Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006780.1 Corchorus capsularis cultivar CVL-1 contig06801, 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: 67730
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:32 original size:11 final size:11
Alignment explanation
Indices: 3--71 Score: 74
Period size: 11 Copynumber: 6.5 Consensus size: 11
1 GA
3 TTATATA-ATT
1 TTATATATATT
13 ATATATATATATT
1 -T-TATATATATT
26 TTATATA-A--
1 TTATATATATT
*
34 TTATATATATA
1 TTATATATATT
*
45 TTATATATTTT
1 TTATATATATT
56 TTATATATATT
1 TTATATATATT
67 TTATA
1 TTATA
72 CCGAAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.14
9 1 0.02
10 1 0.02
11 31 0.62
12 7 0.14
13 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATATATT
Found at i:71 original size:9 final size:9
Alignment explanation
Indices: 18--61 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
8 TAATTATATA
18 TATATATTT
1 TATATATTT
*
27 TATATAATTA
1 TATAT-ATTT
*
37 TATATATAT
1 TATATATTT
46 TATATATTT
1 TATATATTT
*
55 TTTATAT
1 TATATAT
62 ATATTTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATATTT
Found at i:415 original size:21 final size:21
Alignment explanation
Indices: 389--428 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
379 ACCCGACGAA
389 ATGGTGAACCCCGACGCCGAC
1 ATGGTGAACCCCGACGCCGAC
*
410 ATGGTGAACCCCGGCGCCG
1 ATGGTGAACCCCGACGCCG
429 CCGACAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.38, G:0.33, T:0.10
Consensus pattern (21 bp):
ATGGTGAACCCCGACGCCGAC
Found at i:1553 original size:25 final size:25
Alignment explanation
Indices: 1519--1588 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
1509 TCTTTCGATC
*
1519 CAAACCTTTCTTCTTCGATCAAATT
1 CAAATCTTTCTTCTTCGATCAAATT
*
1544 CAAATCTTTCTTCTTCGATCAGATT
1 CAAATCTTTCTTCTTCGATCAAATT
*
1569 CAGAT-TCTTCTTCTTCGATC
1 CAAATCT-TTCTTCTTCGATC
1589 CTATCATGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (25 bp):
CAAATCTTTCTTCTTCGATCAAATT
Found at i:4646 original size:2 final size:2
Alignment explanation
Indices: 4639--4681 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
4629 CTTATTGTTC
* * *
4639 AT AT AT AT AT AT AT AT AC GT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4681 A
1 A
4682 CACACACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6605 original size:30 final size:32
Alignment explanation
Indices: 6569--6632 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 32
6559 GTTAATAAGC
6569 CATTAAAATTTGAGGGTATA-A-GAGGAAAGT
1 CATTAAAATTTGAGGGTATATATGAGGAAAGT
6599 CATTAAAATTTGAGGGTATATATGAGGAAAGT
1 CATTAAAATTTGAGGGTATATATGAGGAAAGT
6631 CA
1 CA
6633 AGATAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 20 0.62
31 1 0.03
32 11 0.34
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (32 bp):
CATTAAAATTTGAGGGTATATATGAGGAAAGT
Found at i:12526 original size:16 final size:16
Alignment explanation
Indices: 12507--12585 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
12497 CGAACCCGTG
12507 ACCCGAATGACCC-ATA
1 ACCCGAATGACCCGA-A
*
12523 ACCC-AGATGACCCGAG
1 ACCCGA-ATGACCCGAA
* *
12539 ACCCGAATGACCTGTA
1 ACCCGAATGACCCGAA
12555 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
12571 ACCTGAATGACCCGA
1 ACCCGAATGACCCGA
12586 GACATTAACC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.04
16 46 0.90
17 3 0.06
ACGTcount: A:0.34, C:0.35, G:0.19, T:0.11
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:12542 original size:32 final size:32
Alignment explanation
Indices: 12500--12583 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
12490 AACGACCCGA
*
12500 ACCCGTGACCCGAATGACCCATAACCCAGATG
1 ACCCGAGACCCGAATGACCCATAACCCAGATG
**
12532 ACCCGAGACCCGAATGACCTGTAACCCAGATG
1 ACCCGAGACCCGAATGACCCATAACCCAGATG
* *
12564 ACCCGAAACCTGAATGACCC
1 ACCCGAGACCCGAATGACCC
