Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold769.1
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: 756534
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 6000 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:81 original size:44 final size:44
Alignment explanation
Indices: 11--408 Score: 217
Period size: 44 Copynumber: 8.9 Consensus size: 44
1 AGGATAGTGT
* * *
11 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
*
55 CTTCAATCTGCTCCACTGTAACCTCAGGGAAATAAGA-C-CT-G
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
* * * * * *
96 ATGT-GATCTTCTCTACTGTAACTTCAGAGAGATAAGATCT-T--
1 CT-TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
* * * * * **
137 -TT-AATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-TACTAT
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT-CTGG
** * * *
179 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATGG
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA-T-CTCTGG
* * **
225 CTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-CTTTA
1 CTTCAATC-----TG--CT-C-C-ACTGTAACCTCAGGGAGATAAGATCTC-TGG
* * * * * * *
279 TTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-TACTAG
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT-CTGG
* * * *
323 CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTATGG
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA-T-CTCTGG
369 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
1 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
409 GAAATTCTTC
Statistics
Matches: 267, Mismatches: 59, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.00
39 25 0.09
40 2 0.01
41 29 0.11
42 5 0.02
43 3 0.01
44 114 0.43
45 5 0.02
46 44 0.16
47 4 0.01
49 1 0.00
51 2 0.01
53 2 0.01
54 9 0.03
55 2 0.01
56 19 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGG
Found at i:348 original size:144 final size:139
Alignment explanation
Indices: 93--378 Score: 441
Period size: 144 Copynumber: 2.0 Consensus size: 139
83 GAAATAAGAC
* *
93 CTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCTTTTAATCCGCTCCATTGTAATC
1 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTAATCCGCTCCACTGTAATC
* ** *
158 TCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAT
66 TCAAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTAT
223 GGCTTCAAT
131 GGCTTCAAT
232 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-C----TTTTAATCCGCTCCACTG
297 TAA-CTTC-AGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGA
61 TAATC-TCAAG-GAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGA
360 TTACTATGGCTTCAAT
124 TTACTATGGCTTCAAT
376 CTG
1 CTG
379 CTCCACTGTA
Statistics
Matches: 134, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
139 40 0.30
140 1 0.01
143 3 0.02
144 90 0.67
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (139 bp):
CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTAATCCGCTCCACTGTAATC
TCAAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTAT
GGCTTCAAT
Found at i:374 original size:46 final size:43
Alignment explanation
Indices: 289--406 Score: 155
Period size: 46 Copynumber: 2.6 Consensus size: 43
279 TTTTAATCCG
* *
289 CTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAAC-TCAGGGAGATAAGATTACTAGCTTCAATCTA
* *
333 CTCCGCTGTAATCTCAGGGAGATAAGATTACTATGGCTTCAATCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATTACTA--GCTTCAATCTA
379 CTCCACTGTAACCTCAGGGAGATAAGAT
1 CTCCACTGTAA-CTCAGGGAGATAAGAT
407 CTGAAATTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 28 0.43
45 1 0.02
46 36 0.55
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
CTCCACTGTAACTCAGGGAGATAAGATTACTAGCTTCAATCTA
Found at i:593 original size:87 final size:87
Alignment explanation
Indices: 424--678 Score: 273
Period size: 86 Copynumber: 3.0 Consensus size: 87
414 TCTTCGGTCT
* * * * * *
424 ACTCCACTACAACCGAGAGAGGTAAGG-TTTGTCTTCGACCTGCTTCACTGTCAACGCAGGAAGA
1 ACTCCACTACAACCGAGAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
* * * * *
488 TAAAATCAGTTGTCTTCAACCA
66 CAAGATCTGCTATCTTCAACCA
** * *
510 ACTCTTCTACACCCGAGAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGG
1 ACTCCACTACAACCGAGAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
*
575 CAAGATCTGCTATTTTCAACCA
66 CAAGATCTGCTATCTTCAACCA
* ** * * *
597 GCTCCACTGTAACCAATGA-ATGCAAAGC-TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAG
1 ACTCCACTACAACCGA-GAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAG
*
660 GCAAGATCTGCTGTCTTCA
65 GCAAGATCTGCTATCTTCA
679 CTGATCTGTT
Statistics
Matches: 139, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
86 74 0.53
87 63 0.45
88 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (87 bp):
ACTCCACTACAACCGAGAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
CAAGATCTGCTATCTTCAACCA
Found at i:1758 original size:21 final size:21
Alignment explanation
Indices: 1732--1778 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1722 GGTATAGCAA
1732 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
*** *
1753 GATCACTTTATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
1774 GATCA
1 GATCA
1779 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.11, T:0.28
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:1879 original size:8 final size:8
Alignment explanation
Indices: 1868--1943 Score: 95
Period size: 8 Copynumber: 9.6 Consensus size: 8
1858 CTCTTTTTAC
1868 TTTTTCAT
1 TTTTTCAT
1876 TTTTTCAT
1 TTTTTCAT
1884 TTTTTCAT
1 TTTTTCAT
1892 TTTTTCA-
1 TTTTTCAT
1899 TTTTTCAT
1 TTTTTCAT
1907 TTTTTCAT
1 TTTTTCAT
*
1915 CTTCTT--T
1 -TTTTTCAT
1922 TTTTTCAT
1 TTTTTCAT
*
1930 TTTCATCAT
1 TTT-TTCAT
1939 TTTTT
1 TTTTT
1944 TTACTCAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
6 4 0.07
7 8 0.14
8 36 0.61
9 11 0.19
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1886 original size:15 final size:15
Alignment explanation
Indices: 1868--1943 Score: 93
Period size: 15 Copynumber: 4.9 Consensus size: 15
1858 CTCTTTTTAC
1868 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
1883 TTTTTTCATTTTTTCA
1 -TTTTTCATTTTTTCA
1899 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
1914 TCTTCTT--TTTTTTCA
1 T-TT-TTCATTTTTTCA
1929 TTTTCATCATTTTTT
1 TTTT--TCATTTTTT
1944 TTACTCAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 26 0.48
16 17 0.31
17 8 0.15
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:1887 original size:23 final size:24
Alignment explanation
Indices: 1861--1932 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 24
1851 CCTTAGCCTC
1861 TTTTT-ACTTTTTCATTTTTTCAT
1 TTTTTCACTTTTTCATTTTTTCAT
*
1884 TTTTTCATTTTTTCA-TTTTTCAT
1 TTTTTCACTTTTTCATTTTTTCAT
*
1907 TTTTTCATCTTCTT--TTTTTTCAT
1 TTTTTCA-CTTTTTCATTTTTTCAT
1930 TTT
1 TTT
1933 CATCATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 31 0.72
24 12 0.28
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCACTTTTTCATTTTTTCAT
Found at i:1945 original size:23 final size:22
Alignment explanation
Indices: 1875--1945 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
1865 TACTTTTTCA
1875 TTTTTTCATTTTTTCATTTTTT
1 TTTTTTCATTTTTTCATTTTTT
* *
1897 CATTTTTCATTTTTTCATCTTCTT
1 -TTTTTTCATTTTTTCAT-TTTTT
*
1921 TTTTTTCATTTTCATCATTTTTT
1 TTTTTTCATTTT-TTCATTTTTT
1944 TT
1 TT
1946 ACTCAAAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 33 0.80
24 8 0.20
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTCATTTTTTCATTTTTT
Found at i:2808 original size:1 final size:1
Alignment explanation
Indices: 2804--2919 Score: 70
Period size: 1 Copynumber: 116.0 Consensus size: 1
2794 TTGACCTTGA
* * * * * ** **
2804 TTTTTTTATTTTTGTTTTTTTTATTTTTTTTATTTTTTTATTTTTTTGATTTTTTTTGATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** ** ** *
2869 GATTTTTTTGATTTTTTTGATTTTTTTTTGATTTTTTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2920 AGTCTGAACT
Statistics
Matches: 85, Mismatches: 30, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 85 1.00
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (1 bp):
T
Found at i:2816 original size:8 final size:8
Alignment explanation
Indices: 2803--2916 Score: 110
Period size: 8 Copynumber: 14.0 Consensus size: 8
2793 TTTGACCTTG
2803 ATTTTTTT
1 ATTTTTTT
*
2811 ATTTTTGT
1 ATTTTTTT
2819 -TTTTTTT
1 ATTTTTTT
2826 ATTTTTTTT
1 A-TTTTTTT
2835 ATTTTTTT
1 ATTTTTTT
2843 ATTTTTTT
1 ATTTTTTT
2851 GATTTTTTTT
1 -A-TTTTTTT
*
2861 GATTTTTTG
1 -ATTTTTTT
2870 ATTTTTTT
1 ATTTTTTT
2878 GATTTTTTT
1 -ATTTTTTT
2887 GA-TTTTTT
1 -ATTTTTTT
**
2895 -TTTGATT
1 ATTTTTTT
2902 -TTTTTTT
1 ATTTTTTT
2909 ATTTTTTT
1 ATTTTTTT
2917 TTTAGTCTGA
Statistics
Matches: 91, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
7 15 0.16
8 42 0.46
9 25 0.27
10 9 0.10
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2831 original size:10 final size:10
Alignment explanation
Indices: 2804--2918 Score: 98
Period size: 10 Copynumber: 11.7 Consensus size: 10
2794 TTGACCTTGA
2804 TTTTTTTATT
1 TTTTTTTATT
2814 TTTGTTTT-TT
1 TTT-TTTTATT
*
2824 TTATTTTTTTT
1 TT-TTTTTATT
2835 ATTTTTTTA-T
1 -TTTTTTTATT
*
2845 TTTTTTGATT
1 TTTTTTTATT
*
2855 TTTTTTGA--
1 TTTTTTTATT
*
2863 TTTTTTGA-T
1 TTTTTTTATT
*
2872 TTTTTTGA-T
1 TTTTTTTATT
*
2881 TTTTTTGATT
1 TTTTTTTATT
2891 TTTTTTTGATT
1 TTTTTTT-ATT
2902 TTTTTTTATT
1 TTTTTTTATT
2912 TTTTTTT
1 TTTTTTT
2919 TAGTCTGAAC
Statistics
Matches: 94, Mismatches: 3, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.09
9 24 0.26
10 38 0.40
11 22 0.23
12 2 0.02
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:2833 original size:18 final size:18
Alignment explanation
Indices: 2812--2917 Score: 110
Period size: 17 Copynumber: 5.8 Consensus size: 18
2802 GATTTTTTTA
*
2812 TTTTTG-TTTTTTTTATT
1 TTTTTGATTTTTTTTGTT
* *
2829 TTTTTTA-TTTTTTTATT
1 TTTTTGATTTTTTTTGTT
*
2846 TTTTTGATTTTTTTTGAT
1 TTTTTGATTTTTTTTGTT
