Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 62
Found at i:12227938 original size:64 final size:65
Alignment explanation
Indices: 12227824--12227947 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
12227814 AATGCATTTT
* *
12227824 ATGCATCAATGCACTCAAGGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGAC
1 ATGCATCAATGCACTCAAGGTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGAC
*
12227889 ATGCATCGATGCACTC-AGGCTATTT-TG-AAACATCGAATGCACTTCATGCATCGATGCAC
1 ATGCATCAATGCACTCAAGG-T-TTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
12227948 TCTTAGTGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
64 33 0.61
65 18 0.33
66 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (65 bp):
ATGCATCAATGCACTCAAGGTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGAC
Found at i:12227947 original size:17 final size:19
Alignment explanation
Indices: 12227919--12227967 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12227909 TATTTTGAAA
12227919 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
12227937 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
12227956 CACCGATGCACT
1 CATCGATGCACT
12227968 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:12231995 original size:37 final size:37
Alignment explanation
Indices: 12231942--12232687 Score: 743
Period size: 37 Copynumber: 20.2 Consensus size: 37
12231932 TCGGTACCCG
* * *
12231942 TGTTATGTTACATAGAAATGGGTGTCTTATGTAGACA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* *
12231979 TGTTATGTTACTTAGAAATGGGTGTCTTATGTAGACA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* *
12232016 TGTTATGTTAATTGGAAATGGGTGTCTGATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* * * *
12232053 TGTTATTTTACTTGGAAATAGGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
*
12232090 TGTTACGTTACTTGGAAATGGG-GTCTTATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* * * *
12232126 TGTTACGTTACATGGAAATAGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAAT-GG-GTGTCTTATGTAGATA
* * * *
12232165 TGTTATATTACATGGAAATGGGGGTCTTATGAAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* *
12232202 TGTTCTGTTACTTGGAAATGGGGGTCTTATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* *
12232239 TATTATGTTACTTGGAAATGGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAATGGGTG--TCTTATGTAGATA
* * * * * *
12232278 TGTTATGTTACATAGAAAGGGGTCTGTTATGT--ACA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* * *
12232313 ---TATGTTACATAGAAATGGGTGTCTGATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
*
12232347 TGTTATGTTACTTGGAAATGGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAATGGGTG--TCTTATGTAGATA
* *
12232386 TGTTATGTTGCTTGGAAATGGG-GTCTTATGTAAATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* * *
12232422 TGTTACGTTACTTGGAAATAGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAAT-GG-GTGTCTTATGTAGATA
* *
12232461 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
* * *
12232498 TGTTATGTTATTTGGAAATGGGTATCTCTTATGT--ACA
1 TGTTATGTTACTTGGAAATGGG--TGTCTTATGTAGATA
* * *
12232535 ---TATGTTACATAGAAATGGGTGTCTCTTATGT--ACA
1 TGTTATGTTACTTGGAAATGGGTG--TCTTATGTAGATA
* * *
12232569 ---TATGTTACATAGAAATGGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAATGGGTG--TCTTATGTAGATA
***
12232605 TGTTATGTTACACAGAAATGGGTGTCTTATGTAGATA
1 TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
*
12232642 TGTTATGTTACTTGGAAATGGGTGTCTCTTATGTACATA
1 TGTTATGTTACTTGGAAATGGGTG--TCTTATGTAGATA
12232681 TGTTATG
1 TGTTATG
12232688 CTTTTCGTCC
Statistics
Matches: 607, Mismatches: 76, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
32 26 0.04
34 60 0.10
35 2 0.00
36 61 0.10
37 283 0.47
38 7 0.01
39 168 0.28
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (37 bp):
TGTTATGTTACTTGGAAATGGGTGTCTTATGTAGATA
Found at i:12232220 original size:76 final size:76
Alignment explanation
Indices: 12231942--12232687 Score: 824
Period size: 76 Copynumber: 10.1 Consensus size: 76
12231932 TCGGTACCCG
* * * * *
12231942 TGTTATGTTACATAGAAATGGGTGTCTTATGTAGACATGTTATGTTACTTAGAAAT-GG-GTGTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
* *
12232005 TTATGTAGACA
66 TTATGTACATA
* * *
12232016 TGTTATGTTA-ATTGGAAATGGGTGTCTGATGTAGATATGTTATTTTACTTGGAAATA-G-GTCT
1 TGTTATGTTACA-TGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCT
12232078 CTTATGTACATA
65 CTTATGTACATA
* * * *
12232090 TGTTACGTTACTTGGAAAT-GGGGTCTTATGTAGATATGTTACGTTACATGGAAATAGGTGTCTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
12232154 TTATGTACATA
66 TTATGTACATA
* * * **
12232165 TGTTATATTACATGGAAATGGGGGTCTTATGAAGATATGTTCTGTTACTTGGAAAT-GG-GGGTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
*
12232228 TTATGTAGATA
66 TTATGTACATA
* * * * * * *
12232239 TATTATGTTACTTGGAAATGGGTGTCTCTTATGTACATATGTTATGTTACATAG-AA-AGGGGTC
1 TGTTATGTTACATGGAAATGGG-G-GTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTC
*
12232302 TGTTATGTAC--A
64 TCTTATGTACATA
* * * *
12232313 ---TATGTTACATAGAAATGGGTGTCTGATGTAGATATGTTATGTTACTTGGAAATGGGTGTCTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
12232375 TTATGTACATA
66 TTATGTACATA
* * * *
12232386 TGTTATGTTGCTTGGAAAT-GGGGTCTTATGTAAATATGTTACGTTACTTGGAAATAGGTGTCTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
12232450 TTATGTACATA
66 TTATGTACATA
* * *
12232461 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTATTTGGAAATGGGTATCTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
12232526 TTATGTAC--A
66 TTATGTACATA
* * * * * *
12232535 ---TATGTTACATAGAAATGGGTGTCTCTTATGT--ACA---TATGTTACATAGAAATGGGTGTC
1 TGTTATGTTACATGGAAATGGG-G-GTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTC
12232592 TCTTATGTACATA
64 TCTTATGTACATA
** * *
12232605 TGTTATGTTACACAGAAATGGGTGTCTTATGTAGATATGTTATGTTACTTGGAAATGGGTGTCTC
1 TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
12232670 TTATGTACATA
66 TTATGTACATA
12232681 TGTTATG
1 TGTTATG
12232688 CTTTTCGTCC
Statistics
Matches: 565, Mismatches: 77, Indels: 58
0.81 0.11 0.08
Matches are distributed among these distances:
68 29 0.05
69 24 0.04
70 3 0.01
71 59 0.10
72 1 0.00
73 62 0.11
74 114 0.20
75 107 0.19
76 166 0.29
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (76 bp):
TGTTATGTTACATGGAAATGGGGGTCTTATGTAGATATGTTATGTTACTTGGAAATAGGTGTCTC
TTATGTACATA
Found at i:12232550 original size:34 final size:34
Alignment explanation
Indices: 12232242--12232685 Score: 260
Period size: 39 Copynumber: 12.2 Consensus size: 34
12232232 GTAGATATAT
* *
12232242 TATGTTACTTGGAAATGGGTGTCTCTTATGTACATA
1 TATGTTACATAGAAATGGGTGTCTCTTATGTAC--A
*
12232278 TGTTATGTTACATAGAAA-GGG-GTCTGTTATGTACA
1 ---TATGTTACATAGAAATGGGTGTCTCTTATGTACA
* **
12232313 TATGTTACATAGAAATGGGTGTCTGATGTA-GATATGT
1 TATGTTACATAGAAATGGGTGTCT-CT-TATG-TA-CA
* *
12232350 TATGTTACTTGGAAATGGGTGTCTCTTATGTACA
1 TATGTTACATAGAAATGGGTGTCTCTTATGTACA
* * *
12232384 TATGTTATGTTGCTTGGAAATGGG-G--TCTTATGTAAA
1 TATGTTA-----CATAGAAATGGGTGTCTCTTATGTACA
* *
12232420 TATGTTACGTTACTTGGAAATAGGTGTCTCTTATGTACATA
1 TATGTTAC---A--TAGAAATGGGTGTCTCTTATGTAC--A
* * *
12232461 TGTTATGTTACATGGAAATGGG-G-GTCTTATGTAGA
1 ---TATGTTACATAGAAATGGGTGTCTCTTATGTACA
* * *
12232496 TATGTTATGTTATTTGGAAATGGGTATCTCTTATGTACA
1 TATGTTA---CA--TAGAAATGGGTGTCTCTTATGTACA
12232535 TATGTTACATAGAAATGGGTGTCTCTTATGTACA
1 TATGTTACATAGAAATGGGTGTCTCTTATGTACA
12232569 TATGTTACATAGAAATGGGTGTCTCTTATGTACATA
1 TATGTTACATAGAAATGGGTGTCTCTTATGTAC--A
* *
12232605 TGTTATGTTACACAGAAATGGGTG--TCTTATGTAGATA
1 ---TATGTTACATAGAAATGGGTGTCTCTTATGT--ACA
* *
12232642 TGTTATGTTACTTGGAAATGGGTGTCTCTTATGTACA
1 ---TATGTTACATAGAAATGGGTGTCTCTTATGTACA
12232679 TATGTTA
1 TATGTTA
12232686 TGCTTTTCGT
Statistics
Matches: 333, Mismatches: 31, Indels: 87
0.74 0.07 0.19
Matches are distributed among these distances:
31 1 0.00
32 22 0.07
33 3 0.01
34 74 0.22
35 9 0.03
36 34 0.10
37 86 0.26
38 5 0.02
39 89 0.27
41 2 0.01
44 8 0.02
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.41
Consensus pattern (34 bp):
TATGTTACATAGAAATGGGTGTCTCTTATGTACA
Found at i:12232914 original size:23 final size:23
Alignment explanation
Indices: 12232865--12232914 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
12232855 TTCACTCTCT
* * ** *
12232865 AAAATATTATAAGTTTATTTCTT
1 AAAATATTATAAATTCATCCCTA
12232888 AAAATATTATAAATTCATCCCTA
1 AAAATATTATAAATTCATCCCTA
12232911 AAAA
1 AAAA
12232915 CAATCATGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAATATTATAAATTCATCCCTA
Found at i:12232984 original size:45 final size:47
Alignment explanation
Indices: 12232933--12233025 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 47
12232923 TGTGTGTCCG
*
12232933 TGTCGAATGTTGACGACA-T-GTATTTCAAAAAGAAAAAGAAGAAAA
1 TGTCGAATGTTGACGACAGTCGTACTTCAAAAAGAAAAAGAAGAAAA
*
12232978 TGTCGAATGTTGACGATATGTCGTACTTCAAAAAGAAAAAGAAGAAAA
1 TGTCGAATGTTGACGACA-GTCGTACTTCAAAAAGAAAAAGAAGAAAA
12233026 GTTAAAGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 17 0.40
47 1 0.02
48 25 0.58
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (47 bp):
TGTCGAATGTTGACGACAGTCGTACTTCAAAAAGAAAAAGAAGAAAA
Found at i:12235822 original size:41 final size:41
Alignment explanation
Indices: 12235765--12235846 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
12235755 GGAAAGAAAC
12235765 GGACCTTGTATAATCACCCTGAACTTCTAAAGTCGTAGAGT
1 GGACCTTGTATAATCACCCTGAACTTCTAAAGTCGTAGAGT
12235806 GGACCTTGTATAATCACCCTGAACTTCTAAAGTCGTAGAGT
1 GGACCTTGTATAATCACCCTGAACTTCTAAAGTCGTAGAGT
12235847 TTATAAGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (41 bp):
GGACCTTGTATAATCACCCTGAACTTCTAAAGTCGTAGAGT
Found at i:12245031 original size:42 final size:42
Alignment explanation
Indices: 12244984--12245282 Score: 492
Period size: 42 Copynumber: 7.1 Consensus size: 42
12244974 AATTGAAGGA
**
12244984 AGTTT-CCATGGTTCCTTTCCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCA-GGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
* *
12245026 AGTTTCCCAGGTTCCTTTGCTGTGTGCAAAGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
12245068 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
* *
12245110 AGTTTCCCAGGTTTCTTTGTTGTGTGCAGGGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
* *
12245152 AGTTTCCCCGGTTCCTTTGTTGTGTGCAATGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
* *
12245194 AGTTTACCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
12245236 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
1 AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
12245278 AGTTT
1 AGTTT
12245283 TCCTAGGCTC
Statistics
