Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005413.1 Corchorus capsularis cultivar CVL-1 contig05431, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22035
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:363 original size:25 final size:26
Alignment explanation
Indices: 331--381 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
321 TATATAATAT
331 ATAATATAGACTTATAATT-TTTTGA
1 ATAATATAGACTTATAATTATTTTGA
*
356 ATAATATAGACTTATATTTATTTTGA
1 ATAATATAGACTTATAATTATTTTGA
382 CCGAATAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (26 bp):
ATAATATAGACTTATAATTATTTTGA
Found at i:388 original size:27 final size:26
Alignment explanation
Indices: 333--400 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
323 TATAATATAT
* *
333 AATATAGACTTATAATT-TTTTGAAT
1 AATATAGACTTATATTTATTTTGAAG
*
358 AATATAGACTTATATTTATTTTGACCG
1 AATATAGACTTATATTTATTTTGA-AG
385 -A-ATAGACTTATATTTA
1 AATATAGACTTATATTTA
401 ACTTCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 31 0.82
26 7 0.18
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (26 bp):
AATATAGACTTATATTTATTTTGAAG
Found at i:2291 original size:12 final size:12
Alignment explanation
Indices: 2271--2316 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2261 AACAACCATA
*
2271 ATATACATGACG
1 ATATACATGATG
*
2283 ATATGCATGATG
1 ATATACATGATG
*
2295 ATAAACATGATG
1 ATATACATGATG
*
2307 ATATGCATGA
1 ATATACATGA
2317 AATGTTGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (12 bp):
ATATACATGATG
Found at i:5286 original size:306 final size:304
Alignment explanation
Indices: 4518--5302 Score: 927
Period size: 306 Copynumber: 2.5 Consensus size: 304
4508 TGTTCGGGTT
* * *
4518 TTGTGACGCCCCAAGATCCCAGATCAAGAGGATG-CGGTGATCTATTGTGGTTTATATAATAGAG
1 TTGTGACGCCCCAAGATCCCACATCATGAGGATGTCAG-GATCTATTGTGGTTTATAT-ATAGAG
*
4582 ATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGCCAAAGT
64 ATCCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGG-CAAAGC
* *
4647 GGACAATACCTCACAGGTTGGGCCGGGTCTCTACAGTTGGTATCATAGCTTTAACCGGGCGTGTA
128 GGACAATACCTCACAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAACCGGACGTGTA
** *
4712 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCTGCGCCCGGT
193 GCAGGAGCTAAGTGCTACACCGTGGGA----GGT----G-CACCGTTAAAATCCCTGCGCCCGGT
* *
4777 TGGTCTTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGA
249 GGGTCTTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGCGTAGA
* * * * * * * * *
4833 TTGTGACGCCCCAAAACCCCACAACATGAGGATGTGATGATCCATTATGATTTATATATAAAGAT
1 TTGTGACGCCCCAAGATCCCACATCATGAGGATGTCAGGATCTATTGTGGTTTATATATAGAGAT
* * * * *
4898 CCAACCC-AACTTGTGAGGTGCCTTTTGGGAAAGGTAAATTCGTGAGGCCTTTTGGGTCAAAGCG
66 CCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCC-TTTGGG-CAAAGCG
* * * * * * * *
4962 GACAATACTTTACAGGTTGGGTCGGATCACTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAG
129 GACAATACCTCACAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAACCGGACGTGTAG
* *
5027 CAGGAGCTAAGTGCTACACCGTGGGA-GT-CACCTTTAAAAT-CTTGGCGCCCGGTGGGTCTTGG
