Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 149 of 226
Found at i:48989387 original size:40 final size:41
Alignment explanation
Indices: 48989301--48989388 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
48989291 TTTTTAATAA
* * * * *
48989301 ATAATAAAATTATTAAAAATTGTTAGAAATTTTTAAATATTG
1 ATAA-AAAATTATTAAAAATTATTAGAAATTATAAAAGATCG
48989343 -TAAAAAATTATTAAAAATTATTAGAAATTATAAAAGA-CG
1 ATAAAAAATTATTAAAAATTATTAGAAATTATAAAAGATCG
48989382 ATAAAAA
1 ATAAAAA
48989389 TTAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 36 0.90
41 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (41 bp):
ATAAAAAATTATTAAAAATTATTAGAAATTATAAAAGATCG
Found at i:48993112 original size:54 final size:54
Alignment explanation
Indices: 48993030--48993137 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
48993020 ACTCCCCTAG
*
48993030 GTACGGCCCTATTAACAAAGCCGTCAACAAATGATATTGTTCTCATGTTAGGGT
1 GTACGGCCCTATTAACAAAGCCCTCAACAAATGATATTGTTCTCATGTTAGGGT
*
48993084 GTACGGCCCTATTAACAAAGCCCTCAACAAATGGTATTGTTCTCATGTTAGGGT
1 GTACGGCCCTATTAACAAAGCCCTCAACAAATGATATTGTTCTCATGTTAGGGT
48993138 TTTGTCTCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (54 bp):
GTACGGCCCTATTAACAAAGCCCTCAACAAATGATATTGTTCTCATGTTAGGGT
Found at i:48997354 original size:32 final size:32
Alignment explanation
Indices: 48997305--48997380 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
48997295 TAACAAGTTC
* *
48997305 AATTAATCAAT-ATAAGTTATCAAATTAAATT
1 AATTAATTAATAATAAGTTATCAAATTAAAGT
*
48997336 AATTAATTAATAATAAGTTATTAAATTAAAGT
1 AATTAATTAATAATAAGTTATCAAATTAAAGT
* *
48997368 AATGAATTTATAA
1 AATTAATTAATAA
48997381 GTTTATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (32 bp):
AATTAATTAATAATAAGTTATCAAATTAAAGT
Found at i:49003180 original size:17 final size:17
Alignment explanation
Indices: 49003158--49003190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49003148 TATTGGGTAG
*
49003158 GTTTTGTTTTGTTTTGT
1 GTTTTGTCTTGTTTTGT
49003175 GTTTTGTCTTGTTTTG
1 GTTTTGTCTTGTTTTG
49003191 ATTTTGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.24, T:0.73
Consensus pattern (17 bp):
GTTTTGTCTTGTTTTGT
Found at i:49003726 original size:44 final size:45
Alignment explanation
Indices: 49003678--49003861 Score: 193
Period size: 44 Copynumber: 4.2 Consensus size: 45
49003668 GACCTACAGT
* * *
49003678 AACTTCAGAGG-TATAGGATTCA-TCGTTTTAATCCGCTCCACTGC
1 AACTTCAGAGGAGATAGGATT-AGTAGCTTTAATCCGCTCCACTGC
*
49003722 AACTTCA-AGGAGATAGGATTAGTAGCTTTAATCTGCTCCACTGC
1 AACTTCAGAGGAGATAGGATTAGTAGCTTTAATCCGCTCCACTGC
* * * *
49003766 AACTTCAG-GGAGATAAGATTGGTATCTTTAA-CCTGCTCCACTGT
1 AACTTCAGAGGAGATAGGATTAGTAGCTTTAATCC-GCTCCACTGC
* * *
49003810 AACTTCAG-GGAGATAGGATTAGTATCTTCAA-CCTGCCCCACTGC
1 AACTTCAGAGGAGATAGGATTAGTAGCTTTAATCC-GCTCCACTGC
49003854 AACTTCAG
1 AACTTCAG
49003862 GGGGATAAAG
Statistics
Matches: 122, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
43 5 0.04
44 117 0.96
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
AACTTCAGAGGAGATAGGATTAGTAGCTTTAATCCGCTCCACTGC
Found at i:49003862 original size:44 final size:44
Alignment explanation
Indices: 49003704--49004050 Score: 312
Period size: 44 Copynumber: 7.9 Consensus size: 44
49003694 GATTCATCGT
* * *
49003704 TTTAATCC-GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGC
1 TTTAA-CCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTATC
* *
49003748 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTATC
* *
49003792 TTTAACCTGCTCCACTGTAACTTCAGGGAGATAGGATTAGTATC
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTATC
* * * *
49003836 TTCAACCTGCCCCACTGCAACTTCAGGGGGATAA-AGTTTGCTATC
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAG-TATC
* ** * *
49003881 TTCAGTCTGCTCCACTACAACTTTAGGGAGATAAGACTT-GTATC
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTATC
* * * * * *
49003925 TTTAACCTACCCCACTGCAACTTTAGGGGGCTAA-AGTTTGTTAT-
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAG-TATC
* * * *
49003969 TTTAACCTGCTCTACTACAACTTCAGAGAGATAAGGTT--TATGGC
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAT--C
** *
49004013 TTTAATTTGCTCCACTGCAAGTTCAGGGAGATAAGATT
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATT
49004051 TGTAGCCCAT
Statistics
Matches: 246, Mismatches: 47, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.01
43 5 0.02
44 199 0.81
45 36 0.15
46 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTATC
Found at i:49003991 original size:133 final size:133
Alignment explanation
Indices: 49003753--49004050 Score: 316
Period size: 133 Copynumber: 2.2 Consensus size: 133
49003743 GTAGCTTTAA
* * * *
49003753 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTTAACCTGCTCCACTGTAACTTCAG
1 TCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTTAACCTACCCCACTGCAACTTCAG
* *
49003818 GGAGATAGGATTAGTATCTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAAGTTTGCTATCTT
66 GGAGATAAGATTAGTATCTTCAACCTGCCCCACTACAACTTCAGGGGGATAAAGTTTGCTATCTT
49003883 CAG
131 CAG
* *
49003886 TCTGCTCCACTACAACTTTAGGGAGATAAGACTT-GTATCTTTAACCTACCCCACTGCAACTTTA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGA-TTGGTATCTTTAACCTACCCCACTGCAACTTCA
* * * * * * * * * * **
49003950 GGGGGCTAA-AGTTTGTTAT-TTTAACCTGCTCTACTACAACTTCAGAGAGATAAGGTTT-ATGG
65 GGGAGATAAGA-TTAG-TATCTTCAACCTGCCCCACTACAACTTCAGGGGGATAAAGTTTGCTAT
* *
49004012 CTTTAA
128 CTTCAG
* * *
49004018 TTTGCTCCACTGCAAGTTCAGGGAGATAAGATT
1 TCTGCTCCACTACAACTTCAGGGAGATAAGATT
49004051 TGTAGCCCAT
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
131 2 0.01
132 33 0.24
133 96 0.71
134 5 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (133 bp):
TCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTTAACCTACCCCACTGCAACTTCAG
GGAGATAAGATTAGTATCTTCAACCTGCCCCACTACAACTTCAGGGGGATAAAGTTTGCTATCTT
CAG
Found at i:49004030 original size:177 final size:177
Alignment explanation
Indices: 49003712--49004046 Score: 388
Period size: 177 Copynumber: 1.9 Consensus size: 177
49003702 GTTTTAATCC
* * * * *
49003712 GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTACAACTTCAAGGAGATAAGATTAGTAGCTTTAACCTACCCCACTGCAACTTCAGGGA
** * *
49003777 GATAAGATTGGTATCTTTAACCTGCTCCACTGTAACTTCAGGGAGATAGGATTAGTATCTTCAAC
66 GATAAGATTGGTATCTTTAACCTGCTCCACTACAACTTCAGAGAGATAGGATTAGTAGCTTCAAC
*
49003842 CTGCCCCACTGCAACTTCAGGGGGATAAAGTTTGCTATCTTCAGTCT
131 CTGCCCCACTGCAACTTCAGGGAGATAAAGTTTGCTATCTTCAGTCT
* * * *
49003889 GCTCCACTACAACTTTAGGGAGATAAGACTT-GTATCTTTAACCTACCCCACTGCAACTTTAGGG
1 GCTCCACTACAACTTCAAGGAGATAAGA-TTAGTAGCTTTAACCTACCCCACTGCAACTTCAGGG
* * * * * * * *
49003953 GGCTAAAGTTTGTTAT-TTTAACCTGCTCTACTACAACTTCAGAGAGATAAGGTTTA-TGGCTTT
65 AGAT-AAGATTGGTATCTTTAACCTGCTCCACTACAACTTCAGAGAGAT-AGGATTAGTAGCTTC
** * *
49004016 AATTTGCTCCACTGCAAGTTCAGGGAGATAA
128 AACCTGCCCCACTGCAACTTCAGGGAGATAA
49004047 GATTTGTAGC
Statistics
Matches: 129, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
177 112 0.87
178 17 0.13
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (177 bp):
GCTCCACTACAACTTCAAGGAGATAAGATTAGTAGCTTTAACCTACCCCACTGCAACTTCAGGGA
GATAAGATTGGTATCTTTAACCTGCTCCACTACAACTTCAGAGAGATAGGATTAGTAGCTTCAAC
CTGCCCCACTGCAACTTCAGGGAGATAAAGTTTGCTATCTTCAGTCT
Found at i:49004196 original size:45 final size:45
Alignment explanation
Indices: 49004059--49004459 Score: 361
Period size: 45 Copynumber: 9.0 Consensus size: 45
49004049 TTTGTAGCCC
* * *
49004059 ATCTTCGATTTACTTCGCTGCCAATACAGGAAGACAAGACCTGTT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
* * * * *** * *
49004104 ATCTTCGACCTACTCCACCGCTGCT-CAGGGAGACAAGATCTACT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
* *
49004148 ATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATC-GATT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG-CT
* * * *
49004193 ATCTTGGACCTACTTCGCTGCCAATACAAGAAGACAAGATCTACT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
* *
49004238 ATCTTCGACCTACTCTACTACTG-C--T-CAAGG-AGACAAGATCTGCT
1 ATCTTCGATCTACT-T-C-GCTGCCAATAC-AGGAAGACAAGATCTGCT
* * * * *
49004282 ATATTTGATCGACTTCACTGCCAATACAGGAAGACAAGATCTGTT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
* * *
49004327 ATCTTC-AGTCTACTTCGTTGTCAATACAAGAAGACAAGA-CTTGCT
1 ATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCT
* * * *
49004372 ATCTTTGATCTGCTTCACTGCCAATCCAGGAAGACAAGATCTGCT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
* * *
49004417 ATCTTCTATCTACTTCGTTGCGAATACAGGAAGACAAGATCTG
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
49004460 TTGCTTTCAG
Statistics
Matches: 280, Mismatches: 60, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
41 4 0.01
42 2 0.01
43 1 0.00
44 62 0.22
45 203 0.73
46 3 0.01
47 2 0.01
48 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
Found at i:49004306 original size:134 final size:132
Alignment explanation
Indices: 49004069--49004461 Score: 445
Period size: 134 Copynumber: 2.9 Consensus size: 132
49004059 ATCTTCGATT
* * * * *
49004069 TACTTCGCTGCCAATACAGGAAGACAAGACCTGTTATCTTCGACCTACTCCACCGCTGCTCAGGG
1 TACTTCGCTGCCAATACAAGAAGACAAGA-CTGCTATCTTCGACCTACTCTA-CACTGCTCAAGG
* * *
49004134 AGACAAGATCTACTATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATC-GATTATCTT
64 AGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG-TTATCTT
*
49004198 -GGACC
128 CAG-CC
*
49004203 TACTTCGCTGCCAATACAAGAAGACAAGATCTACTATCTTCGACCTACTCTACTACTGCTCAAGG
1 TACTTCGCTGCCAATACAAGAAGACAAGA-CTGCTATCTTCGACCTACTCTAC-ACTGCTCAAGG
* * *
49004268 AGACAAGATCTGCTATATTTGATCGACTTCACTGCCAATACAGGAAGACAAGATCTGTTATCTTC
64 AGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTC
*
49004333 AGTC
129 AGCC
* * * * * *
49004337 TACTTCGTTGTCAATACAAGAAGACAAGACTTGCTATCTTTGATCTGCT-T-CACTGCCAATCCA
1 TACTTCGCTGCCAATACAAGAAGACAAGAC-TGCTATCTTCGACCTACTCTACACTG-C--TCAA
* *
49004400 GGAAGACAAGATCTGCTATCTTCT-ATCTACTTCGTTGCGAATACAGGAAGACAAGATCTGTT
62 GG-AGACAAGATCTGCTATCTT-TGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTT
49004462 GCTTTCAGCA
Statistics
Matches: 223, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
131 4 0.02
132 2 0.01
133 3 0.01
134 159 0.71
135 54 0.24
136 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (132 bp):
TACTTCGCTGCCAATACAAGAAGACAAGACTGCTATCTTCGACCTACTCTACACTGCTCAAGGAG
ACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAG
CC
Found at i:49004690 original size:44 final size:44
Alignment explanation
Indices: 49004583--49004848 Score: 257
Period size: 44 Copynumber: 6.0 Consensus size: 44
49004573 GTGTATTCGA
* * *
49004583 TCTGCTTCGCTGTCAGTACAGGAAGGTAAGATCTACTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGCTATCTTCAG
** * * *
49004628 TCTGCTTTACTATCAGTACAGGAAGGCAAGGCTGGTGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGCTATCTTCAG
* * * ** *
49004671 ATCTACTTCACTGTCAGTACTGGAACACAAGACTTGCTATCTTCAG
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGC-TGCTATCTTCAG
*
49004717 TCTGCTTCGCTGTCAGTACAGGAA-GCAAGACCTGCTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGCTATCTTCAG
* * * * * *
49004761 TTTACTTCGCTGTCAGTATAGGAAGGCAAGGCTGGTGTCTTCAA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGCTATCTTCAG
* * *
