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author dave
date Mon, 10 Jun 2019 16:04:10 -0400
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inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  72
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 70 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 83 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 3 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 3
njobc = 4
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  91
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1- 108
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  92
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 76 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1- 118
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1- 115
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  94
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  87
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 80 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 84 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 82 - 75 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     3 / 3 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     3 / 3 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 4

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4 
 -> OK
Segment   1/  1    1-  91
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     
001-0004-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  78
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  73
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  84
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  88
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1- 105
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  77
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 76 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 79 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 80 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  97
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  72
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  97
001-0000-1 (thread    1) identical     
001-0000-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  89
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 95 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
2 x 70 - 70 d
outputhat23=1
treein = 0
compacttree = 0
stacksize: 8192 kb
generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
    0 / 2 (by thread   0) 
tbfast-pair (nuc) Version 7.407
alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

outputhat23=1
Loading 'hat3.seed' ... 
done.
Writing hat3 for iterative refinement
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
tbutree = 1, compacttree = 0
Constructing a UPGMA tree ... 

    0 / 2
done.

Progressive alignment ... 

STEP     1 /1 (thread    0) 
done.
tbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
Loading 'hat3' ... done.
generating a scoring matrix for nucleotide (dist=200) ... done


    0 / 2
Segment   1/  1    1-  95
001-0000-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 L-INS-i (Probably most accurate, very slow)
 Iterative refinement method (<1) with LOCAL pairwise alignment information

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 71 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 110 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 4
njobc = 5
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 90 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 107 - 99 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
###################################################################
# WARNING: Group 2 is forced to be a monophyletic cluster.
###################################################################
Reallocated inconsistentpairlist, size=2

done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     3 / 3 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     3 / 3 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 4

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4 
 -> OK
Segment   1/  1    1- 156
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     
001-0004-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 91 - 78 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     4 / 4 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     4 / 4 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 5

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5 
 -> OK
Segment   1/  1    1- 108
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-1 (thread    1) identical     
001-0006-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 117 - 114 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     3 / 3 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     3 / 3 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 4

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4 
 -> OK
Segment   1/  2    1-  62
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     

Converged.

Reached 1
Segment   2/  2   62- 134
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     
001-0004-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 78 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 102 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 3 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 3
njobc = 4
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 84 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 4
njobc = 5
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
3 x 72 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 2 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 2
njobc = 3
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 99 - 76 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
###################################################################
# WARNING: Group 2 is forced to be a monophyletic cluster.
###################################################################

done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     3 / 3 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     3 / 3 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 4

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4 
 -> OK
Segment   1/  1    1- 103
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     
001-0004-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 101 - 72 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     4 / 4 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     4 / 4 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 5

Checking subalignment 1:
 1  2  3 
 -> OK

Checking subalignment 2:
 4  5 
 -> OK
Segment   1/  1    1- 102
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 95 - 71 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     3 / 3 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 4 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 4
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     3 / 3 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 4 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 2
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 4

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4 
 -> OK
Segment   1/  1    1- 114
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-1 (thread    1) identical     
001-0004-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 102 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 3 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 3
njobc = 4
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 115 - 96 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     5 / 5 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     5 / 5 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 6

Checking subalignment 1:
 1  2  3 
 -> OK

Checking subalignment 2:
 4  5  6 
 -> OK
Segment   1/  1    1- 154
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-1 (thread    1) identical     
001-0008-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 110 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 5
njobc = 6
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
4 x 108 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 3 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 3
njobc = 4
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 93 - 87 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     4 / 4 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     4 / 4 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 5

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5 
 -> OK
Segment   1/  1    1- 102
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-1 (thread    1) identical     
001-0006-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
8 x 98 - 87 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 5
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     7 / 7 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     7 / 7 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 8 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 5
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 8

Checking subalignment 1:
 1  2  3 
 -> OK

Checking subalignment 2:
 4  5  6  7  8 
 -> OK
Segment   1/  1    1- 105
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
5 x 97 - 74 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     4 / 4 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 5 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 5
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     4 / 4 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 3
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 5

Checking subalignment 1:
 1  2  3 
 -> OK

Checking subalignment 2:
 4  5 
 -> OK
Segment   1/  1    1- 109
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-1 (thread    1) identical     
001-0006-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 106 - 87 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     5 / 5 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     5 / 5 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 6

