Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:1872642 original size:201 final size:200
Alignment explanation
Indices: 1872258--1872961 Score: 961
Period size: 201 Copynumber: 3.5 Consensus size: 200
1872248 TTTTCTAACT
* * *
1872258 AAACCGGTTTATTTATACCGG-TAACATTGCAAATTTACCTATTACATTATAATTTTCGGTTTCG
1 AAACCGGTATATTTATACCGGAT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCG
* * * * *
1872322 ATAATT-TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCATGCACCTC-GTTGGGC
65 AT-GTTCTTGGGATCGACAC-TTTTATAAATGTATCGACACTTTATGCATGCACCCCTTTTGGGC
* * *
1872384 ATTCATTCTGG-AAAAAAGTATCGACACAAACTT-AAAAAGTGTCGATACATTATGTAGAACTAT
128 ATTCATTCTGGAAAAAAAGTATCGACACAAA-TTCCACAAGTGTCGATACATTATGTAGACCTAT
1872447 TTTCTCATA
192 TTTCTCATA
* * * * * * *
1872456 AAACCAGTATATTTCTATCGGGTACATTGTAAATTTACCTATTATATTGTAATTATCAGTTTCGA
1 AAACCGGTATATTTATACCGGATACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
1872521 TGTTCTTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCAT
66 TGTTCTTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCATGCACCCCTTTTGGGCAT
* *
1872586 TCATTCTGGAAAAAAAGTATTGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCT
130 TCATTCTGGAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTT
1872651 CTCATA
195 CTCATA
* * * * * * * *
1872657 AAACTGGTCTATTTATACCGGTTACATTGAAAAATTACATATTACATTGTAATTATGGGTTTCGA
1 AAACCGGTATATTTATACCGGATACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
1872722 TGTTCTTGGGATCGACACTTATTATAAATGTATCGACACTTTATGCTTGCACCCCTTTTGGGCAT
66 TGTTCTTGGGATCGACACTT-TTATAAATGTATCGACACTTTATGCATGCACCCCTTTTGGGCAT
* *
1872787 TCATTTTGGACAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTT
130 TCATTCTGGAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTT
1872852 CTCATA
195 CTCATA
* * * *
1872858 AAATCGGTAAATTTATACCGGATACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCAA
1 AAACCGGTATATTTATACCGGATACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
1872923 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
66 TGTTCTTGGGATCGACAC-TTTTATAAATGTATCGACAC
1872962 ATATTTAGGT
Statistics
Matches: 448, Mismatches: 50, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
197 3 0.01
198 69 0.15
199 30 0.07
200 19 0.04
201 325 0.73
202 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
AAACCGGTATATTTATACCGGATACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTCTTGGGATCGACACTTTTATAAATGTATCGACACTTTATGCATGCACCCCTTTTGGGCATT
CATTCTGGAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTC
TCATA
Found at i:1874023 original size:15 final size:15
Alignment explanation
Indices: 1874003--1874031 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1873993 GGAGGTTGTA
1874003 GTTGAGAAGAGCTTG
1 GTTGAGAAGAGCTTG
1874018 GTTGAGAAGAGCTT
1 GTTGAGAAGAGCTT
1874032 TGAGAAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (15 bp):
GTTGAGAAGAGCTTG
Found at i:1874961 original size:201 final size:201
Alignment explanation
Indices: 1874322--1875489 Score: 1876
Period size: 201 Copynumber: 5.8 Consensus size: 201
1874312 TATGAAATTT
* * ** *
1874322 AAAAATGTATCGACACAAATT-TAAAATGTGTTTATACATTATGTAGACTTATTCTCTCATAAAA
1 AAAAA-GTATCGACACAAATTCCACAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAA
* *
1874386 CCGGTCTATTTATACCGGTTACATTGAAACATTACCTATTACATTGTAATTATGGGTTTAGATGT
64 CCGGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGT
* * * *
1874451 TTTTGGGATTGACACTTATTATAAATGCATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCA
129 TCTTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCA
*
1874516 TTCTGGAA
194 TTCTGGAC
* * * *
1874524 AAAAAGTATCGACACAAATTCCACAAGTGTAGATACATTATGTATACATATTCTATCATAAAACC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
** * ** * *
1874589 GGAATATTTATACCGATTACATTGAAATTTTACATATTACATTGTAATTATGGGTTTCGAT-TTT
66 GGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTC
* * *
1874653 TTGGCATCGACACTTTTTA-AAATGTATCGACACTTTATGTGTGCACCCCTTTTGGGCATTCATT
131 TTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
1874717 CTGGAC
196 CTGGAC
* *
1874723 AAAAAGTATCGACACAAA-TCCTACAAGTTTTGATACATTATGTAGACCTATTCTCTCATAAAAC
1 AAAAAGTATCGACACAAATTCC-ACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* *
1874787 TGGTCTATTTATACCGGTTACATTGAAAAATTACCTCTTACATTGTAATTATGGGTTTCGATGTT
65 CGGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTT
*
1874852 CTTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGACATTCAT
130 CTTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCAT
*
1874917 TCTGGTC
195 TCTGGAC
* *
1874924 AAAAAGTATCGACACAAATTCCACAATTGTCGATACATTATGTAGACCTATTCTCTCATAAAACT
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1874989 GGTCTATTTATACCGGTTACATTGAAAAATTACCTCTTACATTGTAATTATGGGTTTCGATGTTC
66 GGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTC
1875054 TTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
131 TTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
1875119 CTGGAC
196 CTGGAC
*
1875125 AAAAAGTATTGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1875190 GGTCTATTTATACCGGTTATATTGAAAAATTACATATTACATTGTAATTATGGGTTTCGATGTTC
66 GGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTC
* * *
1875255 TTGGGATCGACACTTATTATAAATGTATCGACACTTTATGCTTGCACCCCTTTTGGGTATTCATT
131 TTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
*
1875320 TTGGAC
196 CTGGAC
*
1875326 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1875391 GGTCTATTTATACCGGTTACATTGAAAATTTACCTATTATATTGTAATTATGGGTTTCGATGTTC
66 GGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTC
1875456 TTGGGATCGACACTTCTTATAAATGTATCGACAC
131 TTGGGATCGACACTTCTTATAAATGTATCGACAC
1875490 ATATGTTTAC
Statistics
Matches: 900, Mismatches: 61, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
198 3 0.00
199 157 0.17
200 38 0.04
201 691 0.77
202 11 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTCTATTTATACCGGTTACATTGAAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTC
TTGGGATCGACACTTCTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
CTGGAC
Found at i:1875962 original size:19 final size:19
Alignment explanation
Indices: 1875938--1875986 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1875928 TTACATTCAC
1875938 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
**
1875957 ATACAAAATTATAAATTTT
1 ATACAAAATTATAAATCGT
1875976 ATACAAAATTA
1 ATACAAAATTA
1875987 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1880630 original size:182 final size:181
Alignment explanation
Indices: 1880064--1880615 Score: 792
Period size: 182 Copynumber: 3.1 Consensus size: 181
1880054 AACCCAAGTG
*
1880064 TCGATACATTTTTATAAAGTATCGACACTTTATATGCGCTATTACTGCTTCTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCA
* *
1880129 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTGGCTCTTTACCAGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
*
1880194 TGTC-----A-ACCGGTTTTATCATATTTTTACATGTTATATTGTTATAGA
131 TGTCATTTTAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGA
* *
1880239 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTTTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * * * *
1880304 AAAGTGTCGATTCTTATAATAAAATATCGACAATTTTAACATATTCGGTGGTTCTTTACCGGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
* * *
1880369 TGTAATTTTTAGACTGGTTTTATCATATTTTTACTTGTTATATTGTTATGGA
131 TGTCA-TTTTAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGA
* * * * *
1880421 TCAATACATTTTTTTAAAATATCGACACTTTATAAACGCTATTACTGCTTGTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * * * *
1880486 AAAGTGTTGATACTTATAGTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
* * * *
1880551 TGTCATTTTGAGACCGGTTTTGTCATATTTTTACGTGTTATATTGCTACGGA
131 TGTCATTTT-AGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGA
1880603 TCGATACATTTTT
1 TCGATACATTTTT
1880616 TATTTGTATC
Statistics
Matches: 332, Mismatches: 37, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
175 124 0.37
181 5 0.02
182 203 0.61
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
TCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCA
AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
TGTCATTTTAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGA
Found at i:1884266 original size:3 final size:3
Alignment explanation
Indices: 1884258--1884294 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1884248 TTTTAATTTA
1884258 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1884295 GATATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1884610 original size:23 final size:23
Alignment explanation
Indices: 1884582--1884625 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1884572 TCGGATTAAA
1884582 ATTT-AAACCAAATTAATTAAATT
1 ATTTAAAACC-AATTAATTAAATT
*
1884605 ATTTAAAATCAATTAATTAAA
1 ATTTAAAACCAATTAATTAAA
1884626 ATTTTGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTTAAAACCAATTAATTAAATT
Found at i:1887116 original size:30 final size:30
Alignment explanation
Indices: 1887082--1887141 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1887072 TCTTGAAAGT
*
1887082 AAATTAAATGGTTACGCTAGCTGTTGGTTG
1 AAATTAAATGGTTACGCTAGCTGTCGGTTG
*
1887112 AAATTAAATGGTTACTCTAGCTGTCGGTTG
1 AAATTAAATGGTTACGCTAGCTGTCGGTTG
1887142 GGAAGAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (30 bp):
AAATTAAATGGTTACGCTAGCTGTCGGTTG
Found at i:1891893 original size:22 final size:22
Alignment explanation
