Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006192.1 Kokia drynarioides strain JFW-HI SEQ_120761, 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: 4732
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Found at i:1059 original size:55 final size:53
Alignment explanation
Indices: 959--1272 Score: 196
Period size: 53 Copynumber: 6.1 Consensus size: 53
949 GTCAAGGTGT
* *
959 GTGTGTGTATACTATTTGGAGGCACACGAGTTGGCACACGGGTGTGTGTCAAG
1 GTGTGTGTATACTATTTGGAGGCACACGAGCTGACACACGGGTGTGTGTCAAG
* * *
1012 GTGTGTGTATACTATTTCGAGGCACACG-GACTGACATACGGGTGTGTGTCAGG
1 GTGTGTGTATACTATTTGGAGGCACACGAG-CTGACACACGGGTGTGTGTCAAG
* * *
1065 GATTGTGTGTATACTGTTTGGAGG--CAC-A--TG------GGCT-TGTGTCAGG
1 G--TGTGTGTATACTATTTGGAGGCACACGAGCTGACACACGGGTGTGTGTCAAG
* *** * *
1108 GTGTGTGTATACTATTTGGAGGCACACGGGCTGACACACGAACGTGTGTTAGG
1 GTGTGTGTATACTATTTGGAGGCACACGAGCTGACACACGGGTGTGTGTCAAG
* * * * *
1161 GTGTGTGTATAC-AGTTCT-G-GGCAGACGAACTGTCACATCCGCGTGTGT-T-AGG
1 GTGTGTGTATACTA-TT-TGGAGGCACACGAGCTGACACA--CGGGTGTGTGTCAAG
* * * ** * * *
1213 GTGTTTGTATACTGTTTTGAGGCACATAAGCTGACACATGGGCGTGTGTCAGG
1 GTGTGTGTATACTATTTGGAGGCACACGAGCTGACACACGGGTGTGTGTCAAG
1266 GTGTGTG
1 GTGTGTG
1273 CATATTGTTT
Statistics
Matches: 204, Mismatches: 32, Indels: 50
0.71 0.11 0.17
Matches are distributed among these distances:
41 20 0.10
43 13 0.06
44 3 0.01
46 2 0.01
50 2 0.01
51 7 0.03
52 35 0.17
53 96 0.47
54 7 0.03
55 19 0.09
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.30
Consensus pattern (53 bp):
GTGTGTGTATACTATTTGGAGGCACACGAGCTGACACACGGGTGTGTGTCAAG
Found at i:1126 original size:41 final size:42
Alignment explanation
Indices: 1056--1139 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
1046 CATACGGGTG
* *
1056 TGTGTCAGGGATTGTGTGTATACTGTTTGGAGGCACATGGGCT
1 TGTGTCAGGGA-TGTGTGTATACTATTTGGAGGCACACGGGCT
1099 TGTGTCAGGG-TGTGTGTATACTATTTGGAGGCACACGGGCT
1 TGTGTCAGGGATGTGTGTATACTATTTGGAGGCACACGGGCT
1140 GACACACGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 29 0.74
43 10 0.26
ACGTcount: A:0.17, C:0.13, G:0.37, T:0.33
Consensus pattern (42 bp):
TGTGTCAGGGATGTGTGTATACTATTTGGAGGCACACGGGCT
Found at i:1746 original size:40 final size:40
Alignment explanation
Indices: 1693--1810 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
1683 ACTACTTGAG
* *
1693 AATATTT--ATTGAACTAGCAGTGACACTGTTAACACTGC
1 AATATTTCAATTGAACTGGCAGTGACACTGTAAACACTGC
* * * *
1731 AATATTTCAATTGAACCGGTAGTGATACTGTAAACACTAC
1 AATATTTCAATTGAACTGGCAGTGACACTGTAAACACTGC
* * * *
1771 AAGATTACAATTGATCTGGCAGTGACACTATAAACACTGC
1 AATATTTCAATTGAACTGGCAGTGACACTGTAAACACTGC
1811 GATGTGTCAT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 7 0.11
40 57 0.89
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (40 bp):
AATATTTCAATTGAACTGGCAGTGACACTGTAAACACTGC
Found at i:2974 original size:53 final size:53
Alignment explanation
Indices: 2801--3023 Score: 230
Period size: 55 Copynumber: 4.1 Consensus size: 53
2791 TTTAGGGGGT
* * * * * *
2801 GTGTGTGTATATTGTTTGGAGGCACATGGGTTGGCACATGGACGTGTGTCAGG
1 GTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
* * * * * ** * *
2854 GATTATGTGTATACTATTTAGAGGCACACGGGTTGGCACACAGGCGTTTGTCAGGG
1 G--TGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCA-AG
2910 TGTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
1 -GTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
* ** * *
2964 GTGTGTGTATACTGTTTTAAGGCACATGGGCTGATACATGGGCGTATGTCAAG
