Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015008.1 Corchorus capsularis cultivar CVL-1 contig15029, 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: 21406
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:600 original size:21 final size:22
Alignment explanation
Indices: 571--613 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
561 TCGCTCGGTC
*
571 TCTAACAAA-CTAACAATCACA
1 TCTAACAAACCAAACAATCACA
*
592 TCTACCAAACCAAACAATCACA
1 TCTAACAAACCAAACAATCACA
614 CACACCCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (22 bp):
TCTAACAAACCAAACAATCACA
Found at i:1130 original size:66 final size:66
Alignment explanation
Indices: 1024--1153 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
1014 GACTTTTTGG
*
1024 TCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTG
1 TCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGACTTGCTTG
1089 A
66 A
* *
1090 TCATTTCTCAATTGATTTTAATAGAGTAGTGGAATTACTAAAAGATCTCTACCAAGACTTGCTT
1 TCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGACTTGCTT
1154 TTGGAGTTAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (66 bp):
TCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGACTTGCTTG
A
Found at i:3342 original size:22 final size:22
Alignment explanation
Indices: 3313--3365 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3303 AACATCAAAT
*
3313 TTTGATAATCT-CCCTTT-ATAA
1 TTTGATAA-CTGCCCTTTGAAAA
3334 TGTTGATAACTGCCCTTTGAAAA
1 T-TTGATAACTGCCCTTTGAAAA
3357 TTTGATAAC
1 TTTGATAAC
3366 CACCTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (22 bp):
TTTGATAACTGCCCTTTGAAAA
Found at i:3511 original size:22 final size:22
Alignment explanation
Indices: 3486--3637 Score: 103
Period size: 22 Copynumber: 6.9 Consensus size: 22
3476 TATCCTATGC
*
3486 AATTTTGATAACCACTATTTGT
1 AATTTTGATAACCACCATTTGT
* *
3508 AATTTTGATAACCTCGA-TTG-
1 AATTTTGATAACCACCATTTGT
**
3528 AATTTTTGATAACCACCACATGT
1 AA-TTTTGATAACCACCATTTGT
* ** *
3551 AATTTTGATAACGACCCCTTAT
1 AATTTTGATAACCACCATTTGT
* * *
3573 AATTTTGATAACC-TCATATGA
1 AATTTTGATAACCACCATTTGT
* * *
3594 AATTTTTTTGGTAACCATCTTTTGT
1 AA---TTTTGATAACCACCATTTGT
*
3619 AATTTTGATAACCTCCATT
1 AATTTTGATAACCACCATT
3638 AAAATTTTCA
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.02
21 20 0.20
22 58 0.59
23 2 0.02
24 10 0.10
25 7 0.07
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (22 bp):
AATTTTGATAACCACCATTTGT
Found at i:3555 original size:65 final size:64
Alignment explanation
Indices: 3357--3600 Score: 204
Period size: 65 Copynumber: 3.7 Consensus size: 64
3347 CCTTTGAAAA
* * * * *
3357 TTTGATAACCACCTATATTTTAATTTTGAAAACCTCAATTGGAA-TTTTGACAACTGCCCTATAT
1 TTTGATAACCA-CTAT-TTGTAATTTTGATAACCTCGATT-GAATTTTTGACAACTACCC-ATGT
3421 AAT
62 AAT
* * * * * * * * * *
3424 TATGATAGCCATTCTTTGAAATTTTAATAACTTCGATTGAAATTTTGACAACTATCCTATGCAAT
1 TTTGATAACCACTATTTGTAATTTTGATAACCTCGATTGAATTTTTGACAACTA-CCCATGTAAT
* *
3489 TTTGATAACCACTATTTGTAATTTTGATAACCTCGATTGAATTTTTGATAACCACCACATGTAAT
1 TTTGATAACCACTATTTGTAATTTTGATAACCTCGATTGAATTTTTGACAACTACC-CATGTAAT
* *** *
3554 TTTGATAACGACCCCTTATAATTTTGATAACCTC-ATATGAAATTTTT
1 TTTGATAACCACTATTTGTAATTTTGATAACCTCGAT-TG-AATTTTT
3601 TTGGTAACCA
Statistics
Matches: 141, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
64 7 0.05
65 114 0.81
66 11 0.08
67 9 0.06
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (64 bp):
TTTGATAACCACTATTTGTAATTTTGATAACCTCGATTGAATTTTTGACAACTACCCATGTAAT
Found at i:3623 original size:46 final size:47
Alignment explanation
Indices: 3572--3683 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 47
3562 CGACCCCTTA
*
3572 TAATTTTGATAACCTCATATGAAA-TTT-TTTTGGTAACCATCTTTTG
1 TAATTTTGATAACCTCAT-TAAAATTTTATTTTGGTAACCATCTTTTG
3618 TAATTTTGATAACCTCCATTAAAATTTTCAAATTTTGGTAACCATCTTTTG
1 TAATTTTGATAACCT-CATTAAAATTTT---ATTTTGGTAACCATCTTTTG
3669 TAA-TTTGATAACCTC
1 TAATTTTGATAACCTC
3684 CATAACATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
46 19 0.32
47 6 0.10
49 1 0.02
50 11 0.19
51 22 0.37
