Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_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: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1842302 original size:18 final size:18
Alignment explanation
Indices: 1842249--1842303 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
1842239 TTGAGGGATT
*
1842249 ATAGTGGTCCTTCGGGAT
1 ATAGTGGTCCTTCGGGAC
*
1842267 ATAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTCGGGAC
**
1842285 ATAGTGGTTATTCGGGAC
1 ATAGTGGTCCTTCGGGAC
1842303 A
1 A
1842304 AATATTCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:1851203 original size:2 final size:2
Alignment explanation
Indices: 1851190--1851224 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1851180 TCAATCTACA
* *
1851190 AT AT AA AT AT AT AT AT AT AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1851225 ATTTAAGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1851209 original size:14 final size:14
Alignment explanation
Indices: 1851190--1851222 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1851180 TCAATCTACA
1851190 ATATAAATATATAT
1 ATATAAATATATAT
1851204 ATATAAATATATAT
1 ATATAAATATATAT
1851218 ATATA
1 ATATA
1851223 TAATTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAAATATATAT
Found at i:1851405 original size:13 final size:13
Alignment explanation
Indices: 1851383--1851434 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
1851373 ACTCTCAATA
*
1851383 TGCGTTATAAATG
1 TGCGTCATAAATG
1851396 TGCGTCATAAATG
1 TGCGTCATAAATG
*
1851409 TGTGTCATAAATG
1 TGCGTCATAAATG
* *
1851422 CGTGTCATAAATG
1 TGCGTCATAAATG
1851435 CGTGTCACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (13 bp):
TGCGTCATAAATG
Found at i:1851428 original size:26 final size:26
Alignment explanation
Indices: 1851382--1851441 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
1851372 GACTCTCAAT
*
1851382 ATGCGT-T-ATAAATGTGCGTCATAA
1 ATGCGTGTCATAAATGCGCGTCATAA
* *
1851406 ATGTGTGTCATAAATGCGTGTCATAA
1 ATGCGTGTCATAAATGCGCGTCATAA
1851432 ATGCGTGTCA
1 ATGCGTGTCA
1851442 CAGATTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 5 0.17
25 1 0.03
26 24 0.80
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (26 bp):
ATGCGTGTCATAAATGCGCGTCATAA
Found at i:1851435 original size:13 final size:13
Alignment explanation
Indices: 1851389--1851441 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
1851379 AATATGCGTT
* *
1851389 ATAAATGTGCGTC
1 ATAAATGCGTGTC
*
1851402 ATAAATGTGTGTC
1 ATAAATGCGTGTC
1851415 ATAAATGCGTGTC
1 ATAAATGCGTGTC
1851428 ATAAATGCGTGTC
1 ATAAATGCGTGTC
1851441 A
1 A
1851442 CAGATTTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (13 bp):
ATAAATGCGTGTC
Found at i:1863107 original size:32 final size:31
Alignment explanation
Indices: 1863071--1863140 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1863061 AGAGACTAGC
1863071 TAGTGTGACATTCAGATAATGCACAACAGAGT
1 TAGTGTG-CATTCAGATAATGCACAACAGAGT
* * *
1863103 TAGTGTTGTATTTAGATAATGCACAACAGTGT
1 TAGTG-TGCATTCAGATAATGCACAACAGAGT
*
1863135 CAGTGT
1 TAGTGT
1863141 CATATTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 1 0.03
32 30 0.91
33 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (31 bp):
TAGTGTGCATTCAGATAATGCACAACAGAGT
Found at i:1863147 original size:32 final size:32
Alignment explanation
Indices: 1863084--1863148 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1863074 TGTGACATTC
* **
1863084 AGATAATGCACAACAGAGTTAGTGTTGTATTT
1 AGATAATGCACAACAGAGTCAGTGTCATATTT
*
1863116 AGATAATGCACAACAGTGTCAGTGTCATATTT
1 AGATAATGCACAACAGAGTCAGTGTCATATTT
1863148 A
1 A
1863149 TAGAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (32 bp):
AGATAATGCACAACAGAGTCAGTGTCATATTT
Found at i:1883780 original size:24 final size:24
Alignment explanation
Indices: 1883753--1883833 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
1883743 CGAAGTGCCA
* *
1883753 CGTATAATTTGCCCCGATGAACCG
1 CGTAGAATTTGCCCCGAAGAACCG
* * *
1883777 CGTAGAAGTTGTCCCGAAGGACCG
1 CGTAGAATTTGCCCCGAAGAACCG
* * *
1883801 CGTAGAATTTGTCCCAAAGAACCA
1 CGTAGAATTTGCCCCGAAGAACCG
*
1883825 TGTAGAATT
1 CGTAGAATT
1883834 GTCCCGGAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCCCCGAAGAACCG
Found at i:1883823 original size:48 final size:47
Alignment explanation
Indices: 1883753--1883845 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 47
1883743 CGAAGTGCCA
* * * *
1883753 CGTATAATTTGCCCCGATGAACCGCGTAGAAGTTGTCCCGAAGGACCG
1 CGTAGAATTTGCCCCAAAGAACCACGTAGAA-TTGTCCCGAAGGACCG
* * *
1883801 CGTAGAATTTGTCCCAAAGAACCATGTAGAATTGTCCCGGAGGAC
1 CGTAGAATTTGCCCCAAAGAACCACGTAGAATTGTCCCGAAGGAC
1883846 AACATTGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 13 0.34
48 25 0.66
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (47 bp):
CGTAGAATTTGCCCCAAAGAACCACGTAGAATTGTCCCGAAGGACCG
Found at i:1887343 original size:23 final size:22
Alignment explanation
Indices: 1887285--1887358 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
1887275 GAGCCTTTAT
* *
1887285 GGGGTATTGATATCCTTTCATA
1 GGGGTATTGATACCCATTCATA
* *
1887307 GGGGTGTTGGTACCCATTCATA
1 GGGGTATTGATACCCATTCATA
*
1887329 GGGGGTATTGATACCTATTCATA
1 -GGGGTATTGATACCCATTCATA
*
1887352 TGGGTAT
1 GGGGTAT
1887359 CAGTATCTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 24 0.56
23 19 0.44
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (22 bp):
GGGGTATTGATACCCATTCATA
Found at i:1888835 original size:43 final size:43
Alignment explanation
Indices: 1888773--1888864 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
1888763 CCAAAACAAA
* *
1888773 AATTAGGAAATAAGTTGGAAAGCTAGTAATAGCTCCAACATAG
1 AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
* * *
1888816 TATTAGGAAATAAGTTGGAAAGATGGTAATTGCTCCAAAATAG
1 AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
1888859 AATTAG
1 AATTAG
1888865 ACATATTACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (43 bp):
AATTAGGAAATAAGTTGGAAAGATAGTAATAGCTCCAAAATAG
Found at i:1890543 original size:31 final size:30
Alignment explanation
Indices: 1890508--1890584 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
1890498 AACTGATACA
* * *
1890508 CATTATCTAAATGTGAACCTTACATATTGTG
1 CATTATCTAAATG-CAACATGACATATTGTG
* *
1890539 CATTATTTGAATGCAACATGACATATTGTG
1 CATTATCTAAATGCAACATGACATATTGTG
* *
1890569 CATTATTTGAATGCAA
1 CATTATCTAAATGCAA
1890585 ACCTGACTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 30 0.73
31 11 0.27
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (30 bp):
CATTATCTAAATGCAACATGACATATTGTG
Found at i:1896731 original size:56 final size:56
Alignment explanation
Indices: 1896659--1896769 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
1896649 AGAAAGTATT
*
1896659 CGTGCATATATAATTATATTCTATTTGATATTTACCAATTATTTTTTGTTCCTATG
1 CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTATG
* *
1896715 CGTGTATATATAATTATCTTCTATGTGATATTTACCAATTATTTTTTGTTCCTAT
1 CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTAT
1896770 TCGTCTAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (56 bp):
CGTGCATATATAATTATATTCTATGTGATATTTACCAATTATTTTTTGTTCCTATG
Found at i:1898451 original size:24 final size:23
Alignment explanation
Indices: 1898418--1898464 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1898408 GCCCAGCTTT
* *
1898418 CAGCTTCCCACGATGGACCACTGC
1 CAGCTGCCCA-GAGGGACCACTGC
*
1898442 CAGCTGCCCAGGGGGACCACTGC
1 CAGCTGCCCAGAGGGACCACTGC
1898465 ACCTCTGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (23 bp):
CAGCTGCCCAGAGGGACCACTGC
Found at i:1899232 original size:12 final size:13
Alignment explanation
Indices: 1899187--1899231 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1899177 CGCCCCGATT
1899187 ACCCGATTACCCG
1 ACCCGATTACCCG
1899200 ACCCGATTACCCG
1 ACCCGATTACCCG
*
1899213 GCCCGA-TACCCG
1 ACCCGATTACCCG
1899225 ACCCGAT
1 ACCCGAT
1899232 AAATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.22, C:0.47, G:0.18, T:0.13
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:1905143 original size:20 final size:20
Alignment explanation
Indices: 1905114--1905152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1905104 AGAGCATATA
*
1905114 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1905134 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1905153 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1906311 original size:23 final size:23
Alignment explanation
Indices: 1906284--1906348 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1906274 CACAATTTTA
* *
1906284 TTTGTCACGACATTTCTATCCCT
1 TTTGTCACGACATTTCCATCCAT
1906307 TTTGTCACGACATTTCCATCCAT
1 TTTGTCACGACATTTCCATCCAT
* * *
1906330 TTTTTCATGACATCTCCAT
1 TTTGTCACGACATTTCCAT
1906349 TTGCTTCTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.08, T:0.43
Consensus pattern (23 bp):
TTTGTCACGACATTTCCATCCAT
Found at i:1920910 original size:3 final size:3
Alignment explanation
Indices: 1920902--1920935 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1920892 TCCAGAGTTC
*
1920902 TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1920936 TCATACGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:1922186 original size:18 final size:18