Indices: 1891868--1891912 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1891858 ATACCTAATA
1891868 TTTACTTTTTGTTTCATTTTAG
1 TTTACTTTTTGTTTCATTTTAG
1891890 TTTACTTTTTGTTTCATTTTAG
1 TTTACTTTTTGTTTCATTTTAG
1891912 T
1 T
1891913 ACTCATCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (22 bp):
TTTACTTTTTGTTTCATTTTAG
Found at i:1893692 original size:16 final size:18
Alignment explanation
Indices: 1893673--1893709 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
1893663 TTATTAATTA
1893673 TATAAA-ATATAA-AAAC
1 TATAAATATATAATAAAC
1893689 TATAAATTATATAATAAAC
1 TATAAA-TATATAATAAAC
1893708 TA
1 TA
1893710 ATATTGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAATATATAATAAAC
Found at i:1895717 original size:3 final size:3
Alignment explanation
Indices: 1895709--1895737 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1895699 GTGAAAACAC
1895709 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1895738 ATCAAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1899304 original size:3 final size:3
Alignment explanation
Indices: 1899296--1899326 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1899286 AACCCCACAA
1899296 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1899327 TAAATGGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1900389 original size:2 final size:2
Alignment explanation
Indices: 1900384--1900417 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1900374 TTTTTTTTAA
1900384 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
1900418 TTGTCTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1903486 original size:81 final size:81
Alignment explanation
Indices: 1903351--1903805 Score: 696
Period size: 81 Copynumber: 5.6 Consensus size: 81
1903341 ACTTAGTGAT
* * * *
1903351 GCATAATTGACACTTTTCTGTCAAATGCACAACTAGACAATTAATATTTTACTCAAAGACATTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
* *
1903416 ACGTTTCATCTAAATG
66 ACCTTTCATCTAACTG
* *
1903432 GCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTTTACTCAAAGGCATTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
*
1903497 ACCTTTCATCTAAATG
66 ACCTTTCATCTAACTG
* * * *
1903513 ACATAATTGACACATTTCTATCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGACATTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
1903578 ACCTTTCATCTAACTG
66 ACCTTTCATCTAACTG
* * *
1903594 GCATAATTGACACCTTTTTGTCAAATGCACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
1903659 ACCTTTCATCTAACTG
66 ACCTTTCATCTAACTG
* *
1903675 ACATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
1903740 ACCTTTCATCTAACTG
66 ACCTTTCATCTAACTG
* * * * *
1903756 GCATAATTGACACATTTTTTTCAAATGCATAGCTAGGCAA-TAATCTTTTA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTA
1903806 TTTAAAACAA
Statistics
Matches: 346, Mismatches: 28, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
80 10 0.03
81 336 0.97
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (81 bp):
GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGCATTTA
ACCTTTCATCTAACTG
Found at i:1906169 original size:19 final size:20
Alignment explanation
Indices: 1906142--1906179 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1906132 CACAATCTGG
*
1906142 TAAATTTAAAAAA-TATATT
1 TAAAATTAAAAAATTATATT
1906161 TAAAATTAAAAAATTATAT
1 TAAAATTAAAAAATTATAT
1906180 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATTAAAAAATTATATT
Found at i:1906939 original size:29 final size:30
Alignment explanation
Indices: 1906895--1906952 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1906885 CATTTTGAGT
*
1906895 AACGAAATGAAACGTTAGGCACCAAACTGG
1 AACGAAATAAAACGTTAGGCACCAAACTGG
*
1906925 AACGAAA-AAAACGTTAGGCACTAAACTG
1 AACGAAATAAAACGTTAGGCACCAAACTG
1906953 AAAAAACGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (30 bp):
AACGAAATAAAACGTTAGGCACCAAACTGG
Found at i:1911133 original size:36 final size:37
Alignment explanation
Indices: 1911045--1911149 Score: 126
Period size: 37 Copynumber: 2.9 Consensus size: 37
1911035 TGGAACTAAG
* *
1911045 TCAATCTTAAGCCTTCA-CAAAAAAGGATTGAAGCAAA
1 TCAATCTTAAGCCTTCACCAAAGAA-GAGTGAAGCAAA
1911082 TCAATCTTAAGCCTTCACCAAAGAAGAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACCAAAGAAGAGTGAAGCAAA
* * * *
1911119 -CCATCTTAAACCTTCACCGAAG-ACAGTGAAG
1 TCAATCTTAAGCCTTCACCAAAGAAGAGTGAAG
1911150 TACCACATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 8 0.13
36 19 0.31
37 28 0.46
38 6 0.10
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACCAAAGAAGAGTGAAGCAAA
Found at i:1911456 original size:42 final size:41
Alignment explanation
Indices: 1911390--1911491 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
1911380 TTCACAACTT
* * * *
1911390 ATAAGTCCTTCAGGTCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG
* * *
1911431 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAAGATG
1 -ATAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG
* *
1911473 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGTCATC
1911492 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG
Found at i:1911677 original size:214 final size:214
Alignment explanation
Indices: 1911188--1911825 Score: 956
Period size: 214 Copynumber: 3.0 Consensus size: 214
1911178 GTGAAGAAAC
*
1911188 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAA
* *
1911253 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGTAGGATGTTTTCACATGAATTTGGAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
1911318 TGAAAAAAATGATGTTTTAAAAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
131 TG--AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTC
1911383 ACAACTTATAAGTCCTTCAGG
194 ACAACTTATAAGTCCTTCAGG
*
1911404 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAA
*
1911469 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGATTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * * *
1911534 TGAAAAATGATATTTTAAGAAGATGGAATTTTTTAAAATGAAGAATGCAATTTTCAAAATTTCAT
131 TGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCAC
* * **
1911599 AATTTATAAGTCTTTTGGG
196 AACTTATAAGTCCTTCAGG
* *
1911618 CCATCAGAAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGCCTTTTGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAA
* * ** **
1911683 GATGACAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTTGAAAATGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * * * * *
1911748 TGAGAAAATGATGTTTGAAGATGATGAAATTTTTGGAAACT-AAGAATGCGATTTCCATAATTTC
131 TGA-AAAATGATGTTTTAAGAAGATGGAATTTTT-GAAAATGAAGAATGCGATTTTCAAAATTTC
1911812 AC-ACTTAGTAAGTC
194 ACAACTTA-TAAGTC
1911826 TTTCGAGCAT
Statistics
Matches: 383, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
214 199 0.52
215 53 0.14
216 131 0.34
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (214 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCAC
AACTTATAAGTCCTTCAGG
Found at i:1915080 original size:17 final size:17
Alignment explanation
Indices: 1915054--1915100 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
1915044 CAATTTGTTG
*
1915054 TTTTAATTAAAATTAAT
1 TTTTATTTAAAATTAAT
1915071 TTTTATTTAAAATTAAT
1 TTTTATTTAAAATTAAT
1915088 TTTTATTTAAAAT
1 TTTTATTTAAAAT
1915101 GACAATGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATTTAAAATTAAT
Found at i:1917985 original size:13 final size:13
Alignment explanation
Indices: 1917967--1917993 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1917957 CATAGTTGAA
1917967 CAGTCTTCATATG
1 CAGTCTTCATATG
1917980 CAGTCTTCATATG
1 CAGTCTTCATATG
1917993 C
1 C
1917994 GCGTCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1918024 original size:22 final size:22
Alignment explanation
Indices: 1917996--1918038 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1917986 TCATATGCGC
1917996 GTCTGTATTGGGAAGTAATCCT
1 GTCTGTATTGGGAAGTAATCCT
1918018 GTCTGTATTGGGAAGTAATCC
1 GTCTGTATTGGGAAGTAATCC
1918039 CTGCAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
GTCTGTATTGGGAAGTAATCCT
Found at i:1923558 original size:21 final size:19
Alignment explanation
Indices: 1923532--1923577 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1923522 TTTTATATAT
*
1923532 TATATAATATATATGATAATA
1 TATATAATA-ATATCA-AATA
*
1923553 TATATAATAATTTCAAATA
1 TATATAATAATATCAAATA
1923572 TATATA
1 TATATA
1923578 GTTTTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATAATAATATCAAATA
Found at i:1923617 original size:14 final size:14
Alignment explanation
Indices: 1923598--1923625 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1923588 ATATGATATA
1923598 GTTTTTGAAAACAT
1 GTTTTTGAAAACAT
1923612 GTTTTTGAAAACAT
1 GTTTTTGAAAACAT
1923626 ATAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
GTTTTTGAAAACAT
Found at i:1923641 original size:38 final size:38
Alignment explanation
Indices: 1923588--1923767 Score: 174
Period size: 38 Copynumber: 4.7 Consensus size: 38
1923578 GTTTTTAAAG
* * *
1923588 ATATGATATAGTTTTTGAAAACATGTTTTTGAAAACAT
1 ATATAATATAATTTTTGAAAACATATTTTTGAAAACAT
*
1923626 ATA-ATATATAATTTTTTTTAAAGA-ACTATTTTTGAAAACAT
1 ATATA-ATATAA--TTTTTGAAA-ACA-TATTTTTGAAAACAT
* *
1923667 ATATAATATAGTTTTTGAAAACGTATTTTTGAAAAC--
1 ATATAATATAATTTTTGAAAACATATTTTTGAAAACAT
* *
1923703 ATATAATATATAGTTTT-AAAA-AAATGTTTTGAAAACAT
1 ATATAATATA-ATTTTTGAAAACATAT-TTTTGAAAACAT
*
1923741 ATATAATATAATTTTTGAAGACATATT
1 ATATAATATAATTTTTGAAAACATATT
1923768 ATTTTGAATA
Statistics
Matches: 115, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
35 2 0.02
