Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 13 of 198
Found at i:4179825 original size:31 final size:31
Alignment explanation
Indices: 4179790--4179886 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
4179780 AATAAATACC
4179790 AAAAAATTATTTT-AAAAT-TTTAAAAAAATTA
1 AAAAAATTATTTTAAAAATATTT--AAAAATTA
* *
4179821 AAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATTATTTTAAAAATATTTAAAAATTA
** *
4179852 AAAAAA-T-TTAAAAAAAGTATTTTAAAATTA
1 AAAAAATTATTTTAAAAA-TATTTAAAAATTA
4179882 AAAAA
1 AAAAA
4179887 TTTAAAAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.12
30 19 0.32
31 25 0.42
32 5 0.08
33 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAAAATTATTTTAAAAATATTTAAAAATTA
Found at i:4179837 original size:12 final size:11
Alignment explanation
Indices: 4179806--4179848 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4179796 TTATTTTAAA
*
4179806 ATTTTAAAAAA
1 ATTTTAAAAAT
**
4179817 ATTAAAAAAAGT
1 ATTTTAAAAA-T
4179829 ATTTTAAAAAT
1 ATTTTAAAAAT
4179840 ATTTTAAAA
1 ATTTTAAAA
4179849 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:4179868 original size:41 final size:42
Alignment explanation
Indices: 4179791--4179878 Score: 144
Period size: 41 Copynumber: 2.1 Consensus size: 42
4179781 ATAAATACCA
4179791 AAAAATTATTTTAAAATTTTAAAAAAATTAAAAAAAGTATTTT
1 AAAAATTATTTTAAAA-TTTAAAAAAATTAAAAAAAGTATTTT
4179834 AAAAA-TATTTTAAAA-TTAAAAAAATTTAAAAAAAGTATTTT
1 AAAAATTATTTTAAAATTTAAAAAAA-TTAAAAAAAGTATTTT
4179875 AAAA
1 AAAA
4179879 TTAAAAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
40 9 0.20
41 20 0.45
42 10 0.23
43 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (42 bp):
AAAAATTATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTT
Found at i:4179884 original size:29 final size:28
Alignment explanation
Indices: 4179831--4179905 Score: 118
Period size: 27 Copynumber: 2.7 Consensus size: 28
4179821 AAAAAAGTAT
4179831 TTTAAAAA-TATTTTAAAATTAAAAAAA
1 TTTAAAAAGTATTTTAAAATTAAAAAAA
4179858 TTTAAAAAAAGTATTTTAAAATT-AAAAAA
1 TTT--AAAAAGTATTTTAAAATTAAAAAAA
4179887 TTTAAAAAGTATTTTAAAA
1 TTTAAAAAGTATTTTAAAA
4179906 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
27 19 0.42
29 14 0.31
30 12 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTAAAAAGTATTTTAAAATTAAAAAAA
Found at i:4179887 original size:38 final size:38
Alignment explanation
Indices: 4179809--4179933 Score: 139
Period size: 38 Copynumber: 3.2 Consensus size: 38
4179799 TTTTAAAATT
**
4179809 TTAAAAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTT--AAA-ATTAAAAAA
4179849 TTAAAAAAATTTAAAAAAAGTATTTTAAAATTAAAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAATTAAAAAA
* *
4179887 TTTAAAAAGTATTT--TAAAAGTATTTTAAAATTAAAAAA
1 -TTAAAAA-AATTTAAAAAAAGTATTTTAAAATTAAAAAA
*
4179925 ATAAAAAAA
1 TTAAAAAAA
4179934 ATAAATATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
36 1 0.01
37 6 0.08
38 30 0.39
39 10 0.13
40 13 0.17
41 16 0.21
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (38 bp):
TTAAAAAAATTTAAAAAAAGTATTTTAAAATTAAAAAA
Found at i:4179904 original size:12 final size:12
Alignment explanation
Indices: 4179887--4179916 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
4179877 AATTAAAAAA
4179887 TTTAAAAAGTAT
1 TTTAAAAAGTAT
4179899 TTT-AAAAGTAT
1 TTTAAAAAGTAT
4179910 TTTAAAA
1 TTTAAAA
4179917 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
TTTAAAAAGTAT
Found at i:4179904 original size:68 final size:70
Alignment explanation
Indices: 4179790--4179934 Score: 215
Period size: 68 Copynumber: 2.1 Consensus size: 70
4179780 AATAAATACC
*
4179790 AAAAAATTATTTTAAAATTTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAAAAGTATTTTAAAA-TTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
*
4179855 AAATTTA
65 AAA-TAA
* *
4179862 AAAAAAGTATTTTAAAA-TT-AAAAAATT-TAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAA
1 AAAAAAGTATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
4179924 AATAA
66 AATAA
4179929 AAAAAA
1 AAAAAA
4179935 TAAATATATT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
67 8 0.12
68 35 0.51
69 8 0.12
70 2 0.03
72 16 0.23
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (70 bp):
AAAAAAGTATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
AATAA
Found at i:4180856 original size:2 final size:2
Alignment explanation
Indices: 4180844--4180877 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4180834 ATAAAATAAT
*
4180844 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4180878 ATGTTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4182107 original size:24 final size:24
Alignment explanation
Indices: 4182080--4182136 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
4182070 TGTCGAAACA
4182080 TATGCTCCGACATATCATCCAATT
1 TATGCTCCGACATATCATCCAATT
*
4182104 TATGCTCCGACATATCCTCCAATT
1 TATGCTCCGACATATCATCCAATT
4182128 TATGCTCCG
1 TATGCTCCG
4182137 GCGTACGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.33
Consensus pattern (24 bp):
TATGCTCCGACATATCATCCAATT
Found at i:4187893 original size:39 final size:40
Alignment explanation
Indices: 4187828--4187918 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
4187818 GCTCTTAAAT
*
4187828 AAATTACTGAATCTTTTAAATAATTATTAAATTTCATACA
1 AAATTACTGAATCTTTTAAATAATTATTAAATCTCATACA
* *
4187868 AAATTACTG-ATTTTTTAAA-ACATTATTAAATCTCTTACA
1 AAATTACTGAATCTTTTAAATA-ATTATTAAATCTCATACA
* *
4187907 ATATTAATGAAT
1 AAATTACTGAAT
4187919 AACTTACAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.02
39 32 0.73
40 11 0.25
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (40 bp):
AAATTACTGAATCTTTTAAATAATTATTAAATCTCATACA
Found at i:4188816 original size:20 final size:20
Alignment explanation
Indices: 4188793--4188831 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4188783 AATCTCATAC
*
4188793 AATATTATTGAATCTCTTGT
1 AATATTACTGAATCTCTTGT
*
4188813 AATATTACTGAATTTCTTG
1 AATATTACTGAATCTCTTG
4188832 CTTGGAATCC
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:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (20 bp):
AATATTACTGAATCTCTTGT
Found at i:4196276 original size:40 final size:39
Alignment explanation
Indices: 4196232--4196401 Score: 214
Period size: 39 Copynumber: 4.5 Consensus size: 39
4196222 AAATATATTT
* * *
4196232 ATTTTTTAAAATTTTAAAATATTTTTTACATAATTTTTTA
1 ATTTTTT-AAATTTTAAAATATTTTTAAAATACTTTTTTA
4196272 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT-A
4196312 ATTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
4196350 A-TTTTT-AA-TTT-AAATA-TTTT-AAATAC-TTTTTA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
4196382 A-TTTTAAAATTTTTAAAATA
1 ATTTTTTAAA-TTTTAAAATA
4196402 AAAATGGGCC
Statistics
Matches: 121, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
32 11 0.09
33 8 0.07
34 4 0.03
35 8 0.07
36 8 0.07
37 7 0.06
38 2 0.02
39 58 0.48
40 15 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (39 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:4196322 original size:8 final size:9
Alignment explanation
Indices: 4196263--4196338 Score: 52
Period size: 8 Copynumber: 8.2 Consensus size: 9
4196253 TTTTTTACAT
4196263 AATTTTTT-
1 AATTTTTTA
4196271 AATTTTTTA
1 AATTTTTTA
*
4196280 AA-TTTTAA
1 AATTTTTTA
4196288 AATATTTTTAAA
1 AAT-TTTTT--A
4196300 ATACTTTTTTA
1 A-A-TTTTTTA
4196311 AATTTTTT-
1 AATTTTTTA
*
4196319 AA-TTTTAA
1 AATTTTTTA
4196327 AATATTTTTA
1 AAT-TTTTTA
4196337 AA
1 AA
4196339 ATACTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
7 4 0.07
8 19 0.35
9 8 0.15
10 12 0.22
11 2 0.04
12 2 0.04
13 6 0.11
14 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
AATTTTTTA
Found at i:4197559 original size:20 final size:20
Alignment explanation
Indices: 4197531--4197574 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4197521 TACAAAGCTT
* *
4197531 ATATCTTACTCAAGTTAACA
1 ATATATTACGCAAGTTAACA
4197551 ATATATTACGCAAGTTAACA
1 ATATATTACGCAAGTTAACA
4197571 ATAT
1 ATAT
4197575 GTACCATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (20 bp):
ATATATTACGCAAGTTAACA
Found at i:4197681 original size:17 final size:16
Alignment explanation
Indices: 4197653--4197705 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
4197643 TTTGGTTCGC
4197653 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4197669 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
4197686 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4197702 TGTA
1 TGTA
4197706 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:4197962 original size:18 final size:17
Alignment explanation
Indices: 4197941--4197975 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4197931 TTATTATTAA
*
4197941 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
4197959 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4197976 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:4200378 original size:18 final size:18
Alignment explanation
Indices: 4200355--4200389 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4200345 GTTTCAGACG
4200355 TGAGAAAGAAATGAGAAA
1 TGAGAAAGAAATGAGAAA
4200373 TGAGAAAGAAATGAGAA
1 TGAGAAAGAAATGAGAA
4200390 GACGGCTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
TGAGAAAGAAATGAGAAA
Found at i:4203635 original size:12 final size:13
Alignment explanation
Indices: 4203612--4203650 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4203602 TTTTTTATAG
*
4203612 ATAATTTTTTTAT
1 ATAATTTATTTAT
*
4203625 ATAA-TTATTTAA
1 ATAATTTATTTAT
4203637 ATAATTTATTTAT
1 ATAATTTATTTAT
