Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2784
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, 508
Length: 848
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Found at i:246 original size:13 final size:13
Alignment explanation
Indices: 228--253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
218 AAGCCAAGAC
228 AACTTACATAAAT
1 AACTTACATAAAT
241 AACTTACATAAAT
1 AACTTACATAAAT
254 TAAATAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AACTTACATAAAT
Found at i:297 original size:25 final size:25
Alignment explanation
Indices: 277--369 Score: 70
Period size: 25 Copynumber: 3.7 Consensus size: 25
267 TGACTTACAT
*
277 TATACATAACCTT-CTTAACTTACAT
1 TATACATAA-CTTACATAACTTACAT
* *
302 TATACATTACTTACATAACTTACAG
1 TATACATAACTTACATAACTTACAT
327 TACTTACATAA--TACATAA--TACAT
1 TA--TACATAACTTACATAACTTACAT
*
350 AACTTACATAACTTACATAA
1 TA--TACATAACTTACATAA
370 TACATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
23 14 0.25
24 3 0.05
25 34 0.60
27 6 0.11
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.35
Consensus pattern (25 bp):
TATACATAACTTACATAACTTACAT
Found at i:322 original size:9 final size:9
Alignment explanation
Indices: 239--369 Score: 111
Period size: 9 Copynumber: 15.4 Consensus size: 9
229 ACTTACATAA
239 ATAACTTAC
1 ATAACTTAC
* *
248 ATAAATTAA
1 ATAACTTAC
257 ATAACTTAC
1 ATAACTTAC
*
266 ATGACTTAC
1 ATAACTTAC
*
275 ATTA--TAC
1 ATAACTTAC
282 ATAACCTT-C
1 ATAA-CTTAC
*
291 TTAACTTAC
1 ATAACTTAC
*
300 ATTA--TAC
1 ATAACTTAC
*
307 ATTACTTAC
1 ATAACTTAC
316 ATAACTTAC
1 ATAACTTAC
325 AGT-ACTTAC
1 A-TAACTTAC
334 ATAA--TAC
1 ATAACTTAC
341 ATAA--TAC
1 ATAACTTAC
348 ATAACTTAC
1 ATAACTTAC
357 ATAACTTAC
1 ATAACTTAC
366 ATAA
1 ATAA
370 TACATAAAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
7 27 0.27
8 4 0.04
9 68 0.67
10 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
ATAACTTAC
Found at i:343 original size:7 final size:7
Alignment explanation
Indices: 331--376 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
321 TTACAGTACT
331 TACATAA
1 TACATAA
338 TACATAA
1 TACATAA
345 TACATAA
1 TACATAA
352 CTTACATAA
1 --TACATAA
361 CTTACATAA
1 --TACATAA
370 TACATAA
1 TACATAA
377 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:354 original size:32 final size:32
Alignment explanation
Indices: 245--376 Score: 133
Period size: 34 Copynumber: 4.0 Consensus size: 32
235 ATAAATAACT
* * * *
245 TACATAAATTAAATAACTTACATGACTTACATTA
1 TACATAACTTACATAACTTACAT-A-ATACATAA
* * *
279 TACATAACCTT-CTTAACTTACATTATACATTACT
1 TACATAA-CTTACATAACTTACATAATACA-TA-A
313 TACATAACTTACAGT-ACTTACATAATACATAA
1 TACATAACTTACA-TAACTTACATAATACATAA
345 TACATAACTTACATAACTTACATAATACATAA
1 TACATAACTTACATAACTTACATAATACATAA
377 AAATATATCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
31 1 0.01
32 34 0.41
33 6 0.07
34 38 0.46
35 3 0.04
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.35
Consensus pattern (32 bp):
TACATAACTTACATAACTTACATAATACATAA
Found at i:367 original size:59 final size:60
Alignment explanation
Indices: 239--369 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 60
229 ACTTACATAA
* * *
239 ATAACTTACATAAATTAAATAACTTACATGACTTACATTATACATAACCTTCTTAACTTAC
1 ATAACTTACATAAATTAAATAACTTACATGACTTACATAATACATAA-CTACATAACTTAC
* * * *
300 ATTA--TACATTACTTACATAACTTACA-GTACTTACATAATACATAA-TACATAACTTAC
1 ATAACTTACATAAATTAAATAACTTACATG-ACTTACATAATACATAACTACATAACTTAC
357 ATAACTTACATAA
1 ATAACTTACATAA
370 TACATAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
57 13 0.22
58 1 0.02
59 41 0.71
61 3 0.05
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (60 bp):
ATAACTTACATAAATTAAATAACTTACATGACTTACATAATACATAACTACATAACTTAC
Done.