Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008997.1 Corchorus capsularis cultivar CVL-1 contig09018, 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: 31108
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:363 original size:7 final size:6
Alignment explanation
Indices: 333--366 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
323 AAAGCAAAGC
*
333 AAATCT AAATCT AAATCC AAATCT AAAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT -AAATCT AAA
367 GCAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (6 bp):
AAATCT
Found at i:371 original size:18 final size:17
Alignment explanation
Indices: 328--372 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
318 AAAATAAAGC
328 AAAGCAAATCTAAATCT
1 AAAGCAAATCTAAATCT
*
345 AAATCCAAATCTAAAATCT
1 AAA-GCAAATCT-AAATCT
364 AAAGCAAAT
1 AAAGCAAAT
373 TAATAAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAGCAAATCTAAATCT
Found at i:379 original size:13 final size:13
Alignment explanation
Indices: 363--410 Score: 96
Period size: 13 Copynumber: 3.7 Consensus size: 13
353 ATCTAAAATC
363 TAAAGCAAATTAA
1 TAAAGCAAATTAA
376 TAAAGCAAATTAA
1 TAAAGCAAATTAA
389 TAAAGCAAATTAA
1 TAAAGCAAATTAA
402 TAAAGCAAA
1 TAAAGCAAA
411 CAATAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:7013 original size:41 final size:41
Alignment explanation
Indices: 6966--7045 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
6956 TAAATAAAAA
*
6966 TTAAAAAGCAGAAACAGAAA-AATAAAAAT-ATATTTTTTTAT
1 TTAAAAAG-AAAAACAGAAAGAA-AAAAATAATATTTTTTTAT
* *
7007 TTAAAAAGAAAAACGGAAAGAAAAAATTAATATTTTTTT
1 TTAAAAAGAAAAACAGAAAGAAAAAAATAATATTTTTTT
7046 TTAAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 14 0.41
41 20 0.59
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (41 bp):
TTAAAAAGAAAAACAGAAAGAAAAAAATAATATTTTTTTAT
Found at i:7465 original size:18 final size:18
Alignment explanation
Indices: 7437--7481 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
7427 AAAACAAAGC
7437 AAATCAAATCT-AAATCT
1 AAATCAAATCTAAAATCT
7454 AAATCTAAATCTAAAATCT
1 AAATC-AAATCTAAAATCT
*
7473 AAAGCAAAT
1 AAATCAAAT
7482 TAATAAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATCAAATCTAAAATCT
Found at i:7472 original size:7 final size:6
Alignment explanation
Indices: 7437--7475 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
7427 AAAACAAAGC
7437 AAATC- AAATCT AAATCT AAATCT AAATCT AAAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT -AAATCT AAA
7476 GCAAATTAAT
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:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:12753 original size:17 final size:19
Alignment explanation
Indices: 12731--12766 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
12721 TAATCAAGGT
12731 CTAAACTAA-ATA-ATTAA
1 CTAAACTAAGATAGATTAA
12748 CTAAACTAAGATAGATTAA
1 CTAAACTAAGATAGATTAA
12767 AGGCCCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (19 bp):
CTAAACTAAGATAGATTAA
Found at i:24165 original size:39 final size:39
Alignment explanation
Indices: 24122--24200 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
24112 TAGAATTTAA
24122 ATCTAAAATTAAATTCTTACCTTAATTATTAGGCAATAT
1 ATCTAAAATTAAATTCTTACCTTAATTATTAGGCAATAT
24161 ATCTAAAATTAAATTCTTACCTTAATTATTAGGCAATAT
1 ATCTAAAATTAAATTCTTACCTTAATTATTAGGCAATAT
24200 A
1 A
24201 ACAAGCGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.41
Consensus pattern (39 bp):
ATCTAAAATTAAATTCTTACCTTAATTATTAGGCAATAT
Found at i:25414 original size:17 final size:18
Alignment explanation
Indices: 25389--25422 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25379 AATTTTTAAA
25389 AAAATATATATTTTTTTT
1 AAAATATATATTTTTTTT
25407 AAAA-ATATATTTTTTT
1 AAAATATATATTTTTTT
25423 AATCAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAAATATATATTTTTTTT
Done.