49004805 TCTGCTTCGCTATCAATACAGGAAGGCAAGATCTGCTATCTTCA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGCTATCTTCA
49004849 CTGATCTGTT
Statistics
Matches: 178, Mismatches: 37, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
43 1 0.01
44 105 0.59
45 71 0.40
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (44 bp):
TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGCTATCTTCAG
Found at i:49004835 original size:133 final size:134
Alignment explanation
Indices: 49004583--49004848 Score: 356
Period size: 133 Copynumber: 2.0 Consensus size: 134
49004573 GTGTATTCGA
* * * *
49004583 TCTGCTTCGCTGTCAGTACAGGAAGGTAAGATCTACTATCTTCAGTCTGCTTTACTATCAGTACA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGACCTACTATCTTCAGTCTACTTCACTATCAGTACA
* * * *
49004648 GGAAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGTCAGTACTGGAACACAAGA-CTTGCTATC
66 GGAAGGCAAGGCTGGTGTCTTCAATCTACTTCACTATCAATACAGGAACACAAGATC-TGCTATC
49004712 TTCAG
130 TTCAG
* * * * *
49004717 TCTGCTTCGCTGTCAGTACAGGAA-GCAAGACCTGCTATCTTCAGTTTACTTCGCTGTCAGTATA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGACCTACTATCTTCAGTCTACTTCACTATCAGTACA
* * **
49004781 GGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTATCAATACAGGAAGGCAAGATCTGCTATCT
66 GGAAGGCAAGGCTGGTGTCTTCAATCTACTTCACTATCAATACAGGAACACAAGATCTGCTATCT
49004846 TCA
131 TCA
49004849 CTGATCTGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
133 89 0.78
134 25 0.22
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (134 bp):
TCTGCTTCGCTGTCAGTACAGGAAGGCAAGACCTACTATCTTCAGTCTACTTCACTATCAGTACA
GGAAGGCAAGGCTGGTGTCTTCAATCTACTTCACTATCAATACAGGAACACAAGATCTGCTATCT
TCAG
Found at i:49004841 original size:89 final size:90
Alignment explanation
Indices: 49004581--49004848 Score: 294
Period size: 89 Copynumber: 3.0 Consensus size: 90
49004571 TGGTGTATTC
* * * * **
49004581 GATCTGCTTCGCTGTCAGTACAGGAAGGTAAGATCTACTATCTTCAGTCTGCTTTACTATCAGTA
1 GATCTACTTCGCTGTCAGTATAGGAAGGCAAGA-CTGCTATCTTCAGTCTGCTTCGCTATCAGTA
* * *
49004646 CAGGAAGGCAAG-GCTGGTGTCTTC-
65 CAGGAAGGCAAGACCTGCTATCTTCA
* ** *
49004670 GATCTACTTCACTGTCAGTACT-GGAACACAAGACTTGCTATCTTCAGTCTGCTTCGCTGTCAGT
1 GATCTACTTCGCTGTCAGTA-TAGGAAGGCAAGAC-TGCTATCTTCAGTCTGCTTCGCTATCAGT
49004734 ACAGGAA-GCAAGACCTGCTATCTTCA
64 ACAGGAAGGCAAGACCTGCTATCTTCA
* * * * * *
49004760 G-TTTACTTCGCTGTCAGTATAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTATCAATAC
1 GATCTACTTCGCTGTCAGTATAGGAAGGCAAGACTGCTATCTTCAGTCTGCTTCGCTATCAGTAC
*
49004824 AGGAAGGCAAGATCTGCTATCTTCA
66 AGGAAGGCAAGACCTGCTATCTTCA
49004849 CTGATCTGTT
Statistics
Matches: 149, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
88 38 0.26
89 110 0.74
90 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (90 bp):
GATCTACTTCGCTGTCAGTATAGGAAGGCAAGACTGCTATCTTCAGTCTGCTTCGCTATCAGTAC
AGGAAGGCAAGACCTGCTATCTTCA
Found at i:49010739 original size:74 final size:72
Alignment explanation
Indices: 49010598--49010740 Score: 196
Period size: 74 Copynumber: 2.0 Consensus size: 72
49010588 TTGGGTTTAG
* * *
49010598 AAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTTTCAAATCCCGAGATCGTTTAAAACT
1 AAAAAGGATCATGCCCAGTAAGTTAGCAAACGATCTTTTTTCAAATCCCGAGATCGTTTAAAACT
49010663 TGAGAGA
66 TGAGAGA
* * * * *
49010670 AAAAAGGATCATGCCCAGTAAGTTAGCAAATGATCTCTTTTTTTAATTCCTGAGATCGTTTAGAA
1 AAAAAGGATCATGCCCAGTAAGTTAGCAAACGA--TCTTTTTTCAAATCCCGAGATCGTTTAAAA
49010735 CTTGAG
64 CTTGAG
49010741 TTTGAAAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 29 0.48
74 32 0.52
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (72 bp):
AAAAAGGATCATGCCCAGTAAGTTAGCAAACGATCTTTTTTCAAATCCCGAGATCGTTTAAAACT
TGAGAGA
Found at i:49011283 original size:2 final size:2
Alignment explanation
Indices: 49011276--49011300 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49011266 GCATGAATAC
49011276 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
49011301 AATAGGTTAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49012101 original size:20 final size:20
Alignment explanation
Indices: 49012064--49012101 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49012054 AAAAACTCAA
*
49012064 AAATAAAGTAAAATAAAAGT
1 AAATAAAGTAAAAGAAAAGT
49012084 AAAT-AAGTATAAAGAAAA
1 AAATAAAGTA-AAAGAAAA
49012102 AAAAAACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (20 bp):
AAATAAAGTAAAAGAAAAGT
Found at i:49012533 original size:17 final size:17
Alignment explanation
Indices: 49012511--49012544 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49012501 GTATTGGGTA
*
49012511 GGTTTTGTTTTGTTTTG
1 GGTTTTGTCTTGTTTTG
49012528 GGTTTTGTCTTGTTTTG
1 GGTTTTGTCTTGTTTTG
49012545 ATTTCGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.29, T:0.68
Consensus pattern (17 bp):
GGTTTTGTCTTGTTTTG
Found at i:49019382 original size:3 final size:3
Alignment explanation
Indices: 49019364--49019420 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
49019354 GTTATTTTTG
* * * *
49019364 TAT TAT GAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
49019413 TAT TAT TA
1 TAT TAT TA
49019421 GTTTTATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:49019796 original size:15 final size:12
Alignment explanation
Indices: 49019762--49019824 Score: 67
Period size: 12 Copynumber: 5.1 Consensus size: 12
49019752 TTATATTCTT
49019762 TATATTTTATAA
1 TATATTTTATAA
49019774 TATATTTTATACA
1 TATATTTTATA-A
49019787 TAGGTATTTTAT-A
1 TA--TATTTTATAA
*
49019800 TATA-TATATATA
1 TATATTTTATA-A
49019812 TATATTTTATAA
1 TATATTTTATAA
49019824 T
1 T
49019825 TCACATATGC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 4 0.09
11 2 0.05
12 18 0.42
13 11 0.26
15 8 0.19
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTTTATAA
Found at i:49023917 original size:10 final size:10
Alignment explanation
Indices: 49023902--49023971 Score: 65
Period size: 10 Copynumber: 7.3 Consensus size: 10
49023892 AATAAATAAT
49023902 AAAATTATTA
1 AAAATTATTA
*
49023912 AAAATTGTTA
1 AAAATTATTA
* *
49023922 GAAATTTTTA
1 AAAATTATTA
* *
49023932 AATATT-GTA
1 AAAATTATTA
49023941 AAAATTA-TA
1 AAAATTATTA
49023950 AAAATTATTA
1 AAAATTATTA
*
49023960 GAAATTA-TA
1 AAAATTATTA
49023969 AAA
1 AAA
49023972 GACGATAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 20 0.41
10 29 0.59
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (10 bp):
AAAATTATTA
Found at i:49023964 original size:19 final size:18
Alignment explanation
Indices: 49023903--49023971 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
49023893 ATAAATAATA
49023903 AAATTATTAAAAATTGTTAG
1 AAATTA-TAAAAATT-TTAG
* * * *
49023923 AAATTTTTAAATATTGTAA
1 AAA-TTATAAAAATTTTAG
49023942 AAATTATAAAAATTATTAG
1 AAATTATAAAAATT-TTAG
49023961 AAATTATAAAA
1 AAATTATAAAA
49023972 GACGATAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 9 0.23
19 18 0.46
20 10 0.26
21 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
AAATTATAAAAATTTTAG
Found at i:49023981 original size:38 final size:38
Alignment explanation
Indices: 49023902--49023990 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
49023892 AATAAATAAT
* * * * *
49023902 AAAATTATTAAAAATTGTTAGAAATTTTTAAATATTGTA
1 AAAATTA-TAAAAATTATTAGAAATTATAAAAGATCGTA
49023941 AAAATTATAAAAATTATTAGAAATTATAAAAGA-CGATA
1 AAAATTATAAAAATTATTAGAAATTATAAAAGATCG-TA
49023979 AAAATT-TAAAAA
1 AAAATTATAAAAA
49023991 AAAGTTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
37 7 0.16
38 30 0.68
39 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (38 bp):
AAAATTATAAAAATTATTAGAAATTATAAAAGATCGTA
Found at i:49023983 original size:19 final size:19
Alignment explanation
Indices: 49023939--49023990 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
49023929 TTAAATATTG
**
49023939 TAAAAATTATAAAAATTAT
1 TAAAAATTATAAAAACGAT
*
49023958 TAGAAATTATAAAAGACGA-
1 TAAAAATTATAAAA-ACGAT
49023977 TAAAAATT-TAAAAA
1 TAAAAATTATAAAAA
49023991 AAAGTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 5 0.18
19 20 0.71
20 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (19 bp):
TAAAAATTATAAAAACGAT
Found at i:49030516 original size:60 final size:60
Alignment explanation
Indices: 49030446--49030564 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
49030436 CATTCAAAAA
49030446 GATGTGGTGCTCTTGAATGCAATTGATTGTGATTGAAAATTGAAGTGAAGTTGATGGAAT
1 GATGTGGTGCTCTTGAATGCAATTGATTGTGATTGAAAATTGAAGTGAAGTTGATGGAAT
49030506 GATGTGGTGCTCTTGAATGCAATTGATTGTGATTGAAAATTGAAGTGAAGTTGATGGAA
1 GATGTGGTGCTCTTGAATGCAATTGATTGTGATTGAAAATTGAAGTGAAGTTGATGGAA
49030565 AATAAGTTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.34
Consensus pattern (60 bp):
GATGTGGTGCTCTTGAATGCAATTGATTGTGATTGAAAATTGAAGTGAAGTTGATGGAAT
Found at i:49032967 original size:2 final size:2
Alignment explanation
Indices: 49032960--49033007 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
49032950 TACTAAATTA
* *
49032960 AT AT AT AT CT AC AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49033001 AT AT AT A
1 AT AT AT A
49033008 CGCATACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49036126 original size:32 final size:32
Alignment explanation
Indices: 49036089--49036151 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
49036079 TAACCAATAT
*
49036089 AAGTTATCAAATTAAACTAATTAATTAATAAC
1 AAGTTATCAAATTAAACTAATGAATTAATAAC
* * * *
49036121 AAGTTATTAAATTCAAGTAATGAATTTATAA
1 AAGTTATCAAATTAAACTAATGAATTAATAA
49036152 GTTTATAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (32 bp):
AAGTTATCAAATTAAACTAATGAATTAATAAC
Found at i:49039986 original size:13 final size:13
Alignment explanation
Indices: 49039968--49039997 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49039958 ACATTTTGTA
49039968 AATCAATAATTTG
1 AATCAATAATTTG
49039981 AATCAATAATTTG
1 AATCAATAATTTG
49039994 AATC
1 AATC
49039998 TTATATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (13 bp):
AATCAATAATTTG
Found at i:49042567 original size:3 final size:3
Alignment explanation
Indices: 49042559--49042594 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
49042549 AATAATTTGA
49042559 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
49042595 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:49042919 original size:15 final size:14
Alignment explanation
Indices: 49042895--49042928 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
49042885 TACCTACGTA
*
49042895 TATATGTACATATTT
1 TATATATACATA-TT
49042910 TATATATACATATT
1 TATATATACATATT
49042924 TATAT
1 TATAT
49042929 GTTCTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATATACATATT
Found at i:49049631 original size:21 final size:21
Alignment explanation
Indices: 49049607--49049647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49049597 CAAATTTTAA
*
49049607 AAATTATTTAAAAAA-TCATAT
1 AAATTA-TAAAAAAATTCATAT
49049628 AAATTATAAAAAAATTCATA
1 AAATTATAAAAAAATTCATA
49049648 AAAAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTATAAAAAAATTCATAT
Found at i:49050169 original size:18 final size:17
Alignment explanation
Indices: 49050129--49050172 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
49050119 TTAAAATTTT
* *
49050129 GTTTATAATTTTTTTAT
1 GTTTTTAATTTTTTTAA
