Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1839201 original size:18 final size:19
Alignment explanation
Indices: 1839159--1839198 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1839149 TTTGGTTCAC
*
1839159 GGAATGTAAGATTACTAGTG
1 GGAATGTAAGATTACCAG-G
1839179 GGAATGTAAGATTACCAGG
1 GGAATGTAAGATTACCAGG
1839198 G
1 G
1839199 AATAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1843752 original size:23 final size:24
Alignment explanation
Indices: 1843726--1843815 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 24
1843716 TCAAATTTGA
*
1843726 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
1843749 ATTCTGATCTGATA-TTTACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
1843772 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
*
1843796 ATTATGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1843816 TTGAATTATG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 33 0.60
24 22 0.40
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:1843832 original size:24 final size:24
Alignment explanation
Indices: 1843776--1843825 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1843766 ACATGGATTC
*
1843776 TGATCTGATACATGACCTGAATTA
1 TGATATGATACATGACCTGAATTA
* *
1843800 TGATATGATACTTGACTTGAATTA
1 TGATATGATACATGACCTGAATTA
1843824 TG
1 TG
1843826 TTTTGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (24 bp):
TGATATGATACATGACCTGAATTA
Found at i:1843940 original size:35 final size:35
Alignment explanation
Indices: 1843893--1843967 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1843883 TGGAGGAAGA
* *
1843893 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
1843928 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
1843963 TTACT
1 TTACT
1843968 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:1849147 original size:23 final size:24
Alignment explanation
Indices: 1849121--1849210 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 24
1849111 TCAAATTTGA
*
1849121 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
1849144 ATTCTGATCTGATA-TTTACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
1849167 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
*
1849191 ATTATGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1849211 TTGAATTATG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 33 0.60
24 22 0.40
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:1849227 original size:24 final size:24
Alignment explanation
Indices: 1849171--1849220 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1849161 ACATGGATTC
*
1849171 TGATCTGATACATGACCTGAATTA
1 TGATATGATACATGACCTGAATTA
* *
1849195 TGATATGATACTTGACTTGAATTA
1 TGATATGATACATGACCTGAATTA
1849219 TG
1 TG
1849221 TTTTGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (24 bp):
TGATATGATACATGACCTGAATTA
Found at i:1849336 original size:35 final size:35
Alignment explanation
Indices: 1849289--1849363 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1849279 TGGAGGAAGA
* *
1849289 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
1849324 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
1849359 TTACT
1 TTACT
1849364 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:1850057 original size:2 final size:2
Alignment explanation
Indices: 1850046--1850074 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1850036 ACCCCCTAAC
1850046 TA TA -A 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
1850075 CACACACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1853595 original size:23 final size:24
Alignment explanation
Indices: 1853569--1853626 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
1853559 TTGATTTAAT
1853569 ATATTGTAAATTA-TTTTAT-ATTA
1 ATATT-TAAATTATTTTTATAATTA
*
1853592 ATATTTATA-TATTTTTATAATTA
1 ATATTTAAATTATTTTTATAATTA
*
1853615 AAATTTAAATTA
1 ATATTTAAATTA
1853627 AAAAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 9 0.31
23 16 0.55
24 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATTTAAATTATTTTTATAATTA
Found at i:1855085 original size:34 final size:33
Alignment explanation
Indices: 1855033--1855097 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
1855023 TTCATTAAAC
*
1855033 TTTTTTATATTTTAAATTTTGTAAAAAAAATATA
1 TTTTTTATAATTTAAATTTT-TAAAAAAAATATA
*
1855067 TTTTTTATGAATTT-AATTTTTAAAGAAAATA
1 TTTTTTAT-AATTTAAATTTTTAAAAAAAATA
1855098 AATAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 14 0.50
35 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (33 bp):
TTTTTTATAATTTAAATTTTTAAAAAAAATATA
Found at i:1862633 original size:49 final size:49
Alignment explanation
Indices: 1862561--1862658 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1862551 TACCATTGGG
1862561 TCGTTAAGTGATAAACGACATTGATATTGACGATAATTTCTATAAATGT
1 TCGTTAAGTGATAAACGACATTGATATTGACGATAATTTCTATAAATGT
1862610 TCGTTAAGTGATAAACGACATTGATATTGACGATAATTTCTATAAATGT
1 TCGTTAAGTGATAAACGACATTGATATTGACGATAATTTCTATAAATGT
1862659 GATGATGTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (49 bp):
TCGTTAAGTGATAAACGACATTGATATTGACGATAATTTCTATAAATGT
Found at i:1864207 original size:18 final size:18
Alignment explanation
Indices: 1864156--1864198 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1864146 CCAATGGAAT
1864156 GCCGACAATGTAATAATA
1 GCCGACAATGTAATAATA
1864174 GCCGACAATGTAATAATA
1 GCCGACAATGTAATAATA
1864192 GCCGACA
1 GCCGACA
1864199 TTGACATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (18 bp):
GCCGACAATGTAATAATA
Found at i:1864876 original size:44 final size:44
Alignment explanation
Indices: 1864808--1864897 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
1864798 CTAATATGCC
* *
1864808 ACCGTTTACTGTAGAGAAGTATTCAAAGTTTCATCAATTTTTAA
1 ACCGTTTACTGTAGAGAAGCATTCAAAATTTCATCAATTTTTAA
1864852 ACCGTTTACTGTAGAGAAGCATTCAAAATTTCATCAATTTTTAA
1 ACCGTTTACTGTAGAGAAGCATTCAAAATTTCATCAATTTTTAA
1864896 AC
1 AC
1864898 TTCATCAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (44 bp):
ACCGTTTACTGTAGAGAAGCATTCAAAATTTCATCAATTTTTAA
Found at i:1864903 original size:17 final size:18
Alignment explanation
Indices: 1864881--1864915 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1864871 CATTCAAAAT
1864881 TTCATCAA-TTTTTAAAC
1 TTCATCAATTTTTTAAAC
1864898 TTCATCAATTTTTTAAAC
1 TTCATCAATTTTTTAAAC
1864916 CATAGCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCATCAATTTTTTAAAC
Found at i:1867649 original size:22 final size:21
Alignment explanation
Indices: 1867621--1867662 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1867611 CTTCTAAATA
1867621 ACTGAGTCAACTCGCTTGAGTC
1 ACTGAGTCAACTCGC-TGAGTC
*
1867643 ACTGAGTTAACTCGCTGAGT
1 ACTGAGTCAACTCGCTGAGT
1867663 TGAACCGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
ACTGAGTCAACTCGCTGAGTC
Found at i:1871436 original size:166 final size:166
Alignment explanation
Indices: 1871162--1871493 Score: 646
Period size: 166 Copynumber: 2.0 Consensus size: 166
1871152 CATCTAGGGA
*
1871162 TGGACCGAGTGGAGTGTTGGTGTGCGATCGCACCGTTGAAATTTGAATTTTTTTATATTTTAGGT
1 TGGACCGAGTGGAGTGTTGGTGTGCGATCGCACCGTTGAAATTTGAATTTTTTTATATTTTAGGA
*
1871227 TTTTGTTATATATTTTTGATTGATTATCAAATTTCACGCTTTTAAAATTTTATAACTTCACACTC
66 TTTTGTTATATATTTTTGATTGATTATCAAATTTCACGCTTTTAAAATTTTATAACTTCACACCC
1871292 TACAATTTGTAATATAACTTCTTGAATTCGTATCTC
131 TACAATTTGTAATATAACTTCTTGAATTCGTATCTC
1871328 TGGACCGAGTGGAGTGTTGGTGTGCGATCGCACCGTTGAAATTTGAATTTTTTTATATTTTAGGA
1 TGGACCGAGTGGAGTGTTGGTGTGCGATCGCACCGTTGAAATTTGAATTTTTTTATATTTTAGGA
1871393 TTTTGTTATATATTTTTGATTGATTATCAAATTTCACGCTTTTAAAATTTTATAACTTCACACCC
66 TTTTGTTATATATTTTTGATTGATTATCAAATTTCACGCTTTTAAAATTTTATAACTTCACACCC
1871458 TACAATTTGTAATATAACTTCTTGAATTCGTATCTC
131 TACAATTTGTAATATAACTTCTTGAATTCGTATCTC
1871494 CTGGCATAAA
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 164 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (166 bp):
TGGACCGAGTGGAGTGTTGGTGTGCGATCGCACCGTTGAAATTTGAATTTTTTTATATTTTAGGA
TTTTGTTATATATTTTTGATTGATTATCAAATTTCACGCTTTTAAAATTTTATAACTTCACACCC
TACAATTTGTAATATAACTTCTTGAATTCGTATCTC
Found at i:1873008 original size:16 final size:17
Alignment explanation
Indices: 1872977--1873015 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1872967 AATAAAATTT
1872977 TAAAATAAGCATAATTAA
1 TAAAATAA-CATAATTAA
1872995 TAAAATAA-ATAATTAA
1 TAAAATAACATAATTAA
1873011 -AAAAT
1 TAAAAT
1873016 TGAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
18 8 0.38
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAATAACATAATTAA
Found at i:1875911 original size:20 final size:20
Alignment explanation
Indices: 1875886--1875927 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1875876 GGCAATGAAC
*
1875886 CGGCTGAAAACAGGTAGAAT
1 CGGCTGAAAACAGGTAAAAT
*
1875906 CGGCTGAAAACCGGTAAAAT
1 CGGCTGAAAACAGGTAAAAT
1875926 CG
1 CG
1875928 AGGTGAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (20 bp):
CGGCTGAAAACAGGTAAAAT
Found at i:1881285 original size:18 final size:17
