Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001484.1 Hibiscus syriacus cultivar Beakdansim tig00002880_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: 1039362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:563789 original size:3 final size:3
Alignment explanation
Indices: 563775--563884 Score: 94
Period size: 3 Copynumber: 36.7 Consensus size: 3
563765 GAGGCATGCT
* * * * * * *
563775 CAG CAA CAG CAG CAG CAG CAG CAA CAG CAA CAG CAA CAA CAG CAA CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * *
563823 CAG CAA CAG CAG CAA CAG CAG CAG CAG CAG CAG CAA CAA CAA CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
*
563871 CAG CAG CAA CAG CA
1 CAG CAG CAG CAG CA
563885 ACCCCAGCAG
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:563885 original size:6 final size:6
Alignment explanation
Indices: 563775--563886 Score: 104
Period size: 6 Copynumber: 19.2 Consensus size: 6
563765 GAGGCATGCT
* * * * *
563775 CAGCAA CAGCAG CAGCAG CAGCAA CAGCAA CAGCAA CAACAG CAACAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
* * * * *
563823 CAGCAA CAG--- CAGCAA CAGCAG CAGCAG CAGCAG CAACAA CAACAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
*
563868 CAGCAG CAGCAA CAGCAA C
1 CAGCAA CAGCAA CAGCAA C
563887 CCCAGCAGTC
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.03
6 88 0.97
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:569113 original size:29 final size:29
Alignment explanation
Indices: 569081--569146 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
569071 TACCTTTGTT
569081 CTTCCAACAGTTTATATTTTCATCATGCA
1 CTTCCAACAGTTTATATTTTCATCATGCA
*
569110 CTTCCAACAGTTTATATTTTTATCATGCA
1 CTTCCAACAGTTTATATTTTCATCATGCA
569139 CTTCCAAC
1 CTTCCAAC
569147 GAAAGATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (29 bp):
CTTCCAACAGTTTATATTTTCATCATGCA
Found at i:569835 original size:14 final size:14
Alignment explanation
Indices: 569816--569885 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
569806 TTAAATGATA
*
569816 AACGAACATAAATG
1 AACGAACATAAACG
569830 AACGAACATAAACG
1 AACGAACATAAACG
* * *
569844 AAC--AGAT--GCA
1 AACGAACATAAACG
* *
569854 AACGAACACAAATG
1 AACGAACATAAACG
569868 AACGAACATAAACG
1 AACGAACATAAACG
569882 AACG
1 AACG
569886 GATACAAACG
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
10 4 0.10
12 5 0.12
14 32 0.78
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:569845 original size:24 final size:24
Alignment explanation
Indices: 569813--569955 Score: 103
Period size: 24 Copynumber: 5.8 Consensus size: 24
569803 CATTTAAATG
*
569813 ATAAACGAACATAAATGAACGAAC
1 ATAAACGAACATAAACGAACGAAC
*
569837 ATAAACGAACAGATGCAAACGAAC-ACAA
1 ATAAACGAAC--AT--AAACGAACGA-AC
* * *
569865 ATGAACGAACATAAACGAACGGAT
1 ATAAACGAACATAAACGAACGAAC
* * *
569889 ACAAACGAACATAAACGAAAGAAT
1 ATAAACGAACATAAACGAACGAAC
* *
569913 GTAAATGAACATAAACGAAC--AC
1 ATAAACGAACATAAACGAACGAAC
* *
569935 AATAAATGAACATAAATGAAC
1 -ATAAACGAACATAAACGAAC
569956 ATAACAAATG
Statistics
Matches: 96, Mismatches: 16, Indels: 15
0.76 0.13 0.12
Matches are distributed among these distances:
22 1 0.01
23 18 0.19
24 55 0.57
26 4 0.04
27 1 0.01
28 17 0.18
ACGTcount: A:0.57, C:0.17, G:0.14, T:0.12
Consensus pattern (24 bp):
ATAAACGAACATAAACGAACGAAC
Found at i:569867 original size:38 final size:38
Alignment explanation
Indices: 569815--569899 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
569805 TTTAAATGAT
* *
569815 AAACGAACATAAATGAACGAACATAAACGAACAGATGC
1 AAACGAACACAAATGAACGAACATAAACGAACAGATAC
*
569853 AAACGAACACAAATGAACGAACATAAACGAACGGATAC
1 AAACGAACACAAATGAACGAACATAAACGAACAGATAC
569891 AAACGAACA
1 AAACGAACA
569900 TAAACGAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.08
Consensus pattern (38 bp):
AAACGAACACAAATGAACGAACATAAACGAACAGATAC
Found at i:569944 original size:23 final size:23
Alignment explanation
