Mercurial > repos > dave > pipelign

annotate test-data/files/input.merge.2.fas @ 0:9a3a2e04f47a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dave
date Mon, 10 Jun 2019 16:04:10 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
1 >K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
2 ---------------------------CTACCTCTTCTTCTGCTAGACTGCC-------A
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
3 TTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
4 >K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
5 -------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA-------G
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
6 TCTAGCAGAAGAAGAGGTAGTAAT-------TAGATC-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
7 >K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
8 ---TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AAGC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
9 CCCAGAAGACGAAGGG----------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
10 >K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
11 GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC-----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
12 -TTGGCACTTATCTGGGA-------------CGATCT-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
13 >K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
14 TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
15 TCTGTCTCT-------------------------CTC-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
16 >K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
17 CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
18 CTAGGAAAATGTCTA-----------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
19 >K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
20 -----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
21 CTAGGAAAATGTCTAAC-----------------AGC-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
22 >K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
23 ----TGC-----TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
24 TTCCCTAAAAAATTAGC-----------------CTGTCT----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
25 >K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
26 AAGTGCAA------------------GCAATCTGATTCACCCGATTTCTTCC-------A
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
27 ATTATGATGACAGGTGTAGGTCCTACTAATACAGT---------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
28 >K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
29 GAT---------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
30 ----------------------------GGTTTTATAGACATCACTATGAAAGCCCTCAT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
31 CCAAGAAAAAGTTCAGAAGTACACA------------------TCCCACTAGG-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
32 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
33 >K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
34 AA----------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
35 -------------------------------TTTATCAAGAGCCATTTAAAAATCTGAAA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
36 ACAGGAAAATATGCAAGAATGAGGGG--------------TGCCCACACTAAT-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
37 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
38 >K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
39 AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
40 -----AGGAAGCAACCACCACTCTATT-----------------------TTGTGCATC-
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
41 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
42 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
43 >K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
44 AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
45 -----AGCCAGTAGATCCTAGACTAT-------------------------AGCCCTGG-
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
46 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
47 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
48 >K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
49 --------------------------------------GGAGCT----AGAACGAT----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
50 -----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGG
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
51 A-----------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
52 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
53 >K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
54 ----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
55 TTGTGGGGCTGTTGGCTCTGGTCTGCT---------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
56 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
57 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
58 >K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
59 TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
60 TGGTGGGGCAGTTGGCTCTGGTC-------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
61 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
62 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
63 >K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
64 A-------------------------------------GGGATTATGGAAAACAGA----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
65 -----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG----
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
66 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
67 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
68 >K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
69 ------------CGGGCACAC----------------------------ACT--------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
70 ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
71 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
72 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
73 >K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
74 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
75 -CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
76 CAGA----------------------------------------GAGCTCCCA-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
77 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
78 >K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
79 ---------------------------------------------------------TGC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
80 TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
81 TATT-------------------------------------------GACCAC-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
82 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
83 >K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
84 ------------GCTGCTCCC----------------------------ACCCTATCTTG
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
85 TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
86 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
87 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
88 >K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
89 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
90 TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
91 TAAA--------------------------------------CAGCAGTTGTT-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
92 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
93 >K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
94 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
95 --------------------------------TGCCAAGGATCCGTTCACTAA--TCGAA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
96 TGGA---------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
97 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
98 >K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
99 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
100 TTCTGGGAAGTTCAAT----------------TAGGAATACCACATCCCGCAGGGTTAAA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
101 AAAG---------AAAAAATCAGT------------------AACAGTACTGG-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
102 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
103 >K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
104 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
105 CTATG------TTTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
106 TAAAT----TGCTTGTAACTCAGTC-----------------TTCTGATTTGT-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
107 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
108 >K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
109 ------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
110 TCCCAAAGAAGACAAG----ATATCCTTGATC----------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
111 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
112 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
113 >K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
114 ------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
115 TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA----------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
116 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
117 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
118 >K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
119 -------------------------------------------------GGCTAATTCAC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
120 TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
121 -------------------------------------------GCTACTTCCC-------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
122 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
123 >K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
124 ---------------------------------ACAACGGAATTGG---AGGAAATGAAC
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
125 CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT----------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
126 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
127 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
128 >K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
129 -----------------------------------AATAGTACTTT---CCTGATTCCAG
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
130 CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG--------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
131 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
132 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
133 >K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
134 -----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
135 CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATCAG--------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
136 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
137 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
138 >K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
139 --------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
140 CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA-----------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
141 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
142 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
143 >K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
144 -----------------------------------------ACAGC---GACGAAGAGCT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
145 CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA--------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
146 --------------------------------------------TTACAT----------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
147 --
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
148 >K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
149 ------------------------------------------------------------
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
150 -------------------------------------AGCCATTGCTCTCCAA--TTACT
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
151 GTGA---------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTCCATCTAAAA
9a3a2e04f47a Uploaded
dave
parents:
diff changeset
152 AT