Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009824.1 Corchorus capsularis cultivar CVL-1 contig09845, 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: 50642
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1171 original size:26 final size:25
Alignment explanation
Indices: 1142--1271 Score: 82
Period size: 26 Copynumber: 5.0 Consensus size: 25
1132 TGTACGGGTC
1142 GTACGCGCGAGGTCACGTGTGGAGTT
1 GTACGCG-GAGGTCACGTGTGGAGTT
* * *
1168 GTACTTCGGAGGTCACGTGTTGAAGGT
1 GTAC-GCGGAGGTCACGTG-TGGAGTT
* * *
1195 ATCCGTTGGAGGTCACGTGTGGAGTT
1 GTACG-CGGAGGTCACGTGTGGAGTT
* * * *
1221 GTACTTCGAAGATCACGTGTGG-GATC
1 GTAC-GCGGAGGTCACGTGTGGAG-TT
* *
1247 GTACGTTGGAGGTTACGTGTGGAGT
1 GTACG-CGGAGGTCACGTGTGGAGT
1272 GCCAGTTGGC
Statistics
Matches: 76, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
25 1 0.01
26 53 0.70
27 22 0.29
ACGTcount: A:0.18, C:0.15, G:0.38, T:0.28
Consensus pattern (25 bp):
GTACGCGGAGGTCACGTGTGGAGTT
Found at i:1237 original size:53 final size:52
Alignment explanation
Indices: 1150--1271 Score: 165
Period size: 53 Copynumber: 2.3 Consensus size: 52
1140 TCGTACGCGC
* * * *
1150 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGT-TGAAGGTATCCGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTA--CGTTG
*
1203 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGATCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTACGTTG
*
1255 GAGGTTACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
1272 GCCAGTTGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
52 21 0.34
53 36 0.58
54 5 0.08
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTACGTTG
Found at i:1332 original size:15 final size:15
Alignment explanation
Indices: 1312--1356 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1302 TTGTGGTCAT
*
1312 AGGTGGTCGATCGCC
1 AGGTGGTCGAGCGCC
1327 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
1342 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
1357 GGGCTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.11, C:0.27, G:0.47, T:0.16
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Found at i:1462 original size:15 final size:15
Alignment explanation
Indices: 1442--1471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1432 TTGTGGTCAT
1442 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
1457 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
1472 GAGCTTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.50, T:0.13
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Found at i:1486 original size:24 final size:24
Alignment explanation
Indices: 1457--1514 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
1447 GTCGAGCGCC
1457 AGGTGGTCGGGCGCCGAGCTTTGG
1 AGGTGGTCGGGCGCCGAGCTTTGG
* *
1481 AGGTGGTCGAGCGCCGGGCTTTGG
1 AGGTGGTCGGGCGCCGAGCTTTGG
1505 AGGTGGTCGG
1 AGGTGGTCGG
1515 ACGCTGTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.09, C:0.19, G:0.52, T:0.21
Consensus pattern (24 bp):
AGGTGGTCGGGCGCCGAGCTTTGG
Found at i:1577 original size:23 final size:23
Alignment explanation
Indices: 1507--1582 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1497 GGCTTTGGAG
* *
1507 GTGGTCGGACGCTGTCCTTAGAG
1 GTGGTCGGACGCTGGCCTTAGAA
* *
1530 GTGGTCGGTCGCTAGG--TTCACAA
1 GTGGTCGGACGCT-GGCCTT-AGAA
*
1553 GTGGTCGGACGCTGGCCTTGGAA
1 GTGGTCGGACGCTGGCCTTAGAA
1576 GTGGTCG
1 GTGGTCG
1583 AGCGCCAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 4 0.10
23 35 0.83
24 3 0.07
ACGTcount: A:0.13, C:0.21, G:0.41, T:0.25
Consensus pattern (23 bp):
GTGGTCGGACGCTGGCCTTAGAA
Found at i:1732 original size:15 final size:15
Alignment explanation
Indices: 1712--1747 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1702 CATCTTTCTT
1712 TTTCTTGCTTTCCTC
1 TTTCTTGCTTTCCTC
* *
1727 TTTCTTGGTTTCTTC
1 TTTCTTGCTTTCCTC
1742 TTTCTT
1 TTTCTT
1748 CTTCTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.08, T:0.67
Consensus pattern (15 bp):
TTTCTTGCTTTCCTC
Found at i:1752 original size:21 final size:22
Alignment explanation
Indices: 1719--1771 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1709 CTTTTTCTTG
