Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 123 of 208
Found at i:40481826 original size:129 final size:129
Alignment explanation
Indices: 40481618--40482048 Score: 515
Period size: 129 Copynumber: 3.3 Consensus size: 129
40481608 GGTTTGTTAT
* * * * * * *
40481618 CTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAAACTTGTCATGGTGTGATCCGCTCTACTGC
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTG----GATGCGATCTGCTCTACTGC
** * * * *
40481683 AACTTTAGAGAGATAAGATCTGTCATTTTAATCCGCTTCACTGTAACTTCAG-GAAGATATGA-T
61 AACTTTAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGAG-AGATAGGACT
* **
40481746 TGATTT
125 AG-TAA
*
40481752 CTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
* *
40481817 TAGATAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCAGAGAGATAGGACTAGTAA
66 TAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGACTAGTAA
*
40481881 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCAATCTGCTCTACTGCAACTT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
* * * * * *
40481946 CAAAGAGATAAGATCTATGGTTTTAATCCACTCCACTGCAACTTTAGGGTGATAGGACTAGTAA
66 TAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGACTAGTAA
* * * *
40482010 CTTCAATCTGCTTCACTACAACTTCAGGGAAATAAGATT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
40482049 TGTTGGCTTT
Statistics
Matches: 262, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
129 224 0.85
130 3 0.01
133 3 0.01
134 32 0.12
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
TAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGACTAGTAA
Found at i:40481940 original size:85 final size:88
Alignment explanation
Indices: 40481850--40482091 Score: 251
Period size: 85 Copynumber: 2.8 Consensus size: 88
40481840 TAATACACTC
* ** *
40481850 CACTGCAACTTCAGAGAGATAGGACTAGTAACTTCAATCTACTCCACTGCAACTTCAGGGAGATA
1 CACTGCAACTTCAGAGAGATAAGACTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATA
* *
40481915 AGA-TTG-GA-TGCAATCTGC-T
66 AGACTAGTAACTGCAATCTGCTT
* * * * *
40481934 CTACTGCAACTTCAAAGAGATAAGATCTA-TGGTTTTAATCCACTCCACTGCAACTTTAGGGTGA
1 C-ACTGCAACTTCAGAGAGATAAGA-CTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
* *
40481998 TAGGACTAGTAACTTCAATCTGCTT
64 TAAGACTAGTAACTGCAATCTGCTT
* * * * * *
40482023 CACTACAACTTCAGGGAAATAAGATTTGTTGGCTTTAATCTTCTCCACTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGAGAGATAAGACTAG-TGGCTTTAATCTACTCCACTGCAACTTCAGGGAGAT
40482088 AAGA
65 AAGA
40482092 ATTGTCATCT
Statistics
Matches: 125, Mismatches: 25, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
84 1 0.01
85 53 0.42
86 5 0.04
87 2 0.02
88 28 0.22
89 36 0.29
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (88 bp):
CACTGCAACTTCAGAGAGATAAGACTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATA
AGACTAGTAACTGCAATCTGCTT
Found at i:40482045 original size:88 final size:89
Alignment explanation
Indices: 40481885--40482088 Score: 220
Period size: 89 Copynumber: 2.3 Consensus size: 89
40481875 TAGTAACTTC
* * * * * *
40481885 AATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTG-GA-TGCAATCTGCTCTACTGCAACTTC
1 AATCCACTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTCAATCTGCTCTACTACAACTTC
* *
40481947 AAAGAGATAAGATCT-ATGGTTTT
66 AAAGAAATAAGATCTGATGGCTTT
* *
40481970 AATCCACTCCACTGCAACTTTAGGGTGATAGGACTAGTAACTTCAATCTGCT-TCACTACAACTT
1 AATCCACTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTCAATCTGCTCT-ACTACAACTT
** * *
40482034 CAGGGAAATAAGATTTGTTGGCTTT
65 CAAAGAAATAAGATCTGATGGCTTT
**
40482059 AATCTTCTCCACTGCAACTTCAGGGAGATA
1 AATCCACTCCACTGCAACTTCAGGGAGATA
40482089 AGAATTGTCA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
85 29 0.30
86 2 0.02
87 2 0.02
88 31 0.32
89 32 0.33
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (89 bp):
AATCCACTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTCAATCTGCTCTACTACAACTTC
AAAGAAATAAGATCTGATGGCTTT
Found at i:40482079 original size:45 final size:45
Alignment explanation
Indices: 40481547--40482091 Score: 242
Period size: 44 Copynumber: 12.4 Consensus size: 45
40481537 CGCTCCAGTA
* * * * * * *
40481547 CAACTTCAGGGAGATAGGATTAG-TAGCTTAAATTTGCTCCATTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * * * ** * * * *
40481591 CAAATTCAGGTAGATAAGGTTTGTTATCTTCAGTCTGCTCTACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * * * ** *
40481636 CAACTTCAGGGAGATAAAACTTGTCATGG-TGTGATCCGCTCTACTG
1 CAACTTCAGGGAGATAAGA-TT-TGATGGCTTTAATCTACTCCACTG
* * * *** ** *
40481682 CAACTTTAGAGAGATAAGATCTG-TCATTTTAATCCGCTTCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * * ** *
40481726 TAACTTCAGGAAGATATGA-TTGATTTCTTCAATCTACTCCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * * * *
40481770 CAACTTTAGGGAGATAAGATTGGAT-GC---GATCTGCTCTACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* ** * *
40481811 CAACTTTAGATAGATAAGATCTG-TGGTTTTAATAC-ACTCCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAAT-CTACTCCACTG
* * * * ** *
40481855 CAACTTCAGAGAGATAGGACTAG-TAACTTCAATCTACTCCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * *
40481899 CAACTTCAGGGAGATAAGATTGGAT-GC---AATCTGCTCTACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
** * * *
40481940 CAACTTCAAAGAGATAAGATCT-ATGGTTTTAATCCACTCCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * * * * ** * * * *
40481984 CAACTTTAGGGTGATAGGACTAG-TAACTTCAATCTGCTTCACTA
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
* * *
40482028 CAACTTCAGGGAAATAAGATTTGTTGGCTTTAATCTTCTCCACTG
1 CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
40482073 CAACTTCAGGGAGATAAGA
1 CAACTTCAGGGAGATAAGA
40482092 ATTGTCATCT
Statistics
Matches: 363, Mismatches: 119, Indels: 37
0.70 0.23 0.07
Matches are distributed among these distances:
40 3 0.01
41 62 0.17
43 4 0.01
44 192 0.53
45 70 0.19
46 30 0.08
47 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGATTTGATGGCTTTAATCTACTCCACTG
Found at i:40482329 original size:45 final size:45
Alignment explanation
Indices: 40482257--40482744 Score: 479
Period size: 45 Copynumber: 11.0 Consensus size: 45
40482247 AACTATTGTG
* * *
40482257 TCTTTGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * *
40482302 TCTTCAATCTGCTCCGCTGTCAGTACAGTAAGGCAAG-GCTGGTG
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
40482346 TCTTCGATTTGCTTCGCTGCCGGTACATGAAGGCATGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * * *
40482391 TCTTCAATCTGCTCCGCTGTCAATATAGGAATG-AAG-GCTAG-TG
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT-GCTA
* * * *
40482434 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTACTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * *
40482479 TCTTC-AGTCTGC-TCTGCTGTCAGTACAGGAAGGCAAG-GCTGATG
1 TCTTCGA-TCTGCTTC-GCTGTCAGTACAGGAAGGCAAGATCTGCTA
40482523 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * *
40482568 TCTTCGATCTACTTTGCTGCCAATACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * *
40482613 TCTTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
40482658 TCTTCAATCTGCTCCGCTGTTAGTACAGGAAGGCAAG-GCTGGTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
*
40482702 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
40482745 AACTTCATTG
Statistics
Matches: 352, Mismatches: 80, Indels: 22
0.78 0.18 0.05
Matches are distributed among these distances:
43 30 0.09
44 112 0.32
45 210 0.60
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
Found at i:40482405 original size:89 final size:89
Alignment explanation
Indices: 40482254--40482744 Score: 624
Period size: 89 Copynumber: 5.5 Consensus size: 89
40482244 ACAAACTATT
* * * *
40482254 GTGTCTTTGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
*
40482319 TGTCAGTACAGTAAGGCAAGGCTG
66 TGTCAGTACAGGAAGGCAAGGCTG
* * * *
40482343 GTGTCTTCGATTTGCTTCGCTGCCGGTACATGAAGGCATGATCTGCTATCTTCAATCTGCTCCGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
* * * *
40482408 TGTCAATATAGGAATG-AAGGCTA
66 TGTCAGTACAGGAAGGCAAGGCTG
* * * * *
40482431 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTACTATCTTCAGTCTGCTCTGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
40482496 TGTCAGTACAGGAAGGCAAGGCTG
66 TGTCAGTACAGGAAGGCAAGGCTG
* * * * **
40482520 ATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCGATCTACTTTGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
* * * * *
40482585 TGCCAATACAAGAAGACAAGATCTG
66 TGTCAGTACAGGAAGGCAAG-GCTG
* * * * * * *
40482610 CTATCTTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTCAATCTGCTCCGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
*
40482675 TGTTAGTACAGGAAGGCAAGGCTG
66 TGTCAGTACAGGAAGGCAAGGCTG
*
40482699 GTATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
40482745 AACTTCATTG
Statistics
Matches: 336, Mismatches: 64, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
88 75 0.22
89 190 0.57
90 71 0.21
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (89 bp):
GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCGC
TGTCAGTACAGGAAGGCAAGGCTG
Found at i:40482557 original size:177 final size:176
Alignment explanation
Indices: 40482253--40482744 Score: 646
Period size: 177 Copynumber: 2.8 Consensus size: 176
40482243 TACAAACTAT
* * * *
40482253 TGTGTCTTTGATCTGCTTCACTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCCG
1 TGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGGCAAGAT-TTCTATCTTCAATCTGCTCCG
* * * * *
40482318 CTGTCAGTACAGTAAGGCAAGGCTGGTGTCTTCGATTTGCTTCGCTGCCGGTACATGAAGGCATG
65 CTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAG
* * * *
40482383 ATCTGCTATCTTCAATCTGCTCCGCTGTCAATATAGGAATG-AAG-GC
130 ATCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAA-GAAAGAGC
* * * *
40482429 TAGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTACTATCTTCAGTCTGCTCT
1 T-GTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGGCAAGATTT-CTATCTTCAATCTGCTCC
* *
40482494 GCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAA
64 GCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAA
* ** *
40482559 GATCTGCTATCTTCGATCTACTTTGCTGCCAATACAAGAAGACAAGATC
129 GATCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAAGA-AAGAGC
* * * *
40482608 TGCTATCTTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTCAATCTGCTCC
1 TG-TGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGGCAAGAT-TTCTATCTTCAATCTGCTCC
* *
40482673 GCTGTTAGTACAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAA
64 GCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAA
40482738 GATCTGC
129 GATCTGC
40482745 AACTTCATTG
Statistics
Matches: 274, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
176 3 0.01
177 144 0.53
178 4 0.01
179 121 0.44
180 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (176 bp):
TGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGGCAAGATTTCTATCTTCAATCTGCTCCGC
TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGA
TCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAAGAAAGAGC
Found at i:40483848 original size:7 final size:7
Alignment explanation
Indices: 40483836--40483913 Score: 68
