Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2243
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, 612
Length: 1020
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Found at i:31 original size:23 final size:23
Alignment explanation
Indices: 1--45 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
*
1 TTACATAATACATTACTTTTAAC
1 TTACATAATACATAACTTTTAAC
24 TTACATAATACATAACTTTTAA
1 TTACATAATACATAACTTTTAA
46 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (23 bp):
TTACATAATACATAACTTTTAAC
Found at i:98 original size:38 final size:39
Alignment explanation
Indices: 21--113 Score: 152
Period size: 38 Copynumber: 2.4 Consensus size: 39
11 CATTACTTTT
*
21 AACTTACATAATACATAACTTTTAAAATTTTTTTATATA
1 AACTTACATAATACATAACTTATAAAATTTTTTTATATA
* *
60 AACTTACATGATACATAACTTAT-ATATTTTTTTATATA
1 AACTTACATAATACATAACTTATAAAATTTTTTTATATA
98 AACTTACATAATACAT
1 AACTTACATAATACAT
114 TTAACTTACA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 29 0.58
39 21 0.42
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.44
Consensus pattern (39 bp):
AACTTACATAATACATAACTTATAAAATTTTTTTATATA
Found at i:129 original size:9 final size:9
Alignment explanation
Indices: 98--505 Score: 271
Period size: 9 Copynumber: 46.0 Consensus size: 9
88 TTTTTATATA
98 AACTTACAT
1 AACTTACAT
107 AA--TACATTT
1 AACTTACA--T
116 AACTTACAT
1 AACTTACAT
*
125 AACTTACAC
1 AACTTACAT
134 AACTTACAT
1 AACTTACAT
143 AACCTT-CAT
1 AA-CTTACAT
152 AA--TACATTT
1 AACTTACA--T
161 AACTTACAT
1 AACTTACAT
170 AACTTACAT
1 AACTTACAT
* *
179 AA--TGCAA
1 AACTTACAT
186 AACTTACAT
1 AACTTACAT
*
195 AAC-AAC-T
1 AACTTACAT
*
202 TACTTACAT
1 AACTTACAT
*
211 AACATACAT
1 AACTTACAT
* *
220 TACTTA-AA
1 AACTTACAT
*
228 ATATTTACAT
1 A-ACTTACAT
238 AA--TACAT
1 AACTTACAT
245 AACTTAGTACAT
1 AAC-T--TACAT
**
257 AGTTTACAT
1 AACTTACAT
266 AA--TACAT
1 AACTTACAT
273 AACTTAGTACAT
1 AAC-T--TACAT
285 AACTTACAT
1 AACTTACAT
* **
294 AAATT-TTT
1 AACTTACAT
** *
302 TTC-TAAAT
1 AACTTACAT
** *
310 TGCTTACAA
1 AACTTACAT
* *
319 AAATTATAT
1 AACTTACAT
328 AACTTACAT
1 AACTTACAT
337 AACTTACATT
1 AACTTACA-T
*
347 AA-TTAAAT
1 AACTTACAT
355 AACTTACAT
1 AACTTACAT
364 AACTTACAT
1 AACTTACAT
373 AACTTACAT
1 AACTTACAT
*
382 AACTTAAAT
1 AACTTACAT
391 AACTTACAT
1 AACTTACAT
400 AACTTACAT
1 AACTTACAT
*
409 ATCTTACAT
1 AACTTACAT
*
418 AACTTATAT
1 AACTTACAT
* *
427 AAATTAAAT
1 AACTTACAT
*
436 AACTTAAAT
1 AACTTACAT
445 AACTTACAT
1 AACTTACAT
*
454 AATTTACAT
1 AACTTACAT
463 AACTTACAT
1 AACTTACAT
472 AACTTACAT
1 AACTTACAT
481 -A-TTACAT
1 AACTTACAT
*
488 AACCTT-CCT
1 AA-CTTACAT
497 AACTTACAT
1 AACTTACAT
506 TATTGTTTAA
Statistics
Matches: 312, Mismatches: 53, Indels: 68
0.72 0.12 0.16
Matches are distributed among these distances:
6 1 0.00
7 35 0.11
8 17 0.05
9 225 0.72
10 10 0.03
11 10 0.03
12 14 0.04
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:206 original size:16 final size:18
Alignment explanation
Indices: 187--225 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
177 ATAATGCAAA
187 ACTTACATAACA-AC-TT
1 ACTTACATAACATACATT
203 ACTTACATAACATACATT
1 ACTTACATAACATACATT
221 ACTTA
1 ACTTA
226 AAATATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.57
17 2 0.10
18 7 0.33
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (18 bp):
ACTTACATAACATACATT
Found at i:269 original size:28 final size:28
Alignment explanation
Indices: 230--295 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
220 TACTTAAAAT
230 ATTTACATAATACATAACTTAGTACATA
1 ATTTACATAATACATAACTTAGTACATA
*
258 GTTTACATAATACATAACTTAGTACATA
1 ATTTACATAATACATAACTTAGTACATA
*
286 ACTTACATAA
1 ATTTACATAA
296 ATTTTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTTACATAATACATAACTTAGTACATA
Done.