Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 141 of 163
Found at i:46247913 original size:19 final size:20
Alignment explanation
Indices: 46247871--46247913 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
46247861 TCATGCTTTC
*
46247871 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
46247891 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
46247909 TATTC
1 TATTC
46247914 CACAATCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:46248114 original size:38 final size:39
Alignment explanation
Indices: 46248042--46248175 Score: 105
Period size: 38 Copynumber: 3.5 Consensus size: 39
46248032 ATCAGATTGG
* * * *
46248042 CACCCAGTGTCTCATCGGA--TAGTTCAAAGCAAAGTTGA
1 CACCCAGTGTCTCATCGAACCTAG-CCGAAGTAAAGTTGA
* *
46248080 CACCTAGTGTCTCATCG-GCCTAGCCGAAGTAAAG-TGA
1 CACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTTGA
* * * * *
46248117 TACCCAGTATCTCATCGAATCTATCCGAAGTAAAATAGTGA
1 CACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAGT--TGA
*
46248158 CACCCAGTGTCTTATCGA
1 CACCCAGTGTCTCATCGA
46248176 CTCAAGGTCG
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 17 0.23
38 37 0.49
39 3 0.04
41 18 0.24
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTTGA
Found at i:46248313 original size:18 final size:17
Alignment explanation
Indices: 46248267--46248320 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
46248257 TTTCCAATTC
46248267 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
46248284 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
46248302 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
46248320 T
1 T
46248321 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:46256484 original size:16 final size:17
Alignment explanation
Indices: 46256465--46256508 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
46256455 CTTTTTCTCC
46256465 CTGTTTCGTTTCTA-TT
1 CTGTTTCGTTTCTATTT
46256481 CTGTTTC-TTTCTATTT
1 CTGTTTCGTTTCTATTT
*
46256497 CT-TTTTGTTTCT
1 CTGTTTCGTTTCT
46256509 TTTTATGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.05, C:0.18, G:0.09, T:0.68
Consensus pattern (17 bp):
CTGTTTCGTTTCTATTT
Found at i:46256872 original size:33 final size:32
Alignment explanation
Indices: 46256824--46256895 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
46256814 TATTTATCAT
*
46256824 ATAAAA-ATCTTTTACTAATTA-ATAATAAATA
1 ATAAAATATCTTTTACTAACTATAT-ATAAATA
46256855 ATAAAATATCTTTTTACTAACTATATATAAATA
1 ATAAAATATC-TTTTACTAACTATATATAAATA
46256888 ATACAAAT
1 ATA-AAAT
46256896 GTACTCATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.17
32 3 0.08
33 21 0.58
34 6 0.17
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (32 bp):
ATAAAATATCTTTTACTAACTATATATAAATA
Found at i:46260364 original size:17 final size:18
Alignment explanation
Indices: 46260318--46260366 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
46260308 ATGAGGCGCC
46260318 ATAAGTAAAA-ATATATGT
1 ATAA-TAAAATATATATGT
* *
46260336 AAAATTAAATATATAT-T
1 ATAATAAAATATATATGT
46260353 ATAATAAAATATAT
1 ATAATAAAATATAT
46260367 TTACTTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAATAAAATATATATGT
Found at i:46261671 original size:23 final size:26
Alignment explanation
Indices: 46261640--46261697 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 26
46261630 ATCAACTCTT
46261640 ATGAGCTTACC-GT-TTCAGCTC-GA
1 ATGAGCTTACCAGTCTTCAGCTCGGA
* *
46261663 TTGAGCTTACCATTCTTCAGCTCGGA
1 ATGAGCTTACCAGTCTTCAGCTCGGA
46261689 ATGAGCTTA
1 ATGAGCTTA
46261698 TCGATCATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 1 0.03
25 8 0.28
26 10 0.34
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (26 bp):
ATGAGCTTACCAGTCTTCAGCTCGGA
Found at i:46262292 original size:24 final size:24
Alignment explanation
Indices: 46262265--46262311 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46262255 TAATAATAAA
*
46262265 ATACATGTGTAATAAAATATATAC
1 ATACATGTGAAATAAAATATATAC
* *
46262289 ATACATTTGAAATAAAATGTATA
1 ATACATGTGAAATAAAATATATA
46262312 ATTTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (24 bp):
ATACATGTGAAATAAAATATATAC
Found at i:46262406 original size:16 final size:17
Alignment explanation
Indices: 46262385--46262416 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
46262375 TATAAAACAA
46262385 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
46262401 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
46262417 GCTTAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:46263412 original size:24 final size:22
Alignment explanation
Indices: 46263361--46263412 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
46263351 AGCACGACAA
46263361 TGCTCTCTGTTTAGCACATCTG
1 TGCTCTCTGTTTAGCACATCTG
*
46263383 TGCTCTCTGTTTAGCAC-TTTAG
1 TGCTCTCTGTTTAGCACATCT-G
46263405 TGCTCTCT
1 TGCTCTCT
46263413 ATTCATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (22 bp):
TGCTCTCTGTTTAGCACATCTG
Found at i:46264853 original size:10 final size:10
Alignment explanation
Indices: 46264840--46264907 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
46264830 TTATAATAAT
46264840 AAAAGAAAAGA
1 AAAAG-AAAGA
46264851 AAAAGAAAGA
1 AAAAGAAAGA
*
46264861 AAGAACAAACGA
1 AA-AAGAAA-GA
* *
46264873 AATAGAAGGGA
1 AAAAGAA-AGA
46264884 AAAAGAAAGA
1 AAAAGAAAGA
46264894 AAAAGGAAAGA
1 AAAA-GAAAGA
46264905 AAA
1 AAA
46264908 TGAGAAAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 13 0.28
11 30 0.64
12 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.22, T:0.01
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:46264914 original size:29 final size:29
Alignment explanation
Indices: 46264841--46264914 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
46264831 TATAATAATA
*
46264841 AAAGAAAAGAAAAAGAAAGAAAGAACAAACG
1 AAAGAAAAG-AGAA-AAAGAAAGAACAAACG
* * * *
46264872 AAATAGAAGGGAAAAAGAAAGAA-AAAGG
1 AAAGAAAAGAGAAAAAGAAAGAACAAACG
46264900 AAAGAAAATGAGAAA
1 AAAGAAAA-GAGAAA
46264915 GACCAAAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 10 0.29
29 15 0.44
30 2 0.06
31 7 0.21
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (29 bp):
AAAGAAAAGAGAAAAAGAAAGAACAAACG
Found at i:46265873 original size:37 final size:40
Alignment explanation
Indices: 46265780--46265918 Score: 106
Period size: 41 Copynumber: 3.5 Consensus size: 40
46265770 GACTGCGAGT
* **
46265780 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGCCAATTTACTA-TTCGGATTAAGC
* * *
46265821 CAATGAGGCACTGGGTGCCAATTTACT-TT-GG-TTTAGC
1 CGATGAGACACTGGGTGCCAATTTACTATTCGGATTAAGC
* * * * * *
46265858 CGATGAGACACTGGGTGTCAAATTATTTCTTCGAATT-ATC
1 CGATGAGACACTGGGTGCCAATTTA-CTATTCGGATTAAGC
* *
46265898 CGATGATACACTAGGTGCCAA
1 CGATGAGACACTGGGTGCCAA
46265919 ACTGGTGCGT
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
37 24 0.31
38 3 0.04
39 4 0.05
40 21 0.27
41 26 0.33
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGCCAATTTACTATTCGGATTAAGC
Found at i:46274085 original size:8 final size:8
Alignment explanation
Indices: 46274072--46274241 Score: 340
Period size: 8 Copynumber: 21.2 Consensus size: 8
46274062 CATCATATCC
46274072 TTCATGTT
1 TTCATGTT
46274080 TTCATGTT
1 TTCATGTT
46274088 TTCATGTT
1 TTCATGTT
46274096 TTCATGTT
1 TTCATGTT
46274104 TTCATGTT
1 TTCATGTT
46274112 TTCATGTT
1 TTCATGTT
46274120 TTCATGTT
1 TTCATGTT
46274128 TTCATGTT
1 TTCATGTT
46274136 TTCATGTT
1 TTCATGTT
46274144 TTCATGTT
1 TTCATGTT
46274152 TTCATGTT
1 TTCATGTT
46274160 TTCATGTT
1 TTCATGTT
46274168 TTCATGTT
1 TTCATGTT
46274176 TTCATGTT
1 TTCATGTT
46274184 TTCATGTT
1 TTCATGTT
46274192 TTCATGTT
1 TTCATGTT
46274200 TTCATGTT
1 TTCATGTT
46274208 TTCATGTT
1 TTCATGTT
46274216 TTCATGTT
1 TTCATGTT
46274224 TTCATGTT
1 TTCATGTT
46274232 TTCATGTT
1 TTCATGTT
46274240 TT
1 TT
46274242 ATTAAGGAGG
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 162 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (8 bp):
TTCATGTT
Found at i:46280950 original size:22 final size:23
Alignment explanation
Indices: 46280928--46280969 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46280918 AAGCTATTTA
46280928 AAAT-TTTTT-AATTTTTGAATT
1 AAATCTTTTTAAATTTTTGAATT
46280949 AAATCTTTTTAAATTTTTGAA
1 AAATCTTTTTAAATTTTTGAA
46280970 AACTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
AAATCTTTTTAAATTTTTGAATT
Found at i:46285260 original size:161 final size:162
Alignment explanation
Indices: 46284995--46285319 Score: 643
Period size: 161 Copynumber: 2.0 Consensus size: 162
46284985 CAAACCCCAG
46284995 AACTGGCACAGCTGTGAGGGCAGTATCGTAAATAAATCCAAACATTAACCCCACTTTTCACTCAT
1 AACTGGCACAGCTGTGAGGGCAGTATCGTAAATAAATCCAAACATTAACCCCACTTTTCACTCAT
46285060 TTTTATTACATTAAATCCATTCAAGATCCAACTTTGCCATCAAGAAACCCATTTTTTCCCACCAG
66 TTTTATTACATTAAATCCATTCAAGATCCAACTTTGCCATCAAGAAACCCATTTTTTCCCACCAG
46285125 ACGACGCCAAAGAATTTTAAA-GAAAAAAAAA
131 ACGACGCCAAAGAATTTTAAAGGAAAAAAAAA
