Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015868.1 Corchorus capsularis cultivar CVL-1 contig15889, 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: 12472
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Found at i:1568 original size:32 final size:32
Alignment explanation
Indices: 1532--1641 Score: 184
Period size: 32 Copynumber: 3.4 Consensus size: 32
1522 GCGGAGCCTC
*
1532 CCCACTAGGACGGCTCTGCCACGGTTAGCCGT
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
1564 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
* *
1596 CCCACTAGGACGGCTCTACCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
*
1628 CCCACTAGGGCGGC
1 CCCACTAGGACGGC
1642 AAGGCTTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.16, C:0.41, G:0.28, T:0.15
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
Found at i:2205 original size:2 final size:2
Alignment explanation
Indices: 2188--2225 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
2178 ATGACCTGTT
2188 TA TA TA T- TA TA CTA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
2226 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4231 original size:445 final size:441
Alignment explanation
Indices: 3558--4387 Score: 1081
Period size: 445 Copynumber: 1.9 Consensus size: 441
3548 ACTAAATAAC
*
3558 ATAAAGTAGAAAAGTAGGAGGGTCATTTGATAAATACATCCAAATAAATAACTGTTTGTGAATGG
1 ATAAAGTAGAAAAGTAGGAGGGTCATTTGATAAATACATCCAAATAAATAAATGTTTGTGAAT-G
* * *
3623 GGAGATCTTGAAACATAAAAATTCTCTTTTGAACCCTTCATGAAACTCGTAAATTAAATTTAATC
65 GGAGATCTTGAAACATAAAAATTCTCCTTTGAACCCTTAATGAAACTCGTAAATCAAATTTAATC
* * * * *
3688 GGGTTCTTCATCAAAGTAAATCATGCAATAACCTTTTAAGCGACACATGAATAACTTTAATCGGA
130 GGATCCTTCATCAAAGTAAATCATGCAATAACCTTTTAACCGAAACATAAATAACTTTAATCGGA
* * * *
3753 CATTTGGATCAAAAATTATATGGTATTAAATAGACCGGCAATCGAACCCACCAAATTT-GAAAAG
195 CATGTGGATCAAAAATTATATGGTATCAAATAGACCGGCAATCAAAACCACCAAATTTCG-AAAG
* * * *
3817 CATTTTCTTTG-TTTGAAAC-TTAAAATTGGCTTTTGAGTCCTTTATGAAAGTTGTAGATCATGA
259 CA-TTT-TTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTACATCATGA
** * * *
3880 AATTGCCTTTTAAATAGGCACATGAATCACCTTAATCGGACAAATAGAACAAAACAATAAAAAAA
322 AATCACCTTTT-AATAGACACATGAATCACCTTAATCAGACAAATAGAA-AAAAAAATAAAAAAA
3945 AATTAAAGTTGATCGCATTAAATCGATTAAAATAAAATTAGTAAAGAATTAAGTAGT
385 AATTAAAGTTGATCGCATTAAATCGATTAAAATAAAATTAGTAAAGAATTAAGTAGT
* *
4002 ATAAAGTAGAAATA-TATGAGGGTCATTTGATAAATA-ATCCAATTAAGA-AAATGTTCAT-TG-
1 ATAAAGTAGAAA-AGTAGGAGGGTCATTTGATAAATACATCCAAATAA-ATAAATGTT--TGTGA
* **
4062 AT-GGAGATGTTGAAACATAAAAATT-TCCTTT-AACCCTTAATGAAACTCGTTTATCAAATTTA
62 ATGGGAGATCTTGAAACATAAAAATTCTCCTTTGAACCCTTAATGAAACTCGTAAATCAAATTTA
* * * *
4124 GCTTCCGGATCCTTCATGAAATTCGTAAATCATGCAATAACCTTTTAACCGAAACTTAAATAATT
127 --AT-CGGATCCTTCATCAAA---GTAAATCATGCAATAACCTTTTAACCGAAACATAAATAACT
** *
4189 TTAATCGGACATGTGGATTGAAAATTATA-GGATATCAAATAGACCGGCAATTAAAACCACCAAA
186 TTAATCGGACATGTGGATCAAAAATTATATGG-TATCAAATAGACCGGCAATCAAAACCACCAAA
*
4253 TTTCGGAAGCATTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAC
250 TTTCGAAAGCATTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAC
** *
4318 ATCATGAAATCACCTTTTAATAGACAGTTGAATCACCTTAATCAGACAAATAGAAAAAAAAATAC
315 ATCATGAAATCACCTTTTAATAGACACATGAATCACCTTAATCAGACAAATAGAAAAAAAAATAA
4383 AAAAA
380 AAAAA
4388 TAAAAGTCAA
Statistics
Matches: 334, Mismatches: 38, Indels: 29
0.83 0.09 0.07
Matches are distributed among these distances:
439 27 0.08
440 5 0.01
441 23 0.07
442 13 0.04
443 34 0.10
444 81 0.24
445 150 0.45
446 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (441 bp):
ATAAAGTAGAAAAGTAGGAGGGTCATTTGATAAATACATCCAAATAAATAAATGTTTGTGAATGG
GAGATCTTGAAACATAAAAATTCTCCTTTGAACCCTTAATGAAACTCGTAAATCAAATTTAATCG
GATCCTTCATCAAAGTAAATCATGCAATAACCTTTTAACCGAAACATAAATAACTTTAATCGGAC
ATGTGGATCAAAAATTATATGGTATCAAATAGACCGGCAATCAAAACCACCAAATTTCGAAAGCA
TTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTACATCATGAAATC
ACCTTTTAATAGACACATGAATCACCTTAATCAGACAAATAGAAAAAAAAATAAAAAAAAATTAA
AGTTGATCGCATTAAATCGATTAAAATAAAATTAGTAAAGAATTAAGTAGT
Found at i:5733 original size:444 final size:447
Alignment explanation
Indices: 4952--5814 Score: 1080
Period size: 444 Copynumber: 1.9 Consensus size: 447
4942 TTTAAGCATA
* * * * *
4952 AAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTGGAAAAGTATGAGGGTAATT
1 AAATCGAGTAAGATAGAATTAGTAAAGGACTAAGCAGCATAAAGTAGAAAAATATGAGGGTAATT
* * *
5017 TGATATATAATCCAAATAAGAAAATGTTTATTAATGGAGATTTTGAAACATAAAAAATTTCCTTT
66 TGATAAATAATCCAAATAAGAAAATGTTAATTAATGGAGATCTTGAAACATAAAAAATTTCCTTT
* * * **
5082 TTAACCCTTCATGAAACTCGTAGATTAAATGTAGCTTTTGGGTCCTTCATCAAAGTTGTAAATCA
131 TTAACCCTTCATGAAACTCGTAGATCAAATGTAGCTTTCGGGTCATTCATCAAAGTCATAAATCA
* * * * *
5147 TGCAATAACATTTTAACCGACAATTGAATAACTTTAATCAGACATATGCATCAAAAATTATATGG
196 TGCAATAACATTTCAACCGACAATTAAATAACTTCAATCAGACATATGCATCAAAAATTATACGA
* ** * * * * ** *
5212 TATTAAAAAGACCGGCAATTGAACCCACCAAATTTGAAAAGCATTTTCTTTAATCGAAACATAAA
261 TATTAAAAAGACCGCCAATAAAAACAACAAAATTTCAAAAGCATTTTCTAGAATCCAAACATAAA
* * * * *
5277 AATTGGCTTTTGAATCCTTTATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGGAAC-C-TG
326 AATTGCCTTTTGAATCCTTCATGAAAATTATAGATCATGAAATCACCTTTTAATA-G-ACGCTTG
*
5340 AATCACCTTAATCGGACAAATA-AATCAAAAGATTTTAAAAAAATAAAGCTGAAGCGTT
389 AATCACCTTAATCGGACAAATAGAATAAAAAGATTTTAAAAAAATAAAGCTGAAGCGTT
* * * *
5398 AAATCGATTAAGAT-GGATTAGTAAAGGACTAAGCAGCATAAAGTAGAAAAATATGAGGTTCATT
1 AAATCGAGTAAGATAGAATTAGTAAAGGACTAAGCAGCATAAAGTAGAAAAATATGAGGGTAATT
* *
5462 TGATAAATAATCCAATTAAGAAAATGTTAATTGATGGAGATCTTGAAACAT-AAAAATTT-CTTT
66 TGATAAATAATCCAAATAAGAAAATGTTAATTAATGGAGATCTTGAAACATAAAAAATTTCCTTT
* * * *
5525 TTGAACCTTTCATGAAACTCGTCA-ATCAAATTTAGCTTTCGGGTCATTCATGAAAGTCATATAT
131 TT-AACCCTTCATGAAACTCGT-AGATCAAATGTAGCTTTCGGGTCATTCATCAAAGTCATAAAT
* * * * * * *
5589 CATGCAATAACCTTTCAACCGACACTTAAATAAGTTCAATCGGATATGTGGA-CAAAAAATTATA
194 CATGCAATAACATTTCAACCGACAATTAAATAACTTCAATCAGACATATGCATC-AAAAATTATA
*
5653 CGATATTAAATAA-ACCGCCAATAAAAACAACAAAATTTCAGAAGCACTTTT-TAGAATCCAAAC
258 CGATATTAAA-AAGACCGCCAATAAAAACAACAAAATTTCAAAAGCA-TTTTCTAGAATCCAAAC
* * * *
5716 ATTAAAATTGCCTTTTGAGTTCTTCATGAAAATTATAGATCATGAGATCACCTTTTAATAGACGC
321 ATAAAAATTGCCTTTTGAATCCTTCATGAAAATTATAGATCATGAAATCACCTTTTAATAGACGC
*
5781 TTGAATCATCTTAATCGGACAAATAGAATAAAAA
