Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006809.1 Kokia drynarioides strain JFW-HI SEQ_121408, 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: 3156
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1519 original size:26 final size:25
Alignment explanation
Indices: 1490--1559 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 25
1480 AATGAGTTCC
1490 TGCAGCGACAATTTTGGGCAT-GCTCA
1 TGCAGCGAC-ATTTTGGGCATCG-TCA
*
1516 TGCAGCGACATTTCTGGACATCGTCA
1 TGCAGCGACATTT-TGGGCATCGTCA
*
1542 TGCAGTGACTATTTTGGG
1 TGCAGCGAC-ATTTTGGG
1560 TGCAATTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.11
26 29 0.76
27 5 0.13
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (25 bp):
TGCAGCGACATTTTGGGCATCGTCA
Found at i:1619 original size:38 final size:38
Alignment explanation
Indices: 1527--1607 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
1517 GCAGCGACAT
* * *
1527 TTCTGGACATCGTCATGCAGTGACTATTTTGGGTGCAA
1 TTCTGGACATCATCATGCAGTGACAATTCTGGGTGCAA
*
1565 TTCTGGACATCATCATGTAGTGACAATTCTGGGTGCAA
1 TTCTGGACATCATCATGCAGTGACAATTCTGGGTGCAA
1603 TTCTG
1 TTCTG
1608 AATAGACTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (38 bp):
TTCTGGACATCATCATGCAGTGACAATTCTGGGTGCAA
Done.