Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009065.1 Corchorus capsularis cultivar CVL-1 contig09086, 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: 41248
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:2558 original size:42 final size:42
Alignment explanation
Indices: 2478--2593 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
2468 AAGGGTCGAA
* *
2478 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGTCCCATGCGT
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTCCCATGCGT
* *
2520 TGGCCGGTTGTGGCCGGTTGCCCCATGCGTTG-CTCCATGCGT
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTC-CCATGCGT
** *
2562 TGGCCGGTCATGGCCGGATGCTCCATGCGATG
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATG
2594 GTGGTCGGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.08, C:0.29, G:0.38, T:0.25
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTCCCATGCGT
Found at i:4464 original size:30 final size:31
Alignment explanation
Indices: 4430--4512 Score: 123
Period size: 33 Copynumber: 2.6 Consensus size: 31
4420 TTCTTTTCAC
4430 CCAAAACAGAATTATTTTCAATGC-CATCAA
1 CCAAAACAGAATTATTTTCAATGCTCATCAA
* *
4460 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGC--TCATCAA
4493 CCAAAACAGAATTATTTTCA
1 CCAAAACAGAATTATTTTCA
4513 TCACAATTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 23 0.49
33 24 0.51
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28
Consensus pattern (31 bp):
CCAAAACAGAATTATTTTCAATGCTCATCAA
Found at i:4497 original size:33 final size:30
Alignment explanation
Indices: 4430--4509 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
4420 TTCTTTTCAC
*
4430 CCAAAACAGAATTATTTTCAATGCCATCAA
1 CCAAAACAGAATTATTTGCAATGCCATCAA
*
4460 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGC---CATCAA
4493 CCAAAACAGAATTATTT
1 CCAAAACAGAATTATTT
4510 TCATCACAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 23 0.51
33 22 0.49
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (30 bp):
CCAAAACAGAATTATTTGCAATGCCATCAA
Found at i:6031 original size:11 final size:11
Alignment explanation
Indices: 6015--6044 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6005 TTCTGGTCGA
6015 ATTTTTTTTTT
1 ATTTTTTTTTT
6026 ATTTTTTTTTT
1 ATTTTTTTTTT
6037 ATATTTTT
1 AT-TTTTT
6045 CGATATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:6034 original size:13 final size:13
Alignment explanation
Indices: 6016--6044 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6006 TCTGGTCGAA
6016 TTTTTTTTT-TAT
1 TTTTTTTTTATAT
6028 TTTTTTTTTATAT
1 TTTTTTTTTATAT
6041 TTTT
1 TTTT
6045 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTATAT
Found at i:7140 original size:42 final size:42
Alignment explanation
Indices: 7060--7175 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
7050 AAGGGTCGAA
* *
7060 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGTCCCATGCGT
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTCCCATGCGT
* * *
7102 TGGCCGGTTGTGGCTGGTTGCCCCATGCGTTG-CTCCATGCGT
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTC-CCATGCGT
** *
7144 TGGCCGGTCATGGCCGGATGCTCCATGCGATG
