Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g01122.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: 1900
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Found at i:373 original size:81 final size:81
Alignment explanation
Indices: 288--973 Score: 1054
Period size: 81 Copynumber: 8.5 Consensus size: 81
278 GAGGTGACGA
* *
288 GTTTGGAAGACAAGTATGCTACGGCTTACTTTTACAAAACTTCTGATTCTGAAAGCCATGGCGAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
353 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
* * **** * * *
369 GTTTGGAAGATAAATATGCTAATATTTACTTCCACAAAACTTCTGATTCTGAAAGCCATGGCGAC
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
434 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
* * ** * * *
450 GTTTGGAAGATAAATATGCTA-ATCTTTACTTCCACAAAACTTCTGATTCTGAAAGCCATTGCGA
1 GTTTGGAAGACAAGTATGCTACGGC-TTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGA
514 AGGGAAAGAAGTGAAGG
65 AGGGAAAGAAGTGAAGG
531 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
596 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
612 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
677 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
* *
693 GTTTGGAAGACAAGTATACTACGGCTTACTTTCACAAAACTTCTGATTCTGAAAGCCATGGCGAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
758 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
774 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
839 GGGAAAGAAGTGAAGG
66 GGGAAAGAAGTGAAGG
* * * *
855 GTTTGGAAGACAAATATGCTACTGCTTATTTTCATC-AAACTTCTAATTCTGAAAGCCATGGTGA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCA-CAAAACTTCTAATTCTGAAAGCCATGGCGA
* *
919 AAGGAAAGCAA-TGAAGA
65 AGGGAAAG-AAGTGAAGG
* * * *
936 GTTTGGAAGACAAATATTCCACAGCTTACTTTCACAAA
1 GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAA
974 GCGTTTGATT
Statistics
Matches: 565, Mismatches: 35, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
80 1 0.00
81 560 0.99
82 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (81 bp):
GTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAA
GGGAAAGAAGTGAAGG
Found at i:400 original size:162 final size:160
Alignment explanation
Indices: 120--973 Score: 966
Period size: 162 Copynumber: 5.3 Consensus size: 160
110 GGCAATGCAG
* * * * *
120 GAAGGGATTTGGAAGAAAAATATGCTACAGCTTACTTTCACAAAACTTCTGATTCTGCAAA-TCA
1 GAAGGG-TTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTG-AAAGCCA
** * ** * ** * *
184 CT-TTG-ATGGAGGTGATGTGAAGAATTTGGAAGACAAATATTCTACGGCTTACTTCCACAAAGC
64 -TGGCGAAGGGA-AAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCACAAAAC
* * ** * *
247 TTTTGATGCTGAAA-ATCTTGATAGAGAAAAGGAGGT
127 TTCTGATTCTGAAACATCGCGA-AG-GGAAA-GAAGT
* * * *
283 GACGAGTTTGGAAGACAAGTATGCTACGGCTTACTTTTACAAAACTTCTGATTCTGAAAGCCATG
1 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
* ****
348 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGATAAATATGCTAATATTTACTTCCACAAAACTTCT
66 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCACAAAACTTCT
* *
413 GATTCTGAAAGCCATGGCGACGGGAAAGAAGT
131 GATTCTGAAA--CATCGCGAAGGGAAAGAAGT
* * ** * *
445 GAAGGGTTTGGAAGATAAATATGCTA-ATCTTTACTTCCACAAAACTTCTGATTCTGAAAGCCAT
1 GAAGGGTTTGGAAGACAAGTATGCTACGGC-TTACTTTCACAAAACTTCTAATTCTGAAAGCCAT
* * *
509 TGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTC
65 GGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCACAAAACTTC
* *
574 TAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
130 TGATTCTGAAA--CATCGCGAAGGGAAAGAAGT
607 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
1 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
* * *
672 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATACTACGGCTTACTTTCACAAAACTTCT
66 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCACAAAACTTCT
*