2864 TTTTTGA-TTTTTTTGATT
1 TTTTTGATTTTTTTTG-TT
2882 TTTTTGATTTTTTTTTGATTT
1 TTTTTGA-TTTTTTTTG--TT
*
2903 TTTTTTATTTTTTTT
1 TTTTTGATTTTTTTT
2918 TTAGTCTGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
17 29 0.38
18 23 0.30
20 16 0.21
21 8 0.11
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (18 bp):
TTTTTGATTTTTTTTGTT
Found at i:2917 original size:9 final size:9
Alignment explanation
Indices: 2812--2917 Score: 117
Period size: 9 Copynumber: 11.6 Consensus size: 9
2802 GATTTTTTTA
*
2812 TTTTTGTTT
1 TTTTTATTT
2821 TTTTTATTT
1 TTTTTATTT
2830 TTTTTA-TT
1 TTTTTATTT
2838 TTTTTATTT
1 TTTTTATTT
*
2847 TTTTGATTT
1 TTTTTATTT
2856 TTTTTGA-TT
1 TTTTT-ATTT
*
2865 TTTTGATTT
1 TTTTTATTT
*
2874 TTTTGATTT
1 TTTTTATTT
*
2883 TTTTGATTTT
1 TTTTTA-TTT
2893 TTTTTGATTTT
1 TTTTT-A-TTT
2904 TTTTTATTT
1 TTTTTATTT
2913 TTTTT
1 TTTTT
2918 TTAGTCTGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
8 9 0.10
9 59 0.68
10 9 0.10
11 10 0.11
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (9 bp):
TTTTTATTT
Found at i:8305 original size:23 final size:23
Alignment explanation
Indices: 8286--8339 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
8276 TGTATACACG
8286 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* *
8309 TACATAATAATAATA-ATAGTAA
1 TACATAATAAAAATATATACTAA
8331 TAC-TAATAA
1 TACATAATAA
8340 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:8320 original size:3 final size:3
Alignment explanation
Indices: 8289--8359 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
8279 ATACACGTAC
* * * *
8289 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
8336 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
8360 CAAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:8846 original size:11 final size:12
Alignment explanation
Indices: 8826--8863 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
8816 AGAAAAAAAA
8826 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
8839 GAAGAGAGAAGG
1 GAAGAGAGAAGG
8851 G-AGAGAGAAGG
1 GAAGAGAGAAGG
8862 GA
1 GA
8864 GGGGGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:15953 original size:22 final size:22
Alignment explanation
Indices: 15928--15983 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
15918 TAAAACTTTT
15928 AAAATTTTTAAAAAGATTAATA
1 AAAATTTTTAAAAAGATTAATA
* ** *
15950 AAAATTTTCAAAAATTTTAATT
1 AAAATTTTTAAAAAGATTAATA
*
15972 AAGATTTTTAAA
1 AAAATTTTTAAA
15984 TATTCAGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
AAAATTTTTAAAAAGATTAATA
Found at i:18983 original size:69 final size:69
Alignment explanation
Indices: 18906--19044 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
18896 AATAATTACA
18906 CGAATCAATTAAATTAATCTAAAAAAAATTAAGCTCTAGCCATCCATGTCAACCAAAGCTTATTT
1 CGAATCAATTAAATTAATCTAAAAAAAATTAAGCTCTAGCCATCCATGTCAACCAAAGCTTATTT
18971 TATT
66 TATT
*
18975 CGAATCAATTAAATTAATCTAAAAAAAATTAAGCTCTAGCCATCCATGTCAAGCAAAGCTTATTT
1 CGAATCAATTAAATTAATCTAAAAAAAATTAAGCTCTAGCCATCCATGTCAACCAAAGCTTATTT
19040 TATT
66 TATT
19044 C
1 C
19045 AAGTTAATTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32
Consensus pattern (69 bp):
CGAATCAATTAAATTAATCTAAAAAAAATTAAGCTCTAGCCATCCATGTCAACCAAAGCTTATTT
TATT
Found at i:24225 original size:27 final size:27
Alignment explanation
Indices: 24184--24286 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
24174 TAGTATTGGC
*
24184 GCCTATTTGGAAGGCTCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
*
24211 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
* * *
24238 GCCTATGTAGCAGGCGCCAATGGTGGT
1 GCCTATTTGGAAGGCGCCAATGGTGGT
* *
24265 GCC-ATATTAGAAGGTGCCAATG
1 GCCTAT-TTGGAAGGCGCCAATG
24287 CTGTGATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.03
27 65 0.97
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.25
Consensus pattern (27 bp):
GCCTATTTGGAAGGCGCCAATGGTGGT
Found at i:24390 original size:18 final size:20
Alignment explanation
Indices: 24348--24394 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
24338 AAAACGGAAG
24348 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
24368 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
24386 AAAGAAGAA
1 AAAGAAGAA
24395 AAAAAGTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:24397 original size:22 final size:23
Alignment explanation
Indices: 24344--24397 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
24334 TACAAAAACG
*
24344 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
24368 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
24389 GAAGAAAAA
1 GAAGAAAAA
24398 AAGTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:31627 original size:16 final size:15
Alignment explanation
Indices: 31596--31637 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
31586 ACAAAATCAA
*
31596 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
31611 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
31627 ATAAAAATTAA
1 ATAAAAGTTAA
31638 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:31717 original size:38 final size:38
Alignment explanation
Indices: 31674--31755 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
31664 AAAAAGTCAG
31674 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
31712 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
31750 TTATAA
1 TTATAA
31756 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:31865 original size:60 final size:60
Alignment explanation
Indices: 31789--31910 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
31779 ATACTAAACT
* * * * * *
31789 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
31849 AAACACAAAAATTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
31909 AA
1 AA
31911 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:32028 original size:49 final size:49
Alignment explanation
Indices: 31955--32272 Score: 500
Period size: 49 Copynumber: 6.5 Consensus size: 49
31945 CCCGACATTA
31955 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
* *
32004 CAATATTCATACAAAATTATAATATTACAACATTCATACAAAAAAATAT-
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT-TG
*
32053 -AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
*
32101 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATAT-
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT-TG
*
32150 -AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
* * * *
32198 CAATATTCATACAAAACTATAATATTACAATATTCATACAAAAAATTTA
1 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
*
32247 TAATATTCATACAAAATTACAATATT
1 CAATATTCATACAAAATTACAATATT
32273 CATACAAAAA
Statistics
Matches: 246, Mismatches: 17, Indels: 12
0.89 0.06 0.04
Matches are distributed among these distances:
47 2 0.01
48 87 0.35
49 155 0.63
50 2 0.01
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (49 bp):
CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
Found at i:32068 original size:97 final size:97
Alignment explanation
Indices: 31956--32268 Score: 581
Period size: 97 Copynumber: 3.2 Consensus size: 97
31946 CCGACATTAC
*
31956 AATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
*
32021 TATAATATTACAACATTCATACAAAAAAATAT
66 TATAATATTACAATATTCATACAAAAAAATAT
32053 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
32118 TATAATATTACAATATTCATACAAAAAAATAT
66 TATAATATTACAATATTCATACAAAAAAATAT
*
32150 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAC
1 AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
*
32215 TATAATATTACAATATTCATACAAAAAATTTAT
66 TATAATATTACAATATTCATACAAAAAA-ATAT
32248 AATATTCATACAAAATTACAA
1 AATATTCATACAAAATTACAA
32269 TATTCATACA
Statistics
Matches: 211, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
97 187 0.89
98 24 0.11
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (97 bp):
AATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
TATAATATTACAATATTCATACAAAAAAATAT
Found at i:32119 original size:146 final size:145
Alignment explanation
Indices: 31951--32272 Score: 504
Period size: 146 Copynumber: 2.2 Consensus size: 145
31941 ATATCCCGAC
31951 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT-TGCAATATTCATA
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATAT--AATATTCATA
* * *
32015 CAAAATTATAATATTACAACATTCATACAAAAAAATAT-AATATTCATACAAAATTACAAAATTA
64 CAAAATTACAAAATTACAACATTCATACAAAAAAAT-TCAATATTCATACAAAACTACAAAATTA
32079 CAATATTCATACAAAAAA
128 CAATATTCATACAAAAAA
* *
32097 ATTGCAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATATAATATTCATACA
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATATAATATTCATACA
* * *
32162 AAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTACA
66 AAATTACAAAATTACAACATTCATACAAAAAAATT-CAATATTCATACAAAACTACAAAATTACA
32227 ATATTCATACAAAAAA
130 ATATTCATACAAAAAA
* *
32243 TTTATAATATTCATACAAAATTACAATATT
1 ATTACAATATTCATACAAAATTACAATATT
32273 CATACAAAAA
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
144 1 0.01
145 43 0.27
146 116 0.72
147 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (145 bp):
ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATATAATATTCATACA
AAATTACAAAATTACAACATTCATACAAAAAAATTCAATATTCATACAAAACTACAAAATTACAA
TATTCATACAAAAAA
Found at i:32251 original size:30 final size:27
Alignment explanation
Indices: 31951--32272 Score: 267
Period size: 27 Copynumber: 13.1 Consensus size: 27
31941 ATATCCCGAC
* *
31951 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAACTATAAT
31978 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAACTATAAT
* *
32000 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAACTATAAT
*
32027 ATTACAACATTCATACAAAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
* * *
32051 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAACTATAAT
32075 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAACTATAAT
* *
32097 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAACTATAAT
32124 ATTACAATATTCATACAAAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
* * *
32148 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAACTATAAT
32172 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAACTATAAT
*
32194 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAACTATAAT
32221 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
* * *
32244 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAACTATAAT
32270 ATT
1 ATT
32273 CATACAAAAA
Statistics
Matches: 252, Mismatches: 11, Indels: 64
0.77 0.03 0.20
Matches are distributed among these distances:
21 29 0.12
22 59 0.23
23 25 0.10
24 18 0.07
25 8 0.03
26 21 0.08
27 92 0.37
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAACTATAAT
Found at i:32273 original size:68 final size:66
Alignment explanation
Indices: 32124--32283 Score: 175
Period size: 68 Copynumber: 2.3 Consensus size: 66
32114 AAATTATAAT
32124 ATTACAATATTCATACAAAAAAATATAATATTCATACAAAATTACAAAATTACAATATTCATACA
1 ATTACAATATTCATACAAAAAAATATAATATTCATAC-AAA-TACAAAATTACAATATTCATAC-
32189 AAAAA
63 -AAAA
* * *
32194 ATTGCAATATTCATACAAAACTATAATATTACAATATTCATAC-AA-A-AAATTTATAATATTCA
1 ATTACAATATTCATACAAAA--A-AATA-T--AATATTCATACAAATACAAAATTACAATATTCA
32256 TAC-AAA
60 TACAAAA
32262 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
32284 TTACTAATCC
Statistics
Matches: 80, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
65 1 0.01
66 1 0.01
68 22 0.28
70 19 0.24
71 17 0.21
72 2 0.03
73 4 0.05
74 3 0.04
76 11 0.14
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.31
Consensus pattern (66 bp):
ATTACAATATTCATACAAAAAAATATAATATTCATACAAATACAAAATTACAATATTCATACAAA
A
Found at i:32395 original size:22 final size:21
Alignment explanation
Indices: 32169--32406 Score: 100
Period size: 22 Copynumber: 11.1 Consensus size: 21
32159 ACAAAATTAC
*
32169 AAAATTACAATATTCATACAAA
1 AAAATTAAAATATTCATAC-AA
**
32191 AAAATTGCAATATTCATAC--
1 AAAATTAAAATATTCATACAA
* *
32210 AAAACTATAATATTACAATATTCATACA
1 AAAATTAAAATATT-C-ATA--C--A-A
*
32238 AAAAATTTATAATATTCATAC--
1 AAA-A-TTAAAATATTCATACAA
*
32259 AAAATTACAATATTCATACAA
1 AAAATTAAAATATTCATACAA
** * * *
32280 AAAATTACTA-ATCCAAAACTA
1 AAAATTAAAATATTC-ATACAA
* * *
32301 TAAA-TACAAAT-TTAATTATAA
1 AAAATTA-AAATATTCA-TACAA
*
32322 AATAATTACAATATTCATAC--
1 AA-AATTAAAATATTCATACAA
* *
32342 AACATTACAATATTCATA-AA
1 AAAATTAAAATATTCATACAA
*
32362 AAAATTATAATATTCATACAA
1 AAAATTAAAATATTCATACAA
32383 AAAATTTAAAATATTCATACAA
1 AAAA-TTAAAATATTCATACAA
32405 AA
1 AA
32407 TTCTAATCTA
Statistics
Matches: 166, Mismatches: 26, Indels: 48
0.69 0.11 0.20
Matches are distributed among these distances:
19 40 0.24
20 26 0.16
21 33 0.20
22 43 0.26
23 6 0.04
26 1 0.01
28 6 0.04
29 2 0.01
30 9 0.05
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTAAAATATTCATACAA
Found at i:32593 original size:14 final size:15
Alignment explanation
Indices: 32576--32607 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
32566 TTTCTTTCTT
32576 TCTTCTTCTCC-TTC
1 TCTTCTTCTCCTTTC
32590 TCTTCTTCTCCTTTC
1 TCTTCTTCTCCTTTC
32605 TCT
1 TCT
32608 CTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
TCTTCTTCTCCTTTC
Found at i:32608 original size:17 final size:17
Alignment explanation
Indices: 32569--32610 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
32559 TACCTTTTTT
*
32569 CTTTCTTTCTTCTTCTC
1 CTTTCTCTCTTCTTCTC
32586 C--T-TCTCTTCTTCTC
1 CTTTCTCTCTTCTTCTC
32600 CTTTCTCTCTT
1 CTTTCTCTCTT
32611 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 1 0.05
17 7 0.33
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
CTTTCTCTCTTCTTCTC
Found at i:33410 original size:13 final size:13
Alignment explanation
Indices: 33392--33417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33382 TTTTTTTGAA
33392 AAAAATACGGGTC
1 AAAAATACGGGTC
33405 AAAAATACGGGTC
1 AAAAATACGGGTC
33418 GGGTCGGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (13 bp):
AAAAATACGGGTC
Found at i:33622 original size:17 final size:17
Alignment explanation
Indices: 33600--33641 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
33590 AGAAAAAAAA
33600 AAGAGAGAAAGGAGAAG
1 AAGAGAGAAAGGAGAAG
33617 -A-AGAG-AAGGAGAAG
1 AAGAGAGAAAGGAGAAG
*
33631 AAGAAAGAAAG
1 AAGAGAGAAAG
33642 AAAAAAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
14 9 0.43
15 5 0.24
16 4 0.19
17 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (17 bp):
AAGAGAGAAAGGAGAAG
Found at i:33625 original size:14 final size:15
Alignment explanation
Indices: 33603--33634 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
33593 AAAAAAAAAG
33603 AGAGAAAGGAGAAGA
1 AGAGAAAGGAGAAGA
33618 AGAG-AAGGAGAAGA
1 AGAGAAAGGAGAAGA
33632 AGA
1 AGA
33635 AAGAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
AGAGAAAGGAGAAGA
Found at i:33827 original size:20 final size:20
Alignment explanation
Indices: 33802--33984 Score: 90
Period size: 22 Copynumber: 8.8 Consensus size: 20
33792 TTTAGATTAG
*
33802 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
33822 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
33844 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
* *
33863 AATGTTGTATGAATATTGTA
1 AATTTTGTATGAATATTATA
* * *
33883 ATTATTTTATAATTAA-ATT-TG
1 A--ATTTTGT-ATGAATATTATA
* * *
33904 TATTTATAGTTTTG--GATTAGTA
1 AATTT-T-G-TATGAATATTA-TA
* *
33926 ATTTTTTGTATGAATATTGT-
1 A-ATTTTGTATGAATATTATA
33946 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTATA
33966 AATTTTTTGTATGAATATT
1 AA--TTTTGTATGAATATT
33985 GTAATATTAT
Statistics
Matches: 122, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
19 36 0.30
20 28 0.23
21 4 0.03
22 47 0.39
23 7 0.06
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:33875 original size:19 final size:19
Alignment explanation
Indices: 33828--33884 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
33818 TTTAAATTTT
* *
33828 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
33848 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
33867 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
33885 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:34006 original size:27 final size:25
Alignment explanation
Indices: 33938--34210 Score: 274
Period size: 27 Copynumber: 11.1 Consensus size: 25
33928 TTTTTGTATG
*
33938 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
33965 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
33987 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
*
34013 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
34036 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
34061 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
34084 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
34110 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
34133 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
34158 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
34181 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
34208 AAT
1 AAT
34211 GTGGGGATAT
Statistics
Matches: 210, Mismatches: 9, Indels: 54
0.77 0.03 0.20
Matches are distributed among these distances:
21 26 0.12
22 52 0.25
23 7 0.03
24 26 0.12
25 14 0.07
26 5 0.02
27 80 0.38
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.55
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:34068 original size:48 final size:48
Alignment explanation
Indices: 33938--34252 Score: 424
Period size: 49 Copynumber: 6.5 Consensus size: 48
33928 TTTTTGTATG
*
33938 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGT
* *
33987 AATATTATAGTTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATT--ATATTTTTTTGTATGAATATTGT
*
34036 AATTTTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
*
34084 AATATTATAATTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATT--ATATTTTTTTGTATGAATATTGT
*
34133 AATTTTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
* * * ** *
34181 AATATTGTAATTTTGTATGAATATTGTA-ATGTGGGGAT--ATATTGT
1 AATATTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
34226 AATATTGTAATTTTTTGTATGAATATT
1 AATATTGTAA--TTTTGTATGAATATT
34253 GTAATTATTT
Statistics
Matches: 241, Mismatches: 17, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
45 17 0.07
47 22 0.09
48 91 0.38
49 109 0.45
50 1 0.00
51 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (48 bp):
AATATTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGT
Found at i:34101 original size:97 final size:97
Alignment explanation
Indices: 33942--34206 Score: 494
Period size: 97 Copynumber: 2.7 Consensus size: 97
33932 TGTATGAATA
* *
33942 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
34007 ATATTGCAATTTTTTTGTATGAATATTGTAATT
65 ATATTGCAATTTTTTTGTATGAATATTGTAATT
34040 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
34105 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
*
34137 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
34202 TATTG
66 TATTG
34207 TAATGTGGGG
Statistics
Matches: 164, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
97 141 0.86
98 23 0.14
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (97 bp):
TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
TATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:34451 original size:38 final size:38
Alignment explanation
Indices: 34406--34487 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
34396 CATATAAAGT
34406 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
34444 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
34482 TTATAA
1 TTATAA
34488 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:34565 original size:15 final size:15
Alignment explanation
Indices: 34524--34565 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
34514 GTTAACTCAT
*
34524 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
