Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012584.1 Corchorus capsularis cultivar CVL-1 contig12605, 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: 27162
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1939 original size:2 final size:2
Alignment explanation
Indices: 1934--1962 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1924 GGAGAGAGTA
1934 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1963 CTTTAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3831 original size:40 final size:39
Alignment explanation
Indices: 3770--3851 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
3760 CTTGATCTTT
*
3770 CTAATAATTAAGGAAATAAATTAAATCCAGCTTTAGCACC
1 CTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAGC-CC
* *
3810 CTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAGCCC
3849 CTA
1 CTA
3852 GTTATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 5 0.13
40 34 0.87
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (39 bp):
CTAATAATTAAGGAAAGAAATTAAATCCAGCTTTAGCCC
Found at i:3956 original size:13 final size:13
Alignment explanation
Indices: 3938--3964 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3928 TAAGTTTTCC
3938 AGGGACAAATTGG
1 AGGGACAAATTGG
3951 AGGGACAAATTGG
1 AGGGACAAATTGG
3964 A
1 A
3965 TGTAGCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.37, T:0.15
Consensus pattern (13 bp):
AGGGACAAATTGG
Found at i:6113 original size:109 final size:109
Alignment explanation
Indices: 5917--6191 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 109
5907 ACTATTATAG
* *
5917 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTATTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
5982 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
6031 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
6096 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
6140 TTTTACTCTACTAAAAACTCTATTTTTATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
6192 TAGTTTTTTT
Statistics
Matches: 155, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
108 7 0.05
109 121 0.78
110 3 0.02
111 2 0.01
114 22 0.14
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:7200 original size:16 final size:16
Alignment explanation
Indices: 7179--7212 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
7169 CTCAAGCTTT
7179 TAGGCTATAAGACATA
1 TAGGCTATAAGACATA
7195 TAGGCTATAAGACATA
1 TAGGCTATAAGACATA
7211 TA
1 TA
7213 TCTTTTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (16 bp):
TAGGCTATAAGACATA
Found at i:14352 original size:229 final size:229
Alignment explanation
Indices: 13946--14380 Score: 843
Period size: 229 Copynumber: 1.9 Consensus size: 229
13936 GCAGCTGCCA
*
13946 TTCAAGTACAAGAACAGGTGCATTTCCAATCTTCAAGTCATGATATAACTAGACTTTTAACTTTT
1 TTCAAGTACAAGAACAGGTGCATTTCCAATCTTCAAGTCATGATATAACTAGACTGTTAACTTTT
14011 TGCCTTCGCTAATTAGGACAGAATAGCTACCCAAATTTTTATGATGAATCATTCTTCATGACTTA
66 TGCCTTCGCTAATTAGGACAGAATAGCTACCCAAATTTTTATGATGAATCATTCTTCATGACTTA
14076 GAGCCATTCTTCTTTGTATTGGATATGCTGGTTAGCTTGAGCTGGAAAACTTAAATCTCTGAGTT
131 GAGCCATTCTTCTTTGTATTGGATATGCTGGTTAGCTTGAGCTGGAAAACTTAAATCTCTGAGTT
14141 GATACGAAAATCTCTGAGATTGGAAATGCACCTG
