Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010041.1 Corchorus capsularis cultivar CVL-1 contig10062, 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: 52942
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:531 original size:5 final size:5
Alignment explanation
Indices: 521--570 Score: 82
Period size: 5 Copynumber: 9.6 Consensus size: 5
511 TTTGAAAGTC
521 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
571 AGTATAAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.75
6 11 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:561 original size:2 final size:2
Alignment explanation
Indices: 524--630 Score: 64
Period size: 2 Copynumber: 54.5 Consensus size: 2
514 GAAAGTCTAT
524 TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * ** *
560 TA TA TA TA TA TA GTA TA AA TCA AA GA CA TGG CC TA AA TA TA TA
1 TA TA TA TA TA TA -TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA
603 TA TA TA TA TA TA TA TA TA CTA TA TA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA T
631 TTGTACTGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 20
0.71 0.11 0.17
Matches are distributed among these distances:
1 6 0.07
2 71 0.87
3 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10781 original size:100 final size:100
Alignment explanation
Indices: 10625--10804 Score: 306
Period size: 100 Copynumber: 1.8 Consensus size: 100
10615 ACAAATTGAT
* * * * *
10625 TTTCGGTGGACAAGAATAGTTATGGGTTTTGGTCAGAATTTTACTAGTAGGTTTCTATTTTTATG
1 TTTCGGTGGACAAAAATAGTTATGGGTTTTGGTAAAAATTTTACTAGGAAGTTTCTATTTTTATG
10690 GTAACTAGAATTATACGGTATAGCCCGCGGAAAAG
66 GTAACTAGAATTATACGGTATAGCCCGCGGAAAAG
*
10725 TTTCGGTGGATAAAAATAGTTATGGGTTTTGGTAAAAATTTTACTAGGAAGTTTCTATTTTTATG
1 TTTCGGTGGACAAAAATAGTTATGGGTTTTGGTAAAAATTTTACTAGGAAGTTTCTATTTTTATG
10790 GTAACTAGAATTATA
66 GTAACTAGAATTATA
10805 GGCTATATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
100 74 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (100 bp):
TTTCGGTGGACAAAAATAGTTATGGGTTTTGGTAAAAATTTTACTAGGAAGTTTCTATTTTTATG
GTAACTAGAATTATACGGTATAGCCCGCGGAAAAG
Found at i:16512 original size:33 final size:33
Alignment explanation
Indices: 16467--16534 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
16457 ATTAAGATTC
16467 AAGGTTTATAAATTAAAATTTACAATATGTCAA
1 AAGGTTTATAAATTAAAATTTACAATATGTCAA
* *
16500 AAGGTTTGTAAATTAAAATTTACAATATTTCAA
1 AAGGTTTATAAATTAAAATTTACAATATGTCAA
16533 AA
1 AA
16535 TATTTTGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (33 bp):
AAGGTTTATAAATTAAAATTTACAATATGTCAA
Found at i:20436 original size:12 final size:12
Alignment explanation
Indices: 20421--20468 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
20411 TTAGGAATGG
20421 CTTCAGGAACGA
1 CTTCAGGAACGA
20433 CTTCAGGAACGA
1 CTTCAGGAACGA
*
20445 CGTCAGGAACGA
1 CTTCAGGAACGA
*
20457 CATCAGGAACGA
1 CTTCAGGAACGA
20469 GAATATCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.27, T:0.12
Consensus pattern (12 bp):
CTTCAGGAACGA
Found at i:21115 original size:21 final size:22
Alignment explanation
Indices: 21081--21125 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
21071 CAAAAGAACG
*
21081 AAATAAAAGGAACAAACAAACT
1 AAATAAAAGCAACAAACAAACT
21103 AAAT-AAAGCAACAAACAAACT
1 AAATAAAAGCAACAAACAAACT
21124 AA
1 AA
21126 CTCAGACCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.09
Consensus pattern (22 bp):
AAATAAAAGCAACAAACAAACT
Found at i:21196 original size:54 final size:54
Alignment explanation
Indices: 21114--21224 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
21104 AATAAAGCAA
21114 CAAACAAACTAACTCAGACCAGGGAGCGAGTACACAATATCCCATTAACAAAAT
1 CAAACAAACTAACTCAGACCAGGGAGCGAGTACACAATATCCCATTAACAAAAT
* *
21168 CAAACAAACTAACTCAGACCAGGGAGCGAGTACACAATCTCCTATTAACAAAAT
1 CAAACAAACTAACTCAGACCAGGGAGCGAGTACACAATATCCCATTAACAAAAT
21222 CAA
1 CAA
21225 CAGCCACTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (54 bp):
CAAACAAACTAACTCAGACCAGGGAGCGAGTACACAATATCCCATTAACAAAAT
Found at i:21787 original size:3 final size:3
Alignment explanation
Indices: 21779--21808 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21769 ATTGGCCCAT
21779 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21809 AAACCCACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30310 original size:37 final size:37
Alignment explanation
Indices: 30269--30339 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
30259 ATATAATTAT
* *
30269 TCATAAAGTTATGTATATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTATATATGAAAAGACATGTATTGA
*
30306 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTATATATGAAAAGACATGTAT
30340 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTATATATGAAAAGACATGTATTGA
Found at i:30980 original size:2 final size:2
Alignment explanation
Indices: 30973--30999 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30963 TATCAATGAG
30973 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 A
31000 AGTTCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31597 original size:31 final size:32
Alignment explanation
Indices: 31544--31607 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
31534 TAGTGGAGTG
31544 TGTTGGTTTCTTAAAGAAAC-AAAGAGATATA
1 TGTTGGTTTCTTAAAGAAACAAAAGAGATATA
* *
31575 TGTTGGTTTCTTAGAA-ATACAAAAGAGTTATA
1 TGTTGGTTTCTTA-AAGAAACAAAAGAGATATA
31607 T
1 T
31608 CACTATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTTGGTTTCTTAAAGAAACAAAAGAGATATA
Found at i:32852 original size:37 final size:37
Alignment explanation
Indices: 32802--32872 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
32792 ATATAATTAT
* *
32802 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
32839 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
32873 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:34220 original size:18 final size:18
Alignment explanation
Indices: 34193--34231 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
34183 AATTTTACAA
34193 TTTAAAAAAGTAAACTAT
1 TTTAAAAAAGTAAACTAT
*
34211 TTTAAGAAAGTAAACTAT
1 TTTAAAAAAGTAAACTAT
34229 TTT
1 TTT
34232 GATATTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
TTTAAAAAAGTAAACTAT
Found at i:44109 original size:29 final size:30
Alignment explanation
Indices: 44057--44116 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
44047 ACTATTGCGT
44057 TAAGGACATTTTGCTCCCTGAACTT-CAAA
1 TAAGGACATTTTGCTCCCTGAACTTCCAAA
* *
44086 TAAGGATATTTTG-TCCCTTTAACTTCCAAA
1 TAAGGACATTTTGCTCCC-TGAACTTCCAAA
44116 T
1 T
44117 TCAGACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (30 bp):
TAAGGACATTTTGCTCCCTGAACTTCCAAA
Found at i:49726 original size:12 final size:12
Alignment explanation
Indices: 49709--49733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49699 GAGCAAATTG
49709 TGAAGGAGCAGC
1 TGAAGGAGCAGC
49721 TGAAGGAGCAGC
1 TGAAGGAGCAGC
49733 T
1 T
49734 AAAGAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.40, T:0.12
Consensus pattern (12 bp):
TGAAGGAGCAGC
Done.