Mercurial > repos > yhoogstrate > segmentation_fold

changeset 4:21e619c46cb5 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 61ba605ef9eb63914a248fe389860daa2249af69
author yhoogstrate
date Wed, 02 Mar 2016 05:47:07 -0500
parents 59ab674be4b5
children fd7f0bf0f5b6
files README.rst energy-estimation-utility.xml scan-for-segments.xml segmentation-fold.xml test-data/SNORD114-4-revised.scan-for-segments.txt test-data/SNORD118-revised.scan-for-segments.txt test-data/SNORD13-revised.scan-for-segments.txt test-data/SNORD48-revised.scan-for-segments.txt test-data/segments_truncated.2.out.txt test-data/segments_truncated.out.txt test-data/test_01.dbn test-data/test_02.dbn test-data/test_03.dbn test-data/test_04.dbn test-data/test_05.dbn test-data/test_06.dbn test-data/test_07.dbn test-data/test_08.dbn test-data/test_09.dbn test-data/test_10.dbn test-data/test_11.dbn test-data/test_12.dbn test-data/test_13.dbn test-data/test_14.dbn test-data/test_15.dbn test-data/test_16.dbn test-data/test_17.dbn test-data/test_18.dbn test-data/test_19.dbn test-data/test_20.dbn test-data/test_21.dbn test-data/test_22.dbn test-data/test_23.dbn test-data/test_24.dbn test-data/test_25.dbn test-data/test_26.dbn test-data/test_27.dbn test-data/test_28.dbn tool_dependencies.xml
diffstat 39 files changed, 105 insertions(+), 288 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Mon Feb 29 10:43:37 2016 -0500
+++ b/README.rst	Wed Mar 02 05:47:07 2016 -0500
@@ -5,6 +5,11 @@
 
 Segmentation-fold: An algorithm for predicting RNA 2D structures including K-turns
 
+Installation
+------------
+
+Requires a C++11 compliant compiler!
+
 Development
 -----------
 
--- a/energy-estimation-utility.xml	Mon Feb 29 10:43:37 2016 -0500
+++ b/energy-estimation-utility.xml	Wed Mar 02 05:47:07 2016 -0500
@@ -1,8 +1,8 @@
-<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.0_0">
+<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.0">
     <description>Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold</description>
     
     <requirements>
-        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
@@ -77,7 +77,7 @@
             <param  name="do_randomization" value="false" />
             <param  name="shuffle_n_times" value="0" />
             
-            <output name="output_list" file="segments_truncated.out.txt" />
+            <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. -->
         </test>
         <test>
             <param  name="use_custom_xml" value="true" />
@@ -85,7 +85,7 @@
             <param  name="do_randomization" value="false" />
             <param  name="shuffle_n_times" value="1" />
             
-            <output name="output_list" file="segments_truncated.out.txt" lines_diff="8" />
+            <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
         </test>
     </tests>
     
--- a/scan-for-segments.xml	Mon Feb 29 10:43:37 2016 -0500
+++ b/scan-for-segments.xml	Wed Mar 02 05:47:07 2016 -0500
@@ -1,8 +1,8 @@
-<tool id="scan_for_segments" name="scan-for-segments" version="1.6.0_0">
+<tool id="scan_for_segments" name="scan-for-segments" version="1.6.0">
     <description>Scan for the presence of segments in sequences using segmentation-fold</description>
     
     <requirements>
-        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
--- a/segmentation-fold.xml	Mon Feb 29 10:43:37 2016 -0500
+++ b/segmentation-fold.xml	Wed Mar 02 05:47:07 2016 -0500
@@ -1,8 +1,8 @@
-<tool id="segmentation_fold" name="segmentation-fold" version="1.6.0_0">
+<tool id="segmentation_fold" name="segmentation-fold" version="1.6.2_0">
     <description>RNA-Folding including predefined segments including K-turns</description>
     
