Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012061.1 Corchorus olitorius cultivar O-4 contig12094, 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: 7421
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Found at i:499 original size:4 final size:4
Alignment explanation
Indices: 488--702 Score: 64
Period size: 4 Copynumber: 56.0 Consensus size: 4
478 AAGATTTTTT
* * * *
488 TTTA -TTA TTTA TTCA CT-A TTTA TCTA TTTA TTTA TTT- TTAA CTATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA
* * * * ** *
535 TCTA TTTA TTTA -CTA TTTA TCTA TTTA TTTT TTTAA ACTA -TTA TCTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
* * ** * *
582 TTTA TTTA -CTA TTTT TTTA TTT- TTT- TTTCA ACTA -TTA TCTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA
* * *
627 TTTA -CTA TTTA TCTT- TTTA TTTA -TT- TTTA ATTA -TTA TCTA TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
671 TTTA -CTA TTTA TTTTT TTTA TTTA TTAA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
703 GCTATTATCT
Statistics
Matches: 149, Mismatches: 42, Indels: 40
0.65 0.18 0.17
Matches are distributed among these distances:
3 34 0.23
4 104 0.70
5 9 0.06
6 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:517 original size:19 final size:19
Alignment explanation
Indices: 511--647 Score: 75
Period size: 19 Copynumber: 6.9 Consensus size: 19
501 CACTATTTAT
*
511 CTATTTATTTATTT-TTAA
1 CTATTTATCTATTTATTAA
*
529 CTA-TTATCTATTTATTTA
1 CTATTTATCTATTTATTAA
547 CTATTTATCTATTTATTTTTTTAAA
1 CTATTTATCTATTTA-----TT-AA
*
572 CTA-TTATCTATTTATTTA
1 CTATTTATCTATTTATTAA
* * *
590 CTATTTTTTTATTTTTTTTTCAA
1 CTATTTATCTA---TTTATT-AA
* *
613 CTA-TTATCTACTTATTTA
1 CTATTTATCTATTTATTAA
*
631 CTATTTATCTTTTTATT
1 CTATTTATCTATTTATT
648 TATTTTTAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 27
0.68 0.11 0.20
Matches are distributed among these distances:
17 9 0.10
18 17 0.19
19 33 0.37
22 10 0.11
23 4 0.04
24 13 0.14
25 4 0.04
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (19 bp):
CTATTTATCTATTTATTAA
Found at i:550 original size:44 final size:44
Alignment explanation
Indices: 489--726 Score: 299
Period size: 44 Copynumber: 5.5 Consensus size: 44
479 AGATTTTTTT
*
489 TTAT-TATTTATTCACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
*
532 TTATCTATTTATTTACTATTTATCTATTTATTT-TTTTAAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
*
575 TTATCTATTTATTTACTA-TT-T-T-TTTATTTTTTTTTCAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTT-AACTA
* * *
616 TTATCTACTTATTTACTATTTATCTTTTTATTTATTTTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * *
660 TTATCTATTTATTTACTATTTATTTTTTTTATTTATTAATTTAGCTA
1 TTATCTATTTATTTACTATTTA-TCTATTTATTTATT--TTTAACTA
* *
707 TTATCTATTCATTTATTATT
1 TTATCTATTTATTTACTATT
727 ATTATCCTTT
Statistics
Matches: 173, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
39 7 0.04
40 5 0.03
41 23 0.13
42 4 0.02
43 32 0.18
44 53 0.31
45 25 0.14
47 24 0.14
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:633 original size:84 final size:84
Alignment explanation
Indices: 512--694 Score: 280
Period size: 84 Copynumber: 2.2 Consensus size: 84
502 ACTATTTATC
* *
512 TATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATCTATTTATTT-TTTTAAACTAT
1 TATTTATTTTTTTTTAACTATTATCTACTTATTTACTATTTATCTATTTATTTATTTTAAACTAT
576 TATCTATTTATTTACTATT
66 TATCTATTTATTTACTATT