1 TGGCCGGTTGTGGCCGGATGCCCCATGCGATG
7176 GTGGCCGGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 61 0.98
ACGTcount: A:0.08, C:0.28, G:0.38, T:0.26
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGCCCCATGCGATGTCCCATGCGT
Found at i:8853 original size:28 final size:28
Alignment explanation
Indices: 8821--8874 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
8811 ACGACAAACA
8821 GTACGGACGCGCTAAAGAC-GTCAACACT
1 GTACGGACGCGCTAAAG-CTGTCAACACT
* *
8849 GTACGGACGTGCTGAAGCTGTCAACA
1 GTACGGACGCGCTAAAGCTGTCAACA
8875 GCCTGCCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.17
Consensus pattern (28 bp):
GTACGGACGCGCTAAAGCTGTCAACACT
Found at i:13734 original size:111 final size:111
Alignment explanation
Indices: 13613--13837 Score: 396
Period size: 111 Copynumber: 2.0 Consensus size: 111
13603 GTAAAATTTC
*
13613 AAAAATTGAACCACAAAACCAAGTAACATCAAAATCTCACATCCATTCAGACTTCAAATTACCAC
1 AAAAATTGAACCACAAAACCAAGTAACATCAAAATCTCACATCCATTCAAACTTCAAATTACCAC
*
13678 AAAACTTATATACCACTAAAAACCCACACGGTGTTAAAACAAAACA
66 AAAACTTATATACCACTAAAAACCCACACGGTATTAAAACAAAACA
*
13724 AAAAATTGAACCACAAAACCAAGTAACATCAAAATCTCATATCCATTCAAACTTCAAATTACCAC
1 AAAAATTGAACCACAAAACCAAGTAACATCAAAATCTCACATCCATTCAAACTTCAAATTACCAC
** *
13789 AAAACTTATATACCACTAAAAACCCACGTGGTATTAAAACAAAATA
66 AAAACTTATATACCACTAAAAACCCACACGGTATTAAAACAAAACA
13835 AAA
1 AAA
13838 CAAAACAAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (111 bp):
AAAAATTGAACCACAAAACCAAGTAACATCAAAATCTCACATCCATTCAAACTTCAAATTACCAC
AAAACTTATATACCACTAAAAACCCACACGGTATTAAAACAAAACA
Found at i:15051 original size:65 final size:66
Alignment explanation
Indices: 14976--15113 Score: 244
Period size: 65 Copynumber: 2.1 Consensus size: 66
14966 AGACACTAAA
*
14976 ATCTGTTAATGACAAGACAGAGAAAAATGTCAAGGC-AAATATGCAACACAACAGCTACTTTAGG
1 ATCTGTTAATGACAAGACAGAGAAAAATGTCAAGACAAAATATGCAACACAACAGCTACTTTAGG
15040 C
66 C
*
15041 ATCTGTTAATGACAAGACATAGAAAAATGTCAAGACAAAATATGCAACACAACAGCTACTTTAGG
1 ATCTGTTAATGACAAGACAGAGAAAAATGTCAAGACAAAATATGCAACACAACAGCTACTTTAGG
15106 C
66 C
15107 -TCTGTTA
1 ATCTGTTA
15114 TACCAAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
65 41 0.59
66 29 0.41
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (66 bp):
ATCTGTTAATGACAAGACAGAGAAAAATGTCAAGACAAAATATGCAACACAACAGCTACTTTAGG
C
Found at i:17850 original size:102 final size:102
Alignment explanation
Indices: 17674--17877 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
17664 TTTTTTCAAA
17674 CTAGAGGTATTGAGTTCAAAACCCATTACTTACAAAAGTTTTTCAACATTTTTTCCAAATAAAAA
1 CTAGAGGTATTGAGTTCAAAACCCATTACTTACAAAAGTTTTTCAACATTTTTTCCAAATAAAAA
17739 ATCGGTTCAACCGGTTCGGATCTGGGTTAACTACCGG
66 ATCGGTTCAACCGGTTCGGATCTGGGTTAACTACCGG
17776 CTAGAGGTATTGAGTTCAAAACCCATTACTTACAAAAGTTTTTCAACATTTTTTCCAAATAAAAA
1 CTAGAGGTATTGAGTTCAAAACCCATTACTTACAAAAGTTTTTCAACATTTTTTCCAAATAAAAA
*
17841 ATCGGTTCAACCGGTTCGGGTCTGGGTTAACTACCGG
66 ATCGGTTCAACCGGTTCGGATCTGGGTTAACTACCGG
17878 ATTTTCCGGG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (102 bp):
CTAGAGGTATTGAGTTCAAAACCCATTACTTACAAAAGTTTTTCAACATTTTTTCCAAATAAAAA
ATCGGTTCAACCGGTTCGGATCTGGGTTAACTACCGG