Alignment explanation
Indices: 1922163--1922233 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
1922153 GAGGGATTAC
1922163 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1922181 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1922199 AGAGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1922217 AGTGGTTCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1922234 AATATTCAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.18, C:0.21, G:0.34, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1928796 original size:15 final size:15
Alignment explanation
Indices: 1928785--1928817 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1928775 GTAAGAATAC
1928785 AACGTCTAAGAAGAA
1 AACGTCTAAGAAGAA
*
1928800 AACGTCAAAGAAGAA
1 AACGTCTAAGAAGAA
1928815 AAC
1 AAC
1928818 ATTAAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (15 bp):
AACGTCTAAGAAGAA
Found at i:1928824 original size:15 final size:15
Alignment explanation
Indices: 1928792--1928832 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1928782 TACAACGTCT
*
1928792 AAGAAGAAAACGTCA
1 AAGAAGAAAACATCA
*
1928807 AAGAAGAAAACATTA
1 AAGAAGAAAACATCA
1928822 AAGAAGGAAAA
1 AAGAA-GAAAA
1928833 AGAAAACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.66, C:0.07, G:0.20, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACATCA
Found at i:1932774 original size:51 final size:51
Alignment explanation
Indices: 1932664--1932774 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
1932654 AACTTGTTGA
*
1932664 AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGACGGAAAAAGAGAAAGT
1 AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGACGGAAAAAGAGAAAGG
*
1932715 AAAGGAAGAGG-GTAAAGGAGAAGGGACACCGTAA-A-GGAAAAAG-GAAGAGG
1 AAAAGAAGAGGAG-AAAGGAGAAGGGACACCG-AAGACGGAAAAAGAGAA-AGG
1932765 AGAAAGAAGA
1 A-AAAGAAGA
1932775 AGGGACACCG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
49 3 0.06
50 12 0.23
51 36 0.68
52 2 0.04
ACGTcount: A:0.54, C:0.06, G:0.37, T:0.03
Consensus pattern (51 bp):
AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGACGGAAAAAGAGAAAGG
Found at i:1934729 original size:2 final size:2
Alignment explanation
Indices: 1934722--1934844 Score: 187
Period size: 2 Copynumber: 62.5 Consensus size: 2
1934712 TCAATCTACA
1934722 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1934763 -T AT TT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1934804 CT AT AT TT AT 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 AT AT AT AT AT A
1934845 ATTTCTGAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
1 2 0.02
2 107 0.98
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1935199 original size:85 final size:85
Alignment explanation
Indices: 1934904--1935164 Score: 416
Period size: 85 Copynumber: 3.1 Consensus size: 85
1934894 GACGTGTGCA
** * * *
1934904 TCAATGACATGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGTTA-
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
*** *
1934968 AGAAGATTTATAACGGGGGCT
66 CTTA-ATTTATGACGGGGGCT
1934989 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
1935054 CTTAATTTATGACGGGGGCT
66 CTTAATTTATGACGGGGGCT
*
1935074 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
1935139 CTTAATTTATGACGGGGGCT
66 CTTAATTTATGACGGGGGCT
1935159 TCAATG
1 TCAATG
1935165 GCACTCAAAG
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 164 0.99
86 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (85 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAT
CTTAATTTATGACGGGGGCT
Found at i:1941392 original size:2 final size:2
Alignment explanation
Indices: 1941385--1941427 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1941375 TTAATCTACA
1941385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1941427 A
1 A
1941428 ATTTACGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1941616 original size:13 final size:13
Alignment explanation
Indices: 1941589--1941627 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1941579 TTCAATATGC
1941589 GTCATAAAT--GT
1 GTCATAAATGCGT
1941600 GTCATAAATGCGT
1 GTCATAAATGCGT
1941613 GTCATAAATGCGT
1 GTCATAAATGCGT
1941626 GT
1 GT
1941628 TACAGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:1961191 original size:17 final size:19
Alignment explanation
Indices: 1961158--1961196 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1961148 TTTAACAACT
1961158 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
1961177 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
1961195 TA
1 TA
1961197 ATACAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Found at i:1962556 original size:29 final size:28
Alignment explanation
Indices: 1962506--1962574 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
1962496 ACCATTTTAA
*
1962506 AAAATAGCACCCTTTTTAAATTAATTACT
1 AAAATAGCA-CCTTTTCAAATTAATTACT
*
1962535 AAAATAGCACCTATTTCGAATTAATTACT
1 AAAATAGCACCT-TTTCAAATTAATTACT
1962564 AAAATAGCACC
1 AAAATAGCACC
1962575 CGGTTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAATAGCACCTTTTCAAATTAATTACT
Found at i:1962590 original size:7 final size:7
Alignment explanation
Indices: 1962575--1962620 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
1962565 AAATAGCACC
1962575 CGGTTAA
1 CGGTTAA
*
1962582 CGGTCAA
1 CGGTTAA
1962589 CGGTTAA
1 CGGTTAA
*
1962596 TGGTTAA
1 CGGTTAA
*
1962603 CGGTCAA
1 CGGTTAA
1962610 CGGTTAA
1 CGGTTAA
1962617 CGGT
1 CGGT
1962621 CGGGTCTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (7 bp):
CGGTTAA
Found at i:1962600 original size:21 final size:21
Alignment explanation
Indices: 1962576--1962616 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1962566 AATAGCACCC
1962576 GGTTAACGGTCAACGGTTAAT
1 GGTTAACGGTCAACGGTTAAT
1962597 GGTTAACGGTCAACGGTTAA
1 GGTTAACGGTCAACGGTTAA
1962617 CGGTCGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTTAACGGTCAACGGTTAAT
Found at i:1962652 original size:12 final size:13
Alignment explanation
Indices: 1962621--1962656 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1962611 GGTTAACGGT
*
1962621 CGGGTCTGGTCAA
1 CGGGTCGGGTCAA
1962634 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1962647 -GGGTCGGGTC
1 CGGGTCGGGTC
1962657 GGGTCGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1962662 original size:22 final size:22
Alignment explanation
Indices: 1962634--1962682 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1962624 GTCTGGTCAA
* *
1962634 CGGGTCGGGTCAA-GGGTCGGGT
1 CGGGTC-GATCAACGGGTCAGGT
1962656 CGGGTCGATCAACGGGTCAGGT
1 CGGGTCGATCAACGGGTCAGGT
1962678 CGGGT
1 CGGGT
1962683 TGGAACCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.18
Consensus pattern (22 bp):
CGGGTCGATCAACGGGTCAGGT
Found at i:1962671 original size:17 final size:17
Alignment explanation
Indices: 1962618--1962679 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
1962608 AACGGTTAAC
*
1962618 GGTCGGGTCTGGTCAACG
1 GGTCGGGTC-GATCAACG
* ****
1962636 GGTCGGGTCAAGGGTCG
1 GGTCGGGTCGATCAACG
1962653 GGTCGGGTCGATCAACG
1 GGTCGGGTCGATCAACG
*
1962670 GGTCAGGTCG
1 GGTCGGGTCG
1962680 GGTTGGAACC
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCGATCAACG
Found at i:1975891 original size:9 final size:9
Alignment explanation
Indices: 1975877--1975914 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1975867 GCTGGAAAAT
1975877 CGGTTTGAC
1 CGGTTTGAC
1975886 CGGTTTTGAC
1 CGG-TTTGAC
1975896 CGGTTTGAC
1 CGGTTTGAC
*
1975905 CGGTCTGAC
1 CGGTTTGAC
1975914 C
1 C
1975915 TGACCCAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.11, C:0.26, G:0.32, T:0.32
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:1975947 original size:12 final size:12
Alignment explanation
Indices: 1975930--1975973 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1975920 CAACCGACCC
1975930 GACCCGACCGTT
1 GACCCGACCGTT
1975942 GACCCGACC--T
1 GACCCGACCGTT
1975952 GAACCCGACCGTT
1 G-ACCCGACCGTT
1975965 GACCCGACC
1 GACCCGACC
1975974 CAAACCGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.07
11 8 0.28
12 17 0.59
13 2 0.07
ACGTcount: A:0.20, C:0.45, G:0.23, T:0.11
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:1975959 original size:23 final size:22
Alignment explanation
Indices: 1975923--1975974 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
1975913 CCTGACCCAA
1975923 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
1975945 CCGACCTGAACCCGACCGTTGAC
1 CCGACCCG-ACCCGACCGTTGAC
1975968 CCGACCC
1 CCGACCC
1975975 AAACCGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:1979959 original size:23 final size:24
Alignment explanation
Indices: 1979891--1979980 Score: 105
Period size: 23 Copynumber: 3.8 Consensus size: 24
1979881 ACTGAAGTGC
1979891 CACGTAGAATTTGTCCCGAAGGAT
1 CACGTAGAATTTGTCCCGAAGGAT
* *
1979915 CGCGTAGAATATT-TCCCAAAGGAT
1 CACGTAGAAT-TTGTCCCGAAGGAT
*
1979939 CACGTAG-ATTTGTCCCGAAGGAC
1 CACGTAGAATTTGTCCCGAAGGAT
* *
1979962 CACATAG-ATTTGTCTCGAA
1 CACGTAGAATTTGTCCCGAA
1979981 TCACCGCGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.04