4203650 A
1 A
4203651 AAATAAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATAATTTATTTAT
Found at i:4204125 original size:2 final size:2
Alignment explanation
Indices: 4204118--4204172 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
4204108 GTAAGCTCAG
4204118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4204160 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
4204173 TGAAAATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4214615 original size:7 final size:7
Alignment explanation
Indices: 4214603--4214630 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4214593 TTTTCTACAT
4214603 TAAGTAA
1 TAAGTAA
4214610 TAAGTAA
1 TAAGTAA
4214617 TAAGTAA
1 TAAGTAA
4214624 TAAGTAA
1 TAAGTAA
4214631 GTCTCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
TAAGTAA
Found at i:4215238 original size:16 final size:17
Alignment explanation
Indices: 4215208--4215241 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4215198 AAGATTATGT
*
4215208 TAAAATATTTTTAAAAA
1 TAAAATATTTCTAAAAA
4215225 TAAAA-ATTTCTAAAAA
1 TAAAATATTTCTAAAAA
4215241 T
1 T
4215242 TCAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATATTTCTAAAAA
Found at i:4216117 original size:19 final size:19
Alignment explanation
Indices: 4216093--4216165 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
4216083 TTTAACATAA
4216093 ATTTTAATATTTTTAATAT
1 ATTTTAATATTTTTAATAT
* * *
4216112 ATTTTAAACAATTTTCATA-
1 ATTTT-AATATTTTTAATAT
* *
4216131 ATTTATACTTATTTTTAAGATT
1 ATTT-TA-ATATTTTTAATA-T
4216153 ATTTTAATATTTT
1 ATTTTAATATTTT
4216166 AGAATTATTG
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
19 10 0.25
20 24 0.60
21 2 0.05
22 4 0.10
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (19 bp):
ATTTTAATATTTTTAATAT
Found at i:4227861 original size:18 final size:19
Alignment explanation
Indices: 4227838--4227886 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
4227828 TTCCTTAGAA
4227838 TTTTTT-GTATTTCCTCAC
1 TTTTTTGGTATTTCCTCAC
4227856 TTTTTTGGTATTTCCTCA-
1 TTTTTTGGTATTTCCTCAC
4227874 TAATTTTTGGTAT
1 T--TTTTTGGTAT
4227887 GTAACACTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 11 0.39
20 10 0.36
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.61
Consensus pattern (19 bp):
TTTTTTGGTATTTCCTCAC
Found at i:4227880 original size:20 final size:20
Alignment explanation
Indices: 4227818--4227886 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
4227808 AATATATATT
* * *
4227818 TTTTTGGTACTTCCTTAGAA
1 TTTTTGGTATTTCCTCATAA
*
4227838 TTTTTTGTATTTCCTCACT--
1 TTTTTGGTATTTCCTCA-TAA
4227857 TTTTTGGTATTTCCTCATAA
1 TTTTTGGTATTTCCTCATAA
4227877 TTTTTGGTAT
1 TTTTTGGTAT
4227887 GTAACACTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 1 0.02
19 16 0.39
20 24 0.59
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTTTGGTATTTCCTCATAA
Found at i:4229383 original size:43 final size:43
Alignment explanation
Indices: 4229307--4229432 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 43
4229297 TCTGACACCG
4229307 TAGTGCATCATCGGATCAACTGAACGAAGTATACTGGCACCTA
1 TAGTGCATCATCGGATCAACTGAACGAAGTATACTGGCACCTA
* * * * *
4229350 TAGTGCATCATTGGA-CAAGTCGAAGGAATTATACTGGCACATA
1 TAGTGCATCATCGGATCAACT-GAACGAAGTATACTGGCACCTA
* * * *
4229393 -AGGTGCATTATCGGATGAACCGAAGCG-ATTATACTGGCAC
1 TA-GTGCATCATCGGATCAACTGAA-CGAAGTATACTGGCAC
4229433 ATAGGTGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
42 5 0.07
43 60 0.88
44 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
TAGTGCATCATCGGATCAACTGAACGAAGTATACTGGCACCTA
Found at i:4229509 original size:44 final size:42
Alignment explanation
Indices: 4229452--4229533 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 42
4229442 TTGTCGGATA
**
4229452 AATCAAAGCAAATATTTTGGAACACGTAAGTGCATCATCAAATG
1 AATCAAAGCAAATATACTGGAACA-G-AAGTGCATCATCAAATG
*
4229496 AATCGAAA-CAAATATACTGGAACAGCAGTGCATCATCA
1 AATC-AAAGCAAATATACTGGAACAGAAGTGCATCATCA
4229534 GATAAACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 12 0.35
43 1 0.03
44 18 0.53
45 3 0.09
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (42 bp):
AATCAAAGCAAATATACTGGAACAGAAGTGCATCATCAAATG
Found at i:4230584 original size:15 final size:15
Alignment explanation
Indices: 4230566--4230607 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4230556 ATAGTTAAGT
4230566 TTATTTTAATTAAAC
1 TTATTTTAATTAAAC
4230581 TTA-TTTAATT-AAC
1 TTATTTTAATTAAAC
*
4230594 TTAATTATAATTAA
1 TT-ATTTTAATTAA
4230608 TTAGGCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 9 0.39
16 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTTTAATTAAAC
Found at i:4230584 original size:29 final size:29
Alignment explanation
Indices: 4230550--4230607 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4230540 CACTTAATTT
* * * *
4230550 ACTTATATAGTTAAGTTTATTTTAATTAA
1 ACTTATATAATTAACTTAATTATAATTAA
*
4230579 ACTTATTTAATTAACTTAATTATAATTAA
1 ACTTATATAATTAACTTAATTATAATTAA
4230608 TTAGGCTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (29 bp):
ACTTATATAATTAACTTAATTATAATTAA
Found at i:4230587 original size:14 final size:15
Alignment explanation
Indices: 4230570--4230607 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4230560 TTAAGTTTAT
4230570 TTTAATTAAACTT-A
1 TTTAATTAAACTTAA
4230584 TTTAATT-AACTTAA
1 TTTAATTAAACTTAA
4230598 TTATAATTAA
1 TT-TAATTAA
4230608 TTAGGCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 10 0.48
15 5 0.24
16 1 0.05
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATTAAACTTAA
Found at i:4231258 original size:21 final size:21
Alignment explanation
Indices: 4231226--4231318 Score: 79
Period size: 20 Copynumber: 4.6 Consensus size: 21
4231216 TTTTATAGTC
*
4231226 CCTCGTAA-TTTTTGTTACTT
1 CCTCATAATTTTTTGTTACTT
*
4231246 CCTCATAATTTTTTGGTA-TT
1 CCTCATAATTTTTTGTTACTT
4231266 CTCTCATAATTTTTTG-TACTT
1 C-CTCATAATTTTTTGTTACTT
* * * * *
4231287 ACTCAGAA-ATTTTATTACTC
1 CCTCATAATTTTTTGTTACTT
4231307 CCTCAT-ATTTTT
1 CCTCATAATTTTT
4231319 GGTACTTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.09
20 29 0.50
21 24 0.41
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (21 bp):
CCTCATAATTTTTTGTTACTT
Found at i:4231279 original size:22 final size:21
Alignment explanation
Indices: 4231226--4231325 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
4231216 TTTTATAGTC
* *
4231226 CCTCGTAA-TTTTTGTTACTT
1 CCTCATAATTTTTTGGTACTT
4231246 CCTCATAATTTTTTGGTA-TT
1 CCTCATAATTTTTTGGTACTT
4231266 CTCTCATAATTTTTT-GTACTT
1 C-CTCATAATTTTTTGGTACTT
* * * *
4231287 ACTCAGAAATTTTAT--TACTC
1 CCTCA-TAATTTTTTGGTACTT
4231307 CCTCAT-A-TTTTTGGTACTT
1 CCTCATAATTTTTTGGTACTT
4231326 TTAGATAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
17 4 0.06
18 1 0.02
19 4 0.06
20 25 0.39
21 30 0.47
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (21 bp):
CCTCATAATTTTTTGGTACTT
Found at i:4231528 original size:19 final size:20
Alignment explanation
Indices: 4231504--4231549 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4231494 CCAAGCAATT
* *
4231504 TTTTTTTGTACTTC-TCATG
1 TTTTTTTCTACTTCTTCATA
4231523 TTTTTTTCTACTTCTTCATA
1 TTTTTTTCTACTTCTTCATA
4231543 TTTTTTT
1 TTTTTTT
4231550 ATATTCCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTTTCTACTTCTTCATA
Found at i:4240835 original size:4 final size:4
Alignment explanation
Indices: 4240826--4240857 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
4240816 AGGAATAATC
4240826 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
4240858 CTAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4248026 original size:14 final size:14
Alignment explanation
Indices: 4247994--4248027 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4247984 TAAGTAAGTC
*
4247994 ATTTTCCAAAAATT
1 ATTTTCCAAAAACT
4248008 ATTTTCCAAAAACT
1 ATTTTCCAAAAACT
*
4248022 GTTTTC
1 ATTTTC
4248028 AGTAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTTTCCAAAAACT
Found at i:4248560 original size:18 final size:19
Alignment explanation
Indices: 4248539--4248575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4248529 TAAAATAATA
4248539 TTAAAT-TAATTATATATG
1 TTAAATATAATTATATATG
4248557 TTAAATAATAATTATATAT
1 TTAAAT-ATAATTATATAT
4248576 TTATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAAATATAATTATATATG
Found at i:4251795 original size:44 final size:44
Alignment explanation
Indices: 4251747--4252367 Score: 134
Period size: 44 Copynumber: 14.1 Consensus size: 44
4251737 CTGTAACCAC
* ** * *
4251747 AGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCTT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* * * *
4251791 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTATTGCCT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* * ** * * * * * *
4251835 AGGGA-AGTAGAAT-TACTAGCTTCAATATACTCTACT-GTAACCAC
1 AGGGAGA-TAAAATCCAAAATCTTCAATCTACTCCACTACT-GCC-T
* ** * * *
4251879 AGGGAGGTAAAATCCGTAATTTTCAATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* * ** * ** *
4251923 AAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* * **** * * * * *
4251967 AGGGA-AGTAGAAT-TATTGGCTTTAATGTACTCCACT-GTAACCAC
1 AGGGAGA-TAAAATCCAAAATCTTCAATCTACTCCACTACT-GCC-T
* * ** * * *
4252011 AGTGAGGTAAAATCCACCATCTTCGATCTACTTCACTACTGCTT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* ** * *
4252055 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGCCT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* * ** * * * * *
4252099 AGGGA-AGTAGAAT-TACTAGCTTCAATGTACTCCACT-GTAACCAC
