Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008812.1 Hibiscus syriacus cultivar Beakdansim tig00111973_pilon, whole genome shotgun sequence
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: 944649
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:461720 original size:20 final size:20
Alignment explanation
Indices: 461692--461748 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
461682 CGGTATCTCT
*
461692 ACCGTTTTTGTCAAACTGAA
1 ACCGATTTTGTCAAACTGAA
461712 ACCGATTTTGTCAAACTGAA
1 ACCGATTTTGTCAAACTGAA
*
461732 ACCGGTTTTGTCAAACT
1 ACCGATTTTGTCAAACT
461749 TTAACATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ACCGATTTTGTCAAACTGAA
Found at i:461950 original size:14 final size:16
Alignment explanation
Indices: 461931--461967 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
461921 TTTTTCAATT
461931 TCCAA-TCA-GTTTTG
1 TCCAATTCATGTTTTG
461945 TCCAATTCATGTTTTG
1 TCCAATTCATGTTTTG
*
461961 TCAAATT
1 TCCAATT
461968 GAAATCGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 3 0.15
16 12 0.60
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (16 bp):
TCCAATTCATGTTTTG
Found at i:462185 original size:30 final size:31
Alignment explanation
Indices: 462130--462192 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
462120 CTTCGTATCG
* *
462130 TTAAATCGACTTTGTTAAGTATTTTATTAAA
1 TTAAACCGACTTTATTAAGTATTTTATTAAA
462161 TTAAACCGACTTTATTAA-TATTTTATTAAA
1 TTAAACCGACTTTATTAAGTATTTTATTAAA
462191 TT
1 TT
462193 TTCGATCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
TTAAACCGACTTTATTAAGTATTTTATTAAA
Found at i:464875 original size:16 final size:15
Alignment explanation
Indices: 464813--464888 Score: 68
Period size: 16 Copynumber: 4.9 Consensus size: 15
464803 AAAATAAAAA
464813 ATAATAATATACCTAAT
1 ATAATAATATA--TAAT
* *
464830 ATGATAA-ATATAAA
1 ATAATAATATATAAT
464844 ATAATAATAATATAAT
1 ATAATAAT-ATATAAT
464860 ATAAATAATATATAAT
1 AT-AATAATATATAAT
464876 A-AA-AACTATATAA
1 ATAATAA-TATATAA
464889 CATATATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.04
14 18 0.35
16 19 0.37
17 12 0.24
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (15 bp):
ATAATAATATATAAT
Found at i:464878 original size:14 final size:14
Alignment explanation
Indices: 464844--464888 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
464834 TAAATATAAA
464844 ATAAT-AATAATAT
1 ATAATAAATAATAT
464857 A-ATATAAATAATAT
1 ATA-ATAAATAATAT
464871 ATAATAAA-AACTAT
1 ATAATAAATAA-TAT
464885 ATAA
1 ATAA
464889 CATATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 5 0.18
14 21 0.75
15 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAAATAATAT
Found at i:464886 original size:25 final size:24
Alignment explanation
Indices: 464867--464912 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
464857 AATATAAATA
*
464867 ATATATAAT-AAAAACTATATAAC
1 ATATATTATCAAAAACTATATAAC
*
464890 ATATATTTTCAAAAACTATATAA
1 ATATATTATCAAAAACTATATAA
464913 TATGTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATATTATCAAAAACTATATAAC
Found at i:464915 original size:22 final size:23
Alignment explanation
Indices: 464876--464950 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 23
464866 AATATATAAT
*
464876 AAAAACTATATAACATATATTTTC
1 AAAAACTATAT-ACATATGTTTTC
464900 AAAAACTATATA-ATATGTTTTC
1 AAAAACTATATACATATGTTTTC
*
464922 AAAATTA-TATATATATATGTTTTC
1 AAAA--ACTATATACATATGTTTTC
464946 AAAAA
1 AAAAA
464951 TCGTTTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
22 14 0.30
23 7 0.15
24 26 0.55
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (23 bp):
AAAAACTATATACATATGTTTTC
Found at i:465059 original size:35 final size:35
Alignment explanation
Indices: 465011--465136 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
465001 AATCTGTTTT
* *
465011 ATATTATGCATTTTCAAAAAGGTATTTTCAAAACC
1 ATATTATACATTTTCAAAAAGGTGTTTTCAAAACC
* ** *
465046 ATATTATATATTTTCAAAAATATGTTTTC-AAACTAT
1 ATATTATACATTTTCAAAAAGGTGTTTTCAAAAC--C
*
465082 ATATTATACATTTTTAAAAAGGTGTTTTCAAAACC
1 ATATTATACATTTTCAAAAAGGTGTTTTCAAAACC
**
465117 ATATTATATGTTTTCAAAAA
1 ATATTATACATTTTCAAAAA
465137 CCGATTTTTG
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
34 4 0.05
35 41 0.55
36 25 0.34
37 4 0.05
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.42
Consensus pattern (35 bp):
ATATTATACATTTTCAAAAAGGTGTTTTCAAAACC
Found at i:468323 original size:15 final size:15
Alignment explanation
Indices: 468303--468337 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
468293 ATGATAATAG
* *
468303 TGAGGTATTTTGGGT
1 TGAGGTATTTAGGGC
468318 TGAGGTATTTAGGGC
1 TGAGGTATTTAGGGC
468333 TGAGG
1 TGAGG
468338 GGATGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.43, T:0.37
Consensus pattern (15 bp):
TGAGGTATTTAGGGC
Found at i:478769 original size:27 final size:27
Alignment explanation
Indices: 478739--478790 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
478729 ATAACATTAA
478739 ATAATAATAATAATAAT-ATAATATAAT
1 ATAATAATAATAA-AATAATAATATAAT
*
478766 ATAATAATTATAAAATAATAATATA
1 ATAATAATAATAAAATAATAATATA
478791 TAATGTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAATAATAATAAAATAATAATATAAT
Found at i:478778 original size:24 final size:22
Alignment explanation
Indices: 478742--478802 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
478732 ACATTAAATA
*
478742 ATAATAATAATAATATAATATAAT
1 ATAATAATTATAATAT-A-ATAAT
*
478766 ATAATAATTATAAAATAATAAT
1 ATAATAATTATAATATAATAAT
478788 AT-ATAATGTATAATA
1 ATAATAAT-TATAATA
478803 AAAAAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.15
22 13 0.39
23 1 0.03
24 14 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATAATTATAATATAATAAT
Found at i:478799 original size:7 final size:7
Alignment explanation
Indices: 478738--478802 Score: 50
Period size: 6 Copynumber: 9.6 Consensus size: 7
478728 AATAACATTA
478738 AATA-AT
1 AATATAT
478744 AATA-AT
1 AATATAT
478750 AATA-AT
1 AATATAT
478756 -ATAATAT
1 AAT-ATAT
478763 AATATAAT
1 AATAT-AT
478771 AAT-TAT
1 AATATAT
*
478777 AAAATAAT
1 AATAT-AT
478785 AATATAT
1 AATATAT
*
478792 AATGTAT
1 AATATAT
478799 AATA
1 AATA
478803 AAAAAAACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 2 0.04
6 17 0.35
7 17 0.35
8 13 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (7 bp):
AATATAT
Found at i:478803 original size:3 final size:3
Alignment explanation
Indices: 478738--478794 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
478728 AATAACATTA
*
478738 AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT -AT AAT AAT TAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
478782 AAT AAT ATAT AAT
1 AAT AAT A-AT AAT
478795 GTATAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:478823 original size:24 final size:24
Alignment explanation
Indices: 478787--478841 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
478777 AAAATAATAA
**
478787 TATATAATGTATAATAAAAAAAAC
1 TATATAACATATAATAAAAAAAAC
* ***
478811 TATATAACATATATTTTCAAAAAC
1 TATATAACATATAATAAAAAAAAC
478835 TATATAA
1 TATATAA
478842 TATGTTTTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
TATATAACATATAATAAAAAAAAC
Found at i:478844 original size:22 final size:24
Alignment explanation
Indices: 478805--478855 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
478795 GTATAATAAA
478805 AAAAACTATATAACATATATTTTC
1 AAAAACTATATAACATATATTTTC
*
478829 AAAAACTATAT-A-ATATGTTTTC
1 AAAAACTATATAACATATATTTTC
478851 AAAAA
1 AAAAA
478856 TTGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 14 0.54
23 1 0.04
24 11 0.42
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAACTATATAACATATATTTTC
Found at i:478919 original size:33 final size:32
Alignment explanation
Indices: 478821--479061 Score: 121
Period size: 35 Copynumber: 7.0 Consensus size: 32
478811 TATATAACAT
*
478821 ATATTTTCAAAAACTATATAATATGTTTTC-AAA
1 ATATTTT-AAAAACTATATTATATG-TTTCAAAA
* * * * * *
478854 A-ATTGTATATATTATA-TATGTTTTTTCAAAA
1 ATATTTTAAAAACTATATTAT-ATGTTTCAAAA
478885 ATCATTTTAAAAAACTATA-TATATGTTTCAAAA