46285156 AACTGGCACAGCTGTGAGGGCAGTATCGTAAATAAATCCAAACATTAACCCCACTTTTCACTCAT
1 AACTGGCACAGCTGTGAGGGCAGTATCGTAAATAAATCCAAACATTAACCCCACTTTTCACTCAT
46285221 TTTTATTACATTAAATCCATTCAAGATCCAACTTTGCCATCAAGAAACCCATTTTTTCCCACCAG
66 TTTTATTACATTAAATCCATTCAAGATCCAACTTTGCCATCAAGAAACCCATTTTTTCCCACCAG
46285286 ACGACGCCAAAGAATTTTAAAGGAAAAAAAAA
131 ACGACGCCAAAGAATTTTAAAGGAAAAAAAAA
46285318 AA
1 AA
46285320 AGAAAAAGAG
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 151 0.93
162 12 0.07
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (162 bp):
AACTGGCACAGCTGTGAGGGCAGTATCGTAAATAAATCCAAACATTAACCCCACTTTTCACTCAT
TTTTATTACATTAAATCCATTCAAGATCCAACTTTGCCATCAAGAAACCCATTTTTTCCCACCAG
ACGACGCCAAAGAATTTTAAAGGAAAAAAAAA
Found at i:46289450 original size:18 final size:20
Alignment explanation
Indices: 46289405--46289457 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
46289395 ATATATAGTA
*
46289405 ATAAATGTTTTATAATAAGAT
1 ATAAATATTTT-TAATAAGAT
*
46289426 ATGAATATTTTTAAT-A-AT
1 ATAAATATTTTTAATAAGAT
*
46289444 ATAAATATGTTTAA
1 ATAAATATTTTTAA
46289458 ACTTTTCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 4 0.14
21 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
ATAAATATTTTTAATAAGAT
Found at i:46297460 original size:18 final size:20
Alignment explanation
Indices: 46297426--46297464 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
46297416 CTCAAAATCA
46297426 TTTTTTTTACAATATTTATT
1 TTTTTTTTACAATATTTATT
46297446 TTTTTTTTA-AA-ATTTATT
1 TTTTTTTTACAATATTTATT
46297464 T
1 T
46297465 CAAATTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTTACAATATTTATT
Found at i:46309613 original size:24 final size:25
Alignment explanation
Indices: 46309585--46309646 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
46309575 AGGAATCTCA
*
46309585 CAAAGAGCCTA-TAACGGGTAGCTC
1 CAAAGAGCCAATTAACGGGTAGCTC
*
46309609 CAAAGAG-CAATTAACGGGTTGCTC
1 CAAAGAGCCAATTAACGGGTAGCTC
46309633 CAAAGAG-CAATTAA
1 CAAAGAGCCAATTAA
46309647 TGGGAAGCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (25 bp):
CAAAGAGCCAATTAACGGGTAGCTC
Found at i:46323663 original size:3 final size:3
Alignment explanation
Indices: 46323655--46323681 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
46323645 ACGAGGTTGT
46323655 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
46323682 ACCCATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:46329396 original size:183 final size:184
Alignment explanation
Indices: 46329088--46329445 Score: 700
Period size: 183 Copynumber: 1.9 Consensus size: 184
46329078 TCACCTAATT
46329088 AAAATAAACAATTAAGCCTCTCGGTTAAAATATTTAAAAAATCATAAAAAAATGAGAAATTATAA
1 AAAATAAACAATTAAGCCTCTCGGTTAAAATATTTAAAAAATCATAAAAAAATGAGAAATTATAA
46329153 ATTATAAAATATAAAAAAATTAAATGTTAAATATTTTAAAATATTTGAAAAATATGAACTTATAA
66 ATTATAAAATATAAAAAAATTAAATGTTAAATATTTTAAAATATTTGAAAAATATGAACTTATAA
46329218 AAATGATAAATAAATATAAAAAATTATAAAAC-ATTTAAAATATATTCCGAATG
131 AAATGATAAATAAATATAAAAAATTATAAAACAATTTAAAATATATTCCGAATG
46329271 AAAATAAACAATTAAGCCTCTCGGTTAAAATATTTAAAAAATCATAAAAAAATGAGAAATTATAA
1 AAAATAAACAATTAAGCCTCTCGGTTAAAATATTTAAAAAATCATAAAAAAATGAGAAATTATAA
46329336 ATTATAAAATATAAAAAAATTAAATGTTAAATATTTTAAAATATTTGAAAAATATGAACTTATAA
66 ATTATAAAATATAAAAAAATTAAATGTTAAATATTTTAAAATATTTGAAAAATATGAACTTATAA
46329401 AAATGATAAATAAATATAAAAAATTATAAAACATATTTAAAATAT
131 AAATGATAAATAAATATAAAAAATTATAAAACA-ATTTAAAATAT
46329446 TTAAAATTTT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
183 162 0.94
185 11 0.06
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (184 bp):
AAAATAAACAATTAAGCCTCTCGGTTAAAATATTTAAAAAATCATAAAAAAATGAGAAATTATAA
ATTATAAAATATAAAAAAATTAAATGTTAAATATTTTAAAATATTTGAAAAATATGAACTTATAA
AAATGATAAATAAATATAAAAAATTATAAAACAATTTAAAATATATTCCGAATG
Found at i:46330019 original size:19 final size:18
Alignment explanation
Indices: 46329963--46330019 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46329953 ATAAGTTCAA
*
46329963 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46329981 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330000 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330019 T
1 T
46330020 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330130 original size:8 final size:9
Alignment explanation
Indices: 46330034--46330725 Score: 81
Period size: 9 Copynumber: 75.3 Consensus size: 9
46330024 TACCTTTTTG
46330034 ATTTTAA-A
1 ATTTTAATA
46330042 TATTTTAAATA
1 -ATTTT-AATA
* *
46330053 AGTTTATTA
1 ATTTTAATA
46330062 ATTTT-ATA
1 ATTTTAATA
*
46330070 ATTTTTTTATA
1 A--TTTTAATA
* *
46330081 A-ATTAGTA
1 ATTTTAATA
*
46330089 ACTTTAATA
1 ATTTTAATA
*
46330098 AATTTATATCA
1 ATTTTA-AT-A
46330109 ATTTTAATA
1 ATTTTAATA
*
46330118 TTTTTAA-A
1 ATTTTAATA
*
46330126 ATTTTTATA
1 ATTTTAATA
* *
46330135 ATTCTTTACA
1 ATT-TTAATA
**
46330145 ATTTTTTTTA
1 A-TTTTAATA
* *
46330155 TTTTTAAGA
1 ATTTTAATA
*
46330164 ATTCTAATA
1 ATTTTAATA
* *
46330173 CCTTTT--TG
1 -ATTTTAATA
46330181 ATTTTAA-A
1 ATTTTAATA
46330189 TATTTTAAATA
1 -ATTTT-AATA
* *
46330200 AGTTTATTA
1 ATTTTAATA
46330209 ATTTT-ATA
1 ATTTTAATA
*
46330217 ATTTTTTTATA
1 A--TTTTAATA
* *
46330228 A-ATTAGTA
1 ATTTTAATA
*
46330236 ACTTTAATA
1 ATTTTAATA
*
46330245 AATTTATATCA
1 ATTTTA-AT-A
46330256 ATTTTAATA
1 ATTTTAATA
*
46330265 TTTTTAA-A
1 ATTTTAATA
*
46330273 ATTTTTATA
1 ATTTTAATA
* *
46330282 ATTCTTTACA
1 ATT-TTAATA
**
46330292 ATTTTTTTTA
1 A-TTTTAATA
* *
46330302 TTTTTAAGA
1 ATTTTAATA
*
46330311 ATTCTAATA
1 ATTTTAATA
* *
46330320 CCTTTT--TG
1 -ATTTTAATA
46330328 ATTTTAA-A
1 ATTTTAATA
46330336 TATTTTAAATA
1 -ATTTT-AATA
* *
46330347 AGTTTATTA
1 ATTTTAATA
46330356 ATTTT-ATA
1 ATTTTAATA
*
46330364 ATTTTTTTATA
1 A--TTTTAATA
* *
46330375 A-ATTAGTA
1 ATTTTAATA
*
46330383 ACTTTAATA
1 ATTTTAATA
*
46330392 AATTTATATCA
1 ATTTTA-AT-A
46330403 ATTTTAATA
1 ATTTTAATA
*
46330412 TTTTTAA-A
1 ATTTTAATA
*
46330420 ATTTTTATA
1 ATTTTAATA
* *
46330429 ATTCTTTACA
1 ATT-TTAATA
**
46330439 ATTTTTTTTA
1 A-TTTTAATA
* *
46330449 TTTTTAAGA
1 ATTTTAATA
*
46330458 ATTCTAATA
1 ATTTTAATA
* *
46330467 CCTTTT--TG
1 -ATTTTAATA
46330475 ATTTTAA-A
1 ATTTTAATA
46330483 TATTTTAAATA
1 -ATTTT-AATA
* *
46330494 AGTTTATTA
1 ATTTTAATA
46330503 ATTTT-ATA
1 ATTTTAATA
*
46330511 ATTTTTTTATA
1 A--TTTTAATA
* *
46330522 A-ATTAGTA
1 ATTTTAATA
*
46330530 ACTTTAATA
1 ATTTTAATA
*
46330539 AATTTATATCA
1 ATTTTA-AT-A
46330550 ATTTTAATA
1 ATTTTAATA
*
46330559 TTTTTAA-A
1 ATTTTAATA
*
46330567 ATTTTTATA
1 ATTTTAATA
* *
46330576 ATTCTTTACA
1 ATT-TTAATA
**
46330586 ATTTTTTTTA
1 A-TTTTAATA
* *
46330596 TTTTTAAGA
1 ATTTTAATA
*
46330605 ATTCTAATA
1 ATTTTAATA
* *
46330614 CCTTTT--TG
1 -ATTTTAATA
46330622 ATTTTAA-A
1 ATTTTAATA
46330630 TATTTTAAATA
1 -ATTTT-AATA
* *
46330641 AGTTTATTA
1 ATTTTAATA
46330650 ATTTT-ATA
1 ATTTTAATA
*
46330658 ATTTTTTTATA
1 A--TTTTAATA
* *
46330669 A-ATTAGTA
1 ATTTTAATA
*
46330677 ACTTTAATA
1 ATTTTAATA
*
46330686 AATTTATATCA
1 ATTTTA-AT-A
46330697 ATTTTAATA
1 ATTTTAATA
*
46330706 TTTTTAA-A
1 ATTTTAATA
*
46330714 ATTTTTATA
1 ATTTTAATA
46330723 ATT
1 ATT
46330726 CTTTACAATT
Statistics
Matches: 484, Mismatches: 130, Indels: 138
0.64 0.17 0.18
Matches are distributed among these distances:
7 16 0.03
8 74 0.15
9 209 0.43
10 122 0.25
11 63 0.13
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTTTAATA
Found at i:46330166 original size:19 final size:18
Alignment explanation
Indices: 46330110--46330166 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46330100 TTTATATCAA
*
46330110 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46330128 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330147 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330166 T
1 T
46330167 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330313 original size:19 final size:18
Alignment explanation
Indices: 46330257--46330313 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46330247 TTTATATCAA
*
46330257 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46330275 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330294 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330313 T
1 T
46330314 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330460 original size:19 final size:18
Alignment explanation
Indices: 46330404--46330460 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46330394 TTTATATCAA
*
46330404 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46330422 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330441 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330460 T
1 T
46330461 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330607 original size:19 final size:18
Alignment explanation
Indices: 46330551--46330607 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46330541 TTTATATCAA
*
46330551 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46330569 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330588 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330607 T