23 28 0.49
24 25 0.44
25 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
CACGTAGAATTTGTCCCGAAGGAT
Found at i:1979992 original size:23 final size:23
Alignment explanation
Indices: 1979890--1979992 Score: 73
Period size: 23 Copynumber: 4.4 Consensus size: 23
1979880 CACTGAAGTG
*
1979890 CCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAG-ATTTGTCCCGAAGCA
* * * *
1979914 TCGCGTAGAATATT-TCCCAAAGGA
1 CCACGTAG-AT-TTGTCCCGAAGCA
* *
1979938 TCACGTAGATTTGTCCCGAAGGA
1 CCACGTAGATTTGTCCCGAAGCA
* * *
1979961 CCACATAGATTTGTCTCGAATCA
1 CCACGTAGATTTGTCCCGAAGCA
*
1979984 CCGCGTAGA
1 CCACGTAGA
1979993 ACCCTCGACT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.03
23 36 0.55
24 25 0.38
25 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CCACGTAGATTTGTCCCGAAGCA
Found at i:1981650 original size:21 final size:22
Alignment explanation
Indices: 1981612--1981659 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1981602 ATAATGTAAA
*
1981612 AAAATAAGTATAGAAAACTCAT
1 AAAATAAGTATAGAAAACACAT
1981634 CAAAATAA-TAT-GAAAACACAT
1 -AAAATAAGTATAGAAAACACAT
1981655 AAAAT
1 AAAAT
1981660 TCAAATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 3 0.12
23 7 0.29
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAATAAGTATAGAAAACACAT
Found at i:1985137 original size:22 final size:22
Alignment explanation
Indices: 1985106--1985160 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1985096 TATCGTAACT
1985106 TTAAG-GTATTTAAGTTAATGA
1 TTAAGAGTATTTAAGTTAATGA
1985127 TTAAGAGTATTTAAGTTAATGA
1 TTAAGAGTATTTAAGTTAATGA
1985149 TTAAGAGTATTT
1 TTAAGAGTATTT
1985161 CAATGCTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (22 bp):
TTAAGAGTATTTAAGTTAATGA
Found at i:1987532 original size:20 final size:20
Alignment explanation
Indices: 1987507--1987552 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1987497 TGATCCCAAA
*
1987507 TCAACATTC-TAACTTAAATT
1 TCAACATCCATAA-TTAAATT
1987527 TCAACATCCAATAATTAAATT
1 TCAACATCC-ATAATTAAATT
1987548 TCAAC
1 TCAAC
1987553 CTTGAATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 12 0.52
22 3 0.13
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (20 bp):
TCAACATCCATAATTAAATT
Found at i:1988707 original size:29 final size:28
Alignment explanation
Indices: 1988619--1988708 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 28
1988609 CACAATATAT
* * *
1988619 AACTTTTGAAAATTTTATTATTGGTCCCTA
1 AACTTTT-AAAATTATATT-TTAGTCACTA
* **
1988649 AACTTTTACAAAGTTTATACTTTAACCACTA
1 AACTTTTA-AAA--TTATATTTTAGTCACTA
1988680 AACTTTTAAAACTTATATTTTAGTCACTA
1 AACTTTTAAAA-TTATATTTTAGTCACTA
1988709 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
29 15 0.32
30 13 0.28
31 14 0.30
32 5 0.11
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (28 bp):
AACTTTTAAAATTATATTTTAGTCACTA
Found at i:1990050 original size:51 final size:51
Alignment explanation
Indices: 1989974--1990088 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 51
1989964 GTAACTATTG
* * * ** *
1989974 AATAAAATAATAATAAACTAAAGATAATATTTTGATTCTATCATAATTCCT
1 AATAAAATAATAATAAACCAAAGATAATATTCTAACCCTATCATAATTCAT
* *
1990025 AATAAAATAATAATAAACCAAAGATAATGTTCTAACCCTATCTTAATTCAT
1 AATAAAATAATAATAAACCAAAGATAATATTCTAACCCTATCATAATTCAT
*
1990076 ACTAAAATAATAA
1 AATAAAATAATAA
1990089 ATCTAATACT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.33
Consensus pattern (51 bp):
AATAAAATAATAATAAACCAAAGATAATATTCTAACCCTATCATAATTCAT
Found at i:1990123 original size:22 final size:22
Alignment explanation
Indices: 1990074--1990123 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1990064 ATCTTAATTC
1990074 ATACTAAA--ATAATAAATCTA
1 ATACTAAAGGATAATAAATCTA
* *
1990094 ATACTAAAGGATAATACATCTT
1 ATACTAAAGGATAATAAATCTA
*
1990116 ATATTAAA
1 ATACTAAA
1990124 TTATATTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
22 17 0.68
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (22 bp):
ATACTAAAGGATAATAAATCTA
Found at i:1992846 original size:107 final size:108
Alignment explanation
Indices: 1992635--1992857 Score: 247
Period size: 108 Copynumber: 2.1 Consensus size: 108
1992625 GTCCTTTTAT
*
1992635 ATTTTGGTCACATGGGAGGACAAAAATTGGTATTTCCCCTTTTTCATACATGTTATATATTGATT
1 ATTTTGGCCACATGGGAGGACAAAAATTGGTATTTCCCCTTTTTCATACATGTTATATATTGATT
* * *
1992700 GTGTTAATTTTTGTTTACTCCCTCTAAGTTAAGCATG-TTTTGC
66 GTG-TAATATTTGTTAACTCCCCCTAAGTTAAGCATGTTTTTGC
* * * * * * * *
1992743 ATTTTGGCCACCTGTGAGGATC-AAAATTGTTATTTTCCCCTTTTTTCTTGCATGTTATGTGTTT
1 ATTTTGGCCACATGGGAGGA-CAAAAATTGGTA-TTTCCCC-TTTTTCATACATGTTATATATTG
* * *
1992807 ATTG-G-AATATTTGTTAACTCCCCCTTATTTAAGCATGTTTTTTC
63 ATTGTGTAATATTTGTTAACTCCCCCTAAGTTAAGCATGTTTTTGC
1992851 ATTTTGG
1 ATTTTGG
1992858 TCATATGTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
107 27 0.28
108 38 0.40
109 9 0.09
110 22 0.23
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (108 bp):
ATTTTGGCCACATGGGAGGACAAAAATTGGTATTTCCCCTTTTTCATACATGTTATATATTGATT
GTGTAATATTTGTTAACTCCCCCTAAGTTAAGCATGTTTTTGC
Found at i:2005878 original size:42 final size:42
Alignment explanation
Indices: 2005819--2005903 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2005809 CTTGGATTCC
2005819 ACCATATTGACAACATCTGCATCCTCCAGCGGGTAGTTATAT
1 ACCATATTGACAACATCTGCATCCTCCAGCGGGTAGTTATAT
2005861 ACCATATTGACAACATCTGCATCCTCCAGCGGGTAGTTATAT
1 ACCATATTGACAACATCTGCATCCTCCAGCGGGTAGTTATAT
2005903 A
1 A
2005904 GACGGAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
ACCATATTGACAACATCTGCATCCTCCAGCGGGTAGTTATAT
Found at i:2009893 original size:91 final size:91
Alignment explanation
Indices: 2009724--2009895 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 91
2009714 TGTTTACCAA
* * * **
2009724 AATAGTCATTTTGGCCCCTATTCTTTTTTTCTAGAGTATTTTAGCCCCCAACATTTTATTTTAGG
1 AATAGTCATTTTGGCCCCTATTCTTTTTTTCTAGAGCATTTTAGCCCCCAACATTTCATATTAAA
*
2009789 GCAAAAAGGCCCCTAACGTTTGACTG
66 GCAAAAAGACCCCTAACGTTTGACTG
* * *
2009815 AATAGTCATTTTGGCCCTTTATTC-TTTTTTCTGGAGCATTTT-GACCCCTAACATTTCATATTA
1 AATAGTCATTTTGGCCC-CTATTCTTTTTTTCTAGAGCATTTTAG-CCCCCAACATTTCATATTA
* *
2009878 AAGTAAAATGACCCCTAA
64 AAGCAAAAAGACCCCTAA
2009896 TTTAAAGCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
90 1 0.01
91 62 0.91
92 5 0.07
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (91 bp):
AATAGTCATTTTGGCCCCTATTCTTTTTTTCTAGAGCATTTTAGCCCCCAACATTTCATATTAAA
GCAAAAAGACCCCTAACGTTTGACTG
Found at i:2011915 original size:220 final size:221
Alignment explanation
Indices: 2011533--2011976 Score: 701
Period size: 220 Copynumber: 2.0 Consensus size: 221
2011523 TTCGCTGCTT
* * * *
2011533 AATAGCTACAGATGATAATAGCATCCATCATAAGAGCTGAGTTTAAAATATTGTTCCCAAATTCA
1 AATAGCTACAGATGATAATAGCATCCATCATAAGAACTGAGTTCAAAATAATGTACCCAAATTCA
** *
2011598 AGCACATAAAGAATGGGCTTTATATAAAATTTCAATCGCAAAGTCATTAAAAAATATATTAAAGT
66 AGCACATAAAGAATGGGCTTTATATAAAATTTCAAAAGCAAAGTCATTAAAAAAGATATTAAAGT
* * * *
2011663 AGGCTTCATAATGTTTTTCCTATACCTGCATGCTGCATCTTTAGTGAGACTGAGAATGTAAG-AC
131 AGGCTTCATAATATTTTTCCTATACCTGCATGCTGAATCTTTAGTGAAAATGAGAATGTAAGAAC
* *
2011727 ACAGGAAAAACTATTTCTTACATTTC
196 ACAAGAAAAACTATTGCTTACATTTC
2011753 AATAGCTACAGATGATAATAGCATCCATCATAAGAACTGAGTTCAAAATAATGTACCCAAATTCA
1 AATAGCTACAGATGATAATAGCATCCATCATAAGAACTGAGTTCAAAATAATGTACCCAAATTCA
* *
2011818 AGCACATAAAGAATGGGCTTTATATAAATTTTCAAAAGCAAAGTCATTAAAAAAGATATTAATGT
66 AGCACATAAAGAATGGGCTTTATATAAAATTTCAAAAGCAAAGTCATTAAAAAAGATATTAAAGT
* * *
2011883 AGGCTTCATCATATTTTTCGTTTACCTGCATGCTGAATCTTTAGTGAAAATGAGAATGTAAGAAA
131 AGGCTTCATAATATTTTTCCTATACCTGCATGCTGAATCTTTAGTGAAAATGAGAATGTAAG--A
2011948 ACACAAGAAAAACTATTGCTTACATTTC
194 ACACAAGAAAAACTATTGCTTACATTTC
2011976 A
1 A
2011977 TGGCAGGAGC
Statistics
Matches: 203, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
220 176 0.87
223 27 0.13
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (221 bp):
AATAGCTACAGATGATAATAGCATCCATCATAAGAACTGAGTTCAAAATAATGTACCCAAATTCA
AGCACATAAAGAATGGGCTTTATATAAAATTTCAAAAGCAAAGTCATTAAAAAAGATATTAAAGT
AGGCTTCATAATATTTTTCCTATACCTGCATGCTGAATCTTTAGTGAAAATGAGAATGTAAGAAC
ACAAGAAAAACTATTGCTTACATTTC
Found at i:2014248 original size:19 final size:19
Alignment explanation
Indices: 2014224--2014296 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
2014214 GGGAACAAAT
2014224 ATTTAGAATTATAATTAAA
1 ATTTAGAATTATAATTAAA
2014243 ATTTAGAATTATAATTAAA
1 ATTTAGAATTATAATTAAA
2014262 ATTTAGAATTATAATTAAA
1 ATTTAGAATTATAATTAAA
2014281 ATTTAGAATTATAATT
1 ATTTAGAATTATAATT
2014297 GTATTCTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTAGAATTATAATTAAA
Found at i:2014258 original size:13 final size:13
Alignment explanation
Indices: 2014236--2014296 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
2014226 TTAGAATTAT
*
2014236 AATTAAAATTTAG
1 AATTATAATTTAG
*
2014249 AATTATAA-TTAA
1 AATTATAATTTAG
* *
2014261 AATT-TAGAATTAT
1 AATTATA-ATTTAG
*
2014274 AATTAAAATTTAG
1 AATTATAATTTAG
2014287 AATTATAATT
1 AATTATAATT
2014297 GTATTCTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 27 0.71
14 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (13 bp):
AATTATAATTTAG
Found at i:2014296 original size:6 final size:6
