Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008793.1 Hibiscus syriacus cultivar Beakdansim tig00111937_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: 720278
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:416073 original size:65 final size:66
Alignment explanation
Indices: 415956--416078 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 66
415946 ACTTGAGACA
* * *
415956 TTTTTCTCTTAAAACAAATATCGTTTCACTTGAGTCATTTTTCTTCGGAAACAAATTTCAAAGTT
1 TTTTTCTCTAAAAACAAATATCGTTTCACTTGAGACATTTTTCTTCGAAAACAAATTTCAAAGTT
416021 G
66 G
* * *
416022 TTTTTCT-TAAAAACAAATTTTGTTTCACTTGAGACATTTTTC-TCTTAAAACAAATTT
1 TTTTTCTCTAAAAACAAATATCGTTTCACTTGAGACATTTTTCTTC-GAAAACAAATTT
416079 TGTTTAACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 2 0.04
65 41 0.82
66 7 0.14
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (66 bp):
TTTTTCTCTAAAAACAAATATCGTTTCACTTGAGACATTTTTCTTCGAAAACAAATTTCAAAGTT
G
Found at i:416098 original size:102 final size:103
Alignment explanation
Indices: 415838--416101 Score: 433
Period size: 102 Copynumber: 2.6 Consensus size: 103
415828 ACAAAATGTC
* *
415838 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACATTTTCCTTCGGAA
1 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTCGGAA
415903 CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTCT
66 CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTCT
* *
415941 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATATCGTTTCACTTGAG-TCATTTTTCTTCGGA
1 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGAT-ATTTTTCTTCGGA
*
416005 A-ACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
65 ACACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTCT
* * *
416043 GTTTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTAACGTGAGATATTTTTCT
1 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCT
416102 CTCAAAACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 88 0.59
103 61 0.41
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (103 bp):
GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTCGGAA
CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTCT
Found at i:416334 original size:36 final size:36
Alignment explanation
Indices: 416240--416353 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 36
416230 AACAAAATCT
416240 TTGA-ATATGTTTCCCTTGAAACAAAATTTTGTCTCCC
1 TTGAGATA-GTTTCCCTTGAAAC-AAATTTTGTCTCCC
* ** **
416277 TTGAGACAGTTT-TTTTGAAACAAATTTTGTCTTTC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCC
* * * *
416312 TTGAGATAGTTTCCCTTAAAACAGACTTTGTCTCGC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCC
416348 TTGAGA
1 TTGAGA
416354 CATTTTTTTC
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
35 23 0.37
36 29 0.47
37 8 0.13
38 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCC
Found at i:416660 original size:52 final size:53
Alignment explanation
Indices: 416570--416720 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 53
416560 AAAGACTTTT
* * *
416570 AGAAACTAAGCCTGATTTTTCAGGGGTTTCTCGATGTTTTCAAATGAACTTGAA
1 AGAAACTAAGCCTGACTTTT-AGGGGTTTCTTGATGTTTTCAAATGAACTTCAA
* * * * *
416624 AGAAGCTAAACCTGA-TTTTAGGGGTTTCTTAATGTTTTTAAATGAATTTCAA
1 AGAAACTAAGCCTGACTTTTAGGGGTTTCTTGATGTTTTCAAATGAACTTCAA
* ** *
416676 AGAAATTAAGCCT-ACTTTTAGGTATTTCTTGATATTTTCAAATGA
1 AGAAACTAAGCCTGACTTTTAGGGGTTTCTTGATGTTTTCAAATGA
416721 GTTTTTAGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
51 1 0.01
52 63 0.78
53 4 0.05
54 13 0.16
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (53 bp):
AGAAACTAAGCCTGACTTTTAGGGGTTTCTTGATGTTTTCAAATGAACTTCAA
Found at i:426529 original size:24 final size:25
Alignment explanation
Indices: 426480--426535 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
426470 GATGAAACAT
*
426480 AACATAAAAATATCAATACAAC-AA
1 AACATTAAAATATCAATACAACAAA
* *
426504 AACATTAAAATAT-AATTCAAATAAA
1 AACATTAAAATATCAATAC-AACAAA
426529 AACATTA
1 AACATTA
426536 TACTTTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 14 0.52
25 9 0.33
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.23
Consensus pattern (25 bp):
AACATTAAAATATCAATACAACAAA
Found at i:427937 original size:21 final size:21
Alignment explanation
Indices: 427911--427956 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
427901 ACTTAATTCT
427911 GCATCCACTAATTAAATTTCA
1 GCATCCACTAATTAAATTTCA
427932 GCATCCACTAATTAAATTTCA
1 GCATCCACTAATTAAATTTCA
427953 GCAT
1 GCAT
427957 TGAATACCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (21 bp):
GCATCCACTAATTAAATTTCA
Found at i:433659 original size:20 final size:20
Alignment explanation
Indices: 433634--433754 Score: 64
Period size: 20 Copynumber: 5.4 Consensus size: 20
433624 TATGGAATCC
433634 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCA
* *
433654 TTTCATGCATTTAATTTATGACATCC
1 TTTCATGC-CTT-A---ATG-CATCA
*
433680 TTTCATACCTTAATGCATC-
1 TTTCATGCCTTAATGCATCA
* *
433699 TGTTCATGCATTTTTAGTTATGACATCC
1 T-TTCATGC---CTTA---ATG-CATCA
433727 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCA
433747 TTTCATGC
1 TTTCATGC
433755 ATTTCATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 30
0.67 0.07 0.26
Matches are distributed among these distances:
19 1 0.01
20 30 0.38
21 8 0.10
22 1 0.01
23 3 0.04
24 4 0.05
25 5 0.06
26 14 0.18
27 11 0.14
28 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCA
Found at i:433738 original size:47 final size:46
Alignment explanation
Indices: 433621--433780 Score: 225
Period size: 46 Copynumber: 3.5 Consensus size: 46
433611 CGTTTGTTTC
433621 ATTTATGGA-ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
1 ATTTAT-GACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
* *
433667 ATTTATGACATCCTTTCATACCTTAATGCATC-TGTTCATGCATTTTT
1 ATTTATGACATCCTTTCATGCCTTAATGCATCAT-TTCATGCA-TTTA
* *
433714 AGTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTC
1 ATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
* *
433760 ATTTAAGGCATCCTTTCATGC
1 ATTTATGACATCCTTTCATGC
433781 ATTTCAGTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.03
46 57 0.56
47 41 0.40
48 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (46 bp):
ATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
Found at i:433868 original size:93 final size:93
Alignment explanation
Indices: 433762--434165 Score: 534
Period size: 93 Copynumber: 4.3 Consensus size: 93
433752 TGCATTTCAT
*
433762 TTAAGGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
1 TTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
* *
433827 ATTTTAATTTATGGT-ATCCTTTCATGCC
66 ATTTTTAGTTAT-GTCATCCTTTCATGCC
* * *
433855 TTAATGCATCCTTTCATGCATTTTAGTGATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
1 TTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
*
433920 ATTTTTAGTTATGTCATCCTTTGATGCC
66 ATTTTTAGTTATGTCATCCTTTCATGCC
* * *
433948 TTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATTC
1 TTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
434013 ATTTTTAGTTATGTCATCCTTTCATGCATTTC
66 ATTTTTAGTTATGTCATCCTTTCATGC----C
* * * *
434045 ATTTATGGCATCCTTTCATGC-CTT-A---AT-GCATTCTTTCATGCCTTAATGCATCTATTCAT
1 -TTAAT-GCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCAT
*
434104 GCATTTTTAGTTATGACATCCTTTCATGCC
64 GCATTTTTAGTTATGTCATCCTTTCATGCC
* *
434134 TTAATGCATCCGTTCATGCATTTTTAGTTATG
1 TTAATGCATCCTTTCATGCA-TTTCAGTTATG
434166 AATTCGGTTT
Statistics
Matches: 275, Mismatches: 22, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
87 13 0.05
88 4 0.01
89 3 0.01
90 1 0.00
92 2 0.01
93 228 0.83
94 2 0.01
97 2 0.01
98 6 0.02
99 14 0.05
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (93 bp):
TTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
ATTTTTAGTTATGTCATCCTTTCATGCC
Found at i:433988 original size:212 final size:208
Alignment explanation
Indices: 433621--434085 Score: 630
Period size: 212 Copynumber: 2.2 Consensus size: 208
433611 CGTTTGTTTC
* * *
433621 ATTTATGGAATCCTTTCATGCCTTAATGCATCATTTCATGCATTTAATTTATGACATCCTTTCAT
1 ATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAAGTGATGACATCCTTTCAT
*
433686 ACCTTAATGCATCTGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTC
66 ACCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTC
* *
433751 ATGCATTTCATTTAAGGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGC-CTTA-ATG
131 ATGCATTTCATTTAAGGCATCCTTTCATGC-CTT-A---AT-GCATCCGTTCATGCTCTTATATG
433814 -CATCCATTCATGCATTTTA
190 TCATCCATTCATGCA-TTTA
* * *
433833 ATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTGATGGCATCCTTTCAT
1 ATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAAGTGATGACATCCTTTCAT
* * * *
433898 GCCTTAATGCATCCGTTCATGCATTTTTAGTTATGTCATCCTTTGATGCCTTAATGCATCCTTTC
66 ACCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTC
* * *
433963 ATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATTCATTTTTAGTTATGTC
131 ATGCATTTCATTTAAGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC--TCTTA--TATGTC
* *
434028 ATCCTTTCATGCATTTC
192 ATCCATTCATGCATTTA
* *
434045 ATTTATGGCATCCTTTCATGCCTTAATGCATTCTTTCATGC
1 ATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
434086 CTTAATGCAT
Statistics
Matches: 226, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
206 12 0.05
207 2 0.01
209 3 0.01
210 1 0.00
211 2 0.01
212 193 0.85
213 13 0.06
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.44
Consensus pattern (208 bp):
ATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAAGTGATGACATCCTTTCAT
ACCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTC
ATGCATTTCATTTAAGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCTCTTATATGTCATCC
ATTCATGCATTTA
Found at i:434166 original size:47 final size:47
Alignment explanation
Indices: 433762--434165 Score: 488
Period size: 47 Copynumber: 8.7 Consensus size: 47
433752 TGCATTTCAT
* *
433762 TTAAGGCATCCTTTCATGCA-TTTCAGTTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
* * * *
433808 TTAATGCATCCATTCATGCATTTTAATTTATGGTATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
*
433855 TTAATGCATCCTTTCATGCA-TTTTAGTGATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
* * *
433901 TTAATGCATCCGTTCATGCATTTTTAGTTATGTCATCCTTTGATGCC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
* *
433948 TTAATGCATCCTTTCATGCA-TTTCATTTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
* * *
433994 TTAATGCATCCGTTCATTCATTTTTAGTTATGTCATCCTTTCATGCATTTC
1 TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGC----C
* * *
434045 ATTTATGGCATCCTTTCATGC---CTTA---AT-GCATTCTTTCATGCC
1 -TTAAT-GCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