Alignment explanation
Indices: 1881262--1881299 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
1881252 ATTTGATTTG
1881262 AATTAAACTAAACCGTAA
1 AATTAAACTAAACCG-AA
1881280 AATTAAACTAAACCGAA
1 AATTAAACTAAACCGAA
1881297 AAT
1 AAT
1881300 CATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (17 bp):
AATTAAACTAAACCGAA
Found at i:1884833 original size:2 final size:2
Alignment explanation
Indices: 1884826--1884853 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1884816 TGTGAATTCG
1884826 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
1884854 TCGAATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1886991 original size:2 final size:2
Alignment explanation
Indices: 1886984--1887027 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1886974 TGCATTGCCA
1886984 AT AT AT AT -T 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
1887025 AT A
1 AT A
1887028 ATTGCTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1888769 original size:205 final size:208
Alignment explanation
Indices: 1888393--1888808 Score: 622
Period size: 205 Copynumber: 2.0 Consensus size: 208
1888383 CAATATTTTT
*
1888393 ATCTATCGTGTTTAAAAAAGGGAGGAAAGCTTATCGATATTCTTCAAATAGGCTTTAGTTGAGAT
1 ATCTACCGTGTTTAAAAAAGGGAGGAAAGCTTATCGATATTCTTCAAATAGGCTTTAGTTGAGAT
* * **
1888458 CCGATTTGACATTTAACGTTTAAATCAAGGACTAGTTTGATGTAAAGACCTGATTGGTGATAGGA
66 CCGATTTGACATTTAACGCTAAAATCAAGGACTAGTTTGATAAAAAGACCTGATTGGTGATAGGA
* * *
1888523 AATCGATTCTACGAGGACTTAATTAGAATGTTTTGAAGTTTGAAGACTAATTTAGAATTTAAATC
131 AATCGATTATACGAGGACTTAATTAGAATGCTTTAAAGTTTGAAGACTAATTTAGAATTTAAATC
1888588 AT-GGTCAGGGAC
196 ATGGGTCAGGGAC
*
1888600 ATCTACCGTGTTT-AAAAAGGG-GGAAAGCTTATCGATATTCTTCGAATAGGCTTTAGTTGAGAT
1 ATCTACCGTGTTTAAAAAAGGGAGGAAAGCTTATCGATATTCTTCAAATAGGCTTTAGTTGAGAT
* * * * * *
1888663 CTGATTTGATATTTAAGGCTAAAATTAATGATTAGTTTGATAAAAAGACCTGATTGGTGATAGGA
66 CCGATTTGACATTTAACGCTAAAATCAAGGACTAGTTTGATAAAAAGACCTGATTGGTGATAGGA
* * * * *
1888728 AATTGATTATATGAGGACTTTATTATAATGCTTTAAAGTTTGAAGACTAATTTAGAATTTAAATT
131 AATCGATTATACGAGGACTTAATTAGAATGCTTTAAAGTTTGAAGACTAATTTAGAATTTAAATC
*
1888793 ATGGGTCAGTGAC
196 ATGGGTCAGGGAC
1888806 ATC
1 ATC
1888809 CAGTGTAATT
Statistics
Matches: 187, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
205 155 0.83
206 20 0.11
207 12 0.06
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (208 bp):
ATCTACCGTGTTTAAAAAAGGGAGGAAAGCTTATCGATATTCTTCAAATAGGCTTTAGTTGAGAT
CCGATTTGACATTTAACGCTAAAATCAAGGACTAGTTTGATAAAAAGACCTGATTGGTGATAGGA
AATCGATTATACGAGGACTTAATTAGAATGCTTTAAAGTTTGAAGACTAATTTAGAATTTAAATC
ATGGGTCAGGGAC
Found at i:1890946 original size:60 final size:59
Alignment explanation
Indices: 1890795--1890956 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 59
1890785 CTCTCATTTC
* * * * *
1890795 AAATTAGTCCTTAAAC-TTTAAATATTTCAATTTCATCCTTC-AACTATGATTTTATTGT
1 AAATTAGTCCTTAAACTTTTAGATCTTTCAATTTCATCC-CCAAACTATGATTTCATTCT
* ***
1890853 AAATTAGTCCTTAAACTTTT-GAACAACCTAATTTCATCCCCAAACTATGAATTTCATTCT
1 AAATTAGTCCTTAAACTTTTAGATCTTTC-AATTTCATCCCCAAACTATG-ATTTCATTCT
* * *
1890913 AAATTGGTCCCTAAACTTTTAGATCTTTCAATTTCATCGCCAAA
1 AAATTAGTCCTTAAACTTTTAGATCTTTCAATTTCATCCCCAAA
1890957 TTCATCCAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
58 19 0.23
59 20 0.24
60 40 0.48
61 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (59 bp):
AAATTAGTCCTTAAACTTTTAGATCTTTCAATTTCATCCCCAAACTATGATTTCATTCT
Found at i:1895681 original size:110 final size:113
Alignment explanation
Indices: 1895514--1895743 Score: 405
Period size: 111 Copynumber: 2.0 Consensus size: 113
1895504 AATGTTTAGC
1895514 ATTTGCATGTTTCAATGAATTAAAATTATATCAATGGATGTTAAAAGTGCATTTTTAAATG-TTT
1 ATTT-CATGTTTCAATGAATTAAAATTATA-CAATGGATGTTAAAAGTGCATTTTTAAATGTTTT
1895578 TATAAAAGAAGAAGTGTACGTGGAACAACCTCCAGGTTTTGAAGATTCAA
64 TATAAAAGAAGAAGTGTACGTGGAACAACCTCCAGGTTTTGAAGATTCAA
1895628 ATTTCATGTTTCAATGAATTAAAA-TAT-CAAATGGATGTT-AAAGTGCATTTTTAAATGTTTTT
1 ATTTCATGTTTCAATGAATTAAAATTATAC-AATGGATGTTAAAAGTGCATTTTTAAATGTTTTT
1895690 ATAAAAGAAGAAGTGTACGTGGAACAACCTCCAGGTTTTGAAGATTCAA
65 ATAAAAGAAGAAGTGTACGTGGAACAACCTCCAGGTTTTGAAGATTCAA
1895739 ATTTC
1 ATTTC
1895744 CGGATCATGT
Statistics
Matches: 114, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
110 19 0.17
111 68 0.60
112 3 0.03
113 20 0.18
114 4 0.04
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (113 bp):
ATTTCATGTTTCAATGAATTAAAATTATACAATGGATGTTAAAAGTGCATTTTTAAATGTTTTTA
TAAAAGAAGAAGTGTACGTGGAACAACCTCCAGGTTTTGAAGATTCAA
Found at i:1897118 original size:18 final size:19
Alignment explanation
Indices: 1897095--1897152 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 19
1897085 ATTTGGTGCA
*
1897095 GAGGGAATCGA-TCCCCCT
1 GAGGGAACCGATTCCCCCT
1897113 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
1897134 GAAGGGAACCGATTCCCCC
1 G-AGGGAACCGATTCCCCC
1897153 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
21 2 0.06
22 17 0.49
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.17
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:1900041 original size:14 final size:12
Alignment explanation
Indices: 1900007--1900031 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1899997 TCAAGCAACT
1900007 AGAATCAAAGAG
1 AGAATCAAAGAG
1900019 AGAATCAAAGAG
1 AGAATCAAAGAG
1900031 A
1 A
1900032 AAGCATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (12 bp):
AGAATCAAAGAG
Found at i:1902762 original size:26 final size:26
Alignment explanation
Indices: 1902707--1902763 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1902697 GGTCTTTGTT
*
1902707 ATATTTTTAATAAGTTAATATAAAAT
1 ATATTTTTAATAAGTTAATATAAAAG
1902733 ATATTTTTAA-AA-TTAATATATATAAG
1 ATATTTTTAATAAGTTAATATA-A-AAG
1902759 ATATT
1 ATATT
1902764 ATGAGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 8 0.29
25 3 0.11
26 17 0.61
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATTTTTAATAAGTTAATATAAAAG
Found at i:1917272 original size:22 final size:22
Alignment explanation
Indices: 1917246--1917289 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1917236 AACTAGAAAT
1917246 TTGCGAACAACAAAAAGAATAG
1 TTGCGAACAACAAAAAGAATAG
1917268 TTGCGAACAACAAAAAGAATAG
1 TTGCGAACAACAAAAAGAATAG
1917290 AATAATCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (22 bp):
TTGCGAACAACAAAAAGAATAG
Found at i:1918522 original size:27 final size:26
Alignment explanation
Indices: 1918473--1918523 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1918463 TAAGCTTTGG
*
1918473 AATTTTAAAATTAATTCCCTTTTTTT
1 AATTTTAAAATTAATTCCATTTTTTT
1918499 AATTTTAATAATTTAA-TCCATTTTT
1 AATTTTAA-AA-TTAATTCCATTTTT
1918524 ATGTTACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 10 0.45
28 4 0.18
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTTTAAAATTAATTCCATTTTTTT
Found at i:1919714 original size:31 final size:31
Alignment explanation
Indices: 1919676--1919741 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
1919666 AACGCCTGTG
1919676 CACCTAAAATGATAAC-GAAGAAAAAGTTAGA
1 CACCTAAAATGATAACAG-AGAAAAAGTTAGA
*
1919707 CACCTAAAATGATAACAGAGAAAACGTTAGA
1 CACCTAAAATGATAACAGAGAAAAAGTTAGA
1919738 CACC
1 CACC
1919742 AAGATGTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (31 bp):
CACCTAAAATGATAACAGAGAAAAAGTTAGA
Found at i:1922211 original size:231 final size:234
Alignment explanation
Indices: 1921805--1922267 Score: 792
Period size: 231 Copynumber: 2.0 Consensus size: 234
1921795 TCGACTCGAA
*
1921805 TTTTTAAAGTATAAATCCAATCGGATCCAACCCGACCCTATAAAAAAGGATTTAATTAAAATAAT
1 TTTTTAAAGTATAAATCCAATCGGATCCAACCCAACCCTATAAAAAAGGATTTAATTAAAATAAT
* *
1921870 AATATTTTTTTTAAAAAATTATATTATTAGCCTTGGTCGGATCGGAGTGTTTCACCCTCCACCTG
66 AATATTTTTTTTAAAAAATTATATTATTAGCCTTGGTCGGATCGGAATGTTTCACCCTCCACCCG
1921935 AACCCGACCGGACCTCACCCCTTAAAAATCGACCCGATCCGAACCT-AATT-TTTTTATAAAAAA
131 AACCCGACCGGACCTCACCCCTTAAAAATCGACCCGATCCGAACCTAAATTATTTTT-TAAAAAA
* *
1921998 ATCCGACCCTATCGAGTCAATTCAAATTAAATTACCATCAT
195 ATCC-AACCTATCGAATCAATTCAAATTAAATTACCATCAT
*
1922039 TTTTTAAAGTATAAATCCGATCGGATCCAACCCAACCCTAT-AAAAAGGATTTAATTAAAATAAT
1 TTTTTAAAGTATAAATCCAATCGGATCCAACCCAACCCTATAAAAAAGGATTTAATTAAAATAAT
*
1922103 AATA-TTTTTTT-AAATATTATATTATTAGCCTTGGTCGGATCGGAATGTTTCACCCTCCACCCG
66 AATATTTTTTTTAAAAAATTATATTATTAGCCTTGGTCGGATCGGAATGTTTCACCCTCCACCCG
*
1922166 AACCCGACCGGACCTCGCCCCTTAAAAATCGACCCGATCCGAACCTAAATTATTTTTTAAAAAAA
131 AACCCGACCGGACCTCACCCCTTAAAAATCGACCCGATCCGAACCTAAATTATTTTTTAAAAAAA
*
1922231 TCCAACCTATCGAATCAATTCAAATTAAATTATCATC
196 TCCAACCTATCGAATCAATTCAAATTAAATTACCATC
1922268 CCTAGTCTTT
Statistics
Matches: 218, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
231 125 0.57
232 22 0.10
233 32 0.15
234 39 0.18
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30
Consensus pattern (234 bp):
TTTTTAAAGTATAAATCCAATCGGATCCAACCCAACCCTATAAAAAAGGATTTAATTAAAATAAT
AATATTTTTTTTAAAAAATTATATTATTAGCCTTGGTCGGATCGGAATGTTTCACCCTCCACCCG
