Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014633.1 Corchorus capsularis cultivar CVL-1 contig14654, 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: 24480
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:847 original size:148 final size:148
Alignment explanation
Indices: 579--877 Score: 589
Period size: 148 Copynumber: 2.0 Consensus size: 148
569 TTTTTTTAAG
579 AATAAAATTAATTTCATTATATAACATCCGGGTTACAAACATCAGGTGGCAAAGACCTGTACCGC
1 AATAAAATTAATTTCATTATATAACATCCGGGTTACAAACATCAGGTGGCAAAGACCTGTACCGC
644 ACACAAGTTACAAACTTTGTCAAAGCAAATTTCGCTAACCTATGAGCACAAAAATTAGCTTCTCT
66 ACACAAGTTACAAACTTTGTCAAAGCAAATTTCGCTAACCTATGAGCACAAAAATTAGCTTCTCT
709 CTTAACATGAACAAACGA
131 CTTAACATGAACAAACGA
727 AATAAAATTAATTTCATTATATAACATCCGGGTTACAAACATCAGGTGGCAAAGACCTGTACCGC
1 AATAAAATTAATTTCATTATATAACATCCGGGTTACAAACATCAGGTGGCAAAGACCTGTACCGC
792 ACACAAGTTACAAACTTTGTCAAAGCAAATTTCGCTAACCTATGAGCACAAAAATTAGCTTCTCT
66 ACACAAGTTACAAACTTTGTCAAAGCAAATTTCGCTAACCTATGAGCACAAAAATTAGCTTCTCT
*
857 CTTAATATGAACAAACGA
131 CTTAACATGAACAAACGA
875 AAT
1 AAT
878 GTTATCGAAA
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 150 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (148 bp):
AATAAAATTAATTTCATTATATAACATCCGGGTTACAAACATCAGGTGGCAAAGACCTGTACCGC
ACACAAGTTACAAACTTTGTCAAAGCAAATTTCGCTAACCTATGAGCACAAAAATTAGCTTCTCT
CTTAACATGAACAAACGA
Found at i:3684 original size:20 final size:22
Alignment explanation
Indices: 3658--3702 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3648 GTAGGTACCA
3658 CTCTCTCTCTCCTA-ATGAGAGT
1 CTCTCTCTCT-CTATATGAGAGT
*
3680 CTCTCTCTCTCTATCTGAGAGT
1 CTCTCTCTCTCTATATGAGAGT
3702 C
1 C
3703 CTCCCTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.16, C:0.33, G:0.13, T:0.38
Consensus pattern (22 bp):
CTCTCTCTCTCTATATGAGAGT
Found at i:3759 original size:7 final size:7
Alignment explanation
Indices: 3723--3756 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3713 TGTTAGGGTT
3723 TTTTTCC
1 TTTTTCC
3730 TTTTTCC
1 TTTTTCC
3737 TTTTTCC
1 TTTTTCC
*
3744 TTTTTCT
1 TTTTTCC
3751 TTTTTC
1 TTTTTC
3757 TTTCTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:5505 original size:24 final size:23
Alignment explanation
Indices: 5477--5521 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
5467 TTGTTTATAC
5477 CTCAACAAAAGTGTTTCTAAATAA
1 CTCAA-AAAAGTGTTTCTAAATAA
*
5501 CTCAATAAAGTGTTTCTAAAT
1 CTCAAAAAAGTGTTTCTAAAT
5522 TTTCTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (23 bp):
CTCAAAAAAGTGTTTCTAAATAA
Found at i:5732 original size:20 final size:21
Alignment explanation
Indices: 5699--5740 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5689 AATTAGTACA
* *
5699 AAAAAGTTTAATAAGGTTATT
1 AAAAACTTTAATAAAGTTATT
5720 AAAAACTTT-ATAAAGTTATT
1 AAAAACTTTAATAAAGTTATT
5740 A
1 A
5741 TAAGGTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAACTTTAATAAAGTTATT
Found at i:14444 original size:159 final size:159
Alignment explanation
Indices: 14149--14474 Score: 571
Period size: 159 Copynumber: 2.1 Consensus size: 159
14139 AAACACATTA
* * *