Found at i:20561 original size:82 final size:83
Alignment explanation
Indices: 20434--20793 Score: 441
Period size: 84 Copynumber: 4.4 Consensus size: 83
20424 ATCATTTGTT
* * *
20434 TTTCTTATTTCCTTATTAGTTACG-AAATAATTTCTGGGTTTAGCTTTGTTTGTTGCGATTTTGG
1 TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGCTTTGTTTGTTGCGATTTTGG
20498 AGTTGCCATTTGTTT-GA
66 AGTTGCCATTTGTTTCGA
* * * *
20515 TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTAGGTTTAGCTTTTTTTGTTGGGAGTTTGG
1 TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGCTTTGTTTGTTGCGATTTTGG
*
20580 AGTTGCCAATTTGTTTCGT
66 AGTTGCC-ATTTGTTTCGA
* *
20599 TTTTTTATTTCCTTATGAATTTCGAAAATAATTTCTCGGG-TTAGC-TTGCTTTGTTGAGATTTT
1 TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCT-GGGTTTAGCTTTG-TTTGTTGCGATTTT
* **
20662 GGAGTTGTCATTTGTTTCTT
64 GGAGTTGCCATTTGTTTCGA
* * * *
20682 TTTTTTATTTCCTTATGAATTTCGAAATTAAATTATGGGTTTAGCTTTG--T-TTGCGATTTTGG
1 TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGCTTTGTTTGTTGCGATTTTGG
* * *
20744 AGTAGCCCTTTATTT-GA
66 AGTTGCCATTTGTTTCGA
*
20761 TTTCTTATATCCTTATGAATTTCGAAAA-AATTT
1 TTTCTTATTTCCTTATGAATTTCGAAAATAATTT
20794 TCCTTATTCA
Statistics
Matches: 243, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
78 4 0.02
79 25 0.10
80 22 0.09
81 22 0.09
82 46 0.19
83 58 0.24
84 64 0.26
85 2 0.01
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (83 bp):
TTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGCTTTGTTTGTTGCGATTTTGG
AGTTGCCATTTGTTTCGA
Found at i:20645 original size:166 final size:162
Alignment explanation
Indices: 20427--20793 Score: 438
Period size: 166 Copynumber: 2.2 Consensus size: 162
20417 CGAATCCATC
* * * *
20427 ATTTGTTTTTCTTATTTCCTTATTAGTTACG-AAATAATTTCTGGGTTTAGCTTTG-TTTGTTGC
1 ATTTGTTTTT-TTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGC-TTGCTTTGTTGA
* *
20490 GATTTTGGAGTTGCCATTTGTTT-GATTTCTTATTTCCTTATGAATTTCGAAAATAATTTCTAGG
64 GATTTTGGAGTTGCCATTTGTTTCGATTTCTTATTTCCTTATGAATTTCGAAAATAAATTATAGG
* * *
20554 TTTAGCTTTTTTTGTTGGGAGTTTGGAGTTGCCAATTT
129 TTTAGC--TTTGT-TTGCGAGTTTGGAGTAGCC-ATTT
*
20592 GTTTCGTTTTTTTATTTCCTTATGAATTTCGAAAATAATTTCTCGGG-TTAGCTTGCTTTGTTGA
1 ATTT-GTTTTTTTATTTCCTTATGAATTTCGAAAATAATTTCT-GGGTTTAGCTTGCTTTGTTGA
* ** * * *
20656 GATTTTGGAGTTGTCATTTGTTTCTTTTTTTTATTTCCTTATGAATTTCGAAATTAAATTATGGG
64 GATTTTGGAGTTGCCATTTGTTTCGATTTCTTATTTCCTTATGAATTTCGAAAATAAATTATAGG
* *
20721 TTTAGCTTTGTTTGCGATTTTGGAGTAGCCCTTT
129 TTTAGCTTTGTTTGCGAGTTTGGAGTAGCCATTT
* * *
20755 ATTTGATTTCTTATATCCTTATGAATTTCGAAAA-AATTT
1 ATTTGTTTTTTTATTTCCTTATGAATTTCGAAAATAATTT
20794 TCCTTATTCA
Statistics
Matches: 175, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
161 5 0.03
162 27 0.15
163 6 0.03
164 16 0.09
165 27 0.15
166 51 0.29
167 43 0.25
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (162 bp):
ATTTGTTTTTTTATTTCCTTATGAATTTCGAAAATAATTTCTGGGTTTAGCTTGCTTTGTTGAGA
TTTTGGAGTTGCCATTTGTTTCGATTTCTTATTTCCTTATGAATTTCGAAAATAAATTATAGGTT
TAGCTTTGTTTGCGAGTTTGGAGTAGCCATTT
Found at i:22710 original size:32 final size:33
Alignment explanation
Indices: 22674--22756 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 33
22664 AGATGAATGT
