Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013914.1 Corchorus capsularis cultivar CVL-1 contig13935, 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: 53653
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--40 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AAGTAC
7 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 CTCAATTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1398 original size:1 final size:1
Alignment explanation
Indices: 1392--1422 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1382 AAAAGAAGGG
1392 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1423 CCACATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2745 original size:3 final size:3
Alignment explanation
Indices: 2737--2773 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
2727 CTACAATTTG
2737 TAT TAT TAT TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2774 GTACTCTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.19
3 25 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6342 original size:2 final size:2
Alignment explanation
Indices: 6329--6368 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
6319 CTTCACCAAT
6329 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6369 GTTTCATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7290 original size:36 final size:36
Alignment explanation
Indices: 7250--7324 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
7240 GTATAATTTG
*
7250 AAACTAATTCATTTATATATAATA-ATATACATATAT
1 AAACTAATTC-TTCATATATAATATATATACATATAT
* * *
7286 AAACTAATTCTTCATTTATATTATATATATATATAT
1 AAACTAATTCTTCATATATAATATATATACATATAT
7322 AAA
1 AAA
7325 TATATATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 10 0.29
36 24 0.71
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (36 bp):
AAACTAATTCTTCATATATAATATATATACATATAT
Found at i:7771 original size:45 final size:45
Alignment explanation
Indices: 7721--7809 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
7711 GATTACTTCT
7721 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
*
7766 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCA
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCA
7810 ATACTCTAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:8378 original size:23 final size:23
Alignment explanation
Indices: 8313--8382 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
8303 CAATTGAGAA
8313 AAGACCAAAAAGTTTAGTTATTT
1 AAGACCAAAAAGTTTAGTTATTT
** ***
8336 AATCCCCTCAAG--TAGTTATTT
1 AAGACCAAAAAGTTTAGTTATTT
8357 AAGACCAAAAAGTTTAGTTATTT
1 AAGACCAAAAAGTTTAGTTATTT
8380 AAG
1 AAG
8383 TAATCTGCCA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
21 16 0.46
23 19 0.54
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (23 bp):
AAGACCAAAAAGTTTAGTTATTT
Found at i:8405 original size:44 final size:41
Alignment explanation
Indices: 8312--8419 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
8302 TCAATTGAGA
** *
8312 AAAGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGTAGTT
1 AAAGACCAAAAAGTTTAGTTATTTAATAACCTCAAGTAGGT
*
8353 ATTTAAGACCAAAAAGTTTAGTTATTTAAGTAATCTGCCAAGTAGGT
1 A---AAGACCAAAAAGTTTAGTTATTTAA-TAACCT--CAAGTAGGT
* *
8400 AAAGACGAAAAAGATTAGTT
1 AAAGACCAAAAAGTTTAGTT
8420 CTCTAGCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
41 1 0.02
44 42 0.76
45 3 0.05
47 9 0.16
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (41 bp):
AAAGACCAAAAAGTTTAGTTATTTAATAACCTCAAGTAGGT
Found at i:8686 original size:167 final size:166
Alignment explanation
Indices: 8376--8746 Score: 471
Period size: 167 Copynumber: 2.2 Consensus size: 166
8366 AAGTTTAGTT
* * * * ** **
8376 ATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCT
1 ATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAATCAAGACT
* * * *
8441 TGATGGGGATCTTTTATTAATTCCACCACTCTATTCAAGTTCATTGAGAAATGACCAAAAAAATT
66 TGATAGGGATCTTTTAGTAATCCCACCACTCTATTAAAGTTCATTGAGAAATGACCAAAAAAATT
* *
8506 ACTTATTTAATCCCTTCAAGAATCAAAAGTTAGGAC
