Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005081.1 Corchorus capsularis cultivar CVL-1 contig05099, 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: 18528
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1886 original size:16 final size:17
Alignment explanation
Indices: 1855--1887 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1845 GGAAGGTATT
*
1855 AATAAGTAAAATTTAAA
1 AATAAGTAAAAATTAAA
1872 AATAA-TAAAAATTAAA
1 AATAAGTAAAAATTAAA
1888 GAAATAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AATAAGTAAAAATTAAA
Found at i:2917 original size:23 final size:23
Alignment explanation
Indices: 2846--2946 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
2836 TCACACTCTG
* *
2846 AAATTTTGAT-AAT-TCACTATG
1 AAATTTTGATAAATCTCCCTATA
* * ** *
2867 AAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAATCTCCCTATA
*
2889 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTCCCTATA
2912 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAATCTCCCTATA
2935 AAATTTTGATAA
1 AAATTTTGATAA
2947 CTTTCTTTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
21 11 0.16
22 15 0.22
23 41 0.61
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTCCCTATA
Found at i:3023 original size:22 final size:22
Alignment explanation
Indices: 2529--3120 Score: 174
Period size: 22 Copynumber: 27.1 Consensus size: 22
2519 TTTTATGATG
2529 TCATTATGAAATTTTGATAACC
1 TCATTATGAAATTTTGATAACC
* *
2551 T-TTCTATGAAATTTTAATAA--
1 TCAT-TATGAAATTTTGATAACC
* * * *
2571 TGATACTATGGAATTTCGAGAACC
1 TCAT--TATGAAATTTTGATAACC
** **
2595 TTTTTAT-AAATTTTTTTTAACC
1 TCATTATGAAA-TTTTGATAACC
* *
2617 TTC-TTATGAAATTTTGTTAATC
1 -TCATTATGAAATTTTGATAACC
** * * *
2639 TCCCTAAGGAATTTTGA-AGATC
1 TCATTATGAAATTTTGATA-ACC
* * *
2661 TCAATATGGAATTTTGATAACTT
1 TCATTATGAAATTTTGATAAC-C
2684 TCCA--ATGAAATTTTGATAACC
1 T-CATTATGAAATTTTGATAACC
* * * *
2705 AACACTATGAGATGTTGATAACC
1 -TCATTATGAAATTTTGATAACC
* *
2728 TCCA-TATGATATATTGATAACC
1 T-CATTATGAAATTTTGATAACC
* * *
2750 ACATTATGAAAATTTAATAACC
1 TCATTATGAAATTTTGATAACC
* *
2772 TCCA-TATGATATATTGATAACC
1 T-CATTATGAAATTTTGATAACC
* * * *
2794 ACATTATGAAAATTTAAAAACC
1 TCATTATGAAATTTTGATAACC
* *
2816 TCAATATG-AATTGTT-AGTAATC
1 TCATTATGAAATT-TTGA-TAACC
* * * *
2838 ACACTCTGAAATTTTGATAA-T
1 TCATTATGAAATTTTGATAACC
* *
2859 TCACTATGAAATTGTGATAACC
1 TCATTATGAAATTTTGATAACC
* *
2881 TCGTTATGAAATTTTGATAAATCT
1 TCATTATGAAATTTTGAT-AA-CC
* * *
2905 TC-CTATAAAATTTTGATAAATC
1 TCATTATGAAATTTTGAT-AACC
** * *
2927 TCCCTATAAAATTTTGATAACTT
1 TCATTATGAAATTTTGATAAC-C
* *
2950 TC-TTTTGAAATCTTGATAA--
1 TCATTATGAAATTTTGATAACC
*
2969 -C--TA-CAAATTTTGATAACC
1 TCATTATGAAATTTTGATAACC
* **
2987 TTC-CTATGATTTTTTGATAACC
1 -TCATTATGAAATTTTGATAACC
** *
3009 TCATTATGAAATTTTTTTAATC
1 TCATTATGAAATTTTGATAACC
** * *
3031 TCCCTATGAAATTTTGATCTACA
1 TCATTATGAAATTTTGAT-AACC
*
3054 T-ACTATGAAATTTTGATAACCC
1 TCATTATGAAATTTTGATAA-CC
*
3076 TC-TTATGAAAATTTT-A-AAAC
1 TCATTATG-AAATTTTGATAACC
* * *
3096 TAAACTATGAAATTTTGATATCC
1 T-CATTATGAAATTTTGATAACC
3119 TC
1 TC
3121 CCTGAAATTT
Statistics
Matches: 420, Mismatches: 106, Indels: 88
0.68 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
20 4 0.01
21 48 0.11
22 271 0.65
23 77 0.18
24 7 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TCATTATGAAATTTTGATAACC
Found at i:3307 original size:22 final size:22
Alignment explanation