1 T
46330608 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330754 original size:19 final size:18
Alignment explanation
Indices: 46330698--46330754 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
46330688 TTTATATCAA
*
46330698 TTTTAATATTTTTAAAAT
1 TTTTATTATTTTTAAAAT
* *
46330716 TTTTATAATTCTTTACAAT
1 TTTTATTATT-TTTAAAAT
*
46330735 TTTTTTTATTTTTAAGAAT
1 TTTTATTATTTTTAA-AAT
46330754 T
1 T
46330755 CTAATACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTATTTTTAAAAT
Found at i:46330885 original size:147 final size:147
Alignment explanation
Indices: 46329959--46330862 Score: 1808
Period size: 147 Copynumber: 6.1 Consensus size: 147
46329949 GTTTATAAGT
46329959 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330024 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330089 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330106 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330171 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330236 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330253 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330318 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330383 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330400 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330465 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330530 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330547 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330612 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330677 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330694 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
1 TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
46330759 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
66 TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
46330824 ACTTTAATAAATTTATA
131 ACTTTAATAAATTTATA
46330841 TCAATTTTAATATTTTTAAAAT
1 TCAATTTTAATATTTTTAAAAT
46330863 ATAATATATT
Statistics
Matches: 757, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 757 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (147 bp):
TCAATTTTAATATTTTTAAAATTTTTATAATTCTTTACAATTTTTTTTATTTTTAAGAATTCTAA
TACCTTTTTGATTTTAAATATTTTAAATAAGTTTATTAATTTTATAATTTTTTTATAAATTAGTA
ACTTTAATAAATTTATA
Found at i:46331786 original size:5 final size:5
Alignment explanation
Indices: 46331778--46331802 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46331768 TTGCAAGTGA
46331778 GGGGT GGGGT GGGGT GGGGT GGGGT
1 GGGGT GGGGT GGGGT GGGGT GGGGT
46331803 AGGGATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
GGGGT
Found at i:46339705 original size:255 final size:255
Alignment explanation
Indices: 46339254--46339766 Score: 1026
Period size: 255 Copynumber: 2.0 Consensus size: 255
46339244 TCAATGTTGG
46339254 TTTGAACAATAAAAAAAAAAAAAAAAAAAGGGTGAGAGTGCATGTGAAGCCTTTTTGTACATTGA
1 TTTGAACAATAAAAAAAAAAAAAAAAAAAGGGTGAGAGTGCATGTGAAGCCTTTTTGTACATTGA
46339319 ACACTTACCCACATATAAATACACTGTACTTCTTCACAGTGTTAGGTATTCAACCTTTTTTGCTT
66 ACACTTACCCACATATAAATACACTGTACTTCTTCACAGTGTTAGGTATTCAACCTTTTTTGCTT
46339384 TCTCTTGGGGATATAACTTGTTAATCATCCACTTGCTACTTGTTTGACTATCAATTAATCAATTT
131 TCTCTTGGGGATATAACTTGTTAATCATCCACTTGCTACTTGTTTGACTATCAATTAATCAATTT
46339449 GTTTTATATATTAAATGTTTAAAGTTGGTACCAAACACATATATTTTCATTATTCCACAT
196 GTTTTATATATTAAATGTTTAAAGTTGGTACCAAACACATATATTTTCATTATTCCACAT
46339509 TTTGAACAATAAAAAAAAAAAAAAAAAAAGGGTGAGAGTGCATGTGAAGCCTTTTTGTACATTGA
1 TTTGAACAATAAAAAAAAAAAAAAAAAAAGGGTGAGAGTGCATGTGAAGCCTTTTTGTACATTGA
46339574 ACACTTACCCACATATAAATACACTGTACTTCTTCACAGTGTTAGGTATTCAACCTTTTTTGCTT
66 ACACTTACCCACATATAAATACACTGTACTTCTTCACAGTGTTAGGTATTCAACCTTTTTTGCTT
46339639 TCTCTTGGGGATATAACTTGTTAATCATCCACTTGCTACTTGTTTGACTATCAATTAATCAATTT
131 TCTCTTGGGGATATAACTTGTTAATCATCCACTTGCTACTTGTTTGACTATCAATTAATCAATTT
46339704 GTTTTATATATTAAATGTTTAAAGTTGGTACCAAACACATATATTTTCATTATTCCACAT
196 GTTTTATATATTAAATGTTTAAAGTTGGTACCAAACACATATATTTTCATTATTCCACAT
46339764 TTT
1 TTT
46339767 TGTTTTCTTT
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 258 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (255 bp):
TTTGAACAATAAAAAAAAAAAAAAAAAAAGGGTGAGAGTGCATGTGAAGCCTTTTTGTACATTGA
ACACTTACCCACATATAAATACACTGTACTTCTTCACAGTGTTAGGTATTCAACCTTTTTTGCTT
TCTCTTGGGGATATAACTTGTTAATCATCCACTTGCTACTTGTTTGACTATCAATTAATCAATTT
GTTTTATATATTAAATGTTTAAAGTTGGTACCAAACACATATATTTTCATTATTCCACAT
Found at i:46346873 original size:1 final size:1
Alignment explanation
Indices: 46346867--46346933 Score: 134
Period size: 1 Copynumber: 67.0 Consensus size: 1
46346857 AACCTGTCTC
46346867 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46346932 TT
1 TT
46346934 AAATATATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46347467 original size:24 final size:23
Alignment explanation
Indices: 46347429--46347473 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
46347419 TTGTGTATAA
*
46347429 ATAAATAATTATATTAATTTAAT
1 ATAAAAAATTATATTAATTTAAT
*
46347452 ATAAAAAATATATATTTATTTA
1 ATAAAAAAT-TATATTAATTTA
46347474 TCTAAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAAAAATTATATTAATTTAAT
Found at i:46347557 original size:19 final size:19
Alignment explanation
Indices: 46347520--46347557 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
46347510 ATAGTTGCAC
*
46347520 CAAATTAAAATATTTATAT
1 CAAATTAAAATATTAATAT
46347539 CAAATTATAAAT-TTAATAT
1 CAAATTA-AAATATTAATAT
46347558 TTATTCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
CAAATTAAAATATTAATAT
Found at i:46354173 original size:43 final size:43
Alignment explanation
Indices: 46354116--46354324 Score: 248
Period size: 43 Copynumber: 4.9 Consensus size: 43
46354106 CGCTTACAGA
*
46354116 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTGTGC
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTGC
* **
46354159 AAAAAACGCCGCTAAAGATCATGTTCTCTAGCGGCGC-TAAG-
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTGC
* * * *
46354200 AAAAAACGCCACTAAAGATCGTGTTCTTTAGCGGCGCTTGGGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTGC
*
46354243 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TATC
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGT-GC
* * *
46354286 TACAAACGCCGCTAAA-AGT-AGTGTGCTTTAGCGGCGCTT
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
46354325 ATTTCAGAAA
Statistics
Matches: 144, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
41 34 0.24
42 6 0.04
43 104 0.72
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGTGC
Found at i:46354255 original size:84 final size:86
Alignment explanation
Indices: 46354102--46354280 Score: 281
Period size: 84 Copynumber: 2.1 Consensus size: 86
46354092 CTAACTTTTT
* * * *
46354102 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTGTGCAAAAAACG
1 GCGGCGC-TACAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACG
46354167 CCGCTAAAGATCATGTTCTCTA
65 CCGCTAAAGATCATGTTCTCTA
*
46354189 GCGGCGCTA-AG-AAAAAACGCCACTAAAGATCGTGTTCTTTAGCGGCGCTTGGGAAAAAAACGC
1 GCGGCGCTACAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACGC
*
46354252 CGCTAAAGATCATGTTCTTTA
66 CGCTAAAGATCATGTTCTCTA
46354273 GCGGCGCT
1 GCGGCGCT
46354281 TTATCTACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
84 75 0.87
85 2 0.02
86 2 0.02
87 7 0.08
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (86 bp):
GCGGCGCTACAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACGC
CGCTAAAGATCATGTTCTCTA
Found at i:46354820 original size:21 final size:21
Alignment explanation
Indices: 46354761--46354822 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
46354751 TGAACCTTTG
* * *
46354761 CTTCTCTCGCTGCGGCATCTG
1 CTTCTCTCGCTGCAGCCTCTA
46354782 CTTCTCTCGCTGCAGCCTCTA
1 CTTCTCTCGCTGCAGCCTCTA
* *
46354803 CTTCCCTCGCTGCCGCCTCT
1 CTTCTCTCGCTGCAGCCTCT
46354823 GTTTTAAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.05, C:0.45, G:0.18, T:0.32
Consensus pattern (21 bp):
CTTCTCTCGCTGCAGCCTCTA
Found at i:46361722 original size:27 final size:24
Alignment explanation
Indices: 46361691--46361749 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 24
46361681 ACTATTCCAG
46361691 GTTATGTAAGTTGTGTAATATATTT
1 GTTATGTAAGTTGTGT-ATATATTT
* *
46361716 AAGTTATGTAAGTTTTGTTTATATTT
1 --GTTATGTAAGTTGTGTATATATTT
46361742 GTTATGTA
1 GTTATGTA
46361750 TGCTATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 8 0.27
26 7 0.23
27 15 0.50
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (24 bp):
GTTATGTAAGTTGTGTATATATTT
Found at i:46361840 original size:13 final size:15
Alignment explanation
Indices: 46361821--46361861 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
46361811 CATATAAGTT
46361821 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
