Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014683.1 Kokia drynarioides strain JFW-HI SEQ_129722, 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: 373346
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 290 characters in sequence are not A, C, G, or T
Found at i:12995 original size:15 final size:15
Alignment explanation
Indices: 12971--13004 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12961 TAAACCACAT
*
12971 AAAT-TTTACGTGAA
1 AAATCTTTACGGGAA
12985 AAATCTTTACGGGAA
1 AAATCTTTACGGGAA
13000 AAATC
1 AAATC
13005 AAGAGCAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (15 bp):
AAATCTTTACGGGAA
Found at i:13144 original size:49 final size:49
Alignment explanation
Indices: 13086--13271 Score: 189
Period size: 49 Copynumber: 3.7 Consensus size: 49
13076 GAAAATTTTT
13086 TTATTCTAATCAATATCAAATA-AATGAAGTGTAGTAAAATTGAAAAATC
1 TTATTCTAATCAATATCAAATAGAA-GAAGTGTAGTAAAATTGAAAAATC
* * * * *
13135 TTATTCTAATCAATATTACATAGAAGAAGCGT-TTAACTTCAAGGTTGAAAAAATT
1 TTATTCTAATCAATATCAAATAGAAGAAGTGTAGTAA----AA--TTG-AAAAATC
*
13190 TTATTCTAATCAATATCAAATA-AATGAAGTGTAGTAAAGTTGAAAAATC
1 TTATTCTAATCAATATCAAATAGAA-GAAGTGTAGTAAAATTGAAAAATC
* * *
13239 TTATTCTATTCAATGTTAAATAGAAGAAGTGTA
1 TTATTCTAATCAATATCAAATAGAAGAAGTGTA
13272 ATTTTATACA
Statistics
Matches: 112, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
48 3 0.03
49 59 0.53
50 7 0.06
52 3 0.03
54 5 0.04
55 32 0.29
56 3 0.03
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (49 bp):
TTATTCTAATCAATATCAAATAGAAGAAGTGTAGTAAAATTGAAAAATC
Found at i:13207 original size:104 final size:105
Alignment explanation
Indices: 13061--13267 Score: 353
Period size: 104 Copynumber: 2.0 Consensus size: 105
13051 CAAGAAGAAT
**
13061 TTTAACTTCAAGGTTGAAAATTTTTTTATTCTAATCAATATCAAATAAATGAAGTGTAGTAAAAT
1 TTTAACTTCAAGGTTGAAAATAATTTTATTCTAATCAATATCAAATAAATGAAGTGTAGTAAAAT
*
13126 TGAAAAATCTTATTCTAATCAATATTACATAGAAGAAGCG
66 TGAAAAATCTTATTCTAATCAATATTAAATAGAAGAAGCG
*
13166 TTTAACTTCAAGGTTGAAAA-AATTTTATTCTAATCAATATCAAATAAATGAAGTGTAGTAAAGT
1 TTTAACTTCAAGGTTGAAAATAATTTTATTCTAATCAATATCAAATAAATGAAGTGTAGTAAAAT
* *
13230 TGAAAAATCTTATTCTATTCAATGTTAAATAGAAGAAG
66 TGAAAAATCTTATTCTAATCAATATTAAATAGAAGAAG
13268 TGTAATTTTA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 76 0.79
105 20 0.21
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (105 bp):
TTTAACTTCAAGGTTGAAAATAATTTTATTCTAATCAATATCAAATAAATGAAGTGTAGTAAAAT
TGAAAAATCTTATTCTAATCAATATTAAATAGAAGAAGCG
Found at i:29126 original size:4 final size:4
Alignment explanation
Indices: 29117--29143 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29107 ATATCCTTCT
29117 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
29144 TTGCATTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:34726 original size:219 final size:219
Alignment explanation
Indices: 34347--34784 Score: 876
Period size: 219 Copynumber: 2.0 Consensus size: 219
34337 AAACAAGGGA
34347 ATAGGGATTTAGCTGTGTACCATTTTATCCTTTCAGTATGTTAGGAAGCCAGTTGACTTGAATCA
1 ATAGGGATTTAGCTGTGTACCATTTTATCCTTTCAGTATGTTAGGAAGCCAGTTGACTTGAATCA
34412 TAGAAAAAAGATGGCTCTTTCACATTCCATATACCTAGCCTCCCATTACAAGATCTGAATCCAAA
66 TAGAAAAAAGATGGCTCTTTCACATTCCATATACCTAGCCTCCCATTACAAGATCTGAATCCAAA
34477 TCCTCCAAGTTGAAGTCCCAAGTTCTAAAAATTATAGTGCTCCTTTATTTACTTTAAATAAGGTT
131 TCCTCCAAGTTGAAGTCCCAAGTTCTAAAAATTATAGTGCTCCTTTATTTACTTTAAATAAGGTT
34542 CACCTACATGTTGGAGGCACAAGG
196 CACCTACATGTTGGAGGCACAAGG
34566 ATAGGGATTTAGCTGTGTACCATTTTATCCTTTCAGTATGTTAGGAAGCCAGTTGACTTGAATCA
1 ATAGGGATTTAGCTGTGTACCATTTTATCCTTTCAGTATGTTAGGAAGCCAGTTGACTTGAATCA
34631 TAGAAAAAAGATGGCTCTTTCACATTCCATATACCTAGCCTCCCATTACAAGATCTGAATCCAAA
66 TAGAAAAAAGATGGCTCTTTCACATTCCATATACCTAGCCTCCCATTACAAGATCTGAATCCAAA
34696 TCCTCCAAGTTGAAGTCCCAAGTTCTAAAAATTATAGTGCTCCTTTATTTACTTTAAATAAGGTT
131 TCCTCCAAGTTGAAGTCCCAAGTTCTAAAAATTATAGTGCTCCTTTATTTACTTTAAATAAGGTT
34761 CACCTACATGTTGGAGGCACAAGG
196 CACCTACATGTTGGAGGCACAAGG
34785 TGAGAGTGTT
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 219 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (219 bp):
ATAGGGATTTAGCTGTGTACCATTTTATCCTTTCAGTATGTTAGGAAGCCAGTTGACTTGAATCA
TAGAAAAAAGATGGCTCTTTCACATTCCATATACCTAGCCTCCCATTACAAGATCTGAATCCAAA
TCCTCCAAGTTGAAGTCCCAAGTTCTAAAAATTATAGTGCTCCTTTATTTACTTTAAATAAGGTT
CACCTACATGTTGGAGGCACAAGG
Found at i:46618 original size:33 final size:33
Alignment explanation
Indices: 46576--46641 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
46566 AGGCTATGTA
46576 AGGCATACATCAATAGCCAGATTTTGTTAAAGG
1 AGGCATACATCAATAGCCAGATTTTGTTAAAGG
46609 AGGCATACATCAATAGCCAGATTTTGTTAAAGG
1 AGGCATACATCAATAGCCAGATTTTGTTAAAGG
46642 CTCATAGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (33 bp):
AGGCATACATCAATAGCCAGATTTTGTTAAAGG
Found at i:48277 original size:33 final size:33
