Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1853746 original size:39 final size:37
Alignment explanation
Indices: 1853703--1853825 Score: 117
Period size: 39 Copynumber: 3.1 Consensus size: 37
1853693 AATAATAATA
*
1853703 ATAATAAATAAATATAAAAAGTATTTTTTAAAAAACTAT
1 ATAAT-AATAAATTTAAAAAGT-TTTTTTAAAAAACTAT
1853742 ATAAT-ATAAATTTTTAAAAATGTTTCTTTT-AAAAACTAT
1 ATAATAATAAA--TTTAAAAA-GTTT-TTTTAAAAAACTAT
*
1853781 ATATTATATAAAATTTCAAAAA-TGTTTTTTAAAAAACTAT
1 ATAATA-AT-AAATTT-AAAAAGT-TTTTTTAAAAAACTAT
1853821 ATAAT
1 ATAAT
1853826 TTTCAAAAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
37 5 0.07
39 32 0.45
40 24 0.34
41 7 0.10
42 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATAATAAATTTAAAAAGTTTTTTTAAAAAACTAT
Found at i:1853784 original size:41 final size:40
Alignment explanation
Indices: 1853726--1853823 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 40
1853716 ATAAAAAGTA
* *
1853726 TTTTTTAAAAAAC--TATATAATATAAATTTTTAAAAATG
1 TTTTTTAAAAAACTATATATAATATAAAATTTCAAAAATG
* *
1853764 TTTCTTTTAAAAACTATATATTATATAAAATTTCAAAAATG
1 TTT-TTTAAAAAACTATATATAATATAAAATTTCAAAAATG
1853805 TTTTTTAAAAAACTATATA
1 TTTTTTAAAAAACTATATA
1853824 ATTTTCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 3 0.06
39 9 0.17
40 15 0.29
41 25 0.48
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (40 bp):
TTTTTTAAAAAACTATATATAATATAAAATTTCAAAAATG
Found at i:1853835 original size:41 final size:40
Alignment explanation
Indices: 1853726--1853835 Score: 136
Period size: 41 Copynumber: 2.8 Consensus size: 40
1853716 ATAAAAAGTA
* *
1853726 TTTTTTAAAAAACTATATAA-TAT-AAATTTTTAAAAATG
1 TTTTTTAAAAAACTATATAATTATAAAAATTTCAAAAATG
*
1853764 TTTCTTTTAAAAACTATAT-ATTATATAAAATTTCAAAAATG
1 TTT-TTTAAAAAACTATATAATTATA-AAAATTTCAAAAATG
*
1853805 TTTTTTAAAAAACTATATAATTTTCAAAAAT
1 TTTTTTAAAAAACTATATAATTAT-AAAAAT
1853836 GTTTTTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 4 0.07
39 17 0.28
40 14 0.23
41 25 0.41
42 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (40 bp):
TTTTTTAAAAAACTATATAATTATAAAAATTTCAAAAATG
Found at i:1853841 original size:31 final size:31
Alignment explanation
Indices: 1853785--1853875 Score: 141
Period size: 30 Copynumber: 2.9 Consensus size: 31
1853775 AACTATATAT
*
1853785 TATATAAAATTTCAAAAATGTTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATG-TTTTTAAAAAAC
1853818 TATATAATTTTCAAAAATGTTTTT-AAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAAC
1853848 TATATAATTTTCAAAAATG-TTTTAAAAA
1 TATATAATTTTCAAAAATGTTTTTAAAAA
1853876 TGACCAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
29 4 0.07
30 29 0.52
31 5 0.09
32 13 0.23
33 5 0.09
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAAC
Found at i:1853961 original size:37 final size:38
Alignment explanation
Indices: 1853880--1854038 Score: 196
Period size: 38 Copynumber: 4.2 Consensus size: 38
1853870 TAAAAATGAC
* *
1853880 CAAAAATGTTTTCAAAAACTATATATTATGTAAGTTTT
1 CAAAAATGTTTTTAAAAACTATATATTATATAAGTTTT
* *
1853918 CAAAAATGCTTTAAAAAACTATATATTATATAAGTTTT
1 CAAAAATGTTTTTAAAAACTATATATTATATAAGTTTT
* *
1853956 C-AAAATGATTTTAAAAACTATATGTTATATATA-TTTT
1 CAAAAATGTTTTTAAAAACTATATATTATATA-AGTTTT
* * *
1853993 CTAAAATATTTTTAAAAACTATATATTATATACGTATTTT
1 CAAAAATGTTTTTAAAAACTATATATTATATAAG--TTTT
1854033 CAAAAA
1 CAAAAA
1854039 CCGTTTGCAA
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
37 32 0.30
38 64 0.61
40 9 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (38 bp):
CAAAAATGTTTTTAAAAACTATATATTATATAAGTTTT
Found at i:1853973 original size:75 final size:75
Alignment explanation
Indices: 1853882--1854024 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
1853872 AAAATGACCA
* *
1853882 AAAATGTTTTCAAAAACTATATATTATGTA-AGTTTTCAAAAATGCTTTAAAAAACTATATATTA
1 AAAATGTTTTCAAAAACTATATATTATATATA-TTTTCAAAAATACTTTAAAAAACTATATATTA
1853946 TATAAGTTTTC
65 TATAAGTTTTC
* * * *
1853957 AAAATGATTTT-AAAAACTATATGTTATATATATTTTCTAAAATATTTTTAAAAACTATATATTA
1 AAAATG-TTTTCAAAAACTATATATTATATATATTTTCAAAAATACTTTAAAAAACTATATATTA
1854021 TATA
65 TATA
1854025 CGTATTTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
75 55 0.92
76 5 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (75 bp):
AAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAAATACTTTAAAAAACTATATATTAT
ATAAGTTTTC
Found at i:1861190 original size:29 final size:28
Alignment explanation
Indices: 1861158--1861219 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
1861148 AAAATGTCCG
*
1861158 GAAACATTATTAGACATTAAAAAATAACC
1 GAAACATTATTAGACACT-AAAAATAACC
*
1861187 GAAAACATTATTAGACGCTAAAAATAACC
1 G-AAACATTATTAGACACTAAAAATAACC
1861216 GAAA
1 GAAA
1861220 ATATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 3 0.10
29 12 0.40
30 15 0.50
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.21
Consensus pattern (28 bp):
GAAACATTATTAGACACTAAAAATAACC
Found at i:1861220 original size:29 final size:30
Alignment explanation
Indices: 1861159--1861220 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
1861149 AAATGTCCGG
*
1861159 AAACATTATTAGACATTAAAAAATAACCGA
1 AAACATTATTAGACACTAAAAAATAACCGA
*
1861189 AAACATTATTAGACGCT-AAAAATAACCGA
1 AAACATTATTAGACACTAAAAAATAACCGA
1861218 AAA
1 AAA
1861221 TATAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (30 bp):
AAACATTATTAGACACTAAAAAATAACCGA
Found at i:1863460 original size:2 final size:2
Alignment explanation
Indices: 1863453--1863485 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1863443 AGCGAAAATG
1863453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1863486 CAACACTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1871367 original size:3 final size:3
Alignment explanation
Indices: 1871359--1871390 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1871349 TATCCTAGAA
1871359 ATT ATT ATT ATT ATT ATT ATT ATT ATT GATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT A
1871391 ATCTAAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1872822 original size:45 final size:42
Alignment explanation
Indices: 1872774--1872858 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
1872764 AAAATAAAAT
* * *
1872774 TATTATAAATTATATTAATTATTTATTAAAATAAGAATAATA
1 TATTATTAACTATATTAATTACTTATTAAAATAAGAATAATA
* * *
1872816 TATTATTAACTATATTCATTACTTGTTAAAATAATAATAATA
1 TATTATTAACTATATTAATTACTTATTAAAATAAGAATAATA
1872858 T
1 T
1872859 TAAGCTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (42 bp):
TATTATTAACTATATTAATTACTTATTAAAATAAGAATAATA
Found at i:1872882 original size:15 final size:16
Alignment explanation
Indices: 1872841--1872888 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
1872831 TCATTACTTG
*
1872841 TTAAAATAATAATAATA
1 TTAAAATATTAA-AATA
**
1872858 TTAAGCTATTAAAA-A
1 TTAAAATATTAAAATA
1872873 TTAAAATATTAAAATA
1 TTAAAATATTAAAATA
1872889 AAATTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 13 0.52
16 3 0.12
17 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TTAAAATATTAAAATA
Found at i:1872883 original size:8 final size:8
Alignment explanation
Indices: 1872841--1872888 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
1872831 TCATTACTTG
1872841 TTAAAATA
1 TTAAAATA
*
1872849 ATAATAATA
1 TTAA-AATA
**
1872858 TTAAGCTA
1 TTAAAATA
1872866 TTAAAA-A
1 TTAAAATA
1872873 TTAAAATA
1 TTAAAATA
1872881 TTAAAATA
1 TTAAAATA
1872889 AAATTATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.22
8 18 0.56
9 7 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (8 bp):
TTAAAATA
Found at i:1873011 original size:17 final size:17
Alignment explanation
Indices: 1872989--1873021 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1872979 TTATTAATAA
*
1872989 TTTATTAAAATGATATT
1 TTTATTAAAATAATATT
1873006 TTTATTAAAATAATAT
1 TTTATTAAAATAATAT
1873022 ATTAACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTATTAAAATAATATT
Found at i:1873904 original size:31 final size:32
Alignment explanation
Indices: 1873869--1873932 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1873859 TAAATACCAA
* *
1873869 CAAGTAC-ATTACCTTCCAATCCACGTAAGTT
1 CAAGTACTATTACCTTCAAATCCACATAAGTT
*
1873900 CAAGTACTTTTACCTTCAAATCCACATAAGTT
1 CAAGTACTATTACCTTCAAATCCACATAAGTT
1873932 C
1 C
1873933 GATGGTCGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (32 bp):
CAAGTACTATTACCTTCAAATCCACATAAGTT
Found at i:1875051 original size:40 final size:40
Alignment explanation
Indices: 1874996--1875076 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1874986 ACATTCCCCA
1874996 AAACTAGAATAAACACATCAGTCTGTCAAAAACTATTTGT
1 AAACTAGAATAAACACATCAGTCTGTCAAAAACTATTTGT
1875036 AAACTAGAATAAACACATCAGTCTGTCAAAAACTATTTGT
1 AAACTAGAATAAACACATCAGTCTGTCAAAAACTATTTGT
1875076 A
1 A
1875077 CCGTGAGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (40 bp):
AAACTAGAATAAACACATCAGTCTGTCAAAAACTATTTGT
Found at i:1881646 original size:200 final size:200
Alignment explanation
Indices: 1881147--1881653 Score: 526
Period size: 202 Copynumber: 2.5 Consensus size: 200
1881137 ATTTCAAACC
* *
1881147 ATTTTGAACGTGATTTTT-ACACCGCTTATAATGTCTCGTATGTGTCAATATTAGCCTTAATTGA
1 ATTTTGAACGTGATTTTTAAC-CCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTTAATTGA
* * * ** * * * *
1881211 AACATAAGTATCAATACTACATCTCTAATCTTATAAATGATGAAAAGTTTCCAACTAACTTCCCA
65 AAGATAA-AATCAATACTACATCTCTAATCTTATAAATTACAAAAAATTTCAAACTAACTACACA
* * *
1881276 AAAATACTCCCTGAAGATGCCTATAAAGCCATGTTGACTTCTTCTTCATGTAGAAAACTAACCTT
129 AAAATACTCCCTAAAGATGCCTATAAAGCCATGTTAACTTCTTCTTCATGTACAAAACTAACCTT
1881341 TGGAACT
194 TGGAACT
* * * * * * *
1881348 ATTTTGAATGCGATTTTTACCCCCTCTTACAATGTCTTGTATGTGACGATTTTA-CCTTGAATTG
1 ATTTTGAACGTGATTTTTA-ACCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTT-AATTG
* * ** *
1881412 AAAGATACATTACAATACTATGTCTCTAATCTTATAAATTACAAAAAATTTCAAATTAACTACAC
64 AAAGATAAAAT-CAATACTACATCTCTAATCTTATAAATTACAAAAAATTTCAAACTAACTACAC
* *
1881477 -AAAATAACT-CCTCAAATATGCCTATCAAA-CCATTTTAACATT-TTCTTCATGCT-CAAAAC-
128 AAAAAT-ACTCCCT-AAAGATGCCTAT-AAAGCCATGTTAAC-TTCTTCTTCATG-TACAAAACT
* *
1881536 AAGCTTTTGAACT
188 AACCTTTGGAACT
* * * * *
1881549 ATTTTCAACGTGATTTTTAACCCGCTTACAATATCTCATATGTGTCGATATTAGTCTTAACTGAA
1 ATTTTGAACGTGATTTTTAACCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTTAATTGAA
* *
1881614 AGATAAAACTCAATACTACACCTATAATCTTATAAATTAC
66 AGATAAAA-TCAATACTACATCTCTAATCTTATAAATTAC
1881654 GAAATTTTTA
Statistics
Matches: 247, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
200 65 0.26
201 60 0.24
202 115 0.47
203 7 0.03
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (200 bp):
ATTTTGAACGTGATTTTTAACCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTTAATTGAA
AGATAAAATCAATACTACATCTCTAATCTTATAAATTACAAAAAATTTCAAACTAACTACACAAA
AATACTCCCTAAAGATGCCTATAAAGCCATGTTAACTTCTTCTTCATGTACAAAACTAACCTTTG
GAACT
Found at i:1882442 original size:21 final size:22
Alignment explanation
Indices: 1882388--1882451 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
1882378 CGTGTGAACT
1882388 TTTAAAAA-ATTATATTAAAAA
1 TTTAAAAATATTATATTAAAAA
*
1882409 TTTAATAGTATATTA-A-TAAAAA
1 TTTAA-A-AATATTATATTAAAAA
