Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013801.1 Corchorus capsularis cultivar CVL-1 contig13822, 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: 20255
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:274 original size:15 final size:14
Alignment explanation
Indices: 254--294 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
244 GCTATGCTCA
*
254 TCTTTTTTTTTTCTT
1 TCTTTTTTTTTT-GT
269 TCTTTTCTTTTTTGT
1 TCTTTT-TTTTTTGT
284 TCTTTTTTTTT
1 TCTTTTTTTTT
295 AGATTTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (14 bp):
TCTTTTTTTTTTGT
Found at i:286 original size:10 final size:9
Alignment explanation
Indices: 258--293 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
248 TGCTCATCTT
258 TTTTTTTTC
1 TTTTTTTTC
*
267 TTTCTTTTC
1 TTTTTTTTC
276 TTTTTTGTTC
1 TTTTTT-TTC
286 TTTTTTTT
1 TTTTTTTT
294 TAGATTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:293 original size:19 final size:19
Alignment explanation
Indices: 257--292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
247 ATGCTCATCT
*
257 TTTTTTTTTCTTTCTTTTC
1 TTTTTTGTTCTTTCTTTTC
276 TTTTTTGTTCTTT-TTTT
1 TTTTTTGTTCTTTCTTTT
293 TTAGATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTCTTTCTTTTC
Found at i:7531 original size:21 final size:21
Alignment explanation
Indices: 7505--7546 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7495 TTGATAAGAA
7505 AAGAACTGACAAGATTTGAAT
1 AAGAACTGACAAGATTTGAAT
7526 AAGAACTGACAAGATTTGAAT
1 AAGAACTGACAAGATTTGAAT
7547 TATGACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (21 bp):
AAGAACTGACAAGATTTGAAT
Found at i:13527 original size:29 final size:30
Alignment explanation
Indices: 13461--13531 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 30
13451 GCGGCGTCCA
13461 ACGTGGCATGCCACGTGGACAAAAAAAATGAC
1 ACGTGGCATGCCACGTGGAC--AAAAAATGAC
13493 ACGTGGCATGCCACGTGGAC-AAAAATGAC
1 ACGTGGCATGCCACGTGGACAAAAAATGAC
*
13522 ATGTGGCATG
1 ACGTGGCATG
13532 TATCCTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 18 0.47
32 20 0.53
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.15
Consensus pattern (30 bp):
ACGTGGCATGCCACGTGGACAAAAAATGAC
Found at i:13601 original size:31 final size:31
Alignment explanation
Indices: 13547--13684 Score: 107
Period size: 31 Copynumber: 4.5 Consensus size: 31
13537 TTTTGTGCAC
* * * * **
13547 GTGGCATGCCATGTGCCATTTTTTGAAACAT
1 GTGGCATACCACGTGTCACTTTTTGGTACAT
*
13578 GTGGCATACCACGTGTCACTTTTTGGTACAC
1 GTGGCATACCACGTGTCACTTTTTGGTACAT
* * *
13609 GTGGCGTGA-CATGTGTCACTTTTGGGTACAT
1 GTGGCAT-ACCACGTGTCACTTTTTGGTACAT
* * * * *
13640 GTGGCGTGCCACATATCACTTTTTGGTACAC
1 GTGGCATACCACGTGTCACTTTTTGGTACAT
* *
13671 GTGGCGTGCCACGT
1 GTGGCATACCACGT
13685 CGGACACCGT
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
GTGGCATACCACGTGTCACTTTTTGGTACAT
Found at i:13610 original size:62 final size:62
Alignment explanation
Indices: 13544--13681 Score: 177
Period size: 62 Copynumber: 2.2 Consensus size: 62
13534 TCCTTTTGTG
* * * * *
13544 CACGTGGCATGCCATGTGCCATTTTTTGAAACATGTGGCATACCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCATGTGCCACTTTTGGAAACATGTGGCATACCACATATCACTTTTTGGTA
* * ** * *
13606 CACGTGGCGTGACATGTGTCACTTTTGGGTACATGTGGCGTGCCACATATCACTTTTTGGTA
1 CACGTGGCGTGCCATGTGCCACTTTTGGAAACATGTGGCATACCACATATCACTTTTTGGTA
13668 CACGTGGCGTGCCA
1 CACGTGGCGTGCCA
13682 CGTCGGACAC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (62 bp):
CACGTGGCGTGCCATGTGCCACTTTTGGAAACATGTGGCATACCACATATCACTTTTTGGTA
Found at i:14393 original size:22 final size:21
Alignment explanation
Indices: 14359--14399 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14349 GTGGATTTCC
* *
14359 TCTATTTGGTACCCACTCCCCT
1 TCTATTCGATACCCA-TCCCCT
14381 TCTATTCGATACCCATCCC
1 TCTATTCGATACCCATCCC
14400 TCATTTTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.41, G:0.07, T:0.34
Consensus pattern (21 bp):
TCTATTCGATACCCATCCCCT
Done.