Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014801.1 Kokia drynarioides strain JFW-HI SEQ_129843, 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: 399286
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 406 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:371740 original size:14 final size:14
Alignment explanation
Indices: 371718--371772 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
371708 ACATATTACT
*
371718 TTTAGGGTTTAAGA
1 TTTAAGGTTTAAGA
371732 TTTAAGGTTT-AGA
1 TTTAAGGTTTAAGA
* *
371745 GTTTAGGGTTTATGA
1 -TTTAAGGTTTAAGA
371760 TTTAAGGTTTAAG
1 TTTAAGGTTTAAG
371773 GTACTGTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 3 0.09
14 29 0.85
15 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTTAAGGTTTAAGA
Found at i:383179 original size:21 final size:21
Alignment explanation
Indices: 383153--383199 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
383143 TGTTGGTTCG
* *
383153 AAGGATAAAAAGAGGAAGCGT
1 AAGGATAAAAAGAAGAAACGT
*
383174 AAGGATAAGAAGAAGAAACGT
1 AAGGATAAAAAGAAGAAACGT
383195 AAGGA
1 AAGGA
383200 GGTACGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.04, G:0.32, T:0.09
Consensus pattern (21 bp):
AAGGATAAAAAGAAGAAACGT
Done.