Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010000.1 Corchorus capsularis cultivar CVL-1 contig10021, 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: 17470
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:77 original size:30 final size:31
Alignment explanation
Indices: 41--107 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
31 GCGCAAATAG
41 GTCCCTGAAGTGAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTGAACTTAAGTGAGCAATTGA
* * * *
71 GTCCCTGAAGTTAAGTTAATTGAGCAATTGG
1 GTCCCTGAAGTGAACTTAAGTGAGCAATTGA
102 GTCCCT
1 GTCCCT
108 CACCAAACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (31 bp):
GTCCCTGAAGTGAACTTAAGTGAGCAATTGA
Found at i:2143 original size:2 final size:2
Alignment explanation
Indices: 2136--2176 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2126 GACCCCTTTA
2136 AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT -T 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
2175 AT
1 AT
2177 CGGTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2151 original size:10 final size:10
Alignment explanation
Indices: 2136--2176 Score: 61
Period size: 9 Copynumber: 4.4 Consensus size: 10
2126 GACCCCTTTA
2136 ATATATATAT
1 ATATATATAT
2146 ATATATATAT
1 ATATATATAT
2156 -TAT-TATAT
1 ATATATATAT
2164 AT-TATATAT
1 ATATATATAT
2173 ATAT
1 ATAT
2177 CGGTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.21
9 11 0.39
10 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATATATAT
Found at i:9587 original size:2 final size:2
Alignment explanation
Indices: 9580--9615 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
9570 CTCGAACAAC
* *
9580 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9616 GCACTTTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:9595 original size:10 final size:10
Alignment explanation
Indices: 9580--9615 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
9570 CTCGAACAAC
9580 ATATATATAG
1 ATATATATAG
*
9590 ATATATATAT
1 ATATATATAG
9600 ATATATATAG
1 ATATATATAG
9610 ATATAT
1 ATATAT
9616 GCACTTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (10 bp):
ATATATATAG
Found at i:9877 original size:80 final size:82
Alignment explanation
Indices: 9780--9941 Score: 267
Period size: 82 Copynumber: 2.0 Consensus size: 82
9770 TTCACTGTGA
* **
9780 AAAATTTTTATGATTCT-C-GCTTATTTATATGAATTATAT-AGCTTTTTATTGATTATCCTTTT
1 AAAATTTTTATGATTCTCCTGCTTATTTATATGAATTAGATAAGC-TTTTATTGATTATCAATTT
9842 CCAATTAAATTTAGTATT
65 CCAATTAAATTTAGTATT
9860 AAAATTTTTATGATTCTCCTGCTTATTTATATGAATTAGATAAGCTTTTATTGATTATCAATTTC
1 AAAATTTTTATGATTCTCCTGCTTATTTATATGAATTAGATAAGCTTTTATTGATTATCAATTTC
9925 CAATTAAATTTAGTATT
66 CAATTAAATTTAGTATT
9942 CTGTCATTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
80 17 0.22
81 1 0.01
82 55 0.72
83 3 0.04
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (82 bp):
AAAATTTTTATGATTCTCCTGCTTATTTATATGAATTAGATAAGCTTTTATTGATTATCAATTTC
CAATTAAATTTAGTATT
Found at i:11466 original size:22 final size:22
Alignment explanation
Indices: 11441--11497 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
11431 CATTATTATA
11441 AAATTTTAGTAACCACACTATG
1 AAATTTTAGTAACCACACTATG
* * **
11463 AAATTTT-GATAAGCTCTTTATG
1 AAATTTTAG-TAACCACACTATG
11485 AAATTTTAGTAAC
1 AAATTTTAGTAAC
11498 ATTCGTATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (22 bp):