49050146 GATTTTTAATATTTTTTAA
1 G-TTTTTAAT-TTTTTTAA
49050165 GTTTTTAA
1 GTTTTTAA
49050173 AAGGGATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (17 bp):
GTTTTTAATTTTTTTAA
Found at i:49055258 original size:29 final size:30
Alignment explanation
Indices: 49055198--49055328 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
49055188 TTTTGAAATT
* * ***
49055198 TTTTTTAAATTTACATTTTAACCCTTGTAC
1 TTTTCTAAATTTACATTTTGACCCTCAAAC
49055228 TTTT-TGAAATTTACATTTTGACCC-CAAAC
1 TTTTCT-AAATTTACATTTTGACCCTCAAAC
*
49055257 TTTTCTAAAATTTACATTTTGACCC-CAAAA
1 TTTTCT-AAATTTACATTTTGACCCTCAAAC
** *
49055287 TTTTCTAAAACTACATTTTGACCCTTAAAC
1 TTTTCTAAATTTACATTTTGACCCTCAAAC
*
49055317 TTTCTCAAAATT
1 TTT-TCTAAATT
49055329 GCACTTTAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
29 23 0.27
30 56 0.67
31 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTTCTAAATTTACATTTTGACCCTCAAAC
Found at i:49055268 original size:30 final size:30
Alignment explanation
Indices: 49055226--49055328 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
49055216 TAACCCTTGT
*
49055226 ACTTTT-TGAAATTTACATTTTGACCCCAA
1 ACTTTTCTAAAATTTACATTTTGACCCCAA
49055255 ACTTTTCTAAAATTTACATTTTGACCCCAA
1 ACTTTTCTAAAATTTACATTTTGACCCCAA
* * *
49055285 AATTTTCTAAAA-CTACATTTTGACCCTTAA
1 ACTTTTCTAAAATTTACATTTTGACCC-CAA
49055315 AC-TTTCTCAAAATT
1 ACTTTTCT-AAAATT
49055329 GCACTTTAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 24 0.38
30 40 0.62
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (30 bp):
ACTTTTCTAAAATTTACATTTTGACCCCAA
Found at i:49055767 original size:7 final size:7
Alignment explanation
Indices: 49055757--49055781 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49055747 ACACAACACA
49055757 CAACAAG
1 CAACAAG
49055764 CAACAAG
1 CAACAAG
49055771 CAACAAG
1 CAACAAG
49055778 CAAC
1 CAAC
49055782 CAAAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.32, G:0.12, T:0.00
Consensus pattern (7 bp):
CAACAAG
Found at i:49055965 original size:20 final size:19
Alignment explanation
Indices: 49055942--49055987 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
49055932 AAATAGAAGA
*
49055942 GAAAGAAAAGAGAGGAAAGG
1 GAAAGAAAAGAGA-AAAAGG
*
49055962 GAAAGAGAAGAGAAAAAGG
1 GAAAGAAAAGAGAAAAAGG
*
49055981 AAAAGAA
1 GAAAGAA
49055988 GAGGAGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAGAGAAAAAGG
Found at i:49056144 original size:11 final size:11
Alignment explanation
Indices: 49056113--49056169 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
49056103 AGAAGAAAGG
49056113 AGAAAGAAAAA
1 AGAAAGAAAAA
49056124 AG--AG-AAAA
1 AGAAAGAAAAA
49056132 AGAAAGAAAAA
1 AGAAAGAAAAA
49056143 AGAAA-ATAAAA
1 AGAAAGA-AAAA
* *
49056154 AAACAATAAAAA
1 AGA-AAGAAAAA
49056166 AGAA
1 AGAA
49056170 TAAAAGCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
8 6 0.16
9 2 0.05
10 3 0.08
11 18 0.47
12 8 0.21
13 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.04
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:49056144 original size:26 final size:26
Alignment explanation
Indices: 49056074--49056148 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 26
49056064 GCTGGGGCTC
*
49056074 AAAAGAAAGAAAAAGTAAAGGGAAGACGA
1 AAAAGAAAGAAAAAG-AAA--AAAGACGA
* *
49056103 AGAAGAAAGGAGAAAGAAAAAAGA-GA
1 AAAAGAAA-GAAAAAGAAAAAAGACGA
49056129 AAAAGAAAGAAAAAAGAAAA
1 AAAAGAAAG-AAAAAGAAAA
49056149 TAAAAAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 1 0.03
26 18 0.46
27 4 0.10
29 10 0.26
30 6 0.15
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (26 bp):
AAAAGAAAGAAAAAGAAAAAAGACGA
Found at i:49056371 original size:19 final size:18
Alignment explanation
Indices: 49056342--49056377 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49056332 GGCTTTGGTA
49056342 ATTTTTTTAATCTATTTT
1 ATTTTTTTAATCTATTTT
*
49056360 ATTTTATTTAATGTATTT
1 ATTTT-TTTAATCTATTT
49056378 AAATGGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTTTTAATCTATTTT
Found at i:49056624 original size:21 final size:21
Alignment explanation
Indices: 49056599--49056643 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
49056589 AAAAATATTC
49056599 AAAAA-TCTTCGTATTTTAAAA
1 AAAAATTC-TCGTATTTTAAAA
*
49056620 AAAAATTCTCGTATTTTAATA
1 AAAAATTCTCGTATTTTAAAA
49056641 AAA
1 AAA
49056644 TCCCGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAAATTCTCGTATTTTAAAA
Found at i:49056976 original size:35 final size:33
Alignment explanation
Indices: 49056885--49057052 Score: 110
Period size: 35 Copynumber: 4.7 Consensus size: 33
49056875 AAAATTCGTA
*
49056885 TTTCAAAAATTGTCATGTTTTCAA-AATTGTCGTGT
1 TTTCAAAAATTCTC--GTTTTCAATAATT-TCGTGT
49056920 TTT-AAAAATTCTAGCGTTTTCAATAATTTCCGTGT
1 TTTCAAAAATTCT--CGTTTTCAATAATTT-CGTGT
* *
49056955 TTTCAAAAATTCTCGTATTTCAAAAACTTTCTTGT
1 TTTCAAAAATTCTCGT-TTTCAATAA-TTTCGTGT
49056990 TTTCAGAAAAAAAATTTCTCTGTTTT--ATAAATTTTCGTGT
1 TTTC-----AAAAA-TTCTC-GTTTTCAAT-AA-TTTCGTGT
*
49057030 TTTCAAAAATTCTAGTATTTCAA
1 TTTCAAAAATTCTCGT-TTTCAA
49057053 AATAAAATTT
Statistics
Matches: 108, Mismatches: 7, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
33 2 0.02
34 27 0.25
35 36 0.33
36 14 0.13
39 1 0.01
40 18 0.17
41 8 0.07
42 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (33 bp):
TTTCAAAAATTCTCGTTTTCAATAATTTCGTGT
Found at i:49056977 original size:17 final size:16
Alignment explanation
Indices: 49056880--49056999 Score: 64
Period size: 18 Copynumber: 6.8 Consensus size: 16
49056870 AAGAAAAAAT
*
49056880 TCGTATTTCAAAAATTG
1 TCGT-TTTCAAAAATTC
*
49056897 TCATGTTTTC-AAAATTG
1 TC--GTTTTCAAAAATTC
*
49056914 TCGTGTTTTAAAAATTC
1 TCGT-TTTCAAAAATTC
*
49056931 TAGCGTTTTCAATAATT-
1 T--CGTTTTCAAAAATTC
49056948 TCCGTGTTTTCAAAAATTC
1 T-C--GTTTTCAAAAATTC
49056967 TCGTATTTCAAAAACTTTC
1 TCGT-TTTCAAAAA--TTC
*
49056986 TTGTTTTCAGAAAA
1 TCGTTTTCA-AAAA
49057000 AAAATTTCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
15 2 0.02
16 6 0.07
17 28 0.34
18 31 0.37
19 16 0.19
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (16 bp):
TCGTTTTCAAAAATTC
Found at i:49057039 original size:18 final size:18
Alignment explanation
Indices: 49056885--49057440 Score: 225
Period size: 17 Copynumber: 30.5 Consensus size: 18
49056875 AAAATTCGTA
* *
49056885 TTTCAAAAATTGTCATGT
1 TTTCAAAAATTTTCGTGT
*
49056903 TTTC-AAAATTGTCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
49056920 TTT-AAAAATTCTAGCGT
1 TTTCAAAAATTTTCGTGT
* *
49056937 TTTCAATAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
* *
49056955 TTTCAAAAATTCTCGT-A
1 TTTCAAAAATTTTCGTGT
* *
49056972 TTTCAAAAACTTTCTTGT
1 TTTCAAAAATTTTCGTGT
49056990 TTTCAGAAAAAAAATTTCTC-TGT
1 TTTC-----AAAAATTT-TCGTGT
*
49057013 TTT-ATAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
49057030 TTTCAAAAATTCTAGT-A
1 TTTCAAAAATTTTCGTGT
*
49057047 TTTCAAAATAAAATTTT-ATGT
1 TTTC---A-AAAATTTTCGTGT
49057068 TTT-AAAAATTTTCTGTGTTTT
1 TTTCAAAAATTTTC-GTG---T
* *
49057089 TTTTAAAAATTTCCCGTGT
1 TTTCAAAAATTT-TCGTGT
** * *
49057108 TTTCAAAAATTCCCTTAT
1 TTTCAAAAATTTTCGTGT
* *
49057126 TTT-AAAAACTTTCTTGTT
1 TTTCAAAAATTTTCGTG-T
* * *
49057144 TTTCAGAAAAAAATTCCCTGT
1 TTTC---AAAAATTTTCGTGT
*
49057165 TTT-ATAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
49057182 TTTCAAAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
49057200 TTTTAAAATTTTTGGTGAT
1 TTTCAAAAATTTTCGTG-T
* ** * *
49057219 ATAAAAAAAATTTCCTGT
1 TTTCAAAAATTTTCGTGT
* *
49057237 TTTCAAAGAAAATTTCATG-
1 TTTC-AA-AAATTTTCGTGT
**
49057256 TTTCAAAAATCCTCGTG-
1 TTTCAAAAATTTTCGTGT
*
49057273 TTTCAAAAA-ATTC-TGT
1 TTTCAAAAATTTTCGTGT
* *
49057289 GTTTC-AAAATTTTTGCGT
1 -TTTCAAAAATTTTCGTGT
*
49057307 TCTCAAAAATTTCTCGT-T
1 TTTCAAAAATTT-TCGTGT
* *
49057325 TTTCAAAAATTGTCATG-
1 TTTCAAAAATTTTCGTGT
**
49057342 TTTCGCAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
49057360 TGT-AAAAATTTTCAG-GT
1 TTTCAAAAATTTTC-GTGT
*
49057377 TTTCAGAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
49057395 TTCTAAAAAATTCTCGTG-
1 TT-TCAAAAATTTTCGTGT
* *
49057413 TTTCACAAAAATTCCGTGT
1 TTTCA-AAAATTTTCGTGT
49057432 TTTCAAAAA
1 TTTCAAAAA
49057441 AAAATGGTGT
Statistics
Matches: 401, Mismatches: 91, Indels: 92
0.69 0.16 0.16
Matches are distributed among these distances:
15 2 0.00
16 16 0.04
17 137 0.34
18 132 0.33
19 47 0.12
20 12 0.03
21 18 0.04
22 21 0.05
23 14 0.03
24 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:49057095 original size:22 final size:22
Alignment explanation
Indices: 49057067--49057110 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49057057 AAATTTTATG
* *
49057067 TTTTAAAAATTTTCTGTGTTTT
1 TTTTAAAAATTTCCCGTGTTTT
49057089 TTTTAAAAATTTCCCGTGTTTT
1 TTTTAAAAATTTCCCGTGTTTT
49057111 CAAAAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTTAAAAATTTCCCGTGTTTT
Found at i:49057184 original size:17 final size:17
Alignment explanation
Indices: 49057162--49057211 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
49057152 AAAAATTCCC
49057162 TGTTTTATAAATTTTCG
1 TGTTTTATAAATTTTCG
* *
49057179 TGTTTTCAAAAATTCTCG
1 TGTTTT-ATAAATTTTCG
49057197 TGTTTT-TAAAATTTT
1 TGTTTTAT-AAATTTT
49057212 TGGTGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (17 bp):
TGTTTTATAAATTTTCG
Found at i:49057258 original size:92 final size:92
Alignment explanation
Indices: 49057129--49057303 Score: 212
Period size: 92 Copynumber: 1.9 Consensus size: 92
49057119 CCCTTATTTT
* * * * * **
49057129 AAAAACTTTCTTGTTTTTCAGAAAAAAATTCCCTGTTTTATAAATTTTCGTGTTTTC-AAAAATT
1 AAAAAATTTCCTGTTTTTCAGAAAAAAATTCCATGTTTCAAAAATCCTCGTG-TTTCAAAAAATT
*
49057193 CTCGTGTTTTTAAAATTTTTGGTGATATAA
65 CT-GTG-TTTCAAAATTTTTGGTGATATAA
* *
49057223 AAAAAATTTCCTG-TTTTCA-AAGAAAATTTCATGTTTCAAAAATCCTCGTGTTTCAAAAAATTC
1 AAAAAATTTCCTGTTTTTCAGAAAAAAATTCCATGTTTCAAAAATCCTCGTGTTTCAAAAAATTC
49057286 TGTGTTTCAAAATTTTTG
66 TGTGTTTCAAAATTTTTG
49057304 CGTTCTCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
90 13 0.19
91 7 0.10
92 33 0.47
93 6 0.09
94 11 0.16
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (92 bp):
AAAAAATTTCCTGTTTTTCAGAAAAAAATTCCATGTTTCAAAAATCCTCGTGTTTCAAAAAATTC
TGTGTTTCAAAATTTTTGGTGATATAA
Found at i:49057261 original size:19 final size:20
Alignment explanation
Indices: 49057225--49057262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49057215 TGATATAAAA
*
49057225 AAAATTTCCTGTTTTCAAAG
1 AAAATTTCATGTTTTCAAAG
49057245 AAAATTTCATG-TTTCAAA
1 AAAATTTCATGTTTTCAAA
49057263 AATCCTCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAATTTCATGTTTTCAAAG
Found at i:49057324 original size:17 final size:19
Alignment explanation
Indices: 49057294--49057335 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
49057284 TCTGTGTTTC
*
49057294 AAAATTTTTGCG-TTCTCA
1 AAAATTTCTGCGTTTCTCA
*
49057312 AAAATTTCT-CGTTTTTCA
1 AAAATTTCTGCGTTTCTCA
49057330 AAAATT
1 AAAATT
49057336 GTCATGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (19 bp):
AAAATTTCTGCGTTTCTCA
Found at i:49057344 original size:52 final size:52
Alignment explanation
Indices: 49057258--49057402 Score: 127
Period size: 52 Copynumber: 2.8 Consensus size: 52
49057248 ATTTCATGTT
* * * *
49057258 TCAAAAA-TCCTCGTGTTTCAAAAAATTCTGTGTTTC-AAAATTTTTGCGTTC
