Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007877.1 Hibiscus syriacus cultivar Beakdansim tig00110253_pilon, 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: 614694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:4314 original size:21 final size:21
Alignment explanation
Indices: 4296--4381 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
4286 ATGAAGCAAA
*
4296 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
4317 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
4338 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
4359 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
4380 GG
1 GG
4382 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:4382 original size:21 final size:21
Alignment explanation
Indices: 4304--4392 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
4294 AAGGAAACAG
* *
4304 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
4326 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
4346 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
4367 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
4388 AGAGA
1 AGAGA
4393 TAAGTAATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:4933 original size:42 final size:43
Alignment explanation
Indices: 4817--4936 Score: 106
Period size: 42 Copynumber: 2.8 Consensus size: 43
4807 AAAAATTTAC
* *
4817 TGCGGCGTTTTGGAA-GA-AAACGCCGCTAAACATCAACGACTAT
1 TGCGGCG-TTT-GAATGACAAACGCCGCTAAATATCAACAACTAT
** * * *
4860 TGCGGCGTTTGTCTGCCAAATGCCG-TTAATATCAA-AACCTAT
1 TGCGGCGTTTGAATGACAAACGCCGCTAAATATCAACAA-CTAT
*
4902 TGCGGCGTTT-AATGATAAACGCCGCTAAATATCAA
1 TGCGGCGTTTGAATGACAAACGCCGCTAAATATCAA
4937 TACATTTTGC
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
41 11 0.18
42 35 0.58
43 14 0.23
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
TGCGGCGTTTGAATGACAAACGCCGCTAAATATCAACAACTAT
Found at i:5063 original size:13 final size:13
Alignment explanation
Indices: 5021--5062 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
5011 CGCCGCAAAC
5021 TTTAGCGGCGCTATT
1 TTTAGCGGCG--ATT
5036 TTTAGCGGCGA-T
1 TTTAGCGGCGATT
5048 TTTAGCGGC-ATT
1 TTTAGCGGCGATT
5060 TTT
1 TTT
5063 TTTTACGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 14 0.54
13 1 0.04
15 10 0.38
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (13 bp):
TTTAGCGGCGATT
Found at i:5429 original size:6 final size:7
Alignment explanation
Indices: 5403--5428 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5393 TTTTTTTGTT
5403 GGGGGGA
1 GGGGGGA
5410 GGGGGGA
1 GGGGGGA
5417 GGGGGGA
1 GGGGGGA
5424 GGGGG
1 GGGGG
5429 ATTTTCCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.88, T:0.00
Consensus pattern (7 bp):
GGGGGGA
Found at i:5822 original size:37 final size:36
Alignment explanation
Indices: 5756--5830 Score: 114
Period size: 37 Copynumber: 2.1 Consensus size: 36
5746 AAGGAAAATA
*
5756 TTGTCATCTTGTATAAATTTGGATATGTTGTCATAT
1 TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
* *
5792 TTGTCATCTTTTTATAAATTTAGATGTGTTGTCATAT
1 TTGTCATC-TTGTATAAATTTAGATATGTTGTCATAT
5829 TT
1 TT
5831 TGTAAACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (36 bp):
TTGTCATCTTGTATAAATTTAGATATGTTGTCATAT
Found at i:6044 original size:12 final size:11
Alignment explanation
Indices: 6026--6190 Score: 51
Period size: 11 Copynumber: 13.9 Consensus size: 11
6016 GTAGGTTCAA
*
6026 ATTCGAGTTTG
1 ATTCGAGCTTG
6037 AGTTCGAGCTTG
1 A-TTCGAGCTTG
* *
6049 ATTCGAACTTAA
1 ATTCGAGCTT-G
* *
6061 AATCGAGCTTC
1 ATTCGAGCTTG
* *
6072 AATCGAGCTCG
1 ATTCGAGCTTG
*
6083 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
6096 AATCGAGCTCG
1 ATTCGAGCTTG
*
6107 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
6120 AATCGAGCTCG
1 ATTCGAGCTTG
*
6131 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
6144 AATCGAGCTCG
1 ATTCGAGCTTG
*
6155 AGTCTCGAGCTTC
1 A-T-TCGAGCTTG
* *
6168 AATCGAGCTCG
1 ATTCGAGCTTG
6179 AGTCTCGAGCTT
1 A-T-TCGAGCTT
6191 CAATCGAGTT
Statistics
Matches: 108, Mismatches: 34, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
11 51 0.47
12 18 0.17
13 39 0.36
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (11 bp):
ATTCGAGCTTG
Found at i:6093 original size:24 final size:24
Alignment explanation
Indices: 6063--6198 Score: 272
Period size: 24 Copynumber: 5.7 Consensus size: 24
6053 GAACTTAAAA
6063 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
6087 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
6111 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
6135 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
6159 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
6183 TCGAGCTTCAATCGAG
1 TCGAGCTTCAATCGAG
6199 TTCCTGAAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 112 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCGAGTC
Found at i:9437 original size:20 final size:20
Alignment explanation
Indices: 9404--9452 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
9394 ATTTTGAAAT
* * *
9404 TTATTTTTATAAAAATATTA
1 TTATTTTAAAAAAAACATTA
*
9424 TTATTTTAAAAAAAACCTTA
1 TTATTTTAAAAAAAACATTA
9444 TT-TTTTAAA
1 TTATTTTAAA
9453 TTACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTTAAAAAAAACATTA
Found at i:19262 original size:60 final size:60
Alignment explanation
Indices: 19176--19289 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
19166 AAATGGTTCA
* *
19176 TTGACTATAGGATGTTGTTTAATTGAGT-CTCTCGACTATTAAAAGTTACAAAATAATCTT
1 TTGACTATAGGATGTCGTTTAATTGAGTCCTC-CAACTATTAAAAGTTACAAAATAATCTT
* * *
19236 TTGACTATAGGGTGTCGCTTT-GTTGAGTCCTCCAACTATTAAAAGTTATAAAAT
1 TTGACTATAGGATGTCG-TTTAATTGAGTCCTCCAACTATTAAAAGTTACAAAAT
19290 GGTTATTTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 41 0.87
61 6 0.13
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.39
Consensus pattern (60 bp):
TTGACTATAGGATGTCGTTTAATTGAGTCCTCCAACTATTAAAAGTTACAAAATAATCTT
Found at i:22851 original size:22 final size:22
Alignment explanation
Indices: 22826--22900 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
22816 TCATTTCTTT
22826 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
22848 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
22870 AGGCCTTGTTGAATAAATGTTC
1 AGGCCTTGTTGAATAAATGTTC
22892 AGGCGCTTG
1 AGGC-CTTG
22901 AGGTGAAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 48 0.92
23 4 0.08
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (22 bp):
AGGCCTTGTTGAATAAATGTTC
Found at i:32036 original size:9 final size:9
Alignment explanation
Indices: 32019--32070 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
32009 ATAAACAAGG
*
32019 TAAAGAAAA
1 TAAATAAAA
*
32028 CAAATAAAA
1 TAAATAAAA
**
32037 TACAATGGAA
1 TA-AATAAAA
32047 -AAATAAAA
1 TAAATAAAA
32055 TAAATAAAA
1 TAAATAAAA
32064 TAAATAA
1 TAAATAA
32071 GTAAGATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
8 5 0.15
9 24 0.71
10 5 0.15
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (9 bp):
TAAATAAAA
Found at i:32395 original size:9 final size:9
Alignment explanation
Indices: 32381--32405 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
32371 AATAATGAAT
32381 AAAAAAATA
1 AAAAAAATA
32390 AAAAAAATA
1 AAAAAAATA
32399 AAAAAAA
1 AAAAAAA
32406 ATATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:33115 original size:37 final size:37
Alignment explanation
Indices: 33065--33167 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 37
33055 GTGCTTGTGG
* * * * *
33065 ATCATATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
33102 ATCATATTTTTAGGAGTTTGAATCCTAG-AAAATTTT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
33138 ATCCTATTTTTAGGAGTTTGAATCATAGTA
1 ATCATATTTTTAGGAGTTTGAATCATAGTA
33168 CGACGAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 31 0.55
37 25 0.45
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:34015 original size:105 final size:105
Alignment explanation
Indices: 33711--34268 Score: 759
Period size: 105 Copynumber: 5.3 Consensus size: 105
33701 GCATTGTTCC
* * ** *
33711 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-TTTGTTGACA
* * * * *
33775 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
* *
33817 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGA-A-T--GAA-ATTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
* * *
33877 CAACGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
33917 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