12584 GAGACATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.32, C:0.37, G:0.19, T:0.12
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCATAACCCAGATG
Found at i:12719 original size:21 final size:21
Alignment explanation
Indices: 12694--12740 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12684 TACAATTTAT
12694 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
12715 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
12736 ATTAT
1 ATTAT
12741 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:13199 original size:7 final size:7
Alignment explanation
Indices: 13187--13238 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
13177 AACCCGCCCA
13187 ACCCGAG
1 ACCCGAG
*
13194 ACCCGAA
1 ACCCGAG
13201 ACCCGAATG
1 ACCCG-A-G
13210 ACCCGAG
1 ACCCGAG
13217 ACCCGAACG
1 ACCCG-A-G
13226 ACCCGAG
1 ACCCGAG
13233 ACCCGA
1 ACCCGA
13239 ATAACTCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 24 0.62
8 4 0.10
9 11 0.28
ACGTcount: A:0.33, C:0.42, G:0.23, T:0.02
Consensus pattern (7 bp):
ACCCGAG
Found at i:13212 original size:16 final size:16
Alignment explanation
Indices: 13193--13280 Score: 99
Period size: 16 Copynumber: 5.6 Consensus size: 16
13183 CCCAACCCGA
13193 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
13209 GACCCGAGACCCGAAC
1 GACCCGAAACCCGAAT
*
13225 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
* *
13241 AACTCG-AACCC-AGAT
1 GACCCGAAACCCGA-AT
*
13256 GACCCAAAACCCGAAT
1 GACCCGAAACCCGAAT
13272 GACCCGAAA
1 GACCCGAAA
13281 AAACTGCATG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
16 48 0.81
17 1 0.02
ACGTcount: A:0.38, C:0.38, G:0.19, T:0.06
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:15480 original size:18 final size:19
Alignment explanation
Indices: 15457--15494 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
15447 GTGCATGAGC
*
15457 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
15475 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
15494 T
1 T
15495 AATGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:16826 original size:18 final size:19
Alignment explanation
Indices: 16792--16829 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16782 GTCCATCGTT
*
16792 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
16811 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
16829 A
1 A
16830 GCCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:17504 original size:30 final size:30
Alignment explanation
Indices: 17470--17531 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
17460 ATTTTTATCT
17470 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
17500 TGACTTTCCTCTTATACCCTTAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
17530 TG
1 TG
17532 GCTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:19541 original size:38 final size:38
Alignment explanation
Indices: 19490--19567 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
19480 AGGATCATCC
19490 ATTCCTACCATATCAATCAATCCAACAAATAAATTAAT
1 ATTCCTACCATATCAATCAATCCAACAAATAAATTAAT
19528 ATTCCTACCATATCAATCAATCCAACAAATAAATTAAT
1 ATTCCTACCATATCAATCAATCCAACAAATAAATTAAT
19566 AT
1 AT
19568 ATGGTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.29
Consensus pattern (38 bp):
ATTCCTACCATATCAATCAATCCAACAAATAAATTAAT
Found at i:33900 original size:7 final size:7
Alignment explanation
Indices: 33885--33915 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
33875 GGTCCCTCTG
33885 TTTTCTT
1 TTTTCTT
*
33892 TTTTTTT
1 TTTTCTT
33899 TTTTCTT
1 TTTTCTT
33906 TTTTCTT
1 TTTTCTT
33913 TTT
1 TTT
33916 CTTCTAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:33907 original size:13 final size:13
Alignment explanation
Indices: 33885--33918 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
33875 GGTCCCTCTG
*
33885 TTTTCTTTTTTTTT
1 TTTTC-TTTTTTCT
