Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011483.1 Corchorus capsularis cultivar CVL-1 contig11504, 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: 31881
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1126 original size:22 final size:23
Alignment explanation
Indices: 1091--1137 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1081 GTAGTTAATC
*
1091 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
1113 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
1136 AT
1 AT
1138 TAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:1422 original size:22 final size:21
Alignment explanation
Indices: 1393--1436 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1383 CAAAAGTGTA
1393 AAAAGGGGGGCAGTATTTAGC
1 AAAAGGGGGGCAGTATTTAGC
* *
1414 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCAGTATTTAGC
1435 AA
1 AA
1437 TCCAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGCAGTATTTAGC
Found at i:2743 original size:14 final size:14
Alignment explanation
Indices: 2717--2754 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2707 GTCCAAAGAA
2717 ATGAAAA-AAGCAT
1 ATGAAAATAAGCAT
*
2730 ATTAAAATAAGCAT
1 ATGAAAATAAGCAT
2744 ATGAAAATAAG
1 ATGAAAATAAG
2755 TTATACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (14 bp):
ATGAAAATAAGCAT
Found at i:3149 original size:21 final size:21
Alignment explanation
Indices: 3123--3166 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3113 ACATATTAAT
3123 AACTTACATGTTTAGTTGAGA
1 AACTTACATGTTTAGTTGAGA
*
3144 AACTTACATTTTTAGTTGAGA
1 AACTTACATGTTTAGTTGAGA
3165 AA
1 AA
3167 GAATTTGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
AACTTACATGTTTAGTTGAGA
Found at i:4817 original size:2 final size:2
Alignment explanation
Indices: 4810--4842 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4800 TTCTTCAATA
4810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4843 AGTTGTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5717 original size:324 final size:324
Alignment explanation
Indices: 5121--5929 Score: 1293
Period size: 324 Copynumber: 2.5 Consensus size: 324
5111 GTCTTTATTT
* * *
5121 GTTCAATTAAATTATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTCTAGTTGA
1 GTTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCTGA
* * * * * *
5186 ACCATTTCTTCAGTTCATTTTCTGGTATTTTGAACCATATTAA-GTTTAGTACATCGATAACAAT
66 ACCATTTCTTCAGTTTATTTTCAGGGATTTTGAACCATA-TAAGGTTTAGTACAACGGTGACAAT
* *
5250 GGTGCTGATGAAGGCCAACCTGCATCGTTGCCATATGAGATTGATCAATGCTTAAAAAAAAGCTA
130 GGTGCTGATGAAGACCAACCTACATCGTTGCCATATGAGATTGATCAATGCTTAAAAAAAAGCTA
* * *
5315 ACTAGGATATTATATGTAGAACATGATACTTACAATTATGATAAACTTCATGACAAGCCAAACCA
195 ACTAGGATATTATATGTAAAACAGGATACTTACAACTATGATAAACTTCATGACAAGCCAAACCA
* * *
5380 CCAGTAGTCCAAACCATTCCAACGGTTTGAGTCTTTATTTATTTAATCAACTATTGTAATGGAAA
260 CCAGTACTCCAAACAATTCCAACGGTTCGAGTCTTTATTTATTTAATCAACTATTGTAATGGAAA
5445 GTTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCTGA
1 GTTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCTGA
* * *
5510 ACCATTTCTTCAGTTTATTTTAAGGGATTTTGAACCATATAAGGTTCAGTACAGCGGTGACAATG
66 ACCATTTCTTCAGTTTATTTTCAGGGATTTTGAACCATATAAGGTTTAGTACAACGGTGACAATG
*
5575 GTGCTGATGAAGACCAACCTACATCGTT-CCATATGAGATTGATCAATGCTTAAAAACCAAGCTA
131 GTGCTGATGAAGACCAACCTACATCGTTGCCATATGAGATTGATCAATGCTTAAAAA-AAAGCTA
* **
5639 ACTAGGATATTATATGTAAAACAGGATACTTACAACTATGATAATCTTCATGACAAGCCAAATTA
195 ACTAGGATATTATATGTAAAACAGGATACTTACAACTATGATAAACTTCATGACAAGCCAAACCA
* * *
5704 CCAGTACTCCAAACAATTCCAACGGTTCGAGTCTTTATTTGTTTTATCAACTGTTGTAATGGAAA
260 CCAGTACTCCAAACAATTCCAACGGTTCGAGTCTTTATTTATTTAATCAACTATTGTAATGGAAA
* *
5769 ATTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCCGA
1 GTTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCTGA
5834 ACCATTTCTTCAGTTTATTTTCAGGGATTTTGAACCATATAAGGTTTAGTACAACGGTGACAATG
66 ACCATTTCTTCAGTTTATTTTCAGGGATTTTGAACCATATAAGGTTTAGTACAACGGTGACAATG
5899 GTGCTGATGAA-AGCCAACC-AGCATCGTTGCC
131 GTGCTGATGAAGA-CCAACCTA-CATCGTTGCC
5930 GCATCAGCTT
Statistics
Matches: 449, Mismatches: 31, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
323 33 0.07