1 AT-ATTTT-AAAAACTATATTATATGTTTCAAAA
*
478918 ATATTTTCAAAACTATATTATATACGTTTTCAAAA
1 ATATTTTAAAAACTATATTATAT--G-TTTCAAAA
* * *
478953 ACTGTTTTTAAAACTATATATTATACGTTTTCAAAA
1 A-TATTTTAAAAAC--TATATTATATG-TTTCAAAA
* * * *
478989 AGGTGTTTTCAAAACCATATTATATATTTTCAAAA
1 A--TATTTTAAAAACTATATTATAT-GTTTCAAAA
* *
479024 ATGTGTTTTTAAAACTATATATTATATGTTTCCAAAA
1 A--TATTTTAAAAAC--TATATTATATGTTT-CAAAA
479061 A
1 A
479062 AGTGTTTTCA
Statistics
Matches: 165, Mismatches: 26, Indels: 30
0.75 0.12 0.14
Matches are distributed among these distances:
30 6 0.04
31 21 0.13
32 14 0.08
33 16 0.10
34 11 0.07
35 38 0.23
36 24 0.15
37 26 0.16
38 9 0.05
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (32 bp):
ATATTTTAAAAACTATATTATATGTTTCAAAA
Found at i:478941 original size:36 final size:36
Alignment explanation
Indices: 478900--479091 Score: 200
Period size: 37 Copynumber: 5.4 Consensus size: 36
478890 TTTAAAAAAC
*
478900 TATATATATGTTTCAAAAA-TATTTTCAAAACTATA
1 TATATATATGTTTCAAAAAGTGTTTTCAAAACTATA
* * *
478935 T-TATATACGTTTTCAAAAACTGTTTTTAAAACTATA
1 TATATATATG-TTTCAAAAAGTGTTTTCAAAACTATA
* *
478971 TAT-TATACGTTTTCAAAAAGGTGTTTTCAAAACCATA
1 TATATATATG-TTTCAAAAA-GTGTTTTCAAAACTATA
*
479008 T-TATATAT-TTTCAAAAATGTGTTTTTAAAACTATA
1 TATATATATGTTTCAAAAA-GTGTTTTCAAAACTATA
*
479043 TAT-TATATGTTTCCAAAAAAGTGTTTTCAAAACCATA
1 TATATATATGTTT-C-AAAAAGTGTTTTCAAAACTATA
*
479080 T-TATCTATGTTT
1 TATATATATGTTT
479092 TTAAAAAACC
Statistics
Matches: 134, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
34 7 0.05
35 40 0.30
36 37 0.28
37 45 0.34
38 5 0.04
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (36 bp):
TATATATATGTTTCAAAAAGTGTTTTCAAAACTATA
Found at i:479046 original size:72 final size:70
Alignment explanation
Indices: 478895--479083 Score: 253
Period size: 72 Copynumber: 2.7 Consensus size: 70
478885 ATCATTTTAA
* *
478895 AAAACTATATA-TAT-G-TTTCAAAAA-TATTTTCAAAACTATATTATATACGTTTTCAAAAACT
1 AAAACTATATATTATAGTTTTCAAAAAGTGTTTTCAAAACCATATTATATAC-TTTTCAAAAACT
478956 GTTTTT
65 GTTTTT
478962 AAAACTATATATTATACGTTTTCAAAAAGGTGTTTTCAAAACCATATTATATA-TTTTCAAAAAT
1 AAAACTATATATTATA-GTTTTCAAAAA-GTGTTTTCAAAACCATATTATATACTTTTCAAAAA-
*
479026 GTGTTTTT
63 CTGTTTTT
*
479034 AAAACTATATATTATATGTTTCCAAAAAAGTGTTTTCAAAACCATATTAT
1 AAAACTATATATTATA-GTTTTC-AAAAAGTGTTTTCAAAACCATATTAT
479084 CTATGTTTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
67 11 0.10
68 3 0.03
70 1 0.01
71 19 0.17
72 49 0.45
73 26 0.24
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (70 bp):
AAAACTATATATTATAGTTTTCAAAAAGTGTTTTCAAAACCATATTATATACTTTTCAAAAACTG
TTTTT
Found at i:479060 original size:37 final size:35
Alignment explanation
Indices: 478900--479080 Score: 183
Period size: 35 Copynumber: 5.1 Consensus size: 35
478890 TTTAAAAAAC
*
478900 TATA-TATATGTTTCAAAAA-TATTTTCAAAACTA
1 TATATTATATGTTTCAAAAAGTGTTTTCAAAACTA
* * *
478933 TAT-TATATACGTTTTCAAAAACTGTTTTTAAAACTA
1 TATAT-TATATG-TTTCAAAAAGTGTTTTCAAAACTA
* *
478969 TATATTATACGTTTTCAAAAAGGTGTTTTCAAAACCA
1 TATATTATATG-TTTCAAAAA-GTGTTTTCAAAACTA
*
479006 TAT-TATATAT-TTTCAAAAATGTGTTTTTAAAACTA
1 TATAT-TATATGTTTCAAAAA-GTGTTTTCAAAACTA
*
479041 TATATTATATGTTTCCAAAAAAGTGTTTTCAAAACCA
1 TATATTATATGTTT-C-AAAAAGTGTTTTCAAAACTA
479078 TAT
1 TAT
479081 TATCTATGTT
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
33 3 0.02
34 5 0.04
35 39 0.31
36 36 0.29
37 37 0.30
38 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (35 bp):
TATATTATATGTTTCAAAAAGTGTTTTCAAAACTA
Found at i:479900 original size:7 final size:7
Alignment explanation
Indices: 479874--479924 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
479864 TTGACCTAAT
479874 ATAATAA
1 ATAATAA
479881 AT-AT-A
1 ATAATAA
479886 A-AAT-A
1 ATAATAA
479891 ATAATAA
1 ATAATAA
479898 ATAAT-A
1 ATAATAA
479904 AT-ATAA
1 ATAATAA
*
479910 ATAATAT
1 ATAATAA
479917 ATAATAA
1 ATAATAA
479924 A
1 A
479925 AAAACTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 8 0.22
6 11 0.30
7 18 0.49
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAATAA
Found at i:479933 original size:16 final size:16
Alignment explanation
Indices: 479870--479936 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
479860 AGCTTTGACC
*
479870 TAATATAATAAATATA
1 TAATATAAAAAATATA
* *
479886 AAATAATAATAAATA-A
1 TAAT-ATAAAAAATATA
*
479902 TAATATAAATAATATA
1 TAATATAAAAAATATA
479918 TAATA-AAAAAACTATA
1 TAATATAAAAAA-TATA
479934 TAA
1 TAA
479937 CATACATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.30
16 20 0.47
17 10 0.23
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATATAAAAAATATA
Found at i:480037 original size:21 final size:23
Alignment explanation
Indices: 480007--480062 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
479997 TTCAAAAATC
*
480007 GTTTTAAAAAACTATA-TATAT-
1 GTTTTCAAAAACTATATTATATA
480028 GTTTTC-AAAACTATATTATATA
1 GTTTTCAAAAACTATATTATATA
480050 CGTTTTCAAAAAC
1 -GTTTTCAAAAAC
480063 CTTTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.30
21 10 0.33
23 6 0.20
24 5 0.17
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (23 bp):
GTTTTCAAAAACTATATTATATA
Found at i:480039 original size:20 final size:22
Alignment explanation
Indices: 480014--480060 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
480004 ATCGTTTTAA
480014 AAAACTATA-TATAT-GTTTTC
1 AAAACTATATTATATAGTTTTC
480034 AAAACTATATTATATACGTTTTC
1 AAAACTATATTATATA-GTTTTC
480057 AAAA
1 AAAA
480061 ACCTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.38
21 5 0.21
23 10 0.42
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAACTATATTATATAGTTTTC
Found at i:480061 original size:57 final size:59
Alignment explanation
Indices: 479982--480096 Score: 155
Period size: 57 Copynumber: 2.0 Consensus size: 59
479972 AAAAATTATA
* * *
479982 TATATTATATATGTTTTCAAAAATC-GTTTTAAAA-AACTATA-TATATGTTTTCAAAAC
1 TATATTATATACGTTTTCAAAAACCTGTTTTAAAATAA-TATATTATACGTTTTCAAAAC
* *
480039 TATATTATATACGTTTTCAAAAACCTTTTTTAAAATTATATATTATACGTTTTCAAAA
1 TATATTATATACGTTTTCAAAAACCTGTTTTAAAATAATATATTATACGTTTTCAAAA
480097 AGGTATTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 23 0.46
58 12 0.24
59 15 0.30
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (59 bp):
TATATTATATACGTTTTCAAAAACCTGTTTTAAAATAATATATTATACGTTTTCAAAAC
Found at i:480086 original size:36 final size:37
Alignment explanation
Indices: 480029--480206 Score: 188
Period size: 36 Copynumber: 4.9 Consensus size: 37
480019 TATATATATG
*
480029 TTTTCAAAACTATATTATATACGTTTTCAAAAACCT-
1 TTTTCAAAACTATATTATATACGTTTTCAAAAACGTA
* * *
480065 TTTTTAAAATTATA-TATTATACGTTTTCAAAAAGGTA
1 TTTTCAAAACTATATTA-TATACGTTTTCAAAAACGTA
* * *
480102 TTTTCAAAACTATATTATATA--TTTTAAAAAATGTG
1 TTTTCAAAACTATATTATATACGTTTTCAAAAACGTA
* * *
480137 CTTTCAAAACTATA-TATTATATGTTTTCAAAAAGGT-
1 TTTTCAAAACTATATTA-TATACGTTTTCAAAAACGTA
* *
480173 TTTTCAAAACCATATTATATATGTTTTCAAAAAC
1 TTTTCAAAACTATATTATATACGTTTTCAAAAAC
480207 TGATTAAATA
Statistics
Matches: 120, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
34 2 0.02
35 30 0.25
36 57 0.47
37 29 0.24
38 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATTATATACGTTTTCAAAAACGTA
Found at i:480212 original size:23 final size:23
Alignment explanation
Indices: 480173--480217 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
480163 TCAAAAAGGT
* *
480173 TTTTCAAAACCATATTATATATG
1 TTTTCAAAAACATATTAAATATG
480196 TTTTCAAAAAC-TGATTAAATAT
1 TTTTCAAAAACAT-ATTAAATAT
480218 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTTCAAAAACATATTAAATATG
Found at i:480282 original size:44 final size:42
Alignment explanation
Indices: 480184--480282 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 42
480174 TTTCAAAACC
*
480184 ATATTATATATGTTTTCAAAAACTGATTAAATATATATATAT
1 ATATTATATATGTTTTCAAAAACTGATTAAAAATATATATAT
*
480226 ATATATATTATATGTTTTCAAAAA-TAGTTTCAAAAAT-TATACTAT
1 ATAT-TA-TATATGTTTTCAAAAACT-GATT-AAAAATATATA-TAT
480271 ATTATTATATAT
1 A-TATTATATAT
480283 AGTAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
42 4 0.08
