Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012513.1 Corchorus capsularis cultivar CVL-1 contig12534, 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: 18939
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--45 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TA
3 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45 C
1 C
46 CCTCCCTCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:547 original size:16 final size:15
Alignment explanation
Indices: 528--576 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
518 AGTAGAAAAG
528 AAAGAGAGAAAAGAAA
1 AAAGAGA-AAAAGAAA
*
544 AAAGA-AAGAA-AAA
1 AAAGAGAAAAAGAAA
557 AAAGAGAAAAGAGAAA
1 AAAGAGAAAA-AGAAA
573 AAAG
1 AAAG
577 TGTTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 6 0.21
15 2 0.07
16 12 0.43
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAGAAAAAGAAA
Found at i:560 original size:29 final size:29
Alignment explanation
Indices: 521--576 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
511 GGAAGAGAGT
*
521 AGAAAAGAAAGAGAGAAA-AGAAAAAAGAA
1 AGAAAAAAAAGAGA-AAAGAGAAAAAAGAA
550 AGAAAAAAAAGAGAAAAGAGAAAAAAG
1 AGAAAAAAAAGAGAAAAGAGAAAAAAG
577 TGTTTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (29 bp):
AGAAAAAAAAGAGAAAAGAGAAAAAAGAA
Found at i:575 original size:20 final size:20
Alignment explanation
Indices: 523--568 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
513 AAGAGAGTAG
* *
523 AAAAGAAAGAGAGAAAAGAA
1 AAAAGAAAGAAAAAAAAGAA
*
543 AAAAGAAAGAAAAAAAAGAG
1 AAAAGAAAGAAAAAAAAGAA
563 AAAAGA
1 AAAAGA
569 GAAAAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGAAAAAAAAGAA
Found at i:2530 original size:15 final size:15
Alignment explanation
Indices: 2510--2540 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2500 ACAAGTTCTG
2510 GACAAAATTCCAAAA
1 GACAAAATTCCAAAA
*
2525 GACAAAATTCTAAAA
1 GACAAAATTCCAAAA
2540 G
1 G
2541 GCATCACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (15 bp):
GACAAAATTCCAAAA
Found at i:3529 original size:14 final size:14
Alignment explanation
Indices: 3510--3538 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3500 TTCTTCATAT
3510 TAGAGTTAAAATTA
1 TAGAGTTAAAATTA
3524 TAGAGTTAAAATTA
1 TAGAGTTAAAATTA
3538 T
1 T
3539 GGGTTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (14 bp):
TAGAGTTAAAATTA
Found at i:16870 original size:19 final size:18
Alignment explanation
Indices: 16846--16881 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16836 TGAAGATTTC
16846 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
16865 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
16882 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.