Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009147.1 Corchorus capsularis cultivar CVL-1 contig09168, 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: 39503
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1080 original size:15 final size:15
Alignment explanation
Indices: 1039--1082 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
1029 CGTTGGTTAA
*
1039 AAAAATAACAGAAATT
1 AAAAATAA-AAAAATT
1055 ATAAGAATAAAAAAATT
1 A-AA-AATAAAAAAATT
1072 AAAAATAAAAA
1 AAAAATAAAAA
1083 GTAATAGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.32
16 3 0.12
17 9 0.36
18 5 0.20
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:1674 original size:13 final size:13
Alignment explanation
Indices: 1656--1680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1646 AGATTTAGCC
1656 ATGTTAATATTGA
1 ATGTTAATATTGA
1669 ATGTTAATATTG
1 ATGTTAATATTG
1681 TATTCTTGGC
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTTAATATTGA
Found at i:2041 original size:35 final size:35
Alignment explanation
Indices: 1966--2045 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
1956 TATGTTTCTG
* * * *
1966 TATGTTTGAGCATGTTTGTGATTTGGCTTTGTGAC
1 TATGTTTGAGCATGTATCTAATTTGGCTTTATGAC
* * *
2001 CATGTTTGAGCATGTATCTAATTTTGTTTTATGAC
1 TATGTTTGAGCATGTATCTAATTTGGCTTTATGAC
2036 TATGTTTGAG
1 TATGTTTGAG
2046 TATATCTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.19, C:0.09, G:0.24, T:0.49
Consensus pattern (35 bp):
TATGTTTGAGCATGTATCTAATTTGGCTTTATGAC
Found at i:2512 original size:30 final size:30
Alignment explanation
Indices: 2476--2582 Score: 124
Period size: 30 Copynumber: 3.6 Consensus size: 30
2466 ATGAAGTAAT
** * *
2476 AGTGGAAGACAACAATGTCAATCTGCAGCC
1 AGTGGAAGACAACAATGGGAATCAGCAGCA
* *
2506 AGTGGAAGACAACAATGGGGACCAGCAGCA
1 AGTGGAAGACAACAATGGGAATCAGCAGCA
* * *
2536 AGTGGAAGATAACAATGGGAATCGGCAACA
1 AGTGGAAGACAACAATGGGAATCAGCAGCA
*
2566 AGTGGAAGATAACAATG
1 AGTGGAAGACAACAATG
2583 TTGAAGAGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.13
Consensus pattern (30 bp):
AGTGGAAGACAACAATGGGAATCAGCAGCA
Found at i:2852 original size:15 final size:15
Alignment explanation
Indices: 2828--2882 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
2818 TGCTGGGGTT
2828 GGGCCATCTACTACA
1 GGGCCATCTACTACA
* *
2843 GGGCCTTCTACTGCTA
1 GGGCCATCTACTAC-A
*
2859 -GGCCATCTACTAAA
1 GGGCCATCTACTACA
*
2873 GGGCCTTCTA
1 GGGCCATCTA
2883 ATGCATCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (15 bp):
GGGCCATCTACTACA
Found at i:3933 original size:26 final size:25
Alignment explanation
Indices: 3892--3980 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 25
3882 AGCACAAGGT
*
3892 ACTTTCTG-TTTTTTATAAGTGTATA
1 ACTTT-TGTTTTTTTATAAGTGTCTA
3917 ACTATTTGTTTTTTTATAAGTGTCTA
1 ACT-TTTGTTTTTTTATAAGTGTCTA
* *
3943 ACTGTCT-ATTTTTTATAAGTGTCTA
1 ACT-TTTGTTTTTTTATAAGTGTCTA
3968 ACTTTCTGTTTTT
1 ACTTT-TGTTTTT
3981 ATAGGCTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 1 0.02
25 26 0.48
26 27 0.50
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.57
Consensus pattern (25 bp):
ACTTTTGTTTTTTTATAAGTGTCTA
Found at i:3954 original size:25 final size:25
Alignment explanation
Indices: 3900--3980 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
3890 GTACTTTCTG
* * *
3900 TTTTTTATAAGTGTATAACTATTTGT
1 TTTTTTATAAGTGTCTAACTATCT-A
*
3926 TTTTTTATAAGTGTCTAACTGTCTA
1 TTTTTTATAAGTGTCTAACTATCTA
* *
3951 TTTTTTATAAGTGTCTAACTTTCTG
1 TTTTTTATAAGTGTCTAACTATCTA
3976 TTTTT
1 TTTTT
3981 ATAGGCTCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
25 28 0.57
26 21 0.43
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (25 bp):
TTTTTTATAAGTGTCTAACTATCTA
Found at i:13663 original size:29 final size:29
Alignment explanation
Indices: 13621--13678 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
13611 TAACTATCCA
13621 TTTTGGGACAAATTGACCCCTTAACTTTT
1 TTTTGGGACAAATTGACCCCTTAACTTTT
13650 TTTTGGGACAAATTGACCCCTTAACTTTT
1 TTTTGGGACAAATTGACCCCTTAACTTTT
13679 AAAAACAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTGGGACAAATTGACCCCTTAACTTTT
Found at i:14163 original size:28 final size:29
