Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005770.1 Kokia drynarioides strain JFW-HI SEQ_120034, 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: 55314
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:621 original size:34 final size:33
Alignment explanation
Indices: 575--658 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 33
565 TTTTGAAGTT
*
575 TAAATTTAATTTAAAATAAATCCAAACTCAAAA
1 TAAATTAAATTTAAAATAAATCCAAACTCAAAA
* * * *
608 TAAGTTTAAATTTAAAATAAATTCAAACTTAAAT
1 TAA-ATTAAATTTAAAATAAATCCAAACTCAAAA
*
642 TAAATTAAAATTAAAAT
1 TAAATTAAATTTAAAAT
659 TTAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 15 0.35
34 28 0.65
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (33 bp):
TAAATTAAATTTAAAATAAATCCAAACTCAAAA
Found at i:659 original size:17 final size:17
Alignment explanation
Indices: 613--659 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
603 CAAAATAAGT
*
613 TTAAATTTAAAA-TAAA
1 TTAAAATTAAAATTAAA
*
629 TTCAAACTT-AAATTAAA
1 TT-AAAATTAAAATTAAA
646 TTAAAATTAAAATT
1 TTAAAATTAAAATT
660 TAAAATTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAATTAAAATTAAA
Found at i:4858 original size:31 final size:30
Alignment explanation
Indices: 4793--4864 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
4783 GTTACGTTTA
* *
4793 ACAAAACAGTCATTCAACTTTGAAAATGTG
1 ACAAAACAGTCACTAAACTTTGAAAATGTG
*
4823 ACAAAACAGTCACTAAAGTTATCGAAAA-GTG
1 ACAAAACAGTCACTAAACTT-T-GAAAATGTG
*
4854 ACAAAATAGTC
1 ACAAAACAGTC
4865 CTCTTGTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (30 bp):
ACAAAACAGTCACTAAACTTTGAAAATGTG
Found at i:4974 original size:27 final size:26
Alignment explanation
Indices: 4943--4997 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
4933 TTCTTCCTTT
4943 TTCATCCACTACCACTTATTCCTCATC
1 TTCATCCACTACCACTT-TTCCTCATC
* *
4970 TTCATCTACTACCACTTTTTCTCATC
1 TTCATCCACTACCACTTTTCCTCATC
4996 TT
1 TT
4998 TTTTCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (26 bp):
TTCATCCACTACCACTTTTCCTCATC
Found at i:5824 original size:27 final size:26
Alignment explanation
Indices: 5785--5836 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
5775 TAAAAAAAAT
5785 ATGAGAAAAAGTGGTAGTGGATGAAG
1 ATGAGAAAAAGTGGTAGTGGATGAAG
*
5811 ATGAGGAATAAGTGGTAGTGGATGAA
1 ATGA-GAAAAAGTGGTAGTGGATGAA
5837 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.21
Consensus pattern (26 bp):
ATGAGAAAAAGTGGTAGTGGATGAAG
Found at i:14706 original size:23 final size:23
Alignment explanation
Indices: 14599--14709 Score: 116
Period size: 23 Copynumber: 4.8 Consensus size: 23
14589 AATATTAATA
*
14599 AATATGATTTAT-CATCAAATATT
1 AATATGATTTATGC-TTAAATATT
* *
14622 AATATGATTTGTGCTCAAATATT
1 AATATGATTTATGCTTAAATATT
* * *
14645 AATGTGATATATGATTAAATATT
1 AATATGATTTATGCTTAAATATT
* * *
14668 AGTGTAATTTATGCTTAAATATT
1 AATATGATTTATGCTTAAATATT
*
14691 AATATGATTTGTGCTTAAA
1 AATATGATTTATGCTTAAA
14710 GAATTAAGAT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 72 0.99
24 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (23 bp):
AATATGATTTATGCTTAAATATT
Found at i:16907 original size:24 final size:24
Alignment explanation
Indices: 16876--16925 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