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5  6 
 -> OK
Segment   1/  1    1- 127
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-1 (thread    1) identical     
001-0008-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
8 x 101 - 91 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 5
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     7 / 7 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     7 / 7 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 8 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 5
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 8

Checking subalignment 1:
 1  2  3  4  5 
 -> OK

Checking subalignment 2:
 6  7  8 
 -> OK
Segment   1/  1    1- 102
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-1 (thread    1) identical     
001-0012-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 99 - 85 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
###################################################################
# WARNING: Group 2 is forced to be a monophyletic cluster.
###################################################################
Reallocated inconsistentpairlist, size=2

done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     5 / 5 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     5 / 5 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 6

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5  6 
 -> OK
Segment   1/  1    1- 123
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-1 (thread    1) identical     
001-0008-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 115 - 94 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     5 / 5 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 6 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 6
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     5 / 5 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 4
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 6

Checking subalignment 1:
 1  2  3  4 
 -> OK

Checking subalignment 2:
 5  6 
 -> OK
Segment   1/  1    1- 141
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
7 x 120 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 6
njobc = 7
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 99 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 5
njobc = 6
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
9 x 104 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 8 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 8
njobc = 9
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
6 x 108 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 5 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 5
njobc = 6
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
8 x 126 - 83 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 6
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     7 / 7 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 8 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 8
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     7 / 7 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 8 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 6
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 8

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5  6  7  8 
 -> OK
Segment   1/  1    1- 130
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-1 (thread    1) identical     
001-0012-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
7 x 100 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 6
njobc = 7
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
7 x 140 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 6 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 6
njobc = 7
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
13 x 128 - 123 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 7
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 13 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 13
   10 / 13
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    12 / 12 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 13 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 13
   10 / 13
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    12 / 12 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 13 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 7
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 13
   10 / 13

Checking subalignment 1:
 1  2  3  4  5  6 
 -> OK

Checking subalignment 2:
 7  8  9  10  11  12  13 
 -> OK
Segment   1/  1    1- 163
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-1 (thread    1) identical     
001-0022-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
10 x 130 - 111 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 6
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     9 / 9 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     9 / 9 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 10 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 6
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 10

Checking subalignment 1:
 1  2  3  4 
 -> OK

Checking subalignment 2:
 5  6  7  8  9  10 
 -> OK
Segment   1/  1    1- 142
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
16 x 129 - 101 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 8
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 16 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 16
   10 / 16
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    15 / 15 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 16 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 16
   10 / 16
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    15 / 15 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 16 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 8
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 16
   10 / 16

Checking subalignment 1:
 1  2  3  4  5  6  7  8 
 -> OK

Checking subalignment 2:
 9  10  11  12  13  14  15  16 
 -> OK
Segment   1/  1    1- 152
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-1 (thread    1) identical     
001-0028-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
10 x 108 - 96 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 7
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     9 / 9 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     9 / 9 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 10 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 7
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 10

Checking subalignment 1:
 1  2  3 
 -> OK

Checking subalignment 2:
 4  5  6  7  8  9  10 
 -> OK
Segment   1/  1    1- 122
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-1 (thread    1) identical     
001-0016-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
8 x 140 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 7 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 7
njobc = 8
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
17 x 151 - 113 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 13
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 17 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 17
   10 / 17
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    16 / 16 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 17 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 17
   10 / 17
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    16 / 16 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 17 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 13
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 17
   10 / 17

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13 
 -> OK

Checking subalignment 2:
 14  15  16  17 
 -> OK
Segment   1/  1    1- 166
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-1 (thread    1) identical     
001-0030-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
11 x 141 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 10 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 10
njobc = 11
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
22 x 157 - 112 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 16
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 22 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 22
   10 / 22
   20 / 22
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    21 / 21 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 22 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 22
   10 / 22
   20 / 22
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    21 / 21 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 22 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 16
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 22
   10 / 22
   20 / 22

Checking subalignment 1:
 1  2  3  4  5  6 
 -> OK

Checking subalignment 2:
 7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22 
 -> OK
Segment   1/  1    1- 170
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-1 (thread    1) identical     
001-0040-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
12 x 121 - 96 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 10
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 12 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 12
###################################################################
# WARNING: Group 2 is forced to be a monophyletic cluster.
###################################################################
Reallocated inconsistentpairlist, size=2

