Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2461
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: 9952
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Found at i:115 original size:38 final size:39
Alignment explanation
Indices: 64--306 Score: 241
Period size: 39 Copynumber: 6.3 Consensus size: 39
54 ACCCAAGTAT
* * *
64 CTTCGGGATTTAGCCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCGGATATAATCACTCGCACAAATGC
* ** * *
102 CTTCGGGTCTTAGCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCGGATATAATCACTCGCACAAATGC
141 CTTCGGGACTTAGCCCGGATATAA-C-CTCGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAATCACTCGCACAAATGC
* * *
179 CTTCGGGACTTAGCCCGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCGGATA-TAATCACTCGCACAAATGC
* *
218 CTTCGGGACTTAGCCGGA-ATTAGTAACTCGCACAAATG-
1 CTTCGGGACTTAGCCGGATA-TAATCACTCGCACAAATGC
* * *
256 CTTCGGGACTTAGCCGGA-ATTAATCACTAGCAACACATGT
1 CTTCGGGACTTAGCCGGATA-TAATCACTCGC-ACAAATGC
296 CTTC-GGACTTA
1 CTTCGGGACTTA
307 ACCCCGTTAG
Statistics
Matches: 177, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
36 1 0.01
37 6 0.03
38 78 0.44
39 80 0.45
40 12 0.07
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAATCACTCGCACAAATGC
Found at i:153 original size:39 final size:39
Alignment explanation
Indices: 64--273 Score: 243
Period size: 38 Copynumber: 5.5 Consensus size: 39
54 ACCCAAGTAT
* ** *
64 CTTCGGGATTTAGCCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCGGATATAGTCACTCGCACAAATGC
* * * *
102 CTTCGGGTCTTAGCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCGGATATAGTCACTCGCACAAATGC
*
141 CTTCGGGACTTAGCCCGGATATA-AC-CTCGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAGTCACTCGCACAAATGC
* *
179 CTTCGGGACTTAGCCCGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCGGATA-TAGTCACTCGCACAAATGC
*
218 CTTCGGGACTTAGCCGGA-ATTAGTAACTCGCACAAATG-
1 CTTCGGGACTTAGCCGGATA-TAGTCACTCGCACAAATGC
256 CTTCGGGACTTAGCCGGA
1 CTTCGGGACTTAGCCGGA
274 ATTAATCACT
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
36 1 0.01
37 6 0.04
38 68 0.45
39 67 0.45
40 8 0.05
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAGTCACTCGCACAAATGC
Found at i:191 original size:77 final size:76
Alignment explanation
Indices: 64--306 Score: 271
Period size: 77 Copynumber: 3.2 Consensus size: 76
54 ACCCAAGTAT
* * * * *
64 CTTCGGGATTTAGCCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCGG-ATATGGTC
1 CTTCGGGACTTAGCCGGATATAA-C-CTCGCACAAATGCCTTCGGGACTTAGCCGGAAT-TAGTA
*
127 ACTAGCATAAATGC
63 ACTAGCACAAATGC
*
141 CTTCGGGACTTAGCCCGGATATAACCTCGCACAAATGCCTTCGGGACTTAGCCCGAATTAGTAAC
1 CTTCGGGACTTAG-CCGGATATAACCTCGCACAAATGCCTTCGGGACTTAGCCGGAATTAGTAAC
*
206 TCGCACAAATGC
65 TAGCACAAATGC
* *
218 CTTCGGGACTTAGCCGGAATTAGTAA-CTCGCACAAATG-CTTCGGGACTTAGCCGGAATTAATC
1 CTTCGGGACTTAGCCGG-A-TA-TAACCTCGCACAAATGCCTTCGGGACTTAGCCGGAATTAGTA
* *
281 ACTAGCAACACATGT
63 ACTAGC-ACAAATGC
296 CTTC-GGACTTA
1 CTTCGGGACTTA
307 ACCCCGTTAG
Statistics
Matches: 145, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
76 11 0.08
77 95 0.66
78 36 0.25
79 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (76 bp):
CTTCGGGACTTAGCCGGATATAACCTCGCACAAATGCCTTCGGGACTTAGCCGGAATTAGTAACT
AGCACAAATGC
Found at i:8163 original size:40 final size:40
Alignment explanation
Indices: 8119--8305 Score: 297
Period size: 40 Copynumber: 4.7 Consensus size: 40
8109 GCTACTTGCT
*
8119 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
8159 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
8199 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
** * *
8239 CAAATGCCTTCGGG-CTTAGCCCGAAT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
8277 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
8306 CATCCAAATA
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 23 0.17
39 21 0.15
40 92 0.68
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Done.