     <requirements>
-        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.6.2">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
--- a/test-data/SNORD114-4-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/SNORD114-4-revised.scan-for-segments.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -1,49 +1,27 @@
->SNORD114-4 x Kt-CD-box.AGA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UAA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-42.dra
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CUG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.AGG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-42.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Loop-E-Motif.bac
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.ACG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.ACA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-G2nA-SAMribo.bsu
+>SNORD114-4 x Kt-CD-box.UAU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-CD-box.UGU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UGG
+>SNORD114-4 x Kt-CD-box.CAU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-42.tth
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UCA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UCG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-7 G2nA SAM riboswitch (H. marismortui)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UAG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GAA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CGG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-15.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
-.(((((((((.......))))))(.(.((((..((..((((((..........)))))).))..)))).).))))	.((((((.((.(((.((.....((((((.(....)....))))))..)...)))).......)).....))))))	-8.12001228333
->SNORD114-4 x Kt-CD-box.CAG
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((....(((.((.....((((......))))((....))...)...))))...(((....))).))))))	-6.4197063446
+>SNORD114-4 x Kt-U4b.hsa
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-U4b.hsa
+>SNORD114-4 x Kt-CD-box.GGU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-7 (E. coli)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
@@ -51,26 +29,14 @@
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-58.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UUG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-46.tth
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.AUG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UUA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-SAM-ribo.tte
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-23.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GCG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.UGA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-38.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CCG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-46.dra
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-CD-box.CGU
@@ -81,44 +47,28 @@
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-46.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GAG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CAA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-c-di-GMP-II.cac
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-11 (T. thermophilus)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.AUA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GGA
+>SNORD114-4 x Kt-CD-box.AAU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-L30e.sce
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CCA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-7 (T. thermophilus)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GCA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GUG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-42.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-U4a.hsa
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CUA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.AAG
+>SNORD114-4 x Kt-G2nA-SAMribo.bsu
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
-.(((((((((.......))))))(.(.((((..((..((((((..........)))))).))..)))).).))))	((((((((((.......))))))(((......)))...)))).(((((...(.((.......)).)....)))))	-6.19940757751
->SNORD114-4 x Kt-CD-box.GUA
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.GGG
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 x Kt-CD-box.CGA
+>SNORD114-4 x Kt-CD-box.GAU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-11.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 x Kt-46.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((...(((((.......((((......)))).((((((..........)))))).....)))))))))))	1.99971199036
--- a/test-data/SNORD118-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/SNORD118-revised.scan-for-segments.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -1,48 +1,27 @@
->SNORD118 x Kt-CD-box.AGA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UAA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-42.dra
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CUG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.AGG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-42.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Loop-E-Motif.bac
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.ACG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.ACA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-G2nA-SAMribo.bsu
+>SNORD118 x Kt-CD-box.UAU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-CD-box.UGU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UGG
+>SNORD118 x Kt-CD-box.CAU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	.(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))).	3.380651474
 >SNORD118 x Kt-42.tth
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UCA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UCG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-7 G2nA SAM riboswitch (H. marismortui)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UAG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GAA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CGG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-15.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CAG
+>SNORD118 x Kt-U4b.hsa
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-U4b.hsa
+>SNORD118 x Kt-CD-box.GGU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-7 (E. coli)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
@@ -50,74 +29,47 @@
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-58.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UUG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-46.tth
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.AUG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UUA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-SAM-ribo.tte
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-23.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GCG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.UGA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-38.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CCG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-46.dra
