Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 53 of 54
Found at i:12528544 original size:42 final size:41
Alignment explanation
Indices: 12528461--12528559 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
12528451 AGGGTGTCAA
** *
12528461 AGTGCATCCATGCACCCTTGCAGTGCTTCCATGCATCCATGC
1 AGTGCATCCATGCA-CCTCACAGTGCATCCATGCATCCATGC
*
12528503 AGTGCATCCATGCACCTACACTAGTGCATCGATGCAT-CATGC
1 AGTGCATCCATGCACCT-CAC-AGTGCATCCATGCATCCATGC
12528545 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12528560 TCAAACACCG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.06
42 35 0.69
43 13 0.25
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (41 bp):
AGTGCATCCATGCACCTCACAGTGCATCCATGCATCCATGC
Found at i:12528550 original size:20 final size:20
Alignment explanation
Indices: 12528479--12528653 Score: 85
Period size: 20 Copynumber: 8.8 Consensus size: 20
12528469 CATGCACCCT
* *
12528479 TGCAGTGCTTCCATGCATCCA
1 TGCAGTGCATCGATGCAT-CA
* *
12528500 TGCAGTGCATCCATGCACCTA
1 TGCAGTGCATCGATGCATC-A
**
12528521 CACTAGTGCATCGATGCATCA
1 TGC-AGTGCATCGATGCATCA
*
12528542 TGCAGTGCATCCATGCA-C-
1 TGCAGTGCATCGATGCATCA
** *
12528560 T-CA-AACACCGAATGCA--A
1 TGCAGTGCATCG-ATGCATCA
* *
12528577 T-TAGTGCATCGATGCATCC
1 TGCAGTGCATCGATGCATCA
* *
12528596 TTCTGTGCATCGATGCATCA
1 TGCAGTGCATCGATGCATCA
* * *
12528616 AGCCTGTGCATCGATGCATCC
1 TG-CAGTGCATCGATGCATCA
* *
12528637 TGCTGTGCATCCATGCA
1 TGCAGTGCATCGATGCA
12528654 CGAAGGCTGC
Statistics
Matches: 119, Mismatches: 26, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
16 3 0.03
17 14 0.12
18 5 0.04
19 2 0.02
20 43 0.36
21 38 0.32
22 14 0.12
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (20 bp):
TGCAGTGCATCGATGCATCA
Found at i:12531956 original size:29 final size:30
Alignment explanation
Indices: 12531886--12531945 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12531876 AAATTTAAGG
12531886 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
* *
12531917 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
12531946 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:12532055 original size:21 final size:21
Alignment explanation
Indices: 12532025--12532123 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
12532015 AGGGTGTCAA
*
12532025 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCATGC
* *
12532046 AGTGCTTCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
* **
12532067 AGTGCATCCATGCACCTACAC
1 AGTGCATCCATGCACCCATGC
* *
12532088 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATGC
12532109 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12532124 TCAAACACCG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 13 0.21
21 36 0.58
22 13 0.21
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:12532072 original size:13 final size:13
Alignment explanation
Indices: 12532056--12532080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12532046 AGTGCTTCCA
12532056 TGCATCCATGCAG
1 TGCATCCATGCAG
12532069 TGCATCCATGCA
1 TGCATCCATGCA
12532081 CCTACACTAG
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:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:12532108 original size:42 final size:41
Alignment explanation
Indices: 12532025--12532123 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
12532015 AGGGTGTCAA
** *
12532025 AGTGCATCCATGCACCCTTGCAGTGCTTCCATGCATCCATGC
1 AGTGCATCCATGCA-CCTCACAGTGCATCCATGCATCCATGC
*
12532067 AGTGCATCCATGCACCTACACTAGTGCATCGATGCAT-CATGC
1 AGTGCATCCATGCACCT-CAC-AGTGCATCCATGCATCCATGC
12532109 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12532124 TCAAACACCG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.06
42 35 0.69
43 13 0.25
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (41 bp):
AGTGCATCCATGCACCTCACAGTGCATCCATGCATCCATGC
Found at i:12532114 original size:20 final size:20
Alignment explanation
Indices: 12532043--12532217 Score: 85
Period size: 20 Copynumber: 8.8 Consensus size: 20
12532033 CATGCACCCT
* *
12532043 TGCAGTGCTTCCATGCATCCA
1 TGCAGTGCATCGATGCAT-CA
* *
12532064 TGCAGTGCATCCATGCACCTA
1 TGCAGTGCATCGATGCATC-A
**
12532085 CACTAGTGCATCGATGCATCA
1 TGC-AGTGCATCGATGCATCA
*
12532106 TGCAGTGCATCCATGCA-C-
1 TGCAGTGCATCGATGCATCA
** *
12532124 T-CA-AACACCGAATGCA--A
1 TGCAGTGCATCG-ATGCATCA
* *
12532141 T-TAGTGCATCGATGCATCC
1 TGCAGTGCATCGATGCATCA
* *
12532160 TTCTGTGCATCGATGCATCAA
1 TGCAGTGCATCGATGCATC-A
* * *
12532181 GGCTGTGCATCGATGCATCC
1 TGCAGTGCATCGATGCATCA
* *
12532201 TGCTGTGCATCCATGCA
1 TGCAGTGCATCGATGCA
12532218 CGAAGGCTGC
Statistics
Matches: 119, Mismatches: 26, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
16 3 0.03
17 14 0.12
18 5 0.04
19 2 0.02
20 44 0.37
21 37 0.31
22 14 0.12
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCAGTGCATCGATGCATCA
Found at i:12532191 original size:41 final size:41
Alignment explanation
Indices: 12532144--12532226 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
12532134 AATGCAATTA
* *
12532144 GTGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCA-CGAAGGCT
12532185 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
12532226 G
1 G
12532227 CAACGGCTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
Found at i:12532359 original size:20 final size:22
Alignment explanation
Indices: 12532321--12532360 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
12532311 TTTGAGTAGA
12532321 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
12532343 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
12532361 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:12540870 original size:21 final size:22
Alignment explanation
Indices: 12540837--12540877 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
12540827 TTAAATAAAA
12540837 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
12540859 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
12540878 CCTGTCCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:12542542 original size:27 final size:27
Alignment explanation
Indices: 12542498--12542611 Score: 78
Period size: 27 Copynumber: 4.3 Consensus size: 27
12542488 CCTCTATTAA
*
12542498 TTTAATATTAATTA-GATAAATATAAAT
1 TTTAA-ATTATTTATGATAAATATAAAT
* *
12542525 TTTAAATTATTTATGATAAAAAAATAAT
1 TTTAAATTATTTATGATAAATATA-AAT
* *
12542553 TTTTAA-TATTTATG-T-AATTTAAA-
1 TTTAAATTATTTATGATAAATATAAAT
* * *
12542576 TTTATATTATATGATCATAAATA-AATAT
1 TTTAAATTAT-TTATGATAAATATAA-AT
12542604 TTTAAATT
1 TTTAAATT
12542612 TAATTTATAA
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.06
24 5 0.08
25 6 0.09
26 11 0.17
27 25 0.38
28 15 0.23
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTAAATTATTTATGATAAATATAAAT
Found at i:12542641 original size:23 final size:23
Alignment explanation
Indices: 12542598--12542680 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
12542588 GATCATAAAT
* *
12542598 AAATATTTTAA-ATTTAATTTATA
1 AAATAATTTAATATTT-TTTTATA
12542621 AAATAATTTAATATTTTTTTA-A
1 AAATAATTTAATATTTTTTTATA
* *
12542643 ACATATATTTAATTATTTTTATTTTA
1 AAATA-ATTTAA-TATTTTT-TTATA
12542669 AAATAAATTTAA
1 AAAT-AATTTAA
12542681 AAATAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.10
23 20 0.41
24 11 0.22
25 2 0.04
26 10 0.20
27 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATAATTTAATATTTTTTTATA
Found at i:12552252 original size:21 final size:22
Alignment explanation
Indices: 12552219--12552259 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
12552209 TTAAATAAAA
12552219 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
12552241 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
12552260 CCTGTCCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:12553918 original size:27 final size:27
Alignment explanation
Indices: 12553874--12553987 Score: 78
Period size: 27 Copynumber: 4.3 Consensus size: 27
12553864 CCTCTATTAA
*
12553874 TTTAATATTAATTA-GATAAATATAAAT
1 TTTAA-ATTATTTATGATAAATATAAAT
* *
12553901 TTTAAATTATTTATGATAAAAAAATAAT
1 TTTAAATTATTTATGATAAATATA-AAT
* *
12553929 TTTTAA-TATTTATG-T-AATTTAAA-
1 TTTAAATTATTTATGATAAATATAAAT
* * *
12553952 TTTATATTATATGATCATAAATA-AATAT
1 TTTAAATTAT-TTATGATAAATATAA-AT
12553980 TTTAAATT
1 TTTAAATT
12553988 TAATTTATAA
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.06
24 5 0.08
25 6 0.09
26 11 0.17
27 25 0.38
28 15 0.23
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTAAATTATTTATGATAAATATAAAT
Found at i:12554017 original size:23 final size:23
Alignment explanation
Indices: 12553974--12554056 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
12553964 GATCATAAAT
* *
12553974 AAATATTTTAA-ATTTAATTTATA
1 AAATAATTTAATATTT-TTTTATA
12553997 AAATAATTTAATATTTTTTTA-A
1 AAATAATTTAATATTTTTTTATA
* *
12554019 ACATATATTTAATTATTTTTATTTTA
1 AAATA-ATTTAA-TATTTTT-TTATA
12554045 AAATAAATTTAA
1 AAAT-AATTTAA
12554057 AAATAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.10
23 20 0.41
24 11 0.22
25 2 0.04
26 10 0.20
27 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATAATTTAATATTTTTTTATA
Found at i:12557478 original size:16 final size:16