*
33982 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
* *
34022 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
34087 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
** * * * * *
34127 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
* *
34192 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
* * *
34232 GAGTAGCACGATATCCTCCGTTGTGGAGTTGAAATTG
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTG
34269 TGGATGTTTG
Statistics
Matches: 409, Mismatches: 34, Indels: 16
0.89 0.07 0.03
Matches are distributed among these distances:
100 85 0.21
101 2 0.00
102 4 0.01
104 3 0.01
105 253 0.62
106 37 0.09
107 1 0.00
108 24 0.06
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
Found at i:37091 original size:55 final size:55
Alignment explanation
Indices: 37032--37462 Score: 392
Period size: 55 Copynumber: 7.9 Consensus size: 55
37022 ACTTGAAAAG
** ** *
37032 ATCTTCAAATGGCGGGTATGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACA
1 ATCTTCAAATAACGGGTCCGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAATA
* * * * * * *
37087 ATCTTCATAAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTCAAATA
1 ATCTTCA-AATAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
* *
37143 ATCTCCAACA-AACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAATA
1 ATCTTCAA-ATAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAATA
37198 ATCTTC-AATAACCGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCG----
1 ATCTTCAAATAA-CGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
* * * *
37249 ATCTTC-AATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACA
1 ATCTTCAAAT-AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
* * *
37304 ATCTTCCATAA-AACGGGTCCGCTCTCTATTTCTTCAGAGAGTAT-AGAACTCGAAAA
1 ATCTT-CA-AATAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAATA
* * * *
37360 ATCTTC-AATAAACAGGTCCGCTTCCTATTCTTTCAGAGAGTATAGGACTC----A
1 ATCTTCAAAT-AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
* * *
37411 ATCTTTAACA-AACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGA
1 ATCTTCAA-ATAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGA
37463 TCTTCATAAA
Statistics
Matches: 313, Mismatches: 40, Indels: 48
0.78 0.10 0.12
Matches are distributed among these distances:
51 85 0.27
52 3 0.01
53 4 0.01
54 5 0.02
55 124 0.40
56 89 0.28
57 1 0.00
58 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
ATCTTCAAATAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
Found at i:37346 original size:162 final size:161
Alignment explanation
Indices: 37051--37460 Score: 563
Period size: 162 Copynumber: 2.5 Consensus size: 161
37041 TGGCGGGTAT
* *
37051 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCG----ATCTTCA-AAAAACGTGTCTGCTCCCTA
* *
37115 TTCATTCAGAGAGTATAAGACTCAAATAATCTCCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
60 TTCCTTCAGAGAGTATAAGACTCAAACAATCTCCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
* * *
37180 GAGTATAGAACTCGAATAATCTTCAATAACCGGGTCC
125 GAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCC
* *
37217 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCGCTCCCTATTCCTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAAAAACGTGTCTGCTCCCTATTCCTT
* ** *
37282 CAGAGAGTATAGGACTTGAACAATCTTCCATA-AAACGGGTCCGCTCTCTATTTCTTCAGAGAGT
66 CAGAGAGTATAAGACTCAAACAATC-TCCA-ACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGT
37346 ATAGAACTCGAAAAATCTTCAATAAACAGGTCC
129 ATAGAACTCGAAAAATCTTCAATAAACAGGTCC
* * * * * *
37379 GCTTCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTCTGCTCCCTATTCCTT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAAAAACGTGTCTGCTCCCTATTCCTT
37444 CAGAGAGTATAAGACTC
66 CAGAGAGTATAAGACTC
37461 GATCTTCATA
Statistics
Matches: 219, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
161 42 0.19
162 145 0.66
163 1 0.00
166 30 0.14
167 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (161 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAAAAACGTGTCTGCTCCCTATTCCTT
CAGAGAGTATAAGACTCAAACAATCTCCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT
AGAACTCGAAAAATCTTCAATAAACAGGTCC
Found at i:38804 original size:23 final size:22
Alignment explanation
Indices: 38778--38832 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38768 TGAACCCTCC
*
38778 TTTTATTTCTCTTTTTTTTTCAT
1 TTTTATTTCTC-TCTTTTTTCAT
* *
38801 TTTTCTCTTTTCTCTTTTTTCAT
1 TTTTAT-TTCTCTCTTTTTTCAT
38824 TTTTCATTT
1 TTTT-ATTT
38833 TTTCCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATTTCTCTCTTTTTTCAT
Found at i:38840 original size:16 final size:16
Alignment explanation
Indices: 38793--38843 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
38783 TTTCTCTTTT
38793 TTTTTCA-TTTTTCTC-
1 TTTTTCATTTTTTC-CA
38808 TTTTCTC-TTTTTT-CA
1 TTTT-TCATTTTTTCCA
38823 TTTTTCATTTTTTCCA
1 TTTTTCATTTTTTCCA
38839 TTTTT
1 TTTTT
38844 TTCGTTTCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 14 0.45
16 14 0.45
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCATTTTTTCCA
Found at i:38842 original size:23 final size:23
Alignment explanation
Indices: 38797--38843 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
38787 TCTTTTTTTT
*
38797 TCATTTTTCTCTTTTCTCTTTTT
1 TCATTTTTCTCTTTTCTCATTTT
*
38820 TCATTTTTCATTTTTTC-CATTTT
1 TCATTTTTC-TCTTTTCTCATTTT
38843 T
1 T
38844 TTCGTTTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (23 bp):
TCATTTTTCTCTTTTCTCATTTT
Found at i:38890 original size:8 final size:9
Alignment explanation
Indices: 38791--38890 Score: 54
Period size: 9 Copynumber: 11.7 Consensus size: 9
38781 TATTTCTCTT
38791 TTTTTTTCA
1 TTTTTTTCA
*
38800 TTTTTCTC-
1 TTTTTTTCA
*
38808 -TTTTCTC-
1 TTTTTTTCA
38815 -TTTTTTCA
1 TTTTTTTCA
38823 --TTTTTCA
1 TTTTTTTCA
*
38830 TTTTTTCCA
1 TTTTTTTCA
*
38839 TTTTTTTCG
1 TTTTTTTCA
**
38848 TTTCGTT-A
1 TTTTTTTCA
*
38856 TTATTATT-A
1 TT-TTTTTCA
38865 TTATTATTTCA
1 TT-TT-TTTCA
38876 TTTTTTTCA
1 TTTTTTTCA
38885 TTTTTT
1 TTTTTT
38891 CTTCTTTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
7 20 0.27
8 2 0.03
9 45 0.61
10 4 0.05
11 3 0.04
ACGTcount: A:0.12, C:0.13, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:38898 original size:17 final size:17
Alignment explanation
Indices: 38878--38911 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38868 TTATTTCATT
*
38878 TTTTTCATTTTTTCTTC
1 TTTTTCATTTATTCTTC
*
38895 TTTTTTATTTATTCTTC
1 TTTTTCATTTATTCTTC
38912 AAGCGAAATA
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:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTATTCTTC
Found at i:48590 original size:46 final size:49
Alignment explanation
Indices: 48529--48630 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 49
48519 TGTTATCCAC
*
48529 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATTC-AA
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGAA
*
48576 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGAA
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGAA
48625 AAAAAT
1 AAAAAT
48631 GAAAATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
46 28 0.56
47 8 0.16
48 6 0.12
49 8 0.16
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (49 bp):
AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGAA
Found at i:52524 original size:18 final size:18
Alignment explanation
Indices: 52484--52525 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
52474 TTGAACCCAC
52484 CTTTTTGTTCTTTTCTTT
1 CTTTTTGTTCTTTTCTTT
*
52502 TTTTTTGTTCTTTT-TTCT
1 CTTTTTGTTCTTTTCTT-T
52520 CTTTTT
1 CTTTTT
52526 TCTATCTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
CTTTTTGTTCTTTTCTTT
Found at i:63279 original size:12 final size:12
Alignment explanation
Indices: 63243--63285 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
63233 ATTTTTTTTT
63243 AAAAAAAAAT-A
1 AAAAAAAAATGA
* *
63254 ATAATAATAATGA
1 A-AAAAAAAATGA
63267 AAAAAAAAATGA
1 AAAAAAAAATGA
63279 AAAAAAA
1 AAAAAAA
63286 TAATATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 1 0.04
12 23 0.88
13 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:63287 original size:25 final size:24
Alignment explanation
Indices: 63243--63289 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
63233 ATTTTTTTTT
* *
63243 AAAAAAAAATAATAATAATAATGA
1 AAAAAAAAATAAAAAAAATAATGA
63267 AAAAAAAAATGAAAAAAAATAAT
1 AAAAAAAAAT-AAAAAAAATAAT