14149 ATAAGTACCTATACATTAAAAAGCACATCAAGCATAGACTACGAAACATTTTCTTTCTTGATCAA
1 ATAAGCACCTAAACATTAAAAAGCACATCAAGCATAGACTACAAAACATTTTCTTTCTTGATCAA
* * * * *
14214 GGTAAATGAAGTTTATATGCAGCTTTCAATTCTTTAATATAAGAGAATTCTAAACATTGTATCAA
66 GGTAAATGAAGCTTATATGCAGCTTTCAATTCTTGAATATAAGAGAATTCTAAACAATATAGCAA
*
14279 CTCAATTTTGTATCTAGTAACAAATCAAC
131 CCCAATTTTGTATCTAGTAACAAATCAAC
14308 ATAAGCACCTAAACATTAAAAAGCACATCAAGCATAGACTACAAAACATTTTCTTTCTTGATCAA
1 ATAAGCACCTAAACATTAAAAAGCACATCAAGCATAGACTACAAAACATTTTCTTTCTTGATCAA
14373 GGTAAATGAAGCTTATATGCAGCTTTCAATTCTTGAATATAAGAGAATTCTAAACAATATAGCAA
66 GGTAAATGAAGCTTATATGCAGCTTTCAATTCTTGAATATAAGAGAATTCTAAACAATATAGCAA
14438 CCCAATTTTGTATCTAGTAACAAATCAAC
131 CCCAATTTTGTATCTAGTAACAAATCAAC
14467 ATAAGCAC
1 ATAAGCAC
14475 AGCCAGTGCA
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (159 bp):
ATAAGCACCTAAACATTAAAAAGCACATCAAGCATAGACTACAAAACATTTTCTTTCTTGATCAA
GGTAAATGAAGCTTATATGCAGCTTTCAATTCTTGAATATAAGAGAATTCTAAACAATATAGCAA
CCCAATTTTGTATCTAGTAACAAATCAAC
Found at i:23069 original size:6 final size:6
Alignment explanation
Indices: 23060--23107 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
23050 AGAATTAATC
*
23060 TATCTA TATCTA TATC-- TATCTA TATCTA TATCTA TATTTA TA-CTA
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA
23105 TAT
1 TAT
23108 TAAAATGTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 29 0.78
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:23078 original size:16 final size:16
Alignment explanation
Indices: 23057--23094 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
23047 AAAAGAATTA
23057 ATCTATCTATATCTAT
1 ATCTATCTATATCTAT
23073 ATCTATCTATATCTAT
1 ATCTATCTATATCTAT
23089 ATCTAT
1 ATCTAT
23095 ATTTATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCTATCTATATCTAT
Found at i:23844 original size:33 final size:33
Alignment explanation
Indices: 23807--23870 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
23797 TCTACGGGAT
23807 AACCTGAGGAATTTGATGATTTCTTTATGGCAC
1 AACCTGAGGAATTTGATGATTTCTTTATGGCAC
23840 AACCTGAGGAATTTGATGATTTCTTTATGGC
1 AACCTGAGGAATTTGATGATTTCTTTATGGC
23871 CAAAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (33 bp):
AACCTGAGGAATTTGATGATTTCTTTATGGCAC
Found at i:23966 original size:79 final size:82
Alignment explanation
Indices: 23876--24041 Score: 230
Period size: 79 Copynumber: 2.0 Consensus size: 82
23866 ATGGCCAAAA
*
23876 AGAAAGGGTAGAGTTCCTATTGATCAAAATAGGCCTAGCCTGGCC-A-C-TCAGGTAACTCTCTT
1 AGAAAGGGTAGAGTTCCTATTGATCAAAATAGGCCTAGCCTGGCCAATCTTCAGGTAACTCCCTT
23938 CTTTTGGCCAATTATTT
66 CTTTTGGCCAATTATTT
* * *
23955 AGAAATGGTAGAGTTTCTATTGATCAAAATAGGCCTGGCCTGGCCAATTTAATCTTCAGGTAACT
1 AGAAAGGGTAGAGTTCCTATTGATCAAAATAGGCCTAGCCTGGCC-----AATCTTCAGGTAACT
24020 CCCTTCTTTTGGCCAATTATTT
61 CCCTTCTTTTGGCCAATTATTT
24042 TGTATACGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
79 42 0.56
85 1 0.01
86 1 0.01
87 31 0.41
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (82 bp):
AGAAAGGGTAGAGTTCCTATTGATCAAAATAGGCCTAGCCTGGCCAATCTTCAGGTAACTCCCTT
CTTTTGGCCAATTATTT
Done.