Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 9 of 141
Found at i:2637264 original size:25 final size:25
Alignment explanation
Indices: 2637230--2637280 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2637220 CATTTTTAAC
2637230 CAAAAAATAGAAAAGAATATTGATT
1 CAAAAAATAGAAAAGAATATTGATT
2637255 CAAAAAATAGAAAAGAATATTGATT
1 CAAAAAATAGAAAAGAATATTGATT
2637280 C
1 C
2637281 GAAGATTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (25 bp):
CAAAAAATAGAAAAGAATATTGATT
Found at i:2639296 original size:31 final size:31
Alignment explanation
Indices: 2639258--2639317 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2639248 CTAATGACTG
* *
2639258 AAAAAGAAAAA-TTCGAATATTTGGGTGACCA
1 AAAAAGAAAAAGTT-AAATAGTTGGGTGACCA
2639289 AAAAAGAAAAAGTTAAATAGTTGGGTGAC
1 AAAAAGAAAAAGTTAAATAGTTGGGTGAC
2639318 TACTAGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.22
Consensus pattern (31 bp):
AAAAAGAAAAAGTTAAATAGTTGGGTGACCA
Found at i:2640470 original size:2 final size:2
Alignment explanation
Indices: 2640465--2640490 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2640455 ATATATATAT
2640465 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2640491 CATACGCAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2642184 original size:3 final size:3
Alignment explanation
Indices: 2642176--2642208 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2642166 ATACTGTTAG
2642176 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA- AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
2642209 CACTAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2645775 original size:21 final size:22
Alignment explanation
Indices: 2645735--2645777 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2645725 TGTTAAAATT
2645735 TATTTTAAGTATTTAATATTTTG
1 TATTTTAAG-ATTTAATATTTTG
*
2645758 TATTTTAA-ATTTATTATTTT
1 TATTTTAAGATTTAATATTTT
2645778 TTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TATTTTAAGATTTAATATTTTG
Found at i:2651102 original size:25 final size:25
Alignment explanation
Indices: 2651056--2651105 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2651046 TAAAATTAAA
* *
2651056 TAAATAAATTTTTTATATAAAAAAT
1 TAAATAAAATTTTGATATAAAAAAT
2651081 TAAATAAAATTTTGA-ATGAAAAAAT
1 TAAATAAAATTTTGATAT-AAAAAAT
2651106 ATATAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TAAATAAAATTTTGATATAAAAAAT
Found at i:2651796 original size:18 final size:18
Alignment explanation
Indices: 2651775--2651825 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
2651765 CTAAAATATT
2651775 TATAATTGTTTCTAAAAA
1 TATAATTGTTTCTAAAAA
*
2651793 TATAA---TTACT-AAAA
1 TATAATTGTTTCTAAAAA
2651807 TATAATTGTTTCTAGAAAA
1 TATAATTGTTTCTA-AAAA
2651826 AGTCTCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
17 4 0.15
18 5 0.19
19 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (18 bp):
TATAATTGTTTCTAAAAA
Found at i:2654473 original size:30 final size:30
Alignment explanation
Indices: 2654418--2654474 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2654408 CAAATTATAC
*
2654418 CAAATTAAAGCACTAACAAAGACTAAATCT
1 CAAATTAAAGCACTAAAAAAGACTAAATCT
2654448 CAAATTAAA-CA-TAATAAAAGAACTAAA
1 CAAATTAAAGCACTAA-AAAAG-ACTAAA
2654475 AGCTTTCCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 6 0.25
30 15 0.62
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (30 bp):
CAAATTAAAGCACTAAAAAAGACTAAATCT
Found at i:2655009 original size:21 final size:21
Alignment explanation
Indices: 2654985--2655027 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2654975 TTTTTAAATT
2654985 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
*
2655006 TAAATATTAATATAAAGTATA
1 TAAATATTAATATAAAATATA
2655027 T
1 T
2655028 TTTTAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:2657046 original size:21 final size:21
Alignment explanation
Indices: 2657022--2657064 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2657012 TATTTAAATT
2657022 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
2657043 TAAATTTTAATATAAAGTATA
1 TAAATTTTAATATAAAATATA
2657064 T
1 T
2657065 TTTTAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:2665891 original size:24 final size:24
Alignment explanation
Indices: 2665850--2665901 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2665840 TTAGCACTTC
* * *
2665850 GTGGTGGCCTTCTTGGTGGTGGAG
1 GTGGTGGCCTCCTAGGTGGCGGAG
*
2665874 GTGGTGGTCTCCTAGGTGGCGGAG
1 GTGGTGGCCTCCTAGGTGGCGGAG
2665898 GTGG
1 GTGG
2665902 AGGTGGTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.13, G:0.52, T:0.29
Consensus pattern (24 bp):
GTGGTGGCCTCCTAGGTGGCGGAG
Found at i:2665901 original size:30 final size:30
Alignment explanation
Indices: 2665867--2665926 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2665857 CCTTCTTGGT
*
2665867 GGTGGAGGTGGTGGTCTCCTAGGTGGCGGA
1 GGTGGAGGTGGTGGTCTCCTAGGTGACGGA
*
2665897 GGTGGAGGTGGTGGTCTCCTTGGTGACGGA
1 GGTGGAGGTGGTGGTCTCCTAGGTGACGGA
2665927 AGTCTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.10, C:0.13, G:0.52, T:0.25
Consensus pattern (30 bp):
GGTGGAGGTGGTGGTCTCCTAGGTGACGGA
Found at i:2665937 original size:18 final size:18
Alignment explanation
Indices: 2665910--2665944 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2665900 GGAGGTGGTG
2665910 GTCTCCTTGGTGACGGAA
1 GTCTCCTTGGTGACGGAA
*
2665928 GTCTCTTTGGTGACGGA
1 GTCTCCTTGGTGACGGA
2665945 GGTGGAGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (18 bp):
GTCTCCTTGGTGACGGAA
Found at i:2665945 original size:48 final size:50
Alignment explanation
Indices: 2665879--2666152 Score: 219
Period size: 60 Copynumber: 5.0 Consensus size: 50
2665869 TGGAGGTGGT
* *
2665879 GGTCTCCTAGGTGGCGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGA-A
1 GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAGA
*
2665928 -GTCTCTTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAGGTGGA
1 GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGA----GA
2665981 GGTGGTGGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAGGTGGA
1 ------GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGA----GA
*
2666041 GGTGGTGGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCGTGGTGACGGAGGTGGA
1 ------GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGA----GA
* * * *
2666101 GGTGGTCCCCGTGGTGACGGAGGTGGAGGTGGTGGTGTCTTTGGTGACGGAG
1 ---GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAG
2666153 GTAGAGGTGG
Statistics
Matches: 203, Mismatches: 10, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
48 44 0.22
53 2 0.01
57 46 0.23
60 111 0.55
ACGTcount: A:0.11, C:0.14, G:0.50, T:0.26
Consensus pattern (50 bp):
GGTCTCCTTGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAGA
Found at i:2665962 original size:30 final size:30
Alignment explanation
Indices: 2665928--2666970 Score: 958
Period size: 30 Copynumber: 33.0 Consensus size: 30
2665918 GGTGACGGAA
*
2665928 GTCTCTTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2665958 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2665988 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2666018 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2666048 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
*
2666078 GTCTCCGTGGTGACGGAGGTGGA---GGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666105 GTCCCCGTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666135 GTGTCTTTGGTGACGGAGGTAGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGAC----G--GAGGTGGAGGTGGTG
* * *
2666171 ATCCCCTAGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2666201 GT-TCCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGAGGTGGTG
*
2666231 GT-TCCCGTGGTGACGGAGGTGGAGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGAGGTGGTG
2666261 GT-TCCTGTGGTGACGGAGGTGGAGGTGGTGGTG
1 GTCTCCT-TGGTGACGGAGGTGGA---GGTGGTG
* * *
2666294 GTCCCCTAGGTGACGGAGGTGGTGGTGGTGGTG
1 GTCTCCTTGGTGACGGA---GGTGGAGGTGGTG
* *
2666327 GTCCCCTAGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
** *
2666357 GTGACTTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
*
2666387 GT-TCCCGTGGTGACGGAGGTGGAGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666417 GT-TCCCGTGGTGACGGAGGTTGAGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666447 GTGTCTTTGGTGACAGAGGTGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGAC------GGAGGTGGAGGTGGTG
*
2666483 GT-TCCCGTGGTGACGGAGGTGGAGGTGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGA---GGTGGTG
* * *
2666516 GTCCCCGTGGTGACAGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666546 GTGGTCCCTGTGGTGATGGAGGTGGAGGTGGTG
1 GT-CT-CCT-TGGTGACGGAGGTGGAGGTGGTG
* *
2666579 GTGTCTTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
*
2666609 GT-TCCCGTGGTGACGGTGACGCCCCGTGGTGACGGAGGTGGAGGTG
1 GTCT-CC-T--T---GGTGACG----GAGGT---GGAGGT---GGTG
* *
2666655 GTGATCCGCTAGGTGACGGAGGTGGAGGTGGTGGTG
1 GT-CT-C-CTTGGTGACGGAGGTGGA---GGTGGTG
* * *
2666691 GTCCCCTAGGTGATGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
* **
2666721 GTGATCCCTGTGGTGATAGAGGTGGAGGTGGTG
1 GT-CT-CCT-TGGTGACGGAGGTGGAGGTGGTG
*
2666754 GTGTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
*
2666784 GT-TCCCGTGGTGACGGAGGTGGAGGTGGTG
1 GTCT-CCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666814 ATC-CGCTAGGTGACGGAGGTGGAGGTGGTG
1 GTCTC-CTTGGTGACGGAGGTGGAGGTGGTG
* *
2666844 GTGGTACCCTAGGTGACGGAGGTGGAGGTGGTG
1 GT-CT--CCTTGGTGACGGAGGTGGAGGTGGTG
* *
2666877 GTGATCCCTGTGGTGATGGAGGTGGAGGTGGTG
1 GT-CT-CCT-TGGTGACGGAGGTGGAGGTGGTG
*
2666910 GTGTCCTTGGTGACGGAGGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
* * *
2666940 GTCCCCTTGGTGATGGATGTGGAGGTGGTG
1 GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
2666970 G
1 G
2666971 AGGTCTTCTT
Statistics
Matches: 873, Mismatches: 72, Indels: 136
0.81 0.07 0.13
Matches are distributed among these distances:
27 26 0.03
29 5 0.01
30 521 0.60
31 10 0.01
32 14 0.02
33 185 0.21
34 6 0.01
35 1 0.00
36 70 0.08
39 7 0.01
40 4 0.00
43 13 0.01
46 6 0.01
48 4 0.00
49 1 0.00
ACGTcount: A:0.12, C:0.12, G:0.51, T:0.25
Consensus pattern (30 bp):
GTCTCCTTGGTGACGGAGGTGGAGGTGGTG
Found at i:2666337 original size:156 final size:159
Alignment explanation
Indices: 2665935--2666970 Score: 1178
Period size: 156 Copynumber: 6.6 Consensus size: 159
2665925 GAAGTCTCTT
* *
2665935 TGGTGACGGAGGTGGAGGTGGTGGTCTCCTTGGTGACGGAGGTGGAGGTGGT-G-GTCTCCTTGG
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
* * *
2665998 TGACGGA---GGTGGAGGTGGTGGTCTCCTTGGTGACGGAGGTGGAGGTGGT-G-GTCTCCTTGG
66 TGACGGAGGTGGTGGAGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
*
2666058 TGACGGAGGTGGAGGTGGTGGTCT-CC-G
131 TGACGGAGGTGGAGGTGGTGGTGTCCCTG
** * *
2666085 TGGTGACGGAGGTGGA---GGTGGTCCCCGTGGTGACGGAGGTGGAGGTGGTGGTGT--CTTTGG
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
*
2666145 TGACGGAGGTAGAGGTGGAGGTGGTGATCCCCTAGGTGACGGAGGTGGAGGTGGTGGT-T-CCCT
66 TGACGGAGGT---GGTGGAGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGTGTCCCCT
2666208 TGGTGACGGAGGTGGAGGTGGTGGT-TCCC-G
128 TGGTGACGGAGGTGGAGGTGGTGGTGTCCCTG
*
2666238 TGGTGACGGAGGTGGAGGTGGTGGT-TCCTGTGGTGACGGAGGTGGAGGTGGTGGTGGTCCCCTA
