Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_197 ID=scaffold_197-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: 9468
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:4335 original size:6 final size:6
Alignment explanation
Indices: 4288--4359 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
4278 AGTGAAGAAA
* * * *
4288 AAAATA AAAATC AAAATC AAAAGC AAAAGC AAAAATAA AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC -AAAAT-C AAAATC AAAATC
* * *
4338 AAAGTC AAAGTC AAAGTC AAAA
1 AAAATC AAAATC AAAATC AAAA
4360 AATGAAAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 48 0.84
7 9 0.16
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:6773 original size:129 final size:129
Alignment explanation
Indices: 6538--7029 Score: 675
Period size: 129 Copynumber: 3.8 Consensus size: 129
6528 ATCAATGAAT
* * *
6538 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAA-
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* * *
6602 TAGCAAGGAAGCAGATTTAAGCCAAAAGTCTTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
66 T-GTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* *
6667 ATTACAAATCTTGTCTCCCTAAATAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* *
6732 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCTCTGGTCAGTAGTGGAATAGGTTGGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * * * *
6796 ATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAAATCTTATCTTCAAG
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* * *
6861 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGCCAGCCGTGGAATAGGTTGGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * **
6925 ATTACAAATCTTGTCTCCCGAAGA-AATAGCGGAGCAAATC-AAGGACGGTGAATCTTATCTTCA
1 ATTACAAATCTTGTCTCCCTAA-ACAGTAGCGGAGCAGATCGAA-GACGACGAATCTTATCTTCA
* * * * *
6988 AGAGTAAGAAAGTAGATTTAAGCCACAAATCCTATCTCCCTG
64 AGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTG
7030 AAGTTGTAGT
Statistics
Matches: 322, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
128 2 0.01
129 319 0.99
130 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (129 bp):
ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
Found at i:7083 original size:44 final size:44
Alignment explanation
Indices: 7020--7436 Score: 254
Period size: 44 Copynumber: 9.6 Consensus size: 44
7010 CCACAAATCC
* * *
7020 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* * * * * * *
7064 TATCTCTCTGAAGTTGTAGTAGAGTAGA-T--CGCATTAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* * * *** * *
7105 TATTTCCCTG-AGATTACAGCGGAGCAGACCGAAG-AAGCAAATCT
1 TATCTCCCTGAAG-TTGCAGTGGAGCAGATTAAAGCAA-TAGATCT
* * *
7149 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAGATCT
* * *
7193 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCAATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAGATCT
* * *
7237 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* ** *
7281 TATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAA-TAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCAATAGATCT
** ** * * *
7325 TATCTATCTGAAGTTGC-GCAGAGTAGA-T-CA-C-ATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT-AGATCT
* * *
7365 TATCTCCCTGAGGTTGCACTGGAGCAGACTGAGAAAGC-A-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-T--TAAAGCAATAGATCT
* *
7409 TATCCCCCTGAAGTTGCAGTGGGGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
7437 CTGACAACAG
Statistics
Matches: 293, Mismatches: 62, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
39 2 0.01
40 22 0.08
41 32 0.11
42 1 0.00
43 13 0.04
44 212 0.72
45 7 0.02
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
Found at i:8197 original size:4 final size:4
Alignment explanation
Indices: 8188--8213 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
8178 CCATTTTTGG
8188 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
8214 GTGCGTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.