Indices: 3216--3409 Score: 91
Period size: 22 Copynumber: 8.7 Consensus size: 22
3206 GAAATACGAC
3216 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * *
3238 TCTGAAAATTTGATAAGCTC-T
1 TATGAAATTTTGATAATCACAT
* * * * *
3259 TCATAAAATTTTGTTGA-CCCCT
1 T-ATGAAATTTTGATAATCACAT
*
3281 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
3304 TATGCAATTTTGATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
*
3327 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
3348 TATGAAATTTTGATAATCTGATC-T
1 TATGAAATTTTGATAATC--A-CAT
*
3372 CTATGAAATTTCGATAATCAC-T
1 -TATGAAATTTTGATAATCACAT
*
3394 CTATGAGA-TTTGATAA
1 -TATGAAATTTTGATAA
3410 CCTTCTATCA
Statistics
Matches: 131, Mismatches: 27, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 16 0.12
22 83 0.63
23 8 0.06
24 4 0.03
25 18 0.14
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:3313 original size:44 final size:44
Alignment explanation
Indices: 3264--3363 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
3254 GCTCTTCATA
* * * *
3264 AAATTTTGTTGACCCCTCTATGAAATTCTGATAATC-ACATTATG
1 AAATTTTGATAACCCCGCTATGAAATTCTGATAA-CAACACTATG
* * * *
3308 CAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATG
1 AAATTTTGATAACCCCGCTATGAAATTCTGATAACAACACTATG
3352 AAATTTTGATAA
1 AAATTTTGATAA
3364 TCTGATCTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCCCGCTATGAAATTCTGATAACAACACTATG
Found at i:3381 original size:25 final size:22
Alignment explanation
Indices: 3279--3443 Score: 119
Period size: 22 Copynumber: 7.5 Consensus size: 22
3269 TTGTTGACCC
*
3279 CTCTATGAAATTCTGATAATCA
1 CTCTATGAAATTTTGATAATCA
* * *
3301 CAT-TATGCAATTTTGATAACCT
1 C-TCTATGAAATTTTGATAATCA
* *
3323 CGCTTTGAAATTTTGATAA-CAA
1 CTCTATGAAATTTTGATAATC-A
*
3345 CACTATGAAATTTTGATAATCTGA
1 CTCTATGAAATTTTGATAATC--A
*
3369 TCTCTATGAAATTTCGATAATCA
1 -CTCTATGAAATTTTGATAATCA
*
3392 CTCTATGAGA-TTTGATAA-C-
1 CTCTATGAAATTTTGATAATCA
* * *
3411 CTTCTATCAAATTTTGGTACTC-
1 C-TCTATGAAATTTTGATAATCA
3433 CT-TATGAAATT
1 CTCTATGAAATT
3444 GAGACTTTTA
Statistics
Matches: 114, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.01
20 16 0.14
21 15 0.13
22 59 0.52
23 3 0.03
24 1 0.01
25 19 0.17
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATCA
Found at i:3489 original size:22 final size:22
Alignment explanation
Indices: 3463--3782 Score: 91
Period size: 22 Copynumber: 14.8 Consensus size: 22
3453 ATAACATTTA
3463 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
3485 CATGAAATATT-AGTAACCT-CC
1 TATGAAATTTTGA-TAACCTCCC
* ** *
3506 TAATGAAATTTTGTTAACGACAC
1 T-ATGAAATTTTGATAACCTCCC
*
3529 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCCC
* *
3551 TATGACATTTTGATAA--TCTC
1 TATGAAATTTTGATAACCTCCC
* * **
3571 TTTGATAATCTTTCTATAAAAT---
1 TATGA-AAT-TTT-GATAACCTCCC
* *
3593 TGTGATAA--TT-A--ACCACCC
1 TATGA-AATTTTGATAACCTCCC
** **
3611 TATGAAATTTCAATAACCAACC
1 TATGAAATTTTGATAACCTCCC
* * * *
3633 TAAGAAATTTTAATTACCTGATCC
1 TATGAAATTTTGATAACCT--CCC
* * * *
3657 TATGAAATTTCGGTAACCACAC
1 TATGAAATTTTGATAACCTCCC
* * *
3679 TATAAAATTTTGATAACTTCCA
1 TATGAAATTTTGATAACCTCCC
* *
3701 TATGAAATTTTGGTAA-C-CAC
1 TATGAAATTTTGATAACCTCCC
3721 TATGGAAA-TTTGATAACCT-CC
1 TAT-GAAATTTTGATAACCTCCC
* * *
3742 TCATGAAATTATAATAACCAT-CT
1 T-ATGAAATTTTGATAACC-TCCC
3765 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
3783 ACATAGACAA
Statistics