Alignment explanation
Indices: 2014230--2014296 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
2014220 AAATATTTAG
* * * * *
2014230 AATTAT AATTAA AATTTAG AATTAT AATTAA AATTTAG AATTAT AATTAA
1 AATTAT AATTAT AA-TTAT AATTAT AATTAT AA-TTAT AATTAT AATTAT
*
2014280 AATTTAG AATTAT AATT
1 AA-TTAT AATTAT AATT
2014297 GTATTCTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 34 0.69
7 15 0.31
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (6 bp):
AATTAT
Found at i:2016540 original size:32 final size:34
Alignment explanation
Indices: 2016504--2016573 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
2016494 CCTTACAAAC
* *
2016504 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
2016536 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
2016570 TCCC
1 TCCC
2016574 CTTTACGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:2016882 original size:21 final size:21
Alignment explanation
Indices: 2016856--2016918 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2016846 CCATAATGGG
*
2016856 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
2016877 GGGAATCGATATCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2016898 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2016919 ATATTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2017054 original size:15 final size:15
Alignment explanation
Indices: 2017034--2017089 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
2017024 CCATGCAGGG
2017034 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
2017049 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
2017065 TGGGGGAATCTGTTCCC
1 --GGGGAATCTGTACCC
2017082 GGGGAATC
1 GGGGAATC
2017090 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
17 3 0.09
18 9 0.26
19 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.20
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:2017112 original size:35 final size:34
Alignment explanation
Indices: 2017032--2017116 Score: 145
Period size: 33 Copynumber: 2.5 Consensus size: 34
2017022 AACCATGCAG
*
2017032 GGGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCT
2017066 -GGGGGAATCTGTTCCCGGGGAATCGATACCCCCT
1 GGGGGGAATCTGTTCCCGGGGAATCGATA-CCCCT
2017100 GGGGGGAATCTGTTCCC
1 GGGGGGAATCTGTTCCC
2017117 CCTGGGGTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 27 0.56
34 5 0.10
35 16 0.33
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (34 bp):
GGGGGGAATCTGTTCCCGGGGAATCGATACCCCT
Found at i:2017128 original size:21 final size:20
Alignment explanation
Indices: 2017082--2017138 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
2017072 ATCTGTTCCC
2017082 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
2017102 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
2017122 GGTGGAATCTGTACCCC
1 GG-GGAATCTGTACCCC
2017139 TTGGACAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.16, C:0.30, G:0.33, T:0.21
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:2017139 original size:20 final size:20
Alignment explanation
Indices: 2017049--2017139 Score: 74
Period size: 20 Copynumber: 4.9 Consensus size: 20
2017039 ATCTGTACCC
*
2017049 GGGGAATC-GATACCCCT-G
1 GGGGAATCTGTTACCCCTGG
2017067 GGGGAATCTGTT--CCC---
1 GGGGAATCTGTTACCCCTGG
*
2017082 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTGTTA-CCCCTGG
*
2017102 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTTACCCCTGG
2017122 GGTGGAATCTG-TACCCCT
1 GG-GGAATCTGTTACCCCT
2017140 TGGACAATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.03
15 8 0.14
17 6 0.10
18 8 0.14
19 2 0.03
20 23 0.39
21 10 0.17
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGGAATCTGTTACCCCTGG
Found at i:2019103 original size:3 final size:3
Alignment explanation
Indices: 2019095--2019132 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2019085 TACGTCCTCA
* *
2019095 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2019133 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2028657 original size:23 final size:23
Alignment explanation
Indices: 2028627--2028671 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2028617 TACTATAATT
2028627 CAAATCCCACTTGTAAAAGTTAA
1 CAAATCCCACTTGTAAAAGTTAA
2028650 CAAATCCCACTTGTAAAAGTTA
1 CAAATCCCACTTGTAAAAGTTA
2028672 CAACTGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (23 bp):
CAAATCCCACTTGTAAAAGTTAA
Found at i:2031500 original size:109 final size:107
Alignment explanation
Indices: 2031261--2031502 Score: 263
Period size: 107 Copynumber: 2.2 Consensus size: 107
2031251 TAAAAAGTCA
* * *
2031261 CTACACATGACCAAAGTGTAAAAACACGCTAAACTTATAAGGACCAAACAGAGAATAACCCAAAA
1 CTACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAAGGACCAAACAGAGAATAACCCAAAA
** * *
2031326 ATACAAAGCATGCAAGAAAAGGGAAAATAACAGTTTTAAATC
66 ATACAAAGCACACAAGAAAAGGGAAAATAAAAGATTTAAATC
* * * * ** * * *
2031368 CTACATATGACCAGAATGAAAAAATACGCTAATGTTAGAGGGGCCAAA-ATATGAATAACCCAAA
1 CTACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAAGGACCAAACAGA-GAATAACCCAAA
**
2031432 AATTACAAAGCACACAATGAAAAGGGAAAATAAAAGATTT-GGTCC
65 AA-TACAAAGCACACAA-GAAAAGGGAAAATAAAAGATTTAAAT-C
*
2031477 CTACAGGTGACCAAAATGTAAAAACA
1 CTACAGATGACCAAAATGTAAAAACA
2031503 TACTAAACCT
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
106 2 0.02
107 52 0.48
108 13 0.12
109 42 0.39
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (107 bp):
CTACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAAGGACCAAACAGAGAATAACCCAAAA
ATACAAAGCACACAAGAAAAGGGAAAATAAAAGATTTAAATC
Found at i:2032911 original size:135 final size:135
Alignment explanation
Indices: 2032636--2033188 Score: 623
Period size: 135 Copynumber: 4.1 Consensus size: 135
2032626 AACTTTCTGC
* * * * * *
2032636 TGGAAATGTTGATCCCTCGAGTAAGGTGTT-GCTGATTCGAAATGTCGTGAATCGAGAAAAGGTT
1 TGGAAATGTTAATCCCTCAAGTGAGGT-TTCACTGATTCAAAATATCGTGAATCGAGAAAAGGTT
* * * * *
2032700 GAACAATTTCTTCTCATTACTAACTTCTTT-TCCCTCAATCGGATGAGTTCATCTCATTAAGAAA
65 GAACAAGTTCTTCTCATTACGAACTT-TTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAAA
*
2032764 TCTTCAT
129 TCTCCAT
* * * ** * * *
2032771 TGGAAATGCTAAACCCTAAAGCAAGGCATT-ACTGATTCAAAAATGTCGTGAATCGAGAAAAGGC
1 TGGAAATGTTAATCCCTCAAGTGAGG-TTTCACTGATTC-AAAATATCGTGAATCGAGAAAAGGT
* * *
2032835 TGAACAAGTTCTTCTCATTAC-AAATTTTTCACCCTCTATCGGATTTA-TTCTTCTCATTATGAA
64 TGAACAAGTTCTTCTCATTACGAACTTTTTCTCCCTCTATCGGA-TGAGTTCTTCTCATTATGAA
* *
2032898 CTCTCTAT
128 ATCTCCAT
* * * * * *
2032906 TGGAAATATTAATCCCTCAAGTGAGGTTTCGCTAATTTC-AAATACCATGAATCGAGCAAAGGTT
1 TGGAAATGTTAATCCCTCAAGTGAGGTTTCACTGA-TTCAAAATATCGTGAATCGAGAAAAGGTT
* * * * * * *
2032970 TAACAAGTTATTCTTATTACGAACTTTTTCTTCCTCTATCAGATGAGTTCTTCTCATTACGAACT
65 GAACAAGTTCTTCTCATTACGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAAAT
2033035 CTCCAT
130 CTCCAT
* *
2033041 TGGAAATGTTAATCCCTCAAGTGAGGTTTCACTGGTTCAAAATATCGTGAATCGAGTAAAGGTTG
1 TGGAAATGTTAATCCCTCAAGTGAGGTTTCACTGATTCAAAATATCGTGAATCGAGAAAAGGTTG
* * *
2033106 AACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTTCTTATTATTATGAAATC
66 AACAAGTTCTTCTCATTACGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAAATC
2033171 TCCAT
131 TCCAT
2033176 TGGAAATGTTAAT
1 TGGAAATGTTAAT
2033189 TGGTTTATCA
Statistics
Matches: 348, Mismatches: 61, Indels: 18
0.81 0.14 0.04
Matches are distributed among these distances:
134 47 0.14
135 253 0.73
136 48 0.14
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (135 bp):
TGGAAATGTTAATCCCTCAAGTGAGGTTTCACTGATTCAAAATATCGTGAATCGAGAAAAGGTTG
AACAAGTTCTTCTCATTACGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAAATC
TCCAT
Found at i:2034169 original size:15 final size:16
Alignment explanation
Indices: 2034151--2034194 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2034141 TTTTCTACTA
2034151 CTTTTTTTTCTTTT-T
1 CTTTTTTTTCTTTTAT
2034166 CTTTTTTTTTCTTTTAT
1 C-TTTTTTTTCTTTTAT
*
2034183 CTTTTGTTTCTT
1 CTTTTTTTTCTT
2034195 AGGCTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 23 0.88
17 2 0.08
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (16 bp):
CTTTTTTTTCTTTTAT
Found at i:2034171 original size:16 final size:17
Alignment explanation
Indices: 2034152--2034187 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2034142 TTTCTACTAC
2034152 TTTTTTTTCTTTT-TCT
1 TTTTTTTTCTTTTATCT
2034168 TTTTTTTTCTTTTATCT
1 TTTTTTTTCTTTTATCT
2034185 TTT
1 TTT
2034188 GTTTCTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTCTTTTATCT
Found at i:2043996 original size:45 final size:45
Alignment explanation
Indices: 2043941--2044245 Score: 333
Period size: 45 Copynumber: 6.8 Consensus size: 45
2043931 ACTATAACAT
* * * * * *
2043941 CTTTTCTATTGATGATGCACCCATATGCATTTCAACTGTAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* * * * *
2043986 CTTTTTTATTGATAATGTACTCATATACATTTCAAC-CATGGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTC-TAGCATA
* *
2044031 CATTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATG
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* * * *
2044076 CTCTTCTGTTGATAATGCACCCCTATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