Matches: 240, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 237 0.99
43 3 0.01
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (42 bp):
AGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTAC
Found at i:12247203 original size:12 final size:12
Alignment explanation
Indices: 12247186--12247219 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12247176 TCAGACGCCA
**
12247186 GCTCGTACTCTT
1 GCTCGTACTCCC
12247198 GCTCGTACTCCC
1 GCTCGTACTCCC
12247210 GCTCGTACTC
1 GCTCGTACTC
12247220 AGAGTATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.18, T:0.32
Consensus pattern (12 bp):
GCTCGTACTCCC
Found at i:12249313 original size:18 final size:17
Alignment explanation
Indices: 12249268--12249384 Score: 89
Period size: 17 Copynumber: 6.8 Consensus size: 17
12249258 TAAGAGTTAG
* *
12249268 TTTAATAAATGAACTAG
1 TTTAATTAATGAACTAC
12249285 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACT-AC
12249303 TTT-ATTCAATGAACT--
1 TTTAATT-AATGAACTAC
* *
12249318 TGTAATCTTGAATGAACTAA
1 TTTAA--TT-AATGAACTAC
* *
12249338 TTTAATGAATGAACTAG
1 TTTAATTAATGAACTAC
12249355 TTTAATTAATGAACTA-
1 TTTAATTAATGAACTAC
*
12249371 TTTAGTTAAATGAA
1 TTTAATT-AATGAA
12249385 GTGCATAGCT
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.02
16 7 0.08
17 47 0.57
18 23 0.28
20 4 0.05
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTAATTAATGAACTAC
Found at i:12257647 original size:2 final size:2
Alignment explanation
Indices: 12257640--12257684 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
12257630 TTGTATAGTG
12257640 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
12257682 TA T
1 TA T
12257685 GTTTGGTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12258235 original size:90 final size:89
Alignment explanation
Indices: 12258083--12258255 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 89
12258073 ACACACCCTT
12258083 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
12258148 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
12258172 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
12258237 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
12258256 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 30 0.38
90 50 0.62
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:12260509 original size:17 final size:18
Alignment explanation
Indices: 12260473--12260519 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
12260463 TATTTTATTA
12260473 TTTTTATTT--CTTTTCT
1 TTTTTATTTAACTTTTCT
12260489 TTTTTATTTAACTTTTCT
1 TTTTTATTTAACTTTTCT
*
12260507 TTTAT-TTTAACTT
1 TTTTTATTTAACTT
12260520 CTTTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 11 0.39
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTTAACTTTTCT
Found at i:12265681 original size:23 final size:23
Alignment explanation
Indices: 12265613--12265673 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
12265603 CAATCTTATA
*
12265613 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
12265636 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
12265659 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
12265674 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:12267044 original size:6 final size:6
Alignment explanation
Indices: 12267029--12267089 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
12267019 GAAAAAATAA
* * *
12267029 AAAAGAG AAAAGG AAAAGG AAAAGG AAAAAGA AAAAGA AAAAGG AAAAGA
1 AAAAG-G AAAAGG AAAAGG AAAAGG -AAAAGG AAAAGG AAAAGG AAAAGG
12267079 AAAAGAG AAAA
1 AAAAG-G AAAA
12267090 AGTGTTTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 34 0.71
7 14 0.29
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:12267051 original size:19 final size:19
Alignment explanation
Indices: 12267029--12267089 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
12267019 GAAAAAATAA
12267029 AAAAGAGAAAAGGAAAAG-G
1 AAAAG-GAAAAGGAAAAGAG
*
12267048 AAAAGGAAAAAGAAAA-AG
1 AAAAGGAAAAGGAAAAGAG
*
12267066 AAAAAGGAAAAGAAAAAGAG
1 -AAAAGGAAAAGGAAAAGAG
12267086 AAAA
1 AAAA
12267090 AGTGTTTAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.31
19 23 0.64
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAAAGGAAAAGGAAAAGAG
Found at i:12267052 original size:12 final size:12
Alignment explanation
Indices: 12267028--12267089 Score: 79
Period size: 12 Copynumber: 4.9 Consensus size: 12
12267018 AGAAAAAATA
12267028 AAAAAGAGAAAAG
1 AAAAAG-GAAAAG
*
12267041 GAAAAGGAAAAGG
1 AAAAAGGAAAA-G
*
12267054 AAAAAGAAAAAG
1 AAAAAGGAAAAG
12267066 AAAAAGGAAAAG
1 AAAAAGGAAAAG
12267078 AAAAAGAGAAAA
1 AAAAAG-GAAAA
12267090 AGTGTTTAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 23 0.53
13 20 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAAG
Found at i:12267155 original size:17 final size:17
Alignment explanation
Indices: 12267129--12267175 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
12267119 CCCTAAATTG
12267129 AAAA-AAAAGAAAAA-A
1 AAAAGAAAAGAAAAATA
12267144 AAAGAGAAAAGAAAAATA
1 AAA-AGAAAAGAAAAATA
12267162 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
12267176 TAAGGTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 21 0.72
18 4 0.14
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAGAAAAATA
Found at i:12270775 original size:30 final size:31
Alignment explanation
Indices: 12270677--12270795 Score: 134
Period size: 31 Copynumber: 3.9 Consensus size: 31
12270667 GATTCGAGGG
*
12270677 TTACCTATGTCCTTCGGGGCATATGGACAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGT
* * ** * *
12270708 TTTCTTATGT-CTTCCATGACATATGAATAGT
1 TTACCTATGTCCTT-CGGGACATATGGACAGT
12270739 TTACCTATGTCCTTCGGGACATATGGACAG-
1 TTACCTATGTCCTTCGGGACATATGGACAGT
* *
12270769 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
12270796 TAGGTCCTTC
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
30 28 0.39
31 40 0.56
32 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGT
Found at i:12271083 original size:23 final size:23
Alignment explanation
Indices: 12271057--12271108 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
12271047 TGATATGAAC
12271057 ATAAGAGATTATACGAACCAAAG
1 ATAAGAGATTATACGAACCAAAG
* *
12271080 ATAAGAGATTATAGGAACCAGAG
1 ATAAGAGATTATACGAACCAAAG
12271103 ATAAGA
1 ATAAGA
12271109 AATATGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (23 bp):
ATAAGAGATTATACGAACCAAAG
Found at i:12273005 original size:25 final size:23
Alignment explanation
Indices: 12272969--12273016 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
12272959 CTTTTCTCCC
12272969 TTATTTTGTTTCTATTTTATTATTT
1 TTATTTTGTTTCT-TTTT-TTATTT
12272994 TTATTTCT-TTTCTTTTTTTATTT
1 TTATTT-TGTTTCTTTTTTTATTT
12273017 AACTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
24 4 0.18
25 11 0.50
26 1 0.05
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
TTATTTTGTTTCTTTTTTTATTT
Found at i:12273013 original size:17 final size:18
Alignment explanation
Indices: 12272991--12273045 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
12272981 TATTTTATTA
12272991 TTTTTATTT-CTTTTCTT
1 TTTTTATTTACTTTTCTT
12273008 TTTTTATTTAACTTTTCTT
1 TTTTTATTT-ACTTTTCTT
* *
12273027 TTATT-TTAACTTTTCTT
1 TTTTTATTTACTTTTCTT
12273044 TT
1 TT
12273046 ATTTTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 20 0.59
18 2 0.06
19 12 0.35
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTTACTTTTCTT
Found at i:12273046 original size:17 final size:17
Alignment explanation
Indices: 12273009--12273055 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
12272999 TCTTTTCTTT
12273009 TTTTA-TTTAACTTTTC
1 TTTTATTTTAACTTTTC
12273025 TTTTATTTTAACTTTTC
1 TTTTATTTTAACTTTTC
12273042 TTTTATTTTAACTT
1 TTTTATTTTAACTT
12273056 CTTTGGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTTAACTTTTC
Found at i:12279408 original size:2 final size:2
Alignment explanation
Indices: 12279401--12279425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12279391 CATCTTCAGA
12279401 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12279426 ACAATCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12288581 original size:32 final size:32
Alignment explanation
Indices: 12288545--12288606 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
12288535 AAATCTTTGG
12288545 ATGTGGGAGGTGTTTTGATTGAGGATCCCAAT
1 ATGTGGGAGGTGTTTTGATTGAGGATCCCAAT
12288577 ATGTGGGAGGTGTTTTGATTGAGGATCCCA
1 ATGTGGGAGGTGTTTTGATTGAGGATCCCA
12288607 GTAAGATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.21, C:0.10, G:0.35, T:0.34
Consensus pattern (32 bp):
ATGTGGGAGGTGTTTTGATTGAGGATCCCAAT
Found at i:12317945 original size:24 final size:24
Alignment explanation
Indices: 12317905--12318007 Score: 77
Period size: 24 Copynumber: 4.3 Consensus size: 24
12317895 GTAAACGGAG
* *
12317905 ATATCA-AAATCAAAACATAATTC
1 ATATCAGATATCAAAACAGAATTC
* *
12317928 ATATCAGATATCAGAACAGAATCC
1 ATATCAGATATCAAAACAGAATTC
* * *
12317952 A-AGTTAGGA-ATCAGAACAGATTTC
1 ATA-TCA-GATATCAAAACAGAATTC
* *
12317976 AGATCAGATGTCAAAACAGAATTC
1 ATATCAGATATCAAAACAGAATTC
*
12318000 AAATCAGA
1 ATATCAGA
12318008 AATTAGATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 9 0.14
24 51 0.81
25 3 0.05
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATATCAGATATCAAAACAGAATTC
Found at i:12319504 original size:38 final size:37
Alignment explanation
Indices: 12319416--12319504 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 37
12319406 TCGGGCCGGG
12319416 TATATATATAATTTAAATTAAATGTATAAATATTATA
1 TATATATATAATTTAAATTAAATGTATAAATATTATA
* * * *
12319453 TATATTTTTTAATTTAAATTAAATTTATTAATATTATA
1 TATA-TATATAATTTAAATTAAATGTATAAATATTATA
12319491 TATATATAATAATT
1 TATATAT-ATAATT
12319505 ATTTTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.14
38 38 0.86
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (37 bp):
TATATATATAATTTAAATTAAATGTATAAATATTATA
Found at i:12319618 original size:29 final size:30
Alignment explanation
Indices: 12319576--12319650 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
12319566 ACCAAATCTG
* *
12319576 TCCCCGTCCCCGTTTAGCATACACGG-TTT
1 TCCCCATCCCCGTTTAGCATAAACGGTTTT
12319605 TCCCCATCCCCGTTTAGCATAAACGGTTTT
1 TCCCCATCCCCGTTTAGCATAAACGGTTTT
12319635 TCCCCATCCCCGTTTA
1 TCCCCATCCCCGTTTA
12319651 ATTCGGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 24 0.56
30 19 0.44
ACGTcount: A:0.16, C:0.39, G:0.13, T:0.32
Consensus pattern (30 bp):
TCCCCATCCCCGTTTAGCATAAACGGTTTT
Found at i:12321095 original size:18 final size:18
Alignment explanation
Indices: 12321074--12321121 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
12321064 AACGGGTCGG