196 GATACGAAAATCTCTGAGATTGGAAATGCACCTG
*
14175 TTCATGTACAAGAACAGGTGCATTTCCAATCTTCAAGTCATGATATAACTAGACTGTTAACTTTT
1 TTCAAGTACAAGAACAGGTGCATTTCCAATCTTCAAGTCATGATATAACTAGACTGTTAACTTTT
14240 TGCCTTCGCTAATTAGGACAGAATAGCTACCCAAATTTTTATGATGAATCATTCTTCATGACTTA
66 TGCCTTCGCTAATTAGGACAGAATAGCTACCCAAATTTTTATGATGAATCATTCTTCATGACTTA
*
14305 GAGCCATTCTTCTTTGTATTGGATATGCTGTTTAGCTTGAGCTGGAAAACTTAAATCTCTGAGTT
131 GAGCCATTCTTCTTTGTATTGGATATGCTGGTTAGCTTGAGCTGGAAAACTTAAATCTCTGAGTT
14370 GATACGAAAAT
196 GATACGAAAAT
14381 ATCAATTACT
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 203 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (229 bp):
TTCAAGTACAAGAACAGGTGCATTTCCAATCTTCAAGTCATGATATAACTAGACTGTTAACTTTT
TGCCTTCGCTAATTAGGACAGAATAGCTACCCAAATTTTTATGATGAATCATTCTTCATGACTTA
GAGCCATTCTTCTTTGTATTGGATATGCTGGTTAGCTTGAGCTGGAAAACTTAAATCTCTGAGTT
GATACGAAAATCTCTGAGATTGGAAATGCACCTG
Found at i:18270 original size:29 final size:29
Alignment explanation
Indices: 18236--18299 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
18226 ACTTTTGCTA
*
18236 CTTTTATCATTTTTACTCTTTTCTCACTCT
1 CTTTTAT-ATATTTACTCTTTTCTCACTCT
*
18266 -TTTTA-ATATTTACTCTTTTCTTACTCT
1 CTTTTATATATTTACTCTTTTCTCACTCT
18293 CTTTTAT
1 CTTTTAT
18300 TGATTACCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 20 0.67
28 5 0.17
29 5 0.17
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (29 bp):
CTTTTATATATTTACTCTTTTCTCACTCT
Found at i:18430 original size:35 final size:36
Alignment explanation
Indices: 18372--18451 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 36
18362 TGATCACCTT
18372 TTACTCTT-TACTGATTACTATTTTACTC-TTACTGA
1 TTAC-CTTCTACTGATTACTATTTTACTCTTTACTGA
18407 TTACCTTCTACTGATTA-TCATTTTACTCTTTACTGA
1 TTACCTTCTACTGATTACT-ATTTTACTCTTTACTGA
18443 TTACCTTCT
1 TTACCTTCT
18452 TACTTTTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
34 4 0.10
35 22 0.52
36 16 0.38
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (36 bp):
TTACCTTCTACTGATTACTATTTTACTCTTTACTGA
Found at i:18432 original size:22 final size:21
Alignment explanation
Indices: 18407--18531 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 21
18397 CTCTTACTGA
18407 TTACCTTCTACTGATTATCATT
1 TTACCTT-TACTGATTATCATT
*
18429 TTACTCTTTACTGATTA-CCTT
1 TTAC-CTTTACTGATTATCATT
* *
18450 CTTACTTTTTACTGATTAAC-TT
1 -TTAC-CTTTACTGATTATCATT
*
18472 CTTACTTTTTACTGATTAAT-ATT
1 -TTAC-CTTTACTGATT-ATCATT
*
18495 TTACTCTTTACTGATTACCATT
1 TTAC-CTTTACTGATTATCATT
* *
18517 TT-GCTCTACTGATTA
1 TTACCTTTACTGATTA
18532 CCGTTTACAA
Statistics
Matches: 90, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.12
21 4 0.04
22 68 0.76
23 7 0.08
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (21 bp):
TTACCTTTACTGATTATCATT
Found at i:18464 original size:44 final size:45
Alignment explanation
Indices: 18407--18533 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 45
18397 CTCTTACTGA
*
18407 TTAC-CTTCTACTGATTATCATTTTACTCTTTACTGATTACCT-TC
1 TTACTCTT-TACTGATTAACATTTTACTCTTTACTGATTACCTATC
* * * *
18451 TTACTTTTTACTGATTAAC-TTCTTACTTTTTACTGATTA-ATATT
1 TTACTCTTTACTGATTAACATT-TTACTCTTTACTGATTACCTATC
* *
18495 TTACTCTTTACTGATTACCATTTTGCTC--TACTGATTACC
