Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1851
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: 5157
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Found at i:56 original size:29 final size:29
Alignment explanation
Indices: 1--752 Score: 1012
Period size: 28 Copynumber: 26.5 Consensus size: 29
1 ACAA-TCAGTGGCACT-CTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
28 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
57 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
86 ACAAGTCAGTGGCACT-CTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
114 ACAAGTCAGTGGCAC-CCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
142 ACAA-TCAGTGGCAC-CCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
169 ACAAGTTAGTGGCA--CCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
196 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
225 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* * *
254 ACAAATTAGTGGCACT--TTTCAAAGACC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
281 ACAAGTCAATGGCAC-CCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
309 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
338 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* * *
367 ACAAATCAGTGGCGCTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
396 ACAAGTCAGTGGCAC-CCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* *
424 ACAAGTTA--GGCAC-CCTTTCAGAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
450 ACAAGTCAGTGGCAC-CCTTTCGAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* * *
478 ACAAGTCAGTGGCAC-CATTGCGAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
506 ACAATTCAGTGGCACT-CTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
*
534 ACAAGTCAGTGGCAC-CCTTTTAAAGCTCAC
1 ACAAGTCAGTGGCACTCCTTTCAAAGC-C-C
*
564 ACAAGTCAGTGGCACTCCTTTTAAAGCTCAC
1 ACAAGTCAGTGGCACTCCTTTCAAAGC-C-C
* * *
595 GCAAGTCAGTGGTAC-CTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
623 ACAAGTCAGTGGCACT-CTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
651 ACAAGTCAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* * *
679 ACGAGTTAGTGGCA-TTCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCC
* *
707 ACGCACGTCAGTGGCAC-CCTTTTAAAGCCC
1 A--CAAGTCAGTGGCACTCCTTTCAAAGCCC
*
737 ATGCAAGTCAATGGCA
1 A--CAAGTCAGTGGCA
753 ACCCTTTTCA
Statistics
Matches: 656, Mismatches: 48, Indels: 39
0.88 0.06 0.05
Matches are distributed among these distances:
26 24 0.04
27 80 0.12
28 270 0.41
29 195 0.30
30 59 0.09
31 28 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
ACAAGTCAGTGGCACTCCTTTCAAAGCCC
Found at i:1282 original size:20 final size:19
Alignment explanation
Indices: 1236--1312 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
1226 TCATACCCTG
* *
1236 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATCA
* *
1256 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
1276 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
1296 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
1313 GTCTTTTTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:1303 original size:40 final size:39
Alignment explanation
Indices: 1236--1313 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1226 TCATACCCTG
* * *
1236 ATGTATCGATGCATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1276 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1314 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2238 original size:23 final size:23
Alignment explanation
Indices: 2211--2265 Score: 96
Period size: 21 Copynumber: 2.5 Consensus size: 23
2201 AGCCTTTGAC
2211 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2234 CATGCA--TTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2255 CATGCATTTTT
1 CATGCATTTTT
2266 AACATGTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 21 0.70
23 9 0.30
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:2272 original size:20 final size:21
Alignment explanation
Indices: 2219--2272 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2209 ACCATGCATT
**
2219 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
2240 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
2261 -TTTTTAACATGT
1 TTTTTTAACATGT
2273 CCCAGCATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Done.