Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_317 ID=scaffold_317-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: 8271
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:576 original size:3 final size:3
Alignment explanation
Indices: 570--611 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
560 TATTAGCCTT
570 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
612 CTTACTTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:618 original size:4 final size:4
Alignment explanation
Indices: 609--665 Score: 105
Period size: 4 Copynumber: 14.2 Consensus size: 4
599 ATTATTATTA
*
609 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TAAC
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC
657 TTAC TTAC T
1 TTAC TTAC T
666 AGTTCTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAC
Found at i:3287 original size:20 final size:20
Alignment explanation
Indices: 3250--3287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3240 ACGGTATCAA
*
3250 AACAAAGGTTAGAGAAATGG
1 AACAAAGGTTAGAAAAATGG
*
3270 AACAAAGGTTGGAAAAAT
1 AACAAAGGTTAGAAAAAT
3288 TAGAGTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (20 bp):
AACAAAGGTTAGAAAAATGG
Found at i:6324 original size:7 final size:7
Alignment explanation
Indices: 6301--6348 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
6291 TTGAGTCAAA
6301 AAAAATG
1 AAAAATG
6308 -AAAATG
1 AAAAATG
6314 -AAAATG
1 AAAAATG
*
6320 AAAAATT
1 AAAAATG
6327 AAAAATG
1 AAAAATG
*
6334 AAAAAAG
1 AAAAATG
6341 TAAAAATG
1 -AAAAATG
6349 GAGAGGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (7 bp):
AAAAATG
Found at i:6344 original size:15 final size:14
Alignment explanation
Indices: 6301--6348 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
6291 TTGAGTCAAA
6301 AAAAATG-AAAA-T
1 AAAAATGAAAAAGT
* *
6313 GAAAATGAAAAATT
1 AAAAATGAAAAAGT
6327 AAAAATGAAAAAAGT
1 AAAAATG-AAAAAGT
6342 AAAAATG
1 AAAAATG
6349 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 6 0.20
13 4 0.13
14 7 0.23
15 13 0.43
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:7759 original size:128 final size:128
Alignment explanation
Indices: 7531--8062 Score: 861
Period size: 128 Copynumber: 4.2 Consensus size: 128
7521 TTGGTGAAAT
*
7531 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTCGAAATTGCAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* *
7596 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGC
66 AAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* * *
7659 CACAAGTCCTATGTCCCTGACCAGTAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCTCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * *
7724 AAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAAGAAGTAGATTTAAGC
66 AAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
7787 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAA-
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
*
7851 ATAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTATAAGGAAGCAGATTTAAGC
66 A-AGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* *
7915 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATCGGTTGGAAATTGCAGATCTTGTCTCCTTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
* * * * *
7980 CAGTAGCGTAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCATATTGAAGC
66 AAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* *
8043 CGATAA-TCCTATCTCCCTGA
1 C-ACAAGTCCTATGTCCCTGA
8063 AGTTGTAGTG
Statistics
Matches: 375, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
127 1 0.00
128 371 0.99
129 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (128 bp):
CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
AAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
Done.