1 GTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
3017 GTGTGTG
1 GTGTGTG
3024 CATATTGTTT
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
53 56 0.39
54 1 0.01
55 83 0.58
56 2 0.01
57 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.35, T:0.31
Consensus pattern (53 bp):
GTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
Found at i:3023 original size:110 final size:109
Alignment explanation
Indices: 2797--3023 Score: 278
Period size: 110 Copynumber: 2.1 Consensus size: 109
2787 ATTTTTTAGG
* * * * *
2797 GGGTGTGTGTGTATATTGTTTGGAGGCACATGGGTTGGCACATGGACGTGTGTCAGGGATTATGT
1 GGGTGTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGACGTGTGTCAAGGA-TATGT
* * *
2862 GTATACTATTTAGAGGCACACGGGTTGGCACACAGGCGTTTGTCA
65 GTATACTATTTAGAGGCACACGGGCTGACACACAGGCGTATGTCA
* *
2907 GGGTGTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAGG-TGTGTG
1 GGGTGTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGACGTGTGTCAAGGATATGTG
* * * **
2971 TATACTGTTTTA-AGGCACATGGGCTGATACATGGGCGTATGTCA
66 TATACT-ATTTAGAGGCACACGGGCTGACACACAGGCGTATGTCA
*
3015 AGGTGTGTG
1 GGGTGTGTG
3024 CATATTGTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
108 44 0.44
109 4 0.04
110 52 0.52
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (109 bp):
GGGTGTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGACGTGTGTCAAGGATATGTG
TATACTATTTAGAGGCACACGGGCTGACACACAGGCGTATGTCA
Found at i:3033 original size:53 final size:53
Alignment explanation
Indices: 2911--3045 Score: 189
Period size: 53 Copynumber: 2.5 Consensus size: 53
2901 TTGTCAGGGT
* * ** *
2911 GTGTGTGTATACTATTTGGAGGCACATGGGCTGACACATGGGCGTGTGTCAAG
1 GTGTGTGCATACTGTTTTAAGGCACATGGGCTGACACATGGGCGTATGTCAAG
* *
2964 GTGTGTGTATACTGTTTTAAGGCACATGGGCTGATACATGGGCGTATGTCAAG
1 GTGTGTGCATACTGTTTTAAGGCACATGGGCTGACACATGGGCGTATGTCAAG
* *
3017 GTGTGTGCATATTGTTTTAAGACACATGG
1 GTGTGTGCATACTGTTTTAAGGCACATGG
3046 TCTGTAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.32
Consensus pattern (53 bp):
GTGTGTGCATACTGTTTTAAGGCACATGGGCTGACACATGGGCGTATGTCAAG
Found at i:3544 original size:40 final size:40
Alignment explanation
Indices: 3451--3544 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
3441 GAAAATTTAT
* * * * *
3451 TGAACTGGCAGTGACACTGTTAATACTACAAGATTTCAAC
1 TGAACTGGCAGTGAAAATGTAAATACTAAAAGATTACAAC
* *
3491 T-AAATCGACAGTGAAAATGTAAATACTAAAAGATTACAAC
1 TGAACT-GGCAGTGAAAATGTAAATACTAAAAGATTACAAC
*
3531 TGAACTGGTAGTGA
1 TGAACTGGCAGTGA
3545 CACTATAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
39 3 0.07
40 36 0.86
41 3 0.07
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (40 bp):
TGAACTGGCAGTGAAAATGTAAATACTAAAAGATTACAAC
Found at i:3668 original size:12 final size:12
Alignment explanation
Indices: 3651--3682 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3641 GGTATCATGT
3651 CTGCATCTGTAA
1 CTGCATCTGTAA
3663 CTGCATCTGTAA
1 CTGCATCTGTAA
*
3675 CTGTATCT
1 CTGCATCT
3683 ATTACATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (12 bp):
CTGCATCTGTAA
Found at i:3696 original size:17 final size:17
Alignment explanation
Indices: 3674--3716 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3664 TGCATCTGTA
*
3674 ACTGTATCTATTACATG
1 ACTGTATCTATGACATG
*
3691 ACTGTATCTATGGCATG
1 ACTGTATCTATGACATG
*
3708 AATGTATCT
1 ACTGTATCT
3717 GTAACTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (17 bp):
ACTGTATCTATGACATG
Done.