324 414 0.92
325 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (324 bp):
GTTCAATTAAATCATATTAGTACATAAAATTAATATAAATCAAAATGAAATTGAATTATAGCTGA
ACCATTTCTTCAGTTTATTTTCAGGGATTTTGAACCATATAAGGTTTAGTACAACGGTGACAATG
GTGCTGATGAAGACCAACCTACATCGTTGCCATATGAGATTGATCAATGCTTAAAAAAAAGCTAA
CTAGGATATTATATGTAAAACAGGATACTTACAACTATGATAAACTTCATGACAAGCCAAACCAC
CAGTACTCCAAACAATTCCAACGGTTCGAGTCTTTATTTATTTAATCAACTATTGTAATGGAAA
Found at i:14564 original size:45 final size:45
Alignment explanation
Indices: 14513--14601 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
14503 AATAAAGTAC
14513 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGG
1 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGG
* * *
14558 TGGAATTACTAAAAGATCTCTACCCCGGATTAATGATGAGCTGG
1 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
14602 AGAAGTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (45 bp):
TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGG
Found at i:16028 original size:3 final size:3
Alignment explanation
Indices: 16020--16052 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16010 AAGTTCTCTC
16020 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16053 GATGATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17598 original size:25 final size:24
Alignment explanation
Indices: 17565--17611 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
17555 AAAATAAATT
17565 ACTTTGTAGTTGTAATTATGGCAA
1 ACTTTGTAGTTGTAATTATGGCAA
*
17589 ACTTCTGTAGTTGTAATTTTGGC
1 ACTT-TGTAGTTGTAATTATGGC
17612 CAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (24 bp):
ACTTTGTAGTTGTAATTATGGCAA
Found at i:17825 original size:22 final size:22
Alignment explanation
Indices: 17800--17851 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
17790 ATGGATGGAG
* *
17800 GTTTGGTATTTGGACCATTCAA
1 GTTTGATATTTAGACCATTCAA
**
17822 GTTTGATATTTAGATTATTCAA
1 GTTTGATATTTAGACCATTCAA
17844 GTTT-ATAT
1 GTTTGATAT
17852 CATTTTGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (22 bp):
GTTTGATATTTAGACCATTCAA
Found at i:18591 original size:22 final size:23
Alignment explanation
Indices: 18556--18602 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
18546 GTAGTTAATC
*
18556 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
18578 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
18601 AT
1 AT
18603 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:18614 original size:22 final size:22
Alignment explanation
Indices: 18567--18616 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
18557 TAAATTAACT
*
18567 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
18589 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
18611 AATTAA
1 AATTAA
18617 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:18617 original size:15 final size:15
Alignment explanation
Indices: 18580--18618 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18570 TAAAACTAAT
*
18580 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
18595 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
18610 AAATTAATT
1 AAACTAATT
18619 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:18676 original size:32 final size:33
Alignment explanation
Indices: 18651--18714 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
18641 TGCCGCCTAT
18651 TTTGGGCGGCATG-CCATGGCCTTGCCACCCAG
1 TTTGGGCGGCATGCCCATGGCCTTGCCACCCAG
* *
18683 TTTGGGCGGCTTGCCCATGG-CATGCCACCCAG
1 TTTGGGCGGCATGCCCATGGCCTTGCCACCCAG
18715 GCTAGGCGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.22
Consensus pattern (33 bp):
TTTGGGCGGCATGCCCATGGCCTTGCCACCCAG
Found at i:18723 original size:32 final size:32
Alignment explanation
Indices: 18655--18725 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
18645 GCCTATTTTG
* ** *
18655 GGCGGCATGCCATGGCCTTGCCACCCAGTTTG
1 GGCGGCATGCCATGGCCATGCCACCCAGGCTA
*
18687 GGCGGCTTGCCCATGG-CATGCCACCCAGGCTA
1 GGCGGCATG-CCATGGCCATGCCACCCAGGCTA
18719 GGCGGCA
1 GGCGGCA
18726 CAGCCCTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.14, C:0.35, G:0.34, T:0.17
Consensus pattern (32 bp):
GGCGGCATGCCATGGCCATGCCACCCAGGCTA
Done.