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (47 bp):
TAATTTTGATAACCTCATTAAAATTTTATTTTGGTAACCATCTTTTG
Found at i:3672 original size:51 final size:49
Alignment explanation
Indices: 3599--3694 Score: 165
Period size: 51 Copynumber: 1.9 Consensus size: 49
3589 TATGAAATTT
3599 TTTTGGTAACCATCTTTTGTAATTTTGATAACCTCCATTAAAATTTTCAAA
1 TTTTGGTAACCATCTTTTGTAA-TTTGATAACCTCCA-TAAAATTTTCAAA
*
3650 TTTTGGTAACCATCTTTTGTAATTTGATAACCTCCATAACATTTT
1 TTTTGGTAACCATCTTTTGTAATTTGATAACCTCCATAAAATTTT
3695 TTAAAGATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 8 0.18
50 14 0.32
51 22 0.50
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (49 bp):
TTTTGGTAACCATCTTTTGTAATTTGATAACCTCCATAAAATTTTCAAA
Found at i:3764 original size:23 final size:22
Alignment explanation
Indices: 3717--3768 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3707 CTTACGAGGC
* *
3717 TTTGACAACAATCTTTTGTAAT
1 TTTGATAACAATCCTTTGTAAT
*
3739 TTTGATAACTATCCTTTGTAAT
1 TTTGATAACAATCCTTTGTAAT
*
3761 TTTTATAA
1 TTTGATAA
3769 ACACTTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (22 bp):
TTTGATAACAATCCTTTGTAAT
Found at i:5758 original size:436 final size:436
Alignment explanation
Indices: 4863--5886 Score: 1167
Period size: 436 Copynumber: 2.3 Consensus size: 436
4853 ACGTGTTGCC
4863 TTTT-TTTTTTTTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATG
1 TTTTATTTTTTTTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATG
* * * * * *
4927 ATCAACAATTTTCATTAAGAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAATAATGCTTACG
66 ATCAACAACTTTCATGAAGGACTCAAAAG-CAATTTTTATG-TTTAATTCTAAAAAATGCTTACG
* * * * * * *
4992 AAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCTACATGTCCGATT
129 AAATTTTGTCGTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCCACATGTCCAATT
* * * * * * * *
5057 GAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGATTTTCATGAAGGACCCGAAA
194 AAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAA
* * *
5122 GCTAAATTTGATTTACGAGTTTCGTGAAGGGTTCAAAAAGGAATTTTTGTGTTTCAAGATCTCCA
259 GCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAAGGAATTTTTATGTTTCAAGATCTCCA
* * * *
5187 CTATAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTAAAT
324 CTATAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTAAAC
* * * ** *
5252 TGCTTAGTCATTTACAAATTATATCTTAATATAACGTTTAAGTTTTATT
389 TACTTAGTCATTGACAAATTATATCGTAATAT-ACGTTTAAACTTCATT
* * * *
5301 TTTTAATTTTTTGTTCTATTTGTCTGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCAT
1 TTTT-ATTTTTTTTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCAT
* * *
5366 GAT-ATACAACTTTCATGAAGGAGTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAAT-CTTC
65 GATCA-ACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGTTT-AATTCTAAAAAATGCTTA
* * **
5429 CTAAA-TTTGTTCGTTTCGGTTGTTGGTCT-ATTTAATACCATATAA-TTTTCGATCCACATGTC
127 CGAAATTTTG-TCGTTTCGATTGCCGGT-TAATTTAATACCATATAATTTTTCG-TCCACATGTC
*
5491 CAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATAATCTACGACTTTCATAAAGAACC
189 CAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACC
* *
5556 CGAAAG-TTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT
254 CGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAAGGAATTTTTATGTTTCAAGAT
* *
5620 CTCTA-T-TAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTA-TT
319 CTCCACTATAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTT
** * * * *
5682 CTATGCTACTTAGTCCTTGCCAAATTCTATCGT-A-CT-CGATTTAACACTTCATT
384 -TAAACTACTTAGTCATTGACAAATTATATCGTAATATACG-TTTAA-ACTTCATT
* * * * **
5735 ATTTTATTTTCTTTATTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAACATAATTTC
1 -TTTTATTTT-TTT-TTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTC
* * *
5800 ATGATCAACAACTTTCATGAAAGACTCAAAAACTAATTTTTATATATTAATTCTAAAAAATGCTT
63 ATGATCAACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGT-TTAATTCTAAAAAATGCTT
***
5865 TTAAAATTTTGT-GATTTCGATT
126 ACGAAATTTTGTCG-TTTCGATT
5887 AATAATCTAT
Statistics
Matches: 493, Mismatches: 74, Indels: 39
