Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010021.1 Kokia drynarioides strain JFW-HI SEQ_124786, 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: 355209
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 84 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:332051 original size:17 final size:18
Alignment explanation
Indices: 331988--332052 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
331978 TTAAAATGGC
*
331988 AAATGT-TATTGAAATAA
1 AAATGTGTATTGAAATAG
*
332005 AAATG-ATATTGAAATAG
1 AAATGTGTATTGAAATAG
332022 AAA-GTG-ATATGAAAT-G
1 AAATGTGTAT-TGAAATAG
332038 AAATGTGTATTGAAA
1 AAATGTGTATTGAAA
332053 ACAAAAATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 7 0.17
17 32 0.78
18 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (18 bp):
AAATGTGTATTGAAATAG
Found at i:338734 original size:22 final size:23
Alignment explanation
Indices: 338691--338736 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
338681 TTAGATTTTA
*
338691 TTTCTTTCATTTAGTTTCTAGTT
1 TTTCTTTCATTTAGATTCTAGTT
338714 TTTCTTTC-TTTAGGATT-TAGTT
1 TTTCTTTCATTTA-GATTCTAGTT
338736 T
1 T
338737 ATTTATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.65
Consensus pattern (23 bp):
TTTCTTTCATTTAGATTCTAGTT
Found at i:344954 original size:15 final size:14
Alignment explanation
Indices: 344914--344957 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
344904 TATATATTTT
344914 TTAAAAAATT-ATA
1 TTAAAAAATTAATA
344927 TATAAAAAA-TAATA
1 T-TAAAAAATTAATA
344941 TTAAAGAAATTAATA
1 TTAAA-AAATTAATA
344956 TT
1 TT
344958 GGTGGCCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.22
14 14 0.52
15 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TTAAAAAATTAATA
Found at i:345764 original size:30 final size:29
Alignment explanation
Indices: 345725--345783 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
345715 GAGTTAGATC
*
345725 AAATCAAAATTTGATGTATAAAATTGCACA
1 AAATCAAAA-TTCATGTATAAAATTGCACA
* * *
345755 AAATTAAAATTCATTTATACAATTGCACA
1 AAATCAAAATTCATGTATAAAATTGCACA
345784 TTAAACCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTCATGTATAAAATTGCACA
Found at i:350869 original size:32 final size:33
Alignment explanation
Indices: 350807--350870 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
350797 GCATGACTAC
*
350807 TAGATACATCTTCTCTAAATACATTAATTAAAG
1 TAGATACATCTACTCTAAATACATTAATTAAAG
*
350840 TAGATACATCTACTCT-AATACATTCATTAAA
1 TAGATACATCTACTCTAAATACATTAATTAAA
350871 TATAACTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (33 bp):
TAGATACATCTACTCTAAATACATTAATTAAAG
Found at i:354814 original size:23 final size:23
Alignment explanation
Indices: 354788--354863 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
354778 ACATAATGAA
354788 TTTCAAGTGAATTTCATAACCCT
1 TTTCAAGTGAATTTCATAACCCT
* *
354811 TTTCAAG-GAGTTGTCCCAAATAA-TC-
1 TTTCAAGTGAATT-T--C--ATAACCCT
354836 TTTCAAGTGAATTTCATAACCCT
1 TTTCAAGTGAATTTCATAACCCT
354859 TTTCA
1 TTTCA
354864 CCACTATCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
21 4 0.10
22 5 0.12
23 14 0.34
25 9 0.22
26 5 0.12
27 4 0.10
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (23 bp):
TTTCAAGTGAATTTCATAACCCT
Done.