** * *
2044121 CTTTTCTGTTGATAATACATCCATATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* ** * *
2044166 CTTTTATGTTGATAATGTACCCATATACATTTCAACTAAAGTATG
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* * *
2044211 TTTTTTTGTTGATAGTGTACCCATATACATTTCAA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAA
2044246 ATATGGCATC
Statistics
Matches: 222, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
45 221 1.00
46 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
Found at i:2044262 original size:90 final size:89
Alignment explanation
Indices: 2043898--2044286 Score: 323
Period size: 90 Copynumber: 4.3 Consensus size: 89
2043888 GTAACCTCCA
* * * * ** * * *
2043898 TTTATGTTTATAATACA-CCATTATGCACTTTAAACTATAACAT-CTTTTCTATTGATGATGCAC
1 TTTATGTTGATAATGCACCCA-TATACA-TTTCAACTATAGTATACTTTTCTGTTGATAATGTAC
* * *
2043961 CCATATGCATTTCAACTGTAGTATAC
64 CCATATACATTTCAACTCTAGCATAC
* * * * * * *
2043987 TTTTTTATTGATAATGTACTCATATACATTTCAACCATGGTATACATTTCTGTTGATAATGTACC
1 -TTTATGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGTACC
*
2044052 CATATACATTTCAACTCTAGCATGC
65 CATATACATTTCAACTCTAGCATAC
* * * * * ** *
2044077 TCTTCTGTTGATAATGCACCCCTATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATACATC
1 T-TTATGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGTACC
*
2044142 CATATGCATTTCAACTCTAGCATAC
65 CATATACATTTCAACTCTAGCATAC
* * ** * *
2044167 TTTTATGTTGATAATGTACCCATATACATTTCAACTAAAGTATGTTTTTTTGTTGATAGTGTACC
1 -TTTATGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGTACC
* * * *
2044232 CATATACATTTCAAATATGGCATCC
65 CATATACATTTCAACTCTAGCATAC
*** *
2044257 ATTTATGCCAATAATGCACCCATATGCATT
1 -TTTATGTTGATAATGCACCCATATACATT
2044287 AGTATTCTCA
Statistics
Matches: 234, Mismatches: 61, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
89 11 0.05
90 220 0.94
91 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (89 bp):
TTTATGTTGATAATGCACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATGTACCC
ATATACATTTCAACTCTAGCATAC
Found at i:2044271 original size:135 final size:135
Alignment explanation
Indices: 2044028--2044286 Score: 311
Period size: 135 Copynumber: 1.9 Consensus size: 135
2044018 CAACCATGGT
* **
2044028 ATACATTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATGCTCTTCTGTTGATAATG
1 ATACATTTATGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATG
* * * * * * *** *
2044093 CACCCCTATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATACATCCATATGCATTTCAACT
66 CACCCATATACATTTCAAATATAGCATACATTTATGCCAATAATACACCCATATGCATTTCAACT
2044158 CTAGC
131 CTAGC
* * * * * *
2044163 ATACTTTTATGTTGATAATGTACCCATATACATTTCAACTAAAGTATGTTTTTTTGTTGATAGTG
1 ATACATTTATGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATG
* * * *
2044228 TACCCATATACATTTCAAATATGGCATCCATTTATGCCAATAATGCACCCATATGCATT
66 CACCCATATACATTTCAAATATAGCATACATTTATGCCAATAATACACCCATATGCATT
2044287 AGTATTCTCA
Statistics
Matches: 101, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
135 101 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (135 bp):
ATACATTTATGTTGATAATGTACCCATATACATTTCAACTAAAGCATGCTCTTCTGTTGATAATG
CACCCATATACATTTCAAATATAGCATACATTTATGCCAATAATACACCCATATGCATTTCAACT
CTAGC
Found at i:2044726 original size:20 final size:20
Alignment explanation
Indices: 2044697--2044752 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
2044687 TGGCCCTTCA
2044697 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
* * *
2044717 GTATCAATACTACTCTATTATG
1 GTATCGATAC--CCCTACTATG
2044739 GTATCGATACCCCT
1 GTATCGATACCCCT
2044753 TTTAGTATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:2044814 original size:94 final size:96
Alignment explanation
Indices: 2044697--2044916 Score: 286
Period size: 96 Copynumber: 2.3 Consensus size: 96
2044687 TGGCCCTTCA
* * * * *
2044697 GTATCGATACCC-CTACTATGGTATCAATACTACTCTATTATGGTATCGATA-CC-CCTTTTAGT
1 GTATCGATACCCTC-ACCATGGTATCAATACTACTATATTATGGTATCAATACCCTCCCTTCAGT
2044759 ATCGATACCAAAATT-AGATTCGATGTAGCCTG
65 ATCGATACCAAAATTAAG-TTCGATGTAGCCTG
* * *
2044791 GTATCGATACCCTCACCATGGTATCGATACTACTATGTTATGGTATCAATACCCTCCCTTCGGTA
1 GTATCGATACCCTCACCATGGTATCAATACTACTATATTATGGTATCAATACCCTCCCTTCAGTA
* **
2044856 TCGATATCAAAATTAAGTTCGATGTTTCCTG
66 TCGATACCAAAATTAAGTTCGATGTAGCCTG
*
2044887 GTATCGATACCCTCACCATGGTATCCATAC
1 GTATCGATACCCTCACCATGGTATCAATAC
2044917 CACATCGCTT
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
94 44 0.40
95 3 0.03
96 61 0.55
97 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (96 bp):
GTATCGATACCCTCACCATGGTATCAATACTACTATATTATGGTATCAATACCCTCCCTTCAGTA
TCGATACCAAAATTAAGTTCGATGTAGCCTG
Found at i:2044957 original size:96 final size:96
Alignment explanation
Indices: 2044756--2044937 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
2044746 TACCCCTTTT
*
2044756 AGTATCGATACCAAAATTAGATTCGATGTAGCCTGGTATCGATACCCTCACCATGGTATCGATAC
1 AGTATCGATACCAAAATTAGATTCGATGTAGCCTGGTATCGATACCCTCACCATGGTATCCATAC
* * * *
2044821 TACTATGTTATGGTATCAATACCCTCCCTTC
66 CACTATGCTATGGTAACAATACCCTCACTTC
* * **
2044852 GGTATCGATATCAAAATTA-AGTTCGATGTTTCCTGGTATCGATACCCTCACCATGGTATCCATA
1 AGTATCGATACCAAAATTAGA-TTCGATGTAGCCTGGTATCGATACCCTCACCATGGTATCCATA
*
2044916 CCAC-ATCGCT-TGGTAACGATAC
65 CCACTAT-GCTATGGTAACAATAC
2044938 TGTTTGACTC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
95 13 0.17
96 62 0.83
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (96 bp):
AGTATCGATACCAAAATTAGATTCGATGTAGCCTGGTATCGATACCCTCACCATGGTATCCATAC
CACTATGCTATGGTAACAATACCCTCACTTC
Found at i:2051162 original size:45 final size:45
Alignment explanation
Indices: 2050871--2051185 Score: 407
Period size: 45 Copynumber: 7.0 Consensus size: 45
2050861 AACAATAACA
* * * * *
2050871 ACTTTTCTGTTGATGATGAACCCTTATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
* *
2050916 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
* *
2050961 ACTTTTCTGTTGATAATGTACACATATACATTTCAACTCTAGCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
* * * * *
2051006 GCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
* * * *
2051051 AC-TTTCTTGTTGATGATGCACCCATATGCATTTCAACTTTAGCAT
1 ACTTTTC-TGTTGATAATGTACCCATATACATTTCAACTATAGCAT
* *
2051096 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAAAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
** *
2051141 ACTTTTCTGTTGATAGCGTACCCATATACATTTCAACTATGGCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
2051186 CCCATATGCG
Statistics
Matches: 239, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
44 3 0.01
45 232 0.97
46 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT
Found at i:2051757 original size:76 final size:76
Alignment explanation
Indices: 2051666--2051826 Score: 227
Period size: 76 Copynumber: 2.1 Consensus size: 76
2051656 ACCCCTTCAA
* **
2051666 GTATCGATACCAAAATTAGCTTCGATGTAGCCTGGTATTGATACCCTCACCATGGTATCGATACT
1 GTATCGATACCAAAATTAGCTTCGATGTAGCCTAGTATCAATACCCTCACCATGGTATCGATACT
2051731 ACTATGCTATG
66 ACTATGCTATG
* * **
2051742 GTATTGATACCAAAATTAGGTTCGATGTTTCCTAGTATCAATACCCTCACCATGGTATCGATACT
1 GTATCGATACCAAAATTAGCTTCGATGTAGCCTAGTATCAATACCCTCACCATGGTATCGATACT
2051807 AC-ATCGCT-TG
66 ACTAT-GCTATG
*
2051817 GTACCGATAC
1 GTATCGATAC
2051827 TATTTGACTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
75 12 0.16
76 63 0.84
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (76 bp):
GTATCGATACCAAAATTAGCTTCGATGTAGCCTAGTATCAATACCCTCACCATGGTATCGATACT
ACTATGCTATG
Found at i:2056180 original size:17 final size:18
Alignment explanation
Indices: 2056158--2056196 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2056148 CCCGGGCCGA
*
2056158 GTTT-GGTATTTATGTTG
1 GTTTGGGTATTTAGGTTG
2056175 GTTTGGGTATTTAGGTTG
1 GTTTGGGTATTTAGGTTG
2056193 GTTT
1 GTTT
2056197 CGGATGGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.10, C:0.00, G:0.33, T:0.56
Consensus pattern (18 bp):
GTTTGGGTATTTAGGTTG
Found at i:2056212 original size:22 final size:22
Alignment explanation
Indices: 2056187--2056241 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2056177 TTGGGTATTT
2056187 AGGTTGGTTTCGG-ATGGGCTTG
1 AGGTTGGTTT-GGCATGGGCTTG
*
2056209 AGGTTGGTTTGGCTTGGGCTTG
1 AGGTTGGTTTGGCATGGGCTTG
*
2056231 AGGTTAGTTTG
1 AGGTTGGTTTG
2056242 TAAATGGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.09, C:0.07, G:0.44, T:0.40
Consensus pattern (22 bp):
AGGTTGGTTTGGCATGGGCTTG
Found at i:2056789 original size:135 final size:135
Alignment explanation
Indices: 2056438--2056942 Score: 636
Period size: 135 Copynumber: 3.7 Consensus size: 135
2056428 AAAAGACCAC
* * * * * *
2056438 GAATCAAGCAAAGGTTAAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTATCGGATAAGTT
1 GAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTT
* * * * * *
2056503 CATCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGCGAGGTGTTGCTGATTTGAAAT
66 CTTCTCATTATAAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGTTTTACTGATTTGAAAT
2056568 GAT-GT
131 G-TCGT
* * * * *
2056573 AAATGGAGAAAATGTTGAACAA-TTCTTCTCATTACGAACTTCTTCTCCCTCTATTGGATGAGTT
1 GAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTT
* * * *
