Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01335.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, 1000
Length: 4425
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Found at i:3233 original size:282 final size:282
Alignment explanation
Indices: 2729--4094 Score: 1835
Period size: 282 Copynumber: 4.9 Consensus size: 282
2719 ATGAAGGCGA
** * *
2729 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
2794 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * *
2859 TCATGGAGGTAACAAATCAAAATTACCTGTTTTCGAGGCAAGGTCTCTGGAGGATATACATAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* *
2924 CTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
*
2989 TCATCAAAAGATACGAAAACTG
261 TCATCAAAAGATACGAAGACTG
* *
3011 AGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGATCAGCTGAAGATATTGATTTGGCTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* *
3075 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCAAGTATGATCGAGAAACTGCCAG
65 GCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
*
3140 ATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAA
* *
3205 GCTGTTCGACAACTTCC-AGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATG
195 GCTGTTCAACAACTTCCGA-AATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATG
* * * * *
3269 AATCATTAACAGATAAGGATACTG
259 AATCATCAAAAGATACGAAGACTG
* * *
3293 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
** * *
3358 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
3423 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* ** * *
3488 CTATTCAACAACTTGTGAAATCTAAT-C--C--A---G-CATATTCTTCAGGCTCAAGGATTGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* **
3544 TCATCAAAAGATGCGAAGACCA
261 TCATCAAAAGATACGAAGACTG
* * *
3566 AGACTAATGTGGTGCTGCCAGTTTTTGAAGCAAGACCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
*
3631 CAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
3696 CCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAAAG
* * *
3761 CTATTCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
3826 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
*
3848 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * * * *
3913 CAACTGCATGAAGGAGCTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACAG
66 CAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA-
* *** * * *
3976 GATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACATA
129 GATCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATA-TACATA
* * ** * * * * *
4040 ATGCTGTCCAACAA-GGCCGGGAATCTGATCCAGCTAAGCTGCCGCATTCTTCAGG
193 AAGCTGTTCAACAACTTCC-GAAATCTAATCCAGCTGAGCCGCCACATTCTTCAGG
4095 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:3788 original size:555 final size:560
Alignment explanation
Indices: 2729--4031 Score: 1865
Period size: 555 Copynumber: 2.3 Consensus size: 560
2719 ATGAAGGCGA
** * *
2729 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGACTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * **
2794 CAACTTCATGAAGGAGTCGACGTTGAGGAAGTAACTGTTCCGAGTATGATCAAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
2859 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACACAAA
* * *
2923 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
195 GCTATTCAACAACTTCCGAAATCTAATCCA-C-GA--CGCCACATTCTTCAGGCTCAAGGAATGA
** * *
2988 ATCATCAAAAGATACGAAAACTGAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGATCAGCTG
256 ATCATCAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTATTCTTGAACCAAGACCAGCCG
*
3053 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACGTTGAGGAAGTAATTGTTCCA
321 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCA
*
3118 AGTATGATCGAGAAACTGCCAGATCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
386 AGTATGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAG
* * * *
3183 ATCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
451 ATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCAGAATCTAATCCAGCTGAGCCGCCAC
* * * * *
3248 ATTCTTCAGGCTT-AAGGAATGAATCATTAACAGATAAGGATACTG
516 ATTCTTCAGG-TTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
* * *
3293 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* *
3358 CAACTTCATGAAGGAGTCAATGTCGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * *
3423 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAG
131 TCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACACAAAG
** * *
3488 CTATTCAACAACTTGTGAAATCTAAT-C-C-A-G-CATATTCTTCAGGCTCAAGGATTGAATCAT
196 CTATTCAACAACTTCCGAAATCTAATCCACGACGCCACATTCTTCAGGCTCAAGGAATGAATCAT
* * * *
3548 CAAAAGATGCGAAGACCAAGACTAATGTGGTGCTGCC-AGTTTTTGAAGCAAGACCAGCCGAAGA
261 CAAAAGATACGAAAACCAAGACTAATGTGGTGCTGCCTA-TTCTTGAACCAAGACCAGCCGAAGA
*
3612 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCGAGTA
325 TATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACATTGAGGAAGTAATTGTTCCAAGTA
* *
3677 TGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTGTTGTCGAGGCAAGATCT
390 TGATCGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTATTGTCGAGGCAAGATCT
* *
3742 CTGGAGGACATAGACAAAGCTATTCAACAACTTCC-GAAATCTAATCCAGCTGAGCTGCCACATT
455 CTGGAGGACATACACAAAGCTATTCAACAACTTCCAG-AATCTAATCCAGCTGAGCCGCCACATT
*
3806 CTTCAGGTTCAAGGAATGAACCATCAAAAGATATGAAGACTG
519 CTTCAGGTTCAAGGAATGAACCATCAAAAGATAAGAAGACTG
*
3848 AGATTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * *
3913 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
3975 GGATGACACAGGTAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA
129 -GATCATGGAGGTAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGA
4032 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.