Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g01756.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: 4272
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Found at i:3121 original size:69 final size:68
Alignment explanation
Indices: 3026--3473 Score: 518
Period size: 69 Copynumber: 6.5 Consensus size: 68
3016 GGGAAAGGTC
* * * * *
3026 CATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAGAGC
1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
3091 TCAT
65 TCAT
** * * * * *
3095 CAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGGGAAGGGC
1 CA-TTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
3160 TCAT
65 TCAT
* * * * *
3164 CTCTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTAAGGGGAAGAGT
1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
*
3229 TCGT
65 TCAT
* * * ** * *
3233 CCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGGGT
1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
3298 TCAT
65 TCAT
* * * * *
3302 CCATATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGGGAAGGGT
1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
*
3367 TCGT
65 TCAT
* * *
3371 CCGTATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
3436 TCAT
65 TCAT
*
3440 CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGC
3474 TTATCATTAT
Statistics
Matches: 328, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
68 4 0.01
69 320 0.98
70 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (68 bp):
CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCT
CAT
Found at i:3383 original size:207 final size:207
Alignment explanation
Indices: 3023--3473 Score: 593
Period size: 207 Copynumber: 2.2 Consensus size: 207
3013 CCAGGGAAAG
* * *
3023 GTCCATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAG
1 GTCC-TTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAG
* * * *
3088 AGCTCATCAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGG
65 AGCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
* * * *
3153 GAAGGGCTCATCTCTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTA
130 GAAGGGCTCATCTCTATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA
*
3218 AGGGGAAGAGTTC
195 AGGGGAAGAGCTC
* * * * ** *
3231 GTCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGG
1 GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA
* * * *
3296 GTTCATCCA-TATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGG
66 GCTCAT-CAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
* * *
3360 GAAGGGTTCGTC-CGTATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTC
130 GAAGGGCTCATCTC-TATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTC
3424 AAGGGGAAGAGCTC
194 AAGGGGAAGAGCTC
* *
3438 AT-CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
1 GTCCT-TGTTTGCAGATTCTGTTCCAAGCACCCCTGC
3474 TTATCATTAT
Statistics
Matches: 211, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
206 3 0.01
207 202 0.96
208 6 0.03
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (207 bp):
GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA
GCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGG
AAGGGCTCATCTCTATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCAA
GGGGAAGAGCTC
Done.