Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010752.1 Corchorus capsularis cultivar CVL-1 contig10773, 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: 58977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:441 original size:2 final size:2
Alignment explanation
Indices: 434--474 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
424 ACATTCTGAT
* *
434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
475 GTATTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:1591 original size:32 final size:32
Alignment explanation
Indices: 1545--1640 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
1535 GCACCGTCAT
* * *
1545 GCCGATGATATGGCATTGCCACGTCGGACCAA
1 GCCGATGATGTGGCATTGCCACATCAGACCAA
1577 GCCGATGATGTGGCATTGCCACATCAGACCAA
1 GCCGATGATGTGGCATTGCCACATCAGACCAA
** * *
1609 AACGATGATGTGGCATTGCAACATAAGACCAA
1 GCCGATGATGTGGCATTGCCACATCAGACCAA
1641 TTTCGTGCGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (32 bp):
GCCGATGATGTGGCATTGCCACATCAGACCAA
Found at i:1870 original size:30 final size:29
Alignment explanation
Indices: 1827--1926 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
1817 GAGAGGGGGT
*
1827 AAAACGTCCAAAATTG-AGATTTCAG-GCGGC
1 AAAATGTCCAAAATTGAAG-TTT-AGAG-GGC
*
1857 AAAATGTCTAAAATTGAAGTTTAGAGGGC
1 AAAATGTCCAAAATTGAAGTTTAGAGGGC
* * *
1886 AAAATGTCCAAAATTAAAGTTTAGATGAC
1 AAAATGTCCAAAATTGAAGTTTAGAGGGC
1915 AAAATGTCCAAA
1 AAAATGTCCAAA
1927 CGCTACAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
29 42 0.68
30 18 0.29
31 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAATGTCCAAAATTGAAGTTTAGAGGGC
Found at i:13849 original size:19 final size:19
Alignment explanation
Indices: 13817--13854 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
13807 TTTCTTTGGG
13817 CTTTGCTTTATTTCTTCTTT
1 CTTTGCTTTATTTC-TCTTT
*
13837 CTTT-CTTTCTTTCTCTTT
1 CTTTGCTTTATTTCTCTTT
13855 TTCCTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (19 bp):
CTTTGCTTTATTTCTCTTT
Found at i:20096 original size:2 final size:2
Alignment explanation
Indices: 20089--20125 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20079 ATGGTCAAAC
20089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20126 CACTTTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21859 original size:2 final size:2
Alignment explanation
Indices: 21854--21879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21844 TGGGAAAAGC
21854 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
21880 CTCCTATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25811 original size:2 final size:2
Alignment explanation
Indices: 25804--25840 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25794 CATGAGAATA
25804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25841 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25845 original size:2 final size:2
Alignment explanation
Indices: 25840--25874 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
25830 ATATATATAT
*
25840 AC AC AC AC AC AC A- AA AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
25875 TTAGAGCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29071 original size:14 final size:14
Alignment explanation
Indices: 29052--29081 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29042 AAATTGAATA
*
29052 ATTTATGAGTACAC
1 ATTTATAAGTACAC
29066 ATTTATAAGTACAC
1 ATTTATAAGTACAC
29080 AT
1 AT
29082 AATTAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (14 bp):
ATTTATAAGTACAC
Found at i:31365 original size:50 final size:50
Alignment explanation
Indices: 31288--31391 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 50
31278 AGATTGAGAG
* * *
31288 AAATGATGGAGACAAGAGTCTCGAGTAGACAAGAGTCTAAGGGGAAAACA
1 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
*
31338 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAATGGAAAAACA
1 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
31388 AAAT
1 AAAT
31392 AACAACTTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (50 bp):
AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
Found at i:32049 original size:22 final size:22
Alignment explanation
Indices: 32024--32081 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
32014 ACCATCATGT
32024 GGCCGAATCTTACGGCCACCAA
1 GGCCGAATCTTACGGCCACCAA
* * *
32046 GGCCGAATCTCATGGCCACCAT
1 GGCCGAATCTTACGGCCACCAA
*
32068 GGCTGAATCTTACG
1 GGCCGAATCTTACG
32082 ACTACAGTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (22 bp):
GGCCGAATCTTACGGCCACCAA
Found at i:37839 original size:50 final size:50
Alignment explanation
Indices: 37762--37865 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
37752 AGATTGAGAG
* *
37762 AAATGATGGAGACAAGAGTCTCGAGTAGACAAGAGTCTAAGGGAAAAACA