Period size: 7 Copynumber: 10.7 Consensus size: 7
40483826 TGGCCTCTCC
40483836 TTTTTCT
1 TTTTTCT
40483843 TTTTTCT
1 TTTTTCT
*
40483850 TTTCTCTTT
1 TTT-T-TCT
40483859 TTCTTTCT
1 TT-TTTCT
40483867 TTTTTCT
1 TTTTTCT
*
40483874 TCTTT-T
1 TTTTTCT
*
40483880 TCTTTCT
1 TTTTTCT
*
40483887 TTTTCCT
1 TTTTTCT
*
40483894 TTTTCCTT
1 TTTTTC-T
40483902 TTTTTCT
1 TTTTTCT
40483909 TTTTT
1 TTTTT
40483914 TTCTCTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
6 6 0.10
7 37 0.62
8 11 0.18
9 5 0.08
10 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:40483858 original size:20 final size:19
Alignment explanation
Indices: 40483835--40483927 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 19
40483825 TTGGCCTCTC
40483835 CTTTTTCTTTTTTCTTTTCT
1 CTTTTTCTTTTTT-TTTTCT
*
40483855 CTTTTTCTTTCTTTTTTCTT
1 CTTTTTCTTTTTTTTTTC-T
*
40483875 CTTTTTC-TTTCTTTTTC-
1 CTTTTTCTTTTTTTTTTCT
40483892 CTTTTTCCTTTTTTTCTTT-T
1 CTTTTT-CTTTTTTT-TTTCT
40483912 -TTTTCTCTATTTTTTT
1 CTTTT-TCT-TTTTTTT
40483928 ATTTTTTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
17 6 0.10
18 1 0.02
19 25 0.40
20 30 0.48
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTCTTTTTTTTTTCT
Found at i:40483867 original size:17 final size:16
Alignment explanation
Indices: 40483835--40483917 Score: 75
Period size: 16 Copynumber: 5.1 Consensus size: 16
40483825 TTGGCCTCTC
40483835 CTTTTTCTTTTTTCTTTT
1 CTTTTTC-TTTTTC-TTT
*
40483853 CTCTTTT-TCTTTCTTT
1 CT-TTTTCTTTTTCTTT
40483869 -TTTCTTCTTTTTCTTT
1 CTTT-TTCTTTTTCTTT
*
40483885 CTTTTTCCTTTTTCCTT
1 CTTTTT-CTTTTTCTTT
40483902 -TTTTTCTTTTT-TTT
1 CTTTTTCTTTTTCTTT
40483916 CT
1 CT
40483918 CTATTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
14 4 0.07
15 10 0.18
16 18 0.33
17 17 0.31
18 2 0.04
19 4 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
CTTTTTCTTTTTCTTT
Found at i:40483924 original size:10 final size:9
Alignment explanation
Indices: 40483849--40483925 Score: 61
Period size: 9 Copynumber: 8.4 Consensus size: 9
40483839 TTCTTTTTTC
40483849 TTTTCTCTT
1 TTTTCTCTT
*
40483858 TTTCTTTCTT
1 TTT-TCTCTT
40483868 TTTTCT-TCT
1 TTTTCTCT-T
*
40483877 TTTTCTTTCT
1 TTTTCTCT-T
40483887 TTTTC-CTT
1 TTTTCTCTT
*
40483895 TTTCCT-TT
1 TTTTCTCTT
*
40483903 TTTTCTTTT
1 TTTTCTCTT
40483912 TTTTCTCTAT
1 TTTTCTCT-T
40483922 TTTT
1 TTTT
40483926 TTATTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
8 13 0.23
9 22 0.39
10 21 0.38
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:40483932 original size:26 final size:24
Alignment explanation
Indices: 40483836--40483932 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 24
40483826 TGGCCTCTCC
* *
40483836 TTTTTCT-TTTTTCTTTTCTCTTT
1 TTTTTCTCTTTTTTTTTTTTCTTT
40483859 TTCTTTCT-TTTTTCTTCTTTTTCTTT
1 TT-TTTCTCTTTTT-TT-TTTTTCTTT
40483885 CTTTTTC-CTTTTTCCTTTTTTTCTTT
1 -TTTTTCTCTTTTT--TTTTTTTCTTT
40483911 TTTTTCTCTATTTTTTTATTTT
1 TTTTTCTCT-TTTTTTT-TTTT
40483933 TTATTGAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
23 2 0.03
24 10 0.16
25 10 0.16
26 32 0.51
27 9 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTCTCTTTTTTTTTTTTCTTT
Found at i:40483934 original size:44 final size:43
Alignment explanation
Indices: 40483836--40483934 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
40483826 TGGCCTCTCC
* *
40483836 TTTTTCTTTTTTCTTTTCTCTTTTTCTTTCTTTTTTCTTCTTT
1 TTTTTTTTTTTTCTTTTCTCCTTTTCTTTCTTTTTTCTTCTTT
* *
40483879 TTCTTTCTTTTTCCTTTT-TCCTTTT-TTTCTTTTTT-TTCTCTAT
1 TT-TTTTTTTTTTCTTTTCTCCTTTTCTTTCTTTTTTCTTCT-T-T
40483922 TTTTTTATTTTTT
1 TTTTTT-TTTTTT
40483935 ATTGAATCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
41 4 0.08
42 14 0.29
43 16 0.33
44 14 0.29
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (43 bp):
TTTTTTTTTTTTCTTTTCTCCTTTTCTTTCTTTTTTCTTCTTT
Found at i:40489796 original size:25 final size:25
Alignment explanation
Indices: 40489768--40489819 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
40489758 CCTATTTAAG
*
40489768 CTAAAAAAATTTCAAAATTTTCATT
1 CTAAAAAAATTTCAAAAATTTCATT
***
40489793 CTAAAATTTTTTCAAAAATTTCATT
1 CTAAAAAAATTTCAAAAATTTCATT
40489818 CT
1 CT
40489820 TCCCACTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (25 bp):
CTAAAAAAATTTCAAAAATTTCATT
Found at i:40493125 original size:26 final size:28
Alignment explanation
Indices: 40493072--40493136 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
40493062 TTTAAAATAC
* *
40493072 TTTTAAAATAATTTTTTTTATTTTTTTAT
1 TTTTAAAATAA-TTTTTTTATATATTTAT
40493101 TTTTAAAATAA-TTTTTTA-ATATTTAT
1 TTTTAAAATAATTTTTTTATATATTTAT
*
40493127 TTTAAAAATA
1 TTTTAAAATA
40493137 GGCCGGGCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 7 0.21
29 11 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTAAAATAATTTTTTTATATATTTAT
Found at i:40493130 original size:39 final size:41
Alignment explanation
Indices: 40493043--40493130 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
40493033 ATATATATTT
*
40493043 TTTATTTT-TATTTTTTAATTTTAAAATACTTTTAAAATAA
1 TTTATTTTATATTTTTTAATTTTAAAATAATTTTAAAATAA
* * **
40493083 TTTTTTTTAT-TTTTTTATTTTTAAAATAATTTTTTAAT-A
1 TTTATTTTATATTTTTTAATTTTAAAATAATTTTAAAATAA
40493122 TTTATTTTA
1 TTTATTTTA
40493131 AAAATAGGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 9 0.22
40 31 0.76
41 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (41 bp):
TTTATTTTATATTTTTTAATTTTAAAATAATTTTAAAATAA
Found at i:40503351 original size:16 final size:18
Alignment explanation
Indices: 40503312--40503353 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
40503302 AAAGTTTATA
40503312 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
40503329 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
40503346 A-ATTTATA
1 ATATTTATA
40503354 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:40507020 original size:18 final size:19
Alignment explanation
Indices: 40506994--40507030 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40506984 ATAGAAAAAA
*
40506994 TTTAGAAAATTTTAAAATT
1 TTTAGAAAATTATAAAATT
40507013 TTTA-AAAATTATAAAATT
1 TTTAGAAAATTATAAAATT
40507031 ACGATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TTTAGAAAATTATAAAATT
Found at i:40507162 original size:10 final size:9
Alignment explanation
Indices: 40507130--40507228 Score: 60
Period size: 9 Copynumber: 10.4 Consensus size: 9
40507120 CACATGGTGT
*
40507130 AAAATGATA
1 AAAATTATA
*
40507139 AAAATTTATT
1 AAAA-TTATA
40507149 AAAATTAATAA
1 AAAATT-AT-A
*
40507160 AAAATCATA
1 AAAATTATA
*
40507169 AAAGTTAT-
1 AAAATTATA
40507177 AAAATATATTA
1 AAAAT-TA-TA
40507188 CAAAA-TATA
1 -AAAATTATA
40507197 AAAA-TATA
1 AAAATTATA
*
40507205 GAAAATTATTT
1 -AAAATTA-TA
40507216 AAAATTATA
1 AAAATTATA
40507225 AAAA
1 AAAA
40507229 AATATGTAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
8 12 0.17
9 26 0.37
10 23 0.32
11 6 0.08
12 4 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:40507214 original size:28 final size:27
Alignment explanation
Indices: 40507130--40507228 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
40507120 CACATGGTGT
* *
40507130 AAAATGATAAAAATTTATTAAAATTAATAA
1 AAAATCATAAAAA-TTA-TAAAATT-ATTA
*
40507160 AAAATCATAAAAGTTATAAAATATATTA
1 AAAATCATAAAAATTATAAAAT-TATTA
* *
40507188 CAAAAT-ATAAAAATATAGAAAATTATTT
1 -AAAATCATAAAAAT-TATAAAATTATTA
*
40507216 AAAATTATAAAAA
1 AAAATCATAAAAA
40507229 AATATGTAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.08
28 27 0.46
29 16 0.27
30 11 0.19
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATCATAAAAATTATAAAATTATTA
Found at i:40507229 original size:10 final size:10
Alignment explanation
Indices: 40507130--40507229 Score: 50
Period size: 10 Copynumber: 10.4 Consensus size: 10
40507120 CACATGGTGT
*
40507130 AAAATGATAA
1 AAAATTATAA
* *
40507140 AAATTTAT-T
1 AAAATTATAA
40507149 AAAATTAATAA
1 AAAATT-ATAA
*
40507160 AAAATCAT-A
1 AAAATTATAA
*
40507169 AAAGTTATAA
1 AAAATTATAA
* *
40507179 AATA-TATTAC
1 AAAATTA-TAA
40507189 AAAA-TAT-A
1 AAAATTATAA
*
40507197 AAAA-TATAG
1 AAAATTATAA
**
40507206 AAAATTATTT
1 AAAATTATAA
40507216 AAAATTATAA
1 AAAATTATAA
40507226 AAAA
1 AAAA
40507230 ATATGTAGAA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
8 7 0.11
9 19 0.29
10 35 0.53
11 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:40507229 original size:20 final size:20
Alignment explanation
Indices: 40507195--40507243 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
40507185 TTACAAAATA
* * * *
40507195 TAAAAATATAGAAAATTATT
1 TAAAATTATAAAAAAATATG
40507215 TAAAATTATAAAAAAATATG
1 TAAAATTATAAAAAAATATG
40507235 TAGAAATTA
1 TA-AAATTA
40507244 GTCTTAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
TAAAATTATAAAAAAATATG
Found at i:40513536 original size:45 final size:44
Alignment explanation
Indices: 40513447--40513539 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
40513437 ATTACAACAT
*
40513447 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
* *
40513491 CATTCCATTCAACCAAACA-ATTGAATTACTATTA-TGCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
40513536 CATT
1 CATT
40513540 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:40513547 original size:16 final size:16
Alignment explanation
Indices: 40513528--40513560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40513518 ACTATTATGC
40513528 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
40513544 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
40513560 C
1 C
40513561 GAACCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:40516814 original size:14 final size:14
Alignment explanation
Indices: 40516795--40516826 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40516785 ATTATGTTAG
40516795 AATTAAAAACACAT
1 AATTAAAAACACAT
40516809 AATT-AAAACACAT
1 AATTAAAAACACAT
40516822 -ATTAA
1 AATTAA
40516827 TGATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:40516909 original size:39 final size:39
Alignment explanation
Indices: 40516805--40516911 Score: 180
Period size: 39 Copynumber: 2.8 Consensus size: 39
40516795 AATTAAAAAC
*
40516805 ACATAATTAAA-ACACATATTAATGATATTCAAACTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
40516843 ACATAATTAAAGACACATATTAATGATGTTCAAGCTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
40516882 ACATAATTAAAGACTCATATTAATGATGTT
1 ACATAATTAAAGACACATATTAATGATGTT
40516912 TACACTAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 11 0.17
39 54 0.83
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (39 bp):
ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
Found at i:40522296 original size:14 final size:14
Alignment explanation
Indices: 40522277--40522308 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40522267 ATTATGTTAG
40522277 AATTAAAAACACAT
1 AATTAAAAACACAT
40522291 AATT-AAAACACAT
1 AATTAAAAACACAT
40522304 -ATTAA
1 AATTAA
40522309 TGATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:40522348 original size:39 final size:38
Alignment explanation
Indices: 40522287--40522401 Score: 135
Period size: 39 Copynumber: 3.0 Consensus size: 38
