Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020476.1 Corchorus olitorius cultivar O-4 contig20509, 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: 41547
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:4042 original size:723 final size:723
Alignment explanation
Indices: 2656--5014 Score: 4262
Period size: 723 Copynumber: 3.3 Consensus size: 723
2646 CGATCAGATA
*
2656 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTTTA
1 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
*
2721 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTTATGTGACGACATGAGGA
66 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACGACATGAGGA
*
2786 CACACATCTTACTACTTGCTCAACAAGGCCGACCATACACAAGGACTTCTAAGTCATTTGCACTC
131 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGGACTTCTAAGTCATTTGCACTC
* *
2851 CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCTATAACG
196 CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCAATAATG
* * * *
2916 CAAACTATGTGAGGTGTGTGTAGGAACAACCTACCATACCACATACCGTAACTTGTTAGACCTAG
261 CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
*
2981 TAACTAACTGATGAGACCAAGATGTTACATGTATTTGGTGTCTATTATTCATGTATTTGATATGT
326 TAACTAACTGATGAGACCAAGATGTTACATGTATTTCGTGTCTATTATTCATGTATTTGATATGT
* *
3046 TTTATATACTATTTTACCCACTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
391 TTTATATGCTATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
*
3111 GCAATATGGTCTAAAATGAAGCTAATTAAATTGAGCTATTTAGAGCACATTAGGATTGAAGCCCA
456 GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTAGAGCACATTAGGATTGAAGCCCA
* *
3176 AAAGAAGACCTCAAGATGGTGTTTTCGACCATAATCCATTGGATGTGGTAAACCATGTGTTGATG
521 AAAGAAGACCTCAAGATGGTGATTTCGACCATAGTCCATTGGATGTGGTAAACCATGTGTTGATG
*
3241 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGTAGATAACTTG
586 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
*
3306 AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTGGTTAAGCATACCTTACTTGGTTGCCC
651 AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTGGTTAAGCATATCTTACTTGGTTGCCC
3371 AAACGATC
716 AAACGATC
3379 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
1 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
* * *
3444 TCTTTACTAGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACTACATGGGGA
66 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACGACATGAGGA
*
3509 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGTACTTCTAAGTCATTTGCACTC
131 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGGACTTCTAAGTCATTTGCACTC
3574 CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCAATAATG
196 CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCAATAATG
3639 CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
261 CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
*
3704 TAACTAACTAATGAGACCAAGATGTTACATGTATTTCGTGTCTATTATTCATGTATTTGATATGT
326 TAACTAACTGATGAGACCAAGATGTTACATGTATTTCGTGTCTATTATTCATGTATTTGATATGT
3769 TTTATATGCTATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
391 TTTATATGCTATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
*
3834 GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTAGAGCACATTAGGATCGAAGCCCA
456 GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTAGAGCACATTAGGATTGAAGCCCA
*
3899 AAAGAAGACCTCAAGATTGTGATTTCGACCATAGTCCATTGGATGTGGTAAACCATGTGTTGATG
521 AAAGAAGACCTCAAGATGGTGATTTCGACCATAGTCCATTGGATGTGGTAAACCATGTGTTGATG
3964 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
586 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
* *
4029 AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTCGTTAAGCATATCTTACTT-GTTGCAC
651 AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTGGTTAAGCATATCTTACTTGGTTGCCC
4093 AAACGATC
716 AAACGATC
4101 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTT--A--GGGATTTATA
1 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
*
4162 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTTATGTGACGACATGAGGA
66 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACGACATGAGGA
* * *
4227 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACTCAAGGACTTCCAAGTCATTTACACTC
131 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGGACTTCTAAGTCATTTGCACTC
*
4292 CCACGTAGGCCGGCTATTATACCTCCCAAAACTAGAATAGGTAACCAAATGTAAATGCAATAATG
196 CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCAATAATG
4357 CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
261 CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
*
4422 TAACTAACTGATGAGACCAAGATGTTACATGTATTTCGTGTCT-TTATTCATGTACTTGATATGT
326 TAACTAACTGATGAGACCAAGATGTTACATGTATTTCGTGTCTATTATTCATGTATTTGATATGT
* * *
4486 TTTACATGATATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAAAGAAAGTT
391 TTTATATGCTATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
* *
4551 GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTGGAGAACATTAGGATTGAAGCCCA
456 GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTAGAGCACATTAGGATTGAAGCCCA
* *
4616 AAAGAGGACCTCAAGATGGTGATTTCGACCAAAGTCCATTGGATGTGGTAAACCATGTGTTGATG
521 AAAGAAGACCTCAAGATGGTGATTTCGACCATAGTCCATTGGATGTGGTAAACCATGTGTTGATG
4681 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
