Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024540.1 Corchorus olitorius cultivar O-4 contig24573, 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: 4580
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2556 original size:4 final size:4
Alignment explanation
Indices: 2547--2670 Score: 64
Period size: 4 Copynumber: 31.0 Consensus size: 4
2537 TAAAAATAAT
* * *
2547 AATA AATA AATA AATA GAT- AATA ACTAA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA AATA AATA AAT-A AATA AATA A-ATA AATA AATA
* * *
2594 AATA AATA GATGA TAATT AA-A AATA AATA AA-A AGATA AAT- AGTA AATA
1 AATA AATA AAT-A -AATA AATA AATA AATA AATA A-ATA AATA AATA AATA
* *
2642 AATA GATA ATAGTT AA-A AATA AATA AATA
1 AATA AATA A-A-TA AATA AATA AATA AATA
2671 GTTAATAGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
3 14 0.16
4 62 0.69
5 10 0.11
6 4 0.04
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:2569 original size:25 final size:25
Alignment explanation
Indices: 2541--2763 Score: 110
Period size: 25 Copynumber: 8.8 Consensus size: 25
2531 GGTAGCTAAA
2541 AATAATAATAAATAAATAAATAGAT
1 AATAATAATAAATAAATAAATAGAT
2566 AATAACTAAAATAAA-AAGATAAATAG-T
1 AATAA-T--AATAAATAA-ATAAATAGAT
* *
2593 AAATAAATAGATGATAATTAA-AAATAAAT
1 -AAT-AATA-AT-A-AATAAATAAATAGAT
2622 AA-AA-AGATAAATAGTAAATAAATAGAT
1 AATAATA-AT-AA-A-TAAATAAATAGAT
* *
2649 AATAGTTAA-AAATAAATAAATAGTT
1 AATA-ATAATAAATAAATAAATAGAT
*
2674 AATAGTTAA-AAATAAATAAATAGA-
1 AATA-ATAATAAATAAATAAATAGAT
* *
2698 AA-AA-AAT-AGTGAATAAATAGAT
1 AATAATAATAAATAAATAAATAGAT
* *
2720 AATAGTTAA-AAATAAATAAATAGAA
1 AATA-ATAATAAATAAATAAATAGAT
* * *
2745 AAAAATAGTGAATAAATAA
1 AATAATAATAAATAAATAA
2764 TAAAAAATCT
Statistics
Matches: 155, Mismatches: 19, Indels: 48
0.70 0.09 0.22
Matches are distributed among these distances:
21 14 0.09
22 2 0.01
23 2 0.01
24 5 0.03
25 72 0.46
26 8 0.05
27 16 0.10
28 27 0.17
29 7 0.05
30 2 0.01
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (25 bp):
AATAATAATAAATAAATAAATAGAT
Found at i:2627 original size:44 final size:44
Alignment explanation
Indices: 2544--2668 Score: 173
Period size: 44 Copynumber: 2.9 Consensus size: 44
2534 AGCTAAAAAT
* * **
2544 AATAATAAATAAATAAATAGATAA-TAACTA-AAATAAAAAGATA
1 AATAGTAAATAAATAGAT-GATAATTAAAAATAAATAAAAAGATA
2587 AATAGTAAATAAATAGATGATAATTAAAAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATGATAATTAAAAATAAATAAAAAGATA
* *
2631 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAA
1 AATAGTAAATAAATAGATGATAATTAAAAATAAATAAA
2669 TAGTTAATAG
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
42 5 0.07
43 20 0.27
44 49 0.66
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (44 bp):
AATAGTAAATAAATAGATGATAATTAAAAATAAATAAAAAGATA
Found at i:2713 original size:46 final size:46
Alignment explanation
Indices: 2663--2766 Score: 192
Period size: 46 Copynumber: 2.3 Consensus size: 46
2653 GTTAAAAATA
*
2663 AATAAATAGTTAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
1 AATAAATAGATAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
2709 AATAAATAGATAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
1 AATAAATAGATAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
2755 AATAAATA-ATAA
1 AATAAATAGATAA
2767 AAAATCTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (46 bp):
AATAAATAGATAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
Found at i:2727 original size:71 final size:69
Alignment explanation
Indices: 2592--2743 Score: 232
Period size: 71 Copynumber: 2.2 Consensus size: 69
2582 AGATAAATAG
* * *
2592 TAAATAAATAGATGATAATTAAAAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTA
1 TAAATAAATAGATAATAATTAAAAATAAATAAAAAAAAAAATAGTAAATAAATAGATAATAGTTA
2657 AAAA
66 AAAA
* * *
2661 TAAATAAATAGTTAATAGTTAAAAATAAATAAATAGAAAAAAATAGTGAATAAATAGATAATAGT
1 TAAATAAATAGATAATAATTAAAAATAAATAAA-A-AAAAAAATAGTAAATAAATAGATAATAGT
2726 TAAAAA
64 TAAAAA
2732 TAAATAAATAGA
1 TAAATAAATAGA
2744 AAAAAATAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
69 30 0.41
70 1 0.01
71 43 0.58
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (69 bp):
TAAATAAATAGATAATAATTAAAAATAAATAAAAAAAAAAATAGTAAATAAATAGATAATAGTTA
AAAA
Found at i:2759 original size:71 final size:70
Alignment explanation
Indices: 2611--2770 Score: 200
Period size: 71 Copynumber: 2.3 Consensus size: 70
2601 AGATGATAAT
* * *
2611 TAAAAATAAATAAA-AAGATAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGTTA
1 TAAAAATAAATAAATAAAAAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGTAA
* **
2675 ATAGT
66 AAAAA
*
2680 TAAAAATAAATAAATAGAAAAAAATAGTGAATAAATAGATAATAGTTAAAAATAAATAAATAG-A
1 TAAAAATAAATAAATA-AAAAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGTA
2744 AAAAAA
65 AAAAAA
**
2750 TAGTGAATAAAT-AATAAAAAA
1 TA-AAAATAAATAAATAAAAAA
2771 TCTTTTTGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 19 0.24
70 10 0.13
71 50 0.63
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (70 bp):
TAAAAATAAATAAATAAAAAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGTAA
AAAAA
Found at i:4475 original size:1 final size:1
Alignment explanation
Indices: 4436--4466 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
4426 TCTGATCATT
*
4436 AAAAAAAAAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4467 CTTAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Done.