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCT-TGGTGACGGAGGTGGAGGTGGTGGT-GTCCCCTT
* * *
2666302 GGTGACGGAGGTGGTGGTGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGTG--ACTTT
64 GGTGACGGAGGTGGTGGAGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTT
2666365 GGTGACGGAGGTGGAGGTGGTGGT-TCCC-G
129 GGTGACGGAGGTGGAGGTGGTGGTGTCCCTG
* * *
2666394 TGGTGACGGAGGTGGAGGTGGTGGT-TCCCGTGGTGACGGAGGTTGAGGTGGTGGTGT--CTTTG
1 TGGTGACGGAGGTGGAGGTGGTGGTGT-CCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTG
* *
2666456 GTGACAGAGGTGGAGGTGGAGGTGGTGGTTCCCGT-GGTGACGGAGGTGGAGGTGGTGGTGGTCC
65 GTGACGGAGGT---GGTGGAGGTGGTGG-TCCCCTAGGTGACGGAGGTGGAGGTGGTGGT-GTCC
* *
2666520 CCGTGGTGACAGAGGTGGAGGTGGTGGTGGTCCCTG
125 CCTTGGTGACGGAGGTGGAGGTGGTGGT-GTCCCTG
* * *
2666556 TGGTGATGGAGGTGGAGGTGGTGGTGTCTTTGGTGACGGAGGTGGAGGTGGTGGT-T-CCCGTGG
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
*
2666619 TGACGGTGACGCCCCGTGGTGACGGAGGTGGAGGTGGTGATCCGCTAGGTGACGGAGGTGGAGGT
66 TGAC-G-GA-G----GTGGT---GGAGGT---GGT-G-G-TCCCCTAGGTGACGGAGGTGGAGGT
* *
2666684 GGTGGTGGTCCCCTAGGTGATGGAGGTGGAGGTGGTGGTGATCCCTG
115 GGTGGT-GTCCCCTTGGTGACGGAGGTGGAGGTGGTGGTG-TCCCTG
** *
2666731 TGGTGATAGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGT-T-CCCGTGG
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
* * * *
2666794 TGACGGA---GGTGGAGGTGGTGATCCGCTAGGTGACGGAGGTGGAGGTGGTGGTGGTACCCTAG
66 TGACGGAGGTGGTGGAGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGT-GTCCCCTTG
2666856 GTGACGGAGGTGGAGGTGGTGGTGATCCCTG
130 GTGACGGAGGTGGAGGTGGTGGTG-TCCCTG
*
2666887 TGGTGATGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGT-G-GTCCCCTTGG
1 TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
*
2666950 TGATGGA--T-GTGGAGGTGGTGG
66 TGACGGAGGTGGTGGAGGTGGTGG
2666971 AGGTCTTCTT
Statistics
Matches: 785, Mismatches: 49, Indels: 98
0.84 0.05 0.11
Matches are distributed among these distances:
147 43 0.05
148 1 0.00
149 2 0.00
150 16 0.02
152 1 0.00
153 99 0.13
154 2 0.00
155 6 0.01
156 338 0.43
157 10 0.01
158 1 0.00
159 42 0.05
161 5 0.01
162 64 0.08
163 1 0.00
164 2 0.00
165 4 0.01
166 3 0.00
169 8 0.01
172 3 0.00
173 3 0.00
174 7 0.01
175 124 0.16
ACGTcount: A:0.12, C:0.12, G:0.52, T:0.25
Consensus pattern (159 bp):
TGGTGACGGAGGTGGAGGTGGTGGTGTCCTTGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
TGACGGAGGTGGTGGAGGTGGTGGTCCCCTAGGTGACGGAGGTGGAGGTGGTGGTGTCCCCTTGG
TGACGGAGGTGGAGGTGGTGGTGTCCCTG
Found at i:2667931 original size:19 final size:18
Alignment explanation
Indices: 2667909--2667956 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
2667899 TGTTTCAATG
*
2667909 AAAATAGTTTTTGGAAAAT
1 AAAAT-GTTTTTGGAAAAA
2667928 AAAATGGTTTTTTGGAAAAA
1 AAAAT-G-TTTTTGGAAAAA
2667948 AAAATGTTT
1 AAAATGTTT
2667957 ATTTTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
20 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.38
Consensus pattern (18 bp):
AAAATGTTTTTGGAAAAA
Found at i:2667941 original size:20 final size:20
Alignment explanation
Indices: 2667916--2667953 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2667906 ATGAAAATAG
*
2667916 TTTTTGGAAAATAAAATGGT
1 TTTTTGGAAAAAAAAATGGT
2667936 TTTTTGGAAAAAAAAATG
1 TTTTTGGAAAAAAAAATG
2667954 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (20 bp):
TTTTTGGAAAAAAAAATGGT
Found at i:2672051 original size:169 final size:169
Alignment explanation
Indices: 2671827--2672137 Score: 489
Period size: 169 Copynumber: 1.8 Consensus size: 169
2671817 TTTCTAGTCC
* * * * *
2671827 AGTCGATTTTGTTGTCTTTTGAATGCTTACCGGCTCTTCATATTTGAATAATATCGATTTGTGCT
1 AGTCGATATTGTTATCTTTTGAATGCTTACCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
*
2671892 CACGAAGCTGCGCTTAGATAAGTAGTAGCTTATTTTTAGTTGTAAATTCAGCTTTTGAATTACTA
66 CACGAAGCTGCGCTTAGAAAAGTAGTAGCTTATTTTTAGTTGTAAATTCAGCTTTTGAATTACTA
2671957 ATGTC-TACGTTTCCTTTTTTTTAATGATCCGTCACCGCA
131 ATG-CGTACGTTTCCTTTTTTTTAATGATCCGTCACCGCA
*
2671996 AGTCGATATTGTTATCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
1 AGTCGATATTGTTATCTTTTGAATGCTTACCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
* * * * * *
2672061 CACGAAGGTTCGCTTAGAAAATTTGTAGTTTATTTTTAGTTGTAAATTCAGCTTTTGAATTACTG
66 CACGAAGCTGCGCTTAGAAAAGTAGTAGCTTATTTTTAGTTGTAAATTCAGCTTTTGAATTACTA
2672126 ATGCGTACGTTT
131 ATGCGTACGTTT
2672138 TGATTTCTCT
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
168 1 0.01
169 127 0.99
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (169 bp):
AGTCGATATTGTTATCTTTTGAATGCTTACCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
CACGAAGCTGCGCTTAGAAAAGTAGTAGCTTATTTTTAGTTGTAAATTCAGCTTTTGAATTACTA
ATGCGTACGTTTCCTTTTTTTTAATGATCCGTCACCGCA
Found at i:2672294 original size:188 final size:193
Alignment explanation
Indices: 2671966--2672538 Score: 775
Period size: 188 Copynumber: 2.9 Consensus size: 193
2671956 AATGTCTACG
*
2671966 TTTCCTT-TTTTTTAATGATCCGTCACCGCAAGTCGATATTGTTATCTTTTGAATGCTTGCCGGC
1 TTTCCTTCTTTTTTAATGATCCGTCACCGCAAGTCGATATTGTTGTCTTTTGAATGCTTGCCGGC
* * *
2672030 TCTTCAGATTCGAACAATATCGATTTGTGCTCACGAAGGTTCGCTTAGAAAATTTGTAGTTTATT
66 TCTTCAGATTCGAACAATATCGATTTGTGCTCACGAAGCTGCGCTTAGAAAAGTTGTAGTTTA-T
* *
2672095 TTTAGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTTTGA-TT-TC-TC-TG-T-TTT
130 TTTAGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTCTAATTTCTCTTCTTGATATTT
* * *
2672153 TTTCCTTCCTTTTTAATGATCCGTCACCGCAAGTCGATATTGTCGTCTTTTGAATGCTTACCGGC
1 TTTCCTTCTTTTTTAATGATCCGTCACCGCAAGTCGATATTGTTGTCTTTTGAATGCTTGCCGGC
*
2672218 TCTTCAGATTCGAAGAATATCGATTTGTGCTCACGAAGCTGCGCTTAGAAATA-TTGTAGTTTAT
66 TCTTCAGATTCGAACAATATCGATTTGTGCTCACGAAGCTGCGCTTAGAAA-AGTTGTAGTTTAT
* * *
2672282 TTTAACTTGTAAATTCAGCTTTTGCATTACTGATGTGTACGTTCTAATTTCTCTATTCTTTTTTG
130 TTT-AGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTCTAATTTCTC--TTC----TTG
2672347 AAATATTT
188 --ATATTT
* *
2672355 TTTCTTTTTTCTTTTTTAATGATCCATCACCGCAAGTCGATATTGTTGTCTTTTGAATGCTTGCC
1 TTTC---CTTCTTTTTTAATGATCCGTCACCGCAAGTCGATATTGTTGTCTTTTGAATGCTTGCC
* * * *
2672420 GGCTCTTCAGATTCGAACAATACCGATTTGTGCTCACGAAACTGCGCCTCGAAAAGTTGTAGTTT
63 GGCTCTTCAGATTCGAACAATATCGATTTGTGCTCACGAAGCTGCGCTTAGAAAAGTTGTAGTTT
* *
2672485 ATTTTAGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTGTAATCTCTC
128 ATTTTAGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTCTAATTTCTC
2672539 AGTTTATTAT
Statistics
Matches: 338, Mismatches: 27, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
187 11 0.03
188 149 0.44
189 3 0.01
190 2 0.01
193 2 0.01
198 2 0.01
201 1 0.00
202 7 0.02
204 45 0.13
205 116 0.34
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (193 bp):
TTTCCTTCTTTTTTAATGATCCGTCACCGCAAGTCGATATTGTTGTCTTTTGAATGCTTGCCGGC
TCTTCAGATTCGAACAATATCGATTTGTGCTCACGAAGCTGCGCTTAGAAAAGTTGTAGTTTATT
TTAGTTGTAAATTCAGCTTTTGAATTACTGATGCGTACGTTCTAATTTCTCTTCTTGATATTT
Found at i:2677604 original size:4 final size:4
Alignment explanation
Indices: 2677587--2677622 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
2677577 TTCCTTAGTT
*
2677587 CATA CATA CGTA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
2677623 TATATACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2678925 original size:14 final size:13
Alignment explanation
Indices: 2678906--2678936 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2678896 TATTTAAGAT
2678906 AAATCCAAATTTCA
1 AAATCCAAATTT-A
2678920 AAATCCAAATTTA
1 AAATCCAAATTTA
2678933 AAAT
1 AAAT
2678937 TTAACACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATCCAAATTTA
Found at i:2686481 original size:14 final size:14
Alignment explanation
Indices: 2686441--2686482 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2686431 AATTTTATGA
2686441 AATTTTTATATTAT
1 AATTTTTATATTAT
*
2686455 -ATATATTATATTAT
1 AAT-TTTTATATTAT
*
2686469 AATTTTTAAATTAT
1 AATTTTTATATTAT
2686483 TTATTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTTATATTAT
Found at i:2691258 original size:64 final size:64
Alignment explanation
Indices: 2691141--2691268 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 64
2691131 TTAAGAACCT
* * * * * *
2691141 TATATCAGGACGCTCATAAAGAGCTGCGGTATGTCCGCAATATATGCAAGATCAATACCAATCA
1 TATAACAGGACGCTCACAAAGAGCTGCGATATGTCCGCAACACATACAAGATCAATACCAATCA
* * *
2691205 TATAACAGGACGCTCACAAAGAGCTGCGATATGTCCGCAACACGTACAGGATCAATACCGATCA
1 TATAACAGGACGCTCACAAAGAGCTGCGATATGTCCGCAACACATACAAGATCAATACCAATCA
2691269 GGATGCTTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (64 bp):
TATAACAGGACGCTCACAAAGAGCTGCGATATGTCCGCAACACATACAAGATCAATACCAATCA
Found at i:2692010 original size:21 final size:22
Alignment explanation
Indices: 2691973--2692016 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2691963 ATTTCAGCAT
2691973 ACCCATCCATGAAAAAATTTTA
1 ACCCATCCATGAAAAAATTTTA
2691995 ACCCATCCAT-AAAAAATTTTA
1 ACCCATCCATGAAAAAATTTTA
2692016 A
1 A
2692017 TACTTTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (22 bp):
ACCCATCCATGAAAAAATTTTA
Found at i:2695430 original size:36 final size:36
Alignment explanation
Indices: 2695404--2696383 Score: 880
Period size: 36 Copynumber: 27.2 Consensus size: 36
2695394 CCAATTCCCC
* * *
2695404 CACCTTCAATGAACCAACCTTTACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
2695440 CACCTCCAATGAACCAACCATT-ACCTCCACCTTTCT
1 CACCTCCAATGAACCAACC-TTCACCTCCACCTCTCT
* *
2695476 CACCTCCAACGAACCAACCTTCACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
2695512 CACCTCCAATGAACCAACCTTCACCTCCACC-CT-T
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
2695546 GCCACCTCCAATGAACCAACCTTCACCTCCACCTTTCT
1 --CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * * *
2695584 CACCACCAATGAACGAACCATCACCTCCACCCCTAT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
2695620 CACCTCCAATGAACCAACCTTCACCTCCACCCCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* *
2695656 CACCTCCAATGAACCAACCTTCATCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
2695692 CACCACCAATGAACGAACCATCACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
2695728 CACCTCCAATGAACCAACCTTCACCTCCACCCCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* * *
2695764 CACCTCCAATGAACCAACCTTCATCTCCAACTTTC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * ** * * *
2695799 CACC-CC--TGCCACC-TCCAATGAACCAGCCCACCCCTGT
1 CACCTCCAATG-AACCAACC--TTCACC--TCCACCTCTCT
* * *
2695836 CACCTCCAATGAACCAACCTTCAGCTCCACCCCTAT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
2695872 CACCTCCAATGAATCAACCTTCACCTCCACCCCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* * *
2695908 CACCTCCAATGAACCAGCCTTCATCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
2695944 CACCACCAATGAACGAACCATCACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
2695980 CACCTCCAATGAACCAACCTTCACCTCCACCCCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* * *
2696016 CACCTCCAATGAACCAGCCTTCATCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * * *
2696052 CACCACCAATGAACGAACCATCACCTCCATCTAAT-T
1 CACCTCCAATGAACCAACCTTCACCTCCACCT-CTCT
**** * * * * * **
2696088 GTGGTTCAAATGTA--TA-CTTGAAGCCTCCACCCCTAG
1 -CACCTCCAATGAACCAACCTT-CA-CCTCCACCTCTCT
* *
2696124 CACCTCCAATGAATCAACCTTCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
