Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014635.1 Corchorus capsularis cultivar CVL-1 contig14656, 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: 28365
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:709 original size:14 final size:14
Alignment explanation
Indices: 690--718 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
680 TGTACCTCTC
690 TTAAAATTTCTTAT
1 TTAAAATTTCTTAT
704 TTAAAATTTCTTAT
1 TTAAAATTTCTTAT
718 T
1 T
719 GAGTCAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTTCTTAT
Found at i:888 original size:72 final size:68
Alignment explanation
Indices: 754--895 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 68
744 CCTCAATAAA
754 ATTTCAAGTTTTGACACTTATAAATGAAAAAAAAAAAACTTGGAGAACTTTCACTCATTTTAAAT
1 ATTTCAAGTTTTGACACTTATAAATGAAAAAAAAAAAACTTGGAGAACTTTCACTCATTTTAAAT
819 TTG
66 TTG
* * *
822 ATTTCAAGTTTTGATACTTATAAGTGAAAAAAAGAAAAAGAACTTGTAGAACTTTCACTCATTTT
1 ATTTCAAGTTTTGACACTTATAAATG--AAAAA-AAAAA-AACTTGGAGAACTTTCACTCATTTT
887 AAATTTG
62 AAATTTG
894 AT
1 AT
896 ATGACTTGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
68 24 0.36
70 5 0.07
71 5 0.07
72 33 0.49
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (68 bp):
ATTTCAAGTTTTGACACTTATAAATGAAAAAAAAAAAACTTGGAGAACTTTCACTCATTTTAAAT
TTG
Found at i:2508 original size:26 final size:26
Alignment explanation
Indices: 2469--2520 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2459 ATTGCCGAAA
2469 CAAACAAATCTTCAACTATACTTGTT
1 CAAACAAATCTTCAACTATACTTGTT
* * * *
2495 CAAATAAATTTTCAATTATATTTGTT
1 CAAACAAATCTTCAACTATACTTGTT
2521 GTTTAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (26 bp):
CAAACAAATCTTCAACTATACTTGTT
Found at i:4667 original size:160 final size:164
Alignment explanation
Indices: 4468--4791 Score: 521
Period size: 160 Copynumber: 2.0 Consensus size: 164
4458 GACCAAACAG
* *
4468 AGAGGAAATTTCATGCAGACCCTAATCCAAAAGCTTCAGTCATATCCAACTTCTGACCAATCAGT
1 AGAGGAAATTTCATGCAGACCCTAACCCAAAAGCTTCAGTCAAATCCAACTTCTGACCAATCAGT
* *
4533 ACGAGTGTAAAACATTCCTTGTACAAATATCAAGCACATTCAC-A-TT-ACT-TGAAGAACACTA
66 ACCAGTGTAAAACATCCCTTGTACAAATATCAAGCACATTCACTATTTAACTCTGAAGAACACTA
4594 ACAACCACACTTTGTAGAAATATCAAGCACATTA
131 ACAACCACACTTTGTAGAAATATCAAGCACATTA
*
4628 AGAGGAAATTTCATGCAGACCCTAACCCAAAATCTTCAGTCAAATCCAACTTCTGACCAATCAGT
1 AGAGGAAATTTCATGCAGACCCTAACCCAAAAGCTTCAGTCAAATCCAACTTCTGACCAATCAGT
* * *
4693 ACCAGTGTACAACATCCCTTGTAGAAATATCAAGCACATTCACATTATTTGAAGTCTGAAGAACA
66 ACCAGTGTAAAACATCCCTTGTACAAATATCAAGCACATTCAC--TATTT-AACTCTGAAGAACA
4758 CTAACAACCACACTTTGTAGAAATATCAAGCACA
128 CTAACAACCACACTTTGTAGAAATATCAAGCACA
4792 ATAAATTTCT
Statistics
Matches: 149, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
160 101 0.68
163 1 0.01
164 2 0.01
166 2 0.01
167 43 0.29
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (164 bp):
AGAGGAAATTTCATGCAGACCCTAACCCAAAAGCTTCAGTCAAATCCAACTTCTGACCAATCAGT
ACCAGTGTAAAACATCCCTTGTACAAATATCAAGCACATTCACTATTTAACTCTGAAGAACACTA
ACAACCACACTTTGTAGAAATATCAAGCACATTA
Found at i:9017 original size:101 final size:101
Alignment explanation
Indices: 8842--9044 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
8832 CTAATTTTGG
8842 AAACAACTTATAAATATGCATTGGGTTTAGAAAGTTGACTTATATTTTGGGACAAAAAAAGCTTC
1 AAACAACTTATAAATATGCATTGGGTTTAGAAAGTTGACTTATATTTTGGGACAAAAAAAGCTTC
8907 TAGAAGGGGATTTATAAAAAGGGACAGAGGAAGTAT
66 TAGAAGGGGATTTATAAAAAGGGACAGAGGAAGTAT
8943 AAACAACTTATAAATATGCATTGGGTTTAGAAAGTTGACTTATATTTTGGGACAAAAAAAGCTTC
1 AAACAACTTATAAATATGCATTGGGTTTAGAAAGTTGACTTATATTTTGGGACAAAAAAAGCTTC
9008 TAGAAGGGGATTTATAAAAAGGGACAGAGGAAGTAT
66 TAGAAGGGGATTTATAAAAAGGGACAGAGGAAGTAT
9044 A
1 A
9045 TGCTGATGCC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (101 bp):
