Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g01960.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: 4777
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Found at i:2401 original size:549 final size:548
Alignment explanation
Indices: 1460--3119 Score: 2475
Period size: 549 Copynumber: 3.0 Consensus size: 548
1450 TGAAGCAAAA
* * *
1460 CAGCTG-GGAGAGGTAAATATAGGACTGCAATCCCAAATTTCAGAACTTGAGATGATGTCAAAAA
1 CAGCTGAGG-GAGGAAAATATAGGACTGCAATCCCAAATTTCAGAACTCGAGATGATATC-AAAA
* * * *
1524 AGAGAGAAGAAGAACTTTTGACTCTCGCAAAGAAATTTGAGGATAATGAGAAAGAATCATTGTCT
64 AGAGACAAGAAGAACTTTTGACTCTCACAAAGAAGTTTGAGGATAATGAGAAAGAATCATTATCT
*
1589 AGAGTGGAGAATCTGACAGTGCAGATCAACAATCTGCTAGCAGACATGGAGTCACTACGCACCCA
129 AGAGTGGAGAATTTGACAGTGCAGATCAACAATCTGCTAGCAGACATGGAGTCACTACGCACCCA
* ** *
1654 GAAAGCTCAGTTGGAAGAACATATTGCAGTAAAAGATGATGAAGCATCGACTCAAGTCAAGAGCT
194 GAAAGCTCAGTTGGAAGAACATATTGTAGTAAAAGGCGATGAAGCATCAACTCAAGTCAAGAGCT
* * * *
1719 TGATGGATCAGATAAAAAATTTGCAGCAGGAGCTGGAGTCCCTGCAGAGTCAGAAAGCAGAACTT
259 TGATGGATCAGATAAATACTTTGCAGCAGGAGCTGGAGTCCCTGCATAGCCAGAAAGCAGAACTT
* * ** *
1784 GAAGTTCAGCTTGAGAGTAAAACTCGAGCTATTTCCGATCATGTGATCAAGATAGAAAATGCAAA
324 GAAGTTCAGCTTGAGAGTAAAACTCAAGCTATTTCCAATCATGTGATTGAGATAGAAAAGGCAAA
* *
1849 AGAAGAGATAGCAAGCAAGACCGAGGATCAACAAAGAGTTCTGCAGGAGAAAGAGGGTTTGCTGG
389 AGAAGAGATAGCAAGCAAGACCGAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTTGG
* * * * **
1914 CACAAATGAAGGAACTAGAATTTGATGTCAATTCTTTAAAGAATCAGAAAGGTGAGTTGGAAGAG
454 CACAAATGAAGGAACTAGAATTTGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAGAG
* * *
1979 GATTTGCGAACTAAAATCAAAGAGAATGGT
519 GACTTGAGAACTAAAATCGAAGAGAATGGT
* * *
2009 CAGCTGAGGGAGGAAAGTTTAGGACTGCAATCCCAAATTTCCGAACTCGAGATGATATCAAAACA
1 CAGCTGAGGGAGGAAAATATAGGACTGCAATCCCAAATTTCAGAACTCGAGATGATATCAAAA-A
* * **
2074 GAGACAAGAAGAACTTTTGACACTCACAAAGAAGTTTGAGGACAATGAGAAAGAATCGCTATCTA
65 GAGACAAGAAGAACTTTTGACTCTCACAAAGAAGTTTGAGGATAATGAGAAAGAATCATTATCTA
* * * *
2139 GAGTGGAGAATTTAACAGTGCAGAGCAACAATTTGCTAGCAGACATGGAGTCCCTACGCACCCAG
130 GAGTGGAGAATTTGACAGTGCAGATCAACAATCTGCTAGCAGACATGGAGTCACTACGCACCCAG
* * *
2204 AAAGCTCAGTTGGAAGAACATATTGTAGTGAAAGGCGATGAAGCATCAACTCAGGTCAAGGGCTT
195 AAAGCTCAGTTGGAAGAACATATTGTAGTAAAAGGCGATGAAGCATCAACTCAAGTCAAGAGCTT
*
2269 GATGGATCAGATAAATACTTTGCAGCAGGAGCTGGAGTCCCTGCATAGCCAGAAAGCAGAACTGG
260 GATGGATCAGATAAATACTTTGCAGCAGGAGCTGGAGTCCCTGCATAGCCAGAAAGCAGAACTTG
* *
2334 AAGTTCAGCTTGAGAGAAAAACTCAAGCTATTTCCAATCATGTGATTGAGATAGAGAAGGCAAAA
325 AAGTTCAGCTTGAGAGTAAAACTCAAGCTATTTCCAATCATGTGATTGAGATAGAAAAGGCAAAA
*