34539 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
34555 TTAAATTTTAT
1 TTAAATTTTAT
34566 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:37906 original size:22 final size:21
Alignment explanation
Indices: 37871--37915 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
37861 ATACCTACTT
*
37871 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
37892 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
37914 TT
1 TT
37916 CTTTCTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:37923 original size:18 final size:18
Alignment explanation
Indices: 37873--37924 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
37863 ACCTACTTTT
37873 TTCTTC-TT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
37889 TTCTTTTCTTCTGCTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
37911 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
37925 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 8 0.27
19 2 0.07
20 6 0.20
22 11 0.37
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.62
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:38030 original size:27 final size:26
Alignment explanation
Indices: 37981--38083 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 26
37971 AAAATCACAG
*
37981 CATTGGCGCCTTCTAATATGGCACCAC
1 CATTGGCGCCTCCTAATA-GGCACCAC
*
38008 CATTGGCGCCTGCTACATAGGCACCAC
1 CATTGGCGCCTCCTA-ATAGGCACCAC
*
38035 CATTGGCGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCT-CCTAATAGGCACCAC
* *
38062 CATTGGAGCCTTCCAAATAGGC
1 CATTGGCGCC-TCCTAATAGGC
38084 GCCAATACTA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
27 63 0.91
28 6 0.09
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.20
Consensus pattern (26 bp):
CATTGGCGCCTCCTAATAGGCACCAC
Found at i:51095 original size:31 final size:31
Alignment explanation
Indices: 51035--51098 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
51025 ATATATTAAT
* * *
51035 TTAATTAATTTGAGTCCTTGTACTATTTGAA
1 TTAATTAATTTGAGTCCATATAATATTTGAA
* *
51066 TTAATTAATTTTAGTCCATATAATTTTTGAA
1 TTAATTAATTTGAGTCCATATAATATTTGAA
51097 TT
1 TT
51099 GGTCAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (31 bp):
TTAATTAATTTGAGTCCATATAATATTTGAA
Found at i:55808 original size:45 final size:45
Alignment explanation
Indices: 55771--55886 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 45
55761 ATGCCATTGT
* * * * *
55771 GTCTTTTAGCTATGGTCTTACTTGTTAGAATTGTGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCGTTAAAATCGTGATGCCATAAC
* *
55816 GTCTTTCAACTATGGTTTTACTCGTTAAAATCGGGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCGTTAAAATCGTGATGCCATAAC
*
55861 GTCTTTCAACCATGGTCTTACTCGTT
1 GTCTTTCAACTATGGTCTTACTCGTT
55887 TTCGGTACGA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTACTCGTTAAAATCGTGATGCCATAAC
Found at i:55899 original size:45 final size:43
Alignment explanation
Indices: 55771--55921 Score: 133
Period size: 45 Copynumber: 3.4 Consensus size: 43
55761 ATGCCATTGT
* * * * *
55771 GTCTTTTAGCTATGGTCTTACTTGTTAGAATTGTGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCGTT--AATCGGGATGCCATAAC
*
55816 GTCTTTCAACTATGGTTTTACTCGTTAAAATCGGGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCGTT--AATCGGGATGCCATAAC
* * **
55861 GTCTTTCAACCATGGTCTTACTCGTT-TTCGGTACGATGCCATAGT
1 GTCTTTCAACTATGGTCTTACTCGTTAATCGG---GATGCCATAAC
*
55906 TTCTTTCAACTATGGT
1 GTCTTTCAACTATGGT
55922 ATTATTTAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
42 4 0.04
45 85 0.96
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (43 bp):
GTCTTTCAACTATGGTCTTACTCGTTAATCGGGATGCCATAAC
Found at i:57159 original size:15 final size:17
Alignment explanation
Indices: 57128--57160 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57118 ATTTATTCGT
57128 TCAAATAACATAAATTA
1 TCAAATAACATAAATTA
57145 TCAAATAA-A-AAATTA
1 TCAAATAACATAAATTA
57160 T
1 T
57161 TATAATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
TCAAATAACATAAATTA
Found at i:58484 original size:85 final size:84
Alignment explanation
Indices: 58287--58630 Score: 401
Period size: 85 Copynumber: 4.1 Consensus size: 84
58277 TTATATACCT
* * * ** * * * * * *
58287 ATATGTATAGGGATGGTCTTCTCCGGTTCATATAGGAGGAAAGGAGTACGATTTATTGGAACCCA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
* * *
58352 AACTGTTCTTTTGGGAATT
66 AAATGTTCTTTTGGAAATC
* *
58371 ACATATATAGGGATAGTCTACTCCGGTTTGTATAGTAGGAACGAAATATGATTTATTGAAACCTA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
58436 AAATGTTCTTTTTGGAAATC
66 AAATGTTC-TTTTGGAAATC
* * * * * *
58456 ATATATATAGGGATAGTCTTCTCTGGTTTGTATAGGAGGAACAAAATATGATCTATGGAAACATA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
58521 AAATGTTCTTTTGGAAATTC
66 AAATGTTCTTTTGGAAA-TC
58541 -TATATATAGGGGATAGTCTACTCCGGTTTGTATAGGAGTG---G-AATATGATTTATTGAAACC
1 ATATATATA-GGGATAGTCTACTCCGGTTTGTATAGGAG-GAACGAAATATGATTTATTGAAACC
*
58601 TAAAATGTTCTTTTGGAAATT
64 TAAAATGTTCTTTTGGAAATC
*
58622 GTATATATA
1 ATATATATA
58631 TCGTTTTTGT
Statistics
Matches: 224, Mismatches: 31, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.00
82 43 0.19
84 76 0.34
85 103 0.46
86 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (84 bp):
ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
AAATGTTCTTTTGGAAATC
Found at i:67222 original size:21 final size:22
Alignment explanation
Indices: 67196--67240 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
67186 TTCTTCCCTG
67196 TTTGTAA-TATTAGAT-TTTGTA
1 TTTGTAAGTATTA-ATCTTTGTA
67217 TTTGTAAGTATTAATCTTTGTA
1 TTTGTAAGTATTAATCTTTGTA
67239 TT
1 TT
67241 ATCTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (22 bp):
TTTGTAAGTATTAATCTTTGTA
Found at i:67272 original size:3 final size:3
Alignment explanation
Indices: 67264--67298 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
67254 GAAATTGATG
* *
67264 TAT TAT TAT TCT TAT TCT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
67299 AGAAACACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:67691 original size:143 final size:143
Alignment explanation
Indices: 67494--67784 Score: 539
Period size: 143 Copynumber: 2.0 Consensus size: 143
67484 TCATAATTCA
*
67494 TTAATGAATGTGGATTTTCTCAAATTAATAACGTTCCTTTAACATCAAATATTATTATGGCAATA
1 TTAATGAATATGGATTTTCTCAAATTAATAACGTTCCTTTAACATCAAATATTATTATGGCAATA
67559 AAATAATTAATAAAAAAGTTTAAATACATTTTTACCCGCACATTCTCTCAATTTGATTTTTATAA
66 AAATAATTAATAAAAAAGTTTAAATACATTTTTACCCGCACATTCTCTCAATTTGATTTTTATAA
67624 TTTTTTTCTTAAT
131 TTTTTTTCTTAAT
*
67637 TTAA-GAATATGGATTTTCTCTAATTAATAACGTTCCCTTTAACATCAAATATTATTATGGCAAT
1 TTAATGAATATGGATTTTCTCAAATTAATAACGTT-CCTTTAACATCAAATATTATTATGGCAAT
*
67701 AAAATAATTAATAAAAAAGTTTAAATACATTTTTACCCGCACATTTTCTCAATTTGATTTTTATA
65 AAAATAATTAATAAAAAAGTTTAAATACATTTTTACCCGCACATTCTCTCAATTTGATTTTTATA
67766 ATTTTTTTCTTAAT
130 ATTTTTTTCTTAAT
67780 TTAAT
1 TTAAT
67785 ATCTAAATTT
Statistics
Matches: 143, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
142 28 0.20
143 115 0.80
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (143 bp):
TTAATGAATATGGATTTTCTCAAATTAATAACGTTCCTTTAACATCAAATATTATTATGGCAATA
AAATAATTAATAAAAAAGTTTAAATACATTTTTACCCGCACATTCTCTCAATTTGATTTTTATAA
TTTTTTTCTTAAT
Found at i:81004 original size:103 final size:102
Alignment explanation
Indices: 80832--81032 Score: 350
Period size: 103 Copynumber: 2.0 Consensus size: 102
80822 GGAAATACGT
80832 AATCTTATTAACATTTTACATACAAGGATATGTGGTAAAAGTACCATAGAAGCTCCTGCACAAAG
1 AATCTTATTAACATTTTACATACAAGGATATGTGGTAAAAGTACCATAGAAGCTCCTGCACAAAG
80897 ACTCAAATTGCATTTTGTCCCTTTTACTAAAAAATAG
66 ACTCAAATTGCATTTTGTCCCTTTTACTAAAAAATAG
* *
80934 AATCTTATTAACATTTTACATATACAAGGATATGT-GTAAAAGTACCGTAGAGGCTCCTGCACAA
1 AATCTTATTAACATTTTAC--ATACAAGGATATGTGGTAAAAGTACCATAGAAGCTCCTGCACAA
*
80998 AGACTCAAATTGCATTTTGTCCTTTTTACTAAAAA
64 AGACTCAAATTGCATTTTGTCCCTTTTACTAAAAA
81033 TAGCTAATTA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
102 19 0.20
103 61 0.65
104 14 0.15
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.32
Consensus pattern (102 bp):
AATCTTATTAACATTTTACATACAAGGATATGTGGTAAAAGTACCATAGAAGCTCCTGCACAAAG
ACTCAAATTGCATTTTGTCCCTTTTACTAAAAAATAG
Found at i:89343 original size:95 final size:95
Alignment explanation
Indices: 89180--89366 Score: 329
Period size: 95 Copynumber: 2.0 Consensus size: 95
89170 CGTCTCTCTT
* *
89180 AAGTTTTGCCATTAAGACCAAGCCAAAAGGAAGCTTCCCTTCACCTCTCATTTTGTGTGAATTCT
1 AAGTTTTGCCATTAAGACCAAGCCAAAAGGAAGCCTCCCTTCACCTCCCATTTTGTGTGAATTCT
*
89245 AAAACTTCGAGCTAGTTATATTCAGGGGCA
66 AAAACTTCAAGCTAGTTATATTCAGGGGCA
* *
89275 AAGTTTTGTCATTAAGATCAAGCCAAAAGGAAGCCTCCCTTCACCTCCCATTTTGTGTGAATTCT
1 AAGTTTTGCCATTAAGACCAAGCCAAAAGGAAGCCTCCCTTCACCTCCCATTTTGTGTGAATTCT
89340 AAAACTTCAAGCTAGTTATATTCAGGG
66 AAAACTTCAAGCTAGTTATATTCAGGG
89367 TAAAGTTAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (95 bp):
AAGTTTTGCCATTAAGACCAAGCCAAAAGGAAGCCTCCCTTCACCTCCCATTTTGTGTGAATTCT
AAAACTTCAAGCTAGTTATATTCAGGGGCA
Found at i:89680 original size:8 final size:8
Alignment explanation
Indices: 89657--89705 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
89647 GATTGGTTCG
89657 ATTAAAAA
1 ATTAAAAA
89665 TTATTAAAAA
1 --ATTAAAAA
89675 ATTAAAAA
1 ATTAAAAA
89683 ATTAAAAA
1 ATTAAAAA
89691 A-T-AAAA
1 ATTAAAAA
89697 A-TAAAAA
1 ATTAAAAA
89704 AT
1 AT
89706 ATAGTTCAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 17 0.46
10 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATTAAAAA
Found at i:91068 original size:3 final size:3
Alignment explanation
Indices: 91060--91093 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
91050 AAATTTAGTA
*
91060 TAT TAT TAT TAT TAT TAT TCT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
91094 TCTATCTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:93983 original size:22 final size:23
Alignment explanation
