Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01539.N1
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, 835
Length: 1392
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Found at i:295 original size:101 final size:100
Alignment explanation
Indices: 3--738 Score: 667
Period size: 101 Copynumber: 7.5 Consensus size: 100
1 GT
* * *
3 TTATAGAAATGTCCTCTTAATTTTGCATTTAATCAAATATTGGTAGGACAGATTGGCTGGGTAGT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAAT-TTGGCAGGACAGTTTGGCTGGGTAGT
* * * *
68 TTGACATGACAATCCATTTCGTCCCAATTTAAATAC
65 TTGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * * * * * *
104 ATATAGAAA--T-ATCTTAATTTTGCATTCCATCAATTTTGGTAGGGCAGTTTCGCTGGGTAGAT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTGGCAGGACAGTTTGGCTGGGTAGTT
* * * *
166 TGACATGACAGTCCATTTCGTCCTAATTTTAATGT
66 TGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
** * *
201 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTAGGCAGGGTAGTTTTGCTAGGTAGT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTT-GGCAGGACAGTTTGGCTGGGTAGT
* * * *
266 TTGGCATGATAGTCAATTTTGTCCCAATTTTAATGC
65 TTGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * * * * *
302 TTATAGAAATGTCTTCTTAATTTTACATTCAATCTAATTTTGGTAGGCCAGTTTGGCCGGATAGT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATC-AAATTTGGCAGGACAGTTTGGCTGGGTAGT
* * * * *
367 TTGCCATTACAGTACATTTCATCCCGATTTGAATGC
65 TTGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * ** **
403 TTATAGAAATGTTCTCTTAATTTTACATTTAATCAAATTTTAACAACACAGTTTGGCTGGGTAGT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAA-TTTGGCAGGACAGTTTGGCTGGGTAGT
* * *
468 TCGGCATGACAGTCCATTTCGTCCAAATTTGAGTGC
65 TTGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * *
504 CTATTGAAATGTCCTCTTAATTTTGCATTCAATCAAATTT-----G--A---T--AT-GGAAGTT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTGGCAGGACAGTTTGGCTGGGTAGTT
* * * *
556 TGGCATGACAGTTCATTTCTTCCTAATTTGAATGT
66 TGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * ** * *
591 TTATAGAAATATTCTCTTAATTTTACATTCAATCAAATTTCGGCACAACAGTTTGGTTGGATAGT
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTT-GGCAGGACAGTTTGGCTGGGTAGT
* *
656 TTGGCATGACAGTCTATTTTGTCCCAATTTGAATGC
65 TTGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
* * * * *
692 TGATAGAAATATTCTCTTAATGTTGCATTCAGTCAAATATTGGCAGG
1 TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAAT-TTGGCAGG
739 GTTGTTTGGC
Statistics
Matches: 511, Mismatches: 103, Indels: 42
0.78 0.16 0.06
Matches are distributed among these distances:
87 70 0.14
88 1 0.00
90 1 0.00
93 1 0.00
95 1 0.00
97 61 0.12
98 22 0.04
99 2 0.00
100 30 0.06
101 315 0.62
102 7 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (100 bp):
TTATAGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTGGCAGGACAGTTTGGCTGGGTAGTT
TGGCATGACAGTCCATTTCGTCCCAATTTGAATGC
Found at i:620 original size:87 final size:87
Alignment explanation
Indices: 465--630 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 87
455 TTGGCTGGGT
* * * *
465 AGTTCGGCATGACAGTCCATTTCGTCCAAATTTGAGTGCCTATTGAAATGTCCTCTTAATTTTGC
1 AGTTCGGCATGACAGTCCATTTCGTCCAAATTTGAATGCCTATAGAAATATCCTCTTAATTTTAC
530 ATTCAATCAAATTTGATATGGA
66 ATTCAATCAAATTTGATATGGA
* * * * ** *
552 AGTTTGGCATGACAGTTCATTTCTTCCTAATTTGAATGTTTATAGAAATATTCTCTTAATTTTAC
1 AGTTCGGCATGACAGTCCATTTCGTCCAAATTTGAATGCCTATAGAAATATCCTCTTAATTTTAC
617 ATTCAATCAAATTT
66 ATTCAATCAAATTT
631 CGGCACAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (87 bp):
AGTTCGGCATGACAGTCCATTTCGTCCAAATTTGAATGCCTATAGAAATATCCTCTTAATTTTAC
ATTCAATCAAATTTGATATGGA
Found at i:711 original size:188 final size:188
Alignment explanation
Indices: 364--729 Score: 484
Period size: 188 Copynumber: 1.9 Consensus size: 188
354 TTGGCCGGAT
* * *
364 AGTTTGCCATTACAGTACATTTCATCCCGATTTGAATGCTTATAGAAATGTTCTCTTAATTTTAC
1 AGTTTGCCATGACAGTACATTTCATCCCAATTTGAATGCTTATAGAAATATTCTCTTAATTTTAC
* * *
429 ATTTAATCAAATTTTAACAACACAGTTTGGCTGGGTAGTTCGGCATGACAGTCCATTTCGTCCAA
66 ATTCAATCAAATTTCAACAACACAGTTTGGCTGGATAGTTCGGCATGACAGTCCATTTCGTCCAA
* * * *
494 ATTTGAGTGCCTATTGAAATGTCCTCTTAATTTTGCATTCAATCAAATTTGATATGGA
131 ATTTGAATGCCTATAGAAATATCCTCTTAATGTTGCATTCAATCAAATTTGATATGGA
* * * * *
552 AGTTTGGCATGACAGTTCATTTCTTCCTAATTTGAATGTTTATAGAAATATTCTCTTAATTTTAC
1 AGTTTGCCATGACAGTACATTTCATCCCAATTTGAATGCTTATAGAAATATTCTCTTAATTTTAC
** * * * * *
617 ATTCAATCAAATTTCGGC-ACAACAGTTTGGTTGGATAGTTTGGCATGACAGTCTATTTTGTCCC
66 ATTCAATCAAATTTCAACAAC-ACAGTTTGGCTGGATAGTTCGGCATGACAGTCCATTTCGTCCA
* *
681 AATTTGAATG-CTGATAGAAATATTCTCTTAATGTTGCATTCAGTCAAAT
130 AATTTGAATGCCT-ATAGAAATATCCTCTTAATGTTGCATTCAATCAAAT
730 ATTGGCAGGG
Statistics
Matches: 152, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
187 4 0.03
188 148 0.97
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (188 bp):
AGTTTGCCATGACAGTACATTTCATCCCAATTTGAATGCTTATAGAAATATTCTCTTAATTTTAC
ATTCAATCAAATTTCAACAACACAGTTTGGCTGGATAGTTCGGCATGACAGTCCATTTCGTCCAA
ATTTGAATGCCTATAGAAATATCCTCTTAATGTTGCATTCAATCAAATTTGATATGGA
Done.