63290 ATAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAAAATAAAAAAAATAATGA
Found at i:63577 original size:18 final size:17
Alignment explanation
Indices: 63556--63598 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
63546 ATATATACAT
*
63556 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATAA
*
63574 ATAATAAAAATAAATAA
1 ATAATAATAATAAATAA
63591 ATAA-AATA
1 ATAATAATA
63599 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:64036 original size:37 final size:37
Alignment explanation
Indices: 63954--64055 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
63944 GTGCTTGTGG
* * * * * *
63954 ATCTTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
63991 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
64028 ATCTTATTTTTAGGAGTTTGAATCCTAG
1 ATCTTATTTTTAGGAGTTTGAATCCTAG
64056 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (37 bp):
ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:64171 original size:2 final size:2
Alignment explanation
Indices: 64164--64204 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
64154 TCATTCCTCT
64164 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
64205 CGAGTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:83170 original size:22 final size:22
Alignment explanation
Indices: 83105--83173 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
83095 TAGCGCCCGA
* *
83105 CGATGGAAGCTGTGACTGCCGA
1 CGATGGAGGCTGTGACTGCCGG
83127 CGATGGAGGCTGTGACTGCCGG
1 CGATGGAGGCTGTGACTGCCGG
83149 CGATGGAGGCTGTGACTGCCGG
1 CGATGGAGGCTGTGACTGCCGG
83171 CGA
1 CGA
83174 AAAAAGAAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.17
Consensus pattern (22 bp):
CGATGGAGGCTGTGACTGCCGG
Found at i:85480 original size:23 final size:23
Alignment explanation
Indices: 85445--85502 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
85435 TACTAAACTG
* *
85445 GACTTGAACCACTTCAATAATTT
1 GACTTAAAACACTTCAATAATTT
85468 GACTTAAAACACTTCAATAATTT
1 GACTTAAAACACTTCAATAATTT
85491 GACTTAAAACAC
1 GACTTAAAACAC
85503 CATCAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (23 bp):
GACTTAAAACACTTCAATAATTT
Found at i:86766 original size:5 final size:5
Alignment explanation
Indices: 86713--86753 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
86703 AGAATGAAAG
86713 GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA G
1 GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA G
86754 AGTGAGAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:88899 original size:24 final size:24
Alignment explanation
Indices: 88872--88920 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
88862 TTCGCTTTAT
88872 TTGAGCTCAAATTTTAGGCTTCAA
1 TTGAGCTCAAATTTTAGGCTTCAA
88896 TTGAGCTCAAATTTTAGGCTTCAA
1 TTGAGCTCAAATTTTAGGCTTCAA
88920 T
1 T
88921 CGAACTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
TTGAGCTCAAATTTTAGGCTTCAA
Found at i:89725 original size:55 final size:55
Alignment explanation
Indices: 89639--89745 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
89629 GTACTCAAAG
* * *
89639 TATGATTCTCATTTTAAATTAATCTCTAAACTTTTAAATATTCCAATTTGATACC
1 TATGATTATCATTCTAAATTAATCTCTAAACTTTTAAACATTCCAATTTGATACC
* *
89694 TATGATTATCATTCTAAATTAATC-CTCAAACTTTTGAACATTTCAATTTGAT
1 TATGATTATCATTCTAAATTAATCTCT-AAACTTTTAAACATTCCAATTTGAT
89746 CCCCAAACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 2 0.04
55 44 0.96
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.45
Consensus pattern (55 bp):
TATGATTATCATTCTAAATTAATCTCTAAACTTTTAAACATTCCAATTTGATACC
Found at i:89772 original size:60 final size:60
Alignment explanation
Indices: 89647--89816 Score: 149
Period size: 55 Copynumber: 2.9 Consensus size: 60
89637 AGTATGATTC
* * * * * *
89647 TCATTTTAAATTAATCTCT-AAACTTTTAAATATTCCAATTTGAT----ACCTATGA-TT
1 TCATTCTAAATTAATCCCTAAAACTTTTAAACATTCAAATTTGATCCCAAACTATGACCT
* *
89701 ATCATTCTAAATTAAT-CCTCAAACTTTTGAACATTTC-AATTTGATCCCCAAACTATGACCT
1 -TCATTCTAAATTAATCCCTAAAACTTTTAAACA-TTCAAATTTGAT-CCCAAACTATGACCT
** * *
89762 TCATTCTAAATTGGTCCCTAAAATTTTTAAACATTCAAATTTTATCCCAAACTAT
1 TCATTCTAAATTAATCCCTAAAACTTTTAAACATTCAAATTTGATCCCAAACTAT
89817 ACATATATGC
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
54 2 0.02
55 33 0.35
56 3 0.03
60 33 0.35
61 22 0.24
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAATCCCTAAAACTTTTAAACATTCAAATTTGATCCCAAACTATGACCT
Found at i:90057 original size:60 final size:58
Alignment explanation
Indices: 89931--90088 Score: 167
Period size: 60 Copynumber: 2.7 Consensus size: 58
89921 GAATTTGGCG
* * *
89931 ATAAAATTGGAATA-TTAAGAAGTTTGAGGACTAATTTAGAAAGGGGTCATAGTTTAGGT
1 ATAAAATTAGAATATTTAA-AAGTTTAAGGACTAATTTA-AAAGGAGTCATAGTTTAGGT
* * * * *
89990 ATGAAATTATAATGTTTGAAAGTTTAAGGAATAATTTAAAATGAGAGTCATAGTTTGAGG-
1 ATAAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAA-G-GAGTCATAGTTT-AGGT
* *
90050 ATAAAATTAGAATATTTAAAAGCTTAAGGACCAATTTAA
1 ATAAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAA
90089 TATACAAATT
Statistics
Matches: 80, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 3 0.04
59 28 0.35
60 46 0.57
61 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (58 bp):
ATAAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAAGGAGTCATAGTTTAGGT
Found at i:90559 original size:57 final size:59
Alignment explanation
Indices: 90497--90610 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 59
90487 GATGTTCCAA
* *
90497 TTTCATCCCTAAACTAAGACTA-TCATTCTAAATTAGTCCTTAAAC-TTTTG-ACATTTG
1 TTTCATCCCTAAAATAAGAC-ACTCATTCTAAATTAGTCCTCAAACGTTTTGAACATTTG
* * *
90554 TTTCATTCCTAAAATATGACACTCATTCTAAATTGGTCCTCAAACGTTTTGAACATT
1 TTTCATCCCTAAAATAAGACACTCATTCTAAATTAGTCCTCAAACGTTTTGAACATT
90611 CCAATTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 1 0.02
57 38 0.78
58 5 0.10
59 5 0.10
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (59 bp):
TTTCATCCCTAAAATAAGACACTCATTCTAAATTAGTCCTCAAACGTTTTGAACATTTG
Found at i:90843 original size:29 final size:29
Alignment explanation
Indices: 90809--90901 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
90799 ATGATCATAA
90809 TTTAAGGATAAAATTAGAATATTCAAAAG
1 TTTAAGGATAAAATTAGAATATTCAAAAG
* * * * *
90838 TTTAAGAACT-AATTTAGAGTGAGTC-ATAG
1 TTTAAGGA-TAAAATTAGAAT-ATTCAAAAG
*
90867 TTTAGGGATAAAATTAGAATATTCAAAAG
1 TTTAAGGATAAAATTAGAATATTCAAAAG
90896 TTTAAG
1 TTTAAG
90902 AACCAATTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.08
29 40 0.83
30 4 0.08
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.33
Consensus pattern (29 bp):
TTTAAGGATAAAATTAGAATATTCAAAAG
Found at i:90888 original size:58 final size:59
Alignment explanation
Indices: 90758--90911 Score: 213
Period size: 58 Copynumber: 2.6 Consensus size: 59
90748 TTTGGGTATG
** *
90758 AAATTAGAATATTCAAAAGTTTGGGGGACCAATTTAGAAAGATGATCATAATTTAAGGATA
1 AAATTAGAATATTCAAAAGTTT-AAGAACCAATTTAG-AAGATGATCATAATTTAAGGATA
* * *
90819 AAATTAGAATATTCAAAAGTTTAAGAACTAATTTAG-AG-TGAGTCATAGTTTAGGGATA
1 AAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAGATGA-TCATAATTTAAGGATA
90877 AAATTAGAATATTCAAAAGTTTAAGAACCAATTTA
1 AAATTAGAATATTCAAAAGTTTAAGAACCAATTTA
90912 AAATAAAAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.04
58 50 0.59
60 10 0.12
61 22 0.26
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.31
Consensus pattern (59 bp):
AAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAGATGATCATAATTTAAGGATA
Found at i:90916 original size:29 final size:29
Alignment explanation
Indices: 90822--90916 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
90812 AAGGATAAAA
*
90822 TTAGAATATTCAAAAGTTTAAGAACTAAT
1 TTAGAATATTCAAAAGTTTAAGAACAAAT
* * * * * * *
90851 TTAGAGTGAGTC-ATAGTTTAGGGATAAAA
1 TTAGAAT-ATTCAAAAGTTTAAGAACAAAT
*
90880 TTAGAATATTCAAAAGTTTAAGAACCAAT
1 TTAGAATATTCAAAAGTTTAAGAACAAAT
*
90909 TTAAAATA
1 TTAGAATA
90917 AAAGATATAG
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
28 3 0.06
29 41 0.87
30 3 0.06
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (29 bp):
TTAGAATATTCAAAAGTTTAAGAACAAAT
Found at i:92264 original size:45 final size:46
Alignment explanation
Indices: 92198--92304 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 46
92188 GGTGCACTAA
* *
92198 GAGTGCATCGATGCATAAAATGCATTCGAT-GTTTCA-AAAGAGCTT
1 GAGTGCATCGATGCATAAAATGCATTCGATAGTTTCATAAA-ACCAT
* * * *
92243 GAGTGCATTGATGCATCAAATGGATTCGATATTTTCATAAAACCAT
1 GAGTGCATCGATGCATAAAATGCATTCGATAGTTTCATAAAACCAT
92289 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
