Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1003
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: 3422
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.32
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:194 original size:21 final size:21
Alignment explanation
Indices: 168--207 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
158 TTGCACAGTG
*
168 TTTTTGGTTTTTTTTTTTTTA
1 TTTTTGGTTTTGTTTTTTTTA
189 TTTTTGGTTTTGTTTTTTT
1 TTTTTGGTTTTGTTTTTTT
208 GGTTTCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (21 bp):
TTTTTGGTTTTGTTTTTTTTA
Found at i:1903 original size:68 final size:68
Alignment explanation
Indices: 1828--1964 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
1818 GCAGAAATTT
1828 TTATCGCGTTGCCTTTGTGATATTTTAGCCGAAAGGTGACGATATAAATAAGCCATCACCCCACA
1 TTATCGCGTTGCCTTTGTGATATTTTAGCCGAAAGGTGACGATATAAATAAGCCATCACCCCACA
1893 CAG
66 CAG
*
1896 TTATCGCGTTGCCTTTGTGATATTTTAGCCGAAAGGTGACGATATAAATAAGCCATCACGCCACA
1 TTATCGCGTTGCCTTTGTGATATTTTAGCCGAAAGGTGACGATATAAATAAGCCATCACCCCACA
1961 CAG
66 CAG
1964 T
1 T
1965 GGATCGAGTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (68 bp):
TTATCGCGTTGCCTTTGTGATATTTTAGCCGAAAGGTGACGATATAAATAAGCCATCACCCCACA
CAG
Done.