40522277 AATTAAAAAC
*
40522287 ACATAATTAAAACACATATTAATGATATT-AAACCTAAG
1 ACATAATTAAAATACATATTAATGATATTCAAA-CTAAG
* * *
40522325 ACATATTTAAAGATACATATTAATTATGTTCAAACTAAG
1 ACATAATTAAA-ATACATATTAATGATATTCAAACTAAG
*
40522364 ACATAATT-AAATACTCATATTAATGATGTTCAAACTAA
1 ACATAATTAAAATA--CATATTAATGATATTCAAACTAA
40522402 AATAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
37 3 0.04
38 12 0.18
39 49 0.73
40 3 0.04
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (38 bp):
ACATAATTAAAATACATATTAATGATATTCAAACTAAG
Found at i:40527292 original size:33 final size:34
Alignment explanation
Indices: 40527219--40527288 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 34
40527209 GATTTAAACA
40527219 AATTAATTACTAACACTTATTTAAGCTGAACTAC
1 AATTAATTACTAACACTTATTTAAGCTGAACTAC
*
40527253 AATTAATT-CTAACACTTATTTGAGCTGAACTA-
1 AATTAATTACTAACACTTATTTAAGCTGAACTAC
40527285 AATT
1 AATT
40527289 TAATAAACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 4 0.11
33 23 0.66
34 8 0.23
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (34 bp):
AATTAATTACTAACACTTATTTAAGCTGAACTAC
Found at i:40529056 original size:18 final size:18
Alignment explanation
Indices: 40529033--40529071 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40529023 CTCTTTTTGC
40529033 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
40529051 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
40529069 TCT
1 TCT
40529072 ATCTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:40532367 original size:33 final size:32
Alignment explanation
Indices: 40532293--40532463 Score: 117
Period size: 28 Copynumber: 5.5 Consensus size: 32
40532283 GAATTTGTTA
40532293 TTTTTTTCTTAATTTGGTACTTAAATTT---T
1 TTTTTTTCTTAATTTGGTACTTAAATTTGACT
* *
40532322 TTTTTATC-TAATTTGGTACTCAAATTTGACAT
1 TTTTTTTCTTAATTTGGTACTTAAATTTGAC-T
* * *
40532354 TTTTTTTCTTAATTTAGTATTTAAAGTTGACGTT
1 TTTTTTTCTTAATTTGGTACTTAAATTTGAC--T
* * *
40532388 TTTTTTTCTTAAGTTGATACATAATATTT---T
1 TTTTTTTCTTAATTTGGTACTTAA-ATTTGACT
**** *
40532418 TTGGGAT-TTAATTTGGTACCTAAATTTGAC-
1 TTTTTTTCTTAATTTGGTACTTAAATTTGACT
*
40532448 TCTTTTTCTTAATTTG
1 TTTTTTTCTTAATTTG
40532464 ATATCTATTT
Statistics
Matches: 105, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
28 22 0.21
29 20 0.19
30 6 0.06
31 8 0.08
32 8 0.08
33 18 0.17
34 20 0.19
35 3 0.03
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (32 bp):
TTTTTTTCTTAATTTGGTACTTAAATTTGACT
Found at i:40532391 original size:34 final size:33
Alignment explanation
Indices: 40532293--40532399 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 33
40532283 GAATTTGTTA
* *
40532293 TTTTTTTCTTAATTTGGTACTTAAA-TT---TT
1 TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
* * * *
40532322 TTTTTATC-TAATTTGGTACTCAAATTTGACAT
1 TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
* *
40532354 TTTTTTTCTTAATTTAGTATTTAAAGTTGACGTT
1 TTTTTTTCTTAATTTAGTACTCAAAGTTGAC-TT
40532388 TTTTTTTCTTAA
1 TTTTTTTCTTAA
40532400 GTTGATACAT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.24
29 9 0.14
32 8 0.13
33 18 0.29
34 13 0.21
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (33 bp):
TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
Found at i:40534502 original size:37 final size:38
Alignment explanation
Indices: 40534419--40534504 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
40534409 CTTAGATTGC
40534419 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAACG
1 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAACG
40534457 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAACG
1 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAACG
*
40534495 -AATTCAAATA
1 AAAGTCAAATA
40534505 ATAAAGATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 9 0.19
38 38 0.81
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (38 bp):
AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAACG
Found at i:40535080 original size:6 final size:6
Alignment explanation
Indices: 40535069--40535093 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40535059 ACAGTACAGG
40535069 CATCAC CATCAC CATCAC CATCAC C
1 CATCAC CATCAC CATCAC CATCAC C
40535094 CAGAGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CATCAC
Found at i:40541585 original size:29 final size:29
Alignment explanation
Indices: 40541552--40541610 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40541542 CACATTTGAG
40541552 TGCCAAAGTAATCTTGGCTAAATTCAATC
1 TGCCAAAGTAATCTTGGCTAAATTCAATC
*
40541581 TGCCAAAGTAGTCTTGGCTAAATTCAATC
1 TGCCAAAGTAATCTTGGCTAAATTCAATC
40541610 T
1 T
40541611 TCTGAACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (29 bp):
TGCCAAAGTAATCTTGGCTAAATTCAATC
Found at i:40547404 original size:30 final size:30
Alignment explanation
Indices: 40547368--40547429 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
40547358 AGTGTCAGGT
* *
40547368 AACCTAGGGTTGAGGATGACGACAACCTTA
1 AACCTAGGGTTGAGGATGACAACAACCCTA
40547398 AACCTAGGGTTGAGGATGACAACAACCCTA
1 AACCTAGGGTTGAGGATGACAACAACCCTA
40547428 AA
1 AA
40547430 TCTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (30 bp):
AACCTAGGGTTGAGGATGACAACAACCCTA
Found at i:40552476 original size:524 final size:524
Alignment explanation
Indices: 40551488--40553055 Score: 2915
Period size: 524 Copynumber: 3.0 Consensus size: 524
40551478 GAGACCGGGG
*
40551488 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCCGTATCAAGTGTGGGTAGTGTGAAGCCTA
1 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
40551553 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
66 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
* * * * *
40551618 TGTTTCTAGTGTGGATCTCGACAACATTGTATTAAAGATTGCCCTCAGAAAATTGAAGAAGAAAA
131 TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
* *
40551683 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGATCACCGAGAAACACCAGAACTA
196 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
* *
40551748 GAGATAGTGGTAAAAGTGTAATGAAGGGTACAGTTGCAAGACCAGAACCTCGAACACCTGCCAGA
261 GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
**
40551813 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCTAATGTGATTACTGGTACATTCTCTCT
326 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
*
40551878 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCACATGTATGTGTGAATT
391 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
40551943 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
456 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
40552008 GGTA
521 GGTA
40552012 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
1 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
40552077 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
66 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
40552142 TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
131 TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
*
40552207 ATTTTAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
196 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
40552272 GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
261 GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
* * *
40552337 GCTTATGCCATACGTGCTTGTGAGGATGCATCATCACCCGACGTGATTACTAGTACATTCTCTCT
326 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
40552402 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
391 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
40552467 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
456 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
40552532 GGTA
521 GGTA
* *
40552536 AAAATTGTATTTGTGTCCTGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
1 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
40552601 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
66 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
40552666 TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
131 TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
*
40552731 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAAAGGTAGACCACCGAGAAACACCGGAACTA
196 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
40552796 GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
261 GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
*
40552861 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCTCCCGATGTGATTACTGGTACATTCTCTCT
326 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
* *
40552926 CTATGATATTGATGTTGTTGCTTTGATTGATCTTGGGTCTACTCATTCATATGTATGTGTGAATT
391 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
40552991 TAGTATCTAA-AAAAA-TTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
456 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
40553054 GG
521 GG
40553056 CAAATATGTT
Statistics
Matches: 1017, Mismatches: 27, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
522 50 0.05
523 5 0.00
524 962 0.95
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (524 bp):
AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
TGTTTCAAGTGTGGCTCTCGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
GAGATAGTGGTAAAAGTATAATGAAGGGTACAGTTGCAAGACCAGAACCTCAAACACCTGCCAGA
GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTA
GGTA
Found at i:40555785 original size:28 final size:28
Alignment explanation
Indices: 40555745--40555802 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40555735 CACTTGACAA
40555745 GTTGGCGGAGTTATATGTTGCTGAAATT
1 GTTGGCGGAGTTATATGTTGCTGAAATT
*
40555773 GTTGGCGGAGTTATATGTTGTTGAAATT
1 GTTGGCGGAGTTATATGTTGCTGAAATT
40555801 GT
1 GT
40555803 GAGATTGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (28 bp):
GTTGGCGGAGTTATATGTTGCTGAAATT
Found at i:40556852 original size:11 final size:12
Alignment explanation
Indices: 40556836--40556868 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
40556826 ATTTGACGGA
40556836 AAAATTTCG-TG
1 AAAATTTCGTTG
40556847 AAAATTTCGTTTG
1 AAAATTTCG-TTG
40556860 AAAATTTCG
1 AAAATTTCG
40556869 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (12 bp):
AAAATTTCGTTG
Found at i:40558130 original size:51 final size:50
Alignment explanation
Indices: 40558070--40558405 Score: 296
Period size: 51 Copynumber: 6.6 Consensus size: 50
40558060 GATGAACACG
* * *
40558070 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATAGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATGGTCACA
* * * * * * * * *
40558121 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAACCTTTGTTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA-ATATGGTCACA
* ** *
40558172 TGTGTAGTACTGTGTGAAGGCTACTACACGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATGGTCACA
* * * * * * * *
40558223 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA-ATATGGTCACA
* * *
40558274 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATGGTCACA
* * * * * * *
40558325 TTTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCAAAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA--TATGGTCACA
