Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019079.1 Corchorus olitorius cultivar O-4 contig19112, 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: 11648
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2128 original size:14 final size:14
Alignment explanation
Indices: 2109--2136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2099 TTTCCATTTT
2109 TTACATGTTCAAAC
1 TTACATGTTCAAAC
2123 TTACATGTTCAAAC
1 TTACATGTTCAAAC
2137 GTGTAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TTACATGTTCAAAC
Found at i:5992 original size:31 final size:29
Alignment explanation
Indices: 5957--6034 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
5947 GGAAGTTTAT
*
5957 GGGCAAACTGTCTTGCATTTTGAAATTCAGG
1 GGGCAAAATGTCTTG-A-TTTGAAATTCAGG
* * *
5988 GGGCAAAATGTCTTGATTTGAAGTTTATG
1 GGGCAAAATGTCTTGATTTGAAATTCAGG
*
6017 GGGCAAAACGTCCTTGAT
1 GGGCAAAATGT-CTTGAT
6035 GCGAAGGGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.49
30 7 0.17
31 14 0.34
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGCAAAATGTCTTGATTTGAAATTCAGG
Found at i:6019 original size:29 final size:30
Alignment explanation
Indices: 5930--6033 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
5920 ATCAGGGGAT
5930 AAAATGTCTTGAATTTGGGAAGTTTAT-GGGC
1 AAAATGTCTTGAATTT--GAAGTTTATGGGGC
* * * * *
5961 AAACTGTCTTGCATTTTGAAATTCAGGGGGC
1 AAAATGTCTTG-AATTTGAAGTTTATGGGGC
5992 AAAATGTCTTG-ATTTGAAGTTTATGGGGC
1 AAAATGTCTTGAATTTGAAGTTTATGGGGC
*
6021 AAAACGTCCTTGA
1 AAAATGT-CTTGA
6034 TGCGAAGGGG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
29 20 0.34
30 10 0.17
31 24 0.41
32 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGTCTTGAATTTGAAGTTTATGGGGC
Found at i:8168 original size:14 final size:14
Alignment explanation
Indices: 8149--8177 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8139 ACTTGTTAAA
8149 TAATGTTAAGTTAT
1 TAATGTTAAGTTAT
8163 TAATGTTAAGTTAT
1 TAATGTTAAGTTAT
8177 T
1 T
8178 GATTAGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TAATGTTAAGTTAT
Found at i:8443 original size:19 final size:19
Alignment explanation
Indices: 8419--8476 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
8409 CAGACGTGGT
8419 AATGCCACGTCGAACCAAA
1 AATGCCACGTCGAACCAAA
* *
8438 AATGCCATGT-G--GC---
1 AATGCCACGTCGAACCAAA
8451 AATGCCACGTCGAACCAAA
1 AATGCCACGTCGAACCAAA
8470 AATGCCA
1 AATGCCA
8477 TGTGGCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
13 9 0.31
14 1 0.03
16 2 0.07
18 1 0.03
19 16 0.55
ACGTcount: A:0.38, C:0.29, G:0.19, T:0.14
Consensus pattern (19 bp):
AATGCCACGTCGAACCAAA
Found at i:8460 original size:32 final size:32
Alignment explanation
Indices: 8414--8556 Score: 259
Period size: 32 Copynumber: 4.5 Consensus size: 32
8404 TATTACAGAC
*
8414 GTGGTAATGCCACGTCGAACCAAAAATGCCAT
1 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
8446 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
1 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
* *
8478 GTGGCAATGCCACATCGAACCAAAAATGTCAT
1 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
8510 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
1 GTGGCAATGCCACGTCGAACCAAAAATGCCAT
8542 GTGGCAATGCCACGT
1 GTGGCAATGCCACGT
8557 TGGATGAAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 106 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (32 bp):
GTGGCAATGCCACGTCGAACCAAAAATGCCAT
Found at i:9003 original size:32 final size:30
Alignment explanation
Indices: 8954--9024 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
8944 ATTAGGGGGT
8954 AAAATGTCTTGACTTTGGGAAGTTCAAGGGAC
1 AAAATGTCTTGACTTT-GGAAGTT-AAGGGAC
*
8986 AAAATG-CTATGATTTTGGAAGTTAAGGGAAC
1 AAAATGTCT-TGACTTTGGAAGTTAAGGG-AC
*
9017 ACAATGTC
1 AAAATGTC
9025 CTGATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 5 0.15
31 16 0.47
32 13 0.38
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (30 bp):
AAAATGTCTTGACTTTGGAAGTTAAGGGAC
Found at i:9507 original size:14 final size:13
Alignment explanation
Indices: 9488--9526 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9478 ACTCAACACT
9488 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
9502 AACTGACTCAACA
1 AACTGACTCAAAA
9515 AACTGACT-AAAA
1 AACTGACTCAAAA
9527 CCCGACAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:9519 original size:13 final size:13
Alignment explanation
Indices: 9477--9522 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
9467 GTCAGACTCA
9477 GACTCAACACTAACT
1 GACTCAACA--AACT
*
9492 GACTCGAAAAAACT
1 GACTC-AACAAACT
9506 GACTCAACAAACT
1 GACTCAACAAACT
9519 GACT
1 GACT
9523 AAAACCCGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:9781 original size:44 final size:44
Alignment explanation
Indices: 9697--9826 Score: 208
Period size: 44 Copynumber: 3.0 Consensus size: 44
9687 GTAGATACTG
*
9697 ATCTAATAATTTTTCCTTAATTTTCCTCTAAATTGA-TTTTTTCT
1 ATCTAAT-ATTTTTCCTTAATTTTCTTCTAAATTGATTTTTTTCT
* *
9741 ATCTAATATTTTTCCTCAATTTTCTTCTAAATTTATTTTTTTCT
1 ATCTAATATTTTTCCTTAATTTTCTTCTAAATTGATTTTTTTCT
*
9785 ATCTAATATTTTTCCTTGATTTTCTTCTAAATTGATTTTTTT
1 ATCTAATATTTTTCCTTAATTTTCTTCTAAATTGATTTTTTT
9827 TCCATCACAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 25 0.32
44 54 0.68
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (44 bp):
ATCTAATATTTTTCCTTAATTTTCTTCTAAATTGATTTTTTTCT
Done.