Alignment explanation
Indices: 12557457--12557488 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12557447 AATGATTTCA
12557457 GCAGGTGAATGAATAG
1 GCAGGTGAATGAATAG
12557473 GCAGGTGAATGAATAG
1 GCAGGTGAATGAATAG
12557489 CTGTGACTAA
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:0.38, C:0.06, G:0.38, T:0.19
Consensus pattern (16 bp):
GCAGGTGAATGAATAG
Found at i:12560263 original size:36 final size:35
Alignment explanation
Indices: 12560194--12560263 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
12560184 AAAGATCAGG
*
12560194 ATAATAACGTAAAAGGTTTTAAAATATCATATAACT
1 ATAATAACGTAAAAGGTTATAAAATAT-ATATAACT
*
12560230 ATAATAATTGTAAAAGGTTCATAAAATAT-TATAA
1 ATAATAA-CGTAAAAGGTT-ATAAAATATATATAA
12560264 AGAGTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 12 0.40
37 10 0.33
38 8 0.27
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (35 bp):
ATAATAACGTAAAAGGTTATAAAATATATATAACT
Found at i:12562941 original size:23 final size:23
Alignment explanation
Indices: 12562912--12562963 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12562902 AGTGTTGTAT
12562912 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
12562935 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
*
12562958 AATATT
1 TATATT
12562964 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:12562975 original size:19 final size:20
Alignment explanation
Indices: 12562951--12563025 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
12562941 TTAAATATCT
*
12562951 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTAAA
*
12562970 TTATTAGAT--TAATATTAAA
1 TTATTA-ATAATATTATTAAA
* *
12562989 TATATAAATAATATTATT-CA
1 T-TATTAATAATATTATTAAA
12563009 TTATTAATAATATTATT
1 TTATTAATAATATTATT
12563026 TCTATGAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 32 0.71
20 7 0.16
21 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (20 bp):
TTATTAATAATATTATTAAA
Found at i:12563156 original size:22 final size:23
Alignment explanation
Indices: 12563128--12563174 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
12563118 TTGATTATTT
12563128 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
12563150 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
12563173 TA
1 TA
12563175 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:12563179 original size:22 final size:22
Alignment explanation
Indices: 12563136--12563179 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12563126 TTTATTATAA
*
12563136 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
12563158 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
12563180 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:12566751 original size:3 final size:3
Alignment explanation
Indices: 12566739--12566773 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
12566729 AAACATAAAC
12566739 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12566774 ATATATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:12566783 original size:8 final size:7
Alignment explanation
Indices: 12566739--12566786 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 7
12566729 AAACATAAAC
12566739 ATAATAA
1 ATAATAA
12566746 ATAAT-A
1 ATAATAA
12566752 ATAAT-A
1 ATAATAA
12566758 ATAATAATA
1 ATAAT-A-A
12566767 ATAATAA
1 ATAATAA
12566774 ATATATAA
1 ATA-ATAA
12566782 ATAAT
1 ATAAT
12566787 GATAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 12 0.32
7 11 0.30
8 8 0.22
9 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAATAA
Found at i:12566784 original size:15 final size:15
Alignment explanation
Indices: 12566715--12566786 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
12566705 AAAATGTTGT
* *
12566715 AATATGTAATTAATA
1 AATATATAAATAATA
*
12566730 AACATA-AACATAATA
1 AATATATAA-ATAATA
12566745 AATA-AT-AATAAT-
1 AATATATAAATAATA
12566757 AATA-ATAATAATAATA
1 AATATAT-A-AATAATA
12566773 AATATATAAATAAT
1 AATATATAAATAAT
12566787 GATAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.13
13 5 0.11
14 4 0.09
15 24 0.52
16 5 0.11
17 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (15 bp):
AATATATAAATAATA
Found at i:12567235 original size:130 final size:133
Alignment explanation
Indices: 12566987--12567313 Score: 459
Period size: 130 Copynumber: 2.5 Consensus size: 133
12566977 CGTCTAAAGG
* * * * *
12566987 TGACAAGGTTCCTACATGATGAGGAAATCT-AGTC-GAGGGATGACACTGCTCATACATGATGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGA-TCTG-GGGATGACACGGCTCATACATGATGAA
* *
12567050 GAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGGGGACGACTGGTTAT
64 GAGTTCTTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
12567115 CTATGGT
127 CTATGGT
*
12567122 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
12567187 AGTTC-TGGCCATC-TA-AA-GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTA
65 AGTTCTTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTA
12567248 TGGT
130 TGGT
* * * *
12567252 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGA
12567314 GGACGGCTGG
Statistics
Matches: 176, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
129 20 0.11
130 83 0.47
131 2 0.01
133 2 0.01
135 39 0.22
136 30 0.17
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (133 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
GTTCTTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAT
GGT
Found at i:12567269 original size:43 final size:42
Alignment explanation
Indices: 12567088--12567284 Score: 184
Period size: 43 Copynumber: 4.5 Consensus size: 42
12567078 ATAACTCGGT
*
12567088 TCCTACGTGATGGGGACGACTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GACTGGTTATCTATGGTTGACACGGC
** *
12567131 TCCTACGTGATGAGGAGATCT-G--ATCTGGGGAATGACACGGC
1 TCCTACGTGATGAGGAGA-CTGGTTATCTATGG-TTGACACGGC
* * * ** * * *
12567172 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAG-ACTGGTTATCT-ATGGT--TGACACGGC
12567218 TCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GACTGGTTATCTATGGTTGACACGGC
12567261 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGA-CTGGT
12567285 CTGGTGATGA
Statistics
Matches: 123, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
40 6 0.05
41 26 0.21
42 6 0.05
43 45 0.37
44 4 0.03
45 6 0.05
46 29 0.24
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (42 bp):
TCCTACGTGATGAGGAGACTGGTTATCTATGGTTGACACGGC
Found at i:12567314 original size:83 final size:85
Alignment explanation
Indices: 12567163--12567323 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 85
12567153 ATCTGGGGAA
* *
12567163 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG-C-TCT--AGGTGATAACACGGTTCCTACATGA
12567228 TGAGGACGACTGGTTATCTATGGT
62 TGAGGACGACTGGTTATCTATGGT
* * *
12567252 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT-GGTGATGACACGGTTCCTACATGATGAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
*
12567315 GACGGCTGG
66 GACGACTGG
12567324 CCATCTTTAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
83 34 0.52
86 3 0.05
89 29 0.44
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (85 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
GACGACTGGTTATCTATGGT
Found at i:12567423 original size:28 final size:28
Alignment explanation
Indices: 12567362--12567423 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
12567352 AAACCAAATT
12567362 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* * *
12567390 AGAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
12567418 AAAGAT
1 AAAGAT
12567424 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:12567605 original size:33 final size:36
Alignment explanation
Indices: 12567557--12567692 Score: 91
Period size: 38 Copynumber: 3.8 Consensus size: 36
12567547 CAAAGATTAG
* *
12567557 TGTTTCGAGAGAAACAAACTCAAAGA-TG-TT-TTT
1 TGTTTCAAGAAAAACAAACTCAAAGATTGTTTGTTT
* * *
12567590 TGTTTTAAGAAAAACATACTCATAGACTTTGTTTGTTT
1 TGTTTCAAGAAAAACAAACTCAAAGA--TTGTTTGTTT
* * * ****
12567628 TGTTTCAAGAAAAACAGATTCAAATGATGGTAAAATT
1 TGTTTCAAGAAAAACAAACTCAAA-GATTGTTTGTTT
*
12567665 TGTTTCCAA-AGAAACAAACTCAAAGATT
1 TGTTT-CAAGAAAAACAAACTCAAAGATT
12567693 TTTCTCAAAG
Statistics
Matches: 78, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
33 21 0.27
36 5 0.06
37 24 0.31
38 26 0.33
39 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (36 bp):
TGTTTCAAGAAAAACAAACTCAAAGATTGTTTGTTT
Found at i:12567900 original size:102 final size:102
Alignment explanation
Indices: 12567720--12567906 Score: 241
Period size: 102 Copynumber: 1.8 Consensus size: 102
12567710 CTCGAGAGAA
* * * * *
12567720 ACAAAATTTTGTTTCCAAAGAAAGAGATTCAATGATTTTTTTTTTGAAAAGACATTGTCATAAGA
1 ACAAAATTTTGTTTCCAAAGAAAGAGACTCAAAGA-TTTTTTCTTCAAAAGAAATTGTCATAAGA
*
12567785 GACAAAACTTTGTTTTTCAGAAAATGGTATCTTAGTGAG
65 GACAAAACATTG-TTTTCAGAAAATGGTATCTTAGTGAG
* * ** *
12567824 ACAAAATTTTGTTTCCAAAGAAATAGCCTCAAAGA-TTTTTCTTCAAAAGAAATTGTTTTAAGGG
1 ACAAAATTTTGTTTCCAAAGAAAGAGACTCAAAGATTTTTTCTTCAAAAGAAATTGTCATAAGAG
*
12567888 ATAAAACATTGTTTTCAGA
66 ACAAAACATTGTTTTCAGA
12567907 GAAACCAACT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
101 8 0.11
102 32 0.45
104 31 0.44
