Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_36 ID=scaffold_36-JGI_221_v2.0
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: 31191
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 289 characters in sequence are not A, C, G, or T
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--33 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 T
2 TA 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
34 CACATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2456 original size:19 final size:19
Alignment explanation
Indices: 2432--2472 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2422 ACCCATATAG
*
2432 TTATTTAGGTAGATAAATC
1 TTATTTAGATAGATAAATC
2451 TTATTTAGATAGATAAATC
1 TTATTTAGATAGATAAATC
2470 TTA
1 TTA
2473 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
TTATTTAGATAGATAAATC
Found at i:2559 original size:41 final size:41
Alignment explanation
Indices: 2496--2588 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
2486 AAGATATTAT
*
2496 AGGAA-TATTTTATTTTATTTTTAGTAGTTTATTAGAAT-A
1 AGGAATTATTTTATCTTATTTTTAGTAGTTTATTAGAATAA
*
2535 AGAGAATTATTTT-TCTTATGTTTTAGTGGTTTATTAGAATAA
1 AG-GAATTATTTTATCTTAT-TTTTAGTAGTTTATTAGAATAA
2577 AGGAATTATTTT
1 AGGAATTATTTT
2589 CCCAATTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
39 2 0.04
40 8 0.17
41 35 0.73
42 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (41 bp):
AGGAATTATTTTATCTTATTTTTAGTAGTTTATTAGAATAA
Found at i:5811 original size:4 final size:4
Alignment explanation
Indices: 5802--5852 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
5792 GTAACGAATT
5802 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5850 ATA
1 ATA
5853 TACCAAAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:7041 original size:26 final size:26
Alignment explanation
Indices: 7012--7064 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
7002 GTCCTATATG
7012 TTATCTGGTGTGCTCTTCTTCTTTAA
1 TTATCTGGTGTGCTCTTCTTCTTTAA
7038 TTATCTGGTGTGCTCTTCTTCTTTAA
1 TTATCTGGTGTGCTCTTCTTCTTTAA
7064 T
1 T
7065 ATTTTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (26 bp):
TTATCTGGTGTGCTCTTCTTCTTTAA
Found at i:12387 original size:13 final size:13
Alignment explanation
Indices: 12369--12403 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12359 GGAATTCATG
12369 CCTTGATGCTGTA
1 CCTTGATGCTGTA
*
12382 CCTTGATGATGTA
1 CCTTGATGCTGTA
12395 CCTTGATGC
1 CCTTGATGC
12404 AGTCCAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (13 bp):
CCTTGATGCTGTA
Found at i:15342 original size:21 final size:21
Alignment explanation
Indices: 15316--15371 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
15306 AACAGCGGTG
*
15316 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
15337 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
15358 GTGGTGAGATTAGA
1 GCGGTGAGATTAGA
15372 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:26810 original size:15 final size:15
Alignment explanation
Indices: 26792--26860 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
26782 AATAAAAAAT
26792 TAATTAATATTTATA
1 TAATTAATATTTATA
*
26807 TAATTAACTA-TTAAA
1 TAATTAA-TATTTATA
26822 TAATT-ATATTTAGTA
1 TAATTAATATTTA-TA
26837 TATATT-ATA-TTATA
1 TA-ATTAATATTTATA
* *
26851 AAAATAATAT
1 TAATTAATAT
26861 ACATACACGT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.09
14 10 0.23
15 22 0.50
16 8 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
TAATTAATATTTATA
Found at i:30648 original size:11 final size:11
Alignment explanation
Indices: 30632--30678 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
30622 GTAATAATAT
*
30632 AATAGCGAAAC
1 AATAGCAAAAC
30643 AATAGCAAAAC
1 AATAGCAAAAC
*
30654 AATA-AAAAAC
1 AATAGCAAAAC
30664 AAT-GACAAAAC
1 AATAG-CAAAAC
30675 AATA
1 AATA
30679 AAAATGCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 8 0.27
11 22 0.73
ACGTcount: A:0.66, C:0.15, G:0.09, T:0.11
Consensus pattern (11 bp):
AATAGCAAAAC
Found at i:30663 original size:21 final size:21
Alignment explanation
Indices: 30639--30682 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
30629 TATAATAGCG
30639 AAACAAT-AGCAAAACAATAAA
1 AAACAATGA-CAAAACAATAAA
30660 AAACAATGACAAAACAATAAA
1 AAACAATGACAAAACAATAAA
30681 AA
1 AA
30683 TGCATCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.73, C:0.14, G:0.05, T:0.09
Consensus pattern (21 bp):
AAACAATGACAAAACAATAAA
Done.