Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017996.1 Corchorus olitorius cultivar O-4 contig18029, 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: 40012
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8349 original size:163 final size:163
Alignment explanation
Indices: 8144--8446 Score: 441
Period size: 163 Copynumber: 1.9 Consensus size: 163
8134 CGCCGCCATA
8144 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCC-CAACTA
1 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCTC--CTA
* * * *
8208 AAACAAAGAAAGTTTACAA-TTTACACCTATAATATATAGCGGCGTTTAGACACAAGACGCCGCT
64 AAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTACACAAAAGACGCCGAT
*
8272 ATTTAGTGGCGTCTAGAAAAGGAAACGCCACTATT
129 ATTTAGCGGCGTCTAGAAAAGGAAACGCCACTATT
*
8307 TTAATATATGGAGGGAGTGATTTTTTTT-TCCCTTTTTTTGGAGGGAAAAATTCCCTCCTCCTAA
1 TTAATATATGGAGGGAGAGATTTTTTTTCT-CCTTTTTTTGGAGGGAAAAATTCCCTCCTCCTAA
* * * * * * *
8371 AATAAATAAATTTTTCAACTCTACGCCTATAATATATAGCGGCGTTTTCTCAAAAGACGCCGATA
65 AACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTACACAAAAGACGCCGATA
8436 TTTAGCGGCGT
130 TTTAGCGGCGT
8447 TTTCTCAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
162 19 0.15
163 104 0.84
164 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (163 bp):
TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCTCCTAAA
ACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTACACAAAAGACGCCGATAT
TTAGCGGCGTCTAGAAAAGGAAACGCCACTATT
Found at i:8442 original size:31 final size:31
Alignment explanation
Indices: 8402--8484 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
8392 TACGCCTATA
*
8402 ATATATAGCGGCGTTTTCTCAAAAGACGCCG
1 ATATTTAGCGGCGTTTTCTCAAAAGACGCCG
*
8433 ATATTTAGCGGCGTTTTCTCAAAAGATGCCG
1 ATATTTAGCGGCGTTTTCTCAAAAGACGCCG
*
8464 CTATTTAGCGGCGTTTTCTCA
1 ATATTTAGCGGCGTTTTCTCA
8485 CACGTCTTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (31 bp):
ATATTTAGCGGCGTTTTCTCAAAAGACGCCG
Found at i:8731 original size:24 final size:24
Alignment explanation
Indices: 8686--8731 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8676 TTATATGAAT
*
8686 ATAAAATATATATATATTTATATA
1 ATAAAATATATATATATATATATA
*
8710 ATAAAATA-ATTTAT-TATATATA
1 ATAAAATATATATATATATATATA
8732 GCGGCGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAAATATATATATATATATATA
Found at i:14782 original size:28 final size:27
Alignment explanation
Indices: 14705--14839 Score: 234
Period size: 28 Copynumber: 4.9 Consensus size: 27
14695 TATTGCCGCG
14705 AGTGGATCCTCCCACTTCGACCCCAGC
1 AGTGGATCCTCCCACTTCGACCCCAGC
14732 AGTGGATCCTCCCACTTCGACCCCAGC
1 AGTGGATCCTCCCACTTCGACCCCAGC
14759 AGTGGATCCTCCCCACTTCGACCCCCAGC
1 AGTGGATCCT-CCCACTTCGA-CCCCAGC
14788 AGTGGATCCTCCCACTTCGACCCCCAGC
1 AGTGGATCCTCCCACTTCGA-CCCCAGC
14816 AGTGGATCCTCCCCACTTCGACCC
1 AGTGGATCCT-CCCACTTCGACCC
14840 GGGTCGGTTC
Statistics
Matches: 105, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
27 37 0.35
28 41 0.39
29 27 0.26
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.19
Consensus pattern (27 bp):
AGTGGATCCTCCCACTTCGACCCCAGC
Found at i:14839 original size:57 final size:56
Alignment explanation
Indices: 14705--14839 Score: 247