12321074 GTCGGGTCGGGTCAACAA
1 GTCGGGTCGGGTCAACAA
*
12321092 GTCGGGTCGGGTCAACAG
1 GTCGGGTCGGGTCAACAA
12321110 GTCGGGTCGGGT
1 GTCGGGTCGGGT
12321122 TGTAACCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.19
Consensus pattern (18 bp):
GTCGGGTCGGGTCAACAA
Found at i:12321121 original size:23 final size:23
Alignment explanation
Indices: 12321060--12321104 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12321050 GCTGGTCAAC
**
12321060 GGTCAACGGGTCGGGTCGGGTCG
1 GGTCAACAAGTCGGGTCGGGTCG
12321083 GGTCAACAAGTCGGGTCGGGTC
1 GGTCAACAAGTCGGGTCGGGTC
12321105 AACAGGTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (23 bp):
GGTCAACAAGTCGGGTCGGGTCG
Found at i:12322483 original size:108 final size:108
Alignment explanation
Indices: 12322298--12322520 Score: 401
Period size: 108 Copynumber: 2.1 Consensus size: 108
12322288 TTTATTATAA
*
12322298 TATATTTGAGTGGAATTTATAAAATTTAAGTCGAGTTGAACTACTAGAATTTTTGTTTCAATTTG
1 TATATTTGAGTGGAATTTATAAAATTTAAGTCGAGTCGAACTACTAGAATTTTTGTTTCAATTTG
* *
12322363 ATTGTAAGTATCTATAACCATATACAATACGTATATATTTCTT
66 ATCGTAAATATCTATAACCATATACAATACGTATATATTTCTT
*
12322406 TATATTTGAGTGGAATTTATAAAATTTAAGTCGAGTCGAACTACTCGAATTTTTGTTTCAATTTG
1 TATATTTGAGTGGAATTTATAAAATTTAAGTCGAGTCGAACTACTAGAATTTTTGTTTCAATTTG
*
12322471 ATCGTAAATATCTATAACCATATACAATATGTATATATTTCTT
66 ATCGTAAATATCTATAACCATATACAATACGTATATATTTCTT
12322514 TATATTT
1 TATATTT
12322521 TTTTATATGT
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (108 bp):
TATATTTGAGTGGAATTTATAAAATTTAAGTCGAGTCGAACTACTAGAATTTTTGTTTCAATTTG
ATCGTAAATATCTATAACCATATACAATACGTATATATTTCTT
Found at i:12323545 original size:32 final size:32
Alignment explanation
Indices: 12323479--12323545 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
12323469 GATGATGTGT
**
12323479 CATATGTCATGTCATCACTTACGTACATTTGA
1 CATATGTCATGTCATCACTTACGTACATCCGA
* *
12323511 CATATGTCATGTCATCGCTTA-TTAACATCCGA
1 CATATGTCATGTCATCACTTACGT-ACATCCGA
12323543 CAT
1 CAT
12323546 GCATCACATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (32 bp):
CATATGTCATGTCATCACTTACGTACATCCGA
Found at i:12325677 original size:34 final size:30
Alignment explanation
Indices: 12325639--12325707 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
12325629 TTGATATAAC
12325639 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
*
12325673 AATTT-ACAAAATGTTTTTGGGCTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
12325702 AATTTA
1 AATTTA
12325708 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:12325718 original size:29 final size:30
Alignment explanation
Indices: 12325648--12325707 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
12325638 CAATTTAAGG
12325648 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
12325679 CAAAATGTTTTTGGGCTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
12325708 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:12325812 original size:29 final size:30
Alignment explanation
Indices: 12325779--12325848 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
12325769 GGTGTCAAAG
**
12325779 TGCATCCATGCACC-CCTGCAGTGCATCCA
1 TGCATCCATGCACCTCCACCAGTGCATCCA
* *
12325808 TGCATCCATGCACCTGCACCAGTGCATCGA
1 TGCATCCATGCACCTCCACCAGTGCATCCA
12325838 TGCA-CCATGCA
1 TGCATCCATGCA
12325849 GTGCATCCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.23, C:0.39, G:0.19, T:0.20
Consensus pattern (30 bp):
TGCATCCATGCACCTCCACCAGTGCATCCA
Found at i:12325819 original size:21 final size:21
Alignment explanation
Indices: 12325777--12325841 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
12325767 AGGGTGTCAA
* *
12325777 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCATCCATGC
12325798 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCATCCATGC
* *
12325819 ACCTGCA-CCAGTGCATCGATGC
1 A-GTGCATCCA-TGCATCCATGC
12325841 A
1 A
12325842 CCATGCAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCATCCATGC
Found at i:12325908 original size:20 final size:20
Alignment explanation
Indices: 12325883--12325996 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
12325873 AATGCAATTA
12325883 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
*
12325903 GTGCATCGATGCATCTTTCT
1 GTGCATCGATGCATCCTTCT
12325923 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
12325943 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
*
12325964 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
12325984 GTGCATCCATGCA
1 GTGCATCGATGCA
12325997 CGAAGGATAC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
20 68 0.80
21 17 0.20
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:12326392 original size:34 final size:32
Alignment explanation
Indices: 12326353--12326422 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
12326343 TTTTGTAAAG
* *
12326353 GGGAAAGGTTCTAGCTTATCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
12326387 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
12326419 GGGA
1 GGGA
12326423 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:12328639 original size:29 final size:30
Alignment explanation
Indices: 12328570--12328629 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
12328560 CAATTTAAGG
12328570 CAAAATGGTTTTTGGACTCGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTCGAATTGAATTTA
*
12328601 CAAAATGTTTTTGGACT-TAATTGAATTTA
1 CAAAATGTTTTTGGACTCGAATTGAATTTA
12328630 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTCGAATTGAATTTA
Found at i:12328767 original size:20 final size:21
Alignment explanation
Indices: 12328699--12328774 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
12328689 AGGGTGTCAA
* **
12328699 AGTGCATCCATGTACCCCTGC
1 AGTGCATCCATGCACCTATGC
**
12328720 AGTGCATCCATGCACCTACAC
1 AGTGCATCCATGCACCTATGC
*
12328741 TAGTGCATCGATGCACC-ATGC
1 -AGTGCATCCATGCACCTATGC
12328762 AGTGCATCCATGC
1 AGTGCATCCATGC
12328775 TCTCAAACAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 12 0.27
21 18 0.40
22 15 0.33
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCTATGC
Found at i:12329246 original size:34 final size:32
Alignment explanation
Indices: 12329207--12329276 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
12329197 TTTTGTAAAG
* *
12329207 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
12329241 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
12329273 GGGA
1 GGGA
12329277 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:12330389 original size:34 final size:34
Alignment explanation
Indices: 12330350--12330415 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
12330340 GATTAAATTT
12330350 AATTTTACTCGTAATTTCATAAACTTGACTAATC
1 AATTTTACTCGTAATTTCATAAACTTGACTAATC
12330384 AATTTTACTCGTAATTTCATAAACTTGACTAA
1 AATTTTACTCGTAATTTCATAAACTTGACTAA
12330416 AAAAATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (34 bp):
AATTTTACTCGTAATTTCATAAACTTGACTAATC
Found at i:12330435 original size:35 final size:34
Alignment explanation
Indices: 12330361--12330431 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
12330351 ATTTTACTCG
** ***
12330361 TAATTTCATAAACTTGACTAATCAATTTTACTCG
1 TAATTTCATAAACTTGACTAAAAAATTTTACAAA
12330395 TAATTTCATAAACTTGACTAAAAAAATTTT-CAAA
1 TAATTTCATAAACTTGACT-AAAAAATTTTACAAA
12330429 TAA
1 TAA
12330432 ATTTTAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (34 bp):
TAATTTCATAAACTTGACTAAAAAATTTTACAAA
Found at i:12330703 original size:2 final size:2
Alignment explanation
Indices: 12330696--12330735 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12330686 TGCAATATGA
12330696 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
12330736 TGTTATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12331404 original size:23 final size:23
Alignment explanation
Indices: 12331354--12331402 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
12331344 TCGCCCCTAC
* *
12331354 TTTTCATCTATCTTTATGACACG
1 TTTTCATCTACCTTTATGAAACG
*
12331377 TTTTCTTCTACCTTT-TGAAACG
1 TTTTCATCTACCTTTATGAAACG
12331399 TTTT
1 TTTT
12331403 TCGACCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.53
Consensus pattern (23 bp):
TTTTCATCTACCTTTATGAAACG
Found at i:12334163 original size:98 final size:98
Alignment explanation
Indices: 12333994--12334190 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
12333984 ATTATTAAAA
12333994 TATAATAATATACATATGTTAATACAAGTTTATCAAAATACTCAGAGCATACCCTTTGATTATAT
1 TATAATAATATACATATGTTAATACAAGTTTATCAAAATACTCAGAGCATACCCTTTGATTATAT
12334059 GCCAACTTTCATTTACATAACAAAAGGACCTAC
66 GCCAACTTTCATTTACATAACAAAAGGACCTAC
12334092 TATAATAATATACATATGTTAATACAAGTTTATCAAAATACTCAGAGCATACCCTTTGATTATAT
1 TATAATAATATACATATGTTAATACAAGTTTATCAAAATACTCAGAGCATACCCTTTGATTATAT
12334157 GCCAACTTTCATTTACATAACAAAAGGACCTAC
66 GCCAACTTTCATTTACATAACAAAAGGACCTAC
12334190 T
1 T
12334191 GATTAAGTTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (98 bp):
TATAATAATATACATATGTTAATACAAGTTTATCAAAATACTCAGAGCATACCCTTTGATTATAT
GCCAACTTTCATTTACATAACAAAAGGACCTAC
Found at i:12334583 original size:23 final size:23
Alignment explanation
Indices: 12334553--12334613 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
12334543 CTCGTATAAA
12334553 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
** *
12334576 TGCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
12334599 TGCACTGTAGTGCCA
1 TGCACCGAAGTGCCA
12334614 TATAAGATTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:12337931 original size:18 final size:19
Alignment explanation
Indices: 12337911--12337992 Score: 100
Period size: 18 Copynumber: 4.4 Consensus size: 19
12337901 GTCGCGAAGG
*
12337911 ACCACTATGTTCCGAAAG-
1 ACCACTATGTCCCGAAAGA
*
12337929 ACCACTGATTGTTCC-AAAGA
1 ACCACT-A-TGTCCCGAAAGA
12337949 ACCACTATGTCCCG-AAGA
1 ACCACTATGTCCCGAAAGA
12337967 ACCACTATGTCCCG-AAGA
1 ACCACTATGTCCCGAAAGA
12337985 ACCACTAT
1 ACCACTAT
12337993 ATATGTCCCG
Statistics
Matches: 59, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
18 41 0.69
19 6 0.10
20 12 0.20
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (19 bp):
ACCACTATGTCCCGAAAGA
Found at i:12337954 original size:38 final size:36
Alignment explanation
Indices: 12337911--12337992 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 36
12337901 GTCGCGAAGG
* *
12337911 ACCACTATGTTCCGAA-AGACCACTGATTGTTCCAAAGA
1 ACCACTATGTCCCGAAGA-ACCACT-A-TGTCCCAAAGA
*
12337949 ACCACTATGTCCCGAAGAACCACTATGTCCCGAAGA
1 ACCACTATGTCCCGAAGAACCACTATGTCCCAAAGA
12337985 ACCACTAT
1 ACCACTAT
12337993 ATATGTCCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
36 17 0.43
37 1 0.03
38 21 0.52
39 1 0.03