386 TTGAATCACCTTAATCGGACAAATAGAATAAAAA
5815 ATACAAAAAT
Statistics
Matches: 352, Mismatches: 57, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
442 2 0.01
443 9 0.03
444 226 0.64
445 102 0.29
446 13 0.04
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (447 bp):
AAATCGAGTAAGATAGAATTAGTAAAGGACTAAGCAGCATAAAGTAGAAAAATATGAGGGTAATT
TGATAAATAATCCAAATAAGAAAATGTTAATTAATGGAGATCTTGAAACATAAAAAATTTCCTTT
TTAACCCTTCATGAAACTCGTAGATCAAATGTAGCTTTCGGGTCATTCATCAAAGTCATAAATCA
TGCAATAACATTTCAACCGACAATTAAATAACTTCAATCAGACATATGCATCAAAAATTATACGA
TATTAAAAAGACCGCCAATAAAAACAACAAAATTTCAAAAGCATTTTCTAGAATCCAAACATAAA
AATTGCCTTTTGAATCCTTCATGAAAATTATAGATCATGAAATCACCTTTTAATAGACGCTTGAA
TCACCTTAATCGGACAAATAGAATAAAAAGATTTTAAAAAAATAAAGCTGAAGCGTT
Found at i:8453 original size:167 final size:166
Alignment explanation
Indices: 8074--8508 Score: 568
Period size: 167 Copynumber: 2.6 Consensus size: 166
8064 TGAGTCATTT
* * * *
8074 GTCAATTGAGAAATGACCAAAAAATTTAGTTATTTAATCCCCTCAAAAATAAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** * * * * *** *
8139 ATAAGTAATCTGCTAAGTAGGTAAAGACGAAAAATGTTAGTTTTCTAGCTCCTCATCAATCCTTG
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAATTCTCTAACTCAAAAGCAATCCTTG
* *
8204 ATAGGGATCATTTATTAATTCCACTACTCTATTCAA
131 ATAGGGATCATTTAGTAATTCCACTACTCTATTAAA
* * *
8240 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
8305 TTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAATAAATTCTCTAACTTCAAAAGCAAGT-CT
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAATTCTCTAAC-TCAAAAGCAA-TCCT
* *
8369 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
129 TGATAGGGATCATTTAGTAATTCCACTACTCTATTAAA
* *
8407 GTCAATTGAGAAATGACCAAAATGTTTAGTTATTTAATCACCTCAAGAATCAAAAGTTATGG-CA
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTA-GGACA
* *
8471 TTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAAT
65 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAT
8509 TAGGTCTCTC
Statistics
Matches: 233, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
166 97 0.42
167 133 0.57
168 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAATTCTCTAACTCAAAAGCAATCCTTG
ATAGGGATCATTTAGTAATTCCACTACTCTATTAAA
Found at i:8656 original size:106 final size:106
Alignment explanation
Indices: 8467--8678 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
8457 CAAAAGTTAT
*
8467 GGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAATTAGGTCTCTCGCTCCTCATTAAT
1 GGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAACTAGGTCTCTCGCTCCTCATTAAT
* * *
8532 CCGGGGTAGGGATTTTTTAGTAATTTCCATATGTTTATTCA
66 CCGGGATAGGGATCTTTTAGTAATTTCCATATATTTATTCA
*
8573 GGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAACTAGTTCTCTCGCTCCTCATTAAT
1 GGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAACTAGGTCTCTCGCTCCTCATTAAT
**
8638 CCGGGATAGGGATCTTTTAGTAATTTTTATATATTTATTCA
66 CCGGGATAGGGATCTTTTAGTAATTTCCATATATTTATTCA
8679 AATAATATGT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (106 bp):
GGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAAAAAACTAGGTCTCTCGCTCCTCATTAAT
CCGGGATAGGGATCTTTTAGTAATTTCCATATATTTATTCA
Done.