Indices: 93926--93972 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
93916 AATATCATTA
* *
93926 CTAACTTTAATTTTTTATTTTTAT
1 CTAATTTTAA-TTTTAATTTTTAT
93950 CTAATTTTAATTTTAATTTTTAT
1 CTAATTTTAATTTTAATTTTTAT
93973 TATTTCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
CTAATTTTAATTTTAATTTTTAT
Found at i:96088 original size:126 final size:131
Alignment explanation
Indices: 95795--96090 Score: 397
Period size: 126 Copynumber: 2.3 Consensus size: 131
95785 GATTGAACTA
95795 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTCGTTATTGCGTTATTTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGT-GTTATTGCGTTATTTTTACTCTTGTTT
* *
95860 GACGCCTACTACTTAATTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCCAA
65 GACGCC-ACTACTTAATTTAAGTATTAGGGTTTAGGGTTTAATTCCCAGCTTAACTATTATCAAA
*
95925 TTC
129 ATC
* * *
95928 ACTGGTTAATTTTTAACTATAATATTATTATGATTGCTGTTATTGCGTTA-TTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTG-TGTTATTGCGTTATTTTTACTCTTGTTT
* * * *
95992 GATG-C-CTAC-TAA-TT-AGTTTTAGGGTTTAGGGTTTAATTCCCAGTTTAACTATTATTAAAA
65 GACGCCACTACTTAATTTAAGTATTAGGGTTTAGGGTTTAATTCCCAGCTTAACTATTATCAAAA
96052 TC
130 TC
* * * *
96054 ATTGGTTAATGTTTAGCTTTATTATGATTGTGATTGT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGT
96091 TGTCATTGTT
Statistics
Matches: 145, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
125 1 0.01
126 71 0.49
127 2 0.01
128 3 0.02
129 4 0.03
131 1 0.01
132 17 0.12
133 45 0.31
134 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (131 bp):
ATTGGTTAATTTTTAACTATATTATGATTATGATTGTGTTATTGCGTTATTTTTACTCTTGTTTG
ACGCCACTACTTAATTTAAGTATTAGGGTTTAGGGTTTAATTCCCAGCTTAACTATTATCAAAAT
C
Found at i:97871 original size:30 final size:30
Alignment explanation
Indices: 97828--97900 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
97818 GTTACAATTT
* * *
97828 GGACTTAATTTGATTCC-TTCTAATATTATAG
1 GGAC-TAAATTGATTCCATT-TAATAATAGAG
97859 GGACTAAATTGA-TCCATTTAATAATAGAG
1 GGACTAAATTGATTCCATTTAATAATAGAG
*
97888 GGACTAACTTGAT
1 GGACTAAATTGAT
97901 ACTGTCCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 23 0.64
30 9 0.25
31 4 0.11
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (30 bp):
GGACTAAATTGATTCCATTTAATAATAGAG
Found at i:102998 original size:22 final size:22
Alignment explanation
Indices: 102970--103013 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
102960 CTTGGAACCA
102970 ATCAGACTCTGGTCAAATCCTT
1 ATCAGACTCTGGTCAAATCCTT
102992 ATCAGACTCTGGTCAAATCCTT
1 ATCAGACTCTGGTCAAATCCTT
103014 TTATCACAAT
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:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (22 bp):
ATCAGACTCTGGTCAAATCCTT
Found at i:109818 original size:15 final size:15
Alignment explanation
Indices: 109792--109832 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
109782 TTTTTATTTG
109792 AATAATTATAAATAAA
1 AATAATTATAAAT-AA
109808 AATAA-TATAAATAA
1 AATAATTATAAATAA
109822 AATAATTATAA
1 AATAATTATAA
109833 TCAGAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 12 0.50
16 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATTATAAATAA
Found at i:110997 original size:29 final size:30
Alignment explanation
Indices: 110958--111015 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
110948 ATTTGACGTG
*
110958 TATATATAATTACAC-TAAATCAAAATTCA
1 TATATAAAATTACACATAAATCAAAATTCA
*
110987 TATATAAAATTACACATTAAATTAAAATT
1 TATATAAAATTACACA-TAAATCAAAATT
111016 TATGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (30 bp):
TATATAAAATTACACATAAATCAAAATTCA
Found at i:112368 original size:25 final size:26
Alignment explanation
Indices: 112333--112385 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
112323 AGTGTAGTAA
* *
112333 AAAAAATTACATATATATA-AATAATT
1 AAAAAATTACACACATATATAAT-ATT
112359 AAAAAA-TACACACATATATAATATT
1 AAAAAATTACACACATATATAATATT
112384 AA
1 AA
112386 TATTTTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAAATTACACACATATATAATATT
Found at i:112661 original size:27 final size:27
Alignment explanation
Indices: 112612--112663 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
112602 GTTAATATAT
* *
112612 AATAAAATTGTAGTTTGACCCTAAATA
1 AATAAAATTGTAATTTAACCCTAAATA
* *
112639 AATAAAATTTTAATTTAATCCTAAA
1 AATAAAATTGTAATTTAACCCTAAA
112664 AACTATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (27 bp):
AATAAAATTGTAATTTAACCCTAAATA
Found at i:113483 original size:19 final size:19
Alignment explanation
Indices: 113443--113481 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
113433 ATTTTTATAT
113443 TATTTTTAATTATTTAAAA
1 TATTTTTAATTATTTAAAA
*
113462 TATTTTT-A-TATTTATAA
1 TATTTTTAATTATTTAAAA
113479 TAT
1 TAT
113482 ATAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAATTATTTAAAA
Found at i:114752 original size:15 final size:16
Alignment explanation
Indices: 114726--114756 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
114716 AGCTTGTCTT
114726 ATAAGTACATATATAG
1 ATAAGTACATATATAG
114742 ATAAG-ACATATATAG
1 ATAAGTACATATATAG
114757 TTAGGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAAGTACATATATAG
Found at i:118186 original size:25 final size:24
Alignment explanation
Indices: 118153--118202 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
118143 AAAATTTTCC
118153 TTAAAAAACACAATTTAATAACTTT
1 TTAAAAAACACAATTTAATAA-TTT
* * *
118178 TTAATAAACATAATTTATTAATTT
1 TTAAAAAACACAATTTAATAATTT
118202 T
1 T
118203 AAATTTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAAAACACAATTTAATAATTT
Found at i:122318 original size:16 final size:16
Alignment explanation
Indices: 122297--122327 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
122287 CGACTCCCAA
122297 AATTTTCTAATTATAT
1 AATTTTCTAATTATAT
*
122313 AATTTTGTAATTATA
1 AATTTTCTAATTATA
122328 ATATGTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTTCTAATTATAT
Found at i:122855 original size:3 final size:3
Alignment explanation
Indices: 122847--122879 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
122837 TAGTTACTAA
122847 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
122880 AGGCCATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:127213 original size:62 final size:63
Alignment explanation
Indices: 127098--127221 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
127088 GAGACTAAGT
* * *
127098 TTTGGAGGGTCTAAATAAAAATTTCAAAAATTTTACGAGTTTGATGAATTTTTTGAAAAAAAA
1 TTTGGAGGATCTAAATAAAAATTTCAAAAATTTTACGAGATTAATGAATTTTTTGAAAAAAAA
* * * **
127161 TTTGG-GGATCTAATTAAAATTTTTAAAAATTTTGTGAGATTAATGAGA-TTTTTGAAAAAAA
1 TTTGGAGGATCTAAATAAAAATTTCAAAAATTTTACGAGATTAATGA-ATTTTTTGAAAAAAA
127222 TTTAAAAGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
62 46 0.88
63 6 0.12
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (63 bp):
TTTGGAGGATCTAAATAAAAATTTCAAAAATTTTACGAGATTAATGAATTTTTTGAAAAAAAA
Found at i:132555 original size:21 final size:20
Alignment explanation
Indices: 132531--132569 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
132521 GTTAAAAATA
132531 ATTATCATTTTCATCATTTGG
1 ATTATCATTTTCAT-ATTTGG
132552 ATTATCATTTTCATATTT
1 ATTATCATTTTCATATTT
132570 TAATCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTATCATTTTCATATTTGG
Found at i:133190 original size:18 final size:17
Alignment explanation
Indices: 133148--133190 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
133138 CCTTTAATTT
*
133148 TGTAATATTTTATATTA
1 TGTAATTTTTTATATTA
* *
133165 TATTATTTTTATATATTA
1 TGTAATTTTT-TATATTA
133183 TGTAATTT
1 TGTAATTT
133191 ATAACACATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:134177 original size:86 final size:86
Alignment explanation
Indices: 134014--134177 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 86
134004 TGCTCGAACT
* * *
134014 CACGTCTACTTGGAGTAGTAAAATTGTCAATACCAACCAAATTAAGACTCAATCTGATTCAATAT
1 CACGTCTACTTAGAGTAGTAAAATTGTCAATACCAACCAAATTAAGACCCAACCTGATTCAATAT
*
134079 AATAAATATGCATCTCAAACC
66 AATAAACATGCATCTCAAACC
* * *
134100 CACGTCTACTTAGATTAGT-AACTATGTCAATACCAACCAGATTAAGACCCAACCTGATTCAATA
1 CACGTCTACTTAGAGTAGTAAAAT-TGTCAATACCAACCAAATTAAGACCCAACCTGATTCAATA
*
134164 TAATAAACGTGCAT
65 TAATAAACATGCAT
134178 TTAATATATA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
85 3 0.04
86 66 0.96
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (86 bp):
CACGTCTACTTAGAGTAGTAAAATTGTCAATACCAACCAAATTAAGACCCAACCTGATTCAATAT
AATAAACATGCATCTCAAACC
Found at i:138181 original size:29 final size:30
Alignment explanation
Indices: 138108--138182 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
138098 CAAAAATTCT
*
138108 AGATAGTTGGGTGACAAAAAAAGACAAAAT
1 AGATAGTTGGGTGACAAAAAAAGACAAAAA
* * * *
138138 TGAATAGTTGAGTGACCAAAATAGA-AAAAA
1 AG-ATAGTTGGGTGACAAAAAAAGACAAAAA
*
138168 AGATAATTGGGTGAC
1 AGATAGTTGGGTGAC
138183 TATTAATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 11 0.31
30 6 0.17
31 19 0.53
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.20
Consensus pattern (30 bp):
AGATAGTTGGGTGACAAAAAAAGACAAAAA
Found at i:143538 original size:381 final size:381
Alignment explanation
Indices: 142901--143594 Score: 1029
Period size: 381 Copynumber: 1.8 Consensus size: 381
142891 AAAATCTAAC
*
142901 CATAAATCAAGTTAACTTTAATCAATGAAATTGTAGCAAAAATTTGTAAACCTGCTCAATTTACA
1 CATAAATCAAGTTAACTTTAATCAATGAAATTGTAGCAAAAATTTGTAAACCTGCTCAATTAACA
* * * * *
142966 GTGTATGAATTACTTATTTTACTAGGATTATATGACAGCTGATGCTTCAAGTCATTTGATCTAAT
66 GTGTATGAAATACTAATTTTACTAGGATTACA-GACAGCAGATGCTTCAAGTCATGTGATCTAAT
* *
143031 TCATAAGCTAGTGAAGTTACTTCGGAAATTAGGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
130 TCATAAACTAGTGAAGTTACTTCGAAAATTAGGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
* * * * *
143096 TGCATTATGTTTTTTTTTTCATCCAAATGCTGCGTTTTTAATCGCAGCTGAGGCTATGGCATTTG
195 TGCATTATGTGTTCTTTTTCATCCAAATGCAGCGTTTTTAATCGCAGATGAGGCGATGGCATTTG
* * *
143161 CATTAGTTAAAAGGGTGTTGATGTTAAATTCTAATGGACTCTT-CATTTTTGTTGAAGTATACAG
