Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011379.1 Corchorus capsularis cultivar CVL-1 contig11400, 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: 12895
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Found at i:658 original size:22 final size:22
Alignment explanation
Indices: 631--699 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
621 AAAGTGATGA
631 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* *
653 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGAGTAA-AATAG
*
675 TATTCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
697 TAA
1 TAA
700 AAAGTAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.05
22 35 0.90
23 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATAG
Found at i:668 original size:7 final size:7
Alignment explanation
Indices: 636--766 Score: 52
Period size: 7 Copynumber: 18.4 Consensus size: 7
626 GATGATAATC
*
636 AGTAAAG
1 AGTAAAA
643 AGTAAAA
1 AGTAAAA
**
650 TAGTAATC
1 -AGTAAAA
658 AGTAAAA
1 AGTAAAA
665 AGTAAGAA
1 AGTAA-AA
* ***
673 GGTATTC
1 AGTAAAA
*
680 AGTAAAG
1 AGTAAAA
687 AGTAAAA
1 AGTAAAA
694 TAGTAAAA
1 -AGTAAAA
**
702 AGTAATG
1 AGTAAAA
**
709 A-TAATC
1 AGTAAAA
715 AGT--AA
1 AGTAAAA
720 AGTAAAA
1 AGTAAAA
**
727 TAGTAATC
1 -AGTAAAA
*
735 AGTAAAG
1 AGTAAAA
*
742 AGTAAAG
1 AGTAAAA
749 AGTAAAA
1 AGTAAAA
756 TAGTAAAA
1 -AGTAAAA
764 AGT
1 AGT
767 GATGATAATC
Statistics
Matches: 92, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
5 3 0.03
6 5 0.05
7 55 0.60
8 29 0.32
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (7 bp):
AGTAAAA
Found at i:705 original size:22 final size:22
Alignment explanation
Indices: 636--766 Score: 80
Period size: 22 Copynumber: 6.1 Consensus size: 22
626 GATGATAATC
**
636 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAGAGTAAAATAGTAAAA
* * ***
658 AGTAAAAAGTAAGAA-GGTATTC
1 AGTAAAGAGTAA-AATAGTAAAA
680 AGTAAAGAGTAAAATAGTAAAA
1 AGTAAAGAGTAAAATAGTAAAA
*
702 AGTAATGA-T--AATCAGT--AA
1 AGTAAAGAGTAAAAT-AGTAAAA
* *
720 AGTAAA-A-TAGTAATCAGTAAAG
1 AGTAAAGAGTA-AAAT-AGTAAAA
742 AGTAAAGAGTAAAATAGTAAAA
1 AGTAAAGAGTAAAATAGTAAAA
764 AGT
1 AGT
767 GATGATAATC
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.02
18 7 0.08
19 3 0.03
20 10 0.12
21 3 0.03
22 53 0.62
23 6 0.07
24 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (22 bp):
AGTAAAGAGTAAAATAGTAAAA
Found at i:706 original size:44 final size:42
Alignment explanation
Indices: 608--706 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 42
598 AGAAGTAATC
*
608 AGTAAAATAGTAAAAAGTGATGATAATCAGTAAAGAGTAAAAT
1 AGTAAAA-AGTAAAAAGTGAAGATAATCAGTAAAGAGTAAAAT
** * *
651 AGTAATCAGTAAAAAGTAAGAAGGTATTCAGTAAAGAGTAAAAT
1 AGTAAAAAGTAAAAAGT--GAAGATAATCAGTAAAGAGTAAAAT
695 AGTAAAAAGTAA
1 AGTAAAAAGTAA
707 TGATAATCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 10 0.21
43 5 0.11
44 32 0.68
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (42 bp):
AGTAAAAAGTAAAAAGTGAAGATAATCAGTAAAGAGTAAAAT
Found at i:746 original size:62 final size:63
Alignment explanation
Indices: 680--798 Score: 204
Period size: 62 Copynumber: 1.9 Consensus size: 63
670 GAAGGTATTC
680 AGTAAAGAGTAAAATAGTAAAAAGTAATGATAATCAGT-AAAGTAAAATAGTAATCAGTAAAG
1 AGTAAAGAGTAAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAG
* *
742 AGTAAAGAGTAAAATAGTAAAAAGTGATGATAATCAGTAAAAAGTAAAATGGTAATC
1 AGTAAAGAGTAAAATAGTAAAAAGTAATGATAATCAGT-AAAAGTAAAATAGTAATC
799 CCATTTTAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
62 37 0.70
64 16 0.30
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.23
Consensus pattern (63 bp):
AGTAAAGAGTAAAATAGTAAAAAGTAATGATAATCAGTAAAAGTAAAATAGTAATCAGTAAAG
Found at i:2630 original size:13 final size:13
Alignment explanation
Indices: 2612--2647 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2602 TTGCATTTAA
2612 AAATGATAATAAT
1 AAATGATAATAAT
*
2625 AAATGATAACAAT
1 AAATGATAATAAT
*
2638 AAATAATAAT
1 AAATGATAAT
2648 GACGATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (13 bp):
AAATGATAATAAT
Done.