*
434087 TTAATGCAT-CTATTCATGCATTTTTAGTTATGACATCCTTTCATGCC
1 TTAATGCATCCT-TTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
*
434134 TTAATGCATCCGTTCATGCATTTTTAGTTATG
1 TTAATGCATCCTTTCATGCATTTTTAGTTATG
434166 AATTCGGTTT
Statistics
Matches: 305, Mismatches: 35, Indels: 35
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.01
40 11 0.04
41 4 0.01
42 1 0.00
43 3 0.01
46 113 0.37
47 150 0.49
48 1 0.00
50 3 0.01
51 1 0.00
52 4 0.01
53 12 0.04
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (47 bp):
TTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC
Found at i:452588 original size:23 final size:23
Alignment explanation
Indices: 452557--452643 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
452547 GTCGAGGGTT
*
452557 CTATATGGTCATTCGGGATAATA-
1 CTATGTGGTCATTCGGGATAA-AC
* * *
452580 TTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCATTCGGGATAAAC
* *
452603 CTATGTGGTCCTTTGGGATAAAC
1 CTATGTGGTCATTCGGGATAAAC
452626 CTATGTGGTCATTCGGGA
1 CTATGTGGTCATTCGGGA
452644 CAATTATGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 1 0.02
23 53 0.98
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGATAAAC
Found at i:452621 original size:46 final size:46
Alignment explanation
Indices: 452557--452646 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
452547 GTCGAGGGTT
* *
452557 CTATATGGTCATTCGGGATAATA-TTATGTGGTCCTTCGGGACAAAC
1 CTATATGGTCATTCGGGATAA-ACCTATGTGGTCATTCGGGACAAAC
* * *
452603 CTATGTGGTCCTTTGGGATAAACCTATGTGGTCATTCGGGACAA
1 CTATATGGTCATTCGGGATAAACCTATGTGGTCATTCGGGACAA
452647 TTATGTTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (46 bp):
CTATATGGTCATTCGGGATAAACCTATGTGGTCATTCGGGACAAAC
Found at i:461636 original size:3 final size:3
Alignment explanation
Indices: 461619--461700 Score: 141
Period size: 3 Copynumber: 28.0 Consensus size: 3
461609 GGGTTCTAAT
*
461619 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
461666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
461701 CAAATCATGC
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 71 0.95
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:469878 original size:30 final size:30
Alignment explanation
Indices: 469842--469902 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
469832 AAGGATGATG
*
469842 AGTCGGTCATTAATGAGACTGTAACGAAAA
1 AGTCGGTCATTAATGAGAATGTAACGAAAA
*
469872 AGTCGGTCATTAATGAGAATGTAATGAAAA
1 AGTCGGTCATTAATGAGAATGTAACGAAAA
469902 A
1 A
469903 CAAGGCTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (30 bp):
AGTCGGTCATTAATGAGAATGTAACGAAAA
Found at i:474789 original size:4 final size:4
Alignment explanation
Indices: 474780--474868 Score: 58
Period size: 4 Copynumber: 22.0 Consensus size: 4
474770 ACTTCGCTCG
* * *
474780 AAGA AAGA AAGA AAGT AA-A AATA AATAA AATGA AAGAA AATGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AA-GA AAG-A AA-GA AAGA
* * * *
474827 AAAA AAGA AAGA AAAA AAGG ATGA AAGA AA-A AAGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
474869 GAATAAACAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
3 8 0.12
4 45 0.67
5 13 0.19
6 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (4 bp):
AAGA
Found at i:474819 original size:10 final size:10
Alignment explanation
Indices: 474797--474857 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
474787 AAAGAAAGTA
*
474797 AAAAT-AAAT
1 AAAATGAAAG
474806 AAAATGAAAG
1 AAAATGAAAG
474816 AAAATGAAAG
1 AAAATGAAAG
474826 AAAA--AAAG
1 AAAATGAAAG
*
474834 -AAA-GAAAA
1 AAAATGAAAG
474842 AAAGGATGAAAG
1 AAA--ATGAAAG
474854 AAAA
1 AAAA
474858 AAGAAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
7 3 0.07
8 7 0.16
9 7 0.16
10 18 0.42
11 1 0.02
12 7 0.16
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.08
Consensus pattern (10 bp):
AAAATGAAAG
Found at i:476381 original size:133 final size:133
Alignment explanation
Indices: 476135--476509 Score: 504
Period size: 133 Copynumber: 2.8 Consensus size: 133
476125 GAGTTTTCCA
* *
476135 CAAGAAGAAGCGAA-ATGGATCCCTCTCTTTCAAGATTTGATATTCCCT-AAGTAATAGTGGAAC
1 CAAGAAGAAGCGAACA--GATCCATCTCTTTCAAGATTTGATATTCCCTGAA-TAACAGTGGAAC
* * * * * * *
476198 AAGTCTTCCTCGATTAAAACTTCCCTGAAGAATAGTTGAATAAATAAAAGTCCCCATATCTGATT
63 AAGTCTACCTCGATTCAATCTTCCTTGAAGAATAGTGGAATAAATAAAAGTCCCAAGATCTGATT
476263 TTCCCT
128 TTCCCT
* *
476269 CAAGAAGAAGCGTAACAGATCCATCTCTTTCAAGATTTTATATTCCCTGAATAACA-TAGAACAA
1 CAAGAAGAAGCG-AACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAATAACAGTGGAACAA
* * *
476333 GTCTACCTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAAAGTCCCAAGATTTGATTTT
65 GTCTACCTCGATTCAATCTTCCTTGAAGAATAGTGGAATAAATAAAAGTCCCAAGATCTGATTTT
476398 CCCT
130 CCCT
* * * * *
476402 CAAGAAGAAGTAGAACATATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAA
1 CAAGAAGAAG-CGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAATAACAGTGGAACAA
*
476467 GTCTACCTCGATTCAATCTTCCTTGAAGAACAGTGGAATAAAT
65 GTCTACCTCGATTCAATCTTCCTTGAAGAATAGTGGAATAAAT
476510 TAACGTTTCT
Statistics
Matches: 213, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
133 114 0.54
134 94 0.44
135 4 0.02
136 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (133 bp):
CAAGAAGAAGCGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAATAACAGTGGAACAAG
TCTACCTCGATTCAATCTTCCTTGAAGAATAGTGGAATAAATAAAAGTCCCAAGATCTGATTTTC
CCT
Found at i:476707 original size:3 final size:3
Alignment explanation
Indices: 476690--476743 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
476680 GGGTTCTAAT
* * *
476690 TTA TCA TTA -TA TTA TTA TTA TTA CTA TTT TTA TTAA TT- TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
476733 TTA TTA TTA TT
1 TTA TTA TTA TT
476744 TTTAGATTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:476801 original size:18 final size:19
Alignment explanation
Indices: 476774--476809 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
476764 CAACAAAGGT
476774 CCAAACCAAA-TTACAGGC
1 CCAAACCAAATTTACAGGC
*
476792 CCAAATCAAATTTACAGG
1 CCAAACCAAATTTACAGG
476810 TCTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (19 bp):
CCAAACCAAATTTACAGGC
Found at i:477572 original size:14 final size:14
Alignment explanation
Indices: 477553--477579 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
477543 TTTTTATCTT
477553 TTAAAATTATTTTC
1 TTAAAATTATTTTC
477567 TTAAAATTATTTT
1 TTAAAATTATTTT
477580 AAATGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:480285 original size:15 final size:15
Alignment explanation
Indices: 480265--480298 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
480255 AGATGTTAAG
480265 TTTCATAAAGATCAA
1 TTTCATAAAGATCAA
480280 TTTCATAAAGATCAA
1 TTTCATAAAGATCAA
480295 TTTC
1 TTTC
480299 CTTTTCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (15 bp):
TTTCATAAAGATCAA
Found at i:483932 original size:16 final size:16
Alignment explanation
Indices: 483911--483952 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
483901 TACGAATCAT
483911 AATTTTA-ATAGTATAA
1 AATTTTAGATA-TATAA
*
483927 AATTTTAGATATATGA
1 AATTTTAGATATATAA
483943 AATTTTAGAT
1 AATTTTAGAT
483953 CAGATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
AATTTTAGATATATAA
Found at i:484767 original size:28 final size:26
Alignment explanation
Indices: 484711--484777 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 26
484701 TTTTTACCCA
484711 TTAAAATTTTATA--AATTCTCCTAT
1 TTAAAATTTTATATGAATTCTCCTAT
* *
484735 GTAAAATTTTATATGAGTTCTCCCCTAT
1 TTAAAATTTTATATGAATTCT--CCTAT
484763 TTAAAATTTTATATG
1 TTAAAATTTTATATG
484778 TTTGACCCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 12 0.33
26 5 0.14
28 19 0.53
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (26 bp):
TTAAAATTTTATATGAATTCTCCTAT
Found at i:486024 original size:2 final size:2
Alignment explanation
Indices: 486017--486048 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
486007 TTATTTAAAC
*
486017 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486049 GACTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:487401 original size:3 final size:3
Alignment explanation
Indices: 487387--487451 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
487377 AATTATTTCT
* * * *
487387 TAA TAT TAA TAA TAA TAA TAA -AA TAA TTA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
487434 TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
487452 AACCGGGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:487994 original size:123 final size:123
Alignment explanation
Indices: 487713--488285 Score: 868
Period size: 123 Copynumber: 4.7 Consensus size: 123
487703 AGCTAAAGTC
* * *
487713 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-
* * * * * *
487778 TAC-CTGAAAATGGCT-CTGCTGCTCTATCTCCTT-TGTGATAGAATCGAGCAAAGGGTT
65 TCCTCTGGAAAT-GTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
* * *
487835 GAACAAGTTCTTCTTATTATAAAC-TTTACATTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTTTTC-TTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
* *
487899 TTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAAAATCGAGCAAAAGGTT
65 TCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
*
487958 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATTAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
*
488023 CCTCTGGAAATGTTGATGCTGATTTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
66 CCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
*
488081 AAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
488146 CCTTTGGAAATGTTAATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
66 CCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
* * *
488204 GAACAAGTTCTTCCCATTATGAACTTTTTCTTCCTTTTCAGATGAGTTTTTCTCATTATGAAC-T
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
*
488268 CTTTCTGGAAATGTTGAT
66 C-CTCTGGAAATGTTGAT
488286 CCATCGAGTG
Statistics
Matches: 415, Mismatches: 30, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
121 7 0.02
122 81 0.20
123 323 0.78
124 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
CCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
Found at i:488450 original size:36 final size:36
Alignment explanation
Indices: 488324--488450 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
488314 AGTAAAACTG
* *
488324 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAAAAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
* * * ** ***
488360 TCTCAAGGGAGATAAATTATTGTTTTGAGTGAAATTG
1 TCTCAAGCGAGACAAATT-TTGTTTTAAGAAAAAAAA
*
488397 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
* *