16866 TCGAAAATCA
16876 AAACAAATGAAACGTGCAATTTAC
1 AAACAAATGAAACGTGCAATTTAC
16900 AAACAAATGAAACGTGCAATTTAC
1 AAACAAATGAAACGTGCAATTTAC
16924 AA
1 AA
16926 TTCAGTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (24 bp):
AAACAAATGAAACGTGCAATTTAC
Found at i:25297 original size:16 final size:16
Alignment explanation
Indices: 25260--25293 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
25250 CGATTAAAAT
25260 TAATAAAATAAATGAA
1 TAATAAAATAAATGAA
25276 TAATAAAATAAAT-AA
1 TAATAAAATAAATGAA
25291 TAA
1 TAA
25294 ATAACTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAATAAAATAAATGAA
Found at i:28309 original size:20 final size:18
Alignment explanation
Indices: 28262--28368 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
28252 CAAGAAAAAC
28262 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
28279 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
28299 ATTAAATTAATA-AAAGACT
1 ATTAAATTAATATTTA-A-T
*
28318 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
28335 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
28355 ATTAAAATAATATT
1 ATTAAATTAATATT
28369 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
17 17 0.24
18 8 0.11
19 21 0.30
20 24 0.34
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:28356 original size:37 final size:36
Alignment explanation
Indices: 28294--28369 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
28284 GATAATCACT
28294 TTAATATTAAATTAATAAAAGACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAAGACTATTAAAATAA-TA
*
28331 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAAGACTATTAAAATAATA
28367 TTA
1 TTA
28370 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAAGACTATTAAAATAATA
Found at i:34548 original size:27 final size:27
Alignment explanation
Indices: 34518--34593 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
34508 GTATCTGTCA
*
34518 GATAGGCAGCACCAATGGTGCTCATCT
1 GATAGGCAGCACCAATGGTGCCCATCT
**
34545 GATAGGCAGCACCTTTGGTGCCCATCT
1 GATAGGCAGCACCAATGGTGCCCATCT
* *
34572 -AGTAGGCGGCACCAGTGGTGCC
1 GA-TAGGCAGCACCAATGGTGCC
34594 ATACAAATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (27 bp):
GATAGGCAGCACCAATGGTGCCCATCT
Found at i:42553 original size:26 final size:26
Alignment explanation
Indices: 42518--42568 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
42508 ATAAACCCTA
42518 AACATAATTAATGAAATACAAACATG
1 AACATAATTAATGAAATACAAACATG
*
42544 AACATAATTAATTAAATACAAACAT
1 AACATAATTAATGAAATACAAACAT
42569 AAACTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (26 bp):
AACATAATTAATGAAATACAAACATG
Found at i:43042 original size:18 final size:18
Alignment explanation
Indices: 43021--43078 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
43011 TCGAGCTTGA
* *
43021 GCTCGAGCTCGGGCTCAT
1 GCTCAAGCTCGGGCTCAG
* *
43039 GCTCAAGCTCAGGCTTAG
1 GCTCAAGCTCGGGCTCAG
* *
43057 GCTCAAGCTCGAGCTCGG
1 GCTCAAGCTCGGGCTCAG
43075 GCTC
1 GCTC
43079 GAACTCAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.21
Consensus pattern (18 bp):
GCTCAAGCTCGGGCTCAG
Found at i:45223 original size:12 final size:13
Alignment explanation
