Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009090.1 Corchorus capsularis cultivar CVL-1 contig09111, 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: 30016
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2156 original size:6 final size:6
Alignment explanation
Indices: 2145--2169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2135 CGAAGCTTTT
2145 GGTGCA GGTGCA GGTGCA GGTGCA G
1 GGTGCA GGTGCA GGTGCA GGTGCA G
2170 CATTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGTGCA
Found at i:13786 original size:16 final size:17
Alignment explanation
Indices: 13762--13793 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13752 TTTAGTTTAG
13762 TTTTGCTTTATAATTGC
1 TTTTGCTTTATAATTGC
13779 TTTT-CTTTATAATTG
1 TTTTGCTTTATAATTG
13794 GTACTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (17 bp):
TTTTGCTTTATAATTGC
Found at i:15540 original size:7 final size:7
Alignment explanation
Indices: 15528--15568 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
15518 AATTTTATTT
15528 TAATATA
1 TAATATA
15535 TAATATA
1 TAATATA
*
15542 TATTAT-
1 TAATATA
*
15548 TAATATG
1 TAATATA
15555 TAATATA
1 TAATATA
15562 T-ATATA
1 TAATATA
15568 T
1 T
15569 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (7 bp):
TAATATA
Found at i:15548 original size:22 final size:20
Alignment explanation
Indices: 15523--15564 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
15513 GTAAGAATTT
15523 TATT-TTAATATATAATATA
1 TATTATTAATATATAATATA
*
15542 TATTATTAATATGTAATATA
1 TATTATTAATATATAATATA
15562 TAT
1 TAT
15565 ATATGTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTATTAATATATAATATA
Found at i:15556 original size:41 final size:40
Alignment explanation
Indices: 15465--15562 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 40
15455 AAATCATTTT
15465 TATT-TTAATATGTAAAATATTTTATTAAATAAGAATATA
1 TATTATTAATATGTAAAATATTTTATTAAATAAGAATATA
* * * *
15504 TA-TA-T-ACATGTAAGA-ATTTTATTTTAATATATAATATA
1 TATTATTAATATGTAAAATATTTTA-TTAAATA-AGAATATA
*
15542 TATTATTAATATGTAATATAT
1 TATTATTAATATGTAAAATAT
15563 ATATATGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
36 6 0.13
37 14 0.30
38 11 0.24
39 4 0.09
40 1 0.02
41 8 0.17
42 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (40 bp):
TATTATTAATATGTAAAATATTTTATTAAATAAGAATATA
Found at i:15613 original size:11 final size:11
Alignment explanation
Indices: 15597--15625 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
15587 TTCAAACCGA
15597 AAACCGACCCG
1 AAACCGACCCG
15608 AAACCGACCCG
1 AAACCGACCCG
15619 AAACCGA
1 AAACCGA
15626 TTGGTTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.41, G:0.17, T:0.00
Consensus pattern (11 bp):
AAACCGACCCG
Found at i:16057 original size:20 final size:21
Alignment explanation
Indices: 16034--16076 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
16024 CAAATCAAGG
* *
16034 AATAGGCAATCA-ATCAAAGC
1 AATAAGCAATCATAGCAAAGC
16054 AATAAGCAATCATAGCAAAGC
1 AATAAGCAATCATAGCAAAGC
16075 AA
1 AA
16077 GAAAAAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAGCAATCATAGCAAAGC
Found at i:18378 original size:40 final size:40
Alignment explanation
Indices: 18323--18402 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
18313 TTTGTTGTCG
18323 TTGTAGTATTTGATTTAGTTTGATATAGGATCCCAAAGAA
1 TTGTAGTATTTGATTTAGTTTGATATAGGATCCCAAAGAA
18363 TTGTAGTATTTGATTTAGTTTGATATAGGATCCCAAAGAA
1 TTGTAGTATTTGATTTAGTTTGATATAGGATCCCAAAGAA
18403 AGTTGTCGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (40 bp):
TTGTAGTATTTGATTTAGTTTGATATAGGATCCCAAAGAA
Found at i:18685 original size:2 final size:2
Alignment explanation
Indices: 18674--18733 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
18664 AGGGTTACAT
*
18674 TA TA TA -A TA TA TA TA TA TA TA -A TA TGA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
18715 AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
18734 CTGTCGGGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23392 original size:2 final size:2
Alignment explanation
Indices: 23387--23416 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23377 CTTTATTTAG
23387 AT 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 AT