1 TCAAAAATTTCTCGTTTTTCAAAAATTTC-GTGTTTCGAAAATTTTCGCGTTC
* * * *
49057309 TCAAAAATTTCTCGTTTTTCAAAAATTGTCATGTTTCGCAAATTTTCGTGTTG
1 TCAAAAATTTCTCGTTTTTCAAAAATT-TCGTGTTTCGAAAATTTTCGCGTTC
* * *
49057362 T-AAAAATTT-TCAGGTTTTCAGAAATTTTCGTGTTTCTAAAA
1 TCAAAAATTTCTC-GTTTTTCA-AAAATTTCGTGTTTCGAAAA
49057403 AATTCTCGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
51 9 0.12
52 48 0.63
53 19 0.25
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (52 bp):
TCAAAAATTTCTCGTTTTTCAAAAATTTCGTGTTTCGAAAATTTTCGCGTTC
Found at i:49057441 original size:19 final size:19
Alignment explanation
Indices: 49057383--49057442 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
49057373 AGGTTTTCAG
* *
49057383 AAATTTTCGTGTTTCTAAA
1 AAATTCTCGTGTTTCAAAA
*
49057402 AAATTCTCGTGTTTCACAA
1 AAATTCTCGTGTTTCAAAA
49057421 AAATTC-CGTGTTTTCAAAA
1 AAATTCTCGTG-TTTCAAAA
49057440 AAA
1 AAA
49057443 AATGGTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.11
19 32 0.89
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
AAATTCTCGTGTTTCAAAA
Found at i:49069417 original size:75 final size:75
Alignment explanation
Indices: 49069295--49069847 Score: 602
Period size: 75 Copynumber: 7.3 Consensus size: 75
49069285 AATTAAATTC
* * *
49069295 TTTCAATTTCTATTTTTC-CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACG
1 TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACG
49069359 TC-GAGGTATT
66 TCTGAGGTA-T
*
49069369 TTTCAATTTTTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCA
1 TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT--CA
49069434 CG-CTGAGGTATT
64 CGTCTGAGGTA-T
* *
49069446 TTTCAATTTTTATTTTTTC-CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCAC
1 TTTCAATTTTT-GTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCAC
*
49069510 GAC-GAGGTATTTT
65 GTCTGAGGTA---T
* * *
49069523 TTTCAATTCTTGCTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTTTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
* *
49069588 CATCCTTAGGTAT
64 CGT-CTGAGGTAT
* * *
49069601 CTTCAATTTTTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTGCA-
1 TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT-CAC
49069665 -TCCTGAGGTAT
65 GT-CTGAGGTAT
* ** * *
49069676 TTTCAATTTCTGTTTTTCAAAAAATCAACTCATAACGTGAGAGGTGAGTTGAGCCTC-AGGTCAT
1 TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA-GTCAC
*
49069740 ATCCTGAGGTAT
65 GT-CTGAGGTAT
* * * * * * * * *
49069752 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATACTAGAAGTGAGCTGAGCTTCGGGTTAC
1 TTTCAATTTTTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCAC
49069817 G-CTGAGGTAT
65 GTCTGAGGTAT
* * *
49069827 TTTCAATATCTATTTTTCAAA
1 TTTCAATTTTTGTTTTTCAAA
49069848 GGTAAACTCA
Statistics
Matches: 422, Mismatches: 38, Indels: 38
0.85 0.08 0.08
Matches are distributed among these distances:
74 20 0.05
75 141 0.33
76 78 0.18
77 113 0.27
78 21 0.05
79 43 0.10
80 1 0.00
81 5 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (75 bp):
TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACG
TCTGAGGTAT
Found at i:49069920 original size:150 final size:152
Alignment explanation
Indices: 49069563--49069927 Score: 350
Period size: 151 Copynumber: 2.4 Consensus size: 152
49069553 CTCATATTGC
* * * * * * ** **
49069563 GAGAGGTGAGTTGAGCCTCGGGTCACATCCTTAGGTATCTTCAATTTTTGTTTTTC-AAAAAATC
1 GAGAAGTGAGTTGAACCTCAGGTCACATCCTAAGCTATTTTCAATTTCAGGCTTTCAAAAAAATC
* * * * *
49069627 AACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTGCATCCTGAGGTATTTTCAATTTCTGTTTT
66 AACTCATAATACGAGAAGTGAGCTGAGCCTCGGGTGCATCCTGAGGTATTTTCAATATCTATTTT
* *
49069692 TCAAAAAATCAACTCATAACGT
131 TCAAAAAATAAACTCACAACGT
* * * * * * **
49069714 GAGAGGTGAGTTGAGCCTCAGGTCATATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATC
1 GAGAAGTGAGTTGAACCTCAGGTCACATCCTAAGCTATTTTCAATTTCAGGCTTTCAAAAAAATC
* * *
49069779 AACTCATAATACTAGAAGTGAGCTGAGCTTCGGGT-TA-CGCTGAGGTATTTTCAATATCTATTT
66 AACTCATAATACGAGAAGTGAGCTGAGCCTCGGGTGCATC-CTGAGGTATTTTCAATATCTATTT
**
49069842 TTC-AAAGGTAAACTCACAATC-T
130 TTCAAAAAATAAACTCACAA-CGT
*
49069864 GAGAAGTGAGTTGAACTTC-GGATCGCACA-CC-AAGCTATTTTCAATTTCAGGCTTTCAAAAAA
1 GAGAAGTGAGTTGAACCTCAGG-T--CACATCCTAAGCTATTTTCAATTTCAGGCTTTCAAAAAA
49069926 AT
63 AT
49069928 ATAGACAAAA
Statistics
Matches: 182, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
149 2 0.01
150 59 0.32
151 80 0.44
152 41 0.23
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (152 bp):
GAGAAGTGAGTTGAACCTCAGGTCACATCCTAAGCTATTTTCAATTTCAGGCTTTCAAAAAAATC
AACTCATAATACGAGAAGTGAGCTGAGCCTCGGGTGCATCCTGAGGTATTTTCAATATCTATTTT
TCAAAAAATAAACTCACAACGT
Found at i:49070225 original size:30 final size:30
Alignment explanation
Indices: 49070191--49070335 Score: 136
Period size: 30 Copynumber: 4.8 Consensus size: 30
49070181 AAAAAAATTG
* ***
49070191 AAAATTTACATTTTAACTTCTGTACTTTT-T
1 AAAATTTACATTTTAAC-CCCAAACTTTTCT
* *
49070221 AAAATTTATAGTTTAACCCCAAACTTTTCT
1 AAAATTTACATTTTAACCCCAAACTTTTCT
*
49070251 AAAATTTACATTTTAACCCCAAAATTTTCT
1 AAAATTTACATTTTAACCCCAAACTTTTCT
* *
49070281 AAAA-TTACATTTTGACCCTTAAAC-TTTCT
1 AAAATTTACATTTTAACCC-CAAACTTTTCT
*
49070310 CAAAA-TTACACTTTAACCCCTAAACT
1 -AAAATTTACATTTTAACCCC-AAACT
49070336 CTCAGGAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
29 25 0.26
30 70 0.74
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAATTTACATTTTAACCCCAAACTTTTCT
Found at i:49070346 original size:30 final size:29
Alignment explanation
Indices: 49070232--49070349 Score: 98
Period size: 30 Copynumber: 4.0 Consensus size: 29
49070222 AAATTTATAG
* *
49070232 TTTAACCCC-AAACTTTTCTAAAATTTACAT
1 TTTAACCCCTAAACTTCTC-AAAA-TTACAC
* * *
49070262 TTTAACCCC-AAAATTTTCTAAAATTACAT
1 TTTAACCCCTAAACTTCTC-AAAATTACAC
* *
49070291 TTTGACCCTTAAACTTTCTCAAAATTACAC
1 TTTAACCCCTAAAC-TTCTCAAAATTACAC
49070321 TTTAACCCCTAAAC-TCTCAGGAAATTACA
1 TTTAACCCCTAAACTTCTCA--AAATTACA
49070350 TTTTGGCCCG
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.07
29 13 0.17
30 54 0.71
31 4 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTAACCCCTAAACTTCTCAAAATTACAC
Found at i:49071109 original size:10 final size:10
Alignment explanation
Indices: 49071053--49071134 Score: 65
Period size: 11 Copynumber: 7.4 Consensus size: 10
49071043 GCTGGGGCTC
49071053 AAAAGAAAGA
1 AAAAGAAAGA
49071063 AAAAGTAAAGGGA
1 AAAAG-AAA--GA
*
49071076 AGAAGAAGAAGA
1 AAAAG-A-AAGA
*
49071088 AAGGAGAAAGA
1 AA-AAGAAAGA
*
49071099 AAAAGAGAGA
1 AAAAGAAAGA
49071109 AAAAGAAAGAA
1 AAAAGAAAG-A
49071120 AAAAGAAAAGA
1 AAAAG-AAAGA
49071131 AAAA
1 AAAA
49071135 ACAATAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
10 19 0.33
11 20 0.34
12 8 0.14
13 9 0.16
14 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:49071112 original size:11 final size:11
Alignment explanation
Indices: 49071053--49071148 Score: 58
Period size: 10 Copynumber: 8.6 Consensus size: 11
49071043 GCTGGGGCTC
49071053 AAAAGAAAG-A
1 AAAAGAAAGAA
49071063 AAAAGTAAAGGGAA
1 AAAAG-AAA--GAA
49071077 GAAGAAG-AAGAA
1 -AA-AAGAAAGAA
**
49071089 AGGAGAAAG-A
1 AAAAGAAAGAA
*
49071099 AAAAGAGAG-A
1 AAAAGAAAGAA
49071109 AAAAGAAAGAA
1 AAAAGAAAGAA
49071120 AAAAGAAAAGAA
1 AAAAG-AAAGAA
* *
49071132 AAAA-CAATAA
1 AAAAGAAAGAA
49071142 AAAAGAA
1 AAAAGAA
49071149 TAAAAGCAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
10 31 0.46
11 14 0.21
12 13 0.19
13 1 0.01
14 3 0.04
15 2 0.03
16 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.02
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:49071114 original size:27 final size:26
Alignment explanation
Indices: 49071053--49071135 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
49071043 GCTGGGGCTC
49071053 AAAAGAAAG-AAAAAGTAAAGGGAAGAAGA
1 AAAAGAAAGAAAAAAG-AAA---AAGAAGA
* * *
49071082 AGAAGAAAGGAGAAAGAAAAAGAGAGA
1 AAAAGAAAGAAAAAAGAAAAAGA-AGA
49071109 AAAAGAAAGAAAAAAG-AAAAGAA-A
1 AAAAGAAAGAAAAAAGAAAAAGAAGA
49071133 AAA
1 AAA
49071136 CAATAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 4 0.09
25 1 0.02
26 10 0.21
27 16 0.34
29 11 0.23
30 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (26 bp):
AAAAGAAAGAAAAAAGAAAAAGAAGA
Found at i:49071622 original size:20 final size:21
Alignment explanation
Indices: 49071597--49071640 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
49071587 AAAAATATTC
49071597 AAAAATCCTCGTATTTTAA-A
1 AAAAATCCTCGTATTTTAATA
*
49071617 AAAAATTCTCGTATTTTAATA
1 AAAAATCCTCGTATTTTAATA
49071638 AAA
1 AAA
49071641 TCCCGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAATCCTCGTATTTTAATA
Found at i:49071919 original size:18 final size:18
Alignment explanation
Indices: 49071896--49072501 Score: 216
Period size: 17 Copynumber: 33.4 Consensus size: 18
49071886 AAAATTCGTA
* *
49071896 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTCTCGTGT
*
49071914 TTTC-AAAATTGTCGTGT
1 TTTCAAAAATTCTCGTGT
*
49071931 TTT-AAAAATTCTCGCGT
1 TTTCAAAAATTCTCGTGT
* * *
49071948 TTTCAATAATTCCCCTGT
1 TTTCAAAAATTCTCGTGT
*
49071966 TTTCAAAAATTCTCGT-A
1 TTTCAAAAATTCTCGTGT
*
49071983 TTTCAAAAACTT-TCTTGT
1 TTTCAAAAA-TTCTCGTGT
*
49072001 TTTCAAAAAAAAAAATTC-CCTGT
1 TTTC------AAAAATTCTCGTGT
* *
49072024 TGT-ATAAATT-TCCGTGT
1 TTTCAAAAATTCT-CGTGT
49072041 TTTCAAAAATTCT-G-GT
1 TTTCAAAAATTCTCGTGT
**
49072057 ATTTCAAAATAAAATT-TTATGT
1 -TTTC---A-AAAATTCTCGTGT
*
49072079 TTT-AAAAATTTTCTGTGTTTTTT
1 TTTCAAAAATTCTC-GTG-----T
* *
49072102 TTTAAAAAATTCCCGTGT
1 TTTCAAAAATTCTCGTGT
49072120 TTTCAAAAATTC-C-TGT
1 TTTCAAAAATTCTCGTGT
* *
49072136 ATTTTAAAAACTT-TCTTGTT
1 -TTTCAAAAA-TTCTCGTG-T
*
49072156 TTTCAGAAAAATT-TCCCTGT
1 TTTC--AAAAATTCT-CGTGT
* *
49072176 TTT-ATAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGT
49072193 TTTCAAAAATTC-CG-GT
1 TTTCAAAAATTCTCGTGT
49072209 ATTTCAAAAATTCTCGTGT
1 -TTTCAAAAATTCTCGTGT
* *
49072228 TTTCAAAATTTCTGGTGAT
1 TTTCAAAAATTCTCGTG-T
*** *
49072247 ATAAAAAAAAATT-TCCTGT
1 -T-TTCAAAAATTCTCGTGT
*
49072266 TTTCAAAGAAAATT-TCATG-
1 TTTC--A-AAAATTCTCGTGT
* *
49072285 TTTAAAAAATCCTCGTG-
1 TTTCAAAAATTCTCGTGT
49072302 TTTCAAAAATT-TCCGTG-
1 TTTCAAAAATTCT-CGTGT
* *
49072319 TTTC-AAAATTTTCGCGT
1 TTTCAAAAATTCTCGTGT
*
49072336 TCTCAAAAATTTCTCGT-T
1 TTTCAAAAA-TTCTCGTGT
* *
49072354 TTTCAAAAATTGTCATG-
1 TTTCAAAAATTCTCGTGT
** *
49072371 TTTCGCAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGT
* *
49072389 TGT-AAAAATTTTCAG-GT
1 TTTCAAAAATTCTC-GTGT
* *
49072406 TTTCAGAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGT
*
49072424 TTCTAAAAAATTCTCGTGT
1 TT-TCAAAAATTCTCGTGT
*
49072443 TTCACAAAAATTC-CGTGT
1 TT-TCAAAAATTCTCGTGT
** *
49072461 TTTCAAAAA-AATGGTG-
1 TTTCAAAAATTCTCGTGT
49072477 TTTC-AAAATTCTCGTGT
1 TTTCAAAAATTCTCGTGT
49072494 TTTCAAAA
1 TTTCAAAA
49072502 CAAGAGATTC
Statistics
Matches: 445, Mismatches: 78, Indels: 130
0.68 0.12 0.20
Matches are distributed among these distances:
15 4 0.01
16 42 0.09
17 159 0.36
18 120 0.27
19 43 0.10
20 24 0.05
21 23 0.05
22 2 0.00
23 15 0.03
24 13 0.03
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTCAAAAATTCTCGTGT
Found at i:49072119 original size:23 final size:23
Alignment explanation