586 AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
*
4746 AGAAGATGAAGACAAGAGCCGCCCAATCAAGAGTATGTGGTTAAGCATATCTTACTTGGTTGCCC
651 AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTGGTTAAGCATATCTTACTTGGTTGCCC
4811 AAACGATC
716 AAACGATC
* *
4819 ATATCAAGTCCAAGTGAACAGAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
1 ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
* *
4884 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTTTCATGTGACTACATGAGGA
66 TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACGACATGAGGA
* *
4949 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACTCAAGGAATTCTAAGTCATTTGCACTC
131 CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGGACTTCTAAGTCATTTGCACTC
5014 C
196 C
5015 TAGCTAACCC
Statistics
Matches: 1574, Mismatches: 57, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
717 326 0.21
718 365 0.23
720 2 0.00
722 199 0.13
723 682 0.43
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (723 bp):
ATATCAAGTCCAAGTCAACATAAGTCAAGTATAGGAAACCATATGTGCTTAAATGGGGATTTATA
TCTTTACTTGATGAGCCTAGATCGTTCAACAACTAGATGTGGGTTGTCATGTGACGACATGAGGA
CACACATCTTACTACTTGCTCAACAAGGCCGGCCATACACAAGGACTTCTAAGTCATTTGCACTC
CCACGTAGGCCGGCTATTATACCTCCCAAAATTAGAATAGGTAACCAAATGTAAATGCAATAATG
CAGACTATGTGAGGTGTGTGAAGGAACAACCTACCATACCACATACCATAACCTGTTAGACCTAG
TAACTAACTGATGAGACCAAGATGTTACATGTATTTCGTGTCTATTATTCATGTATTTGATATGT
TTTATATGCTATTTTACCCTCTAATATGACGTTTTGCACTTGTAGGCCTATTTAGAGAGAAAGTT
GCAATATGGTCTAAAATGAAGCTAATTAAATGGAGCTATTTAGAGCACATTAGGATTGAAGCCCA
AAAGAAGACCTCAAGATGGTGATTTCGACCATAGTCCATTGGATGTGGTAAACCATGTGTTGATG
AAGATCATGAAAGTTATCAGTGGAATCCTGAATGATTATCAATGGAGATCTAAGAAGATAACTTG
AGAAGATGAAGACAAGAGCCACCCAATCAAGAGTATGTGGTTAAGCATATCTTACTTGGTTGCCC
AAACGATC
Found at i:21300 original size:21 final size:21
Alignment explanation
Indices: 21274--21320 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21264 AGGCAAAATT
21274 GGTTTCAAAATTGGGATTTAC
1 GGTTTCAAAATTGGGATTTAC
*
21295 GGTTTCAAAATTGGGATTTAT
1 GGTTTCAAAATTGGGATTTAC
21316 GGTTT
1 GGTTT
21321 GGGATTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (21 bp):
GGTTTCAAAATTGGGATTTAC
Found at i:21332 original size:33 final size:33
Alignment explanation
Indices: 21295--21409 Score: 107
Period size: 33 Copynumber: 3.6 Consensus size: 33
21285 TGGGATTTAC
21295 GGTTTCAAAATTGGGATTTATGGTTTGGGATTG
1 GGTTTCAAAATTGGGATTTATGGTTTGGGATTG
* * ** ***
21328 GGTTT-AAGAGTT--G-TTT-TCGAATCAAAGTT-
1 GGTTTCAA-AATTGGGATTTATGGTTTGGGA-TTG
21357 GGTTTCAAAATTGGGATTTATGGTTTGGGATTG
1 GGTTTCAAAATTGGGATTTATGGTTTGGGATTG
21390 GGTTTCAAAATTGGGATTTA
1 GGTTTCAAAATTGGGATTTA
21410 CTTTGAAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
29 12 0.20
30 7 0.12
31 2 0.03
32 7 0.12
33 32 0.53
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.42
Consensus pattern (33 bp):
GGTTTCAAAATTGGGATTTATGGTTTGGGATTG
Found at i:23528 original size:4 final size:4
Alignment explanation
Indices: 23513--23560 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
23503 CTTAGCCTTG
* * * *
23513 TGTT TTTT TGTT TGTT TGTT TGCT TGCT TGCT TGTT TGTT TGTT TGTT
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
23561 GTAATAGACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.06, G:0.23, T:0.71
Consensus pattern (4 bp):
TGTT
Found at i:25669 original size:3 final size:3
Alignment explanation
Indices: 25661--25695 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
25651 TATAAATTCT
25661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25696 TTGGGTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27283 original size:22 final size:22
Alignment explanation
Indices: 27258--27299 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27248 GTTTTTAATA
*
27258 TTCTCTGGTCATTCGGGTTAAC
1 TTCTCGGGTCATTCGGGTTAAC
*
27280 TTCTCGGGTCATTTGGGTTA
1 TTCTCGGGTCATTCGGGTTA
27300 TGGGTTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTAAC
Found at i:29966 original size:3 final size:3
Alignment explanation
Indices: 29960--29991 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29950 GTTTTTTTTC
*
29960 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29992 ATACAAGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:33389 original size:15 final size:15
Alignment explanation
Indices: 33369--33397 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33359 CTACGATTTG
33369 AGCACAAGAATGGCT
1 AGCACAAGAATGGCT
33384 AGCACAAGAATGGC
1 AGCACAAGAATGGC
33398 ATGATCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.28, T:0.10
Consensus pattern (15 bp):
AGCACAAGAATGGCT
Found at i:38407 original size:27 final size:27
Alignment explanation
Indices: 38369--38467 Score: 153
Period size: 27 Copynumber: 3.7 Consensus size: 27
38359 CGACCCGAGG
* *
38369 CGAAGTGGGAGGATCCATTGCTGGTGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
*
38396 CGAAGTGGGAGGATCCACTACTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
38423 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* *
38450 TGAAGTGGGAGGTTCCAC
1 CGAAGTGGGAGGATCCAC
38468 CGCGGCAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.21
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Done.