488433 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
488451 GTATTTGAAA
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 42 0.60
37 28 0.40
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
Found at i:489201 original size:22 final size:22
Alignment explanation
Indices: 489146--489202 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
489136 AATAAAATTT
* * *
489146 TCATTTTTGAAAAGAGACTCTA
1 TCATCTTTGAAGAGAGAATCTA
489168 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
489190 TCATCTTTGAAGA
1 TCATCTTTGAAGA
489203 ATGTAGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:489829 original size:204 final size:208
Alignment explanation
Indices: 489425--489843 Score: 571
Period size: 204 Copynumber: 2.0 Consensus size: 208
489415 TCTTGTTGTT
* * *
489425 AAAATTTCAGTTTCCCTTCTATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGTTT
1 AAAATTTCAGCTTCCCTTCTATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
* *
489490 AAGAAGAAAAACTTCATCTTGCATCAATAAATGAAAATCATATGATCATAACATTGGTTCAGCAC
66 AAGAAGAAAAACTTCATCTTGCATCAATAAATG--AA-CATATGACCAT-A-ATTAGTTCAGCAC
* ** *
489555 CATAATCATTGGTTCATAAAACATTTGGCAATGCATTCATCCTTTCCTGTGGCTTCTACTCAGAT
126 CATAATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTGTGGCTTCTACTCAGAT
489620 GTTCGTAAAACATTTGAC
191 GTTCGTAAAACATTTGAC
* *
489638 AAAATTTCAGCTTCCCTTCTGTGGAAAGAAATCTTCATTATATCTCACTTCTAACCTTGGGGGTA
1 AAAATTTCAGCTTCCCTTCTATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
* * ** *
489703 AATAAGTCAAAA-TTCATCTTGGGTCCATAAATTG-A-A-AT-ACCAT-ATTAGTTCAGCACCAT
66 AAGAAG-AAAAACTTCATCTTGCATCAATAAA-TGAACATATGACCATAATTAGTTCAGCACCAT
* *
489762 AATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTGTTGCTTCTGCTCAGATGTT
129 AATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTGTGGCTTCTACTCAGATGTT
489827 CGTAAAACATTTGAC
194 CGTAAAACATTTGAC
489842 AA
1 AA
489844 CACATTCATC
Statistics
Matches: 186, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
204 91 0.49
207 4 0.02
208 2 0.01
209 1 0.01
211 1 0.01
213 81 0.44
214 6 0.03
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (208 bp):
AAAATTTCAGCTTCCCTTCTATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
AAGAAGAAAAACTTCATCTTGCATCAATAAATGAACATATGACCATAATTAGTTCAGCACCATAA
TCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTGTGGCTTCTACTCAGATGTTCG
TAAAACATTTGAC
Found at i:489857 original size:54 final size:53
Alignment explanation
Indices: 489770--490095 Score: 409
Period size: 54 Copynumber: 6.1 Consensus size: 53
489760 ATAATCACTG
* * * *
489770 GTTCATAAAACATTTGGCAACACATTCATCATTTCCTGTTGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATG-TGCTTCTGCACAGAT
* *
489824 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGTTTCTACACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCTGCACAGAT
* * *
489877 GTTCTTCAAACATTTGACAACACATTCATCATTTCATGTGTCTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTG-CTTCTGCACAGAT
* * * *
489931 GTTCGTAATACATTTGACAACACATTCATCATTTCATGTGGTTTTCGCACCGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCT-GCACAGAT
* * * *
489985 GTTAGTAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTG-CTTCTGCACAGAT
* * * * *
490039 GTTCGTAATACATTTGACAACAGATTTATCCTTTCATGTGGCTTCTTCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT-GCTTCTGCACAGAT
490093 GTT
1 GTT
490096 TGCCAGTGAA
Statistics
Matches: 235, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
53 53 0.23
54 178 0.76
55 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCTGCACAGAT
Found at i:490035 original size:108 final size:108
Alignment explanation
Indices: 489775--490095 Score: 461
Period size: 108 Copynumber: 3.0 Consensus size: 108
489765 CACTGGTTCA
* *
489775 TAAAACATTTGGCAACACATTCATCATTTCCTGT-TGCTTCTGCT-CAGATGTTCGTAAAACATT
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGT-CTTCTG-TACAGATGTTCGTAATACATT
**
489838 TGACAACACATTCATCATTTCATGT-GTTTCTACACAGATGTTCT
64 TGACAACACATTCATCATTTCATGTGGTTTCTACACAGATGTTAG
* *
489882 TCAAACATTTGACAACACATTCATCATTTCATGTGTCTTCTGTACAGATGTTCGTAATACATTTG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
* *
489947 ACAACACATTCATCATTTCATGTGGTTT-TCGCACCGATGTTAG
66 ACAACACATTCATCATTTCATGTGGTTTCT-ACACAGATGTTAG
*
489990 TAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
* * * * *
490055 ACAACAGATTTATCCTTTCATGTGGCTTCTTCACAGATGTT
66 ACAACACATTCATCATTTCATGTGGTTTCTACACAGATGTT
490096 TGCCAGTGAA
Statistics
Matches: 192, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
106 1 0.01
107 81 0.42
108 109 0.57
109 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (108 bp):
TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
ACAACACATTCATCATTTCATGTGGTTTCTACACAGATGTTAG
Found at i:495433 original size:36 final size:36
Alignment explanation
Indices: 495393--495470 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
495383 AGTTTGAAAC
** * *
495393 AAAATGTAATTATGCAAAGATGCAAATACAACAATG
1 AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
*
495429 AAAATGTAAAAATGCAAAGATGCAAATGCAAAAATA
1 AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
495465 AAAATG
1 AAAATG
495471 CAAATTGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (36 bp):
AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
Found at i:495455 original size:14 final size:14
Alignment explanation
Indices: 495435--495474 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
495425 AATGAAAATG
*
495435 TAAAAATGCAAAGA
1 TAAAAATGCAAAAA
**
495449 TGCAAATGCAAAAA
1 TAAAAATGCAAAAA
495463 TAAAAATGCAAA
1 TAAAAATGCAAA
495475 TTGTGCAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (14 bp):
TAAAAATGCAAAAA
Found at i:495488 original size:28 final size:28
Alignment explanation
Indices: 495435--495536 Score: 77
Period size: 28 Copynumber: 3.7 Consensus size: 28
495425 AATGAAAATG
*
495435 TAAAAATGCAAAGATGCAAATGCAAAAA
1 TAAAAATGCAAAGATGCAAATACAAAAA
*
495463 TAAAAATGCAAATTG-TGC-AATACAAAAG
1 TAAAAATGCAAA--GATGCAAATACAAAAA
* * * * **
495491 CAAACAT-AAAAG-TTCAAATGTAAAAA
1 TAAAAATGCAAAGATGCAAATACAAAAA
*
495517 TGAAAATGCAAAGATGCAAA
1 TAAAAATGCAAAGATGCAAA
495537 ATGCAAATGC
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
25 3 0.05
26 11 0.20
27 7 0.13
28 30 0.55
29 3 0.05
30 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.18
Consensus pattern (28 bp):
TAAAAATGCAAAGATGCAAATACAAAAA
Found at i:495523 original size:14 final size:15
Alignment explanation
Indices: 495506--495543 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
495496 ATAAAAGTTC
*
495506 AAATGTAAAAATG-A
1 AAATGCAAAAATGCA
*
495520 AAATGCAAAGATGCA
1 AAATGCAAAAATGCA
495535 AAATGCAAA
1 AAATGCAAA
495544 TGCATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (15 bp):
AAATGCAAAAATGCA
Found at i:498870 original size:2 final size:2
Alignment explanation
Indices: 498863--498900 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
498853 TATTATTTAA
498863 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
498901 GACTAATATA
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:498915 original size:8 final size:9
Alignment explanation
Indices: 498862--498916 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 9
498852 TTATTATTTA
498862 AATATATAT
1 AATATATAT
498871 -ATATATAT
1 AATATATAT
498879 -ATATATAT
1 AATATATAT
498887 -ATATATAT
1 AATATATAT
498895 -ATATATGACT
1 AATATAT-A-T
498905 AATATA-AT
1 AATATATAT
498913 AATA
1 AATA
498917 AAATAATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
8 35 0.81
9 2 0.05
10 1 0.02
11 5 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
AATATATAT
Found at i:500217 original size:3 final size:3
Alignment explanation
Indices: 500209--500258 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
500199 AATTATTTAT
* * * *
500209 TAA TAA TAA TAA -AA TAA TTA TAA TGA TAA TTA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
500256 TAA
1 TAA
500259 AAATTTAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:500239 original size:12 final size:12
Alignment explanation
Indices: 500209--500267 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
500199 AATTATTTAT
*
500209 TAATAATAATAA
1 TAATAATTATAA
500221 -AATAATTATAA
1 TAATAATTATAA
* *
500232 TGATAATTATTA
1 TAATAATTATAA
*
500244 TAATAATAATAA
1 TAATAATTATAA
*
500256 TAAAAATT-TAA
1 TAATAATTATAA
500267 T
1 T
500268 GTCTACACCT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
11 14 0.37
12 24 0.63
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:501707 original size:6 final size:6
Alignment explanation
Indices: 501696--501738 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
501686 TCCTTATTAA
* ** *
501696 TGTTCG TGTTCG TATTTA TGTTCG TGTTCA TGTTCG TGTTCG T
1 TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG T
501739 ATTCAGGTTC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.53
Consensus pattern (6 bp):
TGTTCG
Found at i:501716 original size:18 final size:18
Alignment explanation
Indices: 501690--501724 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
501680 TACCTTTCCT
501690 TATTAATGTTCGTGTTCG
1 TATTAATGTTCGTGTTCG
*
501708 TATTTATGTTCGTGTTC
1 TATTAATGTTCGTGTTC
501725 ATGTTCGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.54
Consensus pattern (18 bp):
TATTAATGTTCGTGTTCG
Found at i:501735 original size:18 final size:18
Alignment explanation
Indices: 501690--501743 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
501680 TACCTTTCCT
* *
501690 TATTAATGTTCGTGTTCG
1 TATTCATGTTCGTGTTCA
*
501708 TATTTATGTTCGTGTTCA
1 TATTCATGTTCGTGTTCA
* * *
501726 TGTTCGTGTTCGTATTCA
1 TATTCATGTTCGTGTTCA
501744 GGTTCATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.15, C:0.13, G:0.20, T:0.52
Consensus pattern (18 bp):
TATTCATGTTCGTGTTCA
Found at i:501748 original size:18 final size:18
Alignment explanation
Indices: 501714--501748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
501704 TTCGTATTTA
* *
501714 TGTTCGTGTTCATGTTCG
1 TGTTCGTATTCAGGTTCG
501732 TGTTCGTATTCAGGTTC
1 TGTTCGTATTCAGGTTC
501749 ATATTAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (18 bp):
TGTTCGTATTCAGGTTCG
Found at i:502592 original size:17 final size:17
Alignment explanation
Indices: 502570--502624 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
502560 AAAATTAAAG
502570 TTTAGTTTTTATTTCAT
1 TTTAGTTTTTATTTCAT
* * *
502587 TTTAG--TATATATCCT
1 TTTAGTTTTTATTTCAT
502602 TTTAGTTTTTATTTCAT
1 TTTAGTTTTTATTTCAT
502619 TTTAGT
1 TTTAGT
502625 ATCATATCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 12 0.40
17 18 0.60
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (17 bp):