Indices: 49072078--49072122 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49072068 AAATTTTATG
* * *
49072078 TTTTAAAAATTTTCTGTGTTTTT
1 TTTTAAAAAATTCCCGTGTTTTT
49072101 TTTTAAAAAATTCCCGTGTTTT
1 TTTTAAAAAATTCCCGTGTTTT
49072123 CAAAAATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTTAAAAAATTCCCGTGTTTTT
Found at i:49072144 original size:17 final size:18
Alignment explanation
Indices: 49072101--49072145 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
49072091 CTGTGTTTTT
*
49072101 TTTTAAAAAATTCCCGTG
1 TTTTAAAAAATTCCCGTA
* *
49072119 TTTTCAAAAATTCCTGTA
1 TTTTAAAAAATTCCCGTA
49072137 TTTTAAAAA
1 TTTTAAAAA
49072146 CTTTCTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAATTCCCGTA
Found at i:49072253 original size:35 final size:35
Alignment explanation
Indices: 49072106--49072254 Score: 97
Period size: 35 Copynumber: 4.1 Consensus size: 35
49072096 TTTTTTTTTA
* * * *
49072106 AAAAATTCCCGTGTTTTCAAAAATTCCTGTATTTT
1 AAAAATTCTCGTGTTTTCAAAAATTCCGGTATATC
* * *
49072141 AAAAACTT-TCTTGTTTTTCAGAAAAATTTCCCTGT-T-TT
1 AAAAA-TTCTCGTG-TTTTC--AAAAA-TT-CCGGTATATC
* * *
49072179 ATAAATTTTCGTGTTTTCAAAAATTCCGGTATTTC
1 AAAAATTCTCGTGTTTTCAAAAATTCCGGTATATC
* * *
49072214 AAAAATTCTCGTGTTTTCAAAATTTCTGGTGATATA
1 AAAAATTCTCGTGTTTTCAAAAATTCCGGT-ATATC
49072250 AAAAA
1 AAAAA
49072255 AAATTTCCTG
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
33 4 0.04
34 3 0.03
35 40 0.43
36 15 0.16
37 7 0.08
38 15 0.16
39 3 0.03
40 5 0.05
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (35 bp):
AAAAATTCTCGTGTTTTCAAAAATTCCGGTATATC
Found at i:49072360 original size:52 final size:51
Alignment explanation
Indices: 49072106--49072501 Score: 177
Period size: 52 Copynumber: 7.4 Consensus size: 51
49072096 TTTTTTTTTA
* * *
49072106 AAAAATTCCCGTGTTTTCAAAAATTCCT-GTATTTT-AAAAACTTTCTTGTTTTTC
1 AAAAATTCTCGTG-TTTCAAAAATTTCTCGT-TTTTCAAAAA-TTTC--GTGTTTC
* * * * *
49072160 AGAAAAATT-TCCCTGTTTTATAAATTT-TCGTGTTTTCAAAAATTCCGGTATTTC
1 --AAAAATTCT-CGTGTTTCAAAAATTTCTCGT-TTTTCAAAAATTTC-GTGTTTC
* *** *
49072214 AAAAATTCTCGTGTTTTC-AAAATTTCTGGTGATATAAAAAAAAATTTCCTGTTTTC
1 AAAAATTCTCGTG-TTTCAAAAATTTCTCGT--T-T-TTCAAAAATTTCGTG-TTTC
* * * *
49072270 AAAGAAAATT-TCATGTTT-AAAAAATCCTCGTGTTTCAAAAATTTCCGTGTTTC
1 --A-AAAATTCTCGTGTTTCAAAAATTTCTCGTTTTTCAAAAATTT-CGTGTTTC
* * *
49072323 -AAAATTTTCGCGTTCTCAAAAATTTCTCGTTTTTCAAAAATTGTCATGTTTC
1 AAAAATTCTCGTGTT-TCAAAAATTTCTCGTTTTTCAAAAATT-TCGTGTTTC
** * * *
49072375 GCAAATTTTCGTGTTGT-AAAAATTT-TCAGGTTTTCAGAAATTTTCGTGTTTC
1 AAAAATTCTCGTGTT-TCAAAAATTTCTC-GTTTTTCA-AAAATTTCGTGTTTC
* ** *
49072427 TAAAAAATTCTCGTGTTTCACAAAAATTC-CGTGTTTTCAAAAAAATGGTGTTTC
1 --AAAAATTCTCGTGTTTCA-AAAATTTCTCGT-TTTTCAAAAATTTCGTGTTTC
49072481 -AAAATTCTCGTGTTTTCAAAA
1 AAAAATTCTCGTG-TTTCAAAA
49072502 CAAGAGATTC
Statistics
Matches: 261, Mismatches: 50, Indels: 63
0.70 0.13 0.17
Matches are distributed among these distances:
49 6 0.02
50 5 0.02
51 18 0.07
52 73 0.28
53 39 0.15
54 37 0.14
55 33 0.13
56 27 0.10
57 12 0.05
58 5 0.02
59 6 0.02
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (51 bp):
AAAAATTCTCGTGTTTCAAAAATTTCTCGTTTTTCAAAAATTTCGTGTTTC
Found at i:49072381 original size:35 final size:35
Alignment explanation
Indices: 49072342--49072469 Score: 109
Period size: 35 Copynumber: 3.6 Consensus size: 35
49072332 GCGTTCTCAA
*
49072342 AAATTTCTCGT-TTTTCAAAAATTGTCATGTTTCGC
1 AAATTT-TCGTGTTTTCAAAAATTCTCATGTTTCGC
* * *
49072377 AAATTTTCGTGTTGT-AAAAATTTTCAGGTTTTCAG-
1 AAATTTTCGTGTTTTCAAAAATTCTCATG-TTTC-GC
* * *
49072412 AAATTTTCGTGTTTCTAAAAAATTCTCGTGTTTCAC
1 AAATTTTCGTGTTT-TCAAAAATTCTCATGTTTCGC
* *
49072448 AAAAATTCCGTGTTTTCAAAAA
1 -AAATTTTCGTGTTTTCAAAAA
49072470 AATGGTGTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
34 15 0.20
35 26 0.35
36 12 0.16
37 22 0.29
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (35 bp):
AAATTTTCGTGTTTTCAAAAATTCTCATGTTTCGC
Found at i:49072470 original size:19 final size:19
Alignment explanation
Indices: 49072412--49072472 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
49072402 AGGTTTTCAG
* *
49072412 AAATTTTCGTGTTTCTAAA
1 AAATTCTCGTGTTTCAAAA
*
49072431 AAATTCTCGTGTTTCACAA
1 AAATTCTCGTGTTTCAAAA
49072450 AAATTC-CGTGTTTTCAAAA
1 AAATTCTCGTG-TTTCAAAA
49072469 AAAT
1 AAAT
49072473 GGTGTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.11
19 33 0.89
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
AAATTCTCGTGTTTCAAAA
Found at i:49076262 original size:2 final size:2
Alignment explanation
Indices: 49076255--49076302 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
49076245 TTAATTTAAG
49076255 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
49076297 TA TA TA
1 TA TA TA
49076303 AGTGTGAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49091008 original size:72 final size:72
Alignment explanation
Indices: 49090853--49091025 Score: 177
Period size: 72 Copynumber: 2.4 Consensus size: 72
49090843 AGAGAATGCG
* * * * ** ** * *
49090853 CAACAAGTGCTGAATCTCAAGCCATCGGTAAAGAACAATTCGATGCTGCTCACACAAGCTTTAGA
1 CAACAAGTGTTGGATCTCAAGCCATTGATAATCAATGATTCGATGCTGCTCACACAAGCTTCAAA
49090918 GAATCTA
66 GAATCTA
* * * *
49090925 CATCAAGTGTTGGATCTTAAGCCATTGATAATCAATGATTCGATGTTGCTCACACTAGCTTCAAA
1 CAACAAGTGTTGGATCTCAAGCCATTGATAATCAATGATTCGATGCTGCTCACACAAGCTTCAAA
*
49090990 GAATCTG
66 GAATCTA
* *
49090997 TAACACA-TGTTGTATCTCAAGCCATTGAT
1 CAACA-AGTGTTGGATCTCAAGCCATTGAT
49091026 CATGATATCC
Statistics
Matches: 81, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
72 80 0.99
73 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (72 bp):
CAACAAGTGTTGGATCTCAAGCCATTGATAATCAATGATTCGATGCTGCTCACACAAGCTTCAAA
GAATCTA
Found at i:49093659 original size:21 final size:21
Alignment explanation
Indices: 49093619--49093659 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49093609 AAAATTTTTT
*
49093619 AAAATCATAAAGAATTATAAA
1 AAAATCATAAAGAATCATAAA
49093640 AAAATCATACAA-AATCATAA
1 AAAATCATA-AAGAATCATAA
49093660 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAATCATAAAGAATCATAAA
Found at i:49093672 original size:27 final size:26
Alignment explanation
Indices: 49093641--49093706 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
49093631 AATTATAAAA
*
49093641 AAATCATACAAAATCATAATATATAT
1 AAATCATAAAAAATCATAATATATAT
* *
49093667 ATAATCATATAAAACCATAATATATAT
1 A-AATCATAAAAAATCATAATATATAT
49093694 AAAT-ATAAAAAAT
1 AAATCATAAAAAAT
49093707 ATTAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.20
26 4 0.11
27 24 0.69
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATCATAAAAAATCATAATATATAT
Found at i:49095667 original size:24 final size:24
Alignment explanation
Indices: 49095610--49095674 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
49095600 TCATAATCAA
* * *
49095610 ATACAAATGCGGACACATATTTAG
1 ATACAGATGCAGACACAAATTTAG
*
49095634 TTACAGATGCAGACACAAATTTAG
1 ATACAGATGCAGACACAAATTTAG
* * *
49095658 ATATATATGCAAACACA
1 ATACAGATGCAGACACA
49095675 GATCTTGCCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (24 bp):
ATACAGATGCAGACACAAATTTAG
Found at i:49098236 original size:20 final size:20
Alignment explanation
Indices: 49098211--49098252 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
49098201 CTAAAAAACA
49098211 TTATTTCTAGGTTAACTTAT
1 TTATTTCTAGGTTAACTTAT
49098231 TTATTTCTAGGTTAACTTAT
1 TTATTTCTAGGTTAACTTAT
49098251 TT
1 TT
49098253 CTACAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (20 bp):
TTATTTCTAGGTTAACTTAT
Found at i:49115320 original size:21 final size:22
Alignment explanation
Indices: 49115296--49115362 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
49115286 TTCCCTTCTC
49115296 TTTTCTCTTCTCTTCTCTT-TT
1 TTTTCTCTTCTCTTCTCTTATT
* *
49115317 TTTTCTCCCTCTTTTCTCTTATT
1 TTTTCT-CTTCTCTTCTCTTATT
49115340 TTCTTCCTCTTTCTCTTCCTCTT
1 TT-TT-CTC-TTCTCTT-CTCTT
49115363 CCTCTTCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 4 0.11
24 3 0.08
25 7 0.19
26 5 0.14
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCTCTTCTCTTCTCTTATT
Found at i:49115329 original size:25 final size:25
Alignment explanation
Indices: 49115300--49115362 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 25
49115290 CTTCTCTTTT
*
49115300 CTCTTCTCTTCTCTTTTTTTTCTCC
1 CTCTTCTCTTCTCTTTATTTTCTCC
*
49115325 CTC-T-T-TTCTC-TTATTTTCTTC
1 CTCTTCTCTTCTCTTTATTTTCTCC
49115346 CTCTTTCTCTTCCTCTT
1 CTC-TTCTCTT-CTCTT
49115363 CCTCTTCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
21 12 0.40
22 5 0.17
23 2 0.07
24 2 0.07
25 5 0.17
26 3 0.10
27 1 0.03
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (25 bp):
CTCTTCTCTTCTCTTTATTTTCTCC
Found at i:49115336 original size:22 final size:21
Alignment explanation
Indices: 49115308--49115356 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
49115298 TTCTCTTCTC
*
49115308 TTCTCTTTTTTTTCTCCCTCT
1 TTCTCTTTATTTTCTCCCTCT
*
49115329 TT-TCTCTTATTTTCTTCCTCT
1 TTCTCT-TTATTTTCTCCCTCT
49115350 TTCTCTT
1 TTCTCTT
49115357 CCTCTTCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTCTTTATTTTCTCCCTCT
Found at i:49115369 original size:6 final size:6
Alignment explanation
Indices: 49115341--49115371 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
49115331 TCTCTTATTT
*
49115341 TCTTCC TCTTTC TCTTCC TCTTCC TCTTCC T
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
49115372 ACATTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTTCC
Found at i:49117960 original size:20 final size:19
Alignment explanation
Indices: 49117909--49117961 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
49117899 TAACAAAGGC
* **
49117909 AAGTATCGATACTTTTGTA
1 AAGTATCAATACTTTTAAA
**
49117928 AAGTATCCGTACTTTTAAA
1 AAGTATCAATACTTTTAAA
49117947 TAAGTATCAATACTT
1 -AAGTATCAATACTT
49117962 AAGTCCAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
AAGTATCAATACTTTTAAA
Found at i:49119733 original size:15 final size:15
Alignment explanation
Indices: 49119713--49119742 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49119703 AGAGATTGGA
49119713 TGCAGTTACTAATTC
1 TGCAGTTACTAATTC
49119728 TGCAGTTACTAATTC
1 TGCAGTTACTAATTC
49119743 ATGATCTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
TGCAGTTACTAATTC
Found at i:49126079 original size:2 final size:2
Alignment explanation
Indices: 49126072--49126106 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
49126062 AAATTGATCA
49126072 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
49126107 TTGTTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:49135769 original size:83 final size:82
Alignment explanation
Indices: 49135630--49135871 Score: 363
Period size: 83 Copynumber: 3.0 Consensus size: 82
49135620 AACATTAGGC
*
49135630 TATCTTTTGTAGTATTTCAGTATTTCAATTCATTAACTCTCTCTGATAAACATGATGTATGAACT
1 TATCTTTTGTAGTATTTCAGTATTTC-ATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
49135695 CATACTTCTCCATTTGCA
65 CATACTTCTCCATTTGCA
*
49135713 TATCTTTTGTAGTATTTCAGTATTTCTATTCATTAACTCTTTCTGATTAACATGATGTATGAACT
1 TATCTTTTGTAGTATTTCAGTATTTC-ATTCATTAACTCTTTCTGATAAACATGATGTATGAACT
49135778 CATACTTCTCCATTTGCA
65 CATACTTCTCCATTTGCA
* *
49135796 TATCTTTTGTAGTATTTC---A----ATTCATTAACTTTTTCTGATAAACATGCTGTATGAACTC
