Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011761.1 Corchorus capsularis cultivar CVL-1 contig11782, 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: 76102
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5877 original size:7 final size:7
Alignment explanation
Indices: 5844--5897 Score: 74
Period size: 7 Copynumber: 7.7 Consensus size: 7
5834 AGGGTGCTGT
5844 TAGTTCA
1 TAGTTCA
5851 TAGTTGC-
1 TAGTT-CA
* *
5858 TAATTCT
1 TAGTTCA
5865 TAGTTCA
1 TAGTTCA
5872 TAGTTCA
1 TAGTTCA
5879 TAGTTCA
1 TAGTTCA
5886 TAGTTCA
1 TAGTTCA
5893 TAGTT
1 TAGTT
5898 GGTTCTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 1 0.02
7 40 0.95
8 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (7 bp):
TAGTTCA
Found at i:6572 original size:20 final size:19
Alignment explanation
Indices: 6526--6574 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
6516 CGAATGCTGT
* *
6526 TAGTCTTAGTTGTTGTTTAG
1 TAGT-TTAGTTGTAGTTTAC
*
6546 TACTTTAGTTGATAGTTTAC
1 TAGTTTAGTTG-TAGTTTAC
6566 TAGTTTAGT
1 TAGTTTAGT
6575 ACATTAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.53
Consensus pattern (19 bp):
TAGTTTAGTTGTAGTTTAC
Found at i:6592 original size:20 final size:20
Alignment explanation
Indices: 6540--6594 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
6530 CTTAGTTGTT
**
6540 GTTTAGTACTTTAGTTGATA
1 GTTTAGTACTTTAGTACATA
* *
6560 GTTTACTAGTTTAGTACATTA
1 GTTTAGTACTTTAGTACA-TA
6581 G-TTAGTACTTTAGT
1 GTTTAGTACTTTAGT
6595 TGATACTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (20 bp):
GTTTAGTACTTTAGTACATA
Found at i:20996 original size:15 final size:15
Alignment explanation
Indices: 20976--21004 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20966 TAAACGTATC
20976 TCGTGTCATGTCGTT
1 TCGTGTCATGTCGTT
20991 TCGTGTCATGTCGT
1 TCGTGTCATGTCGT
21005 GTGCTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.28, T:0.45
Consensus pattern (15 bp):
TCGTGTCATGTCGTT
Found at i:21278 original size:69 final size:69
Alignment explanation
Indices: 21150--21361 Score: 347
Period size: 69 Copynumber: 3.1 Consensus size: 69
21140 TGTAAAAATT
* * *
21150 ATTTCCTTTATATGATTTTATTATGAAAATATATACATATAAAGAACCTATAGGAAAAATTGAAG
1 ATTTCCTTTATATGATTTAACTATG--AACATATACATATAAAGAACCTATAGGAAAAATTGAAG
21215 GGTTTC
64 GGTTTC
*
21221 ATTTCCTTTATATGATTTAACTATGAACATATACATATAAAGAACCTGTAGGAAAAATTGAAGGG
1 ATTTCCTTTATATGATTTAACTATGAACATATACATATAAAGAACCTATAGGAAAAATTGAAGGG
21286 TTTC
66 TTTC
21290 ATTTCCTTTATATGATTTAACTATGAAC--ATACATATAAAGAACCTATAGGAAAAATTGAAGGG
1 ATTTCCTTTATATGATTTAACTATGAACATATACATATAAAGAACCTATAGGAAAAATTGAAGGG
21353 TTTC
66 TTTC
*
21357 TTTTC
1 ATTTC
21362 AAAGGATCCA
Statistics
Matches: 135, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
67 42 0.31
69 70 0.52
71 23 0.17
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (69 bp):
ATTTCCTTTATATGATTTAACTATGAACATATACATATAAAGAACCTATAGGAAAAATTGAAGGG
TTTC
Found at i:27438 original size:17 final size:17
Alignment explanation
Indices: 27416--27449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27406 CAGACACGGT
*
27416 GCATCTACCGGTTGAGC
1 GCATCTACCAGTTGAGC
27433 GCATCTACCAGTTGAGC
1 GCATCTACCAGTTGAGC
27450 TAACAACTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (17 bp):
GCATCTACCAGTTGAGC
Found at i:37403 original size:28 final size:27
Alignment explanation
Indices: 37345--37403 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
37335 TGTTATTAGA
* *
37345 AAAAAGAAGAAGAATATTCTTTACCTT
1 AAAAAGAAAAAGAATATTCTTTACCTC
37372 AAAAAGAAAAATGAATATTC-TTATCCTC
1 AAAAAGAAAAA-GAATATTCTTTA-CCTC
37400 AAAA
1 AAAA
37404 CTCAAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAAAGAAAAAGAATATTCTTTACCTC
Found at i:38731 original size:111 final size:111
Alignment explanation
Indices: 38537--38760 Score: 335
Period size: 111 Copynumber: 2.0 Consensus size: 111
38527 ATTCTATATG
* * *
38537 ATCTTTTTGAAGACTTTACTAAATCTATTAATAGTTTGCTTCAAAGACTTAATCAAGTAATAACA
1 ATCTTTTTAAAGACATTACTAAATCTATTAATAGTTTGCTTCAAAGACTTAAACAAGTAATAACA
*
38602 TATCCATTATAATCCAATAC-AATATCAAGTGATTACA-TCATTCTAC
66 AATCCATTATAATCCAATACGAA-ATCAAGTGATTA-AGTCATTCTAC
* **
38648 ATCTTTTTAAAGACATTACTAATTCTATTAATAGTTTGCTTCATTGACTTAAACAAGTAATAACA
1 ATCTTTTTAAAGACATTACTAAATCTATTAATAGTTTGCTTCAAAGACTTAAACAAGTAATAACA
* *
38713 AATCCATTCTAATCCAATACGGAATCAAGTGATTAAGTCATTCTAC
66 AATCCATTATAATCCAATACGAAATCAAGTGATTAAGTCATTCTAC
38759 AT
1 AT
38761 TTCTACTAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
110 1 0.01
111 100 0.98
112 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (111 bp):
ATCTTTTTAAAGACATTACTAAATCTATTAATAGTTTGCTTCAAAGACTTAAACAAGTAATAACA
AATCCATTATAATCCAATACGAAATCAAGTGATTAAGTCATTCTAC
Found at i:67676 original size:19 final size:19
Alignment explanation
Indices: 67646--67683 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
67636 GAGCGAGTGT
67646 TCCAACTGGGAAAGCTTGCC
1 TCCAACTGGGAAAG-TTGCC
67666 TCCAA-TGGGAAAGTTGCC
1 TCCAACTGGGAAAGTTGCC
67684 GTCCCTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (19 bp):
TCCAACTGGGAAAGTTGCC
Found at i:69425 original size:2 final size:2
Alignment explanation
Indices: 69380--69407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69370 TATCATTATC
69380 AT 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 AT
69408 CAGATCAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.