Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012176.1 Corchorus olitorius cultivar O-4 contig12209, 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: 15125
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:405 original size:22 final size:22
Alignment explanation
Indices: 380--426 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
370 TTTTTAGTTG
*
380 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
402 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
424 AGT
1 AGT
427 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:558 original size:31 final size:31
Alignment explanation
Indices: 523--584 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
513 ATATTCGAAA
523 AATAAGGGTATGATAGGCGATTCAAAAGTTT
1 AATAAGGGTATGATAGGCGATTCAAAAGTTT
554 AATAAGGGTATGATAGGCGATTCAAAAGTTT
1 AATAAGGGTATGATAGGCGATTCAAAAGTTT
585 TACAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATGATAGGCGATTCAAAAGTTT
Found at i:3656 original size:22 final size:22
Alignment explanation
Indices: 3620--3662 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3610 TTTTCCGCAA
* * *
3620 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCATGGACAGGACTTGTC
3642 CAAGTCATGGACAGGACTTGT
1 CAAGTCATGGACAGGACTTGT
3663 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCATGGACAGGACTTGTC
Found at i:3718 original size:21 final size:21
Alignment explanation
Indices: 3692--3733 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3682 TTCAACAGAC
3692 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
3713 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
3734 TCTGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:3734 original size:71 final size:71
Alignment explanation
Indices: 3620--3804 Score: 298
Period size: 71 Copynumber: 2.6 Consensus size: 71
3610 TTTTCCGCAA
* *
3620 CAAGTCCTGGGCAGGAGTTGTCCAAGTCATGGACAGGACTTGTTCTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCATGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC
3685 AACAGAC
65 AACAGAC
* * *
3692 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCATGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
3757 ACAGAC
66 ACAGAC
* *
3763 CAAGTCCTGTGCAGGAGTTGTTAAGTCATGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCATGGGCAGGACTTGT
3805 CCTGTTTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 83 0.80
72 21 0.20
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCATGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:3797 original size:21 final size:21
Alignment explanation
Indices: 3764--3804 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3754 TCAACAGACC
* * *
3764 AAGTCCTGTGCAGGAGTTGTT
1 AAGTCATGGGCAGGACTTGTT
3785 AAGTCATGGGCAGGACTTGT
1 AAGTCATGGGCAGGACTTGT
3805 CCTGTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (21 bp):
AAGTCATGGGCAGGACTTGTT
Found at i:3877 original size:21 final size:19
Alignment explanation
Indices: 3852--3896 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
3842 TTTTTCTTTG
3852 TTCAAATCATCTTCAAACGTC
1 TTCAAATCATCTTC-AA-GTC
* *
3873 TTCAATTGATCTTCAAGTC
1 TTCAAATCATCTTCAAGTC
3892 TTCAA
1 TTCAA
3897 GATGAGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 12 0.55
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (19 bp):
TTCAAATCATCTTCAAGTC
Found at i:4288 original size:30 final size:30
Alignment explanation
Indices: 4249--4359 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
4239 AGGATAAATT
*
4249 ATCA-ATTGACCCACTAAAATTGAAGTTTA
1 ATCACATTGACCCACTAAAATTGAAATTTA
* * *
4278 ATTATATTGACCCCACTAAAATTGAAATTTT
1 ATCACATTGA-CCCACTAAAATTGAAATTTA
* **
4309 ATCACATTGACCCTCATAAAATAAAAGATTT-
1 ATCACATTGACCCAC-TAAAATTGAA-ATTTA
* *
4340 ATAACATTGACCCATTAAAA
1 ATCACATTGACCCACTAAAA
4360 ACGTTGGATG
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 3 0.04
30 14 0.21
31 46 0.69
32 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (30 bp):
ATCACATTGACCCACTAAAATTGAAATTTA
Found at i:9505 original size:31 final size:31
Alignment explanation
Indices: 9467--9526 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
9457 CCCCTGAATC
9467 ACCCTAAACCCAACGGCAGAAGGATTATTTT
1 ACCCTAAACCCAACGGCAGAAGGATTATTTT
* * *
9498 ACCCTAAACCGAATGGGAGAAGGATTATT
1 ACCCTAAACCCAACGGCAGAAGGATTATT
9527 ACTTGCTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
ACCCTAAACCCAACGGCAGAAGGATTATTTT
Done.