Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014511.1 Corchorus olitorius cultivar O-4 contig14544, 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: 21342
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1074 original size:31 final size:31
Alignment explanation
Indices: 1037--1485 Score: 631
Period size: 31 Copynumber: 14.6 Consensus size: 31
1027 AAATTTATTA
* *
1037 TGACAACTTCTGGTGTCTATTGTAAGAACAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* *
1068 TGACAACTTCTGGTGTCAATTATAAGATCA-
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1098 TGACAACTTCTGATGTCAATTGTAAGACCA-
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1128 TGACAACTTCTGGTGTCAATTCTAAGACCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
1159 TGACAACTTCTGGTGTCAATTGTAAGACCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1190 TGACAACTTCTGGTGTCAATTGTAAGATCA-
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* ***
1220 TGACAACTTTTGGTGTCAATTGTAAGGTTAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* * *
1251 TGACAATTTCTGGTGCCAATTGTAAGGCCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* *
1282 TGACAACTTCTGGTGCCAATTGTAAGGCCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* *
1313 TGACAACTTCTGGTGCCAATTGTAAGGCCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1344 TGACAACTTCTGGTGTCAATTGTAAGGCCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
* *
1375 TGACAACTTCTGGTATCAATTGTAAGGCCAT
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1406 TGACAACTTCTGGTGTCAATTGTAAGATCA-
1 TGACAACTTCTGGTGTCAATTGTAAGACCAT
*
1436 TGACAAC-TCTTGGTGTCAATTGTAAGATCA-
1 TGACAACTTC-TGGTGTCAATTGTAAGACCAT
*
1466 TGACAACTTTTGGTGTCAAT
1 TGACAACTTCTGGTGTCAAT
1486 ATATATTTTA
Statistics
Matches: 389, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
29 2 0.01
30 126 0.32
31 261 0.67
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
TGACAACTTCTGGTGTCAATTGTAAGACCAT
Found at i:1235 original size:92 final size:92
Alignment explanation
Indices: 1036--1485 Score: 629
Period size: 92 Copynumber: 4.9 Consensus size: 92
1026 GAAATTTATT
* * * *
1036 ATGACAACTTCTGGTGTCTATTGTAAGAACATTGACAACTTCTGGTGTCAATTATAAGATCA-TG
1 ATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATTG
*
1100 ACAACTTCTGATGTCAATTGTAAGACC
66 ACAACTTCTGGTGTCAATTGTAAGACC
*
1127 ATGACAACTTCTGGTGTCAATTCTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATTG
1 ATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATTG
*
1192 ACAACTTCTGGTGTCAATTGTAAGATC
66 ACAACTTCTGGTGTCAATTGTAAGACC
* *** * * *
1219 ATGACAACTTTTGGTGTCAATTGTAAGGTTATTGACAATTTCTGGTGCCAATTGTAAGGCCATTG
1 ATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATTG
* *
1284 ACAACTTCTGGTGCCAATTGTAAGGCC
66 ACAACTTCTGGTGTCAATTGTAAGACC
* * *
1311 ATTGACAACTTCTGGTGCCAATTGTAAGGCCATTGACAACTTCTGGTGTCAATTGTAAGGCCATT
1 A-TGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATT
* *
1376 GACAACTTCTGGTATCAATTGTAAGGCC
65 GACAACTTCTGGTGTCAATTGTAAGACC
* *
1404 ATTGACAACTTCTGGTGTCAATTGTAAGATCA-TGACAAC-TCTTGGTGTCAATTGTAAGATCA-
1 A-TGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTC-TGGTGTCAATTGTAAGACCAT
*
1466 TGACAACTTTTGGTGTCAAT
64 TGACAACTTCTGGTGTCAAT
1486 ATATATTTTA
Statistics
Matches: 323, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
91 77 0.24
92 134 0.41
93 112 0.35
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (92 bp):
ATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGACCATTG
ACAACTTCTGGTGTCAATTGTAAGACC
Found at i:6456 original size:10 final size:10
Alignment explanation
Indices: 6441--6470 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
6431 ATTGTCCCTA
6441 TATCTATATC
1 TATCTATATC
6451 TATCTATATC