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (36 bp):
ACCACTATGTCCCGAAGAACCACTATGTCCCAAAGA
Found at i:12338000 original size:22 final size:19
Alignment explanation
Indices: 12337900--12338012 Score: 90
Period size: 18 Copynumber: 5.9 Consensus size: 19
12337890 ACTGAATATT
* *
12337900 TGTCGCGAAGGACCAC-TA
1 TGTCCCGAAGAACCACTTA
* *
12337918 TGTTCCGAA-AGACCACTGA
1 TGTCCCGAAGA-ACCACTTA
* *
12337937 TTGTTCCAAAGAACCAC-TA
1 -TGTCCCGAAGAACCACTTA
12337956 TGTCCCGAAGAACCAC-TA
1 TGTCCCGAAGAACCACTTA
12337974 TGTCCCGAAGAACCACTATATA
1 TGTCCCGAAGAACCAC--T-TA
*
12337996 TGTCCCGAAGGACCACT
1 TGTCCCGAAGAACCACT
12338013 CCTTAAGAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 44 0.56
19 2 0.03
20 14 0.18
21 1 0.01
22 17 0.22
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (19 bp):
TGTCCCGAAGAACCACTTA
Found at i:12343153 original size:20 final size:19
Alignment explanation
Indices: 12343112--12343200 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 19
12343102 TATTTGTCCT
*
12343112 GAAGGACCACT-ATGTCCC
1 GAAGGACCACTGATATCCC
*
12343130 GAAGGACCACTGATTATTCC
1 GAAGGACCACTGA-TATCCC
* *
12343150 GAAGAACCA-TTATATCCC
1 GAAGGACCACTGATATCCC
12343168 GAAGGACCACTGTATATGTCCC
1 GAAGGACCACTG-ATA--TCCC
*
12343190 GAAGAACCACT
1 GAAGGACCACT
12343201 CCTTAAAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
18 24 0.42
19 4 0.07
20 15 0.26
22 14 0.25
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (19 bp):
GAAGGACCACTGATATCCC
Found at i:12343177 original size:38 final size:40
Alignment explanation
Indices: 12343106--12343200 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 40
12343096 ATTGAATATT
* * *
12343106 TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTG-ATTA
1 TGTCCCGAAGAACCACTATATCCCGAAGGACCACTGTA-TA
*
12343146 T-T-CCGAAGAACCATTATATCCCGAAGGACCACTGTATA
1 TGTCCCGAAGAACCACTATATCCCGAAGGACCACTGTATA
12343184 TGTCCCGAAGAACCACT
1 TGTCCCGAAGAACCACT
12343201 CCTTAAAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 31 0.66
39 3 0.06
40 13 0.28
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (40 bp):
TGTCCCGAAGAACCACTATATCCCGAAGGACCACTGTATA
Found at i:12343190 original size:22 final size:21
Alignment explanation
Indices: 12343126--12343200 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 21
12343116 GACCACTATG
*
12343126 TCCCGAAGGACCACTG-ATTAT
1 TCCCGAAGAACCACTGTA-TAT
12343147 T-CCGAAGAACCA-T-TATA-
1 TCCCGAAGAACCACTGTATAT
*
12343164 TCCCGAAGGACCACTGTATAT
1 TCCCGAAGAACCACTGTATAT
12343185 GTCCCGAAGAACCACT
1 -TCCCGAAGAACCACT
12343201 CCTTAAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.02
18 12 0.27
19 3 0.07
20 14 0.31
21 1 0.02
22 14 0.31
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
TCCCGAAGAACCACTGTATAT
Found at i:12343905 original size:19 final size:19
Alignment explanation
Indices: 12343877--12343926 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
12343867 CCTTGACGGG
*
12343877 TGCATTGATGCACTATCTA
1 TGCATCGATGCACTATCTA
*
12343896 TGCATCGATGTACTATCTA
1 TGCATCGATGCACTATCTA
*
12343915 TGCATCGGTGCA
1 TGCATCGATGCA
12343927 TAAATCGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (19 bp):
TGCATCGATGCACTATCTA
Found at i:12343984 original size:19 final size:19
Alignment explanation
Indices: 12343960--12344030 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
12343950 TTTAAGTAGG
12343960 TGCATCGATGCACTTCTCA
1 TGCATCGATGCACTTCTCA
12343979 TGCATCGATGCACTTCTCA
1 TGCATCGATGCACTTCTCA
*
12343998 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTTCTCA
12344017 TGCATCGATGCACT
1 TGCATCGATGCACT
12344031 AATTGCATTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTTCTCA
Found at i:12352689 original size:51 final size:51
Alignment explanation
Indices: 12352465--12352987 Score: 462
Period size: 51 Copynumber: 9.8 Consensus size: 51
12352455 ACGAGTCTGT
* *
12352465 TCCCTATTCCTTCAG-GAAGTATAAGACTAGAACAATCTTCATA-AAA-TGTGTCTGC
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACT-TGTCCGC
* * * * * **
12352520 TCTCTATTCATTCATAGAGTATAAGACTTGAACAATCTTCAATAAAACAGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAA-CAAACTTGTCCGC
* * * * ** *
12352576 TCTCTACTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGCCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGC
* * * * *
12352631 TCTCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
**
12352682 TCCCTATTCCTTCAGAGAGTAT-GGAACTCGAGCAATCTTCATA-AAACGGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGG-ACT----CAATCTTCA-ACAAACTTGTCCGC
* * * *
12352737 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCCGC
**
12352792 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* * *
12352843 TCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
12352894 TCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* *
12352945 TCCCTATTCTTTCAGAGAGTATAAGACTCAATCTTCAACAAAC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
12352988 GAATTTGCTT
Statistics
Matches: 406, Mismatches: 45, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
50 2 0.00
51 198 0.49
52 1 0.00
54 2 0.00
55 160 0.39
56 43 0.11
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (51 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
Found at i:12352711 original size:106 final size:102
Alignment explanation
Indices: 12352459--12352988 Score: 487
Period size: 106 Copynumber: 5.0 Consensus size: 102
12352449 CAAATGACGA
* * * *
12352459 GTCTGTTCCCTATTCCTTCAG-GAAGTATAAGACTAGAACAATCTTC-ATAAAATGTGTCTGCTC
1 GTCTGCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCAATAAACTG-GTCCGCTC
* * * * *
12352522 TCTATTCATTCATAGAGTATAAGACTTGAACAATCTTCAATAAAACAG-
60 CCTATTCTTTCAGAGAGTATAGGAC-T---CAATCTTCAA-CAAAC-GT
* * * * * * *
12352570 GTCCGCTCTCTACTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGCCCGCTCTC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAATAAACTGGTCCGCTCCC
*
12352635 TATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGT
62 TATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
*
12352676 GT-TCGCTCCCTATTCCTTCAGAGAGTAT-GGAACTCGAGCAATCTTC-ATAAAACGGGTCCGCT
1 GTCT-GCTCCCTATTCCTTCAGAGAGTATAGG-ACT----CAATCTTCAAT-AAACTGGTCCGCT
* * * * *
12352738 CTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTT
59 CCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCAACAAACGT
* *
12352786 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAACTGGTCCGCTCCCTATT
* * *
12352851 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
* * *
12352888 GTCTGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAACTGGTCCGCTCCCTATT
*
12352953 CTTTCAGAGAGTATAAGACTCAATCTTCAACAAACG
66 CTTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
12352989 AATTTGCTTC
Statistics
Matches: 359, Mismatches: 39, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
102 111 0.31
105 4 0.01
106 116 0.32
107 12 0.03
110 45 0.13
111 64 0.18
112 7 0.02
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAACTGGTCCGCTCCCTATT
CTTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
Found at i:12354369 original size:24 final size:22
Alignment explanation
Indices: 12354338--12354408 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 22
12354328 TTTTCTTCCA
*
12354338 TTTTCCATTTTTTCTTCTCTTTT
1 TTTTCCATTTTTT-TTCTCATTT
12354361 TTTTACCATTTTTTTTCTCA--T
1 TTTT-CCATTTTTTTTCTCATTT
*
12354382 TTTTCCATTCATTTTT-TCATTT
1 TTTTCCATT-TTTTTTCTCATTT
12354404 TTTTC
1 TTTTC
12354409 TTCAAGCGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 8 0.19
21 10 0.24
22 6 0.14
23 9 0.21
24 9 0.21
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCCATTTTTTTTCTCATTT
Found at i:12354372 original size:23 final size:23
Alignment explanation
Indices: 12354320--12354408 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 23
12354310 CTTTTTTCAC
12354320 TTTT-CATTTTTTCTTC-CA---
1 TTTTCCATTTTTTCTTCTCATTT
*
12354338 TTTTCCATTTTTTCTTCTCTTTT
1 TTTTCCATTTTTTCTTCTCATTT
12354361 TTTTACCATTTTTT-TTCTCA--T
1 TTTT-CCATTTTTTCTTCTCATTT
*
12354382 TTTTCCATTCATTT-TT-TCATTT
1 TTTTCCATT-TTTTCTTCTCATTT
12354404 TTTTC
1 TTTTC
12354409 TTCAAGCGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
18 4 0.07
19 12 0.20
20 9 0.15
21 10 0.17
22 6 0.10
23 9 0.15
24 9 0.15
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTCCATTTTTTCTTCTCATTT
Found at i:12354405 original size:44 final size:43
Alignment explanation
Indices: 12354324--12354407 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 43
12354314 TTTCACTTTT
*
12354324 CATTTTTTCTTCCATTTTCCATTTTTTCTTCTCTTTTTTTTAC
1 CATTTTTTCTTCCATTTTCCATTTTTTCTTCTATTTTTTTTAC
12354367 CATTTTTT-TTCTCATTTTTCCATTCATTTT-TTC-ATTTTTTT
1 CATTTTTTCTTC-CA-TTTTCCATT--TTTTCTTCTATTTTTTT
12354408 CTTCAAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
42 3 0.08
43 10 0.28
44 16 0.44
45 3 0.08
46 4 0.11
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (43 bp):
CATTTTTTCTTCCATTTTCCATTTTTTCTTCTATTTTTTTTAC
Found at i:12364073 original size:46 final size:48
Alignment explanation
Indices: 12363998--12364105 Score: 166
Period size: 46 Copynumber: 2.3 Consensus size: 48
12363988 CCATGCTTTG
* *
12363998 TTATTCACAAAAATAAATCCTAACTGCATGATATCTAATTCGCATGC-
1 TTATTCAAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
12364045 TTATTCAAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
12364092 TTTATTCAAAAAAA
1 -TTATTCAAAAAAA
12364106 CGAAAATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
46 27 0.48
47 16 0.29
48 13 0.23
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (48 bp):
TTATTCAAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:12378230 original size:22 final size:22
Alignment explanation
Indices: 12378200--12378254 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
12378190 TATTTGGTGG
* *
12378200 TGTTGTTTTTATGG-ATGTTTAA
1 TGTTATTTTTATGGTATATTT-A
*
12378222 TGTTATTTTAATGGTATATTTA
1 TGTTATTTTTATGGTATATTTA
12378244 TGTTTATTTTT
1 TG-TTATTTTT
12378255 TATATTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (22 bp):
TGTTATTTTTATGGTATATTTA
Found at i:12388849 original size:19 final size:19
Alignment explanation
Indices: 12388817--12388927 Score: 124
Period size: 19 Copynumber: 5.8 Consensus size: 19
12388807 AAAAGTAGCT
12388817 AAATAATAAAAATAAAAATA
1 AAATAAT-AAAATAAAAATA
12388837 AAATAA-AATAATAAAAATAA
1 AAATAATAA-AATAAAAAT-A
12388857 AAATAATAAAAT-AAAATAA
1 AAATAATAAAATAAAAAT-A
12388876 AAATAATAAAATAAAAATA
1 AAATAATAAAATAAAAATA
12388895 ATAA-AATAAAAT-AAAAT-
1 A-AATAATAAAATAAAAATA
*
12388912 AAATAAAAGAAATAAA
1 AAATAATA-AAATAAA
12388928 TTAAAATAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 17