AACCCGACCGGACCTCACCCCTTAAAAATCGACCCGATCCGAACCTAAATTATTTTTTAAAAAAA
TCCAACCTATCGAATCAATTCAAATTAAATTACCATCAT
Found at i:1924244 original size:32 final size:32
Alignment explanation
Indices: 1924203--1924275 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
1924193 TCGTAAACAT
1924203 TAAACGTTACACGTATGACACGAACATGTTCG
1 TAAACGTTACACGTATGACACGAACATGTTCG
* * *
1924235 TAAACGTTACACGTATGACATGGATATGTTCG
1 TAAACGTTACACGTATGACACGAACATGTTCG
*
1924267 TAAATGTTA
1 TAAACGTTA
1924276 AATGAACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (32 bp):
TAAACGTTACACGTATGACACGAACATGTTCG
Found at i:1940129 original size:12 final size:12
Alignment explanation
Indices: 1940112--1940136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1940102 AATCGCTAAC
1940112 GATTTGAGCTCA
1 GATTTGAGCTCA
1940124 GATTTGAGCTCA
1 GATTTGAGCTCA
1940136 G
1 G
1940137 CTTCTAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (12 bp):
GATTTGAGCTCA
Found at i:1942850 original size:28 final size:29
Alignment explanation
Indices: 1942795--1942850 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1942785 TGAATCTATA
*
1942795 TTCTCTCGTCTATTCTCTCATCTTTTCTT
1 TTCTCTCGTCTATTCTCTCATCTATTCTT
*
1942824 TTCT-TCGTCTATTTTCTTC-TCTATTCT
1 TTCTCTCGTCTATTCTC-TCATCTATTCT
1942851 CGAGGTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.07, C:0.29, G:0.04, T:0.61
Consensus pattern (29 bp):
TTCTCTCGTCTATTCTCTCATCTATTCTT
Found at i:1956283 original size:24 final size:23
Alignment explanation
Indices: 1956241--1956285 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1956231 ATTCTTATAC
1956241 TTTATTTATTTTTTCATTATTCT
1 TTTATTTATTTTTTCATTATTCT
1956264 TTTATTCTATATTTTT-ATTATT
1 TTTATT-TAT-TTTTTCATTATT
1956286 TATTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTTATTTTTTCATTATTCT
Found at i:1964574 original size:22 final size:20
Alignment explanation
Indices: 1964520--1964581 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 20
1964510 GTCCAAAATA
1964520 TATTTTTATAGAATAAAACTATT
1 TATTTTTATA-AA-AAAA-TATT
*
1964543 TA-TTTAATAAAAAAATATTAT
1 TATTTTTATAAAAAAATA-T-T
1964564 TATTTTTATAAAAGAAAT
1 TATTTTTATAAAA-AAAT
1964582 CACATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 5 0.15
22 15 0.45
23 6 0.18
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTTTTATAAAAAAATATT
Found at i:1964864 original size:5 final size:5
Alignment explanation
Indices: 1964854--1964879 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1964844 CATATCAAAG
1964854 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
1964880 CGAGGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:1965042 original size:12 final size:13
Alignment explanation
Indices: 1965018--1965048 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1965008 CGGGTTCGGG
1965018 TTCGGGGATTTTT
1 TTCGGGGATTTTT
1965031 TTCGGGGA-TTTT
1 TTCGGGGATTTTT
1965043 TTCGGG
1 TTCGGG
1965049 TTGGGTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.06, C:0.10, G:0.35, T:0.48
Consensus pattern (13 bp):
TTCGGGGATTTTT
Found at i:1965099 original size:2 final size:2
Alignment explanation
Indices: 1965092--1965181 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
1965082 CCGCCCCGAT
* * *
1965092 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA T- TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1965131 TA TA T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1965167 TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1965182 AAATATTTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
1 12 0.17
2 60 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:1965149 original size:34 final size:34
Alignment explanation
Indices: 1965106--1965190 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1965096 TATATATATA
*
1965106 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1965140 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
1965174 TATATATAAAATATTTT
1 TATATATATAATATTTT
1965191 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1965166 original size:9 final size:9
Alignment explanation
Indices: 1965091--1965169 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 9
1965081 CCCGCCCCGA
1965091 TTATATATAT
1 TTATATAT-T
*
1965101 ATATATATAT
1 TTATATAT-T
*
1965111 ATATAATATT
1 TTAT-ATATT
1965121 TTATAT-TT
1 TTATATATT
1965129 TT-TATATT
1 TTATATATT
1965137 AATTATATA-T
1 --TTATATATT
*
1965147 ATA-ATATT
1 TTATATATT
1965155 TTATATATT
1 TTATATATT
1965164 TTATAT
1 TTATAT
1965170 TAATTATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
7 6 0.10
8 11 0.19
9 13 0.22
10 20 0.34
11 8 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATATT
Found at i:1965187 original size:18 final size:18
Alignment explanation
Indices: 1965090--1965188 Score: 88
Period size: 16 Copynumber: 5.9 Consensus size: 18
1965080 CCCCGCCCCG
1965090 ATTATATATAT-ATA-T-
1 ATTATATATATAATATTA
1965105 A-TATATATATAATATT-
1 ATTATATATATAATATTA
* * *
1965121 -TTATATTTTTTATATTA
1 ATTATATATATAATATTA
1965138 ATTATATATATAATATT-
1 ATTATATATATAATATTA
* *
1965155 -TTATATATTTTATATTA
1 ATTATATATATAATATTA
*
1965172 ATTATATATAAAATATT
1 ATTATATATATAATATT
1965189 TTCGGGTTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
14 9 0.14
15 4 0.06
16 27 0.41
18 26 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATATATATAATATTA
Found at i:1967426 original size:2 final size:2
Alignment explanation
Indices: 1967419--1967454 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1967409 AAAAGTTCAA
1967419 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
1967455 CTAGAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1968398 original size:26 final size:26
Alignment explanation
Indices: 1968367--1968419 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1968357 CTATTTTTAT
* *
1968367 ATTAGTGGTGCATTTTAATATATGTC
1 ATTAGTGGTGCATTTCAATAAATGTC
*
1968393 ATTAGTGGTGTATTTCAATAAATGTC
1 ATTAGTGGTGCATTTCAATAAATGTC
1968419 A
1 A
1968420 CTCATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (26 bp):
ATTAGTGGTGCATTTCAATAAATGTC
Found at i:1968932 original size:35 final size:35
Alignment explanation
Indices: 1968893--1968969 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1968883 AACATAAACC
1968893 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* * * * *
1968928 TCAATTACATTGTAAACCTCAAATTTTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1968963 TCAATTT
1 TCAATTT
1968970 GAATGCAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1979919 original size:32 final size:32
Alignment explanation
Indices: 1979878--1979958 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
1979868 ACGTGGTATG
* * *
1979878 TGTCATATCATCATTTTGGGTGACAAAGCACA
1 TGTCATATCATCATTTTAGATGACAAAGAACA
* **
1979910 TGTCATATCATCACTTTAGATGACATGGAACA
1 TGTCATATCATCATTTTAGATGACAAAGAACA
* *
1979942 TGTCATGTAATCATTTT
1 TGTCATATCATCATTTT
1979959 TTGTAGCATG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTCATATCATCATTTTAGATGACAAAGAACA
Found at i:1985475 original size:2 final size:2
Alignment explanation
Indices: 1985468--1985493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1985458 ATAATTTCTC
1985468 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
1985494 AACTATATGT
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):
TA
Found at i:1989732 original size:28 final size:30
Alignment explanation
Indices: 1989655--1989732 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 30
1989645 TTTTTTATTG
*
1989655 TAGGCACTAAAAGTGTAATTAAAAAAAATAT
1 TAGGCACTAAAAAT-TAATTAAAAAAAATAT
* * **
1989686 TAAGCAC-ATATTTTAAATT-AAAAAAA-AT
1 TAGGCACTAAAAATT-AATTAAAAAAAATAT
1989714 TAGGCACTAAAAATTAATT
1 TAGGCACTAAAAATTAATT
1989733 TTAAGTATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
28 12 0.32
29 12 0.32
30 7 0.19
31 6 0.16
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (30 bp):
TAGGCACTAAAAATTAATTAAAAAAAATAT
Found at i:1992681 original size:14 final size:15
Alignment explanation
Indices: 1992662--1992690 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1992652 TACCCACAAA
1992662 TATATAAG-TTTAAG
1 TATATAAGATTTAAG
1992676 TATATAAGATTTAAG
1 TATATAAGATTTAAG
1992691 GTAACGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
TATATAAGATTTAAG
Found at i:1994239 original size:162 final size:163
Alignment explanation
Indices: 1993948--1994290 Score: 478
Period size: 163 Copynumber: 2.1 Consensus size: 163
1993938 TATCGTTAGA
* * *
1993948 ATATTCAAATTAGGGTTTAGGGCTTAAAACACTAATCTGAAAAGACCCCAGGTAAAGGCGGAGAA
1 ATATTCGAATTA-GGTTTAGGGCTTAAAACACTAATCCGAAAAGACCCCAGGTAAAGACGGAGAA
* * * *
1994013 GTTTCTAATCCTACGTCTTAATTTCTAACCCTAGTCTCTACTATCCATGTACACTGTGGTGATCA
65 ATTTCTAATACTACGTCTTAATTTCTAACCCTAATCTCTACTATACATGTACACTGTGGTGATCA
1994078 CTTGATTATAAATGAAACATACGTAAT-AGAAAT
130 CTTGATTATAAATGAAACATACGTAATAAGAAAT
*
1994111 ATATTCGAATTAGGTTTAGGG-TGTAAAACACTGATCCGAAAAGA-CCCAGGTAAAGACGGAGAA