46361835 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
46361849 TTATGTAAGTTAT
1 -TATGTAAGTTAT
46361862 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:46361856 original size:16 final size:16
Alignment explanation
Indices: 46361820--46361898 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
46361810 ACATATAAGT
46361820 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
46361835 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
46361849 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
46361867 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
46361883 TTAAGTAAGTCATGTA
1 TTATGTAAGTTATGTA
46361899 GGCTATGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:46361972 original size:19 final size:20
Alignment explanation
Indices: 46361950--46361996 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
46361940 TTTTTCAAGT
* *
46361950 ATATATAAAATTTTA-ATAA
1 ATATATAAAACTGTATATAA
46361969 ATATATTAAAACTGTATATAA
1 ATATA-TAAAACTGTATATAA
46361990 ATATATA
1 ATATATA
46361997 TATCAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATATAAAACTGTATATAA
Found at i:46362658 original size:50 final size:51
Alignment explanation
Indices: 46362599--46362700 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
46362589 AGGAATAAAT
46362599 ACCTTAAATTGCCTCAATTCCGAAGCAAATCCTGG-AAAAAAAAGACATAA
1 ACCTTAAATTGCCTCAATTCCGAAGCAAATCCTGGAAAAAAAAAGACATAA
46362649 ACCTTAAATTGCCTCAATTCCGAAGCAAATCCTGGAAAAAAAAAGACATAA
1 ACCTTAAATTGCCTCAATTCCGAAGCAAATCCTGGAAAAAAAAAGACATAA
46362700 A
1 A
46362701 TACATTAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 35 0.69
51 16 0.31
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.20
Consensus pattern (51 bp):
ACCTTAAATTGCCTCAATTCCGAAGCAAATCCTGGAAAAAAAAAGACATAA
Found at i:46363284 original size:19 final size:19
Alignment explanation
Indices: 46363260--46363301 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
46363250 AAATTGAATT
46363260 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
46363279 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
46363298 TTCT
1 TTCT
46363302 AATTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTGTTTTCATTTGCATC
Found at i:46363307 original size:19 final size:19
Alignment explanation
Indices: 46363266--46363307 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
46363256 AATTTTCTGT
**
46363266 TTTCATTTGCATCTTCTGT
1 TTTCATTTGCATCTTCTAA
46363285 TTTCATTTGCATCTTCTAA
1 TTTCATTTGCATCTTCTAA
46363304 TTTC
1 TTTC
46363308 TAATTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTCATTTGCATCTTCTAA
Found at i:46364310 original size:163 final size:165
Alignment explanation
Indices: 46364112--46364475 Score: 646
Period size: 163 Copynumber: 2.2 Consensus size: 165
46364102 TCATAATTTT
46364112 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCCCATTTTTCTGGCGTTTTCTACAAAAGCGCCA
1 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCCCATTTTTCTGGCGTTTTCTACAAAAGCGCCA
* *
46364177 CTAACAAATTAAATTCTTCTACTGAAACGACACTGTTTTTTA-G-ATATTTTAAAACA-TTTTTT
66 CTAACAAATTAAATTCTTCTACTGAAACGACACCGATTTTTAGGAAT-TTTTAAAA-ATTTTTTT
46364239 TAATTCATATTT-AAAAACACAATATATAATTACAAA
129 TAATTCATATTTAAAAAACACAATATATAATTACAAA
46364275 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCCCATTTTTCTGGCGTTTTCTACAAAAGCGCCA
1 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCCCATTTTTCTGGCGTTTTCTACAAAAGCGCCA
46364340 CTAACAAATTAAATTCTTCTACTGAAACGACACCGATTTTTAGGAATTTTTAAAAATTGTTTTTT
66 CTAACAAATTAAATTCTTCTACTGAAACGACACCGATTTTTAGGAATTTTTAAAAA-T-TTTTTT
46364405 TAATTCATATTTAAAAAACACAATATATAATTACAAA
129 TAATTCATATTTAAAAAACACAATATATAATTACAAA
46364442 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCC
1 TTGCGGCGTTTACGAATAAAACGCCGCTAATGCC
46364476 NNNNNNNNNN
Statistics
Matches: 193, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
163 106 0.55
164 9 0.05
165 2 0.01
166 18 0.09
167 58 0.30
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (165 bp):
TTGCGGCGTTTACGAATAAAACGCCGCTAATGCCCATTTTTCTGGCGTTTTCTACAAAAGCGCCA
CTAACAAATTAAATTCTTCTACTGAAACGACACCGATTTTTAGGAATTTTTAAAAATTTTTTTTA
ATTCATATTTAAAAAACACAATATATAATTACAAA
Found at i:46365828 original size:41 final size:41
Alignment explanation
Indices: 46365769--46365873 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
46365759 ATATTTTTTT
* *
46365769 GCGGCGCTT-CAACAAAAACGCCGCT-AAACCCTTAACATTA
1 GCGGCGCTTAC-ATAAAAACGCCGCTAAAAACCTTAACATTA
* * *
46365809 GCGGCGTTTATCATAAAAACGCCGCTAAAAATCTTAACTTTA
1 GCGGCGCTTA-CATAAAAACGCCGCTAAAAACCTTAACATTA
*
46365851 GCGTCGCTTACATAAAAACGCCG
1 GCGGCGCTTACATAAAAACGCCG
46365874 GCTAGACCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 8 0.15
41 26 0.47
42 21 0.38
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTACATAAAAACGCCGCTAAAAACCTTAACATTA
Found at i:46366129 original size:39 final size:41
Alignment explanation
Indices: 46366086--46366192 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 41
46366076 ATTTTTTTTG
46366086 GCGGCGTTTT-TGTCAAAACGCCGCTAATG--CATATTTTCA
1 GCGGCGTTTTCTGTCAAAACGCCGCTAATGCTCAT-TTTTCA
* * * *
46366125 GCGGCGTTTTCT-T-AGTAACGCCGCGAAAGCTCATTTTTTA
1 GCGGCGTTTTCTGTCA-AAACGCCGCTAATGCTCATTTTTCA
46366165 GCGGCGTTTTCTGTC-AAACGCCGCTAAT
1 GCGGCGTTTTCTGTCAAAACGCCGCTAAT
46366193 TCCTGACTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
38 1 0.02
39 22 0.40
40 28 0.51
41 4 0.07
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (41 bp):
GCGGCGTTTTCTGTCAAAACGCCGCTAATGCTCATTTTTCA
Found at i:46366185 original size:40 final size:38
Alignment explanation
Indices: 46366079--46366188 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 38
46366069 CGTTGGGATT
* * *
46366079 TTTTTTGGCGGCGTTTT-TGTCAAAACGCCGCTAATGCA
1 TTTTTTAGCGGCGTTTTCTGTC-AAACGCCGCGAAAGCA
*
46366117 TATTTTCAGCGGCGTTTTCT-T-AGTAACGCCGCGAAAGCTCA
1 T-TTTTTAGCGGCGTTTTCTGTCA--AACGCCGCGAAAG--CA
46366158 TTTTTTAGCGGCGTTTTCTGTCAAACGCCGC
1 TTTTTTAGCGGCGTTTTCTGTCAAACGCCGC
46366189 TAATTCCTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 26 0.44
40 26 0.44
41 4 0.07
42 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (38 bp):
TTTTTTAGCGGCGTTTTCTGTCAAACGCCGCGAAAGCA
Found at i:46374770 original size:87 final size:87
Alignment explanation
Indices: 46374621--46374883 Score: 325
Period size: 87 Copynumber: 3.0 Consensus size: 87
46374611 GTTAACGCAG
* * ** * * * *
46374621 GAAGGCAAGATCTGCTATCTTTGACCTGCTCCA-CTTCAACTGAGAGAGGAAAGGTTTGTGTCTT
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTCTT
* *
46374685 TGACCTGTTTCGCTGTCAATGCA
65 TAACCTGCTTCGCTGTCAATGCA
* *
46374708 GAGGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTC
1 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTT
46374773 AACCTGCTTCGCTGTCAATGCA
66 AACCTGCTTCGCTGTCAATGCA
* * *
46374795 GGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAAGCAAAGG-TTGGGTCT
1 -GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGC-AAGGTTTGTGTCT
*
46374859 TTCACCTGCCTTC-CTGTCAATGCA
64 TTAACCTG-CTTCGCTGTCAATGCA
46374883 G
1 G
46374884 GAANNNNNNN
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
87 74 0.48
88 72 0.47
89 8 0.05
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (87 bp):
GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTT
AACCTGCTTCGCTGTCAATGCA
Found at i:46374844 original size:45 final size:45
Alignment explanation
Indices: 46374711--46374844 Score: 143
Period size: 44 Copynumber: 3.0 Consensus size: 45
46374701 CAATGCAGAG
*
46374711 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAG-A
1 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAA
* * * ** *
46374755 GGCAAGGTTTG-TGTCTTCAACCTGCTTCGC-TGTCAA-TGCA-GGAA
1 GGCAAGATCTGTTGTCTTCAACCAGC-TC-CATCACAACCG-AGGGAA
46374799 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAA
1 GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAA
46374844 G
1 G
46374845 CAAAGGTTGG
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
43 16 0.23
44 33 0.48
45 20 0.29
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (45 bp):
GGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAA
Found at i:46374859 original size:88 final size:88
Alignment explanation
Indices: 46374617--46374886 Score: 327
Period size: 88 Copynumber: 3.1 Consensus size: 88
46374607 CGTCGTTAAC
* * ** * * * *
46374617 GCAGGAAGGCAAGATCTGCTATCTTTGACCTGCTCCA-CTTCAACTGAGAG-AGGAAAGGTTTGT
1 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAAGCAAAGGTTTGT
* *
46374680 GTCTTTGACCTGTTTCGCTGTCAAT
65 GTC-TTCACCTGCTTCGCTGTCAAT
* *
46374705 GCA-GAGGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGC-AAGGTTTGTG
1 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAAGCAAAGGTTTGTG
46374768 TCTTCAACCTGCTTCGCTGTCAAT
66 TCTTC-ACCTGCTTCGCTGTCAAT
* *
46374792 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAAGCAAAGG-TTGGG
1 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAAGCAAAGGTTTGTG
46374856 TCTTTCACCTGCCTTC-CTGTCAAT
66 TC-TTCACCTG-CTTCGCTGTCAAT
46374880 GCAGGAA
1 GCAGGAA
46374887 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
86 2 0.01
87 68 0.43
88 78 0.49
89 11 0.07
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (88 bp):
GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAAGCAAAGGTTTGTG
TCTTCACCTGCTTCGCTGTCAAT
Found at i:46378207 original size:20 final size:21
Alignment explanation
Indices: 46378175--46378222 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
46378165 CCATTTTTAC
* *
46378175 TCTTTTCTTTTTTCATTTTTCA
1 TCTTTTC-ATTTTCATTCTTCA
46378197 T-TTTTCATTTTCATTCTTCA
1 TCTTTTCATTTTCATTCTTCA
46378217 TCTTTT
1 TCTTTT
46378223 TCTTTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 13 0.57
21 9 0.39
22 1 0.04
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTCATTTTCATTCTTCA
Found at i:46378209 original size:13 final size:13
Alignment explanation
Indices: 46378177--46378217 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
46378167 ATTTTTACTC
*
46378177 TTTTCTTTTTTCA
1 TTTTCATTTTTCA
46378190 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
*
46378204 TTTTCATTCTTCA
1 TTTTCATTTTTCA
46378217 T
1 T
46378218 CTTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:46378230 original size:7 final size:7
Alignment explanation
Indices: 46378177--46378222 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
46378167 ATTTTTACTC
*
46378177 TTTTCTT
1 TTTTCAT
46378184 TTTTCAT
1 TTTTCAT
46378191 TTTTCAT
1 TTTTCAT
46378198 TTTTCA-
1 TTTTCAT
46378204 TTTTCAT
1 TTTTCAT
*
46378211 TCTTCAT
1 TTTTCAT
46378218 CTTTT
1 -TTTT
46378223 TCTTTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
6 6 0.18
7 25 0.74
8 3 0.09
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCAT
Found at i:46378646 original size:42 final size:43
Alignment explanation
Indices: 46378600--46378689 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
46378590 GCTTTTCATA
**
46378600 TTTTTATTTTGACTTTGATTTATTTCTCT-TTTTC-TTTTTGTT
1 TTTTTATTTTGACTTTGATTT-TTTCTCTCTTTTCATTTTCCTT
* *
46378642 TTTTTATTTTTATTTTGATTTTTTCTCTCTTTTCATTTTCCTT
1 TTTTTATTTTGACTTTGATTTTTTCTCTCTTTTCATTTTCCTT
46378685 TTTTT
1 TTTTT
46378690 TTGAATCGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 7 0.17
42 24 0.57
43 11 0.26
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76
Consensus pattern (43 bp):
TTTTTATTTTGACTTTGATTTTTTCTCTCTTTTCATTTTCCTT
Found at i:46384023 original size:2 final size:2
Alignment explanation
Indices: 46384012--46384045 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
46384002 TGGATAACAT
*
46384012 TA TA -A TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46384046 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46384115 original size:32 final size:31
Alignment explanation
Indices: 46384073--46384134 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
46384063 TTAGAATGAT
*
46384073 AAAGCATAAAAAT-ATAGGTATGTGTATAAAAC
1 AAAGCATAAAAATGATA--TAAGTGTATAAAAC
*
46384105 AAAGCCTAAAAATGATATAAGTGTATAAAA
1 AAAGCATAAAAATGATATAAGTGTATAAAA
46384135 AAAAATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 12 0.44
32 12 0.44
33 3 0.11
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (31 bp):
AAAGCATAAAAATGATATAAGTGTATAAAAC
Found at i:46384246 original size:4 final size:4
Alignment explanation
Indices: 46384237--46384263 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
46384227 TAATAATGAG
46384237 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
46384264 CTGAGTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:46410762 original size:46 final size:46
Alignment explanation
Indices: 46410709--46410848 Score: 244
Period size: 46 Copynumber: 3.0 Consensus size: 46
46410699 ACAATGCCAT
* *
46410709 AACTCAGTATGGTTTCCTTCACTGGAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
46410755 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
46410801 AACTCTGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
46410847 AA
1 AA
46410849 TTTTTCCAGG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:46411090 original size:38 final size:38
Alignment explanation
Indices: 46411038--46411113 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
46411028 ACAATTAATC
*
46411038 ATAAAAATTTAGCCGTATGAACTTACCTGGGCAAATTT
1 ATAAAAATTCAGCCGTATGAACTTACCTGGGCAAATTT
* *
46411076 ATAAAAATTCAGCCGTATGAACTTACTTGGGCCAATTT
1 ATAAAAATTCAGCCGTATGAACTTACCTGGGCAAATTT
46411114 GTAGGATTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (38 bp):
ATAAAAATTCAGCCGTATGAACTTACCTGGGCAAATTT
Found at i:46411675 original size:16 final size:17
Alignment explanation
Indices: 46411639--46411676 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
46411629 TAGATTACAA
46411639 AATTCACTAAATCACAG
1 AATTCACTAAATCACAG
*
46411656 AATTCACTAATTCA-AG
1 AATTCACTAAATCACAG
46411672 AATTC
1 AATTC
46411677 TTCTAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (17 bp):
AATTCACTAAATCACAG
Found at i:46413036 original size:26 final size:25
Alignment explanation
Indices: 46413001--46413070 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
46412991 CAACTCTTTA
* *
46413001 TGAACGTCCTGATATATGGCTC-TT
1 TGAACTTCCTGATATATGGCTCGCT
*
46413025 AATGAGCTTCCT-A-ATATGGCTCGCT
1 --TGAACTTCCTGATATATGGCTCGCT
46413050 TGAACTTCCTGATATATGGCT
1 TGAACTTCCTGATATATGGCT
46413071 ATCCGGAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 9 0.24
24 10 0.27
25 10 0.27
26 8 0.22
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (25 bp):
TGAACTTCCTGATATATGGCTCGCT
Found at i:46415066 original size:20 final size:20
Alignment explanation
Indices: 46415041--46415078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46415031 AAAGGTTAAC
46415041 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
46415061 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
46415079 AATAAAACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:46416018 original size:41 final size:41
Alignment explanation
Indices: 46415942--46416038 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
46415932 ATATGATTAG
* *
46415942 CACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAACGAC
1 CACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACGAC
* **
46415982 CACTAAGTGTGCGAAATTAAATAATGATGTTAAATAACGGG
1 CACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACGAC
46416023 CACTAAGTGTGCGAAA
1 CACTAAGTGTGCGAAA
46416039 CCGAGGTCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.25
41 38 0.75
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (41 bp):
CACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACGAC
Found at i:46416074 original size:40 final size:40
Alignment explanation
Indices: 46416019--46416098 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
46416009 TGTTAAATAA
46416019 CGGGCACTAAGTGTGCGAAACCGAGGTCAATTTGGTTAAG
1 CGGGCACTAAGTGTGCGAAACCGAGGTCAATTTGGTTAAG
46416059 CGGGCACTAAGTGTGCGAAACCGAGGTCAATTTGGTTAAG
1 CGGGCACTAAGTGTGCGAAACCGAGGTCAATTTGGTTAAG
46416099 TGAGAGAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (40 bp):
CGGGCACTAAGTGTGCGAAACCGAGGTCAATTTGGTTAAG
Found at i:46448339 original size:6 final size:6
Alignment explanation
Indices: 46448328--46448357 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
46448318 CAAACAACCG
*
46448328 CCTTCT CCTTCT CCTTCT GCTTCT CCTTCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
46448358 TCTACTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (6 bp):
CCTTCT
Found at i:46450420 original size:23 final size:24
Alignment explanation
Indices: 46450393--46450438 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46450383 TTTGTTTATT
* *
46450393 AATTGTAT-GAATTTTTTAAAATG
1 AATTGTATGGAAATATTTAAAATG
46450416 AATTGTATGGAAATATTTAAAAT
1 AATTGTATGGAAATATTTAAAAT
46450439 AATAAATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (24 bp):
AATTGTATGGAAATATTTAAAATG
Found at i:46450760 original size:355 final size:355
Alignment explanation
Indices: 46450109--46450820 Score: 1415
Period size: 355 Copynumber: 2.0 Consensus size: 355
46450099 TATTCTAATA
*
46450109 TTAACTATCAATATTTTAAAATTAAATGTATATATTATTGTGTTTTAATTTGTTAATCATATTAT
1 TTAACTATCAAGATTTTAAAATTAAATGTATATATTATTGTGTTTTAATTTGTTAATCATATTAT
46450174 TCCCAAAAAAAATATAAATAAAGAAAACTAATCTTATATATAATATTTAAAAGTAAAGCTTCTCA
66 TCCCAAAAAAAATATAAATAAAGAAAACTAATCTTATATATAATATTTAAAAGTAAAGCTTCTCA
46450239 GAAAAAAAAATCTTATGTGATGGCATATAATAAAATTTATGTATTTATTTACTTTTACTTTATAG
131 GAAAAAAAAATCTTATGTGATGGCATATAATAAAATTTATGTATTTATTTACTTTTACTTTATAG
46450304 TTTTCTTTATATGGAATTATTTTGTATGCAATAATCATTTAATTAATTCAATGCTGTGTATCAAT
196 TTTTCTTTATATGGAATTATTTTGTATGCAATAATCATTTAATTAATTCAATGCTGTGTATCAAT
46450369 TGTATGACAATAAATTTGTTTATTAATTGTATGAATTTTTTAAAATGAATTGTATGGAAATATTT
261 TGTATGACAATAAATTTGTTTATTAATTGTATGAATTTTTTAAAATGAATTGTATGGAAATATTT
