Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01335.F3
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: 5356
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Found at i:4164 original size:282 final size:282
Alignment explanation
Indices: 3660--5025 Score: 1835
Period size: 282 Copynumber: 4.9 Consensus size: 282
3650 ATGAAGGCGA
** * *
3660 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
3725 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * *
3790 TCATGGAGGTAACAAATCAAAATTACCTGTTTTCGAGGCAAGGTCTCTGGAGGATATACATAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* *
3855 CTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
*
3920 TCATCAAAAGATACGAAAACTG
261 TCATCAAAAGATACGAAGACTG
* *
3942 AGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGATCAGCTGAAGATATTGATTTGGCTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* *
4006 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCAAGTATGATCGAGAAACTGCCAG
65 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
*
4071 ATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
* *
4136 GCTGTTCGACAACTTCC-AGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATG
195 GCTGTTCAACAACTTCCGA-AATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATG
* * * * *
4200 AATCATTAACAGATAAGGATACTG
259 AATCATCAAAAGATACGAAGACTG
* * *
4224 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
** * *
4289 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
4354 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* ** * *
4419 CTATTCAACAACTTGTGAAATCTAAT-C--C--A---G-CATATTCTTCAGGCTCAAGGATTGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* **
4475 TCATCAAAAGATGCGAAGACCA
261 TCATCAAAAGATACGAAGACTG
* * *
4497 AGACTAATGTGGTGCTGCCAGTTTTTGAAGCAAGACCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
*
4562 CAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
4627 CCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* * *
4692 CTATTCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
4757 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
*
4779 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * * * *
4844 CAACTGCATGAAGGAGCTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACAG
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA-
* *** * * *
4907 GATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACATA
129 GATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATA-TACATA
* * ** * * * * *
4971 ATGCTGTCCAACAA-GGCCGGGAATCTGATCCAGCTAAGCTGCCGCATTCTTCAGG
193 AAGCTGTTCAACAACTTCC-GAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGG
5026 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:4719 original size:555 final size:560
Alignment explanation
Indices: 3660--4962 Score: 1865
Period size: 555 Copynumber: 2.3 Consensus size: 560
3650 ATGAAGGCGA
** * *
3660 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
3725 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
3790 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACACAAA
* * *
3854 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
195 GCTATTCAACAACTTCCGAAATCTAATCCA-C-GA--CGCCACATTCTTCAGGCTCAAGGAATGA
** * *
3919 ATCATCAAAAGATACGAAAACTGAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGATCAGCTG
256 ATCATCAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGACCAGCCG
*
3984 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCA
321 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCA
*
4049 AGTATGATCGAGAAACTGCCAGATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
386 AGTATGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
* * * *
4114 ATCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
451 ATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
* * * * *
4179 ATTCTTCAGGCTT-AAGGAATGAATCATTAACAGATAAGGATACTG
516 ATTCTTCAGG-TTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
* * *
4224 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* *
4289 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
4354 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACACAAAG
** * *
4419 CTATTCAACAACTTGTGAAATCTAAT-C-C-A-G-CATATTCTTCAGGCTCAAGGATTGAATCAT
196 CTATTCAACAACTTCCGAAATCTAATCCACGACGCCACATTCTTCAGGCTCAAGGAATGAATCAT
* * * *
4479 CAAAAGATGCGAAGACCAAGACTAATGTGGTGCTGCC-AGTTTTTGAAGCAAGACCAGCCGAAGA
261 CAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGACCAGCCGAAGA
*
4543 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTA
325 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCAAGTA
* *
4608 TGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCT
390 TGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCT
* *
4673 CTGGAGGACATAGACAAAGCTATTCAACAACTTCC-GAAATCTAATCCAGCTGAGCTGCCACATT
455 CTGGAGGACATACACAAAGCTATTCAACAACTTCCAG-AATCTAATCCAGCTGAGCCGCCACATT
*
4737 CTTCAGGTTCAAGGAATGAACCATCAAAAGATATGAAGACTG
519 CTTCAGGTTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
*
4779 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * *
4844 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
4906 GGATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA
129 -GATCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGA
4963 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.