Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01335.F4
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: 5285
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Found at i:4093 original size:282 final size:282
Alignment explanation
Indices: 3589--4954 Score: 1835
Period size: 282 Copynumber: 4.9 Consensus size: 282
3579 ATGAAGGCGA
** * *
3589 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
3654 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * *
3719 TCATGGAGGTAACAAATCAAAATTACCTGTTTTCGAGGCAAGGTCTCTGGAGGATATACATAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* *
3784 CTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
*
3849 TCATCAAAAGATACGAAAACTG
261 TCATCAAAAGATACGAAGACTG
* *
3871 AGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGATCAGCTGAAGATATTGATTTGGCTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* *
3935 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCAAGTATGATCGAGAAACTGCCAG
65 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
*
4000 ATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
* *
4065 GCTGTTCGACAACTTCC-AGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATG
195 GCTGTTCAACAACTTCCGA-AATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATG
* * * * *
4129 AATCATTAACAGATAAGGATACTG
259 AATCATCAAAAGATACGAAGACTG
* * *
4153 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
** * *
4218 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
4283 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* ** * *
4348 CTATTCAACAACTTGTGAAATCTAAT-C--C--A---G-CATATTCTTCAGGCTCAAGGATTGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* **
4404 TCATCAAAAGATGCGAAGACCA
261 TCATCAAAAGATACGAAGACTG
* * *
4426 AGACTAATGTGGTGCTGCCAGTTTTTGAAGCAAGACCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
*
4491 CAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
4556 CCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* * *
4621 CTATTCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
4686 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
*
4708 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * * * *
4773 CAACTGCATGAAGGAGCTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACAG
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA-
* *** * * *
4836 GATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACATA
129 GATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATA-TACATA
* * ** * * * * *
4900 ATGCTGTCCAACAA-GGCCGGGAATCTGATCCAGCTAAGCTGCCGCATTCTTCAGG
193 AAGCTGTTCAACAACTTCC-GAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGG
4955 TGTAAACAAT
Statistics
Matches: 959, Mismatches: 108, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
273 240 0.25
274 2 0.00
276 1 0.00
277 1 0.00
278 1 0.00
279 1 0.00
280 1 0.00
281 8 0.01
282 702 0.73
283 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (282 bp):
AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
TCATCAAAAGATACGAAGACTG
Found at i:4648 original size:555 final size:560
Alignment explanation
Indices: 3589--4891 Score: 1865
Period size: 555 Copynumber: 2.3 Consensus size: 560
3579 ATGAAGGCGA
** * *
3589 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
3654 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
3719 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACACAAA
* * *
3783 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
195 GCTATTCAACAACTTCCGAAATCTAATCCA-C-GA--CGCCACATTCTTCAGGCTCAAGGAATGA
** * *
3848 ATCATCAAAAGATACGAAAACTGAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGATCAGCTG
256 ATCATCAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGACCAGCCG
*
3913 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCA
321 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCA
*
3978 AGTATGATCGAGAAACTGCCAGATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
386 AGTATGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
* * * *
4043 ATCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
451 ATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
* * * * *
4108 ATTCTTCAGGCTT-AAGGAATGAATCATTAACAGATAAGGATACTG
516 ATTCTTCAGG-TTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
* * *
4153 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* *
4218 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
4283 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACACAAAG
** * *
4348 CTATTCAACAACTTGTGAAATCTAAT-C-C-A-G-CATATTCTTCAGGCTCAAGGATTGAATCAT
196 CTATTCAACAACTTCCGAAATCTAATCCACGACGCCACATTCTTCAGGCTCAAGGAATGAATCAT
* * * *
4408 CAAAAGATGCGAAGACCAAGACTAATGTGGTGCTGCC-AGTTTTTGAAGCAAGACCAGCCGAAGA
261 CAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGACCAGCCGAAGA
*
4472 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTA
325 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCAAGTA
* *
4537 TGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCT
390 TGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCT
* *
4602 CTGGAGGACATAGACAAAGCTATTCAACAACTTCC-GAAATCTAATCCAGCTGAGCTGCCACATT
455 CTGGAGGACATACACAAAGCTATTCAACAACTTCCAG-AATCTAATCCAGCTGAGCCGCCACATT
*
4666 CTTCAGGTTCAAGGAATGAACCATCAAAAGATATGAAGACTG
519 CTTCAGGTTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
*
4708 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * *
4773 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
4835 GGATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA
129 -GATCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGA
4892 ATTACATAAT
Statistics
Matches: 663, Mismatches: 69, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
553 1 0.00
554 7 0.01
555 455 0.69
556 1 0.00
559 1 0.00
561 1 0.00
563 1 0.00
564 194 0.29
565 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (560 bp):
AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
TCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACACAAAG
CTATTCAACAACTTCCGAAATCTAATCCACGACGCCACATTCTTCAGGCTCAAGGAATGAATCAT
CAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGACCAGCCGAAGAT
ATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCAAGTAT
GATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTC
TGGAGGACATACACAAAGCTATTCAACAACTTCCAGAATCTAATCCAGCTGAGCCGCCACATTCT
TCAGGTTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
Done.