Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007335.1 Kokia drynarioides strain JFW-HI SEQ_121951, 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: 71206
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1411 original size:6 final size:6
Alignment explanation
Indices: 1400--1431 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1390 GAAAAGCTTC
1400 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
1432 ATGGGACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:2752 original size:23 final size:25
Alignment explanation
Indices: 2705--2754 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
2695 TTATAAAAAT
2705 TAATTATATTAATTATATATGTTAAA
1 TAATTATATTAATTATATA-GTTAAA
*
2731 TAATTATATTTATT-TATA-TTAAA
1 TAATTATATTAATTATATAGTTAAA
2754 T
1 T
2755 CACTAACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
25 4 0.17
26 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATTATATTAATTATATAGTTAAA
Found at i:30920 original size:2 final size:2
Alignment explanation
Indices: 30909--30940 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30899 ACCTTTTAAC
30909 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30941 GTAAAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46814 original size:23 final size:24
Alignment explanation
Indices: 46704--46815 Score: 78
Period size: 23 Copynumber: 4.9 Consensus size: 24
46694 AAGTTTAATT
* *
46704 TAATTTTTTAAAAATTATAAAATA
1 TAATATTTTAAAATTTATAAAATA
*
46728 TAA-ATTATTAAAA-TAATAAAAT-
1 TAATATT-TTAAAATTTATAAAATA
* *
46750 T-ATATTTT-TATTATTATAAAA-A
1 TAATATTTTAAAAT-TTATAAAATA
* * *
46772 TTATAATTT-AAATTTTTAAAATA
1 TAATATTTTAAAATTTATAAAATA
46795 -AATATTTTAAAATTTATAAAA
1 TAATATTTTAAAATTTATAAAA
46816 ACATAAATTA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 25 0.37
23 30 0.44
24 9 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATATTTTAAAATTTATAAAATA
Found at i:47451 original size:23 final size:22
Alignment explanation
Indices: 47415--47459 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
47405 ATCATAAATA
47415 ATTAATATTGTTATGATTTAAT
1 ATTAATATTGTTATGATTTAAT
* *
47437 ATTAATATTTTTTATTATTTAAT
1 ATTAATA-TTGTTATGATTTAAT
47460 GTAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTAATATTGTTATGATTTAAT
Found at i:63735 original size:2 final size:2
Alignment explanation
Indices: 63730--63760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
63720 ACACACACAC
63730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63761 AAAGCCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67857 original size:2 final size:2
Alignment explanation
Indices: 67852--67878 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67842 TCTCCGCAAG
67852 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
67879 CGTGTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:70357 original size:21 final size:21
Alignment explanation
Indices: 70302--70373 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
70292 TAGTACAGTT
* *
70302 TTCTACCGATACAAGTTTCAG
1 TTCTACCGATACAAGTCTCAC
* * *
70323 TTATATCGAGACAAGTCTCAC
1 TTCTACCGATACAAGTCTCAC
*
70344 TTCTACCGATACAAGTCTTAC
1 TTCTACCGATACAAGTCTCAC
70365 TTCTACCGA
1 TTCTACCGA
70374 CACCAAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTCAC
Done.