TTTAGTTTTTATTTCAT
Found at i:502606 original size:32 final size:33
Alignment explanation
Indices: 502570--502632 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
502560 AAAATTAAAG
502570 TTTAGTTTTTATTTCATTTTAGTAT-ATATCCT
1 TTTAGTTTTTATTTCATTTTAGTATCATATCCT
502602 TTTAGTTTTTATTTCATTTTAGTATCATATC
1 TTTAGTTTTTATTTCATTTTAGTATCATATC
502633 GTTAAATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (33 bp):
TTTAGTTTTTATTTCATTTTAGTATCATATCCT
Found at i:505319 original size:30 final size:30
Alignment explanation
Indices: 505279--505373 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
505269 TATTTAGTGG
*
505279 CCAAATTATAAA-TTTGATAAAGTTTGGTGA
1 CCAAAGTATAAACTTTGA-AAAGTTTGGTGA
*
505309 CCAAAGTATAAACTTTGAAAAGTTTAGTGA
1 CCAAAGTATAAACTTTGAAAAGTTTGGTGA
*
505339 TCAAAGTATAAACTTTGAAAAGTTTAGG-GA
1 CCAAAGTATAAACTTTGAAAAGTTT-GGTGA
505369 CCAAA
1 CCAAA
505374 ATGTAATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
30 52 0.90
31 6 0.10
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (30 bp):
CCAAAGTATAAACTTTGAAAAGTTTGGTGA
Found at i:507283 original size:40 final size:40
Alignment explanation
Indices: 507239--507386 Score: 210
Period size: 40 Copynumber: 3.8 Consensus size: 40
507229 AGGGCACTAA
* *
507239 GTGTACATGGTGGGCATGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
507279 GTGTATA--GTGGGTACGACCTTATGCGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
**
507317 GTGTATATGGTGGGCATAACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
507357 GTGTATATGGTGGGAACGACCTTAGGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
507387 GCACTACGGT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 35 0.37
40 59 0.63
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:507611 original size:46 final size:46
Alignment explanation
Indices: 507491--507611 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 46
507481 GTAAGCATGC
* *
507491 AAATAAGCTTACGAGCTTATGGAAT-ATTGGCAATTATATGGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGACAATTATATGGGTAA
* * * * *
507536 AAATAAGCTTACGAGCTTATGGGACAAATGATAATTATTTTGGT-A
1 AAATAAGCTTACGAGCTTATGGAATAAATGACAATTATATGGGTAA
507581 AAATAAGCTTACGAGCTTATGGAAATAAATG
1 AAATAAGCTTACGAGCTTATGG-AATAAATG
507612 GTAAAATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
45 46 0.71
46 19 0.29
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGACAATTATATGGGTAA
Found at i:510041 original size:21 final size:21
Alignment explanation
Indices: 510015--510064 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
510005 GATGCCAAGA
510015 AGACATGCTCGTTGCAGCCTC
1 AGACATGCTCGTTGCAGCCTC
*
510036 AGACATGCTCGTTGCAGGCTC
1 AGACATGCTCGTTGCAGCCTC
510057 AGACATGC
1 AGACATGC
510065 AAGAGATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (21 bp):
AGACATGCTCGTTGCAGCCTC
Found at i:512892 original size:23 final size:23
Alignment explanation
Indices: 512841--512886 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
512831 CACCGAAAAA
512841 CTAAGAAGGAAAAAGAATATTTT
1 CTAAGAAGGAAAAAGAATATTTT
*
512864 CTAAGAAGGAGAGAA-AATATTTT
1 CTAAGAAGGA-AAAAGAATATTTT
512887 TCAAGAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (23 bp):
CTAAGAAGGAAAAAGAATATTTT
Found at i:513126 original size:35 final size:35
Alignment explanation
Indices: 513087--513190 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 35
513077 ACAAATATTA
513087 TTTTAATTTGAAATATTCAAAAGTATATAATTATC-
1 TTTTAATTTGAAATATTCAAAAG-ATATAATTATCT
* *
513122 TTTTAATATTCAAA-ATT-AAATAGATAATAAATATCT
1 TTTTAAT-TTGAAATATTCAAA-AGAT-ATAATTATCT
* *
513158 TTTTAATTTGATATATTCAAATGA-ATAATTATC
1 TTTTAATTTGAAATATTCAAAAGATATAATTATC
513191 CTACTAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
34 13 0.23
35 24 0.42
36 17 0.30
37 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTTAATTTGAAATATTCAAAAGATATAATTATCT
Found at i:516952 original size:12 final size:13
Alignment explanation
Indices: 516918--516952 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
516908 TATTAATACT
516918 AATTAAAAAATAA
1 AATTAAAAAATAA
*
516931 AATTACAAAAT-A
1 AATTAAAAAATAA
516943 AATTAAAAAA
1 AATTAAAAAA
516953 ATACTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AATTAAAAAATAA
Found at i:517523 original size:116 final size:117
Alignment explanation
Indices: 517376--517605 Score: 309
Period size: 117 Copynumber: 2.0 Consensus size: 117
517366 TGATGTTGGC
* * * * * **
517376 GTTGATCTACCTCCTTTTGTGATAGATTTGAG-TAAAAGTTGAAATTGATCCAGCTCCTTCTGTG
1 GTTGATCTACCTCATTCTGTGATAGAATTGAGCGAAAAGTTGAAATTGATCCAACTCCTTCAATG
* *
517440 CTGGATTAAAATGTTAATCCACCTCATCCTGTGATGGATTTGAAATGTCGAT
66 CTGGATTAAAATGTCAATCCACCTCATCCTATGATGGATTTGAAATGTCGAT
** *
517492 GTTGATCTACCTCATTCTGTGATAGAATTGAGCGAAAAGTTGATGTTGATCCAACTCTTTCAATG
1 GTTGATCTACCTCATTCTGTGATAGAATTGAGCGAAAAGTTGAAATTGATCCAACTCCTTCAATG
* * * *
517557 CTGGATTAAAATGTCGATCCATCTCCTTCTATGATGGATTTGAAATGTC
66 CTGGATTAAAATGTCAATCCACCTCATCCTATGATGGATTTGAAATGTC
517606 AATCCACCTC
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
116 29 0.30
117 68 0.70
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (117 bp):
GTTGATCTACCTCATTCTGTGATAGAATTGAGCGAAAAGTTGAAATTGATCCAACTCCTTCAATG
CTGGATTAAAATGTCAATCCACCTCATCCTATGATGGATTTGAAATGTCGAT
Found at i:517595 original size:33 final size:33
Alignment explanation
Indices: 517534--518233 Score: 744
Period size: 33 Copynumber: 21.1 Consensus size: 33
517524 CGAAAAGTTG
* * ** * *
517534 ATGTTGATCCAACTCTTTCAATGCTGGATTAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * *
517567 ATGTCGATCCATCTCCTTCTATGATGGATTTGAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAG-A
*
517601 ATGTCAATCCACCTC--TCTGTGATGGATTAGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* *
517632 ATGTCGATCCACCTCTTTCTGTGATAGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * *
517665 ATATCGAACCACCACTTTCTGTGATGAATTAGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * *
517698 ATGTAGATCCACCACTTTCTGTGATGAATTAGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* *
517731 ATGTAGATCCACCTCTTTCTGTGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * *
517764 ATATCAAACCACCTCTTTCTGTGATGAATTAGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * * *
517797 ATGTAGATCCACCTCTTTTTGTGATGTATTTGG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
*
517830 ATGTCGATCCACCTCTTT-T-TGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * *
517861 AAGTCGATCCACTTCTTTCTGTGATGGATTAAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* * *
517895 ATATCGATCCACCTCTTTCTATGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * *
517928 ATATCGATCCACCTCTTTCTATGATGGATTTAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGA-TTAGA
* * * * *
517962 ATATTGATCCATCTTTTTCTGTGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
*
517995 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* * * *
518029 ATATGGATCCACCTCTTTCTATGATGGATTTAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGA-TTAGA
* *
518063 ATGTCGATTCACCTCTTTCTGTGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* *
518096 ATATCGATCCACCTCTTTCTGTGATGGATTAAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* * *
518130 ATGTCAATCCACCTCTTTCTATGATGGATTAAAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* *
518164 ATGTCGATCCACTTCTTTCTATGATGGA-TATGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTA-GA
*
518197 ATGTCGATCCACCTCTTTCTGTGATGGATTTGA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
518230 ATGT
1 ATGT
518234 TGATGCTGAT
Statistics
Matches: 566, Mismatches: 89, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
31 41 0.07
32 16 0.03
33 327 0.58
34 180 0.32
35 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (33 bp):
ATGTCGATCCACCTCTTTCTGTGATGGATTAGA
Found at i:517936 original size:67 final size:66
Alignment explanation
Indices: 517534--518226 Score: 764
Period size: 67 Copynumber: 10.5 Consensus size: 66
517524 CGAAAAGTTG
* * ** * * * * *
517534 ATGTTGATCCAACTCTTTCAATGCTGGATTAAAATGTCGATCCATCTCCTTCTATGATGGATTTG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
517599 AA
66 -A
* * * *
517601 ATGTCAATCCACCTC--TCTGTGATGGATTAGAATGTCGATCCACCTCTTTCTGTGATAGATTTG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
517664 A
66 A
* * * * * * * * * *
517665 ATATCGAACCACCACTTTCTGTGATGAATTAGAATGTAGATCCACCACTTTCTGTGATGAATTAG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
517730 A
66 A
* ** * * * *
517731 ATGTAGATCCACCTCTTTCTGTGATGGATTTGAATATCAAACCACCTCTTTCTGTGATGAATTAG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
517796 A
66 A
* * * *** *
517797 ATGTAGATCCACCTCTTTTTGTGATGTATTTGGATGTCGATCCACCTCTTT-T-TGATGGATTTG
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
517860 A
66 A
* * *
517861 AAGTCGATCCACTTCTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AAAATATCGATCCACCTCTTTCTGTGATGGATTT
517926 GA
65 GA
* * * * *
517928 ATATCGATCCACCTCTTTCTATGATGGATTTAAAATATTGATCCATCTTTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGA-TTAAAATATCGATCCACCTCTTTCTGTGATGGATTT
517993 GA
65 GA
* *
517995 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAAATATGGATCCACCTCTTTCTATGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AAAATATCGATCCACCTCTTTCTGTGATGGATTT
*
518060 AAA
65 -GA
* ** *
518063 ATGTCGATTCACCTCTTTCTGTGATGGATTTGAATATCGATCCACCTCTTTCTGTGATGGATTAA
1 ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATT-T
*
518128 AA
65 GA
* * * * * *
518130 ATGTCAATCCACCTCTTTCTATGATGGATTAAAAATGTCGATCCACTTCTTTCTATGATGGATAT
1 ATGTCGATCCACCTCTTTCTGTGATGGATT-AAAATATCGATCCACCTCTTTCTGTGATGGATTT
518195 GA
65 GA
518197 ATGTCGATCCACCTCTTTCTGTGATGGATT
1 ATGTCGATCCACCTCTTTCTGTGATGGATT
518227 TGAATGTTGA
Statistics
Matches: 533, Mismatches: 83, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
64 47 0.09
65 58 0.11
66 146 0.27
67 223 0.42
68 59 0.11
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (66 bp):
ATGTCGATCCACCTCTTTCTGTGATGGATTAAAATATCGATCCACCTCTTTCTGTGATGGATTTG
A
Found at i:518043 original size:101 final size:100
Alignment explanation
Indices: 517534--518233 Score: 804
Period size: 101 Copynumber: 7.0 Consensus size: 100
517524 CGAAAAGTTG
* * * * * * *
517534 ATGTTGATCCAACTCTTTCAATGCTGGA-TTAAAATGTCGATCCATCTCCTTCTATGATGGATTT
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
*
517598 GAAATGTCAATCCACCTC--TCTGTGATGGATTAGA
66 G-AATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * * * * * *
517632 ATGTCGATCCACCTCTTTCTGTGATAGATTT-GAATATCGAACCACCACTTTCTGTGATGAATTA
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* * *
