Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013877.1 Corchorus capsularis cultivar CVL-1 contig13898, 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: 49575
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:1173 original size:122 final size:119
Alignment explanation
Indices: 800--1325 Score: 543
Period size: 115 Copynumber: 4.4 Consensus size: 119
790 CAAACTTTAT
* * * * *
800 CAAATTC-ATTTAAGGATTTACTTAAATCTTAAAAGAATTATGAAAGTTTCCCAAAGGGTATATT
1 CAAATTCGA-TTAAGGATTCACTTAAATCTT-AATGAATTATGAAA--TTACCAAAAGCT-T-TT
* * * * *
864 -AACTAAAGGTTTTAATCACTTAATTAAACCCAAAGTTTTAGG-----TAACCTTGA-TTC
60 AAACAAAAGGTTTTAATTACTTAATTAAACCTAAAGCTTAAGGTCACTTAACCTT-ATTTC
* * *
918 CAAATTCAATTAAGCATTCACTTAAATCTTAATGAATTATTATGAAA-T-CCCAAA--TTTTATT
1 CAAATTCGATTAAGGATTCACTTAAATCTTAATG-A--ATTATGAAATTACCAAAAGCTTTTA--
* * * *
979 AACTATAGGTTATAATCACTTAATTAAACCT--A----AAGGTCACTTAACCTTGATTTC
61 AACAAAAGGTTTTAATTACTTAATTAAACCTAAAGCTTAAGGTCACTTAACCTT-ATTTC
* *
1033 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAACTTACTAAAAGCTTTTAAACC
1 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAA-TTACCAAAAGCTTTTAAACA
1098 AAAGGTTTTAATTACTTAATTAAACCTAAAGCTTAATGGTCACTTAACCTTAATTTC
65 AAAGGTTTTAATTACTTAATTAAACCTAAAGCTTAA-GGTCACTTAACCTT-ATTTC
*
1155 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAA-T-CCCAAAGCTTTTAAACAA
1 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTACCAAAAGCTTTTAAACAA
* * *
1218 AAGGTTTTAATTACTTAATTAAACCTAAAGTTTAAGGTCACTAAACCTTAGTTC
66 AAGGTTTTAATTACTTAATTAAACCTAAAGCTTAAGGTCACTTAACCTTATTTC
*
1272 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATAATGGAAATTACCAAAA
1 CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTAT-GAAATTACCAAAA
1326 AGATTAATTC
Statistics
Matches: 354, Mismatches: 26, Indels: 54
0.82 0.06 0.12
Matches are distributed among these distances:
109 3 0.01
112 11 0.03
113 2 0.01
114 12 0.03
115 94 0.27
116 4 0.01
117 53 0.15
118 44 0.12
119 51 0.14
120 15 0.04
121 2 0.01
122 63 0.18
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (119 bp):
CAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTACCAAAAGCTTTTAAACAA
AAGGTTTTAATTACTTAATTAAACCTAAAGCTTAAGGTCACTTAACCTTATTTC
Found at i:26457 original size:16 final size:16
Alignment explanation
Indices: 26400--26462 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
26390 GAACACGTCT
26400 AAACCCGAACCCGAAA
1 AAACCCGAACCCGAAA
* * *
26416 AAGCTCAAACCCGAAA
1 AAACCCGAACCCGAAA
***
26432 AAATTAGAACCCGAAA
1 AAACCCGAACCCGAAA
26448 AAACCCGAACCCGAA
1 AAACCCGAACCCGAA
26463 TCCAAAAGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.51, C:0.32, G:0.13, T:0.05
Consensus pattern (16 bp):
AAACCCGAACCCGAAA
Found at i:26643 original size:32 final size:32
Alignment explanation
Indices: 26607--26698 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 32
26597 TCTGAATAAA
* * *
26607 ACCCAAACTGAACCCGAACTCGAATTAATCTG
1 ACCCAAATTCAACCCGAACTCGAATTAACCTG
*
26639 ACCCAAATTCAACCCGAA-TCCGAATTGACCTG
1 ACCCAAATTCAACCCGAACT-CGAATTAACCTG
* * *
26671 ACCCAAATTTAACCCGAACCCGACTTAA
1 ACCCAAATTCAACCCGAACTCGAATTAA
26699 ACTCGAACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.37, C:0.34, G:0.11, T:0.18
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACTCGAATTAACCTG
Found at i:27224 original size:11 final size:11
Alignment explanation
Indices: 27181--27218 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27171 TTTCTATATA
*
27181 AAATAAATTATT
1 AAATTAATTA-T
27193 AAA-TAATTAT
1 AAATTAATTAT
27203 AAATTAATTAT
1 AAATTAATTAT
27214 AAATT
1 AAATT
27219 TGTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:29192 original size:17 final size:17
Alignment explanation
Indices: 29170--29202 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29160 TTGCATGTGG
29170 CACGTGACCTAATATGA
1 CACGTGACCTAATATGA
29187 CACGTGACCTAATATG
1 CACGTGACCTAATATG
29203 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
CACGTGACCTAATATGA
Found at i:29705 original size:14 final size:14
Alignment explanation
Indices: 29672--29710 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
29662 AAATTTCCTT
*
29672 AACCCGAAACTAACCT
1 AACCC-AAA-TAACCG
29688 AACCCAAATAACCG
1 AACCCAAATAACCG
29702 AACCCAAAT
1 AACCCAAAT
29711 CCAACCTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.49, C:0.36, G:0.05, T:0.10
Consensus pattern (14 bp):
AACCCAAATAACCG
Found at i:30718 original size:22 final size:24
Alignment explanation
