Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 56 of 226
Found at i:18474901 original size:137 final size:134
Alignment explanation
Indices: 18474661--18474955 Score: 301
Period size: 137 Copynumber: 2.2 Consensus size: 134
18474651 TAGTTTTTTG
* * * * * * *
18474661 GTTAGATGGTTGCAAATACATCCTTGAGTCTCGGGTTAGATTCTTTTCCTATTCACATTTGTATT
1 GTTAGATAGTTGCAATTACATCCTTAAATCTCGGGTTAGATTCTTCTACTACTCACATTTGTATT
* * * *
18474726 TTTTATTTCATGATGCTTCAAGTTTTTTAAAATTTTAATTAATTTTTTACATATTAG-TTATTTT
66 TTTTATTTCATGATGCTTCAACTTTTTT-AAA-TTTAA-T-ATTTTTAACATATTAGCTCATTTC
18474790 ATTAGATC
127 ATTAGATC
* * *
18474798 GTTAGATAGTTGCAATTACATCCTTAAATCTCGAGG-TCGATTCTTCTATTACTCGCATTTGTAT
1 GTTAGATAGTTGCAATTACATCCTTAAATCTCG-GGTTAGATTCTTCTACTACTCACATTTGTA-
* *
18474862 TTTTTTTATTTCATGTTGCTTCAAACTTTATTT-AA-TTAATATTTTTAACATATTAGCTCCTTT
64 -TTTTTTATTTCATGATGCTTC-AACTTT-TTTAAATTTAATATTTTTAACATATTAGCTCATTT
* *
18474925 CGTTAGATG
126 CATTAGATC
* *
18474934 GTTAGATAATTGCGATTACATC
1 GTTAGATAGTTGCAATTACATC
18474956 GAAGTTCCAT
Statistics
Matches: 132, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
135 15 0.11
136 31 0.23
137 54 0.41
138 2 0.02
139 22 0.17
140 5 0.04
141 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.48
Consensus pattern (134 bp):
GTTAGATAGTTGCAATTACATCCTTAAATCTCGGGTTAGATTCTTCTACTACTCACATTTGTATT
TTTTATTTCATGATGCTTCAACTTTTTTAAATTTAATATTTTTAACATATTAGCTCATTTCATTA
GATC
Found at i:18475451 original size:3 final size:3
Alignment explanation
Indices: 18475443--18475467 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18475433 CTGTTGGGAT
18475443 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
18475468 CATTTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18476051 original size:62 final size:61
Alignment explanation
Indices: 18475916--18476052 Score: 159
Period size: 62 Copynumber: 2.2 Consensus size: 61
18475906 AATTTTATTT
* *
18475916 TTTTATTTAAAACTTGAAATTAGTAAAAACTCAATGTTTGGTTTATCATTGTTTAAAATTA
1 TTTTATTTAAAACTTGAAATTAGTAAAAACTCAATGTTTGCTTTATCATTATTTAAAATTA
* * ** * *
18475977 TCTCACTATTAAATTTTGAAATTAGTAAAAA-TCAGTGTTTGCTTTATCATTATTTTAAATTAA
1 TTTTA-T-TTAAAACTTGAAATTAGTAAAAACTCAATGTTTGCTTTATCATTATTTAAAATT-A
18476040 TTTTATGTTAAAA
1 TTTTAT-TTAAAA
18476053 AATGAATGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
61 3 0.05
62 33 0.54
63 25 0.41
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (61 bp):
TTTTATTTAAAACTTGAAATTAGTAAAAACTCAATGTTTGCTTTATCATTATTTAAAATTA
Found at i:18487031 original size:7 final size:7
Alignment explanation
Indices: 18487019--18487071 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
18487009 TCATATAAAC
18487019 ATTTTAA
1 ATTTTAA
18487026 ATTTTAA
1 ATTTTAA
18487033 A-TTTAA
1 ATTTTAA
*
18487039 AATTTAA
1 ATTTTAA
* *
18487046 A-ATTAT
1 ATTTTAA
18487052 ATTTT--
1 ATTTTAA
18487057 ATTTTAA
1 ATTTTAA
18487064 ATTTTAA
1 ATTTTAA
18487071 A
1 A
18487072 AATTATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 10 0.26
7 24 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTTAA
Found at i:18487057 original size:26 final size:27
Alignment explanation
Indices: 18487026--18487084 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
18487016 AACATTTTAA
18487026 ATTTTAAATTTAAAATTT-AAAATTAT
1 ATTTTAAATTTAAAATTTAAAAATTAT
* *
18487052 ATTTT-ATTTTAAATTTTAAAAATTAT
1 ATTTTAAATTTAAAATTTAAAAATTAT
18487078 -TTTTAAA
1 ATTTTAAA
18487085 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTAAATTTAAAATTTAAAAATTAT
Found at i:18487095 original size:21 final size:22
Alignment explanation
Indices: 18487069--18487109 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18487059 TTTAAATTTT
18487069 AAAAATTAT-TTTTAAAAATAA
1 AAAAATTATGTTTTAAAAATAA
*
18487090 AAAAATTATGTTTTTAAAAT
1 AAAAATTATGTTTTAAAAAT
18487110 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAATTATGTTTTAAAAATAA
Found at i:18506454 original size:6 final size:6
Alignment explanation
Indices: 18506437--18506472 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
18506427 TTGGGCATGT
*
18506437 TACATA TGCATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA
18506473 GGGTCATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:18514098 original size:27 final size:27
Alignment explanation
Indices: 18514068--18514238 Score: 132
Period size: 27 Copynumber: 6.3 Consensus size: 27
18514058 CTATCCCTTA
* * *
18514068 TTTACTGTCTCGGCAGACTACCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
* *
18514095 TTTATTGTCCCGACTGG-CTACCCCGTG
1 TTTATTGTCTCGAC-GGACTACCTCGTG
* * ** * *
18514122 TTTATTGTCCCAACAAACTATCTTGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
*
18514149 TTTACTGT-TCTGACGGACTATCCT-GTG
1 TTTATTGTCTC-GACGGACTA-CCTCGTG
* * *
18514176 TTTATTGTCTCGATGGACAATCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
* * *
18514203 TTTACTGTCTCTATGGACTACCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
18514230 TTTATTGTC
1 TTTATTGTC
18514239 CCAATGGACT
Statistics
Matches: 112, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.03
27 104 0.93
28 5 0.04
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (27 bp):
TTTATTGTCTCGACGGACTACCTCGTG
Found at i:18514185 original size:108 final size:108
Alignment explanation
Indices: 18514039--18514242 Score: 250
Period size: 108 Copynumber: 1.9 Consensus size: 108
18514029 AACTGACCTA
* * * *
18514039 TGTTTACTATCCTGGCGGACTATCCCTTATTTACTGTCTCGGCAGACTACCTCGTGTTTATTGTC
1 TGTTTACTATCCTGACGGACTATCCCTTATTTACTGTCTCGACAGACAACCTCGTGTTTACTGTC
18514104 CCGACTGG-CTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
66 CCGA-TGGACTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
* * * * ** *
18514147 TGTTTACTGTTCTGACGGACTAT-CCTGTGTTTATTGTCTCGATGGACAATCTCGTGTTTACTGT
1 TGTTTACTATCCTGACGGACTATCCCT-TATTTACTGTCTCGACAGACAACCTCGTGTTTACTGT
* * *
18514211 CTCTATGGACTACCTCGTGTTTATTGTCCCAA
65 CCCGATGGACTACCCCGTGTTTATTGTCCCAA
18514243 TGGACTATAC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 6 0.08
108 74 0.93
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (108 bp):
TGTTTACTATCCTGACGGACTATCCCTTATTTACTGTCTCGACAGACAACCTCGTGTTTACTGTC
CCGATGGACTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
Found at i:18514246 original size:54 final size:54
Alignment explanation
Indices: 18514089--18514247 Score: 162
Period size: 54 Copynumber: 2.9 Consensus size: 54
18514079 GGCAGACTAC
* * * * *** *
18514089 CTCGTGTTTATTGTCCCGACTGG-CTACCCCGTGTTTATTGTCCCAACAAACTAT
1 CTCGTGTTTACTGTCTCTA-TGGACTACCTCGTGTTTATTGTCCCAATGGACAAT
* * * *
18514143 CTTGTGTTTACTGT-TCTGACGGACTATCCT-GTGTTTATTGTCTCGATGGACAAT
1 CTCGTGTTTACTGTCTCT-ATGGACTA-CCTCGTGTTTATTGTCCCAATGGACAAT
18514197 CTCGTGTTTACTGTCTCTATGGACTACCTCGTGTTTATTGTCCCAATGGAC
1 CTCGTGTTTACTGTCTCTATGGACTACCTCGTGTTTATTGTCCCAATGGAC
18514248 TATACTGGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
53 6 0.07
54 73 0.87
55 5 0.06
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (54 bp):
CTCGTGTTTACTGTCTCTATGGACTACCTCGTGTTTATTGTCCCAATGGACAAT
Found at i:18516721 original size:8 final size:9
Alignment explanation
Indices: 18516690--18516832 Score: 55
Period size: 8 Copynumber: 15.1 Consensus size: 9
18516680 AAATTAATAG
18516690 TAATTTTTA
1 TAATTTTTA
18516699 T-ATTTAATATA
1 TAATTT--T-TA
18516710 TATATTTTTA
1 TA-ATTTTTA
*
18516720 TAATTCTCTA
1 TAATT-TTTA
18516730 TAATTTTTA
1 TAATTTTTA
18516739 -AATTTTCTA
1 TAATTTT-TA
* * *
18516748 CAATACATTCA
1 TAAT--TTTTA
18516759 T-ATTTTTCA
1 TAATTTTT-A
18516768 TAATATATTTA
1 TAAT-T-TTTA
* *
18516779 TAATACTCTA
1 TAAT-TTTTA
18516789 TAATATTTT-
1 TAAT-TTTTA
*
18516798 TAATTTTTC
1 TAATTTTTA
*
18516807 TAATATTT-
1 TAATTTTTA
18516815 TAATTTTTA
1 TAATTTTTA
18516824 T-ATTTTTA
1 TAATTTTTA
18516832 T
1 T
18516833 TGCTATAATA
Statistics
Matches: 105, Mismatches: 13, Indels: 33
0.70 0.09 0.22
Matches are distributed among these distances:
8 31 0.30
9 23 0.22
10 30 0.29
11 12 0.11
12 5 0.05
13 4 0.04
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (9 bp):
TAATTTTTA
Found at i:18516742 original size:18 final size:20
Alignment explanation
Indices: 18516708--18516747 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
18516698 ATATTTAATA
18516708 TATATATTTTTATAATTCTC
1 TATATATTTTTATAATTCTC
*
18516728 TATA-ATTTTTA-AATTTTC
1 TATATATTTTTATAATTCTC
18516746 TA
1 TA
18516748 CAATACATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATTTTTATAATTCTC
Found at i:18516817 original size:17 final size:18
Alignment explanation
Indices: 18516789--18516822 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18516779 TAATACTCTA
18516789 TAATATTTTTAATTTTTC
1 TAATATTTTTAATTTTTC
18516807 TAATA-TTTTAATTTTT
1 TAATATTTTTAATTTTT
18516823 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATATTTTTAATTTTTC
Found at i:18516904 original size:31 final size:29
Alignment explanation
Indices: 18516867--18516946 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 29
18516857 TCTAAATATT
*
18516867 TTAAAAAATAATTAAATC-TGTATAAAATAA
1 TTAAAAAATAATTAAA-CATCT-TAAAATAA
18516897 TTAAAAAATCAATTAAACAATCTTAAAATAA
1 TTAAAAAAT-AATTAAAC-ATCTTAAAATAA
*
18516928 CTAAAAATAATAATTAAAC