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (102 bp):
ACAAAATTTTGTTTCCAAAGAAAGAGACTCAAAGATTTTTTCTTCAAAAGAAATTGTCATAAGAG
ACAAAACATTGTTTTCAGAAAATGGTATCTTAGTGAG
Found at i:12567953 original size:15 final size:15
Alignment explanation
Indices: 12567929--12567972 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
12567919 AAGATGATCT
*
12567929 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
12567944 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
12567959 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
12567973 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:12568025 original size:31 final size:30
Alignment explanation
Indices: 12567961--12568035 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
12567951 AGAGAAAATG
*
12567961 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
12567992 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
12568023 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
12568036 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:12568128 original size:40 final size:40
Alignment explanation
Indices: 12568068--12568147 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
12568058 GTTTTAATAA
12568068 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
12568108 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
12568148 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:12568202 original size:63 final size:64
Alignment explanation
Indices: 12568129--12568253 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
12568119 AATGTGGGTA
* * *
12568129 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
12568192 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
12568254 GGATCCCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:12568366 original size:120 final size:119
Alignment explanation
Indices: 12568151--12568374 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
12568141 GTTGTCTCGA
* *
12568151 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
*
12568216 AGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
* * * **
12568270 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
** *
12568332 AAGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
12568375 ATTTTGTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 16 0.18
120 45 0.51
121 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
Found at i:12568542 original size:37 final size:37
Alignment explanation
Indices: 12568486--12568611 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 37
12568476 GAGACAGATT
12568486 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* ** * *
12568523 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* *
12568556 ---ATTTTTGTTTTAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
12568590 CAAAATTTTGTTTCCAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
12568612 CAAACTCAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
30 18 0.27
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 7 0.11
37 33 0.50
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:12568584 original size:67 final size:66
Alignment explanation
Indices: 12568485--12568639 Score: 278
Period size: 67 Copynumber: 2.4 Consensus size: 66
12568475 AGAGACAGAT
12568485 TCAAAGA-TTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
1 TCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
12568549 C
66 C
*
12568550 TCAAAGATTTTTGTTTTAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGATTTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
12568615 AC
65 AC
12568617 TCAAAGA-TTTTTTTCAAAAGAAA
1 TCAAAGATTTTTTTTCAAAAGAAA
12568640 CAATCTCAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
65 18 0.21
66 8 0.09
67 60 0.70
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (66 bp):
TCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
C
Found at i:12568655 original size:27 final size:28
Alignment explanation
Indices: 12568590--12568658 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
12568580 TTAAGAGAGA
*
12568590 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
12568618 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
12568646 CAAAGATTTTTTT
1 CAAAGATTTTTTT
12568659 TCACAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:12568827 original size:29 final size:29
Alignment explanation
Indices: 12568745--12569015 Score: 177
Period size: 29 Copynumber: 9.4 Consensus size: 29
12568735 AAAACTTTGT
* * *
12568745 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
12568771 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* * *
12568799 TTCAAAAGGAACAGACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
12568828 TTCAAAAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *** *
12568855 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT-
1 TTCAAAAGAAACAAACTC-A-A-AG-----A-TTTTTA
* * *
12568892 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
12568918 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
12568946 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* * *
12568975 TTCTAAAGGAACAAACTCAAAGATTTTTT
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
12569004 TTCAAGAGAAAC
1 TTCAAAAGAAAC
12569016 TGTCTCAAGA
Statistics
Matches: 194, Mismatches: 33, Indels: 33
0.75 0.13 0.13
Matches are distributed among these distances:
25 18 0.09
26 22 0.11
27 19 0.10
28 27 0.14
29 85 0.44
30 2 0.01
34 2 0.01
35 2 0.01
36 1 0.01
37 16 0.08
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:12568899 original size:147 final size:147
Alignment explanation
Indices: 12568698--12569034 Score: 599
Period size: 147 Copynumber: 2.3 Consensus size: 147
12568688 TTTGTTTCAG
* *
12568698 ACTCAAAGA-TTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
*
12568760 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAGACTCCAAGATTT
66 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
12568825 TTATTCAAAAGGAACAA
131 TTATTCAAAAGGAACAA
12568842 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
12568907 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
66 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
*
12568972 TTATTCTAAAGGAACAA
131 TTATTCAAAAGGAACAA
12568989 ACTCAAAGATTTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 ACTCAAAGA--TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
12569035 AAATCGTTTT
Statistics
Matches: 184, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
144 9 0.05
145 6 0.03
146 1 0.01
147 133 0.72
149 35 0.19
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (147 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
TTATTCAAAAGGAACAA
Found at i:12569340 original size:36 final size:35
Alignment explanation
Indices: 12569256--12569353 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 35
12569246 GAGAAAATGA
* *
12569256 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* ** *
12569290 AGTCTCAAATGAGACAAAATTTGTTTTTAGTGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
* *
12569326 TGTCTCAAGCGAGACAAAGTTTATTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
12569354 GAGGAAACGA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
34 20 0.39
35 4 0.08
36 27 0.53
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:12570031 original size:4 final size:4
Alignment explanation
Indices: 12570022--12570063 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
12570012 TTTATGTATC
12570022 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
12570064 GTATACTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:12571270 original size:12 final size:11
Alignment explanation
Indices: 12571242--12571277 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12571232 TCCTCTTTTG
*
12571242 TTCTTTGCTTT
1 TTCTTTGATTT
12571253 TTCTTTGATTT
1 TTCTTTGATTT
12571264 TTGCTTTGATTT
1 TT-CTTTGATTT
12571276 TT
1 TT
12571278 TTTCTTTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:12571287 original size:19 final size:20
Alignment explanation
Indices: 12571263--12571311 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
12571253 TTCTTTGATT
12571263 TTTGCTTTGAT-TTTTTTTC
1 TTTGCTTTGATGTTTTTTTC
12571282 TTTGCTCTT--TGTTTTTTTC
1 TTTGCT-TTGATGTTTTTTTC
*
12571301 TTTGGTTTGAT
1 TTTGCTTTGAT
12571312 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.04, C:0.10, G:0.14, T:0.71
Consensus pattern (20 bp):
TTTGCTTTGATGTTTTTTTC
Found at i:12571980 original size:46 final size:45
Alignment explanation
Indices: 12571888--12571981 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 45
12571878 ATAAATGCAG
* * * * *
12571888 TGTTTCAAGGTGGAAAGGATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
12571933 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
12571979 TGT
1 TGT
12571982 CAAAATTTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 11 0.27
46 30 0.73
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:12574464 original size:31 final size:32
Alignment explanation
Indices: 12574408--12574469 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