Indices: 45201--45238 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
45191 TCAAAAACAA
45201 AAAAATATATAAT
1 AAAAATATATAAT
45214 AAAAAT-TATAAT
1 AAAAATATATAAT
*
45226 AAATAAAATATAA
1 AAA-AATATATAA
45239 ACATACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 9 0.41
13 8 0.36
14 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATATATAAT
Found at i:47990 original size:2 final size:2
Alignment explanation
Indices: 47983--48014 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47973 ACTCCAAGTT
*
47983 TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48015 CAGATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:49110 original size:30 final size:30
Alignment explanation
Indices: 49071--49138 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
49061 AAATTTTAAA
* * *
49071 TTAATAATGA-CAAAATTATATTTTGATTTT
1 TTAAAAATGATCAAAATT-TAATTTAATTTT
*
49101 TTAAAAATGATTAAAATTTAATTTAATTTT
1 TTAAAAATGATCAAAATTTAATTTAATTTT
49131 TTAAAAAT
1 TTAAAAAT
49139 TATAAAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (30 bp):
TTAAAAATGATCAAAATTTAATTTAATTTT
Found at i:51735 original size:41 final size:41
Alignment explanation
Indices: 51690--51963 Score: 323
Period size: 41 Copynumber: 6.7 Consensus size: 41
51680 AAAACGCAAA
* *
51690 CGCCGCTAAAGGTCAGATCATTAGCGGCGTTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
* * *
51731 CGCCGCTAAAGGTCAGAGCATTAGCAGCGTTTATGGGAAAA
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
* * * * *
51772 TGCCGCTAAAGGTCAGAGCAGTAGCGACATTTATAGGAAAA
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
* * *
51813 CACTGCTAAAGGTCAGAGCATTAGCGGCGTTTCTAGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
* ** * * *
51854 CACCGCTAAATATCGGAGCACTAGCGGCGTTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
** * * *
51895 CGCCGCTAAAGGTGGGAGCATTAGTGGCGCTTATAAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
*
51936 CGCCGCTAAAGATCAGAGCATTAGCGGC
1 CGCCGCTAAAGGTCAGAGCATTAGCGGC
51964 ACTTTCTCAT
Statistics
Matches: 196, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 196 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATAGGAAAG
Found at i:51985 original size:82 final size:82
Alignment explanation
Indices: 51692--52003 Score: 234
Period size: 82 Copynumber: 3.8 Consensus size: 82
51682 AACGCAAACG
* * * * ** * *
51692 CCGCTAAAGGTCAGATCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCA
1 CCGCTAAAGATCAGAGCACTAGCGGCCTTTATCAGAAAGCGCAGCTAAAGGTCAGAGCATTAGCG
* ** ***
51757 GCGTTTATGGGAAAATG
66 GCGCTTATAAGAAAGCA
* * * * * * *
51774 CCGCTAAAGGTCAGAGCAGTAGCGACATTTAT-AGGAAAACACTGCTAAAGGTCAGAGCATTAGC
1 CCGCTAAAGATCAGAGCACTAGCGGCCTTTATCA-GAAAGCGCAGCTAAAGGTCAGAGCATTAGC
* * *
51838 GGCGTTTCTAGGAAAGCA
65 GGCGCTTATAAGAAAGCA
* * * ** * ** *
51856 CCGCTAAATATCGGAGCACTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTGGGAGCATTAGTG
1 CCGCTAAAGATCAGAGCACTAGCGGCCTTTATCAGAAAGCGCAGCTAAAGGTCAGAGCATTAGCG
*
51921 GCGCTTATAAGAAAGCG
66 GCGCTTATAAGAAAGCA
* * * * *
51938 CCGCTAAAGATCAGAGCATTAGCGGCACTTTCTCATAAA-CGCAGCTAAAGGTTA-AGCAATAGC
1 CCGCTAAAGATCAGAGCACTAGCGGC-CTTTATCAGAAAGCGCAGCTAAAGGTCAGAGCATTAGC
52001 GGC
65 GGC
52004 ATTTTCCCGT
Statistics
