Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013351.1 Corchorus olitorius cultivar O-4 contig13384, 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: 41398
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5158 original size:16 final size:16
Alignment explanation
Indices: 5137--5171 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5127 GTGCTTCACT
5137 CAAGTTGTGATAAGGG
1 CAAGTTGTGATAAGGG
5153 CAAGTTGTGATAAGGG
1 CAAGTTGTGATAAGGG
5169 CAA
1 CAA
5172 CTTGCACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (16 bp):
CAAGTTGTGATAAGGG
Found at i:7608 original size:35 final size:35
Alignment explanation
Indices: 7585--7652 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
7575 GATTGAAGTA
* *
7585 AACTGAAGAATGATCGCCCTGGATCAATTGAAACT
1 AACTGAAGAAAGACCGCCCTGGATCAATTGAAACT
*
7620 AACTGAAGAAAGACCGCCCTGGGTCAACTTGAA
1 AACTGAAGAAAGACCGCCCTGGATCAA-TTGAA
7653 CCAAGATCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (35 bp):
AACTGAAGAAAGACCGCCCTGGATCAATTGAAACT
Found at i:7681 original size:96 final size:96
Alignment explanation
Indices: 7527--7722 Score: 338
Period size: 96 Copynumber: 2.0 Consensus size: 96
7517 TGAAATAAAT
* ** *
7527 TGAAGAAAGACCACCCTGGGTCAACTTGAAGCAAGATCGTTTTGGATCGATTGAAGTAAACTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTTGAACCAAGATCACTTTGGATCGATTAAAGTAAACTGAA
*
7592 GAATGATCGCCCTGGATCAATTGAAACTAAC
66 GAATGATCACCCTGGATCAATTGAAACTAAC
*
7623 TGAAGAAAGACCGCCCTGGGTCAACTTGAACCAAGATCACTTTGGATCGATTAAAGTAAACTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTTGAACCAAGATCACTTTGGATCGATTAAAGTAAACTGAA
7688 GAATGATCACCCTGGATCAATTGAAACTAAC
66 GAATGATCACCCTGGATCAATTGAAACTAAC
7719 TGAA
1 TGAA
7723 AGACATTTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (96 bp):
TGAAGAAAGACCACCCTGGGTCAACTTGAACCAAGATCACTTTGGATCGATTAAAGTAAACTGAA
GAATGATCACCCTGGATCAATTGAAACTAAC
Found at i:13821 original size:34 final size:34
Alignment explanation
Indices: 13778--13845 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
13768 AGCTCTTACA
*
13778 CCAATGAAGTTACACGGGCCTGCATCACGCCTTT
1 CCAATGAAGTTAAACGGGCCTGCATCACGCCTTT
* * *
13812 CCAATGAAGTTAAATGGGTCTTCATCACGCCTTT
1 CCAATGAAGTTAAACGGGCCTGCATCACGCCTTT
13846 ACAAGTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (34 bp):
CCAATGAAGTTAAACGGGCCTGCATCACGCCTTT
Found at i:22616 original size:21 final size:22
Alignment explanation
Indices: 22573--22618 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
22563 GGCCTTGCTT
**
22573 AAGAGAAGAAGTCGACTTGAGC
1 AAGAGAAGAAGTCGACTAAAGC
*
22595 AAGAGAA-TAGTCGACTAAAGC
1 AAGAGAAGAAGTCGACTAAAGC
22616 AAG
1 AAG
22619 TCGAGAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.46, C:0.13, G:0.28, T:0.13
Consensus pattern (22 bp):
AAGAGAAGAAGTCGACTAAAGC
Found at i:24898 original size:16 final size:15
Alignment explanation
Indices: 24877--24906 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24867 GTATGAATTC
24877 AAATTGATTTCTTGAA
1 AAATTGATTT-TTGAA
24893 AAATTGATTTTTGA
1 AAATTGATTTTTGA
24907 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (15 bp):
AAATTGATTTTTGAA
Found at i:36762 original size:29 final size:31
Alignment explanation
Indices: 36703--36767 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
36693 CAAACAATCT
*
36703 ATCAATTAACTAACAAATAATTGCAATTC-A
1 ATCAATTAACTAACAAATAATGGCAATTCAA
*
36733 ATCAATTAA-TAGCAAGAT-ATGGCAATTCAA
1 ATCAATTAACTAACAA-ATAATGGCAATTCAA
36763 ATCAA
1 ATCAA
36768 CAATTGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (31 bp):
ATCAATTAACTAACAAATAATGGCAATTCAA
Found at i:38585 original size:21 final size:22
Alignment explanation
Indices: 38561--38611 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
38551 CTTCTCCAAT
*
38561 TTCAAAATT-CAATCCTTCA-AC
1 TTCAAAATTCCAA-CATTCACAC
*
38582 TTC-AATTTCCAACATTCACAC
1 TTCAAAATTCCAACATTCACAC
38603 TTCAAAATT
1 TTCAAAATT
38612 ACTCAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.35
Consensus pattern (22 bp):
TTCAAAATTCCAACATTCACAC
Found at i:40726 original size:19 final size:18
Alignment explanation
Indices: 40693--40728 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40683 TGAAAATAAT
40693 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
40711 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
40729 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.