1 -TTAAAA-AATAATTAAAC
18516947 CTTAATATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 10 0.23
31 15 0.35
32 15 0.35
33 3 0.07
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.30
Consensus pattern (29 bp):
TTAAAAAATAATTAAACATCTTAAAATAA
Found at i:18517837 original size:15 final size:15
Alignment explanation
Indices: 18517810--18517856 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
18517800 AATTTAACCA
*
18517810 TATT-TTAACATAAT
1 TATTATTAATATAAT
18517824 TATTATTAATATAAT
1 TATTATTAATATAAT
* *
18517839 TTTTAATAATATGAAT
1 TATTATTAATAT-AAT
18517855 TA
1 TA
18517857 AAAAATCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTATTAATATAAT
Found at i:18527052 original size:12 final size:12
Alignment explanation
Indices: 18527037--18527061 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18527027 AAGTTCTTTG
18527037 CCAAGCTTGCCA
1 CCAAGCTTGCCA
18527049 CCAAGCTTGCCA
1 CCAAGCTTGCCA
18527061 C
1 C
18527062 ATGCAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (12 bp):
CCAAGCTTGCCA
Found at i:18528771 original size:16 final size:18
Alignment explanation
Indices: 18528742--18528778 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
18528732 ATGGAAATAA
*
18528742 TTTTTCTTCTTTCT-ACT
1 TTTTTCCTCTTTCTAACT
18528759 TTTTTCCTC-TTCTAACT
1 TTTTTCCTCTTTCTAACT
18528776 TTT
1 TTT
18528779 CATTTTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCCTCTTTCTAACT
Found at i:18529804 original size:91 final size:91
Alignment explanation
Indices: 18529645--18529827 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
18529635 CATTAGAAAG
* * *
18529645 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGTTGGTACAAAATTAGCATTTTTATTTTC
1 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
18529710 CTTAACTTCCATCTTGACTAGATTAA
66 CTTAACTTCCATCTTGACTAGATTAA
*
18529736 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTATAAAATTAGCATTTTTAGTTCC
1 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
18529801 CTTAACTTCCATCTTGACTAGATTAA
66 CTTAACTTCCATCTTGACTAGATTAA
18529827 T
1 T
18529828 AATCTTCTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (91 bp):
TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
CTTAACTTCCATCTTGACTAGATTAA
Found at i:18532238 original size:23 final size:23
Alignment explanation
Indices: 18532212--18532258 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
18532202 TAAGAGAGGA
* *
18532212 AAATTAATGCAGAAATATCACAC
1 AAATTAATACAAAAATATCACAC
*
18532235 AAATTCATACAAAAATATCACAC
1 AAATTAATACAAAAATATCACAC
18532258 A
1 A
18532259 TGAGATTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATTAATACAAAAATATCACAC
Found at i:18536155 original size:44 final size:45
Alignment explanation
Indices: 18536083--18536526 Score: 272
Period size: 44 Copynumber: 9.8 Consensus size: 45
18536073 ATCTGATGTG
*
18536083 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTATTTTA
** * ** * *
18536127 ATCCGCTCCACTGTAACTTCAGAGAGATAGGAT--TACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTA-TTTTA
* * *
18536171 ATCTACTCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC-CT-G-TT--AT-T--T-TA
*
18536225 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCC---TATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTATTTTA
** * * *
18536267 ATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-CTG---CTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTATTTTA
* * *
18536308 ATCTACTCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC-CT-G-TT--AT-T--T-TA
*
18536362 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTATTTTA
** * ** * *
18536406 ATCCGCTCCACTGTAACTTCAGAGAGATAGGAT--TACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTA-TTTTA
* ** *
18536450 ATCTACTCCGCTGTAA-TTCAGAGAGATAAGATCTCTG--GCTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC-CTGTTATTTTA
* * *
18536493 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATC
18536527 TGAAATTTTT
Statistics
Matches: 310, Mismatches: 56, Indels: 68
0.71 0.13 0.16
Matches are distributed among these distances:
41 32 0.10
42 32 0.10
43 41 0.13
44 122 0.39
45 2 0.01
46 3 0.01
47 2 0.01
48 3 0.01
49 1 0.00
50 2 0.01
51 3 0.01
53 5 0.02
54 62 0.20
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (45 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTGTTATTTTA
Found at i:18536253 original size:54 final size:50
Alignment explanation
Indices: 18536035--18536496 Score: 242
Period size: 44 Copynumber: 9.8 Consensus size: 50
18536025 TTCAGTCTGT
* * *
18536035 TCCACTGCAACATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCT-GCTTCAATCT--T-TGATCTAC
* * **
18536089 TCTACTGTAACTTCAGAGAGATAAGATC-CT--TT--AT-TTTAATCCGC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCTGCTTCAATCTTTGATCTAC
*
18536133 TCCACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTC-A------ATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCT-CT-GCTTCAATCTTTGATCTAC
* *
18536177 TCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCT-GCTTCAATCT--T-TGATCTAC
* * **
18536231 TCTACTGTAACTTCAGAGAGATAAGA--TC--C-T--AT-TTTAATCCGC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCTGCTTCAATCTTTGATCTAC
*
18536273 TCCACTGTAACTTCAGAGAGATAGGA--TCTGCTTC-A------ATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCTGCTTCAATCTTTGATCTAC
* *
18536314 TCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCT-GCTTCAATCT--T-TGATCTAC
* * **
18536368 TCTACTGTAACTTCAGAGAGATAAGATC-CT--TT--AT-TTTAATCCGC
1 TCCACTGTAACTTCAGAGAGATAAGATCTCTGCTTCAATCTTTGATCTAC
*
18536412 TCCACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTC-A------ATCTAC
1 TCCACTGTAACTTCAGAGAGATAAGATCT-CT-GCTTCAATCTTTGATCTAC
*
18536456 TCCGCTGTAA-TTCAGAGAGATAAGATCTCTGGCTTCAATCT
1 TCCACTGTAACTTCAGAGAGATAAGATCTCT-GCTTCAATCT
18536497 GCTCCACTGT
Statistics
Matches: 322, Mismatches: 41, Indels: 97
0.70 0.09 0.21
Matches are distributed among these distances:
41 27 0.08
42 31 0.10
43 26 0.08
44 116 0.36
45 11 0.03
46 3 0.01
47 2 0.01
48 9 0.03
49 3 0.01
50 4 0.01
52 2 0.01
53 4 0.01
54 84 0.26
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (50 bp):
TCCACTGTAACTTCAGAGAGATAAGATCTCTGCTTCAATCTTTGATCTAC
Found at i:18536372 original size:142 final size:141
Alignment explanation
Indices: 18536047--18536497 Score: 840
Period size: 137 Copynumber: 3.2 Consensus size: 141
18536037 CACTGCAACA
*
18536047 TCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
1 TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
18536112 AGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTAC
66 AGATCC-TTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTAC
18536177 TCCGCTGTAATT
130 TCCGCTGTAATT
18536189 TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
1 TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
18536254 AGATCC-TATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGA-T-CT-GCTTCAATCTACT
66 AGATCCTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACT
18536315 CCGCTGTAATT
131 CCGCTGTAATT
18536326 TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
1 TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
18536391 AGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTAC
66 AGATCC-TTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTAC
18536456 TCCGCTGTAA-T
130 TCCGCTGTAATT
18536467 TCAGAGAGATAAGATCTCTGGCTTCAATCTG
1 TCAGAGAGATAAGATCTCTGGCTTCAATCTG
18536498 CTCCACTGTA
Statistics
Matches: 303, Mismatches: 1, Indels: 11
0.96 0.00 0.03
Matches are distributed among these distances:
137 95 0.31
138 2 0.01
139 40 0.13
140 40 0.13
141 34 0.11
142 92 0.30
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (141 bp):
TCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATA
AGATCCTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACT
CCGCTGTAATT
Found at i:18536509 original size:87 final size:88
Alignment explanation
Indices: 18536362--18536521 Score: 216
Period size: 87 Copynumber: 1.8 Consensus size: 88
18536352 ATCTGATGTG
* * * * *
18536362 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCA
18536427 GAGAGATAGGATTACTAGCTTCA
66 GAGAGATAGGATTACTAGCTTCA
* * *
18536450 ATCTACTCCGCTGTAA-TTCAGAGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTC
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCT-TGACTTCAATCCGCTCCACTGTAACCTC
*
18536513 AGGGAGATA
65 AGAGAGATA
18536522 AGATCTGAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 2 0.03
87 46 0.74
88 14 0.23
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (88 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCA
GAGAGATAGGATTACTAGCTTCA
Found at i:18564043 original size:6 final size:6
Alignment explanation
Indices: 18564026--18564061 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
18564016 TTGGGCATGT
*
18564026 TACATA TGCATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA
18564062 GGGTCATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:18571848 original size:27 final size:27
Alignment explanation
Indices: 18571774--18571848 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
18571764 AGGCTATCTC
* *
18571774 GTGTTTACTGTCCTAGTGGACAACCTT