Matches: 183, Mismatches: 44, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
81 10 0.05
82 166 0.91
83 7 0.04
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (82 bp):
CCGCTAAAGATCAGAGCACTAGCGGCCTTTATCAGAAAGCGCAGCTAAAGGTCAGAGCATTAGCG
GCGCTTATAAGAAAGCA
Found at i:54543 original size:41 final size:41
Alignment explanation
Indices: 54480--54696 Score: 244
Period size: 41 Copynumber: 5.4 Consensus size: 41
54470 ATGAGAAAGA
* *
54480 GCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGA
1 GCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTCAGT
* * * **
54521 GTATTAGCGGTGCTTATAAGAAAGCGCCGTTAAAGAACAGT
1 GCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTCAGT
* * * * *
54562 GCATTAGCGGCGCTTATAAGGAAGCGCCGCGAGAGATTAGT
1 GCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTCAGT
*
54603 GCATTAGCGGCGCTTAT---AAAGCGCCGGTAAAGGTCAGT
1 GCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTCAGT
* * *
54641 GCATTAGCGACGCTTATAAAGAAA-TGCCACTAAAGGTCAGT
1 GCATTAGCGGCGCTTAT-AAGAAAGCGCCGCTAAAGGTCAGT
*
54682 GCATTAGCGACGCTT
1 GCATTAGCGGCGCTT
54697 TCTCAGAGCA
Statistics
Matches: 147, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
38 31 0.21
41 113 0.77
42 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTCAGT
Found at i:54683 original size:79 final size:80
Alignment explanation
Indices: 54480--54696 Score: 240
Period size: 79 Copynumber: 2.7 Consensus size: 80
54470 ATGAGAAAGA
* * * *
54480 GCATTAGCGGCGCTTAT-GAGAAAGCGCCGCTAAAGGTCAGAGTATTAGCGGTGCTTATAAGAAA
1 GCATTAGCGGCGCTTATAAAGAAA-CGCCGCTAAAGGTCAGTGCATTAGCGGCGCTTAT-A-AAA
*
54544 GCGCCGTTAAAGAACAGT
63 GCGCCGGTAAAGAACAGT
* * * * * *
54562 GCATTAGCGGCGCTTATAAGGAAGCGCCGCGAGAGATTAGTGCATTAGCGGCGCTTAT-AAAGCG
1 GCATTAGCGGCGCTTATAAAGAAACGCCGCTAAAGGTCAGTGCATTAGCGGCGCTTATAAAAGCG
**
54626 CCGGTAAAGGTCAGT
66 CCGGTAAAGAACAGT
* * * *
54641 GCATTAGCGACGCTTATAAAGAAATGCCACTAAAGGTCAGTGCATTAGCGACGCTT
1 GCATTAGCGGCGCTTATAAAGAAACGCCGCTAAAGGTCAGTGCATTAGCGGCGCTT
54697 TCTCAGAGCA
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
79 64 0.58
82 44 0.40
83 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (80 bp):
GCATTAGCGGCGCTTATAAAGAAACGCCGCTAAAGGTCAGTGCATTAGCGGCGCTTATAAAAGCG
CCGGTAAAGAACAGT
Found at i:54861 original size:27 final size:26
Alignment explanation
Indices: 54829--54911 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
54819 TAACAATTAT
*
54829 TTTAAAACTTATATAAACTAAAAAAA
1 TTTAAAATTTATATAAACTAAAAAAA
* * * **
54855 TTCTAAAATTTTAAAAAAATTATTAAAA
1 TT-TAAAA-TTTATATAAACTAAAAAAA
54883 TTTAAAATTTATATAAACTAAAATAAA
1 TTTAAAATTTATATAAACTAAAA-AAA
54910 TT
1 TT
54912 AAATTATTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
26 13 0.30
27 15 0.35
28 15 0.35
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (26 bp):
TTTAAAATTTATATAAACTAAAAAAA
Found at i:54869 original size:19 final size:19
Alignment explanation
Indices: 54847--54889 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54837 TTATATAAAC
54847 TAAAAAAATT-CTAAAATTT
1 TAAAAAAATTACTAAAA-TT
*
54866 TAAAAAAATTATTAAAATT
1 TAAAAAAATTACTAAAATT
54885 TAAAA
1 TAAAA
54890 TTTATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATTACTAAAATT
Done.