Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2429
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: 17966
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Found at i:1527 original size:40 final size:40
Alignment explanation
Indices: 1355--1520 Score: 289
Period size: 40 Copynumber: 4.2 Consensus size: 40
1345 AACCCAAGTA
* *
1355 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1394 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1434 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
1474 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1514 CCTTCGG
1 CCTTCGG
1521 ATCTTAGTCC
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 13 0.11
40 109 0.89
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:9242 original size:78 final size:79
Alignment explanation
Indices: 9114--9317 Score: 349
Period size: 78 Copynumber: 2.6 Consensus size: 79
9104 AACCCAAGTA
* *
9114 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
9178 TAACT-CACAAATG
66 TAACTCCACAAATG
9191 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
9256 TAACTCGCACAAATG
66 TAACTC-CACAAATG
* *
9271 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGG
9318 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
77 13 0.11
78 54 0.45
80 53 0.44
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTCCACAAATG
Found at i:9324 original size:40 final size:40
Alignment explanation
Indices: 9114--9317 Score: 351
Period size: 40 Copynumber: 5.2 Consensus size: 40
9104 AACCCAAGTA
* *
9114 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
9153 CCTTCGGGACTTAGCCCGGATATAGTAACT--CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
9191 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
9231 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
9271 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
9311 CCTTCGG
1 CCTTCGG
9318 ATCTTAGTCC
Statistics
Matches: 158, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
38 38 0.24
39 13 0.08
40 107 0.68
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:13308 original size:28 final size:28
Alignment explanation
Indices: 13268--13323 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
13258 CGGGGCATTA
13268 GTGAGCCCAAACGGCATCACTAAAACTC
1 GTGAGCCCAAACGGCATCACTAAAACTC
*
13296 GTGAGCCCAAACGGCATCACTAAGACTC
1 GTGAGCCCAAACGGCATCACTAAAACTC
13324 ATAGTGACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.14
Consensus pattern (28 bp):
GTGAGCCCAAACGGCATCACTAAAACTC
Found at i:17180 original size:40 final size:40
Alignment explanation
Indices: 17009--17173 Score: 280
Period size: 40 Copynumber: 4.2 Consensus size: 40
16999 AACCCAAGTA
* *
17009 CCTTC-GGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
17047 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
17087 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
17127 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
17167 CCTTCGG
1 CCTTCGG
17174 ATCTTAGTCC
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
38 5 0.04
39 7 0.06
40 109 0.90
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.