* *
1882431 GTTTAAAAATATAAAATTAAA
1 -TTTAAAAATATTATATTAAA
1882452 TTATTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
21 10 0.29
22 9 0.26
23 11 0.32
24 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTAAAAATATTATATTAAAAA
Found at i:1899488 original size:45 final size:46
Alignment explanation
Indices: 1899439--1899529 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
1899429 GAACATCGAA
* * *
1899439 TGCATTTTATGCATGGATGCAC-ATA-TCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACT-ATGCATCGATGCACTCAG
1899484 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1899530 GGTTTTTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 20 0.49
46 20 0.49
47 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
Found at i:1902839 original size:20 final size:22
Alignment explanation
Indices: 1902791--1902848 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1902781 GCATGGGTAG
1902791 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
1902815 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
1902835 TGCATCGATGCACT
1 TGCATCGATGCACT
1902849 CAAGGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1906186 original size:31 final size:31
Alignment explanation
Indices: 1906151--1906209 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1906141 AACTTAAAAG
* *
1906151 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
1906182 AGTTTTACAATATTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
1906210 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:1907564 original size:30 final size:29
Alignment explanation
Indices: 1907530--1907697 Score: 177
Period size: 30 Copynumber: 5.8 Consensus size: 29
1907520 ACTTTAATAC
1907530 AAACCATATAATATTTCTAACATAGACCA
1 AAACCATATAATATTTCTAACATAGACCA
* *
1907559 TAAACCATATAATGTTT-TAAACATCGA-C-
1 -AAACCATATAATATTTCT-AACATAGACCA
* * *
1907587 AAACCATATAATATTTTTAATATAAACCA
1 AAACCATATAATATTTCTAACATAGACCA
* *
1907616 CAAACCATATAATGTTT-TGAACATCGA-C-
1 -AAACCATATAATATTTCT-AACATAGACCA
1907644 AAACCATATAATATTTCTAACATAGACCA
1 AAACCATATAATATTTCTAACATAGACCA
*
1907673 CAAACCATATAATATTTCTTACATA
1 -AAACCATATAATATTTCTAACATA
1907698 ATCAAAAAGA
Statistics
Matches: 115, Mismatches: 13, Indels: 20
0.78 0.09 0.14
Matches are distributed among these distances:
27 42 0.37
28 4 0.03
29 4 0.03
30 65 0.57
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (29 bp):
AAACCATATAATATTTCTAACATAGACCA
Found at i:1907591 original size:57 final size:57
Alignment explanation
Indices: 1907528--1907685 Score: 271
Period size: 57 Copynumber: 2.8 Consensus size: 57
1907518 TAACTTTAAT
*
1907528 ACAAACCATATAATATTTCTAACATAGACCATAAACCATATAATGTTTTAAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTAAACATCG
* * * *
1907585 ACAAACCATATAATATTTTTAATATAAACCACAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTAAACATCG
1907642 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAAT
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAAT
1907686 ATTTCTTACA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 93 1.00
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (57 bp):
ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTTTAAACATCG
Found at i:1908809 original size:22 final size:22
Alignment explanation
Indices: 1908763--1908844 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
1908753 GCATACACAT
*
1908763 CAAATACATAACAT-CAAACAA
1 CAAATTCATAACATACAAACAA
*
1908784 CAAATTCATAACATACAAACAG
1 CAAATTCATAACATACAAACAA
*
1908806 CAAATTCATAACATACAAATAA
1 CAAATTCATAACATACAAACAA
1908828 CAAATTCATAACATACA
1 CAAATTCATAACATACA
1908845 TACATATACA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
21 13 0.23
22 43 0.77
ACGTcount: A:0.57, C:0.22, G:0.01, T:0.20
Consensus pattern (22 bp):
CAAATTCATAACATACAAACAA
Found at i:1908855 original size:32 final size:32
Alignment explanation
Indices: 1908818--1908884 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1908808 AATTCATAAC
* *
1908818 ATACAAATAACAAATTC-ATAACATACATACAT
1 ATACAAACAACAAATACAAT-ACATACATACAT
*
1908850 ATACAAACAACAAATACAATATATACATACAT
1 ATACAAACAACAAATACAATACATACATACAT
1908882 ATA
1 ATA
1908885 TATATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (32 bp):
ATACAAACAACAAATACAATACATACATACAT
Found at i:1908891 original size:18 final size:19
Alignment explanation
Indices: 1908868--1908908 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1908858 AACAAATACA
*
1908868 ATATATACAT-ACATATAT
1 ATATATAAATAACATATAT
1908886 ATATATAAATCAACATATAT
1 ATATATAAAT-AACATATAT
1908906 ATA
1 ATA
1908909 ATAGCCTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATAAATAACATATAT
Found at i:1915578 original size:4 final size:4
Alignment explanation
Indices: 1915569--1915623 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
1915559 TATACATTGA
* * * *
1915569 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGA ATGA ATGT CTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1915617 ATGT ATG
1 ATGT ATG
1915624 AGTGAGTGAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:1915623 original size:20 final size:21
Alignment explanation
Indices: 1915566--1915624 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1915556 AAATATACAT
1915566 TGAATGTATGTATGTAT-ATA
1 TGAATGTATGTATGTATGATA
*
1915586 TGTATGTATGTATGTATGA-A
1 TGAATGTATGTATGTATGATA
*
1915606 TGAATGTCTGTATGTATGA
1 TGAATGTATGTATGTATGA
1915625 GTGAGTGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.44
Consensus pattern (21 bp):
TGAATGTATGTATGTATGATA
Found at i:1915629 original size:4 final size:4
Alignment explanation
Indices: 1915622--1915647 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1915612 TCTGTATGTA
1915622 TGAG TGAG TGAG TGAG TGAG TGAG TG
1 TGAG TGAG TGAG TGAG TGAG TGAG TG
1915648 TGTGTGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (4 bp):
TGAG
Found at i:1915652 original size:2 final size:2
Alignment explanation
Indices: 1915645--1915796 Score: 279
Period size: 2 Copynumber: 76.5 Consensus size: 2
1915635 GAGTGAGTGA
1915645 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
1915687 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT GT TT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1915729 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1915770 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1915797 AACGAACGAA
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
1 1 0.01
2 144 0.99
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
GT
Found at i:1915815 original size:12 final size:12
Alignment explanation
Indices: 1915800--1915824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1915790 GTGTGTGAAC
1915800 GAACGAACGAAT
1 GAACGAACGAAT
1915812 GAACGAACGAAT
1 GAACGAACGAAT
1915824 G
1 G
1915825 CATGCATATT
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:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (12 bp):
GAACGAACGAAT
Found at i:1916619 original size:61 final size:59
Alignment explanation
Indices: 1916542--1916733 Score: 188
Period size: 60 Copynumber: 3.2 Consensus size: 59
1916532 GTATATACGT
* * * * * *
1916542 ATAGTTT-ATGATGAAATTGGAATGTTGAAAATATTTGGAGACCAATTTAGAATTAAAGTC
1 ATAGTTTGAGGATGAAATTGGAATATTCAAAA-ATTT-GAGACCAATTTAAAATGATAGTC
* ** * * * *
1916602 ATAGTTTGAGTATGAAATTATAATATTCAAAAGTTTAAGTACTAATTTAAAATGATATTC
1 ATAGTTTGAGGATGAAATTGGAATATTCAAAAATTTGAG-ACCAATTTAAAATGATAGTC
* * *
1916662 ATAGTTTAAGGATAAAATTGGAATATTTAAAAATTTAGAGACCAATTTAAAATGATAGTC
1 ATAGTTTGAGGATGAAATTGGAATATTCAAAAATTT-GAGACCAATTTAAAATGATAGTC
*
1916722 ATACTTTGAGGA
1 ATAGTTTGAGGA
1916734 CATGTGTTAC
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
59 2 0.02
60 82 0.79
61 20 0.19
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (59 bp):
ATAGTTTGAGGATGAAATTGGAATATTCAAAAATTTGAGACCAATTTAAAATGATAGTC
Found at i:1926827 original size:64 final size:66
Alignment explanation
Indices: 1926651--1926830 Score: 160
Period size: 64 Copynumber: 2.8 Consensus size: 66
1926641 AATTAAATTG
* * *
1926651 AACATCGAATGCATTTCATGCATCGATGCA--CTTACCATGCACCGATGTA--CTGAGGATTTTA
1 AACATCGAATGCATTTGATGCATCGATGCACCCTT---ATGCACCGATGCACTCTGACGATTTTA
1926712 TGAA
63 TGAA
* * * ** *
1926716 AACATCGAATTCATTTGATGCATCGATGCACCAGC-CATTCATAGATGCACTCTGACTA-TTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACC--CTTATGCACCGATGCACTCTGACGATTTTAT
1926778 G-A
64 GAA
*
1926780 AACATCGAATGCAATTGATGCATCGATGCACCCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACCCTTA-TGCACCGATGCACT
1926831 AAGGGTCTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 42 0.46
65 39 0.42
66 3 0.03
67 5 0.05
69 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCCTTATGCACCGATGCACTCTGACGATTTTATGA
A
Found at i:1927090 original size:11 final size:11
Alignment explanation
Indices: 1927051--1927086 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1927041 ACAAGCAACT
1927051 AGAATCAAGAG
1 AGAATCAAGAG
1927062 AGAATCAAGAG
1 AGAATCAAGAG
1927073 AGAATCAA-AG
1 AGAATCAAGAG
1927083 AGAA
1 AGAA
1927087 ATCATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.58, C:0.08, G:0.25, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:1928188 original size:19 final size:20
Alignment explanation
Indices: 1928164--1928211 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1928154 AACGATTTTC
*
1928164 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1928183 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1928203 TTTTGAAAA
1 TTTTGAAAA
1928212 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1940837 original size:75 final size:75
Alignment explanation
Indices: 1940711--1940861 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
1940701 ACTCTTCCCA
* *
1940711 CTCACCTAGCTTCAGTCGAGCTCGAGATGGTGCGGCAAACTTCTAAGTACTAATCACCCACACAG
1 CTCACCTAGCTTCAGTCGAGCTCGAGATGGTGCAGCAAACTTCTAACTACTAATCACCCACACAG
*
1940776 GCCATTTGGC
66 GCCAATTGGC
* * *
1940786 CTCACCTAGCTTCTGTGGAGCTCGAGATGGTGCAGCAAACTTCTAACTACTAATCGCCCACACAG
1 CTCACCTAGCTTCAGTCGAGCTCGAGATGGTGCAGCAAACTTCTAACTACTAATCACCCACACAG
1940851 GCCAATTGGC
66 GCCAATTGGC
1940861 C
1 C
1940862 AAAACAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (75 bp):
CTCACCTAGCTTCAGTCGAGCTCGAGATGGTGCAGCAAACTTCTAACTACTAATCACCCACACAG
GCCAATTGGC
Found at i:1946041 original size:6 final size:6
Alignment explanation
Indices: 1946031--1946168 Score: 125
Period size: 6 Copynumber: 22.5 Consensus size: 6
1946021 TCCTTAACTT
* * * * *
1946031 CCTTTC TCTTTC TCTTTC TCTTTC CCTTTC TCTTTC CCTTTC TCTTTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
* * ** *
1946079 CCTCTC CCTTTG TTTTTC CCTTTC TCTTTC CCTTTC CCTTTC CCTTTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
* *
1946127 CCTTTC ACGCTTTTC CCTTT- CCTTCTC CCTTGC TCTTTC CCT
1 CCTTTC -C-C-TTTC CCTTTC CCTT-TC CCTTTC CCTTTC CCT
1946169 CTCCTTCTCT
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
5 4 0.04
6 91 0.85
7 6 0.06
8 2 0.02
9 4 0.04
ACGTcount: A:0.01, C:0.43, G:0.02, T:0.54
Consensus pattern (6 bp):
CCTTTC
Found at i:1946318 original size:75 final size:75
