Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015915.1 Corchorus capsularis cultivar CVL-1 contig15936, 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: 21320
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:525 original size:27 final size:26
Alignment explanation
Indices: 487--561 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
477 AAGTAGACTT
* *
487 AAAATGACCAAAATGCCCCTGGTGCGG
1 AAAATGACCAAAATGCCCCTAGTGC-A
* *
514 AAAATGACCAAAATGACCTTAGTGCA
1 AAAATGACCAAAATGCCCCTAGTGCA
* *
540 AAAATTACCAAAATCCCCCTAG
1 AAAATGACCAAAATGCCCCTAG
562 GACTCAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 18 0.45
27 22 0.55
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTAGTGCA
Found at i:1119 original size:10 final size:10
Alignment explanation
Indices: 1104--1128 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1094 GAGGACTCTA
1104 GAATTTTCTG
1 GAATTTTCTG
1114 GAATTTTCTG
1 GAATTTTCTG
1124 GAATT
1 GAATT
1129 GTGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:4504 original size:25 final size:25
Alignment explanation
Indices: 4476--4555 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 25
4466 ACTAATTATC
4476 CTCTTCTTAATTATTACCACTTTTA
1 CTCTTCTTAATTATTACCACTTTTA
* *
4501 CTCTTCTT-TTTCTCTACCA-TTTTA
1 CTCTTCTTAATTAT-TACCACTTTTA
* * *
4525 CTCTT-TGAATTACTGATCACCTTTTA
1 CTCTTCTTAATTA-TTACCA-CTTTTA
4551 CTCTT
1 CTCTT
4556 TACTGATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.02
24 18 0.42
25 14 0.33
26 10 0.23
ACGTcount: A:0.19, C:0.26, G:0.03, T:0.53
Consensus pattern (25 bp):
CTCTTCTTAATTATTACCACTTTTA
Found at i:4760 original size:26 final size:27
Alignment explanation
Indices: 4714--4781 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
4704 CTCTTTACTG
**
4714 ATTACTA-TTTCACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
4740 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
4766 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
4782 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:4905 original size:40 final size:40
Alignment explanation
Indices: 4868--4976 Score: 184
Period size: 40 Copynumber: 2.7 Consensus size: 40
4858 TTTTTACCGA
* *
4868 TTTACTGATTACTTCCTTTACTGTT-ACTCTTGATTACCAT
1 TTTACCGATTACTTCTTTTACT-TTCACTCTTGATTACCAT
4908 TTTACCGATTACTTCTTTTACTTTCACTCTTGATTACCAT
1 TTTACCGATTACTTCTTTTACTTTCACTCTTGATTACCAT
4948 TTTACCGATTACTTCTTTTACTTTCACTC
1 TTTACCGATTACTTCTTTTACTTTCACTC
4977 CATTTTACTG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 2 0.03
40 64 0.97
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (40 bp):
TTTACCGATTACTTCTTTTACTTTCACTCTTGATTACCAT
Found at i:5086 original size:23 final size:24
Alignment explanation
Indices: 5059--5104 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
5049 TGATCTTTTA
5059 CTTTTACTGATTACTT-CTTTACC
1 CTTTTACTGATTACTTCCTTTACC
5082 CTTTTACTGATTACTTCCTTTAC
1 CTTTTACTGATTACTTCCTTTAC
5105 TGATTACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.17, C:0.26, G:0.04, T:0.52
Consensus pattern (24 bp):
CTTTTACTGATTACTTCCTTTACC
Found at i:5103 original size:16 final size:16
Alignment explanation
Indices: 5084--5114 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5074 TCTTTACCCT
5084 TTTACTGATTACTTCC
1 TTTACTGATTACTTCC
5100 TTTACTGATTACTTC
1 TTTACTGATTACTTC
5115 TCTTGGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTACTGATTACTTCC
Found at i:5111 original size:23 final size:22
Alignment explanation
Indices: 5062--5112 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
5052 TCTTTTACTT
*
5062 TTACTGATTACTTCTTTACCCTT
1 TTACTGATTACTTCTTTA-CCTA
5085 TTACTGATTACTTCCTTTA-CTGA
1 TTACTGATTACTT-CTTTACCT-A
5108 TTACT
1 TTACT
5113 TCTCTTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 18 0.72
