Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010213.1 Corchorus capsularis cultivar CVL-1 contig10234, 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: 39233
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:3578 original size:19 final size:20
Alignment explanation
Indices: 3541--3578 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3531 CTGGTTTGTT
*
3541 TTTTTAATTAGTAATGTTCC
1 TTTTTAATGAGTAATGTTCC
3561 TTTTTAATGAGTAA-GTTC
1 TTTTTAATGAGTAATGTTC
3579 TTGCTTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTTTAATGAGTAATGTTCC
Found at i:16839 original size:28 final size:26
Alignment explanation
Indices: 16808--16868 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
16798 TTATTTTAGA
16808 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
16836 CAAACTC--ACAATTTTAATCTCAAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
16860 CAACCTCTT
1 CAAACTCTT
16869 CAAGGTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
28 7 0.23
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:16975 original size:34 final size:34
Alignment explanation
Indices: 16934--17042 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 34
16924 ATATCCACTT
*
16934 AACCCGTAATATATAATTGGAATTGGACTAAGAA
1 AACCCGTAATATATAATTGGAATTGGACTAAAAA
*
16968 AACCCGTAATATATAATTTGAATTGGACTAATAAAA
1 AACCCGTAATATATAATTGGAATTGGACT-A-AAAA
17004 TTCAACCCGTAATATATAATTGGAATTGGACTAAAAA
1 ---AACCCGTAATATATAATTGGAATTGGACTAAAAA
17041 AA
1 AA
17043 TTCAATTTGA
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 30 0.45
35 1 0.01
36 3 0.04
37 4 0.06
38 1 0.01
39 28 0.42
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (34 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAA
Found at i:17013 original size:39 final size:38
Alignment explanation
Indices: 16934--17047 Score: 164
Period size: 39 Copynumber: 3.1 Consensus size: 38
16924 ATATCCACTT
*
16934 AACCCGTAATATATAATTGGAATTGGACT-AAGAA---
1 AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
*
16968 AACCCGTAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACTAA-AAAATTC
17007 AACCCGTAATATATAATTGGAATTGGACTAAAAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACT-AAAAAATTC
17046 AA
1 AA
17048 TTTGATTACT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 28 0.39
35 1 0.01
36 3 0.04
39 37 0.52
40 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (38 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
Found at i:18600 original size:2 final size:2
Alignment explanation
Indices: 18590--18630 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
18580 GTAAAGTGTG
*
18590 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
18631 GATCATATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:18782 original size:13 final size:13
Alignment explanation
Indices: 18766--18798 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18756 TCGGTTTAGA
18766 AAAATTGTTTTTG
1 AAAATTGTTTTTG
*
18779 AAAAATGTTTTTG
1 AAAATTGTTTTTG
18792 AAAATTG
1 AAAATTG
18799 CACTAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (13 bp):
AAAATTGTTTTTG
Found at i:19055 original size:2 final size:2
Alignment explanation
Indices: 19048--19074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19038 TATTTCATGT
19048 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19075 GATAGACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21028 original size:23 final size:24
Alignment explanation
Indices: 21002--21051 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
20992 TCTCAAATTC
21002 AACACAAGTGAAAA-AAGAAAAAT
1 AACACAAGTGAAAAGAAGAAAAAT
* * *
21025 AACATACGTGAAAAGAAGAAAACT
1 AACACAAGTGAAAAGAAGAAAAAT
21049 AAC
1 AAC
21052 CCGACTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.10
Consensus pattern (24 bp):
AACACAAGTGAAAAGAAGAAAAAT