2399 GAAGAGATAGTC-AGCAAGACCAAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTTGG
390 GAAGAGATAG-CAAGCAAGACCGAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTTGG
2463 CACAAATGAAGGAACTAGAATTTGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAGAG
454 CACAAATGAAGGAACTAGAATTTGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAGAG
*
2528 GACCTGAGAACTAAAATCGAAGAGAATGGT
519 GACTTGAGAACTAAAATCGAAGAGAATGGT
* ** * * *
2558 CAGCTGAGGGAGGAAAATATGGGACTGCAATATCAAATTTCAGAACTCGAGAGGGTATTAAAAAC
1 CAGCTGAGGGAGGAAAATATAGGACTGCAATCCCAAATTTCAGAACTCGAGATGATATCAAAAA-
* *
2623 GAGACAAGAAGAACTTTTTACTCTCACAAAGAAGTTTGAGGATAATGAGACAGAATCATTATCTA
65 GAGACAAGAAGAACTTTTGACTCTCACAAAGAAGTTTGAGGATAATGAGAAAGAATCATTATCTA
* * ** * * **
2688 GAGTGGAGAATTTGACAGTGCAGATTAACAATCTGCTAGGAGACATGGAGTTGCTGCGGACTGAG
130 GAGTGGAGAATTTGACAGTGCAGATCAACAATCTGCTAGCAGACATGGAGTCACTACGCACCCAG
*
2753 AAAGCTCAGTTGGAAGAACATATTGTAGTTAAAGGCGATGAAGCATCAAAC-CAAGTCAAGAGCT
195 AAAGCTCAGTTGGAAGAACATATTGTAGTAAAAGGCGATGAAGCATC-AACTCAAGTCAAGAGCT
* * * * * * *
2817 TGATGGATGAAATAAATACATTGCAGCAGAAACTGG-GATCCATGCATAGCCAGAAAGCTGAACT
259 TGATGGATCAGATAAATACTTTGCAGCAGGAGCTGGAG-TCCCTGCATAGCCAGAAAGCAGAACT
* *
2881 TGAAGTTCAGCTTGAGAGTAAAACACAAGCTATTT-CAGATCATATGATTGAGATAGAAAAGGCA
323 TGAAGTTCAGCTTGAGAGTAAAACTCAAGCTATTTCCA-ATCATGTGATTGAGATAGAAAAGGCA
* *
2945 AAAGAAGAGATAGTAAGCAAGACTGAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTT
387 AAAGAAGAGATAGCAAGCAAGACCGAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTT
*
3010 GGCACAAATGAAGGAACTAGAATTGGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAG
452 GGCACAAATGAAGGAACTAGAATTTGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAG
3075 AGGACTTGAGAACTAAAATCGAAGAGAATGGT
517 AGGACTTGAGAACTAAAATCGAAGAGAATGGT
**
3107 CAATTGAGGGAGG
1 CAGCTGAGGGAGG
3120 GAATAGTGAG
Statistics
Matches: 1004, Mismatches: 99, Indels: 16
0.90 0.09 0.01
Matches are distributed among these distances:
548 8 0.01
549 990 0.99
550 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (548 bp):
CAGCTGAGGGAGGAAAATATAGGACTGCAATCCCAAATTTCAGAACTCGAGATGATATCAAAAAG
AGACAAGAAGAACTTTTGACTCTCACAAAGAAGTTTGAGGATAATGAGAAAGAATCATTATCTAG
AGTGGAGAATTTGACAGTGCAGATCAACAATCTGCTAGCAGACATGGAGTCACTACGCACCCAGA
AAGCTCAGTTGGAAGAACATATTGTAGTAAAAGGCGATGAAGCATCAACTCAAGTCAAGAGCTTG
ATGGATCAGATAAATACTTTGCAGCAGGAGCTGGAGTCCCTGCATAGCCAGAAAGCAGAACTTGA
AGTTCAGCTTGAGAGTAAAACTCAAGCTATTTCCAATCATGTGATTGAGATAGAAAAGGCAAAAG
AAGAGATAGCAAGCAAGACCGAGGATCAACAGAGAGTTCTGCAGGAGAAAGAGGGTTTGTTGGCA
CAAATGAAGGAACTAGAATTTGAGGTCATTTCTCTAAAGAACCAGAAAGGTGAACTGGAAGAGGA
CTTGAGAACTAAAATCGAAGAGAATGGT
Done.