1 GTGTTTACTGTCCCAGTGGACAACCCT
* *
18571801 GTGTTTACTGTCCCAATGGACTACCCT
1 GTGTTTACTGTCCCAGTGGACAACCCT
* *
18571828 GTGTTTATTGTCCCAGCGGAC
1 GTGTTTACTGTCCCAGTGGAC
18571849 CATATTGGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
GTGTTTACTGTCCCAGTGGACAACCCT
Found at i:18581157 original size:29 final size:27
Alignment explanation
Indices: 18581109--18581167 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
18581099 GACAAAATGT
18581109 TATATTTGAAATATTATTTGGAATAAATA
1 TATATTTGAAATATTATTT-GAA-AAATA
*
18581138 TATATTTGAAAT-TTCGTTTGAAAAATA
1 TATATTTGAAATATT-ATTTGAAAAATA
18581165 TAT
1 TAT
18581168 TAGATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (27 bp):
TATATTTGAAATATTATTTGAAAAATA
Found at i:18589236 original size:18 final size:18
Alignment explanation
Indices: 18589198--18589236 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18589188 TGGTAGTGGT
*
18589198 AGCGGGAGTGGAAGCGGG
1 AGCGGGAGTGGAAGCGAG
* *
18589216 AGCGGGAGTGGGAGTGAG
1 AGCGGGAGTGGAAGCGAG
18589234 AGC
1 AGC
18589237 AGTAGTGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.59, T:0.08
Consensus pattern (18 bp):
AGCGGGAGTGGAAGCGAG
Found at i:18593574 original size:6 final size:6
Alignment explanation
Indices: 18593563--18593594 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
18593553 TTTATCAAAC
18593563 GGATTG GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GGATTG GG
18593595 GAAAGATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:18593617 original size:6 final size:6
Alignment explanation
Indices: 18593606--18593638 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18593596 AAAGATAGTA
18593606 TATGTG TATGTG TATGTG TATGTG TATGTG TAT
1 TATGTG TATGTG TATGTG TATGTG TATGTG TAT
18593639 ACAGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (6 bp):
TATGTG
Found at i:18595656 original size:2 final size:2
Alignment explanation
Indices: 18595649--18595675 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18595639 CGTCACCAAA
18595649 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 A
18595676 TACATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18596130 original size:12 final size:12
Alignment explanation
Indices: 18596113--18596140 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18596103 CATTTTGAAT
18596113 ATCACATTTTCA
1 ATCACATTTTCA
18596125 ATCACATTTTCA
1 ATCACATTTTCA
18596137 ATCA
1 ATCA
18596141 ATGGATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (12 bp):
ATCACATTTTCA
Found at i:18600403 original size:22 final size:22
Alignment explanation
Indices: 18600377--18600420 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18600367 TTTTATTCAT
*
18600377 TAAT-ATAAATATTCTAATAAAA
1 TAATAATAAAT-TGCTAATAAAA
*
18600399 TAATAATTAATTGCTAATAAAA
1 TAATAATAAATTGCTAATAAAA
18600421 CAGTTGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATAATAAATTGCTAATAAAA
Found at i:18604705 original size:15 final size:16
Alignment explanation
Indices: 18604678--18604707 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18604668 TCAGCCATAA
18604678 TAATTTAAATATAAAG
1 TAATTTAAATATAAAG
18604694 TAATTT-AATATAAA
1 TAATTTAAATATAAA
18604708 ATTCAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTTAAATATAAAG
Found at i:18607014 original size:31 final size:31
Alignment explanation
Indices: 18606976--18607039 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
18606966 AACAAGAATG
18606976 ATAGTCTGCTGCAAGATATATTCCCATTATT
1 ATAGTCTGCTGCAAGATATATTCCCATTATT
18607007 ATAGTCTGCTGCAAGATATATTCCCATTATT
1 ATAGTCTGCTGCAAGATATATTCCCATTATT
18607038 AT
1 AT
18607040 GATTAAGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (31 bp):
ATAGTCTGCTGCAAGATATATTCCCATTATT
Found at i:18611190 original size:95 final size:97
Alignment explanation
Indices: 18610990--18611190 Score: 246
Period size: 95 Copynumber: 2.1 Consensus size: 97
18610980 TCTTCCTCGG
18610990 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACTACTTATCCATACACATTGCAGCAGTAAC
1 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGAC-AC---TCCATACACATTGCAGCAGTAAC
* * *
18611055 CCAAAACCCGGTACTGAATAACCACTGGAAAAAAGA
62 CCAAAACCAGGTACTGAAGAACCACTGAAAAAAAGA
* * *
18611091 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGAC-C-CCATGCATATTGCAGGAGTAACCCAA
1 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACACTCCATACACATTGCAGCAGTAACCC-A
* * * *
18611154 AAACCAGTTA-TGCAGAACCATTGAAAAAAATA
65 AAACCAGGTACTGAAGAACCACTGAAAAAAAGA
18611186 TGGTT
1 TGGTT
18611191 ACAACTCAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
95 43 0.48
96 9 0.10
99 1 0.01
101 36 0.40
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (97 bp):
TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACACTCCATACACATTGCAGCAGTAACCCAA
AACCAGGTACTGAAGAACCACTGAAAAAAAGA
Found at i:18623717 original size:14 final size:15
Alignment explanation
Indices: 18623684--18623719 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
18623674 TTTTTTAAAG
18623684 AAAAATGAATATTAT
1 AAAAATGAATATTAT
*
18623699 AAAAATGAATGTTAT
1 AAAAATGAATATTAT
18623714 AAAAAT
1 AAAAAT
18623720 ATTAATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTAT
Found at i:18624647 original size:28 final size:28
Alignment explanation
Indices: 18624593--18624647 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
18624583 TACTTTCCAT
*
18624593 CCAAAACTTTTACTCCCTCCTACTCCCC
1 CCAAAACTTTTACTCCCTCCCACTCCCC
18624621 CCAAAACTTTTACTCCCATCCCA-TCCC
1 CCAAAACTTTTACTCCC-TCCCACTCCC
18624648 ACCCCCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.24, C:0.49, G:0.00, T:0.27
Consensus pattern (28 bp):
CCAAAACTTTTACTCCCTCCCACTCCCC
Found at i:18633680 original size:30 final size:29
Alignment explanation
Indices: 18633646--18633713 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
18633636 GTTAAGAAAA
* *
18633646 CAATTTAACTCTTTTTGAAAGATTGATGGT
1 CAATTTAACT-TTTTTAAAAGATTGAAGGT
**
18633676 CAATTCGACTTTTTTAAAAGATTGAAGGT
1 CAATTTAACTTTTTTAAAAGATTGAAGGT
18633705 CAAATTTAA
1 C-AATTTAA
18633714 TTAAGAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (29 bp):
CAATTTAACTTTTTTAAAAGATTGAAGGT
Found at i:18635782 original size:15 final size:16
Alignment explanation
Indices: 18635762--18635795 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18635752 ACGTGTTTCT
*
18635762 TATTTTTCATATA-TA
1 TATTTTTAATATACTA
18635777 TATTTTTAATATACTA
1 TATTTTTAATATACTA
18635793 TAT
1 TAT
18635796 AGGGCACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTAATATACTA
Found at i:18651204 original size:21 final size:22
Alignment explanation
Indices: 18651178--18651222 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18651168 ACTATATTTG
18651178 ATAAATTGAAC-A-TAAAATTAA
1 ATAAATT-AACAATTAAAATTAA
*
18651199 ATAAATTTACAATTAAAATTAA
1 ATAAATTAACAATTAAAATTAA
18651221 AT
1 AT
18651223 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 8 0.38
22 11 0.52
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAATTAACAATTAAAATTAA
Found at i:18651734 original size:11 final size:11
Alignment explanation
Indices: 18651710--18651743 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18651700 CCAAACATCT
18651710 AAAAGAAA-AA
1 AAAAGAAAGAA
18651720 AAAAGAAAGAA
1 AAAAGAAAGAA
18651731 AAAAGAAGAGAA
1 AAAAGAA-AGAA
18651743 A
1 A
18651744 TGTATAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 9 0.41
12 5 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:18660626 original size:7 final size:7
Alignment explanation
Indices: 18660604--18660701 Score: 65
Period size: 7 Copynumber: 13.4 Consensus size: 7
18660594 GGTTTTAAAG
*
18660604 TTAATGT
1 TTAAGGT
18660611 TTCAAGGT
1 TT-AAGGT
18660619 TTAAGGTTT
1 TTAAGG--T
18660628 TTAA-GT
1 TTAAGGT
*
18660634 TTAGGGT
1 TTAAGGT
18660641 TTAAGGTT
1 TTAAGG-T
*
18660649 TTTAGGT
1 TTAAGGT
*
18660656 TTAGGGT
1 TTAAGGT
**
18660663 TTGTGGTTT
1 TTAAGG--T
18660672 TTAA-GT
1 TTAAGGT
*
18660678 TTAGGGT
1 TTAAGGT
18660685 TTAAGGT
1 TTAAGGT
18660692 TTAAGGT
1 TTAAGGT
18660699 TTA
1 TTA
18660702 CAATTTTTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
6 8 0.11
7 41 0.58
8 14 0.20
9 8 0.11
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (7 bp):
TTAAGGT
Found at i:18660638 original size:44 final size:44
Alignment explanation
Indices: 18660590--18660701 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
18660580 AACTTAAGGG
*
18660590 TTAGGGTTTTAAAG-TTAATGTTTCAAGGTTTAAGGTTTTTAAGT
1 TTAGGGTTTTAAAGTTTAAGGTTT-AAGGTTTAAGGTTTTTAAGT
* * * **
18660634 TTAGGG-TTTAAGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAAGT
1 TTAGGGTTTTAAAG-TTTAAGGTTTAAGGTTTAAGGTTTTTAAGT
*
18660678 TTAGGG-TTTAAGGTTTAAGGTTTA
1 TTAGGGTTTTAAAGTTTAAGGTTTA
18660702 CAATTTTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 16 0.27
44 36 0.61
45 7 0.12
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (44 bp):
TTAGGGTTTTAAAGTTTAAGGTTTAAGGTTTAAGGTTTTTAAGT
Found at i:18660641 original size:22 final size:22
Alignment explanation
Indices: 18660616--18660693 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
18660606 AATGTTTCAA
18660616 GGTTTAAGGTTTTTAAGTTTAG
1 GGTTTAAGGTTTTTAAGTTTAG
*
18660638 GGTTTAAGGTTTTTAGGTTTAG