40558376 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTATGTGAAGGCTACTACGTG
40558406 AACCGTAAAA
Statistics
Matches: 218, Mismatches: 61, Indels: 12
0.75 0.21 0.04
Matches are distributed among these distances:
50 6 0.03
51 209 0.96
52 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATGGTCACA
Found at i:40558242 original size:102 final size:102
Alignment explanation
Indices: 40558066--40558407 Score: 567
Period size: 102 Copynumber: 3.4 Consensus size: 102
40558056 TATCGATGAA
* * *
40558066 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATAGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTAC
* *
40558131 TAAGTGAAGGCTACAATGTGTACCGAGAACCTTTGTT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
** *
40558168 CACGTGTGTAGTACTGTGTGAAGGCTACTACACGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTAC
40558233 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
40558270 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATTTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTAC
* * *
40558335 TAAGTGAAGGCTACTATGTGTACCAAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
40558372 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA
40558408 CCGTAAAACT
Statistics
Matches: 224, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 224 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:40565246 original size:21 final size:21
Alignment explanation
Indices: 40565213--40565252 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40565203 ACTTATTTGT
* * *
40565213 AAAAGTTGTAAAATATGTGTA
1 AAAAATTGAAAAAAATGTGTA
40565234 AAAAATTGAAAAAAATGTG
1 AAAAATTGAAAAAAATGTG
40565253 ATTTAGTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAATTGAAAAAAATGTGTA
Found at i:40574363 original size:49 final size:49
Alignment explanation
Indices: 40574229--40574364 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 49
40574219 TTATGAGAGG
* * *
40574229 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAAGAGAAC
* * * *
40574279 TCCCATGTAAGACCATATCTGAGATATGCCATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAAGAGAAC
*
40574327 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40574365 TGTTATTATC
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 4 0.06
49 36 0.50
50 32 0.44
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGACAAGAGAAC
Found at i:40612489 original size:56 final size:52
Alignment explanation
Indices: 40612417--40612663 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 52
40612407 ACAAATGTAA
*
40612417 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-CATG
* *
40612473 AGAGGTCCCATGTAAGAGCATGTCTGGGACATGGCATCGGCACCGAGAC--G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
*
40612523 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCACCGAG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
* * * * * *
40612573 AAAGGTTCCC-CGTAACACCATGTCTAGGACATGGCATGGGCACC--TACATG
1 AGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
** * *
40612623 AGAATTCCCATGTAAGACCATATCTGGGATATGGCATTGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC
40612664 GGTACAAGAA
Statistics
Matches: 163, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.02
50 109 0.67
51 4 0.02
52 1 0.01
53 4 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (52 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
Found at i:40615566 original size:45 final size:45
Alignment explanation
Indices: 40615502--40615590 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
40615492 TAGAAAACCG
*
40615502 TTGATTTTTCGTAATTGACACTGCCCCGAGCAACTTTCGTATTCA
1 TTGATTTTTCGTAATTGACACTACCCCGAGCAACTTTCGTATTCA
40615547 TTGATTTTTCGTAATTGACACTACCCCGAGCAACTTTCGTATTC
1 TTGATTTTTCGTAATTGACACTACCCCGAGCAACTTTCGTATTC
40615591 CCTAAGGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (45 bp):
TTGATTTTTCGTAATTGACACTACCCCGAGCAACTTTCGTATTCA
Found at i:40619495 original size:761 final size:760
Alignment explanation
Indices: 40616660--40620406 Score: 5459
Period size: 759 Copynumber: 4.9 Consensus size: 760
40616650 AAGAAAGTCA
* * * * * *
40616660 TATTTTTGTCCTCTAATTTCAACCAGTTCACCCTAACCCTTTGCTCCCAATAAATTTCATCTTTA
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
* * * *
40616725 TCAATCTCTAAATTAAGATGTACTCCAGTATCAATCAAATCAGCCATAATTTCATTAGTTCTGTC
66 TCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAGCCATACTTTCATCAGTTCTGTC
* ** *
40616790 ATGATCTAAGAGAAATTTTATTTTTTCTATTTGCTTCTTCTTTTGCCCTTCCC-TTTTTTGTCTA
131 TTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTTGTCTA
* * * *
40616854 ATTCTAGTAGCCCATCTTACGAGCCCAATTTGTAAAAAATTGATTTTTTCAAAAATATCACCGTG
196 ATTCCAGTAGCCCATCTTACGAGCCCAATCTAT-AAAAATTGAATTTTTCAAAAATATCACCGTG
*
40616919 ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCATGCCTCAA
260 ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCAA
* * * *
40616984 ATTGAAATATCTTACTATACATGTTCTTTGATTCAATATCAATACCAAGCAGTATGGGATAGTGA
325 ATCGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGA
** * * * * *
40617049 TATGAAAAA-AATTCGGTAAATGGTGAAAAACTGCTATTGGAAAAATATCCCTCCGCTCTAAGTT
390 TCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAAGTT
* *
40617113 CGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCCGGCAAATTCCCTCTTTCCCAAGCAA
455 CGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTAA
** * *
40617178 ACCAAGTACCTAAGAAGCCAATATCTGTCAGTTGACATTCCTCTAAAACTTCCATAAACTCCGCC
520 ACCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGCC
* ** * *
40617243 ATCCTGCTCTCTTCTCTTGGTTCACCACCCACATTCTCGAAGGAATAAAGT-ATCTCATTAAAAT
585 ATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAA-TAATCTCGTTAAAAT
* *
40617307 CTCCACAAACCATCCAAGGTAGGCCTTGGATTCGATTTAGGTTTTTTAGTATGCCCCAAGTATTT
649 CTCCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTT
*
40617372 CCTCTATTCTGCGCATAATGGGAGCCATAAAAACCCTTAAACCTATG
714 CCTCTATTCTGCGCATAAAGGGAGCCATAAAAACCCTTAAACCTATG
* * * * *
40617419 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCTA-CCCTTTTACACCCAATACATTTTGCCTTT
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCC-TTTGCTCCCAATACATTTCGTCTTT
* *
40617483 ATCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAACTCAGCCATACTTTCATTAGTTCTGT
65 ATCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAGCCATACTTTCATCAGTTCTGT
* *
40617548 CTTGATCTAAGAGAAATTTTATTTTTTCTGTCAGCTTCTTCTTTCGCCCTTCCTTTTTTTTTGTC
130 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCC-CTTTTTTTGTC
* *
40617613 TAATTCTAGTAGCCTATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCG
194 TAATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAA-TTGAATTTTTCAAAAATATCACCG
* * * * *
40617678 CGATCAACTTGCCACAATCTTCTCATCTCATCCACATAA-ATTCTTCCTTCACCCACCACGCCTC
258 TGATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTC
* *
40617742 AAATCGAAAGACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAATATGGGATAGT
323 AAATCGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGT
* * * *
40617807 GATCGGAAAAA-AATGCGGTAAATGGTGAAAAACTGCTGTCGGGAACGTATCCTTCCACTCTAAG
388 GATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAAG
**
40617871 TTTTCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGT
453 TTCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGT
* *
40617936 AAACCAAGTACTTAAGAAGCTAATATCCATC-GTTGACATTCCTCCAAAACTTCCCTAAACTCCG
518 AAACCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCG
*
40618000 CCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAA
583 CCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAATAATCTCGTTAAAA
* * *
40618065 TCTTCACAAACTATCCAAGGTAAGCCTTGGATTTGATTTAGATTTTTTAGTATGCCCCAAGTATT
648 TCTCCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATT
* *
40618130 TCATCTATTCTGCGCATAAAGGGAGACATAAAAA-CCTGTAAACCTATG
713 TCCTCTATTCTGCGCATAAAGGGAGCCATAAAAACCCT-TAAACCTATG
** *
40618178 TATTTTT-TCCCCTAATTTCAACCAGTTTACTTGAGCCCTTTGCTCCCAATAGATTTCGTCTTTA
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
*
40618242 TCAATCTCTAAATTAAGTTGTACTCTAGTAT-AATCCAAATCAGCCATACTTTCATCAGTTCTGT
66 TCAATCTCTAAATTAAGATGTACTCTAGTATCAA-CCAAATCAGCCATACTTTCATCAGTTCTGT
* *
40618306 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCACCCTTCCCTTTTTTTATCT
130 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTTGTCT
* * *
40618371 AATTCCAGTAGCCCATCTTATGAGCCCAATCTATAAAAAAATGAAATTTTT-AAAAATATCACTG
195 AATTCCAGTAGCCCATCTTACGAGCCCAATCTAT-AAAAATTG-AATTTTTCAAAAATATCACCG
* *
40618435 TGATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACGCACCACACCTC
258 TGATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTC
*
40618500 AAATCAAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGT
323 AAATCGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGT
* * * ** * *
40618565 GATCGAAAAAAGAATGCAGTGAATGGTGAAAAACTATTGTTGGTAACATATCCTTCCACTCTAAG
388 GATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAAG
* * *
40618630 TTCGCCACACCCCTATCAAGCCTTTCATGTATATTCGTCTCTAGCAAATTCCCTCTTGCCCAAGT
453 TTCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGT
* * *
40618695 AAACCAAGTACCTGAGAAGCCAATATCCATCAATTGACATTCCTCCAAAATTTCCCTAAACTCCG
518 AAACCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCG
* *
40618760 CAATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTTTCGAAGGAATAAATAATCTCGTTAAAA
583 CCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAATAATCTCGTTAAAA
* * *
40618825 TCTCCATAAACCATCCAAGGTAAGCCTTGGATTCGATTTATATTTTTTTTCGTATGCCCCAAGTA
648 TCTCCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGA--TTTTTTAGTATGCCCCAAGTA
*
40618890 TTTCCTCTATTCTGCACATAAAGGGAGCCATAAAAACCCTT-AACCTATG
711 TTTCCTCTATTCTGCGCATAAAGGGAGCCATAAAAACCCTTAAACCTATG
* * * * *
40618939 TACTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGTTCCCACTTCATTTTGTCTTTA
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
* * *
40619004 TTAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAACCATACTTTCATCAGTTCAGTC
66 TCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAGCCATACTTTCATCAGTTCTGTC
* * * * *
40619069 TTGATCTAAGAGAAATTTTATTTTTACTGTCAACTTCTTCTTTCACCCTTCCCTTTTTTTCTCTA
131 TTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTTGTCTA
* **
40619134 ATTCCAGTAGCCCATCTTACGAGCCCAATCTATACAAAATTGAATTTTTCAAAAAT-GCACCACG
196 ATTCCAGTAGCCCATCTTACGAGCCCAATCTATA-AAAATTGAATTTTTCAAAAATATCACCGTG
* * * *
40619198 ATCAACTTGCCACAATCGTCTGATCTCATCCACACAATTTTTTTCCTTCACCCACCATGCCTTAA
260 ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCAA
* *
40619263 ATCGAAATACCTCCCTATACATGTTCTTTGATTCAATATCAATATCAAGTAGTATGGGATAGTGA
325 ATCGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGA
* * *
40619328 CCGGAAAAAGAATGCTGTAAATGGTGAAAAACTACTGTTGGAAACATATCCGTCCACTCTAAGTT
390 TCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAAGTT
* * * * * * *
40619393 TGCCACACCCCTTTCAAGCCCTTCTTGTACATTAGTCTCTGGAAAATTCCTTCTTTCCCAAGTAA
455 CGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTAA
* * * *
40619458 ATCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCCAAACTTTCCTAAACTCCGCC
520 ACCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGCC
* * * *
40619523 ATCCTGCTCTGCTCTCTTGGTGCACCACCCACTTTCTCGAAGGGATAAATAATCTCGTTAAAATC
585 ATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAATAATCTCGTTAAAATC
* *
40619588 TCTACAAACCATCCAAGGTAAGCCTTGGATTCAATTTAGATTTTTTAGTATGCCCCAAGTATTTC
650 TCCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTTC
* * *
40619653 CTCTATTCTGCGCATAAGGGGAGCCATAAAAACTCATAAACCTATG
715 CTCTATTCTGCGCATAAAGGGAGCCATAAAAACCCTTAAACCTATG
** *
40619699 TATTTTTGTCCCCTAATTTCAACCAGTTTACTTGAGCCCTATT-CTCCCAATACATTTCATCTTT
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCT-TTGCTCCCAATACATTTCGTCTTT
* * * * *
40619763 ATAAATCTCTAAATTAAAATGTACTCTAGTGTCAATCAAATCAGCCATACTTTCATCAGTTTTGT
65 ATCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAGCCATACTTTCATCAGTTCTGT
40619828 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGC-T-TT-TTTCGCCCTT-CCTTTTTTTGTCT
130 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTTGTCT
** * * * * *
40619889 AATTCCAACAGCACATCTTATGATCCCAATCTGTAAAAATTTGAATTTTTCAAAAATATCACTGT
195 AATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAA-TTGAATTTTTCAAAAATATCACCGT
* *
40619954 GATCAACTTGCCACAATCCTTCT-ATCTCATCCACACAATTTTCTTCCTTCACCTACCACGCCTC
259 GATCAACTTGCCACAAT-CATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTC
* * *
40620018 AAATTGAAATACCTTCCTACACATG-TCTTTTGATTCAATATTAATATCAAGCAGTATGGGATAG
323 AAATCGAAATACCTTCCTATACATGTTC-TTTGATTCAATATCAATATCAAGCAGTATGGGATAG
* * * *
40620082 TGATCAGAAAAAGAATGCGGTAAATGGTG-AAAATTGTTGTTGGAAACATATCCGTCCACTTTAA
387 TGATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAA
** * * * *
40620146 GTTCGCCACACCTTTATCAAGCTTTTCATGTATTTTAGTCTCCGACAAATTCCCTCTTTCCCAAG
452 GTTCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAG
* * * *
40620211 TAAACCAAGTACCTAAGAAACAAATTTCCATCAGTTGAAATTCCTCCAAAACTTCCCTAAACTCC
517 TAAACCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCC
* ** *
40620276 TCCATCCTGCTCTGTTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAA
582 GCCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAATAATCTCGTTAAA
* * *
40620341 ATCTCTATAAACCAT-CAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATTCCCCAAGTAT
647 ATCTCCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTAT
40620405 TT
712 TT
40620407 TGTGACAGCC
Statistics
Matches: 2687, Mismatches: 275, Indels: 56
0.89 0.09 0.02
Matches are distributed among these distances:
755 53 0.02
756 273 0.10
757 240 0.09
758 272 0.10
759 553 0.21
760 510 0.19
761 514 0.19
762 267 0.10
763 5 0.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (760 bp):
TATTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
TCAATCTCTAAATTAAGATGTACTCTAGTATCAACCAAATCAGCCATACTTTCATCAGTTCTGTC
TTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTTGTCTA
ATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTGAATTTTTCAAAAATATCACCGTGA
TCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCAAA
TCGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGAT
CGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCGTCCACTCTAAGTTC
GCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTAAA
CCAAGTACCTAAGAAGCCAATATCCATCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGCCA
TCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAATAATCTCGTTAAAATCT
CCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTTCC
TCTATTCTGCGCATAAAGGGAGCCATAAAAACCCTTAAACCTATG
Found at i:40627336 original size:28 final size:27
Alignment explanation
Indices: 40627279--40627430 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
40627269 TAAATTGTGC
*
40627279 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
40627306 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
40627334 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40627361 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
40627389 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40627416 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40627431 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40627343 original size:55 final size:55
Alignment explanation
Indices: 40627279--40627430 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
40627269 TAAATTGTGC
*
40627279 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
40627334 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
40627389 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
40627431 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:40631840 original size:78 final size:77
Alignment explanation
Indices: 40631756--40631904 Score: 244
Period size: 78 Copynumber: 1.9 Consensus size: 77
40631746 GCATTTTCTG
* *
40631756 TAGAGCATTTTTCAAGGTAGGGTGAGAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTTTTAGCTA
1 TAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTG-TTTTTAGCTA
*
40631821 TGTTCTTTTCTAC
65 GGTTCTTTTCTAC
* *
40631834 TAGAGCATTTTTTAAGGTAGAGTGAAAAAGCTTTAGTCTAAAGGTTTCTTGTTGTTTTTAGCTAG
1 TAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTTTAGCTAG
40631899 GTTCTT
66 GTTCTT
40631905 GTTAGATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 16 0.24
78 50 0.76
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (77 bp):
TAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTTTAGCTAG
GTTCTTTTCTAC
Found at i:40637453 original size:5 final size:5
Alignment explanation
Indices: 40637443--40637468 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40637433 TGAGCATTCG
40637443 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
40637469 AATTTTTGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:40637573 original size:10 final size:10
Alignment explanation
Indices: 40637558--40637583 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40637548 GAGATGAAAT
40637558 TCGAATCAAA
1 TCGAATCAAA
40637568 TCGAATCAAA
1 TCGAATCAAA
40637578 TCGAAT
1 TCGAAT
40637584 ATATTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (10 bp):
TCGAATCAAA
Found at i:40638267 original size:30 final size:31
Alignment explanation
Indices: 40638228--40638287 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
40638218 GGAGGTGGGA
40638228 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
* *
40638259 TGGG-AGGGAGTAAAAGTTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAA
40638288 CAAAAGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
Found at i:40638494 original size:9 final size:9
Alignment explanation
Indices: 40638476--40638512 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40638466 TATAGTTTGA
40638476 TATTCGAAT
1 TATTCGAAT
*
40638485 TATTCAAAT
1 TATTCGAAT
*
40638494 TATTCGAGT
1 TATTCGAAT
40638503 TATTCGAAT
1 TATTCGAAT
40638512 T
1 T
40638513 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40639355 original size:20 final size:20
Alignment explanation
Indices: 40639330--40639381 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40639320 AAGTTTATGT
40639330 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
40639350 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
*
40639370 AAAGTAAATGAA
1 TAAGTAAATGAA
40639382 GTGGTACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:40639386 original size:20 final size:19
Alignment explanation
Indices: 40639331--40639387 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
40639321 AGTTTATGTT
* *
40639331 AAGTAAATGAAATGGAAAGT
1 AAGTAAATG-AATGGTAAGA
40639351 AAGTAAATGGAATGGTAAGA
1 AAGTAAAT-GAATGGTAAGA
40639371 AAGTAAATGAAGTGGTA
1 AAGTAAATGAA-TGGTA
40639388 CATAGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.88
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (19 bp):
AAGTAAATGAATGGTAAGA
Found at i:40653964 original size:71 final size:71
Alignment explanation
Indices: 40653845--40653993 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 71
40653835 TTACTTATTC
* * * * * * * *
40653845 ATAATTTGATGATGCTCACTCAAGCTGTCGGGAATTCGCAATACATGTTGGATCTCAGTCATCGA
1 ATAATTTAATGATGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCCCAGCCATCGA
40653910 TAAAGA
66 TAAAGA
* *
40653916 ATAATTTAATGTTGCTCACTCAAGCTATCGAGAATCCACAACATATGTTGGATCCCAGCCATCGA
1 ATAATTTAATGATGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCCCAGCCATCGA
40653981 TAAAGA
66 TAAAGA
40653987 ATAATTT
1 ATAATTT
40653994 CTATTCAAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (71 bp):
ATAATTTAATGATGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCCCAGCCATCGA
TAAAGA
Found at i:40659921 original size:13 final size:13
Alignment explanation
Indices: 40659903--40659927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40659893 GACGAGGCTC
40659903 CTTTGCTCCTTTA
1 CTTTGCTCCTTTA
40659916 CTTTGCTCCTTT
1 CTTTGCTCCTTT
40659928 GCTGATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.32, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTTGCTCCTTTA
Found at i:40662722 original size:13 final size:13
Alignment explanation
Indices: 40662706--40662758 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
40662696 TTTAAACCAA
*
40662706 ACTTTTCGAAAGC
1 ACTTTTCCAAAGC
* *
40662719 ACTTCTCCAAAGT
1 ACTTTTCCAAAGC
* *
40662732 ACTTTTCCACATC
1 ACTTTTCCAAAGC
*
40662745 ACTTTTCAAAAGC
1 ACTTTTCCAAAGC
40662758 A
1 A
40662759 ATAAAGAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCCAAAGC
Found at i:40663127 original size:11 final size:11
Alignment explanation
Indices: 40663111--40663136 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40663101 GTACCTCCAT
40663111 AATTTTCGTAC
1 AATTTTCGTAC
40663122 AATTTTCGTAC
1 AATTTTCGTAC
40663133 AATT
1 AATT
40663137 CTCCACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTTCGTAC
Found at i:40682582 original size:42 final size:43
Alignment explanation
Indices: 40682536--40682621 Score: 140
Period size: 42 Copynumber: 2.0 Consensus size: 43
40682526 GGTAAACCCA
*
40682536 ACAACCCAAGTTTATCTTC-TCT-TTTTTAAAATTCTTTTTTCT
1 ACAACCCAAGATTATCTTCTTCTCTTTTT-AAATTCTTTTTTCT
40682578 ACAACCCAAGATTATCTTCTTCTCTTTTTAAATTCTTTTTTCT
1 ACAACCCAAGATTATCTTCTTCTCTTTTTAAATTCTTTTTTCT
40682621 A
1 A
40682622 GGATAAAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 18 0.44
43 18 0.44
44 5 0.12
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (43 bp):
ACAACCCAAGATTATCTTCTTCTCTTTTTAAATTCTTTTTTCT
Found at i:40683180 original size:68 final size:68
Alignment explanation
Indices: 40683098--40683302 Score: 340
Period size: 68 Copynumber: 3.0 Consensus size: 68
40683088 GAAGGTAATT
* * *
40683098 TCTCACTTTCTCTATTCTCCTCTCTATGTTGCGACATTTGATCCCCCATGTTGCGACATAACATC
1 TCTCACTTTCTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
40683163 CAG
66 CAG
* *
40683166 TCTCACTTTTTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGTATC
1 TCTCACTTTCTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
40683231 CAG
66 CAG
*
40683234 TCTCACTTTCTCTATTCTGCTCCCTATGTTGCGACATTGGATCCCCCATGTT-CTGACATAGCAT
1 TCTCACTTTCTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGC-GACATAGCAT
40683298 CCAG
65 CCAG
40683302 T
1 T
40683303 ATTGACCCAA
