Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01335.F2
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: 4496
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Found at i:3304 original size:282 final size:282
Alignment explanation
Indices: 2800--4165 Score: 1835
Period size: 282 Copynumber: 4.9 Consensus size: 282
2790 ATGAAGGCGA
** * *
2800 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
2865 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * *
2930 TCATGGAGGTAACAAATCAAAATTACCTGTTTTCGAGGCAAGGTCTCTGGAGGATATACATAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* *
2995 CTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
*
3060 TCATCAAAAGATACGAAAACTG
261 TCATCAAAAGATACGAAGACTG
* *
3082 AGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGATCAGCTGAAGATATTGATTTGGCTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* *
3146 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCAAGTATGATCGAGAAACTGCCAG
65 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
*
3211 ATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
* *
3276 GCTGTTCGACAACTTCC-AGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATG
195 GCTGTTCAACAACTTCCGA-AATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATG
* * * * *
3340 AATCATTAACAGATAAGGATACTG
259 AATCATCAAAAGATACGAAGACTG
* * *
3364 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
** * *
3429 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
3494 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* ** * *
3559 CTATTCAACAACTTGTGAAATCTAAT-C--C--A---G-CATATTCTTCAGGCTCAAGGATTGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* **
3615 TCATCAAAAGATGCGAAGACCA
261 TCATCAAAAGATACGAAGACTG
* * *
3637 AGACTAATGTGGTGCTGCCAGTTTTTGAAGCAAGACCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
*
3702 CAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
3767 CCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* * *
3832 CTATTCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
3897 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
*
3919 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * * * *
3984 CAACTGCATGAAGGAGCTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACAG
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA-
* *** * * *
4047 GATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACATA
129 GATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATA-TACATA
* * ** * * * * *
4111 ATGCTGTCCAACAA-GGCCGGGAATCTGATCCAGCTAAGCTGCCGCATTCTTCAGG
193 AAGCTGTTCAACAACTTCC-GAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGG
4166 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:3859 original size:555 final size:560
Alignment explanation
Indices: 2800--4102 Score: 1865
Period size: 555 Copynumber: 2.3 Consensus size: 560
2790 ATGAAGGCGA
** * *
2800 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
2865 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
2930 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACACAAA
* * *
2994 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
195 GCTATTCAACAACTTCCGAAATCTAATCCA-C-GA--CGCCACATTCTTCAGGCTCAAGGAATGA
** * *
3059 ATCATCAAAAGATACGAAAACTGAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGATCAGCTG
256 ATCATCAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGACCAGCCG
*
3124 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCA
321 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCA
*
3189 AGTATGATCGAGAAACTGCCAGATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
386 AGTATGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
* * * *
3254 ATCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
451 ATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
* * * * *
3319 ATTCTTCAGGCTT-AAGGAATGAATCATTAACAGATAAGGATACTG
516 ATTCTTCAGG-TTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
* * *
3364 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* *
3429 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
3494 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACACAAAG
** * *
3559 CTATTCAACAACTTGTGAAATCTAAT-C-C-A-G-CATATTCTTCAGGCTCAAGGATTGAATCAT
196 CTATTCAACAACTTCCGAAATCTAATCCACGACGCCACATTCTTCAGGCTCAAGGAATGAATCAT
* * * *
3619 CAAAAGATGCGAAGACCAAGACTAATGTGGTGCTGCC-AGTTTTTGAAGCAAGACCAGCCGAAGA
261 CAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGACCAGCCGAAGA
*
3683 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTA
325 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCAAGTA
* *
3748 TGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCT
390 TGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCT
* *
3813 CTGGAGGACATAGACAAAGCTATTCAACAACTTCC-GAAATCTAATCCAGCTGAGCTGCCACATT
455 CTGGAGGACATACACAAAGCTATTCAACAACTTCCAG-AATCTAATCCAGCTGAGCCGCCACATT
*
3877 CTTCAGGTTCAAGGAATGAACCATCAAAAGATATGAAGACTG
519 CTTCAGGTTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
*
3919 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * *
3984 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
4046 GGATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA
129 -GATCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGA
4103 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.