260 CATTAGTT-AAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAG
143225 ATGGATATACGGATATGACTGTAAAAATTTAGAAAAACCTAACCATATTGCCAAGTAA
324 ATGGATATACGGATATGACTGTAAAAATTTAGAAAAACCTAACCATATTGCCAAGTAA
* *
143283 CATAAATCGAGTTAAC-TTAGATCAATGGACA-TGTAGCAAAAATTTGTAAACCTGCTCAATTAA
1 CATAAATCAAGTTAACTTTA-ATCAAT-GAAATTGTAGCAAAAATTTGTAAACCTGCTCAATTAA
* * **
143346 CAGTGTATGAAATACTAATTTTACTAGGATTACA-ATAGCAGGTGCTTCAAGTCATGTGATCTGG
64 CAGTGTATGAAATACTAATTTTACTAGGATTACAGACAGCAGATGCTTCAAGTCATGTGATCTAA
* * *
143410 TTCATAAACTTAGTGCAGTTACTTTGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATC
129 TTCATAAAC-TAGTGAAGTTACTTCGAAAATTAGGATGCTTTAGGTTGATGGGGTTCTTCTAATC
* * **
143475 ACTTCATTATGTGTTCTTTTTCATCCAAATGCAGTGTTTTTAATCTTAGATG-GGACGATGGCAT
193 ACTGCATTATGTGTTCTTTTTCATCCAAATGCAGCGTTTTTAATCGCAGATGAGG-CGATGGCAT
*
143539 TTGCATTAGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCTTTTTTGTT
257 TTGCATTAGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTT
143595 TGAATTGCTA
Statistics
Matches: 277, Mismatches: 30, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
380 65 0.23
381 126 0.45
382 83 0.30
383 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (381 bp):
CATAAATCAAGTTAACTTTAATCAATGAAATTGTAGCAAAAATTTGTAAACCTGCTCAATTAACA
GTGTATGAAATACTAATTTTACTAGGATTACAGACAGCAGATGCTTCAAGTCATGTGATCTAATT
CATAAACTAGTGAAGTTACTTCGAAAATTAGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACT
GCATTATGTGTTCTTTTTCATCCAAATGCAGCGTTTTTAATCGCAGATGAGGCGATGGCATTTGC
ATTAGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAGAT
GGATATACGGATATGACTGTAAAAATTTAGAAAAACCTAACCATATTGCCAAGTAA
Found at i:147835 original size:24 final size:24
Alignment explanation
Indices: 147801--147852 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
147791 TTTCTAGATG
* *
147801 ATTTAATATTTATTAGTATGATAT
1 ATTTAACATTTATTAGTATAATAT
*
147825 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTTATTAGTATAATAT
147849 ATTT
1 ATTT
147853 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTTAACATTTATTAGTATAATAT
Found at i:154484 original size:29 final size:30
Alignment explanation
Indices: 154444--154507 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
154434 TAAGGATCTC
* *
154444 ATCAATTTAGTCCCTCTACTATT-AAATTA
1 ATCAATTCAGTCCCTCTACTATTAAAAATA
*
154473 ATCAATTCAGTCCCTGTACTATTAAAAATA
1 ATCAATTCAGTCCCTCTACTATTAAAAATA
154503 ATCAA
1 ATCAA
154508 ACAAGGCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (30 bp):
ATCAATTCAGTCCCTCTACTATTAAAAATA
Found at i:156072 original size:15 final size:15
Alignment explanation
Indices: 156031--156075 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
156021 ACAAATAATT
156031 TAAAAA-TT-ATAAA
1 TAAAAATTTCATAAA
156044 -AAGAAATATTCATAAA
1 TAA-AAAT-TTCATAAA
156060 TAAAAATTTCATAAA
1 TAAAAATTTCATAAA
156075 T
1 T
156076 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 3 0.11
15 11 0.41
16 9 0.33
17 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (15 bp):
TAAAAATTTCATAAA
Found at i:158472 original size:16 final size:16
Alignment explanation
Indices: 158448--158548 Score: 53
Period size: 16 Copynumber: 6.3 Consensus size: 16
158438 ATTCGGTTCG
*
158448 GGTTAATTTCGAGTTTA
1 GGTT-ATTTTGAGTTTA
* *
158465 GGTTATTTTGAATTTT
1 GGTTATTTTGAGTTTA
* *
158481 GGTCATTTTGAGTTTT
1 GGTTATTTTGAGTTTA
* * * **
158497 GGTCA-CTTCAAATTA
1 GGTTATTTTGAGTTTA
* *
158512 AGTTATTTTGGGTTTA
1 GGTTATTTTGAGTTTA
*
158528 GGTCTATTTTAAGTTT-
1 GGT-TATTTTGAGTTTA
158544 GGTTA
1 GGTTA
158549 GGGGTGTAAA
Statistics
Matches: 62, Mismatches: 20, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
15 10 0.16
16 38 0.61
17 14 0.23
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (16 bp):
GGTTATTTTGAGTTTA
Found at i:163342 original size:23 final size:23
Alignment explanation
Indices: 163299--163348 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
163289 AATTAAATAT
**
163299 ATATTTTTATTATTTTTAATTTA
1 ATATTTTTATTATTTAAAATTTA
*
163322 ATATTTTTATT-TATTAAAATTTT
1 ATATTTTTATTAT-TTAAAATTTA
163345 ATAT
1 ATAT
163349 ATAGTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATATTTTTATTATTTAAAATTTA
Found at i:166489 original size:128 final size:128
Alignment explanation
Indices: 166150--166520 Score: 467
Period size: 130 Copynumber: 2.9 Consensus size: 128
166140 CAAAGAACCG
* * * ** *
166150 CATAAATAATAGTAAAAACAAACACACCAATAAGTTAGGTAGATAACATTTCGGTTTGGATCGGT
1 CATAAACAACAGT-AAAAC-AACACATCAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGAT
** * * * *
166215 TTTGAATAAATTTACAATTACAATGTTTTAGCTTTTAAAAAAGCAATGAACCACATAAGATGAAC
64 TTTGAATAAATTTACGGTTACAATATTCTAGTTTTTAAAAAAGCAAAGAACCACATAAGATGAAC
* * *
166280 CATAAACAACAGTAAAAGTAAACACATCAATAAGTTAGGCGAATAACATTTCGGCTTGGATCGAT
1 CATAAACAACAGTAAAA--CAACACATCAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGAT
* * *
166345 TTTGAACAAATTTACGGTTACAGTATTCTAGTTTTTAAAAAAGCAAAGAGCCACATCAA-ATGAA
64 TTTGAATAAATTTACGGTTACAATATTCTAGTTTTTAAAAAAGCAAAGAACCACAT-AAGATGAA
166409 C
128 C
** *
166410 CATAAACAACAGTGAAAACAA-ACATCAATAAGTTAGGCGGATAACATTTTAGTTTAGATCGATT
1 CATAAACAACAGT-AAAACAACACATCAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATT
* *
166474 TTGAATAAATTTACGGATACAATATTCTAATTTTTAAAAAAGCAAAG
65 TTGAATAAATTTACGGTTACAATATTCTAGTTTTTAAAAAAGCAAAG
166521 CGATTTCGTT
Statistics
Matches: 209, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
128 81 0.39
129 6 0.03
130 116 0.56
131 6 0.03
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (128 bp):
CATAAACAACAGTAAAACAACACATCAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTT
TGAATAAATTTACGGTTACAATATTCTAGTTTTTAAAAAAGCAAAGAACCACATAAGATGAAC
Found at i:174036 original size:5 final size:5
Alignment explanation
Indices: 174028--174114 Score: 106
Period size: 5 Copynumber: 17.2 Consensus size: 5
174018 TTTTTTACTT
*
174028 ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATAAA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA
* *
174080 ATATA ATAT- ATAATA AAATA AAATA ATAT- ATATA A
1 ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA A
174115 AACATAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
4 6 0.08
5 60 0.82
6 3 0.04
7 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:174064 original size:27 final size:26
Alignment explanation
Indices: 174027--174111 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 26
174017 TTTTTTTACT
174027 TATATAATATAATATAATATAATATAA
1 TATATAATATAATA-AATATAATATAA
174054 TATATAATATAATAAAATATAATATAA
1 TATATAATATAAT-AAATATAATATAA
*
174081 TATA-ATATATAATAAA-ATAAAATAA
1 TATATA-ATATAATAAATATAATATAA
174106 TATATA
1 TATATA
174112 TAAAACATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
25 12 0.22
26 5 0.09
27 36 0.67
28 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TATATAATATAATAAATATAATATAA
Found at i:174124 original size:22 final size:22
Alignment explanation
Indices: 174030--174125 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 22
174020 TTTTACTTAT
*
174030 ATAATATAATATAATATAATATA
1 ATAA-ATAATATAATAAAATATA
*
174053 ATATATAATATAATAAAATATA
1 ATAAATAATATAATAAAATATA
*
174075 AT--ATAATATAATATATAATAAA
1 ATAAATAATATAATA-A-AATATA
*
174097 ATAAAATAATATATATAAAACATA
1 AT-AAATAATATA-ATAAAATATA
174121 A-AAAT
1 ATAAAT
174126 CTAAGATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
20 11 0.18
21 1 0.02
22 30 0.48
23 3 0.05
24 5 0.08
25 9 0.15
26 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATAATATAATAAAATATA
Found at i:174124 original size:27 final size:28
Alignment explanation
Indices: 174027--174125 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 28
174017 TTTTTTTACT
* *
174027 TATATAATAT-AATATAATATAATATAA
1 TATAAAATATAAAAATAATATAATATAA
* *
174054 TATATAATATAATAA-AATATAATATAA
1 TATAAAATATAAAAATAATATAATATAA
* *
174081 TATAATATATAATAAAATAAAATAATAT-A
1 TATAAAATAT-A-AAAATAATATAATATAA
*
174110 TATAAAACATAAAAAT
1 TATAAAATATAAAAAT
174126 CTAAGATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
27 35 0.58
28 4 0.07
29 12 0.20
30 9 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAAAATATAAAAATAATATAATATAA
Found at i:176467 original size:20 final size:20
Alignment explanation
Indices: 176442--176480 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
176432 AATTTTAATA
176442 ATAAAAAAATAAATTAAATT
1 ATAAAAAAATAAATTAAATT
* *
176462 ATAAAAATATAATTTAAAT
1 ATAAAAAAATAAATTAAAT
176481 ATTTATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAAAATAAATTAAATT
Found at i:195491 original size:199 final size:197
Alignment explanation
Indices: 195124--195680 Score: 672
Period size: 199 Copynumber: 2.8 Consensus size: 197
195114 GAAGGAAATA
* * *
195124 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATTAGGAAAATGAGATTAGTGGTTAGCTTGG
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAA-TACGAAAACGAGATTAGTGGTTTGCTTGG
* * * ** * *
195189 CAGAGT-AGAAAAAAGGGAAGAAATGGATATAGGATGGTGAAAAACCAAAAAAGAACATTAATGT
65 CAGAGTGA-AAAAAACGGAAGAAATGAATAAAGGATGGTGAAAAACTGAAAAAGAATATGAATGT
* * * * * * **
195253 TTGAGTGTCTTAGGTAGGGAAGAAAATTCCGGCTCACTTAACTGCATTAC-AAAGATTAGCTTTG
129 TTGAGCGTGTTTGGTA-GGAAAAAAATTCTGGCTCACTTAACTGCATTACAAAAGATTAGCATCA
195317 TCTTC
193 TCTTC
* * *
195322 ATTAGCTTTCTTGTTCATGGATAGTAAAGCAAAAATACGAAAACGAGTTTAGTGGTTTGCTTGGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * *
195387 AGAGTGAAAAAAAAAACAGAAG-AATGAATAAAAGAAGGTGAAAAACTGAAAAAGAATATGAATG
66 AGAGTG---AAAAAAACGGAAGAAATGAATAAAGGATGGTGAAAAACTGAAAAAGAATATGAATG
* * *
195451 TTTGAGCGTGTTTGGTAGGAAAAAGAATTCTTGTTCACTTAGCTGCATTACAAAAGATTAGCATC
128 TTTGAGCGTGTTTGGTAGGAAAAA-AATTCTGGCTCACTTAACTGCATTACAAAAGATTAGCATC
195516 ATCTTC
192 ATCTTC
* * * *
195522 GTTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGGAAACAAGATTAGTGGTTTGCTTAGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * * * *
195587 AGAGTG-AAAAATCTGGAAGAAATGGAATTAGGGGTGGTGAAAAACTGAAAAAGAATATGGATGT
66 AGAGTGAAAAAAAC-GGAAGAAAT-GAATAAAGGATGGTGAAAAACTGAAAAAGAATATGAATGT
195651 TTGAGCGTGTTTGGTAGGAAAGAAAATTCT
129 TTGAGCGTGTTTGGTAGGAAA-AAAATTCT
195681 CGCACCTGTT
Statistics
Matches: 307, Mismatches: 42, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
196 6 0.02
197 35 0.11
198 42 0.14
199 131 0.43
200 92 0.30
201 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.28
Consensus pattern (197 bp):
ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
AGAGTGAAAAAAACGGAAGAAATGAATAAAGGATGGTGAAAAACTGAAAAAGAATATGAATGTTT
GAGCGTGTTTGGTAGGAAAAAAATTCTGGCTCACTTAACTGCATTACAAAAGATTAGCATCATCT
TC
Found at i:196015 original size:12 final size:12
Alignment explanation
Indices: 196000--196024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
195990 AAACAATTAT
196000 AAAAAACAAAAC
1 AAAAAACAAAAC
196012 AAAAAACAAAAC
1 AAAAAACAAAAC
196024 A
1 A
196025 GTCTGTTTTT
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:199401 original size:30 final size:31
Alignment explanation
Indices: 199362--199421 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
199352 GGAGGTGGGA
*
199362 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
199393 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
199422 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:203890 original size:41 final size:41
Alignment explanation
Indices: 203845--203927 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
203835 TTGGGTAATT
203845 TTGTGGCCATTATTGGTTCTTGTTCAATTAAGTACTGAAAA
1 TTGTGGCCATTATTGGTTCTTGTTCAATTAAGTACTGAAAA
203886 TTGTGGCCATTATTGGTTCTTGTTCAATTAAGTACTGAAAA
1 TTGTGGCCATTATTGGTTCTTGTTCAATTAAGTACTGAAAA
203927 T
1 T
203928 ACTTTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (41 bp):
TTGTGGCCATTATTGGTTCTTGTTCAATTAAGTACTGAAAA
Found at i:207383 original size:16 final size:16
Alignment explanation
Indices: 207362--207393 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
207352 AATGGTCACC
*
207362 CAACTATTCGGATTTT
1 CAACTATTCAGATTTT
207378 CAACTATTCAGATTTT
1 CAACTATTCAGATTTT
207394 TCTTTTTTGA
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (16 bp):
CAACTATTCAGATTTT
Found at i:210802 original size:306 final size:311
Alignment explanation
Indices: 210214--210839 Score: 996
Period size: 306 Copynumber: 2.0 Consensus size: 311
210204 TTTCTCGATT
* *
210214 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCGATTTGACTTGGTTTGCAGCTTTTTTT
1 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
* *
210279 GGTTAGTGGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACTTGTGCAATAGAGCTTAA
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACATGTGCAATAGAGCTTAA
* * *
210344 TGCGATTCAATAGTGGAAAAATTAGATGTTTCAAATTCATATTTGAGCTGGAAACTATTGATATT
131 TGCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTTAAGCTGGAAACTATTGATATT
* * *
210409 AGAAGAGGTATGGAAATTTGAACTGTTTTACTTGTGTTTTGACTTGGTATTTTGATGTAGGAAGT
196 ACAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTATTTTGATGTAGGAAGT
*
210474 TGCATAATATACTGGAGCTATT-AAAATATGAGGAAATGGTTTTTCC-TTTG
261 TGCATAATATACTGGAGCTATTAAAAAT-TGAGGAAATGGTTTTCCCTTTTG
* * *
210524 TTTTGTTGTTAATTGGAGTTACCTTTGTGATTTAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
1 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
* *
210589 GGTTATTAGTTGTAAGATTTGATTTGAATTTTATAAATTAATACT-CATG-G-AATAGAGCTTAA
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACATGTGCAATAGAGCTTAA
* * * *
210651 TGCGATTTAATA-TAGAGAAATTAGATGGTTCAAATTCCTATTTAAGCTGGAAATTATTGATATT
131 TGCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTTAAGCTGGAAACTATTGATATT
210715 ACAAGAGGTATGGAAATTGGAACTGTTTTAATTGTG-TTTGACTTGGTATTTTGATGTAGGAAGT
196 ACAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTATTTTGATGTAGGAAGT
210779 TGCATAAATATACTGGAGCTATTAAAAATTGAGGAAATGGTTTTCCCTTTTG
261 TGCAT-AATATACTGGAGCTATTAAAAATTGAGGAAATGGTTTTCCCTTTTG
*
210831 TTTTCTTGT
1 TTTTGTTGT
210840 AAAATTGTTA
Statistics
Matches: 292, Mismatches: 21, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
305 33 0.11
306 113 0.39
307 40 0.14
308 1 0.00
309 3 0.01
310 102 0.35
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (311 bp):
TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACATGTGCAATAGAGCTTAA
TGCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTTAAGCTGGAAACTATTGATATT
ACAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTATTTTGATGTAGGAAGT
TGCATAATATACTGGAGCTATTAAAAATTGAGGAAATGGTTTTCCCTTTTG
Found at i:215633 original size:14 final size:14
Alignment explanation
Indices: 215614--215640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
215604 CCTTAAAATT
215614 ATACATAAATTTTG
1 ATACATAAATTTTG
215628 ATACATAAATTTT
1 ATACATAAATTTT
215641 AGGGATAAAT
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:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
ATACATAAATTTTG
Found at i:229210 original size:14 final size:14
Alignment explanation
Indices: 229191--229217 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
229181 AATCGAGCTC
229191 AATAAAATAACAAT
1 AATAAAATAACAAT
229205 AATAAAATAACAA
1 AATAAAATAACAA
229218 CGCTACTTAG
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:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAATAACAAT
Found at i:230604 original size:18 final size:18
Alignment explanation
Indices: 230573--230614 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
230563 AATATGCTTG
*
230573 AATT-AAAATGTAAA-TT
1 AATTAAAAATATAAACTT
230589 AAATTAAAAATATAAACTT
1 -AATTAAAAATATAAACTT
230608 AATTAAA
1 AATTAAA
230615 GTTTTATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTAAAAATATAAACTT
Found at i:233128 original size:5 final size:5
Alignment explanation
Indices: 233115--233148 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
233105 AGACAATGAT
* *
233115 TATGA TATGG TATGG TATGG TATGG TATGA TATG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATG
233149 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (5 bp):
TATGG
Found at i:233138 original size:15 final size:15
Alignment explanation
Indices: 233110--233152 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
233100 ATTCGAGACA
233110 ATGATTATGATATGGT
1 ATGA-TATGATATGGT
* *
233126 ATGGTATGGTATGGT
1 ATGATATGATATGGT
233141 ATGATATGATAT
1 ATGATATGATAT
233153 ATATATATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (15 bp):
ATGATATGATATGGT
Found at i:235717 original size:21 final size:21
Alignment explanation
Indices: 235693--235740 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
235683 TGATCAAAAA
235693 ATAAAATTGAATAATTGAGTG
1 ATAAAATTGAATAATTGAGTG
** ** *
235714 ATAATTTTTCATAATTGAGTT
1 ATAAAATTGAATAATTGAGTG
235735 ATAAAA
1 ATAAAA
235741 AAAATACTAA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
ATAAAATTGAATAATTGAGTG
Found at i:237828 original size:185 final size:191
Alignment explanation
Indices: 237461--237873 Score: 640
Period size: 185 Copynumber: 2.2 Consensus size: 191
237451 GGGTTGTCAT
*
237461 TTGGTTATCTGGTTTTAGTTTATTTCAATTTTACTAGGAATGCGGATCGGTTCGGTACGAGGAAC
1 TTGGTTATCTGGTTTTAGTTTATTTCAATGTTACTAGGAATGCGGATCGGTTCGGTACGAGGAAC
**
237526 GGAAATCGGAACACAAATCGTTACTTATATGACACATTATTCGACAGGGGATAGTCTAATAGGAA
66 AAAAATCGGAACACAAATCGTTAC-TATA-GACACATTATTCGACAGGGGATAGTCTAATAGGAA
* * *
237591 TGAAATGCGATTCATCAGTTTGAATTTATACATATAGCTTTTGTGTTTATATAATC-GAGTCC
129 CGAAATACGATTCATCAGTTTGAATTTATACATATAGCTTTTGAGTTTATATAATCGGAGTCC
* * *
237653 TTGGTTATTTGGTTTTAGTTTATTTCAATGTTACTAGGAATGCTGATCGGTTCGGTACGAGGAGC
1 TTGGTTATCTGGTTTTAGTTTATTTCAATGTTACTAGGAATGCGGATCGGTTCGGTACGAGGAAC
* *
237718 AAAAATCGGAACAC-AA-C-TTA-TATA-ACACCTTATTCGACAGGGGATAGTCTACTAGGAACG
66 AAAAATCGGAACACAAATCGTTACTATAGACACATTATTCGACAGGGGATAGTCTAATAGGAACG
* *
237778 TAATACGATTCATCCGTTTGAATTTATACATATAGCTTTTGAGTTTATATAATCGGAGTCC
131 AAATACGATTCATCAGTTTGAATTTATACATATAGCTTTTGAGTTTATATAATCGGAGTCC
*
237839 TCGGTTATCTGGTTTTAGTTTATTTCAATGTTACT
1 TTGGTTATCTGGTTTTAGTTTATTTCAATGTTACT
237874 TTCAACAATT
Statistics
Matches: 205, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
185 83 0.40
186 39 0.19
187 4 0.02
189 3 0.01
190 1 0.00
191 2 0.01
192 73 0.36
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (191 bp):
TTGGTTATCTGGTTTTAGTTTATTTCAATGTTACTAGGAATGCGGATCGGTTCGGTACGAGGAAC
AAAAATCGGAACACAAATCGTTACTATAGACACATTATTCGACAGGGGATAGTCTAATAGGAACG
AAATACGATTCATCAGTTTGAATTTATACATATAGCTTTTGAGTTTATATAATCGGAGTCC
Found at i:238344 original size:210 final size:215
Alignment explanation
Indices: 237958--238524 Score: 815
Period size: 222 Copynumber: 2.6 Consensus size: 215
237948 GAGTGGTTGT
* *
237958 TTATAGGAAACCTTATTCGGTAGGGGATAGTCTAATAGGAACAAAATACGATTCGTCGGTTTGAA
1 TTATAGGAAACCTTATTCGATA-GGGATAGTCTAATAGGAACGAAATACGATTCGTCGGTTTGAA
* *
238023 TCTATATATATATAGC-TTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGATTGCTA
65 --TGTATACATATAGCTTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGATTGCTA
* * ** *
238087 TTGTT-CATTGATTTTCTTGATTATGTATTTTGAATGGAGGGTTGTCATTGGATTGGTTCGGTAT
128 TTGTTCCATTGATTTTCATGATTATGTACTTTGAATGGAGGGTTGTCATTGGATCAGTTCAGTAT
238151 -G-A-GG-AACGCAAATGGTTAC
193 GGAATGGAAACGCAAATGGTTAC
* * * * *
238170 TTATATGAATCCTTATTCGATAGGGATAGTCTAATAGGAATGAAATACGACTCATCGGTTTGAAT
1 TTATAGGAAACCTTATTCGATAGGGATAGTCTAATAGGAACGAAATACGATTCGTCGGTTTGAAT
*
238235 GTATACATATAGCTTTTGTGTTTATATAATCGAATCGTTAATCATACTGAATTGGATTGCTATTG
66 GTATACATATAGCTTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGATTGCTATTG
238300 TTCCA-TGATTTTCATGATTATGTACTTTGAATGGAGGGTTGTCATTGGATCAGTTCAGTATGAG
131 TTCCATTGATTTTCATGATTATGTACTTTGAATGGAGGGTTGTCATTGGATCAGTTCAGTAT--G
238364 GAATGGAAATTTAAACGCAAATGGTTAC
194 GAATGG------AAACGCAAATGGTTAC
238392 TTATAGGAAACCTTATTCGATAGGGATAGTCTAATAGGAACGAAATACGATTCGTCGGTTTGAAT
