Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013762.1 Corchorus capsularis cultivar CVL-1 contig13783, 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: 67295
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:18900 original size:100 final size:100
Alignment explanation
Indices: 18727--18926 Score: 337
Period size: 100 Copynumber: 2.0 Consensus size: 100
18717 CCCTGGTCTG
*
18727 GTTTTCACCTCTTACTTAGCACTTTACTCAGGAGGTAAAAAAGAACGAAATAGCTTCATGCCACT
1 GTTTTCACCTCTTACTTAGCACTTTACTCAGGAGGTAAAAAAGAACAAAATAGCTTCATGCCACT
*
18792 GATATGTTAAAGCTGATGGGATAATTCACTCGAAT
66 GATATGTTAAAGCTGATAGGATAATTCACTCGAAT
* ** *
18827 GTTTTCACCTCTTATTTAGTGCTTTACTCAGGAGGTAAAAAGGAACAAAATAGCTTCATGCCACT
1 GTTTTCACCTCTTACTTAGCACTTTACTCAGGAGGTAAAAAAGAACAAAATAGCTTCATGCCACT
*
18892 GATATGTTAAAGCTGATAGGATATTTCACTCGAAT
66 GATATGTTAAAGCTGATAGGATAATTCACTCGAAT
18927 CTTCTTTTGG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (100 bp):
GTTTTCACCTCTTACTTAGCACTTTACTCAGGAGGTAAAAAAGAACAAAATAGCTTCATGCCACT
GATATGTTAAAGCTGATAGGATAATTCACTCGAAT
Found at i:28527 original size:45 final size:45
Alignment explanation
Indices: 28454--28544 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
28444 TCTTGATTTG
*
28454 AATCATTCATCTAATCTTTCTTATGCATCTACTTCATTTCCTTTC
1 AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
* * * *
28499 AATCTTTCCTCTAATGTTTCATATGCATCTCCTTCATTTCCTTTC
1 AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
28544 A
1 A
28545 CCAACTTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.21, C:0.27, G:0.03, T:0.48
Consensus pattern (45 bp):
AATCATTCATCTAATCTTTCATATGCATCTACTTCATTTCCTTTC
Found at i:34745 original size:63 final size:63
Alignment explanation
Indices: 34646--34771 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
34636 TTGTTATTAG
34646 AATGTATTGATGGGAATGAGACCAATCTTGTAATGTTGACCTATTAAGACCAAAGGACAACCA
1 AATGTATTGATGGGAATGAGACCAATCTTGTAATGTTGACCTATTAAGACCAAAGGACAACCA
34709 AATGTATTGATGGGAATGAGACCAATCTTGTAATGTTGACCTATTAAGACCAAAGGACAACCA
1 AATGTATTGATGGGAATGAGACCAATCTTGTAATGTTGACCTATTAAGACCAAAGGACAACCA
34772 GATATTAATC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (63 bp):
AATGTATTGATGGGAATGAGACCAATCTTGTAATGTTGACCTATTAAGACCAAAGGACAACCA
Found at i:39044 original size:18 final size:18
Alignment explanation
Indices: 39018--39083 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
39008 AAATTTTGAA
39018 TTTTTTTTCTGTTGATTT
1 TTTTTTTTCTGTTGATTT
* *
39036 TTCTTTTTCT-TTCTATACATT
1 TTTTTTTTCTGTT-GAT---TT
39057 TTTTTTTTCTGTTGATTT
1 TTTTTTTTCTGTTGATTT
39075 TTTTTTTTC
1 TTTTTTTTC
39084 GAATCTTCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 2 0.05
18 22 0.56
21 13 0.33
22 2 0.05
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTTTTTCTGTTGATTT
Found at i:39074 original size:17 final size:17
Alignment explanation
Indices: 39018--39081 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
39008 AAATTTTGAA
39018 TTTTTTTTCTGTTGATT
1 TTTTTTTTCTGTTGATT
* *
39035 TTTCTTTTTCTTTCTATACATT
1 TTT-TTTTTC--TGT-T-GATT
39057 TTTTTTTTCTGTTGATT
1 TTTTTTTTCTGTTGATT
39074 TTTTTTTT
1 TTTTTTTT
39082 TCGAATCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 14 0.37
18 7 0.18
19 2 0.05
20 2 0.05
21 7 0.18
22 6 0.16
ACGTcount: A:0.08, C:0.09, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCTGTTGATT
Found at i:49339 original size:2 final size:2
Alignment explanation
Indices: 49332--49366 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
49322 TTTATTTATT
*
49332 TA TA TA TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49367 AACAGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49349 original size:23 final size:23
Alignment explanation