Indices: 30669--30718 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
30659 TAACAGAAAC
**
30669 TTTATATCAAAATGAATAAAGTAA
1 TTTATATCAAAACAAATAAAGTAA
30693 -TTATAT-AAAACAAATAAAG-AA
1 TTTATATCAAAACAAATAAAGTAA
30714 TTTAT
1 TTTAT
30719 TTACAGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.09
22 15 0.65
23 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
TTTATATCAAAACAAATAAAGTAA
Found at i:33762 original size:18 final size:18
Alignment explanation
Indices: 33724--33762 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33714 ACACCCTATG
*
33724 AAATTCCAAAAATTTCCA
1 AAATTCCAAAAATTTCAA
33742 AAATT-CAAAAATCTTCAA
1 AAATTCCAAAAAT-TTCAA
33760 AAA
1 AAA
33763 ACATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATTCCAAAAATTTCAA
Found at i:41257 original size:6 final size:6
Alignment explanation
Indices: 41241--41285 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
41231 AGACTCTTAT
* *
41241 ATATA- ATATAG ATATAG ATATAG ATATAG ATATAT ATATAA ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
41286 CTATAGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:41290 original size:12 final size:12
Alignment explanation
Indices: 41238--41290 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
41228 TGTAGACTCT
41238 TATATAT-AATA
1 TATATATAAATA
* *
41249 TAGATATAGATA
1 TATATATAAATA
* *
41261 TAGATATAGATA
1 TATATATAAATA
41273 TATATATAAATA
1 TATATATAAATA
*
41285 TCTATA
1 TATATA
41291 GATTACTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
11 6 0.17
12 30 0.83
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (12 bp):
TATATATAAATA
Found at i:41515 original size:16 final size:16
Alignment explanation
Indices: 41497--41571 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 16
41487 ATTTTTGGGT
*
41497 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
**
41513 ACCCGAACCC-AAACA
1 ACCCGAACCCGAAATG
* *
41528 ACCCAAAGCCGAAATG
1 ACCCGAACCCGAAATG
* *
41544 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
*
41560 ACACGAACCCGA
1 ACCCGAACCCGA
41572 TCAACCCGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
15 11 0.23
16 36 0.77
ACGTcount: A:0.44, C:0.39, G:0.12, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:42575 original size:2 final size:2
Alignment explanation
Indices: 42568--42598 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
42558 CATGACCTAA
42568 AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
42599 TTGTACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42606 original size:15 final size:15
Alignment explanation
Indices: 42568--42598 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42558 CATGACCTAA
42568 ATATATA-TATATAT
1 ATATATACTATATAT
42582 ATATATACTATATAT
1 ATATATACTATATAT
42597 AT
1 AT
42599 TTGTACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATACTATATAT
Found at i:42953 original size:15 final size:17
Alignment explanation
Indices: 42923--42955 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
42913 AAAACGACCA
42923 AACCCAGAATTGACCCG
1 AACCCAGAATTGACCCG
42940 AACCCA-AA-TGACCCG
1 AACCCAGAATTGACCCG
42955 A
1 A
42956 CATTTGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.39, C:0.36, G:0.15, T:0.09
Consensus pattern (17 bp):
AACCCAGAATTGACCCG
Found at i:46368 original size:29 final size:29
Alignment explanation
Indices: 46311--46368 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
46301 AACACTTTAA
* * *
46311 AAACTTATTTCCCTATATATAATACATTT
1 AAACTTATTTCCCTAAATATAACAAATTT
46340 AAACTTATTTCCC-AAACTATAACAAATTT
1 AAACTTATTTCCCTAAA-TATAACAAATTT
46369 TGCCAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.40
Consensus pattern (29 bp):
AAACTTATTTCCCTAAATATAACAAATTT
Found at i:47662 original size:29 final size:30
Alignment explanation
Indices: 47608--47665 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
47598 CTCAACTATC
47608 AAGTTTCTATATATATTCTTTCACCAAAAAA
1 AAGTTTCTATATATATTC-TTCACCAAAAAA
*
47639 AAGTTTCTATATATATTC-TGACCAAAA
1 AAGTTTCTATATATATTCTTCACCAAAA
47666 TTAGTAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (30 bp):
AAGTTTCTATATATATTCTTCACCAAAAAA
Found at i:49138 original size:2 final size:2
Alignment explanation
Indices: 49133--49161 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49123 TGCATGTGTC
49133 TA 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 TA T
49162 CCATGTATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.