Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002408.1 Corchorus olitorius cultivar O-4 contig02408, 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, 727
Length: 1213
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Found at i:377 original size:15 final size:16
Alignment explanation
Indices: 353--386 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
343 AGAAATTATA
353 TTATATATATTTCTAT
1 TTATATATATTTCTAT
369 TTATA-ATATTTCTAT
1 TTATATATATTTCTAT
384 TTA
1 TTA
387 GAAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATATATTTCTAT
Found at i:454 original size:21 final size:21
Alignment explanation
Indices: 428--493 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
418 ATTAAGTTAC
428 TAAATTATTATTATAATAATA
1 TAAATTATTATTATAATAATA
* *
449 TAAATTTTTATTATAATATTAGA
1 TAAATTATTATTATAATA--ATA
*
472 TATAATTA-TAATATAATAATA
1 TA-AATTATTATTATAATAATA
493 T
1 T
494 CTAATATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 20 0.54
23 13 0.35
24 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAATTATTATTATAATAATA
Found at i:478 original size:24 final size:24
Alignment explanation
Indices: 432--492 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
422 AGTTACTAAA
*
432 TTATTATTATAATAATATAAATTT
1 TTATTATAATAATAATATAAATTT
*
456 TTATTATAATATTAGATAT-AA-TT
1 TTATTATAATAATA-ATATAAATTT
* *
479 ATAATATAATAATA
1 TTATTATAATAATA
493 TCTAATATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 14 0.45
25 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATTATAATAATAATATAAATTT
Found at i:555 original size:16 final size:16
Alignment explanation
Indices: 490--560 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
480 TAATATAATA
490 ATATCTAATATAG-ATT
1 ATAT-TAATATAGAATT
* *
506 -TA-TAA-ATCGAAAT
1 ATATTAATATAGAATT
**
519 ATATTAATATATTA-T
1 ATATTAATATAGAATT
534 ATTATTAATATAGAATT
1 A-TATTAATATAGAATT
551 ATATTAATAT
1 ATATTAATAT
561 TATAATAGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.07
13 5 0.12
14 2 0.05
15 7 0.17
16 23 0.55
17 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (16 bp):
ATATTAATATAGAATT
Found at i:561 original size:22 final size:24
Alignment explanation
Indices: 524--577 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
514 GAAATATATT
524 AATATATTATATTATTA-ATATAGA
1 AATATATTATATTATTATA-ATAGA
*
548 ATTATATTA-A-TATTATAATAGA
1 AATATATTATATTATTATAATAGA
570 AATATATT
1 AATATATT
578 CTAATAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 17 0.63
23 2 0.07
24 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
AATATATTATATTATTATAATAGA
Found at i:576 original size:16 final size:16
Alignment explanation
Indices: 557--589 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
547 AATTATATTA
557 ATATTATAATAGAAAT
1 ATATTATAATAGAAAT
*
573 ATATTCTAATAGAAAT
1 ATATTATAATAGAAAT
589 A
1 A
590 GAAGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
ATATTATAATAGAAAT
Found at i:674 original size:20 final size:19
Alignment explanation
Indices: 646--757 Score: 63
Period size: 20 Copynumber: 5.8 Consensus size: 19
636 ATAGAATAAA
*
646 AATAGAAATTAATAACAACT
1 AATAAAAATTAATAACAA-T
* *
666 AATATAAATTAATAATAATT
1 AATAAAAATTAATAACAA-T
*
686 GATATAAAAATTTAATAATAA-
1 -A-ATAAAAA-TTAATAACAAT
*
707 AA-AAAAATAGAAT-A-AA-
1 AATAAAAAT-TAATAACAAT
*
723 AATAGAAATTAATAACAACT
1 AATAAAAATTAATAACAA-T
*
743 AATATAAATTAATAA
1 AATAAAAATTAATAA
758 TAATTGATAG
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
16 7 0.09
17 8 0.11
18 10 0.13
19 1 0.01
20 32 0.43
21 1 0.01
22 6 0.08
23 10 0.13
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAAAAATTAATAACAAT
Found at i:782 original size:77 final size:77
Alignment explanation
Indices: 595--775 Score: 317
Period size: 77 Copynumber: 2.3 Consensus size: 77
585 AAATAGAAGT
* *
595 ATTAATAATAAATAATATAAAAAATTTAATAATAAAAAAAAATAGAATAAAAATAGAAATTAATA
1 ATTAATAATAATTGATAT-AAAAATTTAATAATAAAAAAAAATAGAATAAAAATAGAAATTAATA
660 ACAACTAATATAA
65 ACAACTAATATAA
673 ATTAATAATAATTGATATAAAAATTTAATAATAAAAAAAAATAGAATAAAAATAGAAATTAATAA
1 ATTAATAATAATTGATATAAAAATTTAATAATAAAAAAAAATAGAATAAAAATAGAAATTAATAA
738 CAACTAATATAA
66 CAACTAATATAA
*
750 ATTAATAATAATTGATAGTAAGAATT
1 ATTAATAATAATTGATA-TAAAAATT
776 GATAATATAG
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
77 76 0.77
78 23 0.23
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (77 bp):
ATTAATAATAATTGATATAAAAATTTAATAATAAAAAAAAATAGAATAAAAATAGAAATTAATAA
CAACTAATATAA
Found at i:787 original size:18 final size:18
Alignment explanation
Indices: 764--799 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
754 ATAATAATTG
764 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
782 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
800 CATTTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATAGTAAGAATTGATAAT
Found at i:827 original size:17 final size:17
Alignment explanation
Indices: 807--857 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
797 AATCATTTGA
807 ATTGATATATAATTTAG
1 ATTGATATATAATTTAG
824 ATTG---T-TAATTT-G
1 ATTGATATATAATTTAG
836 AATTGATATATAATTTAG
1 -ATTGATATATAATTTAG
854 ATTG
1 ATTG
858 TTAATTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 1 0.04
13 10 0.36
14 1 0.04
16 1 0.04
17 14 0.50
18 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (17 bp):
ATTGATATATAATTTAG
Found at i:835 original size:30 final size:30
Alignment explanation
Indices: 801--863 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
791 ATTGATAATC
801 ATTTGAATTGATATATAATTTAGATTGTTA
1 ATTTGAATTGATATATAATTTAGATTGTTA
831 ATTTGAATTGATATATAATTTAGATTGTTA
1 ATTTGAATTGATATATAATTTAGATTGTTA
861 ATT
1 ATT
864 GGTTTAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.51
Consensus pattern (30 bp):
ATTTGAATTGATATATAATTTAGATTGTTA
Done.