23417 GTAACTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24156 original size:1 final size:1
Alignment explanation
Indices: 24123--24148 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
24113 CGTATTTTTG
24123 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
24149 GCAAAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24200 original size:45 final size:45
Alignment explanation
Indices: 24133--24219 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 45
24123 AAAAAAAAAA
24133 AAAAAAAAAAAAAAAAGCAAAAAATC-ATGATGATTTCGATATTTTGG
1 AAAAAAAAAAAAAAAA-CAAAAAA-CAATGATGATTTCG-TATTTTGG
24180 AAAAAAAAAAAAAAAA-AAAAAACAATGATGATTTCGTATT
1 AAAAAAAAAAAAAAAACAAAAAACAATGATGATTTCGTATT
24220 AACAGAGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 5 0.13
45 18 0.46
47 16 0.41
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (45 bp):
AAAAAAAAAAAAAAAACAAAAAACAATGATGATTTCGTATTTTGG
Found at i:25497 original size:3 final size:3
Alignment explanation
Indices: 25489--25561 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
25479 ATGCTGAAGA
25489 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25537 TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
25562 CTGCAGATGT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29729 original size:30 final size:30
Alignment explanation
Indices: 29684--29756 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
29674 CCTTCTCCTT
* * *
29684 CTCCACCACCGCCTTATGTGTACAAGTCTC
1 CTCCTCCACCACCTTATGAGTACAAGTCTC
29714 CTCCTCCACCACCTTATGAGTACAAGTCTC
1 CTCCTCCACCACCTTATGAGTACAAGTCTC
29744 CTCCTCCACCACC
1 CTCCTCCACCACC
29757 AAAGCATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.21, C:0.45, G:0.10, T:0.25
Consensus pattern (30 bp):
CTCCTCCACCACCTTATGAGTACAAGTCTC
Found at i:29826 original size:15 final size:15
Alignment explanation
Indices: 29798--29827 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29788 AAATCACCAC
*
29798 CACCTCCATCACCTT
1 CACCTCCACCACCTT
29813 CACCTCCACCACCTT
1 CACCTCCACCACCTT
29828 ATGAGTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (15 bp):
CACCTCCACCACCTT
Found at i:29837 original size:48 final size:48
Alignment explanation
Indices: 29785--29949 Score: 179
Period size: 48 Copynumber: 3.4 Consensus size: 48
29775 TCCATACTAC
* * * *
29785 TACAAATCACCACCACCTCCATCACCTTCACCTCCACCACCTTATGAG
1 TACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAA
* * * * * * * *
29833 TACAAGTCTCCACCCCCGCCATCTCCTTCACCACCTCCTCCATACT-AC
1 TACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTA-TGAA
*
29881 TACAAATCACCACCTCCTCCATCACCCTCACCACCACCTCCTTATGAA
1 TACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAA
* *
29929 TACAAGTCTCCACCTCCTCCA
1 TACAAATCACCACCTCCTCCA
29950 CCAAAGCATG
Statistics
Matches: 94, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
47 1 0.01
48 92 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.22
Consensus pattern (48 bp):
TACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAA
Found at i:29978 original size:96 final size:99
Alignment explanation
Indices: 29719--29999 Score: 352
Period size: 96 Copynumber: 2.9 Consensus size: 99
29709 GTCTCCTCCT
*
29719 CCACCACCTTATGAGTACAAGTCTCCTCCTCCACCACCAAAGCATGAGGAACAACCTCCATACTA
1 CCACCACCTTATGAGTACAAGTCTCCACCTCCACCACCAAAGCATGAGGAACAACCTCCATACTA
* *
29784 CTACAAATCACCACCACCTCCATCACCTTCACCT
66 CTACAAATCACCACCACCTCCATCACCCTCACCA
* * * ** * * ** **
29818 CCACCACCTTATGAGTACAAGTCTCCACCCCCGCCATC--TCCTTCA-CCACCTCCTCCATACTA
1 CCACCACCTTATGAGTACAAGTCTCCACCTCCACCACCAAAGCATGAGGAACAACCTCCATACTA
*
29880 CTACAAATCACCACCTCCTCCATCACCCTCACCA
66 CTACAAATCACCACCACCTCCATCACCCTCACCA
* * * * *
29914 CCACCTCCTTATGAATACAAGTCTCCACCTCCTCCACCAAAGCATGAGGAAAAACCCCCATACTA
1 CCACCACCTTATGAGTACAAGTCTCCACCTCCACCACCAAAGCATGAGGAACAACCTCCATACTA
*
29979 CTACAAATCCCCACCACCTCC
66 CTACAAATCACCACCACCTCC
30000 TTCTCCATCT
Statistics
Matches: 147, Mismatches: 32, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
96 77 0.52
97 3 0.02
98 3 0.02
99 64 0.44
ACGTcount: A:0.30, C:0.45, G:0.06, T:0.19
Consensus pattern (99 bp):
CCACCACCTTATGAGTACAAGTCTCCACCTCCACCACCAAAGCATGAGGAACAACCTCCATACTA
CTACAAATCACCACCACCTCCATCACCCTCACCA
Done.