Alignment explanation
Indices: 48238--48306 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
48228 TCCTTACAAC
48238 TTTATTGGCATTAGAAAATGCATATCCCTATTA
1 TTTATTGGCATTAGAAAATGCATATCCCTATTA
48271 TTTATTGGCATTAGAAAATGCATATCCCTATTA
1 TTTATTGGCATTAGAAAATGCATATCCCTATTA
48304 TTT
1 TTT
48307 GGGGGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (33 bp):
TTTATTGGCATTAGAAAATGCATATCCCTATTA
Found at i:56266 original size:2 final size:2
Alignment explanation
Indices: 56259--56302 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
56249 ATGGACTGTG
*
56259 CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
56301 CT
1 CT
56303 ATATATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:56307 original size:2 final size:2
Alignment explanation
Indices: 56302--56328 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56292 TCTCTCTCTC
56302 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
56329 TCTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57688 original size:21 final size:21
Alignment explanation
Indices: 57664--57709 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
57654 TGGTAATAAC
*
57664 GCTATTAACTGAGAACAGATA
1 GCTATTAACTAAGAACAGATA
*
57685 GCTATTAACTAAGAACGGATA
1 GCTATTAACTAAGAACAGATA
57706 GCTA
1 GCTA
57710 ACAATTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (21 bp):
GCTATTAACTAAGAACAGATA
Found at i:60754 original size:27 final size:27
Alignment explanation
Indices: 60724--60776 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
60714 ATTCTAAACC
*
60724 TTGGTGAG-GAAACTCAAGTGTTGGATT
1 TTGGTG-GCGAAACACAAGTGTTGGATT
60751 TTGGTGGCGAAACACAAGTGTTGGAT
1 TTGGTGGCGAAACACAAGTGTTGGAT
60777 GATTTAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.30
Consensus pattern (27 bp):
TTGGTGGCGAAACACAAGTGTTGGATT
Found at i:62265 original size:33 final size:33
Alignment explanation
Indices: 62228--62294 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
62218 ATCATTCTAT
62228 CAATCATATTCATTGGTTTACTCTTATTTTTAA
1 CAATCATATTCATTGGTTTACTCTTATTTTTAA
62261 CAATCATATTCATTGGTTTACTCTTATTTTTAA
1 CAATCATATTCATTGGTTTACTCTTATTTTTAA
62294 C
1 C
62295 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (33 bp):
CAATCATATTCATTGGTTTACTCTTATTTTTAA
Found at i:62997 original size:18 final size:17
Alignment explanation
Indices: 62969--63003 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62959 AAACGAATTC
*
62969 TAAAAGATAAAGTAAAT
1 TAAAAGATAAAATAAAT
62986 TAAAATGATAAAATAAAT
1 TAAAA-GATAAAATAAAT
63004 AATCAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
TAAAAGATAAAATAAAT
Found at i:69224 original size:20 final size:20
Alignment explanation
Indices: 69176--69225 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
69166 CTGCCTAGAC
*
69176 CATGTCTGGTATTGCTCGATG
1 CATG-CTGGTACTGCTCGATG
*
69197 C-TCCCTGGTACTGCTCGATG
1 CAT-GCTGGTACTGCTCGATG
69217 CATGCTGGT
1 CATGCTGGT
69226 GCAGCTGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.34
Consensus pattern (20 bp):
CATGCTGGTACTGCTCGATG
Found at i:80728 original size:18 final size:18
Alignment explanation
Indices: 80701--80742 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
80691 ACTTGAGCTG
*
80701 TTATTGTTTCA-TATTATT
1 TTATTATTTCAGTATTA-T
*
80719 TTATTATTTCAGTTTTAT
1 TTATTATTTCAGTATTAT
80737 TTATTA
1 TTATTA
80743 ATTAGGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTTCAGTATTAT
Found at i:86834 original size:9 final size:9
Alignment explanation
Indices: 86817--86850 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
86807 CTGACACGTG
86817 TTATTTTTA
1 TTATTTTTA
*
86826 TTTTTTTTA
1 TTATTTTTA
86835 TTATTTTTA
1 TTATTTTTA
86844 TATATTT
1 T-TATTT
86851 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTTA
Found at i:87218 original size:17 final size:17
Alignment explanation
Indices: 87186--87218 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
87176 ATTGAAGGAA
87186 AAAATAAAGAAAAAGAG
1 AAAATAAAGAAAAAGAG
87203 AAAA-AAAGAAAGAAGA
1 AAAATAAAGAAA-AAGA
87219 AGGAAGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAATAAAGAAAAAGAG
Found at i:87631 original size:20 final size:21
Alignment explanation
Indices: 87590--87632 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
87580 TAATTTACTT
87590 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
87611 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
87631 TA
1 TA
87633 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:87936 original size:16 final size:16
Alignment explanation
Indices: 87892--87940 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
87882 TAAACCTAGC
*
87892 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
87908 T--TTAA-TATAAAAA
1 TAATTAATTATCAAAA
87921 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
