Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014608.1 Kokia drynarioides strain JFW-HI SEQ_129647, 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: 36586
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:8883 original size:15 final size:16
Alignment explanation
Indices: 8857--8886 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8847 GAGATGAATG
8857 ATTAGACTTCAAATCC
1 ATTAGACTTCAAATCC
8873 ATTAG-CTTCAAATC
1 ATTAGACTTCAAATC
8887 ACCTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (16 bp):
ATTAGACTTCAAATCC
Found at i:15999 original size:22 final size:20
Alignment explanation
Indices: 15959--16022 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 20
15949 TCCTCTATTT
15959 TAAAAAT-AGAAATAAATATA
1 TAAAAATCAGAAA-AAATATA
15979 TAAAAATTCAGAAAAACATATA
1 TAAAAA-TCAGAAAAA-ATATA
*
16001 TGTAAAATCTAGAAAAAATATA
1 T-AAAAATC-AGAAAAAATATA
16023 AAGTATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.16
21 3 0.08
22 18 0.47
23 11 0.29
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (20 bp):
TAAAAATCAGAAAAAATATA
Found at i:16192 original size:36 final size:36
Alignment explanation
Indices: 16099--16203 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 36
16089 AAAATATGAA
* * * *
16099 AATGTAAAAAAATATCTAAAAACTAAAAATATTTTAT
1 AATGTATAAAATTAT-TAAAAAATAAAAATATTTAAT
* *
16136 AATGTATTAAATTATAAAAAAATAAAAATATTTAAT
1 AATGTATAAAATTATTAAAAAATAAAAATATTTAAT
*
16172 AAAT-T-TAAAATTTATTAAAAATTTAAAAATAT
1 -AATGTATAAAA-TTATTAAAAA-ATAAAAATAT
16204 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
35 4 0.07
36 28 0.50
37 24 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (36 bp):
AATGTATAAAATTATTAAAAAATAAAAATATTTAAT
Found at i:16200 original size:19 final size:19
Alignment explanation
Indices: 16158--16203 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
16148 TATAAAAAAA
16158 TAAAAATATTTAATAAATT
1 TAAAAATATTTAATAAATT
*
16177 T-AAAATTTATTAA-AAATT
1 TAAAAATAT-TTAATAAATT
16195 TAAAAATAT
1 TAAAAATAT
16204 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAATATTTAATAAATT
Found at i:16265 original size:25 final size:25
Alignment explanation
Indices: 16218--16292 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
16208 ATTAAAATTA
* * *
16218 AAATTTTATATATTTTATATTTTTAT
1 AAATTTTA-AAATTTAATATTTTTAC
*
16244 AAATTTTAAAATTTAATTTTTTTAC
1 AAATTTTAAAATTTAATATTTTTAC
* *
16269 AAATTATCAAAATTTTTATATTTT
1 AAATT-TTAAAA-TTTAATATTTT
16293 AAATAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 18 0.45
26 13 0.32
27 9 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATTTTAAAATTTAATATTTTTAC
Found at i:16318 original size:17 final size:19
Alignment explanation
Indices: 16278--16322 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
16268 CAAATTATCA
*
16278 AAATTTTTATATTTTAAAT
1 AAATTTTAATATTTTAAAT
16297 AAATTTTAAT-TTTTAAAT
1 AAATTTTAATATTTTAAAT
*
16315 AATTTTTA
1 AAATTTTA
16323 TAATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AAATTTTAATATTTTAAAT
Found at i:33401 original size:5 final size:5
Alignment explanation
Indices: 33348--33398 Score: 75
Period size: 5 Copynumber: 10.2 Consensus size: 5
33338 GGAAAAAAAG
* * *
33348 TGTCG TGTCA TGTCG TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TCTCA
1 TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA
33398 T
1 T
33399 CTCTAGGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (5 bp):
TGTCA
Found at i:34763 original size:13 final size:13
Alignment explanation
Indices: 34747--34797 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
34737 AAATTGAAGG
34747 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
*
34760 AAAAGAGAAAG-A
1 AAAAAAGAAAGAA
*
34772 AATAAAGAAAGAA
1 AAAAAAGAAAGAA
* *
34785 AAAGAAGGAAGAA
1 AAAAAAGAAAGAA
34798 GGAGAAGAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:34806 original size:3 final size:3
Alignment explanation
Indices: 34780--34839 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
34770 GAAATAAAGA
* * * *
34780 AAG AAA AAG AAGG AAG AAG GAG AAG AAG AGG AAG AAG GAG AAG AAG
1 AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
34826 AGG AAG AAG GAG AA
1 AAG AAG AAG AAG AA
34840 AGAAAAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34806 original size:9 final size:9
Alignment explanation
Indices: 34792--34839 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
34782 GAAAAAGAAG
34792 GAAGAAGGA
1 GAAGAAGGA
34801 GAAGAA-GA
1 GAAGAAGGA
34809 GGAAGAAGGA
1 -GAAGAAGGA
34819 GAAGAA-GA
1 GAAGAAGGA
34827 GGAAGAAGGA
1 -GAAGAAGGA
34837 GAA
1 GAA
34840 AGAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.11
9 27 0.77
10 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GAAGAAGGA
Found at i:34813 original size:18 final size:18
Alignment explanation
Indices: 34790--34839 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
34780 AAGAAAAAGA
34790 AGGAAGAAGGAGAAGAAG
1 AGGAAGAAGGAGAAGAAG
34808 AGGAAGAAGGAGAAGAAG
1 AGGAAGAAGGAGAAGAAG
34826 AGGAAGAAGGAGAA
1 AGGAAGAAGGAGAA
34840 AGAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (18 bp):
AGGAAGAAGGAGAAGAAG
Found at i:35534 original size:16 final size:16
Alignment explanation
Indices: 35489--35538 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
35479 TAAACCTAGC
35489 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
35505 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
35519 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
35535 TAAT
1 TAAT
35539 ATTCTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 2 0.07
16 12 0.43
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Done.