Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006892.1 Kokia drynarioides strain JFW-HI SEQ_121493, 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: 61097
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:859 original size:11 final size:12
Alignment explanation
Indices: 832--865 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
822 TTATTTGTTT
*
832 TTAAATTTATTA
1 TTAAATTTATAA
844 TTAAATTTA-AA
1 TTAAATTTATAA
855 TTAAATTTATA
1 TTAAATTTATA
866 TTTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:3664 original size:16 final size:18
Alignment explanation
Indices: 3645--3682 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3635 GATTAATTTT
3645 TATTT-AAAAATAT-ATA
1 TATTTAAAAAATATAATA
3661 TATTTAAAAAATATAATA
1 TATTTAAAAAATATAATA
3679 TATT
1 TATT
3683 AAATGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTAAAAAATATAATA
Found at i:13495 original size:12 final size:14
Alignment explanation
Indices: 13468--13502 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
13458 TTTCTGCTAC
13468 TTTTTCATTTTCAT
1 TTTTTCATTTTCAT
13482 TTTTTC-TTTT-AT
1 TTTTTCATTTTCAT
13494 TTTTTCATT
1 TTTTTCATT
13503 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 6 0.30
14 6 0.30
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTCATTTTCAT
Found at i:20045 original size:31 final size:31
Alignment explanation
Indices: 19988--20047 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19978 ACTAACGTAA
* *
19988 GAAAAATTGCCAAGTTTAGATGCCAAATTAG
1 GAAAAAGTGCCAAGTTTAGATACCAAATTAG
*
20019 GAAAAAGTGTCAAGTTT-GAGTACCAAATT
1 GAAAAAGTGCCAAGTTTAGA-TACCAAATT
20048 GAACAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAAAAGTGCCAAGTTTAGATACCAAATTAG
Found at i:20101 original size:31 final size:30
Alignment explanation
Indices: 19998--20104 Score: 87
Period size: 31 Copynumber: 3.6 Consensus size: 30
19988 GAAAAATTGC
* * * *
19998 CAAGTTTAGATGCCAAATTAGGAAAAAGTGT
1 CAAG-TTAGATACCAAATTAAGAAAAAATAT
* *
20029 CAAGTTTGAGTACCAAATTGAACAAAAAA-A-
1 CAAGTTAGA-TACCAAATT-AAGAAAAAATAT
*
20059 -AA-TTAAATACCAAATTAAGAAAAAATAT
1 CAAGTTAGATACCAAATTAAGAAAAAATAT
20087 CAAGTTCAGATACCAAAT
1 CAAGTT-AGATACCAAAT
20105 ATTATATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
26 8 0.14
27 10 0.17
28 3 0.05
29 4 0.07
30 6 0.10
31 22 0.37
32 6 0.10
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.23
Consensus pattern (30 bp):
CAAGTTAGATACCAAATTAAGAAAAAATAT
Found at i:27581 original size:26 final size:23
Alignment explanation
Indices: 27557--27606 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
27547 TTTAAAAATT
*
27557 TAAAATTTAAAAAATAATAATAAA
1 TAAAATTTAAAAAACAA-AATAAA
*
27581 TATAATTTAAAAAACAAAAT-AA
1 TAAAATTTAAAAAACAAAATAAA
27603 TAAA
1 TAAA
27607 GAAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 3 0.13
24 15 0.65
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATTTAAAAAACAAAATAAA
Found at i:44756 original size:6 final size:7
Alignment explanation
Indices: 44739--44769 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
44729 CAATATCGTC
44739 TTTTTTA
1 TTTTTTA
44746 TTTTTTA
1 TTTTTTA
44753 TTTTTTTA
1 -TTTTTTA
44761 TTTTTTA
1 TTTTTTA
44768 TT
1 TT
44770 GTATTAGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:44759 original size:15 final size:15
Alignment explanation
Indices: 44739--44769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44729 CAATATCGTC
44739 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
44754 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
44769 T
1 T
44770 GTATTAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:52634 original size:65 final size:61
Alignment explanation
Indices: 52556--52674 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 61
52546 TCTAATCTTA
* * * *
52556 CAAAAGTTATAAAATTTTTAATTAAACTCCTTAAATTTTTTTTTTAAAATTCTCATTAATTTTCT
1 CAAAAATTATAAAAATTTGAATTAAACCCCTT-AA---TTTTTTTAAAATTCTCATTAATTTTCT
*
52621 CAAAAATTTTAAAAATTTGAATTAAACCCCTTAATTTTTTTAAAATTCTCATTA
1 CAAAAATTATAAAAATTTGAATTAAACCCCTTAATTTTTTTAAAATTCTCATTA
52675 GACTCCAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
61 20 0.41
64 2 0.04
65 27 0.55
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (61 bp):
CAAAAATTATAAAAATTTGAATTAAACCCCTTAATTTTTTTAAAATTCTCATTAATTTTCT
Done.