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 1 0.01
68 127 0.99
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (68 bp):
TCTCACTTTCTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
CAG
Found at i:40687212 original size:39 final size:39
Alignment explanation
Indices: 40687169--40687267 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
40687159 AACATGTTTC
*
40687169 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTAAA
1 TGAGTATTGTGATATATGCTTCAATGTTATGTGATTAAA
*
40687208 TGAGTATTGTGATATATGCTTCAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTCAATGTTATGTGATTAAA
* *
40687247 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
40687268 AAAAGTGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTCAATGTTATGTGATTAAA
Found at i:40693424 original size:59 final size:59
Alignment explanation
Indices: 40693356--40693474 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
40693346 CTTATGAGCA
40693356 GCCCGTAAATAAATAATAATTAAATAAAATTTTAATAAAAAGAATTTCCTAATTAATAG
1 GCCCGTAAATAAATAATAATTAAATAAAATTTTAATAAAAAGAATTTCCTAATTAATAG
40693415 GCCCGTAAATAAATAATAATTAAATAAAATTTTAATAAAAAGAATTTCCTAATTAATAG
1 GCCCGTAAATAAATAATAATTAAATAAAATTTTAATAAAAAGAATTTCCTAATTAATAG
40693474 G
1 G
40693475 AGGGTAAGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (59 bp):
GCCCGTAAATAAATAATAATTAAATAAAATTTTAATAAAAAGAATTTCCTAATTAATAG
Found at i:40702193 original size:7 final size:7
Alignment explanation
Indices: 40702181--40702205 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40702171 ACTGATTTTC
40702181 TTTCTCT
1 TTTCTCT
40702188 TTTCTCT
1 TTTCTCT
40702195 TTTCTCT
1 TTTCTCT
40702202 TTTC
1 TTTC
40702206 AACTCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCTCT
Found at i:40705059 original size:20 final size:20
Alignment explanation
Indices: 40705023--40705061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40705013 AATTTTTTAA
*
40705023 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
40705043 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
40705062 ATTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:40705234 original size:20 final size:20
Alignment explanation
Indices: 40705198--40705236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40705188 AATTTTTTAA
*
40705198 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
40705218 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
40705237 ATTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:40705395 original size:176 final size:176
Alignment explanation
Indices: 40704904--40705438 Score: 1063
Period size: 176 Copynumber: 3.0 Consensus size: 176
40704894 GAAAGGTTTT
40704904 AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
1 AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
40704969 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
66 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
40705034 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
131 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
40705080 AATATATTGCAGTATTGTATT-AAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
1 AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
40705144 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
66 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
40705209 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
131 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
40705255 AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
1 AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
40705320 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
66 ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
40705385 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
131 TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
40705431 AATATATT
1 AATATATT
40705439 TCTATACATA
Statistics
Matches: 358, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
175 175 0.49
176 183 0.51
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (176 bp):
AATATATTGCAGTATTGTATTAAAAAAAGTTAAGTTGGTCAGTTATCAAAATATAAATTTTCATA
ACCAAATTGATGAACTTAAATGACTTTTAATATATATTATTTGTAATTTTTTAAAAATATATTTA
TAATATAATAAATATATAATACATATAAATTTAAATCAAAAAGTCA
Found at i:40705410 original size:20 final size:20
Alignment explanation
Indices: 40705374--40705412 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40705364 AATTTTTTAA
*
40705374 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
40705394 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
40705413 ATTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:40709882 original size:40 final size:40
Alignment explanation
Indices: 40709784--40710086 Score: 405
Period size: 40 Copynumber: 7.6 Consensus size: 40
40709774 TCCTCGTTCA
* * * * *
40709784 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40709823 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40709863 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40709903 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40709943 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40709983 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
40710023 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40710063 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40710087 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40717868 original size:40 final size:40
Alignment explanation
Indices: 40717770--40718032 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
40717760 TCCTCGTTCA
* * * * *
40717770 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
40717809 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40717849 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
40717889 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
40717929 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
40717969 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
40718009 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40718033 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:40720237 original size:26 final size:24
Alignment explanation
Indices: 40720202--40720253 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
40720192 ACATTTTATG
40720202 AAATTATATTTAATAATAATTATTTT
1 AAATTATATTTAATAAT-A-TATTTT
* *
40720228 AAATTGTATTTAATCATATATTTT
1 AAATTATATTTAATAATATATTTT
40720252 AA
1 AA
40720254 TTAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 15 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTATATTTAATAATATATTTT
Found at i:40720360 original size:18 final size:17
Alignment explanation
Indices: 40720332--40720366 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40720322 ATTATTAAGA
*
40720332 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40720349 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40720367 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40720366 original size:16 final size:16
Alignment explanation
Indices: 40720332--40720386 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
40720322 ATTATTAAGA
40720332 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
40720349 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
40720365 A-TTTAA-TAAAAAAT
1 ATTTTAATTAAAATAT
40720379 ATGTTTAA
1 AT-TTTAA
40720387 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:40720516 original size:18 final size:17
Alignment explanation
Indices: 40720488--40720522 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40720478 AATTATAAGA
*
40720488 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40720505 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40720523 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40720630 original size:156 final size:157
Alignment explanation
Indices: 40720320--40720635 Score: 580
Period size: 156 Copynumber: 2.0 Consensus size: 157
40720310 ATAAGAATAT
40720320 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
* *
40720385 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
40720450 TAATCATTTACCAAAACAAATTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
* *
40720477 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
40720541 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
40720606 TAATCATTTACCAAAACAATTTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
40720633 TAA
1 TAA
40720636 GGATATTCTA
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 148 0.96
157 6 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATCATTTACCAAAACAAATTTATGC
Found at i:40720779 original size:16 final size:16
Alignment explanation
Indices: 40720758--40720793 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40720748 GATTAGTTAT
40720758 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40720774 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40720790 TACA
1 TACA
40720794 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40723252 original size:13 final size:13
Alignment explanation
Indices: 40723234--40723260 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40723224 GTGATATAGG
40723234 TGATATCTAAATA
1 TGATATCTAAATA
40723247 TGATATCTAAATA
1 TGATATCTAAATA
40723260 T
1 T
40723261 TTAAGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TGATATCTAAATA
Found at i:40729171 original size:16 final size:17
Alignment explanation
Indices: 40729135--40729172 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40729125 CTTGAATTTT
40729135 TTTTAATTTCTCTATAA
1 TTTTAATTTCTCTATAA
40729152 TTTTATATTT-TCTA-AA
1 TTTTA-ATTTCTCTATAA
40729168 TTTTA
1 TTTTA
40729173 CATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAATTTCTCTATAA
Found at i:40730002 original size:27 final size:27
Alignment explanation
Indices: 40729954--40730005 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40729944 TTAACTATTG
* *
40729954 TAATTAAAAATATAATATTTAAAATAT
1 TAATTAAAAATATAACACTTAAAATAT
* *
40729981 TAATTAAATATTTAACACTTAAAAT
1 TAATTAAAAATATAACACTTAAAAT
40730006 CATGTATAAC
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATTAAAAATATAACACTTAAAATAT
Found at i:40730230 original size:31 final size:31
Alignment explanation
Indices: 40730192--40730291 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
40730182 ACTATTAAAA
*
40730192 TAGTCACTTTTGTTTCTT-TGGTGTTACATTT
1 TAGTCACTTTTGTTT-TTCTGATGTTACATTT
40730223 TAGTCACTTTTGTTTTTCTGATGTTACATTT
1 TAGTCACTTTTGTTTTTCTGATGTTACATTT
* ***
40730254 TAGTCACTTATG--TTTGAAATGTTACATTT
1 TAGTCACTTTTGTTTTTCTGATGTTACATTT
40730283 TAGTCACTT
1 TAGTCACTT
40730292 ACGTTGTCGT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
29 23 0.37
30 2 0.03
31 38 0.60
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.54
Consensus pattern (31 bp):
TAGTCACTTTTGTTTTTCTGATGTTACATTT
Found at i:40730285 original size:29 final size:30
Alignment explanation
Indices: 40730213--40730292 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
40730203 GTTTCTTTGG
* **
40730213 TGTTACATTTTAGTCACTTTTGTTTTTCTGA
1 TGTTACATTTTAGTCACTTATG-TTTTCAAA