1 TATCTTTTGTAGTATTTCAGTATTTCATTCATTAACTCTTTCTGATAAACATGATGTATGAACTC
**
49135854 ATACTTCTTGATTTGCA
66 ATACTTCTCCATTTGCA
49135871 T
1 T
49135872 TCGAAGTATA
Statistics
Matches: 151, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
75 52 0.34
80 1 0.01
83 98 0.65
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (82 bp):
TATCTTTTGTAGTATTTCAGTATTTCATTCATTAACTCTTTCTGATAAACATGATGTATGAACTC
ATACTTCTCCATTTGCA
Found at i:49135854 original size:75 final size:75
Alignment explanation
Indices: 49135731--49135871 Score: 228
Period size: 75 Copynumber: 1.9 Consensus size: 75
49135721 GTAGTATTTC
* *
49135731 AGTATTTCTATTCATTAACTCTTTCTGATTAACATGATGTATGAACTCATACTTCTCCATTTGCA
1 AGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACTCATACTTCTCCATTTGCA
49135796 TATCTTTTGT
66 TATCTTTTGT
* * **
49135806 AGTATTTCAATTCATTAACTTTTTCTGATAAACATGCTGTATGAACTCATACTTCTTGATTTGCA
1 AGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACTCATACTTCTCCATTTGCA
49135871 T
66 T
49135872 TCGAAGTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (75 bp):
AGTATTTCAATTCATTAACTCTTTCTGATAAACATGATGTATGAACTCATACTTCTCCATTTGCA
TATCTTTTGT
Found at i:49146589 original size:11 final size:11
Alignment explanation
Indices: 49146570--49146613 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
49146560 AACACCTAAC
*
49146570 TTTTTGGGTAA
1 TTTTCGGGTAA
49146581 TTTTCGGGTAA
1 TTTTCGGGTAA
49146592 --TTCGGGTAA
1 TTTTCGGGTAA
49146601 TTTTCGGGTAA
1 TTTTCGGGTAA
49146612 TT
1 TT
49146614 CGGTTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:49146597 original size:9 final size:9
Alignment explanation
Indices: 49146583--49146657 Score: 107
Period size: 9 Copynumber: 8.2 Consensus size: 9
49146573 TTGGGTAATT
49146583 TTCGGGTAA
1 TTCGGGTAA
49146592 TTCGGGTAA
1 TTCGGGTAA
49146601 TTTTCGGGTAA
1 --TTCGGGTAA
*
49146612 TTCGGTTAA
1 TTCGGGTAA
*
49146621 TTCGGTTAA
1 TTCGGGTAA
49146630 -TCGGGTAA
1 TTCGGGTAA
49146638 TTCGGGTAA
1 TTCGGGTAA
49146647 TTCGGGTAA
1 TTCGGGTAA
49146656 TT
1 TT
49146658 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.11
9 45 0.74
11 9 0.15
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:49146600 original size:20 final size:20
Alignment explanation
Indices: 49146575--49146659 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
49146565 CTAACTTTTT
49146575 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
49146595 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* *
49146615 GGTTAA--TTCGGTTAA-TC
1 GGGTAATTTTCGGGTAATTC
49146632 GGGTAA--TTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
49146650 GGGTAATTTT
1 GGGTAATTTT
49146660 TAACCAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.26
18 16 0.28
20 27 0.47
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.40
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:49146640 original size:26 final size:26
Alignment explanation
Indices: 49146583--49146656 Score: 103
Period size: 26 Copynumber: 2.7 Consensus size: 26
49146573 TTGGGTAATT
49146583 TTCGGGTAATTCGGGTAATTTTCGGGTAA
1 TTCGGGTAATTCGGGTAA---TCGGGTAA
* *
49146612 TTCGGTTAATTCGGTTAATCGGGTAA
1 TTCGGGTAATTCGGGTAATCGGGTAA
49146638 TTCGGGTAATTCGGGTAAT
1 TTCGGGTAATTCGGGTAAT
49146657 TTTTAACCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 25 0.61
29 16 0.39
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (26 bp):
TTCGGGTAATTCGGGTAATCGGGTAA
Found at i:49147272 original size:19 final size:19
Alignment explanation
Indices: 49147248--49147284 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
49147238 TAACAATCAC
49147248 ATCCTCA-CTAACCCACCTT
1 ATCCTCATCTAA-CCACCTT
49147267 ATCCTCATCTAACCACCT
1 ATCCTCATCTAACCACCT
49147285 CAGAGTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (19 bp):
ATCCTCATCTAACCACCTT
Found at i:49157821 original size:3 final size:3
Alignment explanation
Indices: 49157774--49157807 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
49157764 CTGAGATTAA
49157774 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
49157808 GTGAGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49157840 original size:18 final size:18
Alignment explanation
Indices: 49157797--49157843 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
49157787 ATAATAATAA
*
49157797 TAATAATAATAGTGAGAT
1 TAATAATTATAGTGAGAT
49157815 TAATAATTATAGTGAGAT
1 TAATAATTATAGTGAGAT
49157833 TAATAATTATA
1 TAATAATTATA
49157844 ACGATGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (18 bp):
TAATAATTATAGTGAGAT
Found at i:49159443 original size:16 final size:16
Alignment explanation
Indices: 49159422--49159461 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
49159412 AAAAAAAAAT
* *
49159422 TTGATTGGTAGTTGAA
1 TTGATTAGTAATTGAA
49159438 TTGATTAGTAATTGAA
1 TTGATTAGTAATTGAA
49159454 TTGATTAG
1 TTGATTAG
49159462 GTTATTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (16 bp):
TTGATTAGTAATTGAA
Found at i:49159485 original size:17 final size:18
Alignment explanation
Indices: 49159433--49159485 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 18
49159423 TGATTGGTAG
49159433 TTGAATTGATTA-G-TAA
1 TTGAATTGATTAGGTTAA
49159449 TTGAATTGATTAGGTT-A
1 TTGAATTGATTAGGTTAA
* *
49159466 TTGATTTG-TTAGTTTAA
1 TTGAATTGATTAGGTTAA
49159483 TTG
1 TTG
49159486 GTTCGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 18 0.56
17 13 0.41
18 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (18 bp):
TTGAATTGATTAGGTTAA
Found at i:49160804 original size:27 final size:29
Alignment explanation
Indices: 49160774--49160829 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
49160764 GAGTCATCAA
* *
49160774 ATTAAATT-AATTAATGAATC-ATAAGTT
1 ATTAAATTAAAGTAATCAATCTATAAGTT
49160801 ATTAAATTAAAGTAATCAATCTATAAGTT
1 ATTAAATTAAAGTAATCAATCTATAAGTT
49160830 TATGATGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 10 0.40
29 7 0.28
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (29 bp):
ATTAAATTAAAGTAATCAATCTATAAGTT
Found at i:49160996 original size:16 final size:16
Alignment explanation
Indices: 49160954--49160996 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
49160944 AAAACTAAAC
*
49160954 ATTTTATTGAAATAAT
1 ATTTTATTTAAATAAT
*
49160970 ATTTTAATTAAGATAAT
1 ATTTTATTTAA-ATAAT
49160987 -TTTTATTTAA
1 ATTTTATTTAA
49160997 TAAATTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTATTTAAATAAT
Found at i:49162485 original size:11 final size:11
Alignment explanation
Indices: 49162469--49162533 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
49162459 AATATATATT
49162469 TATTATTAAAA
1 TATTATTAAAA
49162480 TATTATTATAAA
1 TATTATTA-AAA
*
49162492 T-TTTTTAATAA
1 TATTATTAA-AA
*
49162503 CATT-TTAAGAA
1 TATTATTAA-AA
49162514 TATTATTTAAAA
1 TATTA-TTAAAA
49162526 TTATTATT
1 -TATTATT
49162534 GTTGAAAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 1 0.02
11 24 0.55
12 10 0.23
13 9 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:49162603 original size:31 final size:31
Alignment explanation
Indices: 49162545--49162603 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
49162535 TTGAAAGTTA
* * *
49162545 TTATTAAAATAATTTTGTAATAGTAAATAAT
1 TTATTAAAATAATATTATAATAATAAATAAT
*
49162576 TTATTAAAATAATATTATATTAATAAAT
1 TTATTAAAATAATATTATAATAATAAAT
49162604 TAATAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TTATTAAAATAATATTATAATAATAAATAAT
Found at i:49166224 original size:231 final size:231
Alignment explanation
Indices: 49165803--49166238 Score: 800
Period size: 231 Copynumber: 1.9 Consensus size: 231
49165793 AAACAAAGCA
* *
49165803 CATTGATGTTCGGTACCATTTTGTTCGTGATATCATTGTTCGTGGTGATATTGTTGTGAGCAAAA
1 CATTGATGTTCGGTACCATTTTGTTCATGATATCATTGCTCGTGGTGATATTGTTGTGAGCAAAA
49165868 TTAGTGCTCATGAAAATCATATAGATATCGTGACTAAGTTGCTTCTCATAACCAAGTTTGAGCAT
66 TTAGTGCTCATGAAAATCATATAGATATCGTGACTAAGTTGCTTCTCATAACCAAGTTTGAGCAT
*
49165933 TGCTTAGACTTGGTTGGTGTTCATTGTTGAAGTTAAACCCTTAAGGATTTTTACGGAGGAGGTGG
131 TGCTTAGACTTGGTTGGTGTTCATTGTTGAAGTTAAACCCTTAAGGAGTTTTACGGAGGAGGTGG
49165998 AGAACTTGTTTGAGCATTGCTCGTGGTTGGTGATAT
196 AGAACTTGTTTGAGCATTGCTCGTGGTTGGTGATAT
* *
49166034 CATTGCTGTTCGGTATCATTTTGTTCATGATATCATTGCTCGTGGTGATATTGTTGTGAGCAAAA
1 CATTGATGTTCGGTACCATTTTGTTCATGATATCATTGCTCGTGGTGATATTGTTGTGAGCAAAA
* *
49166099 TTAGTGCTCATGAAAATCATTTAGATATGGTGACTAAGTTGCTTCTCATAACCAAGTTTGAGCAT
66 TTAGTGCTCATGAAAATCATATAGATATCGTGACTAAGTTGCTTCTCATAACCAAGTTTGAGCAT
*
49166164 TGCTTAGACTTGGTTGGTGTTCATTGTTGAAGTTAAACCCTTAAGGAGTTTTATGGAGGAGGTGG
131 TGCTTAGACTTGGTTGGTGTTCATTGTTGAAGTTAAACCCTTAAGGAGTTTTACGGAGGAGGTGG
49166229 AGAACTTGTT
196 AGAACTTGTT
49166239 CGTTGAGAGT
Statistics
Matches: 197, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
231 197 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (231 bp):
CATTGATGTTCGGTACCATTTTGTTCATGATATCATTGCTCGTGGTGATATTGTTGTGAGCAAAA
TTAGTGCTCATGAAAATCATATAGATATCGTGACTAAGTTGCTTCTCATAACCAAGTTTGAGCAT
TGCTTAGACTTGGTTGGTGTTCATTGTTGAAGTTAAACCCTTAAGGAGTTTTACGGAGGAGGTGG
AGAACTTGTTTGAGCATTGCTCGTGGTTGGTGATAT
Found at i:49166348 original size:14 final size:14
Alignment explanation
Indices: 49166329--49166355 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49166319 CATGATAAAA
49166329 TAAAATACAAGTGG
1 TAAAATACAAGTGG
49166343 TAAAATACAAGTG
1 TAAAATACAAGTG
49166356 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:49170997 original size:9 final size:9
Alignment explanation
Indices: 49170981--49171015 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
49170971 TAGGTTGAAA
49170981 AATTAATTT
1 AATTAATTT
*
49170990 AGTTAATTT
1 AATTAATTT
*
49170999 AATTAATTA
1 AATTAATTT
49171008 AATTAATT
1 AATTAATT
49171016 GAATAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:49171254 original size:18 final size:19
Alignment explanation
Indices: 49171225--49171260 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
49171215 AAGTTGTGTT
49171225 TTTAATTTAAATATTATTA
1 TTTAATTTAAATATTATTA
*
49171244 TTTAA-TTAAATCTTATT
1 TTTAATTTAAATATTATT
49171261 TTAACATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATATTATTA
Found at i:49173666 original size:12 final size:12
Alignment explanation
Indices: 49173649--49173673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49173639 CTGAATACTT
49173649 TCAACCCTCTCA
1 TCAACCCTCTCA
49173661 TCAACCCTCTCA
1 TCAACCCTCTCA
49173673 T
1 T
49173674 GGTTTGACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (12 bp):
TCAACCCTCTCA
Found at i:49174654 original size:14 final size:16
Alignment explanation
Indices: 49174625--49174657 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
49174615 ATAAACACTA
49174625 AAAATTTAAGATAGTT
1 AAAATTTAAGATAGTT
49174641 AAAA-TTAA-ATAGTT
1 AAAATTTAAGATAGTT
49174655 AAA
1 AAA
49174658 TGATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAATTTAAGATAGTT
Found at i:49178540 original size:19 final size:19
Alignment explanation
Indices: 49178518--49178557 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
49178508 CATAATCTGA
*
49178518 AATAGAGTTTATAACTAAT
1 AATAGAGTTTATAAATAAT
49178537 AATAGAGTTTATAAATAAT
1 AATAGAGTTTATAAATAAT
49178556 AA
1 AA