Alignment explanation
Indices: 14128--14184 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
14118 TCTCGTTTTT
14128 AAAAGTTAAGGGG-CAATTTGTCCAAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCAAAAA
*
14156 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCAAAAA
14185 TGGATAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCAAAAA
Found at i:15737 original size:21 final size:21
Alignment explanation
Indices: 15711--15761 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
15701 GAATCAATCT
15711 ACATGATTTGAGGACACAGT-A
1 ACATGATTTGAGGACAC-GTCA
*
15732 ACATGATTTGCGGACACGTCA
1 ACATGATTTGAGGACACGTCA
15753 ACATGATTT
1 ACATGATTT
15762 TCGGCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (21 bp):
ACATGATTTGAGGACACGTCA
Found at i:19472 original size:72 final size:72
Alignment explanation
Indices: 19335--19476 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
19325 ACGCCACCCC
* * *
19335 GCAGGATATCCAATGATCTCATAACATTGATCTTTTATATGTCCCGACTTCTGACAGTGTCCACA
1 GCAGGATATCCAATGATCTCATAACATTGATCTTTCATATGTCCCCACTTCTGACAATGTCCACA
19400 CCTTGCA
66 CCTTGCA
* * * * * * *
19407 GCAGGATATCCAATGATCTCATAGCATTGGTCTTTCGTGTG-CCCCACCTTTTGGCAATGTTCAC
1 GCAGGATATCCAATGATCTCATAACATTGATCTTTCATATGTCCCCA-CTTCTGACAATGTCCAC
19471 ACCTTG
65 ACCTTG
19477 GCTTGTCTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 4 0.07
72 55 0.93
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (72 bp):
GCAGGATATCCAATGATCTCATAACATTGATCTTTCATATGTCCCCACTTCTGACAATGTCCACA
CCTTGCA
Found at i:20519 original size:21 final size:21
Alignment explanation
Indices: 20493--20543 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
20483 GAATCAATCT
20493 ACATGATTTGCGGACACGGT-A
1 ACATGATTTGCGGACAC-GTCA
20514 ACATGATTTGCGGACACGTCA
1 ACATGATTTGCGGACACGTCA
20535 ACATGATTT
1 ACATGATTT
20544 TCGGCTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
ACATGATTTGCGGACACGTCA
Found at i:22044 original size:2 final size:2
Alignment explanation
Indices: 22037--22067 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22027 TAGGTGGTTT
22037 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22068 TGCCTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:24574 original size:26 final size:26
Alignment explanation
Indices: 24545--24617 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
24535 TTCTATGGGC
24545 AAGTAAAATCGAAAAAGAATGGATCG
1 AAGTAAAATCGAAAAAGAATGGATCG
* * **
24571 AAGTTAAATGGAGGAAGAATGGATCG
1 AAGTAAAATCGAAAAAGAATGGATCG
*
24597 AAG-AGAAATTGAAAAAGAATG
1 AAGTA-AAATCGAAAAAGAATG
24618 AAAGAGAGCG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.27, T:0.16
Consensus pattern (26 bp):
AAGTAAAATCGAAAAAGAATGGATCG
Found at i:25265 original size:30 final size:30
Alignment explanation
Indices: 25231--25300 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
25221 TTTTTTTTCT
**
25231 TTTCAAGTTTTTCTTTATTG-GTGAAAATCA
1 TTTCAAGTTTTTCTTTA-TGAGCAAAAATCA
* *
25261 TTTCAAGTTTTTTTTTATGAGCAAAAATCG
1 TTTCAAGTTTTTCTTTATGAGCAAAAATCA
25291 TTTCAAGTTT
1 TTTCAAGTTT
25301 CAACAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (30 bp):
TTTCAAGTTTTTCTTTATGAGCAAAAATCA
Found at i:37300 original size:60 final size:59
Alignment explanation
Indices: 37207--37324 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 59
37197 TGAAACATAA
37207 ATTTAGGTTAAAGCAATATTAAGGTTGTATAACTCATCTTGCATTGCATACTGCAATCAG
1 ATTTAGGTTAAAGCAATATTAAGGTTGTATAACTC-TCTTGCATTGCATACTGCAATCAG
* *
37267 ATTTAGGTTACAGCAATATTAAGGTTGTATAACTCTCTTGCATTGCATCCTGCAATCA
1 ATTTAGGTTAAAGCAATATTAAGGTTGTATAACTCTCTTGCATTGCATACTGCAATCA
37325 CTATTTGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 22 0.39
60 34 0.61
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (59 bp):
ATTTAGGTTAAAGCAATATTAAGGTTGTATAACTCTCTTGCATTGCATACTGCAATCAG
Found at i:39419 original size:2 final size:2
Alignment explanation
Indices: 39412--39454 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39402 TGCTGGAAAC
39412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39454 A
1 A
39455 GCTTAAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.