Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015753.1 Corchorus capsularis cultivar CVL-1 contig15774, 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: 28742
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:964 original size:30 final size:29
Alignment explanation
Indices: 891--964 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 29
881 ACTTGTAGCA
891 TTTGGACGTTTTGCCTCCTGAACTTCAAT
1 TTTGGACGTTTTGCCTCCTGAACTTCAAT
*
920 TTTGGACATTTTGCCTCCTGAAC-TCTAAT
1 TTTGGACGTTTTGCCTCCTGAACTTC-AAT
949 TTTGAGACGTTTTGCC
1 TTTG-GACGTTTTGCC
965 CCCTCAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.05
29 29 0.71
30 10 0.24
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (29 bp):
TTTGGACGTTTTGCCTCCTGAACTTCAAT
Found at i:976 original size:29 final size:27
Alignment explanation
Indices: 891--976 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 27
881 ACTTGTAGCA
*
891 TTTGGACGTTTTGCCTCCTGAACTTCAAT
1 TTTGGACGTTTTGCCTCCTAAAC-T-AAT
* *
920 TTTGGACATTTTGCCTCCTGAACTCTAAT
1 TTTGGACGTTTTGCCTCCT-AA-ACTAAT
*
949 TTTGAGACGTTTTGCCCCCTCAAACTAA
1 TTTG-GACGTTTTGCCTCCT-AAACTAA
977 GGGCTCCGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 29 0.62
30 17 0.36
31 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (27 bp):
TTTGGACGTTTTGCCTCCTAAACTAAT
Found at i:1203 original size:29 final size:29
Alignment explanation
Indices: 1133--1213 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
1123 AGTCGTTAGA
1133 TTTAGGGGGCAAAACGTCCCAAAATTGAAG
1 TTTAGGGGGCAAAACGT-CCAAAATTGAAG
* ** * * *
1163 TTCAAAGAGCAAAATGTCCAAGATTGAAG
1 TTTAGGGGGCAAAACGTCCAAAATTGAAG
1192 TTTAGGGGGCAAAACGTCCAAA
1 TTTAGGGGGCAAAACGTCCAAA
1214 CACTACAAGT
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (29 bp):
TTTAGGGGGCAAAACGTCCAAAATTGAAG
Found at i:4581 original size:107 final size:107
Alignment explanation
Indices: 4395--4610 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
4385 AGCTTAGTTT
4395 TTGCCATAGATCTTTAGCTCAACATGTTGCTGCATAAATTCATGAAGAACCAAGCTTGAAACATG
1 TTGCCATAGATCTTTAGCTCAACATGTTGCTGCATAAATTCATGAAGAACCAAGCTTGAAACATG
*
4460 CCAATTAGTCGACCTAAGGGGCTGTTGAAATCGACATTAGGG
66 CCAAATAGTCGACCTAAGGGGCTGTTGAAATCGACATTAGGG
4502 TTGCCATAGAT-TATTAGCTCAACATGTTGCTGCATAAATTCATGAAGAACCAAGCTTGAAACAT
1 TTGCCATAGATCT-TTAGCTCAACATGTTGCTGCATAAATTCATGAAGAACCAAGCTTGAAACAT
4566 GCCAAATAGTCGACCTAAGGGGCTGTTGAAATCGACATTAGGG
65 GCCAAATAGTCGACCTAAGGGGCTGTTGAAATCGACATTAGGG
4609 TT
1 TT
4611 TCCTAACCCT
Statistics
Matches: 107, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
106 1 0.01
107 106 0.99
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (107 bp):
TTGCCATAGATCTTTAGCTCAACATGTTGCTGCATAAATTCATGAAGAACCAAGCTTGAAACATG
CCAAATAGTCGACCTAAGGGGCTGTTGAAATCGACATTAGGG
Found at i:16138 original size:156 final size:155
Alignment explanation
Indices: 15841--16194 Score: 374
Period size: 156 Copynumber: 2.3 Consensus size: 155
15831 TCTCAAACTA
* * *
15841 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAATTTTGCCAGG
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AATTTTACCAGG
* * * **
15906 GGACTTAGATTGTCCACATAAGACTATGGAAAAAATTATAAGTAAAACCGAACTCCCCTTGATGG
65 AGACTTAGATTATCCACATAAGACTATGGAAAAAATTATAAGTAAAACCGAACTCCCCTAGATAA
* * * *****
15971 TGAACTAGGTTTCTCTCCTTGTGTTG
130 AGAACTAGGTTTCACACCCCAAATTG
15997 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAGGCTG-ATTTTCCACCA
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGA-GCTGAATTTT--ACCA
* * * * *
16060 GTAGACTTATATTATCCCCATGAAG-CTATGGGAAAAATTATAAGTAAAACCGAACT-CTCTAGC