1 AGGGAGA-TAAAATCCAAAATCTTCAATCTACTCCACTACT-GCC-T
* * ** * *
4252143 AGTGAGGTAAAATCCGTAATCTTCAATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* ** * * *
4252187 A-GGAGATAAGATCTGAAATCTTCAATCTATTTCCACTGCTGCCC
1 AGGGAGATAAAATCCAAAATCTTCAATCTA-CTCCACTACTGCCT
* * **** * * *
4252231 AGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTA-TAACCAC
1 AGGGAGA-TAAAATCCAAAATCTTCAATCTACTCCACTACT-GCC-T
* **** * * *
4252275 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
* ** * * *
4252319 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
4252363 AGGGA
1 AGGGA
4252368 AGTAGAATTA
Statistics
Matches: 395, Mismatches: 156, Indels: 52
0.66 0.26 0.09
Matches are distributed among these distances:
42 4 0.01
43 88 0.22
44 227 0.57
45 72 0.18
46 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAAATCCAAAATCTTCAATCTACTCCACTACTGCCT
Found at i:4251913 original size:132 final size:132
Alignment explanation
Indices: 4251659--4252571 Score: 1278
Period size: 132 Copynumber: 6.9 Consensus size: 132
4251649 CTGCAACTGC
* * * * *
4251659 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTGCTGACCAGGG-AGATAGGATTACTGA
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGG
* *
4251722 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACT
64 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
4251787 GCTT
129 GCTT
* ** * *
4251791 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * ** * *
4251856 TCAATATACTCTACTGTAACCACAGGGAGGTAAAATCCGTAATTTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
4251921 TT
131 TT
* * *
4251923 AAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * * * *
4251988 TTAATGTACTCCACTGTAACCACAGTGAGGTAAAATCCACCATCTTCGATCTACTTCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
4252053 TT
131 TT
** * *
4252055 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* ** *
4252120 TCAATGTACTCCACTGTAACCACAGTGAGGTAAAATCCGTAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
4252185 TT
131 TT
4252187 A-GGAGATAAGATCTGAAATCTTCAATCTATTTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTA-TTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC
* *
4252251 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTG
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
4252316 CTT
130 CTT
4252319 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* ** *
4252384 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGTCAA
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGC-TC-CACT-AC
4252449 TGC--
128 TGCTT
* * ** ** * *
4252452 AAGAAGGCAAGATCTGCTATCTTTAATTTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
4252517 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCATATTCGATCTGCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
4252572 TCGCTGTCAA
Statistics
Matches: 704, Mismatches: 70, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
131 28 0.04
132 526 0.75
133 144 0.20
134 2 0.00
135 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:4253908 original size:1 final size:1
Alignment explanation
Indices: 4253898--4254072 Score: 107
Period size: 1 Copynumber: 175.0 Consensus size: 1
4253888 GGCCTCTCCA
* ** * * * * * *
4253898 TTTTTCTTTTTTTTTTTTTTTCCTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
4253963 TGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
4254028 TTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4254073 GAATCTGAAC
Statistics
Matches: 122, Mismatches: 52, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 122 1.00
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.85
Consensus pattern (1 bp):
T
Found at i:4253913 original size:6 final size:6
Alignment explanation
Indices: 4253898--4254071 Score: 289
Period size: 6 Copynumber: 28.8 Consensus size: 6
4253888 GGCCTCTCCA
* *
4253898 TTTTTC TTTTT- TTTTT- TTTTTCC TTTTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTT-G TT-TTT-G TTTTTG TTTTTG TTTTTG
4253947 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
4253995 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
4254043 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
4254072 TGAATCTGAA
Statistics
Matches: 163, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
5 10 0.06
6 143 0.88
7 5 0.03
8 5 0.03
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:4258263 original size:98 final size:98
Alignment explanation
Indices: 4258084--4258280 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
4258074 GTACAATAAA
* *
4258084 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTCAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
4258149 CCTCTAGAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
4258182 ACTTCAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTCAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
4258247 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
4258280 A
1 A
4258281 TTATTTTTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTCAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:4259638 original size:19 final size:19
Alignment explanation
Indices: 4259614--4259726 Score: 190
Period size: 19 Copynumber: 5.8 Consensus size: 19
4259604 AATCATATAT
4259614 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
4259633 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
4259652 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4259671 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
4259692 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4259711 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
4259727 CTCAAAAATT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
19 69 0.78
21 19 0.22
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4259697 original size:40 final size:40
Alignment explanation
Indices: 4259614--4259725 Score: 210
Period size: 40 Copynumber: 2.9 Consensus size: 40
4259604 AATCATATAT
4259614 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
4259652 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
4259692 TCTAAGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
4259726 CCTCAAAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
38 28 0.39
40 44 0.61
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:4259698 original size:59 final size:56
Alignment explanation
Indices: 4259607--4259726 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 56
4259597 ATTACAAAAT
*
4259607 CATAT-ATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
*
4259662 CATATCATATCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCTAAGATTACATATCATATCTAAGATTG
4259721 CATATC
1 CATATC
4259727 CTCAAAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
55 5 0.08
56 2 0.03
57 11 0.19
59 41 0.69
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:4262323 original size:25 final size:25
Alignment explanation
Indices: 4262295--4262402 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
4262285 AGGCTCTCAC
* * *
4262295 GAGCTTCCCGTTATTTATCTCTTAT
1 GAGCTTCCCGATACTTAGCTCTTAT
* *
4262320 GAGCTTCCCGATACTTGGCTTTTAT
1 GAGCTTCCCGATACTTAGCTCTTAT
* * * * *
4262345 GAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCCCGA-TACTTAGCTCTTAT
* * * *
4262370 GAGCTTCCCGATATTTGGCTCGTAA
1 GAGCTTCCCGATACTTAGCTCTTAT
4262395 GAGCTTCC
1 GAGCTTCC
4262403 TATTACATGG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
24 2 0.03
25 64 0.94
26 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (25 bp):
GAGCTTCCCGATACTTAGCTCTTAT
Found at i:4262376 original size:50 final size:50
Alignment explanation
Indices: 4262320--4262450 Score: 142
Period size: 50 Copynumber: 2.6 Consensus size: 50
4262310 TATCTCTTAT
** *
4262320 GAGCTTCCCGATACTTGGCTTTTATGAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCCCGATACTTGGCTCGTAAGAGCTTCCT-ATTACATGGCTCGTAG
* ** *
4262370 GAGCTTCCCGATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCGATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
*
4262420 GAGCTTCCC-ATTA-TATGGCTCGAAAGAGCTT
1 GAGCTTCCCGA-TACT-TGGCTCGTAAGAGCTT
4262451 TTCGATTACA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
49 6 0.09
50 64 0.91
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCGATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
Found at i:4262413 original size:25 final size:25
Alignment explanation
Indices: 4262345--4262450 Score: 99
Period size: 25 Copynumber: 4.2 Consensus size: 25
4262335 TGGCTTTTAT
*
4262345 GAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCCT-ATTATATGGCTCGTAA
* *
4262370 GAGCTTCCCGA-TATTTGGCTCGTAA
1 GAGCTT-CCTATTATATGGCTCGTAA
* ** *
4262395 GAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCTATTATATGGCTCGTAA
* *
4262420 GAGCTTCCCATTATATGGCTCGAAA
1 GAGCTTCCTATTATATGGCTCGTAA
4262445 GAGCTT
1 GAGCTT
4262451 TTCGATTACA
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
24 5 0.08
25 57 0.89
26 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTCCTATTATATGGCTCGTAA
Found at i:4262414 original size:75 final size:75
Alignment explanation
Indices: 4262295--4262450 Score: 163
Period size: 75 Copynumber: 2.1 Consensus size: 75
4262285 AGGCTCTCAC
* * * * * *** *
4262295 GAGCTTCCCGTTATTTATCTCTTATGAGCTTCCCGATACTTGGCTTTTATGAGCTTCCTGATTA-
1 GAGCTTCCCGATATTTAGCTCGTAAGAGCTTCCCGATACATGGCTCACATGAGCTTCC-CATTAT
* *
4262359 ATGGCTCGTAG
65 ATGGCTCGAAA
* *
4262370 GAGCTTCCCGATATTTGGCTCGTAAGAGCTT-CCTATTACATGGCTCACATGAGCTTCCCATTAT
1 GAGCTTCCCGATATTTAGCTCGTAAGAGCTTCCCGA-TACATGGCTCACATGAGCTTCCCATTAT