36 24 0.21
37 9 0.08
38 36 0.31
39 11 0.10
40 9 0.08
41 23 0.20
42 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (38 bp):
ATATAATATAATTTTTGAAAACATATTTTTGAAAACAT
Found at i:1923782 original size:2 final size:2
Alignment explanation
Indices: 1923775--1923819 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1923765 ATTATTTTGA
* * * *
1923775 AT AT AT AT AT CT AT CT AT CT AT CT 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
1923817 AT A
1 AT A
1923820 GTTTTTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1925153 original size:15 final size:16
Alignment explanation
Indices: 1925133--1925170 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1925123 ATCATTGACT
1925133 TTTAATTC-TTTTCAA
1 TTTAATTCATTTTCAA
1925148 TTTAA-TCATTTTCAA
1 TTTAATTCATTTTCAA
1925163 TTTGAATT
1 TTT-AATT
1925171 TTCTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 15 0.75
16 2 0.10
17 1 0.05
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTAATTCATTTTCAA
Found at i:1932518 original size:17 final size:17
Alignment explanation
Indices: 1932496--1932540 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1932486 TAAATATTGA
*
1932496 TGTGTCAACCATGATGT
1 TGTGTCAACCACGATGT
1932513 TGTGTCAACCACGATGT
1 TGTGTCAACCACGATGT
1932530 TGAT-TCAACCA
1 TG-TGTCAACCA
1932541 GTTCCAGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (17 bp):
TGTGTCAACCACGATGT
Found at i:1933797 original size:201 final size:201
Alignment explanation
Indices: 1933443--1933980 Score: 607
Period size: 201 Copynumber: 2.7 Consensus size: 201
1933433 CTGTTCACAG
* ** * * * *
1933443 CATAGCTCAAGGAAAGAAGGGTTATCT-CTCAACAAAAACTTTCAAGTTCGATTCAATTCAGCTC
1 CATAGCTTAAGGCGAGAAGGGTTATCTGC-CAACGAAAACTTTCGAGTTCGATTCCATTCAACTC
* * * * *
1933507 GAGGGCATATCAACTGTATAGTAGCAGCGAGGAACTACTTTCTGGTTGAATTTTAAATCGAGATA
65 GAGGGCGTATCAACTGTATGGTAGCAGCGAGGAACTACTTCCTGGTTGAATTTTAAACCGAGGTA
*
1933572 TTTAAGCCCATAAGAAATCCTAGGTTGGCTACGAATTAGCAACAAGGAACTATCTCCCAACCTAA
130 TTTAAGCCCAAAAGAAATCCTAGGTTGGCTACGAATTAGCAACAAGGAACTATCTCCCAACCTAA
1933637 TTTACAA
195 TTTACAA
*
1933644 CATAGCTTAAGGCGAGAAGGGTTATCTGCCAACGAAAACTTTCGAGTTTGATTCCATTCAACTCG
1 CATAGCTTAAGGCGAGAAGGGTTATCTGCCAACGAAAACTTTCGAGTTCGATTCCATTCAACTCG
* *
1933709 AGGGCGTATCAA-TCGTATGGTAGGAGCGAGGAACTACTTCCTGGTTGAATTTTAAACCGAGGTC
66 AGGGCGTATCAACT-GTATGGTAGCAGCGAGGAACTACTTCCTGGTTGAATTTTAAACCGAGGTA
* * * * * **
1933773 TTTAAGCCTAAAAG-AATACCTAGGTTTGCTGCTATTTAGCAACAAGGAACTATCTCCCAGTCTA
130 TTTAAGCCCAAAAGAAAT-CCTAGGTTGGCTACGAATTAGCAACAAGGAACTATCTCCCAACCTA
*
1933837 ATTTACAT
194 ATTTACAA
* * * **** * * * *
1933845 CGTAGTTTAAGTCGAGAAAAAATGTATGTCAACGAAAACTTTCGAGTTCGATTCCATTCATCTCG
1 CATAGCTTAAGGCGAGAAGGGTTATCTGCCAACGAAAACTTTCGAGTTCGATTCCATTCAACTCG
* * * * * ** * * *
1933910 AGGGCGTATTAACTGCATGGTAGTAGCGATGAACTAATTTCC-AATTGAAGTCTAAACCGAGGTG
66 AGGGCGTATCAACTGTATGGTAGCAGCGAGGAACT-ACTTCCTGGTTGAATTTTAAACCGAGGTA
1933974 TTTAAGC
130 TTTAAGC
1933981 AAAGAAGAAG
Statistics
Matches: 286, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
200 4 0.01
201 275 0.96
202 7 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (201 bp):
CATAGCTTAAGGCGAGAAGGGTTATCTGCCAACGAAAACTTTCGAGTTCGATTCCATTCAACTCG
AGGGCGTATCAACTGTATGGTAGCAGCGAGGAACTACTTCCTGGTTGAATTTTAAACCGAGGTAT
TTAAGCCCAAAAGAAATCCTAGGTTGGCTACGAATTAGCAACAAGGAACTATCTCCCAACCTAAT
TTACAA
Found at i:1934386 original size:19 final size:20
Alignment explanation
Indices: 1934364--1934401 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1934354 ATAATTTCAA
1934364 ATATA-CATAGTTTTTGAAG
1 ATATAGCATAGTTTTTGAAG
*
1934383 ATATAGTATAGTTTTTGAA
1 ATATAGCATAGTTTTTGAA
1934402 AACATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (20 bp):
ATATAGCATAGTTTTTGAAG
Found at i:1934414 original size:22 final size:20
Alignment explanation
Indices: 1934370--1934414 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1934360 TCAAATATAC
* *
1934370 ATAGTTTTTGAAGATATAGT
1 ATAGTTTTTGAACATATAAT
1934390 ATAGTTTTTGAAAACATATAAT
1 ATAGTTTTTG--AACATATAAT
1934412 ATA
1 ATA
1934415 TAGTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (20 bp):
ATAGTTTTTGAACATATAAT
Found at i:1934460 original size:24 final size:24
Alignment explanation
Indices: 1934433--1934483 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1934423 TAAAGAACGA
* *
1934433 TTTTTGAAAACTTATAAAATTTAG
1 TTTTTGAAAACATATAAAATATAG
*
1934457 TTTTTGAAAACATATAATATATAG
1 TTTTTGAAAACATATAAAATATAG
1934481 TTT
1 TTT
1934484 AAAAAAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (24 bp):
TTTTTGAAAACATATAAAATATAG
Found at i:1934524 original size:63 final size:62
Alignment explanation
Indices: 1934391--1934508 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
1934381 AGATATAGTA
* * *
1934391 TAGTTTTTGAAAACATATAATATATAGTTTTTTAAAGAACGATTTTTGAAAACTTATAAAATT
1 TAGTTTTTGAAAACATATAATATATAG-TTTTAAAAAAACGAGTTTTGAAAACTTATAAAATT
* *
1934454 TAGTTTTTGAAAACATATAATATATAG-TTTAAAAAAATG-GTTTTGAAAACATATA
1 TAGTTTTTGAAAACATATAATATATAGTTTTAAAAAAACGAGTTTTGAAAACTTATA
1934509 TATATAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 14 0.28
61 9 0.18
63 27 0.54
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (62 bp):
TAGTTTTTGAAAACATATAATATATAGTTTTAAAAAAACGAGTTTTGAAAACTTATAAAATT
Found at i:1940356 original size:23 final size:23
Alignment explanation
Indices: 1940278--1940354 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
1940268 CTGTAGAAAT
*
1940278 AGAGTTTTCTGGTTCTGGTAAAT
1 AGAGTTTTCTGGTTCTGGTAAAC
* *
1940301 AGAGTTTTCTGATTCTTGTAAAC
1 AGAGTTTTCTGGTTCTGGTAAAC
* * *
1940324 AAAGTTTTTTGGTTATGGTAAAC
1 AGAGTTTTCTGGTTCTGGTAAAC
*
1940347 AGGGTTTT
1 AGAGTTTT
1940355 TTCAATTATG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (23 bp):
AGAGTTTTCTGGTTCTGGTAAAC
Found at i:1943902 original size:24 final size:23
Alignment explanation
Indices: 1943858--1943903 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1943848 TCGATTTTGG
**
1943858 TAAACAGATTTTTCTGGTTCTGT
1 TAAACAGATTTTTCTAATTCTGT
*
1943881 TAAACATGATTTTTTTAATTCTG
1 TAAACA-GATTTTTCTAATTCTG
1943904 AAATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (23 bp):
TAAACAGATTTTTCTAATTCTGT
Found at i:1944034 original size:24 final size:23
Alignment explanation
Indices: 1943991--1944042 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1943981 CTAGAAAAGA
*
1943991 TAGGAGTCATCTTTTCTATAAAT
1 TAGGAGTCATCTTTTATATAAAT
*
1944014 TAGGAGATCAT-TTTATATATAAGT
1 TAGGAG-TCATCTTT-TATATAAAT
1944038 TAGGA
1 TAGGA
1944043 TTCAAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
TAGGAGTCATCTTTTATATAAAT
Found at i:1949652 original size:21 final size:21
Alignment explanation
Indices: 1949626--1949665 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1949616 TCCAGATTCG
*
1949626 CAACGCGAACTTCGACTATTA
1 CAACGCGAACTTCAACTATTA
1949647 CAACGCGAACTTCAACTAT
1 CAACGCGAACTTCAACTAT
1949666 CGCATTGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
CAACGCGAACTTCAACTATTA
Found at i:1949714 original size:21 final size:21
Alignment explanation
Indices: 1949684--1949891 Score: 180
Period size: 21 Copynumber: 10.0 Consensus size: 21
1949674 GATTTACATA
*
1949684 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1949705 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1949726 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
1949747 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1949766 TTTCGCGTTGCGATTTATTACAAA
1 -TTCGCGTTGCGA--TAGTCCAAG
1949790 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1949809 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1949832 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1949851 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1949874 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
1949892 AATCGCAACG
Statistics
Matches: 150, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
19 37 0.25
20 2 0.01
21 78 0.52
22 8 0.05
23 20 0.13
24 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1949736 original size:42 final size:41
Alignment explanation
Indices: 1949709--1949891 Score: 296
Period size: 42 Copynumber: 4.4 Consensus size: 41
1949699 TCCAAGTTCG
*
1949709 CGTTGCGATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATT
* *
1949749 CGTTGCGATAGTCGAAGTTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAG-TTCGCGTTGCGA-TTATTCCAAATT
1949792 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
1949834 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
1949876 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
1949892 AATCGCAACG
Statistics
Matches: 137, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
40 17 0.12
41 12 0.09
42 84 0.61
43 24 0.18
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:1950807 original size:42 final size:42
Alignment explanation
Indices: 1950745--1951103 Score: 565
Period size: 42 Copynumber: 8.5 Consensus size: 42
1950735 TGCGATTTTG
* *
1950745 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1950787 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1950829 GAATATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
1950871 GACTATCGTAATGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1950913 GACTATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1950955 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1950997 GACTATCGCAACGAACTTGGAATAAACCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