63 GGAGACTTAGATTATCCACAT-AAGACTATGGAAAAAATTATAAGTAAAACCGAACTCCCCTAG-
* * *
16123 ATAAAGAAGTTGGTTTGACACCCCAAATTG
126 ATAAAGAACTAGGTTTCACACCCCAAATTG
* * * *
16153 TCCTTAACTGAAAAACTTGCATAAGTTTTTCATACGAAGTCT
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
16195 GTTTGAGATG
Statistics
Matches: 164, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
154 5 0.03
155 8 0.05
156 148 0.90
157 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAATTTTACCAGGA
GACTTAGATTATCCACATAAGACTATGGAAAAAATTATAAGTAAAACCGAACTCCCCTAGATAAA
GAACTAGGTTTCACACCCCAAATTG
Found at i:16831 original size:27 final size:27
Alignment explanation
Indices: 16794--16846 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
16784 ATTGCAAGAT
16794 TTTCCTAATTCTGATAGAATCAGGATA
1 TTTCCTAATTCTGATAGAATCAGGATA
16821 TTTCCTAATTCTGATAGAATCAGGAT
1 TTTCCTAATTCTGATAGAATCAGGAT
16847 GGTGCAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (27 bp):
TTTCCTAATTCTGATAGAATCAGGATA
Found at i:17572 original size:27 final size:27
Alignment explanation
Indices: 17535--17594 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
17525 TTAATAAAAT
17535 TTCAT-TTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
*
17561 TTCATATTAATTACAAAAGAATTTACA
1 TTCATATTAATTACAAAAGAAATTACA
17588 TTCATAT
1 TTCATAT
17595 AAAATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (27 bp):
TTCATATTAATTACAAAAGAAATTACA
Found at i:20366 original size:2 final size:2
Alignment explanation
Indices: 20359--20411 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
20349 CAAAGCAAAG
* * * *
20359 TA TA TA TA TA TA TG TG TG TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20401 TA TA TA TA TA T
1 TA TA TA TA TA T
20412 CTTTATGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21233 original size:2 final size:2
Alignment explanation
Indices: 21226--21259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21216 TTGATCAAAC
21226 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21260 AACCCTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23176 original size:31 final size:31
Alignment explanation
Indices: 23141--23218 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
23131 GTCCTAACTG
23141 ATTATATCCTTAATTGCTTGAAATCGA-AAAC
1 ATTATATCCTTAATTGCTTGAAATC-ATAAAC
*
23172 ATTATATCATTAATTGCTTGAAATCATAAAC
1 ATTATATCCTTAATTGCTTGAAATCATAAAC
*
23203 GTTATATCCTTAATTG
1 ATTATATCCTTAATTG
23219 TTTGTTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (31 bp):
ATTATATCCTTAATTGCTTGAAATCATAAAC
Found at i:23375 original size:27 final size:27
Alignment explanation
Indices: 23309--23389 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
23299 TAATATAAAA
*
23309 TATTTTTTAAAAAATATTTTATTTTATTT
1 TATTTTTTAAAAAA-A-TATATTTTATTT
*
23338 T-TATTTT-AAAAAATATATTTTATTT
1 TATTTTTTAAAAAAATATATTTTATTT
23363 TATTTTTTAAAAAAATATATTTTATTT
1 TATTTTTTAAAAAAATATATTTTATTT
23390 AGATCACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.26
26 6 0.13
27 23 0.49
28 5 0.11
29 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTTTAAAAAAATATATTTTATTT
Found at i:24684 original size:22 final size:22
Alignment explanation
Indices: 24659--24951 Score: 129
Period size: 22 Copynumber: 13.1 Consensus size: 22
24649 TTTATTGAAT
24659 TTTCATATGGAGGTTATCAAAA
1 TTTCATATGGAGGTTATCAAAA
* *
24681 TTTCATA-GTTACGTTATCAAAA
1 TTTCATATG-GAGGTTATCAAAA
* *
24703 TTTCCT-TGTGAGGCTATCAAAA
1 TTTCATATG-GAGGTTATCAAAA
* **
24725 TTTCATGCTGTG-TTTTATCAAAA
1 TTTCAT-ATG-GAGGTTATCAAAA
* *
24748 TTTCATA-GTGTGGTTATCGAAA
1 TTTCATATG-GAGGTTATCAAAA
* * * **
24770 TTTCGT-TGGAAGATTTTTGAAA
1 TTTCATATGG-AGGTTATCAAAA