0.82 0.01 0.17
Matches are distributed among these distances:
16 2 0.02
17 4 0.05
18 11 0.13
19 40 0.49
20 23 0.28
21 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.20
Consensus pattern (19 bp):
AAATAATAAAATAAAAATA
Found at i:12388873 original size:33 final size:33
Alignment explanation
Indices: 12388816--12388919 Score: 160
Period size: 33 Copynumber: 3.2 Consensus size: 33
12388806 TAAAAGTAGC
12388816 TAAATAATAAAAAT-A-AAAATAAAATAAAATAA
1 TAAA-AATAAAAATAATAAAATAAAATAAAATAA
12388848 TAAAAATAAAAATAATAAAATAAAATAAAAATAA
1 TAAAAATAAAAATAATAAAATAAAAT-AAAATAA
12388882 T-AAAATAAAAATAATAAAATAAAATAAAATAAA
1 TAAAAATAAAAATAATAAAATAAAATAAAAT-AA
12388915 TAAAA
1 TAAAA
12388920 GAAATAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
31 9 0.13
32 10 0.15
33 37 0.55
34 11 0.16
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (33 bp):
TAAAAATAAAAATAATAAAATAAAATAAAATAA
Found at i:12388932 original size:14 final size:13
Alignment explanation
Indices: 12388817--12388933 Score: 114
Period size: 14 Copynumber: 8.6 Consensus size: 13
12388807 AAAAGTAGCT
12388817 AAATAATAAAAAT-
1 AAATAA-AAAAATA
*
12388830 AAA-AATAAAATA
1 AAATAAAAAAATA
12388842 AAATAATAAAAATAA
1 AAATAA-AAAAAT-A
*
12388857 AAATAATAAAATA
1 AAATAAAAAAATA
12388870 AAATAAAAATAATA
1 AAATAAAAA-AATA
12388884 AAATAAAAATAATA
1 AAATAAAAA-AATA
12388898 AAATAAAATAAA-A
1 AAATAAAA-AAATA
12388911 TAAATAAAAGAAATA
1 -AAATAAAA-AAATA
*
12388926 AATTAAAA
1 AAATAAAA
12388934 TAGAATAAGA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
11 5 0.06
12 5 0.06
13 15 0.17
14 56 0.62
15 9 0.10
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.21
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:12388933 original size:33 final size:31
Alignment explanation
Indices: 12388824--12388941 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 31
12388814 GCTAAATAAT
*
12388824 AAAAATAAAAATAAAATAAAAT-AATAAAAA
1 AAAAATTAAAATAAAATAAAATAAATAAAAA
12388854 TAAAAATAATAAAATAAAATAAAA-ATAATAAAATA
1 -AAAAAT--TAAAATAAAATAAAATA-AATAAAA-A
*
12388889 AAAATAATAAAATAAAATAAAATAAATAAAAGA
1 AAAA-ATTAAAATAAAATAAAATAAATAAAA-A
*
12388922 AATAAATTAAAATAGAATAA
1 AA-AAATTAAAATAAAATAA
12388942 GATGAAAATG
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
31 6 0.08
33 52 0.70
34 14 0.19
35 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (31 bp):
AAAAATTAAAATAAAATAAAATAAATAAAAA
Found at i:12389219 original size:21 final size:22
Alignment explanation
Indices: 12389186--12389237 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
12389176 AAAAATGAAT
* *
12389186 AAATAAATGAAATAAAAATATA
1 AAATATATAAAATAAAAATATA
**
12389208 AAA-ATATAAAATAATGATATA
1 AAATATATAAAATAAAAATATA
12389229 AAATATATA
1 AAATATATA
12389238 TACATATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AAATATATAAAATAAAAATATA
Found at i:12390412 original size:21 final size:21
Alignment explanation
Indices: 12390361--12390418 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
12390351 CCTTACTTTA
12390361 TTTTCCTTTTCTTTT-TTTCTC
1 TTTTCCTTTT-TTTTCTTTCTC
12390382 TTTTCTCTTTCTTTTTCTTTCT-
1 TTTTC-CTTT-TTTTTCTTTCTC
12390404 TTTTCCTTTTTTTTC
1 TTTTCCTTTTTTTTC
12390419 AATTTAGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 13 0.38
23 6 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCCTTTTTTTTCTTTCTC
Found at i:12390417 original size:10 final size:11
Alignment explanation
Indices: 12390376--12390418 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 11
12390366 CTTTTCTTTT
12390376 TTTCTCTTTTCTC
1 TTTCT-TTTTC-C
12390389 TTTCTTTTT-C
1 TTTCTTTTTCC
12390399 TTTCTTTTTCC
1 TTTCTTTTTCC
12390410 TTT-TTTTTC
1 TTTCTTTTTC
12390419 AATTTAGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 16 0.55
11 4 0.14
12 4 0.14
13 5 0.17
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTCC
Found at i:12391282 original size:18 final size:18
Alignment explanation
Indices: 12391259--12391311 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
12391249 ACTGAATATT
12391259 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
12391277 TGTCCCGAATGACTACTA
1 TGTCCCGAAGGACCACTA
*
12391295 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
12391312 CCTTAAGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:12400300 original size:16 final size:15
Alignment explanation
Indices: 12400263--12400301 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12400253 AATATGAATG
*
12400263 TAAAAACATGGAAAA
1 TAAAAATATGGAAAA
12400278 TAGAAAATATGGAAAAA
1 TA-AAAATATGG-AAAA
12400295 TAAAAAT
1 TAAAAAT
12400302 GCAAAGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (15 bp):
TAAAAATATGGAAAA
Found at i:12403647 original size:5 final size:5
Alignment explanation
Indices: 12403627--12403815 Score: 99
Period size: 5 Copynumber: 38.0 Consensus size: 5
12403617 AAAAGTAGCT
*
12403627 AAATA ATAAT- AAATA AAATA AAA-A ATA-A AAATA AAATA AAAT- -AATA
1 AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * *
12403673 AAATA AAATA AAATA AAAT- AAATA AAA-G AAATA AAGTA AAATA GAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * * * * * *
12403721 AGATGA AAATGA CAATAA AAATG GAATC AAATA AAACAA AAAAA AAAGA
1 AAAT-A AAAT-A AAAT-A AAATA AAATA AAATA AAA-TA AAATA AAATA
** * *
12403770 AAACG AAA-A ATAGA AAATA AAATTA TAAATA AAA-A TAAATA AAATA
1 AAATA AAATA AAATA AAATA AAA-TA -AAATA AAATA -AAATA AAATA
12403816 TATATATAAT
Statistics
Matches: 144, Mismatches: 26, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
3 3 0.02
4 19 0.13
5 94 0.65
6 25 0.17
7 3 0.02
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:12403667 original size:23 final size:23
Alignment explanation
Indices: 12403627--12403715 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 23
12403617 AAAAGTAGCT
*
12403627 AAATAATAAT-AAATAAAATAAA
1 AAATAAAAATAAAATAAAATAAA
12403649 AAATAAAAATAAAATAAAATAATA
1 AAATAAAAATAAAATAAAATAA-A
12403673 AAAT-AAAATAAAATAAAATAAA
1 AAATAAAAATAAAATAAAATAAA
* *
12403695 TAAA-AGAAATAAAGTAAAATA
1 -AAATAAAAATAAAATAAAATA
12403716 GAATAAGATG
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
22 10 0.17
23 45 0.75
24 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAAATAAAATAAAATAAA
Found at i:12403668 original size:28 final size:27
Alignment explanation
Indices: 12403627--12403815 Score: 104
Period size: 28 Copynumber: 6.7 Consensus size: 27
12403617 AAAAGTAGCT
12403627 AAATAATAATAAATAAAATAAAAAATAA
1 AAATAA-AATAAATAAAATAAAAAATAA
12403655 AAATAAAATAAAATAATAA-AATAAAAT-A
1 AAATAAAAT-AAATAA-AATAA-AAAATAA
*
12403683 AAATAAAATAAATAAAAGAAATAAAGT-A
1 AAATAAAATAAATAAAATAAA-AAA-TAA
* * *
12403711 AAATAGAATAAGATGAAAAT-GACAATAA
1 AAATAAAATAA-AT-AAAATAAAAAATAA
** *
12403739 AAATGGAATCAAATAAAACAAAAAA-AA
1 AAATAAAAT-AAATAAAATAAAAAATAA
* * *
12403766 AAGA-AAACGAAAAATAGAAA-ATAAAATTAT
1 AA-ATAAA--ATAAATA-AAATA-AAAAATAA
12403796 AAATAAAAATAAATAAAATA
1 AAAT-AAAATAAATAAAATA
12403816 TATATATAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 39
0.71 0.08 0.22
Matches are distributed among these distances:
26 3 0.02
27 24 0.19
28 62 0.49
29 28 0.22
30 7 0.06
31 3 0.02
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (27 bp):
AAATAAAATAAATAAAATAAAAAATAA
Found at i:12404128 original size:20 final size:20
Alignment explanation
Indices: 12404080--12404122 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12404070 AAAGGAAATC
12404080 GGGGTAAAAATCAAAATTAA
1 GGGGTAAAAATCAAAATTAA
12404100 GGGGTAAAAATCAAAATTAA
1 GGGGTAAAAATCAAAATTAA
12404120 GGG
1 GGG
12404123 TCAAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.19
Consensus pattern (20 bp):
GGGGTAAAAATCAAAATTAA
Found at i:12406730 original size:15 final size:15
Alignment explanation
Indices: 12406710--12406740 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12406700 TGGCCCGACA
12406710 ACTTTTCAACGTTGC
1 ACTTTTCAACGTTGC
12406725 ACTTTTCAACGTTGC
1 ACTTTTCAACGTTGC
12406740 A
1 A
12406741 TACAAGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (15 bp):
ACTTTTCAACGTTGC
Found at i:12412562 original size:24 final size:21
Alignment explanation
Indices: 12412535--12412583 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
12412525 ATTAATGATC
*
12412535 TAATTCTATTCCTTTAAAATTTTA
1 TAATTCTATGCC-TT-AAA-TTTA
*
12412559 TAATTTTATGCCTTAAATTTA
1 TAATTCTATGCCTTAAATTTA
12412580 TAAT
1 TAAT
12412584 ATAAGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 2 0.09
24 10 0.43
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATTCTATGCCTTAAATTTA
Found at i:12413664 original size:28 final size:28
Alignment explanation
Indices: 12413624--12413679 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
12413614 ACACATAATT
12413624 CTTTTACATTTTACATTTTAAGGAAGAA
1 CTTTTACATTTTACATTTTAAGGAAGAA
* * *
12413652 CTTTTACCTTTTACTTTTTACGGAAGAA
1 CTTTTACATTTTACATTTTAAGGAAGAA
12413680 GTTAAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (28 bp):
CTTTTACATTTTACATTTTAAGGAAGAA
Found at i:12422501 original size:2 final size:2
Alignment explanation
Indices: 12422440--12422485 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12422430 GTTAATAATT
12422440 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
12422482 TA TA
1 TA TA
12422486 ATTTAAGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12424227 original size:24 final size:24
Alignment explanation
Indices: 12424195--12424251 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
12424185 CACCACATCT
* *
12424195 CATATAAATTGCACCGAAGTGCTA
1 CATAGAAATTGCACCGAAGTGCCA
*
12424219 CGTAGAAATTGCACCGAAGTGCCA
1 CATAGAAATTGCACCGAAGTGCCA
12424243 CATAGAAAT
1 CATAGAAAT
12424252 GTCCCGAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
CATAGAAATTGCACCGAAGTGCCA
Found at i:12424669 original size:21 final size:21
Alignment explanation
Indices: 12424643--12424791 Score: 228
Period size: 21 Copynumber: 7.1 Consensus size: 21
12424633 AATTTAAAAT
* *
12424643 GTGTATCGATGCATTGCTACA
1 GTGTATCGAAGCACTGCTACA
* *
12424664 GTGTATCGATGCATTGCTACA
1 GTGTATCGAAGCACTGCTACA
*
12424685 GTGTATC-AATGCATTGCTACA
1 GTGTATCGAA-GCACTGCTACA
12424706 GTGTATCGAAGCACTGCTACA
1 GTGTATCGAAGCACTGCTACA
12424727 GTGTATCGAAGCACTGCTACA
1 GTGTATCGAAGCACTGCTACA
12424748 GTGTATCGAAGCACTGCTACA
1 GTGTATCGAAGCACTGCTACA
*
12424769 GAGTATCGAAGCACTGCTACA
1 GTGTATCGAAGCACTGCTACA
12424790 GT
1 GT
12424792 AACTGATACA
Statistics
Matches: 122, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
20 1 0.01
21 119 0.98
22 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
GTGTATCGAAGCACTGCTACA
Found at i:12430625 original size:22 final size:22