1 GGTTTAAGGTTTTTAAGTTTAG
**
18660660 GGTTTGTGGTTTTTAAGTTTAG
1 GGTTTAAGGTTTTTAAGTTTAG
18660682 GGTTTAAGGTTT
1 GGTTTAAGGTTT
18660694 AAGGTTTACA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (22 bp):
GGTTTAAGGTTTTTAAGTTTAG
Found at i:18660646 original size:29 final size:28
Alignment explanation
Indices: 18660583--18660649 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
18660573 TATATTTAAC
* * *
18660583 TTAAGGGTTAGGGTTTTAAAGTTAATGT
1 TTAAGGTTTAAGGTTTTAAAGTTAAGGT
* *
18660611 TTCAAGGTTTAAGGTTTTTAAGTTTAGGGT
1 TT-AAGGTTTAAGGTTTTAAAG-TTAAGGT
18660641 TTAAGGTTT
1 TTAAGGTTT
18660650 TTAGGTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.06
29 23 0.72
30 7 0.22
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (28 bp):
TTAAGGTTTAAGGTTTTAAAGTTAAGGT
Found at i:18660689 original size:66 final size:66
Alignment explanation
Indices: 18660616--18660899 Score: 252
Period size: 66 Copynumber: 4.4 Consensus size: 66
18660606 AATGTTTCAA
*
18660616 GGTTTAAGGTTTTTAAGTTTAGGGTTTA-AGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAAGTTT
1 GGTTTAAGGTTTTTAAGTTTAGGGTTTACA-GTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTT
18660680 AG
65 AG
* * *
18660682 GGTTTAAGG--TTT-A----A-GGTTTACAATTTTTAGGTTTATGGTTTGTGGTTTTTAAGTTTA
1 GGTTTAAGGTTTTTAAGTTTAGGGTTTACAGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTTA
18660739 G
66 G
* * ** * ** *
18660740 GGTTTAAGATTTTTAGGTTTAGGGTTT-GTGTTTTTTAAGTTAACAGTTTAG-GGTTTTTAGGTT
1 GGTTTAAGGTTTTTAAGTTTAGGGTTTACAG-TTTTTAAGTTTAGGGTTT-GTGGTTTTTAAGTT
18660803 TAG
64 TAG
** * *
18660806 GGTTTGTGGTTTTTAAGTTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTTGTGTTTTTTAA-TTT
1 GGTTTAAGGTTTTTAAGTTTAGGGTTTACAGTTTTTAAGTTTAGGG-TTTGTGGTTTTTAAGTTT
18660870 AAG
65 -AG
* **
18660873 TGTTT-AGGATTTTTATTTTTAGGGTTT
1 GGTTTAAGG-TTTTTAAGTTTAGGGTTT
18660900 TAAGTTAAGG
Statistics
Matches: 175, Mismatches: 27, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
58 48 0.27
59 2 0.01
60 3 0.02
63 1 0.01
64 3 0.02
65 1 0.01
66 83 0.47
67 34 0.19
ACGTcount: A:0.19, C:0.01, G:0.27, T:0.54
Consensus pattern (66 bp):
GGTTTAAGGTTTTTAAGTTTAGGGTTTACAGTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTTA
G
Found at i:18660715 original size:44 final size:45
Alignment explanation
Indices: 18660622--18660715 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
18660612 TCAAGGTTTA
* ***
18660622 AGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
1 AGGTTTTTAAGTTTAGGGTTTAAGGTTTTAAGGTTTACAATTTGT
*
18660667 -GGTTTTTAAGTTTAGGGTTTAAGG-TTTAAGGTTTACAATTTTT
1 AGGTTTTTAAGTTTAGGGTTTAAGGTTTTAAGGTTTACAATTTGT
18660710 AGGTTT
1 AGGTTT
18660716 ATGGTTTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 14 0.33
44 29 0.67
ACGTcount: A:0.20, C:0.01, G:0.28, T:0.51
Consensus pattern (45 bp):
AGGTTTTTAAGTTTAGGGTTTAAGGTTTTAAGGTTTACAATTTGT
Found at i:18660744 original size:44 final size:43
Alignment explanation
Indices: 18660684--18660899 Score: 218
Period size: 44 Copynumber: 4.9 Consensus size: 43
18660674 AAGTTTAGGG
* *
18660684 TTTAAGGTTTAAGGTTTACAATTTTTAGGTTTATGGTTTGTGGTT
1 TTTAA-GTTTAGGGTTTA-AATTTTTAGGTTTAGGGTTTGTGGTT
*
18660729 TTTAAGTTTAGGGTTTAAGATTTTTAGGTTTAGGGTTTGTGTTT
1 TTTAAGTTTAGGGTTTAA-ATTTTTAGGTTTAGGGTTTGTGGTT
* ** **
18660773 TTTAAGTTAACAGTTTAGGGTTTTTAGGTTTAGGGTTTGTGGTT
1 TTTAAGTTTAGGGTTTA-AATTTTTAGGTTTAGGGTTTGTGGTT
* * *
18660817 TTTAAGTTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTTGTGTTT
1 TTTAAGTTTAGGGTTTA-AATTTTTAGGTTTAGGG-TTTGTGGTT
* * **
18660862 TTTAA-TTTAAGTGTTTAGGATTTTTATTTTTAGGGTTT
1 TTTAAGTTT-AGGGTTTA-AATTTTTAGGTTTAGGGTTT
18660900 TAAGTTAAGG
Statistics
Matches: 145, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 106 0.73
45 38 0.26
ACGTcount: A:0.19, C:0.01, G:0.25, T:0.55
Consensus pattern (43 bp):
TTTAAGTTTAGGGTTTAAATTTTTAGGTTTAGGGTTTGTGGTT
Found at i:18660848 original size:88 final size:89
Alignment explanation
Indices: 18660704--18660899 Score: 297
Period size: 88 Copynumber: 2.2 Consensus size: 89
18660694 AAGGTTTACA
* *
18660704 ATTTTTAGGTTTATGGTTTGTGGTTTTTAAGTTTAGGGTTTAAGATTTTTAGGTTTAGGG-TTTG
1 ATTTTTAGGTTTAGGGTTTGTGGTTTTTAAGTTTAGGGTTTAAGATTTTTAAGTTTAGGGTTTTG
18660768 TGTTTTTTAAGTTAACAGTTTAGG
66 TGTTTTTTAAGTTAACAGTTTAGG
*
18660792 GTTTTTAGGTTTAGGGTTTGTGGTTTTTAAGTTTAGGGTTTATAG-TTTTTAAGTTTAGGGTTTT
1 ATTTTTAGGTTTAGGGTTTGTGGTTTTTAAGTTTAGGGTTTA-AGATTTTTAAGTTTAGGGTTTT
* **
18660856 GTGTTTTTTAATTTAAGTGTTTAGG
65 GTGTTTTTTAAGTTAACAGTTTAGG
**
18660881 ATTTTTATTTTTAGGGTTT
1 ATTTTTAGGTTTAGGGTTT
18660900 TAAGTTAAGG
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 54 0.56
89 43 0.44
ACGTcount: A:0.18, C:0.01, G:0.26, T:0.56
Consensus pattern (89 bp):
ATTTTTAGGTTTAGGGTTTGTGGTTTTTAAGTTTAGGGTTTAAGATTTTTAAGTTTAGGGTTTTG
TGTTTTTTAAGTTAACAGTTTAGG
Found at i:18660870 original size:22 final size:22
Alignment explanation
Indices: 18660705--18660870 Score: 174
Period size: 22 Copynumber: 7.5 Consensus size: 22
18660695 AGGTTTACAA
* *
18660705 TTTTTAGGTTTATGGTTTGTGG
1 TTTTTAAGTTTAGGGTTTGTGG
** *
18660727 TTTTTAAGTTTAGGGTTTAAGA
1 TTTTTAAGTTTAGGGTTTGTGG
* *
18660749 TTTTTAGGTTTAGGGTTTGTGT
1 TTTTTAAGTTTAGGGTTTGTGG
* **
18660771 TTTTTAAGTTAACAGTTTAG-GG
1 TTTTTAAGTTTAGGGTTT-GTGG
*
18660793 TTTTTAGGTTTAGGGTTTGTGG
1 TTTTTAAGTTTAGGGTTTGTGG
* *
18660815 TTTTTAAGTTTAGGGTTTATAG
1 TTTTTAAGTTTAGGGTTTGTGG
*
18660837 TTTTTAAGTTTAGGGTTTTGTGT
1 TTTTTAAGTTTAGGG-TTTGTGG
18660860 TTTTTAA-TTTA
1 TTTTTAAGTTTA
18660871 AGTGTTTAGG
Statistics
Matches: 117, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
21 1 0.01
22 104 0.89
23 12 0.10
ACGTcount: A:0.17, C:0.01, G:0.26, T:0.56
Consensus pattern (22 bp):
TTTTTAAGTTTAGGGTTTGTGG
Found at i:18660899 original size:22 final size:22
Alignment explanation
Indices: 18660684--18660899 Score: 145
Period size: 22 Copynumber: 9.7 Consensus size: 22
18660674 AAGTTTAGGG
* **
18660684 TTTAAGGTTTAAGGTTTACAATT
1 TTTAA-GTTTAGGGTTTAGGATT
* * *
18660707 TTTAGGTTTATGGTTT-GTGGTT
1 TTTAAGTTTAGGGTTTAG-GATT
*
18660729 TTTAAGTTTAGGGTTTAAGATT
1 TTTAAGTTTAGGGTTTAGGATT
* *
18660751 TTTAGGTTTAGGGTTT-GTGTTT
1 TTTAAGTTTAGGGTTTAG-GATT
* ** *
18660773 TTTAAGTTAACAGTTTAGGGTT
1 TTTAAGTTTAGGGTTTAGGATT
* *
18660795 TTTAGGTTTAGGGTTT-GTGGTT
1 TTTAAGTTTAGGGTTTAG-GATT
*
18660817 TTTAAGTTTAGGGTTTA-TAGTT
1 TTTAAGTTTAGGGTTTAGGA-TT
* *
18660839 TTTAAGTTTAGGGTTTTGTGTTT
1 TTTAAGTTTAGGGTTTAG-GATT
*
18660862 TTTAA-TTTAAGTGTTTAGGATT
1 TTTAAGTTT-AGGGTTTAGGATT
**
18660884 TTTATTTTTAGGGTTT
1 TTTAAGTTTAGGGTTT
18660900 TAAGTTAAGG
Statistics
Matches: 150, Mismatches: 32, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.01
22 127 0.85
23 22 0.15
ACGTcount: A:0.19, C:0.01, G:0.25, T:0.55
Consensus pattern (22 bp):
TTTAAGTTTAGGGTTTAGGATT
Found at i:18661519 original size:18 final size:18
Alignment explanation
Indices: 18661496--18661533 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18661486 ACTCGAAAAT
* *
18661496 GATACATATAAGGGTTAG
1 GATACATAAAAGGGCTAG
18661514 GATACATAAAAGGGCTAG
1 GATACATAAAAGGGCTAG
18661532 GA
1 GA
18661534 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.21
Consensus pattern (18 bp):
GATACATAAAAGGGCTAG
Found at i:18663303 original size:11 final size:12
Alignment explanation
Indices: 18663287--18663330 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
18663277 ATTAAATATG
18663287 AATTTGAGA-GA
1 AATTTGAGAGGA
18663298 AATTTG-GAAGGA
1 AATTTGAG-AGGA
18663310 AA-TTGAGAGGA
1 AATTTGAGAGGA
18663321 AATTTGAGAG
1 AATTTGAGAG
18663331 AGGATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:18664371 original size:16 final size:18
Alignment explanation
Indices: 18664345--18664379 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18664335 TTTAAATAAA
18664345 TAAAATATTAAA-TTATT
1 TAAAATATTAAATTTATT
18664362 TAAAAT-TTAAATTTATT
1 TAAAATATTAAATTTATT
18664379 T
1 T
18664380 TGTACAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATATTAAATTTATT
Found at i:18669966 original size:17 final size:17
Alignment explanation
Indices: 18669909--18669969 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
18669899 TAACTTTTTG
18669909 AATTAAATTACTAATAT
1 AATTAAATTACTAATAT
* * *
18669926 AATTCTAATAACCTCTAATTT
1 AATT-AAATTA---CTAATAT
18669947 AATTAAATTACTAATAT
1 AATTAAATTACTAATAT
18669964 AATTAA
1 AATTAA
18669970 TGTACAAGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 16 0.47
18 4 0.12
20 4 0.12
21 10 0.29
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAAATTACTAATAT
Found at i:18671239 original size:13 final size:13
Alignment explanation
Indices: 18671218--18671247 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18671208 ATTTTTTAAA
*
18671218 ATATTTATTTTAT
1 ATATGTATTTTAT
18671231 ATATGTATTTTAT
1 ATATGTATTTTAT
18671244 ATAT
1 ATAT
18671248 TATGATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:18671896 original size:110 final size:110
Alignment explanation
Indices: 18671698--18672102 Score: 636
Period size: 110 Copynumber: 3.7 Consensus size: 110
18671688 TCAAAAAAGG
* *
18671698 AAAATATTTCTAAATAATGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAA-ATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