AAATTTTAGTAACCACACTATG
Found at i:11493 original size:44 final size:44
Alignment explanation
Indices: 11436--11649 Score: 127
Period size: 44 Copynumber: 4.9 Consensus size: 44
11426 AATGACATTA
*
11436 TTATAAAATTTTAGTAACCACACTATGAAATTTTGATAAGCTCT
1 TTATGAAATTTTAGTAACCACACTATGAAATTTTGATAAGCTCT
** * * * * *
11480 TTATGAAATTTTAGTAA-CATTCGTATGTAATTTCGATAATCACA
1 TTATGAAATTTTAGTAACCACAC-TATGAAATTTTGATAAGCTCT
** * * ** * * *
11524 CCATGAAATTAT-GATAACCTCGTTATGAAATTCTGAAAAGCTCC
1 TTATGAAATTTTAG-TAACCACACTATGAAATTTTGATAAGCTCT
* *
11568 CTATGAAATTTT-GATAACCACACTAT-AAA-TTTGATAACCT-T
1 TTATGAAATTTTAG-TAACCACACTATGAAATTTTGATAAGCTCT
** *
11609 CTTATGAAATTAAAATAACCAC-CTTATGAAAATTTTGATAA
1 -TTATGAAATTTTAGTAACCACAC-TATG-AAATTTTGATAA
11650 TCACCCAATG
Statistics
Matches: 126, Mismatches: 35, Indels: 17
0.71 0.20 0.10
Matches are distributed among these distances:
41 1 0.01
42 27 0.21
43 7 0.06
44 82 0.65
45 9 0.07
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (44 bp):
TTATGAAATTTTAGTAACCACACTATGAAATTTTGATAAGCTCT
Found at i:11500 original size:66 final size:66
Alignment explanation
Indices: 11430--11555 Score: 146
Period size: 66 Copynumber: 1.9 Consensus size: 66
11420 TTTTTTAATG
* * * * *
11430 ACATTATTATAAAATTTTAG-TAACCACACTATGAAATTTTGATAAGCTCTTTATGAAATTTTAG
1 ACATTAGTATAAAA-TTTAGATAACCACACCATGAAATTATGATAACCTCGTTATGAAATTTTAG
11494 TA
65 TA
* ** * *
11496 ACATTCGTATGTAATTTCGATAATCACACCATGAAATTATGATAACCTCGTTATGAAATT
1 ACATTAGTATAAAATTTAGATAACCACACCATGAAATTATGATAACCTCGTTATGAAATT
11556 CTGAAAAGCT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
65 4 0.08
66 45 0.92
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (66 bp):
ACATTAGTATAAAATTTAGATAACCACACCATGAAATTATGATAACCTCGTTATGAAATTTTAGT
A
Found at i:11551 original size:22 final size:22
Alignment explanation
Indices: 11526--11649 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
11516 TAATCACACC
*
11526 ATGAAATTATGATAACCTCGTT
1 ATGAAATTATGATAACCTCCTT
* * * *
11548 ATGAAATTCTGAAAAGCTCCCT
1 ATGAAATTATGATAACCTCCTT
* *
11570 ATGAAATTTTGATAACCACAC-T
1 ATGAAATTATGATAACCTC-CTT
*
11592 AT-AAATT-TGATAACCTTCTT
1 ATGAAATTATGATAACCTCCTT
** *
11612 ATGAAATTAAAATAACCACCTT
1 ATGAAATTATGATAACCTCCTT
*
11634 ATGAAAATTTTGATAA
1 ATG-AAATTATGATAA
11650 TCACCCAATG
Statistics
Matches: 79, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.01
20 11 0.14
21 10 0.13
22 47 0.59
23 10 0.13
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (22 bp):
ATGAAATTATGATAACCTCCTT
Found at i:11666 original size:22 final size:22
Alignment explanation
Indices: 11638--11760 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 22
11628 CACCTTATGA
11638 AAATTTTGATAATCACCCAATG
1 AAATTTTGATAATCACCCAATG
** *
11660 AAATTTTGGCAATC-CTTCCTATG
1 AAATTTTGATAATCAC--CCAATG
* * ** *
11683 AAATTTTGGTAACCATACTATG
1 AAATTTTGATAATCACCCAATG
* * *
11705 AAATTTTTATGAA-CTCTCAATG
1 AAATTTTGAT-AATCACCCAATG
11727 AAATTTTGATAATCACACC-ATG
1 AAATTTTGATAATCAC-CCAATG
11749 AAATTTTGATAA
1 AAATTTTGATAA
11761 CTTGTGTATG
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
21 3 0.04
22 56 0.71
23 20 0.25
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAATCACCCAATG
Found at i:11772 original size:44 final size:43
Alignment explanation