Alignment explanation
Indices: 1946224--1946435 Score: 311
Period size: 75 Copynumber: 2.9 Consensus size: 75
1946214 TTCACGGTGT
* *
1946224 TTTTCTTTCTCCCTCTCCTTCTCTCTATCAGAATCACTGCTCTTCTCTCTCTCAGAACGACGCCG
1 TTTTCTTTCTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCTCTCTCAGAACGACGCCG
1946289 ATCTCGATGC
66 ATCTCGATGC
* * *
1946299 TTTTCTTTTTCCCGCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
1 TTTTCTTTCTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCTCTCTCAGAACGACGCCG
*
1946364 TTCTCGATGC
66 ATCTCGATGC
* * * * *
1946374 TTTTCCTTGTCCCTTTCCTTTTCTCTATCGGAATCACCGCTC--CTCTCTCTCGGAACGACGCC
1 TTTTCTTTCTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCTCTCTCAGAACGACGCC
1946436 ATTCCTTATC
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
73 18 0.15
75 106 0.85
ACGTcount: A:0.13, C:0.37, G:0.12, T:0.38
Consensus pattern (75 bp):
TTTTCTTTCTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCTCTCTCAGAACGACGCCG
ATCTCGATGC
Found at i:1949415 original size:84 final size:84
Alignment explanation
Indices: 1949318--1949486 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
1949308 GCCTCCTACC
*
1949318 TTGACATATATATGTAAATATAGAATAATCACCAAAACAATTACACTAAGGGCTTTATAAATGTA
1 TTGACATATATATGTAAATATAGAATAATCACCAAAACAATTACACTAAAGGCTTTATAAATGTA
1949383 ATGAAGGAATTAAAATGCA
66 ATGAAGGAATTAAAATGCA
1949402 TTGACATATATATGTAAATATAGAATAATCACCAAAACAATTACACTAAAGGCTTTATAAATGTA
1 TTGACATATATATGTAAATATAGAATAATCACCAAAACAATTACACTAAAGGCTTTATAAATGTA
1949467 ATGAAGGAATTAAAATGCA
66 ATGAAGGAATTAAAATGCA
1949486 T
1 T
1949487 ACCTGCAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (84 bp):
TTGACATATATATGTAAATATAGAATAATCACCAAAACAATTACACTAAAGGCTTTATAAATGTA
ATGAAGGAATTAAAATGCA
Found at i:1952873 original size:3 final size:3
Alignment explanation
Indices: 1952867--1952930 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
1952857 TTTCCATTTG
* * * *
1952867 ATT ATT ATT -TT TTT ATT ATT AAT A-A ATT AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1952913 ATT AATT -TT ATT A-T ATT A
1 ATT -ATT ATT ATT ATT ATT A
1952931 AAGGCCCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 7 0.14
3 40 0.80
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1952929 original size:26 final size:25
Alignment explanation
Indices: 1952867--1952930 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
1952857 TTTCCATTTG
* *
1952867 ATTATTATTTTTTTATTATTAATAA
1 ATTATTATATTATTATTATTAATAA
* *
1952892 ATTAATATTATTATTATTATTATTAA
1 ATTATTA-TATTATTATTATTAATAA
*
1952918 TTTTATTATATTA
1 -ATTATTATATTA
1952931 AAGGCCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 6 0.19
26 20 0.65
27 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTATTATATTATTATTATTAATAA
Found at i:1953666 original size:13 final size:13
Alignment explanation
Indices: 1953648--1953672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1953638 GCCACTGTAT
1953648 GTGGTGGTCGGCG
1 GTGGTGGTCGGCG
1953661 GTGGTGGTCGGC
1 GTGGTGGTCGGC
1953673 AACGGAGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.60, T:0.24
Consensus pattern (13 bp):
GTGGTGGTCGGCG
Found at i:1958547 original size:15 final size:15
Alignment explanation
Indices: 1958527--1958558 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1958517 GATCAATACC
1958527 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1958542 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1958557 TT
1 TT
1958559 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1965880 original size:18 final size:18
Alignment explanation
Indices: 1965826--1965870 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1965816 ATTATGCTTG
* *
1965826 AAGAAGAAA-AAAAGAAA
1 AAGAAAAAATAAAATAAA
1965843 AAGAAAAAATAAAATAAA
1 AAGAAAAAATAAAATAAA
1965861 AAGAAAAAAT
1 AAGAAAAAAT
1965871 GATGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (18 bp):
AAGAAAAAATAAAATAAA
Found at i:1967634 original size:113 final size:112
Alignment explanation
Indices: 1967431--1968354 Score: 807
Period size: 123 Copynumber: 7.9 Consensus size: 112
1967421 CAAAGATTCA
* * *
1967431 AATTCATCATTTGATGGATCAACTGTTTCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAATA
1 AATTCATCATTAGATGGATCAACT-TTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
1967496 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* * *
1967544 AATTCATCATTCGATGAATCAACTGTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTAGATGGATCAACT-TTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1967609 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* * * *
1967657 AATTCATTATTTGATGGATCAACATTTCCGGAAG-AGTTCATAATGAGAATAACTCATCTGAAG-
1 AATTCATCATTAGATGGATCAAC-TTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* ** *
1967720 A--AAGAAGAAGTTCATAATGAGAATAACTTGTTTAAATTTTTGCTCG
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* ** * * * * *
1967766 AATTCATTACTT-GATGGATCGGCATTGCCAGGTAG-GGTTCATAATGAGAACAACTTATCTGAA
1 AATTCATCA-TTAGATGGATCAAC-TTTCCA-GAAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
1967829 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGATTT
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT-TAACCTTTTGCTTG
* * *
1967880 AATTCATCACTCGATGGATCAACTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCATTAGATGGATCAAC-TTTCCAGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1967945 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATG
64 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* * * *
1967994 -ACTCTATCACATAAAGAGATAGATCTGCATCAACTTTTCCAG-AGAAAGTTTATAATGAGAATA
1 AATTC-AT--CAT-------TAGA--TGGATCAAC-TTTCCAGAAG-AAGTTCATAATGAGAAGA
** * *
1968057 ACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATG
52 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* * **
1968117 -ACTCTATCACAGAAAGAGATAGATCAACATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGA
1 AATTC-AT--C------A-TTAGAT--GGATCAAC-TTTCCAGAAG-AAGTTCATAATGAGAAGA
* * *
1968180 ACTCATCTGAAGAAGG-AGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATG
52 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
* * * * *
1968240 -ACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAAAAG-TGTTCATAATGAGAAGAA
1 AATTC-AT--C------A-TTAGAT--GGATCAAC-TTTCCAGAAGAAGTTCATAATGAGAAGAA
1968303 CTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTT
53 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTT
1968355 ACCTTAATTC
Statistics
Matches: 706, Mismatches: 72, Indels: 57
0.85 0.09 0.07
Matches are distributed among these distances:
109 64 0.09
110 31 0.04
111 2 0.00
112 28 0.04
113 168 0.24
114 44 0.06
115 58 0.08
116 2 0.00
121 1 0.00
122 67 0.09
123 190 0.27
124 34 0.05
125 16 0.02
129 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AATTCATCATTAGATGGATCAACTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
Found at i:1967828 original size:222 final size:222
Alignment explanation
Indices: 1967431--1967990 Score: 696
Period size: 222 Copynumber: 2.5 Consensus size: 222
1967421 CAAAGATTCA
* *
1967431 AATTCATCATTTGATGGATCAACTGTTTCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAATA
1 AATTCATCATTTGATGGATCAACT-TTCCGGAAG-AGTTCATAATGAGAAGAACTCATCTG---A
* * * *
1967496 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCATTCGATGA
61 AGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTTGCTCGAATTCATCATTCGATGA
* * *
1967561 ATCAACTGTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
126 ATCAACTGTGCCAGAAGGAGTTCATAATGAGAACAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* *
1967626 AATGAGAAGAACTTGTT-TAACCTTTTGCTTG
191 AATGAGAAGAACTTGTTCAAACCTTTTGATTG
* *
1967657 AATTCATTATTTGATGGATCAACATTTCCGGAAGAGTTCATAATGAGAATAACTCATCTGAAGAA
1 AATTCATCATTTGATGGATCAAC-TTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
* * * *
1967722 AGAAGAAGTTCATAATGAGAATAACTTGTTTAAATTTTTGCTCGAATTCATTACTT-GATGGATC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTTGCTCGAATTCATCA-TTCGATGAATC
** * *
1967786 GGCAT-TGCCAGGTAGG-GTTCATAATGAGAACAACTTATCTGAAGAAGGAAGAAGAAATTCATA
129 AAC-TGTGCCA-GAAGGAGTTCATAATGAGAACAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* *
1967849 ATGAGAAGAATTTGTTCAAACCTTTTGATTT
192 ATGAGAAGAACTTGTTCAAACCTTTTGATTG
* * *
1967880 AATTCATCACTCGATGGATCAACTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCAAC-TTTCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1967945 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
63 -A--AAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTTGC
1967991 ATGACTCTAT
Statistics
Matches: 290, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
222 122 0.42
223 43 0.15
224 1 0.00
225 56 0.19
226 30 0.10
227 1 0.00
228 37 0.13
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (222 bp):
AATTCATCATTTGATGGATCAACTTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAA
GAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTTGCTCGAATTCATCATTCGATGAATCAA
CTGTGCCAGAAGGAGTTCATAATGAGAACAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAACTTGTTCAAACCTTTTGATTG
Found at i:1968693 original size:3 final size:3
Alignment explanation
Indices: 1968687--1968768 Score: 109
Period size: 3 Copynumber: 28.3 Consensus size: 3
1968677 TTTCCATTTG
* *
1968687 ATT ATT ATT -TT ATT ATT ATT AAT A-A ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1968733 ATT ATT ATT ATT ATT ATT ATT AATT -TT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT A
1968769 AAGGCCCAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
2 7 0.10
3 61 0.86
4 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1969521 original size:13 final size:13
Alignment explanation
Indices: 1969503--1969527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1969493 GCCACCGTAT
1969503 GTGGTGGTCGGCA
1 GTGGTGGTCGGCA
1969516 GTGGTGGTCGGC
1 GTGGTGGTCGGC
1969528 GCCGGAGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.56, T:0.24
Consensus pattern (13 bp):
GTGGTGGTCGGCA
Found at i:1970514 original size:145 final size:141
Alignment explanation
Indices: 1970315--1970575 Score: 348
Period size: 145 Copynumber: 1.8 Consensus size: 141
1970305 TTTTAAATAT
* * ** *
1970315 ATATTTATTTTTCAATATTAAGAAAGTGCAGTCTTAAAGCAACTAGATGTCCATTTTCTTATATT
1 ATATTTATTTTTCAATATTAAGAAAGAGAAGTCTTAAAGCAACTAGATAACCATTTTCTGATATT
* *
1970380 TTTAAATAAATAAATATCTTATTT-TTTAATAATTATATATATTAATCTATTTTTTAATTATTTT
66 TATAAATAAATAAATATCTTATTTATAT-AT-A-TATATATATTAA--TATTTTTTAATTATTTT
1970444 TTAGATAAATGTTTTA
126 TTAGATAAATGTTTTA
** *
1970460 ATATTTATTTTTTTATATTAAGAAA-AGAATTGTCTTAAAGCACCTAGA-AACCATTTTCTGATA
1 ATATTTATTTTTCAATATTAAGAAAGAGAA--GTCTTAAAGCAACTAGATAACCATTTTCTGATA
1970523 TTTATAAATAAATAAATATCTTATTTATATATATATATATATTAATATTTTTT
64 TTTATAAATAAATAAATATCTTATTTATATATATATATATATTAATATTTTTT
1970576 CTTAAAATTA
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
141 8 0.08
143 12 0.12
144 3 0.03
145 62 0.60
146 18 0.17
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (141 bp):
ATATTTATTTTTCAATATTAAGAAAGAGAAGTCTTAAAGCAACTAGATAACCATTTTCTGATATT