2696160 CACCACCAACGAACCAACCTTCACCTCCACCCCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
2696196 CACCTCCAATGAACCAACCTTTACCTCCACC-CTTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTC-TCT
* * *
2696232 CACCTCCAATAAACCAACCTTCACCTTCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * ** * *
2696268 CACCACCAACGAATGAACCATCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
2696304 TACCTCCAATGGACCAACCTTCACCTCCATCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * * *
2696340 CACCACCAATGAACGAACCATCACCTTCACC-CTTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTC-TCT
2696376 CACCTCCA
1 CACCTCCA
2696384 CCTTCATCTC
Statistics
Matches: 761, Mismatches: 149, Indels: 68
0.78 0.15 0.07
Matches are distributed among these distances:
32 4 0.01
33 3 0.00
34 8 0.01
35 23 0.03
36 691 0.91
37 16 0.02
38 9 0.01
39 3 0.00
40 4 0.01
ACGTcount: A:0.27, C:0.46, G:0.06, T:0.22
Consensus pattern (36 bp):
CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
Found at i:2695830 original size:28 final size:28
Alignment explanation
Indices: 2695798--2695851 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2695788 CTCCAACTTT
2695798 CCACCCCTGCCACCTCCAATGAACCAGC
1 CCACCCCTGCCACCTCCAATGAACCAGC
*
2695826 CCACCCCTGTCACCTCCAATGAACCA
1 CCACCCCTGCCACCTCCAATGAACCA
2695852 ACCTTCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.26, C:0.52, G:0.09, T:0.13
Consensus pattern (28 bp):
CCACCCCTGCCACCTCCAATGAACCAGC
Found at i:2696442 original size:45 final size:45
Alignment explanation
Indices: 2696378--2696553 Score: 307
Period size: 45 Copynumber: 3.9 Consensus size: 45
2696368 ACCCTTGTCA
*
2696378 CCTCCACCTTCATCTCCATCACCAAGGAGGACACCACCACCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
* *
2696423 CCTCCACCTTCAACTCCATCACCAAGGAGGACACCACCACCGCCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
*
2696468 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCA
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
*
2696513 CCTCCACCTTCAGCTCCATTACCAAGGAGGACACCACCACC
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACC
2696554 TCCACCACCA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 125 1.00
ACGTcount: A:0.27, C:0.48, G:0.12, T:0.12
Consensus pattern (45 bp):
CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
Found at i:2697710 original size:23 final size:23
Alignment explanation
Indices: 2697667--2697711 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2697657 TTTTTTTAAC
* *
2697667 TTTGAATTCTTCTTAAGTTTTTT
1 TTTGAATACTTCTTAAATTTTTT
2697690 TTTGAATAC-TCTTATAATTTTT
1 TTTGAATACTTCTTA-AATTTTT
2697712 AAATTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTGAATACTTCTTAAATTTTTT
Found at i:2698083 original size:3 final size:3
Alignment explanation
Indices: 2698077--2698101 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2698067 TGTATATAAT
2698077 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2698102 GCAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2708435 original size:105 final size:105
Alignment explanation
Indices: 2708253--2708463 Score: 413
Period size: 105 Copynumber: 2.0 Consensus size: 105
2708243 TCTAACTCTT
*
2708253 CAGGAGTCCATGGATGTTTCTCGTCCCTCTCTAAAAGAACATGAGCTCGATGGTATACGCTCCCA
1 CAGGAGTCCATGGATGTTTCTCATCCCTCTCTAAAAGAACATGAGCTCGATGGTATACGCTCCCA
2708318 ACTGGCCTCCAAGGAATGCTGCTTGAATTTCCTTCCAACA
66 ACTGGCCTCCAAGGAATGCTGCTTGAATTTCCTTCCAACA
2708358 CAGGAGTCCATGGATGTTTCTCATCCCTCTCTAAAAGAACATGAGCTCGATGGTATACGCTCCCA
1 CAGGAGTCCATGGATGTTTCTCATCCCTCTCTAAAAGAACATGAGCTCGATGGTATACGCTCCCA
2708423 ACTGGCCTCCAAGGAATGCTGCTTGAATTTCCTTCCAACA
66 ACTGGCCTCCAAGGAATGCTGCTTGAATTTCCTTCCAACA
2708463 C
1 C
2708464 TTTCTCACTT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (105 bp):
CAGGAGTCCATGGATGTTTCTCATCCCTCTCTAAAAGAACATGAGCTCGATGGTATACGCTCCCA
ACTGGCCTCCAAGGAATGCTGCTTGAATTTCCTTCCAACA
Found at i:2713001 original size:231 final size:230
Alignment explanation
Indices: 2712380--2713068 Score: 825
Period size: 231 Copynumber: 3.0 Consensus size: 230
2712370 GGCTCTTGCA
* * * * *
2712380 TTTTACTATGTACAAAGGTTTCAGTCACAGTAGCAACTGCATCAAT-TCCGTCCTTATTCTTCCT
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTAGCAACTGCAT-TATCT-CATCCTTGTTC-T--T
* * * * *
2712444 CTTGTGTTTATCTTCCCTAA-CCTTTTCTGCTTCCCCATTGTTCCCCAAATTCACCACCTTACTA
61 CTTGTGTTTATCTTTCCTAACCCTTTT-TGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTA
* *
2712508 CTTTCTTTTTCTGCATTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATC
125 CTTTCTTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATC
2712573 TTTACTTTTCTTATGC---------GCCTT-TGGAGATTCCT
190 TTTACTTTTCTTATGCTTTTTATGAGCCTTCT-GAGATTCCT
* * * *
2712605 TTTTACTATGTTCAAGGGTTCCGGTCACAGTACCAACTGCATTAGTCCCATCCTTG-TC--CTTG
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTAGCAACTGCATTA-TCTCATCCTTGTTCTTCTTG
** *
2712667 TGTTTATCTTTCCCGACCCTTTTTGCTTCCCCGTTGTTCTCCAAGTTCATCACCTTGCTACTTTC
65 TGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTC
* * ** * *
2712732 TTGTTCTGTGTTCTTTTTTCCACCTTTACAACTTTCCATTGAAATCTCTTTAACCT-CATCTTTA
130 TTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAA-CTACATCTTTA
*
2712796 CTTTTCTTATGCTTTTTATGAGCCTTCTTAGATTCCT
194 CTTTTCTTATGCTTTTTATGAGCCTTCTGAGATTCCT
** * *
2712833 TTTTACTATGTTTGAGGGTTTCAGTCACAGTAGCAACTGCATTGATCTCATCCCTGTTCTTCTTA
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTAGCAACTGCATT-ATCTCATCCTTGTTCTTCTTG
* * *
2712898 TGTTTGTCTTTCTTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCGCCTTGCTACTTTC
65 TGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTC
* * *
2712963 TTGTTCTGCGTTCTCTTTTCCACCCAAACAAGTTTCCATTGGAATCTCTTCAACTGCATCTTTAC
130 TTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATCTTTAC
* **
2713028 TTGTCTTATGCTTTTTATGAGTGTTCTGAGATTCCT
195 TTTTCTTATGCTTTTTATGAGCCTTCTGAGATTCCT
2713064 TTTTA
1 TTTTA
2713069 TCTGTATCAA
Statistics
Matches: 393, Mismatches: 52, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
219 119 0.30
220 8 0.02
224 3 0.01
225 44 0.11
228 60 0.15
229 4 0.01
230 2 0.01
231 153 0.39
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (230 bp):
TTTTACTATGTTCAAGGGTTTCAGTCACAGTAGCAACTGCATTATCTCATCCTTGTTCTTCTTGT
GTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTCT
TGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATCTTTACT
TTTCTTATGCTTTTTATGAGCCTTCTGAGATTCCT
Found at i:2738719 original size:6 final size:6
Alignment explanation
Indices: 2738710--2738749 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
2738700 TATTTTCCAC
2738710 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
2738750 ATTTATACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:2738768 original size:22 final size:22
Alignment explanation
Indices: 2738743--2738789 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
2738733 TAAATTTAAA
2738743 TTTAAATATTTA-TACT-TTTATT
1 TTTAAA-ATTTAGT-CTCTTTATT
*
2738765 TTTAGAATTTAGTCTCTTTATT
1 TTTAAAATTTAGTCTCTTTATT
2738787 TTT
1 TTT
2738790 CTGATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAAAATTTAGTCTCTTTATT
Found at i:2739174 original size:60 final size:60
Alignment explanation
Indices: 2739103--2739233 Score: 199
Period size: 60 Copynumber: 2.2 Consensus size: 60
2739093 ACTAGTAGTT
* *
2739103 ATCCAATTATTAGTAAATTTCTTTTTTAGTCACTCAATTATGAAAAGTTACAAAATGGTC
1 ATCCAATTATTAGTAAATTTCTTTTTTAGTCACCCAACTATGAAAAGTTACAAAATGGTC
* * * * *
2739163 ATCCAACTATTAGTAAATTTCTTTTTTGGTCACCCACCTATGAAAATTTACAAAGTGGTC
1 ATCCAATTATTAGTAAATTTCTTTTTTAGTCACCCAACTATGAAAAGTTACAAAATGGTC
2739223 ATCCAATTATT
1 ATCCAATTATT
2739234 CAACTTTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (60 bp):
ATCCAATTATTAGTAAATTTCTTTTTTAGTCACCCAACTATGAAAAGTTACAAAATGGTC
Found at i:2743359 original size:2 final size:2
Alignment explanation
Indices: 2743352--2743387 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2743342 GCAACTCAGG
*
2743352 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2743388 ACACACATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:2745692 original size:125 final size:125
Alignment explanation
Indices: 2745544--2745783 Score: 374
Period size: 125 Copynumber: 1.9 Consensus size: 125
2745534 TAATTGAGCT
* * *
2745544 CGAGCTTGAGTAGCTCAATTATATCTTGAACCAAGCTCAAGTTTATAATTAAATGTTCG-ATCAA
1 CGAGCTTGAGTAGCTCAATTATATCTTGAACCAAACTCAAATTTAAAATTAAATGTT-GAATCAA
* * * *
2745608 GCTCAAGCCAAGTATCTTTTGCAAATTTTAACTTGAGTTCGAGTTCGAGCTTGAATATATA
65 GCTCAAGCCAAGTATCTTTTGCAAATTTCAAATCGAGTTCGAGTTCAAGCTTGAATATATA
* *
2745669 CGAGCTTGAGTAGCTCAATTATATTTTGAACTAAACTCAAATTTAAAATTAAATGTTGAATCAAG
1 CGAGCTTGAGTAGCTCAATTATATCTTGAACCAAACTCAAATTTAAAATTAAATGTTGAATCAAG
*
2745734 CTCAAGCCAAGTATCTTTTGCAAATTTCAAATCGAGTTCGGGTTCAAGCT
66 CTCAAGCCAAGTATCTTTTGCAAATTTCAAATCGAGTTCGAGTTCAAGCT
2745784 CGAACTTAGC
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 103 0.99
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (125 bp):
CGAGCTTGAGTAGCTCAATTATATCTTGAACCAAACTCAAATTTAAAATTAAATGTTGAATCAAG
CTCAAGCCAAGTATCTTTTGCAAATTTCAAATCGAGTTCGAGTTCAAGCTTGAATATATA
Found at i:2780398 original size:176 final size:176
Alignment explanation
Indices: 2780104--2780426 Score: 646
Period size: 176 Copynumber: 1.8 Consensus size: 176
2780094 TTTGTCAAAA
2780104 GGGGGGGGGGGGATAATCTATAAAGCATATATATTGTCATGTTTCCATGTGATCAAGGTATTGGA
1 GGGGGGGGGGGGATAATCTATAAAGCATATATATTGTCATGTTTCCATGTGATCAAGGTATTGGA
2780169 ACATGGAACTCATTATTATTTCATTGTTTGAAGCATTTAATAATGGTAAAGCATTGTATCATATA
66 ACATGGAACTCATTATTATTTCATTGTTTGAAGCATTTAATAATGGTAAAGCATTGTATCATATA
2780234 TGTTGGTAAAGGTGATCATGTGTGGAAAAACTGTTTTTATAGAAAG
131 TGTTGGTAAAGGTGATCATGTGTGGAAAAACTGTTTTTATAGAAAG
2780280 GGGGGGGGGGGGATAATCTATAAAGCATATATATTGTCATGTTTCCATGTGATCAAGGTATTGGA
1 GGGGGGGGGGGGATAATCTATAAAGCATATATATTGTCATGTTTCCATGTGATCAAGGTATTGGA
2780345 ACATGGAACTCATTATTATTTCATTGTTTGAAGCATTTAATAATGGTAAAGCATTGTATCATATA
66 ACATGGAACTCATTATTATTTCATTGTTTGAAGCATTTAATAATGGTAAAGCATTGTATCATATA
2780410 TGTTGGTAAAGGTGATC
131 TGTTGGTAAAGGTGATC
2780427 CTATAAGGAG
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 147 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.35
Consensus pattern (176 bp):
GGGGGGGGGGGGATAATCTATAAAGCATATATATTGTCATGTTTCCATGTGATCAAGGTATTGGA
ACATGGAACTCATTATTATTTCATTGTTTGAAGCATTTAATAATGGTAAAGCATTGTATCATATA
TGTTGGTAAAGGTGATCATGTGTGGAAAAACTGTTTTTATAGAAAG
Found at i:2787274 original size:5 final size:5
Alignment explanation
Indices: 2787266--2787290 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2787256 TTCTATTAAC
2787266 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
2787291 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2791936 original size:71 final size:71
Alignment explanation
Indices: 2791844--2791979 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
2791834 CTCCTAACTC
* * *
2791844 TTTTTGGTTTAACTATTTCTTAGGTCACTGCCAAATTCAAATTAGACAATTTGAGCATTGCCCCC
1 TTTTTGGTTTAACTATCTCTTAGGTCACTACCAAATTCAAATTAGACAAATTGAGCATTGCCCCC
2791909 CTAGCT
66 CTAGCT
* * ** **
2791915 TTTTTGGTTTAAGC-GTCTCTTAGGTCCCTATTAAATTTGAATTAGACAAATTGAGCATTGCCCC
1 TTTTTGGTTTAA-CTATCTCTTAGGTCACTACCAAATTCAAATTAGACAAATTGAGCATTGCCCC
2791979 C
65 C
2791980 ATTTCCTTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 54 0.98
