Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_33157
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, 360
Length: 600
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Found at i:188 original size:48 final size:48
Alignment explanation
Indices: 136--277 Score: 178
Period size: 48 Copynumber: 3.0 Consensus size: 48
126 GCCTCCTGTG
** *
136 CATGAACTTCCAAAGAAGCCTCCAACGTATAAACCTACGCCATCAATC
1 CATGAACTTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCAATC
* * *
184 CATGAACCTCCAAAGAAGCCTCCAATGTATAAACCTAAACCACCACTC
1 CATGAACTTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCAATC
* * * *
232 CATGAACTTCCAAAGAAGCCACCGA-TTCATGAACCTAAACCACCAA
1 CATGAACTTCCAAAGAAGCCTCCAACGT-ATAAACCTAAACCACCAA
278 AGCCACCAGT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 1 0.01
48 80 0.99
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (48 bp):
CATGAACTTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCAATC
Found at i:393 original size:177 final size:177
Alignment explanation
Indices: 186--533 Score: 561
Period size: 177 Copynumber: 2.0 Consensus size: 177
176 CATCAATCCA
* *
186 TGAACCTCCAAAGAAGCCTCCAATGTATAAACCTAAACCACCACTCCATGAACTTCCAAAGAAGC
1 TGAACCTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCACTCCATGAACCTCCAAAGAAGC
* * *
251 CACCGATTCATGAACCTAAACCACCAAAGCCACCAGTTCACGAACCTCCAAAGAAAGAGAAACCA
66 CACCGATGCATGAACCTAAACCACCAAAGCCACCAATCCACGAACCTCCAAAGAAAGAGAAACCA
* * *
316 GAACACAAGCCACCAATATATGAACCTCCTAAGAAACCACCAGTCCG
131 GAACACAAGCCACCAATATATGAACATCCAAAAAAACCACCAGTCCG
* * *
363 TGAACCTCCAAAGAAGCCTCCAGCGTATAAACCTAAACCACCAGTTCATGAACCTCCAAAGAAGC
1 TGAACCTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCACTCCATGAACCTCCAAAGAAGC
*
428 CACCGATGCATGAATCTAAACCACCAAAGCCACCAATCCACGAACCTCCAAAGAAAGAGAAACCA
66 CACCGATGCATGAACCTAAACCACCAAAGCCACCAATCCACGAACCTCCAAAGAAAGAGAAACCA
* * *
493 GAACCCAAGCCACCAGTTTATGAACATCCAAAAAAACCACC
131 GAACACAAGCCACCAATATATGAACATCCAAAAAAACCACC
534 TTCTGGTCAC
Statistics
Matches: 156, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 156 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.13
Consensus pattern (177 bp):
TGAACCTCCAAAGAAGCCTCCAACGTATAAACCTAAACCACCACTCCATGAACCTCCAAAGAAGC
CACCGATGCATGAACCTAAACCACCAAAGCCACCAATCCACGAACCTCCAAAGAAAGAGAAACCA
GAACACAAGCCACCAATATATGAACATCCAAAAAAACCACCAGTCCG
Found at i:447 original size:48 final size:47
Alignment explanation
Indices: 349--453 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 47
339 ACCTCCTAAG
* *
349 AAACCACCAGTCCGTGAACCTCCAAAGAAGCCTCCAGCGTATAAACCT
1 AAACCACCAGTCCATGAACCTCCAAAGAAGCCACCAGCG-ATAAACCT
* * *
397 AAACCACCAGTTCATGAACCTCCAAAGAAGCCACCGATGC-ATGAATCT
1 AAACCACCAGTCCATGAACCTCCAAAGAAGCCACC-A-GCGATAAACCT
445 AAACCACCA
1 AAACCACCA
454 AAGCCACCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 47 0.94
49 1 0.02
50 2 0.04
ACGTcount: A:0.38, C:0.34, G:0.13, T:0.14
Consensus pattern (47 bp):
AAACCACCAGTCCATGAACCTCCAAAGAAGCCACCAGCGATAAACCT
Done.