1951039 GACTATCGCAACGAACTTGGAATAAATCGCAATGCAAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1951081 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
1951104 CTATCGCAAT
Statistics
Matches: 290, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 280 0.97
44 10 0.03
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1951110 original size:42 final size:41
Alignment explanation
Indices: 1950745--1951196 Score: 495
Period size: 42 Copynumber: 10.8 Consensus size: 41
1950735 TGCGATTTTG
* *
1950745 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
1950787 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
1950829 GAATATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* * * *
1950871 GACTATCGTAATGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
1950913 GACTATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
1950955 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
1950997 GACTATCGCAACGAACTTGGAATAAACCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* * *
1951039 GACTATCGCAACGAACTTGGAATAAATCGCAATGCAAACTTT
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* * * *
1951081 GACTATCGCAACGCGAACTTGGACT-ATCGCAA--TGAATTTG
1 GACTATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTC
* * * *
1951121 GAATAACTCGCAACGCGAACTTCGACT-ATCGCAA--CGAACTTG
1 GACT-A-TCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTC
*
1951163 GACTATCGCAACGCAAACTTGGACT-ATCGCAACG
1 GACTATCGCAACG--AACTTGGAATAATCGCAACG
1951197 AATTTGGAAT
Statistics
Matches: 366, Mismatches: 36, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
38 2 0.01
40 29 0.08
41 2 0.01
42 322 0.88
44 11 0.03
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
Found at i:1951238 original size:47 final size:45
Alignment explanation
Indices: 1951087--1951259 Score: 152
Period size: 47 Copynumber: 4.0 Consensus size: 45
1951077 CTTTGACTAT
* * *
1951087 CGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAACTCGCAA
1 CGCAACGCAAACTCGGACTATCGCAACGAATTTGGAA-AA-TCGCAA
* * *
1951134 CG---CG--AACTTC-GACTATCGCAACGAACTTGG---A-C-TAT
1 CGCAACGCAAAC-TCGGACTATCGCAACGAATTTGGAAAATCGCAA
*
1951169 CGCAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAA
1 CGCAACGCAAACTCGGACTATCGCAACGAATTTGG-A-AAATCGCAA
*
1951216 CGCAACGCGAACTCGGACTATCGCAACGAATTTGGAAAATCGCA
1 CGCAACGCAAACTCGGACTATCGCAACGAATTTGGAAAATCGCA
1951260 TTGCGATAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
35 3 0.03
36 1 0.01
38 3 0.03
39 1 0.01
40 22 0.22
42 21 0.21
43 1 0.01
44 2 0.02
45 9 0.09
46 2 0.02
47 36 0.36
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (45 bp):
CGCAACGCAAACTCGGACTATCGCAACGAATTTGGAAAATCGCAA
Found at i:1951258 original size:87 final size:82
Alignment explanation
Indices: 1951085--1951259 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
1951075 AACTTTGACT
* * *
1951085 ATCGCAACGCGAACTTGGACTATCGCAATGAATTTGGAATAACTCGCAACGCGAACTTCGACTAT
1 ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGGAATAACACGCAACGCGAACTTCGACTAT
**
1951150 CGCAACGAACTTGGACT
66 CGCAACGAACTTGGAAA
1951167 ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCAACGCGAAC-TCG
1 ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGGAAT-AA---C-ACGCAACGCGAACTTC-
*
1951231 GACTATCGCAACGAATTTGGAAA
60 GACTATCGCAACGAACTTGGAAA
1951254 ATCGCA
1 ATCGCA
1951260 TTGCGATAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
82 38 0.47
83 2 0.02
86 3 0.04
87 38 0.47
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (82 bp):
ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGGAATAACACGCAACGCGAACTTCGACTAT
CGCAACGAACTTGGAAA
Found at i:1952535 original size:19 final size:18
Alignment explanation
Indices: 1952494--1952555 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
1952484 TAATTTAGGG
* *
1952494 TTAGGTTGGTTGAGCGAT
1 TTAGGTTGGTTGAGTGGT
1952512 TTAGGTTGGTTGAGTGGTT
1 TTAGGTTGGTTGAGTGG-T
** *
1952531 TTAGGTTTTTTTAGTGGT
1 TTAGGTTGGTTGAGTGGT
1952549 TTAGGTT
1 TTAGGTT
1952556 TTTAGCTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 23 0.61
19 15 0.39
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.50
Consensus pattern (18 bp):
TTAGGTTGGTTGAGTGGT
Found at i:1952786 original size:2 final size:2
Alignment explanation
Indices: 1952779--1952821 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1952769 GAATGAATGA
1952779 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
1952821 A
1 A
1952822 ATCATTAATA
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:1952883 original size:15 final size:15
Alignment explanation
Indices: 1952865--1952901 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1952855 ATAAAAATAC
1952865 ATAAAATAGAAGAAA
1 ATAAAATAGAAGAAA
*
1952880 ATAAAGTAGAAGAAA
1 ATAAAATAGAAGAAA
1952895 ATAAAAT
1 ATAAAAT
1952902 CACATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (15 bp):
ATAAAATAGAAGAAA
Found at i:1957284 original size:13 final size:14
Alignment explanation
Indices: 1957250--1957288 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1957240 TTGACTATTT
*
1957250 AATATTTTAATGGA
1 AATATTGTAATGGA
1957264 AGATATTGTAATGG-
1 A-ATATTGTAATGGA
1957278 AATATTGTAAT
1 AATATTGTAAT
1957289 TATCAAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AATATTGTAATGGA
Found at i:1969244 original size:45 final size:47
Alignment explanation
Indices: 1969185--1969276 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
1969175 TCAAATAAAT
*
1969185 GCATGCGAACTAGATATCACGCGATTAGG-TTTATTTTT-TGAATAA
1 GCATGCAAACTAGATATCACGCGATTAGGATTTATTTTTGTGAATAA
* * * *
1969230 GCATGCAAATTAGATATCATGCGGTTAGGATTTCTTTTTGTGAATAA
1 GCATGCAAACTAGATATCACGCGATTAGGATTTATTTTTGTGAATAA
1969277 CAAAGCATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 25 0.62
46 8 0.20
47 7 0.17
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (47 bp):
GCATGCAAACTAGATATCACGCGATTAGGATTTATTTTTGTGAATAA
Found at i:1972151 original size:13 final size:13
Alignment explanation
Indices: 1972132--1972205 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
1972122 AACCCGACCC
1972132 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1972145 TACCCGACCCGTT
1 GACCCGACCCGTT
1972158 GACCCGACCCGACCTGTT
1 GACCCGA--C--CC-GTT
*
1972176 GACCCGACCTGTT
1 GACCCGACCCGTT
*
1972189 GACCCAACCCGTT
1 GACCCGACCCGTT
1972202 GACC
1 GACC
1972206 GACATTGACC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
13 36 0.71
14 1 0.02
15 1 0.02
16 1 0.02
17 2 0.04
18 10 0.20
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1972162 original size:31 final size:31
Alignment explanation
Indices: 1972127--1972199 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1972117 GTCATAACCC
*
1972127 GACCCGACCCGACCCGTTTACCCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCCGTT
* *
1972158 GACCCGACCCGACCTGTTGACCCGACCTGTT
1 GACCCGACCCGACCCGTTGACCCGACCCGTT
*
1972189 GACCCAACCCG
1 GACCCGACCCG
1972200 TTGACCGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCGACCCGTT
Found at i:1972167 original size:18 final size:18
Alignment explanation
Indices: 1972146--1972184 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1972136 CGACCCGTTT
1972146 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
1972164 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
1972182 ACC
1 ACC
1972185 TGTTGACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1972198 original size:18 final size:17
Alignment explanation
Indices: 1972146--1972199 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
1972136 CGACCCGTTT
*
1972146 ACCCGACCCGTTGACCC
1 ACCCGACCTGTTGACCC
1972163 GACCCGACCTGTTG----
1 -ACCCGACCTGTTGACCC
1972177 ACCCGACCTGTTGACCC
1 ACCCGACCTGTTGACCC
1972194 AACCCG
1 -ACCCG
1972200 TTGACCGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 13 0.43
18 17 0.57
ACGTcount: A:0.19, C:0.46, G:0.20, T:0.15
Consensus pattern (17 bp):
ACCCGACCTGTTGACCC
Found at i:1974769 original size:24 final size:24
Alignment explanation
Indices: 1974703--1974785 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1974693 ATATTTTATC
* * *
1974703 TGATTTCCGACTTGAATTCTGTTC
1 TGATTTCTGATTTGAATTCTGTTA
*
1974727 TGATTTCTGATTTGGATTCTGTTA
1 TGATTTCTGATTTGAATTCTGTTA
*
1974751 TGATATT-TG-TTCTGAATTCTGTTT
1 TGAT-TTCTGATT-TGAATTCTGTTA
1974775 TGATTTCTGAT
1 TGATTTCTGAT
1974786 ATCTTCGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 4 0.08
24 42 0.86
25 3 0.06
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (24 bp):
TGATTTCTGATTTGAATTCTGTTA
Found at i:1974773 original size:12 final size:12
Alignment explanation
Indices: 1974715--1974783 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1974705 ATTTCCGACT
1974715 TGAATTCTGTTC
1 TGAATTCTGTTC
*
1974727 TGATTTCTGATT-
1 TGAATTCTG-TTC
* *
1974739 TGGATTCTGTTA
1 TGAATTCTGTTC
1974751 TGATATT-TGTTC
1 TGA-ATTCTGTTC
*
1974763 TGAATTCTGTTT
1 TGAATTCTGTTC
*
1974775 TGATTTCTG
1 TGAATTCTG
1974784 ATATCTTCGT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
11 5 0.11
12 36 0.78
13 5 0.11
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:1976870 original size:23 final size:23
Alignment explanation
Indices: 1976840--1976895 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1976830 ACCGGTCATA
*
1976840 ACCCGACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGACCCGTTG
* *
1976863 ACCTGACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGACCCGTTG
1976886 ACCCGACCCG
1 ACCCGACCCG
