Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017379.1 Corchorus olitorius cultivar O-4 contig17412, 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: 16422
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2953 original size:15 final size:15
Alignment explanation
Indices: 2922--2963 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2912 TTACTTTGCT
*
2922 TTGTTTTCTAATTTAA
1 TTGTTTTCT-GTTTAA
2938 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
2953 TTGATTTCTGT
1 TTGTTTTCTGT
2964 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4973 original size:5 final size:5
Alignment explanation
Indices: 4959--4993 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
4949 TTACTGATAG
*
4959 TTTGA GTTGA TTTGA TTTGA TTTGA TTTGA TTTGA
1 TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA
4994 CGAGGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (5 bp):
TTTGA
Found at i:7148 original size:17 final size:17
Alignment explanation
Indices: 7126--7161 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
7116 TGATTTAAAA
7126 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
7143 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
7160 AG
1 AG
7162 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:9725 original size:18 final size:18
Alignment explanation
Indices: 9692--9731 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9682 TACAAAATAT
* *
9692 TGTTCCACTGCCGCAGGA
1 TGTTCCACTACCGCAGAA
*
9710 TGTTCCACTACTGCAGAA
1 TGTTCCACTACCGCAGAA
9728 TGTT
1 TGTT
9732 GCATTTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (18 bp):
TGTTCCACTACCGCAGAA
Found at i:11381 original size:76 final size:76
Alignment explanation
Indices: 11244--11394 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
11234 ACAAGGACCC
* *
11244 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
11309 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
11320 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
11382 GATGGGCTGTGTC
63 GATGGGCAGTGTC
11395 TTAGCTCATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:13549 original size:17 final size:17
Alignment explanation
Indices: 13527--13562 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13517 TGATTTGTAA
13527 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
13544 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
13561 AG
1 AG
13563 CTCTTTGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:14564 original size:21 final size:21
Alignment explanation
Indices: 14540--14603 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 21
14530 GTAATATATA
*
14540 TAATAACTAAAATACTTACAT
1 TAATAACTGAAATACTTACAT
* *
14561 TAATTAAATGTAATA-TT--A-
1 TAA-TAACTGAAATACTTACAT
14579 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTACAT
14600 TAAT
1 TAAT
14604 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 1 0.03
20 1 0.03
21 9 0.27
22 8 0.24
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAACTGAAATACTTACAT
Found at i:14585 original size:39 final size:40
Alignment explanation
Indices: 14528--14608 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
14518 TTTAATTCCT
14528 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
14568 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
14607 AT
1 AT
14609 TCTTAGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:14626 original size:24 final size:25
Alignment explanation
Indices: 14599--14645 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
14589 AATACTTACA
14599 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
14623 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
14646 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Done.