92305 GGATAGTGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 27 0.51
46 23 0.43
47 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATAGTTTCATAAAACCAT
Found at i:96485 original size:3 final size:3
Alignment explanation
Indices: 96479--96542 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
96469 TAATATTTAT
* *
96479 TAA TAA TAA -AA TAA TAA TAA TAA AAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
96526 TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
96543 TTTAAATGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:96493 original size:21 final size:21
Alignment explanation
Indices: 96466--96534 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
96456 TTTGGGCCTG
96466 TAATAATATTTATTAATAATAA
1 TAATAATATTTA-TAATAATAA
*
96488 -AATAATA---ATAATAAAAA
1 TAATAATATTTATAATAATAA
*
96505 TAATAATAATTATAATAATAA
1 TAATAATATTTATAATAATAA
*
96526 TGATAATAT
1 TAATAATAT
96535 AAATAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
21 23 0.59
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
TAATAATATTTATAATAATAA
Found at i:97220 original size:20 final size:20
Alignment explanation
Indices: 97195--97246 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
97185 ACCTGACGGA
97195 TGCATCGATGCATTGCATTG
1 TGCATCGATGCATTGCATTG
97215 TGCATCGATGCATTGCATTG
1 TGCATCGATGCATTGCATTG
97235 TGCATCGATGCA
1 TGCATCGATGCA
97247 CATTCAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (20 bp):
TGCATCGATGCATTGCATTG
Found at i:97264 original size:23 final size:23
Alignment explanation
Indices: 97234--97313 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 23
97224 GCATTGCATT
97234 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* * * *
97257 GTGCATCGGTGCACCTAC-ATG-
1 GTGCATCGATGCACATTCAAGGA
*
97278 GTGTATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
97301 -TGCATCGATGCAC
1 GTGCATCGATGCAC
97314 TGTTAAGTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 14 0.31
22 16 0.36
23 15 0.33
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:102638 original size:65 final size:65
Alignment explanation
Indices: 102563--102699 Score: 190
Period size: 65 Copynumber: 2.1 Consensus size: 65
102553 CGATGCACTC
* * * *
102563 TCGATG-TTTCA-AAATAGCCTGAGTGCATCGATGCATTGCTTGTGCATCGATGCATCAAA-TGC
1 TCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGATAGTGCATCGATGCAT-AAACTGC
102625 AT
64 AT
*
102627 TCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGATAGTGCATCGGTGCATAAACTGCAT
1 TCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGATAGTGCATCGATGCATAAACTGCAT
102692 TCGATGTT
1 TCGATGTT
102700 CAATTTATTC
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
64 9 0.14
65 53 0.82
66 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (65 bp):
TCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGATAGTGCATCGATGCATAAACTGCAT
Found at i:102735 original size:20 final size:20
Alignment explanation
Indices: 102710--102747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
102700 CAATTTATTC
*
102710 ATTGGTGTATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
102730 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
102748 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:120796 original size:21 final size:22
Alignment explanation
Indices: 120772--120906 Score: 113
Period size: 21 Copynumber: 6.3 Consensus size: 22
120762 GACTATCGCA
120772 TTGCGATTTATTCCAAGTT-CG
1 TTGCGATTTATTCCAAGTTGCG
* *
120793 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAGTT-GCG
* * *
120814 TTGCGATTTATTCTAAATT-CC
1 TTGCGATTTATTCCAAGTTGCG
120835 TTGCGATTTATTCCAAGTTTGCG
1 TTGCGATTTATTCCAAG-TTGCG
* *
120858 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAGTT-GCG
* *
120879 CTGCAATTTATTCCAAGTT-CG
1 TTGCGATTTATTCCAAGTTGCG
120900 TTGCGAT
1 TTGCGAT
120907 AATCCAAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
19 9 0.10
20 2 0.02
21 51 0.58
22 2 0.02
23 24 0.27
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (22 bp):
TTGCGATTTATTCCAAGTTGCG
Found at i:120875 original size:65 final size:63
Alignment explanation
Indices: 120772--120906 Score: 207
Period size: 65 Copynumber: 2.1 Consensus size: 63
120762 GACTATCGCA
* * *
120772 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCC
1 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGCTGCAATTTATTCCAAATTCC
* *
120835 TTGCGATTTATTCCAAGTTTGCGTTGCGATAGTCGAAGTTCGCGCTGCAATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAG-TT-CGTTGCGATAGTCGAAGTTCGCGCTGCAATTTATTCCAAATTCC
120900 TTGCGAT
1 TTGCGAT
120907 AATCCAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 17 0.26
64 2 0.03
65 46 0.71
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (63 bp):
TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGCTGCAATTTATTCCAAATTCC
Found at i:121654 original size:21 final size:21
Alignment explanation
Indices: 121628--121759 Score: 146
Period size: 21 Copynumber: 6.3 Consensus size: 21
121618 AACCAGTCGT
*
121628 TGCGATTTTGGACTATCGCAA
1 TGCGATATTGGACTATCGCAA
* *
121649 TGCGATAGTCGACTATCGCAA
1 TGCGATATTGGACTATCGCAA
121670 TGCGA-ACTTGGACTATCGCAA
1 TGCGATA-TTGGACTATCGCAA
* *
121691 TGCGATAGTCGACTATCGCAA
1 TGCGATATTGGACTATCGCAA
121712 TGCGA-ACTTGGACTATCGCAA
1 TGCGATA-TTGGACTATCGCAA
* *
121733 TGCGA-ATATGTA-AATCGCAA
1 TGCGATAT-TGGACTATCGCAA
121753 TGCGATA
1 TGCGATA
121760 GTCCAAGTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.16
21 79 0.83
22 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
TGCGATATTGGACTATCGCAA
Found at i:121681 original size:42 final size:42
Alignment explanation
Indices: 121635--121737 Score: 206
Period size: 42 Copynumber: 2.5 Consensus size: 42
121625 CGTTGCGATT
121635 TTGGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAAC
121677 TTGGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAAC
121719 TTGGACTATCGCAATGCGA
1 TTGGACTATCGCAATGCGA
121738 ATATGTAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAAC
Found at i:121705 original size:63 final size:62
Alignment explanation
Indices: 121638--121762 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 62
121628 TGCGATTTTG
*
121638 GACTATCGCAATGCGATA-GTCGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGATAGTC
1 GACTATCGCAATGCGA-ACGTCGACTATCGCAATGCGAA-TATGGA-AATCGCAATGCGATAGTC
* * *
121701 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACGTCGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTC
121763 CAAGTTCGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
62 19 0.34
63 37 0.66
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (62 bp):
GACTATCGCAATGCGAACGTCGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTC
Found at i:121777 original size:21 final size:21
Alignment explanation
Indices: 121747--121959 Score: 198
Period size: 21 Copynumber: 10.5 Consensus size: 21
121737 AATATGTAAA
*
121747 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
121768 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
121789 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
121809 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
121830 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
121851 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
121871 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
121892 TCGCATTGCGATA----AA--
1 TCGCATTGCGATAGTCCAAGT
*
121907 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
121928 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
121949 TCGCGTTGCGA
1 TCGCATTGCGA
121960 ACCTGAAAAC
Statistics
Matches: 162, Mismatches: 15, Indels: 30
0.78 0.07 0.14
Matches are distributed among these distances:
15 12 0.07
16 1 0.01
17 1 0.01
19 2 0.01
20 33 0.20
21 111 0.69
22 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:121780 original size:83 final size:79
Alignment explanation
Indices: 121685--121945 Score: 300
Period size: 83 Copynumber: 3.2 Consensus size: 79
121675 ACTTGGACTA
* * *
121685 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCATTGCGATAGTCGACTATCGCATTGCGAA-TT-GACTATCGCATTGCG-ATAT-TAAATCG
121750 CAATGCGATAGTCCAAGT
62 CAATGCGATAGTCCAAGT
* * *
121768 TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCGACTATCGCATTGCGAT-TTACATATT
1 TCGCATTGCGATAGT-CGACTATCGCATTGCGA-A-TTGACTATCGCATTGCGATATTA-A-A-T
*
121831 CGCATTGCGATAGTCCAAGT
60 CGCAATGCGATAGTCCAAGT
*