24 5 0.20
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.51
Consensus pattern (22 bp):
TTACTGATTACTTCTTTACCTA
Found at i:8154 original size:15 final size:15
Alignment explanation
Indices: 8134--8168 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
8124 ACTATTGCTA
8134 TATTTTTTGTA-TTAT
1 TATTTTTTGTACTT-T
8149 TATTTTTTGTACTTT
1 TATTTTTTGTACTTT
8164 TATTT
1 TATTT
8169 AAATCAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (15 bp):
TATTTTTTGTACTTT
Found at i:8766 original size:65 final size:64
Alignment explanation
Indices: 8601--8813 Score: 309
Period size: 64 Copynumber: 3.3 Consensus size: 64
8591 TCTACAACTG
* *
8601 TCTTCTGGTGTTCTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAGCCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCA
* * *
8665 TCTTCTGGTGTTCTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTTGAGAAACCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTC-TTGATAAACCA
* * * * *
8730 TCTTCTAGTGTACTTCTTGGCATGATCATCTTCCGATCAACTTCTGAAAACTCTCGATAAACCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCA
* *
8794 TCTTTTGGTGTACTCCTTGA
1 TCTTCTGGTGTACTTCTTGA
8814 AATTTTCTAA
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
64 77 0.58
65 56 0.42
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (64 bp):
TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCA
Found at i:13209 original size:27 final size:27
Alignment explanation
Indices: 13179--13233 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
13169 GGATAGGAAT
*
13179 AAAGAATCAATAGAATATGAGACAAGA
1 AAAGAATCAAAAGAATATGAGACAAGA
* *
13206 AAAGGATCAAAAGGATATGAGACAAGA
1 AAAGAATCAAAAGAATATGAGACAAGA
13233 A
1 A
13234 TGTGGGCCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.13
Consensus pattern (27 bp):
AAAGAATCAAAAGAATATGAGACAAGA
Found at i:14337 original size:13 final size:13
Alignment explanation
Indices: 14319--14343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14309 GCTTTTGAAG
14319 ATGTAAAATGCAT
1 ATGTAAAATGCAT
14332 ATGTAAAATGCA
1 ATGTAAAATGCA
14344 ACCTGCGAAA
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGTAAAATGCAT
Found at i:15765 original size:21 final size:21
Alignment explanation
Indices: 15741--15789 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
15731 TCTCACTAAG
*
15741 TCTGATTTGAAT-TTGAAAACC
1 TCTGATTTAAATCTTGAAAA-C
15762 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
15782 TCTTGATT
1 TC-TGATT
15790 ACCAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:15905 original size:15 final size:14
Alignment explanation
Indices: 15887--15933 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
15877 AATTTTCTGA
15887 TTTTCAGTTTTTCATT
1 TTTTCA-TTTTTC-TT
15903 TTTTCATTTTTC-T
1 TTTTCATTTTTCTT
* *
15916 TTTTCCTTCTTCTT
1 TTTTCATTTTTCTT
15930 TTTT
1 TTTT
15934 GCTTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 5 0.18
15 6 0.21
16 6 0.21
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTTCTT
Found at i:18064 original size:2 final size:2
Alignment explanation
Indices: 18059--18084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18049 GAGAGTTCCT
18059 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
18085 AAGCTGTATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19534 original size:10 final size:11
Alignment explanation
Indices: 19496--19537 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
19486 AAATTATGCA
19496 TATTTTTATAGC
1 TATTTTTATA-C
19508 TATTTTTATA-
1 TATTTTTATAC
*
19518 TACTTTT-TAC
1 TATTTTTATAC
19528 TATTTTTATA
1 TATTTTTATA
19538 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.08
10 12 0.46
11 2 0.08
12 10 0.38
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTTATAC
Done.