2056637 CTTCTCATTATGAACTCTCAATTGGAAATATTAAACCCTTAAGTGAGGTTTTACTGATTTGAAAT
66 CTTCTCATTATAAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGTTTTACTGATTTGAAAT
2056702 GTCGT
131 GTCGT
* * * * * *
2056707 GATTCGAGCAAATGTTGAACAAGTTCTTCTTATTACGAATTTTTTCTCCCTCTATCGGACGAGTT
1 GAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTT
* * * * *
2056772 CTTCTCATTACAAACTCTCAATTGGAAATTTTAATCCCTCAAGTGAGGTTTCATTGATTCGAAAT
66 CTTCTCATTATAAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGTTTTACTGATTTGAAAT
2056837 GTCGT
131 GTCGT
* * **
2056842 GAATCGAGCAAAGGTTGAACAAGTTCTTCTAAGTACGAACTTCTTCTCCCTCTATCAAATGAGTT
1 GAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTT
* * *
2056907 CTTCTTATCATAAACTCTCCATTGGAAATGTTAATC
66 CTTCTCATTATAAACTCTCAATTGGAAATGTTAATC
2056943 AGTTTATCTT
Statistics
Matches: 318, Mismatches: 50, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
133 1 0.00
134 115 0.36
135 202 0.64
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (135 bp):
GAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCGGATGAGTT
CTTCTCATTATAAACTCTCAATTGGAAATGTTAATCCCTCAAGTGAGGTTTTACTGATTTGAAAT
GTCGT
Found at i:2056863 original size:269 final size:270
Alignment explanation
Indices: 2056444--2056940 Score: 660
Period size: 269 Copynumber: 1.8 Consensus size: 270
2056434 CCACGAATCA
* * *
2056444 AGCAAAGGTTAAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTATCGGATAAGTTCATCTC
1 AGCAAAGGTTAAACAAGTTCTTCTCAATACGAACTTCTTCTCCCTCTATCGGACAAGTTCATCTC
** * *
2056509 ATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGCGAGGTGTTGCTGATTTGAAATGATGTA
66 ATTACAAACTCTCAATTGGAAATGTTAATCCCTCAAGCGAGGTGTTGCTGATTCGAAATGATGTA
* * * * ***
2056574 AATGGAGAAAATGTTGAACAA-TTCTTCTCATTACGAACTTCTTCTCCCTCTATTGGATGAGTTC
131 AATCGAGAAAAGGTTGAACAAGTTCTTCTAAGTACGAACTTCTTCTCCCTCTATCAAATGAGTTC
* *
2056638 TTCTCATTATGAACTCTCAATTGGAAATATTAAACCCTTAAGTGAGGTTTTACTGATTTGAAATG
196 TTCTCATCATAAACTCTCAATTGGAAATATTAAACCCTTAAGTGAGGTTTTACTGATTTGAAATG
2056703 TCGTGATTCG
261 TCGTGATTCG
* * * * * * * *
2056713 AGCAAATGTTGAACAAGTTCTTCTTATTACGAATTTTTTCTCCCTCTATCGGACGAGTTCTTCTC
1 AGCAAAGGTTAAACAAGTTCTTCTCAATACGAACTTCTTCTCCCTCTATCGGACAAGTTCATCTC
* *
2056778 ATTACAAACTCTCAATTGGAAATTTTAATCCCTCAAGTGAGGT-TT-CATTGATTCGAAATG-TC
66 ATTACAAACTCTCAATTGGAAATGTTAATCCCTCAAGCGAGGTGTTGC--TGATTCGAAATGAT-
* *
2056840 GTGAATCGAGCAAAGGTTGAACAAGTTCTTCTAAGTACGAACTTCTTCTCCCTCTATCAAATGAG
128 GTAAATCGAGAAAAGGTTGAACAAGTTCTTCTAAGTACGAACTTCTTCTCCCTCTATCAAATGAG
* * *
2056905 TTCTTCTTATCATAAACTCTCCATTGGAAATGTTAA
193 TTCTTCTCATCATAAACTCTCAATTGGAAATATTAA
2056941 TCAGTTTATC
Statistics
Matches: 193, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
267 1 0.01
268 3 0.02
269 123 0.64
270 66 0.34
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (270 bp):
AGCAAAGGTTAAACAAGTTCTTCTCAATACGAACTTCTTCTCCCTCTATCGGACAAGTTCATCTC
ATTACAAACTCTCAATTGGAAATGTTAATCCCTCAAGCGAGGTGTTGCTGATTCGAAATGATGTA
AATCGAGAAAAGGTTGAACAAGTTCTTCTAAGTACGAACTTCTTCTCCCTCTATCAAATGAGTTC
TTCTCATCATAAACTCTCAATTGGAAATATTAAACCCTTAAGTGAGGTTTTACTGATTTGAAATG
TCGTGATTCG
Found at i:2057975 original size:5 final size:5
Alignment explanation
Indices: 2057962--2058096 Score: 57
Period size: 5 Copynumber: 25.6 Consensus size: 5
2057952 TGAACCTTCA
* * *
2057962 TTTTA TTTTC TTTT- TCTTT- TTTTC TTTTAC TTTT- TGTTC TTTTA TTTT-
1 TTTTC TTTTC TTTTC T-TTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TTTTC
* * *
2058010 TTTTG TTCT- TTTTC ATTTTC ATTTTC ATTTTC ATTTTTC ATTTTTAA TTTTC
1 TTTTC TTTTC TTTTC -TTTTC -TTTTC -TTTTC --TTTTC --TTTT-C TTTTC
2058062 -TTTC TTTTTC TTTTC TTTCCTC TTTTC TTTTC TTT
1 TTTTC -TTTTC TTTTC TTT--TC TTTTC TTTTC TTT
2058097 CTTAGGAGTA
Statistics
Matches: 108, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
4 18 0.17
5 44 0.41
6 30 0.28
7 16 0.15
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:2057978 original size:6 final size:6
Alignment explanation
Indices: 2057967--2058096 Score: 65
Period size: 6 Copynumber: 21.3 Consensus size: 6
2057957 CTTCATTTTA
* * *
2057967 TTTTCT TTTTCTTT TTTTCT TTTACT TTTTGT TCTTT-T ATTTTTT TTGTTCT
1 TTTTCT TTTTC--T TTTTCT TTTTCT TTTTCT T-TTTCT -TTTTCT TT-TTCT
* * * **
2058019 TTTTCA TTTTCA TTTTCA TTTTCAT TTTTCAT TTTTAA TTTTC- -TTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTC-T TTTTCT TTTTCT TTTTCT
*
2058067 TTTTC- TTTTC- TTTCCT CTTTTC- TTTTCT TT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT TT
2058097 CTTAGGAGTA
Statistics
Matches: 101, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.04
5 14 0.14
6 52 0.51
7 25 0.25
8 6 0.06
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:2057995 original size:12 final size:11
Alignment explanation
Indices: 2057967--2058096 Score: 76
Period size: 12 Copynumber: 11.7 Consensus size: 11
2057957 CTTCATTTTA
2057967 TTTTCTTTT-T
1 TTTTCTTTTCT
*
2057977 CTTT-TTTTCT
1 TTTTCTTTTCT
*
2057987 TTTAC-TTT-T
1 TTTTCTTTTCT
* *
2057996 TGTTCTTTTAT
1 TTTTCTTTTCT
*
2058007 TTTTTTTGTTCT
1 TTTTCTT-TTCT
*
2058019 TTTTCATTTTCA
1 TTTTC-TTTTCT
2058031 TTTTCATTTTCAT
1 TTTTC-TTTTC-T
2058044 TTTTCATTTT-T
1 TTTTC-TTTTCT
2058055 AATTTTC-TTTCT
1 --TTTTCTTTTCT
2058067 TTTTCTTTTCT
1 TTTTCTTTTCT
*
2058078 TTCCTCTTTTC-
1 TT-TTCTTTTCT
2058089 TTTTCTTT
1 TTTTCTTT
2058097 CTTAGGAGTA
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.08
10 22 0.23
11 19 0.20
12 29 0.31
13 17 0.18
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:2058033 original size:25 final size:24
Alignment explanation
Indices: 2058001--2058053 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2057991 CTTTTTGTTC
**
2058001 TTTTATTTTTTTTGTTC-TTTTTCA
1 TTTTATTTTCATT-TTCATTTTTCA
2058025 TTTTCATTTTCATTTTCATTTTTCA
1 TTTT-ATTTTCATTTTCATTTTTCA
2058050 TTTT
1 TTTT
2058054 TAATTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTTTCATTTTCATTTTTCA
Found at i:2058070 original size:17 final size:16
Alignment explanation
Indices: 2058057--2058099 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
2058047 TCATTTTTAA
2058057 TTTTCTTTC-TTTTTC
1 TTTTCTTTCTTTTTTC
*
2058072 TTTTCTTTCCTCTTTTC
1 TTTTCTTT-CTTTTTTC
2058089 TTTTCTTTCTT
1 TTTTCTTTCTT
2058100 AGGAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 3 0.12
17 13 0.54
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTCTTTTTTC
Found at i:2076850 original size:65 final size:65
Alignment explanation
Indices: 2076713--2076869 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 65
2076703 ACTAAGAGTA
* * * *
2076713 CATCGATGCATCAAGTGCATCCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTG
* * * * *
2076777 CATTGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGTATGG-TAAG
1 CATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-AG
2076840 TG
64 TG
*
2076842 CATCGATGCATGAAATGCATTCGATGTT
1 CATCGATGCATCAAATGCATTCGATGTT
2076870 CAATTTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 24 0.30
65 52 0.66
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTG
Found at i:2076908 original size:65 final size:63
Alignment explanation
Indices: 2076713--2076919 Score: 179
Period size: 65 Copynumber: 3.2 Consensus size: 63
2076703 ACTAAGAGTA
* * * *
2076713 CATCGATGCATCAAGTGCATCCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTGGT
1 CATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGT
2076776 G
63 G
* * * **
2076777 CATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGTATGGTAAGTG
1 CATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTGGTG
* ** *
2076842 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TTATGGTGCATCGATGCATGGATTGG
1 CATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGG
2076905 TG
62 TG
*
2076907 CATCGGTGCATCA
1 CATCGATGCATCA
2076920 CTCTGAAAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 2 0.02
63 3 0.03
64 42 0.37
65 63 0.55
66 4 0.03
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
CATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTG
Found at i:2079030 original size:13 final size:13
Alignment explanation
Indices: 2079002--2079040 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2078992 TGGACAATGT
*
2079002 TTTGAAAA-ACTA
1 TTTGAAAATAATA
2079014 TTTGAAAATAATA
1 TTTGAAAATAATA
*
2079027 TTTGTAAATAATA
1 TTTGAAAATAATA
2079040 T
1 T
2079041 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:2087880 original size:65 final size:65
Alignment explanation
Indices: 2087750--2087906 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 65
2087740 ACTAAGAGTA
* * * * *
2087750 CATCGATGTATCAAGTGCATTCTATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTG
* * *
2087814 CATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCCCAGTGCATCGGTGCATGG-TAAG
1 CATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-AG
2087877 TG
64 TG
*
2087879 CATCGATGCATGAAATGCATTCGATGTT
1 CATCGATGCATCAAATGCATTCGATGTT
2087907 CAATTTAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
64 24 0.30
65 54 0.67
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTG
Found at i:2087945 original size:65 final size:64
Alignment explanation
Indices: 2087750--2087947 Score: 193