18671763 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
65 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
*
18671809 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
18671874 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
* * *
18671919 AAAAATTTCAAAATAAGGCAATATTTTGCATTTGGAAATTTGAGAAAACATGCTCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
* * * *
18671984 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATA-CC-ACTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
* * * *
18672027 CAAAAATTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCT
1 -AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
18672091 GGGTTTCGATTT
65 GGGTGTCGATTT
18672103 CTCGTTTATC
Statistics
Matches: 274, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
108 30 0.11
109 42 0.15
110 198 0.72
111 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (110 bp):
AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
Found at i:18674976 original size:19 final size:19
Alignment explanation
Indices: 18674924--18674977 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
18674914 ATGATTAAAC
18674924 AATTCAATAATAT--ATAT
1 AATTCAATAATATAAATAT
* * *
18674941 AATACAA-AATGTGAAATTT
1 AATTCAATAATAT-AAATAT
18674960 AATTCAATAATATAAATA
1 AATTCAATAATATAAATA
18674978 GTAGACATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
19 13 0.48
20 4 0.15
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (19 bp):
AATTCAATAATATAAATAT
Found at i:18675152 original size:73 final size:72
Alignment explanation
Indices: 18675014--18675169 Score: 212
Period size: 71 Copynumber: 2.2 Consensus size: 72
18675004 AAGGTTTGCA
*
18675014 GAAAATAAAAGTTTTTGGGGAAAGTAAAAGGAAAAAATTTGGGGGTTTGAGGGGAGTAAT-TTTT
1 GAAAGTAAAAGTTTTTGGGGAAAGTAAAAGGAAAAAATTTGGGGGTTTGAGGGGAGTAATATTTT
18675078 TTTAGGG
66 TTTAGGG
*
18675085 G-AAGTAAAAG-TTTTGGAGGAAAAGTAAAAGGAAAAAAGTTTTGGGGGTTTGGGGGGAAGTAA-
1 GAAAGTAAAAGTTTTTGG-GG-AAAGTAAAAGGAAAAAA--TTTGGGGGTTTGAGGGG-AGTAAT
*
18675147 ATTTTTTTGGGG
61 ATTTTTTTAGGG
18675159 GAAAGTAAAAG
1 GAAAGTAAAAG
18675170 GGTTTGAGGA
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
69 6 0.08
70 10 0.13
71 18 0.24
73 16 0.21
74 16 0.21
75 9 0.12
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (72 bp):
GAAAGTAAAAGTTTTTGGGGAAAGTAAAAGGAAAAAATTTGGGGGTTTGAGGGGAGTAATATTTT
TTTAGGG
Found at i:18678199 original size:2 final size:2
Alignment explanation
Indices: 18678192--18678221 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18678182 CCTTATTCAC
18678192 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
18678222 GAATTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18684755 original size:42 final size:41
Alignment explanation
Indices: 18684687--18684855 Score: 142
Period size: 42 Copynumber: 4.0 Consensus size: 41
18684677 TCTCATGAGC
* * * *
18684687 TTCAGTT-AACTCATATGAGTTTTAGTTAAACCCTTCTGGGT
1 TTCAGTTCAGCTCTTATGAGCTTTAGTT-AACCCTTATGGGT
* * *
18684728 TTCAGTTCACCTCTTTTGAGCTTTAGTTTAACCCTAATGGGT
1 TTCAGTTCAGCTCTTATGAGCTTTAG-TTAACCCTTATGGGT
* * * * *
18684770 TTCAGTTTAGCTCTTCTAAGCTTCAGATTAACCTTTATGGGT
1 TTCAGTTCAGCTCTTATGAGCTTTAG-TTAACCCTTATGGGT
* * ** *
18684812 TTCCGTTCAGCTCCTATGAGCTTCCGTTCAACCCTTACGGGT
1 TTCAGTTCAGCTCTTATGAGCTTTAGTT-AACCCTTATGGGT
18684854 TT
1 TT
18684856 TCGTTTAGCA
Statistics
Matches: 103, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
41 9 0.09
42 92 0.89
43 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (41 bp):
TTCAGTTCAGCTCTTATGAGCTTTAGTTAACCCTTATGGGT
Found at i:18686698 original size:36 final size:38
Alignment explanation
Indices: 18686606--18686741 Score: 132
Period size: 38 Copynumber: 3.6 Consensus size: 38
18686596 ATACACCAGT
* *
18686606 TTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATA
1 TTGGCACCCAGTGCCTCATCGGATAATCCGAAGTAATA
* * * *
18686644 ATGTCACCCAGTGTCTCATCGGCTAA-CCGAAGTAA-A
1 TTGGCACCCAGTGCCTCATCGGATAATCCGAAGTAATA
* * *
18686680 TTGGCACCCAATGCCTCATCGAATATATTCGAAGTAATAAA
1 TTGGCACCCAGTGCCTCATCGGATA-ATCCGAAGTAAT--A
* *
18686721 TTGACACCCAGTGTCTCATCG
1 TTGGCACCCAGTGCCTCATCG
18686742 ACTCGAAGTC
Statistics
Matches: 77, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
36 20 0.26
37 9 0.12
38 29 0.38
41 19 0.25
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (38 bp):
TTGGCACCCAGTGCCTCATCGGATAATCCGAAGTAATA
Found at i:18686749 original size:74 final size:72
Alignment explanation
Indices: 18686606--18686750 Score: 195
Period size: 74 Copynumber: 2.0 Consensus size: 72
18686596 ATACACCAGT
* * *
18686606 TTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATAATGTCACCCAGTGTCTCATCGGCTAAC
1 TTGGCACCCAATGCCTCATCAGATAATTCGAAGTAATAATGACACCCAGTGTCTCATCGACT-A-
18686671 CGAAGTAAA
64 CGAAGTAAA
18686680 TTGGCACCCAATGCCTCATC-GAATATATTCGAAGTAATAAATTGACACCCAGTGTCTCATCGAC
1 TTGGCACCCAATGCCTCATCAG-ATA-ATTCGAAGTAAT-AA-TGACACCCAGTGTCTCATCGAC
18686744 T-CGAAGT
62 TACGAAGT
18686751 CGAAGAAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
73 1 0.02
74 28 0.44
75 12 0.19
76 2 0.03
77 21 0.33
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (72 bp):
TTGGCACCCAATGCCTCATCAGATAATTCGAAGTAATAATGACACCCAGTGTCTCATCGACTACG
AAGTAAA
Found at i:18689819 original size:21 final size:21
Alignment explanation
Indices: 18689795--18689877 Score: 139
Period size: 21 Copynumber: 4.0 Consensus size: 21
18689785 CGAACATGCC
* *
18689795 AACAGAAGCTCGTGAGAGCTG
1 AACAGAAGCTCATGAGAGCTA
18689816 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATGAGAGCTA
18689837 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATGAGAGCTA
*
18689858 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCTCATGAGAGCT
18689878 GATGCACCCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCATGAGAGCTA
Found at i:18697835 original size:21 final size:21
Alignment explanation
Indices: 18697798--18697859 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
18697788 ACAGAAACCC
*
18697798 GTAAGAGCT-AAGCAGAAGCTA
1 GTAAGAGCTGAA-TAGAAGCTA
*
18697819 GTAAGAGCTGAATAGAAGCTT
1 GTAAGAGCTGAATAGAAGCTA
* *
18697840 GTGAGAGTTGAATAGAAGCT
1 GTAAGAGCTGAATAGAAGCT
18697860 TGTGAAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.21
Consensus pattern (21 bp):
GTAAGAGCTGAATAGAAGCTA
Found at i:18697860 original size:21 final size:21
Alignment explanation
Indices: 18697811--18697871 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
18697801 AGAGCTAAGC
* *
18697811 AGAAGCTAGTAAGAGCTGAAT
1 AGAAGCTTGTGAGAGCTGAAT
*
18697832 AGAAGCTTGTGAGAGTTGAAT
1 AGAAGCTTGTGAGAGCTGAAT
*
18697853 AGAAGCTTGTGAAAGCTGA
1 AGAAGCTTGTGAGAGCTGA
18697872 TCCACCCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (21 bp):
AGAAGCTTGTGAGAGCTGAAT
Found at i:18699239 original size:48 final size:48
Alignment explanation
Indices: 18699181--18699273 Score: 170
Period size: 48 Copynumber: 1.9 Consensus size: 48
18699171 CTTAACTATA
18699181 AAAACGTTAAAATTTTCTAACT-AAACTTTAATACTAACTTAATAAATC
1 AAAACGTTAAAATTTTCTAA-TGAAACTTTAATACTAACTTAATAAATC
18699229 AAAACGTTAAAATTTTCTAATGAAACTTTAATACTAACTTAATAA
1 AAAACGTTAAAATTTTCTAATGAAACTTTAATACTAACTTAATAA
18699274 CACTCCGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (48 bp):
AAAACGTTAAAATTTTCTAATGAAACTTTAATACTAACTTAATAAATC
Found at i:18703692 original size:23 final size:24
Alignment explanation
Indices: 18703666--18703715 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
18703656 TGATTTTTAA
18703666 ATTTTA-AATTATTTAGAGATAAT
1 ATTTTAGAATTATTTAGAGATAAT
* *
18703689 A-TTTAGATTTATTTAGTGATAAT
1 ATTTTAGAATTATTTAGAGATAAT
18703712 ATTT
1 ATTT
18703716 AGGAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 17 0.74
24 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTTAGAATTATTTAGAGATAAT
Found at i:18703716 original size:23 final size:23
Alignment explanation
Indices: 18703674--18703717 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
18703664 AAATTTTAAA
18703674 TTATTTAGAGATAATATTTAGAT
1 TTATTTAGAGATAATATTTAGAT
*
18703697 TTATTTAGTGATAATATTTAG
1 TTATTTAGAGATAATATTTAG
18703718 GAAAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (23 bp):
TTATTTAGAGATAATATTTAGAT
Found at i:18706011 original size:43 final size:43
Alignment explanation
Indices: 18705947--18706073 Score: 157
Period size: 43 Copynumber: 2.9 Consensus size: 43
18705937 AGGATTTCCG
*
18705947 ATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGTATCGAT
1 ATATGT-TTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* **
18705992 TTATGTTTACGTGTAAGACC-CTGTCTGGGACAATGGCATCGAT
1 ATATGTTTACGTGTAAGACCAC-GTCTGGGACGTTGGCATCGAT
* * *
18706035 ATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
18706074 TGGACGAGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.01
43 60 0.86
44 4 0.06
45 5 0.07
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
ATATGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:18708266 original size:13 final size:13
Alignment explanation
Indices: 18708248--18708277 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18708238 TTTGAATTAT
18708248 TTAGTGATAATAA
1 TTAGTGATAATAA
*
18708261 TTAGTGATAATAT