1 ATATTCGAATTAGGTTTAGGGCT-TAAAACACTAATCCGAAAAGACCCCAGGTAAAGACGGAGAA
* * * **
1994174 ATTTCACTAATAGTACGTCTTAATTTCTAACCCTAATCTCTACTATATATTTA-TTTGTGGTGAT
65 ATTT--CTAATACTACGTCTTAATTTCTAACCCTAATCTCTACTATACATGTACACTGTGGTGAT
* *
1994238 CACTTGATTATAAATGAAACTTGCGTAATAAGAAAT
128 CACTTGATTATAAATGAAACATACGTAATAAGAAAT
*
1994274 ATACTCGAATTAGGTTT
1 ATATTCGAATTAGGTTT
1994291 TCTAAGAAGA
Statistics
Matches: 160, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
161 22 0.14
162 64 0.40
163 74 0.46
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (163 bp):
ATATTCGAATTAGGTTTAGGGCTTAAAACACTAATCCGAAAAGACCCCAGGTAAAGACGGAGAAA
TTTCTAATACTACGTCTTAATTTCTAACCCTAATCTCTACTATACATGTACACTGTGGTGATCAC
TTGATTATAAATGAAACATACGTAATAAGAAAT
Found at i:1996473 original size:21 final size:21
Alignment explanation
Indices: 1996449--1996509 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1996439 AACTTTGAAA
1996449 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1996470 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1996484 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1996505 AAATG
1 AAATG
1996510 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1996555 original size:36 final size:36
Alignment explanation
Indices: 1996441--1996560 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
1996431 TGGCAACCAA
1996441 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1996478 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1996513 CTTTGAAAAATAGTTTTTCAAAATTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1996550 -GTTGAAAAATG
1 CTTTGAAAAATG
1996561 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2001104 original size:35 final size:35
Alignment explanation
Indices: 2001065--2001179 Score: 151
Period size: 35 Copynumber: 3.2 Consensus size: 35
2001055 CAACTTTGAA
*
2001065 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
*
2001100 AAAATGATTTTTAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
2001135 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTG
2001171 AAAAATGAT
1 -AAAATGAT
2001180 AATGTGATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
35 35 0.49
36 14 0.20
37 22 0.31
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (35 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:2001165 original size:37 final size:37
Alignment explanation
Indices: 2001058--2001176 Score: 158
Period size: 36 Copynumber: 3.3 Consensus size: 37
2001048 TGGCAACCAA
*
2001058 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAAATGTTT
2001095 CTTTG-AAAAT-GATTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAG-TTTTTCAAAGTTTGGTAAATGTTT
*
2001130 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
2001167 -GTTGAAAAAT
1 CTTTGAAAAAT
2001177 GATAATGTGA
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
35 24 0.32
36 27 0.36
37 23 0.31
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:2010582 original size:22 final size:22
Alignment explanation
Indices: 2010549--2010591 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2010539 AACCTAATAG
*
2010549 ATTTACACAGT-ATTTATAGGC
1 ATTTACACAGTAAGTTATAGGC
*
2010570 ATTTCACATAGTAAGTTATAGG
1 ATTT-ACACAGTAAGTTATAGG
2010592 AAGTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
ATTTACACAGTAAGTTATAGGC
Found at i:2010746 original size:2 final size:2
Alignment explanation
Indices: 2010739--2010770 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2010729 TTTATTTGAA
2010739 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
2010771 TAAATTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2025524 original size:21 final size:21
Alignment explanation
Indices: 2025495--2025547 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2025485 ATTCTGACTA
2025495 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2025516 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
2025537 TCGCAATGCGA
1 TCGCATTGCGA
2025548 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2025562 original size:20 final size:20
Alignment explanation
Indices: 2025537--2025623 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
2025527 TTTTCCTAAT
2025537 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2025557 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2025578 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2025598 TCGCAATGTGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
2025618 TCGCAA
1 TCGCAA
2025624 AGAGATTTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.02
20 38 0.70
21 15 0.28
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2026509 original size:24 final size:24
Alignment explanation
Indices: 2026482--2026535 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2026472 GTATTCGAAA
2026482 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2026506 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2026530 TTTGAT
1 TTTGAT
2026536 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2028990 original size:20 final size:20
Alignment explanation
Indices: 2028934--2029039 Score: 118
Period size: 20 Copynumber: 5.6 Consensus size: 20
2028924 GACATTCATT
2028934 TGACTATCGCAACGCGG-AA
1 TGACTATCGCAACGCGGAAA
2028953 --A-T-T-GCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
2028968 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
2028988 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
*
2029008 TGACTATCGCAACGCAGAAA
1 TGACTATCGCAACGCGGAAA
2029028 TGACTATCGCAA
1 TGACTATCGCAA
2029040 GGAGAGAATC
Statistics
Matches: 72, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.01
14 8 0.11
15 2 0.03
16 1 0.01
17 2 0.03
18 1 0.01
19 1 0.01
20 53 0.74
21 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:2029070 original size:19 final size:19
Alignment explanation
Indices: 2029046--2029091 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2029036 GCAAGGAGAG
2029046 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2029065 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2029084 AATCGCAA
1 AATCGCAA
2029092 CGAGTGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2029089 original size:52 final size:54
Alignment explanation
Indices: 2028993--2029105 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 54
2028983 GGAAATGACT
* ** ** *
2028993 ATCGCAATGCGGAATTGACTATCGCAACGCAGAAATGACTATCGCAAGGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGAGAGA
* *
2029047 ATCGCAATGC-GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGAGAGA
2029099 ATCGCAA
1 ATCGCAA
2029106 CGAGTGAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 26 0.51
53 15 0.29
54 10 0.20
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (54 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGAGAGA
Found at i:2029103 original size:14 final size:14
Alignment explanation
Indices: 2029084--2029115 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2029074 GCGAAATGAA
2029084 AATCGCAACGAGTG
1 AATCGCAACGAGTG
2029098 AATCGCAACGAGTG
1 AATCGCAACGAGTG
2029112 AATC
1 AATC
2029116 ACAATGCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (14 bp):
AATCGCAACGAGTG
Found at i:2029213 original size:33 final size:34
Alignment explanation
Indices: 2029156--2029251 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
2029146 ATTAGTTTCG
2029156 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
2029190 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
2029223 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2029252 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:2029372 original size:14 final size:14
Alignment explanation
Indices: 2029353--2029389 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2029343 CATCAATTAA
2029353 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2029367 ACAAATCATCTTTT
1 ACAAATCAACATTT
2029381 ACAAATCAA
1 ACAAATCAA
2029390 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2030747 original size:21 final size:18
Alignment explanation
Indices: 2030723--2030767 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
2030713 GAACGGTGGG
2030723 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
2030744 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
2030762 AGGGGA
1 AGGGGA
2030768 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:2030784 original size:42 final size:42
Alignment explanation
Indices: 2030677--2030788 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
2030667 TCTAGAATAT
* * *
2030677 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** * *
2030719 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAATGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
2030761 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
2030789 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:2031287 original size:20 final size:20
Alignment explanation
Indices: 2031260--2031453 Score: 166
Period size: 20 Copynumber: 10.3 Consensus size: 20