72 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (71 bp):
TTTTTGGTTTAACTATCTCTTAGGTCACTACCAAATTCAAATTAGACAAATTGAGCATTGCCCCC
CTAGCT
Found at i:2792493 original size:30 final size:31
Alignment explanation
Indices: 2792459--2792558 Score: 107
Period size: 30 Copynumber: 3.2 Consensus size: 31
2792449 ATTTTTACAG
* *
2792459 ATCTTTTAAAAATATCTA-AATATATTATAT
1 ATCTTTTACAAATATTTAGAATATATTATAT
*
2792489 ATCTTTTAGGCATATATTTAAGAATATATTATAT
1 ATCTTTTA--CAAATATTT-AGAATATATTATAT
*
2792523 AT-TTTT-CAGATATTTAGGAATATATTATAT
1 ATCTTTTACAAATATTTA-GAATATATTATAT
2792553 ATCTTT
1 ATCTTT
2792559 CTTATTTCTG
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
29 1 0.02
30 31 0.52
31 3 0.05
32 6 0.10
33 5 0.08
34 14 0.23
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (31 bp):
ATCTTTTACAAATATTTAGAATATATTATAT
Found at i:2805625 original size:111 final size:112
Alignment explanation
Indices: 2805501--2805724 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 112
2805491 AATTTTTTCT
2805501 ATAATACATTTTTACTCTTTTAATAGTTATATATATAAGAATAAAATAATAATTTTACAGAATGA
1 ATAATACATTTTTACTCTTTTAATAGTTATATATATAAGAATAAAATAATAATTTTACAGAATGA
2805566 AGTGGCGGAACAAGCAATATTACTATAACTGTTCCATATTCACCATA
66 AGTGGCGGAACAAGCAATATTACTATAACTGTTCCATATTCACCATA
2805613 ATAATACA-TTTTACTCTTTTAATAGTTATATATATAAGAATAAAATAATAATTTTACAGAATGA
1 ATAATACATTTTTACTCTTTTAATAGTTATATATATAAGAATAAAATAATAATTTTACAGAATGA
2805677 AGTGGCGGAACAAGCAATATTACTATAACTGTTCCATATTCACCATA
66 AGTGGCGGAACAAGCAATATTACTATAACTGTTCCATATTCACCATA
2805724 A
1 A
2805725 AAAAAAAATT
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 104 0.93
112 8 0.07
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (112 bp):
ATAATACATTTTTACTCTTTTAATAGTTATATATATAAGAATAAAATAATAATTTTACAGAATGA
AGTGGCGGAACAAGCAATATTACTATAACTGTTCCATATTCACCATA
Found at i:2806477 original size:3 final size:3
Alignment explanation
Indices: 2806469--2806525 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
2806459 AAAGCAACTA
2806469 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2806516 TAT TAT TAT T
1 TAT TAT TAT T
2806526 TCCCACTTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2812675 original size:326 final size:327
Alignment explanation
Indices: 2812075--2812723 Score: 1291
Period size: 326 Copynumber: 2.0 Consensus size: 327
2812065 AAGTTCGGTT
2812075 AACCGACCGATTTCGAACCGAATTAACCGTTAACCAAACTTCTAAAAAATTATTAACCGACCCCG
1 AACCGACCGATTTCGAACCGAATTAACCGTTAACCAAACTTCTAAAAAATTATTAACCGACCCCG
2812140 ACCGAATTTAGTCGGTTAACCGAATTAATTCGATTTTACGAAATTTGCACATCCCTAGATTCACA
66 ACCGAATTTAGTCGGTTAACCGAATTAATTCGATTTTACGAAATTTGCACATCCCTAGATTCACA
2812205 TTGAAGTTGAACTGCTCCTTTCTCTTTCTCAATCAACATGTCCAGGTAAGAAAAACAGGCTGGTA
131 TTGAAGTTGAACTGCTCCTTTCTCTTTCTCAATCAACATGTCCAGGTAAGAAAAACAGGCTGGTA
2812270 CACACAACTCTCACATGGGACCTAGCCACGTGATTACTTTCTTAGTTCTATCCTCTCCAGTCCGA
196 CACACAACTCTCACATGGGACCTAGCCACGTGATTACTTTCTTAGTTCTATCCTCTCCAGTCCGA
2812335 TCTTTCGTATATTTTGTTTCAGACAATTTTGCAACTTGTAGTAATATATATGATGAATAAACAGG
261 TCTTTCGTATATTTTGTTTCAGACAATTTTGCAACTTGTAGTAATATATATGATGAATAAACAGG
2812400 TA
326 TA
2812402 AACCGA-CGATTTCGAACCGAATTAACCGTTAACCAAACTTCTAAAAAATTATTAACCGACCCCG
1 AACCGACCGATTTCGAACCGAATTAACCGTTAACCAAACTTCTAAAAAATTATTAACCGACCCCG
2812466 ACCGAATTTAGTCGGTTAACCGAATTAATTCGATTTTACGAAATTTGCACATCCCTAGATTCACA
66 ACCGAATTTAGTCGGTTAACCGAATTAATTCGATTTTACGAAATTTGCACATCCCTAGATTCACA
2812531 TTGAAGTTGAACTGCTCCTTTCTCTTTCTCAATCAACATGTCCAGGTAAGAAAAACAGGCTGGTA
131 TTGAAGTTGAACTGCTCCTTTCTCTTTCTCAATCAACATGTCCAGGTAAGAAAAACAGGCTGGTA
2812596 CACACAACTCTCACATGGGACCTAGCCACGTGATTACTTTCTTAGTTCTATCCTCTCCAGTCCGA
196 CACACAACTCTCACATGGGACCTAGCCACGTGATTACTTTCTTAGTTCTATCCTCTCCAGTCCGA
2812661 TCTTTCGTATATTTTGTTTCAGACAATTTTGCAACTTGTAGTAATATATATGATGAATAAACA
261 TCTTTCGTATATTTTGTTTCAGACAATTTTGCAACTTGTAGTAATATATATGATGAATAAACA
2812724 AACTGGAGAT
Statistics
Matches: 322, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
326 316 0.98
327 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (327 bp):
AACCGACCGATTTCGAACCGAATTAACCGTTAACCAAACTTCTAAAAAATTATTAACCGACCCCG
ACCGAATTTAGTCGGTTAACCGAATTAATTCGATTTTACGAAATTTGCACATCCCTAGATTCACA
TTGAAGTTGAACTGCTCCTTTCTCTTTCTCAATCAACATGTCCAGGTAAGAAAAACAGGCTGGTA
CACACAACTCTCACATGGGACCTAGCCACGTGATTACTTTCTTAGTTCTATCCTCTCCAGTCCGA
TCTTTCGTATATTTTGTTTCAGACAATTTTGCAACTTGTAGTAATATATATGATGAATAAACAGG
TA
Found at i:2821642 original size:7 final size:7
Alignment explanation
Indices: 2821632--2821660 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2821622 ATTTTAGTTA
2821632 AGAATAT
1 AGAATAT
2821639 AGAATAT
1 AGAATAT
2821646 AGAATAT
1 AGAATAT
2821653 AGAATAT
1 AGAATAT
2821660 A
1 A
2821661 TGATCGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (7 bp):
AGAATAT
Found at i:2821938 original size:14 final size:14
Alignment explanation
Indices: 2821921--2821949 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2821911 AAATAATAAC
2821921 AAAAAATTT-AAAT
1 AAAAAATTTCAAAT
2821934 AAAAAATTTCAAAT
1 AAAAAATTTCAAAT
2821948 AA
1 AA
2821950 TATATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAATTTCAAAT
Found at i:2828060 original size:40 final size:40
Alignment explanation
Indices: 2828004--2828084 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2827994 AAGCCTTTCC
*
2828004 TGGCAAGATTGGTAGTTTTTTTATATGGATTCTTGTTTGA
1 TGGCAAGATTGATAGTTTTTTTATATGGATTCTTGTTTGA
2828044 TGGCAAGATTGATAGTTTTTTTATATGGATTCTTGTTTGA
1 TGGCAAGATTGATAGTTTTTTTATATGGATTCTTGTTTGA
2828084 T
1 T
2828085 AGCAGTGGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (40 bp):
TGGCAAGATTGATAGTTTTTTTATATGGATTCTTGTTTGA
Found at i:2838851 original size:30 final size:30
Alignment explanation
Indices: 2838817--2838876 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2838807 GCCAAGTTGC
*
2838817 CTGGTAGACCAATTCTTTTGCATCAGTAGA
1 CTGGTAGACCAATTCTTTTGCATCAATAGA
2838847 CTGGTAGACCAATTCTTTTGCATCAATAGA
1 CTGGTAGACCAATTCTTTTGCATCAATAGA
2838877 TGAGTAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (30 bp):
CTGGTAGACCAATTCTTTTGCATCAATAGA
Found at i:2842087 original size:21 final size:21
Alignment explanation
Indices: 2842056--2842101 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2842046 TGACTATTAA
2842056 AAAATTTAATAAATAAAAAAAT
1 AAAATTTAAT-AATAAAAAAAT
**
2842078 AAAA-TTAATAATATTAAAAT
1 AAAATTTAATAATAAAAAAAT
2842098 AAAA
1 AAAA
2842102 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 5 0.23
22 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTTAATAATAAAAAAAT
Found at i:2842102 original size:21 final size:20
Alignment explanation
Indices: 2842054--2842103 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2842044 CATGACTATT
*
2842054 AAAAAATTTAATAAATAAAA
1 AAAAAAATTAATAAATAAAA
*
2842074 AAATAAAATTAATAATATTAAA
1 AAA-AAAATTAATAA-ATAAAA
*
2842096 ATAAAAAT
1 AAAAAAAT
2842104 ATTTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.60
22 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATTAATAAATAAAA
Found at i:2863675 original size:5 final size:5
Alignment explanation
Indices: 2863665--2863703 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2863655 TCCTAAGATG
* *
2863665 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
2863704 GCTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:2864299 original size:24 final size:24
Alignment explanation
Indices: 2864250--2864333 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
2864240 GCTATTCGGG
* * *
2864250 GCTTCCCATTAATGGCTC-TTTGGA
1 GCTTCCCGTTATTGGCTCGTAT-GA
*
2864274 GCTACCCGTTATTGGCTCGTATGA
1 GCTTCCCGTTATTGGCTCGTATGA
** *
2864298 GCTTCTTGATTA-TGGCTCTTATGA
1 GCTTCCCG-TTATTGGCTCGTATGA
2864322 GCTTCCCGTTAT
1 GCTTCCCGTTAT
2864334 ACAGCCCGGA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
23 3 0.06
24 39 0.83
25 5 0.11
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.39
Consensus pattern (24 bp):
GCTTCCCGTTATTGGCTCGTATGA
Found at i:2864575 original size:15 final size:15
Alignment explanation
Indices: 2864555--2864586 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2864545 GATATGAATT
2864555 ATTATAGAAATGTAC
1 ATTATAGAAATGTAC
2864570 ATTATAGAAATGTAC
1 ATTATAGAAATGTAC
2864585 AT
1 AT
2864587 GTTATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (15 bp):
ATTATAGAAATGTAC
Found at i:2865256 original size:124 final size:124
Alignment explanation
Indices: 2865102--2865349 Score: 415
Period size: 124 Copynumber: 2.0 Consensus size: 124
2865092 TGCATTTGGT
* * *
2865102 ATCTAGGTAAGCATAAGTTTTGGAATGACATATTATTAAATTGTTTATTGAGGTGCCTAAGAGCA
1 ATCTAGGTAAGCATAAGTTTTGGAATGACATATTAATAAATTGTCTATTGAGGTGCCTAAAAGCA
* * *
2865167 CATTGGTTGTATGTGTAGTATGTCAAGTTTAAGACATGATTTTGGTTTGTTTTATGTGC
66 CATTGGTTGTATGTGTAATATGTCAAGTTTAAGACATGATTTTGGTTTATTTTAAGTGC
* *
2865226 ATCTAGGTAAGTATAAGTTTTGGAATGACATTTTAATAAATTGTCTATTGAGGTGCCTAAAAGCA
1 ATCTAGGTAAGCATAAGTTTTGGAATGACATATTAATAAATTGTCTATTGAGGTGCCTAAAAGCA
*
2865291 CATTGGTTGTATGTGTAATATGTCAAGTTTAAGACATGGTTTTGGTTTATTTTAAGTGC
66 CATTGGTTGTATGTGTAATATGTCAAGTTTAAGACATGATTTTGGTTTATTTTAAGTGC
2865350 TTTGATATGG
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 115 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (124 bp):
ATCTAGGTAAGCATAAGTTTTGGAATGACATATTAATAAATTGTCTATTGAGGTGCCTAAAAGCA
CATTGGTTGTATGTGTAATATGTCAAGTTTAAGACATGATTTTGGTTTATTTTAAGTGC
Found at i:2867320 original size:38 final size:38
Alignment explanation
Indices: 2867269--2867345 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
2867259 CTAATTGAAG
*
2867269 AATAAATGACAGAGTCTTTGAGGGAGGGGATTTGGTAT
1 AATAAATGACAGAGTCTTTGAGGGAGGGAATTTGGTAT
2867307 AATAAATGACAGAGTCTTTGAGGGAGGGAATTTGGTAT
1 AATAAATGACAGAGTCTTTGAGGGAGGGAATTTGGTAT
2867345 A
1 A
2867346 TCTCAAACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (38 bp):
AATAAATGACAGAGTCTTTGAGGGAGGGAATTTGGTAT
Found at i:2878017 original size:15 final size:15
Alignment explanation
Indices: 2877997--2878027 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2877987 GGTACTGCAC
*
2877997 ACTATTATTATTATT
1 ACTATTACTATTATT
2878012 ACTATTACTATTATT
1 ACTATTACTATTATT
2878027 A
1 A
2878028 TTATCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
ACTATTACTATTATT
Found at i:2898233 original size:20 final size:20
Alignment explanation
Indices: 2898208--2898246 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2898198 ATAAATTAAT
*
2898208 ATAAATGTTTTAATCATTAG
1 ATAAATGTTTTAATAATTAG
*
2898228 ATAAATTTTTTAATAATTA
1 ATAAATGTTTTAATAATTA
2898247 AATCGTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATAAATGTTTTAATAATTAG
Found at i:2898637 original size:19 final size:18
Alignment explanation
Indices: 2898584--2898637 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
2898574 AATAGAAGTT
*
2898584 TTAAAAATTATTTAACAA
1 TTAAAAATTATTTAATAA
* *
2898602 TTACAAAATTAATTAATGA
1 TTA-AAAATTATTTAATAA
2898621 TTAAAAATTATTATAAT
1 TTAAAAATTATT-TAAT
2898638 TATATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAAAATTATTTAATAA
Found at i:2901652 original size:584 final size:583
Alignment explanation
Indices: 2900671--2901802 Score: 1969
Period size: 584 Copynumber: 1.9 Consensus size: 583
2900661 AATATTTCTG