AAACAACTTATAAATATGCATTGGGTTTAGAAAGTTGACTTATATTTTGGGACAAAAAAAGCTTC
TAGAAGGGGATTTATAAAAAGGGACAGAGGAAGTAT
Found at i:13094 original size:22 final size:24
Alignment explanation
Indices: 13052--13095 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
13042 TTCAAGTGTT
*
13052 TTTCAACGACCTTGTTTCAAATGA
1 TTTCAACGACCCTGTTTCAAATGA
13076 TTTCAAC-ACCCT-TTTCAAAT
1 TTTCAACGACCCTGTTTCAAAT
13096 CTCTTCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTCAACGACCCTGTTTCAAATGA
Found at i:14592 original size:31 final size:31
Alignment explanation
Indices: 14523--14597 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
14513 AAATTGACTA
* *
14523 TAGGGACTTATTTGAGCCGATTTTGCAACGT
1 TAGGGACTCATTTGAGCAGATTTTGCAACGT
* * *
14554 TAAGGACTGATTTGAGTAGATTTTGCAACGT
1 TAGGGACTCATTTGAGCAGATTTTGCAACGT
*
14585 TTGGGACTCATTT
1 TAGGGACTCATTT
14598 AACCAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (31 bp):
TAGGGACTCATTTGAGCAGATTTTGCAACGT
Found at i:15638 original size:130 final size:131
Alignment explanation
Indices: 15454--15717 Score: 345
Period size: 130 Copynumber: 2.0 Consensus size: 131
15444 ATTGTTCTAA
* *
15454 ATTTGGAAAGTTCAGAGAGCAAATGGTCATCGATTGGGAAATTCAAAGGCAAATTGTCGCGATTT
1 ATTTAGAAAGTTCAGAGAGCAAATGGTCATCGATTGGGAAATTCAAAGGCAAATTATCGCGATTT
* *
15519 GAAGTGTAAGGGGGAAAATATTCTTGCCGTTATATATAGTTC-GGG-GGAAAGTGAGCCAAATAA
66 GAAGTGTAAGGAGGAAAATATTCTTGCCGTTATACATAGTTCAGGGAGGAAA-TGAGCCAAATAA
15582 GT
130 GT
* * * * * * *
15584 ATTTAGAAATTTCTGAGAGCAAATTGTTC-TGGATTGGGAAATTCAAGGGTAAATTATCGTGATT
1 ATTTAGAAAGTTCAGAGAGCAAA-TGGTCATCGATTGGGAAATTCAAAGGCAAATTATCGCGATT
* * * * *
15648 TGAAGTTTAAGGAGGAAAGTGTTGTTGCCGTTATACATAGTTCAGGGAGGAGATGAGCCAAATAA
65 TGAAGTGTAAGGAGGAAAATATTCTTGCCGTTATACATAGTTCAGGGAGGAAATGAGCCAAATAA
15713 GT
130 GT
15715 ATT
1 ATT
15718 GGGAGAGTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
130 87 0.76
131 24 0.21
132 4 0.03
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (131 bp):
ATTTAGAAAGTTCAGAGAGCAAATGGTCATCGATTGGGAAATTCAAAGGCAAATTATCGCGATTT
GAAGTGTAAGGAGGAAAATATTCTTGCCGTTATACATAGTTCAGGGAGGAAATGAGCCAAATAAG
T
Found at i:15826 original size:5 final size:5
Alignment explanation
Indices: 15816--15843 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
15806 GGTTTATAAA
15816 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
15844 CCCATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:23944 original size:31 final size:31
Alignment explanation
Indices: 23896--23954 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
23886 TCAAATCAGG
* *
23896 ACATTTTGTCTCCTGAACTTCAAAATTCGTA
1 ACATTTTGACTCCTGAACTCCAAAATTCGTA
*
23927 ACATTTTGAC-CCATGAACTCCCAAATTC
1 ACATTTTGACTCC-TGAACTCCAAAATTC
23955 AAGACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (31 bp):
ACATTTTGACTCCTGAACTCCAAAATTCGTA
Found at i:25102 original size:29 final size:31
Alignment explanation
Indices: 25057--25134 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 31
25047 TGACACCAAA
*
25057 TTGTAAGTAGAGGGACCAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
* * *
25087 TTGT-AGTAGGGGGACCAAGTTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
25117 TTGTAAGTAGAGGGACCA
1 TTGTAAGTAGAGGGACCA
25135 GTACGGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.41
30 12 0.29
31 12 0.29
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:25510 original size:13 final size:13
Alignment explanation
Indices: 25492--25521 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25482 CAATTCCCAG
*
25492 TGAAATTGGGGAT
1 TGAAATTGGAGAT
25505 TGAAATTGGAGAT
1 TGAAATTGGAGAT
25518 TGAA
1 TGAA
25522 CTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (13 bp):
TGAAATTGGAGAT
Done.