TATAAATAAATAAATATCTTATTTATATATATATATATATTAATATTTTTTAATTATTTTTTAGA
TAAATGTTTTA
Found at i:1974277 original size:17 final size:17
Alignment explanation
Indices: 1974257--1974289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1974247 CTCACTAACC
*
1974257 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
1974274 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
1974290 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:1974934 original size:19 final size:19
Alignment explanation
Indices: 1974899--1974944 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1974889 TATTTAGACA
1974899 TTTTGCA-TTTCTTATTTT
1 TTTTGCATTTTCTTATTTT
*
1974917 TTTTGCATTTTGTTATTTT
1 TTTTGCATTTTCTTATTTT
*
1974936 CTTTGCATT
1 TTTTGCATT
1974945 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (19 bp):
TTTTGCATTTTCTTATTTT
Found at i:1978779 original size:165 final size:164
Alignment explanation
Indices: 1978342--1978908 Score: 929
Period size: 164 Copynumber: 3.5 Consensus size: 164
1978332 TTAAGACAAT
* * * * *
1978342 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAATACCTTCGAGTTCGACTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* * * *
1978407 TCAGCTCTATGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCC
66 TCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
*
1978472 CGAGTTCGATTACACTCAGCTTCAAGGGCATATC
131 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
*
1978506 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* *
1978571 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCCAAAGACCCC
66 TCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
1978636 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
131 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * * *
1978670 ATTTACAGCATAACTTAAGTCTAGAAGGGTTGTGT-TCCAACCAAAGACCTTCGAGTTCGACTAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTCGACTAC
*
1978734 GCTCAACTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
64 GCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1978799 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
129 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* *
1978835 ATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACGC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1978900 TCAACTCCA
66 TCAACTCCA
1978909 GACAACGCAA
Statistics
Matches: 375, Mismatches: 25, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
163 1 0.00
164 219 0.58
165 154 0.41
166 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
TCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
Found at i:1979219 original size:106 final size:106
Alignment explanation
Indices: 1978903--1980142 Score: 1762
Period size: 106 Copynumber: 12.0 Consensus size: 106
1978893 ACTACGCTCA
* * * *
1978903 ACTCCAGACAACGCAAGTTCAACCTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1978968 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1979009 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATAAACAATTTCC
1979074 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
1979116 ACTCCAGACAACACAAGTTCAACTTCACGGCGAAGAGACCACTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1979181 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1979222 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1979287 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1979328 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAATAAAC-ATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATAAACAATTTCC
* *
1979392 CAATTTCAGAGCCAATTTCGACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1979434 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAAT--A-AA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1979491 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1979528 ACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAA--T---
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1979588 --TTT-----CCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1979622 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA--T---
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1979682 --TTT-----CCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1979716 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAATCAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1979781 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1979822 TCTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1979887 AATCTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1979928 ACTCGAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1979993 AATTTCAGAACCAATTTCAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1980034 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCAC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * ** *
1980099 AGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1980140 ACT
1 ACT
1980143 TGGAACAATA
Statistics
Matches: 1049, Mismatches: 66, Indels: 38
0.91 0.06 0.03
Matches are distributed among these distances:
94 260 0.25
95 3 0.00
96 2 0.00
97 2 0.00
98 7 0.01
101 3 0.00
103 2 0.00
105 3 0.00
106 662 0.63
107 105 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1979563 original size:43 final size:43
Alignment explanation
Indices: 1979412--1979751 Score: 137
Period size: 43 Copynumber: 7.3 Consensus size: 43
1979402 GCCAATTTCG
* *
1979412 ACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCA
1 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
* *** * * * *
1979455 ACTTCACGACGAAGGGACCGCTGG-CTGTCAATAAACAATTTCCCAATTTCA
1 ACTTCACAACGAA-GGA-TATTGGAC--TC--CAGACAA---CGCAAGTTCA
1979506 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
1 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
** *** ** * * *
1979549 ACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAATTTTC-CAATTTCA
1 ACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA----CGCAAGTTCA
1979600 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
1 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
* *** ** * * *
1979643 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTC-CAATTTCA
1 ACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA----CGCAAGTTCA
*
1979694 ACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCA
1 ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
*
1979737 ACTTCACGACGAAGG
1 ACTTCACAACGAAGG
1979752 GACCGCTGGT
Statistics
Matches: 210, Mismatches: 57, Indels: 60
0.64 0.17 0.18
Matches are distributed among these distances:
42 2 0.01
43 70 0.33
44 10 0.05
45 9 0.04
46 21 0.10
48 21 0.10
49 8 0.04
50 10 0.05
51 57 0.27
52 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
Found at i:1979564 original size:94 final size:95
Alignment explanation
Indices: 1979403--1980098 Score: 921
Period size: 94 Copynumber: 7.0 Consensus size: 95
1979393 AATTTCAGAG
* * *
1979403 CCAATTTCGACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1979468 GGGACCGCTGGCTGTCAATAAACAATTTC-
66 GGGACCGCTGGTTGTCAATAAACAATTTCA
*
1979497 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1979562 GGGACCGCTGGTTGTCAATAAACAATTT-T
66 GGGACCGCTGGTTGTCAATAAACAATTTCA
1979591 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1979656 GGGACCGCTGGTTGTCAATAAACAATTT-T
66 GGGACCGCTGGTTGTCAATAAACAATTTCA
*
1979685 CCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1979750 GGGACCGCTGGTTGTCAATAATCAATTTCCCAATTTCTGA
66 GGGACCGCTGGTTGTCAAT-A--AA-----CAATTTC--A
*
1979790 GCCAATTTCAACTTCACAACGAAGGATATTGGTCTCCAGACAACGCAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1979855 AGGGACCGCTGGTTGTCAATAAACAATTTCTCAATCTCAGA
65 AGGGACCGCTGGTTGTCAATAAACAA----T---T-TC--A
* * * *
1979896 GCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGGCAACGCAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
1979961 AGGGACCGTTGGTTGTCAATAAACAATTTCTCAATTTCAGAA
65 AGGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC---A
* *
1980003 CCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1980068 GGGACCGCTGGTTGTCAACAAACAATTTCA
66 GGGACCGCTGGTTGTCAATAAACAATTTCA
1980098 C
1 C
1980099 AGTTCCAGAG
Statistics
Matches: 545, Mismatches: 27, Indels: 59
0.86 0.04 0.09
Matches are distributed among these distances:
94 264 0.48
95 3 0.01
97 2 0.00
98 10 0.02
102 7 0.01
103 4 0.01
104 1 0.00
105 2 0.00
106 243 0.45
107 2 0.00
108 1 0.00
109 2 0.00
110 1 0.00
114 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (95 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCA
Found at i:1980042 original size:600 final size:607
Alignment explanation
Indices: 1978903--1980096 Score: 1839
Period size: 600 Copynumber: 1.9 Consensus size: 607
1978893 ACTACGCTCA
*
1978903 ACTCCAGACAACGCAAGTTCAACCTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACCTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC-T--C
*
1978968 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGAACTCAAGACAACACAAGTTCAACT
63 --TTT---A-CCAATTTCAACTTCACAACGAAAGATATTGAACTCAAGACAACACAAGTTCAACT
1979033 TCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
122 TCACGACGAAGGGACCGCTGGTTGTCAAAAAAACAAC-T--C--TTT---A-CCAATTTCAACTT
* *
1979098 CACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGGCGAAGAGACCACTGGTT
178 CACAACGAAGGATATTAGACTCCAGACAACACAAGTTCAACTTCACGACGAAGAGACCACTGGTT
1979163 GTCAATAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
243 GTCAATAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
*
1979228 GACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
308 GACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATCTC
1979293 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
373 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* * *
1979358 CGAAGGGACCGCTGGTTGTCAAATAAACATTTCCCAATTTCAGAGCCAATTTCGACTTCACAGCG
438 CGAAGGGACCGCTGGTTGTCAAATAAACATTTCCCAATTTCAGAACCAATTTCAACTTCACAACG
*
1979423 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATA
503 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAACA
1979488 AACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
568 AACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1979528 ACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAA-T-TTT
1 ACTCCAGACAACGCAAGTTCAACCTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTCTTT
* * * *
1979591 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
66 ACCAATTTCAACTTCACAACGAAAGATATTGAACTCAAGACAACACAAGTTCAACTTCACGACGA
*
1979655 AGGGACCGCTGGTTGTC-AATAAACAA-T-TTT-CCAATTTCAACTTCACAACGAAGGATATTAG
131 AGGGACCGCTGGTTGTCAAAAAAACAACTCTTTACCAATTTCAACTTCACAACGAAGGATATTAG
* * * *
1979716 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AATCAATTTCC
196 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGAGACCACTGGTTGTCAATAAAT-AACTTCC
* * *
1979780 CAATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGTCTCCAGACAACGCAAGTTCAAC
260 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAC
* *
1979845 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATCTCAGAGCCAATTTTAACTT
325 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATCTCAGAGCCAATTTCAACTT
* * *
1979910 CACAGCGAAGGATATTGGACTCGAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTT
390 CACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* *
1979975 GTC-AATAAACAATTTCTCAATTTCAGAACCAATTTCAACTTCATAACGAAGGATATTGGACTCC
455 GTCAAATAAAC-ATTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCC
** *
1980039 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
519 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAACAAACAATTTC
1980097 ACAGTTCCAG
Statistics
Matches: 533, Mismatches: 34, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
599 10 0.02
600 376 0.71
605 3 0.01
610 1 0.00
612 8 0.02
613 76 0.14
618 3 0.01
623 1 0.00
625 55 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (607 bp):
ACTCCAGACAACGCAAGTTCAACCTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTCTTT
ACCAATTTCAACTTCACAACGAAAGATATTGAACTCAAGACAACACAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAAAAAAACAACTCTTTACCAATTTCAACTTCACAACGAAGGATATTAG
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGAGACCACTGGTTGTCAATAAATAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATCTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAAATAAACATTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAACAAACAATTTCCCAATTTCA
ACTTCACAACGAAGGATATTGG
Found at i:1982048 original size:29 final size:29
Alignment explanation
Indices: 1982015--1982082 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
1982005 TTTATGGACA
1982015 GGAAACTGTCGTGTTTGCCAAGCGACGGT
1 GGAAACTGTCGTGTTTGCCAAGCGACGGT
1982044 GGAAACTGTCGTGTTTGCCAAGCGACGGT
1 GGAAACTGTCGTGTTTGCCAAGCGACGGT
1982073 GGAAACTGTC
1 GGAAACTGTC
1982083 TTACGAGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.24
Consensus pattern (29 bp):
GGAAACTGTCGTGTTTGCCAAGCGACGGT
Found at i:1986765 original size:19 final size:17
Alignment explanation
Indices: 1986741--1986782 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
1986731 TTAATAATTT
1986741 AATATTAATATCTTTCAAA
1 AATATTAATA-CTTT-AAA
*
1986760 AATATT-ATAGTTTAAA
1 AATATTAATACTTTAAA
1986776 AATATTA
1 AATATTA
1986783 TTAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 3 0.14
19 6 0.29
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTAATACTTTAAA
Found at i:1987711 original size:2 final size:2
Alignment explanation
Indices: 1987706--1987736 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1987696 AAGTAATGTA
1987706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1987737 AAATACCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1993792 original size:2 final size:2
Alignment explanation
Indices: 1993787--1993843 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1993777 GTGTTTCTAT
1993787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1993829 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1993844 TAGTAAATGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1994384 original size:25 final size:25
Alignment explanation
Indices: 1994350--1994399 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1994340 TAAAGTGTAC
1994350 CCATCACAAGTGGTAGATATGTGAT
1 CCATCACAAGTGGTAGATATGTGAT
*
1994375 CCATCACAAGTGGTGGATATGTGAT
1 CCATCACAAGTGGTAGATATGTGAT
1994400 GGATATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (25 bp):
CCATCACAAGTGGTAGATATGTGAT
Found at i:2000770 original size:21 final size:21
Alignment explanation
Indices: 2000744--2000786 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2000734 TAATTTTCAA
2000744 ACATTATTGCACATAATTTTG
1 ACATTATTGCACATAATTTTG
*
2000765 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACATAATTTTG
2000786 A
1 A
2000787 TATTGCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACATAATTTTG
Found at i:2021202 original size:20 final size:20
Alignment explanation
Indices: 2021177--2021227 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2021167 AGAGGGTCAA
* *
2021177 CGGTTCGAGTTGAGTCAGTT
1 CGGTTCGAGTTGAATCAGTC
2021197 CGGTTCGAGTTGAATCAGTC
1 CGGTTCGAGTTGAATCAGTC
*
2021217 CGGTTTGAGTT
1 CGGTTCGAGTT
2021228 AACTCGGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.35
Consensus pattern (20 bp):
CGGTTCGAGTTGAATCAGTC
Found at i:2022519 original size:24 final size:24
Alignment explanation
Indices: 2022459--2022520 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
2022449 CAGTAATACA
* *
2022459 TCAAGGATAATTTCCATACTTTTTT
1 TCAA-GATAATTACCATACTATTTT
*
2022484 TC-AGATACTTACCATA-TATTTT
1 TCAAGATAATTACCATACTATTTT
2022506 TCAAGTATAATTACC
1 TCAAG-ATAATTACC
2022521 TAAAAGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 7 0.23
23 13 0.42
24 9 0.29
25 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (24 bp):
TCAAGATAATTACCATACTATTTT
Found at i:2025177 original size:16 final size:17
Alignment explanation
Indices: 2025156--2025187 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2025146 AAAAGATTGA
2025156 AATCTACAGAA-AAAAG
1 AATCTACAGAAGAAAAG
2025172 AATCTACAGAAGAAAA
1 AATCTACAGAAGAAAA
2025188 AAAAGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (17 bp):
AATCTACAGAAGAAAAG
Found at i:2027238 original size:9 final size:8
Alignment explanation
Indices: 2027226--2027286 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 8
2027216 TTAAAATAAT
2027226 TAATAAACA
1 TAATAAA-A
2027235 TAATTAAAA
1 TAA-TAAAA
2027244 TAATAAAA
1 TAATAAAA
*
2027252 -AACAAAA
1 TAATAAAA
*
2027259 -AA-CAAA
1 TAATAAAA
2027265 TAATAAAA
1 TAATAAAA
2027273 -AATAAAA
1 TAATAAAA
2027280 -AATAAAA
1 TAATAAAA
2027287 ACAGTAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 3 0.07
7 24 0.52
8 8 0.17
9 7 0.15
10 4 0.09
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (8 bp):
TAATAAAA
Found at i:2027242 original size:22 final size:21
Alignment explanation
Indices: 2027215--2027274 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2027205 ACTATGAAAT
*
2027215 ATTAAAATAATTAATAAACATA
1 ATTAAAATAA-TAAAAAACATA
2027237 ATTAAAATAATAAAAAACA-A
1 ATTAAAATAATAAAAAACATA
**
2027257 AAAACAAATAATAAAAAA
1 ATTA-AAATAATAAAAAA
2027275 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 21 0.62
22 10 0.29
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
ATTAAAATAATAAAAAACATA
Found at i:2027260 original size:7 final size:7
Alignment explanation
Indices: 2027239--2027297 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
2027229 TAAACATAAT
2027239 TAAAATAA
1 TAAAA-AA
2027247 TAAAAAA
1 TAAAAAA
*
2027254 CAAAAAA
1 TAAAAAA
* *
2027261 CAAATAA
1 TAAAAAA
2027268 TAAAAAA
1 TAAAAAA
2027275 TAAAAAA
1 TAAAAAA
2027282 TAAAAACA
1 TAAAAA-A
2027290 GTAAAAAA
1 -TAAAAAA
2027298 CCAACATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
7 32 0.71
8 7 0.16
9 6 0.13
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:2027265 original size:21 final size:21
Alignment explanation
Indices: 2027241--2027281 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2027231 AACATAATTA
2027241 AAATAATAAAAAACAAAAAAC
1 AAATAATAAAAAACAAAAAAC
*
2027262 AAATAATAAAAAATAAAAAA
1 AAATAATAAAAAACAAAAAA
2027282 TAAAAACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (21 bp):
AAATAATAAAAAACAAAAAAC
Found at i:2030699 original size:7 final size:7
Alignment explanation
Indices: 2030687--2030715 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2030677 ACAAGTGCAG
2030687 AAAGAAA
1 AAAGAAA
2030694 AAAGAAA
1 AAAGAAA
2030701 AAAGAAA
1 AAAGAAA
2030708 AAAGAAA
1 AAAGAAA
2030715 A
1 A
2030716 GGGGATGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2031613 original size:19 final size:19
Alignment explanation
Indices: 2031589--2031636 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2031579 AAGTTTGAAA
*
2031589 TTAGGATTATCTACTGTTT
1 TTAGGATTATCTACTATTT
**
2031608 TTAGGAATTATCTTTTATTT
1 TTAGG-ATTATCTACTATTT
2031628 TTAGGATTA
1 TTAGGATTA
2031637 AGTTTGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (19 bp):
TTAGGATTATCTACTATTT
Found at i:2041546 original size:194 final size:194
Alignment explanation
Indices: 2041208--2041585 Score: 587
Period size: 194 Copynumber: 1.9 Consensus size: 194
2041198 TTGCGATACC
* * * * *
2041208 TGACTGATATCGCGGAGGTTGGCATCTCCTTTGGTTACTACATTTCCAGTTAGTGGATCTTCTTT
1 TGACCGATATCGCGGAGGTTGGCATCTCCTTTGGTCACTACATTTCCAATTAGTGAAGCTTCTTT
* * * *
2041273 TCTTTTTTGTTCATATCCATAGTAGATCTTATGTTTCCGTTTAGTGAAACTCGGTATGTCGATCT
66 TCTTTTTTATTCATATCCATAGTAGATCATATGATTCCGTTTAGTGAAACTCGGTACGTCGATCT
** *
2041338 TTTGACTGACTTTTATGCCTTGAATATTGTTATCTTGAGCATTTTCCCTTGATTCCTTAAGATG
131 TTTGACCAACTTTTATGCCTTGAATATTGTTATCTTGAGCATCTTCCCTTGATTCCTTAAGATG
*
2041402 TGACCGATATCGCTGAGGTTGGCATCTCCTTTGGTCACTACATTTCCAATTAGTGAAGCTTCTTT
1 TGACCGATATCGCGGAGGTTGGCATCTCCTTTGGTCACTACATTTCCAATTAGTGAAGCTTCTTT
*
2041467 TCTTTTTTATTCATATCCATAGTAGATCATATGATTCCAG-TTAGTGAAACTTGGTACGTCGATC
66 TCTTTTTTATTCATATCCATAGTAGATCATATGATTCC-GTTTAGTGAAACTCGGTACGTCGATC
** *
2041531 TTTTGACCAACTTTTATGCCTTGTGTATTGTTATCTTGAGCGTCTTCCCTTGATT
130 TTTTGACCAACTTTTATGCCTTGAATATTGTTATCTTGAGCATCTTCCCTTGATT
2041586 ACACCGGTGT
Statistics
Matches: 166, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
194 165 0.99
195 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (194 bp):
TGACCGATATCGCGGAGGTTGGCATCTCCTTTGGTCACTACATTTCCAATTAGTGAAGCTTCTTT
TCTTTTTTATTCATATCCATAGTAGATCATATGATTCCGTTTAGTGAAACTCGGTACGTCGATCT
TTTGACCAACTTTTATGCCTTGAATATTGTTATCTTGAGCATCTTCCCTTGATTCCTTAAGATG
Found at i:2049404 original size:16 final size:16
Alignment explanation
Indices: 2049363--2049404 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2049353 AAATAAAGAA
2049363 ATTAAAA-GCAATAAT
1 ATTAAAATGCAATAAT
*
2049378 ATTAAATTGCAA-AAT
1 ATTAAAATGCAATAAT
2049393 ATTAAAAATGCA
1 ATT-AAAATGCA
2049405 TGGTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (16 bp):
ATTAAAATGCAATAAT
Found at i:2050626 original size:3 final size:3
Alignment explanation
Indices: 2050618--2050681 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
2050608 ATTTTTTATT
* **
2050618 TAA TAA TAA TAA TAG T-A TATA TAA TATA TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA
2050664 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2050682 AACGAAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 45 0.87
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2050926 original size:45 final size:45
Alignment explanation
Indices: 2050875--2051559 Score: 1237
Period size: 45 Copynumber: 15.2 Consensus size: 45
2050865 CTTGGAAGAA
* *
2050875 TTACAGATTAACCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2050920 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
*
2050965 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGAC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
*
2051010 TTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
*
2051055 TTACAGATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051100 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051145 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051190 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051235 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
*