1 TTATAGGAAACCTTATTCGATAGGGATAGTCTAATAGGAACGAAATACGATTCGTCGGTTTGAAT
* * * *
238457 GTATGCATGTAGCTTTTGTATTTATATAATTGAATCGTTAGTCATACTGAATTGGATTGCTATTG
66 GTATACATATAGCTTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGATTGCTATTG
238522 TTC
131 TTC
238525 TGTGATCGGG
Statistics
Matches: 316, Mismatches: 25, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
209 12 0.04
210 103 0.33
211 40 0.13
212 19 0.06
213 1 0.00
214 1 0.00
215 2 0.01
222 138 0.44
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (215 bp):
TTATAGGAAACCTTATTCGATAGGGATAGTCTAATAGGAACGAAATACGATTCGTCGGTTTGAAT
GTATACATATAGCTTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGATTGCTATTG
TTCCATTGATTTTCATGATTATGTACTTTGAATGGAGGGTTGTCATTGGATCAGTTCAGTATGGA
ATGGAAACGCAAATGGTTAC
Found at i:240892 original size:18 final size:18
Alignment explanation
Indices: 240871--240906 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
240861 TACATAAAAT
240871 TTTAT-AAATACTAATATA
1 TTTATAAAAT-CTAATATA
240889 TTTATAAAATCTAATATA
1 TTTATAAAATCTAATATA
240907 ATACATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATAAAATCTAATATA
Found at i:241703 original size:16 final size:17
Alignment explanation
Indices: 241667--241698 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
241657 CCAAACACGC
241667 AAACTCAAAATGA-TCT
1 AAACTCAAAATGACTCT
241683 AAACTCAAAATGACTC
1 AAACTCAAAATGACTC
241699 GAACTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.87
17 2 0.13
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (17 bp):
AAACTCAAAATGACTCT
Found at i:242113 original size:7 final size:7
Alignment explanation
Indices: 242101--242129 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
242091 TCTGCAGACA
242101 ACAATGT
1 ACAATGT
242108 ACAATGT
1 ACAATGT
242115 ACAATGT
1 ACAATGT
242122 ACAATGT
1 ACAATGT
242129 A
1 A
242130 AAAGGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (7 bp):
ACAATGT
Found at i:256625 original size:14 final size:14
Alignment explanation
Indices: 256606--256639 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
256596 AATTCGAATT
256606 AAATTATATTT-ATC
1 AAATTATATTTCA-C
256620 AAATTATATTTCAC
1 AAATTATATTTCAC
256634 AAATTA
1 AAATTA
256640 AAAAATTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTATATTTCAC
Found at i:260350 original size:22 final size:23
Alignment explanation
Indices: 260325--260371 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
260315 TAAAACGGGC
260325 ATAAAATAT-ACCAA-AAAATAAA
1 ATAAAAT-TCACCAACAAAATAAA
*
260347 ATAAAATTCACCAACAAAATGAA
1 ATAAAATTCACCAACAAAATAAA
260370 AT
1 AT
260372 TACCAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.66, C:0.13, G:0.02, T:0.19
Consensus pattern (23 bp):
ATAAAATTCACCAACAAAATAAA
Found at i:260371 original size:18 final size:17
Alignment explanation
Indices: 260344--260377 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
260334 ACCAAAAAAT
260344 AAAATAAAATTCACCAAC
1 AAAATAAAATT-ACCAAC
*
260362 AAAATGAAATTACCAA
1 AAAATAAAATTACCAA
260378 AACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATAAAATTACCAAC
Found at i:261622 original size:22 final size:20
Alignment explanation
Indices: 261591--261653 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
261581 CTAGACCAAC
261591 AATAATTAAATAAATAATTAAAA
1 AATAA-TAAA-AAAT-ATTAAAA
* *
261614 ATTCATAAACAAAT-TTAAAA
1 AATAATAAA-AAATATTAAAA
261634 AATAATAAAAAATGATTAAA
1 AATAATAAAAAAT-ATTAAA
261654 CTAGATCAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 5 0.15
22 8 0.24
23 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAAAAAATATTAAAA
Found at i:268700 original size:149 final size:149
Alignment explanation
Indices: 268471--269067 Score: 948
Period size: 149 Copynumber: 4.0 Consensus size: 149
268461 TCCCACAGCC
* * * * * *
268471 ACAGGTATGCCTTGTGTTTGATCTTTACTTGCCTAATTGCCTCTTCGCATTGGAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGAAACTCTTCTGAT
* *
268536 CTCTGTAACTT-TTCTCCAGGACCGAAC-TAAAAAATACGGGTCTTTCCATGTCAATGGTGAAGA
66 CTCTGTAA-TTGTTCTCTAGGACCG-ACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGA
*
268599 TAATAAATCAAATTATGGAAA
129 TAATAAATCAAATGATGGAAA
* *
268620 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATCGCATCTTCACACTGAAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGAAACTCTTCTGAT
268685 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
268750 ATAAATCAAATGATGGAAA
131 ATAAATCAAATGATGGAAA
* * *
268769 ACAGGTATCACTCGTGTTTGATCTTTACTTGCTTGATTGCCTCTTCATACTGAAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGAAACTCTTCTGAT
268834 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
268899 ATAAATCAAATGATGGAAA
131 ATAAATCAAATGATGGAAA
* ** * *
268918 ACAGGTATCCCTCGTGTTTGCA-CTTTACTTGTCTGATTATCTCTTCACACTGGAACTCTTCTAA
1 ACAGGTATCCCTCGTGTTTG-ATCTTTACTTGCCTGATTGCCTCTTCACACTGAAACTCTTCTGA
* *
268982 TCTCTGTAAGTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGAT
65 TCTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGAT
*
269047 AATAAATCAAACGATGGAAA
130 AATAAATCAAATGATGGAAA
269067 A
1 A
269068 AGTGCTGATC
Statistics
Matches: 418, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
148 4 0.01
149 413 0.99
150 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (149 bp):
ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGAAACTCTTCTGAT
CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
ATAAATCAAATGATGGAAA
Found at i:271369 original size:26 final size:27
Alignment explanation
Indices: 271340--271390 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
271330 GGATATTTGA
*
271340 ATTTTCTATAAAAATC-AAAATTTTAG
1 ATTTACTATAAAAATCAAAAATTTTAG
* *
271366 ATTTACTTTAAAATTCAAAAATTTT
1 ATTTACTATAAAAATCAAAAATTTT
271391 TATTATCTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (27 bp):
ATTTACTATAAAAATCAAAAATTTTAG
Found at i:273360 original size:16 final size:17
Alignment explanation
Indices: 273341--273377 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
273331 TAAATTATTA
273341 AAAAAT-TATAAAAAAT
1 AAAAATATATAAAAAAT
*
273357 -AAAATATATTAAAAAT
1 AAAAATATATAAAAAAT
273373 AAAAA
1 AAAAA
273378 AATCTGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAAAAT
Found at i:279590 original size:26 final size:26
Alignment explanation
Indices: 279549--279599 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
279539 TCAATTTCTA
*
279549 TATTTAAAAACTTAAT-AATAGTTTT
1 TATTTAAAAACATAATCAATAGTTTT
279574 TATTTAAAAATCATAATCCAATAGTT
1 TATTTAAAAA-CATAAT-CAATAGTT
279600 GACACTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
28 7 0.32
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (26 bp):
TATTTAAAAACATAATCAATAGTTTT
Found at i:282702 original size:19 final size:19
Alignment explanation
Indices: 282670--282715 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
282660 ACTTGAAATT
282670 ATTA-TTTT-TTTAAAAAA
1 ATTACTTTTATTTAAAAAA
**
282687 ATTACTTTTATTTAAATTA
1 ATTACTTTTATTTAAAAAA
282706 ATTACTTTTA
1 ATTACTTTTA
282716 GAATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
19 17 0.68
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTACTTTTATTTAAAAAA
Found at i:282932 original size:3 final size:3
Alignment explanation
Indices: 282924--282959 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
282914 GTTAAATGCT
282924 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
282960 GCTGTGTCTT
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):
TTA
Found at i:306614 original size:21 final size:23
Alignment explanation
Indices: 306565--306614 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
306555 TTGTTATATC
* *
306565 TATTAAAAATTACATTTATTTAT
1 TATTAAAAATCACATTTATGTAT
306588 TATTAAAAATCA-ATTTATGTA-
1 TATTAAAAATCACATTTATGTAT
306609 TATTAA
1 TATTAA
306615 TATGAGGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 8 0.32
23 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTAAAAATCACATTTATGTAT
Found at i:313937 original size:29 final size:30
Alignment explanation
Indices: 313892--313972 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
313882 AAATTTTTAT
* *
313892 AAAATTGAAATTCAAAAATATAAAAT-TATA
1 AAAATTGAAAATAAAAAATATAAAATAT-TA
*
313922 AAAATTGCAAAA-AAAAAAT-TAAAATATTT
1 AAAATTG-AAAATAAAAAATATAAAATATTA
313951 AAAATTGAAAATAAAAAATATA
1 AAAATTGAAAATAAAAAATATA
313973 GATTTTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.09
29 21 0.48
30 16 0.36
31 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (30 bp):
AAAATTGAAAATAAAAAATATAAAATATTA
Found at i:314380 original size:26 final size:26
Alignment explanation
Indices: 314332--314382 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
314322 AATTTTATAT
**
314332 ATTTTTAATTTTTTTATGCTTTTGTG
1 ATTTTTAATTTTTTTATAATTTTGTG
* *
314358 ATTTTTATTTTTTTTGTAATTTTGT
1 ATTTTTAATTTTTTTATAATTTTGT
314383 ATTATTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (26 bp):
ATTTTTAATTTTTTTATAATTTTGTG
Found at i:314390 original size:19 final size:18
Alignment explanation
Indices: 314324--314390 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
314314 TTTTGCATAA
314324 TTTTA-TATATTTT-TAAT
1 TTTTATTAT-TTTTGTAAT
*
314341 TTTT-TTATGCTTTTGTGAT
1 TTTTATTAT--TTTTGTAAT
*
314360 TTTTATTTTTTTTGTAAT
1 TTTTATTATTTTTGTAAT
314378 TTTGTATTATTTT
1 TTT-TATTATTTT
314391 AATAAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 7 0.17
18 15 0.38
19 15 0.38
20 3 0.08
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTATTATTTTTGTAAT
Found at i:314444 original size:14 final size:14
Alignment explanation
Indices: 314407--314447 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
314397 TTTTATAAAA
314407 AAATTCTATTTTTT
1 AAATTCTATTTTTT
** *
314421 ATTTTATATTTTTT
1 AAATTCTATTTTTT
314435 AAATTCTATTTTT
1 AAATTCTATTTTT
314448 GTAATAACTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
AAATTCTATTTTTT
Done.