87937 TAAT
1 TAAT
87941 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:89319 original size:43 final size:43
Alignment explanation
Indices: 89237--89321 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
89227 ATTAACATGT
* *
89237 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
89280 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
89322 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:89956 original size:45 final size:45
Alignment explanation
Indices: 89889--90025 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
89879 GCATAGCTCA
89889 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
89934 TCAAGTCAAGGATATCAACCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * *
89979 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
90024 TC
1 TC
90026 TATTCTTCTC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:93247 original size:4 final size:4
Alignment explanation
Indices: 93240--93303 Score: 58
Period size: 4 Copynumber: 15.5 Consensus size: 4
93230 AATACATTAC
* * *
93240 CTTT CTTT CCTT C-TT CTTT CTTT CCTCTC CTTC CTTT CTTT CTTT CTTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT CTTT C-TTT
*
93290 CTTT CTTT TTTT CT
1 CTTT CTTT CTTT CT
93304 CGTTTATTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.06
4 39 0.76
5 8 0.16
6 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:93290 original size:9 final size:9
Alignment explanation
Indices: 93241--93303 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
93231 ATACATTACC
93241 TTTCTTTCCT
1 TTTCTTT-CT
93251 TCTTCTTTCT
1 T-TTCTTTCT
* * *
93261 TTCCTCTCC
1 TTTCTTTCT
*
93270 TTCCTTTC-
1 TTTCTTTCT
93278 TTTCTTTCT
1 TTTCTTTCT
93287 TTTCTTTCT
1 TTTCTTTCT
93296 TTT-TTTCT
1 TTTCTTTCT
93304 CGTTTATTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
8 12 0.26
9 24 0.52
10 4 0.09
11 6 0.13
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:93295 original size:17 final size:17
Alignment explanation
Indices: 93240--93303 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
93230 AATACATTAC
93240 CTTTCTTTCCTTCTTCTTT
1 CTTTCTTT-CTT-TTCTTT
* * *
93259 CTTTCCTCTCCTTCCTTT
1 CTTT-CTTTCTTTTCTTT
93277 CTTTCTTTCTTTTCTTT
1 CTTTCTTTCTTTTCTTT
*
93294 CTTTTTTTCT
1 CTTTCTTTCT
93304 CGTTTATTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 19 0.51
18 9 0.24
19 6 0.16
20 3 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTCTTTCTTTTCTTT
Found at i:94739 original size:6 final size:6
Alignment explanation
Indices: 94728--94780 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
94718 ACTATTTCAT
94728 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
94776 CATCA
1 CATCA
94781 TCACCAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCAC
Found at i:100490 original size:43 final size:42
Alignment explanation
Indices: 100427--100514 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
100417 GTTGCAAGGC
* * *
100427 AATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTTGGT
1 AATAAAACATACAATACATTTACTTAATCAAGGAAATCTT-GT
* *
100470 AATAAAAGATATAATACATTTACTTAATCAAGGAAATCTTGT
1 AATAAAACATACAATACATTTACTTAATCAAGGAAATCTTGT
100512 AAT
1 AAT
100515 GAACTCAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 5 0.12
43 35 0.88
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (42 bp):
AATAAAACATACAATACATTTACTTAATCAAGGAAATCTTGT
Found at i:114368 original size:21 final size:21
Alignment explanation
Indices: 114329--114369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
114319 ATAAAAATTT
*
114329 ATAAAATTTACAAAAATATAA
1 ATAAAATTTAAAAAAATATAA
114350 ATAAAA-TTAAAAAAGATATA
1 ATAAAATTTAAAAAA-ATATA
114370 TAGTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAATTTAAAAAAATATAA
Found at i:119066 original size:19 final size:18
Alignment explanation
Indices: 119019--119066 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
119009 CGTTTAACTG
*
119019 ATTTTTTATAATTTTATAA
1 ATTTTTTATATTTTTAT-A
119038 ATTTTTTAT-TTTTT-TA
1 ATTTTTTATATTTTTATA
119054 ATTTATTTATATT
1 ATTT-TTTATATT
119067 AAATTATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 6 0.23
19 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTATATTTTTATA
Found at i:119342 original size:12 final size:12
Alignment explanation
Indices: 119327--119356 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
119317 ATTCTTTTAA
119327 TTTTTTTTTTCT
1 TTTTTTTTTTCT
*
119339 TTTTCTTTTTCT
1 TTTTTTTTTTCT
119351 TTTTTT
1 TTTTTT
119357 AAGTTCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:120616 original size:26 final size:27
Alignment explanation
Indices: 120564--120615 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
120554 GAGGGACACA
120564 AAGTGACGGCACTAAAGGAGGATTTTG
1 AAGTGACGGCACTAAAGGAGGATTTTG
* *
120591 AAGTGGCGGCACTAAGGGAGGATTT
