Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015250.1 Kokia drynarioides strain JFW-HI SEQ_130295, 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: 371457
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 332 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:344058 original size:13 final size:13
Alignment explanation
Indices: 344040--344069 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
344030 AACATTTGAC
*
344040 ATATAAAAATTAT
1 ATATAAAAAATAT
344053 ATATAAAAAATAT
1 ATATAAAAAATAT
344066 ATAT
1 ATAT
344070 CTAAAGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAAAAATAT
Found at i:344295 original size:6 final size:6
Alignment explanation
Indices: 344284--344313 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
344274 AAATATTAAT
344284 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
344314 GATTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:353649 original size:144 final size:143
Alignment explanation
Indices: 353371--353766 Score: 610
Period size: 144 Copynumber: 2.8 Consensus size: 143
353361 TAAATTAGGG
*
353371 TTTTAGTATTTATTTTATATATTTTAGGTAAAAAAACCCATAACAAATTGAAAGAATTAAATT-T
1 TTTTAGTATTTATTTTATATATTTTAAGT-AAAAAACCCATAACAAATTGAAAGAATTAAATTAT
*
353435 TTTTATTTTTT-TATTTTATTTTTATTCAAATTATTTAATTATTTTTTATAAATATTTATTATTT
65 TTTTATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTA-TTTTTATAAATATTTATTATTT
*
353499 ATTGTTAAATTTCAA
129 ATTGTTAAATTACAA
* *
353514 TTTTAGTATTTATTTTATATATTTTAAGTGAAAAACCCATAATAAATTGAAAGAATTAAATTTAT
1 TTTTAGTATTTATTTTATATATTTTAAGTAAAAAACCCATAACAAATTGAAAGAATTAAA-TTAT
* *
353579 TTTTATTTTTTCTGTTTTATTTTTATTTAAATTATTCAATTATTTTTATAAATATTTATTATTTA
65 TTTTATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTTATAAATATTTATTATTTA
353644 TTGTTAAATTACAA
130 TTGTTAAATTACAA
* * *
353658 TTTAAGTATTTATTTTATATATCTTAAGTAAAAAATCCATAACAAATTGAAAGAATT-AA--A--
1 TTTTAGTATTTATTTTATATATTTTAAGTAAAAAACCCATAACAAATTGAAAGAATTAAATTATT
*
353718 TTTA-TTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTATTATAA
66 TTTATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTTATAA
353767 TTTATTTTTA
Statistics
Matches: 235, Mismatches: 15, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
137 42 0.18
138 4 0.02
140 1 0.00
142 29 0.12
143 32 0.14
144 100 0.43
145 27 0.11
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (143 bp):
TTTTAGTATTTATTTTATATATTTTAAGTAAAAAACCCATAACAAATTGAAAGAATTAAATTATT
TTTATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTTTATAAATATTTATTATTTAT
TGTTAAATTACAA
Found at i:353786 original size:13 final size:13
Alignment explanation
Indices: 353755--353791 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
353745 AATTATTTAA
* *
353755 TTATTATTATAAT
1 TTATTTTTAAAAT
353768 TTATTTTTAAAAT
1 TTATTTTTAAAAT
353781 TTATTTTTAAA
1 TTATTTTTAAA
353792 TATCCCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTTTAAAAT
Found at i:354115 original size:13 final size:14
Alignment explanation
Indices: 354106--354149 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
354096 GTTAATATAA
354106 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
354120 AAAT-AAATAATAT
1 AAATAAAATAAAAT
* *
354133 AAACAAATTAAAAT
1 AAATAAAATAAAAT
354147 AAA
1 AAA
354150 CTCTTACCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:367247 original size:154 final size:154
Alignment explanation
Indices: 367034--367320 Score: 574
Period size: 154 Copynumber: 1.9 Consensus size: 154
367024 CAATTTTTAC
367034 TATACAAACAGATCATTCATGTCCTACGGTTATGTATTAAAGGCATCAACTGACATGCATTGCAT
1 TATACAAACAGATCATTCATGTCCTACGGTTATGTATTAAAGGCATCAACTGACATGCATTGCAT
367099 AAAATAGAAAGAAATGCATAAAAATAAATAATTTATTACAGTTAACAATGGGTTTTTACTTAGAA
66 AAAATAGAAAGAAATGCATAAAAATAAATAATTTATTACAGTTAACAATGGGTTTTTACTTAGAA
367164 GTCGCCTGAGGTTTGTGCTTTATT
131 GTCGCCTGAGGTTTGTGCTTTATT
367188 TATACAAACAGATCATTCATGTCCTACGGTTATGTATTAAAGGCATCAACTGACATGCATTGCAT
1 TATACAAACAGATCATTCATGTCCTACGGTTATGTATTAAAGGCATCAACTGACATGCATTGCAT
367253 AAAATAGAAAGAAATGCATAAAAATAAATAATTTATTACAGTTAACAATGGGTTTTTACTTAGAA
66 AAAATAGAAAGAAATGCATAAAAATAAATAATTTATTACAGTTAACAATGGGTTTTTACTTAGAA
367318 GTC
131 GTC
367321 TATTATTCCC
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 133 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (154 bp):
TATACAAACAGATCATTCATGTCCTACGGTTATGTATTAAAGGCATCAACTGACATGCATTGCAT
AAAATAGAAAGAAATGCATAAAAATAAATAATTTATTACAGTTAACAATGGGTTTTTACTTAGAA
GTCGCCTGAGGTTTGTGCTTTATT
Found at i:369623 original size:28 final size:28
Alignment explanation
Indices: 369590--369685 Score: 69
Period size: 28 Copynumber: 3.5 Consensus size: 28
369580 GTTCAAGTAC
369590 CAAATTGGATAAAAAAAAATTTAGGTAA
1 CAAATTGGATAAAAAAAAATTTAGGTAA
* *
369618 CAAA-T---T-AAGAAAAATTGTCAAGGTAC
1 CAAATTGGATAAAAAAAAATT-T--AGGTAA
* * *
369644 CAAATTGGGTAAAAACAAATTTAGATAA
1 CAAATTGGATAAAAAAAAATTTAGGTAA
369672 CAAATTAGGA-AAAA
1 CAAATT-GGATAAAA
369686 TATCAAGTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
23 9 0.17
24 2 0.04
26 9 0.17
27 2 0.04
28 18 0.35
29 2 0.04
30 2 0.04
31 8 0.15
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (28 bp):
CAAATTGGATAAAAAAAAATTTAGGTAA
Found at i:369646 original size:54 final size:53
Alignment explanation
Indices: 369582--369686 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 53
369572 AATACCAAGT
*
369582 TCAAGTACCAAATTGGATAAAAAAAAATTTAGGTAACAAATTAAGAAAAATTG
1 TCAAGTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAATTG
* * *
369635 TCAAGGTACCAAATTGGGTAAAAACAAATTTAGATAACAAATTAGGAAAAAT
1 TCAA-GTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAAT
369687 ATCAAGTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (53 bp):
TCAAGTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAATTG
Done.