2031250 GAAACTTAAA
2031260 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
2031280 ATCACAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
2031300 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2031320 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
2031340 ATCGCAATGC-ATATTTGACT
1 ATCGCAATGCGA-AAATGACT
*
2031360 ATCGCAA--CG-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
2031374 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
2031393 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
* *
2031407 ACCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
2031427 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
2031447 ATCGCAA
1 ATCGCAA
2031454 CGAGAATCGC
Statistics
Matches: 144, Mismatches: 14, Indels: 32
0.76 0.07 0.17
Matches are distributed among these distances:
14 13 0.09
16 10 0.07
17 7 0.05
18 4 0.03
19 8 0.06
20 102 0.71
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:2031460 original size:20 final size:20
Alignment explanation
Indices: 2031422--2031460 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2031412 AACGCGAAAA
* *
2031422 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGAGAATT
2031442 TGACTATCGCAACGAGAAT
1 TGACTATCGCAACGAGAAT
2031461 CGCAATGCGA
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:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAACGAGAATT
Found at i:2031487 original size:18 final size:18
Alignment explanation
Indices: 2031460--2031523 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
2031450 GCAACGAGAA
*
2031460 TCGCAATGCGATTTCATT
1 TCGCATTGCGATTTCATT
2031478 TCGCATTGCGA-TTC-TT
1 TCGCATTGCGATTTCATT
* *
2031494 TCG--TTGCGATAGTCAAAT
1 TCGCATTGCGAT-TTC-ATT
2031512 TCGCATTGCGAT
1 TCGCATTGCGAT
2031524 AGTCATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
16 7 0.19
17 3 0.08
18 14 0.38
20 7 0.19
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:2033411 original size:20 final size:20
Alignment explanation
Indices: 2033388--2033451 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2033378 CTGAAACTTT
2033388 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
2033408 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
2033428 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
2033447 AAATC
1 AAATC
2033452 TCATTGCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2033515 original size:20 final size:20
Alignment explanation
Indices: 2033467--2033515 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
2033457 GCGATTCTCT
*
2033467 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
2033487 CATTACGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2033507 CGTTGCGAT
1 CGTTGCGAT
2033516 TCACTCGTTG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2034125 original size:20 final size:20
Alignment explanation
Indices: 2034102--2034195 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
2034092 CGATAGTCAG
*
2034102 ATTCGCATTGCGGTTTACGT
1 ATTCGCATTGCGATTTACGT
2034122 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
2034142 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2034163 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2034183 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2034196 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2034180 original size:61 final size:60
Alignment explanation
Indices: 2034082--2034195 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
2034072 GCGCTATGTA
* *
2034082 AATCGCATTGCGATAGTCAGATTCGCATTGCGGTTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
** *
2034142 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCGCATTGCGA
2034196 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 15 0.31
61 33 0.69
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:2034258 original size:21 final size:21
Alignment explanation
Indices: 2034192--2034252 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
2034182 TATTCGCATT
* *
2034192 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
2034213 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
2034234 GCGAATTTGGGAAATCGCA
1 GCGAATTTGGGAAATCGCA
2034253 CTGCGATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:2034288 original size:20 final size:21
Alignment explanation
Indices: 2034265--2034320 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 21
2034255 GCGATAGTCA
*
2034265 AAATCGCGTTGCGAAT-CTGG
1 AAATCGCGTTGCGAATACCGG
* **
2034285 AAATTGATTTGCG-ATACCGG
1 AAATCGCGTTGCGAATACCGG
*
2034305 AGATCGCGTTGCGAAT
1 AAATCGCGTTGCGAAT
2034321 TATCGATCGC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (21 bp):
AAATCGCGTTGCGAATACCGG
Found at i:2036954 original size:2 final size:2
Alignment explanation
Indices: 2036947--2036973 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2036937 CCTTGTTACC
2036947 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 T
2036974 GTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2041250 original size:124 final size:124
Alignment explanation
Indices: 2041030--2041277 Score: 496
Period size: 124 Copynumber: 2.0 Consensus size: 124
2041020 GTTAGTAACT
2041030 TCAACAAAAGGGACTTAACATAAAAGGAGGTTAAACAAAATTAATAGCATAGAGACTTAAACCGG
1 TCAACAAAAGGGACTTAACATAAAAGGAGGTTAAACAAAATTAATAGCATAGAGACTTAAACCGG
2041095 ACGAACCGATAACGTAAGATACCATTTCCCCTTAATTTTTTGGTGACCAAAGTCGGTTA
66 ACGAACCGATAACGTAAGATACCATTTCCCCTTAATTTTTTGGTGACCAAAGTCGGTTA
2041154 TCAACAAAAGGGACTTAACATAAAAGGAGGTTAAACAAAATTAATAGCATAGAGACTTAAACCGG
1 TCAACAAAAGGGACTTAACATAAAAGGAGGTTAAACAAAATTAATAGCATAGAGACTTAAACCGG
2041219 ACGAACCGATAACGTAAGATACCATTTCCCCTTAATTTTTTGGTGACCAAAGTCGGTTA
66 ACGAACCGATAACGTAAGATACCATTTCCCCTTAATTTTTTGGTGACCAAAGTCGGTTA
2041278 GACCGATAAC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (124 bp):
TCAACAAAAGGGACTTAACATAAAAGGAGGTTAAACAAAATTAATAGCATAGAGACTTAAACCGG
ACGAACCGATAACGTAAGATACCATTTCCCCTTAATTTTTTGGTGACCAAAGTCGGTTA
Found at i:2042422 original size:21 final size:21
Alignment explanation
Indices: 2042389--2042435 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2042379 TTAAGATTTT
2042389 TATT-TTTATATTATTAAAATA
1 TATTATTTATATTATTAAAA-A
2042410 TATTATTTA-ATTATTAAAAA
1 TATTATTTATATTATTAAAAA
2042430 TATTAT
1 TATTAT
2042436 AAAATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTTATATTATTAAAAA
Found at i:2042445 original size:21 final size:21
Alignment explanation
Indices: 2042398--2042447 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2042388 TTATTTTTAT
**
2042398 ATTATTAAAATATATTATTTA
1 ATTATTAAAATATATTATAAA
2042419 ATTATTAAAA-ATATTATAAA
1 ATTATTAAAATATATTATAAA
2042439 ATATATTAA
1 AT-TATTAA
2042448 TTTAACAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAAAATATATTATAAA
Found at i:2042498 original size:15 final size:14
Alignment explanation
Indices: 2042465--2042504 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2042455 GTTTAAATAT
*
2042465 AATATATAATTATA
1 AATATATTATTATA
2042479 AATATATTATTATAA
1 AATATATTATTAT-A
2042494 AATATATTATT
1 AATATATTATT
2042505 TTAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATATTATTATA
Found at i:2042499 original size:56 final size:54
Alignment explanation
Indices: 2042405--2042508 Score: 147
Period size: 56 Copynumber: 1.9 Consensus size: 54
2042395 TATATTATTA
* *
2042405 AAATATATTATTTAATTATTAAAAATATTATAAAATATATTAATTTAACAGTTT
1 AAATATAATATATAATTATTAAAAATATTATAAAATATATTAATTTAACAGTTT
*
2042459 AAATATAATATATAATTA-TAAATATATTATTATAAAATATATTATTTTAA
1 AAATATAATATATAATTATTAAA-A-A-TATTATAAAATATATTAATTTAA
2042509 TTATTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
53 4 0.09
54 17 0.39
55 1 0.02
56 22 0.50
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (54 bp):
AAATATAATATATAATTATTAAAAATATTATAAAATATATTAATTTAACAGTTT
Found at i:2042513 original size:27 final size:27
Alignment explanation
Indices: 2042430--2042513 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 27
2042420 TTATTAAAAA
* *
2042430 TATTATAAAATATATTAATTTAA-CAGT
1 TATTATAAAATATATTATTTTAATTA-T
* * * *
2042457 T-TAAATATAATATATAATTATAAATATAT
1 TAT-TATAAAATATATTATT-TTAAT-TAT
2042486 TATTATAAAATATATTATTTTAATTAT
1 TATTATAAAATATATTATTTTAATTAT
2042513 T
1 T
2042514 TTAAAATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
26 1 0.02
27 17 0.40
28 7 0.17
29 15 0.36
30 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTATAAAATATATTATTTTAATTAT
Found at i:2045449 original size:136 final size:139
Alignment explanation
Indices: 2045271--2045547 Score: 533
Period size: 136 Copynumber: 2.0 Consensus size: 139
2045261 AATCCTAGCT
2045271 TATTAAGTCAGGGTTAATTACATTTATTTTGGGACTTGGTAGAAACTGTTTGTTCTTGTATAGAG
1 TATTAAGTCAGGGTTAATTACATTTATTTTGGGACTTGGTAGAAACTGTTTGTTCTTGTATAGAG
2045336 GCAATGAGAAGAGTGTGCGCTGAATTGCTCGGGTTCAATCATTAAAGCCACTTTAGTAATCTACT
66 GCAATGAGAAGAGTGTGCGCTGAATTGCTCGGGTTCAATCATTAAAGCCACTTTAGTAATCTACT
2045401 TTTTCAACA
131 TTTTCAACA