1 AAGTGACGGCACTAAAGGAGGATTT
120616 GCCACTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.37, T:0.21
Consensus pattern (27 bp):
AAGTGACGGCACTAAAGGAGGATTTTG
Found at i:120798 original size:15 final size:14
Alignment explanation
Indices: 120753--120803 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
120743 CAAATAAACG
*
120753 GGAAAGAAATAA-A
1 GGAAAGAAAGAAGA
*
120766 -GAAAGAAAGGAGA
1 GGAAAGAAAGAAGA
120779 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAG-A
120794 GGAAAGAAAG
1 GGAAAGAAAG
120804 GTAATATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 9 0.28
13 1 0.03
14 11 0.34
15 11 0.34
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (14 bp):
GGAAAGAAAGAAGA
Found at i:123672 original size:47 final size:47
Alignment explanation
Indices: 123621--123710 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
123611 AATACATAAG
*
123621 TTTACCAATATAATACAAAA-ATAATAATTAAATACCAAAATGGGTTA
1 TTTACCAAAATAATACAAAATAT-ATAATTAAATACCAAAATGGGTTA
* ** * *
123668 TTTACTAAAATGGTACAAAATATATATTTATATACCAAAATGG
1 TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGG
123711 TATCTACACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 34 0.94
48 2 0.06
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (47 bp):
TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGGGTTA
Found at i:123803 original size:16 final size:16
Alignment explanation
Indices: 123782--123830 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
123772 TGATGGAGAT
123782 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
123798 ATTATTTT--TATATT-
1 ATTATTTTGGTA-ATTA
123812 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
123827 ATTA
1 ATTA
123831 GCTTGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:139396 original size:28 final size:28
Alignment explanation
Indices: 139364--139459 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 28
139354 TTAATATTAC
139364 TATATGAAAATT-TTAAATAAATAAAA-AA
1 TATAT-AAAATTATTAAAT-AATAAAATAA
*
139392 TATATAAAATTATTAAATATTAAAATAA
1 TATATAAAATTATTAAATAATAAAATAA
* *
139420 TATAATATATATATATTTAAAAAATAAAA-AA
1 TAT-ATA-AAAT-TA-TTAAATAATAAAATAA
139451 TAATATAAA
1 T-ATATAAA
139460 TAGACTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 12 0.21
28 16 0.29
29 3 0.05
30 4 0.07
31 8 0.14
32 13 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
TATATAAAATTATTAAATAATAAAATAA
Found at i:139691 original size:21 final size:21
Alignment explanation
Indices: 139665--139704 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
139655 TCCTCTAAAA
139665 TTAAAAA-AATAATAATAATCT
1 TTAAAAATAATAA-AATAATCT
139686 TTAAAAATAATAAAATAAT
1 TTAAAAATAATAAAATAAT
139705 AAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAATAATAAAATAATCT
Found at i:151662 original size:32 final size:30
Alignment explanation
Indices: 151595--151676 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
151585 CACTTAATTA
*
151595 AAAAAATTATAATTTAA-TCATTAAATTATT
1 AAAAAATT-TAATTTAATTCATTAAATGATT
* * *
151625 CAAAAAATTTCATTCAATTCATTAAAATGCTT
1 -AAAAAATTTAATTTAATTCATT-AAATGATT
*
151657 AAAAAATTTTATTTAATTCA
1 AAAAAATTTAATTTAATTCA
151677 CCAGGTTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 6 0.14
31 31 0.72
32 6 0.14
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (30 bp):
AAAAAATTTAATTTAATTCATTAAATGATT
Found at i:152411 original size:102 final size:102
Alignment explanation
Indices: 152230--152434 Score: 338
Period size: 102 Copynumber: 2.0 Consensus size: 102
152220 GAAGATGATA
152230 AGAATGAAATAGTTACTGAAAATACTGCATTTGTGCATGGGAAACCACCTCAAGAAGCTGCTGGA
1 AGAATGAAATAGTTACTGAAAATACTGCATTTGTGCATGGGAAACCACCTCAAGAAGCTGCTGGA
* *
152295 CCTCCTAAAGTTGAATCTGATGTGGAAATTCTTAATG
66 CCTCCGAAAGTTGAATCTGATATGGAAATTCTTAATG
* * * *
152332 AGAATGAAATAGTTACTGAAAGTACTGCATTTGTGCATGGGGAACCACTTCAAGATGCTGCTGGA
1 AGAATGAAATAGTTACTGAAAATACTGCATTTGTGCATGGGAAACCACCTCAAGAAGCTGCTGGA
* *
152397 CCTCCGAAATTTGAATCTGATATGGAAATTCTTCATG
66 CCTCCGAAAGTTGAATCTGATATGGAAATTCTTAATG
152434 A
1 A
152435 AAAAGTAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (102 bp):
AGAATGAAATAGTTACTGAAAATACTGCATTTGTGCATGGGAAACCACCTCAAGAAGCTGCTGGA
CCTCCGAAAGTTGAATCTGATATGGAAATTCTTAATG
Found at i:163457 original size:51 final size:52
Alignment explanation
Indices: 163374--163479 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 52
163364 AATAAGAACT
*
163374 TAAACTTTGTCACTTCATTTAACTAAGCTCTTATAATTTTACTACACCCAAA
1 TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACACCCAAA
* * * ** * *
163426 TAAACTTT-TCATTTTATTTAAATAAGTTCTTATTCTTTTATTACATCCAAA
1 TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACACCCAAA
163477 TAA
1 TAA
163480 GCCGTTAAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 38 0.83
52 8 0.17