517696 GAATGTAGATCCACCACTTTCTGTGATGAATTAGA
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * * * * * *
517731 ATGTAGATCCACCTCTTTCTGTGATGGATTT-GAATATCAAACCACCTCTTTCTGTGATGAATTA
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* * * * *
517795 GAATGTAGATCCACCTCTTTTTGTGATGTATTTGG
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* *
517830 ATGTCGATCCACCTCTTT-T-TGATGGATTTGAAA-GTCGATCCACTTCTTTCTGTGATGGATTA
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATT-
** * * *
517892 AAAATATCGATCCACCTCTTTCTATGATGGATTTGA
65 TGAATGTCGATCCACCTCTTTCTGTGATGGATTAGA
* * * * *
517928 ATATCGATCCACCTCTTTCTATGATGGATTTAAAATATTGATCCATCTTTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
*
517993 GAATGTCGATCCACCTCTTTCTGTGATGGATTAAAA
66 GAATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* * *
518029 ATATGGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATTCACCTCTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
* *
518094 GAATATCGATCCACCTCTTTCTGTGATGGATTAAAA
66 GAATGTCGATCCACCTCTTTCTGTGATGGATT-AGA
* * * * *
518130 ATGTCAATCCACCTCTTTCTATGATGGATTAAAAATGTCGATCCACTTCTTTCTATGATGGATAT
1 ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
*
518195 GAATGTCGATCCACCTCTTTCTGTGATGGATTTGA
66 GAATGTCGATCCACCTCTTTCTGTGATGGATTAGA
518230 ATGT
1 ATGT
518234 TGATGCTGAT
Statistics
Matches: 520, Mismatches: 73, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
97 46 0.09
98 96 0.18
99 125 0.24
100 47 0.09
101 206 0.40
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (100 bp):
ATGTCGATCCACCTCTTTCTATGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGATTT
GAATGTCGATCCACCTCTTTCTGTGATGGATTAGA
Found at i:520379 original size:15 final size:15
Alignment explanation
Indices: 520359--520450 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 15
520349 CATGTGCTTC
520359 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
*
520374 TTTTCTCTTGTTTTTTT
1 TTTTCT-TT-TTTCTTT
*
520391 TCCTTTCTTTTTCCTTT
1 T--TTTCTTTTTTCTTT
**
520408 CTTTGATTTTTTCTTT
1 -TTTTCTTTTTTCTTT
*
520424 GTTAT-TTTTTTCTTTT
1 -TTTTCTTTTTTC-TTT
520440 TTTTCTTTTTT
1 TTTTCTTTTTT
520451 TTATCTTTGG
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
15 16 0.27
16 24 0.40
17 12 0.20
18 3 0.05
19 5 0.08
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTCTTT
Found at i:520401 original size:11 final size:11
Alignment explanation
Indices: 520360--520411 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
520350 ATGTGCTTCT
*
520360 TTTCTTTTTTC
1 TTTCTTTTTCC
*
520371 TTT-TTTTCTCT
1 TTTCTTTT-TCC
*
520382 TGTTTTTTTTCC
1 T-TTCTTTTTCC
520394 TTTCTTTTTCC
1 TTTCTTTTTCC
520405 TTTCTTT
1 TTTCTTT
520412 GATTTTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 4 0.12
11 21 0.62
12 5 0.15
13 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCC
Found at i:520435 original size:27 final size:27
Alignment explanation
Indices: 520359--520438 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 27
520349 CATGTGCTTC
* *
520359 TTTTCTTTTTTCTTTTTTTCTCTTGTTTT
1 TTTTCTTTCTT-TTTTTTTCT-TTGTATT
*
520388 TTTTCCTTTCTTTTTCCTTTCTTTG-ATT
1 TTTT-CTTTCTTTTT-TTTTCTTTGTATT
*
520416 TTTTCTTTGTTATTTTTTTCTTT
1 TTTTCTTTCTT-TTTTTTTCTTT
520439 TTTTTCTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 13 0.30
28 9 0.21
29 10 0.23
30 11 0.26
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.79
Consensus pattern (27 bp):
TTTTCTTTCTTTTTTTTTCTTTGTATT
Found at i:520446 original size:24 final size:25
Alignment explanation
Indices: 520414--520478 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
520404 CTTTCTTTGA
*
520414 TTTTTTCTTTGTTATTT-T-TTTCTT
1 TTTTTTCTTTGTT-TTTATCTTTCGT
*
520438 TTTTTTCTTT-TTTTTATCTTTGGT
1 TTTTTTCTTTGTTTTTATCTTTCGT
520462 TTTTTTCTTTGTGTTTT
1 TTTTTTCTTTGT-TTTT
520479 TTCTATATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.09
23 3 0.09
24 24 0.69
25 1 0.03
26 4 0.11
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.82
Consensus pattern (25 bp):
TTTTTTCTTTGTTTTTATCTTTCGT
Found at i:520698 original size:2 final size:2
Alignment explanation
Indices: 520691--520734 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
520681 ACAACAAGGG
520691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
520734 A
1 A
520735 AAAGGATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527253 original size:22 final size:22
Alignment explanation
Indices: 527226--527292 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
527216 CCTAATTAAG
*
527226 AAATAAAATTACAAAATAAATT
1 AAATAAAATTACAAAATAAATA
* *
527248 AAATAAATATTA-AAATTGAATA
1 AAATAAA-ATTACAAAATAAATA
527270 AAATAAAAATTAC-AAAT-AATA
1 AAAT-AAAATTACAAAATAAATA
527291 AA
1 AA
527293 GGAAATCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.16
22 25 0.66
23 7 0.18
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (22 bp):
AAATAAAATTACAAAATAAATA
Found at i:527263 original size:17 final size:16
Alignment explanation
Indices: 527243--527281 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
527233 ATTACAAAAT
*
527243 AAATTAAATAAATATTA
1 AAATTAAATAAA-ATAA
*
527260 AAATTGAATAAAATAA
1 AAATTAAATAAAATAA
527276 AAATTA
1 AAATTA
527282 CAAATAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATTAAATAAAATAA
Found at i:533392 original size:13 final size:13
Alignment explanation
Indices: 533353--533392 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
533343 GAACAAAAAG
533353 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
*
533366 AATAAAAAGAGAA
1 AAAAAAAAGAGAA
533379 AAAAATAAAG-GAA
1 AAAAA-AAAGAGAA
533392 A
1 A
533393 TTGAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:533576 original size:69 final size:69
Alignment explanation
Indices: 533465--533595 Score: 244
Period size: 69 Copynumber: 1.9 Consensus size: 69
533455 GATTCAAACT
* *
533465 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAACACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
533530 TTAA
66 TTAA
533534 ATGAGATTGATCAAACACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGA
1 ATGAGATTGATCAAACACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGA
533596 CCATCAAGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAACACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
TTAA
Found at i:534534 original size:32 final size:32
Alignment explanation
Indices: 534498--534605 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
534488 GCATCTTTGA
534498 AGATTCAACATCAAATGTTGGGGCATTTTTTT
1 AGATTCAACATCAAATGTTGGGGCATTTTTTT
*
534530 AGATTTAACATCAAATGTTGGGGCATTTTTTT
1 AGATTCAACATCAAATGTTGGGGCATTTTTTT
* * * * *
534562 AGATTCAACATCGAATATTGGGACA-TCTTTG
1 AGATTCAACATCAAATGTTGGGGCATTTTTTT
534593 AGAATTCAACATC
1 AG-ATTCAACATC
534606 CTGATGCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 6 0.09
32 62 0.91
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (32 bp):
AGATTCAACATCAAATGTTGGGGCATTTTTTT
Found at i:535308 original size:20 final size:20
Alignment explanation
Indices: 535283--535328 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
535273 GTCAACAAAT
*
535283 AATTTCCCAATTTCAGAGAC
1 AATTTCCCAAATTCAGAGAC
*
535303 AATTTCCCAAATTCAGAGCC
1 AATTTCCCAAATTCAGAGAC
535323 AATTTC
1 AATTTC
535329 AACTTCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
AATTTCCCAAATTCAGAGAC
Found at i:535531 original size:105 final size:106
Alignment explanation
Indices: 535301--535578 Score: 389
Period size: 105 Copynumber: 2.6 Consensus size: 106
535291 AATTTCAGAG
*
535301 ACAATTTCCCAAATT-CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACA
1 ACAATTTCCC-AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* * *
535365 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTTTCAACAA
65 CAAGCTCAACTTCACAACGAAGGGACGGCTGGCTATCAACAA
* *
535407 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA-AGCAC
1 ACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACAC
* **
535471 AAGCTCAACTTCACAGCGAAGGGGTGGCTGGCTATCAACAA
66 AAGCTCAACTTCACAACGAAGGGACGGCTGGCTATCAACAA
* * * * * * *
535512 ACAATTTCCTAGTTCCAGAGCCAATTTTAACTTTACGGCGAAGGATATTGGACTCGAAACAATAC
1 ACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACAC
535577 AA
66 AA
535579 CTTACTTGGA
Statistics
Matches: 153, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
105 95 0.62
106 58 0.38
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACAC
AAGCTCAACTTCACAACGAAGGGACGGCTGGCTATCAACAA
Found at i:535875 original size:65 final size:65
Alignment explanation
Indices: 535806--535930 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 65
535796 AAGTTTTGTC
** * *
535806 TCTCTTGAAACATAAA-CATTGAAAATATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGT
1 TCTCTTGAAACA-AAATCATTGAAAATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAGT
535870 T
65 T
* ** *
535871 TCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 TCTCTTGAAACAAAATCATTGAAAATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
535931 CATTTTCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 3 0.06
65 48 0.94
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (65 bp):
TCTCTTGAAACAAAATCATTGAAAATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAGTT
Found at i:535962 original size:102 final size:102
Alignment explanation
Indices: 535847--536214 Score: 365
Period size: 102 Copynumber: 3.7 Consensus size: 102
535837 CCTTGAAATG
* * *
535847 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCTGTTTCCCTTGAAA
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAAC-ATTTCCCTTGAAA
** ** * * *
535910 CAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTA
64 CAAATTTCGTCTCCCTTGAGACAGGTTCCCTCGAAACAA
* **
535949 AGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACA
* * *
536014 AATTTTGTCTCTCTTGAGATAGGTTCCCTCGAAACAA
66 AATTTCGTCTCCCTTGAGACAGGTTCCCTCGAAACAA
* * *
536051 AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG----A
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACA
* * * * * * *
536112 AATTTTGTCACTCATGA-ATAGTTTCCCTTGAAAC-A
66 AATTTCGTCTCCCTTGAGACAGGTTCCCTCGAAACAA
* * * * * *
536147 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACAGATTCCTTTGAAAC
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA-TTTCCCTTGAAAC
536212 AAA
65 AAA
536215 ATCTTTGAAT
Statistics
Matches: 229, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
96 49 0.21
97 22 0.10
98 15 0.07
101 3 0.01
102 134 0.59
103 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACA
AATTTCGTCTCCCTTGAGACAGGTTCCCTCGAAACAA
Found at i:536085 original size:37 final size:37
Alignment explanation