737 GATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
131 GATTCTGAAA--CATCGCGAAGGGAAAGAAGT
769 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
1 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
* * *
834 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACTGCTTATTTTCATC-AAACTTC
66 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCA-CAAAACTTC
* * * *
898 TAATTCTGAAAGCCATGGTGAAAGGAAAGCAA-T
130 TGATTCTGAAA--CATCGCGAAGGGAAAG-AAGT
* * * * *
931 GAAGAGTTTGGAAGACAAATATTCCACAGCTTACTTTCACAAA
1 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAA
974 GCGTTTGATT
Statistics
Matches: 612, Mismatches: 69, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
161 5 0.01
162 586 0.96
163 16 0.03
164 1 0.00
165 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (160 bp):
GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATGCTACGGCTTACTTCCACAAAACTTCT
GATTCTGAAACATCGCGAAGGGAAAGAAGT
Found at i:555 original size:243 final size:243
Alignment explanation
Indices: 120--973 Score: 1114
Period size: 243 Copynumber: 3.5 Consensus size: 243
110 GGCAATGCAG
* * * *
120 GAAGGGATTTGGAAGAAAAATATGCTACAGCTTACTTTCACAAAACTTCTGATTCTGCAAA-TCA
1 GAAGGG-TTTGGAAGACAAATATGCTACTGCTTACTTTCACAAAACTTCTAATTCTG-AAAGCCA
** * ** * ** * * *
184 CT-TTG-ATGGAGGTGATGTGAAGAATTTGGAAGACAAATATTCTACGGCTTACTTCCACAAAGC
64 -TGGCGAAGGGA-AAGAAGTGAAGGGTTTGGAAGACAAATATACTACAGCTTACTTCCACAAAAC
* * *** * * * *
247 TTTTGATGCTGAAA---ATCTTGATAGAGAAAAGGAGGTGACGAGTTTGGAAGACAAGTATGCTA
127 TTCTGATTCTGAAAGCCATGGCGA-AG-GGAAA-GAAGTGAAGGGTTTGGAAGACAAGTATGCTA
* *
309 CGGCTTACTTTTACAAAACTTCTGATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
189 CGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
* * ** * *
364 GAAGGGTTTGGAAGATAAATATGCTAATATTTACTTCCACAAAACTTCTGATTCTGAAAGCCATG
1 GAAGGGTTTGGAAGACAAATATGCTACTGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
* * * *
429 GCGACGGGAAAGAAGTGAAGGGTTTGGAAGATAAATATGCTA-ATCTTTACTTCCACAAAACTTC
66 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATACTACAGC-TTACTTCCACAAAACTTC
*
493 TGATTCTGAAAGCCATTGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTT
130 TGATTCTGAAAGCCATGGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTT
558 ACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
195 ACTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
* *
607 GAAGGGTTTGGAAGACAAGTATGCTACGGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
1 GAAGGGTTTGGAAGACAAATATGCTACTGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
* * *
672 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATACTACGGCTTACTTTCACAAAACTTCT
66 GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATACTACAGCTTACTTCCACAAAACTTCT
737 GATTCTGAAAGCCATGGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTTA
131 GATTCTGAAAGCCATGGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTTA
802 CTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
196 CTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
*
850 GAAGGGTTTGGAAGACAAATATGCTACTGCTTATTTTCATC-AAACTTCTAATTCTGAAAGCCAT
1 GAAGGGTTTGGAAGACAAATATGCTACTGCTTACTTTCA-CAAAACTTCTAATTCTGAAAGCCAT
* * * * * *
914 GGTGAAAGGAAAGCAA-TGAAGAGTTTGGAAGACAAATATTCCACAGCTTACTTTCACAAA
65 GGCGAAGGGAAAG-AAGTGAAGGGTTTGGAAGACAAATATACTACAGCTTACTTCCACAAA
974 GCGTTTGATT
Statistics
Matches: 542, Mismatches: 58, Indels: 21
0.87 0.09 0.03
Matches are distributed among these distances:
242 5 0.01
243 514 0.95
244 17 0.03
245 2 0.00
246 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (243 bp):
GAAGGGTTTGGAAGACAAATATGCTACTGCTTACTTTCACAAAACTTCTAATTCTGAAAGCCATG
GCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAATATACTACAGCTTACTTCCACAAAACTTCT
GATTCTGAAAGCCATGGCGAAGGGAAAGAAGTGAAGGGTTTGGAAGACAAGTATGCTACGGCTTA
CTTTCACAAAACTTCTAATTCTGAAAGCCATGGCGAAGGGAAAGAAGT
Done.