Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00448.F1
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, 559
Length: 933
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Found at i:238 original size:45 final size:44
Alignment explanation
Indices: 174--554 Score: 384
Period size: 45 Copynumber: 8.5 Consensus size: 44
164 TAAGCCCCCT
*
174 GTTTATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
1 GTTTAT-AACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * * *
219 GTTTATACGCCTCCAAAGAAAGAGAAGCCTGAACCCAAACCACCA
1 GTTTATA-ACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * *
264 GTATATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCA
1 GTTTAT-AACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * * *
309 GTTTATACGCCACCAAAGAAAGAGAAGCCTGAGCCCAAACCACCA
1 GTTTATA-ACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * *
354 GTATATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCA
1 GTTTAT-AACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * * * * *
399 ATTTATATGCCACCAAAGAAAGAGAAGCCTAAGCTTAAACCACCA
1 GTTTATA-ACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * * * *
444 GTGTATGAACCACCAAAGAAGGAGAAACCTGAACCTAAGCCACCA
1 GTTTAT-AACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
* * * * * * *
489 GTTTATGCACCTCCAAAGAAAGAAAAACCAGAACCCAAACCACCA
1 GTTTAT-AACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
534 GTTTATAAGCCTCCAAAGAAG
1 GTTTATAA-CCTCCAAAGAAG
555 CCACCAGTGT
Statistics
Matches: 275, Mismatches: 54, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
44 4 0.01
45 268 0.97
46 3 0.01
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (44 bp):
GTTTATAACCTCCAAAGAAGGAGAAGCCTGAGCCTAAACCACCA
Found at i:280 original size:90 final size:90
Alignment explanation
Indices: 177--554 Score: 537
Period size: 90 Copynumber: 4.2 Consensus size: 90
167 GCCCCCTGTT
* * * *
177 TATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTATACGCCTCCAAAGAAAGA
1 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAGA
242 GAAGCCTGAACCCAAACCACCAGTA
66 GAAGCCTGAACCCAAACCACCAGTA
267 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAGA
1 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAGA
*
332 GAAGCCTGAGCCCAAACCACCAGTA
66 GAAGCCTGAACCCAAACCACCAGTA
* *
357 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAATTTATATGCCACCAAAGAAAGA
1 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAGA
** *
422 GAAGCCT-AAGCTTAAACCACCAGTG
66 GAAGCCTGAA-CCCAAACCACCAGTA
* * * * *
447 TATGAACCACCAAAGAAGGAGAAA-CCTGAACCTAAGCCACCAGTTTATGCACCTCCAAAGAAAG
1 TATGAACCTCCAAAGAAGGA-AAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAG
* * * *
511 AAAAACCAGAACCCAAACCACCAGTT
65 AGAAGCCTGAACCCAAACCACCAGTA
537 TAT-AAGCCTCCAAAGAAG
1 TATGAA-CCTCCAAAGAAG
555 CCACCAGTGT
Statistics
Matches: 259, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
89 3 0.01
90 251 0.97
91 5 0.02
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (90 bp):
TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACGCCACCAAAGAAAGA
GAAGCCTGAACCCAAACCACCAGTA
Found at i:349 original size:135 final size:135
Alignment explanation
Indices: 177--554 Score: 451
Period size: 135 Copynumber: 2.8 Consensus size: 135
167 GCCCCCTGTT
*
177 TATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTATACGCCTCCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTATACACCTCCAAAGAAAGA
* * *
242 GAAGCCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCAC
66 AAAGCCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAGCCTAAGCCTAAACCAC
*
307 CAGTT
131 CAGTG
* * * * *
312 TAT-ACGCCACCAAAGAAAGAGAAGCCTGAGCCCAAACCACCAGTATATGA-ACCTCCAAAGAAG
1 TATGA-ACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTAT-ACACCTCCAAAGAAA
* * * * * * * *
375 GAAAAGCCTGAGCCTAAGCCACCAATTTATATG--CCACCAAAGAAAGAGAAGCCTAAGCTTAAA
64 GAAAAGCCTGAACCCAAACCACC-A-GTATATGAACCTCCAAAGAAGGAAAAGCCTAAGCCTAAA
438 CCACCAGTG
127 CCACCAGTG
* * * *
447 TATGAACCACCAAAGAAGGAGAAACCTGAACCTAAGCCACCAGTTTATGCACCTCCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTATACACCTCCAAAGAAAGA
* * *
512 AAAACCAGAACCCAAACCACCAGTTTAT-AAGCCTCCAAAGAAG
66 AAAGCCTGAACCCAAACCACCAGTATATGAA-CCTCCAAAGAAG
555 CCACCAGTGT
Statistics
Matches: 198, Mismatches: 36, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
133 4 0.02
134 2 0.01
135 183 0.92
136 3 0.02
137 6 0.03
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (135 bp):
TATGAACCACCAAAGAAGGAGAAGCCTGAGCCTAAACCACCAGTTTATACACCTCCAAAGAAAGA
AAAGCCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAGCCTAAGCCTAAACCAC
CAGTG
Found at i:820 original size:10 final size:10
Alignment explanation
Indices: 805--830 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
795 ACTCATGTTC
805 TATGTTCTTG
1 TATGTTCTTG
815 TATGTTCTTG
1 TATGTTCTTG
825 TATGTT
1 TATGTT
831 ATGTAGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.62
Consensus pattern (10 bp):
TATGTTCTTG
Done.