Matches: 215, Mismatches: 56, Indels: 54
0.66 0.17 0.17
Matches are distributed among these distances:
15 1 0.00
17 3 0.01
18 4 0.02
19 3 0.01
20 19 0.09
21 18 0.08
22 140 0.65
23 11 0.05
24 15 0.07
25 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:3515 original size:44 final size:44
Alignment explanation
Indices: 3463--3566 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
3453 ATAACATTTA
* *
3463 TATGAAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-C
1 TATGAAATTTTGATAACCACACCATGAAATTATTA-TAACCTCGC
* * * *
3506 TAATGAAATTTTGTTAACGACACTATGAAATTCTTATAACCTCGC
1 T-ATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCGC
*
3551 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
3567 TCTCTTTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
43 1 0.02
44 43 0.86
45 6 0.12
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCGC
Found at i:3687 original size:46 final size:44
Alignment explanation
Indices: 3609--3720 Score: 113
Period size: 46 Copynumber: 2.5 Consensus size: 44
3599 AATTAACCAC
** *
3609 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATTACCTGAT
1 CCTATGAAATTTCGGTAACCACACCTAAGAAATTTTAA-TAACT--T
*
3655 CCTATGAAATTTCGGTAACCACA-CTATA-AAATTTTGATAACTT
1 CCTATGAAATTTCGGTAACCACACCTA-AGAAATTTTAATAACTT
*
3698 CCATATGAAATTTTGGTAACCAC
1 CC-TATGAAATTTCGGTAACCAC
3721 TATGGAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.05
44 19 0.33
45 4 0.07
46 30 0.52
47 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTCGGTAACCACACCTAAGAAATTTTAATAACTT
Found at i:3735 original size:42 final size:43
Alignment explanation
Indices: 3654--3751 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
3644 AATTACCTGA
*
3654 TCCTATGAAATTTCGGTAACCACACTATAAAATTTTGATAACT
1 TCCTATGAAATTTCGGTAACCACACTATAAAATTTTGATAACC
* *
3697 TCCATATGAAATTTTGGTAA-C-CACTATGGAAA-TTTGATAACC
1 TCC-TATGAAATTTCGGTAACCACACTAT-AAAATTTTGATAACC
3739 TCCTCATGAAATT
1 TCCT-ATGAAATT
3752 ATAATAACCA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 26 0.53
43 7 0.14
44 15 0.31
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (43 bp):
TCCTATGAAATTTCGGTAACCACACTATAAAATTTTGATAACC
Found at i:3760 original size:42 final size:44
Alignment explanation
Indices: 3683--3782 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 44
3673 CCACACTATA
* * **
3683 AAATTTTGATAACTTCCATATGAAATTTTGGTAACCA-C-TATGG
1 AAATTTTGATAACCTCCATATGAAATTATAATAACCATCTTAT-G
3726 AAA-TTTGATAACCTCC-TCATGAAATTATAATAACCATCTTATG
1 AAATTTTGATAACCTCCAT-ATGAAATTATAATAACCATCTTATG
3769 AAATTTTGATAACC
1 AAATTTTGATAACC
3783 ACATAGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
41 1 0.02
42 27 0.55
43 8 0.16
44 13 0.27
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACCTCCATATGAAATTATAATAACCATCTTATG
Found at i:3783 original size:22 final size:22
Alignment explanation
Indices: 3602--3783 Score: 133
Period size: 22 Copynumber: 8.3 Consensus size: 22
3592 TTGTGATAAT
* **
3602 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
3624 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
* * *
3646 TTACCTGATCCTATGAAATTTCGG
1 TAACC--ATCCTATGAAATTTTGA
*
3670 TAACCA-CACTATAAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
3692 TAA-CTTCCATATGAAATTTTGG
1 TAACCATCC-TATGAAATTTTGA
3714 TAACCA--CTATGGAAA-TTTGA
1 TAACCATCCTAT-GAAATTTTGA
* *
3734 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
