Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014638.1 Corchorus olitorius cultivar O-4 contig14671, 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: 42412
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 AAAGAAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:485 original size:15 final size:15
Alignment explanation
Indices: 465--496 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
455 TTCTTTCCAC
465 TTGACCTAAAAGAGA
1 TTGACCTAAAAGAGA
*
480 TTGACCTAATAGAGA
1 TTGACCTAAAAGAGA
495 TT
1 TT
497 AGTAACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (15 bp):
TTGACCTAAAAGAGA
Found at i:8563 original size:28 final size:28
Alignment explanation
Indices: 8523--8581 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
8513 TGAACAAGGG
8523 CTTAAAATCATACAAATTTGTATGAAAA
1 CTTAAAATCATACAAATTTGTATGAAAA
8551 CTTAAAATCATACAAATTTGTATGAAAA
1 CTTAAAATCATACAAATTTGTATGAAAA
8579 CTT
1 CTT
8582 GAATTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (28 bp):
CTTAAAATCATACAAATTTGTATGAAAA
Found at i:18495 original size:15 final size:15
Alignment explanation
Indices: 18475--18508 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18465 AAATCCCTGC
18475 TTTAACAATTTAAGT
1 TTTAACAATTTAAGT
* *
18490 TTTAACCATTTGAGT
1 TTTAACAATTTAAGT
18505 TTTA
1 TTTA
18509 TGTTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTAACAATTTAAGT
Found at i:19564 original size:14 final size:14
Alignment explanation
Indices: 19533--19566 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19523 TTAGTAGCTG
**
19533 AAATTTTTAAATTT
1 AAATTTTTAAATCC
19547 AAATTTTTAAATCC
1 AAATTTTTAAATCC
19561 AAATTT
1 AAATTT
19567 CCTCCTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTTTTAAATCC
Found at i:21601 original size:2 final size:2
Alignment explanation
Indices: 21594--21623 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21584 ATTCTATAAA
21594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21624 GGGTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30428 original size:21 final size:21
Alignment explanation
Indices: 30402--30444 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30392 AACAAGACTT
*
30402 TTCAACTATTTCTGGTTTTGG
1 TTCAACTACTTCTGGTTTTGG
*
30423 TTCAACTACTTCTTGTTTTGG
1 TTCAACTACTTCTGGTTTTGG
30444 T
1 T
30445 AGGTTTTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.53
Consensus pattern (21 bp):
TTCAACTACTTCTGGTTTTGG
Found at i:32166 original size:1 final size:1
Alignment explanation
Indices: 32132--32156 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
32122 CGGATGATAT
32132 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
32157 GGGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32317 original size:18 final size:18
Alignment explanation
Indices: 32294--32330 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
32284 TTTTTCCATG
32294 TTTAACAATATATAATAC
1 TTTAACAATATATAATAC
32312 TTTAACAATATATAATAC
1 TTTAACAATATATAATAC
32330 T
1 T
32331 ATAATCGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAACAATATATAATAC
Done.