2051280 TTACAGATGACCCGCAA-GTTTTGAAAACATCATGCACTGAAGGAC
1 TTACAGATGACCCG-AAGGTTTTGAAAACATCATGCACTGAAGGGC
* * *
2051325 TTACAGATGGCCTGAAGGTTTTTAAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGC
* *
2051371 TTACAGATGACCCGAAGGTTTTGAAAACATCACGTACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051416 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051461 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
*
2051506 TTACAGATGACCCGAAGGTTTTGAAAACATCACGCACTGAAGGGC
1 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
2051551 TTACAGATG
1 TTACAGATG
2051560 TGGGAAATAG
Statistics
Matches: 616, Mismatches: 21, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
44 2 0.00
45 571 0.93
46 43 0.07
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (45 bp):
TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
Found at i:2052239 original size:22 final size:22
Alignment explanation
Indices: 2052214--2052298 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
2052204 AAATCCAATA
* *
2052214 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
2052236 AATCTATCATCTTTGAAGAG-G
1 AATCTATCATCTTTGAAGAGAG
*
2052257 AAATATATCATCTTTGAAGAGAG
1 -AATCTATCATCTTTGAAGAGAG
*
2052280 AATTTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
2052299 ATGTAGATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.02
22 55 0.96
23 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:2059099 original size:27 final size:26
Alignment explanation
Indices: 2059037--2059099 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
2059027 TGCAAAGATG
* *
2059037 CAAATGCAAAAATGAAAATGTAAATA
1 CAAATGTAAAAATGAAAATGCAAATA
2059063 CAAACT-TAAAAATGCAAAATGCAAATA
1 CAAA-TGTAAAAATG-AAAATGCAAATA
2059090 CAAATGTAAA
1 CAAATGTAAA
2059100 TATGTGAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 12 0.38
27 20 0.62
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (26 bp):
CAAATGTAAAAATGAAAATGCAAATA
Found at i:2059176 original size:6 final size:7
Alignment explanation
Indices: 2059159--2059199 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
2059149 ATAAAAGTAT
2059159 AAATGCA
1 AAATGCA
2059166 AAATG-A
1 AAATGCA
2059172 AAATGCA
1 AAATGCA
*
2059179 AAGATACA
1 AA-ATGCA
2059187 AAATGC-
1 AAATGCA
2059193 AAATGCA
1 AAATGCA
2059200 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:2059336 original size:43 final size:44
Alignment explanation
Indices: 2059274--2059360 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
2059264 CCGTGCATCA
*
2059274 AACAAAACTTTTACATATAGGGGATAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
*
2059318 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
2059361 TCTAAATCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 33 0.80
44 8 0.20
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
Found at i:2059806 original size:36 final size:36
Alignment explanation
Indices: 2059746--2059817 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
2059736 TCTTACCGTA
* *
2059746 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
* *
2059782 GAATACTTTTGTTATTAATATAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
2059818 TGCATAGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:2061729 original size:16 final size:16
Alignment explanation
Indices: 2061688--2061754 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
2061678 AAATAAAGAA
2061688 ATTAAAA-GCAATAAT
1 ATTAAAATGCAATAAT
*
2061703 ATTAAATTGCAA-AAT
1 ATTAAAATGCAATAAT
*
2061718 ATTAAAAATGC-ATGAT
1 ATT-AAAATGCAATAAT
*
2061734 -TTAAAATGTAA-AAT
1 ATTAAAATGCAATAAT
2061748 A-TAAAAT
1 ATTAAAAT
2061755 CTAAAATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.33
15 16 0.38
16 12 0.29
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (16 bp):
ATTAAAATGCAATAAT
Found at i:2064359 original size:32 final size:33
Alignment explanation
Indices: 2064263--2064361 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2064253 AACTCAACAT
* * *
2064263 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2064296 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2064329 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2064361 A
1 A
2064362 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2064380 original size:21 final size:21
Alignment explanation
Indices: 2064356--2064397 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2064346 ACTTCAAGTT
2064356 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2064377 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
2064398 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2066965 original size:3 final size:3
Alignment explanation
Indices: 2066959--2067026 Score: 84
Period size: 3 Copynumber: 22.0 Consensus size: 3
2066949 TTTTTTTATT
2066959 TAA TAA TAA TAA T-A TATA TAA TATA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TA-A TAA TAA TAA TAA TAA TAA
**
2067006 TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
2067027 AATGAAATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 46 0.79
4 10 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2068039 original size:21 final size:21
Alignment explanation
Indices: 2068015--2068079 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
2068005 CCTTATATTA
2068015 TAAAATTTTAAAATATCAATT
1 TAAAATTTTAAAATATCAATT
* *
2068036 TAAATTTATTAATATTAT-AATT
1 TAAAATT-TTAA-AATATCAATT
* *
2068058 TATAAA-ATTAATATATCAATT
1 TA-AAATTTTAAAATATCAATT
2068079 T
1 T
2068080 TAATTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
20 3 0.09
21 15 0.44
22 10 0.29
23 6 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAATTTTAAAATATCAATT
Found at i:2068426 original size:16 final size:16
Alignment explanation
Indices: 2068405--2068440 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2068395 CGTAGTGGAT
2068405 GCACATGATCAATCCC
1 GCACATGATCAATCCC
2068421 GCACATGATCAATCCC
1 GCACATGATCAATCCC
2068437 GCAC
1 GCAC
2068441 TCCCCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.39, G:0.14, T:0.17
Consensus pattern (16 bp):
GCACATGATCAATCCC
Found at i:2077373 original size:4 final size:4
Alignment explanation
Indices: 2077364--2077606 Score: 76
Period size: 4 Copynumber: 58.8 Consensus size: 4
2077354 AGAACGAATG
* * * *
2077364 AAAT AAAT AAA- ATAAT AAA- AAAT ACAT AAAGG AAAA AAAT AAAG AAA-
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
* * **
2077411 AGAT -AA- AAAT GAAT AAAAT AAAT AAAAT AAAT AAA- AAAT AAGG AAA-
1 AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
2077457 AATAT TAA- AAAT AATAT AACACCT AAAT AAAA ATAAG AATAT AATAC AAAT
1 AA-AT AAAT AAAT AA-AT AA-A--T AAAT AAAT A-AAT AA-AT AA-AT AAAT
* ** *
2077508 AAAT AAAT AAAT AAAT AAAT AAAT AAA- ATAT AAGGG AGAT AAA- AAGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AA-AT
* *
2077556 AAAAGT AAAT -AAT AAAT AAAGA AAAT AAAGA AAAGT AAAT AAAT AAAT
1 -AAA-T AAAT AAAT AAAT AAA-T AAAT AAA-T AAA-T AAAT AAAT AAAT
2077604 AAA
1 AAA
2077607 ATATAACAAG
Statistics
Matches: 179, Mismatches: 33, Indels: 54
0.67 0.12 0.20
Matches are distributed among these distances:
3 23 0.13
4 107 0.60
5 42 0.23
6 4 0.02
7 3 0.02
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:2077376 original size:9 final size:9
Alignment explanation
Indices: 2077364--2077609 Score: 100
Period size: 9 Copynumber: 26.6 Consensus size: 9
2077354 AGAACGAATG
2077364 AAATAAATA
1 AAATAAATA
*
2077373 AAATAATAAA
1 AAATAA-ATA
*
2077383 AAATACATA
1 AAATAAATA
**
2077392 AAGGAAA-A
1 AAATAAATA
*
2077400 AAATAAAGA
1 AAATAAATA
* *
2077409 AAAGATA-A
1 AAATAAATA
*
2077417 AAATGAATA
1 AAATAAATA
2077426 AAATAAATA
1 AAATAAATA
2077435 AAATAAAT-
1 AAATAAATA
2077443 AAA-AAATA
1 AAATAAATA
2077451 AGGAA-AAATA
1 A--AATAAATA
*
2077461 TTAA-AAATA
1 -AAATAAATA
*
2077470 ATATAACACCTA
1 AAATAA-A--TA
*
2077482 AATAAAAATA
1 AA-ATAAATA
2077492 AGAATATAATA
1 A-AATA-AATA
2077503 CAAATAAAT-
1 -AAATAAATA
2077512 AAATAAAT-
1 AAATAAATA
2077520 AAATAAAT-
1 AAATAAATA
2077528 AAATAAAATA
1 AAAT-AAATA
** *
2077538 TAAGGGAGATA
1 -AA-ATAAATA
*
2077549 AAA-AGATA
1 AAATAAATA
2077557 AAAGTAAATAA
1 AAA-TAAAT-A
*
2077568 TAAATAAAGA
1 -AAATAAATA
*
2077578 AAATAAAGA
1 AAATAAATA
2077587 AAAGTAAAT-
1 AAA-TAAATA
2077596 AAATAAATA
1 AAATAAATA
2077605 AAATA
1 AAATA
2077610 TAACAAGAGT
Statistics
Matches: 185, Mismatches: 27, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
7 4 0.02
8 49 0.26
9 68 0.37
10 33 0.18
11 20 0.11
12 8 0.04
13 3 0.02
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:2077519 original size:35 final size:33
Alignment explanation
Indices: 2077364--2077522 Score: 104
Period size: 35 Copynumber: 4.3 Consensus size: 33
2077354 AGAACGAATG
* ** *
2077364 AAATAAATAAAATAATAAAAAATACATAAAGGAAAA
1 AAATAAAT-AAA-AATAAGAAATA-ATAAAATAAAT
*
2077400 AAATAAAGAAAAGATAA-AAATGAATAAAATAAAT
1 AAATAAATAAAA-ATAAGAAAT-AATAAAATAAAT
*
2077434 AAAATAAATAAAAAATAAGGAAAAATATTAAAAATAATAT
1 -AAATAAAT-AAAAATAA-G--AAATAAT-AAAATAA-AT
2077474 AACACCTAAATAAAAATAAGAATATAATACAAATAAAT
1 AA-A--TAAATAAAAATAAGAA-ATAATA-AAATAAAT
2077512 AAATAAATAAA
1 AAATAAATAAA
2077523 TAAATAAATA
Statistics
Matches: 101, Mismatches: 7, Indels: 31
0.73 0.05 0.22
Matches are distributed among these distances:
34 13 0.13
35 27 0.27
36 11 0.11
37 1 0.01
38 9 0.09
39 23 0.23
40 4 0.04
41 8 0.08
42 5 0.05
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (33 bp):
AAATAAATAAAAATAAGAAATAATAAAATAAAT
Found at i:2077684 original size:21 final size:21
Alignment explanation
Indices: 2077651--2077727 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
2077641 AAAATAGAAT
*
2077651 AATAATAACAATAATAACAATA
1 AATAA-AAAAATAATAACAATA
* *
2077673 AATAAAAAAATAGTAA-TATA
1 AATAAAAAAATAATAACAATA
* *
2077693 ATATAAATAAATAGAAAACTAA-A
1 A-ATAAAAAAATA-ATAAC-AATA
*
2077716 AATAAAGAAATA
1 AATAAAAAAATA
2077728 TAGAAAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.09
21 19 0.44
22 17 0.40
23 2 0.05
24 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
AATAAAAAAATAATAACAATA
Found at i:2077719 original size:29 final size:29
Alignment explanation
Indices: 2077661--2077719 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
2077651 AATAATAACA
**
2077661 ATAATAACAATAAATAAAAAAATAGTAAT
1 ATAATAACAATAAATAAAAAAATAAAAAT
* *
2077690 ATAATATA-AATAAATAGAAAACTAAAAAT
1 ATAATA-ACAATAAATAAAAAAATAAAAAT
2077719 A
1 A
2077720 AAGAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (29 bp):
ATAATAACAATAAATAAAAAAATAAAAAT
Found at i:2079778 original size:84 final size:84
Alignment explanation
Indices: 2079653--2081120 Score: 1795
Period size: 84 Copynumber: 17.5 Consensus size: 84
2079643 AATCGAGCTT
* * * * * ** *
2079653 GAAGGTC-TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATGATGCACCTTTGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* **
2079717 GCTGAGTGTAACCGAACT-
66 GCTGAGCGTAGTCGAACTC
*** * * *
2079735 GAAAGGTCTTTTGTTAATAGATAACCTTTCTATCCTTGAGTTATGCTGCAAATGATATGCCTTGG
1 G-AAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGG
* *
2079800 AGCTGAGCGTAGTCAAACTT
65 AGCTGAGCGTAGTCGAACTC
* * * * *
