Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013397.1 Corchorus olitorius cultivar O-4 contig13430, 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: 23736
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:7971 original size:12 final size:13
Alignment explanation
Indices: 7949--7978 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
7939 ACTAGCAATT
7949 AAAATCAATCAAG
1 AAAATCAATCAAG
7962 AAAA-CAATCAAG
1 AAAATCAATCAAG
7974 AAAAT
1 AAAAT
7979 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:9285 original size:19 final size:18
Alignment explanation
Indices: 9252--9287 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9242 AACCTCCAAT
9252 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
9270 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9288 ATGGTCTTCA
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:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:9286 original size:11 final size:11
Alignment explanation
Indices: 9252--9299 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
9242 AACCTCCAAT
9252 TCTTC-AATGA
1 TCTTCAAATGA
9262 TCTTC-AA-G-
1 TCTTCAAATGA
*
9270 TCTTCAAATTA
1 TCTTCAAATGA
*
9281 TCTTCAAATGG
1 TCTTCAAATGA
9292 TCTTCAAA
1 TCTTCAAA
9300 CACGAACTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 7 0.22
11 17 0.53
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (11 bp):
TCTTCAAATGA
Found at i:16805 original size:16 final size:15
Alignment explanation
Indices: 16784--16825 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16774 TTACTCTGCT
16784 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
16800 TTGTTTTATGTTTAA
1 TTGTTTTCTGTTTAA
*
16815 TTGCTTTCTGT
1 TTGTTTTCTGT
16826 CAATCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:18601 original size:58 final size:58
Alignment explanation
Indices: 18511--18626 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
18501 TTATTGAATG
*
18511 AAAAATTTCCTGACTGGTTTAAAACTTATGTGAGTAGTAGTAGTAGTAGCATACAGTT
1 AAAAATTTCCTGACTAGTTTAAAACTTATGTGAGTAGTAGTAGTAGTAGCATACAGTT
18569 AAAAATTTCCTGACTAGTTTAAAACTTATGTGAGTAGTAGTAGTAGTAGCATACAGTT
1 AAAAATTTCCTGACTAGTTTAAAACTTATGTGAGTAGTAGTAGTAGTAGCATACAGTT
18627 TTGGAACTAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (58 bp):
AAAAATTTCCTGACTAGTTTAAAACTTATGTGAGTAGTAGTAGTAGTAGCATACAGTT
Found at i:20782 original size:76 final size:76
Alignment explanation
Indices: 20656--20806 Score: 189
Period size: 76 Copynumber: 2.0 Consensus size: 76
20646 ACAAGGACCC
* *
20656 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
20721 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * **
20732 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGTGTTTTGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTTGCCTGAGAACCCAG
*
20795 ATGGGCTGTGTC
64 ATGGGCAGTGTC
20807 TTAGCTCATC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 58 0.91
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:21790 original size:27 final size:26
Alignment explanation
Indices: 21736--21784 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
21726 ATGATTTAGG
*
21736 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
*
21762 GGTTACTAACGCTCTTTTT-TTTT
1 GGTTACTAACGCCCTTTTTCTTTT
21785 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.53
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Done.