2900671 TTACGTACAACAATTATCTAACTGAAATTAACAAAAAGTAATTTATTAATAGTAATTTAAAATTT
1 TTACGTACAACAATTATCTAACTGAAATTAACAAAAAGTAATTTATTAATAGTAATTTAAAATTT
* *
2900736 AACTAGACTTAATAAATTGAATAACTAAAATGAATAAGCTATAAAAAAAAGAATTAGTATTTTAT
66 AACTAGACTTAATAAATTAAATAACTAAAATGAATAAGCTATAAAAAAAAGAATTAATATTTTAT
* * *
2900801 TTTTATAATTTTATTTCGTAAATTGAATTACCATTATTTAAGTCTCACACATATAGTGGTGGAGC
131 TTGTATAATTTTATTTCGTAAATTGAATTACCATTATTTAAGTCACACACATATAGCGGTGGAGC
* *
2900866 CTATAATTTTTTTTAGGGACGAAATTAAATTATATATCTTTACGATAGTAAAAATATAATTTATT
196 CTATAAATTTTTTTAGGGACGAAATTAAATTATATATCTTTACGACAGTAAAAATATAATTTATT
2900931 ATTTTAATAGCCTATATCTATATAATTTTAAAATAGTTAAATTAAATTTTATTATTTTTAAAAGA
261 ATTTTAATAGCCTATATCTATATAATTTTAAAATAGTTAAATTAAATTTTATTATTTTTAAAAGA
* * *
2900996 TCAAACTACAATTTTACCGTTACTAATCTAAACTTTTATAAATTATAAAAAATTTAAATTTAAAA
326 TCAAAATACAATTTTACCATTACTAATCTAAAATTTTATAAATTATAAAAAATTTAAATTTAAAA
* *
2901061 TTTACTATTTTAAGTGACAGCATAGCACCTGGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAA
391 TTTACTATTTTAAGTGACAGCATAGCACCTGGGTGGAAAGTTAAGTGCCTAACTCTAAGCATAAA
* * *
2901126 ATGAAATTAAGATGTAATGTAAAATTAAAAATGGTAGGTTTCGTATTTATTACGAGGACCAGGAG
456 ATGAAATTAAGATGTAAGGTAAAATTAAAAAGGGTAGGTTTCGTATTTATTACGAGGA-CAGAAG
2901191 ATAGCGGTGGTAGATATATCATCTCATAAAAGCAGTGTCGTTTAACTTACAAAATATTATTTAT
520 ATAGCGGTGGTAGATATATCATCTCATAAAAGCAGTGTCGTTTAACTTACAAAATATTATTTAT
** *
2901255 TTACGTACGCCAATTATCTAACTGAAATTAACAAAAAGTAATTTATTAATAGTATTTTAAAATTT
1 TTACGTACAACAATTATCTAACTGAAATTAACAAAAAGTAATTTATTAATAGTAATTTAAAATTT
*
2901320 AACTAGACTTAATAAATTAAATAACTGAAATGAATAAGCTAT-AAAAAAAGAATTAATATTTTAT
66 AACTAGACTTAATAAATTAAATAACTAAAATGAATAAGCTATAAAAAAAAGAATTAATATTTTAT
*
2901384 TTGTATAATTTTATTTCGTAAATTGAATTACTATTATTTAAGTCACACACATATAGCGGTGGAGC
131 TTGTATAATTTTATTTCGTAAATTGAATTACCATTATTTAAGTCACACACATATAGCGGTGGAGC
* * *
2901449 CTATAAATTTTTTTGGGGACGAAATTAAATTATATATCTTTATGACAGTAAAGATATAATTTTAT
196 CTATAAATTTTTTTAGGGACGAAATTAAATTATATATCTTTACGACAGTAAAAATATAA-TTTAT
*
2901514 TATTTTAATAGCTTATATCTATATAATTTTAAAATAGTTAAATTAAATTTTATTATTTTTAAAAG
260 TATTTTAATAGCCTATATCTATATAATTTTAAAATAGTTAAATTAAATTTTATTATTTTTAAAAG
*
2901579 ATCAAAATACAATTTTACCATTACTAATTTAAAATTTTATAAATTATAAAAAATTTAAATTTAAA
325 ATCAAAATACAATTTTACCATTACTAATCTAAAATTTTATAAATTATAAAAAATTTAAATTTAAA
* * *
2901644 TTTTACTATTTTAAGTGACAGCATGGCACCTGGGTGGAAAGTTAAGTGCCTAGCTCTAAGCATAA
390 ATTTACTATTTTAAGTGACAGCATAGCACCTGGGTGGAAAGTTAAGTGCCTAACTCTAAGCATAA
* *
2901709 AATGAAATTAAGATGTAAGGTAAAATTAAGAAGGGTAGGTTTCGTATTTATTATGAGGACAGAAG
455 AATGAAATTAAGATGTAAGGTAAAATTAAAAAGGGTAGGTTTCGTATTTATTACGAGGACAGAAG
2901774 ATAGCGGTGGTAGATATATCATCTCATAA
520 ATAGCGGTGGTAGATATATCATCTCATAA
2901803 CTTACAAAAT
Statistics
Matches: 517, Mismatches: 30, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
583 170 0.33
584 347 0.67
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (583 bp):
TTACGTACAACAATTATCTAACTGAAATTAACAAAAAGTAATTTATTAATAGTAATTTAAAATTT
AACTAGACTTAATAAATTAAATAACTAAAATGAATAAGCTATAAAAAAAAGAATTAATATTTTAT
TTGTATAATTTTATTTCGTAAATTGAATTACCATTATTTAAGTCACACACATATAGCGGTGGAGC
CTATAAATTTTTTTAGGGACGAAATTAAATTATATATCTTTACGACAGTAAAAATATAATTTATT
ATTTTAATAGCCTATATCTATATAATTTTAAAATAGTTAAATTAAATTTTATTATTTTTAAAAGA
TCAAAATACAATTTTACCATTACTAATCTAAAATTTTATAAATTATAAAAAATTTAAATTTAAAA
TTTACTATTTTAAGTGACAGCATAGCACCTGGGTGGAAAGTTAAGTGCCTAACTCTAAGCATAAA
ATGAAATTAAGATGTAAGGTAAAATTAAAAAGGGTAGGTTTCGTATTTATTACGAGGACAGAAGA
TAGCGGTGGTAGATATATCATCTCATAAAAGCAGTGTCGTTTAACTTACAAAATATTATTTAT
Found at i:2903908 original size:374 final size:373
Alignment explanation
Indices: 2903217--2903966 Score: 1430
Period size: 374 Copynumber: 2.0 Consensus size: 373
2903207 CATAGCACCT
2903217 GGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAAATGAAATTAAGATGTAATGTAAAATTAAAA
1 GGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAAATGAAATTAAGATGTAATGTAAAATTAAAA
2903282 ATGGTAGGTTTCGTATTTATTACGAGGACCAGGAGATAGCGGTGGTAGATATATCATCTCATAAA
66 ATGGTAGGTTTCGTATTTATTACGAGGACCAGGAGATAGCGGTGGTAGATATATCATCTCATAAA
2903347 AGCAGTGTCGTTTAACTTACAAAATATTATTTATTTACGTACGCCAATTATCTAACTGAAATTAA
131 AGCAGTGTCGTTTAACTTACAAAATATTATTTATTTACGTACGCCAATTATCTAACTGAAATTAA
2903412 CAAAAAGTAATTTATTAATAGTATTTTAAAATTTAACTAGACTTAATAAATTAAATAACTGAAAT
196 CAAAAAGTAATTTATTAATAGTATTTTAAAATTTAACTAGACTTAATAAATTAAATAACTGAAAT
*
2903477 GAATAAGCTATAAAAAAAGAATTAATATTTTATTTTTATAATTTTATTTCATAAATTGAATTACT
261 GAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCATAAATTGAATTACT
* *
2903542 ATTATTTAAGTCTCACACATATAGTGGTGGAGACTAT-AATCTTTTTTAG
326 ATTATTTAAGTCACACACATATAGCGGTGGAGACTATAAAT-TTTTTT-G
2903591 GGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAAATGAAATTAAGATGTAATGTAAAATTAAAA
1 GGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAAATGAAATTAAGATGTAATGTAAAATTAAAA
2903656 ATGGTAGGTTTCGTATTTATTACGAGGACCAGGAGATAGCGGTGGTAGATATATCATCTCATAAA
66 ATGGTAGGTTTCGTATTTATTACGAGGACCAGGAGATAGCGGTGGTAGATATATCATCTCATAAA
2903721 AGCAGTGTCGTTTAACTTACAAAATATTATTTATTTACGTACGCCAATTATCTAACTGAAATTAA
131 AGCAGTGTCGTTTAACTTACAAAATATTATTTATTTACGTACGCCAATTATCTAACTGAAATTAA
2903786 CAAAAAGTAATTTATTAATAGTATTTTAAAATTTAACTAGACTTAATAAATTAAATAACTGAAAT
196 CAAAAAGTAATTTATTAATAGTATTTTAAAATTTAACTAGACTTAATAAATTAAATAACTGAAAT
*
2903851 GAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCGTAAATTGAATTACT
261 GAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCATAAATTGAATTACT
*
2903916 ATTATTTAAGTCACACACATATAGCGGTGGAGCCTATAAATTTTTTTG
326 ATTATTTAAGTCACACACATATAGCGGTGGAGACTATAAATTTTTTTG
2903964 GGG
1 GGG
2903967 ACGAAATTAA
Statistics
Matches: 370, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
373 4 0.01
374 363 0.98
375 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (373 bp):
GGGTGGAAAGTTAAGTGTCTAACTCTAAGCATTAAATGAAATTAAGATGTAATGTAAAATTAAAA
ATGGTAGGTTTCGTATTTATTACGAGGACCAGGAGATAGCGGTGGTAGATATATCATCTCATAAA
AGCAGTGTCGTTTAACTTACAAAATATTATTTATTTACGTACGCCAATTATCTAACTGAAATTAA
CAAAAAGTAATTTATTAATAGTATTTTAAAATTTAACTAGACTTAATAAATTAAATAACTGAAAT
GAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCATAAATTGAATTACT
ATTATTTAAGTCACACACATATAGCGGTGGAGACTATAAATTTTTTTG
Found at i:2905555 original size:33 final size:34
Alignment explanation
Indices: 2905488--2905555 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2905478 AATAAAATTT
* *
2905488 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
2905522 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
2905555 A
1 A
2905556 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:2906393 original size:191 final size:191
Alignment explanation
Indices: 2906137--2906520 Score: 678
Period size: 191 Copynumber: 2.0 Consensus size: 191
2906127 TAAATAACTG
*
2906137 AAATGAATAAGCTATAAAAAAAGAATTAATATTTTATTTTTATAATTTTATTTCGTAAATTGAAT
1 AAATGAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCGTAAATTGAAT
* * *
2906202 TACTATTATTTAAGTCTCACACATATAGTGGTGGAGCCTATAAATTTTTTTAGTGACAAAATTAA
66 TACTATTATTTAAGTCACACACATATAGCGGTGGAGCCTATAAATTTTTTTAGGGACAAAATTAA
*
2906267 ATTATATATATTTATGATAGTAAAAATATAATTTTATTATTTTAATAGCCTATATCTATAT
131 ATTATATATATTTATGACAGTAAAAATATAATTTTATTATTTTAATAGCCTATATCTATAT
2906328 AAATGAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCGTAAATTGAAT
1 AAATGAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCGTAAATTGAAT
* *
2906393 TACTATTATTTAAGTCACACACATATAGCGGTGGAGCCTATAAATTTTTTTGGGGACGAAATTAA
66 TACTATTATTTAAGTCACACACATATAGCGGTGGAGCCTATAAATTTTTTTAGGGACAAAATTAA
* * *
2906458 ATTATATATCTTTATGACAGTAAAGATATAATTTTATTATTTTAATAGCTTATATCTATAT
131 ATTATATATATTTATGACAGTAAAAATATAATTTTATTATTTTAATAGCCTATATCTATAT
2906519 AA
1 AA
2906521 TTTTAAAATA
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
191 183 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (191 bp):
AAATGAATAAGCTATAAAAAAAGAATTAATATTTTATTTGTATAATTTTATTTCGTAAATTGAAT
TACTATTATTTAAGTCACACACATATAGCGGTGGAGCCTATAAATTTTTTTAGGGACAAAATTAA
ATTATATATATTTATGACAGTAAAAATATAATTTTATTATTTTAATAGCCTATATCTATAT
Found at i:2907651 original size:454 final size:454
Alignment explanation
Indices: 2906804--2907711 Score: 1672
Period size: 454 Copynumber: 2.0 Consensus size: 454
2906794 CGTTTAACTT
2906804 TCAAAATATTATTTATTTTGATTTATTAATTTTTGCAGTTTTATTTTATTTCTCACAGAAAGGAG
1 TCAAAATATTATTTATTTTGATTTATTAATTTTTGCAGTTTTATTTTATTTCTCACAGAAAGGAG
2906869 TATAACAAATTTAATAATGTGAAGGTTTTTTTTTTTAAACATGTACATTAAATTCTATTACATAA
66 TATAACAAATTTAATAATGTGAAGGTTTTTTTTTTTAAACATGTACATTAAATTCTATTACATAA
* *
2906934 GTGATAAATTCCTCTCTAAGATCTCGTAATAACGCCCTGATGAATATAATAAGAGTTGCAAACCT
131 GTGATAAATTCCTCTCTAAGATCTCGAAATAACGCCCTGATGAATATAATAAGAGTTGCAAACCC
* * *
2906999 TTCCCCAACCCTTTGGGCTTCTCATAAATTACATTTAAATTTCCCCTCTCTTTGCTAATATATTC
196 TTCCCCAACCCTTTGGGCTTCTCATAAATTACAATTAAACTTCCCCTCTCTCTGCTAATATATTC
*
2907064 TATTCTTTTTGTTTATTATGTATAAATCGATGTCAACTTGTGTTGGTTGCTTGTTGAGAATGTGT
261 TATTCTTTTTGTTTATTATATATAAATCGATGTCAACTTGTGTTGGTTGCTTGTTGAGAATGTGT
* *
2907129 TTATTAACTGGTATTTGGCTAAGGGTGAGTTTGGATAGGCGGTGCGTTTACCTGCGGTTGATGTG
326 TTATCAACTGGTATTTGGCTAAGGGTGAGTTTGGATAAGCGGTGCGTTTACCTGCGGTTGATGTG
*
2907194 TGTTTGGATTCGAATGCAGCTATAGTGGTGAGATGAGAATAAAAAATGACCATTATAGACATTA
391 TGTTTGGATTCAAATGCAGCTATAGTGGTGAGATGAGAATAAAAAATGACCATTATAGACATTA
2907258 TCAAAATATTATTTATTTTGATTTATTAATTTTTGCAGTTTTATTTTATTTCTCACAGAAAGGAG
1 TCAAAATATTATTTATTTTGATTTATTAATTTTTGCAGTTTTATTTTATTTCTCACAGAAAGGAG
2907323 TATAACAAATTTAATAATGTGAAGGTTTTTTTTTTTAAACATGTACATTAAATTCTATTACATAA
66 TATAACAAATTTAATAATGTGAAGGTTTTTTTTTTTAAACATGTACATTAAATTCTATTACATAA
*
2907388 GTGATAAATTCCTCTCTAAGATCTCGAAATAATGCCCTGATGAATATAATAAGAGTTGCAAACCC
131 GTGATAAATTCCTCTCTAAGATCTCGAAATAACGCCCTGATGAATATAATAAGAGTTGCAAACCC
* *
2907453 TTCCCCGACCCTTTGGGCTTCTCATAAATTACAATTAAACTTCCCCTCTCTCTGCTTATATATTC
196 TTCCCCAACCCTTTGGGCTTCTCATAAATTACAATTAAACTTCCCCTCTCTCTGCTAATATATTC
2907518 TATTCTTTTTGTTTATTATATATAAATCGATGTCAACTTGTGTTGGTTGCTTGTTGAGAATGTGT
261 TATTCTTTTTGTTTATTATATATAAATCGATGTCAACTTGTGTTGGTTGCTTGTTGAGAATGTGT
* *
2907583 TTGTCAACTGGTATTTGGCTAAGGGTGAGTTTGGATAAGCGGTGCGTTTGCCTGCGGTTGATGTG
326 TTATCAACTGGTATTTGGCTAAGGGTGAGTTTGGATAAGCGGTGCGTTTACCTGCGGTTGATGTG
* *
2907648 TGTTTGGATTCAAATGCAGCTGTAGTGGTGAGATGAGAATAAAAGATGACCATTATAGACATTA
391 TGTTTGGATTCAAATGCAGCTATAGTGGTGAGATGAGAATAAAAAATGACCATTATAGACATTA
2907712 GTTTGCAATG
Statistics
Matches: 438, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
454 438 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (454 bp):
TCAAAATATTATTTATTTTGATTTATTAATTTTTGCAGTTTTATTTTATTTCTCACAGAAAGGAG
TATAACAAATTTAATAATGTGAAGGTTTTTTTTTTTAAACATGTACATTAAATTCTATTACATAA
GTGATAAATTCCTCTCTAAGATCTCGAAATAACGCCCTGATGAATATAATAAGAGTTGCAAACCC
TTCCCCAACCCTTTGGGCTTCTCATAAATTACAATTAAACTTCCCCTCTCTCTGCTAATATATTC
TATTCTTTTTGTTTATTATATATAAATCGATGTCAACTTGTGTTGGTTGCTTGTTGAGAATGTGT
TTATCAACTGGTATTTGGCTAAGGGTGAGTTTGGATAAGCGGTGCGTTTACCTGCGGTTGATGTG
TGTTTGGATTCAAATGCAGCTATAGTGGTGAGATGAGAATAAAAAATGACCATTATAGACATTA
Found at i:2907879 original size:34 final size:33
Alignment explanation
Indices: 2907840--2907903 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
2907830 AATAAAATTT
* *
2907840 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTAT-TTAATAATAAATAATA
* *
