Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018068.1 Corchorus olitorius cultivar O-4 contig18101, 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: 7675
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Found at i:681 original size:24 final size:25
Alignment explanation
Indices: 652--702 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
642 TTATGTGAAC
*
652 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
676 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
701 AA
1 AA
703 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:2671 original size:40 final size:40
Alignment explanation
Indices: 2616--3270 Score: 908
Period size: 40 Copynumber: 16.4 Consensus size: 40
2606 TAAAATACAA
*
2616 ATCATCTTTTTATCAAATTAACTTCAAAATCCTGCACAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* *
2656 ATCATCTTTTTATCAAATTAATTTTAAAATCCTGCACAAG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
*
2696 ATCAT-TGTTTTATCAAATTAATTTCAGAATCCTGCACAGG
1 ATCATCT-TTTTATCAAATTAATTTCAAAATCCTGCACAGG
* *
2736 ATCATCTTTTTATCAAATTAATTTCAAAATCCTACTCAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
2776 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
**
2816 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCTTAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* * *
2856 ATCAT-TGCTTTATCAAATTAATTTCAGAATCCTGCACATG
1 ATCATCT-TTTTATCAAATTAATTTCAAAATCCTGCACAGG
*
2896 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCTCAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* *
2936 ATCAT-TGCTTTATCAAATTAATTTCAGAATCCTGCACAGG
1 ATCATCT-TTTTATCAAATTAATTTCAAAATCCTGCACAGG
* * * *
2976 ATCATCTTTTTATCAAATTAATTTCAGAATCTTACACAAG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
*
3016 ATCATCTTTTTATCAAATTAATTTCAGAATCCTGCACAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
*
3056 ATCATCTTTTTATCAAATTAATTTCAGAATCCTGCACAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* *
3096 ATCAT-TGCTTTATCAAATTAATTTCAGAATCCTGCACAGG
1 ATCATCT-TTTTATCAAATTAATTTCAAAATCCTGCACAGG
* **
3136 ATCATCTTTTTATCAAAGTAATTTCAAAATCCTGCTTAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* * *
3176 ATCATCGTTTTATCAAATTAATTTCAAAATCCTACTCAGG
1 ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
* * * * **
3216 ATCAT-TGCTTTATCAAGTGAATTTCAGAATCCTGTTCAGG
1 ATCATCT-TTTTATCAAATTAATTTCAAAATCCTGCACAGG
3256 ATCAT-TTCTTTATCA
1 ATCATCTT-TTTATCA
3271 TTCAATTTCA
Statistics
Matches: 555, Mismatches: 50, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
39 4 0.01
40 547 0.99
41 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.38
Consensus pattern (40 bp):
ATCATCTTTTTATCAAATTAATTTCAAAATCCTGCACAGG
Found at i:3710 original size:24 final size:24
Alignment explanation
Indices: 3660--3725 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
3650 ATTTCTAATT
**
3660 CAATTTTTCAATTTTACAGGTCAA
1 CAATTTTTCAATTTTACAAATCAA
* **
3684 CAATTTTTCAATTTTGCAAATTTA
1 CAATTTTTCAATTTTACAAATCAA
* *
3708 CAATTTTGCAAATTTACA
1 CAATTTTTCAATTTTACA
3726 TGGTTCATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (24 bp):
CAATTTTTCAATTTTACAAATCAA
Found at i:3713 original size:16 final size:16
Alignment explanation
Indices: 3692--3725 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3682 AACAATTTTT
3692 CAATTTTGCAAATTTA
1 CAATTTTGCAAATTTA
3708 CAATTTTGCAAATTTA
1 CAATTTTGCAAATTTA
3724 CA
1 CA
3726 TGGTTCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (16 bp):
CAATTTTGCAAATTTA
Found at i:3831 original size:25 final size:26
Alignment explanation
Indices: 3803--3851 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3793 GTGCATATCT
*
3803 TTATGATTTCATTTCTTTT-TTATTG
1 TTATGATTGCATTTCTTTTCTTATTG
* *
3828 TTATTATTGGATTTCTTTTCTTAT
1 TTATGATTGCATTTCTTTTCTTAT
3852 GTTTGCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (26 bp):
TTATGATTGCATTTCTTTTCTTATTG
Done.