49178558 AAGGCTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (19 bp):
AATAGAGTTTATAAATAAT
Found at i:49192648 original size:3 final size:3
Alignment explanation
Indices: 49192642--49192685 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
49192632 TTAAAAAAGC
49192642 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49192686 CAGAACTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:49193938 original size:312 final size:310
Alignment explanation
Indices: 49193413--49194052 Score: 770
Period size: 312 Copynumber: 2.1 Consensus size: 310
49193403 ATCGGTTTTA
* * * * * * *
49193413 TAATTAGTTTCGAATCACATGTTTCATTGTTTGTTGTATGTTACTTTTAAATAAGCATTTGTGTT
1 TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACAAGCATTTATGTT
* * ** *
49193478 TTTAAATTTGTGATTTCCACACACATATGTGGGTGATAGAATTTTTAATATATATTAATAATATT
66 TTTAAATTAGTGATTTCCACACACATACGCAGGTAATAGAA-TTTTAATATATATTAATAATATT
* * * * *
49193543 GTTAATTGAGTTGGAGCACAAATCAACTCGATACTAACTCAAAATTGTTGACAAAACCATGATTA
130 GCTAATTGAGTTGGAGCACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGATAA
* * * * * * *
49193608 ATAATTGTAGTACATTTAGTATTGTTTATTTGATGTATTTATGTGCTTAATTTTTGTTTTACTCA
195 ATAAATGAAGTACATTTAGTATTGTTTATCTAATGTATTTATGTGCTTAAATCTCGTTTTACTCA
* *
49193673 CAATCTAATATATATTTTTATTTTAATATCATACATATTTCATATGTTATTATAAT
260 CAAT-T--TA-ATATCTTT-TTTTAATATCATACATATTTCATATGTAATTATAAT
*
49193729 TAATTAATTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACACA-CATTTATG-
1 TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACA-AGCATTTATGT
* * * * * *
49193792 TTTTAAATTAGTGGTTTCCACACGCATACGCATGTAATAGGA-TTT-CTA-GTATTAATAA-AGT
65 TTTTAAATTAGTGATTTCCACACACATACGCAGGTAATAGAATTTTAATATATATTAATAATA-T
* * *
49193853 TGCTAATTGAGTTGGCGACACAAATAAACTCAACACTAACTCATAGTTGTTGACAAAACCATGAT
129 TGCTAATTGAGTTGGAG-CACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGAT
* *
49193918 AAATAAATGAAGTGCATTTAGTATTGTTTATCTAATGTATTTATGTGTTTAAATCTCGTTTTACT
193 AAATAAATGAAGTACATTTAGTATTGTTTATCTAATGTATTTATGTGCTTAAATCTCGTTTTACT
* * * *
49193983 CATAATTTAATCTCTTTTTTTAATATTATACATATTTCATATGTAATTATGAT
258 CACAATTTAATATCTTTTTTTAATATCATACATATTTCATATGTAATTATAAT
*
49194036 TAATTAGTTTTAAACCA
1 TAATTAGTTTCAAACCA
49194053 AGGGCGAAGC
Statistics
Matches: 277, Mismatches: 44, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
307 48 0.17
308 6 0.02
309 2 0.01
310 1 0.00
311 26 0.09
312 104 0.38
313 3 0.01
315 33 0.12
316 53 0.19
317 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (310 bp):
TAATTAGTTTCAAACCACACGTTTCATTATTTATTGTATGTTACTTTTAAACAAGCATTTATGTT
TTTAAATTAGTGATTTCCACACACATACGCAGGTAATAGAATTTTAATATATATTAATAATATTG
CTAATTGAGTTGGAGCACAAATAAACTCAACACTAACTCAAAATTGTTGACAAAACCATGATAAA
TAAATGAAGTACATTTAGTATTGTTTATCTAATGTATTTATGTGCTTAAATCTCGTTTTACTCAC
AATTTAATATCTTTTTTTAATATCATACATATTTCATATGTAATTATAAT
Found at i:49204136 original size:6 final size:6
Alignment explanation
Indices: 49204125--49204150 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49204115 CTACGCCGCT
49204125 GGCGGA GGCGGA GGCGGA GGCGGA GG
1 GGCGGA GGCGGA GGCGGA GGCGGA GG
49204151 AGGAAGGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.69, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:49212681 original size:123 final size:125
Alignment explanation
Indices: 49212372--49212722 Score: 411
Period size: 126 Copynumber: 2.8 Consensus size: 125
49212362 TAATTTCGAG
* ** * * *
49212372 TTGACATTTCTGATAAAATAATATAAAATAGCTTTTAGCAGGATGGTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
49212437 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGAAATAAATAATTATTTTT
66 AAATCGCGCCCTCGTGCACACGCTTTTGCTACAGTAGGTCACGAAAGAAATAA-TATTTTT
* * * *
49212498 TTGATGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * * * *
49212563 AAATTGTGGCCTCGT-CACCACGCTTTTGCTACGGTAGGTTATGTAAGAAAT-A-ATTTTT
66 AAATCGCGCCCTCGTGCA-CACGCTTTTGCTACAGTAGGTCACGAAAGAAATAATATTTTT
* *
49212621 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATACCAGGATGTTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATAGCAGGATGCTATTTGAGAAGAATTTGTG
** * * * *
49212686 AAATCGTACCCTTGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGCACACGCTTTTGCTACAGTAG
49212723 CATGTTTGGG
Statistics
Matches: 190, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
123 92 0.48
124 1 0.01
125 2 0.01
126 95 0.50
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTATAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGCACACGCTTTTGCTACAGTAGGTCACGAAAGAAATAATATTTTT
Found at i:49215959 original size:116 final size:116
Alignment explanation
Indices: 49215755--49215969 Score: 403
Period size: 116 Copynumber: 1.9 Consensus size: 116
49215745 TAAATTGTAC
*
49215755 TAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGTTAG
1 TAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAG
49215820 TACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTAT
66 TACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTAT
* *
49215871 TAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGTTAG
1 TAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAG
49215936 TACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TACCAGTCAAAACATTTTTCCAAATCTAACATTA
49215970 CGTTAAGGTT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 96 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (116 bp):
TAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAG
TACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTAT
Found at i:49216001 original size:23 final size:23
Alignment explanation
Indices: 49215975--49216691 Score: 577
Period size: 23 Copynumber: 29.7 Consensus size: 23
49215965 CATTACGTTA
49215975 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49215998 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
49216021 AGGTTAGGCTAGGGTTTTTAATCAAATT
1 AGG-T----TAGGGTTTTTAATTAAATT
49216049 AGGTTAGGGTTTTTAAGTT-AA--
1 AGGTTAGGGTTTTTAA-TTAAATT
* * *
49216070 GGGTTTAGGGTTTTTCATTGAATT
1 AGG-TTAGGGTTTTTAATTAAATT
49216094 AGGTTAGGGTTTTTAATT-AA--
1 AGGTTAGGGTTTTTAATTAAATT
*
49216114 AGGTTTAGGATTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
49216138 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49216161 AGGTTAGGCTAGGGTTTTTAATTAAATT
1 AGG-T----TAGGGTTTTTAATTAAATT
* *
49216189 AGGCTAGGGTTTTTAATCAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
49216212 ATGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
49216235 AGGTTAGGCTAGAGTTTTTAATCAAATT
1 AGGTTA-G---G-GTTTTTAATTAAATT
**
49216263 AGGTTACAGTTTTTAAGTT-AA--
1 AGGTTAGGGTTTTTAA-TTAAATT
* *
49216284 GGGTTTAGGATTTTTAATTGAATTAGGTT
1 AGG-TTAGGGTTTTTAATT-AA--A--TT
*
49216313 AGGGTTAGGGTTTTTAATT-AAGT
1 A-GGTTAGGGTTTTTAATTAAATT
* *
49216336 -GTTTAGGATTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49216358 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49216381 AGGTTAGGCTAGGGTTTTTAATTAAATT
1 AGG-T----TAGGGTTTTTAATTAAATT
* *
49216409 AGGCTAGGGTTTTTAATCAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
49216432 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
49216455 AGGTTAGGCTAGGGTTTTTAATCAAATT
1 AGG-T----TAGGGTTTTTAATTAAATT
49216483 AGGTTAGGGTTTTTAAGTT-AA--
1 AGGTTAGGGTTTTTAA-TTAAATT
*
49216504 GGGTTTAGGGTTTTTAATTGAATTAGGTT
1 AGG-TTAGGGTTTTTAATT-AA--A--TT
49216533 AGGGTTAGGGTTTTTAATT-AA--
1 A-GGTTAGGGTTTTTAATTAAATT
* *
49216554 GGGTTTAGGATTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
*
49216578 AAGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49216601 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
**
49216624 AGGTTATGGTTTTGGGTTTTTAATTATTTT
1 AGGTTA-------GGGTTTTTAATTAAATT
****
49216654 AGGTTAGGGTTTAGGGTTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
49216677 AGGTTAGGGTTTTTA
1 AGGTTAGGGTTTTTA
49216692 TTACATCAAA
Statistics
Matches: 570, Mismatches: 55, Indels: 138
0.75 0.07 0.18
Matches are distributed among these distances:
20 5 0.01
21 55 0.10
22 46 0.08
23 282 0.49
24 13 0.02
25 4 0.01
27 5 0.01
28 106 0.19
29 29 0.05
30 25 0.04
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:49216027 original size:28 final size:28
Alignment explanation
Indices: 49215966--49216056 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
49215956 CAAATCTAAC
*
49215966 ATTACGTTAAGGTTAGGGTTTTTAATT-A
1 ATTAGGTT-AGGTTAGGGTTTTTAATTAA
49215994 A--A--TTAGGTTAGGGTTTTTAATTAA
1 ATTAGGTTAGGTTAGGGTTTTTAATTAA
* *
49216018 ATTAGGTTAGGCTAGGGTTTTTAATCAA
1 ATTAGGTTAGGTTAGGGTTTTTAATTAA
49216046 ATTAGGTTAGG
1 ATTAGGTTAGG
49216057 GTTTTTAAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 18 0.32
24 4 0.07
26 2 0.04
28 32 0.57
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (28 bp):
ATTAGGTTAGGTTAGGGTTTTTAATTAA
Found at i:49216048 original size:51 final size:47
Alignment explanation
Indices: 49215978--49216636 Score: 597
Period size: 51 Copynumber: 13.7 Consensus size: 47
49215968 TACGTTAAGG
49215978 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
* *
49216025 TAGGCTAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAAGTT-AA--GGGT
1 T----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAATTAGGT
* *
49216074 TTAGGGTTTTTCATTGAATTAGGTTAGGGTTTTTAATT-AA--AGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
*
49216118 TTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
* * *
49216165 TAGGCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATCAAATTATG-
1 T----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
*
49216215 TTAGGGTTTTTAATTAAATTAGGTTAGGCTAGAGTTTTTAATCAAATTAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTA-G---G-GTTTTTAATTAAATTAGGT
** * * *
49216266 TTACAGTTTTTAAGTT-AA--GGGTTTAGGATTTTTAATTGAATTAGGTTAGGG
1 TTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATT-AA--A--TTAGGT
* * *
49216317 TTAGGGTTTTTAATT-AAGT-GTTTAGGATTTTTAATTAAATTAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
49216361 TTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGG-
1 TTAGGGTTTTTAATTAAATTAGG-T----TAGGGTTTTTAATTAAATTAGGT
* * *
49216412 CTAGGGTTTTTAATCAAATTAGGCTAGGGTTTTTAATTAAATTAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
* *
49216459 TAGGCTAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAAGTT-AA--GGGT
1 T----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAATTAGGT
*
49216508 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--GGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGT
* *
49216558 TTAGGATTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
*
49216604 TTAGGGTTTTTAATTAAATTAGGTTATGGTTTT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTT
49216637 GGGTTTTTAA
Statistics
Matches: 524, Mismatches: 39, Indels: 99
0.79 0.06 0.15
Matches are distributed among these distances:
44 73 0.14
45 68 0.13
46 82 0.16
47 12 0.02
48 2 0.00
49 15 0.03
50 54 0.10
51 212 0.40
52 6 0.01
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (47 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
Found at i:49216317 original size:30 final size:29
Alignment explanation
Indices: 49216283--49216420 Score: 85
Period size: 28 Copynumber: 5.2 Consensus size: 29
49216273 TTTTAAGTTA