2907874 AAATATATTTAAATTATTTTATATTAAATA
1 AAATATATTTAAATTATTTAATAATAAATA
2907904 GTAATTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.42
34 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATATATTTAAATTATTTAATAATAAATAATA
Found at i:2910763 original size:34 final size:33
Alignment explanation
Indices: 2910724--2910787 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
2910714 AATAAAATTT
* *
2910724 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTAT-TTAATAATAAATAATA
* *
2910758 AAATATATTTAAATTATTTTATATTAAATA
1 AAATATATTTAAATTATTTAATAATAAATA
2910788 GTAATTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.42
34 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATATATTTAAATTATTTAATAATAAATAATA
Found at i:2912808 original size:30 final size:30
Alignment explanation
Indices: 2912752--2912809 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2912742 TATATCTATA
* * *
2912752 TATTTTTAAAATAGTTAAATTAAATTTTAT
1 TATTTTTAAAAGAGTCAAAATAAATTTTAT
2912782 TATTTTTAAAAGA-TCAAAATACAATTTT
1 TATTTTTAAAAGAGTCAAAATA-AATTTT
2912810 TCTATTACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (30 bp):
TATTTTTAAAAGAGTCAAAATAAATTTTAT
Found at i:2913649 original size:139 final size:140
Alignment explanation
Indices: 2913484--2913763 Score: 526
Period size: 139 Copynumber: 2.0 Consensus size: 140
2913474 CCCACGTCCA
2913484 TACCCTCCTCTTTTTTTCTTTCTTTTTTTTAAAGAACAGATCCCAACCTTTTAAATACTATTTAA
1 TACCCTCCTC-TTTTTTCTTTCTTTTTTTTAAAGAACAGATCCCAACCTTTTAAATACTATTTAA
*
2913549 ATTATGTAGGTCATGTGTATGAAAATATTTATATAACAAAATAAGAATTTATTTAATTTTAAAAA
65 ATTATGTAGGTCATGTGTATGAAAATATATATATAACAAAATAAGAATTTATTTAATTTTAAAAA
2913614 TTTAAAATAAT
130 TTTAAAATAAT
2913625 TACCCTCCTC-TTTTTCTTTCTTTTTTTTAAAGAACAGATCCCAACCTTTTAAATACTATTTAAA
1 TACCCTCCTCTTTTTTCTTTCTTTTTTTTAAAGAACAGATCCCAACCTTTTAAATACTATTTAAA
*
2913689 TTATGTAGGTCATGTGTATGAAAATATATATATATCAAAATAAGAATTTATTTAATTTTAAAAAT
66 TTATGTAGGTCATGTGTATGAAAATATATATATAACAAAATAAGAATTTATTTAATTTTAAAAAT
2913754 TTAAAATAAT
131 TTAAAATAAT
2913764 AATGAACATG
Statistics
Matches: 137, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
139 127 0.93
141 10 0.07
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (140 bp):
TACCCTCCTCTTTTTTCTTTCTTTTTTTTAAAGAACAGATCCCAACCTTTTAAATACTATTTAAA
TTATGTAGGTCATGTGTATGAAAATATATATATAACAAAATAAGAATTTATTTAATTTTAAAAAT
TTAAAATAAT
Found at i:2919368 original size:27 final size:27
Alignment explanation
Indices: 2919337--2919393 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2919327 CATATATTGT
2919337 TGGCATTAGCGGTAAGAATATTCAAAC
1 TGGCATTAGCGGTAAGAATATTCAAAC
*
2919364 TGGCATTATCGGTAAGAATATTCAAAC
1 TGGCATTAGCGGTAAGAATATTCAAAC
2919391 TGG
1 TGG
2919394 AATATATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (27 bp):
TGGCATTAGCGGTAAGAATATTCAAAC
Found at i:2922893 original size:2 final size:2
Alignment explanation
Indices: 2922888--2922914 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2922878 TGTAAAATGC
2922888 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2922915 AAATAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2930786 original size:27 final size:27
Alignment explanation
Indices: 2930755--2930811 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2930745 CATATATTGT
2930755 TGGCATTAGCGGTAAGAATATTCAAAC
1 TGGCATTAGCGGTAAGAATATTCAAAC
*
2930782 TGGCATTATCGGTAAGAATATTCAAAC
1 TGGCATTAGCGGTAAGAATATTCAAAC
2930809 TGG
1 TGG
2930812 AATATATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (27 bp):
TGGCATTAGCGGTAAGAATATTCAAAC
Found at i:2934541 original size:2 final size:2
Alignment explanation
Indices: 2934534--2934560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2934524 NNNNAAATGC
2934534 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2934561 AAATAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2938750 original size:26 final size:26
Alignment explanation
Indices: 2938720--2938771 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2938710 GCTTAGTAAG
* *
2938720 TTCGTATAATGGGAAGTTAACTTACT
1 TTCGTATAACGGGAAATTAACTTACT
2938746 TTCGTATAACGGGAAATTAACTTACT
1 TTCGTATAACGGGAAATTAACTTACT
2938772 ATTCATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (26 bp):
TTCGTATAACGGGAAATTAACTTACT
Found at i:2939202 original size:25 final size:25
Alignment explanation
Indices: 2939129--2939202 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
2939119 CTAATGCAAA
* *
2939129 CATGTAAGCGAGAAGCTCTTTCGAGC
1 CATGTAA-CGGGAAGCTCATTCGAGC
*
2939155 CA--TAACGGGAAGCTTATGT-GAGC
1 CATGTAACGGGAAGCTCAT-TCGAGC
2939178 CATGTAACGGGAAGCTCATTCGAGC
1 CATGTAACGGGAAGCTCATTCGAGC
2939203 TGTATAACGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 15 0.38
24 5 0.12
25 18 0.45
26 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (25 bp):
CATGTAACGGGAAGCTCATTCGAGC
Found at i:2939210 original size:25 final size:23
Alignment explanation
Indices: 2939140--2939215 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
2939130 ATGTAAGCGA
* *
2939140 GAAGCTCTTTCGAGCCATAACGG
1 GAAGCTCATTCGAGCTATAACGG
* *
2939163 GAAGCTTATGT-GAGCCATGTAACGG
1 GAAGCTCAT-TCGAG-C-TATAACGG
2939188 GAAGCTCATTCGAGCTGTATAACGG
1 GAAGCTCATTCGAGC--TATAACGG
2939213 GAA
1 GAA
2939216 TTTCAAGCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
23 10 0.24
24 4 0.10
25 27 0.66
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (23 bp):
GAAGCTCATTCGAGCTATAACGG
Found at i:2939284 original size:27 final size:25
Alignment explanation
Indices: 2939249--2939306 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
2939239 AGTTTTGGAA
*
2939249 AGCCATTAATCAATAAGCTCATGAAAG
1 AGCCATTAATCAAGAAGCTC-T-AAAG
* *
2939276 AGCCTTTAATCAGGAAGCTCTAAAG
1 AGCCATTAATCAAGAAGCTCTAAAG
2939301 AGCCAT
1 AGCCAT
2939307 ATATTGGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 1 0.04
27 17 0.63
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (25 bp):
AGCCATTAATCAAGAAGCTCTAAAG
Found at i:2954179 original size:121 final size:121
Alignment explanation
Indices: 2953965--2954206 Score: 475
Period size: 121 Copynumber: 2.0 Consensus size: 121
2953955 AAAAAACTAA
2953965 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
1 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
*
2954030 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTTATGGATATTTT
66 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
2954086 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
1 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
2954151 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
66 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
2954207 ATTACAAGAA
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (121 bp):
TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
Found at i:2956121 original size:33 final size:35
Alignment explanation
Indices: 2956084--2956180 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
2956074 ATGGTTATAT
2956084 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
2956117 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
2956152 --AAATATTTAAAATTTATAATTCATATATT
1 TTAAATATTTAAAA--TATAATTTATATATT
2956181 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 7 0.14
35 9 0.18
37 6 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:2956380 original size:13 final size:13
Alignment explanation
Indices: 2956361--2956422 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
2956351 TAAACTAAAA
2956361 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
2956374 TTCTCAAAATCAC
1 TTTTCAAAAGCAC
* *
2956387 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
**
2956400 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
2956413 TTTTCAAAAG
1 TTTTCAAAAG
2956423 TAATGAAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:2957158 original size:21 final size:21
Alignment explanation
Indices: 2957129--2957176 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2957119 ATATTGGCAT
*
2957129 ATGATATTGAAAATATCCAGG
1 ATGACATTGAAAATATCCAGG
2957150 ATGACATTGAAAATATCCAGG
1 ATGACATTGAAAATATCCAGG
2957171 ATGACA
1 ATGACA
2957177 GAGATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (21 bp):
ATGACATTGAAAATATCCAGG
Found at i:2957508 original size:18 final size:18
Alignment explanation
Indices: 2957473--2957510 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2957463 GAGTTGATCC
*
2957473 AAATAACTCGATTAATTT
1 AAATAACTCGACTAATTT
2957491 AAATAACTCGAACT-ATTT
1 AAATAACTCG-ACTAATTT
2957509 AA
1 AA
2957511 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (18 bp):
AAATAACTCGACTAATTT
Found at i:2960173 original size:3 final size:3
Alignment explanation
Indices: 2960165--2960197 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2960155 AAGCATAATT
2960165 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2960198 GCTTACAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2966779 original size:15 final size:15
Alignment explanation
Indices: 2966759--2966787 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2966749 AAATAAGTCC
2966759 AATTTATTAAAAAGA
1 AATTTATTAAAAAGA
2966774 AATTTATTAAAAAG
1 AATTTATTAAAAAG
2966788 TTAGAAGCTT
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:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTATTAAAAAGA
Found at i:2984565 original size:199 final size:197
Alignment explanation
Indices: 2984233--2984610 Score: 446
Period size: 199 Copynumber: 1.9 Consensus size: 197
2984223 AGACATTAAG
* *
2984233 AAAAGTCGATGTACCAAATTATGTAAAAAATTAAAGTATAGAGATTAAATTTCAAAGATAAGCAT
1 AAAAGTCGAGGAACCAAATTATGTAAAAAATTAAAGTATAGAGATTAAATTTCAAAGATAAGCAT
* ** * * * *
2984298 AGTATAGGAACCAAAATTGGAATTTGACCATTTTTATGTAATCTTAAAAAAGAAGTAAAAAGTTG
66 AATATAGGAACCAAAATTAAAATTTGACCATTTTGATATAATCTAAAAAAAAAAGTAAAAAGTTG
*** *
2984363 TGTATTT-AGACACT-TGTATGTCAACATTTTAAAT-AGAATGAAGTATTTAGATTGATTATGAT
131 TGTATTTGA-ACA-TGTGTACACCAACATTTT-AATCAGAATGAAATATTTAGATTGATTATGAT
2984425 ATTAT
193 ATTAT
* * * * **
2984430 AAAAGTCGAGGAATCAAATTATGTCAAAAATTAAAGTATAGTGATTAAAGTTT-ATATTTAAGCG
1 AAAAGTCGAGGAACCAAATTATGTAAAAAATTAAAGTATAGAGATTAAA-TTTCAAAGATAA--G
*
2984494 CATAATATAAGG-ATCAAAATTAAAATTTGACCATTGTTGA-ATAATCTAAAAAAAAAAGT-AAA
63 CATAATAT-AGGAACCAAAATTAAAATTTGACCATT-TTGATATAATCTAAAAAAAAAAGTAAAA
2984556 AGATTGTGTATTTGAACATGTGTACACCAACATTTTAATCAGAATGAAATATTTA
126 AG-TTGTGTATTTGAACATGTGTACACCAACATTTTAATCAGAATGAAATATTTA
2984611 ATGTAATGCC
Statistics
Matches: 152, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
197 49 0.32
198 12 0.08
199 84 0.55
200 7 0.05
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.33
Consensus pattern (197 bp):
AAAAGTCGAGGAACCAAATTATGTAAAAAATTAAAGTATAGAGATTAAATTTCAAAGATAAGCAT
AATATAGGAACCAAAATTAAAATTTGACCATTTTGATATAATCTAAAAAAAAAAGTAAAAAGTTG
TGTATTTGAACATGTGTACACCAACATTTTAATCAGAATGAAATATTTAGATTGATTATGATATT
AT
Found at i:2989643 original size:23 final size:22
Alignment explanation
Indices: 2989608--2989681 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
2989598 ATATTTTCAG
2989608 TGTTCATGCTAGAGAATATTTAC
1 TGTTCATGCTAGAGAAT-TTTAC
* *
2989631 TGTTGATGTTAGAGAATTTTAC
1 TGTTCATGCTAGAGAATTTTAC
* * *
2989653 TGTTCATGCCAAAGAATTTTAT