194 CAGGAGCTAAGTGCTACACCGTGGGAGGTGCACCGTTAAAATCCCT-GCGCCCGGTGGGTCTTGG
* * *
5089 TGATTGTGTTGTGTGGGCTTGTC-GTGACGACAAGCCTATAAGG-GCGTAGA
258 TGA-----TTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGCGTAGA
* * * *
5139 TTGTGACGCCCTAAGATCCCACATCGTGAGGATGTTAGGATATATTGTGGTTTATATATAGAGAT
1 TTGTGACGCCCCAAGATCCCACATCATGAGGATGTCAGGATCTATTGTGGTTTATATATAGAGAT
*
5204 CCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGCGAAGCCTTTGGGCGAAAGCGG
66 CCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGC-AAAGCGG
* *
5269 AAAATACCTCGCAGGTTGGGCCGGGTCTCTACAG
130 ACAATACCTCACAGGTTGGGCCGGGTCTCTACAG
5303 GTTTTTAGGC
Statistics
Matches: 396, Mismatches: 64, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
302 2 0.01
303 30 0.08
305 1 0.00
306 106 0.27
307 55 0.14
308 13 0.03
309 2 0.01
313 37 0.09
314 105 0.27
315 45 0.11
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (304 bp):
TTGTGACGCCCCAAGATCCCACATCATGAGGATGTCAGGATCTATTGTGGTTTATATATAGAGAT
CCAACCCAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGCAAAGCGGA
CAATACCTCACAGGTTGGGCCGGGTCTCTACAGTTGGTATCAGAGCTTTAACCGGACGTGTAGCA
GGAGCTAAGTGCTACACCGTGGGAGGTGCACCGTTAAAATCCCTGCGCCCGGTGGGTCTTGGTGA
TTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGCGTAGA
Found at i:6295 original size:314 final size:312
Alignment explanation
Indices: 5724--7778 Score: 2486
Period size: 313 Copynumber: 6.5 Consensus size: 312
5714 TGTTCAGGTT
* * * * * * *
5724 TTGTGACGCCCCAAGATCCCAGATCAAGAGGATGCGGTGATTTATTGGGGTTTATATAATAGAGA
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATAT-ATAGAGA
** * * *
5789 TCCAACCCAAAAATGTGAGGCGCCTTTTGGGAAGGACAAATCCGTGAGGCCTTTGGGCCAAAGTG
65 TCCAACCC-AACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCG
* * * *
5854 GACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTGGTAACAGAACTTTAACCGGGCGTGTAG
129 GACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAG
* * * *
5919 TGGGAGCTAAGTGCTACACTGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGCCGCCCGGTT
194 TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTT
* * * * * *
5984 GGTCCTGGTTATTGTGTAGACTTGTCGAGGACGACAAGTCTATAAGGGGGGTATA
259 GGTCCTGGTGATTGTGTAGGCTTGTCGGGGACGACAAGCCTATAA-GAGGGTAGA
* ** *
6039 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGAT
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATATATAGAGAT
* * * * *
6104 CCAACCCAACATGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGG
66 CCAACCCAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGC-CTTTGGGTCAAAGCGG
** * * * * * * ** *
6169 ACAATATTTTGCAGGTTGGGACGGATCTCTACAGTTGGTATTAGAGCTTTCACTGGATGTGTAGC
130 ACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAGT
* * * *
6234 AGGAGCTAAGTGCTACACCGTCGGAGTGCGTTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTGG
195 GGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTTG
*
6299 GTCCTGGTGATTGTGTTGTGTGGGCTTGTC-GGGACGACAAGCCTATAAGAGGGTAGA
260 GTCCTGGTGA-----TTGTGTAGGCTTGTCGGGGACGACAAGCCTATAAGAGGGTAGA
* * * * *
6356 TTGTAACGCCCAAAGATCCTA-AATCGTGAGGATGTGAGGATATATTGTGGTTTATATATAGAGA
1 TTGTGACGCCCCAAGATCCCACAA-CATGAGGATGTGATGATATATTGTGGTTTATATATAGAGA