* *
1719 CTTTCCTCTTTCTTGGTTTCTT
1 CTTTCTTCTTTCTTAGTTTCTT
*
1741 CTTTCTTC-TTCTTAGTTTCCT
1 CTTTCTTCTTTCTTAGTTTCTT
1762 CTTTC-TCTTT
1 CTTTCTTCTTT
1772 TGCCTCTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 18 0.67
22 7 0.26
ACGTcount: A:0.02, C:0.28, G:0.06, T:0.64
Consensus pattern (22 bp):
CTTTCTTCTTTCTTAGTTTCTT
Found at i:1777 original size:15 final size:15
Alignment explanation
Indices: 1759--1789 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1749 TTCTTAGTTT
*
1759 CCTCTTTCTCTTTTG
1 CCTCTTTATCTTTTG
1774 CCTCTTTATCTTTTG
1 CCTCTTTATCTTTTG
1789 C
1 C
1790 TGCTGCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.32, G:0.06, T:0.58
Consensus pattern (15 bp):
CCTCTTTATCTTTTG
Found at i:1780 original size:36 final size:35
Alignment explanation
Indices: 1704--1780 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
1694 AATTTGTTCA
* *
1704 TCTTTCTTTTTCTTGCTTTCCTCTTTCTTGGTTTCT
1 TCTTTCTTCTTCTTGCTTTCCTCTTTCTT-GTTTCC
1740 TCTTTCTTCTTCTTAG-TTTCCTCTTTCTCT-TTTGCC
1 TCTTTCTTCTTCTT-GCTTTCCTCTTTCT-TGTTT-CC
1776 TCTTT
1 TCTTT
1781 ATCTTTTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 3 0.08
36 31 0.86
37 2 0.06
ACGTcount: A:0.01, C:0.27, G:0.06, T:0.65
Consensus pattern (35 bp):
TCTTTCTTCTTCTTGCTTTCCTCTTTCTTGTTTCC
Found at i:7604 original size:11 final size:10
Alignment explanation
Indices: 7573--7604 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
7563 TTGGGTAGCG
7573 AGAAAATGAA
1 AGAAAATGAA
7583 AGAAAATGAA
1 AGAAAATGAA
7593 AGAAAGATGAA
1 AGAAA-ATGAA
7604 A
1 A
7605 AAACAGTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (10 bp):
AGAAAATGAA
Found at i:14068 original size:3 final size:3
Alignment explanation
Indices: 14060--14093 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
14050 TTTCATCCCC
14060 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14094 TACAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16577 original size:2 final size:2
Alignment explanation
Indices: 16570--16599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16560 CTTTGTTTGT
16570 TA TA TA TA 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
16600 GAAAGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17162 original size:33 final size:33
Alignment explanation
Indices: 17120--17218 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
17110 TTTTGCCCTT
*
17120 AGCCACGGCGGAGCGTCCCCACTAGGGCGGCTC
1 AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
17153 AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
1 AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
* *
17186 AGCCACGGCGGAGCCTCCCCAGTGGGGCGGCTC
1 AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
17219 GACTACTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.14, C:0.40, G:0.36, T:0.09
Consensus pattern (33 bp):
AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
Found at i:17351 original size:33 final size:33
Alignment explanation
Indices: 17291--17385 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
17281 GGCGGCCTGC
* *
17291 CCATGGTGAAGCCACCC-CAGTGGGGCGGCTTGAG
1 CCATGGT-AAGCCACCCTC-CTGAGGCGGCTTGAG
*
17325 CCATGGTAAGCCACGCTCCTGAGGCGGCTTGAG
1 CCATGGTAAGCCACCCTCCTGAGGCGGCTTGAG
* *
17358 CCATGGTAAGCCGCCCTCCTGGGGCGGC
1 CCATGGTAAGCCACCCTCCTGAGGCGGC
17386 ACGGGTCATC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
33 46 0.85
34 8 0.15
ACGTcount: A:0.16, C:0.33, G:0.36, T:0.16
Consensus pattern (33 bp):
CCATGGTAAGCCACCCTCCTGAGGCGGCTTGAG
Found at i:17733 original size:5 final size:5
Alignment explanation
Indices: 17723--17749 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17713 TGAGTGGGGT
17723 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
17750 AATGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:35358 original size:16 final size:16
Alignment explanation
Indices: 35337--35368 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35327 TTGTCATCTG
35337 CCCAATGCACAAAATA
1 CCCAATGCACAAAATA
35353 CCCAATGCACAAAATA
1 CCCAATGCACAAAATA