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-CD-box.CGU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
-.......((.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))).....))	((.(((.(((((((.(.....)....))...))))(.(((....)))((((((((...........)))))))).)).)))))(....)	-14.319940567
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((((...((((((............))...))))...))......(((((((((...........))))))))).....)))......	-15.021024704
 >SNORD118 x Kt-T-box.bsu
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-23.tth
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-46.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GAG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CAA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-c-di-GMP-II.cac
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-11 (T. thermophilus)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.AUA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GGA
+>SNORD118 x Kt-CD-box.AAU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-L30e.sce
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CCA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-7 (T. thermophilus)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GCA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GUG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-42.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-U4a.hsa
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CUA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.AAG
+>SNORD118 x Kt-G2nA-SAMribo.bsu
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GUA
+>SNORD118 x Kt-CD-box.GAU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.GGG
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 x Kt-CD-box.CGA
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))......	-8.30012321472
 >SNORD118 x Kt-11.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 x Kt-46.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
--- a/test-data/SNORD13-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/SNORD13-revised.scan-for-segments.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -1,48 +1,26 @@
->SNORD13 x Kt-CD-box.AGA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UAA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-42.dra
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CUG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.AGG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-42.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Loop-E-Motif.bac
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.ACG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.ACA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-G2nA-SAMribo.bsu
+>SNORD13 x Kt-CD-box.UAU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-CD-box.UGU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UGG
+>SNORD13 x Kt-CD-box.CAU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-42.tth
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UCA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UCG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-7 G2nA SAM riboswitch (H. marismortui)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UAG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GAA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CGG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-15.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CAG
+>SNORD13 x Kt-U4b.hsa
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-U4b.hsa
+>SNORD13 x Kt-CD-box.GGU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-7 (E. coli)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
@@ -50,74 +28,47 @@
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-58.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UUG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-46.tth
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.AUG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UUA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-SAM-ribo.tte
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-23.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GCG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.UGA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-38.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CCG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-46.dra
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-CD-box.CGU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
-(((((.....((.(.(((.(((((.((((((....))))))..((((((........((.(((...))).)).)))))).))))))))).)).)))))	(((((.(.(...((((((.(((((.((((((....))))))..((((((........((.(((...))).)).)))))).))))))))))))))))))	2.15042304993
+(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))))))))))	3.35026359558
 >SNORD13 x Kt-T-box.bsu
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-23.tth
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-46.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GAG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CAA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-c-di-GMP-II.cac
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-11 (T. thermophilus)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.AUA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GGA
+>SNORD13 x Kt-CD-box.AAU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-L30e.sce
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CCA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-7 (T. thermophilus)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GCA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GUG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-42.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-U4a.hsa
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CUA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.AAG
+>SNORD13 x Kt-G2nA-SAMribo.bsu
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GUA
+>SNORD13 x Kt-CD-box.GAU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.GGG
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 x Kt-CD-box.CGA
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).)))))	-9.91994667053
 >SNORD13 x Kt-11.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 x Kt-46.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
--- a/test-data/SNORD48-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/SNORD48-revised.scan-for-segments.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -1,48 +1,26 @@
->SNORD48 x Kt-CD-box.AGA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UAA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-42.dra
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CUG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.AGG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-42.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Loop-E-Motif.bac