121851 TCGCATTGCGATAGTCGACTATCGCATTGCG-ATTTACATATTCGCATTGCG--A-TAAATCGCA
1 TCGCATTGCGATAGTCGACTATCGCATTGCGAATTGAC-TA-TCGCATTGCGATATTAAATCGCA
121912 ATGCGATAGTCCAAGT
64 ATGCGATAGTCCAAGT
121928 TCGCATTGCGATAGTCGA
1 TCGCATTGCGATAGTCGA
121946 AGTTCGCGTT
Statistics
Matches: 156, Mismatches: 13, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
77 38 0.24
78 1 0.01
79 1 0.01
80 7 0.04
81 5 0.03
82 16 0.10
83 83 0.53
84 5 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (79 bp):
TCGCATTGCGATAGTCGACTATCGCATTGCGAATTGACTATCGCATTGCGATATTAAATCGCAAT
GCGATAGTCCAAGT
Found at i:121793 original size:62 final size:62
Alignment explanation
Indices: 121727--121904 Score: 204
Period size: 62 Copynumber: 2.9 Consensus size: 62
121717 ACTTGGACTA
* *
121727 TCGCAATGCGAATATGT-A-AATCGCAATGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAATA-GTCACAATCGCAATGCGAT-GTACATA-TTCGCATTGCGATAGTCCAAGT
* * *
121789 TCGCATTGCG-ATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAATAGTC-ACAATCGCAATGCGATGTACATATTCGCATTGCGATAGTCCAAGT
* * *
121851 TCGCATTGCG-ATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATA
1 TCGCATTGCGAATAGTC-ACAATCGCAATGCGATGTACATATTCGCATTGCGATA
121905 AATCGCAATG
Statistics
Matches: 107, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 89 0.83
63 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (62 bp):
TCGCATTGCGAATAGTCACAATCGCAATGCGATGTACATATTCGCATTGCGATAGTCCAAGT
Found at i:122662 original size:60 final size:61
Alignment explanation
Indices: 122551--122698 Score: 203
Period size: 60 Copynumber: 2.4 Consensus size: 61
122541 GTTTGGGGGC
* * *
122551 CAATTTAGAAA-GAGAGTCATGGTTTAAGGAATGTAATTAGAATATTCAAAAGTTTTAAGA-
1 CAATTTA-AAATGAGAGTCATAGTTTAAGGAATGAAATTAGAATATTCAAAAGTTTAAAGAT
*
122611 CTAATTTAAAATGAGAGTTATAGTTT-AGGAATGAAATTAGAATATTCAAAAGTTTAAAGAT
1 C-AATTTAAAATGAGAGTCATAGTTTAAGGAATGAAATTAGAATATTCAAAAGTTTAAAGAT
* *
122672 CAATTTAAAATGAAAGTCGTAGTTTAA
1 CAATTTAAAATGAGAGTCATAGTTTAA
122699 AGACATATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
60 57 0.74
61 20 0.26
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.33
Consensus pattern (61 bp):
CAATTTAAAATGAGAGTCATAGTTTAAGGAATGAAATTAGAATATTCAAAAGTTTAAAGAT
Found at i:126758 original size:7 final size:7
Alignment explanation
Indices: 126746--126772 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
126736 CGGACACGTT
126746 CATCATC
1 CATCATC
126753 CATCATC
1 CATCATC
126760 CATCATC
1 CATCATC
126767 CATCAT
1 CATCAT
126773 ACATGGGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (7 bp):
CATCATC
Found at i:135240 original size:40 final size:39
Alignment explanation
Indices: 135161--135240 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
135151 ATGTCTCGTC
* * *
135161 TTAAACCGAAAATATTACATTTTTTGTAACATTTTCGAT
1 TTAAACCAAAAATATTAAATTTTTTGTAACATTTCCGAT
*
135200 TTAAACCAAAAATGTTAAACTTTCTTT-TAACATTTCCGAT
1 TTAAACCAAAAATATTAAA-TTT-TTTGTAACATTTCCGAT
135240 T
1 T
135241 GCATATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 16 0.46
40 16 0.46
41 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (39 bp):
TTAAACCAAAAATATTAAATTTTTTGTAACATTTCCGAT
Found at i:143810 original size:2 final size:2
Alignment explanation
Indices: 143803--143861 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
143793 CATGAACCCC
143803 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
143845 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
143862 GGGGTGAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:144274 original size:27 final size:26
Alignment explanation
Indices: 144227--144278 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
144217 AATTTTAAGT
*
144227 TAAATATATAAATAGTTTTAATATTG
1 TAAATATATAAATAATTTTAATATTG
144253 TAAAT-TATAAATAAATTATTAATATT
1 TAAATATATAAAT-AATT-TTAATATT
144279 TTAACTCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAATATATAAATAATTTTAATATTG
Found at i:144388 original size:60 final size:60
Alignment explanation
Indices: 144314--144426 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
144304 GGTCCCCGAT
* *
144314 TATAGGGTGATGCTTTGTTGAGTCCAT-CGACTATTAAAAGTTACAAAATGATCCTTCAAC
1 TATAGGGTGATGCTTTGTTGAGTCC-TCCAACAATTAAAAGTTACAAAATGATCCTTCAAC
*
144374 TATAGGGTGTTGCTTTGTTGAGTCCTCCAACAATTAAAAGTTACAAAATGATC
1 TATAGGGTGATGCTTTGTTGAGTCCTCCAACAATTAAAAGTTACAAAATGATC
144427 ACCCGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (60 bp):
TATAGGGTGATGCTTTGTTGAGTCCTCCAACAATTAAAAGTTACAAAATGATCCTTCAAC
Found at i:144436 original size:60 final size:59
Alignment explanation
Indices: 144300--144436 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 59
144290 TAAAGTAGAC
* * * *
144300 AAATGGTCCCCGATTATAGGGTGATGCTTTGTTGAGTCCATCGACTATTAAAAGTTACA
1 AAATGATCCCCGACTATAGGGTGATGCTTTGTTGAGTCCATCAACAATTAAAAGTTACA
* * *
144359 AAATGATCCTTCAACTATAGGGTGTTGCTTTGTTGAGTCC-TCCAACAATTAAAAGTTACA
1 AAATGATCC-CCGACTATAGGGTGATGCTTTGTTGAGTCCAT-CAACAATTAAAAGTTACA
144419 AAATGATCACCCGACTAT
1 AAATGATC-CCCGACTAT
144437 TTATTACGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
59 9 0.14
60 56 0.85
61 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (59 bp):
AAATGATCCCCGACTATAGGGTGATGCTTTGTTGAGTCCATCAACAATTAAAAGTTACA
Found at i:144788 original size:28 final size:28
Alignment explanation
Indices: 144756--144812 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
144746 TCATCAATTG
*
144756 AACTACAGTCACTTAACTCATACACAAA
1 AACTAAAGTCACTTAACTCATACACAAA
144784 AACTAAAGTCACTTAACTCATACACAAA
1 AACTAAAGTCACTTAACTCATACACAAA
144812 A
1 A
144813 CTTAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.26, G:0.04, T:0.21
Consensus pattern (28 bp):
AACTAAAGTCACTTAACTCATACACAAA
Found at i:145914 original size:6 final size:6
Alignment explanation
Indices: 145903--145932 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
145893 GGGGCTAACT
145903 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
145933 TATATATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCTC
Found at i:148220 original size:22 final size:23
Alignment explanation
Indices: 148186--148228 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
148176 ATATAATAAA
148186 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
148209 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
148229 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:148259 original size:15 final size:15
Alignment explanation
Indices: 148239--148286 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
148229 TATTAGAATA
*
148239 ATTTATTTTAATATT
1 ATTTATTTAAATATT
*
148254 ATTTATTTCAATATT
1 ATTTATTTAAATATT
*
148269 A-TTATTAAAATATT
1 ATTTATTTAAATATT
148283 ATTT
1 ATTT
148287 CTATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTAAATATT
Found at i:148341 original size:33 final size:37
Alignment explanation
Indices: 148299--148384 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
148289 ATAATTTTAT
* *
148299 AAATAAAAATATTA-AGACT-GA-TAAAT-TCTATTA
1 AAATAAAAATATTATAAACTAGATTAAATATATATTA
* *
148332 AAATAAAAATATTATAAATTATATTAAATATATATTA
1 AAATAAAAATATTATAAACTAGATTAAATATATATTA
148369 AAATAAAAATATTATA
1 AAATAAAAATATTATA
148385 TTATATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 14 0.31
34 3 0.07
35 1 0.02
36 5 0.11
37 22 0.49
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (37 bp):
AAATAAAAATATTATAAACTAGATTAAATATATATTA
Found at i:148581 original size:26 final size:23
Alignment explanation
Indices: 148549--148601 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
148539 TTAAAATAAG
148549 AATATAATAGTATCGTATATTATTGT
1 AATATAATAG-A--GTATATTATTGT
*
148575 AATATAATTGAGTATATTATTGT
1 AATATAATAGAGTATATTATTGT
148598 AATA
1 AATA
148602 AAAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 16 0.62
25 1 0.04
26 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (23 bp):
AATATAATAGAGTATATTATTGT
Found at i:148614 original size:20 final size:23
Alignment explanation
Indices: 148563--148606 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
148553 TAATAGTATC
* *
148563 GTATATTATTGTAATATAATTGA
1 GTATATTATTGTAATAAAAATGA
148586 GTATATTATTGTAATAAAAAT
1 GTATATTATTGTAATAAAAAT
148607 ATTATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (23 bp):
GTATATTATTGTAATAAAAATGA
Found at i:148628 original size:25 final size:25
Alignment explanation
Indices: 148564--148635 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
148554 AATAGTATCG