*
40730244 TGTTACATTTTAGTCACTTATG-TTTGAAA
1 TGTTACATTTTAGTCACTTATGTTTTCAAA
40730273 TGTTACATTTTAGTCACTTA
1 TGTTACATTTTAGTCACTTA
40730293 CGTTGTCGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 24 0.53
31 21 0.47
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTTACATTTTAGTCACTTATGTTTTCAAA
Found at i:40730315 original size:31 final size:30
Alignment explanation
Indices: 40730192--40730317 Score: 121
Period size: 31 Copynumber: 4.1 Consensus size: 30
40730182 ACTATTAAAA
* * *
40730192 TAGTCACTTTTGTTTCTTTGGTGTTACATTT
1 TAGTCACTTATGTTTC-GTGATGTTACATTT
*
40730223 TAGTCACTTTTGTTTTTC-TGATGTTACATTT
1 TAGTCACTTATG--TTTCGTGATGTTACATTT
**
40730254 TAGTCACTTATGTTT-GAAATGTTACATTT
1 TAGTCACTTATGTTTCGTGATGTTACATTT
* * *
40730283 TAGTCACTTACGTTGTCGTGTTGTAACATTT
1 TAGTCACTTATGTT-TCGTGATGTTACATTT
40730314 TAGT
1 TAGT
40730318 TACTGAATGT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
29 27 0.33
30 1 0.01
31 49 0.60
33 4 0.05
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (30 bp):
TAGTCACTTATGTTTCGTGATGTTACATTT
Found at i:40732698 original size:13 final size:13
Alignment explanation
Indices: 40732680--40732704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40732670 TCTCGATTTA
40732680 ATCAATCTAATCC
1 ATCAATCTAATCC
40732693 ATCAATCTAATC
1 ATCAATCTAATC
40732705 AAATTCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
ATCAATCTAATCC
Found at i:40736594 original size:28 final size:30
Alignment explanation
Indices: 40736537--40736595 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40736527 GGACTTAGAA
*
40736537 AATATAAAAATATAATATTTTAAATATTTT
1 AATATAAAAATATAATATATTAAATATTTT
*
40736567 AATATAAAAATA-ATTATATTAAAT-TTTT
1 AATATAAAAATATAATATATTAAATATTTT
40736595 A
1 A
40736596 TTAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 10 0.37
30 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATATAAAAATATAATATATTAAATATTTT
Found at i:40736616 original size:37 final size:37
Alignment explanation
Indices: 40736575--40736665 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 37
40736565 TTAATATAAA
* * *
40736575 AATAATTATATTAAATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATTTAAT
*
40736612 AATAATTATATTAAAATATGATTAAATTATTTTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATTTAAT
**
40736649 AATAATCCTATTAAAAT
1 AATAATTATATTAAAAT
40736666 TTAATAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (37 bp):
AATAATTATATTAAAATATGATTAAATTATATTTAAT
Found at i:40736803 original size:16 final size:16
Alignment explanation
Indices: 40736782--40736835 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
40736772 TGAATTATTG
*
40736782 ATTACAACTCTATTCC
1 ATTACAACTCTATTCT
** *
40736798 ATTACAGTTCTATTAT
1 ATTACAACTCTATTCT
*
40736814 ATTATAACTCTATTCT
1 ATTACAACTCTATTCT
40736830 ATTACA
1 ATTACA
40736836 TTTCAAAATC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:40736949 original size:14 final size:14
Alignment explanation
Indices: 40736930--40736964 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40736920 TAACACTTAT
40736930 AAAATTTTATACTA
1 AAAATTTTATACTA
* *
40736944 AAAATTCTATACTT
1 AAAATTTTATACTA
40736958 AAAATTT
1 AAAATTT
40736965 CAATTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTTTATACTA
Found at i:40737087 original size:25 final size:27
Alignment explanation
Indices: 40737041--40737093 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
40737031 CATTTACCTA
* * *
40737041 AAAAAAAGGTAAAAGATGAAAAGGAAC
1 AAAAAAAGGAAAAAGATAAAAAGAAAC
40737068 AAAAAAA-GAAAAAGA-AAAAAGAAAC
1 AAAAAAAGGAAAAAGATAAAAAGAAAC
40737093 A
1 A
40737094 GTAGTTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 7 0.30
27 7 0.30
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAAAGGAAAAAGATAAAAAGAAAC
Found at i:40738722 original size:15 final size:15
Alignment explanation
Indices: 40738702--40738730 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40738692 ACATCAACAT
40738702 TTAAAAAAATAAATA
1 TTAAAAAAATAAATA
40738717 TTAAAAAAATAAAT
1 TTAAAAAAATAAAT
40738731 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAAAAAAATAAATA
Found at i:40738738 original size:15 final size:15
Alignment explanation
Indices: 40738703--40738739 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
40738693 CATCAACATT
*
40738703 TAAAAAAATAAATAT
1 TAAAAAAATAAATAA
40738718 TAAAAAAATAAATTAA
1 TAAAAAAATAAA-TAA
40738734 TAAAAA
1 TAAAAA
40738740 TATATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAAATAAATAA
Found at i:40738911 original size:19 final size:18
Alignment explanation
Indices: 40738898--40738955 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
40738888 CTAAAAAATT
40738898 TAATAATTTA-T-AAAAA
1 TAATAATTTATTAAAAAA
*
40738914 TAATAATTTATTAAAACA
1 TAATAATTTATTAAAAAA
* *
40738932 TAA-AAATTAATAAAAAA
1 TAATAATTTATTAAAAAA
40738949 TATATAA
1 TA-ATAA
40738956 CACCCTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.29
17 14 0.41
18 8 0.24
19 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAATTTATTAAAAAA
Found at i:40738919 original size:16 final size:16
Alignment explanation
Indices: 40738898--40738947 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
40738888 CTAAAAAATT
40738898 TAATAATTTATAAAAA
1 TAATAATTTATAAAAA
40738914 TAATAATTTATTAAAACA
1 TAATAATTTA-TAAAA-A
* *
40738932 TAAAAATTAATAAAAA
1 TAATAATTTATAAAAA
40738948 ATATATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 11 0.37
17 10 0.33
18 9 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAATTTATAAAAA
Found at i:40739830 original size:40 final size:41
Alignment explanation
Indices: 40739786--40739876 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
40739776 AAAAATTTGC
* *
40739786 CACAAGTTTTGTAC-TTTTTGAAAATTTAACCCTCCATATT
1 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTCCATATT
*
40739826 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTTCATATT
1 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTCCATATT
*
40739867 TACAAATTCT
1 CACAAATTCT
40739877 ATCAATTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 12 0.26
41 34 0.74
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (41 bp):
CACAAATTCTGTACTTTTTTGAAAATTTAACCCTCCATATT
Found at i:40747907 original size:12 final size:12
Alignment explanation
Indices: 40747876--40747913 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40747866 CAATAAAATT
*
40747876 ATTTCACA-AAA
1 ATTTCACACATA
*
40747887 ATTTTACACATA
1 ATTTCACACATA
40747899 ATTTCACACATA
1 ATTTCACACATA
40747911 ATT
1 ATT
40747914 AACACAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTTCACACATA
Found at i:40759771 original size:21 final size:22
Alignment explanation
Indices: 40759716--40759791 Score: 102
Period size: 21 Copynumber: 3.5 Consensus size: 22
40759706 GGTAGTTATA
*
40759716 AAATGTTC-GGTGATTTGAAAC
1 AAATGTACTGGTGATTTGAAAC
* *
40759737 ATATGTATTGGTGATTTGAAAC
1 AAATGTACTGGTGATTTGAAAC
*
40759759 AGATGTA-TGGTGATTTGAAAC
1 AAATGTACTGGTGATTTGAAAC
40759780 AAATGTACTGGT
1 AAATGTACTGGT
40759792 AGTCAGAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 25 0.52
22 23 0.48
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (22 bp):
AAATGTACTGGTGATTTGAAAC
Found at i:40760485 original size:42 final size:42
Alignment explanation
Indices: 40760438--40760522 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
40760428 TGCCTTGGAG
40760438 AAAATTTTGCCGTTTTGGTCAAAAAGGGAAGCTTAGTCCACA
1 AAAATTTTGCCGTTTTGGTCAAAAAGGGAAGCTTAGTCCACA
40760480 AAAATTTTGCCGTTTTGGTCAAAAAGGGAAGCTTAGTCCACA
1 AAAATTTTGCCGTTTTGGTCAAAAAGGGAAGCTTAGTCCACA
40760522 A
1 A
40760523 TTCATCGGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAATTTTGCCGTTTTGGTCAAAAAGGGAAGCTTAGTCCACA
Found at i:40762541 original size:26 final size:27
Alignment explanation
Indices: 40762498--40762549 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
40762488 CAAACAGATC
*
40762498 CCAAATACCCACTCAACCTAGCCCAAA
1 CCAAATACCCAATCAACCTAGCCCAAA
*
40762525 CCAAA-ACCCAATTAACCTAGCCCAA
1 CCAAATACCCAATCAACCTAGCCCAA
40762550 CTAATGTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.42, C:0.42, G:0.04, T:0.12
Consensus pattern (27 bp):
CCAAATACCCAATCAACCTAGCCCAAA
Found at i:40762967 original size:20 final size:19
Alignment explanation
Indices: 40762930--40762998 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
40762920 TTTAAGGTGG
*
40762930 TTCTCTTTTCT--TTTTCT
1 TTCTCTTTTCTACGTTTCT
40762947 TTCTCTTTCTCTACGTTTCT
1 TTCTCTTT-TCTACGTTTCT
* **
40762967 TTACTGTTTTCTTTGTTTCT
1 TT-CTCTTTTCTACGTTTCT
*
40762987 TTCTATTTTCTA
1 TTCTCTTTTCTA
40762999 TACGAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 8 0.19
18 3 0.07
19 8 0.19
20 18 0.43
21 5 0.12
ACGTcount: A:0.06, C:0.22, G:0.04, T:0.68
Consensus pattern (19 bp):
TTCTCTTTTCTACGTTTCT
Found at i:40763717 original size:24 final size:24
Alignment explanation
Indices: 40763681--40763726 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40763671 AATATTATAT
* *
40763681 AAATTTACCATGTTTTATTATTCA
1 AAATTTACCATGTATCATTATTCA
**
40763705 AAATTTATTATGTATCATTATT
1 AAATTTACCATGTATCATTATT
40763727 TAAATTTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTACCATGTATCATTATTCA
Found at i:40764046 original size:29 final size:29
Alignment explanation
Indices: 40763992--40764070 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
40763982 CTCTTTCCAA
40763992 TATTTTAACATTTTAATTTATCTC-AACT
1 TATTTTAACATTTTAATTTATCTCAAACT
*
40764020 TATTTTCAACATTGTTAATTTAT-TCAAATT
1 TATTTT-AACATT-TTAATTTATCTCAAACT
*
40764050 TATTTTAACCTTTTAATTTAT
1 TATTTTAACATTTTAATTTAT
40764071 ACATATTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 15 0.33
29 13 0.28
30 18 0.39
ACGTcount: A:0.32, C:0.11, G:0.01, T:0.56
Consensus pattern (29 bp):
TATTTTAACATTTTAATTTATCTCAAACT
Found at i:40777007 original size:175 final size:175
Alignment explanation
Indices: 40776511--40777047 Score: 864
Period size: 174 Copynumber: 3.1 Consensus size: 175
40776501 AAAATGGTGA
* * *
40776511 ATCTGATCTCCCTGAGATTGCAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
40776576 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCAGG
66 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
40776641 TCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTATAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* * *
40776686 ATCTTATCTCCCTGAA-ATTACAGCGGAACAAATTGAAGCCAGTGATCCTATTTCCCTGAG-TTA
1 ATCTTATCTCCCT-AAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
*
40776749 CAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
65 CAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
40776814 GTCTTATCTCCCTGAGATTATAGTGGAATAGACCGAAGAATTACAG
130 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* *
40776860 ATCTTATCTCCCTAAGATTACATCTGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* *
40776925 AGT-GAAGCGGATCAAAATAAAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGATCGCATCAG
66 AGTGGAA-CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * *
40776989 GTCTTATCTCTCTGAGATTACAGTGGAATAGACTGAAGAAATTACAA
130 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG-AATTACAG
40777036 ATCTTATCTCCC
1 ATCTTATCTCCC
40777048 AAGCAGTGTA
Statistics
Matches: 334, Mismatches: 23, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
173 2 0.01
174 164 0.49
175 148 0.44
176 20 0.06
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (175 bp):
ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
Found at i:40777180 original size:100 final size:100
Alignment explanation
Indices: 40777035--40777219 Score: 232
Period size: 100 Copynumber: 1.9 Consensus size: 100
40777025 AGAAATTACA
* * **
40777035 AATCTTATCTCCCAAGCAGTGTAGTGGAGCAGATTAAAGCCACAACGGCGAATCTTACTTCCCCA
1 AATCTTATCTCCCAAGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGAATCTTACTTCCCCA
*
40777100 ACATTGTAGTTAGAA-AGATTGAAGCTGCAATAATG
66 ACATTGCAGTTA-AACAGATTGAAGCTGCAATAATG
* * *
40777135 AATCTTA-CTGCCC-AGTCAGTGCAGTGGAACAGATTGAAGCTACAACAACGAATCTTGCTTCCC
1 AATCTTATCT-CCCAAG-CAGTGCAGTGGAACAGATTAAAGCCACAACAACGAATCTTACTTCCC
**
40777198 TGACATTGCAGTTAAACAGATT
64 CAACATTGCAGTTAAACAGATT
40777220 AAAGTTCGAG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
99 6 0.08
100 66 0.92
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (100 bp):
AATCTTATCTCCCAAGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGAATCTTACTTCCCCA
ACATTGCAGTTAAACAGATTGAAGCTGCAATAATG
Found at i:40777208 original size:50 final size:50
Alignment explanation
Indices: 40777057--40777219 Score: 141
Period size: 50 Copynumber: 3.3 Consensus size: 50
40777047 CAAGCAGTGT
* * * ** *
40777057 AGTGGAGCAGATTAAAGCCACAACGGCGAATCTTACTTCCCCA-ACATTGT
1 AGTGGAACAGATTGAAGCTACAACAACGAATCTTACTT-CCCAGACATTGC
* * * * * * *
40777107 AGTTAGAA-AGATTGAAGCTGCAATAATGAATCTTACTGCCCAGTCAGTGC
1 AG-TGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACATTGC
* *
40777157 AGTGGAACAGATTGAAGCTACAACAACGAATCTTGCTTCCCTGACATTGC
1 AGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACATTGC
**
40777207 AGTTAAACAGATT
1 AGTGGAACAGATT
40777220 AAAGTTCGAG
Statistics
Matches: 86, Mismatches: 24, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
49 8 0.09
50 75 0.87
51 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCAGACATTGC
Found at i:40777471 original size:16 final size:17
Alignment explanation
Indices: 40777431--40777471 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40777421 TTGCCCAGCC
*
40777431 CAAATCAAATAAATAAA
1 CAAATAAAATAAATAAA
*
40777448 CAAA-AAAATATATAAA
1 CAAATAAAATAAATAAA
40777464 -AAATAAAA
1 CAAATAAAA
40777472 ACAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (17 bp):
CAAATAAAATAAATAAA
Found at i:40777485 original size:22 final size:23
Alignment explanation
Indices: 40777441--40777486 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
40777431 CAAATCAAAT
40777441 AAATAAACAAAAAAATATATAAA
1 AAATAAACAAAAAAATATATAAA
* *
40777464 AAATAAA-AACAAAAT-TATTAA
1 AAATAAACAAAAAAATATATAAA
40777485 AA
1 AA
40777487 GTCCATCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAACAAAAAAATATATAAA
Found at i:40777599 original size:26 final size:27
Alignment explanation
Indices: 40777558--40777608 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
40777548 CAAACAGATC
*
40777558 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
40777585 CCAAA-ACCCAATTAACCTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
40777609 GCTAATGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:40778777 original size:24 final size:24
Alignment explanation
Indices: 40778741--40778786 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40778731 AATATTATAT
* *
40778741 AAATTTACCATGTTTTATTATTCA
1 AAATTTACCATGTATCATTATTCA
**
40778765 AAATTTATTATGTATCATTATT
1 AAATTTACCATGTATCATTATT
40778787 TAAATTTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTACCATGTATCATTATTCA
Found at i:40779088 original size:28 final size:28
Alignment explanation
Indices: 40779051--40779128 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
40779041 CTCTTTCCAA
40779051 TATTTTAACATTTTAATTTATCTC-AACT
1 TATTTTAACATTTTAATTTAT-TCAAACT
* *
40779079 TATTTCAACATTGTTAATTTATTCAAATT
1 TATTTTAACATT-TTAATTTATTCAAACT
* *
40779108 TATTTTAGCCTTTTAATTTAT
1 TATTTTAACATTTTAATTTAT
40779129 ACATATTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTTTAACATTTTAATTTATTCAAACT
Found at i:40783607 original size:27 final size:27
Alignment explanation
Indices: 40783577--40783754 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40783567 ATATTGAGTC
* * * *
40783577 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40783604 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40783631 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40783659 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40783686 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40783713 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40783740 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40783755 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40783716 original size:82 final size:81
Alignment explanation
Indices: 40783598--40783753 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40783588 TGCTATATAA
* *
40783598 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40783663 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40783680 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40783744 CACTTAGTGC
65 CACTTAGTGC
40783754 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40791665 original size:27 final size:27
Alignment explanation
Indices: 40791635--40791812 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40791625 ATATTGAGTC
* * * *
40791635 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40791662 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40791689 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40791717 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40791744 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40791771 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40791798 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40791813 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40791774 original size:82 final size:81
Alignment explanation
Indices: 40791656--40791811 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40791646 TGCTATATAA
* *
40791656 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40791721 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40791738 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40791802 CACTTAGTGC
65 CACTTAGTGC
40791812 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40794804 original size:12 final size:12
Alignment explanation
Indices: 40794783--40794832 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
40794773 AAAAACGAAA
*
40794783 TGATTAAAAACT
1 TGATGAAAAACT
* *
40794795 TGATGGAAAATT
1 TGATGAAAAACT
*
40794807 TTATGAAAAGACT
1 TGATGAAAA-ACT
40794820 TGATGAAAAACT
1 TGATGAAAAACT
40794832 T
1 T
40794833 AAAAAGAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:40794922 original size:18 final size:18
Alignment explanation
Indices: 40794899--40794936 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40794889 AGAACTAAAT
*
40794899 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
40794917 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
40794935 GA
1 GA
40794937 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:40796313 original size:22 final size:20
Alignment explanation
Indices: 40796260--40796319 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 20
40796250 GTTTTCTTGC
*
40796260 AAAAATAAAA-ATG-AAAAT
1 AAAAATAAAATAGGAAAAAT
40796278 -AAAATAAAATAGGAAAAAT
1 AAAAATAAAATAGGAAAAAT
40796297 AAATAATAATAATAGGAAAAAT
1 AAA-AATAA-AATAGGAAAAAT
40796319 A
1 A
40796320 TTTTTTTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 9 0.25
18 2 0.06
19 5 0.14
20 2 0.06
21 5 0.14
22 13 0.36
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAATAAAATAGGAAAAAT
Found at i:40798076 original size:73 final size:73
Alignment explanation
Indices: 40797957--40798102 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
40797947 TTGGTCCTTG
*
40797957 TATTTGGGTGGAACTTTCTTTTGCAGTACTGCGGAGACATTTTCTCCTACATGTACTCTTTCGTT
1 TATTTGGGCGGAACTTTCTTTTGCAGTACTGCGGAGACATTTTCTCCTACATGTACTCTTTCGTT
40798022 ACCTATTA
66 ACCTATTA
* *
40798030 TATTTGGGCGGAACTTTCTTTTGCAGTACTGTGGAGACATTTTCTCCTACATGTGCTCTTTCGTT
1 TATTTGGGCGGAACTTTCTTTTGCAGTACTGCGGAGACATTTTCTCCTACATGTACTCTTTCGTT
40798095 ACCTATTA
66 ACCTATTA
40798103 ACCTCCTCTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (73 bp):
TATTTGGGCGGAACTTTCTTTTGCAGTACTGCGGAGACATTTTCTCCTACATGTACTCTTTCGTT
ACCTATTA
Found at i:40800943 original size:12 final size:12
Alignment explanation
Indices: 40800922--40800971 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
40800912 AAAAACGAAA
*
40800922 TGATTAAAAACT
1 TGATGAAAAACT
* *
40800934 TGATGGAAAATT
1 TGATGAAAAACT
*
40800946 TTATGAAAAGACT
1 TGATGAAAA-ACT
40800959 TGATGAAAAACT
1 TGATGAAAAACT
40800971 T
1 T
40800972 AAAAAGAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:40801061 original size:18 final size:18
Alignment explanation
Indices: 40801038--40801075 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40801028 AGAACTAAAT
*
40801038 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
40801056 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
40801074 GA
1 GA
40801076 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:40803706 original size:30 final size:29
Alignment explanation
Indices: 40803664--40803791 Score: 136
Period size: 30 Copynumber: 4.3 Consensus size: 29
40803654 TGCAAATTCA
* *
40803664 ACCCTATAATCATTCATAGTTACACATCAT
1 ACCCTGTAATCATTCATA-TTACATATCAT
*
40803694 ACCTTGTAATCATTC-TCAATTACATATCAT
1 ACCCTGTAATCATTCAT--ATTACATATCAT
*
40803724 ACCCTATAATCATTTTCA-ATTACATATCAT
1 ACCCTGTAATCA--TTCATATTACATATCAT
40803754 ACCCTGTAATCATTTTCA-ATTACATATCAT
1 ACCCTGTAATCA--TTCATATTACATATCAT
40803784 ACCCTGTA
1 ACCCTGTA
40803792 TAATGTGTTA
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.01
30 82 0.94
31 1 0.01
32 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
ACCCTGTAATCATTCATATTACATATCAT
Found at i:40803737 original size:60 final size:59
Alignment explanation
Indices: 40803664--40803788 Score: 189
Period size: 60 Copynumber: 2.1 Consensus size: 59
40803654 TGCAAATTCA
*
40803664 ACCCTATAATCA-TTCATAGTTACACATCATACCTTGTAATCATTCTCAATTACATATCAT
1 ACCCTATAATCATTTCA-A-TTACACATCATACCCTGTAATCATTCTCAATTACATATCAT
* *
40803724 ACCCTATAATCATTTTCAATTACATATCATACCCTGTAATCATTTTCAATTACATATCAT
1 ACCCTATAATCA-TTTCAATTACACATCATACCCTGTAATCATTCTCAATTACATATCAT
40803784 ACCCT
1 ACCCT
40803789 GTATAATGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
60 55 0.92
61 1 0.02
62 4 0.07
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (59 bp):
ACCCTATAATCATTTCAATTACACATCATACCCTGTAATCATTCTCAATTACATATCAT
Done.