* ** * * *
6420 TCCAACCCAACTTATGAGGCGCCTTTTGGGAAGGGTGAATCTGTGTGGCCTTTGGGTCAAAGCGA
65 TCCAACCCAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCGG
* * * * *
6485 ACAATACCTCGTAGGTTGGGCCGGATTTCTACAGTTAATATCAGAGCGTTAACCGGGCGAGTAGT
130 ACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAGT
* * * * * * * *
6550 TGTAGCTAAGTGCTACACCGTTGGAGTGCGGTGGGATCCACCTCTAGAATCCCGGTGCCCGGTCG
195 GGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTTG
* * *
6615 GTCCTGATGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGA
260 GTCCTGGTGATTGTGTAGGCTTGTCGGGGACGACAAGCCTATAA-GAGGGTAGA
** * ** * *
6669 TTGTGACGCCCCAAGATCCCACAACATGAGGAAATTATGATCCATTATGGTTTATATATTGAGAT
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATATATAGAGAT
* * * * *
6734 CCAACCCAACTTGTGAGGTGCCTTTTTGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGG
66 CCAACCCAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGC-CTTTGGGTCAAAGCGG
* * * * * * * ** *
6799 ACAATACTTTGAAGGTTGGGTCGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGC
130 ACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAGT
* * * * *
6864 AGGAGCTAAGTGCTAAACCGTGGAAGTGCGGTGGGAGCCACCTTTAAAATCCCGACGCCCGGTGG
195 GGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTTG
* **
6929 GTCCTGGTGATTGTGTTGTGTGGGCTTGTC-GTCACGACAAGCCTATAAGAGGGTAGA
260 GTCCTGGTGA-----TTGTGTAGGCTTGTCGGGGACGACAAGCCTATAAGAGGGTAGA
* * * * * *
6986 TTTTGACACCCCAAGATCCTACATCATGAAGATGTGAGGATATATTGTGGTTTATATATAGAGAT
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATATATAGAGAT
* * * * *
7051 TCAACCCAAATTTATGGGGCGCCTTTTGGGAAGGGCGAATCCGTGAGGCCTTTGGGTCAAAGCGG
66 CCAACCC-AACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCGG
* *
7116 ATAATACCTCGTAGGTTGGGCCGGAAT-TCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAG
130 ACAATACCTCGCAGGTTGGGCCGG-ATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAG
* *
7180 TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGGCGCCCGGTT
194 TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTT
*
7245 GGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAA-ATGGGTAGA
259 GGTCCTGGTGATTGTGTAGGCTTGTCGGGGACGACAAGCCTATAAGA-GGGTAGA
* *
7299 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGAGGATATATTGTGGTTAATATATAGAGAT
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATATATAGAGAT
* *
7364 CCAACCTAAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGTTCAAAGCGG
66 CCAACC-CAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCGG
* * *
7429 ACAATACCTCGTAGGTTGGGCCGGATTTCTACAGTTAGTATCAGATCTTTAACCGGGCGTGTAGT
130 ACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAGT
* * * * *
7494 GGGAGCTAAGTGCTACTCCGTGGGAGTGCGGTGGGAAGCCACCTCTAGAATTCCCGGTGCCTGGT
195 GGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGG-AGCCACCTTTA-AAATCCCGGCGCCCGGT
* * *
7559 TGGTCCTGATGATTGT-TGGGCTTGTCGGGGACGACAAGCGTATAAGGAGGGTAGA
258 TGGTCCTGGTGATTGTGTAGGCTTGTCGGGGACGACAAGCCTATAA-GAGGGTAGA
* * * * * *
7614 TTGTGACGCTCCAAGATCCCAGATCAAGAGGATGTTG-TTATCTATTGTGGTTTATATAATAGAG