12574398 TGACGAAATG
*
12574408 ACACAAACAAAAGATAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
12574440 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
12574470 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:12578116 original size:3 final size:3
Alignment explanation
Indices: 12578104--12578141 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
12578094 AAACATAAAC
12578104 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12578142 ATATATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12578151 original size:8 final size:7
Alignment explanation
Indices: 12578104--12578154 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 7
12578094 AAACATAAAC
12578104 ATAATAA
1 ATAATAA
12578111 ATAAT-A
1 ATAATAA
12578117 ATAAT-A
1 ATAATAA
12578123 ATAAT-A
1 ATAATAA
12578129 ATAAT-A
1 ATAATAA
12578135 ATAATAA
1 ATAATAA
12578142 ATATATAA
1 ATA-ATAA
12578150 ATAAT
1 ATAAT
12578155 GATAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 24 0.57
7 11 0.26
8 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAATAA
Found at i:12584339 original size:18 final size:18
Alignment explanation
Indices: 12584267--12584331 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
12584257 ACTGAATATT
12584267 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
12584285 TGTCCCGAAGGACAACTGA
1 TGTCCCGAAGGACCACT-A
* *
12584304 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
12584323 TGTCCCGAA
1 TGTCCCGAA
12584332 TGGCCACTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 24 0.60
19 2 0.05
20 14 0.35
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:12584615 original size:24 final size:21
Alignment explanation
Indices: 12584559--12584616 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
12584549 ATATCTTCTC
12584559 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
12584581 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
12584605 GATCACTTTCAT
1 -ATCACTTTCAT
12584617 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:12588412 original size:38 final size:40
Alignment explanation
Indices: 12588361--12588437 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 40
12588351 ACTGAATATT
*
12588361 TGTCCCGAAGGACCACTG-AT-TGTTCCGAATAACCACTA
1 TGTCCCGAAGGACCACTGTATATGTCCCGAATAACCACTA
*
12588399 TGTCCCGAAGGACCACTGTATATGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACTGTATATGTCCCGAATAACCACT
12588438 CCTCAAGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 18 0.51
39 2 0.06
40 15 0.43
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTGTATATGTCCCGAATAACCACTA
Found at i:12588413 original size:18 final size:20
Alignment explanation
Indices: 12588360--12588437 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
12588350 CACTGAATAT
12588360 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* **
12588380 TTGTTCCGAATAACCACT-A
1 TTGTCCCGAAGGACCACTGA
12588399 -TGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTG-A
*
12588419 TATGTCCCGAATGACCACT
1 T-TGTCCCGAAGGACCACT
12588438 CCTCAAGAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.30
19 1 0.02
20 16 0.34
22 16 0.34
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:12588425 original size:22 final size:21
Alignment explanation
Indices: 12588361--12588437 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 21
12588351 ACTGAATATT
12588361 TGTCCCGAAGGACCACTGAT-
1 TGTCCCGAAGGACCACTGATA
* **
12588381 TGTTCCGAATAACCAC---TA
1 TGTCCCGAAGGACCACTGATA
12588399 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTG-ATA
*
12588421 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
12588438 CCTCAAGAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.29
20 13 0.29
22 18 0.40
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:12589159 original size:19 final size:19
Alignment explanation
Indices: 12589135--12589205 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
12589125 TTTAAGTAGG
*
12589135 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTTA
*
12589154 TGCATCGATGCACTCATTA
1 TGCATCGATGCACTCCTTA
12589173 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
12589192 TGCATCGATGCACT
1 TGCATCGATGCACT
12589206 AATTGTATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:12590396 original size:10 final size:9
Alignment explanation
Indices: 12590364--12590388 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12590354 ATAATCATTA
12590364 TAAAAAAAT
1 TAAAAAAAT
12590373 TAAAAAAAT
1 TAAAAAAAT
12590382 TAAAAAA
1 TAAAAAA
12590389 CTATAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:12590472 original size:17 final size:16
Alignment explanation
Indices: 12590447--12590489 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
12590437 TATATTATAA
*
12590447 TTTTTAAAAGA-TAATT
1 TTTTTAAAAAATTAA-T
12590463 TTTTTAAAAAATTAAT
1 TTTTTAAAAAATTAAT
12590479 TTTTTAAAAAA
1 TTTTTAAAAAA
12590490 AATCGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTTAAAAAATTAAT
Found at i:12590490 original size:17 final size:17
Alignment explanation
Indices: 12590458--12590490 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12590448 TTTTAAAAGA
*
12590458 TAATTTTTTTAAAAAAT
1 TAATTTTTTAAAAAAAT
12590475 TAATTTTTTAAAAAAA
1 TAATTTTTTAAAAAAA
12590491 ATCGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTTTTAAAAAAAT
Found at i:12590828 original size:31 final size:31
Alignment explanation
Indices: 12590793--12590869 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
12590783 TATCCGACCT
*
12590793 GAACCCGAATTGAATCGAAA-ATATGATACCC
1 GAACCCGAATTGAATCCAAAGATATGA-ACCC
* * *
12590824 GAACCTGAACTGCATCCAAATGATATGAACCC
1 GAACCCGAATTGAATCCAAA-GATATGAACCC
*
12590856 GTACCCGAGATTGA
1 GAACCCGA-ATTGA
12590870 CCTGGTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
31 16 0.46
32 10 0.29
33 9 0.26
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (31 bp):
GAACCCGAATTGAATCCAAAGATATGAACCC
Found at i:12590921 original size:16 final size:16
Alignment explanation
Indices: 12590898--12590964 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
12590888 TTACCCGACA
12590898 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACC
*
12590914 TATTTTCAACCTGACC
1 TGTTTTCAACCTGACC
* *
12590930 TGTTTTTAACCTGACT
1 TGTTTTCAACCTGACC
*
12590946 TGTTTTTAACCTGACC
1 TGTTTTCAACCTGACC
12590962 TGT
1 TGT
12590965 AAATGATCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.43
Consensus pattern (16 bp):
TGTTTTCAACCTGACC
Found at i:12594617 original size:102 final size:102
Alignment explanation
Indices: 12594449--12594647 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
12594439 AATTAAATTA
12594449 TAAATAAAGGGAGCTAACAACCTTATAAAAGCAATCCGAATGAACAACCAACAACACAAACAAAT
1 TAAATAAAGGGAGCTAACAACCTTATAAAAGCAATCCGAATGAACAACCAACAACACAAACAAAT
12594514 CAAAAGTAGCTACAAATTAAACAATTTATTTAAACTG
66 CAAAAGTAGCTACAAATTAAACAATTTATTTAAACTG
* *
12594551 TAAATAAAGGTAGCTAACAACCTTATAAAAGCTATCCGAATGAACAACCAACAACACAAACAAAT
1 TAAATAAAGGGAGCTAACAACCTTATAAAAGCAATCCGAATGAACAACCAACAACACAAACAAAT
*
12594616 CAACAGTAGCTACAAATTAAACAATTTATTTA
66 CAAAAGTAGCTACAAATTAAACAATTTATTTA
12594648 CCTCTTTCAG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (102 bp):
TAAATAAAGGGAGCTAACAACCTTATAAAAGCAATCCGAATGAACAACCAACAACACAAACAAAT
CAAAAGTAGCTACAAATTAAACAATTTATTTAAACTG
Found at i:12594981 original size:6 final size:6
Alignment explanation
Indices: 12594910--12595041 Score: 83
Period size: 6 Copynumber: 22.5 Consensus size: 6
12594900 CAGGTTTAAA
* * * * *
12594910 TTTGGG -TTGGG TTCGGG TTTGAG TTAGGG TTTAGG -TTGGG TTT-AG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * * * *
12594955 TTAGGG GTTGGG TTTGAG TTTGGG TTTTAGG TTTGGG TTAGGG TTT-GA
1 TTTGGG TTTGGG TTTGGG TTTGGG -TTTGGG TTTGGG TTTGGG TTTGGG
* * * * *
12595003 TTAGGG GTTGGG TTTAGG TTTGGG TTTAGG TTTAGG TTT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTT
12595042 AAGTTAGGTT
Statistics
Matches: 92, Mismatches: 29, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
5 15 0.16
6 72 0.78
7 5 0.05
ACGTcount: A:0.10, C:0.01, G:0.43, T:0.46
Consensus pattern (6 bp):
TTTGGG
Found at i:12595007 original size:48 final size:46
Alignment explanation
Indices: 12594913--12595040 Score: 154
Period size: 48 Copynumber: 2.7 Consensus size: 46
12594903 GTTTAAATTT
** *
12594913 GGGTTGGGTTCGGGTTTGAG-TTAGGGTTTAGGTTGGGTTTAGTTAG
1 GGGTTGGGTTTAGGTTTGGGTTTA-GGTTTAGGTTGGGTTTAGTTAG
*
12594959 GGGTTGGGTTT-GAGTTTGGGTTTTAGGTTTGGGTTAGGGTTT-GATTAG
1 GGGTTGGGTTTAG-GTTTGGG-TTTAGGTTTAGGTT-GGGTTTAG-TTAG
12595007 GGGTTGGGTTTAGGTTTGGGTTTAGGTTTAGGTT
1 GGGTTGGGTTTAGGTTTGGGTTTAGGTTTAGGTT
12595041 TAAGTTAGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
45 1 0.01
46 16 0.22
47 23 0.32
48 31 0.43
49 1 0.01
ACGTcount: A:0.10, C:0.01, G:0.45, T:0.45
Consensus pattern (46 bp):
GGGTTGGGTTTAGGTTTGGGTTTAGGTTTAGGTTGGGTTTAGTTAG
Found at i:12595025 original size:12 final size:12
Alignment explanation
Indices: 12594962--12595055 Score: 72
Period size: 12 Copynumber: 7.9 Consensus size: 12
12594952 TAGTTAGGGG
12594962 TTGGGTTT-GAGT