Found at i:21697 original size:17 final size:18
Alignment explanation
Indices: 21675--21715 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21665 ATATTATATT
21675 TATTTTATAC-TAAAAAA
1 TATTTTATACATAAAAAA
*
21692 TATTTT-TTCATAAAAAA
1 TATTTTATACATAAAAAA
*
21709 TCTTTTA
1 TATTTTA
21716 AACCGGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTTATACATAAAAAA
Found at i:24447 original size:179 final size:177
Alignment explanation
Indices: 24136--24493 Score: 653
Period size: 179 Copynumber: 2.0 Consensus size: 177
24126 TCCATAAACA
*
24136 AATCATTTTTTTGTTGGATTATTTATTAAATGATACTCATACTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGGATTATTTATTAAATGATACTCATACTTTTATAATTTATACTATTTAAT
24201 CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACC
66 CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACC
* *
24266 GATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTTCATGGTCTAC
131 GATCAAGGTGATTCAGATGTCTATTTAAAGGTAATTCCATGGTCTAC
* *
24313 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATATTATTTAA
1 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATACTCATACTTTTATAATTTATACTATTTAA
24378 TCACTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGA
65 TC-CTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGA
24443 CCGATCAAGGTGATTCAGATGTCTATTTAAAGGTAATTCCATGGTCTAC
129 CCGATCAAGGTGATTCAGATGTCTATTTAAAGGTAATTCCATGGTCTAC
24492 AA
1 AA
24494 CTTTCATGAA
Statistics
Matches: 174, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
177 5 0.03
178 58 0.33
179 111 0.64
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (177 bp):
AATCATTTTTTTGTTGGATTATTTATTAAATGATACTCATACTTTTATAATTTATACTATTTAAT
CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACC
GATCAAGGTGATTCAGATGTCTATTTAAAGGTAATTCCATGGTCTAC
Found at i:25217 original size:74 final size:74
Alignment explanation
Indices: 25138--25280 Score: 259
Period size: 74 Copynumber: 1.9 Consensus size: 74
25128 TTTTCAGGTG
* *
25138 ACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTACTTCTACCCTTTTTCGTAATTACACT
1 ACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTACTTCTACCCTTTTTCGTAATTACACA
25203 TTTCGGATA
66 TTTCGGATA
*
25212 ACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTTTTCGTAATTACACA
1 ACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTACTTCTACCCTTTTTCGTAATTACACA
25277 TTTC
66 TTTC
25281 CCTTCCTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.22, C:0.31, G:0.07, T:0.40
Consensus pattern (74 bp):
ACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTACTTCTACCCTTTTTCGTAATTACACA
TTTCGGATA
Found at i:25318 original size:20 final size:21
Alignment explanation
Indices: 25287--25325 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
25277 TTTCCCTTCC
25287 TTAATGGTTTTTAATTAATGT
1 TTAATGGTTTTTAATTAATGT
25308 TTAAT-GTTTTTAATTAAT
1 TTAATGGTTTTTAATTAAT
25326 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TTAATGGTTTTTAATTAATGT
Found at i:28704 original size:84 final size:84
Alignment explanation
Indices: 28562--28730 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
28552 GAGATGAGCC
*
28562 TTATATATAACAATGTTTAACCATCCCATAAGGGGTACAAGAGTCAGACTGCTTGCCCAAACCCA
1 TTATATATAACAATGTTTAACCATCCCATAAGGGGTACAAGAGTCAGACTGCTCGCCCAAACCCA
*
28627 TAGGCCGGATCCAAATAGG
66 TAGGCCAGATCCAAATAGG
28646 TTATATATAACAATGTTTAACCATCCCATAAGGGGTACAAGAGTCAGACTGCTCGCCCAAACCCA
1 TTATATATAACAATGTTTAACCATCCCATAAGGGGTACAAGAGTCAGACTGCTCGCCCAAACCCA
28711 TAGGCCAGATCCAAATAGG
66 TAGGCCAGATCCAAATAGG
28730 T
1 T
28731 CAAGTCTTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (84 bp):
TTATATATAACAATGTTTAACCATCCCATAAGGGGTACAAGAGTCAGACTGCTCGCCCAAACCCA
TAGGCCAGATCCAAATAGG
Found at i:30790 original size:11 final size:11
Alignment explanation
Indices: 30774--30807 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