1976896 TTGACCGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.12
Consensus pattern (23 bp):
ACCCGACCCGACCCGACCCGTTG
Found at i:1976888 original size:13 final size:13
Alignment explanation
Indices: 1976849--1976901 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
1976839 AACCCGACCC
1976849 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1976862 TACCTGACCC---
1 GACCCGACCCGTT
*
1976872 GACCCGACCTGTT
1 GACCCGACCCGTT
1976885 GACCCGACCCGTT
1 GACCCGACCCGTT
1976898 GACC
1 GACC
1976902 GACGTTGACC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
10 7 0.23
13 24 0.77
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1979448 original size:12 final size:12
Alignment explanation
Indices: 1979433--1979502 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
1979423 GATAAATGAC
1979433 CTGAATTCTGTT
1 CTGAATTCTGTT
*
1979445 CTGATTTCTGATT
1 CTGAATTCTG-TT
*
1979458 -TGGATTCTGTT
1 CTGAATTCTGTT
1979469 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
1979481 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1979493 TTGATTTCTG
1 CTGAATTCTG
1979503 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
11 4 0.08
12 41 0.84
13 4 0.08
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1979478 original size:24 final size:24
Alignment explanation
Indices: 1979396--1979504 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1979386 AAATATTTTA
*
1979396 TCTGATTTCTGACTTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGT
*** **
1979420 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGT
*
1979444 TCTGATTTCTGATTTGGATTCTGT
1 TCTGATTTCTGATTTGAATTCTGT
*
1979468 TCTGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGATT-TGAATTCTGT
*
1979492 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1979505 ATCTTCGTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
23 2 0.03
24 66 0.96
25 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATTTGAATTCTGT
Found at i:1979504 original size:48 final size:48
Alignment explanation
Indices: 1979396--1979504 Score: 155
Period size: 48 Copynumber: 2.3 Consensus size: 48
1979386 AAATATTTTA
*
1979396 TCTGATTTCTGACTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* ** **
1979444 TCTGATTTCTGATTTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
1979492 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1979505 ATCTTCGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:1980554 original size:13 final size:13
Alignment explanation
Indices: 1980536--1980563 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1980526 CGTTCTAATA
1980536 TAAAGAGTTGTTC
1 TAAAGAGTTGTTC
1980549 TAAAGAGTTGTTC
1 TAAAGAGTTGTTC
1980562 TA
1 TA
1980564 GGATCAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (13 bp):
TAAAGAGTTGTTC
Found at i:1987395 original size:9 final size:9
Alignment explanation
Indices: 1987362--1987443 Score: 67
Period size: 9 Copynumber: 8.3 Consensus size: 9
1987352 CTTGAAGAAG
1987362 AAATGAAAAA
1 AAATG-AAAA
*
1987372 AAATAGAGGAA
1 AAAT-GA-AAA
1987383 AAATGAAAA
1 AAATGAAAA
*
1987392 AAATTAAAA
1 AAATGAAAA
1987401 AAA-GAAAA
1 AAATGAAAA
1987409 AAATGAAAA
1 AAATGAAAA
1987418 ATGGTGAATGAAAA
1 A-----AATGAAAA
1987432 AAATGAAAA
1 AAATGAAAA
1987441 AAA
1 AAA
1987444 ATAAGAAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
8 7 0.12
9 30 0.50
10 7 0.12
11 7 0.12
14 9 0.15
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (9 bp):
AAATGAAAA
Found at i:1987401 original size:17 final size:17
Alignment explanation
Indices: 1987381--1987520 Score: 60
Period size: 17 Copynumber: 7.8 Consensus size: 17
1987371 AAAATAGAGG
* *
1987381 AAAAATGAAAAAAATTA
1 AAAAAAGAAAAAAATGA
1987398 AAAAAAGAAAAAAATGA
1 AAAAAAGAAAAAAATGA
1987415 AAAATGGTGAATGAAAAAAATGA
1 AAAA-----AA-GAAAAAAATGA
1987438 AAAAAA-ATAAGAAAA-G-
1 AAAAAAGA-AA-AAAATGA
* *
1987454 AGAAAAG-AGAAAATGA
1 AAAAAAGAAAAAAATGA
1987470 AAATGAAA-ATGAAAAAATG-
1 AAA--AAAGA--AAAAAATGA
*
1987489 AAAAAAGAAAAAAA-AA
1 AAAAAAGAAAAAAATGA
1987505 AGAAAAAGAAATAAAA
1 A-AAAAAGAAA-AAAA
1987521 GGAGGGTTCC
Statistics
Matches: 96, Mismatches: 7, Indels: 39
0.68 0.05 0.27
Matches are distributed among these distances:
14 4 0.04
15 2 0.02
16 15 0.16
17 34 0.35
18 14 0.15
19 3 0.03
20 7 0.07
22 2 0.02
23 15 0.16
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAGAAAAAAATGA
Found at i:1987452 original size:9 final size:10
Alignment explanation
Indices: 1987362--1987520 Score: 65
Period size: 10 Copynumber: 15.9 Consensus size: 10
1987352 CTTGAAGAAG
1987362 AAATGAAAAA
1 AAATGAAAAA
**
1987372 AAATAGAGGAA
1 AAAT-GAAAAA
1987383 AAATG-AAAA
1 AAATGAAAAA
*
1987392 AAAT-TAAAA
1 AAATGAAAAA
1987401 AAA-G-AAAA
1 AAATGAAAAA
1987409 AAATGAAAAA
1 AAATGAAAAA
*
1987419 TGGTGAATG-AAAA
1 ----AAATGAAAAA
1987432 AAATGAAAAA
1 AAATGAAAAA
1987442 AAAT-AAGAAA
1 AAATGAA-AAA
*
1987452 AGA-GAAAAGAGA
1 AAATG-AAA-A-A
1987464 AAATGAAAATGA
1 AAATGAAAA--A
1987476 AAATG--AAA
1 AAATGAAAAA
1987484 AAATGAAAAA
1 AAATGAAAAA
1987494 AGAA--AAAAA
1 A-AATGAAAAA
1987503 AAA-GAAAAA
1 AAATGAAAAA
1987512 GAAAT-AAAA
1 -AAATGAAAA
1987521 GGAGGGTTCC
Statistics
Matches: 118, Mismatches: 8, Indels: 46
0.69 0.05 0.27
Matches are distributed among these distances:
8 15 0.13
9 31 0.26
10 36 0.31
11 14 0.12
12 13 0.11
13 5 0.04
14 4 0.03
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:1987459 original size:26 final size:25
Alignment explanation
Indices: 1987357--1987520 Score: 80
Period size: 26 Copynumber: 6.7 Consensus size: 25
1987347 TTTCGCTTGA
1987357 AGAAGAAATGAAAAAAAATAG---AG
1 AGAA-AAATGAAAAAAAATAGAAAAG
* *
1987380 -GAAAAATGAAAAAAATTAAAAAAAG
1 AGAAAAATGAAAAAAAAT-AGAAAAG
* *** *
1987405 AAAAAAATGAAAAATGGT-G-AATG
1 AGAAAAATGAAAAAAAATAGAAAAG
*
1987428 AAAAAAATGAAAAAAAATAAGAAAAG
1 AGAAAAATGAAAAAAAAT-AGAAAAG
1987454 AGAAAAGA-GAAAATGAAAAT-GAAAATG
1 AGAAAA-ATGAAAA--AAAATAGAAAA-G
* *
1987481 A-AAAAATGAAAAAAGAA-AAAAAAA
1 AGAAAAATGAAAAAA-AATAGAAAAG
*
1987505 AGAAAAA-GAAATAAAA
1 AGAAAAATGAAAAAAAA
1987521 GGAGGGTTCC
Statistics
Matches: 109, Mismatches: 16, Indels: 32
0.69 0.10 0.20
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 20 0.18
24 9 0.08
25 15 0.14
26 40 0.37
27 3 0.03
28 5 0.05
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (25 bp):
AGAAAAATGAAAAAAAATAGAAAAG
Found at i:1987461 original size:12 final size:12
Alignment explanation
Indices: 1987431--1987515 Score: 59
Period size: 13 Copynumber: 6.7 Consensus size: 12
1987421 GTGAATGAAA
1987431 AAAATGAAAAAA-
1 AAAA-GAAAAAAG
*
1987443 AATAAGAAAAGAG
1 AA-AAGAAAAAAG
*
1987456 AAAAGAGAAAATG
1 AAAAGA-AAAAAG
1987469 AAAATGAAAATGAA-
1 AAAA-GAAAA--AAG
1987483 AAAATGAAAAAAG
1 AAAA-GAAAAAAG
1987496 AAAA-AAAAAAG
1 AAAAGAAAAAAG
1987507 AAAAAGAAA
1 -AAAAGAAA
1987516 TAAAAGGAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
11 7 0.12
12 18 0.30
13 22 0.37
14 12 0.20
15 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:1987499 original size:6 final size:6
Alignment explanation
Indices: 1987430--1987515 Score: 68
Period size: 6 Copynumber: 13.5 Consensus size: 6
1987420 GGTGAATGAA
* * *
1987430 AAAAATG AAAAA- AAATAAG AAAAGAG AAAAGAG AAAATG AAAATG AAAATG
1 AAAAA-G AAAAAG AAA-AAG AAAA-AG AAAA-AG AAAAAG AAAAAG AAAAAG
1987481 AAAAAATG AAAAAAG AAAAA- AAAAAG AAAAAG AAA
1 -AAAAA-G -AAAAAG AAAAAG AAAAAG AAAAAG AAA
1987516 TAAAAGGAGG
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
5 8 0.11
6 30 0.42
7 26 0.37
8 7 0.10
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:1987569 original size:45 final size:45
Alignment explanation
Indices: 1987518--1987603 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1987508 AAAAGAAATA
* *
1987518 AAAGGAGGGT-TCCAGATGAAAACCCAAAAAGGGCGTCTTGAAACC
1 AAAGGA-GGTCTCAAGATGAAAACCCAAAAAGGGCGACTTGAAACC
* **
1987563 AAAGGAGGTCTCAAGTTGAAAACCCGCAAAGGGCGACTTGA
1 AAAGGAGGTCTCAAGATGAAAACCCAAAAAGGGCGACTTGA
1987604 GTTTTGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (45 bp):
AAAGGAGGTCTCAAGATGAAAACCCAAAAAGGGCGACTTGAAACC
Found at i:1988472 original size:8 final size:8
Alignment explanation
Indices: 1988459--1988483 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1988449 AAATGCATTA
1988459 AATTGCAT
1 AATTGCAT
1988467 AATTGCAT
1 AATTGCAT
1988475 AATTGCAT
1 AATTGCAT
1988483 A
1 A
1988484 CATTTTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (8 bp):
AATTGCAT
Found at i:1988948 original size:55 final size:55
Alignment explanation
Indices: 1988855--1989281 Score: 500
Period size: 55 Copynumber: 7.8 Consensus size: 55
1988845 ATCTTAAGCC
* * * * * * *
1988855 TTCGAGTCTTATACTCCCTAAATAAATAGGAAGAGGACCCGTTAGTTGAAGATTA
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
* *
1988910 TTCGGGTCCTATACTCTCTGAATGAATAAGGAGCGGACCCGTTTGTTGAAGATTA
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
* * * ** * *
1988965 TTTGAGTCCTATACTCTTTGAA-GAAATAGGGAGTGGACATGTTAGTTTAAGATTA
1 TTCGAGTCCTATACTCTCTGAATG-AATAGGGAGCGGACCCGTTTGTTGAAGATTA
*
1989020 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGAACCCGTTTGTTGAAGATTA
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
*
1989075 TTTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
* * * *
1989130 CTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTG
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
* * * * **
1989185 TTCGAGTCTTATACTC-CTTGAATGAATAGGGAGCAGACACATTTGCCGAAGATTGA
1 TTCGAGTCCTATACTCTC-TGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATT-A
