Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012126.1 Corchorus capsularis cultivar CVL-1 contig12147, 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: 37402
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:5880 original size:2 final size:2
Alignment explanation
Indices: 5868--5897 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5858 AAACTCAACA
*
5868 AT AT CT 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
5898 TGTGTGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8525 original size:21 final size:20
Alignment explanation
Indices: 8499--8568 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
8489 CATTATTTTT
8499 AAATTAAACAAATAATAATTG
1 AAATTAAA-AAATAATAATTG
* *
8520 AAATTAATTTGAAAT--TAATTAC
1 AAATTAA---AAAATAATAATT-G
8542 AAATTAAAAAATAATAATTG
1 AAATTAAAAAATAATAATTG
8562 AAATTAA
1 AAATTAA
8569 TTATAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
19 4 0.10
20 7 0.18
21 17 0.44
22 7 0.18
23 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATTAAAAAATAATAATTG
Found at i:10895 original size:95 final size:93
Alignment explanation
Indices: 10745--10917 Score: 244
Period size: 95 Copynumber: 1.8 Consensus size: 93
10735 AGTAATGTGG
* * *
10745 TAAAAATGAAATAGGTAAAAAGATATTAGATTTAATTAAATAAAAATATAGTTTTTAGTTGAA-T
1 TAAAAATAAAATAGGTAAAAAGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTT-AACT
10809 AAAACTATAAAAGTAAAATAGTAAAATGC
65 AAAACTATAAAAGTAAAATAGTAAAATGC
*
10838 TAAAAATAAAATA-GT-ATAAGAATATTAGATTTAATAATTAAATAAAAATAGAATTTTTAGTTA
1 TAAAAATAAAATAGGTAAAAAG-ATATTAGA-TT--TAATTAAATAAAAATAGAATTTTTAGTTA
10901 ACTAAAACTATAAAAGT
62 ACTAAAACTATAAAAGT
10918 TTAGCCATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
91 4 0.06
92 10 0.14
93 14 0.20
94 2 0.03
95 41 0.58
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.32
Consensus pattern (93 bp):
TAAAAATAAAATAGGTAAAAAGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTAACTA
AAACTATAAAAGTAAAATAGTAAAATGC
Found at i:11275 original size:20 final size:20
Alignment explanation
Indices: 11247--11287 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11237 GGGTAATTCA
11247 AAAGATTTACAAGAACTCGT
1 AAAGATTTACAAGAACTCGT
*
11267 AAAGTTTTACAAGAACTCGT
1 AAAGATTTACAAGAACTCGT
11287 A
1 A
11288 CTTTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
AAAGATTTACAAGAACTCGT
Found at i:11654 original size:137 final size:140
Alignment explanation
Indices: 11438--11697 Score: 339
Period size: 137 Copynumber: 1.9 Consensus size: 140
11428 ACTATTATAG
*
11438 TTTTACTAAACTAAAAACTCTATTTTTATTTAAATAAATCTAATATATCCTTATAACTATTTCAT
1 TTTTACTAAACTAAAAACTCTATTTTTATTTAAATAAATATAATATA-CCTTATAACTATTTCAT
* * * * *
11503 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATACATTATAATTTTTTAAATATACTTTTA
65 TTTCACCATTTTACTAATTTAATTAAAAAACTTAGATACATTAGAATTTTTAAAATATACTTTTA
11568 TAGTTTTACAA
130 TAGTTTTACAA
* * ** * *
11579 TTTTACTCAACTAAAAATTCTA-TTTT-TTTATTTAATTATAATATA-CTTAT-ACATATTTTAT
1 TTTTACTAAACTAAAAACTCTATTTTTATTTAAATAAATATAATATACCTTATAAC-TATTTCAT
* **
11640 TTTCATCATTTTACTAATTTAATTAAAAAACTTAGATTTATTAGAATTTTTAAAATAT
65 TTTCACCATTTTACTAATTTAATTAAAAAACTTAGATACATTAGAATTTTTAAAATAT
11698 CTATCTATAC
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
136 2 0.02
137 62 0.60
139 15 0.15
140 4 0.04
141 20 0.19
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (140 bp):
TTTTACTAAACTAAAAACTCTATTTTTATTTAAATAAATATAATATACCTTATAACTATTTCATT
TTCACCATTTTACTAATTTAATTAAAAAACTTAGATACATTAGAATTTTTAAAATATACTTTTAT
AGTTTTACAA
Found at i:13344 original size:25 final size:24
Alignment explanation