Period size: 57 Copynumber: 2.4 Consensus size: 56
14695 TATTGCCGCG
14705 AGTGGATCCT-CCCACTTCGA-CCCCAGCAGTGGATCCTCCCACTTCGACCCCAGC
1 AGTGGATCCTCCCCACTTCGACCCCCAGCAGTGGATCCTCCCACTTCGACCCCAGC
14759 AGTGGATCCTCCCCACTTCGACCCCCAGCAGTGGATCCTCCCACTTCGACCCCCAGC
1 AGTGGATCCTCCCCACTTCGACCCCCAGCAGTGGATCCTCCCACTTCGA-CCCCAGC
14816 AGTGGATCCTCCCCACTTCGACCC
1 AGTGGATCCTCCCCACTTCGACCC
14840 GGGTCGGTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
54 10 0.13
55 10 0.13
56 27 0.35
57 31 0.40
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.19
Consensus pattern (56 bp):
AGTGGATCCTCCCCACTTCGACCCCCAGCAGTGGATCCTCCCACTTCGACCCCAGC
Found at i:16846 original size:12 final size:12
Alignment explanation
Indices: 16821--16855 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16811 CTAATACTAG
* *
16821 TGGCGGTGGAGA
1 TGGCGATGGTGA
16833 TGGCGATGGTGA
1 TGGCGATGGTGA
16845 TGGCGATGGTG
1 TGGCGATGGTG
16856 GTAAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.09, G:0.54, T:0.23
Consensus pattern (12 bp):
TGGCGATGGTGA
Found at i:17238 original size:32 final size:32
Alignment explanation
Indices: 17202--17387 Score: 225
Period size: 32 Copynumber: 5.8 Consensus size: 32
17192 GCGTTAAAAT
*
17202 AAAACGCCCATATTTAGCGGCGTCTGATGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTGATGAAC
17234 AAAACGCCCTTATTTAGCGGCGTCT-ATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTGAT-GAAC
* *
17266 AAAAAGCCCTTATTTAGCGGTGTCT-ATAGAA-
1 AAAACGCCCTTATTTAGCGGCGTCTGAT-GAAC
* * * * *
17297 AAAACGCCTTTATTTAGCAGCATCTGAAGAAG
1 AAAACGCCCTTATTTAGCGGCGTCTGATGAAC
* *
17329 AAAACGCCCTTATTTAGCGGCGTCTGAAGAAAAA
1 AAAACGCCCTTATTTAGCGGCGTCTGATG--AAC
17363 AAAACGCCCTTATTTAGCGGCGTCT
1 AAAACGCCCTTATTTAGCGGCGTCT
17388 ATATTACCAA
Statistics
Matches: 136, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
31 25 0.18
32 84 0.62
34 27 0.20
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTGATGAAC
Found at i:17312 original size:63 final size:64
Alignment explanation
Indices: 17202--17390 Score: 242
Period size: 63 Copynumber: 2.9 Consensus size: 64
17192 GCGTTAAAAT
*
17202 AAAACGCCCATATTTAGCGGCGTCTGAT-GAACAAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTGATAGAA-AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
* * * * * *
17266 AAAAAGCCCTTATTTAGCGGTGTCT-ATAGAAAAAACGCCTTTATTTAGCAGCATCTGA-AGAAG
1 AAAACGCCCTTATTTAGCGGCGTCTGATAGAAAAAACGCCCTTATTTAGCGGCGTCT-ATAGAAC
17329 AAAACGCCCTTATTTAGCGGCGTCTGA-AGAAAAAAAAACGCCCTTATTTAGCGGCGTCTATA
1 AAAACGCCCTTATTTAGCGGCGTCTGATAG---AAAAAACGCCCTTATTTAGCGGCGTCTATA
17391 TTACCAAACG
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
63 53 0.50
64 27 0.25
65 1 0.01
66 25 0.24
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (64 bp):
AAAACGCCCTTATTTAGCGGCGTCTGATAGAAAAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:17365 original size:95 final size:97
Alignment explanation
Indices: 17202--17390 Score: 276
Period size: 95 Copynumber: 2.0 Consensus size: 97
17192 GCGTTAAAAT
* * * *
17202 AAAACGCCCATATTTAGCGGCGTCTGATGAACAAAACGCCCTTATTTAGCGGCGTCTATAG-AAC
1 AAAACGCCCATATTTAGCAGCATCTGAAGAACAAAACGCCCTTATTTAGCGGCGTCTATAGAAAA
*
17266 AAAAA-GCCCTTATTTAGCGGTGTCTATAGAA