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.ACG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.ACA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-G2nA-SAMribo.bsu
+>SNORD48 x Kt-CD-box.UAU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-CD-box.UGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UGG
+>SNORD48 x Kt-CD-box.CAU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-42.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UCA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UCG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-7 G2nA SAM riboswitch (H. marismortui)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UAG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GAA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CGG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-15.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CAG
+>SNORD48 x Kt-U4b.hsa
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-U4b.hsa
+>SNORD48 x Kt-CD-box.GGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-7 (E. coli)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
@@ -50,26 +28,14 @@
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-58.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UUG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-46.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.AUG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UUA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-SAM-ribo.tte
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-23.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GCG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.UGA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-38.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CCG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-46.dra
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-CD-box.CGU
@@ -80,43 +46,29 @@
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-46.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GAG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CAA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-c-di-GMP-II.cac
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-11 (T. thermophilus)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.AUA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GGA
+>SNORD48 x Kt-CD-box.AAU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-L30e.sce
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CCA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-7 (T. thermophilus)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GCA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GUG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-42.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-U4a.hsa
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CUA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.AAG
+>SNORD48 x Kt-G2nA-SAMribo.bsu
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GUA
+>SNORD48 x Kt-CD-box.GAU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.GGG
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 x Kt-CD-box.CGA
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	(((((...(((((((...))).....))))).....(((((............)))))))))....	-10.9206504822
 >SNORD48 x Kt-11.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >SNORD48 x Kt-46.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	((...(((((..((..((((.....)))).))((((.((((((...))))..)).)))))))))))	-1.84962844849
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.2.out.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -0,0 +1,5 @@
+>C/D-box snoRNA (shuffle iteration 1)
+agaggCGUGAUcccaacgUGAuggc
+....((((.......))))......	....(...((((.....)))))...	-9.3900680542
+>Artificial double C/D K-turn construct (shuffle iteration 1)
+uguucugucacggcacauaccuccggUGUGAUggUGAauaguaUGAgaaguaucgugugucagaggcccuaaUGUGAUgccuuaa
--- a/test-data/segments_truncated.out.txt	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/segments_truncated.out.txt	Wed Mar 02 05:47:07 2016 -0500
@@ -1,4 +1,6 @@
->C/D-box snoRNA (shuffle iteration 1)
-cgCGUGAUgagUGAgucagagcacc
->Artificial double C/D K-turn construct (shuffle iteration 1)
-ggcauuaccgacaguccucguaacaggaauaucguacggucUGUGAUaUGAuuucaucguggaacuuUGUGAUcggcgggauUGA
+>C/D-box snoRNA
+GCUCUGACCGAAAGGCGUGAUGAGC
+((((....((.....))....))))	(((((((((....))...)))))))	2.50072479248
+>Artificial double C/D K-turn construct
+GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
+((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.25102996826
--- a/test-data/test_01.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_01.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -32.2572 kcal/mole
+>Sequence length: 34bp, dE: -28.56 kcal/mole, segments: 1
 CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG
 ((((((((((((.......)))...)))))))))
--- a/test-data/test_02.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_02.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -34.4572 kcal/mole
+>Sequence length: 34bp, dE: -30.16 kcal/mole, segments: 1
 CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
 ((((((((((((.......)))...)))))))))
--- a/test-data/test_03.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_03.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 35bp, dE: -31.2572 kcal/mole
+>Sequence length: 35bp, dE: -26.76 kcal/mole, segments: 1
 CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
 ((((((((((((.......))))....))))))))
--- a/test-data/test_04.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_04.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -30.4872 kcal/mole
+>Sequence length: 34bp, dE: -23.19 kcal/mole, segments: 1
 CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG
 ((((((((((..((.....)))...)))))))))
--- a/test-data/test_05.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_05.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -42.5072 kcal/mole
+>Sequence length: 47bp, dE: -34.71 kcal/mole, segments: 1
 CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
 ((((.(((((..((((((((.......)))))))))))...))))))
--- a/test-data/test_06.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_06.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -40.3572 kcal/mole
+>Sequence length: 47bp, dE: -32.56 kcal/mole, segments: 1
 GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
 ((((.(((((..((((((((.......)))))))))))...))))))
--- a/test-data/test_07.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_07.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 31bp, dE: -26.5072 kcal/mole
+>Sequence length: 31bp, dE: -24.51 kcal/mole, segments: 1
 AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
-..(((.(((((....))))...)))).....
+.((((.(((((....))))...)))))....
--- a/test-data/test_08.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_08.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 37bp, dE: -33.7572 kcal/mole
+>Sequence length: 37bp, dE: -29.26 kcal/mole, segments: 1
 UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