Indices: 569853--570001 Score: 138
Period size: 23 Copynumber: 6.3 Consensus size: 23
569843 GAACAGATGC
* *
569853 AAACGAACACAAATGAACGAACAT
1 AAACGAACAC-AATAAATGAACAT
** * *
569877 AAACGAACGGATACAAACGAACAT
1 AAACGAACACA-ATAAATGAACAT
*
569901 AAACGAA-AGAATGTAAATGAACAT
1 AAACGAACACAA--TAAATGAACAT
569925 AAACGAACACAATAAATGAACAT
1 AAACGAACACAATAAATGAACAT
* * *
569948 AAATGAACATAACAAATGAACAT
1 AAACGAACACAATAAATGAACAT
* * *
569971 AATCGAACACAATAAATGATCGT
1 AAACGAACACAATAAATGAACAT
569994 AAACGAAC
1 AAACGAAC
570002 GTAAACAATA
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.01
23 58 0.56
24 41 0.40
25 3 0.03
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (23 bp):
AAACGAACACAATAAATGAACAT
Found at i:570220 original size:24 final size:24
Alignment explanation
Indices: 570188--570259 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
570178 TGGGCTGAAT
*
570188 ATAAATGAACGAACATATACGAAC
1 ATAAATGAACGAACATAAACGAAC
* *
570212 ATAAATGAACGAACATACACGGAC
1 ATAAATGAACGAACATAAACGAAC
*
570236 ATAAATCAACGAACATAAACGAAC
1 ATAAATGAACGAACATAAACGAAC
570260 GGATTACCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.14
Consensus pattern (24 bp):
ATAAATGAACGAACATAAACGAAC
Found at i:570223 original size:14 final size:14
Alignment explanation
Indices: 570188--570228 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
570178 TGGGCTGAAT
570188 ATAAATGAACGAAC
1 ATAAATGAACGAAC
570202 AT--AT--ACGAAC
1 ATAAATGAACGAAC
570212 ATAAATGAACGAAC
1 ATAAATGAACGAAC
570226 ATA
1 ATA
570229 CACGGACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 8 0.35
12 4 0.17
14 11 0.48
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:570253 original size:14 final size:14
Alignment explanation
Indices: 570206--570254 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
570196 ACGAACATAT
*
570206 ACGAACATAAATGA
1 ACGAACATAAATCA
570220 ACGAACAT--A-C-
1 ACGAACATAAATCA
*
570230 ACGGACATAAATCA
1 ACGAACATAAATCA
570244 ACGAACATAAA
1 ACGAACATAAA
570255 CGAACGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
10 7 0.25
12 2 0.07
13 1 0.04
14 18 0.64
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (14 bp):
ACGAACATAAATCA
Found at i:574292 original size:21 final size:21
Alignment explanation
Indices: 574266--574308 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
574256 TTTTCGGGCT
* *
574266 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
574287 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
574308 A
1 A
574309 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:574362 original size:46 final size:47
Alignment explanation
Indices: 574287--574397 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 47
574277 TACCCATTCA
* * *
574287 AGGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAG
1 AGGGGAATCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
* * *
574333 AGGGGAATCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTG
1 AGGGGAATCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
574380 AGGGGAATCGATACCCCC
1 AGGGGAATCGATACCCCC
574398 AAGGGGGGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 26 0.45
47 32 0.55
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (47 bp):
AGGGGAATCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAG
Found at i:574756 original size:29 final size:29
Alignment explanation
Indices: 574722--574793 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
574712 CATATTATGA
**
574722 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
574751 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
574780 TACATGACATGAAT
1 TACATGACATGAAT
574794 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:575158 original size:23 final size:23
Alignment explanation
Indices: 575092--575150 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
575082 ATCATTATAT
*