1 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
*
37812 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAATGGAAAAACA
1 AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
37862 AAAT
1 AAAT
37866 AACAACTTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (50 bp):
AAATGATGGAGACAAGAGTCTCAAGTAGACAAAAGTCTAAGGGAAAAACA
Found at i:39389 original size:2 final size:2
Alignment explanation
Indices: 39382--39418 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39372 TAATATGTAG
39382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39419 TACTAACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45650 original size:203 final size:202
Alignment explanation
Indices: 45294--45691 Score: 559
Period size: 203 Copynumber: 2.0 Consensus size: 202
45284 AGGATTTATA
* * * * *
45294 TATATAATACACAGTCAGTGGAGTTTAGTAGACTGCACAAGCGTGTCTTGAAGGGTGACATGTGT
1 TATACAATACACAGTCAGTGGAGTTTAGAAAACTACACAAGCGTGTCCTGAAGGGTGACATGTGT
* * *
45359 CTCCTAGGAACTAGATTGAAATATTTAAAATTTAATTAATTCAAAAAATGGACATGTGTCAACTC
66 CTCCTAGGAACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGGACATGCGTCAACTC
* * *
45424 CAAAACCCGCTTGTGAGGTCCAAAATTTACACCGCCGGTGTATCATATAATTACCCTTTATATTA
131 CAAAACCCGCTTGTGAGGTCCAAAATTTACACCGCCGATATATCATATAATCACCC-TTATATTA
45489 AGGCAAAT
195 AGGCAAAT
* * *
45497 TATACAATACACCGTCGGTGGAGTTTAGAAAATTACACAAGCG-GATCCTGAAGGGTGACATGTG
1 TATACAATACACAGTCAGTGGAGTTTAGAAAACTACACAAGCGTG-TCCTGAAGGGTGACATGTG
* * *
45561 TCTCTTAGGGACTAGATTGAAATATTTAAAACTTAAATAACTT-AAAAAATGGATATGCGTCAAC
65 TCTCCTAGGAACTAGATTGAAATATTTAAAACTTAAATAA-TTCAAAAAATGGACATGCGTCAAC
* * *
45625 TCTATAACCCGCTTGTG-GAGTCCAAAATTTACACCGCCGATATATCATGTAATCACCCTTATAT
129 TCCAAAACCCGCTTGTGAG-GTCCAAAATTTACACCGCCGATATATCATATAATCACCCTTATAT
45689 TAA
193 TAA
45692 ACTTTGTGAA
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
202 11 0.06
203 159 0.92
204 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (202 bp):
TATACAATACACAGTCAGTGGAGTTTAGAAAACTACACAAGCGTGTCCTGAAGGGTGACATGTGT
CTCCTAGGAACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGGACATGCGTCAACTC
CAAAACCCGCTTGTGAGGTCCAAAATTTACACCGCCGATATATCATATAATCACCCTTATATTAA
GGCAAAT
Found at i:55179 original size:20 final size:18
Alignment explanation
Indices: 55156--55204 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
55146 CAACAGAGTG
*
55156 GTATATTATATACTCATATA
1 GTATATAATATA-T-ATATA
55176 GTATATAATATATATATA
1 GTATATAATATATATATA
55194 -TATATAA-ATAT
1 GTATATAATATAT
55205 TGTTATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 7 0.25
18 5 0.18
19 1 0.04
20 11 0.39
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (18 bp):
GTATATAATATATATATA
Found at i:55187 original size:22 final size:19
Alignment explanation
Indices: 55157--55204 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
55147 AACAGAGTGG
*
55157 TATATTATATACTCATATAGTA
1 TATAATATATA-T-ATATA-TA
55179 TATAATATATATATATATA
1 TATAATATATATATATATA
55198 TA-AATAT
1 TATAATAT
55205 TGTTATGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 5 0.20
19 4 0.16
20 5 0.20
21 1 0.04
22 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TATAATATATATATATATA
Found at i:58852 original size:14 final size:15
Alignment explanation
Indices: 58823--58866 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
58813 CGCCCCACTT
*
58823 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
58838 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
58852 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
58867 ACTGAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:58924 original size:33 final size:35
Alignment explanation
Indices: 58874--58967 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 35
58864 TACACTGAGT
* *
58874 CTCCCCACTAGGACGGC-TCAGCCACGGCG-AAGC
1 CTCCCCACTGGGGCGGCTTCAGCCACGGCGCAAGC
* *
58907 CTCCCCACTGGGGCGGCTTCA-CCATGG-GCAGGC
1 CTCCCCACTGGGGCGGCTTCAGCCACGGCGCAAGC
58940 CGT-CCCACTGGGGCGGCTTC-GCCACGGC
1 C-TCCCCACTGGGGCGGCTTCAGCCACGGC
58968 AGGCCGCCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 46 0.90
34 4 0.08
ACGTcount: A:0.14, C:0.41, G:0.32, T:0.13
Consensus pattern (35 bp):
CTCCCCACTGGGGCGGCTTCAGCCACGGCGCAAGC
Found at i:58964 original size:17 final size:16
Alignment explanation
Indices: 58910--58964 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
58900 GCGAAGCCTC
58910 CCCACTGGGGCGGCTT
1 CCCACTGGGGCGGCTT
*
58926 CACCA-T-GGGCAGGCCGT
1 C-CCACTGGGGC-GG-CTT
58943 CCCACTGGGGCGGCTT
1 CCCACTGGGGCGGCTT
58959 CGCCAC
1 C-CCAC
58965 GGCAGGCCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 13 0.42
18 4 0.13
ACGTcount: A:0.11, C:0.40, G:0.35, T:0.15
Consensus pattern (16 bp):
CCCACTGGGGCGGCTT
Done.