1 TGTTCATGCTAGAGAATTTTAC
2989675 TGTTCAT
1 TGTTCAT
2989682 TCGTCTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 29 0.66
23 15 0.34
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (22 bp):
TGTTCATGCTAGAGAATTTTAC
Found at i:2993188 original size:24 final size:22
Alignment explanation
Indices: 2993152--2993219 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 22
2993142 ATCTGCACCG
*
2993152 TTGAGTGTTTTATCCATACCAT
1 TTGAGTGTTTTATCCACACCAT
**
2993174 TTGAGTAGCTTTTATCTGCACCAT
1 TTGAGT-G-TTTTATCCACACCAT
* *
2993198 TTGAGTGGTTTAACCACACCAT
1 TTGAGTGTTTTATCCACACCAT
2993220 ACTAGCTACT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.46
23 2 0.05
24 18 0.49
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (22 bp):
TTGAGTGTTTTATCCACACCAT
Found at i:2993219 original size:46 final size:43
Alignment explanation
Indices: 2993131--2993219 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 43
2993121 ACGGAGGAAG
* * *
2993131 TTGAGTAGTTTATCTGCACCGTTGAGTGTTTTATCCATACCAT
1 TTGAGTAGTTTATCTGCACCGTTGAGTGGTTTAACCACACCAT
*
2993174 TTGAGTAGCTTTTATCTGCACCATTTGAGTGGTTTAACCACACCAT
1 TTGAGTAG--TTTATCTGCACC-GTTGAGTGGTTTAACCACACCAT
2993220 ACTAGCTACT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 8 0.21
45 12 0.31
46 19 0.49
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (43 bp):
TTGAGTAGTTTATCTGCACCGTTGAGTGGTTTAACCACACCAT
Found at i:3000228 original size:26 final size:26
Alignment explanation
Indices: 3000199--3000250 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3000189 TTCAGTCATT
3000199 TCAGTCAATTAGGGGTCTAGGTAAAC
1 TCAGTCAATTAGGGGTCTAGGTAAAC
3000225 TCAGTCAATTAGGGGTCTAGGTAAAC
1 TCAGTCAATTAGGGGTCTAGGTAAAC
3000251 CTACCGACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (26 bp):
TCAGTCAATTAGGGGTCTAGGTAAAC
Found at i:3010073 original size:24 final size:22
Alignment explanation
Indices: 3010036--3010103 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 22
3010026 ATCTGTACTA
3010036 TTGAGTGGTTTATCCACACTGT
1 TTGAGTGGTTTATCCACACTGT
* ** *
3010058 TTGAGTAGCTTTTATCTTCATTGT
1 TTGAGT-G-GTTTATCCACACTGT
*
3010082 TTGAGTGGTTTAACCACACTGT
1 TTGAGTGGTTTATCCACACTGT
3010104 ACTGGCAGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 16 0.46
23 2 0.06
24 17 0.49
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (22 bp):
TTGAGTGGTTTATCCACACTGT
Found at i:3010240 original size:18 final size:19
Alignment explanation
Indices: 3010217--3010270 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
3010207 TTTATTACTG
*
3010217 GTGGTTTATCCGCAAC-GA
1 GTGGTTTATCCACAACAGA
*
3010235 GTGGTTCATCCACAACGATGA
1 GTGGTTTATCCACAAC-A-GA
3010256 GTGGTTTATCCACAA
1 GTGGTTTATCCACAA
3010271 TGTCGTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 14 0.47
21 16 0.53
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (19 bp):
GTGGTTTATCCACAACAGA
Found at i:3014031 original size:14 final size:14
Alignment explanation
Indices: 3014012--3014051 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3014002 TTGATTGCCA
3014012 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3014026 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3014040 GAAAAATGTTTT
1 GTAAAATGTTTT
3014052 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3014064 original size:34 final size:35
Alignment explanation
Indices: 3014020--3014086 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
3014010 CAGTAAAATG
* *
3014020 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
* *
3014054 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
3014087 CTGATGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:3014072 original size:20 final size:20
Alignment explanation
Indices: 3014035--3014074 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3014025 CGTAAAATGA
**
3014035 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATAATTTACT
*
3014055 TTTCTGTAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
3014075 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:3017234 original size:28 final size:27
Alignment explanation
Indices: 3017199--3017257 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 27
3017189 AAAAATATTT
3017199 CATAAAAGTTGTTTTCAATGAAACAAA
1 CATAAAAGTTGTTTTCAATGAAACAAA
3017226 CATATAAAGTTGTTTTCAATGAAACAAA
1 CATA-AAAGTTGTTTTCAATGAAACAAA
3017254 CATA
1 CATA
3017258 CATTTGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (27 bp):
CATAAAAGTTGTTTTCAATGAAACAAA
Found at i:3021147 original size:24 final size:24
Alignment explanation
Indices: 3021111--3021167 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
3021101 AATACTCTTA
3021111 AAAACCCAA-ACTCATTAATATTT
1 AAAACCCAATACTCATTAATATTT
3021134 AAAACCCAATACTCATTAATATTT
1 AAAACCCAATACTCATTAATATTT
3021158 AAAACCCAAT
1 AAAACCCAAT
3021168 TTGATAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAACCCAATACTCATTAATATTT
Found at i:3021453 original size:77 final size:78
Alignment explanation
Indices: 3021364--3021515 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 78
3021354 AATATTTTTA
3021364 TAATGAATTTAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATA
1 TAATGAATTTAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATA
3021429 ATTATTTGAATTT
66 ATTATTTGAATTT
3021442 TAATGAA-TTAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATA
1 TAATGAATTTAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATA
3021506 ATTATTTGAA
66 ATTATTTGAA
3021516 AAAGATAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.91
78 7 0.09
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (78 bp):
TAATGAATTTAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATA
ATTATTTGAATTT
Found at i:3021531 original size:77 final size:76
Alignment explanation
Indices: 3021373--3021539 Score: 264
Period size: 77 Copynumber: 2.2 Consensus size: 76
3021363 ATAATGAATT
3021373 TAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATAATTATTTGA
1 TAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATAATTATTTGA
** * *
3021438 ATTTTAATGAAT
66 A-TAAAATAAAA
3021450 TAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATAATTATTTGA
1 TAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATAATTATTTGA
3021515 A-AAAGATAAAAA
66 ATAAA-AT-AAAA
3021527 TAAAATAAAATTA
1 TAAAATAAAATTA
3021540 TAAGTACTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
75 1 0.01
76 2 0.02
77 81 0.96
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (76 bp):
TAAAATAAAATTAAAATTAAAAGCAATAAGAAATACTAAATTGAAGAAAAAAGATAATTATTTGA
ATAAAATAAAA
Found at i:3035333 original size:25 final size:24
Alignment explanation
Indices: 3035294--3035375 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 24
3035284 TCATGTACAA
3035294 GTATGCTCAT-ACGAGCTATGAATCG
1 GTATGCT-ATCACGAGCTAT-AATCG
* * *
3035319 GTATGCTTTCTCGAGCTATAGATTG
1 GTATGCTATCACGAGCTATA-ATCG
*
3035344 GTATGCTATCACGAGCTATAAATCA
1 GTATGCTATCACGAGCTAT-AATCG
3035369 GTATGCT
1 GTATGCT
3035376 CACACAAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 2 0.04
25 44 0.94
26 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
GTATGCTATCACGAGCTATAATCG
Found at i:3048257 original size:19 final size:20
Alignment explanation
Indices: 3048217--3048253 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3048207 AATATATTTT
3048217 TTTGTATATGGTGAATTATA
1 TTTGTATATGGTGAATTATA
3048237 TTTG-ATAT-GTGAATTAT
1 TTTGTATATGGTGAATTAT
3048254 TATTATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTGTATATGGTGAATTATA
Found at i:3048512 original size:23 final size:23
Alignment explanation
Indices: 3048486--3048630 Score: 155
Period size: 23 Copynumber: 6.3 Consensus size: 23
3048476 AGTGTTATTG
*
3048486 ATCAGTGGTAGCTACGGCTATAT
1 ATCAGTGGTAGCTACGGCTACAT
** *
3048509 ATCAGTGGTAGCTTTGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
3048532 TTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * *
3048555 ATTAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
3048578 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
* * **
3048601 ATCAATGGTAGCTTCAACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
3048624 ATCAGTG
1 ATCAGTG
3048631 TGGCACTTAT
Statistics
Matches: 98, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 98 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:3048562 original size:46 final size:46
Alignment explanation
Indices: 3048487--3048630 Score: 191
Period size: 46 Copynumber: 3.1 Consensus size: 46
3048477 GTGTTATTGA
*
3048487 TCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTTGACTACATT
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTTGACTACATT
* * *
3048533 TCAGTGGTAGCTACGACTACATATTAGTGGTAG-TTTCGGCTACATT
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTT-GACTACATT
* * ** *
3048579 TCAGTGGTAGCTACGGCTACGTATCAATGGTAGCTTCAACTACATA
1 TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTTGACTACATT
3048625 TCAGTG
1 TCAGTG
3048631 TGGCACTTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 3 0.04
46 79 0.94
47 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (46 bp):
TCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTTGACTACATT
Found at i:3048610 original size:69 final size:69
Alignment explanation
Indices: 3048486--3048630 Score: 173
Period size: 69 Copynumber: 2.1 Consensus size: 69
3048476 AGTGTTATTG
* ** * * *
3048486 ATCAGTGGTAGCTACGGCTATATATCAGTGGTAGCTTTGACTACATTTCAGTGGTAGCTACGACT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGACTACATATCAATGGTAGCTACAACT
3048551 ACAT
66 ACAT
* * * * * * *
3048555 ATTAGTGGTAGTTTCGGCTACATTTCAGTGGTAGCTACGGCTACGTATCAATGGTAGCTTCAACT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGACTACATATCAATGGTAGCTACAACT
3048620 ACAT
66 ACAT
3048624 ATCAGTG
1 ATCAGTG
3048631 TGGCACTTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (69 bp):
ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTACGACTACATATCAATGGTAGCTACAACT
ACAT
Found at i:3058051 original size:26 final size:26
Alignment explanation
Indices: 3058021--3058074 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3058011 AATCGAAGGG
3058021 GTATGCAATATCAGGTTGGTGACTCA
1 GTATGCAATATCAGGTTGGTGACTCA
3058047 GTATGCAATATCAGGTTGGTGACTCA
1 GTATGCAATATCAGGTTGGTGACTCA
3058073 GT
1 GT
3058075 CCTTTCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (26 bp):
GTATGCAATATCAGGTTGGTGACTCA
Found at i:3065790 original size:45 final size:43
Alignment explanation
Indices: 3065722--3065851 Score: 143
Period size: 45 Copynumber: 2.9 Consensus size: 43
3065712 GTTGTGTGCT
*
3065722 TAAAATGAGTAAGATTATAGCTGAAAGATGCTATGGCATCATGA
1 TAAAATGAGTAAGA-CATAGCTGAAAGATGCTATGGCATCATGA
* *** *
3065766 TATAAATGAGTAAGACCATGGCTGAAAGACATTATGGCATCATGG
1 TA-AAATGAGTAAGA-CATAGCTGAAAGATGCTATGGCATCATGA
* *
3065811 TAAACATGACTAAGACAGTAGTTGAAAGATGCTATGGCATC
1 TAAA-ATGAGTAAGACA-TAGCTGAAAGATGCTATGGCATC
3065852 CTAGTAGTCT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
44 6 0.09
45 64 0.91
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (43 bp):
TAAAATGAGTAAGACATAGCTGAAAGATGCTATGGCATCATGA
Found at i:3075349 original size:29 final size:29
Alignment explanation
Indices: 3075245--3075438 Score: 126
Period size: 28 Copynumber: 6.8 Consensus size: 29