2045410 TATTAAGTCAGGGTT-ATTACA-TTA-TTTGGGACTTGGTAGAAACTGTTTGTTCTTGTATAGAG
1 TATTAAGTCAGGGTTAATTACATTTATTTTGGGACTTGGTAGAAACTGTTTGTTCTTGTATAGAG
2045472 GCAATGAGAAGAGTGTGCGCTGAATTGCTCGGGTTCAATCATTAAAGCCACTTTAGTAATCTACT
66 GCAATGAGAAGAGTGTGCGCTGAATTGCTCGGGTTCAATCATTAAAGCCACTTTAGTAATCTACT
2045537 TTTTCAACA
131 TTTTCAACA
2045546 TA
1 TA
2045548 GTGAAAGTCA
Statistics
Matches: 138, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
136 114 0.83
137 3 0.02
138 6 0.04
139 15 0.11
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (139 bp):
TATTAAGTCAGGGTTAATTACATTTATTTTGGGACTTGGTAGAAACTGTTTGTTCTTGTATAGAG
GCAATGAGAAGAGTGTGCGCTGAATTGCTCGGGTTCAATCATTAAAGCCACTTTAGTAATCTACT
TTTTCAACA
Found at i:2051649 original size:28 final size:25
Alignment explanation
Indices: 2051583--2051651 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
2051573 TTTTGAAAAT
* * *
2051583 ATTTTTTAATTTTTAAAAATAATTT
1 ATTTTCTAATTTTTAAAAAAAATTA
2051608 ATTTTCATATATTTTTAAAAAAAAATCTAA
1 ATTTTC-TA-ATTTTT-AAAAAAAAT-T-A
2051638 ATTTTCTAATTTTT
1 ATTTTCTAATTTTT
2051652 TAGAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.14
26 2 0.06
27 6 0.17
28 14 0.39
29 3 0.08
30 6 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTTCTAATTTTTAAAAAAAATTA
Found at i:2056752 original size:14 final size:14
Alignment explanation
Indices: 2056729--2056758 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2056719 ATAGGTAAAA
*
2056729 CGGTAGAAAAAATC
1 CGGTAAAAAAAATC
2056743 CGGTAAAAAAAATC
1 CGGTAAAAAAAATC
2056757 CG
1 CG
2056759 AATTCGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (14 bp):
CGGTAAAAAAAATC
Found at i:2057082 original size:57 final size:57
Alignment explanation
Indices: 2056984--2057114 Score: 165
Period size: 57 Copynumber: 2.3 Consensus size: 57
2056974 TTCGATTTGC
* * ** * *
2056984 GAAATTCGCGTTGCGATAGTTGTGTTTACCTATACATGTAATTAACGTTGCGAATTT
1 GAAAATCGCGTTGCGATAATACTGTTTACATATACAGGTAATTAACGTTGCGAATTT
* *
2057041 GAAAATCGCGTTGCGATAATACTGTTTACATATATC-GGTAATTAGCGTTGCGGATTT
1 GAAAATCGCGTTGCGATAATACTGTTTACATATA-CAGGTAATTAACGTTGCGAATTT
*
2057098 GAAAATCGCGTTTCGAT
1 GAAAATCGCGTTGCGAT
2057115 TTACATATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 63 0.98
58 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (57 bp):
GAAAATCGCGTTGCGATAATACTGTTTACATATACAGGTAATTAACGTTGCGAATTT
Found at i:2057126 original size:20 final size:20
Alignment explanation
Indices: 2057103--2057149 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2057093 GATTTGAAAA
2057103 TCGCGTTTCGATTTACATAT
1 TCGCGTTTCGATTTACATAT
2057123 TCGCGTTTCGATTTACATAT
1 TCGCGTTTCGATTTACATAT
*
2057143 TCCCGTT
1 TCGCGTT
2057150 GCGAATTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (20 bp):
TCGCGTTTCGATTTACATAT
Found at i:2063077 original size:12 final size:12
Alignment explanation
Indices: 2063062--2063093 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2063052 CGATTCTCGG
2063062 CCCAATACCCGA
1 CCCAATACCCGA
*
2063074 CCCAATACCCGG
1 CCCAATACCCGA
2063086 CCCAATAC
1 CCCAATAC
2063094 TCTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.50, G:0.09, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:2067594 original size:2 final size:2
Alignment explanation
Indices: 2067587--2067627 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2067577 CCATTACATT
2067587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2067628 TTCAATTATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2075116 original size:3 final size:3
Alignment explanation
Indices: 2075110--2075138 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2075100 ACGAATTGTC
2075110 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2075139 AATAGTGGTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2075417 original size:3 final size:3
Alignment explanation
Indices: 2075409--2075503 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
2075399 TTTTTATCCA
* *
2075409 TAT TAT TAT TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2075457 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2075504 AATATATTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2075992 original size:20 final size:19
Alignment explanation
Indices: 2075967--2076005 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2075957 GAAACTAGAG
*
2075967 ACAGAGACAGAGAAAAAAAA
1 ACAGAGAAAG-GAAAAAAAA
2075987 ACAGAGAAAGGAAAAAAAA
1 ACAGAGAAAGGAAAAAAAA
2076006 TAAACTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (19 bp):
ACAGAGAAAGGAAAAAAAA
Found at i:2088317 original size:5 final size:5
Alignment explanation
Indices: 2088301--2088381 Score: 78
Period size: 5 Copynumber: 16.2 Consensus size: 5
2088291 ATTATGCTTG
* * *
2088301 AAGAA AAAAA AAGAA AAG-A AAGAA AAGAA AAAAA AAGAA AAGAA AAAAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
*
2088350 ATAGAA AATG-A AA-AA AAGAG AAGAAA AAGAA A
1 A-AGAA AA-GAA AAGAA AAGAA AAG-AA AAGAA A
2088382 GGGGGTCAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
4 7 0.11
5 46 0.74
6 9 0.15
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:2088322 original size:9 final size:9
Alignment explanation
Indices: 2088305--2088382 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
2088295 TGCTTGAAGA
*
2088305 AAAAAAAAG
1 AAAAGAAAG
2088314 AAAAGAAAG
1 AAAAGAAAG
2088323 AAAAG-AA-
1 AAAAGAAAG
2088330 AAAA-AAAG
1 AAAAGAAAG
2088338 AAAAGAAA-
1 AAAAGAAAG
*
2088346 AAAA-ATAG
1 AAAAGAAAG
2088354 AAAATGAAA-
1 AAAA-GAAAG
2088363 AAAAGAGAAG
1 AAAAGA-AAG
2088373 AAAAAGAAAG
1 -AAAAGAAAG
2088383 GGGGTCAAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
7 8 0.14
8 16 0.28
9 22 0.39
10 5 0.09
11 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:2088330 original size:24 final size:24
Alignment explanation
Indices: 2088301--2088382 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
2088291 ATTATGCTTG
2088301 AAGAAAAAAAAAGAAAAGAAAGAA
1 AAGAAAAAAAAAGAAAAGAAAGAA
2088325 AAGAAAAAAAAAGAAAAGAAA-AA
1 AAGAAAAAAAAAGAAAAGAAAGAA
* * * *
2088348 AA-ATAGAAAATGAAAA-AAAGAG
1 AAGAAAAAAAAAGAAAAGAAAGAA
*
2088370 AAGAAAAAGAAAG
1 AAGAAAAAAAAAG
2088383 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.06
22 14 0.29
23 10 0.21
24 21 0.44
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (24 bp):
AAGAAAAAAAAAGAAAAGAAAGAA
Found at i:2088382 original size:15 final size:15
Alignment explanation
Indices: 2088304--2088371 Score: 86
Period size: 15 Copynumber: 4.5 Consensus size: 15
2088294 ATGCTTGAAG
2088304 AAAAA-AAAAG-AAA
1 AAAAAGAAAAGAAAA
*
2088317 AGAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
2088332 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
2088347 AAAATAGAAAATGAAAA
1 AAAA-AGAAAA-GAAAA
*
2088364 AAAGAGAA
1 AAAAAGAA
2088372 GAAAAAGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 21 0.44
16 10 0.21
17 8 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:2088746 original size:18 final size:18
Alignment explanation
Indices: 2088710--2088754 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2088700 CTATTTCAAG
*
2088710 TTCAATTTA--TTTGAGA
1 TTCAATTTATTTTTGAAA
2088726 TTCAATTTATTTTTGAAA
1 TTCAATTTATTTTTGAAA
2088744 TTCAATTTATT
1 TTCAATTTATT
2088755 CTTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
18 17 0.65
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:2089647 original size:83 final size:83
Alignment explanation
Indices: 2089505--2089916 Score: 761
Period size: 83 Copynumber: 4.9 Consensus size: 83
2089495 ATATCTTAGT
2089505 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
2089570 CTGATCTGATTTGGCAGAA
65 CTGATCTGATTTGGCAGAA
* *
2089589 CTAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
2089654 TGATCTGATTTGGCAGAA
66 TGATCTGATTTGGCAGAA
*
2089672 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
2089737 TGATCTGATTTGGCAGAA
66 TGATCTGATTTGGCAGAA
2089755 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
2089820 CTGATCTGATTTGGCAGAA
65 CTGATCTGATTTGGCAGAA
2089839 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
* *
2089904 TAATCTGGTTTGG
66 TGATCTGATTTGG
2089917 TAAAAATTAC
Statistics
Matches: 319, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
83 208 0.65
84 111 0.35
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTTGGCAGAA
Found at i:2089805 original size:167 final size:166
Alignment explanation
Indices: 2089505--2089916 Score: 761
Period size: 167 Copynumber: 2.5 Consensus size: 166
2089495 ATATCTTAGT
2089505 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
*
2089570 CTGATCTGATTTGGCAGAACTAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
65 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
2089635 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
130 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
*
2089672 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATT
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
*
2089737 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTTTGG
66 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGG
2089802 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
130 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
2089839 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
* *
2089904 TAATCTGGTTTGG
66 TGATCTGATTTGG
2089917 TAAAAATTAC
Statistics
Matches: 238, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
166 81 0.34
167 157 0.66
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (166 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:2090848 original size:113 final size:112
Alignment explanation
Indices: 2090644--2091410 Score: 1236
Period size: 113 Copynumber: 6.8 Consensus size: 112
2090634 ATTCAAATCT
*
2090644 ATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
2090709 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
* *
2090757 ATCAAATTGATGGATTAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2090821 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
64 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2090870 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2090935 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2090983 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
2091048 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTATTTGAATTC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
* * *
2091096 ATCAAATTGATTGATTAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2091160 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
64 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2091209 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
2091274 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TGCTCAAATC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT-CTGAATTC
* * ** *
2091322 TATTACTTGATGGGTTATTTTTTTTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 -ATCACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2091387 AG-AGAAAGTTCATAATGAGAAGAA
64 AGAAG-AAGTTCATAATGAGAAGAA
2091411 CTCATCAAAA
Statistics
Matches: 617, Mismatches: 25, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
111 8 0.01
112 36 0.06
113 451 0.73
114 113 0.18
115 9 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (112 bp):
ATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
Found at i:2091269 original size:339 final size:339
Alignment explanation
Indices: 2090636--2091410 Score: 1394
Period size: 339 Copynumber: 2.3 Consensus size: 339
2090626 TAACAAAGAT
*
2090636 TCAAATCTATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2090701 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTG
2090766 ATGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
130 ATGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
2090831 CATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAG
195 CATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAG
2090896 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
260 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
2090961 GTTCAACC-TTTTGTC
325 GTTCAACCTTTTTG-C
* *
2090976 TGAATTC-ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2091040 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTG
*
2091105 ATTGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
130 ATGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
2091170 CATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAG
195 CATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAG
2091235 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
260 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
2091300 GTTCAACCTTTTTGC
325 GTTCAACCTTTTTGC
* * **
2091315 TCAAATCTATTACTTGATGGGTTATTTTTTTTAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2091380 AGAAAGAAG-AGAAAGTTCATAATGAGAAGAA
65 AGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
2091411 CTCATCAAAA
Statistics
Matches: 417, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
338 4 0.01
339 325 0.78
340 83 0.20
341 5 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (339 bp):
TCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTGA
TGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGA
GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTTGC
Found at i:2091670 original size:3 final size:3
Alignment explanation
Indices: 2091664--2091737 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
2091654 TTTTTATCCA
*
2091664 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2091712 TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2091738 AATATATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2092225 original size:19 final size:18
Alignment explanation
Indices: 2092203--2092240 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2092193 GAAACTAGAG
*
2092203 ACAGAGACAGAGAAAAAAA
1 ACAGAGAAAG-GAAAAAAA
2092222 ACAGAGAAAGGAAAAAAA
1 ACAGAGAAAGGAAAAAAA
2092240 A
1 A
2092241 TAAACTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (18 bp):
ACAGAGAAAGGAAAAAAA
Found at i:2093869 original size:20 final size:20
Alignment explanation
Indices: 2093775--2094143 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2093765 GATTTTCCAT
* ** *
2093775 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2093795 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2093815 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2093835 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2093855 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2093875 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2093895 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2093915 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2093935 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2093955 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2093975 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2093995 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2094015 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2094035 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2094055 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2094075 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2094095 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2094115 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2094135 AATCACAAC
1 AATCGCAAC
2094144 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2094853 original size:24 final size:24
Alignment explanation
Indices: 2094814--2094860 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2094804 AAATTTGGTC
2094814 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2094838 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2094861 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2095051 original size:12 final size:12
Alignment explanation
Indices: 2095034--2095058 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2095024 ATATAATCCT
2095034 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2095046 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2095058 G
1 G
2095059 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2097434 original size:52 final size:53
Alignment explanation
Indices: 2097378--2097654 Score: 331
Period size: 52 Copynumber: 5.2 Consensus size: 53
2097368 AAATCCCAAC
2097378 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
2097430 ATG-AAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* *
2097481 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* * * *
2097533 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GAGAATCGCAATGCGAA
* *
2097590 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GAGAATCGCAATGCGAA
2097642 ATGAAAATCGCAA
1 ATGAAAATCGCAA
2097655 CGAGATAATC
Statistics
Matches: 209, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
50 14 0.07
51 38 0.18
52 119 0.57
53 2 0.01
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
Found at i:2097457 original size:19 final size:19
Alignment explanation
Indices: 2097378--2097654 Score: 337
Period size: 19 Copynumber: 15.7 Consensus size: 19
2097368 AAATCCCAAC
2097378 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
2097398 ATGAAAATCGC-A--CG--
1 ATGAAAATCGCAATGCGAA
*
2097412 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097430 ATG-AAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097448 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
2097463 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097481 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
2097500 ATGAAAATCG-AA-CCGAC
1 ATGAAAATCGCAATGCGAA
2097517 AT---AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
2097533 ATTAAAATCGCAATACGAA
1 ATGAAAATCGCAATGCGAA
2097552 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097571 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097590 ATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAA
2097607 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097623 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
2097642 ATGAAAATCGCAA
1 ATGAAAATCGCAA
2097655 CGAGATAATC
Statistics
Matches: 224, Mismatches: 11, Indels: 45
0.80 0.04 0.16
Matches are distributed among these distances:
13 8 0.04
14 25 0.11
15 3 0.01
16 16 0.07
17 14 0.06
18 21 0.09
19 126 0.56
20 11 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:2097474 original size:33 final size:33
Alignment explanation
Indices: 2097433--2097635 Score: 180
Period size: 33 Copynumber: 5.8 Consensus size: 33
2097423 ATGCGAAATG
2097433 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
* * *
2097466 GAATCGCAATGCGAAATGAAAATCGCAATGCG-
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
* ** *
2097498 AAAT-GAAAAT-CGAACCGACATAATCGCAATGCGAAATTA
1 AAATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GA
*
2097537 AAATCGCAATACGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GA
2097575 AAATCGCAATGCGAAATGAAAATCGCAACGA-A
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
2097607 AGAATCGCAATGCGAAATGAAAATCGCAA
1 A-AATCGCAATGCGAAATGAAAATCGCAA
2097636 TGCGAAATGA
Statistics
Matches: 143, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
31 7 0.05
32 9 0.06
33 64 0.45
34 1 0.01
35 1 0.01
36 2 0.01
38 44 0.31
39 8 0.06
40 7 0.05
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:2097552 original size:71 final size:71
Alignment explanation
Indices: 2097351--2097692 Score: 296
Period size: 71 Copynumber: 4.9 Consensus size: 71
2097341 ACGAAAATAC
* * *
2097351 AATCGCAACGCGAAATG-AAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAAAATCGC-A--
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AATAATCGCAATGC-GAAATTAAAATCGCAATG
*
2097410 CG--A-GAG
63 CGAAATGAA
* *
2097416 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATTAAAATCGCAA
2097475 TGCGAAATGAA
61 TGCGAAATGAA
* *
2097486 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAAATAATCGCAATGCGAAATTAAAATCGCAATGCG
2097550 AAATGAA
65 AAATGAA
*
2097557 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATTAAAATCGCAA
2097617 TGCGAAATGAA
61 TGCGAAATGAA
* *
2097628 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATTA-AAATCGCAATGCG
2097692 A
65 A
2097693 TTTTCATTTC
Statistics
Matches: 231, Mismatches: 16, Indels: 54
0.77 0.05 0.18
Matches are distributed among these distances:
64 8 0.03
65 26 0.11
66 18 0.08
67 4 0.02
68 6 0.03
69 13 0.06
70 30 0.13
71 105 0.45
72 4 0.02
73 7 0.03
74 2 0.01
76 8 0.03
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATTAAAATCGCAATGCGA
AATGAA
Found at i:2097613 original size:142 final size:141
Alignment explanation
Indices: 2097416--2097686 Score: 483
Period size: 142 Copynumber: 1.9 Consensus size: 141
2097406 CGCACGAGAG
*
2097416 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
2097481 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTA-AAATCGC
66 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACATAATCGCAATGCGAAATTATAAA-CGC
2097544 AATACGAAATGAA
129 AATACGAAATGAA
2097557 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
*
2097622 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAACGCA
65 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATAAACGCA
2097687 TTGCGATTTT
Statistics
Matches: 125, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
141 17 0.14
142 103 0.82
143 5 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (141 bp):
AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGAAATTATAAACGCAA
TACGAAATGAA
Found at i:2097792 original size:19 final size:19
Alignment explanation
Indices: 2097683--2097784 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2097673 AAATTATAAA
2097683 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2097702 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2097722 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2097738 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2097755 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2097774 CGCATTGCGAT
1 CGCATTGCGAT
2097785 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2097910 original size:14 final size:14
Alignment explanation
Indices: 2097891--2097927 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2097881 CATCAATTAC
2097891 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2097905 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2097919 ACAAATCAA
1 ACAAATCAA
2097928 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2099850 original size:19 final size:19
Alignment explanation
Indices: 2099826--2099944 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 19
2099816 ATAGTTACTT
* *
2099826 TCGCAACACGAACTTAAAA
1 TCGCAACGCGAACTCAAAA
2099845 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCG-AACTCAAAA
* *
2099864 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAACTCAAAA
*
2099883 TCGCAA--CG-A--CAGAA
1 TCGCAACGCGAACTCAAAA
* * *
2099897 TCGCAATGCGAAAT-GAAA
1 TCGCAACGCGAACTCAAAA
* *
2099915 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAACTCAAAA
*
2099934 TCGCAATGCGA
1 TCGCAACGCGA
2099945 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.11
16 3 0.04
17 3 0.04
18 17 0.21
19 46 0.57
20 3 0.04
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAACTCAAAA
Found at i:2099962 original size:19 final size:19
Alignment explanation
Indices: 2099940--2100067 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2099930 AAAATCGCAA
2099940 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2099959 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2099973 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2099992 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2100006 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2100025 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2100043 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2100063 TGCGA
1 TGCGA
2100068 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.20
19 30 0.34
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2099982 original size:33 final size:33
Alignment explanation
Indices: 2099940--2100031 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2099930 AAAATCGCAA
2099940 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2099973 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2100006 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2100032 TGGTTTCGCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2100270 original size:93 final size:93
Alignment explanation
Indices: 2100111--2100583 Score: 939
Period size: 93 Copynumber: 5.1 Consensus size: 93
2100101 TTGAATGGAT
2100111 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100176 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2100204 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100269 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2100297 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100362 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2100390 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100454 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2100482 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100547 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2100575 AAATTTACT
1 AAATTTACT
2100584 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.24
93 287 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2100556 original size:185 final size:186
Alignment explanation
Indices: 2100111--2100583 Score: 939
Period size: 185 Copynumber: 2.5 Consensus size: 186
2100101 TTGAATGGAT
2100111 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100176 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2100241 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
2100297 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100362 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2100427 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
2100482 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2100547 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2100584 AAGCAATCTA
Statistics
Matches: 287, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
185 155 0.54
186 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2102303 original size:14 final size:14
Alignment explanation
Indices: 2102284--2102373 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2102274 TTGAAATGAA
2102284 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2102298 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2102315 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2102331 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2102350 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2102364 AATCGCAACG
1 AATCGCAACG
2102374 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Done.