43 3 0.06
44 28 0.57
45 11 0.22
46 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (42 bp):
ATATTATATATGTTTTCAAAAACTGATTAAAAATATATATAT
Found at i:480744 original size:21 final size:21
Alignment explanation
Indices: 480687--480745 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
480677 TATGATAAAG
*
480687 TATTAATATAATTAATATAATT
1 TATTAA-ATTATTAATATAATT
* * *
480709 TATT-ATTTTTATAATATTATT
1 TATTAAATTAT-TAATATAATT
480730 TATTAAATTATTAATA
1 TATTAAATTATTAATA
480746 ATGAATAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.07
21 19 0.66
22 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAAATTATTAATATAATT
Found at i:482231 original size:26 final size:26
Alignment explanation
Indices: 482197--482252 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
482187 TTACACACAT
*
482197 ATTAAAAACATTAACTCTTACATTAC
1 ATTAAAAACATTAACTCATACATTAC
*
482223 ATTAGAAACATTAACTCATACATTAC
1 ATTAAAAACATTAACTCATACATTAC
482249 ATTA
1 ATTA
482253 CAATACAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (26 bp):
ATTAAAAACATTAACTCATACATTAC
Found at i:483556 original size:14 final size:14
Alignment explanation
Indices: 483537--483566 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
483527 GTTATACACT
483537 TAAACGATAAATGC
1 TAAACGATAAATGC
483551 TAAACGATAAATGC
1 TAAACGATAAATGC
483565 TA
1 TA
483567 TAAATCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (14 bp):
TAAACGATAAATGC
Found at i:483889 original size:15 final size:15
Alignment explanation
Indices: 483861--483895 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
483851 AACAACATCC
* *
483861 CCTCAGCCCTAAATA
1 CCTCAACCCAAAATA
483876 CCTCAACCCAAAATA
1 CCTCAACCCAAAATA
483891 CCTCA
1 CCTCA
483896 CTATTATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.43, G:0.03, T:0.17
Consensus pattern (15 bp):
CCTCAACCCAAAATA
Found at i:484736 original size:62 final size:63
Alignment explanation
Indices: 484531--484732 Score: 191
Period size: 62 Copynumber: 3.2 Consensus size: 63
484521 TAATGCTTTC
* * * * * * *
484531 ATGAATACGATAATGCAATTCATGTGTTTGGGGAAAGTTCTCACGAGAGGTCAAAAAGTCTGA
1 ATGAATACGATAATACGATTCATGTATTTGGGAAAAGTCCTCATGAGAGGTCAAAAAATCTGA
* * * * *
484594 ATCAATACGACT-ATACGA-TCTAAGTATTTGGGAAATGTCCTCATGAGAGG-CCAGAAATCTGA
1 ATGAATACGA-TAATACGATTC-ATGTATTTGGGAAAAGTCCTCATGAGAGGTCAAAAAATCTGA
* * *
484656 ATG-A-ACGTTGTAATATGATTCATGTATTTGGGAAAAGTCCTCATGAGAGGTCAAAAAAT-TTA
1 ATGAATACG--ATAATACGATTCATGTATTTGGGAAAAGTCCTCATGAGAGGTCAAAAAATCTGA
484718 ATGAATACGATAATA
1 ATGAATACGATAATA
484733 TGATGATGAA
Statistics
Matches: 109, Mismatches: 21, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
60 3 0.03
61 2 0.02
62 55 0.50
63 45 0.41
64 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (63 bp):
ATGAATACGATAATACGATTCATGTATTTGGGAAAAGTCCTCATGAGAGGTCAAAAAATCTGA
Found at i:487946 original size:40 final size:40
Alignment explanation
Indices: 487885--488046 Score: 252
Period size: 40 Copynumber: 4.0 Consensus size: 40
487875 TGTAGGTTTA
* *
487885 TAATACACTTTTGTGTCTATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
** *
487925 TAATACACTTTGGTGTATATGGTAAGTACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
487965 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
* * *
488005 TAATACACTTCGGTGTATATGGTGGGTACAACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
488045 TA
1 TA
488047 GCACTACGGT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 111 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (40 bp):
TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:488126 original size:20 final size:20
Alignment explanation
Indices: 488096--488146 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
488086 CAGGGTTGTA
* *
488096 TATTGGGTTATTGTCTATTG
1 TATTTGGTTATTGTCTATGG
*
488116 T-TTATGGTTATTTTCTATGG
1 TATT-TGGTTATTGTCTATGG
488136 TATTTGGTTAT
1 TATTTGGTTAT
488147 GGAATAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.16, C:0.04, G:0.22, T:0.59
Consensus pattern (20 bp):
TATTTGGTTATTGTCTATGG
Found at i:488676 original size:21 final size:21
Alignment explanation
Indices: 488652--488691 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
488642 TGTAACAATT
*
488652 ACTGTAGCAGTGT-ATCGATGC
1 ACTGTAACAGT-TCATCGATGC
488673 ACTGTAACAGTTCATCGAT
1 ACTGTAACAGTTCATCGAT
488692 ACAGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
ACTGTAACAGTTCATCGATGC
Found at i:490690 original size:24 final size:23
Alignment explanation
Indices: 490658--490734 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
490648 CATTTAAATG
490658 ATAAACGAAAACAAATGAACGAAC
1 ATAAACG-AAACAAATGAACGAAC
**
490682 ATAAACG-AATGAATGTAAACGAAC
1 ATAAACGAAACAAATG--AACGAAC
*
490706 ATAAAC-AAACACAATAAACGAAC
1 ATAAACGAAACA-AATGAACGAAC
490729 ATAAAC
1 ATAAAC
490735 CAACACAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
22 6 0.14
23 13 0.30
24 22 0.50
25 3 0.07
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (23 bp):
ATAAACGAAACAAATGAACGAAC
Found at i:490727 original size:23 final size:23
Alignment explanation
Indices: 490697--490746 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
490687 CGAATGAATG
490697 TAAACGAACATAAACAAACACAA
1 TAAACGAACATAAACAAACACAA
*
490720 TAAACGAACATAAACCAACACAA
1 TAAACGAACATAAACAAACACAA
490743 TAAA
1 TAAA
490747 GGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.64, C:0.22, G:0.04, T:0.10
Consensus pattern (23 bp):
TAAACGAACATAAACAAACACAA
Found at i:490988 original size:10 final size:10
Alignment explanation
Indices: 490956--490991 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
490946 AACATAAATG
*
490956 AATGCACATA
1 AATGAACATA
*
490966 AACGAACATA
1 AATGAACATA
490976 AATGAACATA
1 AATGAACATA
490986 AATGAA
1 AATGAA
490992 TGAACATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.17
Consensus pattern (10 bp):
AATGAACATA
Found at i:498214 original size:65 final size:65
Alignment explanation
Indices: 498082--498241 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
498072 TGCAGTAAGA
* * * ** *
498082 GTGCATCGATGCATGAAGTACATTCGATG-TTTCAAAATTGCCTGAGTGAATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGAATCGATGCATGTCGT
* * * *
498146 GTGCATCGATGCATCAAATGCTTTCGATGTTTTCATAAA-AACCTGAGTGCATCGATTCATGGT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACCTGAGTGAATCGATGCAT-GTC
498209 GT
64 GT
*
498211 GTGCATCAATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
498242 CAATTTATTC
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 25 0.31
65 51 0.63
66 5 0.06
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGAATCGATGCATGTCGT
Found at i:499376 original size:21 final size:21
Alignment explanation
Indices: 499350--499393 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
499340 CCGGAGGAGG
*
499350 AGGAGAAGCACGAGAAGAGCT
1 AGGAGAAGCACGAGAAGAACT
* *
499371 AGGAGAAGCTCGTGAAGAACT
1 AGGAGAAGCACGAGAAGAACT
499392 AG
1 AG
499394 CTCTCGGAGT
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:0.14, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGAAGCACGAGAAGAACT
Found at i:500975 original size:23 final size:23
Alignment explanation
Indices: 500945--501008 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
500935 GCATGGCTTT
500945 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
500968 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
500990 -TGTATCGATGCACATTCAA
1 GTGCATCGATGCACATTCAA
501009 ATAGATGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 4 0.12
23 15 0.44
24 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:504842 original size:22 final size:21
Alignment explanation
Indices: 504802--504841 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
504792 GAGTTTATTT
504802 TCATTTTTCAATTTTAAAATA
1 TCATTTTTCAATTTTAAAATA
504823 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
504842 ACAACTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:506926 original size:65 final size:65
Alignment explanation
