Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008831.1 Corchorus capsularis cultivar CVL-1 contig08852, 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: 18313
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:99 original size:30 final size:31
Alignment explanation
Indices: 65--131 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
55 AAGAAGGGGC
65 AATCAGCAATTAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
** *
95 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
126 AATCAG
1 AATCAG
132 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:131 original size:31 final size:30
Alignment explanation
Indices: 73--132 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
63 GCAATCAGCA
73 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
1 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
*
103 ATTAAGTTCAATAAGAAAGATGTAATCAGT
1 ATTAAGTTCAATAAGAAA-AAGTAATCAGT
133 AAAAGGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (30 bp):
ATTAAGTTCAATAAGAAAAAGTAATCAGTG
Found at i:151 original size:22 final size:23
Alignment explanation
Indices: 126--185 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
116 AGAAAGATGT
126 AATCAGTAAAAG-GTAAAGCGAC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
148 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
*
170 AGTCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
186 TAGAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:292 original size:107 final size:109
Alignment explanation
Indices: 172--373 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 109
162 AAAGTGATAG
*
172 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-A-AATAATCAGAGTCAAG
1 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
235 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
66 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
*
279 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAA
1 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
* *
344 GTAATAGTAATCAGTAAATCGATAATTAAG
66 GTAATAGAAATCAGTAAATCAATAATTAAG
374 AGTTAAAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 46 0.52
108 1 0.01
109 42 0.47
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (109 bp):
TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
Found at i:308 original size:54 final size:54
Alignment explanation
Indices: 174--373 Score: 264
Period size: 54 Copynumber: 3.7 Consensus size: 54
164 AGTGATAGTC
* *
174 AGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAA-AAAATAATCA
1 AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAATTAATCA
*
227 GAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAATC-
1 -AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAATTAATCA
* *
281 AGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCA
1 AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAATTAATCA
* * *
336 GAGTCAA-AGTAATAGTAATCAGTAAATCGATAATTAAG
1 -AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
374 AGTTAAAATG
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
53 36 0.28
54 53 0.41
55 36 0.28
56 5 0.04
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.24
Consensus pattern (54 bp):
AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAATTAATCA
Found at i:640 original size:66 final size:64
Alignment explanation
Indices: 560--845 Score: 241
Period size: 64 Copynumber: 4.4 Consensus size: 64
550 AATAGCAGGC
* * *
560 AATCAGTAAAAAGTAAAAAGGT-ACCTGA-AAGGGTAAAAAGAGTAATCAGTAAAAGAGTAAAAT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AACAAGAGT-AAAAGAGTAATCAGTAAAA-AGT-AAAT
623 AGT
62 AGT
* * *
626 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAAGTAAATAGT
* * * * *
690 AATCAGT-AAGAGTAAAAAAGGTAAT-AAGTAAGAAGTAAAAG-GAAATCAGT-AAGAGTAAAAA
1 AATCAGTAAAAAGT-AAAAAGGTAATCAA-CAAG-AGTAAAAGAGTAATCAGTAAAAAGTAAATA
751 GGT
63 -GT
* * * * *
754 GATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAA-AGGTAATCAGTAAAAAGCAAA-AG
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAG-AGTAAAAGA-GTAATCAGTAAAAAGTAAATA-
817 GCT
63 G-T
820 -ATCAGTAAAAAGT-AAAAGAGTAATCA
1 AATCAGTAAAAAGTAAAAAG-GTAATCA
846 GTAAAAAAAG
Statistics
Matches: 184, Mismatches: 23, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
63 16 0.09
64 68 0.37
65 46 0.25
66 47 0.26
67 7 0.04
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.18
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAAGTAAATAGT
Found at i:649 original size:22 final size:21
Alignment explanation
Indices: 560--926 Score: 233
Period size: 22 Copynumber: 17.2 Consensus size: 21
550 AATAGCAGGC
560 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
* * **
582 -ACCTG-AAAGGGTAAAAAGAGT
1 AATCAGTAAAAAGT-AAAAG-GT
*
603 AATCAGTAAAAGAGTAAAATAGT
1 AATCAGTAAAA-AGTAAAA-GGT
626 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAGGT
* *
648 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGTAAAA-GGT
*
669 AGTCAGTAAAAAGTAAATA-GT
