Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007411.1 Kokia drynarioides strain JFW-HI SEQ_122030, 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: 28349
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:259 original size:12 final size:12
Alignment explanation
Indices: 237--266 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
227 TCGAAGCATA
237 AAAACAAATAAAT
1 AAAA-AAATAAAT
250 AAAAAAATAAAT
1 AAAAAAATAAAT
262 AAAAA
1 AAAAA
267 GGGAAGGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:452 original size:19 final size:20
Alignment explanation
Indices: 428--466 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
418 AATATCTATC
428 AAAAAACAAAAA-AAAATTT
1 AAAAAACAAAAAGAAAATTT
*
447 AAAAAATAAAAAGAAAATTT
1 AAAAAACAAAAAGAAAATTT
467 CGAAAGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAACAAAAAGAAAATTT
Found at i:5791 original size:12 final size:12
Alignment explanation
Indices: 5776--5809 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5766 ATCCATAAGG
5776 AAATGCAAGAGC
1 AAATGCAAGAGC
*
5788 AAATGCAAGCGC
1 AAATGCAAGAGC
*
5800 AACTGCAAGA
1 AAATGCAAGA
5810 TGATTTGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.09
Consensus pattern (12 bp):
AAATGCAAGAGC
Found at i:13952 original size:38 final size:39
Alignment explanation
Indices: 13779--14204 Score: 348
Period size: 40 Copynumber: 10.9 Consensus size: 39
13769 GCAATAAAGT
* * *
13779 CAATCTCTTACCCTGATCATGGGGCAGATTGAAGTCATCAC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACAT--C
** * * * *
13820 CAATCTCTTACCCCGATCATGGGGCATATTGAAAACACAC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACA-TC
** *
13860 CAATCTCTTACCTCAATCATGGGGCAGATTGAAGACATAC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACAT-C
*
13900 CAATCTCGTACCTTGATCATAGGGCAGATTGAAG-CATC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACATC
* * * *
13938 TAATCTTTTACCTTGATCAGAAGGCAGATTGAAG-CATC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACATC
* * * ** * *
13976 TAATCTTTTACCTTAATCGGAGGGAAGATTGAAGACACAC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACA-TC
* **
14016 CAATATCTTACCCCGATCAT-GAGGCAG-TTGAAG-CATC
1 CAATCTCTTACCTTGATCATAG-GGCAGATTGAAGACATC
* * * * *
14053 CAATCTCTTACCTTAATTAAAAGGCAGATTGAAGACAAAC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGAC-ATC
* *
14093 CAATCTCTTACCTTGATCATAAGGCAGATTGAAG-CATT
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACATC
* * *
14131 CAATCTTTTACCCT-A--ATAAGGCAGATTGAAGACAATC
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGAC-ATC
* * * *
14168 CAATCTCTTACCCTAATCAGAGGGCAGTTTGAAGACA
1 CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACA
14205 AATCATTCTC
Statistics
Matches: 317, Mismatches: 54, Indels: 30
0.79 0.13 0.07
Matches are distributed among these distances:
35 16 0.05
36 1 0.00
37 36 0.11
38 86 0.27
39 15 0.05
40 130 0.41
41 33 0.10
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (39 bp):
CAATCTCTTACCTTGATCATAGGGCAGATTGAAGACATC
Found at i:14239 original size:115 final size:112
Alignment explanation
Indices: 14037--14242 Score: 261
Period size: 115 Copynumber: 1.8 Consensus size: 112
14027 CCCGATCATG
* *
14037 AGGCAGTTGAAGCATCCAATCTCTTACCTTAATTAAAAGGCAGATTGAAGACAAACCAATCTCTT
1 AGGCAGTTGAAGCATCCAATCTCTTACCCTAATCAAAAGGCAGATTGAAGACAAACCAATCTCTT
* *
14102 ACCTTGATCATAAGGCAGATTGAAGCATTCAATCTTTTACCCTAATA
66 ACCTCGATCATAAGGCAAATTGAAGCATTCAATCTTTTACCCTAATA
* * * * *
14149 AGGCAGATTGAAGACAATCCAATCTCTTACCCTAATCAGAGGGCAGTTTGAAGACAAATCATTCT
1 AGGCAG-TTGAAG-C-ATCCAATCTCTTACCCTAATCAAAAGGCAGATTGAAGACAAACCAATCT
* **
14214 CTTATCC-CGGTCATGGGGCAAATTGAAGC
63 CTTA-CCTCGATCATAAGGCAAATTGAAGC
14243 TATCATCCTA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
112 6 0.08
113 6 0.08
114 1 0.01