3075235 TAGGTGTCCA
* *
3075245 TTTAACTGAGATAGCCATAAAGGCATCCT
1 TTTAACAGAGATAGCCACAAAGGCATCCT
* * * **
3075274 TTCTAAAATAGTTAGCCACAAAGGTTTCC-
1 TT-TAACAGAGATAGCCACAAAGGCATCCT
* * *
3075303 TTTAACAGAAATAACCACAAATGCATCCT
1 TTTAACAGAGATAGCCACAAAGGCATCCT
* **
3075332 TTTTACAGAGATAGCCACAAAGGTTTCC-
1 TTTAACAGAGATAGCCACAAAGGCATCCT
* * * * *
3075360 TTTAACATAAATAACCACAAAGGCTTTCT
1 TTTAACAGAGATAGCCACAAAGGCATCCT
* * * **
3075389 TATAACATAGATTGCCGTAAAGG-ATTCC-
1 TTTAACAGAGATAGCCACAAAGGCA-TCCT
*
3075417 TTTAACAGAAATAGCCACAAAG
1 TTTAACAGAGATAGCCACAAAG
3075439 ACTTACTTAT
Statistics
Matches: 120, Mismatches: 41, Indels: 9
0.71 0.24 0.05
Matches are distributed among these distances:
28 56 0.47
29 45 0.38
30 19 0.16
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (29 bp):
TTTAACAGAGATAGCCACAAAGGCATCCT
Found at i:3075357 original size:57 final size:57
Alignment explanation
Indices: 3075236--3075438 Score: 199
Period size: 57 Copynumber: 3.5 Consensus size: 57
3075226 ACCACTATGT
* * * * * * * * *
3075236 AGGTGTCCATTTAACTGAGATAGCCATAAAGGCATCCTTTCTAAAATAGTTAGCCACAA
1 AGGTTTCC-TTTAACAGAAATAACCACAAAGGCATCC-TTATAACAGAGATAGCCACAA
* * *
3075295 AGGTTTCCTTTAACAGAAATAACCACAAATGCATCCTTTTTACAGAGATAGCCACAA
1 AGGTTTCCTTTAACAGAAATAACCACAAAGGCATCCTTATAACAGAGATAGCCACAA
* * * * * **
3075352 AGGTTTCCTTTAACATAAATAACCACAAAGGCTTTCTTATAACATAGATTGCCGTAA
1 AGGTTTCCTTTAACAGAAATAACCACAAAGGCATCCTTATAACAGAGATAGCCACAA
* *
3075409 AGGATTCCTTTAACAGAAATAGCCACAAAG
1 AGGTTTCCTTTAACAGAAATAACCACAAAG
3075439 ACTTACTTAT
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
57 90 0.75
58 23 0.19
59 7 0.06
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (57 bp):
AGGTTTCCTTTAACAGAAATAACCACAAAGGCATCCTTATAACAGAGATAGCCACAA
Found at i:3077626 original size:20 final size:20
Alignment explanation
Indices: 3077603--3077642 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3077593 GAATTAACCT
*
3077603 AAATGCAATGAACTGGTTTA
1 AAATGCAATGAAATGGTTTA
*
3077623 AAATGTAATGAAATGGTTTA
1 AAATGCAATGAAATGGTTTA
3077643 GCAGCAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (20 bp):
AAATGCAATGAAATGGTTTA
Found at i:3082511 original size:33 final size:33
Alignment explanation
Indices: 3082469--3082532 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3082459 AAAGGCTTTG
* *
3082469 TGGTGAGTATTGAACGTAAATGAACGCCTTTTT
1 TGGTGAGTATTGAACGTAAAGGAACACCTTTTT
*
3082502 TGGTGAGTATTGAATGTAAAGGAACACCTTT
1 TGGTGAGTATTGAACGTAAAGGAACACCTTT
3082533 ATGGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (33 bp):
TGGTGAGTATTGAACGTAAAGGAACACCTTTTT
Found at i:3082577 original size:61 final size:61
Alignment explanation
Indices: 3082506--3082728 Score: 293
Period size: 61 Copynumber: 3.7 Consensus size: 61
3082496 CTTTTTTGGT
* * * *
3082506 GAGTATTGAATGTAAAGGAACACCTTTATGGAAAAAATCTGGATAGGAAAGCCTTTGAGGC
1 GAGTACTGAATGTAAAGGAACACCTTTGTGGAAAAACTCTGGATAGGAAAGCCTTTGTGGC
* *
3082567 GAGTACTGAATGTAAAGGAACACCTTTGTGGTAAAACTCTGGATAGGAAAGGCTTTGTGGC
1 GAGTACTGAATGTAAAGGAACACCTTTGTGGAAAAACTCTGGATAGGAAAGCCTTTGTGGC
* * * * * * * * *
3082628 GAGTAGTGAATGTAAAGAAACGCCTATGTGGCAAAACTCTAGACATGAAAGCCTTTGTTGC
1 GAGTACTGAATGTAAAGGAACACCTTTGTGGAAAAACTCTGGATAGGAAAGCCTTTGTGGC
* *
3082689 GAGTACTGAATGTAAAGGACCGCCTTTGTGGAAAAACTCT
1 GAGTACTGAATGTAAAGGAACACCTTTGTGGAAAAACTCT
3082729 AGAAGGGTAA
Statistics
Matches: 141, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 141 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.25
Consensus pattern (61 bp):
GAGTACTGAATGTAAAGGAACACCTTTGTGGAAAAACTCTGGATAGGAAAGCCTTTGTGGC
Found at i:3092275 original size:50 final size:50
Alignment explanation
Indices: 3092210--3092305 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
3092200 ACTACGTCCG
* * *
3092210 GGAAGGTTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACC
1 GGAAAGTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC
3092260 GGAAAGTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 GGAAAGTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
3092306 TATCGAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (50 bp):
GGAAAGTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC
Found at i:3097900 original size:11 final size:12
Alignment explanation
Indices: 3097872--3097904 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3097862 GCCCAAACGT
3097872 CGAAATTTTCGAA
1 CGAAATTTTC-AA
3097885 CGAAATTTTC-A
1 CGAAATTTTCAA
3097896 CGAAATTTT
1 CGAAATTTT
3097905 TTCATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:3104166 original size:50 final size:50
Alignment explanation
Indices: 3104109--3104494 Score: 565
Period size: 50 Copynumber: 7.7 Consensus size: 50
3104099 TCATTCGATA
*
3104109 CACGTAGTAGCCTTCACATAGTACTACACACATGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* *
3104159 CACGTAGTAGCCTTCATATAGTAATACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
*
3104209 CACGTAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
*
3104259 CACGTAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
*
3104309 CACGTAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
* * * *
3104359 CACGTAGTAGCCTTCACATAGTATTACACACGTGACCAAAGCTTTACGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACGGTT
** * * * * *** *
3104410 CATATAGTAGCATTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTT
*
3104461 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
3104495 TTCATCGATA
Statistics
Matches: 306, Mismatches: 28, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
50 233 0.76
51 73 0.24
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
Found at i:3108556 original size:29 final size:30
Alignment explanation
Indices: 3108496--3108564 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
3108486 ATAGTTGAAG
3108496 CCATCCATTTTCATGATTCGATGGTCGTCA
1 CCATCCATTTTCATGATTCGATGGTCGTCA
*
3108526 CCATCCGTTTTCATTG-TT-GATGGTCGTCA
1 CCATCCATTTTCA-TGATTCGATGGTCGTCA
*
3108555 CCATCTATTT
1 CCATCCATTT
3108565 CATAATTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 19 0.54
30 14 0.40
31 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (30 bp):
CCATCCATTTTCATGATTCGATGGTCGTCA
Found at i:3108574 original size:29 final size:29
Alignment explanation
Indices: 3108496--3108575 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
3108486 ATAGTTGAAG
* *
3108496 CCATCCATTTTCATGATTCGATGGTCGTCA
1 CCATCCGTTTTCAT-ATTTGATGGTCGTCA
3108526 CCATCCGTTTTCAT-TGTTGATGGTCGTCA
1 CCATCCGTTTTCATAT-TTGATGGTCGTCA
3108555 CCAT-C-TATTTCATAATTTGAT
1 CCATCCGT-TTTCAT-ATTTGAT
3108576 AGACGAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 1 0.02
28 8 0.18
29 21 0.48
30 14 0.32
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (29 bp):
CCATCCGTTTTCATATTTGATGGTCGTCA
Found at i:3108596 original size:30 final size:30
Alignment explanation
Indices: 3108562--3108746 Score: 128
Period size: 30 Copynumber: 6.2 Consensus size: 30
3108552 TCACCATCTA
* **
3108562 TTTCATAATTTGATAGAC-GAAGTTATCCCT
1 TTTCATAATTCGATAG-CTGAAGCCATCCCT
3108592 TTTCATAATTCGATAGCTGAAGCCATCCCT
1 TTTCATAATTCGATAGCTGAAGCCATCCCT
* * * **
3108622 TTTCATAATTCGATGGTTGTCA-TAATCCCT
1 TTTCATAATTCGATAGCTG-AAGCCATCCCT
* ** * *
3108652 TTTCTTTGTT-GATGGTCAT-CA-CCATCCCT
1 TTTCATAATTCGATAG-C-TGAAGCCATCCCT
* * *
3108681 TTTCATAATTTGATAGCTAAAGCTATCCCT
1 TTTCATAATTCGATAGCTGAAGCCATCCCT
* * *
3108711 TTCCATATTTTGATAGCTGAAGCCATCCCT
1 TTTCATAATTCGATAGCTGAAGCCATCCCT
3108741 TTTCAT
1 TTTCAT
3108747 TGGTCGATGA
Statistics
Matches: 123, Mismatches: 25, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.01
29 23 0.19
30 97 0.79
31 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (30 bp):
TTTCATAATTCGATAGCTGAAGCCATCCCT
Found at i:3108655 original size:118 final size:117
Alignment explanation
Indices: 3108441--3108746 Score: 391
Period size: 118 Copynumber: 2.6 Consensus size: 117
3108431 TGTTACCACC
* * * * *
3108441 CCTTTTCATAGTTCGGTAGCCGAAGCTATCCC-TTTCTATATTTTGATAGTTGAAGCCATCCATT
1 CCTTTTCATAATTTGATAG-CGAAGCTATCCCTTTTC-ATATTTTGATAGCTGAAGCCATCCCTT
* * * *
3108505 TTCATGATTCGATGGTCGTCACCATCCGTTTTCATTGTTGATGGTCGTCACCAT
64 TTCATAATTCGATGGTCGTCACAATCCCTTTTCATTGTTGATGGTCATCACCAT
* * *
3108559 -CTATTTCATAATTTGATAGACGAAGTTATCCCTTTTCATAATTCGATAGCTGAAGCCATCCCTT
1 CCT-TTTCATAATTTGATAG-CGAAGCTATCCCTTTTCATATTTTGATAGCTGAAGCCATCCCTT
* * *
3108623 TTCATAATTCGATGGTTGTCATAATCCCTTTTCTTTGTTGATGGTCATCACCAT
64 TTCATAATTCGATGGTCGTCACAATCCCTTTTCATTGTTGATGGTCATCACCAT
* *
3108677 CCCTTTTCATAATTTGATAGCTAAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTT
1 -CCTTTTCATAATTTGATAGC-GAAGCTATCCCTTTTCATATTTTGATAGCTGAAGCCATCCCTT
3108742 TTCAT
64 TTCAT
3108747 TGGTCGATGA
Statistics
Matches: 162, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
117 2 0.01
118 95 0.59
119 63 0.39
120 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (117 bp):
CCTTTTCATAATTTGATAGCGAAGCTATCCCTTTTCATATTTTGATAGCTGAAGCCATCCCTTTT
CATAATTCGATGGTCGTCACAATCCCTTTTCATTGTTGATGGTCATCACCAT
Found at i:3117156 original size:20 final size:20
Alignment explanation
Indices: 3117115--3117157 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3117105 AAATAATGGG
*
3117115 AAAAAACAAGAAAATAGCAA
1 AAAAAACAAGAAAATAGAAA
3117135 AAAAAACAAGAACAATA-AAA
1 AAAAAACAAGAA-AATAGAAA
3117155 AAA
1 AAA
3117158 TACTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.79, C:0.09, G:0.07, T:0.05
Consensus pattern (20 bp):
AAAAAACAAGAAAATAGAAA
Found at i:3119490 original size:21 final size:20
Alignment explanation
Indices: 3119452--3119490 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3119442 GTAAATGATG
*
3119452 TTTTGGCATGATTATAATTA
1 TTTTGGAATGATTATAATTA
*
3119472 TTTTGGAATTGATTGTAAT
1 TTTTGGAA-TGATTATAAT
3119491 ATGGTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTTGGAATGATTATAATTA
Found at i:3125002 original size:15 final size:17
Alignment explanation
Indices: 3124982--3125024 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
3124972 CTTCTTATCC
3124982 AATCATCTTTAT-TC-A
1 AATCATCTTTATCTCGA
*
3124997 AATCATCTATATCTCGA
1 AATCATCTTTATCTCGA
*
3125014 TATCATCTTTA
1 AATCATCTTTA
3125025 ATCTAATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (17 bp):
AATCATCTTTATCTCGA
Found at i:3130562 original size:22 final size:22
Alignment explanation
Indices: 3130478--3130546 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
3130468 TGTATATGAT
* * *
3130478 TCTAATATGTTTTGCATTTGTA
1 TCTATTATGTTCTGCATCTGTA
*
3130500 TATGATT-TGTTCTGCATCTGTA
1 TCT-ATTATGTTCTGCATCTGTA
3130522 TCTATTATGTTCTGCATCTGTA
1 TCTATTATGTTCTGCATCTGTA
3130544 TCT
1 TCT
3130547 GGTCTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.08
22 35 0.88
23 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (22 bp):
TCTATTATGTTCTGCATCTGTA
Found at i:3131944 original size:17 final size:18
Alignment explanation
Indices: 3131919--3131967 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
3131909 AAATATCTTG
*
3131919 ATAATATCATATTTA-AA
1 ATAAAATCATATTTATAA
*
3131936 ATAAAATCATATTTATAT
1 ATAAAATCATATTTATAA
*
3131954 ATAAAATTATATTT
1 ATAAAATCATATTT
3131968 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAATCATATTTATAA
Done.