Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024097.1 Corchorus olitorius cultivar O-4 contig24130, 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: 15278
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:3777 original size:8 final size:8
Alignment explanation
Indices: 3766--3932 Score: 68
Period size: 8 Copynumber: 21.2 Consensus size: 8
3756 ATAAAAAAGT
3766 AATAGATA
1 AATAGATA
*
3774 AATAAATA
1 AATAGATA
*
3782 AATAGAAA
1 AATAGATA
*
3790 AATAAGTAAA
1 AAT-AG-ATA
3800 AATA-ATA
1 AATAGATA
* *
3807 GATAAATA
1 AATAGATA
*
3815 AAAAGATA
1 AATAGATA
*
3823 AATAGGTA
1 AATAGATA
*
3831 TATAGATA
1 AATAGATA
*
3839 ATTAGATA
1 AATAGATA
*
3847 AATAGGTA
1 AATAGATA
3855 GGAA-A-A-A
1 --AATAGATA
3862 AAGTAGATA
1 AA-TAGATA
*
3871 ATAGTAAATA
1 A-A-TAGATA
3881 AATAGAT-
1 AATAGATA
3888 AATA-ACTA
1 AATAGA-TA
*
3896 AATTGATA
1 AATAGATA
3904 AATA-A-A
1 AATAGATA
3910 AAT--ATA
1 AATAGATA
3916 AATAG-TA
1 AATAGATA
*
3923 AATAAATA
1 AATAGATA
3931 AA
1 AA
3933 AAATATCTTT
Statistics
Matches: 120, Mismatches: 22, Indels: 34
0.68 0.12 0.19
Matches are distributed among these distances:
5 3 0.03
6 9 0.08
7 19 0.16
8 65 0.54
9 8 0.07
10 16 0.13
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.25
Consensus pattern (8 bp):
AATAGATA
Found at i:5702 original size:18 final size:17
Alignment explanation
Indices: 5679--5713 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5669 ATCCCAATCC
*
5679 AACTATTGTTATGATTTA
1 AACTATGGTTATG-TTTA
5697 AACTATGGTTATGTTTA
1 AACTATGGTTATGTTTA
5714 CTGGGGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (17 bp):
AACTATGGTTATGTTTA
Found at i:7298 original size:25 final size:24
Alignment explanation
Indices: 7264--7310 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
7254 ACGTTTGCAC
7264 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
7289 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
7311 TGTAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:7360 original size:39 final size:41
Alignment explanation
Indices: 7301--7382 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 41
7291 ATACCTAAGA
* * *
7301 ATTTAATTAATGTAATTA-TTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTTCAGTTATTATATATATTAC
*
7340 ATTTAATTAATATAAGTATTTTGAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTTCAGTTATTATATATATTAC
7381 AT
1 AT
7383 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 16 0.43
40 13 0.35
41 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (41 bp):
ATTTAATTAATATAAGTATTTTCAGTTATTATATATATTAC
Found at i:7615 original size:2 final size:2
Alignment explanation
Indices: 7598--7640 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
7588 AGTTTAGACT
*
7598 TA TA TA GTA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7641 AAAGTACGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9491 original size:13 final size:13
Alignment explanation
Indices: 9475--9546 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
9465 AAAGGGAGAA
*
9475 AAAAAAAGAAGAG
1 AAAAAAAGAAAAG
*
9488 AAAAATAGAAAAG
1 AAAAAAAGAAAAG
* *
9501 AAAAATAGAAAGG
1 AAAAAAAGAAAAG
9514 AAAAGAAAGAAAAG
1 AAAA-AAAGAAAAG
* *
9528 -AAAAAAGGAAGG
1 AAAAAAAGAAAAG
9540 AAAAAAA
1 AAAAAAA
9547 AAAGGAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 7 0.14
13 36 0.72
14 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:9504 original size:26 final size:26
Alignment explanation
Indices: 9475--9554 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
9465 AAAGGGAGAA
*
9475 AAAAAAAGAAGAGAAAAATAGAAAAG
1 AAAAAAAGAAGAGAAAAAAAGAAAAG
*
9501 AAAAATAGAA-AGGAAAAGAAAGAAAAG
1 AAAAAAAGAAGA-GAAAA-AAAGAAAAG
* *
9528 AAAAAAGGAAG-GAAAAAAA-AAAGG
1 AAAAAAAGAAGAGAAAAAAAGAAAAG
9552 AAA
1 AAA
9555 TTAAGGAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.15
25 4 0.09
26 19 0.41
27 16 0.35
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAAAAAGAAGAGAAAAAAAGAAAAG
Found at i:9547 original size:16 final size:17
Alignment explanation
Indices: 9522--9553 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9512 GGAAAAGAAA
9522 GAAAAGAAAAAAGGAAG
1 GAAAAGAAAAAAGGAAG
9539 GAAAA-AAAAAAGGAA
1 GAAAAGAAAAAAGGAA
9554 ATTAAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAAGGAAG
Found at i:9548 original size:22 final size:26
Alignment explanation
Indices: 9494--9550 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
9484 AGAGAAAAAT
9494 AGAAAAGAAAAATAGAAAGGAAAAGAA
1 AGAAAAGAAAAATAGAAAGG-AAAGAA
*
9521 AGAAAAGAAAAA-AGGAAGGAAA-AA
1 AGAAAAGAAAAATAGAAAGGAAAGAA
9545 A-AAAAG
1 AGAAAAG
9551 GAAATTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.17
24 3 0.10
25 3 0.10
26 6 0.21
27 12 0.41
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (26 bp):
AGAAAAGAAAAATAGAAAGGAAAGAA
Done.