1 TTACTCTTTACTGATTAACATTTTACTCTTTACTGATTACC
18534 GTTTACAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
42 9 0.13
43 3 0.04
44 52 0.76
45 4 0.06
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (45 bp):
TTACTCTTTACTGATTAACATTTTACTCTTTACTGATTACCTATC
Found at i:18608 original size:56 final size:56
Alignment explanation
Indices: 18492--18676 Score: 168
Period size: 56 Copynumber: 3.3 Consensus size: 56
18482 ACTGATTAAT
* * *** *
18492 ATTTTACTCTTTACTGATTACCATT-TTGC-TCTACTGATTACCGTTTACAAATTACT
1 ATTTTACTCTTTACTGATTACC-TTCTTACTTTTACTGATTACC-TTTACTTTTTACC
*
18548 ATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCATTACTTTTTACC
1 ATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCTTTACTTTTTACC
* * * *
18604 ATTTTACTCTTTGAAT--TTA-ATTAC-CA-TTTTACTGGTTACTTCTTTACTTTTTACC
1 ATTTTACTCTTT-ACTGATTACCTT-CTTACTTTTACTGATTAC--CTTTACTTTTTACC
18659 ATTTTACTCTTTACTGAT
1 ATTTTACTCTTTACTGAT
18677 CTCTCTTTAT
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
53 12 0.11
54 5 0.05
55 31 0.29
56 46 0.43
57 14 0.13
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (56 bp):
ATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACCTTTACTTTTTACC
Found at i:18734 original size:26 final size:26
Alignment explanation
Indices: 18705--18758 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
18695 CATTTTACTG
18705 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAATTTA
18731 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTTCACTCTTTGAATTTA
18757 AT
1 AT
18759 CACCATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAATTTA
Found at i:18766 original size:26 final size:26
Alignment explanation
Indices: 18711--18766 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
18701 ACTGATTACT
* *
18711 ATTTTACTCTCTTGAATTTAATTACT
1 ATTTTACTCTCTTGAATTTAATCACC
18737 ATTTTCACTCT-TTGAATTTAATCACC
1 ATTTT-ACTCTCTTGAATTTAATCACC
18763 ATTT
1 ATTT
18767 GTCATTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTTACTCTCTTGAATTTAATCACC
Found at i:18806 original size:33 final size:33
Alignment explanation
Indices: 18732--18814 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
18722 TTGAATTTAA
*
18732 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATT
* *
18766 TGT--CATTTTACTCTTTGAATTTACTTACCATT
1 T-TACCATTTTACTCTTTGAATTTAATCACCATT
18798 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
18815 ACCGATTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.02
32 22 0.51
33 18 0.42
34 1 0.02
35 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.53
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATT
Found at i:18864 original size:40 final size:41
Alignment explanation
Indices: 18820--18897 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
18810 TCTTTACCGA
*
18820 TTTACTGATCACTTCTTTTACTTTTACTC-TTAATTACCAT
1 TTTACTGATCACTTCTTTTACTTTGACTCTTTAATTACCAT
*
18860 TTTACTGATTACTTCTTTTACTTTGACTCTTTAATTAC
1 TTTACTGATCACTTCTTTTACTTTGACTCTTTAATTAC
18898 TGATTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 27 0.77
41 8 0.23
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.54
Consensus pattern (41 bp):
TTTACTGATCACTTCTTTTACTTTGACTCTTTAATTACCAT