Indices: 506787--506946 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
506777 CGCACTAAGA
* * * * * * *
506787 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTAAGTGAATCGATGCATGGCGT
* * *
506851 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTAAGTGAATCGATTCATGGGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACCTAAGTGAATCGATGCATGGCG
506915 T
65 T
*
506916 GTGCAACGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
506947 CAATTTATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 27 0.33
65 53 0.64
66 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTAAGTGAATCGATGCATGGCGT
Found at i:508817 original size:36 final size:36
Alignment explanation
Indices: 508777--508916 Score: 228
Period size: 36 Copynumber: 3.9 Consensus size: 36
508767 ATACAATCTT
*
508777 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
508813 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
508849 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
508885 TCCACCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
508917 ACTTATAAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.21
36 77 0.79
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:508856 original size:13 final size:11
Alignment explanation
Indices: 508799--508899 Score: 62
Period size: 11 Copynumber: 8.5 Consensus size: 11
508789 ATCACGCCTT
508799 TATCATCACCA
1 TATCATCACCA
*
508810 TAGTCCATCTCCA
1 TA-T-CATCACCA
*
508823 TTATCA-CGCCTA
1 -TATCATCACC-A
508835 TATCATCACCA
1 TATCATCACCA
508846 TAGTCCATCACCA
1 TA-T-CATCACCA
*
508859 TTATCA-CGCCTA
1 -TATCATCACC-A
508871 TATCATCACCA
1 TATCATCACCA
*
508882 TATTCCACCACCA
1 TA-T-CATCACCA
508895 TATCA
1 TATCA
508900 CGCCTATATT
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
11 26 0.36
12 16 0.22
13 26 0.36
14 4 0.06
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (11 bp):
TATCATCACCA
Found at i:508878 original size:23 final size:23
Alignment explanation
Indices: 508779--508882 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
508769 ACAATCTTTC
*
508779 CATCACCATTATCA-CGCCTTTAT
1 CATCACCATTATCATCGCC-ATAT
*
508802 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
508825 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
508850 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCC-ATAT
508874 CATCACCAT
1 CATCACCAT
508883 ATTCCACCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 8 0.12
25 14 0.22
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:509397 original size:14 final size:15
Alignment explanation
Indices: 509363--509409 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
509353 AATTTGGAGT
509363 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
509378 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
509392 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
509409 G
1 G
509410 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:513024 original size:36 final size:36
Alignment explanation
Indices: 512976--513150 Score: 259
Period size: 36 Copynumber: 4.9 Consensus size: 36
512966 GATACAATCT
*
512976 TTCCATCACCATTATCACGCCTTTATCATCACCATA
1 TTCCATCACCATTATCACGCCTATATCATCACCATA
*
513012 GTT-CATCTCCATTATCACGCCTATATCATCACCATA
1 -TTCCATCACCATTATCACGCCTATATCATCACCATA
*
513048 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 TTCCATCACCATTATCACGCCTATATCATCACCATA
*
513084 TTCCACCACCA-TATCACG-CTATATCATCACCATA
1 TTCCATCACCATTATCACGCCTATATCATCACCATA
* *
513118 TTCCACCACCA-TATCACGCCTATATTATCACCA
1 TTCCATCACCATTATCACGCCTATATCATCACCA
513151 ACTTATAAAT
Statistics
Matches: 129, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
34 34 0.26
35 21 0.16
36 72 0.56
37 2 0.02
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.30
Consensus pattern (36 bp):
TTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:513078 original size:23 final size:23
Alignment explanation
Indices: 512979--513082 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
512969 ACAATCTTTC
*
512979 CATCACCATTATCA-CGCCTTTAT
1 CATCACCATTATCATCGCC-ATAT
*
513002 CATCACCA-TAGTTCATCTCCAT-T
1 CATCACCATTA--TCATCGCCATAT
* *
513025 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
513050 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCC-ATAT
513074 CATCACCAT
1 CATCACCAT
513083 ATTCCACCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 8 0.12
25 14 0.22
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.31
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:514689 original size:23 final size:24
Alignment explanation
Indices: 514663--514716 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
514653 TAAATTAAAT
* *
514663 AATATACAAAAATATAA-AGCACA
1 AATATACAAAAAAATAATAGCAAA
*
514686 AATATA-AAAAAAATAATTGCAAA
1 AATATACAAAAAAATAATAGCAAA
514709 AATATACA
1 AATATACA
514717 TATTAAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (24 bp):
AATATACAAAAAAATAATAGCAAA
Found at i:519093 original size:21 final size:21
Alignment explanation
Indices: 519062--519108 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
519052 TGTATGAATA
* *
519062 GTAGC-AGTATCGGTACCCTT
1 GTAGCAAGTATCGATACCCCT
519082 GTAGCAAGTATCGATACCCCT
1 GTAGCAAGTATCGATACCCCT
519103 GTAGCA
1 GTAGCA
519109 TTCTAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (21 bp):
GTAGCAAGTATCGATACCCCT
Found at i:519453 original size:18 final size:18
Alignment explanation
Indices: 519422--519458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
519412 ATGTTTAATG
* *
519422 AAAAATATATCAATTGTT
1 AAAAAGATACCAATTGTT
519440 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
519458 A
1 A
519459 CCAATTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:522176 original size:34 final size:33
Alignment explanation
Indices: 522115--522185 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
522105 CCTTTAGAAC
*
522115 TCCCTAGTTTTTCACGGGTTAAACTAG-AACATT
1 TCCCTAGTTTTACACGGGTTAAACTAGAAAC-TT
*
522148 TCCCTAGCTTTTACACGGGATT-AGCTAGAAACTT
1 TCCCTAG-TTTTACACGGG-TTAAACTAGAAACTT
522182 TCCC
1 TCCC
522186 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 7 0.21
34 21 0.64
35 5 0.15
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGTTAAACTAGAAACTT
Found at i:522570 original size:20 final size:21
Alignment explanation
Indices: 522545--522589 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
522535 TGTATGAACA
*
522545 GTAGCA-GTATCGGTACCCAT
1 GTAGCAGGTATCGATACCCAT
*
522565 GTAGCAGGTATCGATACCCCT
1 GTAGCAGGTATCGATACCCAT
522586 GTAG
1 GTAG
522590 TATTCTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
GTAGCAGGTATCGATACCCAT
Found at i:525257 original size:21 final size:21
Alignment explanation
Indices: 525233--525278 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
525223 TTTCAGAGAC
* * *
525233 ACTTACCAAGTTACTTCATCT
1 ACTTACCAAGGTAATGCATCT
525254 ACTTACCAAGGTAATGCATCT
1 ACTTACCAAGGTAATGCATCT
525275 ACTT
1 ACTT
525279 CCACTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (21 bp):
ACTTACCAAGGTAATGCATCT
Found at i:529416 original size:25 final size:25
Alignment explanation
Indices: 529382--529430 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
529372 TGAAACTTTT
529382 TCATGTCACAACATGAGGGATATGA
1 TCATGTCACAACATGAGGGATATGA
529407 TCATGTCACAACATGAGGGATATG
1 TCATGTCACAACATGAGGGATATG
529431 GTCACTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (25 bp):
TCATGTCACAACATGAGGGATATGA
Found at i:531195 original size:2 final size:2
Alignment explanation
Indices: 531184--531221 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
531174 ATATTTATGG
531184 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
531222 TACTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:539096 original size:22 final size:23
Alignment explanation
Indices: 539036--539096 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
539026 ATTTCCTTGT
539036 GAATTTAATTTTCT-TTCATTTC
1 GAATTTAATTTTCTCTTCATTTC
*
539058 GAACTTT-A-GTTCATCTTC-TTTC
1 GAA-TTTAATTTTC-TCTTCATTTC
539080 GAATTTAATTTTCTCTT