* * * * * *
1989241 TT-GATTCTTATACTCCCTGAAGGGATAGGGAGCAGACCCGT
1 TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGT
1989282 CATTCAAATA
Statistics
Matches: 321, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
54 2 0.01
55 315 0.98
56 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (55 bp):
TTCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACCCGTTTGTTGAAGATTA
Found at i:2001631 original size:19 final size:19
Alignment explanation
Indices: 2001607--2001651 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2001597 CAAAACATAA
*
2001607 TAAAAACAA-AATATAAAAG
1 TAAAAA-AATAATAAAAAAG
2001626 TAAAAAAATAATAAAAAAG
1 TAAAAAAATAATAAAAAAG
*
2001645 CAAAAAA
1 TAAAAAA
2001652 CTAGATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (19 bp):
TAAAAAAATAATAAAAAAG
Found at i:2002995 original size:20 final size:21
Alignment explanation
Indices: 2002970--2003022 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
2002960 TGGTTAAGGC
2002970 AGTATCGATACCCTAGG-A-TG
1 AGTATCGATACCCT-GGTACTG
* *
2002990 AGTATCAATACTCTGGTACTG
1 AGTATCGATACCCTGGTACTG
2003011 AGGTATCGATAC
1 A-GTATCGATAC
2003023 TTGACTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 3 0.11
22 9 0.33
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCCTGGTACTG
Found at i:2008528 original size:20 final size:20
Alignment explanation
Indices: 2008503--2008547 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2008493 CTTGGGTACT
*
2008503 GATACTAACCCTTTAGTATC
1 GATACTAAACCTTTAGTATC
*
2008523 GATACTAAACCTTTGGTATC
1 GATACTAAACCTTTAGTATC
*
2008543 AATAC
1 GATAC
2008548 CCACCTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (20 bp):
GATACTAAACCTTTAGTATC
Found at i:2008577 original size:20 final size:20
Alignment explanation
Indices: 2008531--2008568 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2008521 TCGATACTAA
2008531 ACCT-TTGGTATCAATACCC
1 ACCTATTGGTATCAATACCC
*
2008550 ACCTATTGGTATCGATACC
1 ACCTATTGGTATCAATACC
2008569 TCCTGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (20 bp):
ACCTATTGGTATCAATACCC
Found at i:2009896 original size:21 final size:21
Alignment explanation
Indices: 2009867--2009931 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2009857 GGTGTCATAA
*
2009867 AACCCTGTGGGCTCGGTATGT
1 AACCATGTGGGCTCGGTATGT
**
2009888 AACCATGTGGGCTCAATATGT
1 AACCATGTGGGCTCGGTATGT
2009909 AACCATGTGGGCTCGGTATGT
1 AACCATGTGGGCTCGGTATGT
2009930 AA
1 AA
2009932 TCCTGCAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (21 bp):
AACCATGTGGGCTCGGTATGT
Found at i:2012778 original size:24 final size:24
Alignment explanation
Indices: 2012733--2012779 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2012723 GTTATGCCAC
* *
2012733 AAGAGCAGAGAAAATGCGTGTCAT
1 AAGAGCAAAGAAAATGCCTGTCAT
2012757 AAGAGCAAAGAAAAT-CTCTGTCA
1 AAGAGCAAAGAAAATGC-CTGTCA
2012780 CATGGATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (24 bp):
AAGAGCAAAGAAAATGCCTGTCAT
Found at i:2023741 original size:152 final size:152
Alignment explanation
Indices: 2023458--2023756 Score: 517
Period size: 152 Copynumber: 2.0 Consensus size: 152
2023448 AACAGTGGGG
* * *
2023458 TGCAGGAAGCAGGGCTCTTAATCCACTCCAAAGTCATCAAACAATCGGATTCTAAAATGAGCCTA
1 TGCAGGAAGCAAGGCTCTTAATCCACTCCAAAGCCATCAAACAATCAGATTCTAAAATGAGCCTA
* * * * *
2023523 CAACATGCTTAACTCCCCAACTCCATGAAGAGCAGCAACTCTCTTTTAATTGCCAATAGTTTTGC
66 CAACACGCTGAACTCCCCAACTCCATGAAGAGCAGCAACCCTCTTTTAATTGCCAACAGTTCTGC
2023588 CAAAACTGGAGGCCCTGCGGGA
131 CAAAACTGGAGGCCCTGCGGGA
2023610 TGCAGGAAGCAAGGCTCTTAATCCACTCCAAAGCCATCAAACAATCAGATTCTAAAATGAGCCTA
1 TGCAGGAAGCAAGGCTCTTAATCCACTCCAAAGCCATCAAACAATCAGATTCTAAAATGAGCCTA
*
2023675 CAACACGCTGAACTCCCCGACTCCATGAAGAGCAGCAACCCTCTTTTAATTGCCAACAGTTCTGC
66 CAACACGCTGAACTCCCCAACTCCATGAAGAGCAGCAACCCTCTTTTAATTGCCAACAGTTCTGC
2023740 CAAAACTGGAGGCCCTG
131 CAAAACTGGAGGCCCTG
2023757 GACCAGCACT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 138 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (152 bp):
TGCAGGAAGCAAGGCTCTTAATCCACTCCAAAGCCATCAAACAATCAGATTCTAAAATGAGCCTA
CAACACGCTGAACTCCCCAACTCCATGAAGAGCAGCAACCCTCTTTTAATTGCCAACAGTTCTGC
CAAAACTGGAGGCCCTGCGGGA
Found at i:2030233 original size:23 final size:23
Alignment explanation
Indices: 2030191--2030234 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
2030181 TTAAAATTTA
2030191 CAAATACTAAATCAACATATAAT
1 CAAATACTAAATCAACATATAAT
2030214 CAAATCACTAAATCAA-ATATA
1 CAAAT-ACTAAATCAACATATA
2030235 TATTTCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (23 bp):
CAAATACTAAATCAACATATAAT
Found at i:2030414 original size:2 final size:2
Alignment explanation
Indices: 2030407--2030439 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2030397 CCGTATTTCT
2030407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2030440 TCATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2030670 original size:22 final size:22
Alignment explanation
Indices: 2030631--2030680 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2030621 ACTCCGACTG
* * *
2030631 ATAACTTTTTGGGTTATGATTT
1 ATAACATTTTGAGCTATGATTT
*
2030653 ATAACATTTTGAGCTATGCTTT
1 ATAACATTTTGAGCTATGATTT
2030675 -TAACAT
1 ATAACAT
2030681 ATTACCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (22 bp):
ATAACATTTTGAGCTATGATTT
Found at i:2032334 original size:12 final size:12
Alignment explanation
Indices: 2032309--2032338 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2032299 TCGTGACTAG
2032309 AAATTAATCAAA
1 AAATTAATCAAA
2032321 AAATATAATCAAA
1 AAAT-TAATCAAA
2032334 AAATT
1 AAATT
2032339 CTGATGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATTAATCAAA
Found at i:2033419 original size:31 final size:31
Alignment explanation
Indices: 2033377--2033438 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2033367 CTCCATCCGA
* *
2033377 GACCTGACCCGACCAAAATAAAGTTTCACCC
1 GACCCGACCCGACCAAAATAAAGTTACACCC
*
2033408 GACCCGACCCGACCGAAATAAAGTTACACCC
1 GACCCGACCCGACCAAAATAAAGTTACACCC
2033439 AACCTGACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.37, G:0.15, T:0.13
Consensus pattern (31 bp):
GACCCGACCCGACCAAAATAAAGTTACACCC
Found at i:2033859 original size:261 final size:258
Alignment explanation
Indices: 2033404--2034019 Score: 826
Period size: 261 Copynumber: 2.4 Consensus size: 258
2033394 ATAAAGTTTC
* * * *
2033404 ACCCGACCCGACCCGACCGAAATAAAGTTACACCCAACCTGACTCGAATATATGAATTAGAAACC
1 ACCCGACCC-ACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAACC
*
2033469 CAA-CCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAATTAGTGACTTAATTGAAAA
65 CAACCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAA
* *
2033533 AATATATATATATATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGTTAAAATTATATA
130 AATATATATATATATAGAGGGGTATTATTATAATTATTCCTAAATAAATAAGGTAAAATTATATA
2033598 TTTTTTGGGTCGGGTCGGGTA-TTTTCACCCTAAAC-CTG-A-ACCCGACCCGAATATCACACTT
195 ---TTT---TCGGGTCGGGTATTTTTCACCCTAAACTC-GAACACCCGACCCGAATATCACACTT
2033659 AAAAAA
253 AAAAAA
* * *
2033665 ACCCGACCCTACCCGATCAAAATAAAGTTTCACCCGACCCGACCCAAATATATGAATTAGAAACC
1 ACCCGACCC-ACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAACC
2033730 CAACCCGACCCGAAATAATAAAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTG-AA
65 CAACCCGACCCGAAATAAT-AAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAA
*
2033794 AAA-A-AT-TATATATAGAGGGGTATTATTGTAATTATTCCTAAATAAATAAGGTAAAATTATAT
129 AAATATATATATATATAGAGGGGTATTATTATAATTATTCCTAAATAAATAAGGTAAAA-T-TAT
* *
2033856 ATATTTTCGGGTCGGGTATTTTTCACTCTAAACTCGAACTCGACCCGACCTGAATATCACACTTA
192 ATATTTTCGGGTCGGGTATTTTTCACCCTAAACTCGAA--C-ACCCGACCCGAATATCACACTTA
2033921 AAAAA
254 AAAAA
2033926 A--C-A---ACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAG--A---
1 ACCCGACCCACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAACCC
2033980 AACCCGACCCGAAATAAT-AAAAAAA-TATTTTTATTCAATA
66 AACCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATA
2034020 TATGAATAAG
Statistics
Matches: 327, Mismatches: 17, Indels: 37
0.86 0.04 0.10
Matches are distributed among these distances:
246 15 0.05
247 7 0.02
249 18 0.06
252 1 0.00
254 47 0.14
255 12 0.04
256 14 0.04
257 2 0.01
258 4 0.01
259 48 0.15
260 3 0.01
261 95 0.29
262 20 0.06
263 41 0.13
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (258 bp):
ACCCGACCCACCCGACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAACCC
AACCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAA
ATATATATATATATAGAGGGGTATTATTATAATTATTCCTAAATAAATAAGGTAAAATTATATAT
TTTCGGGTCGGGTATTTTTCACCCTAAACTCGAACACCCGACCCGAATATCACACTTAAAAAA
Found at i:2039452 original size:2 final size:2
Alignment explanation
Indices: 2039445--2039481 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2039435 GGATACACAT
2039445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2039482 TGATTTAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2052693 original size:21 final size:21
Alignment explanation
Indices: 2052667--2052709 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2052657 CTTACTCGAT
2052667 ATCAAGTTGCTTTCCACTTGA
1 ATCAAGTTGCTTTCCACTTGA
*
2052688 ATCAAGTTGCTTTCTACTTGA
1 ATCAAGTTGCTTTCCACTTGA
2052709 A
1 A
2052710 CCAACTTATT
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:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (21 bp):
ATCAAGTTGCTTTCCACTTGA
Found at i:2061167 original size:20 final size:20
Alignment explanation