46450434 AAAATAATAAATACGTGTAAATAAACTTTT
326 AAAATAATAAATACGTGTAAATAAACTTTT
46450464 TTAACTATCAAGATTTTAAAATTAAATGTATATATTATTGTGTTTTAATTTGTTAATCATATTAT
1 TTAACTATCAAGATTTTAAAATTAAATGTATATATTATTGTGTTTTAATTTGTTAATCATATTAT
46450529 TCCCAAAAAAAATATAAATAAAGAAAACTAATCTTATATATAATATTTAAAAGTAAAGCTTCTCA
66 TCCCAAAAAAAATATAAATAAAGAAAACTAATCTTATATATAATATTTAAAAGTAAAGCTTCTCA
46450594 GAAAAAAAAATCTTATGTGATGGCATATAATAAAATTTATGTATTTATTTACTTTTACTTTATAG
131 GAAAAAAAAATCTTATGTGATGGCATATAATAAAATTTATGTATTTATTTACTTTTACTTTATAG
46450659 TTTTCTTTATATGGAATTATTTTGTATGCAATAATCATTTAATTAATTCAATGCTGTGTATCAAT
196 TTTTCTTTATATGGAATTATTTTGTATGCAATAATCATTTAATTAATTCAATGCTGTGTATCAAT
46450724 TGTATGACAATAAATTTGTTTATTAATTGTATGAATTTTTTAAAATGAATTGTATGGAAATATTT
261 TGTATGACAATAAATTTGTTTATTAATTGTATGAATTTTTTAAAATGAATTGTATGGAAATATTT
46450789 AAAATAATAAATACGTGTAAATAAACTTTT
326 AAAATAATAAATACGTGTAAATAAACTTTT
46450819 TT
1 TT
46450821 TCAAACGAAT
Statistics
Matches: 356, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
355 356 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (355 bp):
TTAACTATCAAGATTTTAAAATTAAATGTATATATTATTGTGTTTTAATTTGTTAATCATATTAT
TCCCAAAAAAAATATAAATAAAGAAAACTAATCTTATATATAATATTTAAAAGTAAAGCTTCTCA
GAAAAAAAAATCTTATGTGATGGCATATAATAAAATTTATGTATTTATTTACTTTTACTTTATAG
TTTTCTTTATATGGAATTATTTTGTATGCAATAATCATTTAATTAATTCAATGCTGTGTATCAAT
TGTATGACAATAAATTTGTTTATTAATTGTATGAATTTTTTAAAATGAATTGTATGGAAATATTT
AAAATAATAAATACGTGTAAATAAACTTTT
Found at i:46450775 original size:23 final size:24
Alignment explanation
Indices: 46450748--46450793 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46450738 TTTGTTTATT
* *
46450748 AATTGTAT-GAATTTTTTAAAATG
1 AATTGTATGGAAATATTTAAAATG
46450771 AATTGTATGGAAATATTTAAAAT
1 AATTGTATGGAAATATTTAAAAT
46450794 AATAAATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (24 bp):
AATTGTATGGAAATATTTAAAATG
Found at i:46452106 original size:19 final size:18
Alignment explanation
Indices: 46452072--46452107 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46452062 AAAAATAAAA
*
46452072 AAAATAAAAAAGTATTTT
1 AAAATAAAAAAATATTTT
46452090 AAAATAAAAAATATATTT
1 AAAATAAAAAA-ATATTT
46452108 ATTATATATT
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATAAAAAAATATTTT
Found at i:46457838 original size:16 final size:16
Alignment explanation
Indices: 46457819--46457850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46457809 AATAATATTG
46457819 TAAAGAAAAAAGATGA
1 TAAAGAAAAAAGATGA
*
46457835 TAAAGAAAGAAGATGA
1 TAAAGAAAAAAGATGA
46457851 GATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (16 bp):
TAAAGAAAAAAGATGA
Found at i:46468897 original size:22 final size:22
Alignment explanation
Indices: 46468872--46468918 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
46468862 TTGAAAGAAA
46468872 GCAACAAAAATTATAGTTTTTT
1 GCAACAAAAATTATAGTTTTTT
46468894 GCAACAAAAATTATAGTTTTTT
1 GCAACAAAAATTATAGTTTTTT
46468916 GCA
1 GCA
46468919 GAAGTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
GCAACAAAAATTATAGTTTTTT
Found at i:46471346 original size:2 final size:2
Alignment explanation
Indices: 46471341--46471376 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
46471331 AATTCATAAA
*
46471341 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46471377 GCAGGCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46474528 original size:19 final size:19
Alignment explanation
Indices: 46474504--46474542 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
46474494 AACAAAAGAG
46474504 TAAGAAAATTAGGTAAGGT
1 TAAGAAAATTAGGTAAGGT
46474523 TAAGAAAATTAGGTAAGGT
1 TAAGAAAATTAGGTAAGGT
46474542 T
1 T
46474543 TACCAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (19 bp):
TAAGAAAATTAGGTAAGGT
Found at i:46475021 original size:14 final size:14
Alignment explanation
Indices: 46475002--46475033 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
46474992 CGCTGGAAAA
*
46475002 TCCAGAAAATATTT
1 TCCAGAAAACATTT
46475016 TCCAGAAAACATTT
1 TCCAGAAAACATTT
46475030 TCCA
1 TCCA
46475034 CCAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (14 bp):
TCCAGAAAACATTT
Found at i:46498605 original size:14 final size:15
Alignment explanation
Indices: 46498578--46498607 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
46498568 CTGAATTGTA
46498578 TATTAAATATATATT
1 TATTAAATATATATT
46498593 TATTAAA-ATATATT
1 TATTAAATATATATT
46498607 T
1 T
46498608 TTTTTTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAAATATATATT
Found at i:46498638 original size:60 final size:61
Alignment explanation
Indices: 46498549--46498671 Score: 230
Period size: 60 Copynumber: 2.0 Consensus size: 61
46498539 GTTGTAAGAC
46498549 TTTTTTGCCCGGGCCTGGCCTGAATTGTATATTAAATATATATTTATTAA-AATATATTTT
1 TTTTTTGCCCGGGCCTGGCCTGAATTGTATATTAAATATATATTTATTAATAATATATTTT
*
46498609 TTTTTTGCCCGGGCCTGGCCTGAATTGTATATTAAATATATATTTATTAATTATATATTTT
1 TTTTTTGCCCGGGCCTGGCCTGAATTGTATATTAAATATATATTTATTAATAATATATTTT
46498670 TT
1 TT
46498672 GGACTTTTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 50 0.82
61 11 0.18
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (61 bp):
TTTTTTGCCCGGGCCTGGCCTGAATTGTATATTAAATATATATTTATTAATAATATATTTT
Found at i:46498658 original size:15 final size:15
Alignment explanation
Indices: 46498638--46498668 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46498628 CTGAATTGTA
46498638 TATTAAATATATATT
1 TATTAAATATATATT
*
46498653 TATTAATTATATATT
1 TATTAAATATATATT
46498668 T
1 T
46498669 TTTGGACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTAAATATATATT
Found at i:46504906 original size:21 final size:21
Alignment explanation
Indices: 46504859--46504909 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
46504849 ATTTCAATGC
* * *
46504859 AACTACAAAAGGAGGTTACCC
1 AACTTCAAAAGGAGGTGACCA
* *
46504880 ATCTTCAACAGGAGGTGACCA
1 AACTTCAAAAGGAGGTGACCA
46504901 AACTTCAAA
1 AACTTCAAA
46504910 TTGAGTTATC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (21 bp):
AACTTCAAAAGGAGGTGACCA
Found at i:46507608 original size:20 final size:20
Alignment explanation
Indices: 46507583--46507622 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46507573 TGTAAAATGA
*
46507583 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
46507603 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
46507623 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:46507611 original size:34 final size:35
Alignment explanation
Indices: 46507568--46507634 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
46507558 CAGTAAAATA
* *
46507568 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTAGAAAATATTTTAC
46507602 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
46507635 CTGCTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:46516099 original size:53 final size:53
Alignment explanation
Indices: 46516038--46516141 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
46516028 TATGTTCCCT
46516038 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
46516091 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAAT
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAAT
46516142 ATTTTCATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38
Consensus pattern (53 bp):
AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
Found at i:46516251 original size:18 final size:18
Alignment explanation
Indices: 46516213--46516251 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
46516203 TTTACGTTAA
*
46516213 AAATTTTGAATTCTCCGT
1 AAATTTTGAATTCTCAGT
*
46516231 AAATTTTGAATTCTCATT
1 AAATTTTGAATTCTCAGT
46516249 AAA
1 AAA
46516252 CTATTAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
AAATTTTGAATTCTCAGT
Found at i:46538004 original size:23 final size:22
Alignment explanation
Indices: 46537957--46538007 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
46537947 AATTAGTGGG
* *
46537957 TTTTTTTTTTTTCTTGTTTTCC
1 TTTTTTTTTCTTCTTCTTTTCC
46537979 TTTTTTTTTCTT-TTCTTCTTCGC
1 TTTTTTTTTCTTCTTCTT-TTC-C
46538002 TTTTTT
1 TTTTTT
46538008 CTTGACATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTCTTCTTCTTTTCC
Found at i:46538006 original size:24 final size:23
Alignment explanation
Indices: 46537957--46538007 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
46537947 AATTAGTGGG
* **
46537957 TTTTTTTTTTTTCTTGTTTTCCT
1 TTTTTTTTTTTTCTTCTTCGCCT
46537980 TTTTTTTTCTTTTCTTCTTCG-CT
1 TTTTTTTT-TTTTCTTCTTCGCCT
46538003 TTTTT
1 TTTTT
46538008 CTTGACATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTTTTCTTCTTCGCCT
Found at i:46538338 original size:12 final size:11
Alignment explanation
Indices: 46538302--46538359 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
46538292 AGTTTTTTTT
46538302 AAAATTA-AAA
1 AAAATTATAAA
* **
46538312 AAAGTTATTTA
1 AAAATTATAAA
46538323 AAAATTATAAA
1 AAAATTATAAA
46538334 CAAAATTCAT-AA
1 -AAAATT-ATAAA
46538346 AAAATTATAAA
