Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013208.1 Corchorus capsularis cultivar CVL-1 contig13229, 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: 33191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:5352 original size:20 final size:22
Alignment explanation
Indices: 5316--5355 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5306 CAAATTATGC
5316 ATATTTTTATAGCTATTTTTCT
1 ATATTTTTATAGCTATTTTTCT
5338 ATATTTTT-T-GCTATTTTT
1 ATATTTTTATAGCTATTTTT
5356 ATATGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (22 bp):
ATATTTTTATAGCTATTTTTCT
Found at i:5366 original size:20 final size:20
Alignment explanation
Indices: 5327--5366 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5317 TATTTTTATA
* *
5327 GCTATTTTTCTATATTTTTT
1 GCTATTTTTATATATGTTTT
*
5347 GCTATTTTTATATGTGTTTT
1 GCTATTTTTATATATGTTTT
5367 TACCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATATGTTTT
Found at i:6893 original size:13 final size:13
Alignment explanation
Indices: 6875--6922 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
6865 ATAATTATTG
*
6875 TTTGCTTCATTAA
1 TTTGCTTTATTAA
6888 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
6901 ATTGCTTTATTAA
1 TTTGCTTTATTAA
6914 TTTGCTTTA
1 TTTGCTTTA
6923 GATTTAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.58
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:6938 original size:6 final size:6
Alignment explanation
Indices: 6919--6957 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
6909 ATTAATTTGC
6919 TTTAGA TTTAAGA TTTAGA TTTAGA TTTAGA TTT-GA TTT
1 TTTAGA TTT-AGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
6958 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:9166 original size:71 final size:69
Alignment explanation
Indices: 9039--9171 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 69
9029 TTGCTTGAAA
* ** * *
9039 TGCATTGTCATTATATTTATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTTTTCC
1 TGCATTGTCATTATATTAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTTTCC
9104 TTAG
66 TTAG
* *
9108 TGCATTGTCTTTATATATAATTTTAGCATTCAGATGTATTTAAATGGTGCTCCCACCATTTTTT
1 TGCATTGTCATTATAT-TAATTTTAGCATTCAGATGTAATT-AATGGTGCTCCCACCATTTTTT
9172 CATTAGTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 15 0.27
70 20 0.36
71 20 0.36
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (69 bp):
TGCATTGTCATTATATTAATTTTAGCATTCAGATGTAATTAATGGTGCTCCCACCATTTTTTTCC
TTAG
Found at i:13938 original size:6 final size:6
Alignment explanation
Indices: 13927--13953 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13917 AAAGCAAAGC
13927 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
13954 ACAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:15471 original size:17 final size:17
Alignment explanation
Indices: 15449--15484 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15439 AAACAATAAG
15449 TTTTCACTTTTCTTGTC
1 TTTTCACTTTTCTTGTC
15466 TTTTCACTTTTCTTGTC
1 TTTTCACTTTTCTTGTC
15483 TT
1 TT
15485 CAGGACCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.22, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTCACTTTTCTTGTC
Found at i:20125 original size:42 final size:42
Alignment explanation
Indices: 20066--20275 Score: 359
Period size: 42 Copynumber: 5.0 Consensus size: 42
20056 GCGAATTAAC
* *
20066 AATATACATGCATTTTGGGTATATCATTTTGGTTGTCCTGTG
1 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
20108 AATATA-ACTGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
1 AATATACA-TGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
*
20150 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCTGTG
1 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
*
20192 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCATG
1 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
*
20234 AATATGCATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
1 AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
20276 TACTTTGTGT
Statistics
Matches: 159, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
41 1 0.01
42 157 0.99
43 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (42 bp):
AATATACATGCATTTTGGGTATATCATTTTGCTTGTCCCGTG
Found at i:24793 original size:2 final size:2
Alignment explanation
Indices: 24788--24815 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24778 AAAAAACAAA
24788 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
24816 TAATTTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28531 original size:17 final size:17
Alignment explanation
Indices: 28493--28532 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28483 AAAGTTCATT
28493 AAAAAGAAGAAAAAATA
1 AAAAAGAAGAAAAAATA
*
28510 CAAAAGAAGAAGAAAA-A
1 AAAAAGAAGAA-AAAATA
28527 AAAAAG
1 AAAAAG
28533 CCTGCAGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAGAAGAAAAAATA
Found at i:32294 original size:6 final size:6
Alignment explanation
Indices: 32283--32328 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
32273 AATATTTATC
32283 TATCTA TATCTA TATCTA TCTATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA --TATCTA TATCTA TATCTA TATCTA TAT
32329 TAAAAAGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
8 6 0.16
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:32294 original size:10 final size:10
Alignment explanation
Indices: 32279--32315 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
32269 GTTCAATATT
32279 TATCTATCTA
1 TATCTATCTA
* *
32289 TATCTATATC
1 TATCTATCTA
32299 TATCTATCTA
1 TATCTATCTA
32309 TATCTAT
1 TATCTAT
32316 ATCTATACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (10 bp):
TATCTATCTA
Found at i:32302 original size:20 final size:20
Alignment explanation
Indices: 32274--32326 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
32264 TCAAAGTTCA
*
32274 ATATTTATCTATCTATATCT
1 ATATCTATCTATCTATATCT
32294 ATATCTATCTATCTATATCT
1 ATATCTATCTATCTATATCT
32314 ATATCTATACTAT
1 ATATCTAT-CTAT
32327 ATTAAAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATCTATCTATCTATATCT
Done.