2079820 GAAGGTTTTTTGATGGCAGATAACCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCCTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
2079885 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * * * * * *
2079904 TAAGGGC---T-TTAGAAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATAATGGTGCCTTTG
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGG
*
2079965 AGCTGAGCATAGTCGAACTC
65 AGCTGAGCGTAGTCGAACTC
* * * * * * *
2079985 AAAGGTCTTTAGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080050 GCTGAGCGTAGTCAAACTC
66 GCTGAGCGTAGTCGAACTC
* * * *
2080069 GAAGGTCTTTTGTTGGCAGATAACCATTCTATCCTTGAGTTATGCTGCAAATGATATGCCTTAGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080134 GCTGAGCGTAGTCTAACTC
66 GCTGAGCGTAGTCGAACTC
* * *
2080153 GAAGGTC-TTTGGTGGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCCAATGATGTGCCTTGG
1 GAAGGTCTTTTGTTGG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGG
2080217 AGCTGAGCGTAGTCGAACTC
65 AGCTGAGCGTAGTCGAACTC
* * *
2080237 GAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* *
2080302 GCTGAGCGTAGTTGAATTC
66 GCTGAGCGTAGTCGAACTC
* * * * **
2080321 AAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTCAGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080386 GCTGAGCGTAGTCGAATTC
66 GCTGAGCGTAGTCGAACTC
* * * *
2080405 GAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTAGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
**
2080470 G-TCGATTGTAGTCGAACTC
66 GCT-GAGCGTAGTCGAACTC
* ** * * ** * * *
2080489 GAAGGTATTTTAATGGCAGATAACCCTTCTAACCTTGAGCTATATTGTAAATAATGTGCCTTAGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080554 GCCGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
** * *
2080573 GAAGGTCTTTTAATGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATAATGTGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
2080638 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
** * * * *
2080657 GAAGGTCTTTTAATGGCAAATAACCCTTCTAGCCCTGAGCTATGCTGTAAATGATGTGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
2080722 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * *
2080741 GAAGGTC-TTTGGTGGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCTTTGG
1 GAAGGTCTTTTGTTGG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGG
* *
2080805 AGCTGAACGTAGTTGAACTC
65 AGCTGAGCGTAGTCGAACTC
* * * * *
2080825 GAAGGTCTTTGGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGATGCAAATGATATGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080890 GCTGAGTGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
** * *
2080909 GAAGGTCTTTTAATGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2080974 GCTGAGCATTA-TCGAACTC
66 GCTGAGC-GTAGTCGAACTC
* * * *
2080993 GAAGGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
*
2081058 GCTGAGCGTAGTTGAACTC
66 GCTGAGCGTAGTCGAACTC
* *
2081077 GAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATG
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
2081121 TTGTAAATAG
Statistics
Matches: 1201, Mismatches: 169, Indels: 30
0.86 0.12 0.02
Matches are distributed among these distances:
80 35 0.03
81 32 0.03
82 1 0.00
83 22 0.02
84 1062 0.88
85 49 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (84 bp):
GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTC
Found at i:2082457 original size:95 final size:95
Alignment explanation
Indices: 2082255--2082517 Score: 368
Period size: 95 Copynumber: 2.7 Consensus size: 95
2082245 GGCTAGCTAA
* * *
2082255 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTATAG-AT
1 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
2082319 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCCGAATATT
* *
2082353 ATCCATAAAGCTGGGGGGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
*
2082418 TAATCACCTTTATCAGGCTAGCCGAATCTT
66 TAATCACCTTTATCAGGCTAGCCGAATATT
* * *
2082448 ATCCATAAAGCCA-GAGCGTTTAACCAATTGCTTTAGAGGGACATCTCAAGCTTTATTGTATATA
1 ATCCATAAAG-CAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-
2082512 TATAAT
64 TATAAT
2082518 ATTATAATCT
Statistics
Matches: 150, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
94 4 0.03
95 92 0.61
96 9 0.06
97 2 0.01
98 43 0.29
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCCGAATATT
Found at i:2086401 original size:4 final size:4
Alignment explanation
Indices: 2086392--2086549 Score: 56
Period size: 4 Copynumber: 36.8 Consensus size: 4
2086382 AGAACGAATG
* * * * *
2086392 AAAT AAAT AAA- ATAAT AAAA AAAT ACAT AAAGG AAAA AAAT AAAG AAA-
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
*
2086440 AAAT -AA- AAAT GAAT AAAAT AAAT AAAAT AAAT AAAAT AAAT AGAAAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT -AAAT AAAT --AAAT
* * *
2086487 AATAA AAAT AATAT AACACTT AAAT AAAA ATAAG AAGAT -AAT GCAAAT
1 AA-AT AAAT AA-AT AA-A--T AAAT AAAT A-AAT AA-AT AAAT --AAAT
2086535 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
2086550 ACAAATATAA
Statistics
Matches: 118, Mismatches: 16, Indels: 40
0.68 0.09 0.23
Matches are distributed among these distances:
3 10 0.08
4 70 0.59
5 27 0.23
6 8 0.07
7 3 0.03
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:2086431 original size:28 final size:26
Alignment explanation
Indices: 2086400--2086475 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 26
2086390 TGAAATAAAT
2086400 AAAATAATAAAAAAATACATAAAGGAAA
1 AAAATAATAAAAAAATA-A-AAAGGAAA
* *
2086428 AAAATAA-AGAAAAAATAAAAATGAAT
1 AAAATAATA-AAAAAATAAAAAGGAAA
2086454 AAAATAAATAAAATAAATAAAA
1 AAAAT-AATAAAA-AAATAAAA
2086476 TAAATAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.26
27 7 0.17
28 24 0.57
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (26 bp):
AAAATAATAAAAAAATAAAAAGGAAA
Found at i:2086616 original size:19 final size:18
Alignment explanation
Indices: 2086592--2086636 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2086582 AAGATTAAAT
2086592 AAAATAAAGAAAATAAAGA
1 AAAATAAA-AAAATAAAGA
* *
2086611 AAAATAAATAAATAAATA
1 AAAATAAAAAAATAAAGA
2086629 AAATATAA
1 AAA-ATAA
2086637 CAAGAGTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAATAAAAAAATAAAGA
Found at i:2086760 original size:35 final size:33
Alignment explanation
Indices: 2086721--2086812 Score: 89
Period size: 35 Copynumber: 2.7 Consensus size: 33
2086711 AATATAATAT
2086721 AAATAAATAGAAAACTAAAAATAAAGAAATATAGA
1 AAATAAATAGAAAA-TAAAAATAAAGAAATATA-A
* * * *
2086756 AAATATAATAGAAAATATAATTAAATATATATAA
1 AAATA-AATAGAAAATAAAAATAAAGAAATATAA
*
2086790 AAA-AAATAAGAAAA-ATAAATAAA
1 AAATAAAT-AGAAAATAAAAATAAA
2086813 TAAAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 11 0.22
33 7 0.14
34 4 0.08
35 19 0.38
36 9 0.18
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (33 bp):
AAATAAATAGAAAATAAAAATAAAGAAATATAA
Found at i:2086768 original size:12 final size:12
Alignment explanation
Indices: 2086751--2086776 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2086741 ATAAAGAAAT
2086751 ATAGAAAATATA
1 ATAGAAAATATA
2086763 ATAGAAAATATA
1 ATAGAAAATATA
2086775 AT
1 AT
2086777 TAAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
ATAGAAAATATA
Found at i:2086798 original size:23 final size:22
Alignment explanation
Indices: 2086756--2086798 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2086746 GAAATATAGA
* *
2086756 AAATATAATAGAAAATATAATT
1 AAATATAATAAAAAAAATAATT
2086778 AAATATATATAAAAAAAATAA
1 AAATATA-ATAAAAAAAATAA
2086799 GAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATATAATAAAAAAAATAATT
Found at i:2086818 original size:9 final size:9
Alignment explanation
Indices: 2086392--2086633 Score: 112
Period size: 9 Copynumber: 26.6 Consensus size: 9
2086382 AGAACGAATG
2086392 AAATAAATA
1 AAATAAATA
2086401 AAAT-AATA
1 AAATAAATA
2086409 AAA-AAAT-
1 AAATAAATA
* *
2086416 ACATAAAGGA
1 AAATAAA-TA
2086426 AAA-AAATAA
1 AAATAAAT-A
*
2086435 AGAAAAAATAA
1 A-AATAAAT-A
*
2086446 AAATGAATA
1 AAATAAATA
2086455 AAATAAATA
1 AAATAAATA
2086464 AAATAAATA
1 AAATAAATA
2086473 AAATAAATA
1 AAATAAATA
2086482 GAAAT-AATAA
1 -AAATAAAT-A
2086492 AAATAATATA
1 AAATAA-ATA
*
2086502 ACACTTAAATA
1 A-A-ATAAATA
*
2086513 AAA-ATAAGA
1 AAATA-AATA
* *
2086522 AGAT-AATGC
1 AAATAAAT-A
2086531 AAATAAAT-
1 AAATAAATA
2086539 AAATAAATA
1 AAATAAATA
*
2086548 AAACAAATA
1 AAATAAATA
** *
2086557 TAAGGGAGATA
1 -AA-ATAAATA
*
2086568 AAA-AGATA
1 AAATAAATA
2086576 AAAGT-AA-A
1 AAA-TAAATA
* *
2086584 GATTAAATA
1 AAATAAATA
*
2086593 AAATAAAGA
1 AAATAAATA
*
2086602 AAATAAAGAA
1 AAATAAA-TA
2086612 AAATAAAT-
1 AAATAAATA
2086620 AAATAAATA
1 AAATAAATA
2086629 AAATA
1 AAATA
2086634 TAACAAGAGT
Statistics
Matches: 180, Mismatches: 27, Indels: 52
0.69 0.10 0.20
Matches are distributed among these distances:
7 3 0.02
8 44 0.24
9 79 0.44
10 33 0.18
11 18 0.10
12 3 0.02
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (9 bp):
AAATAAATA
Found at i:2111630 original size:18 final size:18
Alignment explanation
Indices: 2111591--2111632 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2111581 GTAAAAAGAT
* *
2111591 ATTAAAATAATAAAAGCG
1 ATTAAAAAAATAAAAGCA
*
2111609 ATTAAAAAAATAAAAGTA
1 ATTAAAAAAATAAAAGCA
2111627 ATTAAA
1 ATTAAA
2111633 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (18 bp):
ATTAAAAAAATAAAAGCA
Found at i:2112943 original size:25 final size:27
Alignment explanation
Indices: 2112893--2112953 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
2112883 GTTAAAAATT
*
2112893 AAATCCACCGAAAGGTGGAATT-AAA-
1 AAATCCACCGAAAGATGGAATTAAAAC
2112918 AAATCCACCGAAA-ATAGG-ATTGAAAAC
1 AAATCCACCGAAAGAT-GGAATT-AAAAC
2112945 AAATCCACC
1 AAATCCACC
2112954 AAACATGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 4 0.13
25 15 0.48
26 3 0.10
27 9 0.29
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (27 bp):
AAATCCACCGAAAGATGGAATTAAAAC
Found at i:2119676 original size:3 final size:3
Alignment explanation
Indices: 2119668--2119698 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2119658 TATAGAAGTA
2119668 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2119699 CAAATTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2120733 original size:13 final size:13
Alignment explanation
Indices: 2120712--2120746 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2120702 CATACCATTA
*
2120712 AGCTGCAGAATAG
1 AGCTCCAGAATAG
2120725 AGCTCCAGAATAG
1 AGCTCCAGAATAG
2120738 AGCTCCAGA
1 AGCTCCAGA
2120747 GATCGGCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (13 bp):
AGCTCCAGAATAG
Found at i:2134970 original size:39 final size:36
Alignment explanation
Indices: 2134928--2135237 Score: 310
Period size: 37 Copynumber: 8.4 Consensus size: 36
2134918 TTATATATGT
*
2134928 ATATATTATTATATAATTTTGAAAACATTTTGAAAATC
1 ATATA-TATTATATAATTTTTAAAACATTTTGAAAA-C
*
2134966 -TATATGA-TATATAGTTTTTAAAACATTTTTGAAAAC
1 ATATAT-ATTATATAATTTTTAAAACA-TTTTGAAAAC
2135002 ATATATATTATATAATTTTTAAAACATTTTGAAAA-
1 ATATATATTATATAATTTTTAAAACATTTTGAAAAC
*
2135037 A-ATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATTATATAATTTTTAAAACATTTTGAAAAC
* * *
2135072 ATATATATATTATATAGTTTTTAAAATATTTTAAAAAAC