4262434 ATGGCTCGAAA
65 ATGGCTCGAAA
4262445 GAGCTT
1 GAGCTT
4262451 TTCGATTACA
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
74 7 0.11
75 59 0.89
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (75 bp):
GAGCTTCCCGATATTTAGCTCGTAAGAGCTTCCCGATACATGGCTCACATGAGCTTCCCATTATA
TGGCTCGAAA
Found at i:4262467 original size:50 final size:50
Alignment explanation
Indices: 4262318--4262469 Score: 123
Period size: 50 Copynumber: 3.0 Consensus size: 50
4262308 TTTATCTCTT
*** * * **
4262318 ATGAGCTTCCCGATACT-TGGCTTTTATGAGCTTCCTGATTA-ATGGCTCGT
1 ATGAGCTTCCCGATA-TATGGCTCGAAAGAGCTTCC-GATTACATGACTCAC
* * * * *
4262368 AGGAGCTTCCCGATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCAC
1 ATGAGCTTCCCGATATATGGCTCGAAAGAGCTTCCGATTACATGACTCAC
*
4262418 ATGAGCTTCCC-ATTATATGGCTCGAAAGAGCTTTTCGATTACAT-ACTCAC
1 ATGAGCTTCCCGA-TATATGGCTCGAAAGAGC-TTCCGATTACATGACTCAC
4262468 AT
1 AT
4262470 AGGCATACCT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
49 6 0.07
50 69 0.81
51 10 0.12
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
ATGAGCTTCCCGATATATGGCTCGAAAGAGCTTCCGATTACATGACTCAC
Found at i:4284821 original size:13 final size:13
Alignment explanation
Indices: 4284805--4284842 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
4284795 TAAACCAAAT
4284805 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
4284818 TTTTTAAAAACAC
1 TTTTCAAAAGCAC
4284831 TTTTCAAAAGCA
1 TTTTCAAAAGCA
4284843 ATGAAGAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:4295777 original size:34 final size:35
Alignment explanation
Indices: 4295733--4295799 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
4295723 CAGTAAAATA
* *
4295733 TTTTCCGTAAAATGA-TTTCTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
* *
4295767 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTAGAAAATATTTT
4295800 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTAGAAAATATTTTAC
Found at i:4295864 original size:32 final size:32
Alignment explanation
Indices: 4295789--4295865 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 32
4295779 TGACTTACTG
* ** *
4295789 GAAAATATTTTCTGGTGTTTGATTGAATCTGT
1 GAAAATATTTTCTGCTGTTTGACAGAATCTCT
* *
4295821 GTAAAATATTTTCTGCTGTTTGACAGATTTTCT
1 G-AAAATATTTTCTGCTGTTTGACAGAATCTCT
4295854 GAAAATATTTTC
1 GAAAATATTTTC
4295866 CGGAAAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 12 0.32
33 26 0.68
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGACAGAATCTCT
Found at i:4297172 original size:27 final size:27
Alignment explanation
Indices: 4297142--4297211 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
4297132 AATAATCAAT
*
4297142 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
4297169 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
4297197 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
4297212 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:4300894 original size:16 final size:16
Alignment explanation
Indices: 4300873--4300904 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4300863 ATCAAGAAAG
4300873 TAGAGGAGGAAAAACA
1 TAGAGGAGGAAAAACA
4300889 TAGAGGAGGAAAAACA
1 TAGAGGAGGAAAAACA
4300905 GCAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.06
Consensus pattern (16 bp):
TAGAGGAGGAAAAACA
Found at i:4304518 original size:41 final size:42
Alignment explanation
Indices: 4304429--4304527 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 42
4304419 ACGTCGCAAA
* *
4304429 CGTTTGCAGCGTTTTTTTCTAAGTGCCGCTAAAGAACATTAT
1 CGTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACATTAT
*
4304471 CTTTAGCAGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGT-T
1 CGTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT-TAT
* *
4304512 CGTTAGCGGCGCTTTT
1 CGTTAGCAGCGTTTTT
4304528 ATAAAAAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.66
42 17 0.34
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
CGTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACATTAT
Found at i:4304870 original size:21 final size:21
Alignment explanation
Indices: 4304844--4304913 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
4304834 TTTGCTCTAT
* *
4304844 TCTGCTTCTCTCGCTGTAGCC
1 TCTGCTTCCCTCGCTGCAGCC
4304865 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
* *
4304886 GCTGCTTCCCTCGCTGCCGCC
1 TCTGCTTCCCTCGCTGCAGCC
4304907 TCTGCTT
1 TCTGCTT
4304914 TAAGTTGTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.03, C:0.44, G:0.20, T:0.33
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:4309443 original size:9 final size:9
Alignment explanation
Indices: 4309429--4309610 Score: 162
Period size: 9 Copynumber: 20.9 Consensus size: 9
4309419 TTTTTATGTA
4309429 TTATGTAAG
1 TTATGTAAG
4309438 TTATGTAAG
1 TTATGTAAG
*
4309447 TTGTGT-A-
1 TTATGTAAG
*
4309454 TTATGTGAG
1 TTATGTAAG
*
4309463 TTATGTGAG
1 TTATGTAAG
4309472 TTATGTAAG
1 TTATGTAAG
*
4309481 TTATGGAAG
1 TTATGTAAG
* *
4309490 TTATTTAAT
1 TTATGTAAG
4309499 TTATGTAAG
1 TTATGTAAG
4309508 TTATGTAAG
1 TTATGTAAG
*
4309517 TTATGTAGG
1 TTATGTAAG
*
4309526 CTATGT-A-
1 TTATGTAAG
* *
4309533 TTATCTAAA
1 TTATGTAAG
*
4309542 TAATGTAAG
1 TTATGTAAG
* *
4309551 TTA-GGAATC
1 TTATGTAA-G
4309560 TTATGT-A-
1 TTATGTAAG
4309567 TTATGTAAG
1 TTATGTAAG
*
4309576 TTATGCAAG
1 TTATGTAAG
* *
4309585 TTATTTAAT
1 TTATGTAAG
4309594 TTATGTAAG
1 TTATGTAAG
4309603 TTATGTAA
1 TTATGTAA
4309611 TTAGAAATTT
Statistics
Matches: 138, Mismatches: 27, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
7 15 0.11
8 7 0.05
9 115 0.83
10 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:4309586 original size:34 final size:35
Alignment explanation
Indices: 4309422--4309610 Score: 149
Period size: 34 Copynumber: 5.4 Consensus size: 35
4309412 TGATATATTT
* *
4309422 TTATGTATTATGTAAGTTATGTAAGTTGT-G--TA
1 TTATGTATTATGTAAGTTATGTAAGTTATGGAATC
* *
4309454 TTATGTGAGTTATGTGAGTTATGTAAGTTATGGAA-G
1 TTATGT-A-TTATGTAAGTTATGTAAGTTATGGAATC
* * **
4309490 TTATTTAATTTATGTAAGTTATGTAAGTTATGTAGGC
1 TTATGT-A-TTATGTAAGTTATGTAAGTTATGGAATC
* * *
4309527 -TATGTATTATCTAAATAATGTAAGTTA-GGAATC
1 TTATGTATTATGTAAGTTATGTAAGTTATGGAATC
* **
4309560 TTATGTATTATGTAAGTTATGCAAGTTATTTAAT-
1 TTATGTATTATGTAAGTTATGTAAGTTATGGAATC
4309594 TTATGTAAGTTATGTAA
1 TTATGT-A-TTATGTAA
4309611 TTAGAAATTT
Statistics
Matches: 124, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
32 6 0.05
33 4 0.03
34 67 0.54
35 6 0.05
36 41 0.33
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (35 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGGAATC
Found at i:4309643 original size:37 final size:37
Alignment explanation
Indices: 4309590--4309671 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
4309580 GCAAGTTATT
* *
4309590 TAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCA
1 TAATATTATCTAAGTTATGTAATTAGAAATTTGATCA
* *
4309626 TAATATTATCTAAGTTATGTAATTCGAAATTTGATCT
1 TAATATTATCTAAGTTATGTAATTAGAAATTTGATCA
4309663 TAATATTAT
1 TAATATTAT
4309672 AAAAGTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (37 bp):
TAATATTATCTAAGTTATGTAATTAGAAATTTGATCA
Found at i:4309684 original size:20 final size:20
Alignment explanation
Indices: 4309659--4309697 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4309649 TCGAAATTTG
4309659 ATCTTAATATTATAAAAGTA
1 ATCTTAATATTATAAAAGTA
*
4309679 ATCTTAATATTATATAAGT
1 ATCTTAATATTATAAAAGT
4309698 TATGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTTAATATTATAAAAGTA
Found at i:4309712 original size:94 final size:93
Alignment explanation
Indices: 4309589--4309763 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 93
4309579 TGCAAGTTAT
* *
4309589 TTAATTTATGTAAGTTATGTAATTAGAAATTTTATCATAATATTATCTAAGTTATGTAATTCGAA
1 TTAATTTATATAAGTTATGTAATTAGAAATTTTATCATAATATTATATAAGTTATGTAATTCGAA
4309654 ATTTGATCTTAATATTATAAAAGTAATC
66 ATTTGATCTTAATATTATAAAAGTAATC
* * * *
4309682 TTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAGTATTGTATAAGTTATGTAATTCGA
1 TTAAT-TTATATAAGTTATGTAATTAGAAATTTTATCATAATATTATATAAGTTATGTAATTCGA
* *
4309747 TATTTTATCTTAATATT
65 AATTTGATCTTAATATT
4309764 GTATAAGTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 5 0.07
94 68 0.93
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (93 bp):
TTAATTTATATAAGTTATGTAATTAGAAATTTTATCATAATATTATATAAGTTATGTAATTCGAA
ATTTGATCTTAATATTATAAAAGTAATC
Found at i:4309732 original size:37 final size:37
Alignment explanation
Indices: 4309679--4309853 Score: 305
Period size: 37 Copynumber: 4.7 Consensus size: 37
4309669 TATAAAAGTA
* *
4309679 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
*
4309716 ATCTTAGTATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
4309753 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
4309790 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
* *
4309827 ATCTTAACATTATATAAGTTATGTAAT
1 ATCTTAATATTGTATAAGTTATGTAAT
4309854 ATTATATAAG
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 132 1.00
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (37 bp):
ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
Found at i:4309900 original size:37 final size:37
Alignment explanation
Indices: 4309850--4309946 Score: 176
Period size: 37 Copynumber: 2.6 Consensus size: 37
4309840 ATAAGTTATG
4309850 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
*
4309887 TAATATTGTATAAGTTATGTAATTCGATATTTTATCT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCT
*
4309924 TAACATTATATAAGTTATGTAAT
1 TAATATTATATAAGTTATGTAAT
4309947 ATTTTATAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49