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (52 bp):
TAAACTTTGTCACTTCATTTAAATAAGCTCTTATAATTTTACTACACCCAAA
Found at i:177265 original size:16 final size:13
Alignment explanation
Indices: 177230--177255 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177220 ACACACCCTC
177230 CATTAAATAACAA
1 CATTAAATAACAA
177243 CATTAAATAACAA
1 CATTAAATAACAA
177256 ATCAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
CATTAAATAACAA
Found at i:177270 original size:23 final size:22
Alignment explanation
Indices: 177235--177321 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 22
177225 CCCTCCATTA
177235 AATAACAACATTAAATAACAAATC
1 AATAA-AA-ATTAAATAACAAATC
* *
177259 AATTAAAAATTAAATTAAAGAAAAC
1 AA-TAAAAATTAAA-T-AACAAATC
*
177284 AA-AAAAATTAAAATAATCAAATT
1 AATAAAAATT-AAATAA-CAAATC
177307 AACTAACAAATTAAA
1 AA-TAA-AAATTAAA
177322 ATATTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
22 2 0.04
23 19 0.38
24 8 0.16
25 16 0.32
26 5 0.10
ACGTcount: A:0.67, C:0.09, G:0.01, T:0.23
Consensus pattern (22 bp):
AATAAAAATTAAATAACAAATC
Found at i:183869 original size:44 final size:44
Alignment explanation
Indices: 183806--183908 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
183796 ACACGGGCTA
* *
183806 GCACATGGGGGTGTGTCCAGGGTACGTGTCTATACTGTTTGGAG
1 GCACACGGGGGTGTGTCCAGGGTACGTGTCTATACTATTTGGAG
**
183850 GCACACGGGGGTGTGTCCAGGGTGTGTGTCTATACTATTTGGAG
1 GCACACGGGGGTGTGTCCAGGGTACGTGTCTATACTATTTGGAG
*
183894 GCACACGGGCGTGTG
1 GCACACGGGGGTGTG
183909 CCTGAACTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.16, C:0.17, G:0.40, T:0.27
Consensus pattern (44 bp):
GCACACGGGGGTGTGTCCAGGGTACGTGTCTATACTATTTGGAG
Found at i:184723 original size:17 final size:17
Alignment explanation
Indices: 184701--184754 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
184691 GCATCTGTAA
184701 CTGTATCTCTAATTCTT
1 CTGTATCTCTAATTCTT
*
184718 CTGTATCTGTAA-----
1 CTGTATCTCTAATTCTT
184730 CTGTATCTCTAATTCTT
1 CTGTATCTCTAATTCTT
*
184747 TTGTATCT
1 CTGTATCT
184755 GTAACTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
12 11 0.38
17 18 0.62
ACGTcount: A:0.19, C:0.20, G:0.09, T:0.52
Consensus pattern (17 bp):
CTGTATCTCTAATTCTT
Found at i:184725 original size:29 final size:29
Alignment explanation
Indices: 184693--184795 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
184683 ACATGACTGC
184693 ATCTGTAACTGTATCTCTAATTCTTCTGT
1 ATCTGTAACTGTATCTCTAATTCTTCTGT
*
184722 ATCTGTAACTGTATCTCTAATTCTTTTGT
1 ATCTGTAACTGTATCTCTAATTCTTCTGT
**
184751 ATCTGTAACTGTATCTCTGACA-T-GACTGT
1 ATCTGTAACTGTATCTCT-A-ATTCTTCTGT
184780 ATCTGTAACTGTATCT
1 ATCTGTAACTGTATCT
184796 GTATTATTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
29 65 0.96
30 2 0.03
31 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (29 bp):
ATCTGTAACTGTATCTCTAATTCTTCTGT
Found at i:184735 original size:12 final size:12
Alignment explanation
Indices: 184718--184798 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
184708 TCTAATTCTT
184718 CTGTATCTGTAA
1 CTGTATCTGTAA
*
184730 CTGTATCTCTAA
1 CTGTATCTGTAA
184742 TTCTTTTGTATCTGTAA
1 --C---TGTATCTGTAA
*
184759 CTGTATCTCTGACATGA
1 CTGTA--TCTG---TAA
184776 CTGTATCTGTAA
1 CTGTATCTGTAA
184788 CTGTATCTGTA
1 CTGTATCTGTA
184799 TTATTTCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
12 28 0.51
14 5 0.09
15 5 0.09
17 17 0.31
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (12 bp):
CTGTATCTGTAA
Found at i:198091 original size:18 final size:20
Alignment explanation
Indices: 198059--198096 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
198049 TTAATTATTT
198059 TATATTATATGAAATAAATA
1 TATATTATATGAAATAAATA
198079 TATATTAT-T-AAATAAATA
1 TATATTATATGAAATAAATA
198097 AAAATAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATTATATGAAATAAATA
Found at i:202291 original size:16 final size:16
Alignment explanation
Indices: 202269--202310 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
202259 ATTTTATATT
202269 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
202285 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
202301 AATTTAATAT
1 ATTTTAATAT
202311 AATTAATTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:204527 original size:26 final size:26
Alignment explanation
Indices: 204497--204567 Score: 65
Period size: 29 Copynumber: 2.6 Consensus size: 26
204487 TGAAATAATG
*
204497 ATTTAATATAAATATATTTAATTATT
1 ATTTAATATAAATATATATAATTATT
204523 ATTTAACATATATAAT-TAATATAATTATT
1 ATTT-A-ATATA-AATAT-ATATAATTATT
*
204552 TTTATAATAT-AATATA
1 ATT-TAATATAAATATA
204568 CTTGAGTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
26 8 0.22
27 2 0.05
28 10 0.27
29 16 0.43
30 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTAATATAAATATATATAATTATT
Found at i:208398 original size:19 final size:18
