Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_35589
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: 4468
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Found at i:1951 original size:54 final size:54
Alignment explanation
Indices: 1869--1980 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
1859 GAGCTGTGAT
* * *
1869 TTCAAAGGATGTTTCATCCAAGCAAAAAGTTCAGAAGGTTGACGATACAAAGAC
1 TTCAAAGGATGTTTCATCCAAGCAAAAAGGTCAAAAGGTTGACCATACAAAGAC
* * * *
1923 TTCAAAGGATTTTTCATCCGAGCAAAAAGGTCAAAAGGTTGACCTTACAAAGCC
1 TTCAAAGGATGTTTCATCCAAGCAAAAAGGTCAAAAGGTTGACCATACAAAGAC
1977 TTCA
1 TTCA
1981 GACTATCCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (54 bp):
TTCAAAGGATGTTTCATCCAAGCAAAAAGGTCAAAAGGTTGACCATACAAAGAC
Found at i:3072 original size:36 final size:33
Alignment explanation
Indices: 2918--3050 Score: 212
Period size: 33 Copynumber: 4.0 Consensus size: 33
2908 GGAGTTGGAC
* * * * *
2918 CACCACCGCCACCACTACCTCCAGGGGGAGGAG
1 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
2951 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
1 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
*
2984 CACCACCTCCGCCACCACCTCCTGGTGGAGGAG
1 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
3017 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
1 CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
3050 C
1 C
3051 TCCTGGCCCT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.21, C:0.45, G:0.25, T:0.09
Consensus pattern (33 bp):
CACCACCTCCGCCACCACCTCCTGGAGGAGGAG
Done.