3756 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
3778 TAACCA
1 TAACCA
3784 CATAGACAAG
Statistics
Matches: 125, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
20 12 0.10
21 14 0.11
22 79 0.63
23 4 0.03
24 16 0.13
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:5246 original size:37 final size:37
Alignment explanation
Indices: 5151--5252 Score: 141
Period size: 38 Copynumber: 2.7 Consensus size: 37
5141 CAGATTATCT
*
5151 AAATTCAAATAGGACGTTGGAGACAAAGACAAAAAGCA
1 AAATT-AAATAGGACGTTGGAAACAAAGACAAAAAGCA
* ** *
5189 AAATTAGATACAACGATTGGAAACAAAGACAAAAGGCA
1 AAATTAAATAGGACG-TTGGAAACAAAGACAAAAAGCA
5227 AAATTAAATAGGACGTTGGAAACAAA
1 AAATTAAATAGGACGTTGGAAACAAA
5253 AAGTCAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 18 0.33
38 37 0.67
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.15
Consensus pattern (37 bp):
AAATTAAATAGGACGTTGGAAACAAAGACAAAAAGCA
Found at i:5413 original size:30 final size:32
Alignment explanation
Indices: 5368--5434 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
5358 TTTAATAATG
* * *
5368 ACAATTTAGAAATATGTTTTAATAA-AAGGGT
1 ACAATTGAGAAATATGTTTTAAAAATAAGAGT
5399 ACAATTGA-AAATATGTTTTAAAAATAAGAGT
1 ACAATTGAGAAATATGTTTTAAAAATAAGAGT
5430 ACAAT
1 ACAAT
5435 CGGAAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (32 bp):
ACAATTGAGAAATATGTTTTAAAAATAAGAGT
Found at i:10681 original size:62 final size:62
Alignment explanation
Indices: 10584--10708 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
10574 CTTTTAAATA
**
10584 TAAAATATAAATATGTAACAATTAACATAATAAATAACAAACAAATAATGGTGAGGAAGGGC
1 TAAAATATAAATATGTAACAATTAACATAATAAATAACAAACAAATAACAGTGAGGAAGGGC
*
10646 TAAAATATAAATATGTAACAATTAACATAATAAATAACAAACAAATAACAGTGAGGGAGGGC
1 TAAAATATAAATATGTAACAATTAACATAATAAATAACAAACAAATAACAGTGAGGAAGGGC
10708 T
1 T
10709 CGACTAGCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.22
Consensus pattern (62 bp):
TAAAATATAAATATGTAACAATTAACATAATAAATAACAAACAAATAACAGTGAGGAAGGGC
Found at i:14005 original size:20 final size:21
Alignment explanation
Indices: 13969--14007 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13959 CCAAACTAAA
13969 TGCACTTAATCATTTTTTTCT
1 TGCACTTAATCATTTTTTTCT
13990 TGCACTTAAT-ATTTTTTT
1 TGCACTTAATCATTTTTTT
14008 GGTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (21 bp):
TGCACTTAATCATTTTTTTCT
Found at i:14458 original size:32 final size:32
Alignment explanation
Indices: 14417--14479 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
14407 CTAACAAAGC
*
14417 ACACAAAGTGATAAAAAACCCACACATATATT
1 ACACAAAGTGACAAAAAACCCACACATATATT
* * *
14449 ACACAAAGTGGCACAAAACCCATACATATAT
1 ACACAAAGTGACAAAAAACCCACACATATAT
14480 ATGTAGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.24, G:0.08, T:0.17
Consensus pattern (32 bp):
ACACAAAGTGACAAAAAACCCACACATATATT
Found at i:18447 original size:31 final size:31
Alignment explanation
Indices: 18378--18479 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
18368 TCCTTTTGTG
* * * **
18378 CACGTGGCATGTCACGTGCCATTTTTTGAAA
1 CACGTGGCATGACACGTGTCACTTTTTGGTA
* * *
18409 CATGTGGCATGCCACGTGTTACTTTTTGGTA
1 CACGTGGCATGACACGTGTCACTTTTTGGTA
* * *
18440 CACGTGGCGTGACATGTGTCACTTTTTTGTA
1 CACGTGGCATGACACGTGTCACTTTTTGGTA
*
18471 CATGTGGCA
1 CACGTGGCA
18480 CGACTTTTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (31 bp):
CACGTGGCATGACACGTGTCACTTTTTGGTA
Done.