Alignment explanation
Indices: 12430564--12430630 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
12430554 GAGTCGAGGG
* **
12430564 ATATACAGTGGTCCTTTAGGAC
1 ATATACAGTGGTCATTCGGGAC
* * *
12430586 ATATACAATGGTCTTTCGGGAT
1 ATATACAGTGGTCATTCGGGAC
12430608 ATATACAGTGGTCATTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
12430630 A
1 A
12430631 AATTTCATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (22 bp):
ATATACAGTGGTCATTCGGGAC
Found at i:12434412 original size:22 final size:22
Alignment explanation
Indices: 12434387--12434451 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
12434377 GAGTCGAGGG
12434387 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
12434409 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGGGAC
12434431 ATATACAGTGGTCCTTCGGGA
1 ATATACAGTGGTCCTTCGGGA
12434452 AAAATTTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCGGGAC
Found at i:12435836 original size:23 final size:23
Alignment explanation
Indices: 12435809--12435922 Score: 165
Period size: 23 Copynumber: 5.0 Consensus size: 23
12435799 GTGCCATATA
* *
12435809 TTTGTCCCAAAGGACTATATAGT
1 TTTGTCCCGAAGGACTACATAGT
* *
12435832 TTTGTCCTGAAGGACCACATAGT
1 TTTGTCCCGAAGGACTACATAGT
*
12435855 TTTATCCCGAAGGACTACATAGT
1 TTTGTCCCGAAGGACTACATAGT
12435878 TTTGTCCCGAAGGACTACATAGT
1 TTTGTCCCGAAGGACTACATAGT
* *
12435901 TTTGTCCCGAATGACCACATAG
1 TTTGTCCCGAAGGACTACATAG
12435923 AACCCTCAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (23 bp):
TTTGTCCCGAAGGACTACATAGT
Found at i:12449320 original size:20 final size:20
Alignment explanation
Indices: 12449297--12449339 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12449287 AATCCACCAC
*
12449297 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
12449317 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
12449337 ATG
1 ATG
12449340 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:12449442 original size:23 final size:23
Alignment explanation
Indices: 12449405--12449463 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
12449395 AGGAGTTATC
*
12449405 AAAGACCACATAGTTTTGTCCCG
1 AAAGACCACATAGTTTTATCCCG
* * *
12449428 AAGGACTACATAGTTTTATTCCG
1 AAAGACCACATAGTTTTATCCCG
12449451 AAAGACCACATAG
1 AAAGACCACATAG
12449464 AACCCTCGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (23 bp):
AAAGACCACATAGTTTTATCCCG
Found at i:12452711 original size:22 final size:22
Alignment explanation
Indices: 12452683--12452726 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12452673 TTTAAATATA
*
12452683 ATTTTAGTTATCATAATAAATT
1 ATTTTAGTTATAATAATAAATT
12452705 ATTTTAGTTATAATAATAAATT
1 ATTTTAGTTATAATAATAAATT
12452727 CAAAATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTTAGTTATAATAATAAATT
Found at i:12453086 original size:196 final size:193
Alignment explanation
Indices: 12452767--12453545 Score: 873
Period size: 196 Copynumber: 4.0 Consensus size: 193
12452757 ATTATGGTAA
* * * * * *
12452767 TTTATTTAGACACAATAACAAATTAATTTAGTTAAAATAAAAAATATGTTAAATTTCTTT-AGTC
1 TTTATTTAGTCACAATAACATATTAAATTAGTTAAAATAAAAATTATGTCAAATTTATTTCA-TC
* * ** * * * * *
12452831 AAAATATTTTCTCAAAATAACAAATTATGACAAATTTAAATAGTTATAATAATAATTTATAATAA
65 ACAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAACAA
* * *
12452896 ATATTAATTTCTCAATATAAAAAAGTATGACAAATAATATTTTTTCACAATAATAAATTATAAC
130 ATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTATAAC
* * * * *
12452960 TTTATTTAGTCAAAATAACATATTAAAATTAGTCAAAATAAAAACTTACGTTAAATTTATTTCGT
1 TTTATTTAGTCACAATAACATATT-AAATTAGTTAAAATAAAAA-TTATGTCAAATTTATTTCAT
* *
12453025 CACAATATTGTTTTCAAAATAACAACTTTTGA-AAATTTTATTTAATCAAAATAACAATTTATAA
64 CACAATATT-TTCTCAAAATAACAAATTTTGACAAA-TTTATTTAATCAAAATAACAATTTATAA
* * * * *
12453089 CAAATATTAATTTCTCAATATAAAAAATTATGAAAAACACTATTCTTTTACAATAACAAATTGTA
127 CAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTATA
12453154 AC
192 AC
* * ** * *
12453156 AAATTTATTTAGTTATAATAACATGGTAAATTCATTTAAAATAAAAATTTATGTCAAATATATTT
1 ---TTTATTTAGTCACAATAACATATTAAATT-AGTTAAAATAAAAA-TTATGTCAAATTTATTT
* * **
12453221 CATCACAATATTTTCTCAAAATAACAACTTTTGACAAATTTGTTTAATCTTAATAACAATTTATA
61 CATCACAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCAAAATAACAATTTATA
* * * *
12453286 ACAAATATTGATTTCTCAAT-TAAAAAATTATGACAAATAACATTCTTTCACAAAAATAAATTGT
126 ACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAA-T-T
*
12453350 AACAAC
189 -ATAAC
* ** *
12453356 TTTATTTAGTTACAATAACACGTTAAATTTAGTTAAAATAAAAGTTATGTCAAATTTATTTCATC
1 TTTATTTAGTCACAATAACATATTAAA-TTAGTTAAAATAAAAATTATGTCAAATTTATTTCATC
* * ** * *
12453421 ACAATATTTTGTCAAAATAAAAAAATCGTGACAAATTTATTTAATCCAAACAACAAATTTATAAC
65 ACAATATTTTCTCAAAAT-AACAAATTTTGACAAATTTATTTAATCAAAATAAC-AATTTATAAC
* *
12453486 AAATATTAA-TTCTCAATATAAAAAATTGTGACAAGTAATATTCTTTCACAATAACAAATT
128 AAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATT
12453546 GTAGCATAAT
Statistics
Matches: 495, Mismatches: 74, Indels: 31
0.82 0.12 0.05
Matches are distributed among these distances:
193 21 0.04
194 17 0.03
195 26 0.05
196 137 0.28
197 105 0.21
198 125 0.25
199 61 0.12
200 3 0.01
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (193 bp):
TTTATTTAGTCACAATAACATATTAAATTAGTTAAAATAAAAATTATGTCAAATTTATTTCATCA
CAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAACAAA
TATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTATAAC
Found at i:12453395 original size:197 final size:197
Alignment explanation
Indices: 12452767--12453548 Score: 911
Period size: 198 Copynumber: 4.0 Consensus size: 197
12452757 ATTATGGTAA
* * * * *
12452767 TTTATTTAGACACAATAACAAATT-AATTTAGTTAAAATAAAAAATATGTTAAATTTCTTT-AGT
1 TTTATTTAGTCACAATAACATATTAAATTTAGTTAAAATAAAAATTATGTCAAATTTATTTCA-T
* * ** * * *
12452830 CAAAATATTTTCTCAAAATAACAAATTATGACAAATTTAAATAGT-TATAATAATAATTTATAAT
65 CACAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCTA-AATAACAATTTATAAC
* * * *
12452894 AAATATTAATTTCTCAATATAAAAAAGTATGACAAATAATATTTTTTCACAATAATAAA-T-T-A
129 AAATATTAATTTCTCAATATAAAAAATTATGACAAATAACATTCTTTCACAATAACAAATTGTAA
*
12452956 TAAC
194 CAAC
* * * * * *
12452960 TTTATTTAGTCAAAATAACATATTAAAATTAGTCAAAATAAAAACTTACGTTAAATTTATTTCGT
1 TTTATTTAGTCACAATAACATATTAAATTTAGTTAAAATAAAAA-TTATGTCAAATTTATTTCAT
* * *
12453025 CACAATATTGTTTTCAAAATAACAACTTTTGA-AAATTTTATTTAATCAAAATAACAATTTATAA
65 CACAATATT-TTCTCAAAATAACAAATTTTGACAAA-TTTATTTAATCTAAATAACAATTTATAA
*
12453089 CAAATATTAATTTCTCAATATAAAAAATTATGA-AAA-ACACTATTCTTTTACAATAACAAATTG
128 CAAATATTAATTTCTCAATATAAAAAATTATGACAAATA-AC-ATTCTTTCACAATAACAAATTG
*
12453152 TAACAAA
191 TAACAAC
* * ** * * *
12453159 TTTATTTAGTTATAATAACATGGTAAATTCATTTAAAATAAAAATTTATGTCAAATATATTTCAT
1 TTTATTTAGTCACAATAACATATTAAATTTAGTTAAAATAAAAA-TTATGTCAAATTTATTTCAT
* * *
12453224 CACAATATTTTCTCAAAATAACAACTTTTGACAAATTTGTTTAATCTTAATAACAATTTATAACA
65 CACAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCTAAATAACAATTTATAACA
* * *
12453289 AATATTGATTTCTCAAT-TAAAAAATTATGACAAATAACATTCTTTCACAAAAATAAATTGTAAC
130 AATATTAATTTCTCAATATAAAAAATTATGACAAATAACATTCTTTCACAATAACAAATTGTAAC
12453353 AAC
195 AAC
* ** *
12453356 TTTATTTAGTTACAATAACACGTTAAATTTAGTTAAAATAAAAGTTATGTCAAATTTATTTCATC
1 TTTATTTAGTCACAATAACATATTAAATTTAGTTAAAATAAAAATTATGTCAAATTTATTTCATC
* * ** * *
12453421 ACAATATTTTGTCAAAATAAAAAAATCGTGACAAATTTATTTAATCCAAACAACAAATTTATAAC
66 ACAATATTTTCTCAAAAT-AACAAATTTTGACAAATTTATTTAATCTAAATAAC-AATTTATAAC
* * *
12453486 AAATATTAA-TTCTCAATATAAAAAATTGTGACAAGTAATATTCTTTCACAATAACAAATTGTA
129 AAATATTAATTTCTCAATATAAAAAATTATGACAAATAACATTCTTTCACAATAACAAATTGTA
12453549 GCATAATTAT
Statistics
Matches: 502, Mismatches: 70, Indels: 29
0.84 0.12 0.05
Matches are distributed among these distances:
193 21 0.04
194 18 0.04
195 30 0.06
196 124 0.25
197 113 0.23
198 128 0.25
199 68 0.14
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (197 bp):
TTTATTTAGTCACAATAACATATTAAATTTAGTTAAAATAAAAATTATGTCAAATTTATTTCATC
ACAATATTTTCTCAAAATAACAAATTTTGACAAATTTATTTAATCTAAATAACAATTTATAACAA
ATATTAATTTCTCAATATAAAAAATTATGACAAATAACATTCTTTCACAATAACAAATTGTAACA
AC
Found at i:12453540 original size:395 final size:393
Alignment explanation
Indices: 12452798--12453563 Score: 999
Period size: 395 Copynumber: 1.9 Consensus size: 393
12452788 ATTAATTTAG
* * *
12452798 TTAAAATAAAAAATATGTTAAATTTCTTTAGTCAAAATATTTTCTCAAAATAACAAATTATGACA
1 TTAAAATAAAAAATATGTCAAATATATTTAGTCAAAATATTTTCTCAAAATAACAAATTATGACA
* * *
12452863 AATTTAAATAGTTATAATAATAATTTATAATAAATATTAATTTCTCAATATAAAAAAGTATGACA
66 AATTTAAATAATTATAATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAAGTATGACA
* * * * *
12452928 AATAATATTTTTTCACAATAATAAATTATAACTTTATTTAGTCAAAATAACATATTAAAATTAGT
131 AATAACATTCTTTCACAAAAATAAATTACAACTTTATTTAGTCAAAATAACACATTAAAATTAGT
* * * * * **
12452993 CAAAATAAAAACTTACGTTAAATTTATTTCGTCACAATATTGTTTTCAAAATAACAACTTTTGAA
196 CAAAATAAAAACTTACGTCAAATTTATTTCATCACAATATTGTTGTCAAAATAAAAAATCGTGAA
*
12453058 AATTTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAA
261 AATTTTATTTAATCAAAACAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAA
* *
12453123 AAACACTATTCTTTTACAATAACAAATTGTAACA-AATTTATTTAGTTATAATAACATGGTAAAT
326 AAACAATATTCTTTCACAATAACAAATTGTAACATAA-TTATTTAGTTATAATAACATGGTAAAT
12453187 TCAT
390 TCAT
* * * *
12453191 TTAAAATAAAAATTTATGTCAAATATATTTCA-TCACAATATTTTCTCAAAATAACAACTTTTGA
1 TTAAAATAAAAA-ATATGTCAAATATATTT-AGTCAAAATATTTTCTCAAAATAACAAATTATGA
*** * *
12453255 CAAATTTGTTTAATCT-TAATAACAATTTATAACAAATATTGATTTCTCAAT-TAAAAAATTATG
64 CAAATTTAAATAAT-TATAATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAAGTATG
* * *
12453318 ACAAATAACATTCTTTCACAAAAATAAATTGTAACAACTTTATTTAGTTACAATAACACGTTAAA
128 ACAAATAACATTCTTTCACAAAAATAAA-T-T-ACAACTTTATTTAGTCAAAATAACACATTAAA
* * * *
12453383 TTTAGTTAAAAT-AAAAGTTATGTCAAATTTATTTCATCACAATATT-TTGTCAAAATAAAAAAA
190 ATTAGTCAAAATAAAAACTTACGTCAAATTTATTTCATCACAATATTGTTGTCAAAAT-AAAAAA
*
12453446 TCGTGACAAA-TTTATTTAATCCAAACAACAAATTTATAACAAATATTAA-TTCTCAATATAAAA
254 TCGTGA-AAATTTTATTTAATCAAAACAAC-AATTTATAACAAATATTAATTTCTCAATATAAAA
* * ** *
12453509 AATTGTGACAAGTAATATTCTTTCACAATAACAAATTGTAGCATAATTATTTAGT
317 AATTATGAAAAACAATATTCTTTCACAATAACAAATTGTAACATAATTATTTAGT
12453564 AAAAAAATTA
Statistics
Matches: 320, Mismatches: 43, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
393 48 0.15
394 94 0.29
395 117 0.37
396 61 0.19
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (393 bp):
TTAAAATAAAAAATATGTCAAATATATTTAGTCAAAATATTTTCTCAAAATAACAAATTATGACA
AATTTAAATAATTATAATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAAGTATGACA
AATAACATTCTTTCACAAAAATAAATTACAACTTTATTTAGTCAAAATAACACATTAAAATTAGT
CAAAATAAAAACTTACGTCAAATTTATTTCATCACAATATTGTTGTCAAAATAAAAAATCGTGAA
AATTTTATTTAATCAAAACAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGAA
AAACAATATTCTTTCACAATAACAAATTGTAACATAATTATTTAGTTATAATAACATGGTAAATT
CAT
Found at i:12457339 original size:82 final size:81
Alignment explanation
Indices: 12457200--12458056 Score: 675
Period size: 81 Copynumber: 10.7 Consensus size: 81
12457190 TGGTATATTC
* * ** ** * *
12457200 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGGGTCTGCTCTGCTTTTC-TCTCAGGGGAGAT
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCAT-TCAGGGGAAAT
* * *
12457264 CACACTTAATTTGTGCCT
64 AAGACTTGATTTGTGCCT
* * * * * *
12457282 ATTTTTCGGGTAGATAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAATT
1 CTTTTTCGGGTAGACATATCAAT-TTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
*
12457347 AGACTTGATTTGGGCCT
65 AGACTTGATTTGTGCCT
* * * *
12457364 CTTTTTTCAGGTAGACAAATCAATGTTGGAAGACGTGC-CTGTTCCACCATTCATTCAGGGGAAA
1 C-TTTTTCGGGTAGACATATCAAT-TTGGAAGACGT-CTCTGCTCCACTATTCATTCAGGGGAAA
*
12457428 TCAA-ACTTGATTTGTGACT
63 T-AAGACTTGATTTGTGCCT
* * * * * * *
12457447 CATTTTT-GGGTAGGCAAATCAATTTTGGAAGACGTTTTTGTTCTACCATTCATTCAGGGGAAAT
1 C-TTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAAT
* * *
12457511 CAGACTTGATCTATGCCT
64 AAGACTTGATTTGTGCCT
* * * * * * * *
12457529 CTTTTTCGGGTAGACAAATAAATATTAGAATACGTGTTTGCTCCGCCATTCATTCAGGGGAAAT-
1 CTTTTTCGGGTAGACATATCAAT-TTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
*
12457593 ---C---ATATGTGCCT
65 AGACTTGATTTGTGCCT
* * *
12457604 CTTCTTCGAGTAGACATATCAATTTTGGAATACG---C-G-T-C-C-ATTCATTCAGGGGAAAT-
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
*
12457660 AGACTTGATTTTTGCCT
65 AGACTTGATTTGTGCCT
* * * * *
12457677 CTTTTTTGAGTAGACAGATCAACTTTGGAAGACGTCTCTACTCCACTATTCATTCA-GGGAGATA
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
* * *
12457741 AGACTCGATCTGTTCCT
65 AGACTTGATTTGTGCCT
* * * * *
12457758 CTTCTTCGGGTAGACATATCAACTTTGGAAGTCTTCTCTACTCCACTATTCATTCA-GGGAGATA
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
** * *
12457822 AGACTCAATATGTACCT
65 AGACTTGATTTGTGCCT
* * * * **
12457839 CTTCTTCGGGTAGACATATCTATTTTGGAAGACGTCTCTGCTCCATTATTCATTCA-AGGAGGTA
1 CTTTTTCGGGTAGACATATC-AATTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
* *
12457903 AGACTCGATTTGTGACT
65 AGACTTGATTTGTGCCT
* * * *
12457920 CTTTTTTGGGTAGACATATCAACTTTGGAAGAAGTCTCTGCTCTACTATTCATTCA-GGGAGATA
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATA
*
12457984 AGA-TTCGATTTATGCCT
65 AGACTT-GATTTGTGCCT
* * *
12458001 CTTTTTCGGGTAGACATATCAACTTTAGAAAACGTCTCTGCTCCATTATTCATTCA
1 CTTTTTCGGGTAGACATATCAA-TTTGGAAGACGTCTCTGCTCCACTATTCATTCA
12458057 TGGAGATAAG
Statistics
Matches: 648, Mismatches: 98, Indels: 59
0.80 0.12 0.07
Matches are distributed among these distances:
67 17 0.03
68 1 0.00
69 1 0.00
70 2 0.00
71 1 0.00
73 37 0.06
75 35 0.05
76 2 0.00
78 2 0.00
79 1 0.00
80 9 0.01
81 286 0.44
82 174 0.27
83 79 0.12
84 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (81 bp):
CTTTTTCGGGTAGACATATCAATTTGGAAGACGTCTCTGCTCCACTATTCATTCAGGGGAAATAA
GACTTGATTTGTGCCT
Found at i:12457497 original size:165 final size:164
Alignment explanation
Indices: 12457253--12457594 Score: 443
Period size: 165 Copynumber: 2.1 Consensus size: 164
12457243 TGCTTTTCTC
* * * *
12457253 TCAGGGGAGATCACACTTAATTTGTGCCTATTTTTCGGGTAGATAAATCAATGTTGGAAGACGTG
1 TCAGGGGAAATCAAACTTAATTTGTGACTATTTTTCGGGTAGACAAATCAATGTTGGAAGACGTG
* * *
12457318 TCTGCTCCACCATTCATTCAGGGGAAATTAGACTTGATTTGGGCCTCTTTTTTCAGGTAGACAAA
66 TCTGCTCCACCATTCATTCAGGGGAAATCAGACTTGATCTAGGCCTC-TTTTTCAGGTAGACAAA
* * * *
12457383 TCAATGTTGGAAGACGTGCCTGTTCCACCATTCAT
130 TAAATATTAGAAGACGTGCCTGCTCCACCATTCAT
* * *
12457418 TCAGGGGAAATCAAACTTGATTTGTGACTCATTTTT-GGGTAGGCAAATCAATTTTGGAAGACGT
1 TCAGGGGAAATCAAACTTAATTTGTGACT-ATTTTTCGGGTAGACAAATCAATGTTGGAAGACGT
* * * * * *
12457482 TTTTGTTCTACCATTCATTCAGGGGAAATCAGACTTGATCTATGCCTCTTTTTCGGGTAGACAAA
65 GTCTGCTCCACCATTCATTCAGGGGAAATCAGACTTGATCTAGGCCTCTTTTTCAGGTAGACAAA
* ** *
12457547 TAAATATTAGAATACGTGTTTGCTCCGCCATTCAT
130 TAAATATTAGAAGACGTGCCTGCTCCACCATTCAT
12457582 TCAGGGGAAATCA
1 TCAGGGGAAATCA
12457595 TATGTGCCTC
Statistics
Matches: 152, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
164 56 0.37
165 90 0.59
166 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (164 bp):
TCAGGGGAAATCAAACTTAATTTGTGACTATTTTTCGGGTAGACAAATCAATGTTGGAAGACGTG
TCTGCTCCACCATTCATTCAGGGGAAATCAGACTTGATCTAGGCCTCTTTTTCAGGTAGACAAAT
AAATATTAGAAGACGTGCCTGCTCCACCATTCAT
Found at i:12458021 original size:243 final size:239
Alignment explanation
Indices: 12457277--12458067 Score: 752
Period size: 243 Copynumber: 3.3 Consensus size: 239
12457267 ACTTAATTTG
* * * * *
12457277 TGCCTATTTTTCGGGTAGATAAATCAA-TGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGG
1 TGCCTCTTTTTCGGGTAGACAAATCAACTATTAGAAGACGTCTCTGCTCCACCATTCATTCA-GG
* * * * * * * * *
12457341 GAAATTAGACTTGATTTGGGCCTCTTTTTTCAGGTAGACAAATCAATGTTGGAAGACGTGCCTGT
65 GAGATAAGAC-TCATATGTGCCTC-TTCTTCGGGTAGACATATCAATTTTGGAAGACGT-CCTG-
* ** * * *
12457406 TCCACCATTCATTCAGGGGAAATCAA-ACTTGATTTGTGACTCATTTTTGGGTAGGCAAATCAAT
126 TCCA--ATTCATTCA-AGGAGGT-AAGACTTGATTTGTGACTCTTTTTTGGGTAGACAAATCAAC
* * * * * *
12457470 TTTGGAAGACGTTTTTGTTCTACCATTCATTCAGGGGAAATCAGACTT-GATCTA
187 TTTGGAAGACGTCTCTGCTCTACTATTCATTCA-GGGAGATAAGA-TTCGATCTA
* * * * *
12457524 TGCCTCTTTTTCGGGTAGACAAAT-AAATATTAGAATACGTGTTTGCTCCGCCATTCATTCAGGG
1 TGCCTCTTTTTCGGGTAGACAAATCAACTATTAGAAGACGTCTCTGCTCCACCATTCATTCAGGG
* *
12457588 -G--AA-A-TCATATGTGCCTCTTCTTCGAGTAGACATATCAATTTTGGAATACG--C-GTCC-A
66 AGATAAGACTCATATGTGCCTCTTCTTCGGGTAGACATATCAATTTTGGAAGACGTCCTGTCCAA
* * * * *
12457644 TTCATTC-AGG-GGAAATAGACTTGATTTTTGCCTCTTTTTTGAGTAGACAGATCAACTTTGGAA
131 TTCATTCAAGGAGG-TA-AGACTTGATTTGTGACTCTTTTTTGGGTAGACAAATCAACTTTGGAA
* * * *
12457707 GACGTCTCTACTCCACTATTCATTCAGGGAGATAAGACTCGATCTG
194 GACGTCTCTGCTCTACTATTCATTCAGGGAGATAAGATTCGATCTA
* * * * * * * *
12457753 TTCCTCTTCTTCGGGTAGACATATCAACT-TTGGAAGTCTTCTCTACTCCACTATTCATTCAGGG
1 TGCCTCTTTTTCGGGTAGACAAATCAACTATTAGAAGACGTCTCTGCTCCACCATTCATTCAGGG
* *
12457817 AGATAAGACTCAATATGTACCTCTTCTTCGGGTAGACATATCTATTTTGGAAGACGTCTCTGCTC
66 AGATAAGACTC-ATATGTGCCTCTTCTTCGGGTAGACATATCAATTTTGGAAGACGTC-CTG-TC
* *
12457882 CATTATTCATTCAAGGAGGTAAGACTCGATTTGTGACTCTTTTTTGGGTAGACATATCAACTTTG
128 CA--ATTCATTCAAGGAGGTAAGACTTGATTTGTGACTCTTTTTTGGGTAGACAAATCAACTTTG
* *
12457947 GAAGAAGTCTCTGCTCTACTATTCATTCAGGGAGATAAGATTCGATTTA
191 GAAGACGTCTCTGCTCTACTATTCATTCAGGGAGATAAGATTCGATCTA
* * ** *
12457996 TGCCTCTTTTTCGGGTAGACATATCAACT-TTAGAAAACGTCTCTGCTCCATTATTCATTCATGG
1 TGCCTCTTTTTCGGGTAGACAAATCAACTATTAGAAGACGTCTCTGCTCCACCATTCATTCAGGG
12458060 AGATAAGA
66 AGATAAGA
12458068 GTTGAGATTG
Statistics
Matches: 445, Mismatches: 77, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
228 2 0.00
229 64 0.14
230 62 0.14
231 8 0.02
232 2 0.00
233 1 0.00
234 5 0.01
235 41 0.09
236 1 0.00
238 1 0.00
239 28 0.06
240 13 0.03
242 1 0.00
243 154 0.35
244 4 0.01
245 2 0.00
246 5 0.01
247 51 0.11
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (239 bp):
TGCCTCTTTTTCGGGTAGACAAATCAACTATTAGAAGACGTCTCTGCTCCACCATTCATTCAGGG
AGATAAGACTCATATGTGCCTCTTCTTCGGGTAGACATATCAATTTTGGAAGACGTCCTGTCCAA
TTCATTCAAGGAGGTAAGACTTGATTTGTGACTCTTTTTTGGGTAGACAAATCAACTTTGGAAGA
CGTCTCTGCTCTACTATTCATTCAGGGAGATAAGATTCGATCTA
Found at i:12458123 original size:36 final size:37
Alignment explanation
Indices: 12458072--12458159 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 37
12458062 ATAAGAGTTG
12458072 AGATTGATTTGCTTCACTACTCTTCCGTGAAGAC-TA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGACTTA
* * * *
12458108 AGATTGATTTACTTCAGTACTCTTTCGTGAAGTCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGACTTA
12458145 AGATTGATTTGCTTC
1 AGATTGATTTGCTTC
12458160 GAATATCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 30 0.65
37 16 0.35
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (37 bp):
AGATTGATTTGCTTCACTACTCTTCCGTGAAGACTTA
Found at i:12473440 original size:22 final size:22
Alignment explanation
Indices: 12473415--12473463 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
12473405 GGTTCTACGC
12473415 GGTCCTTCAGGAAT-ATCTATGT
1 GGTCCTTC-GGAATAATCTATGT
* *
12473437 GGTCATTCGGGATAATCTATGT
1 GGTCCTTCGGAATAATCTATGT
12473459 GGTCC
1 GGTCC
12473464 ATAGAGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (22 bp):
GGTCCTTCGGAATAATCTATGT
Found at i:12474525 original size:29 final size:29
Alignment explanation
Indices: 12474462--12474636 Score: 93
Period size: 29 Copynumber: 6.1 Consensus size: 29
12474452 TTGACCGGAA
*
12474462 GATATTTTAGTAATTATTTTGAAAATGGT
1 GATATTTTAGTAATTATTTTAAAAATGGT
* *
12474491 GATATTTTGGTAATTATTTTAAAAA-GTTT
1 GATATTTTAGTAATTATTTTAAAAATG-GT
* * * *
12474520 GCTATTTTCGTAATTTTTTTAATAAAAAAAAGGT
1 GATATTTTAGTAA-TTATTT--T--AAAAATGGT
*
12474554 GATAATTT-GT--TT-TTTT---AA-G-T
1 GATATTTTAGTAATTATTTTAAAAATGGT
*
12474574 GATATTTTAGTAATTATTTTAAAAAGGGT
1 GATATTTTAGTAATTATTTTAAAAATGGT
* * *
12474603 GATATGTTCGTAAATATTTGTTAAAAA-GGT
1 GATATTTTAGTAATTA-TT-TTAAAAATGGT
12474633 GATA
1 GATA
12474637 ATTGTGTAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 35
0.71 0.08 0.21
Matches are distributed among these distances:
20 8 0.07
21 3 0.03
22 2 0.02
23 2 0.02
24 4 0.03
27 3 0.03
28 2 0.02
29 52 0.45
30 16 0.14
31 7 0.06
32 1 0.01
33 2 0.02
34 12 0.10
35 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (29 bp):
GATATTTTAGTAATTATTTTAAAAATGGT
Found at i:12474685 original size:10 final size:12
Alignment explanation
Indices: 12474661--12474692 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
12474651 TTGAGACCAT
12474661 CTTTGACCAGAA
1 CTTTGACCAGAA
12474673 CTTTGACC-G-A
1 CTTTGACCAGAA
12474683 CTTTGACCAG
1 CTTTGACCAG
12474693 CCATTAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (12 bp):
CTTTGACCAGAA
Found at i:12480642 original size:29 final size:29
Alignment explanation
Indices: 12480608--12480676 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
12480598 CCGTTGACCG
12480608 GGTGATATTTT-AGTAATTATTTTGAAAAT
1 GGTGATATTTTGA-TAATTATTTTGAAAAT
12480637 GGTGATATTTTGATAATTATTTTGAAAAT
1 GGTGATATTTTGATAATTATTTTGAAAAT
*
12480666 GGTGTTATTTT
1 GGTGATATTTT
12480677 CTTTCGTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (29 bp):
GGTGATATTTTGATAATTATTTTGAAAAT
Found at i:12480725 original size:29 final size:29
Alignment explanation
Indices: 12480693--12480795 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