49216283 AGGGTTTAGGATTTTTAATTGAATTAGGTT
1 AGGGTTTAGGATTTTTAATT-AATTAGGTT
*
49216313 AGGG-TTAGGGTTTTTAATT-A--A-G-T
1 AGGGTTTAGGATTTTTAATTAATTAGGTT
49216336 ---GTTTAGGATTTTTAATTAA--A--TT
1 AGGGTTTAGGATTTTTAATTAATTAGGTT
*
49216358 A-GG-TTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTTAGGATTTTTAATT-AATTAGGTT
* * *
49216386 A-GG-CTAGGGTTTTTAATTAAATTAGGCT
1 AGGGTTTAGGATTTTTAATT-AATTAGGTT
49216414 AGGGTTT
1 AGGGTTT
49216421 TTAATCAAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.01
21 14 0.16
22 3 0.03
23 15 0.17
24 4 0.04
25 1 0.01
26 1 0.01
27 1 0.01
28 29 0.32
29 16 0.18
30 5 0.06
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (29 bp):
AGGGTTTAGGATTTTTAATTAATTAGGTT
Found at i:49216366 original size:50 final size:51
Alignment explanation
Indices: 49216271--49216368 Score: 171
Period size: 50 Copynumber: 1.9 Consensus size: 51
49216261 TTAGGTTACA
*
49216271 GTTTTTAAGTTAAGGGTTTAGGATTTTTAATTGAATTAGGTTAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTAGG
*
49216322 GTTTTTAA-TTAAGTGTTTAGGATTTTTAATTAAATTAGGTTAGGGTT
1 GTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTT
49216369 TTTAATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 37 0.82
51 8 0.18
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.48
Consensus pattern (51 bp):
GTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTAGG
Found at i:49216419 original size:220 final size:219
Alignment explanation
Indices: 49215979--49216636 Score: 1113
Period size: 220 Copynumber: 3.0 Consensus size: 219
49215969 ACGTTAAGGT
*
49215979 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
1 TAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
*
49216044 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTCATTG-A--A--TTA-GGTTAGGG
66 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGG
49216103 TTTTTAATTAAAGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
131 TTTTTAATT-AAGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
49216168 GCTAGGGTTTTTAATTAAATTAGGC
195 GCTAGGGTTTTTAATTAAATTAGGC
* *
49216193 TAGGGTTTTTAATCAAATTATGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGAGTTTTTAATC
1 TAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
** *
49216258 AAATTAGGTTACAGTTTTTAAGTTAAGGGTTTAGGATTTTTAATTGAATTAGGTTAGGGTTAGGG
66 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGG
49216323 TTTTTAATTAAGTGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
131 TTTTTAATTAAG-GTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
49216388 GCTAGGGTTTTTAATTAAATTAGGC
195 GCTAGGGTTTTTAATTAAATTAGGC
*
49216413 TAGGGTTTTTAATCAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
1 TAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
49216478 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGG
66 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGG
*
49216543 TTTTTAATTAAGGGTTTAGGATTTTTAATTAAATTAAGTTAGGGTTTTTAATTAAATTAGG-T--
131 TTTTTAATTAA-GGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49216605 --TAGGGTTTTTAATTAAATTAGGT
195 GCTAGGGTTTTTAATTAAATTAGGC
*
49216628 TATGGTTTT
1 TAGGGTTTT
49216637 GGGTTTTTAA
Statistics
Matches: 420, Mismatches: 16, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
214 104 0.25
215 31 0.07
217 1 0.00
219 7 0.02
220 276 0.66
221 1 0.00
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (219 bp):
TAGGGTTTTTAATCAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATC
AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGG
TTTTTAATTAAGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
CTAGGGTTTTTAATTAAATTAGGC
Found at i:49216554 original size:50 final size:49
Alignment explanation
Indices: 49216484--49216649 Score: 182
Period size: 50 Copynumber: 3.4 Consensus size: 49
49216474 AATCAAATTA
49216484 GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAG
1 GGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAATT-AATTAGGTTAG
*
49216535 GGTTAGGGTTTTTAATTAAGGGTTTAGGATTTTTAATTAA--A--TTA-
1 GGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAATTAGGTTAG
* *
49216579 AGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTATG
1 GGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATT-AATTAGGTTA-G
* *
49216632 GTTTTGGGTTTTTAATTA
1 GGTTAGGGTTTTTAATTA
49216650 TTTTAGGTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
44 16 0.16
45 5 0.05
46 14 0.14
47 5 0.05
49 3 0.03
50 22 0.22
51 18 0.18
52 1 0.01
53 14 0.14
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (49 bp):
GGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAATTAGGTTAG
Found at i:49216641 original size:30 final size:30
Alignment explanation
Indices: 49216604--49216671 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
49216594 TTAAATTAGG
*
49216604 TTAGGGTTTTTAATTAAATTAGGTTATGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
* **
49216634 TTTGGGTTTTTAATTATTTTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
49216664 TTAGGGTT
1 TTAGGGTT
49216672 AAATTAGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:49216641 original size:53 final size:53
Alignment explanation
Indices: 49216584--49216689 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
49216574 AATTAAGTTA
** *
49216584 GGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTATGGTTTT
1 GGGTTTTTAATTAAATTAGGTTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
** **
49216637 GGGTTTTTAATTATTTTAGGTTAGGGTTTAGGGTTAAATTAGGTTAGGGTTTT
1 GGGTTTTTAATTAAATTAGGTTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
49216690 TATTACATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (53 bp):
GGGTTTTTAATTAAATTAGGTTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
Found at i:49217231 original size:18 final size:18
Alignment explanation
Indices: 49217205--49217239 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49217195 CGGAAAAGGA
* *
49217205 TACATATAAGGGTTAGGG
1 TACAAATAAGGGCTAGGG
49217223 TACAAATAAGGGCTAGG
1 TACAAATAAGGGCTAGG
49217240 AAACGCACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (18 bp):
TACAAATAAGGGCTAGGG
Found at i:49217898 original size:7 final size:7
Alignment explanation
Indices: 49217886--49217910 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49217876 AGTTATATAC
49217886 ATACATA
1 ATACATA
49217893 ATACATA
1 ATACATA
49217900 ATACATA
1 ATACATA
49217907 ATAC
1 ATAC
49217911 TAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:49219127 original size:22 final size:22
Alignment explanation
Indices: 49219102--49219157 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
49219092 AAATATGGAT
*
49219102 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
49219124 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
49219146 TTGAGAGGAATT
1 TTGAGA-GAATT
49219158 GAGAGGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:49219174 original size:12 final size:11
Alignment explanation
Indices: 49219114--49219176 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 11
49219104 GAGAGAATTT
49219114 TTGA-AGGAAA
1 TTGAGAGGAAA
*
49219124 TTGAGA-GAATT
1 TTGAGAGGAA-A
49219135 TTG-GAAGGAAA
1 TTGAG-AGGAAA
49219146 TTGAGAGG-AA
1 TTGAGAGGAAA
49219156 TTGAGAGGAAA
1 TTGAGAGGAAA
49219167 TATGAGAGGA
1 T-TGAGAGGA
49219177 TTTGTTTGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 18 0.41
11 14 0.32
12 12 0.27
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:49226455 original size:9 final size:9
Alignment explanation
Indices: 49226441--49226711 Score: 177
Period size: 9 Copynumber: 32.1 Consensus size: 9
49226431 AACTTATTTA
49226441 TTATGTAAG
1 TTATGTAAG
49226450 TTATGTAAG
1 TTATGTAAG
*
49226459 TTGTGTAAG
1 TTATGTAAG
49226468 TTATGTAAG
1 TTATGTAAG
*
49226477 CTATGTAAG
1 TTATGTAAG
*
49226486 TTGTGT-A-
1 TTATGTAAG
* *
49226493 TTATGAAAC
1 TTATGTAAG
49226502 TTATGTAAG
1 TTATGTAAG
*
49226511 TTGTGT-A-
1 TTATGTAAG
*
49226518 TTATG-ATGG
1 TTATGTA-AG
49226527 TTATGTAAG
1 TTATGTAAG
*
49226536 TTGTGT-A-
1 TTATGTAAG
49226543 TTATGTAAG
1 TTATGTAAG
*
49226552 TTATGTTAG
1 TTATGTAAG
*
49226561 TTGTGT-A-
1 TTATGTAAG
* *
49226568 TTATGAAAC
1 TTATGTAAG
49226577 TTATGTAAG
1 TTATGTAAG
*
49226586 TTATGT--C
1 TTATGTAAG
49226593 TTATGTAAG
1 TTATGTAAG
*
49226602 TGATGT-AG
1 TTATGTAAG
*
49226610 AATATGT-A-
1 -TTATGTAAG
49226618 TTATGTAAG
1 TTATGTAAG
*
49226627 TTATGTCAG
1 TTATGTAAG
*
49226636 TTGTGT-A-
1 TTATGTAAG
*
49226643 TTATGTAAA
1 TTATGTAAG
49226652 TTATGT-A-
1 TTATGTAAG
49226659 TTATGTAAG
1 TTATGTAAG
*
49226668 TTATGTAAT
1 TTATGTAAG
*
49226677 TTGTGT-A-
1 TTATGTAAG
*
49226684 TTATGTAAC
1 TTATGTAAG
* *
49226693 TTATTTAAT
1 TTATGTAAG
49226702 TTATGTAAG
1 TTATGTAAG
49226711 T
1 T
49226712 GTGTATTATT
Statistics
Matches: 204, Mismatches: 37, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
7 44 0.22
8 16 0.08
9 143 0.70
10 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:49226506 original size:25 final size:25
Alignment explanation
Indices: 49226439--49226658 Score: 237
Period size: 25 Copynumber: 8.7 Consensus size: 25
49226429 ATAACTTATT
*
49226439 TATTATGTAAGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
49226464 TAAGTTATGTAAGCTATGTAAGTTGTG
1 T-A-TTATGAAAGTTATGTAAGTTGTG
*
49226491 TATTATGAAACTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
**
49226516 TATTATGATGGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
49226541 TATTATGTAAGTTATGTTAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
49226566 TATTATGAAACTTATGTAAGTTATG
1 TATTATGAAAGTTATGTAAGTTGTG
* * * * *
49226591 TCTTATGTAAGTGATGT-AGAATATG
1 TATTATGAAAGTTATGTAAG-TTGTG
* *
49226616 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
49226641 TATTATGTAAA-TTATGTA
1 TATTATG-AAAGTTATGTA
49226659 TTATGTAAGT
Statistics
Matches: 164, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
24 2 0.01
25 133 0.81
26 6 0.04
27 23 0.14
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (25 bp):
TATTATGAAAGTTATGTAAGTTGTG
Found at i:49226521 original size:16 final size:16
Alignment explanation
Indices: 49226434--49226674 Score: 143
Period size: 16 Copynumber: 14.4 Consensus size: 16
49226424 TAGGAATAAC
*
49226434 TTATTTATTATGTAAG
1 TTATGTATTATGTAAG
*
49226450 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
*
49226468 TTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGTAAG
* * *
49226486 TTGTGTATTATGAAAC
1 TTATGTATTATGTAAG
*
49226502 TTATGTAAGTTGTGT-A-
1 TTATGT-A-TTATGTAAG
*
49226518 TTATGATGGTTATGTAAG
1 TTATG-T-ATTATGTAAG
*
49226536 TTGTGTATTATGTAAG
1 TTATGTATTATGTAAG
*
49226552 TTATGTTAGTTGTGT-A-
1 TTATG-TA-TTATGTAAG
*
49226568 TTATGAAACTTATGTAAG
1 TTATG-TA-TTATGTAAG
*
49226586 TTATGTCTTATGTAAG
1 TTATGTATTATGTAAG
* *
49226602 TGATGTAGAATATGT-A-
1 TTATGT--ATTATGTAAG
*
49226618 TTATGTAAGTTATGTCAG
1 TTATGT-A-TTATGTAAG
* *
49226636 TTGTGTATTATGTAAA
1 TTATGTATTATGTAAG
49226652 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
49226668 TTATGTA
1 TTATGTA
49226675 ATTTGTGTAT
Statistics
Matches: 174, Mismatches: 35, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.01
16 102 0.59
17 14 0.08
18 57 0.33
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Done.