0.81 0.12 0.06
Matches are distributed among these distances:
432 2 0.00
433 5 0.01
434 11 0.02
435 9 0.02
436 167 0.34
437 18 0.04
438 74 0.15
439 108 0.22
440 99 0.20
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (436 bp):
TTTTATTTTTTTTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATG
ATCAACAACTTTCATGAAGGACTCAAAAGCAATTTTTATGTTTAATTCTAAAAAATGCTTACGAA
ATTTTGTCGTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCCACATGTCCAATTAA
AGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATAAAGAACCCGAAAGC
TAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAAGGAATTTTTATGTTTCAAGATCTCCACT
ATAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTAAACTA
CTTAGTCATTGACAAATTATATCGTAATATACGTTTAAACTTCATT
Found at i:9029 original size:17 final size:17
Alignment explanation
Indices: 9007--9041 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
8997 GAAATAGCCA
9007 AAAAAAAGAAATGTTCTGT
1 AAAAAAA-AAA-GTTCTGT
9026 AAAAAAAAAAGTTCTG
1 AAAAAAAAAAGTTCTG
9042 ATCGTCGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (17 bp):
AAAAAAAAAAGTTCTGT
Found at i:9930 original size:146 final size:147
Alignment explanation
Indices: 9666--9957 Score: 541
Period size: 146 Copynumber: 2.0 Consensus size: 147
9656 GTAACACATA
9666 AAATTTCTAAGTCTAAAAATAAGACAAGAAAGATTGGAGCCAAATAATAATTTTATTGATCGATG
1 AAATTTCTAAGTCTAAAAATAAGACAAGAAAGATTGGAGCCAAATAATAATTTTATTGATCGATG
*
9731 AATGTAAGTACAATCTTTGGAAATTCTAATAATAAGAAATTGTCCTCTGATTCTTCTTCTTCGCA
66 AATGCAAGTACAATCTTTGGAAATTCTAATAATAAGAAATTGTCCTCTGATTCTTCTTCTTCGCA
9796 AAATT-TGCTTCAAGAG
131 AAATTCTGCTTCAAGAG
* *
9812 AAATTTCTAAGTCTAAAAATAAGACAAGAAAGATTGGAGTCAAATAATAATTTTATTGATTGATG
1 AAATTTCTAAGTCTAAAAATAAGACAAGAAAGATTGGAGCCAAATAATAATTTTATTGATCGATG
*
9877 AATGCAGGTACAATCTTTGGAAATTCTAATAATAAGAAATTGTCCTCTGATTCTTCTTCTTCGCA
66 AATGCAAGTACAATCTTTGGAAATTCTAATAATAAGAAATTGTCCTCTGATTCTTCTTCTTCGCA
9942 AAATTCTGCTTCAAGA
131 AAATTCTGCTTCAAGA
9958 TTTGTTTCAA
Statistics
Matches: 141, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
146 131 0.93
147 10 0.07
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (147 bp):
AAATTTCTAAGTCTAAAAATAAGACAAGAAAGATTGGAGCCAAATAATAATTTTATTGATCGATG
AATGCAAGTACAATCTTTGGAAATTCTAATAATAAGAAATTGTCCTCTGATTCTTCTTCTTCGCA
AAATTCTGCTTCAAGAG
Found at i:11336 original size:7 final size:7
Alignment explanation
Indices: 11320--11358 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
11310 TATTAATTAG
11320 TGAAGAC
1 TGAAGAC
*
11327 TGAGGAC
1 TGAAGAC
11334 TGAAGAC
1 TGAAGAC
11341 TGAAGAC
1 TGAAGAC
11348 TGAAGAC
1 TGAAGAC
11355 TGAA
1 TGAA
11359 ATTAAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.31, T:0.15
Consensus pattern (7 bp):
TGAAGAC
Found at i:12110 original size:13 final size:13
Alignment explanation
Indices: 12092--12131 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
12082 TATAACTTTA
12092 ACAATTGAATTTG
1 ACAATTGAATTTG
*
12105 ACAATTGAA-TTC
1 ACAATTGAATTTG
12117 ACAATTGAATTTG
1 ACAATTGAATTTG
12130 AC
1 AC
12132 TCCTCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (13 bp):
ACAATTGAATTTG
Found at i:12122 original size:12 final size:12
Alignment explanation
Indices: 12092--12127 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
12082 TATAACTTTA
*
12092 ACAATTGAATTTG
1 ACAATTGAA-TTC
12105 ACAATTGAATTC
1 ACAATTGAATTC
12117 ACAATTGAATT
1 ACAATTGAATT
12128 TGACTCCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (12 bp):
ACAATTGAATTC
Found at i:13691 original size:30 final size:28
Alignment explanation
Indices: 13654--13718 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
13644 TACTGCTTCC
13654 TTTTTTTTTGTTAAAATAGAATACTAGTT
1 TTTTTTTTTGTTAAAATAGAATACTA-TT
* ***
13683 TCTTTTTTTTTTTTTGATAGAATACTATT
1 T-TTTTTTTTGTTAAAATAGAATACTATT
13712 TTTTTTT
1 TTTTTTT
13719 AAGAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 6 0.19
29 4 0.13
30 21 0.68
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.65
Consensus pattern (28 bp):
TTTTTTTTTGTTAAAATAGAATACTATT
Done.