Consensus pattern (37 bp):
TAATATTATATAAGTTATGTAATTCGATATTTTATCT
Found at i:4309916 original size:93 final size:93
Alignment explanation
Indices: 4309757--4309996 Score: 435
Period size: 93 Copynumber: 2.6 Consensus size: 93
4309747 TATTTTATCT
*
4309757 TAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGAT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGAT
4309822 ATTTTATCTTAACATTATATAAGTTATG
66 ATTTTATCTTAACATTATATAAGTTATG
4309850 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGAT
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGAT
4309915 ATTTTATCTTAACATTATATAAGTTATG
66 ATTTTATCTTAACATTATATAAGTTATG
* * * *
4309943 TAATATTTTATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTA
1 TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTA
4309997 AGAAATGTTA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 142 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (93 bp):
TAATATTATATAAGTTATGTAATTCGATATTTTATCTTAATATTGTATAAGTTATGTAATTCGAT
ATTTTATCTTAACATTATATAAGTTATG
Found at i:4309947 original size:56 final size:56
Alignment explanation
Indices: 4309887--4309996 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 56
4309877 TATTTTATCT
* *
4309887 TAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTATG
1 TAATATTGTATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGTTATG
* *
4309943 TAATATTTTATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTA
1 TAATATTGTATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGTTA
4309997 AGAAATGTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (56 bp):
TAATATTGTATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGTTATG
Found at i:4312297 original size:147 final size:146
Alignment explanation
Indices: 4312086--4312428 Score: 384
Period size: 147 Copynumber: 2.3 Consensus size: 146
4312076 CGGCCTCGTA
* * * *
4312086 TCGATAAATGCTAAAACATTTTTGCGGCGTTTTAATTAAAGCGCCACTAACTATAAATCAAAACG
1 TCGATAAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAATCAAAACG
* * * * * * *
4312151 CAGTCGTTTCATCAACACTTACCTCAAACCCGTGGCGTTTTCAAAAAATCGCCACTAATAACATT
66 AAGTCATTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAA-AGCCACTAATAACATA
* * * *
4312216 TAAAAAATGGCAGCATT
130 GAAAAAACGACAACATT
* *
4312233 TCTATAAATGTTAGAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATC-AAAC
1 TCGATAAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAA-ATCAAAAC
* * * ** *
4312297 GAAGTCATTTCCCCAACAGTTAACTCAATCTTGTGGCGTTTCCAAAAAAAGCCACTAATACCATA
65 GAAGTCATTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAAGCCACTAATAACATA
*
4312362 GACAAAACGACAACATT
130 GAAAAAACGACAACATT
** * * *
4312379 TCGATAAA-CATAACTACAATTTTGCGGCGTTTCATGTAAAGCGCCACTAA
1 TCGATAAATGTTAA-AACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAA
4312429 TAGCAACGTA
Statistics
Matches: 163, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
145 2 0.01
146 65 0.40
147 93 0.57
148 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (146 bp):
TCGATAAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAATCAAAACG
AAGTCATTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAAGCCACTAATAACATAG
AAAAAACGACAACATT
Found at i:4312553 original size:19 final size:19
Alignment explanation
Indices: 4312529--4312565 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4312519 CGCCGTTCCC
*
4312529 CTTCCCAGTTACAGGATAA
1 CTTCCCACTTACAGGATAA
4312548 CTTCCCACTTACAGGATA
1 CTTCCCACTTACAGGATA
4312566 CAAATTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (19 bp):
CTTCCCACTTACAGGATAA
Found at i:4313946 original size:114 final size:111
Alignment explanation
Indices: 4313748--4314131 Score: 391
Period size: 114 Copynumber: 3.4 Consensus size: 111
4313738 GCTTGTTAAT
* * *
4313748 AAACGCCGCTAAATCCCCCAATGCTAAGTAAAACGACCTCGTTGGGCTTAGGTTT-TTTGCGGCG
1 AAACGCCGCTAAATCCCCGAATGCTCAG-AAAACGACGTCGTT-GGCTTAGGTTTCTTTGCGGCG
* *
4313812 CTTTCCAAAAAATGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCTCCAT
64 C-TTCC-AAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAA
* * * *
4313862 AAACGCCGCTAAATCCCCGAATACTCAGAGAACGGCGTCGTTCGGCTTATGTTTCTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTT-GGCTTAGGTTTCTTTGCGGCGC
* ** * * *
4313927 TTCCACAGAAACGCCGCTAAAGTACTAAACATTGGCGGCG-TTAC-CTCAA
65 TTCCA-A-AAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT-CTC-CAA
* * *
4313976 AAACGCCGCTAAGTCACCGAATGCTCAGAAAACGACGTCGTTGGTCTTAGGTTTCTTTGCGGTGA
1 AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTTGG-CTTAGGTTTCTTTGCGGCG-
* * * *
4314041 ATTCTCAAAAATGCCGCTAAATCCCTGAGCTTTAGCGGCGCTTCAT-AAA
64 CTTC-CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC-TCCAA
* *
4314090 AAATGCCGCTAAATCCCCGAATG-TGCGGAAAACGACGTCGTT
1 AAACGCCGCTAAATCCCCGAATGCT-CAGAAAACGACGTCGTT
4314132 CGGCCGAGGT
Statistics
Matches: 221, Mismatches: 37, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
112 1 0.00
113 32 0.14
114 180 0.81
115 6 0.03
116 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (111 bp):
AAACGCCGCTAAATCCCCGAATGCTCAGAAAACGACGTCGTTGGCTTAGGTTTCTTTGCGGCGCT
TCCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAA
Found at i:4314212 original size:40 final size:40
Alignment explanation
Indices: 4314164--4314254 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
4314154 TTATAGAAAT
4314164 CGCCGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
1 CGCCGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
*
4314204 CGCTGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
1 CGCCGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
4314244 CGCCGCTAATG
1 CGCCGCTAATG
4314255 ATTGATCTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (40 bp):
CGCCGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
Found at i:4314269 original size:40 final size:40
Alignment explanation
Indices: 4314164--4314270 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
4314154 TTATAGAAAT
* *
4314164 CGCCGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
1 CGCCGCTAATGATTATTCTGCAGCGGCGTTTTCCGTAAAG
* * *
4314204 CGCTGCTAATGCTTATTCTTCAGCGGCGTTTTCCGTAAAG
1 CGCCGCTAATGATTATTCTGCAGCGGCGTTTTCCGTAAAG
*
4314244 CGCCGCTAATGATTGA-TCTGGAGCGGC
1 CGCCGCTAATGATT-ATTCTGCAGCGGC
4314271 ATTTGTTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 60 0.98
41 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (40 bp):
CGCCGCTAATGATTATTCTGCAGCGGCGTTTTCCGTAAAG
Found at i:4314389 original size:2 final size:2
Alignment explanation
Indices: 4314382--4314406 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4314372 AGAAAAATTG
4314382 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4314407 AAATTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4314722 original size:60 final size:61
Alignment explanation
Indices: 4314597--4314730 Score: 152
Period size: 59 Copynumber: 2.2 Consensus size: 61
4314587 TTATTAAGAC
* *
4314597 ATCTTTTTTGGTCA-TCCAACTATAAAAAATTACAAAATGTTACTCAACTATTACTAAATT
1 ATCTTTTTTGGTCACTCCAACTATAAAAAATTACAAAATGTCACCCAACTATTACTAAATT
* * * *
4314657 -TCTTTTTTGGTCACT-CAATTATGAAAAGTTACAAAATAGTCACCCAACTATT-C-AATTTT
1 ATCTTTTTTGGTCACTCCAACTATAAAAAATTACAAAAT-GTCACCCAACTATTACTAA-ATT
*
4314716 ATCTTTTTTAGTCAC
1 ATCTTTTTTGGTCAC
4314731 CATTGGGATA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 2 0.03
59 35 0.56
60 26 0.41
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (61 bp):
ATCTTTTTTGGTCACTCCAACTATAAAAAATTACAAAATGTCACCCAACTATTACTAAATT
Found at i:4315317 original size:55 final size:55
Alignment explanation
Indices: 4315224--4315354 Score: 131
Period size: 57 Copynumber: 2.3 Consensus size: 55
4315214 TGATAGTTGG
* * * * **
4315224 GTGACCATTTTGTAACTTTTTCATAGTTAGGTGAC-AAAAAAATACTAATAGTTAA
1 GTGACCATTTTATAAC-TTTTAATAATTAGATGACAAAAAAAATACTAATAACTAA
4315279 GTGACCATTTTATAACTTTTAATAATT-GATCGATCAAAAAAAAATACTAATAACTAA
1 GTGACCATTTTATAACTTTTAATAATTAGAT-GA-C-AAAAAAAATACTAATAACTAA
* *
4315336 GTGACTACTTGTATAACTT
1 GTGACCA-TTTTATAACTT
4315355 ACCCAAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
53 2 0.03
54 11 0.17
55 16 0.25
57 24 0.38
58 10 0.16
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (55 bp):
GTGACCATTTTATAACTTTTAATAATTAGATGACAAAAAAAATACTAATAACTAA
Found at i:4315575 original size:18 final size:18
Alignment explanation
Indices: 4315552--4315586 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4315542 TTGAAATAAT
*
4315552 ATTTTTTAAATAATAAAC
1 ATTTTTTAAAAAATAAAC
4315570 ATTTTTTAAAAAATAAA
1 ATTTTTTAAAAAATAAA
4315587 AATGTTAATA
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:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTTTAAAAAATAAAC
Found at i:4318296 original size:27 final size:27
Alignment explanation
Indices: 4318266--4318321 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 27
4318256 TATTTTAAAA
4318266 TTAA-TTAATATTATTATAAAAATATTT
1 TTAATTTAATATTATTAT-AAAATATTT
*
4318293 TTAATTTTTAATATTTTTATAAAATATTT
1 TTAA--TTTAATATTATTATAAAATATTT
4318322 CAATTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
29 9 0.36
30 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAATTTAATATTATTATAAAATATTT
Found at i:4320218 original size:25 final size:25
Alignment explanation
Indices: 4320174--4320223 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4320164 TTCCGTGTGC
*
4320174 GAAAAAATAATATTAATTATGATTT
1 GAAAAAATAATATTAATTATAATTT
*
4320199 GAAAGAAATAATATT-TTTATAATTT
1 GAAA-AAATAATATTAATTATAATTT