Indices: 49323--49368 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
49313 TATTTACTAT
* *
49323 TTATTTATTTATATATATATAAA
1 TTATATATATATATATATATAAA
49346 TTATATATATATATATATATAAA
1 TTATATATATATATATATATAAA
49369 CAGAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATATATATATATATATAAA
Found at i:50559 original size:3 final size:3
Alignment explanation
Indices: 50551--50583 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
50541 GAAAATTCAC
50551 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50584 CATCATCATC
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:50588 original size:3 final size:3
Alignment explanation
Indices: 50582--50614 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
50572 AATAATAATA
*
50582 ATC ATC ATC ATC ATC ATG ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
50615 TCAAGAGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:56158 original size:2 final size:2
Alignment explanation
Indices: 56151--56184 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56141 CTTGTGTAAT
56151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56185 AAAGAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60086 original size:122 final size:122
Alignment explanation
Indices: 59954--60197 Score: 488
Period size: 122 Copynumber: 2.0 Consensus size: 122
59944 AAATTTATAA
59954 ACTTCATTATTCATGAAATTATGACCATAATAACAGTTTGTTTATTGAATTTGTTGGTAAATAAT
1 ACTTCATTATTCATGAAATTATGACCATAATAACAGTTTGTTTATTGAATTTGTTGGTAAATAAT
60019 AATATATAGGTTCTTTGATAAACAACATAGATATTTTTAATACAAAGTATATTAAAC
66 AATATATAGGTTCTTTGATAAACAACATAGATATTTTTAATACAAAGTATATTAAAC
60076 ACTTCATTATTCATGAAATTATGACCATAATAACAGTTTGTTTATTGAATTTGTTGGTAAATAAT
1 ACTTCATTATTCATGAAATTATGACCATAATAACAGTTTGTTTATTGAATTTGTTGGTAAATAAT
60141 AATATATAGGTTCTTTGATAAACAACATAGATATTTTTAATACAAAGTATATTAAAC
66 AATATATAGGTTCTTTGATAAACAACATAGATATTTTTAATACAAAGTATATTAAAC
60198 TTGATAACCT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (122 bp):
ACTTCATTATTCATGAAATTATGACCATAATAACAGTTTGTTTATTGAATTTGTTGGTAAATAAT
AATATATAGGTTCTTTGATAAACAACATAGATATTTTTAATACAAAGTATATTAAAC
Found at i:60986 original size:2 final size:2
Alignment explanation
Indices: 60979--61005 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60969 AAAATACTAG
60979 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
61006 TGTATATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61206 original size:14 final size:14
Alignment explanation
Indices: 61189--61218 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61179 CTTATAATTT
*
61189 ATTAGAAATAATAA
1 ATTAGAAATAACAA
61203 ATTAGAAATAACAA
1 ATTAGAAATAACAA
61217 AT
1 AT
61219 AATTACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (14 bp):
ATTAGAAATAACAA
Found at i:61595 original size:21 final size:22
Alignment explanation
Indices: 61569--61625 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
61559 TTAGGTTTTA
*
61569 ATTATTAAAAATAATTA-AATT
1 ATTATTAAAAATAATTATAAAT
61590 ATTATTAAAAA-AATTATAAAT
1 ATTATTAAAAATAATTATAAAT
*
61611 ATTTTTAAGAAATAA
1 ATTATTAA-AAATAA
61626 ATTACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 3 0.10
23 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTATTAAAAATAATTATAAAT
Found at i:62496 original size:31 final size:31
Alignment explanation
Indices: 62458--62517 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
62448 GTCTCAAACG
*
62458 TTGCAAAACCGGCTCGAATCAATCCCTAACA
1 TTGCAAAACCGGCTCAAATCAATCCCTAACA
* * *
62489 TTGCAAAATCGGCTTAAATCAGTCCCTAA
1 TTGCAAAACCGGCTCAAATCAATCCCTAA
62518 AATCAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.23
Consensus pattern (31 bp):
TTGCAAAACCGGCTCAAATCAATCCCTAACA
Done.