Indices: 2061131--2061168 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2061121 ATCCTATTCT
**
2061131 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2061151 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2061169 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2063067 original size:27 final size:27
Alignment explanation
Indices: 2063028--2063080 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2063018 CAGTTTTAGT
2063028 TTATTTTAATATTTAATTT-TTTTAAA
1 TTATTTTAATATTTAATTTATTTTAAA
*
2063054 TTATATTTAATATTTATTTTATTTTAA
1 TTAT-TTTAATATTTAATTTATTTTAA
2063081 TACTTCATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 14 0.58
28 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATTTTAATATTTAATTTATTTTAAA
Found at i:2063430 original size:51 final size:56
Alignment explanation
Indices: 2063375--2063517 Score: 139
Period size: 53 Copynumber: 2.7 Consensus size: 56
2063365 CTATGAATTT
2063375 AATATTAATAAAATAT-TTTAAT-ATCATTT-TAATAA-A-AATATTA-ATTATTAA
1 AATATTAATAAAATATATTTAATAAT-ATTTATAATAATATAATATTATATTATTAA
* *
2063426 AATATT--TAAAATATATTTATTAATATTTATAATAATATAATATTATATTTTTAA
1 AATATTAATAAAATATATTTAATAATATTTATAATAATATAATATTATATTATTAA
* * *
2063480 TAT-TATAATAAAATA-A-TAAATTATA-TTATAATAATATA
1 AATAT-TAATAAAATATATTTAATAATATTTATAATAATATA
2063518 TAAGATATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
49 8 0.10
50 9 0.12
51 14 0.18
52 1 0.01
53 21 0.27
54 16 0.21
55 1 0.01
56 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (56 bp):
AATATTAATAAAATATATTTAATAATATTTATAATAATATAATATTATATTATTAA
Found at i:2063473 original size:22 final size:23
Alignment explanation
Indices: 2063426--2063489 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
2063416 TAATTATTAA
* *
2063426 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
2063447 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
2063470 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
2063490 AAATAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:2063504 original size:18 final size:18
Alignment explanation
Indices: 2063481--2063515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2063471 TATTTTTAAT
2063481 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
2063499 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
2063516 TATAAGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:2063508 original size:23 final size:25
Alignment explanation
Indices: 2063479--2063531 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
2063469 TATATTTTTA
*
2063479 ATATTATAATAA-A-ATAATAAATT
1 ATATTATAATAATATATAAGAAATT
*
2063502 ATATTATAATAATATATAAGATATT
1 ATATTATAATAATATATAAGAAATT
2063527 ATATT
1 ATATT
2063532 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATTATAATAATATATAAGAAATT
Found at i:2063525 original size:20 final size:23
Alignment explanation
Indices: 2063479--2063529 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2063469 TATATTTTTA
*
2063479 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAATAAATG
*
2063502 ATATTATAATAATAT-AT-AA-G
1 ATATTATAATAAAATAATAAATG
2063522 ATATTATA
1 ATATTATA
2063530 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 2 0.08
23 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATAAATG
Found at i:2063583 original size:56 final size:55
Alignment explanation
Indices: 2063465--2063624 Score: 150
Period size: 54 Copynumber: 2.9 Consensus size: 55
2063455 TAATAATATA
*
2063465 ATATTATATTTTTAATATTATAATAA-A-ATAATAAATTATATTATAATAATATATAAG
1 ATATTATATTTTT-AT-TT-TAATAATATATAATAAATTAT-TAATAATAATATATAAG
* **
2063522 ATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAA-AATTTATATT
1 ATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAATAATATATAAG
* *** *
2063576 AT-TTATTAATTTTATAGAAATAATAT-TATTAAATTATTAATAATGAATA
1 ATATTA-TATTTTTATTTTAATAATATATAATAAATTATTAATAAT-AATA
2063625 ATATTATCTA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
53 19 0.22
54 31 0.35
55 11 0.12
56 14 0.16
57 13 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (55 bp):
ATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAATAATATATAAG
Found at i:2063646 original size:27 final size:25
Alignment explanation
Indices: 2063461--2063654 Score: 80
Period size: 27 Copynumber: 7.6 Consensus size: 25
2063451 TTTATAATAA
* *
2063461 TATAAT-ATTATATTTTTAATATTAT
1 TATAATAATAATATTATTAA-ATTAT
* * *
2063486 AATAA-AATAATA-AATTATATTAT
1 TATAATAATAATATTATTAAATTAT
* * * *
2063509 AATAATATATAAGA-TATTATATTTT
1 TATAATA-ATAATATTATTAAATTAT
** *
2063534 TATTTTAATAATATATAATAAATTAT
1 TATAATAATAATAT-TATTAAATTAT
*
2063560 TAATAA-AATTTATATTATTTATTAATT-T
1 T-ATAATAA-TAATATTA-TTA--AATTAT
2063588 TATAGA-AATAATATTATTAAATTAT
1 TATA-ATAATAATATTATTAAATTAT
*
2063613 TAATAATGAATAATATTATCTATATATAT
1 T-ATAAT-AATAATATTAT-TAAAT-TAT
*
2063642 T-TAATATTAATAT
1 TATAATAATAATAT
2063655 AATAATCTAA
Statistics
Matches: 130, Mismatches: 22, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
23 10 0.08
24 13 0.10
25 30 0.23
26 26 0.20
27 34 0.26
28 9 0.07
29 8 0.06
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (25 bp):
TATAATAATAATATTATTAAATTAT
Found at i:2063699 original size:23 final size:23
Alignment explanation
Indices: 2063673--2063717 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2063663 AATAATATTT
2063673 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
2063696 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
2063718 ATATAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:2063836 original size:20 final size:21
Alignment explanation
Indices: 2063812--2063862 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2063802 TTAATAAAAT
*
2063812 TATAAAAATATTTTTTTAATA
1 TATAAAAATATTATTTTAATA
2063833 -ATAAATAA-ATTATTTTAATA
1 TATAAA-AATATTATTTTAATA
*
2063853 TTTAAAAATA
1 TATAAAAATA
2063863 ATAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAAAATATTATTTTAATA
Found at i:2069187 original size:20 final size:21
Alignment explanation
Indices: 2069164--2069202 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2069154 ATAACAAAAC
*
2069164 ATTTT-TTTAAAAAAATTAAG
1 ATTTTCTTGAAAAAAATTAAG
*
2069184 ATTTTCTTGAAAATAATTA
1 ATTTTCTTGAAAAAAATTA
2069203 CCTCTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTCTTGAAAAAAATTAAG
Found at i:2069263 original size:2 final size:2
Alignment explanation
Indices: 2069256--2069284 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2069246 GATAAACAAG
2069256 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 A
2069285 CCTGTGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2071074 original size:41 final size:41
Alignment explanation
Indices: 2071029--2071106 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2071019 TTAAACGCCG
*
2071029 CTATAGACTCATACAATAGTGACATTTTTAAAGAAACACCA
1 CTATAGAATCATACAATAGTGACATTTTTAAAGAAACACCA
* * * * *
2071070 CTATAGAATCGTATAATCGTGGCGTTTTTAAAGAAAC
1 CTATAGAATCATACAATAGTGACATTTTTAAAGAAAC
2071107 GACACAAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (41 bp):
CTATAGAATCATACAATAGTGACATTTTTAAAGAAACACCA
Found at i:2071332 original size:114 final size:113
Alignment explanation
Indices: 2071126--2071345 Score: 280
Period size: 114 Copynumber: 1.9 Consensus size: 113
2071116 GACTCAAACT
* * ** *
2071126 ATAGTGGCGTTTATTGTGAAAATGCCGCCAAAATGTGCACATTAGTGATGTTTTACTAGAAAAAC
1 ATAGTGGCGTTTATTGTGAAAATGCCGCAAAAACGCACACATTAGTGACGTTTTACTAGAAAAAC
* *
2071191 GCCGCAAAAAGATAACATTGCCCCTCCCTTGCTCGATCCCTAGCGTACC
66 ACCGCAAAAAGATAACATTGCCCCTCCC-TGCCCGATCCCTAGCGTACC
* * * * * *
2071240 ATAGTGGCGTTTGTTGTGCAAATGCCGTAAAAACGCACACATTAGTGGCGTTTTA-TTGGAAAAC
1 ATAGTGGCGTTTATTGTGAAAATGCCGCAAAAACGCACACATTAGTGACGTTTTACTAGAAAAAC
* *
2071304 ACCGCAAAAGGATAACATATGCCTCTCCCTGCCCGATCCCTA
66 ACCGCAAAAAGATAACAT-TGCCCCTCCCTGCCCGATCCCTA
2071346 AAATTCATTT
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
113 35 0.39
114 55 0.61
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (113 bp):
ATAGTGGCGTTTATTGTGAAAATGCCGCAAAAACGCACACATTAGTGACGTTTTACTAGAAAAAC
ACCGCAAAAAGATAACATTGCCCCTCCCTGCCCGATCCCTAGCGTACC
Found at i:2071453 original size:21 final size:21
Alignment explanation
Indices: 2071429--2071531 Score: 125
Period size: 21 Copynumber: 4.9 Consensus size: 21
2071419 GTCGCACCCA
* *
2071429 ATCACCATCTTCGTGCCTCCG
1 ATCACCATCGTCGCGCCTCCG
*
2071450 ATCACCATCGTCGTGCCTCCG
1 ATCACCATCGTCGCGCCTCCG
* * *
2071471 ATCACCATCTTCGCCCCTCTG
1 ATCACCATCGTCGCGCCTCCG
* *
2071492 GTCACCATCGTCGCACCTCCG
1 ATCACCATCGTCGCGCCTCCG
*
2071513 ATCACCATTGTCGCGCCTC
1 ATCACCATCGTCGCGCCTC
2071532 TAATGACTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.15, C:0.45, G:0.16, T:0.25
Consensus pattern (21 bp):
ATCACCATCGTCGCGCCTCCG
Found at i:2071532 original size:42 final size:42
Alignment explanation
Indices: 2071415--2071532 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 42
2071405 CTTCAGCCTA
* * *
2071415 CATCGTCGCA-C-CCAATCACCATCTTCGTGCCTCCGATCAC
1 CATCGTCGCACCTCCGATCACCATCTTCGCGCCTCTGATCAC
** * *
2071455 CATCGTCGTGCCTCCGATCACCATCTTCGCCCCTCTGGTCAC
1 CATCGTCGCACCTCCGATCACCATCTTCGCGCCTCTGATCAC
2071497 CATCGTCGCACCTCCGATCACCAT-TGTCGCGCCTCT
1 CATCGTCGCACCTCCGATCACCATCT-TCGCGCCTCT
2071533 AATGACTCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 8 0.12
41 2 0.03
42 55 0.85
ACGTcount: A:0.15, C:0.45, G:0.15, T:0.25
Consensus pattern (42 bp):
CATCGTCGCACCTCCGATCACCATCTTCGCGCCTCTGATCAC