4320224 TATAACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (25 bp):
GAAAAAATAATATTAATTATAATTT
Found at i:4322004 original size:17 final size:19
Alignment explanation
Indices: 4321982--4322016 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
4321972 CTAAAATAGT
4321982 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
4321999 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
4322017 TCGAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:4328277 original size:21 final size:21
Alignment explanation
Indices: 4328253--4328296 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4328243 TCATTGTTAT
* *
4328253 ATACTTATAATAACATTTGAG
1 ATACGTATAACAACATTTGAG
*
4328274 ATACGTGTAACAACATTTGAG
1 ATACGTATAACAACATTTGAG
4328295 AT
1 AT
4328297 TCCAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (21 bp):
ATACGTATAACAACATTTGAG
Found at i:4329334 original size:21 final size:21
Alignment explanation
Indices: 4329300--4329342 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
4329290 CTCTCTTAAC
4329300 AAAAATTTAAAAATTTTCAAAAA
1 AAAAATTT-AAAATTTT-AAAAA
4329323 AAAAATTT-AAATTTTAAAAA
1 AAAAATTTAAAATTTTAAAAA
4329343 TCCAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
23 8 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATTTAAAATTTTAAAAA
Found at i:4329423 original size:11 final size:11
Alignment explanation
Indices: 4329407--4329455 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
4329397 ATATATATAT
4329407 AAAATCTAAAA
1 AAAATCTAAAA
*
4329418 AAAATCTAAAG
1 AAAATCTAAAA
* *
4329429 AATATATAAAA
1 AAAATCTAAAA
*
4329440 AAATTCTAAAA
1 AAAATCTAAAA
*
4329451 TAAAT
1 AAAAT
4329456 AAATTTGGGG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAATCTAAAA
Found at i:4329452 original size:20 final size:22
Alignment explanation
Indices: 4329413--4329458 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4329403 ATATAAAATC
*
4329413 TAAAAAAAATCTAAAGAATATA
1 TAAAAAAAATCTAAAGAATAAA
*
4329435 TAAAAAAATTCT-AA-AATAAA
1 TAAAAAAAATCTAAAGAATAAA
4329455 TAAA
1 TAAA
4329459 TTTGGGGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAAAAATCTAAAGAATAAA
Found at i:4333729 original size:45 final size:45
Alignment explanation
Indices: 4333679--4334076 Score: 510
Period size: 45 Copynumber: 8.8 Consensus size: 45
4333669 AAAGTGTAGG
* * * **
4333679 TCTTGTCTTTCTATATTGGCAGTGAAGTAGATCAAAGATAGTAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* * *
4333724 TCTTGTCTTCCTATATTTGTAGTGAAGTAGATTGAAAATAACAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
4333769 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* * * *
4333814 TCTTTTCTTCCTGTATTGGTAGTGAAGTAGATCAAAGATAGCAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* ** *
4333859 TCTTGTCTTCCTATATTAGTAGTGGTGTAGATCGAAGATAACAAA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* * * * *
4333904 TCTTGTTTTTCTGTATTGGCAGTGAAGTAGATCAAAGATAGA-AGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATA-ACAGA
* * *
4333949 TCTTGTCTTCCTACATTGGTAGCGGAGTAGATCGAAGATAACAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* *
4333994 TCTTGTCTTCCCATATTGGTAGCGAAGTAGATCGAAGATAACAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
* * * *
4334039 TATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
1 TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGA
4334077 CTGAATAAAC
Statistics
Matches: 304, Mismatches: 47, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
44 1 0.00
45 302 0.99
46 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (45 bp):
TCTTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAACAGA
Found at i:4335610 original size:3 final size:3
Alignment explanation
Indices: 4335604--4335649 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
4335594 TTTTATCATC
* *
4335604 ATT ATT ATT ATT ATT ATTT ATT ATT ATT AAT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4335650 TCCACGTACG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4335632 original size:25 final size:25
Alignment explanation
Indices: 4335595--4335646 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
4335585 TTTTTTTCTT
* *
4335595 TTTATCATCATTATTATTATTATTA
1 TTTATCATCATTAATATTATAATTA
* *
4335620 TTTATTATTATTAATATTATAATTA
1 TTTATCATCATTAATATTATAATTA
4335645 TT
1 TT
4335647 ATTTCCACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATCATCATTAATATTATAATTA
Found at i:4338941 original size:16 final size:16
Alignment explanation
Indices: 4338922--4338953 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4338912 TCTAAATGAC
*
4338922 AATTGTTCTAAACATA
1 AATTGTCCTAAACATA
4338938 AATTGTCCTAAACATA
1 AATTGTCCTAAACATA
4338954 TTTGTTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (16 bp):
AATTGTCCTAAACATA
Found at i:4346258 original size:11 final size:11
Alignment explanation
Indices: 4346242--4346273 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4346232 TTTTATGATG
4346242 ACTATATAAAA
1 ACTATATAAAA
4346253 ACTATATAAAA
1 ACTATATAAAA
4346264 A-TAT-TAAAA
1 ACTATATAAAA
4346273 A
1 A
4346274 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 12 0.57
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (11 bp):
ACTATATAAAA
Found at i:4348256 original size:2 final size:2
Alignment explanation
Indices: 4348249--4348273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4348239 TTAGAGATGA
4348249 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
4348274 TTTCTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4350060 original size:44 final size:44
Alignment explanation
Indices: 4349906--4350043 Score: 258
Period size: 44 Copynumber: 3.1 Consensus size: 44
4349896 GTCTCGACTT
*
4349906 TCATTTTCATATACTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
*
4349950 TTATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
4349994 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
4350038 TCATTT
1 TCATTT
4350044 ATTGAATACA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
Found at i:4350641 original size:13 final size:13
Alignment explanation
Indices: 4350622--4350698 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
4350612 AACACTCAAT
*
4350622 TTCTCAAAAGCAT
1 TTCTCAAAAGCAC
*
4350635 TTATCAAAAGCAC
1 TTCTCAAAAGCAC
*
4350648 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
4350661 TTTTCAAAAGCAC
1 TTCTCAAAAGCAC
4350674 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
4350687 TTCTCAAAAGCA
1 TTCTCAAAAGCA
4350699 ATAAAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:4353522 original size:16 final size:15
Alignment explanation
Indices: 4353496--4353530 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
4353486 TAATGCTCTG
4353496 TTAGTGGAACAAATT
1 TTAGTGGAACAAATT
4353511 TTAGTCGGAACAAATT
1 TTAGT-GGAACAAATT
4353527 TTAG
1 TTAG
4353531 CCGGTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (15 bp):
TTAGTGGAACAAATT
Found at i:4366572 original size:21 final size:21
Alignment explanation
Indices: 4366518--4366578 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
4366508 TATTATAAAT
*
4366518 TTTATTTAATAATAAA-AATC
1 TTTAGTTAATAATAAAGAATC
4366538 TTTAGTTTAATAATAAAGAA-C
1 TTTAG-TTAATAATAAAGAATC
*
4366559 TTTAGTTAATTAATCAAGAA
1 TTTAGTTAA-TAATAAAGAA
4366579 ATAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 8 0.22
21 26 0.72
22 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTAGTTAATAATAAAGAATC
Found at i:4366572 original size:24 final size:21
Alignment explanation
Indices: 4366514--4366565 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4366504 AATATATTAT
4366514 AAAT-TTTA-TTTAATAATAA
1 AAATCTTTAGTTTAATAATAA
4366533 AAATCTTTAGTTTAATAATAA
1 AAATCTTTAGTTTAATAATAA
4366554 AGAA-CTTTAGTT
1 A-AATCTTTAGTT
4366566 AATTAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 20 0.67
22 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (21 bp):
AAATCTTTAGTTTAATAATAA
Found at i:4375234 original size:14 final size:14
Alignment explanation
Indices: 4375215--4375279 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
4375205 ATTTTATAAT
4375215 TATATTTAAAACTA
1 TATATTTAAAACTA
* *
4375229 TATATTTGAAGCTA
1 TATATTTAAAACTA
4375243 TA-ACTTTAAAA-TA
1 TATA-TTTAAAACTA
*
4375256 AATATTT-AAACTGA
1 TATATTTAAAACT-A
*
4375270 AATATTTAAA
1 TATATTTAAA
4375280 GTCTTTTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.07
13 8 0.20
14 28 0.68
15 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (14 bp):
TATATTTAAAACTA
Found at i:4377199 original size:23 final size:22
Alignment explanation
Indices: 4377161--4377203 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
4377151 AAATCTCCTA
4377161 AAAATCCAAATAAAATAAAATC
1 AAAATCCAAATAAAATAAAATC
4377183 AAAATCTCTAAAT-AAATAAAA
1 AAAATC-C-AAATAAAATAAAA
4377204 CTACTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATCCAAATAAAATAAAATC
Found at i:4378365 original size:43 final size:42
Alignment explanation
Indices: 4378316--4378620 Score: 207
Period size: 43 Copynumber: 7.2 Consensus size: 42
4378306 CTAATGCCAA
* * *
4378316 GGAGATAGGATTAGG-TCTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGATT-GGAT-TTCAATCTACTCCACTGCAACTTCAG
* * * * * *
4378359 GGAGATAAGACTT-AATGT-GATCTGCT-CTCTGCAACCTCAG
1 GGAGATAAGA-TTGGATTTCAATCTACTCCACTGCAACTTCAG
* * *
4378399 AGAGATAAGATCCGTGATTT-AATCCACTCCACTGCAACTTCAG
1 GGAGATAAGAT-TG-GATTTCAATCTACTCCACTGCAACTTCAG
* * *
4378442 GGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAG
1 GGAGATAAGATTGGAT-TTCAATCTACTCCACTGCAACTTCAG
* * * * * *
