Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013649.1 Corchorus olitorius cultivar O-4 contig13682, 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: 29301
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:9339 original size:12 final size:13
Alignment explanation
Indices: 9322--9354 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
9312 TCTTTCCCTT
9322 TCCACA-CAAAAA
1 TCCACAGCAAAAA
9334 TCCACATGCAAAAA
1 TCCACA-GCAAAAA
9348 TCCACAG
1 TCCACAG
9355 ATCTTACCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 1 0.05
14 12 0.63
ACGTcount: A:0.48, C:0.33, G:0.06, T:0.12
Consensus pattern (13 bp):
TCCACAGCAAAAA
Found at i:11590 original size:30 final size:30
Alignment explanation
Indices: 11508--11602 Score: 115
Period size: 30 Copynumber: 3.1 Consensus size: 30
11498 ACCTTTTTTT
11508 TAAGCAAATTCAAAAGAAGATTTT-GAAAAC
1 TAAG-AAATTCAAAAGAAGATTTTGGAAAAC
11538 TAAGATAATTCCCAAAAGAAGATTTTGGAAAA-
1 TAAGA-AATT--CAAAAGAAGATTTTGGAAAAC
*
11570 TAGAGAAATTCAAAATAAGATTTTGG-AAAC
1 TA-AGAAATTCAAAAGAAGATTTTGGAAAAC
11600 TAA
1 TAA
11603 TAAAGTTGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
29 5 0.09
30 25 0.43
32 20 0.34
33 8 0.14
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (30 bp):
TAAGAAATTCAAAAGAAGATTTTGGAAAAC
Found at i:13302 original size:22 final size:22
Alignment explanation
Indices: 13271--13328 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
13261 GTTGTAGCTC
* *
13271 TATGGTAGCAATAAATCTGACT
1 TATGGCAGCAATAAATCTAACT
13293 TATGGCAGCAATAAATCTAACT
1 TATGGCAGCAATAAATCTAACT
* *
13315 TCTAGCAGCAATAA
1 TATGGCAGCAATAA
13329 GAACTGAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (22 bp):
TATGGCAGCAATAAATCTAACT
Found at i:13772 original size:29 final size:29
Alignment explanation
Indices: 13730--13789 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
13720 CACGATAAAT
13730 GATTACTTAAGCAAGCTATTTGATTTGAA
1 GATTACTTAAGCAAGCTATTTGATTTGAA
13759 GATTACTTAAGCAAGCTATTTGATTTGAA
1 GATTACTTAAGCAAGCTATTTGATTTGAA
13788 GA
1 GA
13790 CAGTAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (29 bp):
GATTACTTAAGCAAGCTATTTGATTTGAA
Found at i:17796 original size:96 final size:95
Alignment explanation
Indices: 17607--17796 Score: 224
Period size: 96 Copynumber: 2.0 Consensus size: 95
17597 TCATTATTTA
* * *
17607 AACTTTTATAGTTTTACTCAACTGAAAACTCTATTTATATTTAATTAAATCTAATATCCTTGTAA
1 AACTTTTACAGTTTTACTCAACTGAAAACTCTATTTATAATTAATTAAATCTAATATCCTTATAA
*
17672 CTTTTTATTTTACCATTTTAATACTTTAATT
66 CTTTTTATTTTAACATTTTAATA-TTTAATT
* * * **
17703 AACTTTTACAGTTTTATTCTACTGAAAACTCTATTTTTAATTAATTAAAATC-AATATTTTTATA
1 AACTTTTACAGTTTTACTCAACTGAAAACTCTATTTATAATTAATT-AAATCTAATATCCTTATA
*
17767 GA-TATTTTCTTTTTAACATTTTAAT-TTTAA
65 -ACT-TTTT-ATTTTAACATTTTAATATTTAA
17797 AAAATTGGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
96 56 0.70
97 10 0.12
98 14 0.17
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (95 bp):
AACTTTTACAGTTTTACTCAACTGAAAACTCTATTTATAATTAATTAAATCTAATATCCTTATAA
CTTTTTATTTTAACATTTTAATATTTAATT
Found at i:20603 original size:21 final size:21
Alignment explanation
Indices: 20579--20643 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
20569 AATTCTCTGT
20579 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * **
20600 AAATCATAGAAA-ATTCTTCGT-
1 AAATTA-AGAAATACTCAAC-TC
20621 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
20642 AA
1 AA
20644 GTCCTGATTC
