Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016931.1 Corchorus olitorius cultivar O-4 contig16964, 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: 16709
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Found at i:3963 original size:54 final size:54
Alignment explanation
Indices: 3883--4536 Score: 802
Period size: 54 Copynumber: 12.1 Consensus size: 54
3873 ACAAAAACTT
** * * *
3883 TTCTTGGAGCGACCACACTAGATCATCTGAAGATCAACTCTGATCATCGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
** *
3937 TTCTTAAAATGACCGCACTGGATCATCTGTA-GATCAACTCTGAT-ATTCGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTG-AGGATCAACTCTGATCATT-GAAAAC
* * ** * *
3991 TTCTTGAAACGACCATAC-CGAATCATCTG-GAGATCAACTTTGATC-TTCGAAAAC
1 TTCTTGGAATGACCGCACTAG-ATCATCTGAG-GATCAACTCTGATCATT-GAAAAC
* * *
4045 TTCTTGGAATGACCGCACTGGATTATCTGAGGATCAACTCTGATCAATGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* * * * * * *
4099 ATCTTGGAATAACTGCACTAGATCATTTGAAGATCAACTCTAATCATTGTAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* * * *
4153 TTCTTGGACTGACCACACTAGATCATCTGAGGATAAACTCTGATCATTGTAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* * *
4207 TTCTTGGACTGACCACACTAGATCATCTGAGGATCAACTCTGATCATTGTAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* *
4261 TTCTTGGATTGACCGCACTAGATCATTTGAGGATCAACTCTGATCATTGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* * *
4315 TTCTTGGAATGACCGCGCTGGACCATCTGAGGATCAACTCTGATCATTGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
*
4369 TTCTTGGAATGACCGCACTAGATCATCTGAGGATTAACTCTGATCATTGAAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
* *
4423 TTCTTGGAATGACCGCACTAGATCATCTGGGGATCAACTCTGATCACT-AGAAAC
1 TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGA-AAAC
* * *
4477 TTCTTGGAATGACCGCACAAGATCAAT-TG-GAGATCAACTCTGATCATCGTAAAC
1 TTCTTGGAATGACCGCACTAGATC-ATCTGAG-GATCAACTCTGATCATTGAAAAC
4531 TTCTTG
1 TTCTTG
4537 AAATAAGATC
Statistics
Matches: 526, Mismatches: 61, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
53 5 0.01
54 515 0.98
55 6 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (54 bp):
TTCTTGGAATGACCGCACTAGATCATCTGAGGATCAACTCTGATCATTGAAAAC
Found at i:4553 original size:35 final size:35
Alignment explanation
Indices: 4505--4711 Score: 324
Period size: 35 Copynumber: 5.9 Consensus size: 35
4495 AAGATCAATT
*
4505 GGAGATCAACTCTGATCATCGTAAACTTCTTGAAA
1 GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
** *
4540 TAAGATCAACTCTGATCGTCGAAAACTTCTTGAAA
1 GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
* *
4575 CGAGATAAACTCTGATCATCGAAAACTTCTTGAAA
1 GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
*
4610 GGAGATAAACTCTGATCATCGAAAACTTCTTGAAA
1 GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
*
4645 TGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
1 GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
* *
4680 GGAGATCAACTTTGATAATCGAAAACTTCTTG
1 GGAGATCAACTCTGATCATCGAAAACTTCTTG
4712 GAATGACCAC
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 158 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (35 bp):
GGAGATCAACTCTGATCATCGAAAACTTCTTGAAA
Found at i:4839 original size:54 final size:54
Alignment explanation
Indices: 4719--5046 Score: 423
Period size: 54 Copynumber: 6.1 Consensus size: 54
4709 TTGGAATGAC
* * * * *
4719 CACATGGGTCATTTGGAA-ATCAATTTAGATCTCTGAAAGCTT-TAAGAAAGACCG
1 CACA-GGGTCATCT-GAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
* * * * *
4773 CACAGGGTCATCTTAAAATCAATTTAGATCTCTGAAAACTTTTATGAAAGACCG
1 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
4827 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
1 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
* *
4881 CACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAATACCG
1 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
* * * ** *
4935 CACAGGGCCATTTGATG-TCAACTTAGGTCTTTGAAAACTTCTATGAAAGACCG
1 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
* *
4988 CACAGGGT--TATGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAATACCG
1 CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
5040 CACAGGG
1 CACAGGG
5047 CTGTTTGATC
Statistics
Matches: 245, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
51 5 0.02
52 41 0.17
53 70 0.29
54 129 0.53
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
CACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
Found at i:5172 original size:22 final size:22
Alignment explanation
Indices: 5144--5191 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5134 AACACCTGTA
*
5144 CTTGAC-TCTTCATCTACCCTTT
1 CTTGACTTCTTC-TCTACCCATT
*
5166 CTTGACTTCTTCTTTACCCATT
1 CTTGACTTCTTCTCTACCCATT
5188 CTTG
1 CTTG
5192 GCTATTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (22 bp):
CTTGACTTCTTCTCTACCCATT
Found at i:6997 original size:6 final size:6
Alignment explanation
Indices: 6986--7027 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
6976 TTCTTTCACA
6986 TTTTCT TTTTCT TTTTCT TTTTCT GCTTTTCTT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT --TTTTC-T TTTTCT TTT
7028 GCTAATGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 22 0.67
7 5 0.15
8 5 0.15
9 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:15301 original size:24 final size:25
Alignment explanation
Indices: 15255--15300 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
15245 CACCTCCCAA
*
15255 ACCCTAGACTTCATTAGCCTTTTAT
1 ACCCTAGACTTCATTACCCTTTTAT
15280 ACCCTAGAC-TCATT-CCCTTTT
1 ACCCTAGACTTCATTACCCTTTT
15301 TGTTTGGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.39
Consensus pattern (25 bp):
ACCCTAGACTTCATTACCCTTTTAT
Done.