1 TTGGGTTTAG-GT
12594974 TTGGGTTTTAGGT
1 TTGGG-TTTAGGT
12594987 TTGGG-TTAGGGT
1 TTGGGTTTA-GGT
* *
12594999 TT--GATTAGGGG
1 TTGGGTTTA-GGT
12595010 TTGGGTTTAGGT
1 TTGGGTTTAGGT
12595022 TTGGGTTTAGGT
1 TTGGGTTTAGGT
* *
12595034 TTAGGTTTAAG-
1 TTGGGTTTAGGT
*
12595045 TTAGGTTTAGG
1 TTGGGTTTAGG
12595056 GTTTAGGTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
10 1 0.01
11 21 0.30
12 33 0.47
13 14 0.20
14 1 0.01
ACGTcount: A:0.13, C:0.00, G:0.40, T:0.47
Consensus pattern (12 bp):
TTGGGTTTAGGT
Found at i:12595042 original size:6 final size:6
Alignment explanation
Indices: 12595013--12595064 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
12595003 TTAGGGGTTG
* *
12595013 GGTTTA GGTTTG GGTTTA GGTTTA GGTTTA AG-TTA GGTTTA GGGTTTA
1 GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA -GGTTTA
12595061 GGTT
1 GGTT
12595065 CAAGTTAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 4 0.10
6 30 0.75
7 6 0.15
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (6 bp):
GGTTTA
Found at i:12595069 original size:24 final size:24
Alignment explanation
Indices: 12595025--12595078 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
12595015 TTTAGGTTTG
*
12595025 GGTTTA-GGTTTAGGTTTAAGTTA
1 GGTTTAGGGTTTAGGTTCAAGTTA
12595048 GGTTTAGGGTTTAGGTTCAAGTTA
1 GGTTTAGGGTTTAGGTTCAAGTTA
*
12595072 GGGTTAG
1 GGTTTAG
12595079 TGACAGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (24 bp):
GGTTTAGGGTTTAGGTTCAAGTTA
Found at i:12595793 original size:16 final size:15
Alignment explanation
Indices: 12595753--12595880 Score: 76
Period size: 14 Copynumber: 8.7 Consensus size: 15
12595743 TAATTTTTTA
12595753 AATTAACTATT-T-AT
1 AATTAA-TATTATAAT
12595767 AATTAATATTATAAT
1 AATTAATATTATAAT
*
12595782 AATT-ATA-TATTAT
1 AATTAATATTATAAT
12595795 AATTAATATTCAT-AT
1 AATTAATATT-ATAAT
*
12595810 AATTAATA-TA-ATT
1 AATTAATATTATAAT
* *
12595823 AATATAAAATTATATT
1 AAT-TAATATTATAAT
* *
12595839 AATATAATATAATTTAT
1 AAT-TAATATTA-TAAT
*
12595856 AATTTATAATT-T-AT
1 AATTAAT-ATTATAAT
12595870 AATTAATATTA
1 AATTAATATTA
12595881 ATATAAAATA
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
13 21 0.23
14 26 0.28
15 20 0.22
16 18 0.20
17 7 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATATTATAAT
Found at i:12595799 original size:28 final size:26
Alignment explanation
Indices: 12595753--12595880 Score: 96
Period size: 28 Copynumber: 4.4 Consensus size: 26
12595743 TAATTTTTTA
12595753 AATTAACTATTTATAATTAATATTATAAT
1 AATTAA-TA-TTATAATTAATATTAT-AT
12595782 AATTATATATTATAATTAATATTCATAT
1 AATTA-ATATTATAATTAATATT-ATAT
* *
12595810 AATTAATATAATTAATATAAAATTATATT
1 AATTAATATTA-TAAT-TAATATTATA-T
*
12595839 AATATAATATAATTTATAATTTATAATT-TAT
1 AAT-T-A-AT-A-TTATAATTAAT-ATTATAT
12595870 AATTAATATTA
1 AATTAATATTA
12595881 ATATAAAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 25
0.73 0.04 0.22
Matches are distributed among these distances:
26 3 0.04
27 6 0.07
28 30 0.36
29 20 0.24
30 3 0.04
31 5 0.06
32 6 0.07
33 8 0.10
34 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTAATATTATAATTAATATTATAT
Found at i:12595820 original size:9 final size:9
Alignment explanation
Indices: 12595764--12595878 Score: 63
Period size: 9 Copynumber: 13.3 Consensus size: 9
12595754 ATTAACTATT
12595764 TATAATTAA
1 TATAATTAA
*
12595773 TATTA-TAA
1 TATAATTAA
* *
12595781 TAATTATATAT
1 T-ATAAT-TAA
12595792 TATAATT-A
1 TATAATTAA
*
12595800 -AT-ATTCA
1 TATAATTAA
12595807 TATAATTAA
1 TATAATTAA
12595816 TATAATTAA
1 TATAATTAA
12595825 TATAA--AA
1 TATAATTAA
12595832 T-TATATTAA
1 TATA-ATTAA
12595841 TATAATATAA
1 TATAAT-TAA
12595851 TTTATAATT--
1 --TATAATTAA
12595860 TATAATT--
1 TATAATTAA
12595867 TATAATTAA
1 TATAATTAA
12595876 TAT
1 TAT
12595879 TAATATAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 30
0.71 0.04 0.25
Matches are distributed among these distances:
6 5 0.06
7 21 0.24
8 6 0.07
9 35 0.41
10 9 0.10
11 4 0.05
12 6 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
TATAATTAA
Found at i:12595836 original size:57 final size:57
Alignment explanation
Indices: 12595766--12595889 Score: 132
Period size: 57 Copynumber: 2.2 Consensus size: 57
12595756 TAACTATTTA
* * *
12595766 TAAT-TAATATTATAATAAT-T-ATAT-A-TTATAATTAATATTCATATAATTAATATAAT
1 TAATATAAAATTATAATAATATAATATAATTTATAATTAATAAT-TTATAATT-A-AT-AT
* *
12595822 TAATATAAAATTATATTAATATAATATAATTTATAATTTATAATTTATAATTAATAT
1 TAATATAAAATTATAATAATATAATATAATTTATAATTAATAATTTATAATTAATAT
12595879 TAATATAAAAT
1 TAATATAAAAT
12595890 ATAGTATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
56 4 0.07
57 26 0.45
58 3 0.05
59 5 0.09
60 8 0.14
61 12 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.48
Consensus pattern (57 bp):
TAATATAAAATTATAATAATATAATATAATTTATAATTAATAATTTATAATTAATAT
Found at i:12595858 original size:7 final size:7
Alignment explanation
Indices: 12595846--12595873 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12595836 ATTAATATAA
12595846 TATAATT
1 TATAATT
12595853 TATAATT
1 TATAATT
12595860 TATAATT
1 TATAATT
12595867 TATAATT
1 TATAATT
12595874 AATATTAATA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATAATT
Found at i:12595906 original size:82 final size:76
Alignment explanation
Indices: 12595764--12595975 Score: 210
Period size: 75 Copynumber: 2.8 Consensus size: 76
12595754 ATTAACTATT
*
12595764 TATAATTAATATTATAATAATTATATATTATAATTAATATTCATATAATTAATATAATTAATATA
1 TATAATTAATATTATAAT-ATTATATATTATAATTAATATTAATATAATTAATATAATTAATATA
12595829 AAATTATATTAA
65 AAATTATATTAA
*
12595841 TATAATATAAT-TTATAAT-TTATA-ATTTATAATTAATATTAATATAA--AATAT-AGT-ATAT
1 TATAAT-TAATATTATAATATTATATA-TTATAATTAATATTAATATAATTAATATAATTAATAT
*
12595899 AACATTAATATTAA
64 AAAATT-ATATTAA
* * * * * *
12595913 TATAAACTATATGTTATAA-ATTATATAGTATAGTT--TATAAACTATAGTTAATATAATTAATA
1 TAT-AATTA-ATATTATAATATTATATATTATAATTAATATTAA-TATAATTAATATAATTAATA
12595975 T
63 T
12595976 TAATATAATA
Statistics
Matches: 113, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
71 9 0.08
72 19 0.17
73 13 0.12
74 18 0.16
75 31 0.27
76 2 0.02
77 17 0.15
78 4 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (76 bp):
TATAATTAATATTATAATATTATATATTATAATTAATATTAATATAATTAATATAATTAATATAA
AATTATATTAA
Found at i:12595909 original size:31 final size:29
Alignment explanation
Indices: 12595866--12596054 Score: 123
Period size: 31 Copynumber: 6.0 Consensus size: 29
12595856 AATTTATAAT
12595866 TTAT-AATTAATATTAATATAAAATATAG
1 TTATAAATTAATATTAATATAAAATATAG
*
12595894 TATATAACATTAATATTAATATAAACTATATG
1 T-TATAA-ATTAATATTAATATAAAATATA-G
* *
12595926 TTATAAATTATATAGTATAGTTTATAAACTATAG
1 TTATAAATTA-ATA-T-TA--ATATAAAATATAG
12595960 TTAATATAATTAATATTAATAT--AATATAG
1 TT-ATA-AATTAATATTAATATAAAATATAG
*
12595989 TTTATAAACTATATACTATATTAATATAAATTATAG
1 -TTAT-AA--AT-TA--ATATTAATATAAAATATAG
* * *
12596025 TTAAGATAATTAACATTAATATAAACTATA
1 TT-ATA-AATTAATATTAATATAAAATATA
12596055 TAGTACATTA
Statistics
Matches: 131, Mismatches: 8, Indels: 41
0.73 0.04 0.23
Matches are distributed among these distances:
28 1 0.01
29 12 0.09
30 8 0.06
31 50 0.38
32 5 0.04
33 6 0.05
34 16 0.12
35 20 0.15
36 13 0.10
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
TTATAAATTAATATTAATATAAAATATAG
Found at i:12595950 original size:14 final size:14
Alignment explanation
Indices: 12595933--12595994 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
12595923 ATGTTATAAA
*
12595933 TTATATAGTATAGT
1 TTATATAATATAGT
12595947 TTATA-AACTATAGT
1 TTATATAA-TATAGT
*
12595961 TAATATAATTAATA-T
1 TTATATAA-T-ATAGT
*
12595976 TAATATAATATAGT
1 TTATATAATATAGT
12595990 TTATA
1 TTATA
12595995 AACTATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.10
14 21 0.52
15 12 0.30
16 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATATAATATAGT
Found at i:12595980 original size:15 final size:15
Alignment explanation
Indices: 12595960--12596048 Score: 56
Period size: 15 Copynumber: 5.6 Consensus size: 15
12595950 TAAACTATAG
12595960 TTAATATAATTAATA
1 TTAATATAATTAATA
*
12595975 TTAATATAATATAGTTTA
1 TTAATATAAT-TA--ATA
* *
12595993 TAAACTATATACT-ATA
1 TTAA-TATA-ATTAATA
12596009 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
* *
12596024 GTTAAGATAATTAACA
1 -TTAATATAATTAATA
12596040 TTAATATAA
1 TTAATATAA
12596049 ACTATATAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
15 30 0.53
16 16 0.28
18 5 0.09
19 5 0.09
20 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:12596062 original size:22 final size:22
Alignment explanation
Indices: 12596037--12596139 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
12596027 AAGATAATTA
12596037 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
12596059 ACATTAATATAAACTATAGT-GT
1 ACATTAATATAAACTATA-TAGT
* * * *
12596081 --ATAAATTATATACCATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
12596101 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
12596123 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
12596140 TGAATATAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.09
21 23 0.35
22 32 0.49
23 4 0.06