 ((((((((((((((......)))...)))))))))))
--- a/test-data/test_09.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_09.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 37bp, dE: -30.8072 kcal/mole
+>Sequence length: 37bp, dE: -26.31 kcal/mole, segments: 1
 UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
 ((((((((((((((......)))...)))))))))))
--- a/test-data/test_10.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_10.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 109bp, dE: -76.7072 kcal/mole
+>Sequence length: 109bp, dE: -66.21 kcal/mole, segments: 1
 CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
-((((((((((((.(((((((((...(((.(((..(..((((((.(((.((((....)))).)))))))))))))...)))....))))))))))))....)))))))))
+((((((((((((.(((((((((...(((.....(((.((((((.(((.((((....)))).))))))))).)))...)))....))))))))))))....)))))))))
--- a/test-data/test_11.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_11.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -46.6072 kcal/mole
+>Sequence length: 53bp, dE: -42.71 kcal/mole, segments: 1
 GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
 ((((.(((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_12.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_12.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -50.2072 kcal/mole
+>Sequence length: 53bp, dE: -46.31 kcal/mole, segments: 1
 GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_13.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_13.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -43.5072 kcal/mole
+>Sequence length: 53bp, dE: -39.61 kcal/mole, segments: 1
 GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_14.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_14.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -37.9072 kcal/mole
+>Sequence length: 53bp, dE: -34.01 kcal/mole, segments: 1
 CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
 ((.((..((..(((...((.((((((......)))))))))))..))..))))
--- a/test-data/test_15.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_15.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -37.8572 kcal/mole
+>Sequence length: 49bp, dE: -32.16 kcal/mole, segments: 1
 CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG
 (.((((((((...(((((((((((....))))))))))))))))))).)
--- a/test-data/test_16.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_16.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -43.4072 kcal/mole
+>Sequence length: 50bp, dE: -34.51 kcal/mole, segments: 1
 UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
-(((((...(((...((((((((..((....)))))))))))))..)))))
+(((((..((((...((((((((.((.....)))))))))))))).)))))
--- a/test-data/test_17.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_17.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -37.3072 kcal/mole
+>Sequence length: 49bp, dE: -30.91 kcal/mole, segments: 1
 UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
 (((((((.((...((((((((.((....)).)))))))))).)))))))
--- a/test-data/test_18.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_18.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -37.7072 kcal/mole
+>Sequence length: 50bp, dE: -30.61 kcal/mole, segments: 1
 UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
 (((((...(((...(((((((((((....))))))))))))))..)))))
--- a/test-data/test_19.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_19.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 30bp, dE: -28.4572 kcal/mole
+>Sequence length: 30bp, dE: -24.46 kcal/mole, segments: 1
 UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
-((((((((.(((.....)))..))))))))
+((((((((.((((...))))..))))))))
--- a/test-data/test_20.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_20.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 22bp, dE: -23.2072 kcal/mole
+>Sequence length: 22bp, dE: -19.11 kcal/mole, segments: 1
 GCCAAUGAGGUUUAUCCGAGGC
 (((...((((.....)))))))
--- a/test-data/test_21.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_21.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -27.7072 kcal/mole
+>Sequence length: 34bp, dE: -22.71 kcal/mole, segments: 1
 ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
 (((((.(((...(((((....)))))))))))))
--- a/test-data/test_22.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_22.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 25bp, dE: -24.4072 kcal/mole
+>Sequence length: 25bp, dE: -18.01 kcal/mole, segments: 1
 GCUCUGACCGAAAGGCGUGAUGAGC
 (((((((((....))...)))))))
--- a/test-data/test_23.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_23.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 85bp, dE: -70.4144 kcal/mole
+>Sequence length: 85bp, dE: -60.91 kcal/mole, segments: 2
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
-((((((((...(((((..(((......(((((((((((((.....))))))))...)))))...))).....)))))))))))))
+((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))
--- a/test-data/test_24.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_24.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -29.0072 kcal/mole
+>Sequence length: 34bp, dE: -25.41 kcal/mole, segments: 1
 GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC
 ((((((...(((((((.....)))))))))))))
--- a/test-data/test_25.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_25.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 26bp, dE: -24.7072 kcal/mole
+>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1
 GGUGGAGGGACUGGCCCGAUGAAACC
 (((((((((.....)))...))))))
--- a/test-data/test_26.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_26.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 55bp, dE: -42.1072 kcal/mole
+>Sequence length: 55bp, dE: -33.71 kcal/mole, segments: 1
 GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
-((((((...(((((((....(((((((....))))...))).)))))))))))))
+((((((...(((((((...(((...)))(((...))).....)))))))))))))
--- a/test-data/test_27.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_27.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 36bp, dE: -26.2072 kcal/mole
+>Sequence length: 36bp, dE: -22.71 kcal/mole, segments: 1
 AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU
 (((...(((((((((((.....))))))))))))))
--- a/test-data/test_28.dbn	Mon Feb 29 10:43:37 2016 -0500
+++ b/test-data/test_28.dbn	Wed Mar 02 05:47:07 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 26bp, dE: -24.7072 kcal/mole
+>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1
 GGUGAAGGGACUGGCCCGACGAAACC
 (((((((((.....)))...))))))
--- a/tool_dependencies.xml	Mon Feb 29 10:43:37 2016 -0500
+++ b/tool_dependencies.xml	Wed Mar 02 05:47:07 2016 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="segmentation-fold" version="1.6.0">
-        <repository changeset_revision="5b89079b53e2" name="package_segmentation_fold_1_6_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="segmentation-fold" version="1.1.0">
+        <repository changeset_revision="fba0d6f9dd67" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>