Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CCACVL1_25597
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, 795
Length: 1326
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Found at i:139 original size:6 final size:6
Alignment explanation
Indices: 124--173 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
114 AAAACAAGCC
* * *
124 CAACAA CAACAG CAACAT CAACAT C-A-A- CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
169 CAACA
1 CAACA
174 ACAAGCGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 2 0.05
6 34 0.87
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (6 bp):
CAACAG
Found at i:139 original size:12 final size:12
Alignment explanation
Indices: 124--177 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
114 AAAACAAGCC
124 CAACAACAACAG
1 CAACAACAACAG
*
136 CAACATC-A-A-
1 CAACAACAACAG
*
145 CATCAACAACAG
1 CAACAACAACAG
*
157 CAACAGCAACAG
1 CAACAACAACAG
169 CAACAACAA
1 CAACAACAA
178 GCGATTTCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 2 0.06
12 24 0.73
ACGTcount: A:0.56, C:0.33, G:0.07, T:0.04
Consensus pattern (12 bp):
CAACAACAACAG
Found at i:145 original size:15 final size:15
Alignment explanation
Indices: 127--176 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
117 ACAAGCCCAA
*
127 CAACAACAGCAACAT
1 CAACAACAGCAACAG
* *
142 CAACATCAACAACAG
1 CAACAACAGCAACAG
157 ---CAACAGCAACAG
1 CAACAACAGCAACAG
169 CAACAACA
1 CAACAACA
177 AGCGATTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
12 10 0.37
15 17 0.63
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (15 bp):
CAACAACAGCAACAG
Found at i:151 original size:21 final size:21
Alignment explanation
Indices: 127--176 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
117 ACAAGCCCAA
* *
127 CAACAACAGCAACATCAACAT
1 CAACAACAGCAACAGCAACAG
148 CAACAACAGCAACAGCAACAG
1 CAACAACAGCAACAGCAACAG
169 CAACAACA
1 CAACAACA
177 AGCGATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.34, G:0.08, T:0.04
Consensus pattern (21 bp):
CAACAACAGCAACAGCAACAG
Found at i:335 original size:18 final size:18
Alignment explanation
Indices: 312--350 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
302 CTTCTAATTT
*
312 ACAACCACCACCACAACA
1 ACAACCACCACAACAACA
* *
330 ACAACCCCCGCAACAACA
1 ACAACCACCACAACAACA
348 ACA
1 ACA
351 GCAGCAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (18 bp):
ACAACCACCACAACAACA
Found at i:358 original size:12 final size:12
Alignment explanation
Indices: 343--431 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
333 ACCCCCGCAA
343 CAACAACAGCAG
1 CAACAACAGCAG
* *
355 CAACAGCCTCCGCAG
1 CAACA---ACAGCAG
*
370 CAGCAACAGCAG
1 CAACAACAGCAG
* *
382 CCACAACAGCAA
1 CAACAACAGCAG
**
394 CAACAACAGCCT
1 CAACAACAGCAG
*
406 CAA-AATCAGCAA
1 CAACAA-CAGCAG
*
418 CAGCAACAGCAG
1 CAACAACAGCAG
430 CA
1 CA
432 GCAGCAGAAG
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
11 2 0.04
12 44 0.77
13 2 0.04
15 9 0.16
ACGTcount: A:0.44, C:0.37, G:0.16, T:0.03
Consensus pattern (12 bp):
CAACAACAGCAG
Found at i:400 original size:24 final size:26
Alignment explanation
Indices: 373--430 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
363 TCCGCAGCAG
*
373 CAACAGCAGC-CACAA-CAGCAACAA
1 CAACAGCAGCTCAAAATCAGCAACAA
*
397 CAACAGC--CTCAAAATCAGCAACAG
1 CAACAGCAGCTCAAAATCAGCAACAA
421 CAACAGCAGC
1 CAACAGCAGC
431 AGCAGCAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 4 0.14
24 22 0.79
26 1 0.04
ACGTcount: A:0.47, C:0.36, G:0.14, T:0.03
Consensus pattern (26 bp):
CAACAGCAGCTCAAAATCAGCAACAA
Found at i:418 original size:21 final size:21
Alignment explanation
Indices: 368--419 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
358 CAGCCTCCGC
* *
368 AGCAGCAACAGCAGCCACAAC
1 AGCAGCAACAACAGCCACAAA
* *
389 AGCAACAACAACAGCCTCAAA
1 AGCAGCAACAACAGCCACAAA
*
410 ATCAGCAACA
1 AGCAGCAACA
420 GCAACAGCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.13, T:0.04
Consensus pattern (21 bp):
AGCAGCAACAACAGCCACAAA
Found at i:433 original size:12 final size:12
Alignment explanation
Indices: 366--444 Score: 54
Period size: 12 Copynumber: 6.6 Consensus size: 12
356 AACAGCCTCC
366 GCAGCAGCAACA
1 GCAGCAGCAACA
378 GCAGCCA-CAACA
1 GCAG-CAGCAACA
* *
390 GCAACAACAACA
1 GCAGCAGCAACA
** *
402 GCCTCA-AAATCA
1 GCAGCAGCAA-CA
*
414 GCAACAGCAACA
1 GCAGCAGCAACA
*
426 GCAGCAGCAGCA
1 GCAGCAGCAACA
*
438 GAAGCAG
1 GCAGCAG
445 ATTCGACCGT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 4 0.08
12 45 0.85
13 4 0.08
ACGTcount: A:0.44, C:0.33, G:0.20, T:0.03
Consensus pattern (12 bp):
GCAGCAGCAACA
Done.