1 TTAGTGATAATAA
18708274 TTAG
1 TTAG
18708278 ATTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (13 bp):
TTAGTGATAATAA
Found at i:18709623 original size:45 final size:44
Alignment explanation
Indices: 18709574--18709700 Score: 200
Period size: 45 Copynumber: 2.8 Consensus size: 44
18709564 ATGCTAGAAA
*
18709574 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCAATATTCTAT
1 CGAGTAAGACCATGACTGAAAGACATTATGGCATCAA-ATTCTAT
18709619 CGAGTAAGACCATGACTGAAAGACATTATGGCATCACAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACATTATGGCATCA-AATTCTAT
** *
18709664 CGAGTAAGACCATGGTTGAAAGACACTATGGCATCAA
1 CGAGTAAGACCATGACTGAAAGACATTATGGCATCAA
18709701 GACGAGAATA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
44 1 0.01
45 75 0.97
46 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (44 bp):
CGAGTAAGACCATGACTGAAAGACATTATGGCATCAAATTCTAT
Found at i:18713583 original size:25 final size:25
Alignment explanation
Indices: 18713555--18713619 Score: 58
Period size: 26 Copynumber: 2.6 Consensus size: 25
18713545 CCCGATATAT
*
18713555 GGCTCTTCGGAGCTTCTTGATTAAA
1 GGCTATTCGGAGCTTCTTGATTAAA
* * * *
18713580 GGCTATTTGTGAGTTTCTTGGTTAAT
1 GGCTATTCG-GAGCTTCTTGATTAAA
* *
18713606 GGCTTTTCGTAGCT
1 GGCTATTCGGAGCT
18713620 ACCCGTTATT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.43
Consensus pattern (25 bp):
GGCTATTCGGAGCTTCTTGATTAAA
Found at i:18714776 original size:42 final size:42
Alignment explanation
Indices: 18714703--18714785 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
18714693 CAGCCATGTG
* *
18714703 TAACACACGGCCTACCACACGAGTGTCTGTTTTGGTCGTGTA
1 TAACACACGGCCTACCACACGAGCGTCTGTTTTGGCCGTGTA
* *
18714745 TAACACATGGCCTACCACACGGGCG-CGTGTTTTGGCCGTGT
1 TAACACACGGCCTACCACACGAGCGTC-TGTTTTGGCCGTGT
18714786 GTCCCCTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (42 bp):
TAACACACGGCCTACCACACGAGCGTCTGTTTTGGCCGTGTA
Found at i:18722259 original size:15 final size:15
Alignment explanation
Indices: 18722239--18722268 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18722229 AATCGGCTAA
18722239 AAAGAGTTTACCTAT
1 AAAGAGTTTACCTAT
18722254 AAAGAGTTTACCTAT
1 AAAGAGTTTACCTAT
18722269 TAAGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AAAGAGTTTACCTAT
Found at i:18722560 original size:19 final size:20
Alignment explanation
Indices: 18722520--18722567 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
18722510 ATTACAAAAT
18722520 AATTCAAAATAAATTTCAAA
1 AATTCAAAATAAATTTCAAA
**
18722540 AATTCAAAAT-AATTTTTAA
1 AATTCAAAATAAATTTCAAA
18722559 AATTCAAAA
1 AATTCAAAA
18722568 CATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTCAAAATAAATTTCAAA
Found at i:18722579 original size:19 final size:19
Alignment explanation
Indices: 18722520--18722589 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
18722510 ATTACAAAAT
*
18722520 AATTCAAAATAAATTTCAAA
1 AATTCAAAAT-AATTTTAAA
*
18722540 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
*
18722559 AATTCAAAA-CATTTATAAAAA
1 AATTCAAAATAATTT-T--AAA
18722580 AATTCAAAAT
1 AATTCAAAAT
18722590 TTATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.10
19 17 0.40
20 10 0.24
21 11 0.26
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:18722615 original size:27 final size:25
Alignment explanation
Indices: 18722569--18722618 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
18722559 AATTCAAAAC
*
18722569 ATTTATAAAAAAATTCAAAATTTAT
1 ATTTATAAAAAAATTAAAAATTTAT
*
18722594 ATTTTTAAAAAAATGATAAAAATTT
1 ATTTATAAAAAAAT--TAAAAATTT
18722619 CAAAAACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
27 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTTATAAAAAAATTAAAAATTTAT
Found at i:18726492 original size:16 final size:17
Alignment explanation
Indices: 18726462--18726493 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18726452 TTTAAATAAA
18726462 AAATTTATATATTTTTT
1 AAATTTATATATTTTTT
18726479 AAATTTAT-TATTTTT
1 AAATTTATATATTTTT
18726494 CCAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AAATTTATATATTTTTT
Found at i:18728037 original size:16 final size:15
Alignment explanation
Indices: 18728010--18728039 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
18728000 AAGAAGAGTG
18728010 AGAGAAAAGAGAGAA
1 AGAGAAAAGAGAGAA
18728025 AGAGAAAACGAGAGA
1 AGAGAAAA-GAGAGA
18728040 TATGTGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAGAAAAGAGAGAA
Found at i:18731654 original size:18 final size:18
Alignment explanation
Indices: 18731601--18731654 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
18731591 AACTTCAACA
* *
18731601 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
18731620 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
18731638 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
18731655 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:18733185 original size:9 final size:9
Alignment explanation
Indices: 18733173--18733248 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
18733163 AAATTAATCA
18733173 AATTAACCG
1 AATTAACCG
* *
18733182 AATTACCCA
1 AATTAACCG
18733191 AATTAACCG
1 AATTAACCG
*
18733200 AATTACCCG
1 AATTAACCG
*
18733209 AATTATCCG
1 AATTAACCG
18733218 AATTAACCG
1 AATTAACCG
*
18733227 AATTACCCG
1 AATTAACCG
*
18733236 AATTAACCA
1 AATTAACCG
18733245 AATT
1 AATT
18733249 GAATCACTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:18733185 original size:18 final size:18
Alignment explanation
Indices: 18733164--18733248 Score: 107
Period size: 18 Copynumber: 4.7 Consensus size: 18
18733154 TTTGGTTAAA
*
18733164 AATTAATCAAATTAACCG
1 AATTAACCAAATTAACCG
*
18733182 AATTACCCAAATTAACCG
1 AATTAACCAAATTAACCG
* * *
18733200 AATTACCCGAATTATCCG
1 AATTAACCAAATTAACCG
* *
18733218 AATTAACCGAATTACCCG
1 AATTAACCAAATTAACCG
18733236 AATTAACCAAATT
1 AATTAACCAAATT
18733249 GAATCACTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.26
Consensus pattern (18 bp):
AATTAACCAAATTAACCG
Found at i:18733193 original size:27 final size:27
Alignment explanation
Indices: 18733163--18733248 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
18733153 TTTTGGTTAA
* * *
18733163 AAATTAATCAAATTAACCGAATTACCC
1 AAATTAACCAAATTACCCGAATTAACC
* *
18733190 AAATTAACCGAATTACCCGAATTATCC
1 AAATTAACCAAATTACCCGAATTAACC
* *
18733217 GAATTAACCGAATTACCCGAATTAACC
1 AAATTAACCAAATTACCCGAATTAACC
18733244 AAATT
1 AAATT
18733249 GAATCACTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATTAACCAAATTACCCGAATTAACC
Found at i:18735206 original size:20 final size:20
Alignment explanation
Indices: 18735181--18735218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18735171 AAAAATTCAA
18735181 AAAAATATAAAAAT-ATTTTT
1 AAAAAT-TAAAAATCATTTTT
18735201 AAAAATTAAAAATCATTT
1 AAAAATTAAAAATCATTT
18735219 AAATTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTAAAAATCATTTTT
Found at i:18741778 original size:39 final size:39
Alignment explanation
Indices: 18741735--18741813 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
18741725 TCGAGTTATT
*
18741735 TAAGTTAATCAATTTATTCAGATCAACTCGAATAAAAAA
1 TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
*
18741774 TAAGTTAATCAAGTTATTCGGATCAACTCGAATAAAAAA
1 TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
18741813 T
1 T
18741814 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (39 bp):
TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
Found at i:18742268 original size:16 final size:16
Alignment explanation
Indices: 18742247--18742277 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18742237 AATTCCTTTA
18742247 AAATTAGAAATATTAT
1 AAATTAGAAATATTAT
*
18742263 AAATTAGTAATATTA
1 AAATTAGAAATATTA
18742278 AATTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATTAGAAATATTAT
Found at i:18750158 original size:30 final size:31
Alignment explanation
Indices: 18750122--18750179 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
18750112 AAAAAAAGTT
*
18750122 ACTTAAAT-AAAACTTACGAATAGTTCAGTA
1 ACTTAAATGAAAACTTACGAATAATTCAGTA
*
18750152 ACTTAAATGAAAACTTTCGAATAATTCA
1 ACTTAAATGAAAACTTACGAATAATTCA
18750180 AAGATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
ACTTAAATGAAAACTTACGAATAATTCAGTA
Found at i:18753719 original size:21 final size:21
Alignment explanation
Indices: 18753695--18753739 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18753685 AAAAATTGTC
* * * *
18753695 AATATTTAATTATTTAATTTT
1 AATATTCAAATATATAAATTT
18753716 AATATTCAAATATATAAATTT
1 AATATTCAAATATATAAATTT
18753737 AAT
1 AAT
18753740 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTCAAATATATAAATTT
Found at i:18754097 original size:20 final size:19
Alignment explanation
Indices: 18754064--18754102 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18754054 ATAGATAGGC
*
18754064 AAAAATTTATTTTTTAAAAT
1 AAAAATTTA-GTTTTAAAAT
*
18754084 AAAAATTTGGTTTTAAAAT
1 AAAAATTTAGTTTTAAAAT
18754103 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AAAAATTTAGTTTTAAAAT
Found at i:18755406 original size:16 final size:17
Alignment explanation
Indices: 18755373--18755407 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18755363 ATTTGAATCA
*
18755373 TTTTTAATTGCTATATT
