Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004197.1 Kokia drynarioides strain JFW-HI SEQ_117433, 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: 23512
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17048 original size:30 final size:28
Alignment explanation
Indices: 17013--17191 Score: 142
Period size: 29 Copynumber: 6.1 Consensus size: 28
17003 GGAGGATTTG
* * *
17013 GGGTCAAAATGTTATCTTTGGAAATTTTGG
1 GGGTCAAAATGTAAT-TTTGGAAAGTTT-A
* * * *
17043 GGGTCAGAATGTGATTTTTAGAAAGTTCAA
1 GGGTCAAAATGT-AATTTTGGAAAGTT-TA
*
17073 GGGTCAAAATGCAATTTTGGAAAAGTTTA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTA
* *
17102 GGGTTAAAATGTAATTTTGGAAAAGTTCA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTA
* *
17131 AGGTCAAAATGTAATTTTGGAAATGTTTG
1 GGGTCAAAATGTAATTTTGGAAA-GTTTA
* * * *
17160 GGGTTAAAATATTATTTTTGGAAAGTTCA
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTA
17189 GGG
1 GGG
17192 ACCTCTTGAG
Statistics
Matches: 119, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
28 3 0.03
29 68 0.57
30 47 0.39
31 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTA
Found at i:17164 original size:58 final size:59
Alignment explanation
Indices: 17013--17188 Score: 198
Period size: 58 Copynumber: 3.0 Consensus size: 59
17003 GGAGGATTTG
* * * * *
17013 GGGTCAAAATGTTATCTTTGGAAAT-TTTGGGGGTCAGAATGTGATTTT-TAGAAAGTTCAA
1 GGGTCAAAATGTAAT-TTTGGAAATGTTT-GGGGTTAAAATGTAATTTTGGA-AAAGTTCAA
* * *
17073 GGGTCAAAATGCAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTCAA
1 GGGTCAAAATGTAATTTTGGAAATGTTTGGGGTTAAAATGTAATTTTGGAAAAGTTCAA
* *
17132 -GGTCAAAATGTAATTTTGGAAATGTTTGGGGTTAAAATATTATTTTTGG-AAAGTTCA
1 GGGTCAAAATGTAATTTTGGAAATGTTTGGGGTTAAAAT-GTAATTTTGGAAAAGTTCA
17189 GGGACCTCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
58 43 0.43
59 40 0.40
60 17 0.17
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTGGAAATGTTTGGGGTTAAAATGTAATTTTGGAAAAGTTCAA
Found at i:18072 original size:3 final size:3
Alignment explanation
Indices: 18064--18103 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18054 TTTTGTTTTC
18064 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18104 CTTGCTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20593 original size:58 final size:58
Alignment explanation
Indices: 20520--20635 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
20510 ATCAACAAAT
* *
20520 TAAACGCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACAATCATAAAC
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACAATCATAAAC
* * * *
20578 TAAACCCAACTATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACAATCATAAAC
20636 AACTTTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 3 0.06
58 48 0.94
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.33
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACAATCATAAAC
Found at i:20882 original size:18 final size:19
Alignment explanation
Indices: 20859--20895 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20849 TTATTTGACT
20859 TTTTTTGTGTTGTT-TTTA
1 TTTTTTGTGTTGTTGTTTA
*
20877 TTTTTTGTTTTGTTGTTTA
1 TTTTTTGTGTTGTTGTTTA
20896 GAATGGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.00, G:0.16, T:0.78
Consensus pattern (19 bp):
TTTTTTGTGTTGTTGTTTA
Found at i:20997 original size:20 final size:19
Alignment explanation
Indices: 20957--20997 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
20947 GTTATTGTTG
*
20957 TTACTTGAATTTATGTTAT
1 TTACTTGAATTTATCTTAT
*
20976 TTACTTGAACTTTTTCTTAT
1 TTACTTGAA-TTTATCTTAT
20996 TT
1 TT
20998 TTTTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.61
Consensus pattern (19 bp):
TTACTTGAATTTATCTTAT
Found at i:21616 original size:6 final size:7
Alignment explanation
Indices: 21606--21630 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21596 CTAAAAAGTA
21606 AAAAAAT
1 AAAAAAT
21613 AAAAAAT
1 AAAAAAT
21620 AAAAAAT
1 AAAAAAT
21627 AAAA
1 AAAA
21631 TTTGAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Done.