1 --ATATATATTATATAATTTTTAAAACATTTT-GAAAAC
*
2135111 TTATATATATTATATAATTTTTAAAACGTTTTTGAAAA-
1 --ATATATATTATATAATTTTTAAAAC-ATTTTGAAAAC
2135149 ATATATATAATATATAAGTTTTTAAAACAATTTTTG-AAA-
1 ATATATAT--TATATAA-TTTTTAAAAC-A-TTTTGAAAAC
* * * * **
2135188 ATATAAATTATATAGTTTTGAAAATTATTTTTTAAAC
1 ATATATATTATATAATTTTTAAAA-CATTTTGAAAAC
2135225 ATATATATTATAT
1 ATATATATTATAT
2135238 GGTTTTAGAA
Statistics
Matches: 236, Mismatches: 19, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
34 32 0.14
35 5 0.02
36 48 0.20
37 55 0.23
38 34 0.14
39 53 0.22
40 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
ATATATATTATATAATTTTTAAAACATTTTGAAAAC
Found at i:2134976 original size:34 final size:34
Alignment explanation
Indices: 2134928--2135237 Score: 269
Period size: 39 Copynumber: 8.4 Consensus size: 34
2134918 TTATATATGT
*
2134928 ATATATTATTATATAATTTTGAAAACATTTTGAAA
1 ATATA-TATTATATAATTTTTAAAACATTTTGAAA
* *
2134963 ATCTATATGATATATAGTTTTTAAAACATTTTTGAAAA
1 ATATATAT--TATATAATTTTTAAAACA-TTTTG-AAA
2135001 CATATATATTATATAATTTTTAAAACATTTTGAAA
1 -ATATATATTATATAATTTTTAAAACATTTTGAAA
* *
2135036 AAATATATTATATAGTTTTTAAAACATTTTGAAAACA
1 ATATATATTATATAATTTTTAAAACATTTTG--AA-A
* * *
2135073 TATATATATTATATAGTTTTTAAAATATTTTAAAAAA
1 -ATATATATTATATAATTTTTAAAACATTTT--GAAA
*
2135110 CTTATATATATTATATAATTTTTAAAACGTTTTTGAAAA
1 ---ATATATATTATATAATTTTTAAAAC-ATTTTG-AAA
2135149 ATATATATAATATATAAGTTTTTAAAACAATTTTTGAAA
1 ATATATAT--TATATAA-TTTTTAAAAC-A-TTTTGAAA
* * * * *
2135188 ATATAAATTATATAGTTTTGAAAATTATTTTTTAAA
1 ATATATATTATATAATTTTTAAAA-CA-TTTTGAAA
2135224 CATATATATTATAT
1 -ATATATATTATAT
2135238 GGTTTTAGAA
Statistics
Matches: 232, Mismatches: 22, Indels: 40
0.79 0.07 0.14
Matches are distributed among these distances:
34 32 0.14
35 7 0.03
36 48 0.21
37 42 0.18
38 40 0.17
39 54 0.23
40 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (34 bp):
ATATATATTATATAATTTTTAAAACATTTTGAAA
Found at i:2134989 original size:36 final size:35
Alignment explanation
Indices: 2134937--2135211 Score: 241
Period size: 36 Copynumber: 7.5 Consensus size: 35
2134927 TATATATTAT
* *
2134937 TATATAATTTTGAAAACATTTTGAAAATCTATATGA
1 TATATAGTTTTTAAAACATTTTGAAAATCTATAT-A
2134973 TATATAGTTTTTAAAACATTTTTGAAAA-CATATATA
1 TATATAGTTTTTAAAACA-TTTTGAAAATC-TATATA
* **
2135009 TTATATAATTTTTAAAACATTTTGAAAAAATATAT-
1 -TATATAGTTTTTAAAACATTTTGAAAATCTATATA
*
2135044 TATATAGTTTTTAAAACATTTTGAAAACATATATATA
1 TATATAGTTTTTAAAACATTTTG-AAA-ATCTATATA
* * *
2135081 TTATATAGTTTTTAAAATATTTTAAAAAACTTATATATA
1 -TATATAGTTTTTAAAACATTTT-GAAAA--TCTATATA
* * *
2135120 TTATATAATTTTTAAAACGTTTTTGAAAAATATATATAA
1 -TATATAGTTTTTAAAAC-ATTTTG-AAAATCTATAT-A
* *
2135159 TATATAAGTTTTTAAAACAATTTTTGAAAATATAAAT-
1 TATAT-AGTTTTTAAAAC-A-TTTTGAAAATCTATATA
*
2135196 TATATAGTTTTGAAAA
1 TATATAGTTTTTAAAA
2135212 TTATTTTTTA
Statistics
Matches: 206, Mismatches: 17, Indels: 32
0.81 0.07 0.13
Matches are distributed among these distances:
34 22 0.11
35 3 0.01
36 49 0.24
37 37 0.18
38 36 0.17
39 46 0.22
40 13 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
TATATAGTTTTTAAAACATTTTGAAAATCTATATA
Found at i:2135321 original size:13 final size:13
Alignment explanation
Indices: 2135254--2135338 Score: 52
Period size: 13 Copynumber: 6.6 Consensus size: 13
2135244 AGAAAATGTT
*
2135254 TTTATTATATTTA
1 TTTATTTTATTTA
2135267 TTTATTATTA-TTA
1 TTTATT-TTATTTA
* *
2135280 -TTATTATATTTT
1 TTTATTTTATTTA
** *
2135292 TTGTACCTTCTTT-
1 TT-TATTTTATTTA
2135305 TTTATTTTATTTA
1 TTTATTTTATTTA
2135318 TTTATTTT-TATTA
1 TTTATTTTAT-TTA
*
2135331 CTTATTTT
1 TTTATTTT
2135339 TTTCTCTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
11 2 0.04
12 15 0.27
13 30 0.55
14 8 0.15
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:2137672 original size:20 final size:20
Alignment explanation
Indices: 2137627--2137719 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
2137617 TTCAAGCTTG
* * *
2137627 ATGAAATTAATTTTTAAATT
1 ATGAAATTTATTTTAAAAAT
*
2137647 CT-AAATTTATTTTAAAAAT
1 ATGAAATTTATTTTAAAAAT
2137666 ATGAAATTTATTTTAAAAAAT
1 ATGAAATTTATTTT-AAAAAT
* * *
2137687 ATTAAAATTAATTTTTAAAAT
1 A-TGAAATTTATTTTAAAAAT
*
2137708 ATTAAATTTATT
1 ATGAAATTTATT
2137720 ATTATTTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.25
20 21 0.35
21 13 0.22
22 11 0.18
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (20 bp):
ATGAAATTTATTTTAAAAAT
Found at i:2137731 original size:24 final size:21
Alignment explanation
Indices: 2137630--2137713 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
2137620 AAGCTTGATG
2137630 AAATTAATTTTT-AAAT-TCT-
1 AAATTAATTTTTAAAATAT-TA
* * *
2137649 AAATTTATTTTAAAAATA-TG
1 AAATTAATTTTTAAAATATTA
* *
2137669 AAATTTATTTTAAAAAATATTA
1 AAATTAATTTT-TAAAATATTA
2137691 AAATTAATTTTTAAAATATTA
1 AAATTAATTTTTAAAATATTA
2137712 AA
1 AA
2137714 TTTATTATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.20
20 15 0.27
21 18 0.33
22 11 0.20
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
AAATTAATTTTTAAAATATTA
Found at i:2138431 original size:82 final size:80
Alignment explanation
Indices: 2138323--2138556 Score: 289
Period size: 82 Copynumber: 2.9 Consensus size: 80
2138313 GGAAATATAT
*
2138323 GTTTAATATTTAAATTTAAACA-ATATTATTATCTATTTAAATTTAGATATTAAAAAAGTTTTGG
1 GTTTAATATTTAAATTTAAA-AGATATTATTATCTA-TTAAATTTAGATATTAAAAGAGTTTTGG
*
2138387 TTGGAGTAAACTCTCAG
64 TTGGACTAAACTCTCAG
* * *
2138404 GTTTAATATTATAAATTTAAAAGATATTATAATATGCTTAAATTTAGATATTAAAAGAGTTTTGG
1 GTTTAATATT-TAAATTTAAAAGATATTATTATCT-ATTAAATTTAGATATTAAAAGAGTTTTGG
** *
2138469 TTAAATTAAAACTCTCAG
64 TTGGACT-AAACTCTCAG
* *
2138487 ATTTAATATTTTAAATTTAAAAGATATTATTATCTA-T---TTTAGATATTAAAAGAGTTTTAGT
1 GTTTAATA-TTTAAATTTAAAAGATATTATTATCTATTAAATTTAGATATTAAAAGAGTTTTGGT
2138548 TGGACTAAA
65 TGGACTAAA
2138557 ACTCACTCGA
Statistics
Matches: 133, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
77 3 0.02
78 26 0.20
81 12 0.09
82 51 0.38
83 39 0.29
84 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (80 bp):
GTTTAATATTTAAATTTAAAAGATATTATTATCTATTAAATTTAGATATTAAAAGAGTTTTGGTT
GGACTAAACTCTCAG
Found at i:2144539 original size:123 final size:120
Alignment explanation
Indices: 2144290--2144551 Score: 260
Period size: 123 Copynumber: 2.2 Consensus size: 120
2144280 GGGTTTGTTT
* * *
2144290 AGAAACGCCACTAAAGTACTAGGTTTTAGCAGTGTTTGCCTAAGGCCACAATATATGTACCCTAC
1 AGAAATGCCACTAAAGTACTAGGTTTTAGCAGCGTTTGCCTAACGCCACAATATATGTACCCTAC
* * * ** **
2144355 TGCAGCGTTTGTTTAAAAACTCCACTAAAGAACTATTCTTTTTAAGCATTTGTTT
66 TGCAGCGTTTATTTAAAAACGCCACTAAAGAACTATTCGTTGCAAGCATTTGTAA
* ** *
2144410 AGAAATGCCACTAAAGTACTAGGTTTTAGCGGCGTTTTTCTAAAAACGCCACAATATATGTATCC
1 AGAAATGCCACTAAAGTACTAGGTTTTAGCAGCGTTTGCCT---AACGCCACAATATATGTACCC
* * * *
2144475 TATTGCAGTGTTTATTTAAAAA-GCCACTAAAGTACTTATAT-GTTGCAA-CGTTTGTGAA
63 TACTGCAGCGTTTATTTAAAAACGCCACTAAAGAAC-TAT-TCGTTGCAAGCATTTGT-AA
* * *
2144533 ATAAATGTCGCTAAAGTAC
1 AGAAATGCCACTAAAGTAC
2144552 GAGTGTTAGC
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
120 36 0.31
122 17 0.15
123 61 0.53
124 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (120 bp):
AGAAATGCCACTAAAGTACTAGGTTTTAGCAGCGTTTGCCTAACGCCACAATATATGTACCCTAC
TGCAGCGTTTATTTAAAAACGCCACTAAAGAACTATTCGTTGCAAGCATTTGTAA
Found at i:2148467 original size:4 final size:4
Alignment explanation
Indices: 2148453--2148503 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
2148443 GAGGGAAGAA
* * * *
2148453 TATG CATG TATG TATG TATA TATG TATG CATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2148501 TAT
1 TAT
2148504 CACCAGAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:2150809 original size:21 final size:20
Alignment explanation
Indices: 2150766--2150805 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2150756 TTGAAGTTTC
*
2150766 AAAAATAACAAATTGGTCAT
1 AAAAATAACAAATAGGTCAT
*
2150786 AAAAATATCAAATAGGTCAT
1 AAAAATAACAAATAGGTCAT
2150806 TAAATAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAATAACAAATAGGTCAT
Found at i:2154122 original size:13 final size:12
Alignment explanation
Indices: 2154092--2154121 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2154082 AAAAAGAGAG
2154092 AAAAAATTATTT
1 AAAAAATTATTT
2154104 AAAAAATTATTT
1 AAAAAATTATTT
2154116 AAAAAA
1 AAAAAA
2154122 ACAAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAATTATTT
Found at i:2154159 original size:20 final size:20
Alignment explanation
Indices: 2154136--2154183 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2154126 AACAAAATAA
2154136 AAATAAATAAACAAAAAATT-
1 AAATAAATAAA-AAAAAATTG
* *
2154156 AAATTAAATTAAAAAAAGTTG
1 AAA-TAAATAAAAAAAAATTG
2154177 AAATAAA
1 AAATAAA
2154184 ATAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (20 bp):
AAATAAATAAAAAAAAATTG
Found at i:2154163 original size:21 final size:20
Alignment explanation
Indices: 2154124--2154187 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
2154114 TTAAAAAAAC
* * *
2154124 AAAACAAAATAAAAATAAAT
1 AAAAAAAAATTAAATTAAAT
2154144 AAACAAAAAATTAAATTAAAT
1 AAA-AAAAAATTAAATTAAAT
* * *
2154165 TAAAAAAAGTTGAAATAAAAT
1 AAAAAAAAATT-AAATTAAAT
2154186 AA
1 AA
2154188 TAATAATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (20 bp):
AAAAAAAAATTAAATTAAAT
Found at i:2155479 original size:15 final size:14
Alignment explanation
Indices: 2155459--2155515 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
2155449 CTGAAACGAG
2155459 AAAAAAATAAGTAAT
1 AAAAAAATAA-TAAT
2155474 AAAAAAATAATAAT
1 AAAAAAATAATAAT
*
2155488 AAATAACGATAATAAT
1 AAA-AA-AATAATAAT
2155504 AATAATAAATAA
1 AA-AA-AAATAA
2155516 ATATAAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 7 0.19
15 12 0.33
16 15 0.42
17 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (14 bp):
AAAAAAATAATAAT
Found at i:2155521 original size:22 final size:22
Alignment explanation
Indices: 2155479--2155521 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2155469 GTAATAAAAA
*
2155479 AATAATAATAAATAACGATAAT
1 AATAATAATAAATAAAGATAAT
*
2155501 AATAATAATAAATAAATATAA
1 AATAATAATAAATAAAGATAA
2155522 AACTATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAATAATAAATAAAGATAAT
Found at i:2155703 original size:39 final size:38
Alignment explanation
Indices: 2155639--2155832 Score: 198
Period size: 39 Copynumber: 5.1 Consensus size: 38
2155629 TTTCAAAAAC
* *
2155639 TATATAATTTTTAAAAATGTTTTAAAAATTATATATTA
1 TATATAGTTTTCAAAAATGTTTTAAAAATTATATATTA
* *
2155677 TATATCAGTTTTCAAGAATGCTTTAAAAAATTATATATTA
1 TATAT-AGTTTTCAAAAATG-TTTTAAAAATTATATATTA
**
2155717 TATA-AGTTTTCAAAAAATGATTTTAAAAACCATATATTA
1 TATATAGTTTTC-AAAAATG-TTTTAAAAATTATATATTA
* * * * *
2155756 TATAT-TTTTTCTAAAATATTTTCAAAATTATATATCA
1 TATATAGTTTTCAAAAATGTTTTAAAAATTATATATTA
* * *
2155793 TATATA-TTTTC-AAAATGTTTTCAATATTATATAATA
1 TATATAGTTTTCAAAAATGTTTTAAAAATTATATATTA
2155829 TATA
1 TATA
2155833 CATATATATT
Statistics
Matches: 131, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
36 25 0.19
37 25 0.19
38 17 0.13
39 42 0.32
40 22 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATAGTTTTCAAAAATGTTTTAAAAATTATATATTA
Done.