Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018336.1 Corchorus olitorius cultivar O-4 contig18369, 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: 31335
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:4335 original size:19 final size:20
Alignment explanation
Indices: 4296--4336 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4286 CGTTATTAAC
*
4296 ATATAAAAATTTTTCTGAAA
1 ATATAAAAATTTCTCTGAAA
*
4316 ATATAAGAATTTCT-TGAAA
1 ATATAAAAATTTCTCTGAAA
4335 AT
1 AT
4337 GCAGTCTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAAAAATTTCTCTGAAA
Found at i:4468 original size:93 final size:93
Alignment explanation
Indices: 4301--4485 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 93
4291 TTAACATATA
*
4301 AAAATTTTTCTGAAAATATAAGAATTTCTTGAAAATGCAGTCTTACATTAAACATATGGCACTTA
1 AAAATTTTTCTGAAAATATAAGAATTTCTTGAAAATGCAGTCTTACATTAAACATATGACACTTA
4366 AAAAATAAGATTCAATTGTCTCAAACAT
66 AAAAATAAGATTCAATTGTCTCAAACAT
* *
4394 AAAATTTTTCTGAAAATATAAGAATTTCTTGAAAATGTAGTCTTACATTAAATATATGACACTTA
1 AAAATTTTTCTGAAAATATAAGAATTTCTTGAAAATGCAGTCTTACATTAAACATATGACACTTA
* *
4459 TAAACTAAGATTCAATTGTCTCAAACA
66 AAAAATAAGATTCAATTGTCTCAAACA
4486 CTAATTCTTG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (93 bp):
AAAATTTTTCTGAAAATATAAGAATTTCTTGAAAATGCAGTCTTACATTAAACATATGACACTTA
AAAAATAAGATTCAATTGTCTCAAACAT
Found at i:5662 original size:20 final size:20
Alignment explanation
Indices: 5633--5670 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5623 TTATTACCTC
* *
5633 ATTAGGCTACTGCTCTTAAT
1 ATTAGACTACTACTCTTAAT
5653 ATTAGACTACTACTCTTA
1 ATTAGACTACTACTCTTA
5671 TGTTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
ATTAGACTACTACTCTTAAT
Found at i:8192 original size:18 final size:18
Alignment explanation
Indices: 8169--8312 Score: 87
Period size: 18 Copynumber: 7.5 Consensus size: 18
8159 TCTTAAGTTT
8169 GCTCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
* * *
8187 GCTCCGTGTTTATCTCAACT-T
1 GCTCCGTG--CA--ACAACTAA
*
8208 GCCCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
* *
8226 GCTCCGTGCTTATCTCAACT-T
1 GCTCCGTGC--A--ACAACTAA
8247 GCTCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
* *
8265 GCTCCGTGCTTATCTCAACT-T
1 GCTCCGTGC--A--ACAACTAA
8286 GCTCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
8304 GCTCCGTGC
1 GCTCCGTGC
8313 TTATCTTATC
Statistics
Matches: 95, Mismatches: 16, Indels: 30
0.67 0.11 0.21
Matches are distributed among these distances:
17 15 0.16
18 34 0.36
19 3 0.03
20 3 0.03
21 25 0.26
22 15 0.16
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (18 bp):
GCTCCGTGCAACAACTAA
Found at i:8215 original size:39 final size:39
Alignment explanation
Indices: 8167--8318 Score: 286
Period size: 39 Copynumber: 3.9 Consensus size: 39
8157 TATCTTAAGT
*
8167 TTGCTCCGTGCAACAACTAAGCTCCGTGTTTATCTCAAC
1 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
*
8206 TTGCCCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
1 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
8245 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
1 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
8284 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCT
1 TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCT
8319 TATCTCAGGC
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (39 bp):
TTGCTCCGTGCAACAACTAAGCTCCGTGCTTATCTCAAC
Found at i:8251 original size:21 final size:21
Alignment explanation
Indices: 8187--8294 Score: 88
Period size: 21 Copynumber: 5.4 Consensus size: 21
8177 CAACAACTAA
*
8187 GCTCCGTGTTTATCTCAACTT
1 GCTCCGTGCTTATCTCAACTT
* * *
8208 GCCCCGTGC--A--ACAACTAA
1 GCTCCGTGCTTATCTCAACT-T
8226 GCTCCGTGCTTATCTCAACTT
1 GCTCCGTGCTTATCTCAACTT
* *
8247 GCTCCGTGC--A--ACAACTAA
1 GCTCCGTGCTTATCTCAACT-T
8265 GCTCCGTGCTTATCTCAACTT
1 GCTCCGTGCTTATCTCAACTT
8286 GCTCCGTGC
1 GCTCCGTGC
8295 AACAACTAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
17 10 0.15
18 17 0.26
19 2 0.03
20 2 0.03
21 25 0.38
22 10 0.15
ACGTcount: A:0.19, C:0.34, G:0.17, T:0.30
Consensus pattern (21 bp):
GCTCCGTGCTTATCTCAACTT
Found at i:8510 original size:13 final size:13
Alignment explanation
Indices: 8492--8516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8482 ACGTTAATTG
8492 TTTTCTTTTGAAC
1 TTTTCTTTTGAAC
8505 TTTTCTTTTGAA
1 TTTTCTTTTGAA
8517 TAACAACATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTCTTTTGAAC
Found at i:9177 original size:18 final size:17
Alignment explanation
Indices: 9150--9193 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
9140 TCACAGCTAA
9150 TTAATATTTATTATTAT
1 TTAATATTTATTATTAT
*
9167 TTAATTATTTATTTTTAT
1 TTAA-TATTTATTATTAT
*
9185 TGAATATTT
1 TTAATATTT
9194 CTAACTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTAATATTTATTATTAT
