Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009141.1 Corchorus capsularis cultivar CVL-1 contig09162, 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: 11045
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1804 original size:109 final size:109
Alignment explanation
Indices: 1648--2014 Score: 596
Period size: 109 Copynumber: 3.5 Consensus size: 109
1638 AGTTTAGCCT
1648 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1713 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAAAC
1757 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
*
1822 AATAATTTATTGTTATAGGGTTTTAGAAAT-AAA-ATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAAAC
*
1864 TAATTTCACTAAGTTTAGCCCCAAATT--AA--TT-TTTTTATTTTAAGGGTAAATTTCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1924 AATAATTTATTGTTATAGGG-TTTAGAAATAAAATATAT--AAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAAAC
* ** *
1965 TAA-TTCACTAAATTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
2015 TAGAAAAATT
Statistics
Matches: 244, Mismatches: 7, Indels: 19
0.90 0.03 0.07
Matches are distributed among these distances:
99 8 0.03
100 13 0.05
101 17 0.07
102 51 0.21
103 5 0.02
104 15 0.06
105 2 0.01
107 35 0.14
108 3 0.01
109 95 0.39
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (109 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAAAC
Found at i:10175 original size:22 final size:22
Alignment explanation
Indices: 10105--10405 Score: 154
Period size: 22 Copynumber: 13.5 Consensus size: 22
10095 ATATTTTTAT
** * *
10105 AAATTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTCCATATG
* *
10127 AAATTTTGTTAACCTCTC-TAAG
1 AAATTTTGATAACCTC-CATATG
* * *
10149 GAATTTTGAAAACCTCAATATG
1 AAATTTTGATAACCTCCATATG
*
10171 AAATTTTGATAACTTCCCA-ATG
1 AAATTTTGATAACCT-CCATATG
**
10193 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACCTCCA-TATG
* *
10216 AGATATTGATAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
* * * **
10238 ATATATTGATAACCACGTTATG
1 AAATTTTGATAACCTCCATATG
* * *
10260 AAAATTTAAAAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
*
10282 -AATTGTT-AGTAA--TCACACTCTG
1 AAATT-TTGA-TAACCTC-CA-TATG
*
10304 AACTTTTGATAA--TCACACTATG
1 AAATTTTGATAACCTC-CA-TATG
*
10326 AAATTGTGATAACCTCGC-TATG
1 AAATTTTGATAACCTC-CATATG
* *
10348 AAATTTTGATAAATCTTCC-TATA
1 AAATTTTGAT-AA-CCTCCATATG
* *
10371 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCATATG
10394 AAATTTTGATAA
1 AAATTTTGATAA
10406 ATGTCACGAT
Statistics
Matches: 220, Mismatches: 43, Indels: 32
0.75 0.15 0.11
Matches are distributed among these distances:
20 2 0.01
21 8 0.04
22 147 0.67
23 57 0.26
24 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATG
Found at i:10374 original size:23 final size:23
Alignment explanation
Indices: 10307--10407 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 23
10297 CACTCTGAAC
* * *
10307 TTTTGAT-AATCACACTATGAAA
1 TTTTGATAAATCTCCCTATAAAA
* * * *
10329 TTGTGAT-AACCTCGCTATGAAA
1 TTTTGATAAATCTCCCTATAAAA
*
10351 TTTTGATAAATCTTCCTATAAAA
1 TTTTGATAAATCTCCCTATAAAA
*
10374 TTTTGATAAACCTCCCTATAAAA
1 TTTTGATAAATCTCCCTATAAAA
10397 TTTTGATAAAT
1 TTTTGATAAAT
10408 GTCACGATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 24 0.36
23 42 0.64
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTTGATAAATCTCCCTATAAAA
Found at i:10398 original size:46 final size:45
Alignment explanation
Indices: 10321--10407 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
10311 GATAATCACA
* * *
10321 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATAAAATTGTGATAACCTCCCTATAAAATTTTGATAAATCTTC
*
10366 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAAAT
1 CTATAAAATTGTGAT-AACCTCCCTATAAAATTTTGATAAAT
10408 GTCACGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.35
46 24 0.65
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (45 bp):
CTATAAAATTGTGATAACCTCCCTATAAAATTTTGATAAATCTTC
