Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009644.1 Kokia drynarioides strain JFW-HI SEQ_124362, 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: 362035
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:284168 original size:16 final size:16
Alignment explanation
Indices: 284143--284194 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
284133 AGTCACGTAT
*
284143 AAAAATAAAGAAGAAG
1 AAAAAGAAAGAAGAAG
*
284159 AAAAAGAAAGCA-AAG
1 AAAAAGAAAGAAGAAG
*
284174 AAAAAGAGAA-AAGCAG
1 AAAAAGA-AAGAAGAAG
284190 AAAAA
1 AAAAA
284195 TTATATATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAGAAG
Found at i:286848 original size:17 final size:17
Alignment explanation
Indices: 286826--286864 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
286816 CTAAATAAAT
286826 AAAATGCAGA-GACAATA
1 AAAATGCA-ATGACAATA
*
286843 AAAATGCAATGACAATT
1 AAAATGCAATGACAATA
286860 AAAAT
1 AAAAT
286865 AAATGCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:295220 original size:24 final size:23
Alignment explanation
Indices: 295185--295230 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
295175 AAGAGTTAAT
295185 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAATGCAAAT-TAAAATAAA
*
295209 TTGTCAGA-GCAAATTAAGATAA
1 TTGTCA-ATGCAAATTAAAATAA
295231 GATGAGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (23 bp):
TTGTCAATGCAAATTAAAATAAA
Found at i:315205 original size:17 final size:17
Alignment explanation
Indices: 315150--315210 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
315140 CATCAAATTC
*
315150 CCATTATCATTGCATTT
1 CCATTGTCATTGCATTT
** *
315167 TAATTGTCACTGCATTT
1 CCATTGTCATTGCATTT
*
315184 GCATTGTCATTGCATTT
1 CCATTGTCATTGCATTT
315201 CCATTTGTCA
1 CCA-TTGTCA
315211 GTGTATTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 29 0.83
18 6 0.17
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (17 bp):
CCATTGTCATTGCATTT
Found at i:316643 original size:21 final size:20
Alignment explanation
Indices: 316597--316649 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
316587 TTGTGCTAAC
316597 TCTACCGATACAAATATGAA
1 TCTACCGATACAAATATGAA
*
316617 TTCTACCGATACAAGTCATGCAA
1 -TCTACCGATACAAAT-ATG-AA
316640 -CTACCGATAC
1 TCTACCGATAC
316650 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.83
22 3 0.10
23 2 0.07
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (20 bp):
TCTACCGATACAAATATGAA
Found at i:317301 original size:24 final size:24
Alignment explanation
Indices: 317266--317331 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
317256 TTTAACTCAC
317266 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
317290 ACGAGCCAAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
317314 ACGAGCCCAGAATGGTTA
1 ACGAGCCCAGAATGGTTA
317332 ACCAGTATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:318512 original size:12 final size:12
Alignment explanation
Indices: 318495--318519 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
318485 ACTTATTTAC
318495 AATCTAGCCTTA
1 AATCTAGCCTTA
318507 AATCTAGCCTTA
1 AATCTAGCCTTA
318519 A
1 A
318520 GCTAATTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
AATCTAGCCTTA
Found at i:329173 original size:13 final size:14
Alignment explanation
Indices: 329155--329188 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
329145 TCTTCCTAAA
329155 GAAATTTTGT-CAC
1 GAAATTTTGTCCAC
*
329168 GAAATTTTGTCCTC
1 GAAATTTTGTCCAC
329182 GAAATTT
1 GAAATTT
329189 CCTACTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
GAAATTTTGTCCAC
Found at i:333141 original size:19 final size:19
Alignment explanation
Indices: 333117--333163 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
333107 GCATACATGA
333117 TTCCACTAACCACACACGG
1 TTCCACTAACCACACACGG
333136 TTCCACTAACCACACACGG
1 TTCCACTAACCACACACGG
333155 TTCCACTAA
1 TTCCACTAA
333164 TTAGACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.40, G:0.09, T:0.19
Consensus pattern (19 bp):
TTCCACTAACCACACACGG
Found at i:333171 original size:19 final size:19
Alignment explanation
Indices: 333117--333185 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
333107 GCATACATGA
*
333117 TTCCACTAACCACACACGG
1 TTCCACTAATCACACACGG
*
333136 TTCCACTAACCACACACGG
1 TTCCACTAATCACACACGG
* * **
333155 TTCCACTAATTAGACACAA
1 TTCCACTAATCACACACGG
333174 TTCCACTAATCA
1 TTCCACTAATCA
333186 AATACCATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.35, C:0.36, G:0.07, T:0.22
Consensus pattern (19 bp):
TTCCACTAATCACACACGG
Found at i:335034 original size:20 final size:21
Alignment explanation
Indices: 334996--335035 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
334986 ATGTATTCAT
* *
334996 TATTTTTCTTTTAATAATAAG
1 TATTTTTCTTTAAAAAATAAG
335017 TATTTTTC-TTAAAAAATAA
1 TATTTTTCTTTAAAAAATAA
335036 AAATCTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTTTTCTTTAAAAAATAAG
Found at i:337910 original size:16 final size:16
Alignment explanation
Indices: 337891--337921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
337881 TTGAAAAAAT
337891 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
337907 TTTCAAATTTATATG
1 TTTCAAATATATATG
337922 CACTGACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:338303 original size:63 final size:63
Alignment explanation
Indices: 338235--338361 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
338225 GATATCTAAT
*
338235 ATTACAATTTTTTTATACAATAATAGAGATAAAGATAGAATTACATGATTTAAATTTGTAAAC
1 ATTACAATTTTTTTATACAATAATAGAGATAAAGATAGAATTACACGATTTAAATTTGTAAAC
338298 ATTACAATTTTTTTATACAATAATAGAGATAAAGATAGAATTACACGATTTAAATTTGTAAAC
1 ATTACAATTTTTTTATACAATAATAGAGATAAAGATAGAATTACACGATTTAAATTTGTAAAC
338361 A
1 A
338362 ATGAGTGTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (63 bp):
ATTACAATTTTTTTATACAATAATAGAGATAAAGATAGAATTACACGATTTAAATTTGTAAAC
Found at i:349368 original size:21 final size:21
Alignment explanation
Indices: 349330--349369 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
349320 GATGTATTTC
* *
349330 GATGTGTCTCATGCGTATTCG
1 GATGTGTCGCATGAGTATTCG
*
349351 GATGTGTCGGATGAGTATT
1 GATGTGTCGCATGAGTATT
349370 TGTATCGAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (21 bp):
GATGTGTCGCATGAGTATTCG
Found at i:350012 original size:17 final size:17
Alignment explanation
Indices: 349990--350025 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
349980 CTACTGGATG
349990 GGGTAAAACTAGTAGGA
1 GGGTAAAACTAGTAGGA
350007 GGGTAAAACTAGTAGGA
1 GGGTAAAACTAGTAGGA
350024 GG
1 GG
350026 CCCAATGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.17
Consensus pattern (17 bp):
GGGTAAAACTAGTAGGA
Done.