Found at i:2079941 original size:18 final size:18
Alignment explanation
Indices: 2079918--2079952 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2079908 ACTGAATATT
*
2079918 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
2079936 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
2079953 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:2087785 original size:33 final size:33
Alignment explanation
Indices: 2087748--2087811 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
2087738 TCGGTGGATA
2087748 TATCCTATAGAGAGGTGATGGTTGTGTTATATG
1 TATCCTATAGAGAGGTGATGGTTGTGTTATATG
2087781 TATCCTATAGAGAGGTGATGGTTGTGTTATA
1 TATCCTATAGAGAGGTGATGGTTGTGTTATA
2087812 CATATTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.06, G:0.30, T:0.39
Consensus pattern (33 bp):
TATCCTATAGAGAGGTGATGGTTGTGTTATATG
Found at i:2090127 original size:12 final size:12
Alignment explanation
Indices: 2090100--2090142 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2090090 CGAAAGAAGC
2090100 AGAGAG-AGCAA
1 AGAGAGAAGCAA
*
2090111 CGAGAGAAGCAA
1 AGAGAGAAGCAA
*
2090123 AGAGAGAAGCAG
1 AGAGAGAAGCAA
2090135 AGAGAGAA
1 AGAGAGAA
2090143 CAACATTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.53, C:0.09, G:0.37, T:0.00
Consensus pattern (12 bp):
AGAGAGAAGCAA
Found at i:2092422 original size:20 final size:19
Alignment explanation
Indices: 2092381--2092428 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2092371 AACGATTTTC
*
2092381 TTTTGAAAACAAAAATAGA
1 TTTTGAAAACAAAAATAAA
* *
2092400 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAAT-AAA
2092420 TTTTGAAAA
1 TTTTGAAAA
2092429 AGGATTTTCT
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 (19 bp):
TTTTGAAAACAAAAATAAA
Found at i:2092554 original size:34 final size:32
Alignment explanation
Indices: 2092515--2092584 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
2092505 TTTTGTAAAG
* *
2092515 GGGAAAGGTTGTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* * *
2092549 GGGAAATGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
2092581 GGGA
1 GGGA
2092585 GTTTGTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:2093156 original size:2 final size:2
Alignment explanation
Indices: 2093149--2093208 Score: 63
Period size: 2 Copynumber: 31.5 Consensus size: 2
2093139 TTATAAAACA
* * * *
2093149 AT AT AT AT -T AT AT AT TT AT AT A- AT AT AA AA AC A- 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
2093188 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2093209 ATAAAGAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2093285 original size:8 final size:8
Alignment explanation
Indices: 2093274--2093324 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
2093264 ATAAAAAATG
2093274 TATATGTA
1 TATATGTA
2093282 TATAT-TAA
1 TATATGT-A
*
2093290 CTAGTATATA
1 -TA-TATGTA
*
2093300 TATATATA
1 TATATGTA
2093308 TATATGTA
1 TATATGTA
2093316 TATATGTA
1 TATATGTA
2093324 T
1 T
2093325 TTGAGTGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 1 0.03
8 28 0.74
9 4 0.11
10 4 0.11
11 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (8 bp):
TATATGTA
Found at i:2094761 original size:24 final size:24
Alignment explanation
Indices: 2094734--2094781 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2094724 AAGCTAAAGC
*
2094734 TAGATTATCTAGGATACCAAAGTT
1 TAGAGTATCTAGGATACCAAAGTT
*
2094758 TAGAGTCTCTAGGATACCAAAGTT
1 TAGAGTATCTAGGATACCAAAGTT
2094782 CTATACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (24 bp):
TAGAGTATCTAGGATACCAAAGTT
Found at i:2104023 original size:24 final size:24
Alignment explanation
Indices: 2103991--2104040 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2103981 GACCCTAGCA
2103991 GTTTTATAATACCATGCTCAATTG
1 GTTTTATAATACCATGCTCAATTG
2104015 GTTTTATAATACCATGCTCAATTG
1 GTTTTATAATACCATGCTCAATTG
2104039 GT
1 GT
2104041 AACAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (24 bp):
GTTTTATAATACCATGCTCAATTG
Found at i:2120210 original size:2 final size:2
Alignment explanation
Indices: 2120203--2120228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2120193 CCACCACCAA
2120203 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
2120229 TGTAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2120335 original size:2 final size:2
Alignment explanation
Indices: 2120322--2120351 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2120312 CGAATTATTG
*
2120322 AT AT AC 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
2120352 TTGTTGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2126731 original size:18 final size:18
Alignment explanation
Indices: 2126677--2126739 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
2126667 TTAAATTCTT
*
2126677 ATTAATTTATATATCTTAA
1 ATTAAATTA-ATATCTTAA
* * * *
2126696 CTTAAATTCACATATTAA
1 ATTAAATTAATATCTTAA
2126714 ATTAAATTAATATCTTAA
1 ATTAAATTAATATCTTAA
2126732 GATTAAAT
1 -ATTAAAT
2126740 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAATTAATATCTTAA
Found at i:2127103 original size:28 final size:29
Alignment explanation
Indices: 2127025--2127127 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 29
2127015 ATATATGTAA
* * *
2127025 TAAGTCAAAATAAAAATAAGATATATTTT
1 TAAGTTAAGATAAAAATAAAATATATTTT
*
2127054 TAAAACTTAAGATAAAAATAAAATATA-TTT
1 T--AAGTTAAGATAAAAATAAAATATATTTT
* *
2127084 TAAGTTAAGATAATATTAAAATATATTTT
1 TAAGTTAAGATAAAAATAAAATATATTTT
*
2127113 TAAGTTAAAATAAAA
1 TAAGTTAAGATAAAA
2127128 GTTATCTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
28 21 0.34
29 17 0.27
30 4 0.06
31 20 0.32
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (29 bp):
TAAGTTAAGATAAAAATAAAATATATTTT
Found at i:2127125 original size:29 final size:29
Alignment explanation
Indices: 2127025--2127186 Score: 127
Period size: 29 Copynumber: 5.7 Consensus size: 29
2127015 ATATATGTAA
* *
2127025 TAAGTCAAAATAAAAATAAGATATATTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* *
2127054 TAAAACTTAAGATAAAAATAAAATATA-TTT
1 T--AAGTTAAAATAAAAATAAAATATATTTT
* * *
2127084 TAAGTTAAGATAATATTAAAATATATTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* *
2127113 TAAGTTAAAATAAAAGT----TATCTTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* * * * *
2127138 TAGGTTAAAACAAGAATAAAATAGATTTAA
1 TAAGTTAAAATAAAAATAAAATATATTT-T
*
2127168 TAATTTAAAATAAAAATAA
1 TAAGTTAAAATAAAAATAA
2127187 TTTTTTAATG
Statistics
Matches: 103, Mismatches: 22, Indels: 15
0.74 0.16 0.11
Matches are distributed among these distances:
25 20 0.19
28 21 0.20
29 23 0.22
30 19 0.18
31 20 0.19
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAGTTAAAATAAAAATAAAATATATTTT
Found at i:2128756 original size:17 final size:19
Alignment explanation
Indices: 2128736--2128773 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2128726 TTATTTTTAG
2128736 TGAAA-ATTTTT-TAGGCA
1 TGAAACATTTTTCTAGGCA
2128753 TGAAACCATTTTTCTAGGCA
1 TGAAA-CATTTTTCTAGGCA
2128773 T
1 T
2128774 AGTTGTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (19 bp):
TGAAACATTTTTCTAGGCA
Found at i:2130329 original size:15 final size:15
Alignment explanation
Indices: 2130309--2130349 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2130299 ATTTAATTAA
2130309 TGTGGAGGATATATC
1 TGTGGAGGATATATC
2130324 TGTGGAGGATATATC
1 TGTGGAGGATATATC
*
2130339 TGAGGAGGATA
1 TGTGGAGGATA
2130350 CATGAGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (15 bp):
TGTGGAGGATATATC
Found at i:2137572 original size:21 final size:21
Alignment explanation
Indices: 2137546--2137605 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
2137536 CATATGAAAT
*
2137546 TTGTCCCGAAGGACCACTGTA
1 TTGTCCAGAAGGACCACTGTA
2137567 TTGTCCAGAAGGACCACTGTA
1 TTGTCCAGAAGGACCACTGTA
* *
2137588 TTGTCCTGAATGACCACT
1 TTGTCCAGAAGGACCACT
2137606 ATAACCCTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
TTGTCCAGAAGGACCACTGTA
Found at i:2143137 original size:2 final size:2
Alignment explanation
Indices: 2143130--2143171 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2143120 GTATTCCTTT
2143130 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
2143172 GATAGGTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2146380 original size:144 final size:144
Alignment explanation
Indices: 2146115--2146402 Score: 443
Period size: 144 Copynumber: 2.0 Consensus size: 144
2146105 TCTTAAAGTA
* * * *
2146115 CATAAAACACCATAATAAAAGACATAATTAAAGTCTATAAACATAAATGATAAACAAATAATGTT
1 CATAAAACACCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGACAAACAAATAATATT
* * * *
2146180 TTTGTTCTTTGGCACAACATTCTAAAATTTCGCGCAATACTTGTGACATATGATACTCTAGTATT
66 TTTGTTCTTTAGCACAACATTCTAAAATTTCGCGCAATACTTGTGACATATCATACTCCAGAATT
2146245 ACAATCATCATTCT
131 ACAATCATCATTCT
* *
2146259 CATAAAACACCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGGCAAACATATAATATT
1 CATAAAACACCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGACAAACAAATAATATT
* * *
2146324 TTTGTTCTTTAGCACAACATTCTCAAATTTCAGC-CAATACTTGTGACTTCTCATACTCCAGAAT
66 TTTGTTCTTTAGCACAACATTCTAAAATTTC-GCGCAATACTTGTGACATATCATACTCCAGAAT
2146388 TACAATCATCATTCT
130 TACAATCATCATTCT
2146403 TTATTTCCTC
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
144 128 0.98
145 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (144 bp):
CATAAAACACCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGACAAACAAATAATATT
TTTGTTCTTTAGCACAACATTCTAAAATTTCGCGCAATACTTGTGACATATCATACTCCAGAATT
ACAATCATCATTCT
Done.