Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013723.1 Kokia drynarioides strain JFW-HI SEQ_128751, whole genome shotgun sequence
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: 31124
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:18431 original size:12 final size:12
Alignment explanation
Indices: 18414--18438 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18404 ATTTTACATC
18414 TATTTTATTTTA
1 TATTTTATTTTA
18426 TATTTTATTTTA
1 TATTTTATTTTA
18438 T
1 T
18439 GCTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:26786 original size:40 final size:40
Alignment explanation
Indices: 26726--26806 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
26716 GAACCCTCAA
* *
26726 TATAAAGCAACCCTCTTAGCTAGCCTATGAGTATTCTTTT
1 TATAAAGCAACCCCCATAGCTAGCCTATGAGTATTCTTTT
* *
26766 TATAAAGCAACCCCCATAGCTAGCTTATGAGTATTTTTTT
1 TATAAAGCAACCCCCATAGCTAGCCTATGAGTATTCTTTT
26806 T
1 T
26807 TCTTCTTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (40 bp):
TATAAAGCAACCCCCATAGCTAGCCTATGAGTATTCTTTT
Found at i:27168 original size:247 final size:247
Alignment explanation
Indices: 26732--27225 Score: 988
Period size: 247 Copynumber: 2.0 Consensus size: 247
26722 TCAATATAAA
26732 GCAACCCTCTTAGCTAGCCTATGAGTATTCTTTTTATAAAGCAACCCCCATAGCTAGCTTATGAG
1 GCAACCCTCTTAGCTAGCCTATGAGTATTCTTTTTATAAAGCAACCCCCATAGCTAGCTTATGAG
26797 TATTTTTTTTTCTTCTTGAGTAAGTTTCTCTTTTTCTTTCTTTTGGTGACCTTATGATTTTGTCA
66 TATTTTTTTTTCTTCTTGAGTAAGTTTCTCTTTTTCTTTCTTTTGGTGACCTTATGATTTTGTCA
26862 CTTTTTCACATGTTTTCTTACTCATAATTCTTTTTACTTCTACTCATTTTTTTCTTTTCTTTTTG
131 CTTTTTCACATGTTTTCTTACTCATAATTCTTTTTACTTCTACTCATTTTTTTCTTTTCTTTTTG
26927 ATTTGTCTCCTTTTTTTTGGCTAAACTATGGTTCATACATTATATTGAGTTT
196 ATTTGTCTCCTTTTTTTTGGCTAAACTATGGTTCATACATTATATTGAGTTT
26979 GCAACCCTCTTAGCTAGCCTATGAGTATTCTTTTTATAAAGCAACCCCCATAGCTAGCTTATGAG
1 GCAACCCTCTTAGCTAGCCTATGAGTATTCTTTTTATAAAGCAACCCCCATAGCTAGCTTATGAG
27044 TATTTTTTTTTCTTCTTGAGTAAGTTTCTCTTTTTCTTTCTTTTGGTGACCTTATGATTTTGTCA
66 TATTTTTTTTTCTTCTTGAGTAAGTTTCTCTTTTTCTTTCTTTTGGTGACCTTATGATTTTGTCA
27109 CTTTTTCACATGTTTTCTTACTCATAATTCTTTTTACTTCTACTCATTTTTTTCTTTTCTTTTTG
131 CTTTTTCACATGTTTTCTTACTCATAATTCTTTTTACTTCTACTCATTTTTTTCTTTTCTTTTTG
27174 ATTTGTCTCCTTTTTTTTGGCTAAACTATGGTTCATACATTATATTGAGTTT
196 ATTTGTCTCCTTTTTTTTGGCTAAACTATGGTTCATACATTATATTGAGTTT
27226 CCTATGTTTA
Statistics
Matches: 247, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 247 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (247 bp):
GCAACCCTCTTAGCTAGCCTATGAGTATTCTTTTTATAAAGCAACCCCCATAGCTAGCTTATGAG
TATTTTTTTTTCTTCTTGAGTAAGTTTCTCTTTTTCTTTCTTTTGGTGACCTTATGATTTTGTCA
CTTTTTCACATGTTTTCTTACTCATAATTCTTTTTACTTCTACTCATTTTTTTCTTTTCTTTTTG
ATTTGTCTCCTTTTTTTTGGCTAAACTATGGTTCATACATTATATTGAGTTT
Done.