Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005110.1 Kokia drynarioides strain JFW-HI SEQ_118934, 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: 10082
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2728 original size:18 final size:18
Alignment explanation
Indices: 2705--2743 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2695 AGTATGTATA
2705 GATTATAGGAAGCTGAAT
1 GATTATAGGAAGCTGAAT
*
2723 GATTATAGGAAGCTGAGT
1 GATTATAGGAAGCTGAAT
2741 GAT
1 GAT
2744 GCAATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (18 bp):
GATTATAGGAAGCTGAAT
Found at i:6335 original size:135 final size:135
Alignment explanation
Indices: 6088--6356 Score: 459
Period size: 135 Copynumber: 2.0 Consensus size: 135
6078 TTTCTCTAGC
6088 TGTACAAGTTGATTATACCATCTGTACACTTACGCAAATCTAGCGTGTTCATCAGATAGTTGTCA
1 TGTACAAGTTGATTATACCATCTGTACACTTACGCAAATCTAGCGTGTTCATCAGATAGTTGTCA
* *
6153 GTTGCGATGACAGTTCTAGGCGTAAATTTGGATGTTATTTTGCAACGACAACTCTGTACACCTTC
66 GTTGCGACGACAGTTCTAAGCGTAAATTTGGATGTTATTTTGCAACGACAACTCTGTACACCTTC
6218 ATGCT
131 ATGCT
* * *
6223 TGTACAAGTTGATTATACCAGT-TGTACACTTACGCAAATTTGGCGTGTTCATCAGATAGTTTTC
1 TGTACAAGTTGATTATACCA-TCTGTACACTTACGCAAATCTAGCGTGTTCATCAGATAGTTGTC
* *
6287 AGTTGCGACGACAGTTCTAAGCGTAAATTTTGATGTTATTTTGTAACGACAACTCTGTACACCTT
65 AGTTGCGACGACAGTTCTAAGCGTAAATTTGGATGTTATTTTGCAACGACAACTCTGTACACCTT
6352 CATGC
130 CATGC
6357 ATTGATCCTT
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
135 125 0.99
136 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (135 bp):
TGTACAAGTTGATTATACCATCTGTACACTTACGCAAATCTAGCGTGTTCATCAGATAGTTGTCA
GTTGCGACGACAGTTCTAAGCGTAAATTTGGATGTTATTTTGCAACGACAACTCTGTACACCTTC
ATGCT
Done.