1 GAATTTAATTTTCTCTT
539097 ATTCTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
21 6 0.19
22 17 0.53
23 9 0.28
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (23 bp):
GAATTTAATTTTCTCTTCATTTC
Found at i:544292 original size:2 final size:2
Alignment explanation
Indices: 544285--544334 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
544275 ATGGTATAAC
* *
544285 AT AT AT AT AT AT AT -T GT AT AGT AC AT -T A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
544325 AT AT AT AT AT
1 AT AT AT AT AT
544335 TACTATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:547402 original size:19 final size:19
Alignment explanation
Indices: 547378--547425 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
547368 CTTCTAGAAA
*
547378 TGGTCCAACCGGATTAAAC
1 TGGTCCAAACGGATTAAAC
547397 TGGTCCAAACGGATTAAAC
1 TGGTCCAAACGGATTAAAC
547416 TGGTCCAAAC
1 TGGTCCAAAC
547426 CAGTCTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (19 bp):
TGGTCCAAACGGATTAAAC
Found at i:547453 original size:20 final size:20
Alignment explanation
Indices: 547430--547485 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
547420 CCAAACCAGT
*
547430 CTAAACCAAGTCAACCCAAC
1 CTAAACCGAGTCAACCCAAC
*
547450 CTAAACCGAGTCAACCCGAC
1 CTAAACCGAGTCAACCCAAC
*
547470 CTGAACCGAGTCAACC
1 CTAAACCGAGTCAACC
547486 AGACCTGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.39, G:0.12, T:0.11
Consensus pattern (20 bp):
CTAAACCGAGTCAACCCAAC
Found at i:547490 original size:20 final size:20
Alignment explanation
Indices: 547433--547493 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
547423 AACCAGTCTA
* *
547433 AACCAAGTCAACCCA-ACCTA
1 AACCGAGTCAA-CCAGACCTG
*
547453 AACCGAGTCAACCCGACCTG
1 AACCGAGTCAACCAGACCTG
547473 AACCGAGTCAACCAGACCTG
1 AACCGAGTCAACCAGACCTG
547493 A
1 A
547494 CCCGTTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.10
Consensus pattern (20 bp):
AACCGAGTCAACCAGACCTG
Found at i:547581 original size:22 final size:22
Alignment explanation
Indices: 547522--547588 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
547512 ACCCGTTAAT
*
547522 CGGTCTGACCGTTGAATTTGAC
1 CGGTCTGACCGTTGACTTTGAC
* * *
547544 CGGTATAACCATTGACTTTGAC
1 CGGTCTGACCGTTGACTTTGAC
* *
547566 CGGTCTGACTGTTGACCTTGAC
1 CGGTCTGACCGTTGACTTTGAC
547588 C
1 C
547589 AAAAAAGTCA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (22 bp):
CGGTCTGACCGTTGACTTTGAC
Found at i:556824 original size:29 final size:30
Alignment explanation
Indices: 556792--556855 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
556782 CTCACAACTC
*
556792 CCTCTCAACCGAG-AAATTAATA-CA-ACAAT
1 CCTCTCAACC-AGTAAA-TAACACCAGACAAT
556821 CCTCTCAACCAGTAAATAACACCAGACAAT
1 CCTCTCAACCAGTAAATAACACCAGACAAT
556851 CCTCT
1 CCTCT
556856 TATATTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 15 0.48
30 10 0.32
ACGTcount: A:0.41, C:0.33, G:0.06, T:0.20
Consensus pattern (30 bp):
CCTCTCAACCAGTAAATAACACCAGACAAT
Found at i:563912 original size:23 final size:24
Alignment explanation
Indices: 563886--563945 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
563876 ATTATTGGCG
563886 AACATGTTCGTTTAACGT-TT-GTA
1 AACATGTTCGTTTAA-GTATTCGTA
*
563909 AACATATTCGTTT-AGTATTCGTA
1 AACATGTTCGTTTAAGTATTCGTA
563932 AACATGTTCGTTTA
1 AACATGTTCGTTTA
563946 GCGTCCGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 27 0.84
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (24 bp):
AACATGTTCGTTTAAGTATTCGTA
Found at i:564153 original size:24 final size:22
Alignment explanation
Indices: 564126--564169 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
564116 GATAGCAAGA
564126 TTATAAATGAATCAATAAACGAGC
1 TTATAAATGAA-C-ATAAACGAGC
**
564150 TTATTCATGAACATAAACGA
1 TTATAAATGAACATAAACGA
564170 ACCGGACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 1 0.06
24 9 0.50
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (22 bp):
TTATAAATGAACATAAACGAGC
Found at i:564839 original size:2 final size:2
Alignment explanation
Indices: 564832--564891 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
564822 GTTTTCTTGA
564832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
564874 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
564892 TACGTTCTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573953 original size:30 final size:29
Alignment explanation
Indices: 573888--573956 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
573878 ATGAGCTAAT
*
573888 AATGAGCTAAGATAAATATCAAATGTATG
1 AATGAGCTAAGATAAATATCAAATGAATG
*
573917 AGATGAGCTAAGAT-AATGATCATATGAATTG
1 A-ATGAGCTAAGATAAAT-ATCAAATGAA-TG
573948 AATGAGCTA
1 AATGAGCTA
573957 GAATAAGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 4 0.11
30 28 0.80
31 3 0.09
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (29 bp):
AATGAGCTAAGATAAATATCAAATGAATG
Found at i:575519 original size:17 final size:17
Alignment explanation
Indices: 575492--575529 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
575482 CATCCTCATT
575492 TTTTCTGTTCTTATATTC
1 TTTTCTGTTCTT-TATTC
*
575510 TTTT-TGTTCTTTCTTC
1 TTTTCTGTTCTTTATTC
575526 TTTT
1 TTTT
575530 AGAGTTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTCTGTTCTTTATTC
Found at i:580089 original size:16 final size:16
Alignment explanation
Indices: 580070--580100 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
580060 AATATATAAC
*
580070 TACAAAAATAATTGAT
1 TACAAAAAAAATTGAT
580086 TACAAAAAAAATTGA
1 TACAAAAAAAATTGA
580101 ATGTTATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TACAAAAAAAATTGAT
Found at i:580252 original size:19 final size:19
Alignment explanation
Indices: 580214--580253 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
580204 ACAATATATG
*
580214 TTATAACTATAATTAAAAT
1 TTATAACTATAAATAAAAT
*
580233 TTATAACTATAAATATAAT
1 TTATAACTATAAATAAAAT
580252 TT
1 TT
580254 GTCACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATAACTATAAATAAAAT
Found at i:581991 original size:2 final size:2
Alignment explanation
Indices: 581984--582012 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
581974 TAGCTTTTGA
581984 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
582013 TTGTTATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:582238 original size:17 final size:18
Alignment explanation
Indices: 582216--582253 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
582206 GGTTTCATAT
582216 TAAATA-ATTGCATATTA
1 TAAATAGATTGCATATTA
582233 TAAATAGTATTGCATATTA
1 TAAATAG-ATTGCATATTA
582252 TA
1 TA
582254 TTAGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TAAATAGATTGCATATTA
Found at i:582262 original size:19 final size:19
Alignment explanation
Indices: 582212--582262 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
582202 ATATGGTTTC
*
582212 ATATTAAATAATTGCATATT
1 ATATTAGAT-ATTGCATATT
*
582232 ATAAATAG-TATTGCATATT
1 AT-ATTAGATATTGCATATT
582251 ATATTAGATATT
1 ATATTAGATATT
582263 AAATAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 3 0.12
21 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (19 bp):
ATATTAGATATTGCATATT
Found at i:583045 original size:39 final size:39
Alignment explanation
Indices: 583002--583150 Score: 140
Period size: 39 Copynumber: 3.8 Consensus size: 39
582992 CATATACACC
* * * *
583002 TGGTAGGGGCTTACCTTGTGCACAAAG-CAGAGGAGCTTA
1 TGGTAAGGACTTACCCTGAGCACAAAGAC-GAGGAGCTTA
* *
583041 TGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGCATG
1 TGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGCTTA
* * ** * *
583080 CGGTAAGGACTTACCCTGGGCACAAATTCGAGGAGGATGA
1 TGGTAAGGACTTACCCTGAGCACAAAGACGAGGA-GCTTA
* *
583120 -GGTAAGGACTTACCCTGAGCATAAAGTCGAG
1 TGGTAAGGACTTACCCTGAGCACAAAGACGAG
583151 AAGACTGCGG
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 89 0.98
40 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (39 bp):
TGGTAAGGACTTACCCTGAGCACAAAGACGAGGAGCTTA
Found at i:583163 original size:39 final size:39
Alignment explanation
Indices: 583042--583185 Score: 157
Period size: 39 Copynumber: 3.7 Consensus size: 39
