Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015769.1 Corchorus olitorius cultivar O-4 contig15802, 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: 2793
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Found at i:475 original size:47 final size:47
Alignment explanation
Indices: 406--500 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
396 TATATATATA
406 TATATATATTATAGTGTTTAATAATAAGTTAAAATATTATTTATAGT
1 TATATATATTATAGTGTTTAATAATAAGTTAAAATATTATTTATAGT
453 TATATATATTATAGTGTTTAATAATAAGTTAAAATATTATTTATAGT
1 TATATATATTATAGTGTTTAATAATAAGTTAAAATATTATTTATAGT
500 T
1 T
501 TTAACTGTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (47 bp):
TATATATATTATAGTGTTTAATAATAAGTTAAAATATTATTTATAGT
Found at i:1185 original size:16 final size:17
Alignment explanation
Indices: 1166--1198 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1156 TTGATGTTTT
1166 GAATAATAAAAA-TAAA
1 GAATAATAAAAAGTAAA
1182 GAATAATAAAAAGTAAA
1 GAATAATAAAAAGTAAA
1199 AAAATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
GAATAATAAAAAGTAAA
Found at i:1456 original size:24 final size:22
Alignment explanation
Indices: 1394--1458 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
1384 TGGAAACATT
*
1394 TTTGCAGAGCATTATTTACCAC
1 TTTGCAGAGCATTATTTTCCAC
1416 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
1438 TTTGCAGAGTGCATTATTTTC
1 TTTGCAGA--GCATTATTTTC
1459 TTCAACTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 29 0.73
24 11 0.28
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTGCAGAGCATTATTTTCCAC
Found at i:1562 original size:24 final size:24
Alignment explanation
Indices: 1487--1564 Score: 110
Period size: 22 Copynumber: 3.4 Consensus size: 24
1477 TTATTAGAAA
*
1487 CATTATTTACCACTTTGCAGAGT-
1 CATTATTTTCCACTTTGCAGAGTG
*
1510 -ATTATTTTCTACTTTGCAGA--G
1 CATTATTTTCCACTTTGCAGAGTG
1531 CATTATTTTCCACTTTGCAGAGTG
1 CATTATTTTCCACTTTGCAGAGTG
1555 CATTATTTTC
1 CATTATTTTC
1565 TTCAACTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 37 0.77
24 11 0.23
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (24 bp):
CATTATTTTCCACTTTGCAGAGTG
Found at i:1579 original size:106 final size:106
Alignment explanation
Indices: 1394--1595 Score: 368
Period size: 106 Copynumber: 1.9 Consensus size: 106
1384 TGGAAACATT
1394 TTTGCAGAGCATTATTTACCACTTTGCAGAGCATTATTTTCCACTTTGCAGAGTGCATTATTTTC
1 TTTGCAGAGCATTATTTACCACTTTGCAGAGCATTATTTTCCACTTTGCAGAGTGCATTATTTTC
1459 TTCAACTTCAGCTTTGCATTATTAGAAACATTATTTACCAC
66 TTCAACTTCAGCTTTGCATTATTAGAAACATTATTTACCAC
* * *
1500 TTTGCAGAGTATTATTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGAGTGCATTATTTTC
1 TTTGCAGAGCATTATTTACCACTTTGCAGAGCATTATTTTCCACTTTGCAGAGTGCATTATTTTC
*
1565 TTCAACTTCAGCTTTGCATTATTGGAAACAT
66 TTCAACTTCAGCTTTGCATTATTAGAAACAT
1596 CTTTGCAGAG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (106 bp):
TTTGCAGAGCATTATTTACCACTTTGCAGAGCATTATTTTCCACTTTGCAGAGTGCATTATTTTC
TTCAACTTCAGCTTTGCATTATTAGAAACATTATTTACCAC
Done.