33899 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
33912 TTTTCTT
1 TTTTCTT
33919 CTAGCTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:36600 original size:18 final size:18
Alignment explanation
Indices: 36577--36611 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36567 GGGTTGGGGT
*
36577 TGGAGCTGGTCCCAATGA
1 TGGAGCTAGTCCCAATGA
*
36595 TGGAGCTAGTGCCAATG
1 TGGAGCTAGTCCCAATG
36612 GTGGTGTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (18 bp):
TGGAGCTAGTCCCAATGA
Found at i:37622 original size:16 final size:16
Alignment explanation
Indices: 37598--37628 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37588 CATGGAACTT
*
37598 AAAATAATTATTGAAA
1 AAAAAAATTATTGAAA
37614 AAAAAAATTATTGAA
1 AAAAAAATTATTGAA
37629 TACTCAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAAAATTATTGAAA
Found at i:47943 original size:10 final size:10
Alignment explanation
Indices: 47928--47958 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
47918 CCTGCTTTTT
47928 ATGTCTATCA
1 ATGTCTATCA
47938 ATGTCTATCA
1 ATGTCTATCA
47948 ATGTCTATCA
1 ATGTCTATCA
47958 A
1 A
47959 GAAAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (10 bp):
ATGTCTATCA
Found at i:55806 original size:11 final size:11
Alignment explanation
Indices: 55782--55816 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55772 TTGACAGCGC
55782 AACAAAAACAA
1 AACAAAAACAA
* *
55793 AACGAAAACGA
1 AACAAAAACAA
55804 AACAAAAACAA
1 AACAAAAACAA
55815 AA
1 AA
55817 AACGGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:58148 original size:13 final size:14
Alignment explanation
Indices: 58130--58162 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
58120 ACGCTACTAA
58130 CGAACCC-ATGGCT
1 CGAACCCAATGGCT
58143 CGAACCCAATGGCT
1 CGAACCCAATGGCT
58157 CGAACC
1 CGAACC
58163 GCTGCACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.27, C:0.39, G:0.21, T:0.12
Consensus pattern (14 bp):
CGAACCCAATGGCT
Found at i:61201 original size:16 final size:16
Alignment explanation
Indices: 61180--61231 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
61170 TATATATTTA
61180 ATTTAATTTCTCCTAT
1 ATTTAATTTCTCCTAT
61196 ATTTAA-TTCT--T-T
1 ATTTAATTTCTCCTAT
*
61208 -TTGAATTGTCTCCTAT
1 ATTTAATT-TCTCCTAT
61224 ATTTAATT
1 ATTTAATT
61232 CTTGGTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
11 4 0.14
12 2 0.07
13 4 0.14
15 5 0.18
16 7 0.25
17 6 0.21
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTTAATTTCTCCTAT
Found at i:62572 original size:13 final size:14
Alignment explanation
Indices: 62549--62578 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
62539 AGCAAAACAG
62549 AAAGACAAACCCAA
1 AAAGACAAACCCAA
62563 AAAGAC-AACCCAA
1 AAAGACAAACCCAA
62576 AAA
1 AAA
62579 CCAAGCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.67, C:0.27, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAGACAAACCCAA
Found at i:65838 original size:15 final size:15
Alignment explanation
Indices: 65818--65847 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65808 GAGAAAGAGA
65818 CTGTTAATGGAGTAG
1 CTGTTAATGGAGTAG
65833 CTGTTAATGGAGTAG
1 CTGTTAATGGAGTAG
65848 ATTGAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
CTGTTAATGGAGTAG
Found at i:67571 original size:30 final size:29
Alignment explanation
Indices: 67498--67575 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
67488 ACTTGTAGCA
67498 TTTGGACGTTTTGCCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
*
67527 TTTGGACATTTTGCCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
67556 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
67576 CAACCTAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 31 0.67
30 15 0.33
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.38
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTGAACTTCAAT
Done.