1 AAAATTATAAA
46538357 AAA
1 AAA
46538360 TATATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
10 8 0.21
11 20 0.53
12 8 0.21
13 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:46538355 original size:10 final size:10
Alignment explanation
Indices: 46538302--46538360 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
46538292 AGTTTTTTTT
46538302 AAAATTA-AA
1 AAAATTATAA
*
46538311 AAAAGTTATTTA
1 AAAA-TTA-TAA
46538323 AAAATTATAAA
1 AAAATTAT-AA
46538334 CAAAATTCATAA
1 -AAAATT-ATAA
46538346 AAAATTATAA
1 AAAATTATAA
46538356 AAAAT
1 AAAAT
46538361 ATATTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 4 0.10
10 13 0.31
11 10 0.24
12 13 0.31
13 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:46538484 original size:21 final size:22
Alignment explanation
Indices: 46538458--46538507 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
46538448 TGTTATTTTT
46538458 ATTTTTATTAA-TAATTTTATA
1 ATTTTTATTAAGTAATTTTATA
**
46538479 ATTTTTA-TAAGTTTTTTTATA
1 ATTTTTATTAAGTAATTTTATA
46538500 ATTTTTAT
1 ATTTTTAT
46538508 GGTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTTTATTAAGTAATTTTATA
Found at i:46538514 original size:21 final size:21
Alignment explanation
Indices: 46538472--46538515 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
46538462 TTATTAATAA
46538472 TTTTATAATTTTTATAAGTTT
1 TTTTATAATTTTTATAAGTTT
*
46538493 TTTTATAATTTTTAT-GGTTT
1 TTTTATAATTTTTATAAGTTT
46538513 TTT
1 TTT
46538516 AATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTATAATTTTTATAAGTTT
Found at i:46544022 original size:12 final size:12
Alignment explanation
Indices: 46543980--46544022 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
46543970 TAGAATACTT
*
46543980 AAAAAA-TAGAA
1 AAAAAATTATAA
*
46543991 AAAAAATTGT-A
1 AAAAAATTATAA
46544002 AAAAAATTATAA
1 AAAAAATTATAA
46544014 AAAAAATTA
1 AAAAAATTA
46544023 AAATTGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:46544056 original size:20 final size:20
Alignment explanation
Indices: 46544019--46544058 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46544009 TATAAAAAAA
* * *
46544019 ATTAAAATTGATATAAACTT
1 ATTAAAAATCATAAAAACTT
46544039 ATTAAAAATCATAAAAACTT
1 ATTAAAAATCATAAAAACTT
46544059 GAACTAGACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (20 bp):
ATTAAAAATCATAAAAACTT
Found at i:46544449 original size:9 final size:9
Alignment explanation
Indices: 46544437--46544502 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
46544427 TTATGAATTT
46544437 TTTTTATAA
1 TTTTTATAA
46544446 TTTTTATAA
1 TTTTTATAA
*
46544455 GTTTATATTAA
1 -TTTTTA-TAA
* *
46544466 TTTTAATACTT
1 TTTTTATA--A
46544477 TTTTTATAA
1 TTTTTATAA
*
46544486 TTTTTATGA
1 TTTTTATAA
46544495 TTTTTATA
1 TTTTTATA
46544503 GAATTTAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
9 26 0.58
10 9 0.20
11 10 0.22
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:46544486 original size:20 final size:19
Alignment explanation
Indices: 46544435--46544512 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 19
46544425 TTTTATGAAT
* *
46544435 TTTTTTTATAATTTTTATA
1 TTTTTATATAATTTTAATA
**
46544454 AGTTTATATTAATTTTAATA
1 TTTTTATA-TAATTTTAATA
* *
46544474 CTTTTTTTATAATTTTTATGA
1 -TTTTTATATAATTTTAAT-A
*
46544495 TTTTTATAGAA-TTTAATA
1 TTTTTATATAATTTTAATA
46544513 CGTTTTTATN
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
18 1 0.02
19 10 0.22
20 28 0.62
21 6 0.13
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATATAATTTTAATA
Found at i:46544508 original size:40 final size:39
Alignment explanation
Indices: 46544435--46544519 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
46544425 TTTTATGAAT
*
46544435 TTTTTTTATAATTTTTATAAGTTTATATTAATTTTAATAC
1 TTTTTTTATAATTTTTATAAGTTTATATGAA-TTTAATAC
* *
46544475 TTTTTTTATAATTTTTATGA-TTTTTATAGAATTTAATAC
1 TTTTTTTATAATTTTTATAAGTTTATAT-GAATTTAATAC
*
46544514 GTTTTT
1 TTTTTT
46544520 ATNNNNNNNN
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (39 bp):
TTTTTTTATAATTTTTATAAGTTTATATGAATTTAATAC
Found at i:46545011 original size:11 final size:10
Alignment explanation
Indices: 46544951--46545013 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
46544941 AATTTTTTAA
46544951 TTAATAATTTT
1 TTAAT-ATTTT
46544962 TATAAT-TTTT
1 T-TAATATTTT
**
46544972 TTCTTATTTT
1 TTAATATTTT
46544982 TTAATATTTT
1 TTAATATTTT
**
46544992 TTAGGATTTT
1 TTAATATTTT
46545002 TTAATCATTTT
1 TTAAT-ATTTT
46545013 T
1 T
46545014 ATGAGAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 2 0.05
10 28 0.68
11 7 0.17
12 4 0.10
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (10 bp):
TTAATATTTT
Found at i:46555415 original size:16 final size:16
Alignment explanation
Indices: 46555394--46555425 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46555384 GTTTTGTTGC
*
46555394 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
46555410 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
46555426 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:46568479 original size:24 final size:25
Alignment explanation
Indices: 46568422--46568479 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
46568412 TAGCTTTCAT
*
46568422 GAGCATCCCATTATATAGTTCTTGC
1 GAGCATCCCATTATATAGCTCTTGC
**
46568447 GAGTTTCCCATTA-ATAGCTCTTTG-
1 GAGCATCCCATTATATAGCTC-TTGC
46568471 GAGCATCCC
1 GAGCATCCC
46568480 GATTGTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (25 bp):
GAGCATCCCATTATATAGCTCTTGC
Found at i:46568705 original size:24 final size:25
Alignment explanation
Indices: 46568632--46568705 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
46568622 TCGCTTGAAC
* *
46568632 CTTCCCGATAT-TAGCTCGTATGAG
1 CTTCCCGTTATATGGCTCGTATGAG
* *
46568656 CTTCCCGTTATATGGCTCGAAAGAG
1 CTTCCCGTTATATGGCTCGTATGAG
**
46568681 CTTCTTGTTA-A-GTGCTCGTATGAG
1 CTTCCCGTTATATG-GCTCGTATGAG
46568705 C
1 C
46568706 ATTCGCGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 21 0.52
25 18 0.45
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (25 bp):
CTTCCCGTTATATGGCTCGTATGAG
Found at i:46571432 original size:16 final size:16
Alignment explanation
Indices: 46571411--46571459 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
46571401 ATCATGTAAC
46571411 TATTTTCATATACATA
1 TATTTTCATATACATA
*
46571427 TATTTTCCACAT-CATA
1 TATTTT-CATATACATA
46571443 TA--TTCATATAACATA
1 TATTTTCATAT-ACATA
46571458 TA
1 TA
46571460 CATTTCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 6 0.21
16 12 0.43
17 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTTCATATACATA
Found at i:46571720 original size:25 final size:25
Alignment explanation
Indices: 46571692--46571911 Score: 80
Period size: 25 Copynumber: 8.9 Consensus size: 25
46571682 TATCCGGGCT
46571692 ATATAACAGGAAGCTCATAAGAGCC
1 ATATAACAGGAAGCTCATAAGAGCC
* **
46571717 ATAT-TCAGGAAGCTCATGCGAGCC
1 ATATAACAGGAAGCTCATAAGAGCC
* *
46571741 A-ATAACGGGTAGCTC-TAAAGAGCC
1 ATATAACAGGAAGCTCAT-AAGAGCC
* ** * *
46571765 AT-TAATCAGAAAGCTCCGAATAGTC
1 ATATAA-CAGGAAGCTCATAAGAGCC
* * * *
46571790 ATATATCGGGAAGTTCA-AGCGAGCC
1 ATATAACAGGAAGCTCATA-AGAGCC
* ***
46571815 ATAT--CGGGAAGCTCCGGAGAGCC
1 ATATAACAGGAAGCTCATAAGAGCC
* *
46571838 AT-TAATCATGAAGCTCACAAAGAGCC
1 ATATAA-CAGGAAGCTCA-TAAGAGCC
* * ** *
46571864 -TTTAATCAAGAAGCTCCGAAAAGCC
1 ATATAA-CAGGAAGCTCATAAGAGCC
* *
46571889 ATATAACGGGATGCTCATAAGAG
1 ATATAACAGGAAGCTCATAAGAG
46571912 ATACGGTTTG
Statistics
Matches: 139, Mismatches: 42, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
22 1 0.01
23 19 0.14
24 36 0.26
25 58 0.42
26 25 0.18
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (25 bp):
ATATAACAGGAAGCTCATAAGAGCC
Found at i:46571793 original size:73 final size:73
Alignment explanation
Indices: 46571716--46571853 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 73
46571706 TCATAAGAGC
* * *
46571716 CATAT-TCAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCTAAAGAGCCATTAATCA-GAAAGC
1 CATATATCAGGAAGCTCAAGCGAGCC-ATAACGGGAAGCTCCAAAGAGCCATTAATCATG-AAGC
46571779 TCCGAATAGT
64 TCCGAATAGT
* * * **
46571789 CATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGGAGAGCCATTAATCATGAAGCTC
1 CATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCATTAATCATGAAGCTC
46571854 ACAAAGAGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 37 0.67
74 18 0.33
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (73 bp):
CATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCATTAATCATGAAGCTC
CGAATAGT
Found at i:46571836 original size:23 final size:23
Alignment explanation
Indices: 46571792--46571839 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
46571782 GAATAGTCAT
* *
46571792 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
**
46571815 ATATCGGGAAGCTCCGGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
46571838 AT
1 AT
46571840 TAATCATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:46575499 original size:17 final size:17