Found at i:10418 original size:46 final size:45
Alignment explanation
Indices: 10326--10418 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 45
10316 TCACACTATG
* * * *
10326 AAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCCTATA
1 AAATTGTGATAACCTCCCTATAAAATTTTGATAAATCGTCCGATA
*
10371 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAAT-GTCACGATA
1 AAATTGTGAT-AACCTCCCTATAAAATTTTGATAAATCGTC-CGATA
10417 AA
1 AA
10419 TCTCCATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 11 0.27
46 30 0.73
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (45 bp):
AAATTGTGATAACCTCCCTATAAAATTTTGATAAATCGTCCGATA
Found at i:10512 original size:73 final size:73
Alignment explanation
Indices: 10393--10540 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
10383 ACCTCCCTAT
10393 AAAATTTTGATAAATGTCACGATAAATCTCCATTGACACCAGAAATTGTCAATGGTGTTACAATT
1 AAAATTTTGATAAATGTCACGATAAATCTCCATTGACACCAGAAATTGTCAATGGTGTTACAATT
10458 GACACCAG
66 GACACCAG
10466 AAAATTTTGATAAATGTCACGATAAATCTCCATTGACACCAGAAATTGTCAATGGTGTTACAATT
1 AAAATTTTGATAAATGTCACGATAAATCTCCATTGACACCAGAAATTGTCAATGGTGTTACAATT
10531 GACACCAG
66 GACACCAG
10539 AA
1 AA
10541 GTTGTCAATG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (73 bp):
AAAATTTTGATAAATGTCACGATAAATCTCCATTGACACCAGAAATTGTCAATGGTGTTACAATT
GACACCAG
Found at i:10615 original size:30 final size:30
Alignment explanation
Indices: 10497--10746 Score: 365
Period size: 30 Copynumber: 8.2 Consensus size: 30
10487 ATAAATCTCC
* * * *
10497 ATTGACACCAGAAATTGTCAATGGTGTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCA
* *
10528 ATTGACACCAGAAGTTGTCAATGATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCA
*
10559 AATGACACCAGAAGTTGTCAATGATTTTGCA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCA
*
10590 ATTGACACCATAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
10620 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
* *
10650 ATTGACACCAGAAGTTGTCATCATTTTGAA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
10680 ATTGACACCATAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
10710 ATTGACACCATAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
10740 ATTGACA
1 ATTGACA
10747 AGCAATTGAC
Statistics
Matches: 205, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
30 132 0.64
31 73 0.36
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATTTTGCA
Found at i:10665 original size:60 final size:60
Alignment explanation
Indices: 10497--10985 Score: 609
Period size: 60 Copynumber: 7.8 Consensus size: 60
10487 ATAAATCTCC
* * * * * *
10497 ATTGACACCAGAAATTGTCAATGGTGTTACAATTGACACCAGAAGTTGTCAATGATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACCAGAAGTTGTC-ATGATTTTGCA
* *
10559 AATGACACCAGAAGTTGTCAATGATTTTGCAATTGACACCATAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
* *
10620 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATCATTTTGAA
1 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
* *
10680 ATTGACACCATAAGTTGTCATGATTTTGCAATTGACACCATAAGTTGTCATGATTTTGCAATTGA
1 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA--TT----TT--
10745 CAAGCA
58 ---GCA
* * * *
10751 ATTGACACCAGAAGTTGTCATGATCTTGCAAATGACACCAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
* *
10811 AATGACACCAGAAGTTGTCATGATTTTGCACTTGACACCAGAAGTTGTCATGATTTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA-TTTTGCA
*
10872 ATTGACACCGGAAGTTGTCATGATTTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGA-TTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
** * *
10933 ATTGACACTTGAAGATGTCATGATTTTATTCAATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCATGA-TTT-TGCAATTGACACCAGAAGTTGTCAT
10986 ATACACCATG
Statistics
Matches: 378, Mismatches: 35, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
60 139 0.37
61 84 0.22
62 99 0.26
65 2 0.01
66 2 0.01
69 1 0.00
71 51 0.13
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (60 bp):
ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
Found at i:10766 original size:41 final size:41
Alignment explanation
Indices: 10707--10787 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
10697 TCATGATTTT
* * *
10707 GCAATTGACACCATAAGTTGTCATGATTTTGCAATTGACAA
1 GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACAA
10748 GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACA
1 GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACA
10788 CCAGAAGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACAA
Found at i:10826 original size:101 final size:101
Alignment explanation
Indices: 10647--10939 Score: 394
Period size: 101 Copynumber: 3.0 Consensus size: 101
10637 TCATGATTTT
* *
10647 GCAATTGACACCAGAAGTTGTCATCATTTTG-AAATTGACACCATAAGTTGTCATGATTTTGCAA
1 GCAATTGACACCAGAAGTTGTCATGATTTTGCAAA-TGACACCAGAAGTTGTCATGATTTTGCAA
*
10711 TTGACACCATAAGTTGTCATGATTTTGCAATTGACAA
65 TTGACACCAGAAGTTGTCATGATTTTGCAATTGACAA
* * * *
10748 GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACACCAGAAGTTGTCATGATCTTACAAA
1 GCAATTGACACCAGAAGTTGTCATGATTTTGCAAATGACACCAGAAGTTGTCATGATTTTGCAAT
10813 TGACACCAGAAGTTGTCATGA--TT----TTG-C-A
66 TGACACCAGAAGTTGTCATGATTTTGCAATTGACAA
* *
10841 -C--TTGACACCAGAAGTTGTCATGATTTTTGCAATTGACACCGGAAGTTGTCATGATTTTTGCA
1 GCAATTGACACCAGAAGTTGTCATGA-TTTTGCAAATGACACCAGAAGTTGTCATGA-TTTTGCA
10903 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACA
64 ATTGACACCAGAAGTTGTCATGATTTTGCAATTGACA
10940 CTTGAAGATG
Statistics
Matches: 168, Mismatches: 13, Indels: 23
0.82 0.06 0.11
Matches are distributed among these distances:
90 22 0.13
91 27 0.16
92 28 0.17
93 1 0.01
94 3 0.02
95 3 0.02
98 3 0.02
99 3 0.02
101 75 0.45
102 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (101 bp):
GCAATTGACACCAGAAGTTGTCATGATTTTGCAAATGACACCAGAAGTTGTCATGATTTTGCAAT
TGACACCAGAAGTTGTCATGATTTTGCAATTGACAA
Found at i:10856 original size:131 final size:121
Alignment explanation
Indices: 10748--10985 Score: 350
Period size: 122 Copynumber: 1.9 Consensus size: 121
10738 CAATTGACAA
* * * *
10748 GCAATTGACACCAGAAGTTGTCATGATCTTGCAAATGACACCAGAAGTTGTCATGATCTTACAAA
1 GCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAAT
*
10813 TGACACCAGAAGTTGTCATGATTTTGCACTTGACACCAGAAGTTGTCATGATTTTT
66 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTT
* *
10869 GCAATTGACACCGGAAGTTGTCATGATTTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAA
1 GCAATTGACACCAGAAGTTGTCATGA-TTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAA
** * *
10934 TTGACACTTGAAGATGTCATGATTTTATTCAATTGACACCAGAAGTTGTCAT
65 TTGACACCAGAAGTTGTCATGA-TTT-TGCAATTGACACCAGAAGTTGTCAT
10986 ATACACCATG
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
121 25 0.24
122 52 0.50
123 3 0.03
124 23 0.22
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (121 bp):
GCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAAT
TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTT
Found at i:10877 original size:31 final size:30
Alignment explanation
Indices: 10748--10985 Score: 341
Period size: 30 Copynumber: 7.8 Consensus size: 30
10738 CAATTGACAA
*
10748 GCAATTGACACCAGAAGTTGTCATGATCTT
1 GCAATTGACACCAGAAGTTGTCATGATTTT
* *
10778 GCAAATGACACCAGAAGTTGTCATGATCTT
1 GCAATTGACACCAGAAGTTGTCATGATTTT
* *
10808 ACAAATGACACCAGAAGTTGTCATGATTTT
1 GCAATTGACACCAGAAGTTGTCATGATTTT
*
10838 GCACTTGACACCAGAAGTTGTCATGATTTTT
1 GCAATTGACACCAGAAGTTGTCATGA-TTTT
*
10869 GCAATTGACACCGGAAGTTGTCATGATTTTT
1 GCAATTGACACCAGAAGTTGTCATGA-TTTT
10900 GCAATTGACACCAGAAGTTGTCATGATTTT
1 GCAATTGACACCAGAAGTTGTCATGATTTT
** *
10930 GCAATTGACACTTGAAGATGTCATGATTTTAT
1 GCAATTGACACCAGAAGTTGTCATGA-TTT-T
*
10962 TCAATTGACACCAGAAGTTGTCAT
1 GCAATTGACACCAGAAGTTGTCAT
10986 ATACACCATG
Statistics
Matches: 189, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
30 107 0.57
31 61 0.32
32 21 0.11
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (30 bp):
GCAATTGACACCAGAAGTTGTCATGATTTT
Done.