Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_144 ID=scaffold_144-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: 11518
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.29
Warning! 550 characters in sequence are not A, C, G, or T
Found at i:5300 original size:9 final size:9
Alignment explanation
Indices: 5283--5341 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
5273 ATCCAAAAAA
5283 AAAAACAAC
1 AAAAACAAC
*
5292 AACAACAAC
1 AAAAACAAC
5301 AAAAACAA-
1 AAAAACAAC
*
5309 AAAAGCAAC
1 AAAAACAAC
5318 AAAAA-AAC
1 AAAAACAAC
*
5326 AAAAAAGAAC
1 -AAAAACAAC
5336 AAAAAC
1 AAAAAC
5342 TAAAAACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 10 0.24
9 29 0.69
10 3 0.07
ACGTcount: A:0.78, C:0.19, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAACAAC
Found at i:5309 original size:6 final size:6
Alignment explanation
Indices: 5276--5365 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
5266 AAATTCAATC
* * * *
5276 CAAAAA AAAAAA CAACAA CAACAA CAAAAA CAAAAAA GCAACAA -AAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C-AAAAA -CAAAAA CAAAAA
*
5325 C-AAAA -AAGAA CAAAAA CTAAAAA CAAAAA -AAGAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA C-AAAAA CAAAAA CAA-AAA CAAAAA
5366 AAACCTCTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
5 13 0.19
6 37 0.54
7 17 0.25
8 1 0.01
ACGTcount: A:0.80, C:0.16, G:0.03, T:0.01
Consensus pattern (6 bp):
CAAAAA
Found at i:5310 original size:23 final size:21
Alignment explanation
Indices: 5292--5369 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
5282 AAAAAACAAC
5292 AACAACAACAAAAAC-AAAAA
1 AACAACAACAAAAACAAAAAA
*
5312 AGCAACAA-AAAAACAAAAAA
1 AACAACAACAAAAACAAAAAA
*
5332 GAACAAAAACTAAAAACAAAAAA
1 -AACAACAAC-AAAAACAAAAAA
*
5355 AGA-AACAAAAAAAAC
1 A-ACAACAACAAAAAC
5370 CTCTACCGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.12
20 12 0.25
21 12 0.25
22 5 0.10
23 13 0.27
ACGTcount: A:0.79, C:0.15, G:0.04, T:0.01
Consensus pattern (21 bp):
AACAACAACAAAAACAAAAAA
Found at i:5317 original size:26 final size:23
Alignment explanation
Indices: 5276--5368 Score: 93
Period size: 25 Copynumber: 4.0 Consensus size: 23
5266 AAATTCAATC
*
5276 CAAAAAAAAAAACAACAACAACAA
1 CAAAAAAAAAAACAACAA-AAAAA
5300 CAAAAACAAAAAAGCAACAAAAAAA
1 CAAAAA-AAAAAA-CAACAAAAAAA
*
5325 CAAAAAAGAACAAA-AAC-TAAAAA
1 CAAAAAA-AA-AAACAACAAAAAAA
*
5348 CAAAAAAAGAAACAA-AAAAAA
1 CAAAAAAAAAAACAACAAAAAA
5369 CCTCTACCGG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.05
22 7 0.12
23 12 0.20
24 10 0.17
25 18 0.31
26 9 0.15
ACGTcount: A:0.81, C:0.15, G:0.03, T:0.01
Consensus pattern (23 bp):
CAAAAAAAAAAACAACAAAAAAA
Found at i:5361 original size:35 final size:35
Alignment explanation
Indices: 5278--5366 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
5268 ATTCAATCCA
5278 AAAAAAAAAACAACAACAACAACAAAAACAAAAAAGC
1 AAAAAAAAAACAA-AA-AACAACAAAAACAAAAAAGC
* * *
5315 AACAAAAAAACAAAAAAGAACAAAAACTAAAAA-C
1 AAAAAAAAAACAAAAAACAACAAAAACAAAAAAGC
5349 AAAAAAAGAAACAAAAAA
1 AAAAAAA-AAACAAAAAA
5367 AACCTCTACC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
34 7 0.15
35 26 0.55
36 2 0.04
37 12 0.26
ACGTcount: A:0.81, C:0.15, G:0.03, T:0.01
Consensus pattern (35 bp):
AAAAAAAAAACAAAAAACAACAAAAACAAAAAAGC
Found at i:5889 original size:15 final size:15
Alignment explanation
Indices: 5871--5917 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
5861 AAAAAGATAT
5871 GAAAAAATAAAAATG
1 GAAAAAATAAAAATG
5886 G-AAAAATGAAAAATG
1 GAAAAAAT-AAAAATG
*
5901 GAAAAAGTAAAAATG
1 GAAAAAATAAAAATG
5916 GA
1 GA
5918 GAGGCTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 18 0.62
16 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
GAAAAAATAAAAATG
Found at i:5890 original size:8 final size:8
Alignment explanation
Indices: 5879--5917 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
5869 ATGAAAAAAT
5879 AAAAATGG
1 AAAAATGG
5887 AAAAAT-G
1 AAAAATGG
5894 AAAAATGG
1 AAAAATGG
*
5902 AAAAA-GT
1 AAAAATGG
5909 AAAAATGG
1 AAAAATGG
5917 A
1 A
5918 GAGGCTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (8 bp):
AAAAATGG
Found at i:9687 original size:100 final size:100
Alignment explanation
Indices: 9514--10287 Score: 1071
Period size: 100 Copynumber: 7.7 Consensus size: 100
9504 TGGGCGTTGT
* *
9514 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCTGACAGTGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
** *
9579 AGCCACAACGGTGGATCTTACTTCCCCGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
9614 AGTGGAGCAGATTGAAGTTACAACGGCGAATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
*
9679 AGCCACAACGGCAGATCTTACTTCCCTGGCGATGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * * *
9714 AGTGGAGCAGATTGAAGTCACAACTGCGGATCTGGTTTCCTCAACAGGGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
**
9779 AGCCACAACGGCAGATCTTACTTCCCCAGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
9814 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTTCCCGACAGTGCAACTAAAAAGGTTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
* **
9879 AGCTACAACGGTGGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
9914 AGTAGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCTCGACAATGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
* *
9979 AGCCACAACGGCGGATCTTACTTCCCTGGCGGTAC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
10014 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTTAAAAGTTTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
* * *
10079 AGCCACAACAGCATATCTTACTTCCCTGGCAGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
10114 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCTGACAGTGTAATTTAAAATTCTTT
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAA-TTAAAA-----A
** ** * *
10179 TTTTGAAGCCACAATAGCAGATCTTACTTACCTGGCGGTGT
60 GATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * * ** *
10220 AGTAGAGCAGATTGAAGTCATAACGGCGGATCTGATTTCTTCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
10285 AGC
66 AGC
10288 ATCAATTCTT
Statistics
Matches: 596, Mismatches: 72, Indels: 12
0.88 0.11 0.02
Matches are distributed among these distances:
100 506 0.85
101 5 0.01
105 6 0.01
106 79 0.13
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (100 bp):
AGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGTGCAATTAAAAAGATTGA
AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
Done.