Indices: 536014--536086 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
536004 CCTTGAAATG
* * *
536014 AATTTTGTCTCTCTTGAGATAGGTTCCCTCGAAACAA
1 AATTTTGTCTCCCTTAAGACAGGTTCCCTCGAAACAA
* * *
536051 AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTAAGACAGGTTCCCTCGAAACA
536087 TAAACATTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (37 bp):
AATTTTGTCTCCCTTAAGACAGGTTCCCTCGAAACAA
Found at i:536177 original size:96 final size:100
Alignment explanation
Indices: 535951--536197 Score: 367
Period size: 102 Copynumber: 2.5 Consensus size: 100
535941 TGGAACTAAG
* *
535951 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG-AA-GAA
* *
536016 TTTTGTCTCTCTTGAGATAGGTTCCCTCGAAACAAAA
64 TTTTGTCACTCATGAGATAGGTTCCCTCGAAACAAAA
*
536053 TTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG-A-AATT
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAGAATT
* *
536116 TTGTCACTCATGA-ATAGTTTCCCTTGAAAC-AAA
66 TTGTCACTCATGAGATAGGTTCCCTCGAAACAAAA
* *
536149 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
536198 GATTCCTTTG
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
96 49 0.36
97 15 0.11
98 15 0.11
100 1 0.01
102 55 0.41
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (100 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAGAATT
TTGTCACTCATGAGATAGGTTCCCTCGAAACAAAA
Found at i:536299 original size:21 final size:21
Alignment explanation
Indices: 536275--536336 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
536265 TTCTTTTTGA
536275 AGTTTTTGTCTCTCTTGAGAC
1 AGTTTTTGTCTCTCTTGAGAC
*
536296 AG----T-T-TCTCTTGAAAC
1 AGTTTTTGTCTCTCTTGAGAC
**
536311 AAATTTTGTCTCTCTTGAGAC
1 AGTTTTTGTCTCTCTTGAGAC
536332 AGTTT
1 AGTTT
536337 CCCTTGAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 1 0.03
19 1 0.03
20 1 0.03
21 15 0.50
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (21 bp):
AGTTTTTGTCTCTCTTGAGAC
Found at i:536325 original size:36 final size:36
Alignment explanation
Indices: 536278--536346 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
536268 TTTTTGAAGT
*
536278 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
536314 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
536347 TTCAATCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:540844 original size:23 final size:23
Alignment explanation
Indices: 540818--540863 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
540808 CACCACAGCT
* *
540818 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
540841 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
540864 TATAAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:541673 original size:63 final size:63
Alignment explanation
Indices: 541573--541694 Score: 190
Period size: 63 Copynumber: 1.9 Consensus size: 63
541563 CTTAAGGAGG
* * *
541573 TGCATCGATGCATTGAGGACATTCGATGTTCATTTAATTGAAAATGCATCGATGCACTCCTTA
1 TGCATCGATGCACTAAGGACATTCGATGTTCAATTAATTGAAAATGCATCGATGCACTCCTTA
* **
541636 TGCATCGATGCACTAATGACATTCGATGTTCAATTAATTGAGGATGCATCGATGCACTC
1 TGCATCGATGCACTAAGGACATTCGATGTTCAATTAATTGAAAATGCATCGATGCACTC
541695 TACCCAGAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCACTAAGGACATTCGATGTTCAATTAATTGAAAATGCATCGATGCACTCCTTA
Found at i:543025 original size:38 final size:38
Alignment explanation
Indices: 542935--543309 Score: 323
Period size: 37 Copynumber: 9.5 Consensus size: 38
542925 TTTTTTAAAA
*
542935 AAAACTA-ATATTATATATATTTTCGAAAATTGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
*
542972 AAAACTATACA-TATATATATTTTCGAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
* *
543009 AAAACTATACATTATATATACTTTCGAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
*
543047 AAAACTATATATTATATATATTTTC-AAAAACGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
* * * **
543084 AAAAAATGTTTTCAAAACTTTGTAATATATATATTT-TCAAAATGTTTTC
1 --AAAA------CTATA-TAT-T-ATATATAT-TTTCGAAAAATGTTTTC
* ****
543133 AAAACTATATATTATATAT-TTTTCAAAAAAAAAATTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
543170 AAAACTATATATTATATATATAGTTTC-AAAAATGTTTTC
1 AAAACTATATATTATATATAT--TTTCGAAAAATGTTTTC
* * *
543209 AAAACTATAT-TCTATATATAATTTCAAAAAATGTTTTT
1 AAAACTATATAT-TATATATATTTTCGAAAAATGTTTTC
***
543247 AAAACTATATTATATATATATATATATATTTTTAAAATGTTTTC
1 AAAAC--TA-TATAT-TATATATAT-T-TTCGAAAAATGTTTTC
543291 AAAACTATATATTATATAT
1 AAAACTATATATTATATAT
543310 GTTAATATAA
Statistics
Matches: 279, Mismatches: 32, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
36 3 0.01
37 85 0.30
38 74 0.27
39 31 0.11
40 15 0.05
41 11 0.04
42 11 0.04
43 1 0.00
44 17 0.06
45 3 0.01
46 2 0.01
47 5 0.02
48 8 0.03
49 13 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (38 bp):
AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
Found at i:543028 original size:75 final size:76
Alignment explanation
Indices: 542935--543309 Score: 284
Period size: 75 Copynumber: 4.8 Consensus size: 76
542925 TTTTTTAAAA
* * *
542935 AAAACTA-ATATTATATATAT-TTTCGAAAATTGTTTTCAAAACTATACATATATATATTTTCGA
1 AAAACTATACATTATATATATATTTCGAAAAATGTTTTCAAAACTATACATATATATATTTTCAA
542998 AAAATGTTTTC
66 AAAATGTTTTC
* *
543009 AAAACTATACATTATATATA-CTTTCGAAAAATGTTTTCAAAACTATATATTATATATATTTTC-
1 AAAACTATACATTATATATATATTTCGAAAAATGTTTTCAAAACTATACA-TATATATATTTTCA
*
543072 AAAAACGTTTTC
65 AAAAATGTTTTC
* * * *
543084 AAAAAATGTTTTCAAAACTTTGTAATATATATATTTTC--AAAATGTTTTCAAAACTATATAT-T
1 --AAAA------CTATAC-AT-T-ATATATATA-TTTCGAAAAATGTTTTCAAAACTATACATAT
****
543146 ATATATTTTTCAAAAAAAAAATTC
54 ATATA-TTTTCAAAAAATGTTTTC
* *
543170 AAAACTATATATTATATATATAGTTTC-AAAAATGTTTTCAAAACTATATTC-TATATATAATTT
1 AAAACTATACATTATATATATA-TTTCGAAAAATGTTTTCAAAACTATA--CATATATATATTTT
*
543233 CAAAAAATGTTTTT
63 CAAAAAATGTTTTC
* *** *
543247 AAAACTATATTATATATATATATATATATTTTTAAAATGTTTTCAAAACTATATAT-TATATAT
1 AAAAC--TA-TACAT-TATATATATAT-TTCGAAAAATGTTTTCAAAACTATACATATATATAT
543310 GTTAATATAA
Statistics
Matches: 244, Mismatches: 28, Indels: 52
0.75 0.09 0.16
Matches are distributed among these distances:
74 7 0.03
75 61 0.25
76 34 0.14
77 23 0.09
78 9 0.04
79 2 0.01
80 12 0.05
81 13 0.05
82 20 0.08
83 4 0.02
84 11 0.05
85 7 0.03
86 37 0.15
88 4 0.02
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (76 bp):
AAAACTATACATTATATATATATTTCGAAAAATGTTTTCAAAACTATACATATATATATTTTCAA
AAAATGTTTTC
Found at i:543089 original size:50 final size:49
Alignment explanation
Indices: 543030--543136 Score: 160
Period size: 50 Copynumber: 2.2 Consensus size: 49
543020 TTATATATAC
* *
543030 TTTCGAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAACGT
1 TTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTC-AAAACGT
* * *
543080 TTTCAAAAAATGTTTTCAAAACTTTGTAATATATATATTTTCAAAATGT
1 TTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAACGT
543129 TTTCAAAA
1 TTTCAAAA
543137 CTATATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
49 14 0.27
50 38 0.73
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (49 bp):
TTTCAAAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAACGT
Found at i:543094 original size:13 final size:13
Alignment explanation
Indices: 543067--543100 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
543057 ATTATATATA
543067 TTTTC-AAAAACG
1 TTTTCAAAAAACG
*
543079 TTTTCAAAAAATG
1 TTTTCAAAAAACG
543092 TTTTCAAAA
1 TTTTCAAAA
543101 CTTTGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAAACG
Found at i:543120 original size:25 final size:24
Alignment explanation
Indices: 543042--543125 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
543032 TCGAAAAATG
* *
543042 TTTTCAAAACTATATATTATATATA
1 TTTTCAAAACT-TTTAATATATATA
* *
543067 TTTTCAAAAACGTTTTCAA-A-AAATG
1 TTTTC-AAAAC-TTTT-AATATATATA
543092 TTTTCAAAACTTTGTAATATATATA
1 TTTTCAAAACTTT-TAATATATATA
543117 TTTTCAAAA
1 TTTTCAAAA
543126 TGTTTTCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
23 5 0.11
24 7 0.15
25 25 0.53
26 8 0.17
27 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTCAAAACTTTTAATATATATA
Found at i:543141 original size:25 final size:24
Alignment explanation
Indices: 543062--543142 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
543052 TATATATTAT
*
543062 ATATATTTTCAAAAACGTTTTCAAA
1 ATATATTTTC-AAAATGTTTTCAAA
* * *
543087 AAATGTTTTCAAAACT-TTGT-AATA
1 ATATATTTTCAAAA-TGTTTTCAA-A
543111 TATATATTTTCAAAATGTTTTCAAA
1 -ATATATTTTCAAAATGTTTTCAAA
543136 ACTATAT
1 A-TATAT
543143 ATTATATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
23 2 0.05
24 10 0.23
25 29 0.67
26 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (24 bp):
ATATATTTTCAAAATGTTTTCAAA
Found at i:543162 original size:86 final size:87
Alignment explanation
Indices: 542991--543161 Score: 265
Period size: 88 Copynumber: 2.0 Consensus size: 87
542981 CATATATATA
* *
542991 TTTTCGAAAAATGTTTTCAAAACTATACATTATATATACTTTCGAAAAATGTTTTCAAAACTATA
1 TTTTCAAAAAATGTTTTCAAAACTATACAATATATATACTTTC-AAAAATGTTTTCAAAACTATA
543056 TATTATATATATTTTCAAAAACG
65 TATTATATATATTTTCAAAAACG
* ** *
543079 TTTTCAAAAAATGTTTTCAAAACTTTGTAATATATATATTTTC-AAAATGTTTTCAAAACTATAT
1 TTTTCAAAAAATGTTTTCAAAACTATACAATATATATACTTTCAAAAATGTTTTCAAAACTATAT
543143 ATTATATAT-TTTTCAAAAA
66 ATTATATATATTTTCAAAAA
543162 AAAAATTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
85 10 0.13
86 30 0.39
88 37 0.48
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (87 bp):
TTTTCAAAAAATGTTTTCAAAACTATACAATATATATACTTTCAAAAATGTTTTCAAAACTATAT
ATTATATATATTTTCAAAAACG
Found at i:543171 original size:86 final size:87
Alignment explanation
Indices: 542997--543173 Score: 241
Period size: 86 Copynumber: 2.0 Consensus size: 87
542987 TATATTTTCG
*
542997 AAAAATGTTTTCAAAACTATACATTATATATACTTTCGAAAAATGTTTTCAAAACTATATATTAT
1 AAAAATGTTTTCAAAACTATACAATATATATACTTTC-AAAAATGTTTTCAAAACTATATATTAT
****
543062 ATATATTTTCAAAAACGTTTTCA
65 ATATATTTTCAAAAAAAAATTCA
* ** *
543085 AAAAATGTTTTCAAAACTTTGTAATATATATATTTTC-AAAATGTTTTCAAAACTATATATTATA
1 AAAAATGTTTTCAAAACTATACAATATATATACTTTCAAAAATGTTTTCAAAACTATATATTATA
543149 TAT-TTTTCAAAAAAAAAATTCA
66 TATATTTTC-AAAAAAAAATTCA
543171 AAA
1 AAA
543174 CTATATATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
85 5 0.06
86 42 0.53
88 32 0.41
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.41
Consensus pattern (87 bp):
AAAAATGTTTTCAAAACTATACAATATATATACTTTCAAAAATGTTTTCAAAACTATATATTATA
TATATTTTCAAAAAAAAATTCA
Found at i:543318 original size:44 final size:44
Alignment explanation
Indices: 543236--543327 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
543226 ATAATTTCAA
* * *
543236 AAAATGTTTTTAAAACTATATTATATATATATATATATATTTTT
1 AAAATGTTTTCAAAACTATATTATATATATATATATATAATATT
*