Indices: 13298--13354 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
13288 GTCGGCCTTG
*
13298 AATTT-TTTAATGTTTAATTATTA
1 AATTTATTTAATATTTAATTATTA
* *
13321 AATTTATTTAATATCTTTATTATTC
1 AATTTATTTAATAT-TTAATTATTA
*
13346 GATTTATTT
1 AATTTATTT
13355 TACAATTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.18
24 7 0.25
25 16 0.57
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:13699 original size:3 final size:3
Alignment explanation
Indices: 13691--13729 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13681 AGGTAAAATT
13691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13730 TAAATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:14184 original size:49 final size:50
Alignment explanation
Indices: 14112--14249 Score: 188
Period size: 49 Copynumber: 2.7 Consensus size: 50
14102 TTAGTAATTA
*
14112 ACATTAAAAAGGGCCAAGGAAATTAGTAATTTAAATATAACCTAA-TATT
1 ACATTAAAAAGGGCCAAAGAAATTAGTAATTTAAATATAACCTAATTATT
*
14161 ACATTAAAAAGAGCCAAAGAAATTAGTAATTTAAATATAACCTAATGTTTATT
1 ACATTAAAAAGGGCCAAAGAAATTAGTAATTTAAATATAACCTAA---TTATT
** * *
14214 ACATTTTAAAGGGCCAAACAAATTAGTAATATAAAT
1 ACATTAAAAAGGGCCAAAGAAATTAGTAATTTAAAT
14250 TAGTATTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
49 43 0.55
53 35 0.45
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (50 bp):
ACATTAAAAAGGGCCAAAGAAATTAGTAATTTAAATATAACCTAATTATT
Found at i:17104 original size:6 final size:6
Alignment explanation
Indices: 17087--17136 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
17077 AATTAAAAGG
* * *
17087 AAAGAA AGAGAA AAAGAA TAAGAA TAAACAA AAAGAAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAAG-AA AAAGAA AAAGAA
17137 GTGAAAACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 26 0.72
7 10 0.28
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:17447 original size:57 final size:58
Alignment explanation
Indices: 17386--17495 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 58
17376 CTTACCTGCA
*
17386 AAAATGGGAGCCAGGAGGTAGGAGGAAGAGAGAGAAGGAGAAATCG-GGGAAAGATTG
1 AAAATGGGAGCCAGGAGATAGGAGGAAGAGAGAGAAGGAGAAATCGAGGGAAAGATTG
* * *
17443 AAAATGGGAGCCGGGAGATAGGAGGAAGAGAGAGAAGGATAAATTGAGGGAAA
1 AAAATGGGAGCCAGGAGATAGGAGGAAGAGAGAGAAGGAGAAATCGAGGGAAA
17496 AGATGAGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 42 0.88
58 6 0.12
ACGTcount: A:0.44, C:0.05, G:0.43, T:0.09
Consensus pattern (58 bp):
AAAATGGGAGCCAGGAGATAGGAGGAAGAGAGAGAAGGAGAAATCGAGGGAAAGATTG
Found at i:18529 original size:20 final size:20
Alignment explanation
Indices: 18514--18551 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18504 TGTCTTTATT
18514 TTCTTA-TTTCTTTCTTTTA
1 TTCTTATTTTCTTTCTTTTA
*
18533 TTGTTATTTTCTTTCTTTT
1 TTCTTATTTTCTTTCTTTT
18552 TATTGGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (20 bp):
TTCTTATTTTCTTTCTTTTA
Found at i:23235 original size:21 final size:20
Alignment explanation
Indices: 23211--23271 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
23201 AATTGGTTAG
23211 ATATGATTAAGTTGCGTTTTA
1 ATAT-ATTAAGTTGCGTTTTA
*
23232 ATAT-TT---TT-CGTATTA
1 ATATATTAAGTTGCGTTTTA
*
23247 AAATAATTAAGTTGCGTTTTA
1 ATAT-ATTAAGTTGCGTTTTA
23268 ATAT
1 ATAT
23272 TTTTCGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
16 2 0.07
17 2 0.07
19 2 0.07
20 2 0.07
21 13 0.43
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
ATATATTAAGTTGCGTTTTA
Found at i:23263 original size:36 final size:36
Alignment explanation
Indices: 23216--23291 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
23206 GTTAGATATG
23216 ATTAAGTTGCGTTTTAATATTTTTCGTATTAAAATA