1 TTGTGACGCCCCAAGATCCCACAACATGAGGATG-TGATGATATATTGTGGTTTATAT-ATAGAG
* *
7678 ATCCAACCCAAACTTGTGAGGCACCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGTCAAAGC
64 ATCCAACCC-AACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGC
*
7743 GGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAG
128 GGACAATACCTCGCAGGTTGGGCCGGATCTCTACAG
7779 GTTTTTGGGC
Statistics
Matches: 1482, Mismatches: 229, Indels: 57
0.84 0.13 0.03
Matches are distributed among these distances:
311 13 0.01
312 34 0.02
313 370 0.25
314 311 0.21
315 128 0.09
316 231 0.16
317 301 0.20
318 68 0.05
319 26 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (312 bp):
TTGTGACGCCCCAAGATCCCACAACATGAGGATGTGATGATATATTGTGGTTTATATATAGAGAT
CCAACCCAACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCGGA
CAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAGTG
GGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTTGG
TCCTGGTGATTGTGTAGGCTTGTCGGGGACGACAAGCCTATAAGAGGGTAGA
Found at i:7006 original size:630 final size:631
Alignment explanation
Indices: 5724--7778 Score: 2871
Period size: 630 Copynumber: 3.3 Consensus size: 631
5714 TGTTCAGGTT
* * * * * *
5724 TTGTGACGCCCCAAGATCCCAGATCAAGAGGATGCG-GTGATTTATTGGGGTTTATATAATAGAG
1 TTGTGACGCCCCAAGATCCTAAATCATGAGGATGTGAG-GATATATTGTGGTTTATATAATAGAG
** * * * *
5788 ATCCAACCCAAAAATGTGAGGCGCCTTTTGGGAAGGACAAATCCGTGAGGCCTTTGGGCCAAAGT
65 ATCCAACCCAAACTTATGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGC
* * * *
5853 GGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAGTTGGTAACAGAACTTTAACCGGGCGTGTA
130 GGACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTA
* *
5918 GTGGGAGCTAAGTGCTACACTGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGCCGCCCGGT
195 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGGCGCCCGGT
* * * * * * *
5983 TGGTCCTGGTTATTGTGTAGACTTGTCGAGGACGACAAGTCTATAAGGGGGGTATATTGTGACGC
260 TGGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGATTGTGACGC
6048 CCCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGATCCAACCCAA
325 CCCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGATCCAACCCAA
* *
6113 CATGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATATTT
390 CTTGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATACTT
* *
6178 TGCAGGTTGGGACGGATCTCTACAGTTGGTATTAGAGCTTTCACTGGATGTGTAGCAGGAGCTAA
455 TGAAGGTTGGGACGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGCAGGAGCTAA
*
6243 GTGCTACACCGTCGGAGTGCGTTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTGGGTCCTGGTG
520 GTGCTACACCGT-GGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTGGGTCCTGGTG
6308 ATTGTGTTGTGTGGGCTTGTCGGGACGACAAGCCTATAAGAGGGTAGA
584 ATTGTGTTGTGTGGGCTTGTCGGGACGACAAGCCTATAAGAGGGTAGA
* * *
6356 TTGTAACGCCCAAAGATCCTAAATCGTGAGGATGTGAGGATATATTGTGGTTTATAT-ATAGAGA
1 TTGTGACGCCCCAAGATCCTAAATCATGAGGATGTGAGGATATATTGTGGTTTATATAATAGAGA
** * *
6420 TCCAACCC-AACTTATGAGGCGCCTTTTGGGAAGGGTGAATCTGTGTGGCCTTTGGGTCAAAGCG
66 TCCAACCCAAACTTATGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCG
* * * * * *
6484 AACAATACCTCGTAGGTTGGGCCGGATTTCTACAGTTAATATCAGAGCGTTAACCGGGCGAGTAG
