Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010770.1 Corchorus capsularis cultivar CVL-1 contig10791, 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: 9681
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:404 original size:18 final size:18
Alignment explanation
Indices: 383--438 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
373 ATAAAAGTAA
383 ATATATATTTATTATAAT
1 ATATATATTTATTATAAT
401 ATATATA---ATTATAAT
1 ATATATATTTATTATAAT
416 -TATA-ATTTA-TATAAT
1 ATATATATTTATTATAAT
*
431 AAATATAT
1 ATATATAT
439 ATAAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 14 0.44
16 4 0.12
17 2 0.06
18 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTTATTATAAT
Found at i:413 original size:15 final size:15
Alignment explanation
Indices: 382--508 Score: 81
Period size: 13 Copynumber: 8.5 Consensus size: 15
372 TATAAAAGTA
*
382 AATATATATTTATTAT
1 AATATATA-TAATTAT
398 AATATATATAATTAT
1 AATATATATAATTAT
* *
413 AATTATAATTTATATAAT
1 AA-TAT-ATATA-ATTAT
431 AAATATATATAA--AGT
1 -AATATATATAATTA-T
446 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
461 -TTATATAT-ATTAT
1 AATATATATAATTAT
*
474 -ATATATA-AAGTA-
1 AATATATATAATTAT
*
486 AATACATATAATTAT
1 AATATATATAATTAT
501 AATATATA
1 AATATATA
509 ATTTATATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
13 24 0.27
14 11 0.12
15 24 0.27
16 12 0.14
17 8 0.09
18 7 0.08
19 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:428 original size:41 final size:41
Alignment explanation
Indices: 383--517 Score: 88
Period size: 41 Copynumber: 3.3 Consensus size: 41
373 ATAAAAGTAA
*
383 ATATATATTTATTATAATATATATAATTATAATTATAATTT
1 ATATATATATATTATAATATATATAATTATAATTATAATTT
* * *
424 ATATA-ATA-AATAT-ATATAAAGTAAATATATAA-T-TACTTT
1 ATATATATATATTATAATATATA-T-AAT-TATAATTATAATTT
* *
463 ATATATATTATATATATAA-AGTAAATACA-TATAATTATAATAT
1 ATATATA-TATAT-TATAATA-TATATA-ATTATAATTATAATTT
*
506 ATA-ATTTATATT
1 ATATATATATATT
518 TATTATTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
38 6 0.08
39 15 0.20
40 8 0.11
41 22 0.30
42 5 0.07
43 13 0.18
44 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
ATATATATATATTATAATATATATAATTATAATTATAATTT
Found at i:506 original size:39 final size:38
Alignment explanation
Indices: 352--516 Score: 126
Period size: 39 Copynumber: 4.2 Consensus size: 38
342 CGAGTTATTT
* * * *
352 ATTTATATATAAAATAAAGTTATAAAAGTA-AATATAT-
1 ATTTATATATAAAGTAAA-TAATATAATTATAATATATA
*
389 ATTTAT-TATAATA-TATATAATTATAATTATAATTTATATA
1 ATTTATATATAA-AGTAAATAA-TATAATTATAA--TATATA
* *
429 ATAAATATATATAAAGTAAAT-ATATAATTACT-TTATATA
1 AT--TTATATATAAAGTAAATAATATAATTA-TAATATATA
468 TATTATATATATAAAGTAAATACATATAATTATAATATATA
1 -ATT-TATATATAAAGTAAATA-ATATAATTATAATATATA
509 ATTTATAT
1 ATTTATAT
517 TTATTATTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
35 2 0.02
36 14 0.14
37 9 0.09
39 32 0.31
40 8 0.08
41 23 0.22
42 6 0.06
43 9 0.09
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (38 bp):
ATTTATATATAAAGTAAATAATATAATTATAATATATA
Found at i:509 original size:13 final size:12
Alignment explanation
Indices: 399--516 Score: 82
Period size: 13 Copynumber: 9.5 Consensus size: 12
389 ATTTATTATA
399 ATATATATAATT
1 ATATATATAATT
411 ATA-ATTATAATT
1 ATATA-TATAATT
*
423 -TATATAATAAAT
1 ATATAT-ATAATT
*
435 ATATATA-AAGT
1 ATATATATAATT
*
446 AAATATATAATT
1 ATATATATAATT
*
458 ACTTTATATATATT
1 A-TATATATA-ATT
*
472 ATATATATAAAGTAA
1 ATATATAT-AA-T-T
*
487 ATACATATAATT
1 ATATATATAATT
499 ATAATATATAATT
1 AT-ATATATAATT
512 -TATAT
1 ATATAT
517 TTATTATTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
11 17 0.20
12 24 0.29
13 28 0.33
14 8 0.10
15 7 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATATATATAATT
Found at i:1690 original size:10 final size:10
Alignment explanation
Indices: 1669--1723 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
1659 AAATAAAGAA
1669 AACAAG-AAG
1 AACAAGTAAG
1678 AACAAGTAAG
1 AACAAGTAAG
1688 AACAAGTAAG
1 AACAAGTAAG
** *
1698 AACTTGTATG
1 AACAAGTAAG
*
1708 AAAAAGTGAAG
1 AACAAGT-AAG
1719 AACAA
1 AACAA
1724 CAAAGAACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
9 6 0.17
10 24 0.67
11 6 0.17
ACGTcount: A:0.58, C:0.09, G:0.20, T:0.13
Consensus pattern (10 bp):
AACAAGTAAG
Found at i:5183 original size:33 final size:32
Alignment explanation
Indices: 5146--5214 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
5136 CTTGCTCAAC
** *
5146 TTGTAAAGGTGTGATGAAGGCCCGTGAACTTCA
1 TTGTAAAGACGTGATGAAGGCCCG-CAACTTCA
*
5179 TTGTAACGACGTGATGAAGGCCCGCAACTTCA
1 TTGTAAAGACGTGATGAAGGCCCGCAACTTCA
5211 TTGT
1 TTGT
5215 GTGTAAGAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (32 bp):
TTGTAAAGACGTGATGAAGGCCCGCAACTTCA
Found at i:9491 original size:20 final size:21
Alignment explanation
Indices: 9454--9492 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9444 TGAAAAAATA
9454 ATATGATTTGTTTGATTTACT
1 ATATGATTTGTTTGATTTACT
* *
9475 ATAT-ATTTTTTTTATTTA
1 ATATGATTTGTTTGATTTA
9493 AATGGGCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (21 bp):
ATATGATTTGTTTGATTTACT
Done.