543280 AAAATGTTTTCAAAACTATA-TAT-TATATATGTTAATATAATATT
1 AAAATGTTTTCAAAACTATATTATATATATAT-AT-ATATAATATT
543324 AAAA
1 AAAA
543328 ACCCCAGACG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 7 0.17
43 4 0.10
44 31 0.74
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (44 bp):
AAAATGTTTTCAAAACTATATTATATATATATATATATAATATT
Found at i:543318 original size:46 final size:45
Alignment explanation
Indices: 543236--543317 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
543226 ATAATTTCAA
*
543236 AAAATGTTTTTAAAACTATATTATATATATATATAT-ATATTTTT
1 AAAATGTTTTCAAAACTATATTATATATATATATATAATATTTTT
*
543280 AAAATGTTTTCAAAACTATA-TAT-TATATATGT-TAATAT
1 AAAATGTTTTCAAAACTATATTATATATATATATATAATAT
543318 AATATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 12 0.34
43 3 0.09
44 19 0.54
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (45 bp):
AAAATGTTTTCAAAACTATATTATATATATATATATAATATTTTT
Found at i:544242 original size:29 final size:29
Alignment explanation
Indices: 544210--544271 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
544200 AAAAAATTGG
*
544210 TTAATTCAGTTCGATTAATAATTTTCAAA
1 TTAATTCAATTCGATTAATAATTTTCAAA
* *
544239 TTAATTCAATTCGGTTAATAATTTTTAAA
1 TTAATTCAATTCGATTAATAATTTTCAAA
544268 TTAA
1 TTAA
544272 CCGAATCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (29 bp):
TTAATTCAATTCGATTAATAATTTTCAAA
Found at i:544491 original size:26 final size:28
Alignment explanation
Indices: 544436--544496 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
544426 AAAAAAATTG
* *
544436 TTAATTCGGTTTGGTTAATAATTTTTAAA
1 TTAATTCGGTTCGGTT-ATAATTTTCAAA
544465 TTAATTCGGTTCGG-T-TAATTTTCAAA
1 TTAATTCGGTTCGGTTATAATTTTCAAA
*
544491 TAAATT
1 TTAATT
544497 TTAGTTCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.52
28 1 0.03
29 13 0.45
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (28 bp):
TTAATTCGGTTCGGTTATAATTTTCAAA
Found at i:545377 original size:28 final size:29
Alignment explanation
Indices: 545346--545400 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
545336 TGTTTATACT
*
545346 ACTAACTTTT-AATTTTATCAATTATAGC
1 ACTAAATTTTGAATTTTATCAATTATAGC
* *
545374 ACTAAATTTTGATTTTTTTCAATTATA
1 ACTAAATTTTGAATTTTATCAATTATA
545401 TTATTGAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (29 bp):
ACTAAATTTTGAATTTTATCAATTATAGC
Found at i:546374 original size:40 final size:39
Alignment explanation
Indices: 546325--546403 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
546315 TATTAAAATA
*
546325 TATTATTTAATTATTAA-AAATATAATA-AAATATATTATT
1 TATTATTTAAATA-TAATAAATA-AATATAAATATATTATT
*
546364 TATTAGTTTAAATATAATAAATAATTATAAATATATTATT
1 TATTA-TTTAAATATAATAAATAAATATAAATATATTATT
546404 ATAAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 11 0.31
40 24 0.69
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (39 bp):
TATTATTTAAATATAATAAATAAATATAAATATATTATT
Found at i:546380 original size:31 final size:32
Alignment explanation
Indices: 546318--546391 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
546308 TTTGTATTAT
546318 TAAAATATATTATTTAATTATTAAAAATATAA
1 TAAAATATATTATTTAATTATTAAAAATATAA
*
546350 TAAAATATATTATTT-ATTAGTT-TAAATATAA
1 TAAAATATATTATTTAATTA-TTAAAAATATAA
546381 T-AAATA-ATTAT
1 TAAAATATATTAT
546392 AAATATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 5 0.12
30 5 0.12
31 13 0.32
32 17 0.43
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
TAAAATATATTATTTAATTATTAAAAATATAA
Found at i:546395 original size:10 final size:11
Alignment explanation
Indices: 546315--546402 Score: 57
Period size: 10 Copynumber: 8.5 Consensus size: 11
546305 ATTTTTGTAT
546315 TATTA-AAATA
1 TATTATAAATA
*
546325 TATTATTTAAT-
1 TATTA-TAAATA
*
546336 TATTAAAAATA
1 TATTATAAATA
*
546347 TAATA-AAATA
1 TATTATAAATA
**
546357 TATTATTTAT-
1 TATTATAAATA
546367 TAGTT-TAAATA
1 TA-TTATAAATA
546378 TA--ATAAATA
1 TATTATAAATA
546387 -ATTATAAATA
1 TATTATAAATA
546397 TATTAT
1 TATTAT
546403 TATAAAATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
8 1 0.02
9 6 0.10
10 29 0.49
11 20 0.34
12 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
TATTATAAATA
Found at i:546404 original size:14 final size:15
Alignment explanation
Indices: 546387--546418 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
546377 ATAATAAATA
546387 ATTAT-AAATATATT
1 ATTATAAAATATATT
546401 ATTATAAAATATATT
1 ATTATAAAATATATT
546416 ATT
1 ATT
546419 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:563011 original size:21 final size:21
Alignment explanation
Indices: 562987--563027 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
562977 TGGGTTGGCT
562987 GTAACTGGGCTCCTACTATTG
1 GTAACTGGGCTCCTACTATTG
563008 GTAACTGGGCTCCTACTATT
1 GTAACTGGGCTCCTACTATT
563028 AGGCCTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
GTAACTGGGCTCCTACTATTG
Found at i:564122 original size:19 final size:19
Alignment explanation
Indices: 564081--564124 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
564071 CTTGGCTGAT
***
564081 TGGGTCGGATCTTTGGCTT
1 TGGGTCGGATCTTTGGAAC
*
564100 TGGGTCGGATCTTTGTAAC
1 TGGGTCGGATCTTTGGAAC
564119 TGGGTC
1 TGGGTC
564125 TGGGTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.36, T:0.39
Consensus pattern (19 bp):
TGGGTCGGATCTTTGGAAC
Found at i:564144 original size:27 final size:28
Alignment explanation
Indices: 564113--564168 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
564103 GTCGGATCTT
564113 TGTAACTGGG-TCTGGGTTCTG-GTTGGC
1 TGTAACTGGGCTCTGGGTT-TGAGTTGGC
* *
564140 TGTAATTGGGCTCTTGGTTTGAGTTGGC
1 TGTAACTGGGCTCTGGGTTTGAGTTGGC
564168 T
1 T
564169 TGATTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.09, C:0.12, G:0.38, T:0.41
Consensus pattern (28 bp):
TGTAACTGGGCTCTGGGTTTGAGTTGGC
Found at i:564431 original size:36 final size:35
Alignment explanation
Indices: 564362--564431 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
564352 GTGGGAATTC
*
564362 TAATTTTCTATAATTAAAATATGTGTACCCACTAA
1 TAATTTTCTATAATTAAAATATGTGTAACCACTAA
*
564397 TAATTCTT-TATAATTAGAAA-ATGGTGTAATCACTA
1 TAATT-TTCTATAATTA-AAATAT-GTGTAACCACTA
564432 TCCTTACCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (35 bp):
TAATTTTCTATAATTAAAATATGTGTAACCACTAA
Found at i:565668 original size:25 final size:21
Alignment explanation
Indices: 565625--565700 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 21
565615 TAAAATAAAT
565625 ATTTTTTATTTAAATATTATATA
1 ATTTTTTATTTAAATA-T-TATA
565648 ATTTTTTATTCTTGAAA-ATTATA
1 ATTTTTTA-T-TT-AAATATTATA
*
565671 ATTTTTTA---AGATTATTATA
1 ATTTTTTATTTA-AATATTATA
565690 ATTTTTTATTT
1 ATTTTTTATTT
565701 TTCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 14 0.32
23 20 0.45
24 2 0.05
25 3 0.07
26 3 0.07
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTTTTATTTAAATATTATA
Found at i:565733 original size:42 final size:41
Alignment explanation
Indices: 565636--565739 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 41
565626 TTTTTTATTT
* * * *
565636 AAATATTATATAATTTTTTATTCTTGAAAATTATAATTTTTT
1 AAATTTTA-ATAATTTTTTATTCTTCAAAATTATAAGTTTTG
*
565678 AAGATTATT-ATAATTTTTTATTTTTCAAAATT-TATAGTTTTG
1 AA-ATT-TTAATAATTTTTTATTCTTCAAAATTATA-AGTTTTG
*
565720 AAATTTTAAATAATATTTTA
1 AAATTTT-AATAATTTTTTA
565740 AAATTTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
40 2 0.04
41 5 0.10
42 40 0.78
43 2 0.04
44 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (41 bp):
AAATTTTAATAATTTTTTATTCTTCAAAATTATAAGTTTTG
Found at i:567002 original size:124 final size:116
Alignment explanation
Indices: 566864--567094 Score: 291
Period size: 116 Copynumber: 1.9 Consensus size: 116
566854 TTATTATATT
* * **
566864 TTAATAAATTAAATTAAAAACATGACTCATAAATATTAATATACTATTTTTTAAATTAATGCAAG
1 TTAATAAATTAAATTAAAAACATGACCCATAAATATTAATAAACTA--AATTAAA--AA--C-AG
* * * *
566929 AGGTCTATAAACTTATTTTTTATTGATTTATTTTTCTCATCATAACGTTAAAAATTATA
59 -GGCCCATAAACTTATTTTTTATTGACTTATTGTTCTCATCATAACGTTAAAAATTATA
* * *
566988 TTAATATATTAAATTAAAAGCATGACCCATAAATATTAATAAACTAAATTAGAAACAGGGCCCAT
1 TTAATAAATTAAATTAAAAACATGACCCATAAATATTAATAAACTAAATTAAAAACAGGGCCCAT
567053 AAACTTATTTTTTATTGACTTATTGTTCTCATCATAACGTTA
66 AAACTTATTTTTTATTGACTTATTGTTCTCATCATAACGTTA
567095 TGTCAATTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 45 0.47
117 2 0.02
118 1 0.01
120 2 0.02
122 4 0.04
124 42 0.44
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (116 bp):
TTAATAAATTAAATTAAAAACATGACCCATAAATATTAATAAACTAAATTAAAAACAGGGCCCAT
AAACTTATTTTTTATTGACTTATTGTTCTCATCATAACGTTAAAAATTATA
Found at i:567036 original size:35 final size:35
Alignment explanation
Indices: 566985--567055 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
566975 GTTAAAAATT
* * *
566985 ATATTAATATATTAAATTA-AAAGCATGACCCATAA
1 ATATTAATAAACTAAATTAGAAA-CAGGACCCATAA
*
567020 ATATTAATAAACTAAATTAGAAACAGGGCCCATAA
1 ATATTAATAAACTAAATTAGAAACAGGACCCATAA
567055 A
1 A
567056 CTTATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAGAAACAGGACCCATAA
Found at i:574513 original size:54 final size:54
Alignment explanation
Indices: 574480--574913 Score: 564
Period size: 54 Copynumber: 8.0 Consensus size: 54
574470 TGCACTCATG
574480 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * * * * *
574534 GTGCCGAAACAGTTATTCATCTACATAAGATAAATTTCGTGAAATGCATACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * *
574588 GTGCTGAAACGATTATTCATCCACATAGGATGAA-TCCTGTGAAATACACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCC-GTGAAATGCACACTTA
* * * * *
574642 GTTCCGAAATGATTATTCATTCACATAGAATGAATTCCGTGAAATGCACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* *
574696 GTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTAAAATGCACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * * * * * * *
574750 GTTCTGAAACTGTTATTCATCCAGATATGATGAATTTCATGAAATACACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * *
574804 GTGCTGAAACTGTTATTCATCCACATAGGATGAATTCCGTGAAATTCACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * * * *
574858 GTGCCAAAATGGTTATTCATCCATATAGGATGAATTCCGTGAAATACACAATTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
574912 GT
1 GT
574914 TCCAAATTGG
Statistics
Matches: 327, Mismatches: 51, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
53 2 0.01
54 322 0.98
55 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (54 bp):
GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
Found at i:575280 original size:22 final size:20
Alignment explanation
Indices: 575238--575309 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 20
575228 TAGCCCTTCA
575238 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