131 GACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAG
* * * * *
6549 TTGTAGCTAAGTGCTACACCGTTGGAGTGCGGTGGGATCCACC-TCTAGAATCCCGGTGCCCGGT
196 TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGT-TAGAATCCCGGCGCCCGGT
* *
6613 CGGTCCTGATGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGATTGTGACGC
260 TGGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGATTGTGACGC
** *
6678 CCCAAGATCCCACAACATGAGGAAATTATGATCCATTATGGTTTATATATTGAGATCCAACCCAA
325 CCCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGATCCAACCCAA
*
6743 CTTGTGAGGTGCCTTTTTGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATACTT
390 CTTGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATACTT
*
6808 TGAAGGTTGGGTCGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGCAGGAGCTAA
455 TGAAGGTTGGGACGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGCAGGAGCTAA
* *
6873 GTGCTAAACCGTGGAAGTGCGGTGGGAGCCACCTTTAAAATCCCGACGCCCGGTGGGTCCTGGTG
520 GTGCTACACCGTGG-AGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTGGGTCCTGGTG
**
6938 ATTGTGTTGTGTGGGCTTGTCGTCACGACAAGCCTATAAGAGGGTAGA
584 ATTGTGTTGTGTGGGCTTGTCGGGACGACAAGCCTATAAGAGGGTAGA
* * * *
6986 TTTTGACACCCCAAGATCCTACATCATGAAGATGTGAGGATATATTGTGGTTTATAT-ATAGAGA
1 TTGTGACGCCCCAAGATCCTAAATCATGAGGATGTGAGGATATATTGTGGTTTATATAATAGAGA
* * * *
7050 TTCAACCCAAATTTATGGGGCGCCTTTTGGGAAGGGCGAATCCGTGAGGCCTTTGGGTCAAAGCG
66 TCCAACCCAAACTTATGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCG
* *
7115 GATAATACCTCGTAGGTTGGGCCGGAAT-TCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTA
131 GACAATACCTCGCAGGTTGGGCCGG-ATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTA
7179 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGGCGCCCGGT
195 GTGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGGCGCCCGGT
*
7244 TGGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAA-ATGGGTAGATTGTGACGC
260 TGGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGATTGTGACGC
* * ** * * *
7308 CCCAAGATCCCACAACATGAGGATGTGAGGATATATTGTGGTTAATATATAGAGATCCAACCTAA
325 CCCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGATCCAACC-CA
* * * ** *
7373 ACTTGTGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGC-CTTTGGTTCAAAGCGGACAATACC
389 ACTTGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATACT
* * * * * * * * ** **
7437 TCGTAGGTTGGGCCGGATTTCTACAGTTAGTATCAGATCTTTAACCGGGCGTGTAGTGGGAGCTA
454 TTGAAGGTTGGGACGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGCAGGAGCTA
* * * * * *
7502 AGTGCTACTCCGTGGGAGTGCGGTGGGAAGCCACCTCTAGAATTCCCGGTGCCTGGTTGGTCC--
519 AGTGCTACACCGT-GGAGTGCGGTGGG-AGCCACCTTTA-AAATCCCGGCGCCCGGTGGGTCCTG
* *
7565 -TGA-TG-ATTGT-TGGGCTTGTCGGGGACGACAAGCGTATAAGGAGGGTAGA
581 GTGATTGTGTTGTGTGGGCTTGTC-GGGACGACAAGCCTATAA-GAGGGTAGA
* * * * ** *
7614 TTGTGACGCTCCAAGATCCCAGATCAAGAGGATGTTG-TTATCTATTGTGGTTTATATAATAGAG
1 TTGTGACGCCCCAAGATCCTAAATCATGAGGATG-TGAGGATATATTGTGGTTTATATAATAGAG
* * *
7678 ATCCAACCCAAACTTGTGAGGCACCTTTTGGGAAGGGCAAATCCGTGAAGCCTTTGGGTCAAAGC
65 ATCCAACCCAAACTTATGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGC
*
7743 GGACAATACCTCGCAGGTTGGGCCGGGTCTCTACAG
130 GGACAATACCTCGCAGGTTGGGCCGGATCTCTACAG
7779 GTTTTTGGGC
Statistics
Matches: 1262, Mismatches: 146, Indels: 33
0.88 0.10 0.02
Matches are distributed among these distances:
626 10 0.01
627 19 0.02
628 56 0.04
629 103 0.08
630 732 0.58
631 274 0.22
632 67 0.05
633 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (631 bp):
TTGTGACGCCCCAAGATCCTAAATCATGAGGATGTGAGGATATATTGTGGTTTATATAATAGAGA
TCCAACCCAAACTTATGAGGCGCCTTTTGGGAAGGGCAAATCCGTGAGGCCTTTGGGTCAAAGCG
GACAATACCTCGCAGGTTGGGCCGGATCTCTACAGTTAGTATCAGAGCTTTAACCGGGCGTGTAG
TGGGAGCTAAGTGCTACACCGTGGGAGTGCGGTGGGAGCCACCGTTAGAATCCCGGCGCCCGGTT
GGTCCTGGTGATTGTGTAGGCTTATCGGGGACGACAAGCCTATAAGGTGGGTAGATTGTGACGCC
CCAAGATCCCACAACATGAGGATGTTATGATCCATTATGGTTTATATATAGAGATCCAACCCAAC
TTGTGAGGTGCCTTTTGGGAAGGGTAAATCCGTGAGGCGTTTTGGGCCAAAGCGGACAATACTTT
GAAGGTTGGGACGGATCTCTACAGTTGGTATCAGAGCTTTCACTGGATGTGTAGCAGGAGCTAAG
TGCTACACCGTGGAGTGCGGTGGGAGCCACCTTTAAAATCCCGGCGCCCGGTGGGTCCTGGTGAT
TGTGTTGTGTGGGCTTGTCGGGACGACAAGCCTATAAGAGGGTAGA
Found at i:10797 original size:16 final size:14
Alignment explanation
Indices: 10767--10794 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10757 AACTAGAAAA
10767 GGAGAAGGGGAGAG
1 GGAGAAGGGGAGAG
10781 GGAGAAGGGGAGAG
1 GGAGAAGGGGAGAG
10795 AGGTGCGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
GGAGAAGGGGAGAG
Found at i:11344 original size:78 final size:79
Alignment explanation
Indices: 11192--11355 Score: 224
Period size: 78 Copynumber: 2.1 Consensus size: 79
11182 AACTTTTATA
11192 ATTTTACTCAACTATAAAAACTCTATATTTATTTAACTAAATCTAATATCTTCATAACTATTTTA
1 ATTTTACTCAAC-ATAAAAACTCTATATTTATTTAACTAAATCTAATATCTTCATAACTATTTTA
* **
11257 TTTTTCCATTTTACC
65 GTTCACCATTTTACC
* * *
11272 ATTTTACTCGAC-TAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTT-ATAACTATTTTA
1 ATTTTACTCAACATAAAAACTCTATATTTATTTAACTAAATCTAATAT-CTTCATAACTATTTTA
* *
11335 GTTCACCATTTTGCT
65 GTTCACCATTTTACC
11350 ATTTTA
1 ATTTTA
11356 GTTAAAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 61 0.81
79 3 0.04
80 11 0.15
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (79 bp):
ATTTTACTCAACATAAAAACTCTATATTTATTTAACTAAATCTAATATCTTCATAACTATTTTAG
TTCACCATTTTACC
Found at i:12085 original size:13 final size:13
Alignment explanation
Indices: 12049--12087 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12039 AGTTTTTTTA
**
12049 ATATTTATTTCTT
1 ATATTTATTTAAT
*
12062 AAATTTATTTAAT
1 ATATTTATTTAAT
12075 ATATTTATTTAAT
1 ATATTTATTTAAT
12088 CTACTACCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTATTTAAT
Found at i:12478 original size:20 final size:20
Alignment explanation
Indices: 12438--12487 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
12428 TATCATAAAT
*
12438 TATTCATATAACAAGTTTTG
1 TATTCATATAATAAGTTTTG
12458 TATTCATATAATAA-TTATTG
1 TATTCATATAATAAGTT-TTG
12478 T-TT-ATATAAT
1 TATTCATATAAT
12488 GAAATTTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 17 0.61
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATTCATATAATAAGTTTTG
Done.