Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009543.1 Corchorus olitorius cultivar O-4 contig09575, 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: 8367
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1367 original size:47 final size:47
Alignment explanation
Indices: 1313--1409 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
1303 TGTATGTGCA
* *
1313 TTTAATTATATTGTATTTGATGTACTAACAATGTATGGACTAATTTG
1 TTTAATTATATTATATTTGATGTACTAACAATATATGGACTAATTTG
1360 TTTAATTATATTATATTTGATGTACTAACAATATATGGACTAATTTG
1 TTTAATTATATTATATTTGATGTACTAACAATATATGGACTAATTTG
1407 TTT
1 TTT
1410 GGGTTCCAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (47 bp):
TTTAATTATATTATATTTGATGTACTAACAATATATGGACTAATTTG
Found at i:4572 original size:30 final size:30
Alignment explanation
Indices: 4531--4611 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
4521 CAATCCGCTG
* *
4531 CTGCCATGTCATCCTGTTGACCGAGTCAAA
1 CTGCCACGTCATCCTGTTGACCAAGTCAAA
4561 CTGCCACGTCATCCTGTTGACCAAGTCAAA
1 CTGCCACGTCATCCTGTTGACCAAGTCAAA
*
4591 CTGCCACATCATCCTGTTGAC
1 CTGCCACGTCATCCTGTTGAC
4612 TGTTGACCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.26
Consensus pattern (30 bp):
CTGCCACGTCATCCTGTTGACCAAGTCAAA
Found at i:4667 original size:48 final size:49
Alignment explanation
Indices: 4592--4686 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 49
4582 CAAGTCAAAC
* * *
4592 TGCCACATCATCCTGTTGACTGTTGACCAGACAACCTGCCATGTCATCT
1 TGCCACATCATCCTCTTGACCGTTGACCAGACAACCTGCCACGTCATCT
* * *
4641 TGCCACGTCATCC-CTTGACCGTTGACCGGTCAACCTGCCACGTCAT
1 TGCCACATCATCCTCTTGACCGTTGACCAGACAACCTGCCACGTCAT
4687 TGAGTTTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 28 0.70
49 12 0.30
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.26
Consensus pattern (49 bp):
TGCCACATCATCCTCTTGACCGTTGACCAGACAACCTGCCACGTCATCT
Found at i:4900 original size:18 final size:19
Alignment explanation
Indices: 4877--4919 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
4867 TATTTTCTGT
4877 CTGTTTGACCTC-TTGGTC
1 CTGTTTGACCTCTTTGGTC
4895 CTGTTTGACCTCTTTGGTC
1 CTGTTTGACCTCTTTGGTC
*
4914 CCGTTT
1 CTGTTT
4920 TCTGCTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.05, C:0.28, G:0.21, T:0.47
Consensus pattern (19 bp):
CTGTTTGACCTCTTTGGTC
Found at i:4935 original size:48 final size:48
Alignment explanation
Indices: 4851--5043 Score: 191
Period size: 48 Copynumber: 4.1 Consensus size: 48
4841 AGTTTGCTCC
* * *
4851 GTTTGACCTTTC-GACCTATTTTCTG-TCTGTTTGACCTCTTGGTCCT
1 GTTTGACCTTTCGGTCCTGTTTTCTGCTATGTTTGACCTCTTGGTCCT
* * * *
4897 GTTTGACCTCTTTGGTCCCGTTTTCTGCT-TGTTCGACCTCTTGGCCCT
1 GTTTGACCT-TTCGGTCCTGTTTTCTGCTATGTTTGACCTCTTGGTCCT
* * *
4945 GTTTGACCTTTCGGTCATGTTTTATGCCTAT-TTTGACCCCTTGGTCCT
1 GTTTGACCTTTCGGTCCTGTTTTCTG-CTATGTTTGACCTCTTGGTCCT
** * *
4993 GTTTGACCTTTCAATCCTGTTTTCTGC-CTGATTGACCT-TTGGGTCCT
1 GTTTGACCTTTCGGTCCTGTTTTCTGCTATGTTTGACCTCTT-GGTCCT
5040 GTTT
1 GTTT
5044 TTTAGCCCTT
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
46 12 0.10
47 32 0.27
48 74 0.62
49 2 0.02
ACGTcount: A:0.08, C:0.26, G:0.19, T:0.46
Consensus pattern (48 bp):
GTTTGACCTTTCGGTCCTGTTTTCTGCTATGTTTGACCTCTTGGTCCT
Found at i:6753 original size:19 final size:19
Alignment explanation
Indices: 6714--6754 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6704 GGTAGTTAAA
* * *
6714 AGAGTGAGTATGAGGAGAG
1 AGAGTGAGTAGGAAGAAAG
6733 AGAGTGAGTAGGAAGAAAG
1 AGAGTGAGTAGGAAGAAAG
6752 AGA
1 AGA
6755 ATAGGGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (19 bp):
AGAGTGAGTAGGAAGAAAG
Found at i:7521 original size:16 final size:16
Alignment explanation
Indices: 7497--7552 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
7487 GGTTAAGTCA
7497 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
*
7513 GGCTT-GGGT-TATGTCG
1 GG-TTCGGGTAT-TTTCG
7529 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
7545 GGTTCGGG
1 GGTTCGGG
7553 CTCGGGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.09
16 28 0.82
17 3 0.09
ACGTcount: A:0.05, C:0.12, G:0.43, T:0.39
Consensus pattern (16 bp):
GGTTCGGGTATTTTCG
Found at i:7533 original size:32 final size:32
Alignment explanation
Indices: 7486--7546 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
7476 GGGCGGGTTC
7486 GGGTTAAGTCAGGTTCGGGTATTTTCGGGCTT
1 GGGTTAAGTCAGGTTCGGGTATTTTCGGGCTT
* *
7518 GGGTTATGTCGGGTTCGGGTATTTTCGGG
1 GGGTTAAGTCAGGTTCGGGTATTTTCGGG
7547 TTCGGGCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.11, G:0.41, T:0.38
Consensus pattern (32 bp):
GGGTTAAGTCAGGTTCGGGTATTTTCGGGCTT
Found at i:8026 original size:31 final size:31
Alignment explanation
Indices: 7991--8062 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
7981 TAAATTATTG
*
7991 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
8022 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
8053 CAAATTAAAA
1 CAAATTAAAA
8063 GCTGATAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Done.