   10 / 12
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    11 / 11 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 12 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 12
   10 / 12
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    11 / 11 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 12 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 10
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 12
   10 / 12

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10 
 -> OK

Checking subalignment 2:
 11  12 
 -> OK
Segment   1/  1    1- 122
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-1 (thread    1) identical     
001-0020-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
10 x 142 - 88 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 8
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP     9 / 9 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 10 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 10
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP     9 / 9 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 10 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 8
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 10

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5  6  7  8  9  10 
 -> OK
Segment   1/  1    1- 157
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-1 (thread    1) identical     
001-0016-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
21 x 168 - 155 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 17
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 21 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 21
   10 / 21
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    20 / 20 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 21 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 21
   10 / 21
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    20 / 20 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 21 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 17
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 21
   10 / 21

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17 
 -> OK

Checking subalignment 2:
 18  19  20  21 
 -> OK
Segment   1/  1    1- 209
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-1 (thread    1) identical     
001-0038-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
12 x 141 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 11 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.
   10 / 11 (by thread   0) 

##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 11
njobc = 12
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
24 x 169 - 74 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 22
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 24 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 24
   10 / 24
   20 / 24
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    23 / 23 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 24 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 24
   10 / 24
   20 / 24
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    23 / 23 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 24 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 22
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 24
   10 / 24
   20 / 24

Checking subalignment 1:
 1  2 
 -> OK

Checking subalignment 2:
 3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24 
 -> OK
Segment   1/  1    1- 174
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-0 (thread    1) skip     

001-0043-1 (thread    1) skip     

001-0044-1 (thread    1) identical     
001-0044-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
13 x 121 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 12 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 12
njobc = 13
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
26 x 186 - 107 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 21
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 26 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 26
   10 / 26
   20 / 26
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    25 / 25 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 26 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 26
   10 / 26
   20 / 26
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    25 / 25 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 26 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 21
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 26
   10 / 26
   20 / 26

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21 
 -> OK

Checking subalignment 2:
 22  23  24  25  26 
 -> OK
Segment   1/  1    1- 199
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-0 (thread    1) skip     

001-0043-1 (thread    1) skip     

001-0044-0 (thread    1) skip     

001-0045-1 (thread    1) skip     

001-0046-0 (thread    1) skip     

001-0047-1 (thread    1) skip     

001-0048-1 (thread    1) identical     
001-0048-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
25 x 173 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 24 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 24
njobc = 25
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
23 x 142 - 130 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 13
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 23 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 23
   10 / 23
   20 / 23
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    22 / 22 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 23 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 23
   10 / 23
   20 / 23
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    22 / 22 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 23 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 13
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 23
   10 / 23
   20 / 23

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13 
 -> OK

Checking subalignment 2:
 14  15  16  17  18  19  20  21  22  23 
 -> OK
Segment   1/  1    1- 155
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-1 (thread    1) identical     

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
38 x 198 - 155 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 26
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 38 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 38
   10 / 38
   20 / 38
   30 / 38
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    37 / 37 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 38 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 38
   10 / 38
   20 / 38
   30 / 38
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    37 / 37 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 38 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 26
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 38
   10 / 38
   20 / 38
   30 / 38

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26 
 -> OK

Checking subalignment 2:
 27  28  29  30  31  32  33  34  35  36  37  38 
 -> OK
Segment   1/  1    1- 205
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-0 (thread    1) skip     