131 ACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGAA
*
8542 ATTTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGT-AAGA
1 ATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACT-CAAAA-TCAAGA
* *
8606 CTTGGTAGGGATCTTTTAGTAATCCCACTACTCTATTAAAG-TCAATTGAGAAATGACC-AAAAA
64 CTTGATAGGGATCTTTTAGTAATCCCACCACTCTATTAAAGTTC-ATTGAGAAATGACCAAAAAA
* * * * *
8669 GTCTAGTTATTTAATCCCCTCAAGATTTAAAAGTTGGGAA
128 AT-TACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGAA
8709 ATTTAAGTAATCTGCCAAGT-GGAAAAAGACGAAAAAAA
1 ATTTAAGTAATCTGCCAAGTAGG-AAAAGACGAAAAAAA
8747 ATTAGTTATC
Statistics
Matches: 177, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
166 57 0.32
167 119 0.67
168 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (166 bp):
ATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAATCAAGACT
TGATAGGGATCTTTTAGTAATCCCACCACTCTATTAAAGTTCATTGAGAAATGACCAAAAAAATT
ACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGAA
Found at i:8838 original size:21 final size:20
Alignment explanation
Indices: 8812--8851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
8802 TGTTTATTCA
*
8812 AATAATATGTAGTATATATAT
1 AATAATATATAG-ATATATAT
8833 AATAATATATAGATATATA
1 AATAATATATAGATATATA
8852 AACTAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATATATAGATATATAT
Found at i:8874 original size:2 final size:2
Alignment explanation
Indices: 8867--8906 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
8857 ATTCTTCATT
*
8867 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8907 TCAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9897 original size:127 final size:127
Alignment explanation
Indices: 9738--10044 Score: 569
Period size: 127 Copynumber: 2.4 Consensus size: 127
9728 GATTGAATCA
* * *
9738 AATTAATTCTTATAAATATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGTTACTAAATGA
1 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
9803 CAATAATTATTGTATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
66 CAATAATTATTGTATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
*
9865 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGG
1 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
9930 CAATAATTATTGTATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
66 CAATAATTATTGTATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
*
9992 AATTAATTCCTATAATTATTGGTTTGTTTCTTATCTTAATATCAAATATCAAT
1 AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAAT
10045 TATTATTGTC
Statistics
Matches: 175, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 175 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (127 bp):
AATTAATTCCTATAATTATTGGTTTGTTTTTTATCTTAATATCAAATATCAATGATACTAAATGA
CAATAATTATTGTATTTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
Found at i:13228 original size:26 final size:27
Alignment explanation
Indices: 13197--13265 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 27
13187 ATAATATTTT
*
13197 AATTATTCCATTATTTTTT-TAACATA
1 AATTATTCCATTATTTTTTCTAACAAA
*
13223 AATTATTCCATTATTTTTTGCTAAGAAA
1 AATTATTCCATTATTTTTT-CTAACAAA
13251 AATTATTCCATTATT
1 AATTATTCCATTATT
13266 AATTATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 19 0.49
28 20 0.51
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.51
Consensus pattern (27 bp):
AATTATTCCATTATTTTTTCTAACAAA
Found at i:13414 original size:37 final size:37
Alignment explanation
Indices: 13326--13414 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
13316 GCTTTTGGTT
* * * *
13326 TCCAATGTCCTATTTAATTTTGGCTTTAGTCTTTGTT
1 TCCAACGTCCTATTTAATTTTGACTTTAGTCTTTATC
** *
13363 TCCAACGTTGTATTTAATTTT-ACTTTTTGTCTTTATC
1 TCCAACGTCCTATTTAATTTTGAC-TTTAGTCTTTATC
13400 TCCAACGTCCTATTT
1 TCCAACGTCCTATTT
13415 GGGATTAGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 1 0.02
37 41 0.98
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.53
Consensus pattern (37 bp):
TCCAACGTCCTATTTAATTTTGACTTTAGTCTTTATC