Period size: 65 Copynumber: 3.1 Consensus size: 64
2087740 ACTAAGAGTA
* * * * * *
2087750 CATCGATGTATCAAGTGCATTCTATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCACAGTGCATCGATGCATGGTTGGTG
* * **
2087814 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCCCAGTGCATCGGTGCATGGTAAGTG
1 CATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCACAGTGCATCGATGCATGGTTGGTG
* ** ** **
2087879 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTTATGGTGCATCGATGCATGGATTGGT
1 CATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCACAGTGCATCGATGCATGG-TTGGT
2087943 G
64 G
2087944 CATC
1 CATC
2087948 ACTATGGAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
63 3 0.03
64 43 0.39
65 60 0.55
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCACAGTGCATCGATGCATGGTTGGTG
Found at i:2090051 original size:13 final size:13
Alignment explanation
Indices: 2090023--2090061 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2090013 TGGGCAATGT
*
2090023 TTTGAAAA-ACTA
1 TTTGAAAATAATA
2090035 TTTGAAAATAATA
1 TTTGAAAATAATA
*
2090048 TTTGTAAATAATA
1 TTTGAAAATAATA
2090061 T
1 T
2090062 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:2096350 original size:64 final size:62
Alignment explanation
Indices: 2096264--2096466 Score: 203
Period size: 66 Copynumber: 3.1 Consensus size: 62
2096254 TGCACTAAAA
* *
2096264 GTGCATCAATGCATAAAGTGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAA-TGCATTCGATGTTTCAAAATATCCATAGTGCATCGATGCATGG-TG
* *
2096328 GTGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA-ATCCTTAGTGCATCGGTGCATGGT
1 GTGCATCGATGCAT-AAATGCATTCGATG--TTTCA-AAATATCCATAGTGCATCGATGCATGGT
*
2096392 AA
62 -G
* ** * *
2096394 GTGCATCGATGCATGAAATGCATTGGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCAAAAT-ATCCATAGTGCATCGATGCATGG--T
2096458 G
62 G
2096459 GTGCATCG
1 GTGCATCG
2096467 GTGTATCACT
Statistics
Matches: 116, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 43 0.37
65 12 0.10
66 53 0.46
67 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCAAAATATCCATAGTGCATCGATGCATGGTG
Found at i:2096398 original size:66 final size:65
Alignment explanation
Indices: 2096240--2096424 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 65
2096230 ACCGTTGGAC
* ** *
2096240 CCTTAGTTCATCGGTGCACT-AAAAGTGCATCAATGCATAAAGTGCATTCGATG--TTTCAAAAT
1 CCTTAGTGCATCGGTGCA-TGGTAAGTGCATCGATGCATAAA-TGCATTCGATGTTTTTCAAAAT
2096302 AG
64 AG
* * *
2096304 CCATAGTGCATCGATGCATGGCT-GGTGCATCGATGCATCAAATGCATTCGATGTTTTTCATAAA
1 CCTTAGTGCATCGGTGCATGG-TAAGTGCATCGATGCAT-AAATGCATTCGATGTTTTTCA-AAA
*
2096368 -AT
63 TAG
*
2096370 CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGCATTGGATGTT
1 CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCAT-AAATGCATTCGATGTT
2096425 CAATTTAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
63 1 0.01
64 39 0.39
65 4 0.04
66 54 0.53
67 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATAAATGCATTCGATGTTTTTCAAAATAG
Found at i:2110455 original size:19 final size:19
Alignment explanation
Indices: 2110431--2110484 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
2110421 GTCAACTCTT
2110431 GTCAAAGTCAATGGGTCAG
1 GTCAAAGTCAATGGGTCAG
** *
2110450 GTCAAAGTCAACAGCTCAG
1 GTCAAAGTCAATGGGTCAG
2110469 GTCAAAGTCAATGGGT
1 GTCAAAGTCAATGGGT
2110485 TGGTTGAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (19 bp):
GTCAAAGTCAATGGGTCAG
Found at i:2113132 original size:17 final size:17
Alignment explanation
Indices: 2113098--2113135 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2113088 TTATGTGATC
*
2113098 ACATTTAATACGGGATT
1 ACATTTAATACGGAATT
*
2113115 ACATTTAATACGTAATT
1 ACATTTAATACGGAATT
2113132 ACAT
1 ACAT
2113136 GCACTTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (17 bp):
ACATTTAATACGGAATT
Found at i:2113344 original size:31 final size:31
Alignment explanation
Indices: 2113301--2113363 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2113291 GAGTCGAGGG
* *
2113301 TTACCTATGTTCTATAGGACATATGGATAGT
1 TTACCTAGGTTCTATAGGACATATGGACAGT
* * *
2113332 TTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TTACCTAGGTTCTATAGGACATATGGACAGT
2113363 T
1 T
2113364 ACCGAGGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTAGGTTCTATAGGACATATGGACAGT
Found at i:2113383 original size:30 final size:31
Alignment explanation
Indices: 2113315--2113383 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
2113305 CTATGTTCTA
* * * *
2113315 TAGGACATATGGATAGTTTACCTAGGTTCTT
1 TAGGACCTATGGACAGTTTACCGAGGATCTT
*
2113346 TGGGACCTATGGACAG-TTACCGAGGATCTT
1 TAGGACCTATGGACAGTTTACCGAGGATCTT
*
2113376 TATGACCT
1 TAGGACCT
2113384 CTAGATAGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (31 bp):
TAGGACCTATGGACAGTTTACCGAGGATCTT
Found at i:2117302 original size:28 final size:28
Alignment explanation
Indices: 2117262--2117319 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2117252 TCGTTAGATG
2117262 ATAACTAAGCTTAAGGAAAGCTTAAGTT
1 ATAACTAAGCTTAAGGAAAGCTTAAGTT
2117290 ATAACTAAGCTTAAGGAAAGCTTAAGTT
1 ATAACTAAGCTTAAGGAAAGCTTAAGTT
2117318 AT
1 AT
2117320 CTTAAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (28 bp):
ATAACTAAGCTTAAGGAAAGCTTAAGTT
Found at i:2118414 original size:17 final size:17
Alignment explanation
Indices: 2118388--2118431 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2118378 TATGATTTAT
*
2118388 GTGATCACATTTAATAC
1 GTGATTACATTTAATAC
*
2118405 GTGATTACATTTAATAT
1 GTGATTACATTTAATAC
*
2118422 GTAATTACAT
1 GTGATTACAT
2118432 GCACTTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (17 bp):
GTGATTACATTTAATAC
Found at i:2118652 original size:31 final size:31
Alignment explanation
Indices: 2118596--2118658 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2118586 GAGTCGAGGG
* *
2118596 TTACCTATGTTCTACGGGAAATATGGATAGT
1 TTACCTAGGTTCTACGGGAAATATGGACAGT
* **
2118627 TTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TTACCTAGGTTCTACGGGAAATATGGACAGT
2118658 T
1 T
2118659 ATCAAGGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (31 bp):
TTACCTAGGTTCTACGGGAAATATGGACAGT
Found at i:2118689 original size:30 final size:30
Alignment explanation
Indices: 2118617--2118716 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
2118607 CTACGGGAAA
* * ***
2118617 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCAAGGATCTTTATGACC
* *
2118648 TATGGACAGTTATCAAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
* *
2118678 TTTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
*
2118708 TCTGGATAG
1 TATGGATAG
2118717 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
30 49 0.86
31 8 0.14
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCAAGGATCTTTATGACC
Found at i:2128683 original size:23 final size:23
Alignment explanation
Indices: 2128653--2128697 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2128643 TACTATAATT
2128653 CAAATCCCACTTGTAAAAGTTAA
1 CAAATCCCACTTGTAAAAGTTAA
2128676 CAAATCCCACTTGTAAAAGTTA
1 CAAATCCCACTTGTAAAAGTTA
2128698 CAACTGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (23 bp):
CAAATCCCACTTGTAAAAGTTAA
Found at i:2133954 original size:19 final size:19
Alignment explanation
Indices: 2133913--2133957 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2133903 ATATGATTCT
* **
2133913 TATGTGTCATATGTTATTG
1 TATGTGTCACATGTTATAC
*
2133932 TATGTGTTACATGTTATAC
1 TATGTGTCACATGTTATAC
2133951 TATGTGT
1 TATGTGT
2133958 ATTCCATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (19 bp):
TATGTGTCACATGTTATAC
Found at i:2134436 original size:23 final size:23
Alignment explanation
Indices: 2134410--2134471 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
2134400 AGAATTTGAT
2134410 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCATTCGGGACATTTCTAC
2134433 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCATTCGGGACATTTCTAC
2134456 GTGGTCATTCGGGACA
1 GTGGTCATTCGGGACA
2134472 ATCTTATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (23 bp):
GTGGTCATTCGGGACATTTCTAC
Found at i:2136719 original size:13 final size:13
Alignment explanation
Indices: 2136680--2136720 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2136670 TCCTATGACA
*
2136680 TTATTATGGATAT
1 TTATTTTGGATAT
* *
2136693 CTATGTTGGATAT
1 TTATTTTGGATAT
2136706 TTATTTTGGATAT
1 TTATTTTGGATAT
2136719 TT
1 TT
2136721 TTGGATTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (13 bp):
TTATTTTGGATAT
Found at i:2136866 original size:19 final size:18
Alignment explanation
Indices: 2136831--2136865 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2136821 ATGAAAAACA
2136831 TTTTTGATTAAATTTTTG
1 TTTTTGATTAAATTTTTG
2136849 TTTTTGA-TATAATTTTT
1 TTTTTGATTA-AATTTTT
2136866 TAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTTGATTAAATTTTTG
Found at i:2137420 original size:32 final size:32
Alignment explanation
Indices: 2137384--2137449 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
2137374 CAACAAGCAA
*
2137384 ATAGAGTCAAATTTGTATTC-AACAGTGTCTTT
1 ATAGAGCCAAATTTGTATTCGAA-AGTGTCTTT
*
2137416 ATAGAGCCAAATTTGTATTCGAATGTGTCTTT
1 ATAGAGCCAAATTTGTATTCGAAAGTGTCTTT
2137448 AT
1 AT