* ** *
22674 TGTATTTTGAAGTTAA-ATGTTGAATATTTATA
1 TGTATTTTGAACTTAATAAATTGAATATTCATA
22706 TGTATTTTGAACTTAATTAAATTGAATATTCATA
1 TGTATTTTGAACTTAA-TAAATTGAATATTCATA
22740 TGTATTTTGAACTTAAT
1 TGTATTTTGAACTTAAT
22757 TTATGTATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 15 0.33
33 1 0.02
34 29 0.64
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
TGTATTTTGAACTTAATAAATTGAATATTCATA
Found at i:22741 original size:34 final size:34
Alignment explanation
Indices: 22693--22757 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
22683 AAGTTAAATG
*
22693 TTGAATATTTATATGTATTTTGAACTTAATTAAA
1 TTGAATATTCATATGTATTTTGAACTTAATTAAA
22727 TTGAATATTCATATGTATTTTGAACTTAATT
1 TTGAATATTCATATGTATTTTGAACTTAATT
22758 TATGTATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (34 bp):
TTGAATATTCATATGTATTTTGAACTTAATTAAA
Found at i:34858 original size:32 final size:33
Alignment explanation
Indices: 34822--34923 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 33
34812 CCGACCATTG
*
34822 CTTGGAGAAG-CC-GCGCAACACCTGCCACATGA
1 CTTGGAGAAGCCCGGC-CAACACCGGCCACATGA
* *
34854 CTTGGAGAGGCCCGGCCACCACCGGCCACATGA
1 CTTGGAGAAGCCCGGCCAACACCGGCCACATGA
* ** *
34887 CTCGGCCATGCCCGGCC-ACAACCGGCCACATGA
1 CTTGGAGAAGCCCGGCCAAC-ACCGGCCACATGA
34920 CTTG
1 CTTG
34924 ACCATGCCCG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 10 0.17
33 46 0.79
34 2 0.03
ACGTcount: A:0.23, C:0.39, G:0.26, T:0.12
Consensus pattern (33 bp):
CTTGGAGAAGCCCGGCCAACACCGGCCACATGA
Found at i:34929 original size:33 final size:33
Alignment explanation
Indices: 34845--34952 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
34835 CGCAACACCT
* * *
34845 GCCACATGACTTGGA-GAGGCCCGGCCACCACCG
1 GCCACATGACTT-GACCATGCCCGGCCACAACCG
* *
34878 GCCACATGACTCGGCCATGCCCGGCCACAACCG
1 GCCACATGACTTGACCATGCCCGGCCACAACCG
** *
34911 GCCACATGACTTGACCATGCCCGGATACAACTG
1 GCCACATGACTTGACCATGCCCGGCCACAACCG
34944 GCCACATGA
1 GCCACATGA
34953 TCCTTTAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 1 0.02
33 63 0.98
ACGTcount: A:0.24, C:0.39, G:0.25, T:0.12
Consensus pattern (33 bp):
GCCACATGACTTGACCATGCCCGGCCACAACCG
Found at i:38588 original size:33 final size:33
Alignment explanation
Indices: 38473--38576 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
38463 TTCTTTTCAC
* *
38473 CCAAAGCAGAATTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
38503 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
38536 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
38569 GCAAAACA
1 CCAAAACA
38577 TATTTGTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
30 21 0.33
33 43 0.67
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:38640 original size:33 final size:33
Alignment explanation
Indices: 38603--38699 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
38593 AATTAGCATC
* **
38603 CAAAACAGATTTAGTTTCATCATAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* *
38636 CAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
38669 CAAATTAGGTTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
38700 TCTAATACAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Done.