* * *
148564 TATATTATTGTAAT-ATAAT-TGAG
1 TATATTATTGTAATAAAAATATTAT
148587 TATATTATTGTAATAAAAATATTAT
1 TATATTATTGTAATAAAAATATTAT
*
148612 TATATTATAT-TAGTAAAAATATTA
1 TATATTAT-TGTAATAAAAATATTA
148636 ATTAAATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.33
24 4 0.10
25 23 0.55
26 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
TATATTATTGTAATAAAAATATTAT
Found at i:148645 original size:25 final size:25
Alignment explanation
Indices: 148600--148647 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
148590 ATTATTGTAA
*
148600 TAAAAATATTATTATATTATATTAG
1 TAAAAATATTATTATAATATATTAG
148625 TAAAAATATTAATTA-AATATATT
1 TAAAAATATT-ATTATAATATATT
148648 TTAAATACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAAAATATTATTATAATATATTAG
Found at i:153144 original size:16 final size:16
Alignment explanation
Indices: 153125--153196 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
153115 AATTAAATTA
153125 TTAAT-TTTAGTTTATT
1 TTAATATTTA-TTTATT
153141 TTAATATTTATTTA-T
1 TTAATATTTATTTATT
* *
153156 TTAA-ATCATATGTAATAT
1 TTAATAT-TTAT-TTAT-T
*
153174 TTAATTTTTATTTTATT
1 TTAATATTTA-TTTATT
153191 TTAATA
1 TTAATA
153197 CTTGTAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 11 0.26
17 10 0.23
18 10 0.23
19 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAATATTTATTTATT
Found at i:153463 original size:21 final size:21
Alignment explanation
Indices: 153417--153457 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
153407 TAAATACTAA
*
153417 AAAAATTAAAATTGATAGTTT
1 AAAAATTAAAATTCATAGTTT
153438 AAAAATT-AAATTCATAGTTT
1 AAAAATTAAAATTCATAGTTT
153458 TTAAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAATTAAAATTCATAGTTT
Found at i:154081 original size:17 final size:16
Alignment explanation
Indices: 154059--154105 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
154049 TATTTTGTGC
154059 TTAATTTATTTAAGTAT
1 TTAATTTATTTAA-TAT
154076 TTAATTTATTTAATAT
1 TTAATTTATTTAATAT
* *
154092 TTTATTTAATTAAT
1 TTAATTTATTTAAT
154106 TTTTTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTAATTTATTTAATAT
Found at i:163549 original size:20 final size:20
Alignment explanation
Indices: 163521--163575 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
163511 ATAATGTTAT
163521 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
* *
163541 CAGGATATCTACACCATAGA
1 CAGGGTATCTATACCATAGA
*
163561 CAGGGTATATATACC
1 CAGGGTATCTATACC
163576 TCAGTTAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:164567 original size:43 final size:43
Alignment explanation
Indices: 164458--164568 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 43
164448 TGATGTTTAA
*
164458 CGACGTTTTT-TCTAAAAACGCCGCAAATGGTTTTGAGAAGTAG
1 CGACGTTTTTCTC-AAAAATGCCGCAAATGGTTTTGAGAAGTAG
* * * * ** *
164501 CGGCGTTTTACT-TAAAATCGCCGCAATAT-GTTTTGATATTTTG
1 CGACGTTTTTCTCAAAAAT-GCCGCAA-ATGGTTTTGAGAAGTAG
164544 CGACGTTTTTCTCAAAAATGCCGCA
1 CGACGTTTTTCTCAAAAATGCCGCA
164569 GTAAGTTATG
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
42 4 0.08
43 41 0.77
44 8 0.15
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (43 bp):
CGACGTTTTTCTCAAAAATGCCGCAAATGGTTTTGAGAAGTAG
Found at i:164594 original size:43 final size:44
Alignment explanation
Indices: 164498--164596 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 44
164488 TTTTGAGAAG
* * * *
164498 TAGCGGCGTTTTACTTAAAATCGCCGCAATATGTTTTGATATTT
1 TAGCGGCGTTTTTCTAAAAATCGCCGCAATAAGTTATGATATTT
* * *
164542 T-GCGACGTTTTTCTCAAAAAT-GCCGCAGTAAGTTATG-TTTTT
1 TAGCGGCGTTTTTCT-AAAAATCGCCGCAATAAGTTATGATATTT
164584 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
164597 ATCGAAAACG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
42 5 0.11
43 34 0.76
44 6 0.13
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (44 bp):
TAGCGGCGTTTTTCTAAAAATCGCCGCAATAAGTTATGATATTT
Found at i:164680 original size:44 final size:43
Alignment explanation
Indices: 164629--164748 Score: 143
Period size: 44 Copynumber: 2.7 Consensus size: 43
164619 TTGAGAATTA
164629 GCGGCGTTTCTAGTGCAAAAACGCCGCTAAATGCATGGTATATT
1 GCGGCGTTTCTAGTGC-AAAACGCCGCTAAATGCATGGTATATT
** **
164673 GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTTTGGTATATT
1 GCGGCGTTTCTAGTGCA-AAACGCCGCTAAATGCATGGTATATT
* *
164717 GCGACATTTCTAGTTTGC-AAACGCCGCTAAAT
1 GCGGCGTTTCTAG--TGCAAAACGCCGCTAAAT
164749 AACACAGGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 63 0.97
46 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTCTAGTGCAAAACGCCGCTAAATGCATGGTATATT
Found at i:168931 original size:52 final size:52
Alignment explanation
Indices: 168868--169026 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
168858 TAACAACAAA
168868 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
* *
168920 ATACATTATAATTTAGAAACATTAAAGTACTTATGCGTAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
168972 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
169024 ATA
1 ATA
169027 TTGTTCAGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:171340 original size:31 final size:31
Alignment explanation
Indices: 171298--171453 Score: 228
Period size: 31 Copynumber: 5.0 Consensus size: 31
171288 AGGGTCGAGG
*
171298 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
171329 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
171360 GTTTACCTA-GATTCTTCGGGACATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
*
171391 GTTTACCTTTGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
171422 GATTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
171453 G
1 G
171454 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
30 2 0.02
31 111 0.97
32 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:171711 original size:18 final size:18
Alignment explanation
Indices: 171688--171822 Score: 105
Period size: 18 Copynumber: 7.5 Consensus size: 18
171678 AATATTAATA
*
171688 CATGATAGTGATAGAGAT
1 CATGATAATGATAGAGAT
**
171706 CATGATAATGATATCGAT
1 CATGATAATGATAGAGAT
* *
171724 GATAATAATGATAGAGAT
1 CATGATAATGATAGAGAT
*
171742 CATGATAATGATATTA-AT
1 CATGATAATGATA-GAGAT
** *
171760 GTTGA-AAGAGATAGAGAT
1 CATGATAA-TGATAGAGAT
**
171778 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
*
171796 -GTGGATAATGATAGAGAT
1 CAT-GATAATGATAGAGAT
*
171814 TATGATAAT
1 CATGATAAT
171823 ATTATTGACG
Statistics
Matches: 88, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
17 4 0.05
18 80 0.91
19 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:171737 original size:36 final size:36
Alignment explanation
Indices: 171696--171830 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
171686 TACATGATAG
*
171696 TGATAGAGATCATGATAATGATATCGATGAT-AATAA
1 TGATAGAGATCATGATAATGATATTGATG-TGAATAA
*
171732 TGATAGAGATCATGATAATGATATTAATGTTGAA-AGA
1 TGATAGAGATCATGATAATGATATTGATG-TGAATA-A
*
171769 -GATAGAGATCATGATAATGATATTGATGTGGATAA
1 TGATAGAGATCATGATAATGATATTGATGTGAATAA
*
171804 TGATAGAGATTATGATAAT-ATTATTGA
1 TGATAGAGATCATGATAATGA-TATTGA
171831 CGTTGTTAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
35 5 0.06
36 80 0.91
37 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (36 bp):
TGATAGAGATCATGATAATGATATTGATGTGAATAA
Found at i:177195 original size:24 final size:24
Alignment explanation
Indices: 177168--177239 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
177158 CGTTCATTTA
177168 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* *
177192 CGTTCGGTTACGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
177216 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
177240 TCATTCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:177197 original size:14 final size:14
Alignment explanation
Indices: 177178--177233 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
177168 CGTTCGTGAA
177178 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
177192 CGTTCGGTTA----
1 CGTTCGGTTATGTT
*
177202 CGTTCGTTTATGTT
1 CGTTCGGTTATGTT
177216 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
177230 CGTT
1 CGTT
177234 TATGTTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
14 27 0.75
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:177996 original size:10 final size:10
Alignment explanation
Indices: 177981--178072 Score: 56
Period size: 10 Copynumber: 9.7 Consensus size: 10
177971 GGGTCTCCAA
177981 CGTTTATGTT
1 CGTTTATGTT
177991 CGTTTATGTT
1 CGTTTATGTT
*
178001 CG--TGT-TT
1 CGTTTATGTT
178008 CGTTTATGTT