2137450 TTCACTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
ATAGAGCCAAATTTGTATTCGAAAGTGTCTTT
Found at i:2144347 original size:2 final size:2
Alignment explanation
Indices: 2144334--2144401 Score: 95
Period size: 2 Copynumber: 35.0 Consensus size: 2
2144324 GTTTTTCTAG
*
2144334 AT AT AG AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2144375 AT AT AT AT -T AT CT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2144402 GATTTCATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2147571 original size:85 final size:84
Alignment explanation
Indices: 2147456--2147616 Score: 243
Period size: 85 Copynumber: 1.9 Consensus size: 84
2147446 TGTAAGTCAT
* * *
2147456 ACAAATGTGTGTCATTTTCATTTATGATGGGGGCTTCAATGACACGCAATGTAAGC-CATACATG
1 ACAAAAGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACACGCAATG--AGCACATAAATG
2147520 CGTGTCATAAATTTATGACAC
64 CGTGTCATAAATTTATGACAC
* *
2147541 ACAAAAGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACGCGCAATGAGCATCATAAATGT
1 ACAAAAGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACACGCAATGAGCA-CATAAATGC
2147606 GTGTCATAAAT
65 GTGTCATAAAT
2147617 GTGTGTCATA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
83 3 0.04
85 66 0.96
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (84 bp):
ACAAAAGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACACGCAATGAGCACATAAATGCG
TGTCATAAATTTATGACAC
Found at i:2147612 original size:13 final size:13
Alignment explanation
Indices: 2147596--2147626 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2147586 GCAATGAGCA
2147596 TCATAAATGTGTG
1 TCATAAATGTGTG
2147609 TCATAAATGTGTG
1 TCATAAATGTGTG
2147622 TCATA
1 TCATA
2147627 GATTTATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (13 bp):
TCATAAATGTGTG
Found at i:2152139 original size:23 final size:23
Alignment explanation
Indices: 2152113--2152161 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2152103 TAAATTATTC
2152113 TAATATTTTAAAAAT-AATAATAT
1 TAAT-TTTTAAAAATAAATAATAT
*
2152136 TAATTTTTTAAAATAAATAATAT
1 TAATTTTTAAAAATAAATAATAT
2152159 TAA
1 TAA
2152162 CTGTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATTTTTAAAAATAAATAATAT
Found at i:2152857 original size:10 final size:10
Alignment explanation
Indices: 2152844--2152868 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2152834 ATAAATTTAA
2152844 ATAATATCAT
1 ATAATATCAT
2152854 ATAATATCAT
1 ATAATATCAT
2152864 ATAAT
1 ATAAT
2152869 TCCAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATATCAT
Found at i:2153980 original size:19 final size:19
Alignment explanation
Indices: 2153965--2154015 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2153955 CAGCTTACTG
2153965 TCAAATTCATAGCTTATTT
1 TCAAATTCATAGCTTATTT
*
2153984 TCAAATTCATAGTTTATTT
1 TCAAATTCATAGCTTATTT
2154003 TCAAATTCATAGC
1 TCAAATTCATAGC
2154016 CTAATGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
TCAAATTCATAGCTTATTT
Found at i:2157232 original size:21 final size:22
Alignment explanation
Indices: 2157203--2157248 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2157193 ATAATTGAAA
*
2157203 TTAAATTATTTTATAA-ATATT
1 TTAAATTATTATATAATATATT
*
2157224 TTAATTTATTATATAATTATATT
1 TTAAATTATTATATAA-TATATT
2157247 TT
1 TT
2157249 TTGAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAAATTATTATATAATATATT
Found at i:2157481 original size:25 final size:24
Alignment explanation
Indices: 2157447--2157493 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2157437 TTATGTTTAG
*
2157447 ATTTTTTTTAAAAAATTAAATAAT
1 ATTTTTTTTAAAAAATAAAATAAT
2157471 ATTTTATTTTAAAAAATAAAATA
1 ATTTT-TTTTAAAAAATAAAATA
2157494 TAAACATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTTTTTTAAAAAATAAAATAAT
Found at i:2173485 original size:26 final size:26
Alignment explanation
Indices: 2173456--2173507 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2173446 TCATATCAAT
*
2173456 AATCCTGTTAACTATTGGTGTCTTGA
1 AATCCTGTTAACTATTGGTGCCTTGA
2173482 AATCCTGTTAACTATTGGTGCCTTGA
1 AATCCTGTTAACTATTGGTGCCTTGA
2173508 TTGGTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (26 bp):
AATCCTGTTAACTATTGGTGCCTTGA
Found at i:2177123 original size:2 final size:2
Alignment explanation
Indices: 2177118--2177164 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2177108 AAATCTAAGG
2177118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2177160 AT AT A
1 AT AT A
2177165 ATTGACACGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2181485 original size:19 final size:18
Alignment explanation
Indices: 2181444--2181485 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2181434 TATTTTTTCA
*
2181444 AATTA-TTTTGAACTTTG
1 AATTATTTTTGAAATTTG
*
2181461 AATTATTTTTGAAATATTT
1 AATTATTTTTGAAAT-TTG
2181480 AATTAT
1 AATTAT
2181486 GCCCAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (18 bp):
AATTATTTTTGAAATTTG
Found at i:2184040 original size:2 final size:2
Alignment explanation
Indices: 2184033--2184069 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2184023 AATTGATTAA
2184033 AT AT AT 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 AT AT AT A
2184070 GCTTAAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2198978 original size:19 final size:18
Alignment explanation
Indices: 2198934--2198985 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
2198924 CCTACATATG
* *
2198934 ACATAATTATATTTACAAG
1 ACATAA-TATATATACAAC
2198953 ACTATAATATATATACACAC
1 AC-ATAATATATATACA-AC
*
2198973 ACATAAAATATAT
1 ACATAATATATAT
2198986 GCATATACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (18 bp):
ACATAATATATATACAAC
Found at i:2198991 original size:25 final size:27
Alignment explanation
Indices: 2198963--2199017 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
2198953 ACTATAATAT
*
2198963 ATATACACACACATAA-A-ATATATGC
1 ATATACACACACATAATACATATATAC
*
2198988 ATATACACGCACATAATACATATATAC
1 ATATACACACACATAATACATATATAC
2199015 ATA
1 ATA
2199018 CACGCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 1 0.04
27 10 0.38
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (27 bp):
ATATACACACACATAATACATATATAC
Found at i:2199018 original size:25 final size:23
Alignment explanation
Indices: 2198959--2199023 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
2198949 CAAGACTATA
*
2198959 ATATATATACACACACATAAAAT
1 ATATATATACACGCACATAAAAT
2198982 ATATGCATATACACGCACATAATACAT
1 ATAT--ATATACACGCACATAA-A-AT
*
2199009 ATATACATACACGCA
1 ATATATATACACGCA
2199024 TATTCTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 4 0.11
25 25 0.69
26 1 0.03
27 6 0.17
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.25
Consensus pattern (23 bp):
ATATATATACACGCACATAAAAT
Found at i:2199472 original size:18 final size:18
Alignment explanation
Indices: 2199451--2199494 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2199441 TTAATGAACC
*
2199451 AATTTGGGGCTGTTGGCT
1 AATTTGGGGCTGTTGACT
*
2199469 AATTTGGGGTTGTTGACT
1 AATTTGGGGCTGTTGACT
*
2199487 AGTTTGGG
1 AATTTGGG
2199495 AGAATCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.07, G:0.39, T:0.41
Consensus pattern (18 bp):
AATTTGGGGCTGTTGACT
Found at i:2202702 original size:216 final size:215
Alignment explanation
Indices: 2202250--2202936 Score: 1109
Period size: 202 Copynumber: 3.3 Consensus size: 215
2202240 ATTTAAAAAT
*
2202250 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAA-AACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
2202314 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAATACTAAATTATAC
66 GGATCAAATC-AAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
2202379 CCATTT-AAAAGTTATGGGCCAATTAAAAAATAAAAATAAGTAATAAGTATGGGTCAATTTTAGA
130 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGA
2202443 TGCAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
2202464 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
2202529 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATC-AAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
2202594 CCATTTAAAAAGTTACGAGCCAATTAAAAAATAGAAATAAGTAACAAGTATGGGT-ATATTTCAG
130 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCA-ATTTTAG
*
2202658 ATGCAAATAAAATTTGGAGCAC
194 ATGCAAATAAAATTTGGAGGAC
* *
2202680 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
2202745 GGATCAAATC-----------GA-T-TGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACA
66 GGATCAAATCAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
2202797 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGAT
131 CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGAT
*
2202862 GCAAATAAAATTTGGTGGAC
196 GCAAATAAAATTTGGAGGAC
*
2202882 TAAATTGAATAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
2202937 AAGGGATCAA
Statistics
Matches: 448, Mismatches: 21, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
202 168 0.38
203 2 0.00
204 1 0.00
214 47 0.10
215 86 0.19
216 144 0.32
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (215 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACC
CATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGAT
GCAAATAAAATTTGGAGGAC
Done.