Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019581.1 Corchorus olitorius cultivar O-4 contig19614, 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: 4024
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:49 original size:13 final size:12
Alignment explanation
Indices: 18--51 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
8 GTTGATATCC
18 TCTTTTCTTTTTT
1 TCTTTT-TTTTTT
*
31 TCTTTTTTTTTG
1 TCTTTTTTTTTT
43 TCTTTTTTT
1 TCTTTTTTT
52 AGAAATGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:676 original size:19 final size:20
Alignment explanation
Indices: 652--691 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
642 GTTAAAGACT
652 AGGCCCAAA-CGAAACAAAG
1 AGGCCCAAACCGAAACAAAG
671 AGGCCCAAACCGAAACAAAG
1 AGGCCCAAACCGAAACAAAG
691 A
1 A
692 ACCAAGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.53, C:0.28, G:0.20, T:0.00
Consensus pattern (20 bp):
AGGCCCAAACCGAAACAAAG
Found at i:966 original size:6 final size:6
Alignment explanation
Indices: 955--987 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
945 TGAATTTACA
*
955 CAAAAT CAAAAT TAAAAT CAAAAT CAAAAT CAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAA
988 TCCGAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
CAAAAT
Found at i:3581 original size:40 final size:40
Alignment explanation
Indices: 3515--3985 Score: 574
Period size: 40 Copynumber: 11.8 Consensus size: 40
3505 AGGATGATCC
* * * *
3515 TGAAATTAA-ATGATAAAGA-AATGATCCTGAACAGGATTC
1 TGAAATTAATTTGATAAA-ACAATGATCCTGAGCAGGGTTT
* * * * *
3554 TGAAATTCAATTT-ATAGAGCAATGATCCTGAGTAAGATTT
1 TGAAATT-AATTTGATAAAACAATGATCCTGAGCAGGGTTT
* * * * *
3594 TGAAATTAGTTTGATAAAGCAATGGTCCTGAGCAGGATTC
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
* * *
3634 TGAAATTAACTAGATAAAATAATGATCCTGAGCAGGGTTT
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
* *
3674 TGAAATTAATTTGATAAAA-AGATGATCCTGAGCAGGATTC
1 TGAAATTAATTTGATAAAACA-ATGATCCTGAGCAGGGTTT
* * *
3714 TGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTT
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
3754 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
*
3794 TGAAATTAATTTGATAAAACAATGATCCTGAGAAGGGTTT
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
* *
3834 TGAAATTAATTTGATAAAA-AGATGATCCTGAGCAGGATTC
1 TGAAATTAATTTGATAAAACA-ATGATCCTGAGCAGGGTTT
* * *
3874 TGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTT
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
* *
3914 TGAAATTAATTTGATAAAACAATGATCCTGAGTAGGGTTC
1 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
* * *
3954 TGAAATTAATTTAATAAAGCAAAGATCCTGAG
1 TGAAATTAATTTGATAAAACAATGATCCTGAG
3986 TAGGATTGTG
Statistics
Matches: 374, Mismatches: 50, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
39 13 0.03
40 358 0.96
41 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (40 bp):
TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTT
Found at i:3623 original size:80 final size:79
Alignment explanation
Indices: 3515--3985 Score: 640
Period size: 80 Copynumber: 5.9 Consensus size: 79
3505 AGGATGATCC
* * *
3515 TGAAATTAA-ATGATAAAGAAATGATCCTGAACAGGATTCTGAAATTCAATTT-ATAGAGCAATG
1 TGAAATTAATTTGATAAA-AAATGATCCTGAGCAGGATTCTGAAATT-AATTTGATAAAGCAATG
* * *
3578 ATCCTGAGTAAGATTT
64 ATCCTGAGCAGGGTTT
* * * * * **
3594 TGAAATTAGTTTGATAAAGCAATGGTCCTGAGCAGGATTCTGAAATTAACTAGATAAAATAATGA
1 TGAAATTAATTTGATAAA-AAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
3659 TCCTGAGCAGGGTTT
65 TCCTGAGCAGGGTTT
* *
3674 TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGA
1 TGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
3739 TCCTGAGCAGGGTTT
65 TCCTGAGCAGGGTTT
* * *
3754 TGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGA
1 TGAAATTAATTTGATAAAA-AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
*
3819 TCCTGAGAAGGGTTT
65 TCCTGAGCAGGGTTT
* *
3834 TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGA
1 TGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
3899 TCCTGAGCAGGGTTT
65 TCCTGAGCAGGGTTT
* * * *
3914 TGAAATTAATTTGATAAAACAATGATCCTGAGTAGGGTTCTGAAATTAATTTAATAAAGCAAAGA
1 TGAAATTAATTTGATAAAA-AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGA
3979 TCCTGAG
65 TCCTGAG
3986 TAGGATTGTG
Statistics
Matches: 346, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
79 13 0.04
80 331 0.96
81 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (79 bp):
TGAAATTAATTTGATAAAAAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGAT
CCTGAGCAGGGTTT
Done.