001-0043-1 (thread    1) skip     

001-0044-0 (thread    1) skip     

001-0045-1 (thread    1) skip     

001-0046-0 (thread    1) skip     

001-0047-1 (thread    1) skip     

001-0048-0 (thread    1) skip     

001-0049-1 (thread    1) skip     

001-0050-0 (thread    1) skip     

001-0051-1 (thread    1) skip     

001-0052-0 (thread    1) skip     

001-0053-1 (thread    1) skip     

001-0054-0 (thread    1) skip     

001-0055-1 (thread    1) skip     

001-0056-0 (thread    1) skip     

001-0057-1 (thread    1) skip     

001-0058-0 (thread    1) skip     

001-0059-1 (thread    1) skip     

001-0060-0 (thread    1) skip     

001-0061-1 (thread    1) skip     

001-0062-0 (thread    1) skip     

001-0063-1 (thread    1) skip     

001-0064-0 (thread    1) skip     

001-0065-1 (thread    1) skip     

001-0066-0 (thread    1) skip     

001-0067-1 (thread    1) skip     

001-0068-0 (thread    1) skip     

001-0069-1 (thread    1) skip     

001-0070-0 (thread    1) skip     

001-0071-1 (thread    1) skip     

001-0072-1 (thread    1) identical     
001-0072-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
34 x 182 - 104 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 25
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 34 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 34
   10 / 34
   20 / 34
   30 / 34
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    33 / 33 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 34 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 34
   10 / 34
   20 / 34
   30 / 34
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    33 / 33 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 34 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 25
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 34
   10 / 34
   20 / 34
   30 / 34

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9 
 -> OK

Checking subalignment 2:
 10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34 
 -> OK
Segment   1/  1    1- 188
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-0 (thread    1) skip     

001-0043-1 (thread    1) skip     

001-0044-0 (thread    1) skip     

001-0045-1 (thread    1) skip     

001-0046-0 (thread    1) skip     

001-0047-1 (thread    1) skip     

001-0048-0 (thread    1) skip     

001-0049-1 (thread    1) skip     

001-0050-0 (thread    1) skip     

001-0051-1 (thread    1) skip     

001-0052-0 (thread    1) skip     

001-0053-1 (thread    1) skip     

001-0054-0 (thread    1) skip     

001-0055-1 (thread    1) skip     

001-0056-0 (thread    1) skip     

001-0057-1 (thread    1) skip     

001-0058-0 (thread    1) skip     

001-0059-1 (thread    1) skip     

001-0060-0 (thread    1) skip     

001-0061-1 (thread    1) skip     

001-0062-0 (thread    1) skip     

001-0063-1 (thread    1) skip     

001-0064-1 (thread    1) identical     
001-0064-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
24 x 154 - 70 d
nadd = 1
generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 23 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done
All-to-all alignment.


##### writing hat3
pairlocalalign (nuc) Version 7.407
alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
1 thread(s)

nadd = 1
ppenalty_ex = -10
nthread = 1
blosum 62 / kimura 200
sueff_global = 0.100000
norg = 23
njobc = 24
Loading 'hat3' ... 
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Loading 'hat2n' (aligned sequences - new sequences) ... done.
Loading 'hat2i' (aligned sequences) ... done.

0 / 1 (thread 0)                    
c

Combining ..
0 / 1
 0 / 1

   done.                      


   done.                      

addsingle (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 Multi-INS-fragment (Not tested.)
 ?

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
38 x 187 - 149 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 34
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 38 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 38
   10 / 38
   20 / 38
   30 / 38
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    37 / 37 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 38 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 38
   10 / 38
   20 / 38
   30 / 38
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    37 / 37 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 38 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 34
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 38
   10 / 38
   20 / 38
   30 / 38

Checking subalignment 1:
 1  2  3  4 
 -> OK

Checking subalignment 2:
 5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38 
 -> OK
Segment   1/  1    1- 216
001-0000-0 (thread    1) skip     