Indices: 11633--11784 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 43
11623 ATAACCACCT
** *
11633 TATGAAAATTTTGATAATCAC-CCAATGAAATTTTGGCAATCCTTCC
1 TATG-AAATTTTGATAATCACACC-ATGAAATTTTGATAA--CTTTC
* * * * * *
11679 TATGAAATTTTGGTAACCATACTATGAAATTTTTATGAACTCTC
1 TATGAAATTTTGATAATCACACCATGAAATTTTGAT-AACTTTC
* *
11723 AATGAAATTTTGATAATCACACCATGAAATTTTGATAACTTGTG
1 TATGAAATTTTGATAATCACACCATGAAATTTTGATAACTT-TC
*
11767 TATGAAATTGTGATAATC
1 TATGAAATTTTGATAATC
11785 TACTTGTAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
43 4 0.05
44 50 0.60
45 23 0.27
46 7 0.08
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAATCACACCATGAAATTTTGATAACTTTC
Found at i:13064 original size:6 final size:6
Alignment explanation
Indices: 13053--13102 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 6
13043 AAGAATACAA
*
13053 TAAAAT TAAAAT T-AAAT T-AAAT T-AAAT T-AAAT TAAAAG TAAAA-
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
13096 TAAAAT T
1 TAAAAT T
13103 TCAGCCTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 25 0.61
6 16 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
TAAAAT
Found at i:13069 original size:5 final size:5
Alignment explanation
Indices: 13055--13088 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
13045 GAATACAATA
13055 AAATT AAAATT AAATT AAATT AAATT AAATT AAA
1 AAATT -AAATT AAATT AAATT AAATT AAATT AAA
13089 AGTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:13081 original size:15 final size:16
Alignment explanation
Indices: 13055--13102 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
13045 GAATACAATA
13055 AAATTAAAATTAAATT
1 AAATTAAAATTAAATT
13071 AAATT-AAATTAAATT
1 AAATTAAAATTAAATT
* *
13086 AAAAGTAAAATAAAATT
1 -AAATTAAAATTAAATT
13103 TCAGCCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 9 0.32
17 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATTAAAATTAAATT
Found at i:16054 original size:30 final size:29
Alignment explanation
Indices: 15996--16054 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
15986 CCGTGCAGAT
* *
15996 CAATTTGGGATATAACGTTTCAGAAACGA
1 CAATTTAGGATATAACGTTACAGAAACGA
*
16025 CAATTTAGGATATAACGTTACTTGAAACGA
1 CAATTTAGGATATAACGTTAC-AGAAACGA
16055 TCAAATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (29 bp):
CAATTTAGGATATAACGTTACAGAAACGA
Found at i:16256 original size:31 final size:30
Alignment explanation
Indices: 16195--16276 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
16185 TGATCATTTT
* * **
16195 TTATATCCTTAAATGATCACTTTTTGAAACG
1 TTATATCCTAAAATGATC-GTTTTAAAAACG
16226 TTATATCCTAAAATGATCGTTTTCAAAAACG
1 TTATATCCTAAAATGATCGTTTT-AAAAACG
* *
16257 TTATATCCCAAATTGATCGT
1 TTATATCCTAAAATGATCGT
16277 GGCAGCAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (30 bp):
TTATATCCTAAAATGATCGTTTTAAAAACG
Found at i:16302 original size:31 final size:31
Alignment explanation
Indices: 16221--16302 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
16211 TCACTTTTTG
* **
16221 AAACGTTATATCCTAAAATGATCGTTTTCAA
1 AAACGTTATATCCTAAATTGATCGTTGGCAA
* *
16252 AAACGTTATATCCCAAATTGATCG-TGGCAGC
1 AAACGTTATATCCTAAATTGATCGTTGGCA-A
*
16283 AAACGTTATATCCTGAATTG
1 AAACGTTATATCCTAAATTG
16303 GTTATTTAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (31 bp):
AAACGTTATATCCTAAATTGATCGTTGGCAA
Done.