Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold933
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: 4112
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Found at i:171 original size:7 final size:7
Alignment explanation
Indices: 161--233 Score: 83
Period size: 8 Copynumber: 9.7 Consensus size: 7
151 TAAACCAAAA
161 ACCCTAC
1 ACCCTAC
168 ACCCTAC
1 ACCCTAC
*
175 AACCCTAAA
1 -ACCCT-AC
184 ACCCTAC
1 ACCCTAC
*
191 ACCCTAAA
1 ACCCT-AC
199 ACCCTAC
1 ACCCTAC
206 ACCCTAC
1 ACCCTAC
213 ACCCTAC
1 ACCCTAC
220 AACCCTAC
1 -ACCCTAC
228 AACCCT
1 -ACCCT
234 CAACCCCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
7 28 0.48
8 29 0.50
9 1 0.02
ACGTcount: A:0.36, C:0.51, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAC
Found at i:237 original size:7 final size:7
Alignment explanation
Indices: 1--505 Score: 393
Period size: 7 Copynumber: 69.9 Consensus size: 7
1 AAACCCT
1 AAACCCT
8 AAAACCCT
1 -AAACCCT
16 AAAACCCT
1 -AAACCCT
24 AAAACCCT
1 -AAACCCT
32 AAAACCC-
1 -AAACCCT
39 AAACCCCT
1 AAA-CCCT
*
47 AACCCCT
1 AAACCCT
54 AAACCCT
1 AAACCCT
61 AAACCC-
1 AAACCCT
*
67 AGACCCT
1 AAACCCT
*
74 AAACCCC
1 AAACCCT
*
81 AACCCCCT
1 AA-ACCCT
89 -AACCCT
1 AAACCCT
95 AAAACCC-
1 -AAACCCT
*
102 AAACCCC
1 AAACCCT
109 AAACCCCT
1 AAA-CCCT
*
117 AACCCCT
1 AAACCCT
*
124 AACCCCT
1 AAACCCT
*
131 AAACCAT
1 AAACCCT
**
138 AAACCAA
1 AAACCCT
145 AAACCCT
1 AAACCCT
**
152 AAACCAA
1 AAACCCT
159 AAACCCT
1 AAACCCT
*
166 ACACCCT
1 AAACCCT
173 ACAACCCT
1 A-AACCCT
181 AAAACCCT
1 -AAACCCT
*
189 ACACCCT
1 AAACCCT
196 AAAACCCT
1 -AAACCCT
*
204 ACACCCT
1 AAACCCT
*
211 ACACCCT
1 AAACCCT
218 ACAACCCT
1 A-AACCCT
226 ACAACCCT
1 A-AACCCT
* *
234 CAACCCC
1 AAACCCT
*
241 AAACCCC
1 AAACCCT
248 AAATCCC-
1 AAA-CCCT
*
255 AACCCCCT
1 AA-ACCCT
263 AAAACCCT
1 -AAACCCT
271 AAACCCT
1 AAACCCT
278 AAAACCCT
1 -AAACCCT
286 -AACCCT
1 AAACCCT
292 AAAACCCT
1 -AAACCCT
300 AAACCCT
1 AAACCCT
307 AAACCCTT
1 AAACCC-T
315 AAAACCCT
1 -AAACCCT
323 AAACCCT
1 AAACCCT
330 AAACCCTT
1 AAACCC-T
338 AAACCCT
1 AAACCCT
* *
345 AAAACCA
1 AAACCCT
*
352 AAACCCC
1 AAACCCT
*
359 AAACCCC
1 AAACCCT
*
366 CAACCCTT
1 AAACCC-T
374 AAACCCT
1 AAACCCT
381 AAACCCT
1 AAACCCT
388 AAA-CCT
1 AAACCCT
394 CAAACCCT
1 -AAACCCT
*
402 AAACCCC
1 AAACCCT
409 AAACCCT
1 AAACCCT
*
416 AAACCCC
1 AAACCCT
423 AAA-CCT
1 AAACCCT
429 -AACCCTT
1 AAACCC-T
*
436 AAACCCC
1 AAACCCT
*
443 AAAGCCT
1 AAACCCT
450 AAAAACCCT
1 --AAACCCT
459 -AACCCT
1 AAACCCT
*
465 AAACACT
1 AAACCCT
472 AAAACCCT
1 -AAACCCT
*
480 -AACCCC
1 AAACCCT
*
486 ACACCCT
1 AAACCCT
*
493 AAACCCC
1 AAACCCT
500 AAACCC
1 AAACCC
506 AAAAAGACGC
Statistics
Matches: 412, Mismatches: 52, Indels: 67
0.78 0.10 0.13
Matches are distributed among these distances:
5 2 0.00
6 42 0.10
7 230 0.56
8 123 0.30
9 15 0.04
ACGTcount: A:0.42, C:0.46, G:0.00, T:0.11
Consensus pattern (7 bp):
AAACCCT
Found at i:791 original size:31 final size:31
Alignment explanation
Indices: 736--800 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
726 GATATTCCTA
*
736 GAATAGCTTAATCCATGTTAGGATATCCCGG
1 GAATAGCTTAATCCACGTTAGGATATCCCGG
** * *
767 GAATAGCTTAATTGACGTTGGGATATCCCTG
1 GAATAGCTTAATCCACGTTAGGATATCCCGG
798 GAA
1 GAA
801 AATCTCTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (31 bp):
GAATAGCTTAATCCACGTTAGGATATCCCGG
Found at i:2059 original size:17 final size:17
Alignment explanation
Indices: 2037--2070 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2027 GCTTTTTTTT
2037 ATTATTCTTAATATAAA
1 ATTATTCTTAATATAAA
*
2054 ATTATTTTTAATATAAA
1 ATTATTCTTAATATAAA
2071 TATAGATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTCTTAATATAAA
Found at i:3564 original size:23 final size:23
Alignment explanation
Indices: 3537--3591 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
3527 AAATACTTTA
3537 AATTTTATTAGCCAATCATAAAT
1 AATTTTATTAGCCAATCATAAAT
* *
3560 AATTTTATCAGCCACTCATAAAT
1 AATTTTATTAGCCAATCATAAAT
3583 AATTTTATT
1 AATTTTATT
3592 GTTAGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (23 bp):
AATTTTATTAGCCAATCATAAAT
Done.