1 TTTTTAATTGCTAAATT
18755390 TTTTTAATT-CTAAATT
1 TTTTTAATTGCTAAATT
18755406 TT
1 TT
18755408 CAGTCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTAATTGCTAAATT
Found at i:18760301 original size:48 final size:48
Alignment explanation
Indices: 18760235--18760368 Score: 187
Period size: 48 Copynumber: 2.8 Consensus size: 48
18760225 CGAGATAATG
* * * *
18760235 GGAATCCAAGTGGCGGCTGGAGTCGAGAACAAAGGGATAGAGATTACA
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
**
18760283 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTATG
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
* * *
18760331 GGAATCCGAGCGGTGGCTGGGGCCAAGAACAAAGGGAT
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGAT
18760369 CGGAACACCC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.32, C:0.15, G:0.40, T:0.13
Consensus pattern (48 bp):
GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
Found at i:18760818 original size:18 final size:20
Alignment explanation
Indices: 18760795--18760837 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18760785 TTGGTACATA
*
18760795 TTTTAC-TAAATTGT-TTTT
1 TTTTACATAAATTGTGTTTC
*
18760813 TTTTACATAATTTGTGTTTC
1 TTTTACATAAATTGTGTTTC
18760833 TTTTA
1 TTTTA
18760838 TTATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTACATAAATTGTGTTTC
Found at i:18762072 original size:27 final size:26
Alignment explanation
Indices: 18762016--18762082 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 26
18762006 ATTATATATT
* *
18762016 AAATATATAT-TTTTTACTTTTAATT
1 AAATATAAATATTTTTACTTTTAATC
* *
18762041 GAATATTAAATATTTTTATTTTTAATC
1 AAATA-TAAATATTTTTACTTTTAATC
*
18762068 AAATATATATATTTT
1 AAATATAAATATTTT
18762083 ATATATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.12
26 13 0.38
27 17 0.50
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
AAATATAAATATTTTTACTTTTAATC
Found at i:18770457 original size:20 final size:20
Alignment explanation
Indices: 18770434--18770474 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18770424 TTAAATCCAT
* *
18770434 TTGATTTAAATCAAATCAAA
1 TTGATTGAAATCAAATAAAA
*
18770454 TTGATTGGAATCAAATAAAA
1 TTGATTGAAATCAAATAAAA
18770474 T
1 T
18770475 CATGATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (20 bp):
TTGATTGAAATCAAATAAAA
Found at i:18772336 original size:33 final size:34
Alignment explanation
Indices: 18772291--18772399 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 34
18772281 AATGCAACAT
* *
18772291 ACATGC-TATAACAGATCA-ATATGGTAGCAA-TA
1 ACATGCTTATAACAGAT-ATATATAGCAGCAATTA
*
18772323 ACATGCTTATAACAAATATATATAGCAGCAATTA
1 ACATGCTTATAACAGATATATATAGCAGCAATTA
* * * *
18772357 TCATGCTTATAACAGAT-TATGATAGTAGTAATAA
1 ACATGCTTATAACAGATATAT-ATAGCAGCAATTA
*
18772391 ACTTGCTTA
1 ACATGCTTA
18772400 ACATGTATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
32 7 0.11
33 22 0.35
34 34 0.54
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (34 bp):
ACATGCTTATAACAGATATATATAGCAGCAATTA
Found at i:18772719 original size:27 final size:27
Alignment explanation
Indices: 18772687--18772837 Score: 119
Period size: 27 Copynumber: 5.4 Consensus size: 27
18772677 AACAGGGGAC
18772687 AAAATTGTAAAATCTAAAAAATAGGGG
1 AAAATTGTAAAATCTAAAAAATAGGGG
* * *
18772714 ATAATTGTAAAATATAAAAAA-ATGGGA
1 AAAATTGTAAAATCTAAAAAATA-GGGG
* * * *
18772741 AAAACTGTAAAATCTGAAGAATAGGTGC
1 AAAATTGTAAAATCTAAAAAATAGG-GG
* *
18772769 AAAACTATAAAA--TAAGAAAAGTAAGGGG
1 AAAATTGTAAAATCTAA-AAAA-T-AGGGG
*
18772797 AAAATTGTAAAATTTGAAAAAAATAGGGG
1 AAAATTGTAAAATCT--AAAAAATAGGGG
18772826 CAAAATTGTAAA
1 -AAAATTGTAAA
18772838 TTTGTAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
26 3 0.03
27 43 0.44
28 25 0.26
29 8 0.08
30 13 0.13
31 4 0.04
32 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (27 bp):
AAAATTGTAAAATCTAAAAAATAGGGG
Found at i:18776454 original size:22 final size:22
Alignment explanation
Indices: 18776426--18776472 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
18776416 ATAAAATAAA
* *
18776426 TTTATTTTAATCAAATTAATAT
1 TTTATTTTAATCAAACTAAAAT
*
18776448 TTTATTTTGATCAAACTAAAAT
1 TTTATTTTAATCAAACTAAAAT
18776470 TTT
1 TTT
18776473 TCATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATTTTAATCAAACTAAAAT
Found at i:18786677 original size:117 final size:117
Alignment explanation
Indices: 18786471--18786705 Score: 416
Period size: 117 Copynumber: 2.0 Consensus size: 117
18786461 ACTCGCCATC
*
18786471 TGGCGAATTGTGTGATTGTGCTTGCAGTTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
1 TGGCGAATTATGTGATTGTGCTTGCAGTTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
*
18786536 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTGAACTTACTTAGTTACCTT
66 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
* * *
18786588 TGGCGAGTTATGTGATTGTGGTTGCAGTTATAAAAGGATCTGCTTGAAGTATTAGTAAATAGTTA
1 TGGCGAATTATGTGATTGTGCTTGCAGTTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
*
18786653 AATGTTTTCATCTGGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
66 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
18786705 T
1 T
18786706 CCTTATCAGG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (117 bp):
TGGCGAATTATGTGATTGTGCTTGCAGTTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
Found at i:18792156 original size:14 final size:14
Alignment explanation
Indices: 18792137--18792173 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
18792127 TTTAAAAATT
18792137 AAAAAATTATTTTA
1 AAAAAATTATTTTA
18792151 AAAAAATTATTTTA
1 AAAAAATTATTTTA
18792165 AAAAAATTA
1 AAAAAATTA
18792174 AAAATCGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAAATTATTTTA
Found at i:18792192 original size:27 final size:27
Alignment explanation
Indices: 18792162--18792215 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
18792152 AAAAATTATT
18792162 TTAAAAAAAT-TAAAAATCGTTAAAATA
1 TTAAAAAAATATAAAAAT-GTTAAAATA
* * *
18792189 TTAAAGAAGTATAAAAATTTTAAAATA
1 TTAAAAAAATATAAAAATGTTAAAATA
18792216 CATATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
TTAAAAAAATATAAAAATGTTAAAATA
Found at i:18793281 original size:4 final size:4
Alignment explanation
Indices: 18793272--18793302 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
18793262 CTTTTTATTA
18793272 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
18793303 ATATATCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:18796246 original size:43 final size:43
Alignment explanation
Indices: 18796198--18796526 Score: 329
Period size: 43 Copynumber: 7.7 Consensus size: 43
18796188 TATTACATAT
* * * *
18796198 CGATGCCACTGTCCCAGACAGGGTCTTATGCGAAATCAAATAA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* *
18796241 CGATGCCAATGTCCCAGACATGGTTTTATACGTAATCACAGT-A
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCA-AATAA
* * * * * * *
18796284 CAATGCTAATGTCCCAGACATGGTCTTACATGTTATCACATAT
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* * * *
18796327 CGATGCCACTGTCCCAGACAGGGTCCTATACGTAATCACAGT-A
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCA-AATAA
* * * * * * *
18796370 CAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATAT
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* * * *
18796413 CGATGCCACTGTCCCAGACAGGGTCTTATACGAAATCATATAA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* *
18796456 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACATTA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* * *
18796499 CAATGTCAATGTCCCAAACATGGTCTTA
1 CGATGCCAATGTCCCAGACATGGTCTTA
18796527 CATGTTATCA
Statistics
Matches: 227, Mismatches: 55, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
42 2 0.01
43 222 0.98
44 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
Found at i:18796357 original size:86 final size:86
Alignment explanation
Indices: 18796200--18796483 Score: 390
Period size: 86 Copynumber: 3.3 Consensus size: 86
18796190 TTACATATCG
* * *** ** * * * *
18796200 ATGCCACTGTCCCAGACAGGGTCTTATGCGAAATCAAATAACGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
*
18796265 TTTATACGTAATCACAGTACA
66 CTTATACGTAATCACAGTACA
*
18796286 ATGCTAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
*
18796351 CCTATACGTAATCACAGTACA
66 CTTATACGTAATCACAGTACA
*
18796372 ATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
* * *
18796437 CTTATACGAAATCATA-TAACG
66 CTTATACGTAATCACAGT-ACA
18796458 ATGCCAATGTCCCAGACATGGTCTTA
1 ATGCCAATGTCCCAGACATGGTCTTA
18796484 TACGTAATCA
Statistics
Matches: 176, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 1 0.01
86 175 0.99
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (86 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
CTTATACGTAATCACAGTACA
Found at i:18796408 original size:129 final size:129
Alignment explanation
Indices: 18796169--18796536 Score: 461
Period size: 129 Copynumber: 2.9 Consensus size: 129
18796159 TGTCATATCA
* * * * *
18796169 CAGATATGTTCTTACATGTTATTACATATCGATGCCACTGTCCCAGACAGGGTCTTATGCGAAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
* * * * * * *
18796234 CA-AATAACGATGCCAATGTCCCAGACATGGTTTTATACGTAATCACAGTA-CAATGCTAATGTC
66 CACAAT-ACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACA-TATCAATGCCAATGTC