115 63 0.81
116 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (112 bp):
AGGCAGTTGAAGCATCCAATCTCTTACCCTAATCAAAAGGCAGATTGAAGACAAACCAATCTCTT
ACCTCGATCATAAGGCAAATTGAAGCATTCAATCTTTTACCCTAATA
Found at i:14241 original size:155 final size:153
Alignment explanation
Indices: 13847--14201 Score: 380
Period size: 155 Copynumber: 2.3 Consensus size: 153
13837 CATGGGGCAT
* * * * *
13847 ATTGAAAACACACCAATCTCTTACCTCAATCATGGGGCAGATTGAAGACATACCAATCTCGTACC
1 ATTGAAGACACACCAATATCTTACCCCAATCATGAGGCAG-TTGAAG-CAT-CCAATCTCTTACC
** * * * * * *
13912 TTGATCATAGGGCAGATTGAAG-C-ATCTAATCTTTTACCTTGATCAGAAGGCAGATTGAAGCAT
63 TCAATCAAAAGGCAAATTGAAGACAAACCAATCTCTTACCTTGATCAGAAGGCAGATTGAAGCAT
* *
13975 CTAATCTTTTACCTTAATCGGAGGGAAG
128 CTAATCTTTTACCCTAAT--GAAGGAAG
* *
14003 ATTGAAGACACACCAATATCTTACCCCGATCATGAGGCAGTTGAAGCATCCAATCTCTTACCTTA
1 ATTGAAGACACACCAATATCTTACCCCAATCATGAGGCAGTTGAAGCATCCAATCTCTTACCTCA
* * *
14068 ATTAAAAGGCAGATTGAAGACAAACCAATCTCTTACCTTGATCATAAGGCAGATTGAAGCAT-TC
66 ATCAAAAGGCAAATTGAAGACAAACCAATCTCTTACCTTGATCAGAAGGCAGATTGAAGCATCT-
*
14132 AATCTTTTACCCTAAT-AAGGCAG
130 AATCTTTTACCCTAATGAAGGAAG
* *
14155 ATTGAAGACA-ATCCAATCTCTTACCCTAATCA-GAGGGCAGTTTGAAG
1 ATTGAAGACACA-CCAATATCTTACCCCAATCATGA-GGCAG-TTGAAG
14202 ACAAATCATT
Statistics
Matches: 173, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
151 3 0.02
152 37 0.21
153 36 0.21
154 5 0.03
155 57 0.33
156 35 0.20
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (153 bp):
ATTGAAGACACACCAATATCTTACCCCAATCATGAGGCAGTTGAAGCATCCAATCTCTTACCTCA
ATCAAAAGGCAAATTGAAGACAAACCAATCTCTTACCTTGATCAGAAGGCAGATTGAAGCATCTA
ATCTTTTACCCTAATGAAGGAAG
Found at i:14242 original size:193 final size:194
Alignment explanation
Indices: 13779--14242 Score: 562
Period size: 193 Copynumber: 2.4 Consensus size: 194
13769 GCAATAAAGT
* *
13779 CAATCTCTTACCCTGATCATG-GGGCAGATTGAAGTCATCACCAATCTCTTACCCCGATCATGGG
1 CAATCTCTTACCCTAATCA-GAGGGCAGATTGAAGACA-CACCAATCTCTTACCCCGATCATGGG
* * *** *
13843 GCATATTGAAAACACACCAATCTCTTACCTCAATCATGGGGCAGATTGAAGACATACCAATCTCG
64 GCAAATTG-AAGCACACCAATCTCTTACCTCAATCAAAAGGCAGATTGAAGACAAACCAATCTCG
* *
13908 TACCTTGATCATAGGGCAGATTGAAGCATCTAATCTTTTACCTTGATCAGAAGGCAGATTGAAGC
128 TACCTTGATCATAAGGCAGATTGAAGCATCTAATCTTTTACCCTGA-CAGAAGGCAGATTGAAGC
13973 ATC
192 ATC
* * * * * * *
13976 TAATCTTTTACCTTAATCGGAGGGAAGATTGAAGACACACCAATATCTTACCCCGATCATGAGGC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGC
* * * * *
14041 -AGTTGAAGCA-TCCAATCTCTTACCTTAATTAAAAGGCAGATTGAAGACAAACCAATCTCTTAC
66 AAATTGAAGCACACCAATCTCTTACCTCAATCAAAAGGCAGATTGAAGACAAACCAATCTCGTAC
*
14104 CTTGATCATAAGGCAGATTGAAGCAT-TCAATCTTTTACCCT-A-ATAAGGCAGATTGAAGACAA
131 CTTGATCATAAGGCAGATTGAAGCATCT-AATCTTTTACCCTGACAGAAGGCAGATTGAAG-C-A
14166 TC
193 TC
* * * * * *
14168 CAATCTCTTACCCTAATCAGAGGGCAGTTTGAAGACAAATCATTCTCTTATCCCGGTCATGGGGC
1 CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGC
14233 AAATTGAAGC
66 AAATTGAAGC
14243 TATCATCCTA
Statistics
Matches: 225, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
190 15 0.07
191 1 0.00
192 57 0.25
193 90 0.40
194 4 0.02
195 3 0.01
196 27 0.12
197 28 0.12
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (194 bp):
CAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGC
AAATTGAAGCACACCAATCTCTTACCTCAATCAAAAGGCAGATTGAAGACAAACCAATCTCGTAC
CTTGATCATAAGGCAGATTGAAGCATCTAATCTTTTACCCTGACAGAAGGCAGATTGAAGCATC
Found at i:18175 original size:17 final size:18
Alignment explanation
Indices: 18148--18186 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
18138 TCTTTTTGTC
* *
18148 AAACTATTGATGAAGATG
1 AAACTATTGATAAAGATA
18166 AAAC-ATTGATAAAGATA
1 AAACTATTGATAAAGATA
18183 AAAC
1 AAAC
18187 GTAAACAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (18 bp):
AAACTATTGATAAAGATA
Done.