Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018212.1 Corchorus olitorius cultivar O-4 contig18245, 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: 12972
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:385 original size:102 final size:102
Alignment explanation
Indices: 218--421 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
208 AAAAATATCT
218 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
1 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
*
283 AAATAGACGCCGCTATAGTCAATTTCAGAAAATCATA
66 AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
320 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
1 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
*
385 AAAAAGATGCCGCTATAGTCAATTTCAGAAAATCATA
66 AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
422 TAGCGGCGTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (102 bp):
CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
Found at i:7893 original size:26 final size:27
Alignment explanation
Indices: 7864--7917 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
7854 TGTTTTGGAT
7864 TGTTTTTGATTGAT-TATATATTATTC
1 TGTTTTTGATTGATATATATATTATTC
7890 TGTTTTTGATTGATCATATATATTATTC
1 TGTTTTTGATTGAT-ATATATATTATTC
7918 CCCAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (27 bp):
TGTTTTTGATTGATATATATATTATTC
Found at i:12454 original size:33 final size:33
Alignment explanation
Indices: 12417--12757 Score: 167
Period size: 33 Copynumber: 10.6 Consensus size: 33
12407 GGTAATACTA
12417 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * * **
12450 ATTTGGTAATCAAAGTAAAAAGA-AAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * * *
12482 ACTGGGTAACTAAAGT--------TATA-TGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* *
12506 ATTTGGTAATTAAAGTTAAAAGAGTAAAGTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* ** ** *
12539 ATTTGGTAATCAAAGTAAAAAGAAAAAAAAGGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGG-T
**
12573 ATTTGGTAATTAAAACAAAAAGAGT-AATATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAT-TGGT
**** *
12606 AAAAAG-AGATTAAAGTAAAAAGAGTAAAATGGT
1 ATTTGGTA-ATTAAAGTAAAAAGAGTAAATTGGT
** * ** * *
12639 AAAAT-GAAATT-TGGTAGCTAAAG-TTAAA-TGGT
1 -ATTTGGTAATTAAAGTA--AAAAGAGTAAATTGGT
* *
12671 ATTCGGTAATTAGAA-TAAAAAGAGTAAATTGAT
1 ATTTGGTAATTA-AAGTAAAAAGAGTAAATTGGT
* *
12704 ATTTGGTAAATATAGTAAAAAGAGTAAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGT-AAATTGGT
*
12738 ATTTGATAATTAAAGTAAAA
1 ATTTGGTAATTAAAGTAAAA
12758 TTGGTAAAAA
Statistics
Matches: 224, Mismatches: 60, Indels: 47
0.68 0.18 0.14
Matches are distributed among these distances:
24 15 0.07
25 2 0.01
31 5 0.02
32 38 0.17
33 108 0.48
34 56 0.25
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (33 bp):
ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
Found at i:12642 original size:16 final size:17
Alignment explanation
Indices: 12589--12642 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
12579 TAATTAAAAC
*
12589 AAAAAGAGTAATATGGT
1 AAAAAGAGTAAAATGGT
*
12606 AAAAAGAGATTAAA--GT
1 AAAAAGAG-TAAAATGGT
12622 AAAAAGAGTAAAATGGT
1 AAAAAGAGTAAAATGGT
12639 AAAA
1 AAAA
12643 TGAAATTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 14 0.45
18 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (17 bp):
AAAAAGAGTAAAATGGT
Found at i:12765 original size:34 final size:33
Alignment explanation
Indices: 12677--12811 Score: 96
Period size: 34 Copynumber: 3.9 Consensus size: 33
12667 TGGTATTCGG
*
12677 TAATTAGAA-TAAAAAGAGT-AAATTGATATTTGG
1 TAATTA-AAGTAAAAAG-GTAAAATTGATATTTGA
* * *
12710 TAAATATAGTAAAAAGAGTAAAATTGGTATTTGA
1 TAATTAAAGTAAAAAG-GTAAAATTGATATTTGA
* *
12744 TAATTAAAGTAAAATTGGTAAAAAGATATGGTATTT-A
1 TAATTAAAGTAAAA-AGGT--AAA-AT-TGATATTTGA
* *
12781 GTAATTAAAGGAAAAGGGTAAAATTGATATT
1 -TAATTAAAGTAAAAAGGTAAAATTGATATT
12812 CAGTAATCAG
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
32 1 0.01
33 21 0.25
34 28 0.33
35 4 0.05
36 3 0.04
37 6 0.07
38 21 0.25
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.33
Consensus pattern (33 bp):
TAATTAAAGTAAAAAGGTAAAATTGATATTTGA
Done.