18796297 C
129 C
*
18796298 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCCTATACGTAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
* * *
18796363 CACAGTACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCGATGCCACTGTCC
66 CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCAATGCCAATGTCC
* * * ** * * * *
18796427 CAGACAGGGTCTTATACGAAATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
* *
18796492 CACATTACAATGTCAATGTCCCAAACATGGTCTTACATGTTATCA
66 CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCA
18796537 AATCTTGATA
Statistics
Matches: 209, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
128 2 0.01
129 205 0.98
130 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (129 bp):
CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCAATGCCAATGTCC
Found at i:18796512 original size:86 final size:86
Alignment explanation
Indices: 18796200--18796526 Score: 388
Period size: 86 Copynumber: 3.8 Consensus size: 86
18796190 TTACATATCG
* * ** * * * *
18796200 ATGCCACTGTCCCAGACAGGGTCTTATGCGAAATCAAATAACGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGGT
*
18796265 TTTATACGTAATCACAGTACA
66 CTTATACGTAATCACAGTACA
* * * *
18796286 ATGCTAATGTCCCAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGGT
*
18796351 CCTATACGTAATCACAGTACA
66 CTTATACGTAATCACAGTACA
* * * *
18796372 ATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGGT
* * *
18796437 CTTATACGAAATCATA-TAACG
66 CTTATACGTAATCACAGT-ACA
* * * * *
18796458 ATGCCAATGTCCCAGACATGGTCTTATACGTAATCACAT-TACAATGTCAATGTCCCAAACATGG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT-CGATGCCAATGTCCCAGACAGGG
18796522 TCTTA
65 TCTTA
18796527 CATGTTATCA
Statistics
Matches: 210, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
85 2 0.01
86 208 0.99
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (86 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGGT
CTTATACGTAATCACAGTACA
Found at i:18810079 original size:20 final size:21
Alignment explanation
Indices: 18810035--18810079 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
18810025 TTAAAATACT
* * *
18810035 TTTAAAATATTTTTTTTTATT
1 TTTAAAATATATTTTTTAATG
18810056 TTTAAAATA-ATTTTTTAATG
1 TTTAAAATATATTTTTTAATG
18810076 TTTA
1 TTTA
18810080 TTAAAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAAAATATATTTTTTAATG
Found at i:18828923 original size:36 final size:36
Alignment explanation
Indices: 18828883--18828952 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
18828873 ATCATTTAAT
* *
18828883 CCAAACTTAATCTCCTAACTTCTAACAAGTAATCTG
1 CCAAACTCAATCTCCTAACTTCTAACAAGAAATCTG
* *
18828919 CCAAACTCAATCTCCTATCTTCTCACAAGAAATC
1 CCAAACTCAATCTCCTAACTTCTAACAAGAAATC
18828953 GACTAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (36 bp):
CCAAACTCAATCTCCTAACTTCTAACAAGAAATCTG
Found at i:18831414 original size:20 final size:21
Alignment explanation
Indices: 18831371--18831414 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18831361 TTACTTGGAA
*
18831371 TTTTTTTTATTTTAACATGGT
1 TTTTTTTTATTTTAACATGAT
* *
18831392 TTTTTTTTCTTTTTA-ATGAT
1 TTTTTTTTATTTTAACATGAT
18831412 TTT
1 TTT
18831415 GACTGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTTTTTTATTTTAACATGAT
Found at i:18832698 original size:27 final size:27
Alignment explanation
Indices: 18832668--18832734 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
18832658 AGGGAAGCAG
18832668 GTTGGCGGCACCAAACAAGGGAACCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
** *
18832695 GTTGGCGGCACCAAACAAGGGTTCCTT
1 GTTGGCGGCACCAAACAAGGGAACCCT
18832722 GTTGGCGGCACCA
1 GTTGGCGGCACCA
18832735 CCCTTGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGAACCCT
Found at i:18832834 original size:10 final size:10
Alignment explanation
Indices: 18832819--18832902 Score: 68
Period size: 10 Copynumber: 8.8 Consensus size: 10
18832809 AAAATAATGA
18832819 AAAGGAAAGG
1 AAAGGAAAGG
*
18832829 ATAGGAAA-G
1 AAAGGAAAGG
* *
18832838 AAAGAAAAAG
1 AAAGGAAAGG
18832848 -AAGGAAAGG
1 AAAGGAAAGG
18832857 AAAGGAAAGG
1 AAAGGAAAGG
**
18832867 GGAGGAAA-G
1 AAAGGAAAGG
* *
18832876 AAAGAAAAAG
1 AAAGGAAAGG
*
18832886 -AAGGAAAGA
1 AAAGGAAAGG
18832895 AAAGGAAA
1 AAAGGAAA
18832903 AGAGAAGAGA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 26 0.46
10 31 0.54
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (10 bp):
AAAGGAAAGG
Found at i:18832837 original size:38 final size:35
Alignment explanation
Indices: 18832798--18832960 Score: 120
Period size: 38 Copynumber: 4.5 Consensus size: 35
18832788 GAAGAAAGAA
* *
18832798 AGGAAGAAAGAAAAATAATGAAAAGGAAAGGATAGG
1 AGGAAGAAAGAAAAAGAA-GAAAAGGAAAGGAAAGG
*
18832834 A--AAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGGGG
1 AGGAAGAAAGAAAAAGAAGAAAAGGAAAGGAAA--GG
* * *
18832869 AGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAAG
1 AGG-AAGAAAGAAAAAGAAGAAAAGGAAAGGAAAGG
* * *
18832905 AGAAGAGAAAAAAAAAAGAAAGAAGAA-GAAGAGGGAAGG
1 AGGA-AG-AAAGAAAAAG-AAGAA-AAGGAA-AGGAAAGG
18832944 AAGGAA-AAA-AAAAAGAA
1 -AGGAAGAAAGAAAAAGAA
18832961 AATAAGGTAA
Statistics
Matches: 104, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
33 13 0.12
34 14 0.13
35 6 0.06
36 12 0.12
37 12 0.12
38 35 0.34
39 9 0.09
40 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (35 bp):
AGGAAGAAAGAAAAAGAAGAAAAGGAAAGGAAAGG
Found at i:18832921 original size:18 final size:18
Alignment explanation
Indices: 18832874--18832927 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
18832864 AGGGGAGGAA
18832874 AGAAAGAAAAAGAAG-GAA-
1 AGAAA-AAAAA-AAGAGAAG
**
18832892 AGAAAAGGAAAAGAGAAG
1 AGAAAAAAAAAAGAGAAG
18832910 AGAAAAAAAAAAGA-AAG
1 AGAAAAAAAAAAGAGAAG
18832927 A
1 A
18832928 AGAAGAAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.10
17 10 0.33
18 17 0.57
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAAGAGAAG
Found at i:18832931 original size:18 final size:18
Alignment explanation
Indices: 18832880--18832931 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
18832870 GGAAAGAAAG
* *
18832880 AAAAAGAAGGAAAGAAAAG
1 AAAAAGAAAG-AAGAAAAA
*
18832899 GAAAAGAGAAG-AGAAAAA
1 AAAAAGA-AAGAAGAAAAA
18832917 AAAAAGAAAGAAGAA
1 AAAAAGAAAGAAGAA
18832932 GAAGAGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.11
18 16 0.59
19 6 0.22
20 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAGAAAAA
Found at i:18832931 original size:36 final size:37
Alignment explanation
Indices: 18832880--18832961 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 37
18832870 GGAAAGAAAG
*
18832880 AAAAAGAAGGAAAGAA-AAG-GAAAAGAGAAGAGAAAAA
1 AAAAAGAAAGAAAGAAGAAGAGAAAAG-GAAG-GAAAAA
**
18832917 AAAAAGAAAG-AAGAAGAAGAGGGAAGGAAGGAAAAA
1 AAAAAGAAAGAAAGAAGAAGAGAAAAGGAAGGAAAAA
18832953 AAAAAGAAA
1 AAAAAGAAA
18832962 ATAAGGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 20 0.50
37 16 0.40
38 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAGAAAGAAGAAGAGAAAAGGAAGGAAAAA
Found at i:18833666 original size:8 final size:8
Alignment explanation
Indices: 18833653--18833677 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18833643 AATATTTTGG
18833653 TAATATTT
1 TAATATTT
18833661 TAATATTT
1 TAATATTT
18833669 TAATATTT
1 TAATATTT
18833677 T
1 T
18833678 TGTAATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATATTT
Found at i:18833779 original size:27 final size:28
Alignment explanation
Indices: 18833729--18833797 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
18833719 AATAAAAAAA
18833729 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
18833757 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
18833784 TTACCAAAATATAT
1 TTACCAAAATATAT
18833798 CAAAAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.57
28 12 0.30
29 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:18836094 original size:15 final size:14
Alignment explanation
Indices: 18836054--18836082 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18836044 TTTTTGTATC
18836054 AATTTAATTATTCT
1 AATTTAATTATTCT
18836068 AATTTAATTATTCT
1 AATTTAATTATTCT
18836082 A
1 A
18836083 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:18836343 original size:14 final size:14
Alignment explanation
Indices: 18836326--18836360 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
18836316 CTTTCATCCC
18836326 CTTTCCTTTTCTTT
1 CTTTCCTTTTCTTT
*
18836340 CTTTCTTTTTCTTT
1 CTTTCCTTTTCTTT
18836354 CTTTCCT
1 CTTTCCT
18836361 CTCTTTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
CTTTCCTTTTCTTT
Found at i:18836355 original size:38 final size:38
Alignment explanation
Indices: 18836294--18836396 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 38
18836284 ATAAATTTTT
* *
18836294 TTTTCTCTTCTTCCTTTCT-TTTCTTTCATCCCCTTTCC
1 TTTTCT-TTCTTTCTTTTTCTTTCTTTCATCCCCTTTCC
* * *
18836332 TTTTCTTTCTTTCTTTTTCTTTCTTTCCTCTCTTTTCC
1 TTTTCTTTCTTTCTTTTTCTTTCTTTCATCCCCTTTCC
* *
18836370 TTTTCCTTCTTT-TTCTTTCTTCCTTTC
1 TTTTCTTTCTTTCTT-TTTCTTTCTTTC
18836397 TTTCTTCTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 12 0.21
38 44 0.79
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTTCTTTCTTTCTTTTTCTTTCTTTCATCCCCTTTCC
Done.