583032 AGGAGCTTAT
* *
583042 GGTAAGGACTTACCCTGAGCACAAAGACGAGGAG-CATGC
1 GGTAAGGACTTACCCTGAGCACAAAGTCGAGAAGAC-TGC
* * * *
583081 GGTAAGGACTTACCCTGGGCACAAATTCGAGGAGGA-TGA
1 GGTAAGGACTTACCCTGAGCACAAAGTCGA-GAAGACTGC
*
583120 GGTAAGGACTTACCCTGAGCATAAAGTCGAGAAGACTGC
1 GGTAAGGACTTACCCTGAGCACAAAGTCGAGAAGACTGC
* * * *
583159 GGTAAGGTCTTATCCTGTGCACTAAGT
1 GGTAAGGACTTACCCTGAGCACAAAGT
583186 ATAGGGGCCT
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
38 4 0.05
39 80 0.93
40 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (39 bp):
GGTAAGGACTTACCCTGAGCACAAAGTCGAGAAGACTGC
Found at i:583820 original size:21 final size:22
Alignment explanation
Indices: 583791--583832 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
583781 TTCTTGAATC
583791 AAATCCTAAAAA-AATAAGCAA
1 AAATCCTAAAAACAATAAGCAA
*
583812 AAATGCTAAAAACAATAAGCA
1 AAATCCTAAAAACAATAAGCA
583833 TTTTCGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (22 bp):
AAATCCTAAAAACAATAAGCAA
Found at i:585775 original size:21 final size:21
Alignment explanation
Indices: 585734--585777 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
585724 GGGTTTTTTA
*
585734 GGATGAACATTGGATGAGTTT
1 GGATGAACATTGAATGAGTTT
585755 GGATGAACATTTGAATG-GTTT
1 GGATGAACA-TTGAATGAGTTT
585776 GG
1 GG
585778 GAAAATTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (21 bp):
GGATGAACATTGAATGAGTTT
Found at i:595725 original size:7 final size:7
Alignment explanation
Indices: 595713--595831 Score: 170
Period size: 7 Copynumber: 17.0 Consensus size: 7
595703 AAATATGATG
595713 AAGAAAA
1 AAGAAAA
595720 AAGAAAA
1 AAGAAAA
595727 AAGAAAA
1 AAGAAAA
595734 AAGAAAA
1 AAGAAAA
595741 AAGAAAA
1 AAGAAAA
595748 AAGAAAA
1 AAGAAAA
595755 AAGAAAA
1 AAGAAAA
595762 AAGAAAA
1 AAGAAAA
595769 AAGAAAA
1 AAGAAAA
595776 AAG-AAA
1 AAGAAAA
595782 AAG-AAA
1 AAGAAAA
*
595788 AAGAAGA
1 AAGAAAA
*
595795 AAGAAGA
1 AAGAAAA
*
595802 AAGAAGA
1 AAGAAAA
*
595809 AAGAAGA
1 AAGAAAA
595816 AAGAAGAA
1 AAGAA-AA
595824 AATGAAAA
1 AA-GAAAA
595832 GGGGGTTCAA
Statistics
Matches: 107, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
6 12 0.11
7 87 0.81
8 5 0.05
9 3 0.03
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:595727 original size:1 final size:1
Alignment explanation
Indices: 595716--595789 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
595706 TATGATGAAG
* * * * * * * * *
595716 AAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
595781 AAAGAAAAA
1 AAAAAAAAA
595790 GAAGAAAGAA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:596736 original size:13 final size:13
Alignment explanation
Indices: 596704--596728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
596694 GATGAAACCG
596704 TGAAACCATGAGA
1 TGAAACCATGAGA
596717 TGAAACCATGAG
1 TGAAACCATGAG
596729 TTGGAACCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (13 bp):
TGAAACCATGAGA
Found at i:597882 original size:17 final size:18
Alignment explanation
Indices: 597860--597897 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
597850 AGTTTCATAT
597860 TAAATA-ATTGCATATTA
1 TAAATAGATTGCATATTA
597877 TAAATAGTATTGCATATTA
1 TAAATAG-ATTGCATATTA
597896 TA
1 TA
597898 TTAGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TAAATAGATTGCATATTA
Found at i:597906 original size:19 final size:19
Alignment explanation
Indices: 597856--597906 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
597846 ATATAGTTTC
*
597856 ATATTAAATAATTGCATATT
1 ATATTAGAT-ATTGCATATT
*
597876 ATAAATAG-TATTGCATATT
1 AT-ATTAGATATTGCATATT
597895 ATATTAGATATT
1 ATATTAGATATT
597907 AAAAAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 3 0.12
21 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (19 bp):
ATATTAGATATTGCATATT
Found at i:603604 original size:14 final size:14
Alignment explanation
Indices: 603577--603640 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 14
603567 GAGAATTAAG
*
603577 AAAATAAAGAAAAAT
1 AAAACAAAG-AAAAT
*
603592 AAATCAAAGAAAAT
1 AAAACAAAGAAAAT
*
603606 AAAACAACAAACGAAAT
1 AAAACAA-AGA--AAAT
603623 AAAACAAAGAAAAT
1 AAAACAAAGAAAAT
603637 AAAA
1 AAAA
603641 AGACGAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 19 0.46
15 9 0.22
16 2 0.05
17 11 0.27
ACGTcount: A:0.77, C:0.08, G:0.06, T:0.09
Consensus pattern (14 bp):
AAAACAAAGAAAAT
Found at i:603854 original size:13 final size:13
Alignment explanation
Indices: 603830--603868 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
603820 GGGAGATAAA
603830 AAAATGATAAAAAG
1 AAAAT-ATAAAAAG
603844 AAAATATAAAAAG
1 AAAATATAAAAAG
603857 AAAATATAAAAA
1 AAAATATAAAAA
603869 AACTAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAATATAAAAAG
Found at i:603869 original size:22 final size:24
Alignment explanation
Indices: 603850--603894 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
603840 AAAGAAAATA
603850 TAAAAAGA-A-AATATAAAAAAAC
1 TAAAAAGATAGAATATAAAAAAAC
*
603872 TAAATAGATAGAATATAAAAAAA
1 TAAAAAGATAGAATATAAAAAAA
603895 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 12 0.60
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (24 bp):
TAAAAAGATAGAATATAAAAAAAC
Found at i:603877 original size:15 final size:13
Alignment explanation
Indices: 603827--603870 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
603817 TAAGGGAGAT
603827 AAAAAAATGATAAA
1 AAAAAAAT-ATAAA
*
603841 AAGAAAATATAAA
1 AAAAAAATATAAA
*
603854 AAGAAAATATAAA
1 AAAAAAATATAAA
603867 AAAA
1 AAAA
603871 CTAAATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAATATAAA
Found at i:603891 original size:24 final size:24
Alignment explanation
Indices: 603859--603914 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
603849 ATAAAAAGAA
603859 AATATAAAAAAACTAA-ATAGATAG
1 AATATAAAAAAACTAATATA-ATAG
* *
603883 AATATAAAAAAAGTAATATAATAT
1 AATATAAAAAAACTAATATAATAG
603907 AATATAAA
1 AATATAAA
603915 TAGAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (24 bp):
AATATAAAAAAACTAATATAATAG
Found at i:603949 original size:35 final size:35
Alignment explanation
Indices: 603836--603976 Score: 141
Period size: 36 Copynumber: 4.0 Consensus size: 35
603826 TAAAAAAATG
*
603836 ATAAAAAGAAAATATAAAAAGAA-AATATAAAA-AA
1 ATAAATAGAAAATATAAAAA-AATAATATAAAATAA
*
603870 ACTAAATAGATAGAATATAAAAAAAGTAATATAATATAA
1 A-TAAATAGA-A-AATATAAAAAAA-TAATATAAAATAA
603909 TATAAATAGAAAA-ATAAAAAAAGTAATATAAAATAA
1 -ATAAATAGAAAATATAAAAAAA-TAATATAAAATAA
* *
603945 ATAAATAG-AAA-ACAAAAAAATAAT-GAAAATAA
1 ATAAATAGAAAATATAAAAAAATAATATAAAATAA
603977 GGAATATAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
32 7 0.07
33 4 0.04
34 12 0.13
35 15 0.16
36 25 0.26
37 12 0.13
38 9 0.09
39 10 0.11
40 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (35 bp):
ATAAATAGAAAATATAAAAAAATAATATAAAATAA
Found at i:603991 original size:41 final size:37
Alignment explanation
Indices: 603888--603992 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 37
603878 GATAGAATAT
* *
603888 AAAAAAAGT--AATATAATATAATATAAATAGAAAAAT
1 AAAAAAAGTAAAATAAAATATAAT-TAAATAGAAAAAA
*
603924 AAAAAAAGTAATATAAAATA-AA-TAAATAGAAAACAA
1 AAAAAAAGTAAAATAAAATATAATTAAATAGAAAA-AA
603960 AAAAATAA-TGAAAATAAGGAATATAATTAAATA
1 AAAAA-AAGT-AAAATAA--AATATAATTAAATA
603993 AATAGAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
35 11 0.20
36 16 0.29
37 10 0.18
38 7 0.12
39 4 0.07
40 2 0.04
41 6 0.11
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (37 bp):
AAAAAAAGTAAAATAAAATATAATTAAATAGAAAAAA
Found at i:614519 original size:14 final size:14
Alignment explanation
Indices: 614492--614555 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 14
614482 GAGAATTAAC
*
614492 AAAATAAAGAAAAAT
1 AAAACAAAG-AAAAT
*
614507 AAATCAAAGAAAAT
1 AAAACAAAGAAAAT
*
614521 AAAACAACAAACAAAAT
1 --AA-AACAAAGAAAAT
614538 AAAACAAAGAAAAT
1 AAAACAAAGAAAAT
614552 AAAA
1 AAAA
614556 AGACGAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 20 0.49
15 9 0.22
16 2 0.05
17 10 0.24
ACGTcount: A:0.78, C:0.08, G:0.05, T:0.09
Consensus pattern (14 bp):
AAAACAAAGAAAAT