Alignment explanation
Indices: 208376--208426 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
208366 TTTTATGAAC
208376 TTTTTTTAATAATTTTTA
1 TTTTTTTAATAATTTTTA
208394 GTTTTTTTGAAT-ATTTTTA
1 -TTTTTTT-AATAATTTTTA
208413 TATTTTTTAA-AATT
1 T-TTTTTTAATAATT
208427 ACTTATTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.21
19 20 0.69
20 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTTTTAATAATTTTTA
Found at i:208399 original size:20 final size:19
Alignment explanation
Indices: 208376--208426 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
208366 TTTTATGAAC
208376 TTTTTTTAATAATTTTTAGT
1 TTTTTTTAATAATTTTTA-T
*
208396 TTTTTTGAAT-ATTTTTAT
1 TTTTTTTAATAATTTTTAT
*
208414 ATTTTTTAA-AATT
1 TTTTTTTAATAATT
208427 ACTTATTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.41
19 7 0.26
20 9 0.33
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTTTAATAATTTTTAT
Found at i:208399 original size:30 final size:28
Alignment explanation
Indices: 208359--208422 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
208349 TATAATTCTC
*
208359 TTTTAATTTTTATGAACTTTTTTTAATAAT
1 TTTTAATTTTTATGAA-TATTTTT-ATAAT
* * *
208389 TTTTAGTTTTTTTGAATATTTTTATATT
1 TTTTAATTTTTATGAATATTTTTATAAT
208417 TTTTAA
1 TTTTAA
208423 AATTACTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 9 0.31
29 6 0.21
30 14 0.48
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTTAATTTTTATGAATATTTTTATAAT
Found at i:215498 original size:17 final size:17
Alignment explanation
Indices: 215473--215509 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
215463 GTACGTGTTG
215473 TTTAACAGATACAATAA
1 TTTAACAGATACAATAA
* *
215490 TTTACCAGATACAATTA
1 TTTAACAGATACAATAA
215507 TTT
1 TTT
215510 TCTATACGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTAACAGATACAATAA
Found at i:217014 original size:3 final size:3
Alignment explanation
Indices: 217006--217031 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
216996 TTTTAAAATA
217006 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
217032 TGCGACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:219907 original size:5 final size:5
Alignment explanation
Indices: 219897--219921 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
219887 ATCCCCCATG
219897 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
219922 TGATCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:234166 original size:27 final size:27
Alignment explanation
Indices: 234136--234198 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
234126 TAAAAATAAA
* * * * *
234136 GAAAATTAATATTTTAAGTACCTAATT
1 GAAAATTAAAAATTTAAATACCAAAAT
*
234163 G-AAATAAAAAATTTAAATACCAAAAT
1 GAAAATTAAAAATTTAAATACCAAAAT
234189 GAAAATTAAA
1 GAAAATTAAA
234199 TACACTGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (27 bp):
GAAAATTAAAAATTTAAATACCAAAAT
Found at i:235051 original size:3 final size:3
Alignment explanation
Indices: 235043--235073 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
235033 TAGACTTTTG
235043 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
235074 ACCTTAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:251146 original size:3 final size:3
Alignment explanation
Indices: 251131--251165 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
251121 ACAATTGGAT
* *
251131 CAA CAA CAG CAA CAA CAA CCA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
251166 GTTCGTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.37, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:263932 original size:9 final size:9
Alignment explanation
Indices: 263918--263947 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
263908 AGTTTACTAC
263918 TTTTCTTCT
1 TTTTCTTCT
263927 TTTTCTTCT
1 TTTTCTTCT
*
263936 TCTTCTTCT
1 TTTTCTTCT
263945 TTT
1 TTT
263948 CTTGCTCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:264301 original size:6 final size:6
Alignment explanation
Indices: 264294--264335 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
264284 TGGAACAAGA
* * *
264294 AGAAGA AGAAGC AGAAGC AGAAGC AGAAAC AGAAAC AGAAGC
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC
264336 TGAGGTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:271662 original size:15 final size:17
Alignment explanation
Indices: 271642--271675 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
271632 TGCCCACTTG
271642 TTTTTCT-TCC-TTTTT
1 TTTTTCTCTCCATTTTT
271657 TTTTTCTCTCCATTTTT
1 TTTTTCTCTCCATTTTT
271674 TT
1 TT
271676 GGTTTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTCTCCATTTTT
Found at i:273807 original size:24 final size:23
Alignment explanation
Indices: 273774--273823 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
273764 AGAAATAATC
*
273774 TTTTAGTTAAACTCTGTTTAATTG
1 TTTTAATTAAACTCTG-TTAATTG