4378485 AGAGATAAGACTT-GA-TGCGATCTGCT-CTCTGCAACCTC-G
1 GGAGATAAGA-TTGGATTTCAATCTACTCCACTGCAACTTCAG
* *
4378524 GAGAGATAAGATCTGTGATTT-AATCCACTCCACTGTAACTTCAG
1 G-GAGATAAGAT-TG-GATTTCAATCTACTCCACTGCAACTTCAG
* *
4378568 GGAGATAGGATTGGTTCTTCAATCTACTCCACTGCAACTTCAG
1 GGAGATAAGATTGGAT-TTCAATCTACTCCACTGCAACTTCAG
*
4378611 AGAGATAAGA
1 GGAGATAAGA
4378621 CTTGATGCGA
Statistics
Matches: 199, Mismatches: 45, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
39 3 0.02
40 41 0.21
41 17 0.09
42 23 0.12
43 109 0.55
44 6 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
GGAGATAAGATTGGATTTCAATCTACTCCACTGCAACTTCAG
Found at i:4378461 original size:126 final size:126
Alignment explanation
Indices: 4378316--4378707 Score: 615
Period size: 126 Copynumber: 3.1 Consensus size: 126
4378306 CTAATGCCAA
* * * *
4378316 GGAGATAGGATTAGG-TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTAATGTGAT
1 GGAGATAGGATT-GGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGAT
* *
4378380 CTGCTCTCTGCAACCTCAGAGAGATAAGATCCGTGATTTAATCCACTCCACTGCAACTTCAG
65 CTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTTCAG
4378442 GGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGATC
1 GGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGATC
*
4378507 TGCTCTCTGCAACCTCGGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTTCAG
66 TGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTTCAG
*
4378568 GGAGATAGGATTGGTTCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGATC
1 GGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGATC
* * * * * *
4378633 TGCTCTCTGCAACATCAGAAAGATAAGATCTATATGTTTTAATCCACTCCATTGTAACTTCAA
66 TGCTCTCTGCAACCTCAGAGAGATAAGATC--TGTGATTTAATCCACTCCACTGTAACTTCAG
*
4378696 GGAGATATGATT
1 GGAGATAGGATT
4378708 ATTTACTTCA
Statistics
Matches: 247, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
125 2 0.01
126 207 0.84
128 38 0.15
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (126 bp):
GGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCGATC
TGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTTCAG
Found at i:4378766 original size:50 final size:49
Alignment explanation
Indices: 4378712--4379007 Score: 200
Period size: 50 Copynumber: 5.9 Consensus size: 49
4378702 ATGATTATTT
* * *
4378712 ACTTCAATCTGTTTAACTGCAGTGTCAGGGAAACAAGATTCGCCGCCGTG
1 ACTTCAATCT-TTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTG
** * * * ** *
4378762 ACTTCAATCTATTCCACTACACTGCCAGGGAAGTAAGATCCGCCGTTGTG
1 ACTTCAATCT-TTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTG
* * *
4378812 GCTTCAATCTTTTAAATTGCAATATCAGGGAAACCAA-ATCCGCCGTCGTG
1 ACTTCAATCTTTT-AACTGCAATGTCAGGGAAA-CAAGATCCGCCGTCGTG
* * * ** * * ** *
4378862 GCTTCAATATACTCCACTACACCT-TCAGGGAAGTAAGATCCGCCGTTGTG
1 ACTTCAATCT-TTTAACTGCA-ATGTCAGGGAAACAAGATCCGCCGTCGTG
* * * * *
4378912 GCTTCAATCTTTTAAATTGCAATGTCGGGGAAACCAGATCCGCCGTTGTG
1 ACTTCAATCTTTT-AACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTG
* * * * *
4378962 GCTTCAATCTTTTTAATTGCAATGTTAAGGAAACCAGATCCGCCGT
1 ACTTCAATC-TTTTAACTGCAATGTCAGGGAAACAAGATCCGCCGT
4379008 TGTAGCTTTA
Statistics
Matches: 192, Mismatches: 46, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
49 6 0.03
50 178 0.93
51 8 0.04
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (49 bp):
ACTTCAATCTTTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTG
Found at i:4378856 original size:100 final size:100
Alignment explanation
Indices: 4378713--4378971 Score: 362
Period size: 100 Copynumber: 2.6 Consensus size: 100
4378703 TGATTATTTA
* * * * * *
4378713 CTTCAATCTGTTT-AACTGCAGTGTCAGGGAAA-CAAGATTCGCCGCCGTGACTTCAATCTATTC
1 CTTCAATCT-TTTAAATTGCAATGTCAGGGAAACCAA-ATCCGCCGTCGTGGCTTCAATCTACTC
4378776 CACTACA-CTGCCAGGGAAGTAAGATCCGCCGTTGTGG
64 CACTACACCT-CCAGGGAAGTAAGATCCGCCGTTGTGG
* *
4378813 CTTCAATCTTTTAAATTGCAATATCAGGGAAACCAAATCCGCCGTCGTGGCTTCAATATACTCCA
1 CTTCAATCTTTTAAATTGCAATGTCAGGGAAACCAAATCCGCCGTCGTGGCTTCAATCTACTCCA
*
4378878 CTACACCTTCAGGGAAGTAAGATCCGCCGTTGTGG
66 CTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
* * *
4378913 CTTCAATCTTTTAAATTGCAATGTCGGGGAAACCAGATCCGCCGTTGTGGCTTCAATCT
1 CTTCAATCTTTTAAATTGCAATGTCAGGGAAACCAAATCCGCCGTCGTGGCTTCAATCT
4378972 TTTTAATTGC
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
99 3 0.02
100 134 0.94
101 5 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTCAGGGAAACCAAATCCGCCGTCGTGGCTTCAATCTACTCCA
CTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:4378984 original size:150 final size:149
Alignment explanation
Indices: 4378797--4379069 Score: 402
Period size: 150 Copynumber: 1.8 Consensus size: 149
4378787 CAGGGAAGTA
* *
4378797 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCAGGGAAACCAAATCCGCCGTCGTG
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCAAGGAAACCAAATCCGCCGTCGTA
*
4378862 GCTTCAATATACTCCACTACACCTTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAA
66 GCTTCAATATACTCCACTACA-CTTCAGGGAAGCAAGATCCGCCGTTGTGGCTTCAATCTTTTAA
4378927 ATTGCAATGTCGGGGAAACC
130 ATTGCAATGTCGGGGAAACC
* * * * *
4378947 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAAGGAAACCAGATCCGCCGTTGTA
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCAAGGAAACCAAATCCGCCGTCGTA
* * ** * * *
4379012 GCTTTAATCTGTTCCACTACACTTCGGGGAAGCAAGATTCGCCGTTGTGGGTTCAATC
66 GCTTCAATATACTCCACTACACTTCAGGGAAGCAAGATCCGCCGTTGTGGCTTCAATC
4379070 CGTTCCACTG
Statistics
Matches: 108, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
149 33 0.31
150 75 0.69
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (149 bp):
AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCAAGGAAACCAAATCCGCCGTCGTA
GCTTCAATATACTCCACTACACTTCAGGGAAGCAAGATCCGCCGTTGTGGCTTCAATCTTTTAAA
TTGCAATGTCGGGGAAACC
Found at i:4379008 original size:50 final size:50
Alignment explanation
Indices: 4378797--4379021 Score: 254
Period size: 50 Copynumber: 4.5 Consensus size: 50
4378787 CAGGGAAGTA
*
4378797 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCAGGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAACC
* * * ** ** * * * ***
4378847 AAATCCGCCGTCGTGGCTTCAATATACTCCACTACACCT-TCAGGGAAGTA
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCA-ATGTCAGGGAAACC
*
4378897 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAACC
* * *
4378947 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAAGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAACC
* *
4378997 AGATCCGCCGTTGTAGCTTTAATCT
1 AGATCCGCCGTTGTGGCTTCAATCT
4379022 GTTCCACTAC
Statistics
Matches: 140, Mismatches: 33, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
49 1 0.01
50 138 0.99
51 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAACC
Found at i:4379330 original size:100 final size:100
Alignment explanation
Indices: 4379157--4379340 Score: 244
Period size: 100 Copynumber: 1.8 Consensus size: 100
4379147 TAACGCCAGG
* *
4379157 GAGATAAGATCCGCCGTCGTGGCTTCAATCTACTCCGCTGCAATGCCAAAAAAATAAGACCCGCC
1 GAGATAAGATCCGCCGTCGTGGCTTCAATCTACTCCGCTGCAACGCCAAAAAAATAAGACCCACC
4379222 GTTGTGGCTTCAATCTTTTTAATTACAATGCCAAA
66 GTTGTGGCTTCAATCTTTTTAATTACAATGCCAAA
* * * * * * ** *
4379257 GAGATAGGATTCGCCTTTGTGGCTTCAATCTGCTCTGCTG-AGACGCCAGGAAAATAAGATCCAC
1 GAGATAAGATCCGCCGTCGTGGCTTCAATCTACTCCGCTGCA-ACGCCAAAAAAATAAGACCCAC
*
4379321 CGTTGTGGCTTCAGTCTTTT
65 CGTTGTGGCTTCAATCTTTT
4379341 CCATTGCAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 70 0.99
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (100 bp):
GAGATAAGATCCGCCGTCGTGGCTTCAATCTACTCCGCTGCAACGCCAAAAAAATAAGACCCACC
GTTGTGGCTTCAATCTTTTTAATTACAATGCCAAA
Found at i:4379474 original size:88 final size:88
Alignment explanation
Indices: 4379368--4379544 Score: 266
Period size: 88 Copynumber: 2.0 Consensus size: 88
4379358 CGATAAGACG
* *
4379368 GGTATCTTCGATCTGCTTCGCTACCAGTACAGGAAGGCAAGATCTG-TCATTTTCAACCTACTCC
1 GGTATCTTCGATCTGCTTCGCTACCAATACAGGAAGACAAGATCTGCT-ATTTTCAACCTACTCC
4379432 ACTGCTACCCAGGGAGACAAGGCT
65 ACTGCTACCCAGGGAGACAAGGCT
* * *
4379456 GGTATCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTATTCCA
1 GGTATCTTCGATCTGCTTCGCTACCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
* * *
4379521 CTGCTGCTCAGGGAGATAAGGCT
66 CTGCTACCCAGGGAGACAAGGCT
4379544 G
1 G
4379545 AAGTTTCACC
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 79 0.99
89 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (88 bp):
GGTATCTTCGATCTGCTTCGCTACCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
CTGCTACCCAGGGAGACAAGGCT
Found at i:4380790 original size:13 final size:13
Alignment explanation
Indices: 4380774--4380811 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
4380764 CCATTTTTAC
4380774 TTTTTCATTTTCA
1 TTTTTCATTTTCA
*
4380787 TTTTTCGTTTTCA
1 TTTTTCATTTTCA
4380800 TCTTTTCATTTT
1 T-TTTTCATTTT
4380812 TTTCACATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.11, C:0.16, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:4386214 original size:23 final size:22
Alignment explanation
Indices: 4386176--4386218 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
4386166 AAATCTCCTA
4386176 AAAATCCAAATAAAATAAAATC
1 AAAATCCAAATAAAATAAAATC
4386198 AAAATCTCTAAAT-AAATAAAA
1 AAAATC-C-AAATAAAATAAAA
4386219 CTACTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATCCAAATAAAATAAAATC
Found at i:4386664 original size:20 final size:20
Alignment explanation
Indices: 4386639--4386686 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
4386629 ACATTAGAAA
*
4386639 ATATAAAAATGGA-AATAAAT