12480683 TAATTTTAAA
*
12480693 AAAAAAATGATAATTTCATAAATTTTTTT
1 AAAAAAGTGATAATTTCATAAATTTTTTT
* *
12480722 AAAAAAGTGAT-ATTTTAGT-AATTATTTTG
1 AAAAAAGTGATAATTTCA-TAAATT-TTTTT
** * *
12480751 AAAAGGGTGATATTTTCATAAATATTTCTT
1 AAAAAAGTGATAATTTCATAAAT-TTTTTT
*
12480781 AAAAAGGTGATAATT
1 AAAAAAGTGATAATT
12480796 GTGTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.16
29 25 0.43
30 23 0.40
31 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.42
Consensus pattern (29 bp):
AAAAAAGTGATAATTTCATAAATTTTTTT
Found at i:12482405 original size:19 final size:19
Alignment explanation
Indices: 12482381--12482419 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12482371 TCATTGTTTT
*
12482381 ATATTGTTCATAATGCCTC
1 ATATTGCTCATAATGCCTC
12482400 ATATTGCTCATAATGCCTC
1 ATATTGCTCATAATGCCTC
12482419 A
1 A
12482420 CTAAGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
ATATTGCTCATAATGCCTC
Found at i:12488156 original size:22 final size:23
Alignment explanation
Indices: 12488124--12488183 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
12488114 AGTCGAGGGT
*
12488124 TCTACGCGGTCCTTCGGGACA-A
1 TCTACGTGGTCCTTCGGGACATA
* * *
12488146 TCTATGTGGTCCTTCGGGATATT
1 TCTACGTGGTCCTTCGGGACATA
12488169 TCTACGTGGTCCTTC
1 TCTACGTGGTCCTTC
12488184 AGGATAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.35
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACATA
Found at i:12488177 original size:23 final size:22
Alignment explanation
Indices: 12488123--12488189 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
12488113 GAGTCGAGGG
* *
12488123 TTCTACGCGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGATA
* *
12488145 ATCTATGTGGTCCTTCGGGATA
1 TTCTACGTGGTCCTTCGGGATA
*
12488167 TTTCTACGTGGTCCTTCAGGATA
1 -TTCTACGTGGTCCTTCGGGATA
12488190 AATTCTACAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.34
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGGATA
Found at i:12490128 original size:3 final size:3
Alignment explanation
Indices: 12490120--12490196 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
12490110 TGATCTCATT
12490120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12490168 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12490197 TTACCCTAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12494753 original size:27 final size:27
Alignment explanation
Indices: 12494723--12494774 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
12494713 AAAATACAAG
12494723 TTTTCAAA-GTTCTGAATTTTTTTAATA
1 TTTTCAAATGTTCTG-ATTTTTTTAATA
* *
12494750 TTTTCAAATTTTTTGATTTTTTTAA
1 TTTTCAAATGTTCTGATTTTTTTAA
12494775 AAAAGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (27 bp):
TTTTCAAATGTTCTGATTTTTTTAATA
Found at i:12495672 original size:18 final size:16
Alignment explanation
Indices: 12495640--12495670 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12495630 AATATTGAAA
12495640 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
12495656 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
12495671 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:12497484 original size:40 final size:40
Alignment explanation
Indices: 12497408--12497486 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
12497398 TTGACAATTT
*
12497408 ATCTTTTTAATTTAGATATAAGATCATCAATTGATGATTC
1 ATCTTTTTAATTTAAATATAAGATCATCAATTGATGATTC
12497448 ATCTTCTTTAATTTAAATATAAGATCA-C-ATTAGATGATT
1 ATCTT-TTTAATTTAAATATAAGATCATCAATT-GATGATT
12497487 ATGCTACAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 3 0.08
40 13 0.36
41 20 0.56
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (40 bp):
ATCTTTTTAATTTAAATATAAGATCATCAATTGATGATTC
Found at i:12497842 original size:44 final size:45
Alignment explanation
Indices: 12497757--12497873 Score: 202
Period size: 44 Copynumber: 2.6 Consensus size: 45
12497747 AGAGGACAAG
12497757 AATAAC-TCTGGAGGAACAACATTTGACTCCAGAGCTGCAACATCA
1 AATAACTTC-GGAGGAACAACATTTGACTCCAGAGCTGCAACATCA
12497802 AATAACTTCGGAGGAACAACA-TTGACTCCAGAGCTGCAACATCA
1 AATAACTTCGGAGGAACAACATTTGACTCCAGAGCTGCAACATCA
*
12497846 AATAACTTCAGAGGAACAACATTTGACT
1 AATAACTTCGGAGGAACAACATTTGACT
12497874 TTGGAGGTAC
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
44 43 0.62
45 24 0.35
46 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (45 bp):
AATAACTTCGGAGGAACAACATTTGACTCCAGAGCTGCAACATCA
Found at i:12497857 original size:24 final size:24
Alignment explanation
Indices: 12497786--12497858 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
12497776 CATTTGACTC
12497786 CAGAGCTGCAACATCAAATAACTT
1 CAGAGCTGCAACATCAAATAACTT
* * * * *
12497810 CGGAG--G-AACAAC-ATTGACTC
1 CAGAGCTGCAACATCAAATAACTT
12497830 CAGAGCTGCAACATCAAATAACTT
1 CAGAGCTGCAACATCAAATAACTT
12497854 CAGAG
1 CAGAG
12497859 GAACAACATT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 9 0.26
21 5 0.14
22 2 0.06
23 5 0.14
24 14 0.40
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (24 bp):
CAGAGCTGCAACATCAAATAACTT
Found at i:12497865 original size:24 final size:24
Alignment explanation
Indices: 12497794--12497867 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
12497784 TCCAGAGCTG
*
12497794 CAACATCAAATAACTTCGGAGGAA
1 CAACATCAAATAACTTCAGAGGAA
* * ***
12497818 CAACAT----TGACTCCAGAGCTG
1 CAACATCAAATAACTTCAGAGGAA
12497838 CAACATCAAATAACTTCAGAGGAA
1 CAACATCAAATAACTTCAGAGGAA
12497862 CAACAT
1 CAACAT
12497868 TTGACTTTGG
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
20 14 0.40
24 21 0.60
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (24 bp):
CAACATCAAATAACTTCAGAGGAA
Found at i:12499688 original size:18 final size:18
Alignment explanation
Indices: 12499665--12499706 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12499655 TAGGTTGGAT
12499665 CGGGTCGAGTCAAAAAGA
1 CGGGTCGAGTCAAAAAGA
* *
12499683 CGGGTCGGGTCAAACAGA
1 CGGGTCGAGTCAAAAAGA
*
12499701 TGGGTC
1 CGGGTC
12499707 AGGTTAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.38, T:0.14
Consensus pattern (18 bp):
CGGGTCGAGTCAAAAAGA
Found at i:12503086 original size:24 final size:21
Alignment explanation
Indices: 12503024--12503088 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
12503014 ATATACGTTT
* *
12503024 TATGATCAGT-AA-AGTACGG
1 TATGAACAGTGAACAGTACCG
*
12503043 TATGAACAGTGAACAATACCG
1 TATGAACAGTGAACAGTACCG
12503064 TATGAACAGTGGTGAACAGTACCG
1 TATGAACA---GTGAACAGTACCG
12503088 T
1 T
12503089 GAACAATGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.24
20 2 0.05
21 13 0.35
24 13 0.35
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (21 bp):
TATGAACAGTGAACAGTACCG
Found at i:12503226 original size:21 final size:21
Alignment explanation
Indices: 12503202--12503242 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12503192 AATTTTAAAA
12503202 CATTCATCAT-TATACATTTAC
1 CATTCA-CATATATACATTTAC
*
12503223 CATTTACATATATACATTTA
1 CATTCACATATATACATTTA
12503243 AAACATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (21 bp):
CATTCACATATATACATTTAC
Found at i:12503913 original size:18 final size:18
Alignment explanation
Indices: 12503886--12503920 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12503876 CCGCGTAGAA
*
12503886 ATGTCTCGAATGACCACT
1 ATGTCCCGAATGACCACT
12503904 ATGTCCCGAATGACCAC
1 ATGTCCCGAATGACCAC
12503921 ATATCACATT
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:0.31, G:0.17, T:0.23
Consensus pattern (18 bp):
ATGTCCCGAATGACCACT
Found at i:12504708 original size:24 final size:24
Alignment explanation
Indices: 12504655--12504708 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12504645 CATTTTAGGA
* *
12504655 GTCACTTCTTACCATAGTAACTCT
1 GTCACTTCTTACCATAATAACTAT
*
12504679 GCCACTTCTTACCATAATAACTAT
1 GTCACTTCTTACCATAATAACTAT
12504703 GTCACT
1 GTCACT
12504709 GGCTCATCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (24 bp):
GTCACTTCTTACCATAATAACTAT
Found at i:12507286 original size:31 final size:30
Alignment explanation
Indices: 12507197--12507286 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 30
12507187 AACACATGCC
* *
12507197 ACATGTTCCAAGTGATGATAT-ATCATGTGT
1 ACATGTTCAAAGTGATGATATGA-CATATGT
* *
12507227 A-ATGTGTCCAAATTGATGATGTGACATATGTT
1 ACATGT-T-CAAAGTGATGATATGACATATG-T
*
12507259 ACATGTTCAAAGTGACGATATGACATAT
1 ACATGTTCAAAGTGATGATATGACATAT
12507287 ATTGTGCATA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 4 0.08
30 2 0.04
31 34 0.71
32 4 0.08
33 4 0.08
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (30 bp):
ACATGTTCAAAGTGATGATATGACATATGT
Found at i:12521480 original size:31 final size:33
Alignment explanation
Indices: 12521444--12521510 Score: 111
Period size: 31 Copynumber: 2.1 Consensus size: 33
12521434 TATATATTTC
12521444 ATACAGTAAGGCCTATTCCA-TCGGGA-TATAT
1 ATACAGTAAGGCCTATTCCATTCGGGATTATAT
*
12521475 ATACAGTAAGGCCTATTCCATTGGGGATTATAT
1 ATACAGTAAGGCCTATTCCATTCGGGATTATAT
12521508 ATA
1 ATA
12521511 AAGCATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 20 0.61
32 5 0.15
33 8 0.24
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (33 bp):
ATACAGTAAGGCCTATTCCATTCGGGATTATAT
Found at i:12524067 original size:18 final size:19
Alignment explanation
Indices: 12524043--12524102 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
12524033 TGATTTTTAG
12524043 ATTTTTAATTTAATATAAT
1 ATTTTTAATTTAATATAAT
*
12524062 -TTTTTATTTTAATATATAT
1 ATTTTTAATTTAATATA-AT
*
12524081 ATTTATTAATATAATAATAAT
1 ATTT-TTAATTTAAT-ATAAT
12524102 A
1 A
12524103 AAATTATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.44
19 2 0.06
20 3 0.09
21 11 0.32
22 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTAATTTAATATAAT
Found at i:12527098 original size:13 final size:13
Alignment explanation
Indices: 12527018--12527091 Score: 121
Period size: 13 Copynumber: 5.7 Consensus size: 13
12527008 TGCGTCATGA
*
12527018 ATTTATGACGTGC
1 ATTTATGACGCGC
* *
12527031 ATTTATGACACGT
1 ATTTATGACGCGC
12527044 ATTTATGACGCGC
1 ATTTATGACGCGC
12527057 ATTTATGACGCGC
1 ATTTATGACGCGC
12527070 ATTTATGACGCGC
1 ATTTATGACGCGC
12527083 ATTTATGAC
1 ATTTATGAC
12527092 ACTCATTGCG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:12527179 original size:13 final size:13
Alignment explanation
Indices: 12527161--12527205 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
12527151 ATAAATTTAG
12527161 CGCATTTATGACA
1 CGCATTTATGACA
* *
12527174 CGCATTTATAACG
1 CGCATTTATGACA
12527187 CGCATTTATGACA
1 CGCATTTATGACA
*
12527200 CTCATT
1 CGCATT
12527206 GCTCGTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (13 bp):
CGCATTTATGACA
Done.