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.35
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:12596188 original size:20 final size:22
Alignment explanation
Indices: 12596158--12596249 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 22
12596148 AACTATAGGT
12596158 TACATAT--ATAGTT-TATATA
1 TACATATAAATAGTTATATATA
*
12596177 -ACATATAAATAGATTGTATATA
1 TACATATAAATAG-TTATATATA
*
12596199 TACATATACTATAGGTTATATATA
1 TACATATA-AATA-GTTATATATA
* *
12596223 TACACTATACATAGTT-TATACA
1 TACA-TATAAATAGTTATATATA
12596245 TACAT
1 TACAT
12596250 GATACATGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.10
20 4 0.07
21 3 0.05
22 15 0.25
23 10 0.16
24 18 0.30
25 5 0.08
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
TACATATAAATAGTTATATATA
Found at i:12596218 original size:22 final size:23
Alignment explanation
Indices: 12596171--12596256 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 23
12596161 ATATATAGTT
* * *
12596171 TATATA-ACATATAAATAGATTG
1 TATATATACATATACATAGGTTA
12596193 TATATATACATATACTATAGGTTA
1 TATATATACATATAC-ATAGGTTA
12596217 TATATATACACTATACATA-GTT-
1 TATATATACA-TATACATAGGTTA
*
12596239 TATACATACATGATACAT
1 TATATATACAT-ATACAT
12596257 GTACTATAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.02
22 21 0.38
23 10 0.18
24 19 0.34
25 5 0.09
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (23 bp):
TATATATACATATACATAGGTTA
Found at i:12596307 original size:24 final size:23
Alignment explanation
Indices: 12596274--12596318 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12596264 AAGTTACATA
*
12596274 TATAGTTTACATGTATAAATATAT
1 TATAGGTTACAT-TATAAATATAT
*
12596298 TATAGGTTACATTATATATAT
1 TATAGGTTACATTATAAATAT
12596319 TAACTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
TATAGGTTACATTATAAATATAT
Found at i:12596352 original size:14 final size:14
Alignment explanation
Indices: 12596333--12596391 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
12596323 TATTGTTTAT
12596333 GTTTAGTGTTTAGG
1 GTTTAGTGTTTAGG
*
12596347 GTTTAG-GGTTAGG
1 GTTTAGTGTTTAGG
* **
12596360 ATTTAAAGTTTAGG
1 GTTTAGTGTTTAGG
12596374 GTTTAGTGTTTAGG
1 GTTTAGTGTTTAGG
12596388 GTTT
1 GTTT
12596392 TTATAAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
GTTTAGTGTTTAGG
Found at i:12596483 original size:49 final size:48
Alignment explanation
Indices: 12596388--12596483 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
12596378 AGTGTTTAGG
* ** * *
12596388 GTTTTTATAAACTATATACTTTATTAATTTATATAGTTTATGTATATT
1 GTTTCTATAAACTATATAAGTAATTAATTTATATAGTTTATATATATT
*
12596436 GTTTCTATAAACTATATAAGTAATTTACTTTATAT-GATTTATATATAT
1 GTTTCTATAAACTATATAAGTAA-TTAATTTATATAG-TTTATATATAT
12596484 ATATACTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 20 0.50
49 20 0.50
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (48 bp):
GTTTCTATAAACTATATAAGTAATTAATTTATATAGTTTATATATATT
Found at i:12596790 original size:2 final size:2
Alignment explanation
Indices: 12596783--12596921 Score: 53
Period size: 2 Copynumber: 71.0 Consensus size: 2
12596773 TGTTTCTTTA
* * *
12596783 AT AT AT AT AT AT AT -T CT AT AT AT -T ACT -T AT AT TT GT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
12596822 AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
12596861 AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC AT AT AT AGT TT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
12596903 AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT A-T AT AT
12596922 TAATATAAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
1 9 0.09
2 86 0.83
3 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12596872 original size:79 final size:79
Alignment explanation
Indices: 12596788--12596988 Score: 228
Period size: 79 Copynumber: 2.5 Consensus size: 79
12596778 CTTTAATATA
* * *
12596788 TATATATATTCTATA-TAT-TACTTATATTTGTTATACATACATATATATACTATATTAATATAA
1 TATATATATTATATAGTATATACATATA-TAGTT-TACATACATATATATACTATATTAATATAA
*
12596851 ATTATAACATATAAAC
64 ATAATAACATATAAAC
* * * *
12596867 TATATATTTTATATAGTTTATACATATATAGTTTATATATATATATATACTATATTAATATAAAT
1 TATATATATTATATAGTATATACATATATAGTTTACATACATATATATACTATATTAATATAAAT
***
12596932 AATATTTTATAAAC
66 AATAACATATAAAC
* * *
12596946 TATATACT-TTTTATAGTTTATACATATATAGTTTATATACATA
1 TATATA-TATTATATAGTATATACATATATAGTTTACATACATA
12596989 GTTTACATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 92 0.87
80 7 0.07
81 7 0.07
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.48
Consensus pattern (79 bp):
TATATATATTATATAGTATATACATATATAGTTTACATACATATATATACTATATTAATATAAAT
AATAACATATAAAC
Found at i:12596906 original size:13 final size:13
Alignment explanation
Indices: 12596876--12597208 Score: 146
Period size: 13 Copynumber: 24.5 Consensus size: 13
12596866 CTATATATTT
12596876 TATATAGTTTATACA
1 TATATAGTTTAT--A
12596891 TATATAGTTTATA
1 TATATAGTTTATA
*
12596904 TATATA-TATATA
1 TATATAGTTTATA
* * *
12596916 CTATATTAATATAAA
1 -TATA-TAGTTTATA
*
12596931 TA-ATATTTTATAAA
1 TATATAGTTTAT--A
*
12596945 CTATATA-CTT-T-
1 -TATATAGTTTATA
12596956 T-TATAGTTTATACA
1 TATATAGTTTAT--A
12596970 TATATAGTTTATA
1 TATATAGTTTATA
* *
12596983 TACATAGTTTACA
1 TATATAGTTTATA
12596996 TATATAGTTTATA
1 TATATAGTTTATA
* *
12597009 TACATAGTTTACA
1 TATATAGTTTATA
12597022 TATATAGTTTATA
1 TATATAGTTTATA
*
12597035 TACATAGTTTATA
1 TATATAGTTTATA
* *
12597048 TGTATAGTTCACATA
1 TATATAGTT--TATA
* * *
12597063 AAAATAATTTATA
1 TATATAGTTTATA
12597076 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
12597093 TTATATAGTTTATA
1 -TATATAGTTTATA
**
12597107 -ATATA-AATATA
1 TATATAGTTTATA
* *
12597118 GTTTATAATTT-TA
1 -TATATAGTTTATA
* *
12597131 TATACAGTTGACATA
1 TATATAGTT--TATA
* *
12597146 AATATAATTTATA
1 TATATAGTTTATA
12597159 TATATAGTTTATAATA
1 TATATAG-TT-T-ATA
12597175 TAAATATAGTTTATA
1 T--ATATAGTTTATA
*
12597190 TATA-ATTTTATA
1 TATATAGTTTATA
12597202 TTATATA
1 -TATATA
12597209 TATATTATAT
Statistics
Matches: 242, Mismatches: 43, Indels: 67
0.69 0.12 0.19
Matches are distributed among these distances:
9 4 0.02
10 3 0.01
11 5 0.02
12 28 0.12
13 104 0.43
14 14 0.06
15 55 0.23
16 11 0.05
17 5 0.02
18 13 0.05
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:12596995 original size:26 final size:26
Alignment explanation
Indices: 12596966--12597056 Score: 164
Period size: 26 Copynumber: 3.5 Consensus size: 26
12596956 TTATAGTTTA
12596966 TACATATATAGTTTATATACATAGTT
1 TACATATATAGTTTATATACATAGTT
12596992 TACATATATAGTTTATATACATAGTT
1 TACATATATAGTTTATATACATAGTT
12597018 TACATATATAGTTTATATACATAGTT
1 TACATATATAGTTTATATACATAGTT
* *
12597044 TATATGTATAGTT
1 TACATATATAGTT
12597057 CACATAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (26 bp):
TACATATATAGTTTATATACATAGTT
Found at i:12597000 original size:79 final size:79
Alignment explanation
Indices: 12596824--12596988 Score: 269
Period size: 79 Copynumber: 2.1 Consensus size: 79
12596814 TTTGTTATAC
*
12596824 ATACATATATATACTATATTAATATAAATTATAACATATAAACTATATATTTTATATAGTTTATA
1 ATACATATATATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATA
12596889 CATATATAGTTTAT
66 CATATATAGTTTAT
* ***
12596903 ATATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTT-TATAGTTTAT
1 ATACATATATATACTATATTAATATAAATAATAACATATAAACTATATA-TTTTATATAGTTTAT
12596967 ACATATATAGTTTAT
65 ACATATATAGTTTAT
12596982 ATACATA
1 ATACATA
12596989 GTTTACATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 75 0.95
80 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (79 bp):
ATACATATATATACTATATTAATATAAATAATAACATATAAACTATATATTTTATATAGTTTATA
CATATATAGTTTAT
Found at i:12597116 original size:18 final size:18
Alignment explanation
Indices: 12597072--12597194 Score: 77
Period size: 18 Copynumber: 7.3 Consensus size: 18
12597062 AAAAATAATT
* *
12597072 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
12597090 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
12597108 TATAAATATAGTTTATAA
1 TATAAATATAGTTTATAA
* * * *
12597126 TTTTATATACAG--T-TGA
1 -TATAAATATAGTTTATAA
* *
12597142 CATAAATATA-ATT-T-A
1 TATAAATATAGTTTATAA
12597157 TAT--ATATAGTTTATAA
1 TATAAATATAGTTTATAA
12597173 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
12597190 TATAA
1 TATAA
12597195 TTTTATATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
13 5 0.06
14 2 0.02
15 10 0.12
16 8 0.10
17 8 0.10
18 41 0.49
19 9 0.11
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:12597181 original size:31 final size:30
Alignment explanation
Indices: 12597143--12597212 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
12597133 TACAGTTGAC
12597143 ATAAATATAATTTATATATATAGTTTATAAT
1 ATAAATATAATTTATATATA-AGTTTATAAT
* * *
12597174 ATAAATATAGTTTATATATAATTTTATATT
1 ATAAATATAATTTATATATAAGTTTATAAT
*
12597204 ATATATATA
1 ATAAATATA
12597213 TTATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
ATAAATATAATTTATATATAAGTTTATAAT
Found at i:12598432 original size:43 final size:43
Alignment explanation
Indices: 12598379--12598478 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
12598369 CCGATTTTGT
*