Found at i:18927 original size:41 final size:41
Alignment explanation
Indices: 18813--18930 Score: 107
Period size: 40 Copynumber: 2.9 Consensus size: 41
18803 ATTTTACTCT
* * * * *
18813 TTACCGATTT-ACTGATCACTTCTTTTACTTTTACTC-TTAA
1 TTACC-ATTTCACTGATTACATCTCTTACCTTGACTCTTTAA
* * * *
18853 TTACCATTTTACTGATTACTTCTTTTACTTTGACTCTTTAA
1 TTACCATTTCACTGATTACATCTCTTACCTTGACTCTTTAA
*
18894 TTACTGATTTCACTGATTA-ATCTCTTACCTTGACTCT
1 TTAC-CATTTCACTGATTACATCTCTTACCTTGACTCT
18931 GGATTATCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 4 0.06
40 29 0.43
41 23 0.34
42 12 0.18
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (41 bp):
TTACCATTTCACTGATTACATCTCTTACCTTGACTCTTTAA
Found at i:22421 original size:39 final size:39
Alignment explanation
Indices: 22378--22454 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
22368 AGACACCCGC
22378 TTATTCCGGAGAAA-AAGAAAGAGACCAATCCATGGTCGA
1 TTATTCCGGAGAAACAA-AAAGAGACCAATCCATGGTCGA
** *
22417 TTATTGTGGTGAAACTAAAAAGAGACCAATCCATGGTC
1 TTATTCCGGAGAAAC-AAAAAGAGACCAATCCATGGTC
22455 AACTTTTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 20 0.61
41 2 0.06
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (39 bp):
TTATTCCGGAGAAACAAAAAGAGACCAATCCATGGTCGA
Found at i:22477 original size:45 final size:43
Alignment explanation
Indices: 22426--22615 Score: 123
Period size: 50 Copynumber: 4.1 Consensus size: 43
22416 ATTATTGTGG
*
22426 TGAAACTAAAAAGAGACCAATCC-ATGGTCAACTTTTGATAACTGT
1 TGAAACTAAAAA-AGACCAATCCTA-GGTCAAC-TTTGATAACTGC
* ** *
22471 TGAAACTTAAAAAGACCTGTTCTGAGGTCAACTTTGATAACTGC
1 TGAAACTAAAAAAGACCAATCCT-AGGTCAACTTTGATAACTGC
*
22515 TGAAACTTAAAAAAAAAAAGA-CATATTCTGAGGTCAACTTTGATAACTGC
1 TGAAAC-T-----AAAAAAGACCA-ATCCT-AGGTCAACTTTGATAACTGC
** ** * *
22565 TGAAAACCTTTAAAAGACCTGTTCTGAGGCCAACTTTGATAACTGC
1 TG-AAA-CTAAAAAAGACCAATCCT-AGGTCAACTTTGATAACTGC
22611 TGAAA
1 TGAAA
22616 ACTGAGAAAG
Statistics
Matches: 120, Mismatches: 13, Indels: 24
0.76 0.08 0.15
Matches are distributed among these distances:
44 24 0.20
45 22 0.18
46 33 0.28
47 1 0.01
49 1 0.01
50 34 0.28
51 4 0.03
52 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.27
Consensus pattern (43 bp):
TGAAACTAAAAAAGACCAATCCTAGGTCAACTTTGATAACTGC
Found at i:22529 original size:46 final size:45
Alignment explanation
Indices: 22451--22647 Score: 236
Period size: 46 Copynumber: 4.2 Consensus size: 45
22441 ACCAATCCAT
*
22451 GGTCAACTTTTGATAACTGTTG-AAACTTAAAAAGACCTGTTCTGA
1 GGTCAAC-TTTGATAACTGCTGAAAACTTAAAAAGACCTGTTCTGA
* *
22496 GGTCAACTTTGATAACTGCTG-AAACTTAAAAAAAAAAAGACATATTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTT------AAAAAGACCTGTTCTGA
*
22546 GGTCAACTTTGATAACTGCTGAAAACCTTTAAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAA-CTTAAAAAGACCTGTTCTGA
* * *
22592 GGCCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTTAAAAAGACCTGTTCTGA
*
22637 GGTCGACTTTG
1 GGTCAACTTTG
22648 GTGATCTTAT
Statistics
Matches: 132, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
44 19 0.14
45 33 0.25
46 38 0.29
50 36 0.27
51 3 0.02
52 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (45 bp):
GGTCAACTTTGATAACTGCTGAAAACTTAAAAAGACCTGTTCTGA
Done.