Found at i:614536 original size:17 final size:17
Alignment explanation
Indices: 614511--614544 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
614501 AAAAATAAAT
*
614511 CAAAGAAAATAAAACAA
1 CAAACAAAATAAAACAA
614528 CAAACAAAATAAAACAA
1 CAAACAAAATAAAACAA
614545 AGAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.15, G:0.03, T:0.06
Consensus pattern (17 bp):
CAAACAAAATAAAACAA
Found at i:614822 original size:25 final size:25
Alignment explanation
Indices: 614794--614842 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
614784 ATATATATAT
614794 ATAAATAA-ATAGATAGAATATAAAA
1 ATAAATAATATA-ATAGAATATAAAA
* *
614819 ATAAGTAATATAATATAATATAAA
1 ATAAATAATATAATAGAATATAAA
614843 TAGAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (25 bp):
ATAAATAATATAATAGAATATAAAA
Found at i:614914 original size:39 final size:38
Alignment explanation
Indices: 614792--614923 Score: 117
Period size: 39 Copynumber: 3.3 Consensus size: 38
614782 ATATATATAT
* *
614792 ATATAAATAAATAGATAGAATATAAAAATAAGTAAT-A-TA
1 ATATAAATAAATAGA-A-AACA-AAAAATAAGAAATAAGTA
* *
614831 ATATAATATAAATAGAAAACTAATAAATAA-ATAGTAATGTA
1 ATATAA-ATAAATAGAAAAC-AAAAAATAAGA-AATAA-GTA
*
614872 ATATAAATAAATAGAAAACAAAAAATAAGGAAATAAGAA
1 ATATAAATAAATAGAAAACAAAAAATAA-GAAATAAGTA
*
614911 ATATAATTAAATA
1 ATATAAATAAATA
614924 TATATATATA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
38 11 0.14
39 31 0.40
40 26 0.34
41 9 0.12
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.26
Consensus pattern (38 bp):
ATATAAATAAATAGAAAACAAAAAATAAGAAATAAGTA
Found at i:614984 original size:5 final size:5
Alignment explanation
Indices: 614976--615009 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
614966 AATAAGTAAG
614976 AATAA AAT-A AATAA GAATAA AATAA AATAA AATA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATA
615010 TGAAACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:614999 original size:20 final size:19
Alignment explanation
Indices: 614959--615006 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
614949 ATAATTATAA
614959 AAAATGAAATAAGTAAGAAT
1 AAAAT-AAATAAGTAAGAAT
614979 AAAATAAATAAGAATAA-AAT
1 AAAATAAATAAG--TAAGAAT
614999 AAAATAAA
1 AAAATAAA
615007 ATATGAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.27
20 16 0.62
21 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AAAATAAATAAGTAAGAAT
Found at i:615009 original size:15 final size:15
Alignment explanation
Indices: 614965--615001 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
614955 ATAAAAAATG
*
614965 AAATAAGTAAGAATA
1 AAATAAATAAGAATA
614980 AAATAAATAAGAATA
1 AAATAAATAAGAATA
614995 AAATAAA
1 AAATAAA
615002 ATAAAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (15 bp):
AAATAAATAAGAATA
Found at i:615478 original size:19 final size:20
Alignment explanation
Indices: 615443--615482 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
615433 CGATAGATCG
*
615443 TCCAAACCTCATTTTAAAAA
1 TCCAAACCGCATTTTAAAAA
615463 TCCAAACCGC-TTTTAAAAA
1 TCCAAACCGCATTTTAAAAA
615482 T
1 T
615483 TGGCCTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (20 bp):
TCCAAACCGCATTTTAAAAA
Found at i:618991 original size:18 final size:17
Alignment explanation
Indices: 618970--619038 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 17
618960 TGGGTATTTA
618970 TTATTTAATTATTATTAT
1 TTATTTAA-TATTATTAT
*
618988 TTA-TTACTATT-TT-T
1 TTATTTAATATTATTAT
619002 TTATTTAATATTATTCAT
1 TTATTTAATATTATT-AT
*
619020 TTTTTGGTAATATTATTAT
1 TTATT--TAATATTATTAT
619039 AAGTAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.10
15 9 0.21
16 6 0.14
17 3 0.07
18 8 0.19
19 2 0.05
20 10 0.24
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATTTAATATTATTAT
Found at i:620599 original size:23 final size:22
Alignment explanation
Indices: 620569--620656 Score: 108
Period size: 23 Copynumber: 4.0 Consensus size: 22
620559 ATCAGATTGT
620569 CCAGGGGGTACAGATTCCCCTCC
1 CCAGGGGGTACAGATTCCCC-CC
620592 CCAGGGGG-ATCAGATT-CCCCC
1 CCAGGGGGTA-CAGATTCCCCCC
* *
620613 CAAGGGGGTACCGATTCCCCCCC
1 CCAGGGGGTACAGATT-CCCCCC
*
620636 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
620657 TGTCTAACGG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.24
22 10 0.17
23 34 0.59
ACGTcount: A:0.17, C:0.41, G:0.27, T:0.15
Consensus pattern (22 bp):
CCAGGGGGTACAGATTCCCCCC
Found at i:620619 original size:20 final size:21
Alignment explanation
Indices: 620571--620634 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
620561 CAGATTGTCC
*
620571 AGGGGGTACAGATTCCCCTCCCCA
1 AGGGGATACAGATT--CC-CCCCA
*
620595 GGGGGAT-CAGATTCCCCCCA
1 AGGGGATACAGATTCCCCCCA
* *
620615 AGGGGGTACCGATTCCCCCC
1 AGGGGATACAGATTCCCCCC
620635 CCCAGGGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 10 0.29
21 13 0.38
23 6 0.18
24 5 0.15
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (21 bp):
AGGGGATACAGATTCCCCCCA
Found at i:620622 original size:44 final size:44
Alignment explanation
Indices: 620571--620656 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
620561 CAGATTGTCC
*
620571 AGGGGGTACAGATTCCCCTCCCCAGGGGG-ATCAGATTCCCCCCA
1 AGGGGGTACAGATTCCCCCCCCCAGGGGGTA-CAGATTCCCCCCA
* *
620615 AGGGGGTACCGATTCCCCCCCCCAGGGGGTACCGATTCCCCC
1 AGGGGGTACAGATTCCCCCCCCCAGGGGGTACAGATTCCCCC
620657 TGTCTAACGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.17, C:0.40, G:0.28, T:0.15
Consensus pattern (44 bp):
AGGGGGTACAGATTCCCCCCCCCAGGGGGTACAGATTCCCCCCA
Found at i:625483 original size:268 final size:272
Alignment explanation
Indices: 624951--625553 Score: 892
Period size: 268 Copynumber: 2.2 Consensus size: 272
624941 GCCATCCCTA
* * * *
624951 CTCAACATACCATGAATTTATAAAGGTTTTCATTAACAACCAAAATATTTTTGGGTTTAGGGTTC
1 CTCAACATACCATGAATTTATAAAGGTTTTCAGTAATAACTAAAATATTTTAGGGTTTAGGGTTC
* * **
625016 CAAAATTAATATACAATAAATAATATAAGTAACTATTGATTTTTGTGAACCCTAAACCCTAAAAT
66 CAAAATTAATATACAACAAATAATATAAGTAACCATTGATTTTTGCAAACCCTAAACCCTAAAAT
* * * * *
625081 ATTTTGTTTGTTACTAAAAACCCTAAACTTAAACCCTACAACCTAAATCCTAACCATTCTCCCTC
131 ATTTTGGTTATTACTAAAAACCC--AAC-TAAACCATACAACCTAAACCCTAACCATTCTCCATC
* *
625146 CAATGAATTTCTTCTTATAAAAAATAAATATGTAACCACCATCATGGTAGATATCACCATCCTCT
193 CAATCAATTTCTTCTTATAAAAAAGAAATATGTAACCACCATCATGGTAGATATCACCATCCTCT
*
625211 ACCCCTTTCATTGCC
258 ACCCCTTTCATCGCC
*
625226 CTCAACATACCATGAATTTATAAAGGTTTTCAGTAATAACTAAAATATTTTAGGGTTTAGGGTTT
1 CTCAACATACCATGAATTTATAAAGGTTTTCAGTAATAACTAAAATATTTTAGGGTTTAGGGTTC
625291 CAAAATTAATATACAACAAATAATATAAGTAACCATTGA-TTTTGCAAACCCTAAACCCTAAAAT
66 CAAAATTAATATACAACAAATAATATAAGTAACCATTGATTTTTGCAAACCCTAAACCCTAAAAT
** *
625355 ATTTTGGTTATTGTTGAAAA-CC-A-TAAACCATA-AACCCTAAACCCTAACCATTCTCCATCCA
131 ATTTTGGTTATTACTAAAAACCCAACTAAACCATACAA-CCTAAACCCTAACCATTCTCCATCCA
*
625416 ATCAATTTCTTCTTATAAAAAAGAAATATGTAACCACCATCATGGTAGATATTACCATCCTCTAC
195 ATCAATTTCTTCTTATAAAAAAGAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTAC
*
625481 CCCTTTCATCGTC
260 CCCTTTCATCGCC
* * * * *
625494 CTCAACATACCGTGAATTTATAAAGATTTTTAGCAATAACTAAAAGATTTTAGGGTTTAG
1 CTCAACATACCATGAATTTATAAAGGTTTTCAGTAATAACTAAAATATTTTAGGGTTTAG
625554 TGGCGACCAA
Statistics
Matches: 300, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
267 2 0.01
268 160 0.53
270 1 0.00
273 2 0.01
274 38 0.13
275 97 0.32
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (272 bp):
CTCAACATACCATGAATTTATAAAGGTTTTCAGTAATAACTAAAATATTTTAGGGTTTAGGGTTC
CAAAATTAATATACAACAAATAATATAAGTAACCATTGATTTTTGCAAACCCTAAACCCTAAAAT
ATTTTGGTTATTACTAAAAACCCAACTAAACCATACAACCTAAACCCTAACCATTCTCCATCCAA
TCAATTTCTTCTTATAAAAAAGAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACC
CCTTTCATCGCC
Found at i:626306 original size:29 final size:29
Alignment explanation
Indices: 626264--626359 Score: 156
Period size: 29 Copynumber: 3.3 Consensus size: 29
626254 GTTCGAACGT
*
626264 AGGTCGCCAGGTGATCCGAGCAACCAAGG
1 AGGTCGCCAGGTGATCCGAGCGACCAAGG
626293 AGGTCGCCAGGTGATCCGAGCGACCAAGG
1 AGGTCGCCAGGTGATCCGAGCGACCAAGG
* *
626322 AGGTCGCCAGGTGATCCGATCGACCAAGA
