Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003974.1 Kokia drynarioides strain JFW-HI SEQ_117070, 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: 25977
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3402 original size:48 final size:47
Alignment explanation
Indices: 3330--3425 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 47
3320 CAGTTACGAA
3330 CTTCATGGTCAATCCCTCCGCTTCTAAAATAGGCTCCCTTCTTAACT
1 CTTCATGGTCAATCCCTCCGCTTCTAAAATAGGCTCCCTTCTTAACT
*
3377 CNTTCATGGTCAATCCTTCCGCTTCTAAAATAGGCTCCCTTCTTAACT
1 C-TTCATGGTCAATCCCTCCGCTTCTAAAATAGGCTCCCTTCTTAACT
3425 C
1 C
3426 GACACTCACC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.34
Consensus pattern (47 bp):
CTTCATGGTCAATCCCTCCGCTTCTAAAATAGGCTCCCTTCTTAACT
Found at i:6963 original size:21 final size:21
Alignment explanation
Indices: 6917--6963 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6907 CTAAGGATGG
* *
6917 TTCTACCAATACAAGTGATAC
1 TTCTACCAAAACAAGTCATAC
* *
6938 ATCTACCAAAACAAGTCATGC
1 TTCTACCAAAACAAGTCATAC
6959 TTCTA
1 TTCTA
6964 TCGATATTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (21 bp):
TTCTACCAAAACAAGTCATAC
Found at i:7695 original size:18 final size:18
Alignment explanation
Indices: 7672--7741 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
7662 CGATCTAGTA
*
7672 ATGCTCAAATGAGCCAGT
1 ATGCTCAAACGAGCCAGT
* *
7690 ATGCTCAAATGAGCTAGT
1 ATGCTCAAACGAGCCAGT
*
7708 ATGCTCTAACGAGCCAGT
1 ATGCTCAAACGAGCCAGT
*
7726 ATGCTCTAACGAGCCA
1 ATGCTCAAACGAGCCA
7742 ATTTGCAGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (18 bp):
ATGCTCAAACGAGCCAGT
Found at i:9082 original size:51 final size:51
Alignment explanation
Indices: 8999--9137 Score: 224
Period size: 51 Copynumber: 2.7 Consensus size: 51
8989 TAAACGAAAG
** *
8999 GGTCCGATGACTAAGTGTCATCGTGAGCGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATAATGAGTGAATGAATCCTTTATGGATTAAT
* *
9050 GGTTCGATGACTAAGTGTCATTATGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATAATGAGTGAATGAATCCTTTATGGATTAAT
*
9101 GGTCCGATGACTAAGTGTCATAATGAGTAAATGAATC
1 GGTCCGATGACTAAGTGTCATAATGAGTGAATGAATC
9138 TTGAGTAATA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATAATGAGTGAATGAATCCTTTATGGATTAAT
Found at i:15622 original size:51 final size:51
Alignment explanation
Indices: 15561--15741 Score: 290
Period size: 51 Copynumber: 3.5 Consensus size: 51
15551 TAAATGAAAG
* *
15561 GGTCCAATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
* *
15612 GGTCCGATGACTAAGTGTCATCATGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
*
15663 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
* * *
15714 GGTCTGATGACTAAATGTCTTCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
15742 TTATGGATTC
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 120 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
Found at i:16434 original size:24 final size:21
Alignment explanation
Indices: 16380--16434 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
16370 GACTTGAGTT
*
16380 GTATCGGTAGTTAAATTGTGA
1 GTATCGGTAGTTAAATTATGA
* *
16401 GTATCAGTAGTTATATGTATGGAA
1 GTATCGGTAGTTAAAT-TAT-G-A
16425 GTATCGGTAG
1 GTATCGGTAG
16435 ATTGCATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.52
22 2 0.07
23 1 0.04
24 10 0.37
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (21 bp):
GTATCGGTAGTTAAATTATGA
Found at i:17897 original size:36 final size:36
Alignment explanation
Indices: 17850--17921 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
17840 GTGGCCTCTC
17850 CTCGATGTGGAGCTTAAACAAAGATAAAATACATGT
1 CTCGATGTGGAGCTTAAACAAAGATAAAATACATGT
17886 CTCGATGTGGAGCTTAAACAAAGATAAAATACATGT
1 CTCGATGTGGAGCTTAAACAAAGATAAAATACATGT
17922 TACAAGCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
CTCGATGTGGAGCTTAAACAAAGATAAAATACATGT
Found at i:21064 original size:22 final size:23
Alignment explanation
Indices: 21025--21069 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
21015 GATCTTTTGA
21025 TTCTGGTCCCTGTGTTGTGACAT
1 TTCTGGTCCCTGTGTTGTGACAT
*
21048 TTCTTGTCCC-GTGTTGTGACAT
1 TTCTGGTCCCTGTGTTGTGACAT
21070 AGTGATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.44
Consensus pattern (23 bp):
TTCTGGTCCCTGTGTTGTGACAT
Done.