1 TATCTATATC
6461 TATACTATAT
1 TAT-CTATAT
6471 TAAAAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (10 bp):
TATCTATATC
Found at i:6459 original size:16 final size:15
Alignment explanation
Indices: 6438--6468 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6428 ATAATTGTCC
6438 CTATATCTATATCTAT
1 CTATATCTATA-CTAT
6454 CTATATCTATACTAT
1 CTATATCTATACTAT
6469 ATTAAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
CTATATCTATACTAT
Found at i:6670 original size:63 final size:62
Alignment explanation
Indices: 6597--6791 Score: 154
Period size: 63 Copynumber: 3.2 Consensus size: 62
6587 ATTTTTATTT
6597 AATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAGAAA
1 AATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTA-AAA
* * * *** * *** *
6660 AATTATATATATTAATATAT-TTTAT-AGT-TTTACTCAACTA-AAAACT-CTATTTTTATT---
1 AATTA-A-ATA-TAATATATCCTTATAACTATTTAAT-TTTTACCATTTTACTATTTTAATTAAA
*
6717 T
62 A
*
6718 AATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACAATTTTAATTAAAAA
1 AATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATT-AAAA
*
6781 AATTATATATA
1 AATTAAATATA
6792 TTAGAATTTT
Statistics
Matches: 93, Mismatches: 26, Indels: 26
0.64 0.18 0.18
Matches are distributed among these distances:
55 8 0.09
56 7 0.08
57 5 0.05
58 12 0.13
59 9 0.10
62 10 0.11
63 22 0.24
64 5 0.05
65 7 0.08
66 8 0.09
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (62 bp):
AATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAA
Found at i:6772 original size:58 final size:58
Alignment explanation
Indices: 6589--6777 Score: 147
Period size: 58 Copynumber: 3.2 Consensus size: 58
6579 AAAACTCTAT
* *
6589 TTTTATTTAATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACTA
1 TTTTAATTAATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACAA
* * * ***
6647 TTTTAATTAGA--AAA-ATTATATAT-ATTA-ATA-TATTTTATAGTTTTACTCAACTAAAAACT
1 TTTTAATTA-ATTAAATATAATATATCCTTATA-ACTA-TTTA-ATTTTTAC-C-A-T-TTTA--
*
6706 CTAT
56 C-AA
*
6710 TTTTATTTAATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACAA
1 TTTTAATTAATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACAA
6768 TTTTAATTAA
1 TTTTAATTAA
6778 AAAAATTATA
Statistics
Matches: 96, Mismatches: 18, Indels: 34
0.65 0.12 0.23
Matches are distributed among these distances:
54 3 0.03
55 8 0.08
56 15 0.16
57 4 0.04
58 19 0.20
59 3 0.03
60 1 0.01
61 1 0.01
62 3 0.03
63 9 0.09
64 4 0.04
65 15 0.16
66 8 0.08
67 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (58 bp):
TTTTAATTAATTAAATATAATATATCCTTATAACTATTTAATTTTTACCATTTTACAA
Found at i:6804 original size:121 final size:121
Alignment explanation
Indices: 6558--6794 Score: 456
Period size: 121 Copynumber: 2.0 Consensus size: 121
6548 TTGTTTAGAC
6558 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
* *
6623 TATTTAATTTTTACCATTTTACTATTTTAATTAGAAAAATTATATATATTAATATA
66 TATTTAATTTTTACCATTTTACAATTTTAATTAAAAAAATTATATATATTAATATA
6679 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
6744 TATTTAATTTTTACCATTTTACAATTTTAATTAAAAAAATTATATATATTA
66 TATTTAATTTTTACCATTTTACAATTTTAATTAAAAAAATTATATATATTA
6795 GAATTTTTTA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (121 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
TATTTAATTTTTACCATTTTACAATTTTAATTAAAAAAATTATATATATTAATATA
Found at i:8825 original size:13 final size:13
Alignment explanation
Indices: 8807--8831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8797 TTTAATGTTC
8807 TAAATATTATTTA
1 TAAATATTATTTA
8820 TAAATATTATTT
1 TAAATATTATTT
8832 TGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:15475 original size:4 final size:4
Alignment explanation
Indices: 15466--15494 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
