Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012050.1 Corchorus olitorius cultivar O-4 contig12083, 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: 50384
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:713 original size:2 final size:2
Alignment explanation
Indices: 708--742 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
698 TGCGTGTGTG
708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
743 GTCAATTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2864 original size:2 final size:2
Alignment explanation
Indices: 2857--2885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2847 CAAGCAAGAG
2857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2886 TATGTCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6685 original size:18 final size:19
Alignment explanation
Indices: 6662--6698 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6652 ATCAGTTTAC
6662 TTAATTAAAT-TGAATTAA
1 TTAATTAAATATGAATTAA
*
6680 TTAATTATATATGAATTAA
1 TTAATTAAATATGAATTAA
6699 GTTTGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TTAATTAAATATGAATTAA
Found at i:12102 original size:33 final size:32
Alignment explanation
Indices: 12061--12140 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
12051 TATAATTTTT
12061 AAAA-CCCTTAAAGCTGGTATGAAAAAAAAAAA
1 AAAACCCCTTAAAGCTGGTAT-AAAAAAAAAAA
* ** *
12093 AAATCCCCTTAAAGCTTTTCTAAAAAAAAAAA
1 AAAACCCCTTAAAGCTGGTATAAAAAAAAAAA
*
12125 AAAACCCCTTGAAGCT
1 AAAACCCCTTAAAGCT
12141 TCTAATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 28 0.68
33 13 0.32
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.20
Consensus pattern (32 bp):
AAAACCCCTTAAAGCTGGTATAAAAAAAAAAA
Found at i:12470 original size:23 final size:24
Alignment explanation
Indices: 12431--12482 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
12421 TTGTTTAATT
12431 AATT-ACTTATATATTTTATATAC
1 AATTCACTTATATATTTTATATAC
12454 AATTCACTTATAT-TTTTATATAC
1 AATTCACTTATATATTTTATATAC
12477 AATTCA
1 AATTCA
12483 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTCACTTATATATTTTATATAC
Found at i:15383 original size:2 final size:2
Alignment explanation
Indices: 15376--15405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15366 GGTAATTAAC
15376 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
15406 TAACCTTTTC
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:23173 original size:33 final size:34
Alignment explanation
Indices: 23136--23200 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
23126 TTTAGGGATT
23136 GAAAGAG-TACAATTGATGGATGTGAGCCCCGTA
1 GAAAGAGATACAATTGATGGATGTGAGCCCCGTA
*
23169 GAAAGAGTATACAATTGATGTATGTGAGCCCC
1 GAAAGAG-ATACAATTGATGGATGTGAGCCCC
23201 ATACATACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 7 0.24
35 22 0.76
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (34 bp):
GAAAGAGATACAATTGATGGATGTGAGCCCCGTA
Found at i:25526 original size:19 final size:18
Alignment explanation
Indices: 25486--25528 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
25476 CATTTCGTTG
* * *
25486 TTTATTTTAGTATATTAT
1 TTTATTTTACTACATTAA
25504 TTTATTATTACTACATTAA
1 TTTATT-TTACTACATTAA
25523 TTTATT
1 TTTATT
25529 CTCTCATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATTTTACTACATTAA
Found at i:27380 original size:2 final size:2
Alignment explanation
Indices: 27373--27423 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
27363 AATTAGCCTC
27373 TA 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 TA
27415 T- TA T- TA TA T
1 TA TA TA TA TA T
27424 GAGGGATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:30816 original size:5 final size:5
Alignment explanation
Indices: 30790--30833 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
30780 AGGAGTACAA
*
30790 AATAT -ATAT AGT-T AAT-T AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
30834 GTTGTAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 11 0.31
5 24 0.69
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:34726 original size:13 final size:13
Alignment explanation
Indices: 34708--34732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34698 TAGTTTCAGA
34708 TGTGCAAAACATG
1 TGTGCAAAACATG
34721 TGTGCAAAACAT
1 TGTGCAAAACAT
34733 CAAACTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
TGTGCAAAACATG
Found at i:35327 original size:7 final size:7
Alignment explanation
Indices: 35315--35340 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35305 GAAGGTAAGG
35315 TAGGACT
1 TAGGACT
35322 TAGGACT
1 TAGGACT
35329 TAGGACT
1 TAGGACT
35336 TAGGA
1 TAGGA
35341 GTAGGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (7 bp):
TAGGACT
Found at i:41770 original size:6 final size:6
Alignment explanation
Indices: 41759--41786 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41749 AATATCTATC
41759 CATTTT CATTTT CATTTT CATTTT CATT
1 CATTTT CATTTT CATTTT CATTTT CATT
41787 GATGATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:44299 original size:2 final size:2
Alignment explanation
Indices: 44292--44319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44282 CTCTGTACTC
44292 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
44320 TCTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.