*
575258 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACCATG
*
575280 GTATCGATACCCCCTTCCA--
1 GTATCGATA-CCCCTACCATG
575299 GTATCGATACC
1 GTATCGATACC
575310 AAAATTAGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.04
19 9 0.20
20 10 0.22
21 6 0.13
22 18 0.39
23 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:575383 original size:95 final size:95
Alignment explanation
Indices: 575242--575461 Score: 264
Period size: 95 Copynumber: 2.3 Consensus size: 95
575232 CCTTCAGTAT
* *
575242 CGATACCC-CTACCATGGTATCGATACTACCCTACTATGGTATCGATAC-CCCCTTCCAGTATCG
1 CGATACCCTC-ACCATGGTATCGATACTACCATACTATGGTACCGATACTCCCC-TCCAGTATCG
* *
575305 ATACCAAAATTAGCTTCGATGTGGCTTGGTAC
64 ATACCAAAATTAGCTTCGATGTGACCTGGTAC
* * **
575337 CGATACCCTCACCATGGTATCGATACTACTATGCTATGGTACCGATACTCCCCTCTGGTATCGAT
1 CGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATACTCCCCTCCAGTATCGAT
* * * *
575402 ACCAAAATTAGGTTTGATGTTACCTGGTAT
66 ACCAAAATTAGCTTCGATGTGACCTGGTAC
* * * *
575432 CGATACCATTATCATAGTATCGATACTACC
1 CGATACCCTCACCATGGTATCGATACTACC
575462 TCATCAGTAC
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
95 101 0.95
96 5 0.05
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (95 bp):
CGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATACTCCCCTCCAGTATCGAT
ACCAAAATTAGCTTCGATGTGACCTGGTAC
Found at i:579429 original size:15 final size:16
Alignment explanation
Indices: 579390--579431 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
579380 ATAACACTTA
*
579390 AAAGAAAATTTTAAAGT
1 AAAGAAAA-TTAAAAGT
*
579407 AAATAAAATTAAAAG-
1 AAAGAAAATTAAAAGT
579422 AAAGAAAATT
1 AAAGAAAATT
579432 CAATAAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 6 0.27
17 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (16 bp):
AAAGAAAATTAAAAGT
Found at i:581173 original size:20 final size:22
Alignment explanation
Indices: 581128--581175 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
581118 ATACCTTAAT
581128 TCCTAATAAAATAATAAATCTAA
1 TCCTAATAAAATAATAAATC-AA
*
581151 TCCTAA-AAAATAATACATC-A
1 TCCTAATAAAATAATAAATCAA
581171 TCCTA
1 TCCTA
581176 TATTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
22 12 0.50
23 6 0.25
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (22 bp):
TCCTAATAAAATAATAAATCAA
Found at i:581645 original size:61 final size:61
Alignment explanation
Indices: 581550--581671 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
581540 TTATAAGTCA
*
581550 AATCTGGTTGGATCTACATTTCTTCAGGAGTGATAACATCCGAGGGATCTTATCTGTACCT
1 AATCTGGTTGGATCTACATTTCTTCAGGAGTGATAACATCCGAGGGATCTGATCTGTACCT
* *
581611 AATCTGGTTTGATCTCCATTTCTTCAGGAGTGATAACATCCGAGGGATCTGATCTGTACCT
1 AATCTGGTTGGATCTACATTTCTTCAGGAGTGATAACATCCGAGGGATCTGATCTGTACCT
581672 CCTAATCATC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (61 bp):
AATCTGGTTGGATCTACATTTCTTCAGGAGTGATAACATCCGAGGGATCTGATCTGTACCT
Found at i:586838 original size:54 final size:53
Alignment explanation
Indices: 586740--587006 Score: 328
Period size: 54 Copynumber: 5.0 Consensus size: 53
586730 CGTACTCATG
586740 GTGCCAAAACGGTTATTCAT---ATAGGATGAATTCCGTGAAATGCACACTTA
1 GTGCCAAAACGGTTATTCATCCAATAGGATGAATTCCGTGAAATGCACACTTA
* * * *
586790 GTGCCAAAATGGTTATTCATCCACATAGGATAAATTTCGTGAAATGCACTCTTA
1 GTGCCAAAACGGTTATTCATCCA-ATAGGATGAATTCCGTGAAATGCACACTTA
*
586844 GTGCC-AAACGATTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACTTA
1 GTGCCAAAACGGTTATTCATCC-AATAGGATGAATTCCGTGAAATGCACACTTA
* ** *
586897 GTGCCGAAACAGG-TATTCGCCCATATAAGATGAATTCCGTGAAATGCACACTTA
1 GTGCCAAAAC-GGTTATTCATCCA-ATAGGATGAATTCCGTGAAATGCACACTTA
* ** * *
586951 TTATCAAAACGATTATTCATCCAGATAGGATGAATTCCGTGAAATACACACTTA
1 GTGCCAAAACGGTTATTCATCCA-ATAGGATGAATTCCGTGAAATGCACACTTA
587005 GT
1 GT
587007 ACCGAAATTG
Statistics
Matches: 184, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
50 19 0.10
53 48 0.26
54 116 0.63
55 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (53 bp):
GTGCCAAAACGGTTATTCATCCAATAGGATGAATTCCGTGAAATGCACACTTA
Found at i:586886 original size:107 final size:108
Alignment explanation
Indices: 586760--587013 Score: 352
Period size: 107 Copynumber: 2.4 Consensus size: 108
586750 GGTTATTCAT
* *
586760 ATAGGATGAATTCCGTGAAATGCACACTTAGTGCC-AAA-ATGGTTATTCATCCACATAGGATAA
1 ATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACA-GG-TATTCACCCACATAAGATAA
* * *
586823 ATTTCGTGAAATGCACTCTTAGT-GCCAAACGATTATTCATCCAA
64 ATTCCGTGAAATGCACACTTAGTAGCAAAACGATTATTCATCCAA
* * *
586867 ATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGGTATTCGCCCATATAAGATGAAT
1 ATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGGTATTCACCCACATAAGATAAAT
* * *
586932 TCCGTGAAATGCACACTTATTATCAAAACGATTATTCATCCAG
66 TCCGTGAAATGCACACTTAGTAGCAAAACGATTATTCATCCAA
* *
586975 ATAGGATGAATTCCGTGAAATACACACTTAGTACCGAAA
1 ATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
587014 TTGTAACATC
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
107 70 0.53
108 60 0.46
109 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (108 bp):
ATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAGGTATTCACCCACATAAGATAAAT
TCCGTGAAATGCACACTTAGTAGCAAAACGATTATTCATCCAA
Found at i:588849 original size:32 final size:32
Alignment explanation
Indices: 588808--588899 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
588798 AGTCGAGGGT
*
588808 TTACCTATGTTCTATGGAACATATGGACAAAA
1 TTACCTATGTTCTATAGAACATATGGACAAAA
* * * **
588840 TTACCTATG-TCTTTCGAGGCATATGGACAGTA
1 TTACCTATGTTCTATAGA-ACATATGGACAAAA
*
588872 -TACCTATGTTCTAAAGAACATATGGACA
1 TTACCTATGTTCTATAGAACATATGGACA
588900 GTTTACCTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 24 0.49
32 25 0.51
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTATAGAACATATGGACAAAA
Found at i:588894 original size:31 final size:31
Alignment explanation
Indices: 588809--588914 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
588799 GTCGAGGGTT
* **
588809 TACCTATGTTCTATGGAACATATGGACAAAA
1 TACCTATGTTCTATAGAACATATGGACAGTA
* * *
588840 TTACCTATG-TCTTTCGAGGCATATGGACAGTA
1 -TACCTATGTTCTATAGA-ACATATGGACAGTA
* *
588872 TACCTATGTTCTAAAGAACATATGGACAGTT
1 TACCTATGTTCTATAGAACATATGGACAGTA
*
588903 TACCTAGGTTCT
1 TACCTATGTTCT
588915 TCGGGACCTA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
31 37 0.61
32 24 0.39
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTATAGAACATATGGACAGTA
Found at i:588953 original size:30 final size:31
Alignment explanation
Indices: 588892--588958 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
588882 CTAAAGAACA
* *
588892 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAGTTTACCGAGGTTCTTCAGGACC
* * *
588923 TATGGACAG-TTATCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTCAGGACC
588953 TATGGA
1 TATGGA
588959 TAGGTCATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTCAGGACC
Found at i:592607 original size:24 final size:20
Alignment explanation
Indices: 592580--592637 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
592570 GCATGGGTAG
592580 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
592604 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
592624 TGTATCGATGCACT
1 TGCATCGATGCACT
592638 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:595028 original size:20 final size:20
Alignment explanation
Indices: 595003--595057 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
594993 TAGCCCTTCA
595003 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
* *
595023 GTATCGATATTACCCTACTATG
1 GTATCGATA--CCCCTACCATG
595045 GTATCGATACCCC
1 GTATCGATACCCC
595058 CTTACAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:595143 original size:95 final size:96
Alignment explanation
Indices: 595003--595227 Score: 276
Period size: 96 Copynumber: 2.4 Consensus size: 96
594993 TAGCCCTTCA
* *
595003 GTATCGATACCC-CTACCATGGTATCGATATTACCCTACTATGGTATCGATACCCC-CTTAC-AG
1 GTATCGATACCCTC-ACCATGGTATCGATATTACCATACTATGGTATCGATACCCCTCAT-CTAG
* * *
595065 TATTGATACCAAAATTAGCTTCGATGTGGCTTG
64 TATCGATACCAAAATTAGCTTCGATGTGACCTG
* * * *
595098 GTATCAATACCCTCACCATGGTATCGATATTACTATACTATGGTATCGATAGCCCTCATCTGGTA
1 GTATCGATACCCTCACCATGGTATCGATATTACCATACTATGGTATCGATACCCCTCATCTAGTA
* *
595163 TCGATACCAAAATTAGGTTCGATGTTACCTG
66 TCGATACCAAAATTAGCTTCGATGTGACCTG
* * * *
595194 GTATCGATACCCTTATCATAGTATCGATACTACC
1 GTATCGATACCCTCACCATGGTATCGATATTACC
595228 TCATCAGTAC
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
95 50 0.45
96 60 0.55
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (96 bp):
GTATCGATACCCTCACCATGGTATCGATATTACCATACTATGGTATCGATACCCCTCATCTAGTA
TCGATACCAAAATTAGCTTCGATGTGACCTG
Found at i:601797 original size:9 final size:9
Alignment explanation
Indices: 601779--601876 Score: 55
Period size: 9 Copynumber: 11.0 Consensus size: 9
601769 AATATTTGTA
601779 AATATA-AT
1 AATATATAT
601787 AATATATAT
1 AATATATAT
*
601796 AATTTATAT
1 AATATATAT
* *
601805 ATTTTATAT
1 AATATATAT
*
601814 AATAAATATGT
1 AAT--ATATAT
*
601825 AAGATA-AT
1 AATATATAT
601833 AATA-ATAAT
1 AATATAT-AT
601842 AATA-ATAAT
1 AATATAT-AT
*
601851 AACATATAT
1 AATATATAT
601860 AAT-TA-AT
1 AATATATAT
601867 AATACTATAT
1 AATA-TATAT
601877 TATTATAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
7 6 0.08
8 12 0.17
9 43 0.61
10 4 0.06
11 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
AATATATAT
Found at i:601834 original size:3 final size:3
Alignment explanation
Indices: 601828--601870 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
601818 AATATGTAAG
*
601828 ATA ATA ATA ATA ATA ATA ATA ATA A-C ATA TATA ATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA
601871 CTATATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 28 0.80
4 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:602164 original size:20 final size:20
Alignment explanation
Indices: 602139--602176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
602129 AAGCATCATG
602139 CTCGAAAGACTTACAAATGA
1 CTCGAAAGACTTACAAATGA
* *
602159 CTCGAAGGATTTACAAAT
1 CTCGAAAGACTTACAAAT
602177 TCGTGATAAA
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:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (20 bp):
CTCGAAAGACTTACAAATGA
Found at i:615577 original size:16 final size:16
Alignment explanation
Indices: 615556--615589 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
615546 CAAAAGGGGG
*
615556 AGAAGTGTGTGTTTTA
1 AGAAGTGTGTGCTTTA
615572 AGAAGTGTGTGCTTTA
1 AGAAGTGTGTGCTTTA
615588 AG
1 AG
615590 TGTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.38
Consensus pattern (16 bp):
AGAAGTGTGTGCTTTA
Done.