* * * *
595 TTTTTATTTTTTTTTCAACTATTATCTACTTATTTACTATTTATCTTTTTATTTATTTTTAATTA
1 TATTTATTTTTTTTT-AACTATTATCTACTTATTTACTATTTATCTATTTATTTATTTTAAACTA
660 TTATCTATTTATTTACTATT
65 TTATCTATTTATTTACTATT
*
680 TATTT-TTTTTATTTA
1 TATTTATTTTTTTTTA
695 TTAATTTAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
83 14 0.16
84 44 0.49
85 32 0.36
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (84 bp):
TATTTATTTTTTTTTAACTATTATCTACTTATTTACTATTTATCTATTTATTTATTTTAAACTAT
TATCTATTTATTTACTATT
Found at i:702 original size:32 final size:35
Alignment explanation
Indices: 632--731 Score: 91
Period size: 36 Copynumber: 2.8 Consensus size: 35
622 ACTTATTTAC
*
632 TATTTATCTTTTTATTTATTTTTAATTATTATCTATT
1 TATTTATCTATTTATTTATTTTTAATTATTA--TATT
*
669 TATTTA-CTATTTATTT-TTTTTATTTATTA-ATT
1 TATTTATCTATTTATTTATTTTTAATTATTATATT
* *
701 TAGCTATTATCTATTCATTTATTATT-ATTAT
1 TA--T-TTATCTATTTATTTATTTTTAATTAT
732 CCTTTTTTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
32 5 0.09
34 1 0.02
35 15 0.28
36 22 0.42
37 10 0.19
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (35 bp):
TATTTATCTATTTATTTATTTTTAATTATTATATT
Found at i:841 original size:33 final size:33
Alignment explanation
Indices: 771--841 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
761 TCTCTATACC
* * *
771 TATTTATCTTTTTCTTTTTTCAAATTTATTTAT
1 TATTTATCTATTACTTTTTTCAAATTTATTTAA
* *
804 TATTTATCTATTACTTTTTT-TATTTTATTTTAA
1 TATTTATCTATTACTTTTTTCAAATTTA-TTTAA
837 TATTT
1 TATTT
842 TTTTAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (33 bp):
TATTTATCTATTACTTTTTTCAAATTTATTTAA
Found at i:2677 original size:27 final size:27
Alignment explanation
Indices: 2647--2746 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
2637 AGTGAACTTA
*
2647 AAATGACCGAAATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
2674 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
2701 AGATGACCAAAATGCCCCTGAACGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
2728 AAATGACTAACATGCCCCT
1 AAATGACCAAAATGCCCCT
2747 TATGTGACCC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTGC
Found at i:3378 original size:22 final size:22
Alignment explanation
Indices: 3350--3470 Score: 61
Period size: 22 Copynumber: 5.5 Consensus size: 22
3340 TCGTATCAGG
3350 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAGA
* * *
3372 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAACAAAATTTCATAAGA
* ** * *
3393 AGATTCTCGAAATTCCAT-AGTA
1 AGGTTAACAAAATTTCATAAG-A
** **
3415 TCGTTATTAAAATTTCAT-AGTA
1 AGGTTAACAAAATTTCATAAG-A
* *
3437 AGGTTATCAAAATTTCATAAGG
1 AGGTTAACAAAATTTCATAAGA
3459 AGG-TAATCAAAA
1 AGGTTAA-CAAAA
3471 ATAGTGTAAT
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
21 16 0.22
22 54 0.75
23 2 0.03
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAGA
Found at i:4575 original size:22 final size:22
Alignment explanation
Indices: 4550--4629 Score: 124
Period size: 22 Copynumber: 3.5 Consensus size: 22
4540 AATTTTGGAA
*
4550 AGCATTATTTACCACTTTGCAG
1 AGCATTATTTTCCACTTTGCAG
*
4572 AGCATTATTTTCTACTTTGCAG
1 AGCATTATTTTCCACTTTGCAG
4594 AGCATTATTTTCCACTTTGCAG
1 AGCATTATTTTCCACTTTGCAG
4616 AGCGCATTATTTTC
1 A--GCATTATTTTC
4630 TTCAACTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
22 42 0.79
24 11 0.21
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (22 bp):
AGCATTATTTTCCACTTTGCAG
Done.