Alignment explanation
Indices: 46575477--46575509 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46575467 ATATTTAATA
46575477 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
46575494 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
46575510 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:46583639 original size:19 final size:19
Alignment explanation
Indices: 46583601--46583673 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
46583591 TAAAATTCTA
* *
46583601 TAAAAATCATATAAATTAC
1 TAAAAATCATAAAAAGTAC
46583620 TTAAAAAT-ATAAAAAGTAC
1 -TAAAAATCATAAAAAGTAC
* * *
46583639 TAAAATTGATATAAAATTA-
1 TAAAAATCATA-AAAAGTAC
46583658 TAAAAAATCATAAAAA
1 T-AAAAATCATAAAAA
46583674 CTTGAAATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 6 0.14
19 17 0.39
20 21 0.48
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAAATCATAAAAAGTAC
Found at i:46583655 original size:11 final size:10
Alignment explanation
Indices: 46583457--46583665 Score: 52
Period size: 10 Copynumber: 21.6 Consensus size: 10
46583447 TTAAAAAAGT
46583457 TAAAATTATA
1 TAAAATTATA
*
46583467 TAAACTTATA
1 TAAAATTATA
*
46583477 -AATA-T-TA
1 TAAAATTATA
46583484 TAAAA-TAT-
1 TAAAATTATA
*
46583492 TAAAAATATA
1 TAAAATTATA
* *
46583502 AAAAACCTA-A
1 TAAAA-TTATA
*
46583512 T-AAATTCAAA
1 TAAAATT-ATA
46583522 T-AAATTATA
1 TAAAATTATA
* *
46583531 AAAAATTTTA
1 TAAAATTATA
*
46583541 TAACATTA-A
1 TAAAATTATA
** *
46583550 TAAAACACATT
1 TAAAA-TTATA
*
46583561 TAAAA-TATT
1 TAAAATTATA
46583570 TAAAATTTTATA
1 TAAAA--TTATA
**
46583582 TAAACCTAT-
1 TAAAATTATA
*
46583591 TAAAATTCTA
1 TAAAATTATA
*
46583601 TAAAAATCATA
1 T-AAAATTATA
46583612 T-AAATTACT-
1 TAAAATTA-TA
*
46583621 TAAAAATATA
1 TAAAATTATA
* *
46583631 -AAAAGTA-C
1 TAAAATTATA
46583639 TAAAATTGATA
1 TAAAATT-ATA
46583650 TAAAATTATA
1 TAAAATTATA
*
46583660 AAAAAT
1 TAAAAT
46583666 CATAAAAACT
Statistics
Matches: 144, Mismatches: 34, Indels: 42
0.65 0.15 0.19
Matches are distributed among these distances:
7 2 0.01
8 11 0.08
9 49 0.34
10 53 0.37
11 22 0.15
12 7 0.05
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (10 bp):
TAAAATTATA
Found at i:46587554 original size:32 final size:30
Alignment explanation
Indices: 46587509--46587588 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 30
46587499 TGTTTTATAT
46587509 ATTGCC-AAGTTGATTTATATGTAGATACATAC
1 ATTGCCGAA-TTGATTTATATGT--ATACATAC
* *
46587541 ATTGCCGAATTGATTTCTATATGTATATATAT
1 ATTGCCGAATTGA-TT-TATATGTATACATAC
*
46587573 ATTACCGAATTGATTT
1 ATTGCCGAATTGATTT
46587589 GAGATCCCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 1 0.02
31 2 0.05
32 28 0.67
33 4 0.10
34 7 0.17
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
ATTGCCGAATTGATTTATATGTATACATAC
Found at i:46587694 original size:42 final size:43
Alignment explanation
Indices: 46587588--46587742 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 43
46587578 CGAATTGATT
* * *
46587588 TGAGATCCCGTATAAGACTATATCTGGGATATGACATCGGCATCGATT
1 TGAGATCCCGTATAAGACCATAGCTGGGATAT----T-GGCATCGATA
* *
46587636 TGAGATCCCGTATAAGATCATATCTGGGATA-TGGCATCGATA
1 TGAGATCCCGTATAAGACCATAGCTGGGATATTGGCATCGATA
* * *
46587678 TGAGA-CTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATC-CCGTATAAGACCATAGCTGGGATATTGGCATCGATA
* *
46587721 TGAGATTTCCATATAAGACCAT
1 TGAGA-TCCCGTATAAGACCAT
46587743 GTCTGAGACA
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.01
42 33 0.36
43 17 0.19
44 11 0.12
48 29 0.32
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
TGAGATCCCGTATAAGACCATAGCTGGGATATTGGCATCGATA
Found at i:46596337 original size:6 final size:6
Alignment explanation
Indices: 46596328--46596357 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
46596318 AACAAATAAA
46596328 AATTTG AATTTG AATTTG AATTTG AATTTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG
46596358 GGCAAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
AATTTG
Found at i:46599104 original size:3 final size:3
Alignment explanation
Indices: 46599096--46599128 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
46599086 TTGTGTTCTT
*
46599096 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46599129 ATAAGTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:46609590 original size:6 final size:6
Alignment explanation
Indices: 46609579--46609638 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
46609569 GCCATCATCA
* * * *
46609579 CCACCT CCACCT CCACCT CCACCT CCACCC CCCCCT CCACCG CCTCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
**
46609627 CTTCCT CCACCT
1 CCACCT CCACCT
46609639 ATCCCTCGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.12, C:0.68, G:0.02, T:0.18
Consensus pattern (6 bp):
CCACCT
Found at i:46611353 original size:22 final size:22
Alignment explanation
Indices: 46611328--46611371 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
46611318 TTTTTATATA
46611328 TGTGTAGGAAAGAGTTTAAGTT
1 TGTGTAGGAAAGAGTTTAAGTT
46611350 TGTGTAGGAAAGAGTTTAAGTT
1 TGTGTAGGAAAGAGTTTAAGTT
46611372 CTAACCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (22 bp):
TGTGTAGGAAAGAGTTTAAGTT
Found at i:46617733 original size:6 final size:6
Alignment explanation
Indices: 46617724--46617755 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
46617714 TCGCAACCAT
46617724 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
1 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
46617756 TAACAGCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.34, T:0.00
Consensus pattern (6 bp):
AGCCGC
Found at i:46617736 original size:18 final size:18
Alignment explanation
Indices: 46617715--46617754 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
46617705 TCCTCGCAAT
*
46617715 CGCAACCATAGCCGCAGC
1 CGCAACCACAGCCGCAGC
* *
46617733 CGCAGCCGCAGCCGCAGC
1 CGCAACCACAGCCGCAGC
46617751 CGCA
1 CGCA
46617755 GTAACAGCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.47, G:0.28, T:0.03
Consensus pattern (18 bp):
CGCAACCACAGCCGCAGC
Found at i:46617762 original size:18 final size:18
Alignment explanation
Indices: 46617724--46617765 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
46617714 TCGCAACCAT
**
46617724 AGCCGCAGCCGCAGCCGC
1 AGCCGCAGCCGCAGCAAC
*
46617742 AGCCGCAGCCGCAGTAAC
1 AGCCGCAGCCGCAGCAAC
46617760 AGCCGC
1 AGCCGC
46617766 CGTCGCAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.45, G:0.31, T:0.02
Consensus pattern (18 bp):
AGCCGCAGCCGCAGCAAC
Found at i:46621626 original size:28 final size:28
Alignment explanation
Indices: 46621577--46621636 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
46621567 ATGTAAAGAG
* * *
46621577 ATATATATGTATATTTTAAAATTGTGAA
1 ATATATATGTATATTATAAAATTATAAA
46621605 ATATATATGTATA-TATATAAATTATAAA
1 ATATATATGTATATTATA-AAATTATAAA
46621633 ATAT
1 ATAT
46621637 GTGTGCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (28 bp):
ATATATATGTATATTATAAAATTATAAA
Found at i:46623354 original size:30 final size:31
Alignment explanation
Indices: 46623320--46623379 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
46623310 AAACCTTTTA
*
46623320 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
46623350 TTTTCTCCTAAAACTTTTACTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
46623380 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:46624011 original size:5 final size:5
Alignment explanation
Indices: 46624001--46624026 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46623991 GAACAAATAT
46624001 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
46624027 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:46624344 original size:16 final size:17
Alignment explanation
Indices: 46624317--46624348 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
46624307 AAATTTTTTA
46624317 AGTTTGTGGGCTTGTTT
1 AGTTTGTGGGCTTGTTT
46624334 AGTTT-TGGGCTTGTT
1 AGTTTGTGGGCTTGTT
46624349 GGGTTAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.34, T:0.53
Consensus pattern (17 bp):
AGTTTGTGGGCTTGTTT
Found at i:46624546 original size:12 final size:12
Alignment explanation
Indices: 46624522--46624571 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
46624512 CCTTACAGAA
46624522 TCATTTCTCATTT
1 TCATTTC-CATTT
*
46624535 TCATTTTCATTT
1 TCATTTCCATTT
* *
46624547 CCATTTCCGTTT
1 TCATTTCCATTT
*
46624559 TAATTTCCATTT
1 TCATTTCCATTT
46624571 T
1 T
46624572 GAGAAAACTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:46624559 original size:18 final size:18
Alignment explanation
Indices: 46624522--46624570 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
46624512 CCTTACAGAA
*
46624522 TCATTTCTCATTTTCATTT
1 TCATTTC-CATTTCCATTT
*
46624541 TCATTTCCATTTCCGTTT
1 TCATTTCCATTTCCATTT
*
46624559 TAATTTCCATTT
1 TCATTTCCATTT
46624571 TGAGAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCCATTT
Done.