* *
273798 TTTTAATTAAACTTTGTTATTTG
1 TTTTAATTAAACTCTGTTAATTG
273821 TTT
1 TTT
273824 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.60
Consensus pattern (23 bp):
TTTTAATTAAACTCTGTTAATTG
Found at i:275690 original size:24 final size:24
Alignment explanation
Indices: 275662--275724 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
275652 AGAAATAATC
275662 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
275686 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
275710 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
275725 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:278981 original size:20 final size:20
Alignment explanation
Indices: 278956--279017 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
278946 TTTTAGTTTT
278956 TTCAAATCCAAAAAAAAAAA
1 TTCAAATCCAAAAAAAAAAA
**
278976 TTCAAATCCAATTAAAAAAA
1 TTCAAATCCAAAAAAAAAAA
*
278996 TTAAAAAT-CAAGAAAAAAAAA
1 TT-CAAATCCAA-AAAAAAAAA
279017 T
1 T
279018 CTAATCATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (20 bp):
TTCAAATCCAAAAAAAAAAA
Found at i:284833 original size:13 final size:13
Alignment explanation
Indices: 284815--284840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284805 TCGTAAGTTA
284815 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
284828 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
284841 ATAAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:293990 original size:5 final size:5
Alignment explanation
Indices: 293980--294007 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
293970 AAATACACAT
293980 TTGTG TTGTG TTGTG TTGTG TTGTG TTG
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTG
294008 CGTTTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (5 bp):
TTGTG
Found at i:307720 original size:23 final size:22
Alignment explanation
Indices: 307686--307811 Score: 114
Period size: 23 Copynumber: 5.5 Consensus size: 22
307676 ACGCTAGCGC
*
307686 GCTTACTATTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
307709 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
307732 GCTTACTGTTT-GCACCATT-TGT
1 GCTTACTGTTTCGCA-C-TTGTGT
* *
307754 GCCTACTGGATT-GCACTTGTGT
1 GCTTACT-GTTTCGCACTTGTGT
*
307776 GCTTACTATTTCCCCAGCACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
307802 GCTTACTGTT
1 GCTTACTGTT
307812 AAGTACTTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.05
22 22 0.25
23 40 0.46
24 2 0.02
26 19 0.22
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:313346 original size:2 final size:2
Alignment explanation
Indices: 313341--313366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
313331 AAAAAAAAAA
313341 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
313367 TTTTTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317037 original size:19 final size:19
Alignment explanation
Indices: 317013--317050 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
317003 TTTGAAATTG
317013 ATAAAAATCAGA-AGTTGAA
1 ATAAAAATCA-ACAGTTGAA
317032 ATAAAAATCAACAGTTGAA
1 ATAAAAATCAACAGTTGAA
317051 TTGGTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (19 bp):
ATAAAAATCAACAGTTGAA
Found at i:327687 original size:2 final size:2
Alignment explanation
Indices: 327680--327710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
327670 ACTTTGGTTT
327680 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
327711 TCCTTAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:337201 original size:153 final size:153
Alignment explanation
Indices: 336923--337220 Score: 535
Period size: 153 Copynumber: 1.9 Consensus size: 153
336913 GGAGCTTTAG
*
336923 ATTGAGTTTAACAAGGGCCTGGATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
1 ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
336988 AACAACTCTTCTCCAACTGCATTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
66 AACAACTCTTCTCCAACTGCATTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
337053 TTGGAATCCAAAGAACGCCCTGA
131 TTGGAATCCAAAGAACGCCCTGA
*
337076 ATTGAGTTTAACAAGGGTCTGAATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
1 ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
* * *
337141 AACAACTCTTCTCCAACCT-CGTTCTCCCCTCCTGTATATCTAACTTATTTACACCTGCCTCCAG
66 AACAACTCTTCTCCAA-CTGCATTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAA
337205 GTTGGAATCCAAAGAA
130 GTTGGAATCCAAAGAA
337221 TCCATAGATC
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
153 137 0.99
154 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (153 bp):
ATTGAGTTTAACAAGGGCCTGAATCTCACTTTTGACATTATCATCTTTTCTATCCTTGCTTTTGG
AACAACTCTTCTCCAACTGCATTCTCCCCTCCGGTATATCTAACTTATTTACACCTGCCTCCAAG
TTGGAATCCAAAGAACGCCCTGA
Found at i:339522 original size:21 final size:21
Alignment explanation
Indices: 339498--339572 Score: 50