15456 AAAGTGATAC
15466 AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
15495 ACACACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:18753 original size:433 final size:433
Alignment explanation
Indices: 17951--18996 Score: 1323
Period size: 433 Copynumber: 2.4 Consensus size: 433
17941 AATCTAGATA
* ** * * * * * **
17951 AAAAATTATATGATATTAAATAGACCATCAATCGAAACCACAAAA-TATCGAAAGCCTTTTTTAG
1 AAAAATTAAATGATATTAAATAGACCGGCAACCAAAACCACAAAATTTTGGAAA-CATTTTTTTT
* *
18015 AATTGAAACATAAAAATTAGCTTTTGAATCCTTTCAA-GAAAGTTGTATG-TCATGAAATTACCT
65 AATTGAAACATAAAAATTGGCTTTTGAGTCC-TT-AATGAAAGTTGTA-GATCATGAAATTACCT
* * *
18078 TTTAATATACACCTGAATTACCTTAATTGCACAAATAGAACAAAGAAAAAAGAAAAAGCCGAAGC
127 TTTAATAGACACCTGAATTACCTTAATCGGACAAATAG-----A-AAAAAA-AAAAAGCCGAAGC
*** * * * * * * *
18143 GTTAAATCAAATAAGATAGAATTTGTAATGGACTAAGTAGTATAAAGTAGATAAGTATGAGGGTC
185 GTTAAATCAAATAAGATAGAATCAATAAAGAACTAACTAGTATAAAGTACAAAAATATGAGGATC
* *
18208 ATTTGATAAATAATCCAAATAAGAATATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCCC
250 ATTTGAAAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCCC
* * * *
18273 TTTGAACCCTTCATGAAACTCATAGATCAAATTTAACTTTTGGGTCCTTCATGAAAGTCGTAAAT
315 TTTGAACCCTCCATGAAACTCATAAATCAAATTTAACTTTCGGGTCCTTCATGAAAGACGTAAAT
* *
18338 CATGCAATAACCTTTTAACCAACACTTGAATAACTTTAATCGGACATGTGGATC
380 CATGCAATAACCTTCTAACCAACACTTGAATAACTTTAATCAGACATGTGGATC
* * * *
18392 AAAAATTAAATGCTATTAAATAGGCTGGCAACCAAAACCACCAAA-TTTGAGAAAC-TTTATTTT
1 AAAAATTAAATGATATTAAATAGACCGGCAACCAAAACCACAAAATTTTG-GAAACATTT-TTTT
*
18455 TAATTGAAACATAAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGATAATGAAATTACCTTT
64 TAATTGAAACATAAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGATCATGAAATTACCTTT
* * * * * *
18520 TAATAGACATCTTAATCACCTTAATCGGACAAATAGAATAAAAAAAAATCTGAAGCGTTAAATC-
129 TAATAGACACCTGAATTACCTTAATCGGACAAATAGAAAAAAAAAAAAGCCGAAGCGTTAAATCA
* *
18584 GATCAAGATAGAATCAATAAAGAACTAACTAGTATAAAGTACAAAAATATGAGGATTATTTGAAA
194 AAT-AAGATAGAATCAATAAAGAACTAACTAGTATAAAGTACAAAAATATGAGGATCATTTGAAA
* * * *
18649 AATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGCAACATAAAAATTCTCTTTTGAGCC
258 AATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCCCTTTGAACC
* * *
18714 CTCCATGAAACTCGTAAATCAAATTTAGCTTTCGGGTCCTTCATGAAAGACGTAGATCATGCAAT
323 CTCCATGAAACTCATAAATCAAATTTAACTTTCGGGTCCTTCATGAAAGACGTAAATCATGCAAT
* * *
18779 AACCTTCTAACCGACACTTTATTAACTTTAATCAGACATGTGGATC
388 AACCTTCTAACCAACACTTGAATAACTTTAATCAGACATGTGGATC
* * ** *
18825 GAAAATTATATGATATTAAATAGACCGGCAATTAAAACCACAAAATTTTGGAAGCATTTTTTTTA
1 AAAAATTAAATGATATTAAATAGACCGGCAACCAAAACCACAAAATTTTGGAAACATTTTTTTTA
* *
18890 ACTGAAACATAAAAATTGGCTTTTG-GATCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTT
66 ATTGAAACATAAAAATTGGCTTTTGAG-TCCTTAATGAAAGTTGTAGATCATGAAATTACCTTTT
* *
18954 AATAGACACCTGAATTATCTTAATCGGACAAATAGAAGAAAAA
130 AATAGACACCTGAATTACCTTAATCGGACAAATAGAAAAAAAA
18997 TTTTCAAAAT
Statistics
Matches: 525, Mismatches: 72, Indels: 24
0.85 0.12 0.04
Matches are distributed among these distances:
432 3 0.01
433 371 0.71
434 12 0.02
435 1 0.00
439 3 0.01
440 60 0.11
441 71 0.14
442 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (433 bp):
AAAAATTAAATGATATTAAATAGACCGGCAACCAAAACCACAAAATTTTGGAAACATTTTTTTTA
ATTGAAACATAAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGATCATGAAATTACCTTTTA
ATAGACACCTGAATTACCTTAATCGGACAAATAGAAAAAAAAAAAAGCCGAAGCGTTAAATCAAA
TAAGATAGAATCAATAAAGAACTAACTAGTATAAAGTACAAAAATATGAGGATCATTTGAAAAAT
AATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCCCTTTGAACCCTC
CATGAAACTCATAAATCAAATTTAACTTTCGGGTCCTTCATGAAAGACGTAAATCATGCAATAAC
CTTCTAACCAACACTTGAATAACTTTAATCAGACATGTGGATC
Done.