* *
24792 -TTAATTAATTGTGTGGTTATCAAAA
1 TTTCA-T-A-TG-GAGGTTATCAAAA
* *
24817 TTTCTTA-GGAAAGTTATCAAAA
1 TTTCATATGG-AGGTTATCAAAA
** **
24839 AATCATA-GGAAAATTATCAAAA
1 TTTCATATGG-AGGTTATCAAAA
*
24861 TTTCGTATGGAGGTTA-CTAAAA
1 TTTCATATGGAGGTTATC-AAAA
*
24883 TTTCATA-GGTAGGTTATTAAAA
1 TTTCATATGG-AGGTTATCAAAA
* *
24905 TTTCATATTGTGGTTATCAAAA
1 TTTCATATGGAGGTTATCAAAA
** *
24927 TTTCATAAAGAGATTATCAAAA
1 TTTCATATGGAGGTTATCAAAA
24949 TTT
1 TTT
24952 TACGAGGAAA
Statistics
Matches: 204, Mismatches: 48, Indels: 38
0.70 0.17 0.13
Matches are distributed among these distances:
21 11 0.05
22 158 0.77
23 17 0.08
24 5 0.02
25 10 0.05
26 3 0.01
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTCATATGGAGGTTATCAAAA
Found at i:24986 original size:22 final size:22
Alignment explanation
Indices: 24961--25008 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24951 TTACGAGGAA
*
24961 ATTATCACAATTTGAT-ACTGTG
1 ATTATCAAAATTTGATGAC-GTG
*
24983 ATTATCAAAATTTTATGACGTG
1 ATTATCAAAATTTGATGACGTG
25005 ATTA
1 ATTA
25009 CTAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (22 bp):
ATTATCAAAATTTGATGACGTG
Found at i:25265 original size:32 final size:32
Alignment explanation
Indices: 25228--25290 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
25218 TCAAGTTGGG
*
25228 TTGAATTTGGGTCAGTTTAATTCGGGTTCGGA
1 TTGAATTTGGGTCAGGTTAATTCGGGTTCGGA
25260 TTGAATTTGGGTCAGGTTAATTCGGGTTCGG
1 TTGAATTTGGGTCAGGTTAATTCGGGTTCGG
25291 GTTCAGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (32 bp):
TTGAATTTGGGTCAGGTTAATTCGGGTTCGGA
Found at i:25301 original size:32 final size:32
Alignment explanation
Indices: 25231--25303 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
25221 AGTTGGGTTG
* *
25231 AATTTGGGTCAGTTTAATTCGGGTTCGGATTG
1 AATTTGGGTCAGGTTAATTCGGGTTCGGATTC
*
25263 AATTTGGGTCAGGTTAATTCGGGTTCGGGTTC
1 AATTTGGGTCAGGTTAATTCGGGTTCGGATTC
*
25295 AGTTTGGGT
1 AATTTGGGT
25304 TTTGGCCAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (32 bp):
AATTTGGGTCAGGTTAATTCGGGTTCGGATTC
Found at i:27517 original size:17 final size:16
Alignment explanation
Indices: 27478--27533 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
27468 GAATCTGAAT
27478 CCGAAAAAATCCAAAC
1 CCGAAAAAATCCAAAC
* *
27494 CCGAAAAAGTTCAAAC
1 CCGAAAAAATCCAAAC
* *
27510 CTGAAAAAAATCCGAAC
1 CCG-AAAAAATCCAAAC
27527 CCGAAAA
1 CCGAAAA
27534 TTTATGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.54, C:0.27, G:0.11, T:0.09
Consensus pattern (16 bp):
CCGAAAAAATCCAAAC
Found at i:27712 original size:15 final size:15
Alignment explanation
Indices: 27689--27748 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
27679 CAGAACTCGA
*
27689 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
* *
27704 ACCCAAATTCACCCCG
1 ACCCAAATT-AACCTG
*
27720 AACCCAAATTAATCTG
1 -ACCCAAATTAACCTG
27736 ACCCAAATTAACC
1 ACCCAAATTAACC
27749 CAAACCCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 20 0.56
16 7 0.19
17 9 0.25
ACGTcount: A:0.38, C:0.37, G:0.07, T:0.18
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:27722 original size:32 final size:31
Alignment explanation
Indices: 27686--27757 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 31
27676 AAACAGAACT
*
27686 CGAACCCGAATTAACCTGACCCAAATTCACCC
1 CGAACCCGAATTAACCTGACCCAAATT-AACC
* *
27718 CGAACCCAAATTAATCTGACCCAAATTAACC
1 CGAACCCGAATTAACCTGACCCAAATTAACC
*
27749 CAAACCCGA
1 CGAACCCGA
27758 CTCAAACCCG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.39, C:0.38, G:0.08, T:0.15
Consensus pattern (31 bp):
CGAACCCGAATTAACCTGACCCAAATTAACC
Done.