1 AGGTCGCCAGGTGATCCGAGCGACCAAGG
*
626351 AGATCGCCA
1 AGGTCGCCA
626360 TGCGTCCCTG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.27, C:0.28, G:0.33, T:0.11
Consensus pattern (29 bp):
AGGTCGCCAGGTGATCCGAGCGACCAAGG
Found at i:629379 original size:22 final size:23
Alignment explanation
Indices: 629354--629402 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
629344 ATAAAAAAAA
*
629354 TTGACA-CTCTAAAAT-AATTTTT
1 TTGACACCTC-AAAATAAATATTT
629376 TTGACACCTCAAAATAAATATTT
1 TTGACACCTCAAAATAAATATTT
629399 TTGA
1 TTGA
629403 ATTTAACACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
TTGACACCTCAAAATAAATATTT
Found at i:630186 original size:21 final size:21
Alignment explanation
Indices: 630138--630202 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
630128 CACGTTGAAT
*
630138 GCTGAACGGTTCAGCATTCAAC-
1 GCTGAATGGTTC--CATTCAACA
630160 GCTGAATGGTTCCATTCAACA
1 GCTGAATGGTTCCATTCAACA
*
630181 GCTGAATGGCTCCATTCAACA
1 GCTGAATGGTTCCATTCAACA
630202 G
1 G
630203 TAGTAAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.20
21 21 0.52
22 11 0.28
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (21 bp):
GCTGAATGGTTCCATTCAACA
Found at i:644158 original size:20 final size:20
Alignment explanation
Indices: 644135--644198 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
644125 TAGTATTTAG
644135 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
644155 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
644175 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
644194 TTAAA
1 ATAAA
644199 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:644168 original size:19 final size:20
Alignment explanation
Indices: 644144--644193 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
644134 GATAAATTTA
*
644144 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
644163 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
644184 TT-ATAATTTT
1 TTAATAATTTT
644194 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:644196 original size:31 final size:30
Alignment explanation
Indices: 644111--644197 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
644101 TTCGATAATA
* *
644111 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
644142 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
644173 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
644198 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:644951 original size:31 final size:30
Alignment explanation
Indices: 644895--644974 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 30
644885 ATAAAGTTTA
644895 AAAAATTATAAAA-TACTT-ATAAATTTATT
1 AAAAATTATAAAATTA-TTAATAAATTTATT
644924 AAAAGATTATAAAATTATTAATAAATTTATCT
1 AAAA-ATTATAAAATTATTAATAAATTTAT-T
*
644956 AAAAATTATAAAATAATTA
1 AAAAATTATAAAATTATTA
644975 TTATATTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
29 4 0.09
30 11 0.24
31 26 0.57
32 5 0.11
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAAATTATAAAATTATTAATAAATTTATT
Found at i:649547 original size:26 final size:26
Alignment explanation
Indices: 649518--649571 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
649508 ACCAAGTGCA
*
649518 TATGGTGGGCAAGCCCTTATGTGTAT
1 TATGGTGGGCAAGACCTTATGTGTAT
* *
649544 TATGGTGGGCATGACCTTTTGTGTAT
1 TATGGTGGGCAAGACCTTATGTGTAT
649570 TA
1 TA
649572 GCACTTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.39
Consensus pattern (26 bp):
TATGGTGGGCAAGACCTTATGTGTAT
Found at i:657877 original size:20 final size:20
Alignment explanation
Indices: 657854--657911 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
657844 TGAAAAATTA
*
657854 ATTGGTACATTGATGCATGG
1 ATTGGTACATCGATGCATGG
*
657874 ATTGGTGCATCGATGCATGG
1 ATTGGTACATCGATGCATGG
* *
657894 ATTGGTGCATCGGTGCAT
1 ATTGGTACATCGATGCAT
657912 CGGTGCATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.33
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:661985 original size:2 final size:2
Alignment explanation
Indices: 661978--662025 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
661968 CAACCAAACC
661978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
662020 AT AT AT
1 AT AT AT
662026 TAAGTTCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:662452 original size:21 final size:21
Alignment explanation
Indices: 662428--662470 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
662418 CCAGAGGAGG
*
662428 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
662449 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
662470 A
1 A
662471 ACTCCAGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.40, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:665967 original size:23 final size:22
Alignment explanation
Indices: 665929--665971 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
665919 CAATTCCTTT
665929 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
665951 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
665972 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:666257 original size:11 final size:12
Alignment explanation
Indices: 666227--666259 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
666217 TTGGTGCTGG
666227 AAACAAGATATA
1 AAACAAGATATA
*
666239 AAATAAGAT-TA
1 AAACAAGATATA
666250 AAACAAGATA
1 AAACAAGATA
666260 AAGAAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.67, C:0.06, G:0.09, T:0.18
Consensus pattern (12 bp):
AAACAAGATATA
Found at i:671695 original size:26 final size:26
Alignment explanation
Indices: 671664--671789 Score: 243
Period size: 26 Copynumber: 4.8 Consensus size: 26
671654 GCATGGTCTT
671664 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
671690 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
671716 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
671742 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
*
671768 GTGCATCGATGCATAAAATGCA
1 GTGCATCGATGCATCAAATGCA
671790 TTCGATGTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 99 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:671701 original size:17 final size:18
Alignment explanation
Indices: 671664--671781 Score: 65
Period size: 17 Copynumber: 6.8 Consensus size: 18
671654 GCATGGTCTT
*
671664 GTGCATC-GATGCATCAA
1 GTGCATCAGATGCATCGA
* *
671681 ATGCA-CTGAGTGCATCGA
1 GTGCATCAGA-TGCATCGA
*
671699 -TGCATCAAATGCA-CTGA
1 GTGCATCAGATGCATC-GA
*
671716 GTGCATC-GATGCATCAA
1 GTGCATCAGATGCATCGA
* *
671733 ATGCA-CTGAGTGCATCGA
1 GTGCATCAGA-TGCATCGA
*
671751 -TGCATCAAATGCA-CTGA
1 GTGCATCAGATGCATC-GA
671768 GTGCATC-GATGCAT
1 GTGCATCAGATGCAT
671782 AAAATGCATT
Statistics
Matches: 78, Mismatches: 11, Indels: 23
0.70 0.10 0.21
Matches are distributed among these distances:
16 4 0.05
17 43 0.55
18 31 0.40
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (18 bp):
GTGCATCAGATGCATCGA
Found at i:671834 original size:20 final size:20
Alignment explanation
Indices: 671809--671846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
671799 TGAAAAATAA
*
671809 ATTGGTGTATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
671829 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
671847 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:675458 original size:40 final size:40
Alignment explanation
Indices: 675395--675548 Score: 229
Period size: 40 Copynumber: 3.9 Consensus size: 40
675385 GATTAAGCAC
* * *
675395 TTCGGTGCATATGGTGGGTACGACCTTATGTATAATGAAT
1 TTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGCAT
* * *
675435 TTCAGTGCATATGGTGGGCACGACTTTATGTGTAATGCAC
1 TTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGCAT
* *
675475 TTCGGTGCATATGGTGAGCACGACCTTATGTGTAATGCCT
1 TTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGCAT
675515 TT-GGTGCATATGGTGGGCACGACCTTATGTGTAA
1 TTCGGTGCATATGGTGGGCACGACCTTATGTGTAA
675549 GCACTAAGGT
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 31 0.30
40 71 0.70
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (40 bp):
TTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGCAT
Done.