Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03874.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: 3148
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:1491 original size:30 final size:30
Alignment explanation
Indices: 1430--1491 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1420 GGGATGGGAG
* * * **
1430 GGAGTAAAAGTTTTGGGGGAAAAGTGGAAA
1 GGAGTAAAAATTTTGAGAGAAAAGTAAAAA
1460 GGAGTAAAAATTTTGAGAGAAAAGTAAAAA
1 GGAGTAAAAATTTTGAGAGAAAAGTAAAAA
1490 GG
1 GG
1492 TTTGGGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAATTTTGAGAGAAAAGTAAAAA
Found at i:2322 original size:149 final size:150
Alignment explanation
Indices: 1842--2442 Score: 1109
Period size: 149 Copynumber: 4.0 Consensus size: 150
1832 ACTACTAGTA
*
1842 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGTAACCAGTGGT
1 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
1907 GCAGCTGCAAATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCT
66 GCAGCTG--AATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCT
1972 TGGAATAACACCTGCTTATTTG
129 TGGAATAACACCTGCTTATTTG
*
1994 CCAGTCTCACTATCAGCTCGAGTTC-AACTCATTGAATTATGCAAATAGTGCAGCAACCAGTGGT
1 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
2058 GCAGCTGCAAATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCT
66 GCAGCTG--AATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCT
2123 TGGAATAACACCTGCTTATTTG
129 TGGAATAACACCTGCTTATTTG
2145 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
1 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
* *
2210 GCAGCTG-ATAATACTGATGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCATTTTCTTG
66 GCAGCTGAATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCTTG
2274 GAATAACACCTGCTTATTTG
131 GAATAACACCTGCTTATTTG
2294 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
1 CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
2359 GCAGCTG-ATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCTTG
66 GCAGCTGAATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCTTG
2423 GAATAACACCTGCTTATTTG
131 GAATAACACCTGCTTATTTG
2443 TGGCAAACTC
Statistics
Matches: 441, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
149 222 0.50
151 149 0.34
152 70 0.16
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (150 bp):
CCAGTCTCACTATCAGCTCGAGTTCAAACTCATTGAATTATGCAAATAGTGCTGCAACCAGTGGT
GCAGCTGAATAATACTGGTGATTCAGGAGAACCTGGTGTTGGTGGTGTGCCTAATCGTTTTCTTG
GAATAACACCTGCTTATTTG
Done.