Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000866.1 Corchorus olitorius cultivar O-4 contig00866, 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, 768
Length: 1280
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Found at i:496 original size:24 final size:24
Alignment explanation
Indices: 469--529 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
459 TAATAAAAAA
*
469 AGATAAATAGGTATAGAG-ATAAAT
1 AGATAAATAGGTACAGAGAAT-AAT
*
493 AGATAAATAGATACAGAGAATAAT
1 AGATAAATAGGTACAGAGAATAAT
*
517 AAATAAATAGGTA
1 AGATAAATAGGTA
530 GCTAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.18, T:0.23
Consensus pattern (24 bp):
AGATAAATAGGTACAGAGAATAAT
Found at i:540 original size:3 final size:3
Alignment explanation
Indices: 532--558 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
522 AATAGGTAGC
532 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
559 CAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:593 original size:4 final size:4
Alignment explanation
Indices: 578--753 Score: 75
Period size: 4 Copynumber: 44.8 Consensus size: 4
568 AGATAATGGC
* * * * *
578 TAAA TTAA TAAA TAAA -AAGA TAAA T-AG CAAA TAAA TAGA T-AA TAAT
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* ** * **
624 TAAA TTAA TAAA TAAA -AAGA TAAA -ATG TAAA TAAA TAGA T-AA TAGTT
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TA-AA
* * *
671 TAAAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA
1 T-AAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA
* *
717 -AAA TAAA TAAA TAAA TAAA T-AG TAAA TAAA TAGA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
754 TAGTTTAAAA
Statistics
Matches: 123, Mismatches: 32, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
3 18 0.15
4 92 0.75
5 10 0.08
6 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:609 original size:27 final size:27
Alignment explanation
Indices: 560--619 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
550 TAATAATAAC
* * *
560 AAATAAATAGATAATGGCTAAATTAAT
1 AAATAAAAAGATAATAGCTAAATAAAT
587 AAATAAAAAGATAAATAGC-AAATAAAT
1 AAATAAAAAGAT-AATAGCTAAATAAAT
*
614 AGATAA
1 AAATAA
620 TAATTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.23
Consensus pattern (27 bp):
AAATAAAAAGATAATAGCTAAATAAAT
Found at i:636 original size:27 final size:27
Alignment explanation
Indices: 606--665 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
596 GATAAATAGC
* *
606 AAATAAATAGATAATAAT-TAAATTAAT
1 AAATAAAAAGATAA-AATGTAAATAAAT
633 AAATAAAAAGATAAAATGTAAATAAAT
1 AAATAAAAAGATAAAATGTAAATAAAT
*
660 AGATAA
1 AAATAA
666 TAGTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (27 bp):
AAATAAAAAGATAAAATGTAAATAAAT
Found at i:688 original size:25 final size:24
Alignment explanation
Indices: 651--763 Score: 79
Period size: 23 Copynumber: 5.0 Consensus size: 24
641 AGATAAAATG
651 TAAATAAATAGATAATAGTTTAAAA
1 TAAATAAA-AGATAATAGTTTAAAA
676 TAAATAAAAAGATAAATAG--T-AAA
1 TAAAT-AAAAGAT-AATAGTTTAAAA
*
699 TAAAT---AGATAATAGTTAAAAA
1 TAAATAAAAGATAATAGTTTAAAA
*
720 TAAATAAATAAATAAATAG--T-AAA
1 TAAATAAA-AGAT-AATAGTTTAAAA
743 TAAAT---AGATAATAGTTTAAAA
1 TAAATAAAAGATAATAGTTTAAAA
764 AGATTAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 30
0.68 0.04 0.29
Matches are distributed among these distances:
18 10 0.14
19 7 0.10
20 1 0.01
21 11 0.15
23 16 0.23
24 1 0.01
25 12 0.17
26 13 0.18
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (24 bp):
TAAATAAAAGATAATAGTTTAAAA
Found at i:698 original size:44 final size:44
Alignment explanation
Indices: 560--795 Score: 302
Period size: 44 Copynumber: 5.3 Consensus size: 44
550 TAATAATAAC
* * *
560 AAATAAATAGATAATGGCTAAATTAATAAATAAAAAGATAAATAGC
1 AAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATAAATAGT
*
606 AAATAAATAGATAATAATTAAATTAATAAATAAAAAGATAAA-ATGT
1 AAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATAAATA-GT
*
652 AAATAAATAGATAATAGTTTAAAATAAATAAAAAGATAAATAGT
1 AAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGT
696 AAATAAATAGATAATAGTTAAAAATAAATAAATAA-ATAAATAGT
1 AAATAAATAGATAATAGTTAAAAATAAATAAA-AAGATAAATAGT
* *
740 AAATAAATAGATAATAGTTTAAAAA-GATTAAAAA-ATAAATAGT
1 AAATAAATAGATAATAG-TTAAAAATAAATAAAAAGATAAATAGT
*
783 GAATAAATA-ATAA
1 AAATAAATAGATAA
796 AAAAAAAATC
Statistics
Matches: 176, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
42 4 0.02
43 19 0.11
44 82 0.47
45 11 0.06
46 60 0.34
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (44 bp):
AAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGT
Done.