Period size: 21 Copynumber: 3.7 Consensus size: 21
339488 TCATGTAACT
* *
339498 TATATTATAAAAATTTAAATA
1 TATAATATAAAAATATAAATA
* *
339519 TATAATATTATAATATAAATA
1 TATAATATAAAAATATAAATA
*
339540 T-TAA-A-AATAAT-TAAATTA
1 TATAATATAAAAATATAAA-TA
*
339558 TTTATATATAAAAAT
1 TATA-ATATAAAAAT
339573 TAATGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
17 4 0.09
18 8 0.19
19 3 0.07
20 4 0.09
21 19 0.44
22 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATATAAAAATATAAATA
Found at i:339910 original size:19 final size:20
Alignment explanation
Indices: 339866--339910 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
339856 TTTTTATTAC
*
339866 AATTTATGTGTTGAGAAGTG
1 AATTTATGTGTTGAGAAGTA
339886 AA-TTATGATGTTG-GAA-TA
1 AATTTATG-TGTTGAGAAGTA
339904 AATTTAT
1 AATTTAT
339911 AAATCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (20 bp):
AATTTATGTGTTGAGAAGTA
Found at i:340612 original size:3 final size:3
Alignment explanation
Indices: 340606--340632 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
340596 CCCATGGCGG
340606 CGA CGA CGA CGA CGA CGA CGA CGA CGA
1 CGA CGA CGA CGA CGA CGA CGA CGA CGA
340633 TGATGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CGA
Found at i:341617 original size:2 final size:2
Alignment explanation
Indices: 341610--341642 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
341600 ATAAAGAGCT
341610 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
341643 TATATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:345577 original size:23 final size:23
Alignment explanation
Indices: 345469--345565 Score: 176
Period size: 23 Copynumber: 4.2 Consensus size: 23
345459 GGCAACAAAA
* *
345469 AGCACACACAGTGCTAAACAGAG
1 AGCACACAAAGTGCTAATCAGAG
345492 AGCACACAAAGTGCTAATCAGAG
1 AGCACACAAAGTGCTAATCAGAG
345515 AGCACACAAAGTGCTAATCAGAG
1 AGCACACAAAGTGCTAATCAGAG
345538 AGCACACAAAGTGCTAATCAGAG
1 AGCACACAAAGTGCTAATCAGAG
345561 AGCAC
1 AGCAC
345566 GAGACGTGCT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (23 bp):
AGCACACAAAGTGCTAATCAGAG
Found at i:348690 original size:20 final size:21
Alignment explanation
Indices: 348663--348723 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
348653 TTATATAATA
*
348663 TATAAAATAATAAAAATATTT
1 TATAAAATAATAAATATATTT
*
348684 T-TAAAATAATATAATTTATTT
1 TATAAAATAATA-AATATATTT
348705 TATAAAATAA-AAATATATT
1 TATAAAATAATAAATATATT
348724 CGACATTACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.49
21 10 0.29
22 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAAATAATAAATATATTT
Found at i:349621 original size:23 final size:23
Alignment explanation
Indices: 349554--349609 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
349544 NNNNNNNNNN
349554 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
349577 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
349600 CAGAGAGCAC
1 CAGAGAGCAC
349610 GAGACGTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:352734 original size:20 final size:21
Alignment explanation
Indices: 352707--352767 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
352697 TTATATAATA
*
352707 TATAAAATAATAAAAATATTT
1 TATAAAATAATAAATATATTT
*
352728 T-TAAAATAATATAATTTATTT
1 TATAAAATAATA-AATATATTT
352749 TATAAAATAA-AAATATATT
1 TATAAAATAATAAATATATT
352768 CGACATTACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.49
21 10 0.29
22 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAAATAATAAATATATTT
Found at i:354306 original size:16 final size:17
Alignment explanation
Indices: 354273--354321 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
354263 ATTTTAAAAA
* *
354273 ATTTCAAAAACA-TCTT
1 ATTTCAAAAATATTTTT
*
354289 ATTT-AACAATATTTTT
1 ATTTCAAAAATATTTTT
354305 ATTTCAAAAATATTTTT
1 ATTTCAAAAATATTTTT
354322 TGTCCCAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 11 0.41
17 11 0.41
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTCAAAAATATTTTT
Found at i:357557 original size:17 final size:17
Alignment explanation
Indices: 357527--357560 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
357517 ATTTTGACTA
**
357527 TTTAAATTTTTAAAAAT
1 TTTAAATTAGTAAAAAT
357544 TTTAAATTAGTAAAAAT
1 TTTAAATTAGTAAAAAT
357561 AAAATTACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAT
Found at i:368459 original size:45 final size:46
Alignment explanation
Indices: 368385--368474 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
368375 CCCATTGTCT
* * *
368385 TCATCAGTCTTTGTTTTCCACTTCGTTCCATGTTCTGGGTAAGTTA
1 TCATCAGTCTTTGTTTTCCACCTCGTTCCATGTGCCGGGTAAGTTA
*
368431 TCAT-AGTCTTTGTTTTCCACCTCTTTCCATGTGCCGGGTAAGTT
1 TCATCAGTCTTTGTTTTCCACCTCGTTCCATGTGCCGGGTAAGTT
368475 CCTGCATCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (46 bp):
TCATCAGTCTTTGTTTTCCACCTCGTTCCATGTGCCGGGTAAGTTA
Done.