66 AAAAACGCCCTTATTTAGCGGCGTCTATAGAA
** *
17297 AAAACGCCTTTATTTAGCAGCATCTGAAGAAGAAAACGCCCTTATTTAGCGGCGTCTGA-AGAAA
1 AAAACGCCCATATTTAGCAGCATCTGAAGAACAAAACGCCCTTATTTAGCGGCGTCT-ATAGAAA
17361 AAAAAACGCCCTTATTTAGCGGCGTCTATA
65 AAAAAACGCCCTTATTTAGCGGCGTCTATA
17391 TTACCAAACG
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
95 53 0.64
96 8 0.10
97 22 0.27
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (97 bp):
AAAACGCCCATATTTAGCAGCATCTGAAGAACAAAACGCCCTTATTTAGCGGCGTCTATAGAAAA
AAAAACGCCCTTATTTAGCGGCGTCTATAGAA
Found at i:17567 original size:24 final size:24
Alignment explanation
Indices: 17535--17585 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
17525 ACGTGTCCAG
*
17535 ATAGCGGCGTCTAGACGCCGTTAT
1 ATAGCGGCGTCTAGACGCCGCTAT
* *
17559 ATAGTGGCGTCTAGACGCTGCTAT
1 ATAGCGGCGTCTAGACGCCGCTAT
17583 ATA
1 ATA
17586 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (24 bp):
ATAGCGGCGTCTAGACGCCGCTAT
Found at i:25845 original size:72 final size:72
Alignment explanation
Indices: 25728--25865 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 72
25718 CCATCCTGCG
* *
25728 GGATATCCAATGATCTCATAGCACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCGCACCT
1 GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
25793 TGCAGCA
66 TGCAGCA
* * *
25800 GGATATCCAATGATCTCATAACATTGATCTTTCGTGTGCCCCATCTTTTGACAATGTTCACACCT
1 GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
25865 T
66 T
25866 AGCTTGTCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (72 bp):
GGATATCCAATGATCTCATAACACTGATCTTTCATGTGCCCCATCTTTTGACAATGTCCACACCT
TGCAGCA
Found at i:28627 original size:24 final size:21
Alignment explanation
Indices: 28584--28627 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
28574 TAAATAGTTG
28584 ATAATATTATATTTTTTTTTA
1 ATAATATTATATTTTTTTTTA
28605 ATAATCATTAATAGTTTTTTTTT
1 ATAAT-ATT-ATA-TTTTTTTTT
28628 TTTTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 3 0.15
24 9 0.45
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATAATATTATATTTTTTTTTA
Found at i:29746 original size:21 final size:22
Alignment explanation
Indices: 29720--29761 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29710 TATGACTTAA
*
29720 ACTATTTC-ACTATTTTTTTTT
1 ACTATTTCAACTACTTTTTTTT
29741 ACTATTTCAACTACTTTTTTT
1 ACTATTTCAACTACTTTTTTT
29762 AAAAGTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (22 bp):
ACTATTTCAACTACTTTTTTTT
Found at i:29762 original size:21 final size:21
Alignment explanation
Indices: 29720--29762 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29710 TATGACTTAA
*
29720 ACTATTTCACTATTTTTTTTT
1 ACTATTTCACTATCTTTTTTT
29741 ACTATTTCAACTA-CTTTTTTT
1 ACTATTTC-ACTATCTTTTTTT
29762 A
1 A
29763 AAAGTACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.60
Consensus pattern (21 bp):
ACTATTTCACTATCTTTTTTT
Found at i:31476 original size:51 final size:52
Alignment explanation
Indices: 31375--31476 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
31365 GTTCATCAAA
* **
31375 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
31427 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
31477 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Done.