12598379 TATTATTAGACGTTTTACCAAATTTGGTAAAAACGACCGAAAA
1 TATTATTAGACGCTTTACCAAATTTGGTAAAAACGACCGAAAA
* *
12598422 TATTATTAGACGCTTTACCAGATTTGGTAAAAATGACCGAAAA
1 TATTATTAGACGCTTTACCAAATTTGGTAAAAACGACCGAAAA
12598465 TATTATTAGACGCT
1 TATTATTAGACGCT
12598479 ACCAGTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (43 bp):
TATTATTAGACGCTTTACCAAATTTGGTAAAAACGACCGAAAA
Found at i:12598553 original size:23 final size:21
Alignment explanation
Indices: 12598518--12598560 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
12598508 CCGAAAATGT
*
12598518 TAAAAAAATTAATGTTTTAGG
1 TAAAAAAATTAATATTTTAGG
12598539 TAAAAAAATAATAATATTTTAG
1 TAAAAAAAT--TAATATTTTAG
12598561 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
TAAAAAAATTAATATTTTAGG
Found at i:12602492 original size:20 final size:20
Alignment explanation
Indices: 12602467--12602508 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12602457 TAAAGTTTCC
*
12602467 AATAATAACAAAACCGGTAG
1 AATAATAACAAAACCAGTAG
12602487 AATAATAACAAAACCAGTAG
1 AATAATAACAAAACCAGTAG
12602507 AA
1 AA
12602509 AAAATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (20 bp):
AATAATAACAAAACCAGTAG
Found at i:12604590 original size:18 final size:18
Alignment explanation
Indices: 12604567--12604603 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12604557 TGATCCTTCA
12604567 ATTGTATTATAAATGAAT
1 ATTGTATTATAAATGAAT
12604585 ATTGTATTATAAATGAAT
1 ATTGTATTATAAATGAAT
12604603 A
1 A
12604604 ACATAGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTGTATTATAAATGAAT
Found at i:12604730 original size:2 final size:2
Alignment explanation
Indices: 12604725--12604751 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12604715 AATATTTTAA
12604725 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12604752 AATTCAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12605054 original size:14 final size:14
Alignment explanation
Indices: 12605023--12605075 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
12605013 TTTTTTTGTT
*
12605023 AATTTT-AAA-TAC
1 AATTTTAAAATTAA
12605035 AATTTTAAAATTAA
1 AATTTTAAAATTAA
12605049 AATTTTAAAAATTAA
1 AATTTT-AAAATTAA
*
12605064 AATTTGAAAATT
1 AATTTTAAAATT
12605076 TATATATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 6 0.17
13 3 0.08
14 14 0.39
15 13 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
AATTTTAAAATTAA
Found at i:12605061 original size:15 final size:15
Alignment explanation
Indices: 12605035--12605093 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
12605025 TTTTAAATAC
12605035 AATTTT-AAAATTAA
1 AATTTTAAAAATTAA
12605049 AATTTTAAAAATTAA
1 AATTTTAAAAATTAA
* *
12605064 AATTTGAAAATTTATA
1 AATTTTAAAAATTA-A
* *
12605080 TATTTAAAAAATTA
1 AATTTTAAAAATTA
12605094 TTTTTCTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
14 6 0.16
15 20 0.53
16 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTTAAAAATTAA
Found at i:12605470 original size:2 final size:2
Alignment explanation
Indices: 12605459--12605495 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12605449 AATACGAGAA
12605459 AT AT -T 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
12605496 GCGTCAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12609448 original size:22 final size:22
Alignment explanation
Indices: 12609413--12609455 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12609403 TTATAGGAAG
*
12609413 ATAATGTCACAGAGTTTAAAAC
1 ATAATATCACAGAGTTTAAAAC
*
12609435 ATAATATCATAGAGTTTAAAA
1 ATAATATCACAGAGTTTAAAA
12609456 TTATAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (22 bp):
ATAATATCACAGAGTTTAAAAC
Found at i:12612025 original size:45 final size:45
Alignment explanation
Indices: 12611976--12612205 Score: 289
Period size: 45 Copynumber: 5.1 Consensus size: 45
12611966 TATTGGCATG
* * * *
12611976 AAAGGATGCCATAGTTGAAATGTATATGGGTGCATTATAAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
* * * * *
12612021 AAAGGTGTACTAGAGTTGAAATGCATACGAGTGCATTATCAACAGA
1 AAA-GTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
* * *
12612067 AAAGTATGCTAGAGTTGAAATGAATATGGGTACATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
* * * * *
12612112 AAAGTATACTATGGTTGAAATGTATATGGGTACATTATCAACATA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
*
12612157 AAAGTATACTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
12612202 AAAG
1 AAAG
12612206 ATGTTAGAAT
Statistics
Matches: 160, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 124 0.77
46 36 0.22
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (45 bp):
AAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
Found at i:12612104 original size:91 final size:91
Alignment explanation
Indices: 12611949--12612205 Score: 322
Period size: 90 Copynumber: 2.8 Consensus size: 91
12611939 ATAAAAGAAT
*** * * *
12611949 AATGCATACGAGTGCATTATTGGCATG-AAAGGATGCCATAGTTGAAATGTATATGGGTGCATTA
1 AATGCATACGAGTGCATTATCAACA-GAAAAGTATGCTATAGTTGAAATGAATATGGGTGCATTA
* *
12612013 TAAACAGAAAAGGTGTACTA-GAGTTGA
65 TCAACAGAAAAGGTATACTATG-GTTGA
* *
12612040 AATGCATACGAGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGAATATGGGTACATTAT
1 AATGCATACGAGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGAATATGGGTGCATTAT
12612105 CAACAGAAAA-GTATACTATGGTTGA
66 CAACAGAAAAGGTATACTATGGTTGA
* * * * * * *
12612130 AATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATACGAGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGAATATGGGTGCATTAT
12612195 CAACAGAAAAG
66 CAACAGAAAAG
12612206 ATGTTAGAAT
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
90 79 0.55
91 65 0.45
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (91 bp):
AATGCATACGAGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGAATATGGGTGCATTAT
CAACAGAAAAGGTATACTATGGTTGA
Found at i:12612239 original size:90 final size:88
Alignment explanation
Indices: 12611986--12612248 Score: 278
Period size: 90 Copynumber: 2.9 Consensus size: 88
12611976 AAAGGATGCC
* * * *
12611986 ATAGTTGAAATGTATATGGGTGCATTATAAACAGAAAAGGTGTACTAGAGTTGAAATGCATACGA
1 ATAGTTGAAATGAATATGGGTGCATTATCAACAGAAAAGATGT--TAGAGTTGAAATGCATATGA
* * *
12612051 GTGCATTATCAACAGAAAAGTATGCT
64 -TGTATTATCAACATAAAAGTATACT
* * ** *
12612077 AGAGTTGAAATGAATATGGGTACATTATCAACAGAAAAGTATACTATG-GTTGAAATGTATATG-
1 ATAGTTGAAATGAATATGGGTGCATTATCAACAGAAAAG-ATGTTA-GAGTTGAAATGCATATGA
*
12612140 GGTACATTATCAACATAAAAGTATACT
64 TGT--ATTATCAACATAAAAGTATACT
* * *
12612167 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATGTTAGAATTTAAAATGCATAATGA
1 ATAGTTGAAATGAATATGGGTGCATTATCAACAGAAAAGATGTTAG-AGTTGAAATGCAT-ATGA
*
12612232 TGTATTATAAACATAAA
64 TGTATTATCAACATAAA
12612249 TGGAGGTTAC
Statistics
Matches: 141, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
88 2 0.01
89 4 0.03
90 93 0.66
91 39 0.28
92 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (88 bp):
ATAGTTGAAATGAATATGGGTGCATTATCAACAGAAAAGATGTTAGAGTTGAAATGCATATGATG
TATTATCAACATAAAAGTATACT
Found at i:12613249 original size:14 final size:14
Alignment explanation
Indices: 12613230--12613267 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
12613220 TCCAAAATAG
12613230 AAATTTTGTCCCCA
1 AAATTTTGTCCCCA
12613244 AAATTTTGTCCCCA
1 AAATTTTGTCCCCA
12613258 AAATTTTGTC
1 AAATTTTGTC
12613268 ATCCACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (14 bp):
AAATTTTGTCCCCA
Found at i:12614003 original size:10 final size:10
Alignment explanation
Indices: 12613988--12614021 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
12613978 GAGCCAGCTT
12613988 CATACACACA
1 CATACACACA
12613998 CATACACACA
1 CATACACACA
12614008 CATACACACA
1 CATACACACA
12614018 -ATAC
1 CATAC
12614022 TTCATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (10 bp):
CATACACACA
Found at i:12617658 original size:12 final size:12
Alignment explanation
Indices: 12617641--12617665 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12617631 AGAATGAGGC
12617641 ACGATCAAAACT
1 ACGATCAAAACT
12617653 ACGATCAAAACT
1 ACGATCAAAACT
12617665 A
1 A
12617666 AGGCGTCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
ACGATCAAAACT
Found at i:12618782 original size:13 final size:13
Alignment explanation
Indices: 12618761--12618796 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
12618751 AAATCCCTAG
*
12618761 AAATTCTCATTAT
1 AAATACTCATTAT
12618774 AAATACTCATTAT
1 AAATACTCATTAT
12618787 AAATACTCAT
1 AAATACTCAT
12618797 ACATAGCCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATACTCATTAT
Found at i:12625743 original size:45 final size:45
Alignment explanation
Indices: 12625648--12625848 Score: 298
Period size: 45 Copynumber: 4.5 Consensus size: 45
12625638 GGTAAGTATG
* * * *
12625648 AAATAAGCTTACGAGCTTATGAAATAAA-AGCAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGATGGTA
*
12625692 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATGATGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGATGGTA
* *
12625737 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGATGGTA
*
12625782 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTAT-ATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGA-TGGTA