1 CGTTTATGTT
178018 CG----TGTT
1 CGTTTATGTT
*
178024 CATTTATGTT
1 CGTTTATGTT
178034 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
178045 ATGTTCGTGTT
1 -CGTTTATGTT
178056 CGTTTATGTT
1 CGTTTATGTT
178066 CGTTTAT
1 CGTTTAT
178073 TTATTAAATG
Statistics
Matches: 61, Mismatches: 10, Indels: 22
0.66 0.11 0.24
Matches are distributed among these distances:
6 5 0.08
7 4 0.07
8 2 0.03
9 2 0.03
10 37 0.61
11 7 0.11
12 4 0.07
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:178031 original size:16 final size:16
Alignment explanation
Indices: 177987--178076 Score: 130
Period size: 16 Copynumber: 5.7 Consensus size: 16
177977 CCAACGTTTA
*
177987 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
178003 TGTTTCGTTTATGTTCG
1 TG-TTCATTTATGTTCG
178020 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
178036 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
178052 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
178068 T-TT-ATTTAT
1 TGTTCATTTAT
178077 TAAATGAACG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
14 5 0.07
15 2 0.03
16 47 0.67
17 16 0.23
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:179425 original size:20 final size:20
Alignment explanation
Indices: 179380--179425 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
179370 GACCAACAAA
*
179380 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
179400 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
179419 ATCGCAA
1 ATCGCAA
179426 ATTCGCGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:179536 original size:20 final size:20
Alignment explanation
Indices: 179504--179577 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
179494 TTTTCCCAAT
*
179504 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
* ** *
179524 TCGTAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
179545 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
179565 TCGCAACGCGAAT
1 TCGCAACGCGAAT
179578 TGGGAAAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:179547 original size:21 final size:21
Alignment explanation
Indices: 179521--179596 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
179511 GCGAATAAGT
*
179521 AAATCGTAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
179542 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
179562 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
179583 AAATCGCAATGCGA
1 AAATCGCAACGCGA
179597 TACTGACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:179561 original size:41 final size:41
Alignment explanation
Indices: 179504--179596 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
179494 TTTTCCCAAT
*
179504 TCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
179545 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
179586 TCGCAATGCGA
1 TCGCAATGCGA
179597 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:179609 original size:41 final size:41
Alignment explanation
Indices: 179523--179657 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
179513 GAATAAGTAA
* * *
179523 ATCGTAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
179564 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
179605 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
179646 TTCGCAACGCGA
1 ATCGCAACGCGA
179658 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:179610 original size:20 final size:20
Alignment explanation
Indices: 179585--179699 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
179575 AATTGGGAAA
*
179585 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
179605 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
179626 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
179646 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
179666 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
179686 TTCGCAACGCGATA
1 ATCGCAACGCGATA
179700 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:179658 original size:41 final size:41
Alignment explanation
Indices: 179582--179719 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
179572 GCGAATTGGG
* * *
179582 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
179623 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
179665 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
179704 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
179720 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:179915 original size:22 final size:22
Alignment explanation
Indices: 179887--179930 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
179877 TACTCTCTCA
179887 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
179909 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
179931 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:181592 original size:18 final size:18
Alignment explanation
Indices: 181571--181615 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
181561 TCCACTTCGG
*
181571 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
181589 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
181607 GAGCCATCA
1 GAGCCATCA
181616 TCTGATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:182151 original size:19 final size:20
Alignment explanation
Indices: 182101--182162 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
182091 TTACTTTCGT
*
182101 AACACGAAAATGACTATCGC
1 AACACGGAAATGACTATCGC
* *
182121 AACGCGGAAATGGCTATCGC
1 AACACGGAAATGACTATCGC
* **
182141 AATAC-GAAATGAAAATCGC
1 AACACGGAAATGACTATCGC
182160 AAC
1 AAC
182163 GACAAAATCG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AACACGGAAATGACTATCGC
Found at i:182209 original size:19 final size:19
Alignment explanation
Indices: 182136--182217 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
182126 GGAAATGGCT
*
182136 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
182155 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
182169 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
182187 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
182206 ATCGCAATGCGA
1 ATCGCAATGCGA
182218 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:182251 original size:14 final size:14
Alignment explanation
Indices: 182229--182286 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
182219 TTGTGTTTCG
*
182229 CGTTACGATTTTGT
1 CGTTGCGATTTTGT
*
182243 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
182259 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
182275 CATTGCGATTTT
1 CGTTGCGATTTT
182287 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 4 0.11
18 11 0.31
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:182293 original size:33 final size:32
Alignment explanation
Indices: 182224--182302 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
182214 GCGATTTGTG
* *
182224 TTTCGCGTTACGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTCA
182256 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGA-TTTCA
*
182289 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
182303 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCATTGCGATTTCA
Found at i:182299 original size:19 final size:19
Alignment explanation
Indices: 182275--182342 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
182265 GCGATTTTGT
**
182275 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
*
182294 CATTGCGATAGCCATTTCCG
1 CATTGCGATAGTCATTT-CG
*
182314 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCA-TTTCG
*
182334 CGTTGCGAT
1 CATTGCGAT
182343 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 14 0.33
20 25 0.60
21 3 0.07
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:182321 original size:20 final size:19
Alignment explanation
Indices: 182287--182342 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
182277 TTGCGATTTT
*
182287 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
182306 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
182326 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
182343 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:184229 original size:14 final size:14
Alignment explanation
Indices: 184210--184245 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
184200 ATTGTTTAAT
184210 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
184224 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
184238 TGATTTGT
1 TGATTTGT
184246 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:184385 original size:20 final size:20