30764 AAAAAAGTTT
30774 TCTTCTTTTTC
1 TCTTCTTTTTC
*
30785 TCTTCTTTTTT
1 TCTTCTTTTTC
30796 TCTTTCTTTTTC
1 TC-TTCTTTTTC
30808 GACCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTCTTTTTC
Found at i:33795 original size:37 final size:35
Alignment explanation
Indices: 33745--33813 Score: 111
Period size: 37 Copynumber: 1.9 Consensus size: 35
33735 GTTTGCAATA
33745 TTACACATGTGAATATATTTATATGTGTGTGTGTGTG
1 TTACACATGTGAATATA--TATATGTGTGTGTGTGTG
*
33782 TTACACATGTGAATATATATTTGTGTGTGTGT
1 TTACACATGTGAATATATATATGTGTGTGTGT
33814 AGAAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 14 0.45
37 17 0.55
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (35 bp):
TTACACATGTGAATATATATATGTGTGTGTGTGTG
Found at i:38184 original size:27 final size:27
Alignment explanation
Indices: 38146--38199 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38136 AATTTAATCA
*
38146 AATCCAAATTTATGTAATAGTATGTTG
1 AATCCAAATTTATGTAATACTATGTTG
38173 AATCCAAATTTATGTAATACTATGTTG
1 AATCCAAATTTATGTAATACTATGTTG
38200 CTAGGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (27 bp):
AATCCAAATTTATGTAATACTATGTTG
Found at i:38841 original size:22 final size:22
Alignment explanation
Indices: 38799--38842 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38789 TATTCATACG
* *
38799 AAATTGTGATAATCTTCCTATT
1 AAATTATGATAATCTACCTATT
38821 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCTAC-CTATT
38843 TTTTATGACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTACCTATT
Found at i:38899 original size:60 final size:60
Alignment explanation
Indices: 38798--38939 Score: 230
Period size: 60 Copynumber: 2.3 Consensus size: 60
38788 ATATTCATAC
* * *
38798 GAAATTGTGATAATCTTCCTATTAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAATCTTCC--TGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
38860 GAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
1 GAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
*
38920 GAAATTTTGATAACCTTCCT
1 GAAATTTTGATAATCTTCCT
38940 CTGAAATTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 58 0.76
62 18 0.24
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.44
Consensus pattern (60 bp):
GAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
Found at i:38998 original size:20 final size:21
Alignment explanation
Indices: 38975--39021 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
38965 GAATTTCGAG
* *
38975 AACCTTTTTAT-AATTTTTTT
1 AACCTTCTTATAAATTTTGTT
38995 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTAT-AAATTTTGTT
39017 AACCT
1 AACCT
39022 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (21 bp):
AACCTTCTTATAAATTTTGTT
Found at i:39225 original size:23 final size:22
Alignment explanation
Indices: 39003--39233 Score: 91
Period size: 22 Copynumber: 10.5 Consensus size: 22
38993 TTAACCTTCT
* *
39003 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCGC
* * * *
39025 TAAGGAATTTTGA-AGATCTCAC
1 TATGAAATTTTGATA-ACCTCGC
* *
39047 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCGC
*
39070 TAT-AAGATGTTGATAACCTC-C
1 TATGAA-ATTTTGATAACCTCGC
* * * *
39091 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCGC
* * * *
39114 TAAGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCGC
** *
39135 ATATG-AATTGTCAATAA--TCAC
1 -TATGAAATT-TTGATAACCTCGC
* * * **
39156 TCTGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCGC
*
39178 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCGC
39200 TATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCGC
*
39223 TATAAAATTTT
1 TATGAAATTTT
Statistics
Matches: 154, Mismatches: 40, Indels: 29
0.69 0.18 0.13
Matches are distributed among these distances:
20 10 0.06
21 10 0.06
22 98 0.64
23 34 0.22
24 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCGC
Done.