1 AATCAGTAAAAAGTAAA-AGGT
*
690 AATCAGT-AAGAGTAAAAAAGGT
1 AATCAGTAAAAAGT--AAAAGGT
* * *
712 AATAAGTAAGAAGTAAAAGGA
1 AATCAGTAAAAAGTAAAAGGT
*
733 AATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
* * *
754 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGT-AAAAGGT
* *
776 AATCAGCAAGAAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
*
798 AATCAGTAAAAAGCAAAAGGCT
1 AATCAGTAAAAAGTAAAAGG-T
820 -ATCAGTAAAAAGTAAAAGAGT
1 AATCAGTAAAAAGTAAAAG-GT
841 AATCAGT--AAA--AAAAGG-
1 AATCAGTAAAAAGTAAAAGGT
* * *
857 GAGCAG-AAAATAGTAAAGGGT
1 AATCAGTAAAA-AGTAAAAGGT
* *
878 AATCAGTAAAAGAATAAAATGAT
1 AATCAGTAAAA-AGTAAAA-GGT
901 AATCAGT-AAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAGGT
922 AATCA
1 AATCA
927 ACAAGAGTAA
Statistics
Matches: 270, Mismatches: 46, Indels: 59
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.01
17 3 0.01
18 6 0.02
20 31 0.11
21 90 0.33
22 97 0.36
23 37 0.14
24 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAGGT
Found at i:662 original size:43 final size:42
Alignment explanation
Indices: 612--852 Score: 240
Period size: 43 Copynumber: 5.6 Consensus size: 42
602 TAATCAGTAA
*
612 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAA-AGGTAATCAGTAAAAAGTAA-AAGGTAATCAGC
* *
655 AAGAGTAAAATA-GTAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAA-AGGTAATCAGTAAAAAGTAAA-AGGTAATCAGC
* * * *
697 AAGAGTAAAAAAGGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGT-AAAAAGGTAATCAGTAAAAAGTAAAAGGTAATCAGC
* * *
740 AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAAAGGTAATCAGTAAAAAGT-AAAAGGTAATCAGC
* *
783 AAGAAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCT-ATCAGTA
1 AAG-AGTAAAAAGGTAATCAGTAAAAAGTAAAAGG-TAATCAG-C
*
827 AAAAGT-AAAAGAGTAATCAGTAAAAA
1 AAGAGTAAAAAG-GTAATCAGTAAAAA
853 AAGGGAGCAG
Statistics
Matches: 169, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
42 39 0.23
43 105 0.62
44 25 0.15
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAAAGGTAATCAGTAAAAAGTAAAAGGTAATCAGC
Found at i:688 original size:21 final size:22
Alignment explanation
Indices: 560--926 Score: 256
Period size: 21 Copynumber: 17.2 Consensus size: 22
550 AATAGCAGGC
560 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
* * **
582 -ACCTG-AAAGGGTAAAAAGAGT
1 AATCAGTAAAAAGTAAAAAG-GT
603 AATCAGTAAAAGAGTAAAATA-GT
1 AATCAGTAAAA-AGTAAAA-AGGT
*
626 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
*
648 AATCA--ACAAGAGTAAAATA-GT
1 AATCAGTA-AAAAGTAAAA-AGGT
* *
669 AGTCAGTAAAAAGTAAATA-GT
1 AATCAGTAAAAAGTAAAAAGGT
*
690 AATCAGT-AAGAGTAAAAAAGGT
1 AATCAGTAAAAAGT-AAAAAGGT
* * *
712 AATAAGTAAGAAGT-AAAAGGA
1 AATCAGTAAAAAGTAAAAAGGT
*
733 AATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
* * *
754 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGTAAAAAGGT
* *
776 AATCAGCAAGAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
*
798 AATCAGTAAAAAG-CAAAAGGCT
1 AATCAGTAAAAAGTAAAAAGG-T
820 -ATCAGTAAAAAGT-AAAAGAGT
1 AATCAGTAAAAAGTAAAAAG-GT
841 AATCAGT---AA--AAAAAGG-
1 AATCAGTAAAAAGTAAAAAGGT
* * *
857 GAGCAG-AAAATAGT-AAAGGGT
1 AATCAGTAAAA-AGTAAAAAGGT
* * *
878 AATCAGTAAAAGAATAAAATGAT
1 AATCAGTAAAA-AGTAAAAAGGT
*
901 AATCAGT-AAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAAAAAGGT
922 AATCA
1 AATCA
927 ACAAGAGTAA
Statistics
Matches: 268, Mismatches: 48, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
16 4 0.01
17 1 0.00
18 6 0.02
19 3 0.01
20 26 0.10
21 97 0.36
22 91 0.34
23 33 0.12
24 6 0.02
25 1 0.00
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAAAGGT
Found at i:9980 original size:2 final size:2
Alignment explanation
Indices: 9973--10001 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9963 TACAGTTTTA
9973 AT 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 AT A
10002 CTAGTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10129 original size:29 final size:28
Alignment explanation
Indices: 10065--10129 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
10055 TTAAAATAAA
*
10065 ATAA-ATATAAAAATTGATATATTTTTT
1 ATAATATATAAAAATTGATATATTATTT
* *
10092 TTAGGTATATAAAAATTGATATATTAATTT
1 ATA-ATATATAAAAATTGATATATT-ATTT
10122 ATAATATA
1 ATAATATA
10130 ATATGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (28 bp):
ATAATATATAAAAATTGATATATTATTT
Found at i:14423 original size:24 final size:23
Alignment explanation
Indices: 14392--14440 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
14382 AATTGATCAA
14392 CATTAAGGTTTCACGAAAATTTT
1 CATTAAGGTTTCACGAAAATTTT
14415 CATTCAAGGTTTCACGAAAATTTT
1 CATT-AAGGTTTCACGAAAATTTT
14439 CA
1 CA
14441 ATTGGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (23 bp):
CATTAAGGTTTCACGAAAATTTT
Found at i:16333 original size:2 final size:2
Alignment explanation
Indices: 16326--16351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16316 AAAGATAAAG
16326 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
16352 GATGTGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.