Found at i:9815 original size:109 final size:109
Alignment explanation
Indices: 9693--9909 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 109
9683 TATTATATAT
*
9693 ATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATATCAAACAATAC
1 ATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAC
9758 -AAGATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCC
66 AAAG-TGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCC
*
9802 ATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAC
1 ATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAC
9867 AAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
9910 AAAATGACTA
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
109 102 0.97
110 3 0.03
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (109 bp):
ATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAC
AAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCC
Found at i:24517 original size:36 final size:36
Alignment explanation
Indices: 24477--24550 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
24467 TTCACTAATG
*
24477 AAAATTTTATGTTTGAATCCAATATGATCTCTCGAA
1 AAAATTTTATGTTTGAATCCAATATGAACTCTCGAA
24513 AAAATTTTATGTTTGAATCCAATATGAACTCTCGAA
1 AAAATTTTATGTTTGAATCCAATATGAACTCTCGAA
24549 AA
1 AA
24551 GGTTTGCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAATTTTATGTTTGAATCCAATATGAACTCTCGAA
Found at i:28558 original size:10 final size:10
Alignment explanation
Indices: 28511--28560 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
28501 ATTTCCTTAT
28511 TTTCTT-TTC
1 TTTCTTCTTC
28520 TTTTCTTTCTTC
1 -TTTC-TTCTTC
* *
28532 TTCCTTATTC
1 TTTCTTCTTC
28542 TTT-TTCTTC
1 TTTCTTCTTC
28551 TTTCTTCTTC
1 TTTCTTCTTC
28561 GTTATGGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.24
10 17 0.52
11 5 0.15
12 3 0.09
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:28558 original size:26 final size:27
Alignment explanation
Indices: 28503--28565 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
28493 TATTCCAAAT
*
28503 TTCCTTATTTTCTTTTCTTTTCTTTCTTC
1 TTCCTTA--TTCTTTTCTCTTCTTTCTTC
28532 TTCCTTATTCTTTT-TCTTCTTTCTTC
1 TTCCTTATTCTTTTCTCTTCTTTCTTC
*
28558 TTCGTTAT
1 TTCCTTAT
28566 GGGCTAGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 18 0.56
27 7 0.22
29 7 0.22
ACGTcount: A:0.05, C:0.24, G:0.02, T:0.70
Consensus pattern (27 bp):
TTCCTTATTCTTTTCTCTTCTTTCTTC
Found at i:28601 original size:34 final size:34
Alignment explanation
Indices: 28541--28620 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 34
28531 CTTCCTTATT
*
28541 CTTTTTCTTCTTTCTTCTTCGTTATGGGCTAGGCC
1 CTTTTTCTT-TTTCTTCTTCGATATGGGCTAGGCC
*
28576 CTTTTTCTTTTTCTTATTTC-ATATGGGCTAGGCC
1 CTTTTTCTTTTTCTT-CTTCGATATGGGCTAGGCC
28610 CTTTTTCTTTT
1 CTTTTTCTTTT
28621 CTTTTGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
34 30 0.71
35 12 0.29
ACGTcount: A:0.07, C:0.23, G:0.14, T:0.56
Consensus pattern (34 bp):
CTTTTTCTTTTTCTTCTTCGATATGGGCTAGGCC
Found at i:28857 original size:14 final size:14
Alignment explanation
Indices: 28838--28882 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
28828 ATGATTTGAC
28838 AAAATGATATAATG
1 AAAATGATATAATG
28852 AAAATGAT-T--TG
1 AAAATGATATAATG
28863 ACAAATGATATAAT-
1 A-AAATGATATAATG
28877 AAAATG
1 AAAATG
28883 TTTTGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
11 3 0.11
12 7 0.26
13 7 0.26
14 9 0.33
15 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (14 bp):
AAAATGATATAATG
Found at i:28875 original size:26 final size:26
Alignment explanation
Indices: 28827--28888 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
28817 CGTGTCTCTG
28827 AATGATTTGACAAAATGATATAATGAA
1 AATGATTTGACAAAATGATATAAT-AA
28854 AATGATTTGAC-AAATGATATAATAA
1 AATGATTTGACAAAATGATATAATAA
*
28879 AATGTTTTGA
1 AATGATTTGA
28889 ATTTGTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 11 0.32
26 12 0.35
27 11 0.32
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (26 bp):
AATGATTTGACAAAATGATATAATAA
Found at i:29307 original size:18 final size:18
Alignment explanation
Indices: 29284--29323 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
29274 ACTGAAATTT
*
29284 TTTTATAATTATATAACG
1 TTTTATAATTATATAACA
29302 TTTTATAATTATATAACA
1 TTTTATAATTATATAACA
29320 TTTT
1 TTTT
29324 TAGTAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATAATTATATAACA
Found at i:29635 original size:23 final size:23
Alignment explanation
Indices: 29604--29648 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29594 ACTAACAATG
29604 TATTATATAATATTCTTAAAATT
1 TATTATATAATATTCTTAAAATT
*
29627 TATTGTATAATATTCTTAAAAT
1 TATTATATAATATTCTTAAAAT
29649 ATATAACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTATATAATATTCTTAAAATT
Done.