Alignment explanation
Indices: 184362--184426 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
184352 ATCGCAACGA
184362 GATAGCCATTTTCGCGTTGC
1 GATAGCCATTTTCGCGTTGC
*
184382 GATAGCCATTTTCGCGTTAC
1 GATAGCCATTTTCGCGTTGC
184402 GATAGCCATTTTCGCGTTGC
1 GATAGCCATTTTCGCGTTGC
184422 GATAG
1 GATAG
184427 TCAAATGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (20 bp):
GATAGCCATTTTCGCGTTGC
Found at i:185509 original size:24 final size:24
Alignment explanation
Indices: 185482--185535 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
185472 GTATTTGAAA
* *
185482 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
185506 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
185530 TTTGAT
1 TTTGAT
185536 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:188046 original size:19 final size:19
Alignment explanation
Indices: 188024--188154 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
188014 GGAAATTACT
188024 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
188043 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
188057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
188076 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
188090 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
188109 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
188123 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
188142 ATCGCAACGCGAA
1 ATCGCAATGCGAA
188155 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:188066 original size:33 final size:33
Alignment explanation
Indices: 188024--188150 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
188014 GGAAATTACT
188024 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
188057 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
188089 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
188123 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
188151 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:188131 original size:66 final size:66
Alignment explanation
Indices: 188025--188157 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
188015 GAAATTACTA
*
188025 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
188090 T
66 T
*
188091 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
188156 T
66 T
188157 T
1 T
188158 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:188238 original size:19 final size:18
Alignment explanation
Indices: 188181--188239 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
188171 GATTCTCTCG
188181 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
* *
188199 GCTGCGA--TT-ATCTCG-
1 -TTGCGATTTTCATTTCGC
188214 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
188232 ATTGCGAT
1 -TTGCGAT
188240 AGTACTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:188238 original size:33 final size:33
Alignment explanation
Indices: 188150--188239 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
188140 AAATCGCAAC
* * * *
188150 GCGAATTTAATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
*
188183 GCGATTTTCATTTCGCGCTGCGATTATCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
*
188216 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
188240 AGTACTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
Found at i:188365 original size:14 final size:14
Alignment explanation
Indices: 188346--188382 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
188336 CATCAATTAA
188346 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
188360 ACAAATCACCTTTT
1 ACAAATCAACTTTT
188374 ACAAATCAA
1 ACAAATCAA
188383 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:189802 original size:21 final size:21
Alignment explanation
Indices: 189736--189802 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
189726 GTGAATCGGG
*
189736 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
189756 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
189778 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
189799 CTCT
1 CTCT
189803 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:189821 original size:42 final size:41
Alignment explanation
Indices: 189736--189858 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
189726 GTGAATCGGG
* * * *
189736 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
189778 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
189820 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
189859 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:191917 original size:33 final size:33
Alignment explanation
Indices: 191860--191958 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
191850 ACGAGATAAT
191860 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
191894 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
191927 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
191959 CAAAATAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:191952 original size:19 final size:19
Alignment explanation
Indices: 191835--192018 Score: 163
Period size: 19 Copynumber: 10.1 Consensus size: 19
191825 TCTTTTGGTT
*
191835 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
191854 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
191874 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
191892 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
191908 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
191925 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
191941 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
191960 AAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
191979 AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
191998 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
192017 GA
1 GA
192019 TTTTTGTTTC
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.13
15 2 0.01
16 4 0.03
17 3 0.02
18 3 0.02
19 77 0.57
20 27 0.20
21 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:192036 original size:19 final size:19
Alignment explanation
Indices: 192014--192058 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
192004 AAAATCGCAA
*
192014 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
* *
192033 TGCGTTTTTTATTTCGTGT
1 TGCGATTTTTATTTCGCGT
192052 TGCGATT
1 TGCGATT
192059 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:192634 original size:20 final size:20
Alignment explanation
Indices: 192609--192661 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
192599 GCGCTATGTA
192609 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
192629 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
192649 TATCTCGTTGCGA
1 AATCGCGTTGCGA
192662 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:192695 original size:20 final size:20
Alignment explanation
Indices: 192670--192723 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
192660 GATTTTGTAT
192670 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
192690 TATCGCATTACGATAGTCAG
1 TATCGCATTGCGATAGTAAG
192710 TATCGCATTGCGAT
1 TATCGCATTGCGAT
192724 TTTTCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:192708 original size:61 final size:61
Alignment explanation
Indices: 192610--192726 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
192600 CGCTATGTAA
* * * * * *
192610 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
192671 ATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT
192727 TCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:192742 original size:61 final size:61
Alignment explanation
Indices: 192605--192744 Score: 151
Period size: 61 Copynumber: 2.3 Consensus size: 61
192595 AATGGCGCTA
* * * * * *
192605 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTT
* * * *
192665 TGTATTATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTT
192726 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
192745 TTACTTATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
60 5 0.08
61 58 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTT
Found at i:192834 original size:21 final size:21
Alignment explanation
Indices: 192794--192834 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
192784 ACTGTAGACC
**
192794 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
192815 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
192835 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Done.