*
12625827 AAATAAGCTTACAAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
12625849 GATTAAATTG
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 27 0.19
45 115 0.81
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGATGGTA
Found at i:12625800 original size:90 final size:90
Alignment explanation
Indices: 12625648--12625873 Score: 321
Period size: 90 Copynumber: 2.5 Consensus size: 90
12625638 GGTAAGTATG
* * *
12625648 AAATAAGCTTACGAGCTTATGAAATAAA-AGCAAGTATGTTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATGTTGATAAAATAAGCTTACGAGCTTAT
12625712 GGAATAAATGATAAGTATGA-TGGTA
66 GGAATAAATGATAAGTAT-ATTGGTA
* *
12625737 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGATAAAATAAGCTTATGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATGTTGATAAAATAAGCTTACGAGCTTAT
*
12625802 GGAATAAATGGTAAGTATATTGGTA
66 GGAATAAATGATAAGTATATTGGTA
* * * * *
12625827 AAATAAGCTTACAAGCTTATGGGATTAAATTGTAAATATTTTGATAA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATAGTAAGTATGTTGATAA
12625874 GAAATTTTAA
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
89 28 0.23
90 73 0.59
91 22 0.18
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATAAATAGTAAGTATGTTGATAAAATAAGCTTACGAGCTTAT
GGAATAAATGATAAGTATATTGGTA
Found at i:12627447 original size:2 final size:2
Alignment explanation
Indices: 12627440--12627477 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12627430 CCCCGTGACA
12627440 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
12627478 TAGGAAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12638247 original size:30 final size:30
Alignment explanation
Indices: 12638213--12638274 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
12638203 GCAAGTTTCA
*
12638213 TTGTTAATTGATTATTAGTTGA-AATTCAAG
1 TTGTTAATTGATTATTAGGTGATAATT-AAG
**
12638243 TTGTTTTTTGATTATTAGGTGATAATTAAG
1 TTGTTAATTGATTATTAGGTGATAATTAAG
12638273 TT
1 TT
12638275 TAAGGAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.52
Consensus pattern (30 bp):
TTGTTAATTGATTATTAGGTGATAATTAAG
Found at i:12638759 original size:45 final size:46
Alignment explanation
Indices: 12638662--12638764 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 46
12638652 ATTCAACAGG
* * * *
12638662 TACCGATACCCTCTTAAATGAAAAGAATAACATAATGTAATTAGGG
1 TACCGATACCCTCTTAAATGAAAAGAATAACAGAATGCAATGAGGC
* * **
12638708 TACCGATACCCTCTTGAATGAAAA-ATTAACAGAATGCGGTGAGGC
1 TACCGATACCCTCTTAAATGAAAAGAATAACAGAATGCAATGAGGC
12638753 TACCGATACCCT
1 TACCGATACCCT
12638765 AAGAAGGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 26 0.53
46 23 0.47
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (46 bp):
TACCGATACCCTCTTAAATGAAAAGAATAACAGAATGCAATGAGGC
Found at i:12639352 original size:21 final size:21
Alignment explanation
Indices: 12639326--12639386 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
12639316 TGAGGGTTTT
12639326 ATAGGTCCTTCGGGACAACTC
1 ATAGGTCCTTCGGGACAACTC
*
12639347 ATAGGTCATTCGGGACATACTC
1 ATAGGTCCTTCGGGACA-ACTC
*
12639369 ACAGGTCCTTCGGGACAA
1 ATAGGTCCTTCGGGACAA
12639387 ATTTCATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTC
Found at i:12646984 original size:21 final size:21
Alignment explanation
Indices: 12646955--12647016 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
12646945 GTCGAGGGTT
* *
12646955 TCATTGGTCCTTCAGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
12646976 TCATAGGTCTTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
12646997 TCAGAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
12647017 ATTTCATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:12650832 original size:65 final size:65
Alignment explanation
Indices: 12650762--12650897 Score: 193
Period size: 65 Copynumber: 2.1 Consensus size: 65
12650752 CATTAATTAT
* *
12650762 ATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCAATGCATGGCCTGTGCATCGGTACATAAAATG
1 ATTCGATGTTTCAATAA-AACCAGGAGTGCATCAATGCATGGCCTGTGCATCGGTACACAAAATG
12650826 C
65 C
* * * **
12650827 ATTCGATGTTTTAATAAAATCATGAGTGCATCAATGCATGGTTTGTGCATCGGTACACAAAATGC
1 ATTCGATGTTTCAATAAAACCAGGAGTGCATCAATGCATGGCCTGTGCATCGGTACACAAAATGC
12650892 ATTCGA
1 ATTCGA
12650898 ATTAGGGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
65 61 0.97
66 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (65 bp):
ATTCGATGTTTCAATAAAACCAGGAGTGCATCAATGCATGGCCTGTGCATCGGTACACAAAATGC
Found at i:12660100 original size:23 final size:22
Alignment explanation
Indices: 12660071--12660132 Score: 106
Period size: 23 Copynumber: 2.8 Consensus size: 22
12660061 CAGAACCTCC
*
12660071 AGGGGGTATCGATTCCTCTTCA
1 AGGGGGTATCGATTCCCCTTCA
12660093 AGGGGGGTATCGATTCCCCTTCA
1 A-GGGGGTATCGATTCCCCTTCA
12660116 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
12660133 TCTGCACCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (22 bp):
AGGGGGTATCGATTCCCCTTCA
Found at i:12666464 original size:31 final size:31
Alignment explanation
Indices: 12666441--12666550 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
12666431 CATAGATTTT
* *
12666441 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
12666472 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
12666503 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
12666534 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
12666551 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:12670762 original size:31 final size:31
Alignment explanation
Indices: 12670724--12670848 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
12670714 CCCGAAGGAC
* * *
12670724 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
12670755 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12670786 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12670817 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12670848 C
1 C
12670849 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12672355 original size:30 final size:30
Alignment explanation
Indices: 12672321--12672384 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
12672311 GATGAAGAGA
12672321 ATATCTCTTCATCCTTATCCCCTCTAACAT
1 ATATCTCTTCATCCTTATCCCCTCTAACAT
12672351 ATATCTCTTCATCCTTATCCCCTCTAACAT
1 ATATCTCTTCATCCTTATCCCCTCTAACAT
12672381 ATAT
1 ATAT
12672385 ATCCTTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATCTCTTCATCCTTATCCCCTCTAACAT
Found at i:12672393 original size:24 final size:26
Alignment explanation
Indices: 12672328--12672393 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 26
12672318 AGAATATCTC
12672328 TTCATCCTTATCCCCTCTAACATATA
1 TTCATCCTTATCCCCTCTAACATATA
12672354 TCTCTTCATCCTTATCCCCTCTAACATATA
1 ----TTCATCCTTATCCCCTCTAACATATA
12672384 -T-ATCCTTATC
1 TTCATCCTTATC
12672394 ATATTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 9 0.25
25 1 0.03
30 26 0.72
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (26 bp):
TTCATCCTTATCCCCTCTAACATATA
Found at i:12675030 original size:65 final size:65
Alignment explanation
Indices: 12674941--12675097 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
12674931 TACACTTGGG
* * * * * *
12674941 GTGCATCGGTGCACTAATTACATTCGATGTTTCAA-AAGATCTAGGAGTGCATCGATGCATGGCC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAAT-AAGGAGTGCATCGATGCATGGCC
12675005 T
65 T
* * * **
12675006 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAATAATGAGTGCATCGATGTATGGTTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAATAAGGAGTGCATCGATGCATGGCCT
12675071 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
12675098 ATTAGGGTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 75 0.95
66 4 0.05
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAATAAGGAGTGCATCGATGCATGGCCT
Found at i:12677361 original size:20 final size:20
Alignment explanation
Indices: 12677294--12677368 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
12677284 AATGCTACAA
* *
12677294 GAATAGTATCGGTACTGTAT
1 GAATAATATCGATACTGTAT
* * *
12677314 GAATAGTATCGATACTATAC
1 GAATAATATCGATACTGTAT
* * *
12677334 AAACAATATCGATAATGTAT
1 GAATAATATCGATACTGTAT
12677354 GAATAATATCGATAC
1 GAATAATATCGATAC
12677369 CAAACGCACA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
GAATAATATCGATACTGTAT
Found at i:12694874 original size:15 final size:15
Alignment explanation
Indices: 12694835--12694876 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
12694825 AATACTAAAC
12694835 AAATTA-AATAAATA
1 AAATTACAATAAATA
*
12694849 AACATTAACAATAATTA
1 AA-ATT-ACAATAAATA
12694866 AAATTACAATA
1 AAATTACAATA
12694877 GAATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 4 0.17
17 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTACAATAAATA
Found at i:12695828 original size:15 final size:15
Alignment explanation
Indices: 12695808--12695837 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12695798 TCTCCCAAAT
12695808 CCCCACTCGCCTTTG
1 CCCCACTCGCCTTTG
12695823 CCCCACTCGCCTTTG
1 CCCCACTCGCCTTTG
12695838 GTTTTCGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.53, G:0.13, T:0.27
Consensus pattern (15 bp):
CCCCACTCGCCTTTG
Done.