001-0001-1 (thread    1) skip     

001-0002-0 (thread    1) skip     

001-0003-1 (thread    1) skip     

001-0004-0 (thread    1) skip     

001-0005-1 (thread    1) skip     

001-0006-0 (thread    1) skip     

001-0007-1 (thread    1) skip     

001-0008-0 (thread    1) skip     

001-0009-1 (thread    1) skip     

001-0010-0 (thread    1) skip     

001-0011-1 (thread    1) skip     

001-0012-0 (thread    1) skip     

001-0013-1 (thread    1) skip     

001-0014-0 (thread    1) skip     

001-0015-1 (thread    1) skip     

001-0016-0 (thread    1) skip     

001-0017-1 (thread    1) skip     

001-0018-0 (thread    1) skip     

001-0019-1 (thread    1) skip     

001-0020-0 (thread    1) skip     

001-0021-1 (thread    1) skip     

001-0022-0 (thread    1) skip     

001-0023-1 (thread    1) skip     

001-0024-0 (thread    1) skip     

001-0025-1 (thread    1) skip     

001-0026-0 (thread    1) skip     

001-0027-1 (thread    1) skip     

001-0028-0 (thread    1) skip     

001-0029-1 (thread    1) skip     

001-0030-0 (thread    1) skip     

001-0031-1 (thread    1) skip     

001-0032-0 (thread    1) skip     

001-0033-1 (thread    1) skip     

001-0034-0 (thread    1) skip     

001-0035-1 (thread    1) skip     

001-0036-0 (thread    1) skip     

001-0037-1 (thread    1) skip     

001-0038-0 (thread    1) skip     

001-0039-1 (thread    1) skip     

001-0040-0 (thread    1) skip     

001-0041-1 (thread    1) skip     

001-0042-0 (thread    1) skip     

001-0043-1 (thread    1) skip     

001-0044-0 (thread    1) skip     

001-0045-1 (thread    1) skip     

001-0046-0 (thread    1) skip     

001-0047-1 (thread    1) skip     

001-0048-0 (thread    1) skip     

001-0049-1 (thread    1) skip     

001-0050-0 (thread    1) skip     

001-0051-1 (thread    1) skip     

001-0052-0 (thread    1) skip     

001-0053-1 (thread    1) skip     

001-0054-0 (thread    1) skip     

001-0055-1 (thread    1) skip     

001-0056-0 (thread    1) skip     

001-0057-1 (thread    1) skip     

001-0058-0 (thread    1) skip     

001-0059-1 (thread    1) skip     

001-0060-0 (thread    1) skip     

001-0061-1 (thread    1) skip     

001-0062-0 (thread    1) skip     

001-0063-1 (thread    1) skip     

001-0064-0 (thread    1) skip     

001-0065-1 (thread    1) skip     

001-0066-0 (thread    1) skip     

001-0067-1 (thread    1) skip     

001-0068-0 (thread    1) skip     

001-0069-1 (thread    1) skip     

001-0070-0 (thread    1) skip     

001-0071-1 (thread    1) skip     

001-0072-1 (thread    1) identical     
001-0072-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
76 x 215 - 206 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 38
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 76 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 76
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   60 / 76
   70 / 76
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    75 / 75 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 76 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 76
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   60 / 76
   70 / 76
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    75 / 75 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 76 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 38
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 76
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Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38 
 -> OK

Checking subalignment 2:
 39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76 
 -> OK
Segment   1/  1    1- 285
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001-0147-1 (thread    1) skip     

001-0148-1 (thread    1) identical     
001-0148-1 (thread    1) better     

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

inputfile = orig
100 x 273 - 156 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb
nsubalignments = 2
maxmem = 76
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

    1 / 100 (thread    0)
done.

Constructing a UPGMA tree ... 


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   80 / 100
   90 / 100
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 1/2... 

STEP    99 / 99 (thread    0) f
done.

Making a distance matrix from msa.. 

    0 / 100 (thread    0)
done.

Constructing a UPGMA tree ... 


    0 / 100
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   20 / 100
   30 / 100
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   60 / 100
   70 / 100
   80 / 100
   90 / 100
done.

Checking subalignment 1:
 -> OK
Checking subalignment 2:
 -> OK
Progressive alignment 2/2... 

STEP    99 / 99 (thread    0) f
done.

disttbfast (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)

generating a scoring matrix for nucleotide (dist=200) ... done

    0 / 100 (thread    0)dndpre (nuc) Version 7.407
alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
1 thread(s)

minimumweight = 0.000010
autosubalignment = 0.000000
nthread = 1
randomseed = 0
blosum 62 / kimura 200
poffset = 0
niter = 1
sueff_global = 0.100000
nadd = 1
nsubalignments = 2
maxmem = 76
generating a scoring matrix for nucleotide (dist=200) ... done



    0 / 100
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   90 / 100

Checking subalignment 1:
 1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76 
 -> OK

Checking subalignment 2:
 77  78  79  80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99  100 
 -> OK
Segment   1/  1    1- 279
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001-0195-1 (thread    1) skip     

001-0196-1 (thread    1) identical     
001-0196-1 (thread    1) worse      

Converged.

Reached 1
done
dvtditr (nuc) Version 7.407
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-i (Standard)
 Iterative refinement method (max. 1 iterations)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.