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:20786 original size:57 final size:56
Alignment explanation
Indices: 20713--20824 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 56
20703 TTATTTTATA
* *
20713 GAATAATTAAGTAGAGATGGGGGGATAGGAGTTTATTATAACATTTATTGTGTGAAT
1 GAATAATTAAGTAGAGATAGGGGGATAGGA-TTTATTATAACATTTATTGTATGAAT
20770 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
1 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAA
20825 AGGAAATGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 24 0.45
57 29 0.55
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (56 bp):
GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTATGAAT
Found at i:21023 original size:7 final size:7
Alignment explanation
Indices: 21011--21056 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
21001 AAATAATATG
21011 TATAGTA
1 TATAGTA
21018 TATAGTA
1 TATAGTA
21025 TATAGTA
1 TATAGTA
21032 TATAGTA
1 TATAGTA
21039 TATAGTA
1 TATAGTA
21046 TATAGTA
1 TATAGTA
21053 TATA
1 TATA
21057 TGACTGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (7 bp):
TATAGTA
Found at i:21791 original size:132 final size:130
Alignment explanation
Indices: 21576--21843 Score: 428
Period size: 132 Copynumber: 2.0 Consensus size: 130
21566 CATTGTTTAA
*
21576 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
* * * *
21641 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
66 TATTTAATTTTTACCATTTTACTAATTTAATT-AAAAAACTTAGATATATTA-AAATTTTAAAAT
21706 AT
129 AT
* *
21708 ACTTTTATAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
* *
21773 TATTTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTAAAATAT
66 TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTAAAATAT
*
21838 ATTTTT
1 ACTTTT
21844 TAAATGACAT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
130 17 0.13
131 18 0.14
132 91 0.72
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (130 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTAAAATAT
Found at i:23414 original size:27 final size:28
Alignment explanation
Indices: 23384--23457 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
23374 TCCGACGTTT
*
23384 AAGGGCAAAACTGTAATTT-AGTCAACC
1 AAGGGCAAAACTGTAATTTCAGCCAACC
* *
23411 AAGGGTAAAA-TGGTAATTTCAGCCGACC
1 AAGGGCAAAACT-GTAATTTCAGCCAACC
*
23439 AATGGCAAATAC-GTAATTT
1 AAGGGCAAA-ACTGTAATTT
23458 TAACATCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 16 0.42
28 20 0.53
29 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (28 bp):
AAGGGCAAAACTGTAATTTCAGCCAACC
Found at i:25078 original size:30 final size:30
Alignment explanation
Indices: 25042--25102 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
25032 TCAGTAAGAT
25042 ATTAAAATTTGAGGGTATAAGAAAAAAGTC
1 ATTAAAATTTGAGGGTATAAGAAAAAAGTC
*
25072 ATTAAAATTTGAGGGTATAAGAGAAAAGTC
1 ATTAAAATTTGAGGGTATAAGAAAAAAGTC
25102 A
1 A
25103 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAAAAAAGTC
Found at i:26248 original size:45 final size:45
Alignment explanation
Indices: 26194--26290 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
26184 AACAACAACT
* *
26194 AATATTAGCTTTATTTTAATGAATTATATAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATCACATAGAGATGGAGGAGTAG
* * *
26239 AATATTAGCTTTATTTTGATGAATCACCTGGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATCACATAGAGATGGAGGAGTAG
26284 AAT-TTAG
1 AATATTAG
26291 GTAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATCACATAGAGATGGAGGAGTAG
Done.