1 ATTAAGTTGCGTTTTAATATTTTTCGTATTAAAATA
*
23252 ATTAAGTTGCGTTTTAATATTTTTCGTATTGAAATA
1 ATTAAGTTGCGTTTTAATATTTTTCGTATTAAAATA
23288 ATTA
1 ATTA
23292 CTAGATTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (36 bp):
ATTAAGTTGCGTTTTAATATTTTTCGTATTAAAATA
Found at i:23338 original size:20 final size:20
Alignment explanation
Indices: 23297--23337 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
23287 AATTACTAGA
*
23297 TTGCTAAACACTGCCCCCTT
1 TTGCTAAACACCGCCCCCTT
*
23317 TTGCTAAATACCG-CCCCTT
1 TTGCTAAACACCGCCCCCTT
23336 TT
1 TT
23338 TACACTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.20, C:0.37, G:0.10, T:0.34
Consensus pattern (20 bp):
TTGCTAAACACCGCCCCCTT
Found at i:23425 original size:25 final size:25
Alignment explanation
Indices: 23397--23453 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
23387 AACTCTCAAC
*
23397 CTTCAAATC-CCATTTCTAACAACTT
1 CTTCAAATCTCCATTTCTAACAA-AT
*
23422 CTTCAAA-CTTCATTTCTAACAAAT
1 CTTCAAATCTCCATTTCTAACAAAT
23446 CTTCAAAT
1 CTTCAAAT
23454 TCATTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (25 bp):
CTTCAAATCTCCATTTCTAACAAAT
Found at i:23461 original size:24 final size:25
Alignment explanation
Indices: 23407--23459 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
23397 CTTCAAATCC
*
23407 CATTTCTAACAACTTCTTCAAACTT
1 CATTTCTAACAACATCTTCAAACTT
23432 CATTTCTAACAA-ATCTTCAAA-TT
1 CATTTCTAACAACATCTTCAAACTT
23455 CATTT
1 CATTT
23460 TCCTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.26
24 8 0.30
25 12 0.44
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.42
Consensus pattern (25 bp):
CATTTCTAACAACATCTTCAAACTT
Found at i:23498 original size:26 final size:26
Alignment explanation
Indices: 23469--23536 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
23459 TTCCTTCATT
23469 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
23495 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
23521 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
23537 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:23499 original size:15 final size:15
Alignment explanation
Indices: 23469--23536 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
23459 TTCCTTCATT
23469 TTAATCATAAACTAA
1 TTAATCATAAACTAA
23484 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
23495 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
23510 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
23521 TTAAACATAAACTAA
1 TTAATCATAAACTAA
23536 T
1 T
23537 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:26602 original size:15 final size:15
Alignment explanation
Indices: 26558--26603 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
26548 AAAAGGCAGC
*
26558 TTACAACAACTAAAA
1 TTACAACAACTAATA
26573 TTACAACAACT-ATA
1 TTACAACAACTAATA
26587 TTACAACAACTAATA
1 TTACAACAACTAATA
26602 TT
1 TT
26604 CTTTTAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (15 bp):
TTACAACAACTAATA
Found at i:29143 original size:2 final size:2
Alignment explanation
Indices: 29136--29167 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29126 AACCAAGTCA
29136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29168 AGAAGACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34315 original size:15 final size:16
Alignment explanation
Indices: 34288--34329 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
34278 CTTGAAATCT
*
34288 ATAAAAACAAACA-AA
1 ATAAAATCAAACATAA
*
34303 ATTAAATCAAACATAA
1 ATAAAATCAAACATAA
*
34319 GTAAAATCAAA
1 ATAAAATCAAA
34330 ACTAAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (16 bp):
ATAAAATCAAACATAA
Done.