Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015836.1 Corchorus olitorius cultivar O-4 contig15869, 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: 53390
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:14041 original size:107 final size:109
Alignment explanation
Indices: 13853--14069 Score: 357
Period size: 107 Copynumber: 2.0 Consensus size: 109
13843 TCGAATTTAC
* *
13853 TAACCACCTACTCACATATATGATAAGAATCGAGAGAAATAAAAACTCTAAAACTAAAATGATTT
1 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAATAAAAACTCTAAAACTAAAATAATTT
* * *
13918 GCTAGCCACATATCAAGAATGCTCGACGTGCCAGCGCGAGCCGA
66 GCTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
13962 TAACCACCTACTCACATATATGATAAGAACCGAGA-AAA-AAAAACTCTAAAACTAAAATAATTT
1 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAATAAAAACTCTAAAACTAAAATAATTT
* *
14025 GCTAGCCATAAATCAAGAATGCTCAACGCGCCAGCGTGAGCCGA
66 GCTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
14069 T
1 T
14070 CAACTTGTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
107 64 0.63
108 3 0.03
109 34 0.34
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (109 bp):
TAACCACCTACTCACATATATGATAAGAACCGAGAGAAATAAAAACTCTAAAACTAAAATAATTT
GCTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
Found at i:18711 original size:25 final size:26
Alignment explanation
Indices: 18657--18725 Score: 131
Period size: 25 Copynumber: 2.7 Consensus size: 26
18647 TTTTACTACT
18657 AACAGAGAGCGACTCAGCCAAAAAAA
1 AACAGAGAGCGACTCAGCCAAAAAAA
18683 AACAGAGAGCGACTCAGCC-AAAAAA
1 AACAGAGAGCGACTCAGCCAAAAAAA
18708 AACAGAGAGCGACTCAGC
1 AACAGAGAGCGACTCAGC
18726 TAGTCTTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 24 0.56
26 19 0.44
ACGTcount: A:0.49, C:0.25, G:0.22, T:0.04
Consensus pattern (26 bp):
AACAGAGAGCGACTCAGCCAAAAAAA
Found at i:20175 original size:32 final size:32
Alignment explanation
Indices: 20108--20175 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
20098 GGGAAAATGA
*
20108 TGCAATATACAAAATCCTTCATTTTCCAATAC
1 TGCAATACACAAAATCCTTCATTTTCCAATAC
*
20140 TGCATATACACAAAATCTTTCATTTT-CAATAC
1 TGCA-ATACACAAAATCCTTCATTTTCCAATAC
20172 TGCA
1 TGCA
20176 CTAATCACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (32 bp):
TGCAATACACAAAATCCTTCATTTTCCAATAC
Found at i:23192 original size:26 final size:27
Alignment explanation
Indices: 23141--23192 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
23131 ATGGCTGATT
*
23141 AATGATTATTTCATTTTTCACTAAAAA
1 AATGATTATTTCATTTTTCACAAAAAA
*
23168 AATGATTATTTCA-TTTTCAGAAAAA
1 AATGATTATTTCATTTTTCACAAAAA
23193 TGGCATCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (27 bp):
AATGATTATTTCATTTTTCACAAAAAA
Found at i:27471 original size:18 final size:20
Alignment explanation
Indices: 27436--27477 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
27426 TTATTAACTT
*
27436 AAAATAAATTGAAAATTAA-
1 AAAATAAAATGAAAATTAAC
*
27455 AAAATAAAATG-AGATTAAC
1 AAAATAAAATGAAAATTAAC
27474 AAAA
1 AAAA
27478 AGCACTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAATAAAATGAAAATTAAC
Found at i:29451 original size:74 final size:74
Alignment explanation
Indices: 29330--29478 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
29320 TAGTCTTCGG
* *
29330 TGCTCCCGTTGTGATGTTTCCACTTTTCAATGTGATGCTCTCATTCAATCCTGACCATTGGATGC
1 TGCTCCCGTTGTGATGTTCCCACTTTTCAATGTGATCCTCTCATTCAATCCTGACCATTGGATGC
29395 AATATATAT
66 AATATATAT
29404 TGCTCCCGTTGTGATGTTCCCACTTTTCAATGTGATCCTCTCATTCAATCCTGACCATTGGATGC
1 TGCTCCCGTTGTGATGTTCCCACTTTTCAATGTGATCCTCTCATTCAATCCTGACCATTGGATGC
*
29469 AATATCTAT
66 AATATATAT
29478 T
1 T
29479 TTCCTGACCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (74 bp):
TGCTCCCGTTGTGATGTTCCCACTTTTCAATGTGATCCTCTCATTCAATCCTGACCATTGGATGC
AATATATAT
Found at i:32724 original size:14 final size:14
Alignment explanation
Indices: 32705--32733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32695 TCAAAATTCT
32705 ACCACAAATAAATC
1 ACCACAAATAAATC
32719 ACCACAAATAAATC
1 ACCACAAATAAATC
32733 A
1 A
32734 TATCTACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (14 bp):
ACCACAAATAAATC
Found at i:32921 original size:2 final size:2
Alignment explanation
Indices: 32914--32941 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32904 ATTGATATTG
32914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32942 TGTCTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52010 original size:23 final size:23
Alignment explanation
Indices: 51974--52036 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
51964 AAAAATATGC
51974 TATTAT-TATATATAATTGCTAT
1 TATTATATATATATAATTGCTAT
51996 TATTATATATATATAATTGCTAT
1 TATTATATATATATAATTGCTAT
*
52019 TATTATATATATAAAATT
1 TATTATATATATATAATT
52037 ATAAAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (23 bp):
TATTATATATATATAATTGCTAT
Found at i:52427 original size:2 final size:2
Alignment explanation
Indices: 52414--52451 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
52404 TTATACATAC
*
52414 AT AT AT AC AT AT AT AT AT AT AT AT AT AT CA- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
52452 CTCAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:52451 original size:10 final size:11
Alignment explanation
Indices: 52405--52452 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
52395 GCTACTTAAT
*
52405 TATA-CATACA
1 TATATCATATA
52415 TATATACATATA
1 TATAT-CATATA
52427 TATAT-ATATA
1 TATATCATATA
52437 TATATCA-ATA
1 TATATCATATA
52447 TATATC
1 TATATC
52453 TCAATTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 23 0.68
11 1 0.03
12 10 0.29
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (11 bp):
TATATCATATA
Found at i:52456 original size:12 final size:12
Alignment explanation
Indices: 52414--52457 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 12
52404 TTATACATAC
52414 ATATATA-C-AT
1 ATATATATCAAT
52424 ATATATAT--AT
1 ATATATATCAAT
52434 ATATATATCAAT
1 ATATATATCAAT
*
52446 ATATATCTCAAT
1 ATATATATCAAT
52458 TTTTAAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 17 0.57
12 13 0.43
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATATCAAT
Done.