Found at i:13598 original size:33 final size:33
Alignment explanation
Indices: 13501--13582 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
13491 TTTTTACACT
*
13501 GAGCCTCCCCACTAGGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTGGGACGGCTCAGCCACGGCG
13534 GAGCCTCCCCACTGGGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTGGGACGGCTCAGCCACGGCG
13567 GAGCCTCCCCACTGGG
1 GAGCCTCCCCACTGGG
13583 GCAGCTTCGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.16, C:0.43, G:0.32, T:0.10
Consensus pattern (33 bp):
GAGCCTCCCCACTGGGACGGCTCAGCCACGGCG
Found at i:13755 original size:33 final size:33
Alignment explanation
Indices: 13656--13774 Score: 154
Period size: 32 Copynumber: 3.7 Consensus size: 33
13646 AAACTAGCCG
* * *
13656 AGCCGCCCCACTGGGGCGGCCTG-CTCTGGCT-A
1 AGCCGCCCCAGTGGGGCGGCCTGTTTATGG-TGA
* *
13688 AGCCGCCCCAATGGGGCGGCCT-TTCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGTTTATGGTGA
13720 AGCCGCCCCAGTGGGGCGGCCTGTTTATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGTTTATGGTGA
*
13753 AGCCGTCCCAGTGGGGCGGCCT
1 AGCCGCCCCAGTGGGGCGGCCT
13775 CGCCGTGGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
31 1 0.01
32 46 0.60
33 30 0.39
ACGTcount: A:0.12, C:0.34, G:0.37, T:0.18
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGTTTATGGTGA
Found at i:16294 original size:11 final size:11
Alignment explanation
Indices: 16251--16288 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16241 TTCCTATGTA
*
16251 AAATAAATTAT
1 AAATTAATTAT
16262 CAAA-TAATTAT
1 -AAATTAATTAT
16273 AAATTAATTAT
1 AAATTAATTAT
16284 AAATT
1 AAATT
16289 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:31587 original size:2 final size:2
Alignment explanation
Indices: 31580--31608 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31570 AGGTGGTTTA
31580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31609 ACTTTACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45384 original size:6 final size:6
Alignment explanation
Indices: 45375--45419 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
45365 GGAATAATAA
45375 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
45420 GTCACTATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:50849 original size:162 final size:165
Alignment explanation
Indices: 50511--50871 Score: 427
Period size: 162 Copynumber: 2.2 Consensus size: 165
50501 CAGGTGTTTA
* * * *
50511 TTAAAAGGTAATTTCAAGATCTACAACTTT--TGATCAGGACTCAAAAGCCAAAATTTATTTTTC
1 TTAAAAGGTTATTGCATGATCTACGACTTTCATGA-CAGGACTCAAAAGCCAAAATTTATTTTTC
* **
50574 GATTAAAAAAAGTGCTTCTGAAATTTGGTGGTTTCAATTGTCGGTCTATATAATATCATATAATT
65 GATTAAAAAAAGTGCTTCCGAAA--T-GTGGTTTCAATTACCGGTCTATATAATATCATATAATT
* * *
50639 TTCGGTTCACATGTTCGATTAAAGTTATTCAAGTGTCAG
127 TTCGGATCACATGTTCAATTAAAGTTATGCAAGTGTCAG
**
50678 TTAAAAGGTTATTGCATGATCTACGACTTTCATGA-AGGACTCAAAAGCCAATTTTTATTTTTCG
1 TTAAAAGGTTATTGCATGATCTACGACTTTCATGACAGGACTCAAAAGCCAAAATTTATTTTTCG
* * *
50742 ATTCAAAAAAA-TGCTTCCG-AA-GTGGTTTCGATTACCGGTTTATTTAATATCATATAATTTTC
66 ATT-AAAAAAAGTGCTTCCGAAATGTGGTTTCAATTACCGGTCTATATAATATCATATAATTTTC
*
50804 -GATC-CATGTGTCCAATTGAAA-TTATGCAAGTGTCGG
130 GGATCACATGT-T-CAATT-AAAGTTATGCAAGTGTCAG
50840 TTAAAAGGTTATTGCATGATGC-ACGACTTTCA
1 TTAAAAGGTTATTGCATGAT-CTACGACTTTCA
50872 AGAAAGACAC
Statistics
Matches: 171, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
160 5 0.03
161 4 0.02
162 83 0.49
163 4 0.02
166 2 0.01
167 63 0.37
168 7 0.04
169 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (165 bp):
TTAAAAGGTTATTGCATGATCTACGACTTTCATGACAGGACTCAAAAGCCAAAATTTATTTTTCG
ATTAAAAAAAGTGCTTCCGAAATGTGGTTTCAATTACCGGTCTATATAATATCATATAATTTTCG
GATCACATGTTCAATTAAAGTTATGCAAGTGTCAG
Found at i:53629 original size:2 final size:2
Alignment explanation
Indices: 53622--53653 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53612 AGCATCTTCC
53622 AT 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 AT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.