35369 ATTGGGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.06, T:0.12
Consensus pattern (16 bp):
CCCAATGCACAAAATA
Found at i:38566 original size:6 final size:6
Alignment explanation
Indices: 38555--38586 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
38545 AATGGGAACT
38555 GATTGG GATTGG GATTGG GATTGG GATTGG GA
1 GATTGG GATTGG GATTGG GATTGG GATTGG GA
38587 GGGTTCAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.50, T:0.31
Consensus pattern (6 bp):
GATTGG
Found at i:44776 original size:32 final size:34
Alignment explanation
Indices: 44729--44818 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
44719 GATGACCCGT
**
44729 GCCGCCCCAAGAGGGCGGCTT-ACCA-TGGGCAA
1 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAA
*
44761 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAA
44795 GCCGCCCCACTAGGGCGGCTTCAC
1 GCCGCCCCACTAGGGCGGCTTCAC
44819 TATGAATAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
32 19 0.36
33 4 0.08
34 30 0.57
ACGTcount: A:0.17, C:0.39, G:0.32, T:0.12
Consensus pattern (34 bp):
GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAA
Found at i:44835 original size:33 final size:34
Alignment explanation
Indices: 44729--44835 Score: 112
Period size: 34 Copynumber: 3.2 Consensus size: 34
44719 GATGACCCGT
** ** *
44729 GCCGCCCCAAGAGGGCGGCTT-ACCA-TGGGCAA
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
**
44761 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
* *
44795 GCCGCCCCACTAGGGCGGCTTCACTA-TGAATAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
44828 GCCGCCCC
1 GCCGCCCC
44836 GGTGGGGTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 19 0.29
33 16 0.24
34 31 0.47
ACGTcount: A:0.18, C:0.38, G:0.31, T:0.13
Consensus pattern (34 bp):
GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
Found at i:44906 original size:32 final size:31
Alignment explanation
Indices: 44826--44910 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
44816 CACTATGAAT
*
44826 AGGCCGCCCCGGTGGGGTGGCTTAGCCACGGC
1 AGGCCG-CCCGGTGGGGCGGCTTAGCCACGGC
* *
44858 AGGCCGCCCGGTGGGGCGTCTTCGCCACGGC
1 AGGCCGCCCGGTGGGGCGGCTTAGCCACGGC
44889 AGGCCGCGCCGGTGGGGCGGCT
1 AGGCCGC-CCGGTGGGGCGGCT
44911 CGGCTATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 29 0.60
32 19 0.40
ACGTcount: A:0.07, C:0.35, G:0.46, T:0.12
Consensus pattern (31 bp):
AGGCCGCCCGGTGGGGCGGCTTAGCCACGGC
Found at i:45010 original size:33 final size:30
Alignment explanation
Indices: 44968--45078 Score: 96
Period size: 33 Copynumber: 3.5 Consensus size: 30
44958 GTTTTGCTCT
*
44968 AGCCGCCCCACCGAGGCGGCCTGCCTTACGCGA
1 AGCCGCCCCA-TG-GGCGGCCTGCCTTA-GCGA
** * *
45001 AGCCGCCCCATGGGCGGTTTGCCGTGGCGA
1 AGCCGCCCCATGGGCGGCCTGCCTTAGCGA
*
45031 AGCCGCCCCAGTGGGGCGGCCTGCCTATAGTGA
1 AGCCGCCCCA-T-GGGCGGCCTGCCT-TAGCGA
*
45064 AGCCGCTCCAGTGGG
1 AGCCGCCCCA-TGGG
45079 GAGGCTCTGC
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
30 14 0.22
31 11 0.17
32 14 0.22
33 25 0.39
ACGTcount: A:0.14, C:0.37, G:0.36, T:0.14
Consensus pattern (30 bp):
AGCCGCCCCATGGGCGGCCTGCCTTAGCGA
Found at i:45101 original size:33 final size:34
Alignment explanation
Indices: 45020--45118 Score: 100
Period size: 33 Copynumber: 3.0 Consensus size: 34
45010 ATGGGCGGTT
* *
45020 TGCCGTGGC-GAAGCCGCCCCAGTGGGGCGGC-C
1 TGCCGTGGCTGAAGCCGCTCCAGTGGGGAGGCTC
* *
45052 TGCCTATAG-TGAAGCCGCTCCAGTGGGGAGGCTC
1 TGCC-GTGGCTGAAGCCGCTCCAGTGGGGAGGCTC
*
45086 TGCCGTGGCTG-AGCCG-TCCTAATGGGGAGGCTC
1 TGCCGTGGCTGAAGCCGCTCC-AGTGGGGAGGCTC
45119 AGTGTAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
32 7 0.13
33 41 0.75
34 7 0.13
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.17
Consensus pattern (34 bp):
TGCCGTGGCTGAAGCCGCTCCAGTGGGGAGGCTC
Found at i:45187 original size:21 final size:21
Alignment explanation
Indices: 45163--45202 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45153 CAAAAGTGTA
45163 AAAAAT-GGGACGGTATTTAAC
1 AAAAATAGGG-CGGTATTTAAC
*
45184 AAAACTAGGGCGGTATTTA
1 AAAAATAGGGCGGTATTTA
45203 GCAACCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAAC
Done.