1 ATATAAAAATGCAGAA-AAAT
*
4386659 ATATAAAAATTCAGAAAAAT
1 ATATAAAAATGCAGAAAAAT
4386679 ATATAAAA
1 ATATAAAA
4386687 TATAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
ATATAAAAATGCAGAAAAAT
Found at i:4386776 original size:19 final size:18
Alignment explanation
Indices: 4386694--4386776 Score: 53
Period size: 21 Copynumber: 4.3 Consensus size: 18
4386684 AAATATAAAA
4386694 TTAAAATTAAAAAAATATG
1 TTAAAATTAAAAAAAT-TG
*
4386713 --ATAATTGAAAAGAAATTAG
1 TTAAAATT-AAAA-AAATT-G
* * *
4386732 TTGAAATTAATAAAATTA
1 TTAAAATTAAAAAAATTG
4386750 TTACAAAATGTAAAAAAATTG
1 TT--AAAAT-TAAAAAAATTG
4386771 TTAAAA
1 TTAAAA
4386777 AACAATTGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
17 5 0.10
18 7 0.15
19 14 0.29
20 7 0.15
21 15 0.31
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.31
Consensus pattern (18 bp):
TTAAAATTAAAAAAATTG
Found at i:4386819 original size:15 final size:15
Alignment explanation
Indices: 4386799--4386828 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4386789 TAATTTGTTA
*
4386799 ATATAATTTTAAAAT
1 ATATAATTATAAAAT
4386814 ATATAATTATAAAAT
1 ATATAATTATAAAAT
4386829 GTACTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATTATAAAAT
Found at i:4391791 original size:41 final size:41
Alignment explanation
Indices: 4391763--4391944 Score: 283
Period size: 41 Copynumber: 4.4 Consensus size: 41
4391753 TACTTTAGTA
*
4391763 CACCGGCATGAAGCCTGCTAGACATAAAGTCTGAAATAATT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATT
* * *
4391804 CACCGACATTAAGCCTGCTAGACATAAAATCTAAAATAATT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
4391845 CACCGGCATTAAACCTGCTAGACATAAAGTCTGAAATAATT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
4391886 CACCGGCATTAAGCCTGCTAGACATAATGTCTGAAATAATT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATT
** *
4391927 CTTCGGCATTAAACCTGC
1 CACCGGCATTAAGCCTGC
4391945 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 128 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAATT
Found at i:4393953 original size:2 final size:2
Alignment explanation
Indices: 4393946--4393977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4393936 NNNNNNNNNN
4393946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4393978 ATTCATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4404001 original size:16 final size:15
Alignment explanation
Indices: 4403949--4404001 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
4403939 TTAGATTCAG
* *
4403949 ATTTTTCTGGGCTCA
1 ATTTTTTTGGGCTTA
* *
4403964 AGTTTTCTTGGGATTA
1 A-TTTTTTTGGGCTTA
*
4403980 AATTTTTTGGGCTTA
1 ATTTTTTTGGGCTTA
4403995 ATTTTTT
1 ATTTTTT
4404002 CGTGCTCGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.17, C:0.09, G:0.19, T:0.55
Consensus pattern (15 bp):
ATTTTTTTGGGCTTA
Found at i:4404273 original size:5 final size:5
Alignment explanation
Indices: 4404246--4404288 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
4404236 TGTAAAATTC
*
4404246 ATTAT ATTTT ATTAT -TTATT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT ATT
4404289 GTCAATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 28 0.82
6 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATTAT
Found at i:4405680 original size:23 final size:23
Alignment explanation
Indices: 4405649--4405702 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
4405639 CCCCCATCTG
4405649 CTACACACTATCTCTGTCCATCC
1 CTACACACTATCTCTGTCCATCC
* * *
4405672 CTACTCACTATCTCTGTTCATCT
1 CTACACACTATCTCTGTCCATCC
4405695 CTACACAC
1 CTACACAC
4405703 CAAATAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.04, T:0.33
Consensus pattern (23 bp):
CTACACACTATCTCTGTCCATCC
Found at i:4411387 original size:43 final size:43
Alignment explanation
Indices: 4411330--4411490 Score: 196
Period size: 43 Copynumber: 3.7 Consensus size: 43
4411320 GTTTTAAAAA
* *
4411330 AAACGCCGCTAAAGATCATGTCCTTTAGCGGCACTTTTTCTAC
1 AAACGCCGCTAAAGACCATGTCCTTTAGCGGCACTTATTCTAC
*
4411373 AAACGCCGCTAAAGACCATGTCCTTTAGCAGCACTTATTCTAC
1 AAACGCCGCTAAAGACCATGTCCTTTAGCGGCACTTATTCTAC
* * * * * *
4411416 AAACGTCGTTAAAGACCATGTCCTTTAGCGGCGCTTATCCCAT
1 AAACGCCGCTAAAGACCATGTCCTTTAGCGGCACTTATTCTAC
** * **
4411459 AAACTTCGCTAAAGACCGTGAGCTTTAGCGGC
1 AAACGCCGCTAAAGACCATGTCCTTTAGCGGC
4411491 GCTTTTTAAA
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGTCCTTTAGCGGCACTTATTCTAC
Found at i:4411713 original size:19 final size:19
Alignment explanation
Indices: 4411689--4411726 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4411679 TACAAAAATG
*
4411689 TTAAAAGTTAAAATGATAA
1 TTAAAAGTCAAAATGATAA
4411708 TTAAAAGTCAAAATGATAA
1 TTAAAAGTCAAAATGATAA
4411727 AAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (19 bp):
TTAAAAGTCAAAATGATAA
Found at i:4417342 original size:10 final size:10
Alignment explanation
Indices: 4417327--4417352 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4417317 NNNNNNNNNN
4417327 TATATCCATA
1 TATATCCATA
4417337 TATATCCATA
1 TATATCCATA
4417347 TATATC
1 TATATC
4417353 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATCCATA
Found at i:4419546 original size:14 final size:14
Alignment explanation
Indices: 4419527--4419594 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
4419517 ATGACCGTTG
4419527 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
4419541 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
4419556 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
4419569 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
4419582 AAACCTTAAATCT
1 AAACCCTAAATCT
4419595 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:4419550 original size:15 final size:15
Alignment explanation
Indices: 4419530--4419567 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4419520 ACCGTTGAAA
4419530 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
4419545 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
4419560 CCCTAAAT
1 CCCTAAAT
4419568 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:4420145 original size:41 final size:41
Alignment explanation
Indices: 4420081--4420270 Score: 170
Period size: 41 Copynumber: 4.6 Consensus size: 41
4420071 TTTTGTTACT
* ** *
4420081 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAATAC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGATAC
* ** *
4420122 ATTAGCGGCGCTTAGATACAAACGCCGCTAAAGG-CCATAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGATA-C
* * * * * *
4420163 ATTAGTGGCGCTCAGATAAAAACGCCACGAAAGGCCAGAGA-
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAGATAC
* * *
4420204 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGATCAGA-GC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AGATAC
*
4420245 ATTAGCGGCGTTTAGATAAAAACGCC
1 ATTAGCGGCGCTTAGATAAAAACGCC
4420271 ACCAAAAATC
Statistics
Matches: 121, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
40 3 0.02
41 116 0.96
43 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGATAC
Found at i:4420298 original size:41 final size:41
Alignment explanation
Indices: 4420121--4420295 Score: 197
Period size: 41 Copynumber: 4.3 Consensus size: 41
4420111 AAGGTAAATA
* * * *
4420121 CATTAGCGGCGCTTAGATACAAACGCCGCTAAAGGCCATAG
1 CATTAGCGGCGCTTAGATAAAAACGCCACTAAAGACCAGAG
* * * * *
4420162 AATTAGTGGCGCTCAGATAAAAACGCCACGAAAGGCCAGAG
1 CATTAGCGGCGCTTAGATAAAAACGCCACTAAAGACCAGAG
* * * *
4420203 AATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGATCAGAG
1 CATTAGCGGCGCTTAGATAAAAACGCCACTAAAGACCAGAG
* * * *
4420244 CATTAGCGGCGTTTAGATAAAAACGCCACCAAAAATCAGAG
1 CATTAGCGGCGCTTAGATAAAAACGCCACTAAAGACCAGAG
4420285 CATTAGCGGCG
1 CATTAGCGGCG
4420296 TTTTTTACAA
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 116 1.00
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.15
Consensus pattern (41 bp):
CATTAGCGGCGCTTAGATAAAAACGCCACTAAAGACCAGAG
Found at i:4420313 original size:82 final size:82
Alignment explanation
Indices: 4420122--4420295 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
4420112 AGGTAAATAC
* ** * * *
4420122 ATTAGCGGCGCTTAGATACAAACGCCGCTAAAGGCCATAGAATTAGTGGCGCTCAGATAAAAACG
1 ATTAGCGGCGCTCAGATACAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTCAGATAAAAACG
* **
4420187 CCACGAAAGGCCAGAGA
66 CCACCAAAAACCAGAGA
* * *
4420204 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGATCAGAGCATTAGCGGCGTTTAGATAAAAACG
1 ATTAGCGGCGCTCAGATACAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTCAGATAAAAACG
* *
4420269 CCACCAAAAATCAGAGC
66 CCACCAAAAACCAGAGA
4420286 ATTAGCGGCG
1 ATTAGCGGCG
4420296 TTTTTTACAA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.16
Consensus pattern (82 bp):
ATTAGCGGCGCTCAGATACAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTCAGATAAAAACG
CCACCAAAAACCAGAGA
Found at i:4420330 original size:41 final size:41
Alignment explanation
Indices: 4420222--4420359 Score: 136
Period size: 41 Copynumber: 3.4 Consensus size: 41
4420212 CGCTCAGATA
* **
4420222 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGTTTAGATA-
1 AAAACGCCGCCAAAGATCAGAGCATTAGCGGCGTTT-TTTAC
* *
4420263 AAAACGCCACCAAAAATCAGAGCATTAGCGGCGTTTTTTAC
1 AAAACGCCGCCAAAGATCAGAGCATTAGCGGCGTTTTTTAC
* * * * * *
4420304 AAAGCGCCGCGAAAGATCCGATCATTAGCGTCG-CTTTTAC
1 AAAACGCCGCCAAAGATCAGAGCATTAGCGGCGTTTTTTAC
*
4420344 AAAAACGCCGCTAAAG
1 -AAAACGCCGCCAAAG
4420360 GCCCAAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 8 0.10
41 72 0.90
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCCAAAGATCAGAGCATTAGCGGCGTTTTTTAC
Done.