575092 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
575114 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
575137 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
575151 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:580984 original size:21 final size:21
Alignment explanation
Indices: 580960--581000 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
580950 TTTCGGGCTA
* *
580960 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
580981 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
581001 CGAATATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:581057 original size:65 final size:67
Alignment explanation
Indices: 580980--581127 Score: 221
Period size: 65 Copynumber: 2.2 Consensus size: 67
580970 ACCCATTCAA
*
580980 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCC-TCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
581043 -GG
65 GGG
* * *
581045 GGGGAACCGATACCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
581110 GG
66 GG
*
581112 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
581128 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
64 10 0.13
65 43 0.57
66 5 0.07
67 17 0.23
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
GG
Found at i:581461 original size:28 final size:29
Alignment explanation
Indices: 581429--581499 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
581419 CATATTATGA
**
581429 TACATGACATGAATTTGTATTA-ATGTAT
1 TACATGACATGAATTCATATTATATGTAT
581457 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
581486 TACATGACATGAAT
1 TACATGACATGAAT
581500 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 20 0.50
29 20 0.50
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:581831 original size:22 final size:22
Alignment explanation
Indices: 581796--581876 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
581786 ACATCATTAT
* *
581796 GGCACTACGATGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
581818 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
581840 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
581863 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
581877 TTTATACGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 41 0.73
23 15 0.27
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:586971 original size:33 final size:33
Alignment explanation
Indices: 586911--587009 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 33
586901 AAATATGAAA
* * *
586911 AATAAGTTAGTCACCTACCAAG--GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
586942 AATGAGTTGGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
586975 AATAAGTTGGCCACCAACCAAGATGAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
587008 AA
1 AA
587010 CTTGCCAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.30
33 42 0.70
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:588837 original size:62 final size:62
Alignment explanation
Indices: 588740--588870 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 62
588730 TTTCATCGCC
*
588740 TAGAAACCACTACTGGTAAAAAGACAAAAATTAAAATTAGTTGAAAGAATTCCAAACCTATT
1 TAGAAACCACTACTGGTAAAAAGACAAAAATTAAAATTAGTTGAAAGAATTCCAAACATATT
*
588802 TAGAAACCACTGCTGGTAAAAAGACAAAAATTAAAATTAGTTGAAAGAATTCCAAACATATT
1 TAGAAACCACTACTGGTAAAAAGACAAAAATTAAAATTAGTTGAAAGAATTCCAAACATATT
588864 TAGAAAC
1 TAGAAAC
588871 AAACACAATA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (62 bp):
TAGAAACCACTACTGGTAAAAAGACAAAAATTAAAATTAGTTGAAAGAATTCCAAACATATT
Found at i:589756 original size:178 final size:178
Alignment explanation
Indices: 589457--589813 Score: 714
Period size: 178 Copynumber: 2.0 Consensus size: 178
589447 GAGAATAAAT
589457 CGAACATCACACCATCACTATCCCTTAACAAGCCGCCAATGCCTCCTCTTAACCACCTATTTACC
1 CGAACATCACACCATCACTATCCCTTAACAAGCCGCCAATGCCTCCTCTTAACCACCTATTTACC
589522 ATAGCACCGTCCACATTTAGTTTGAAAAAGCCCAAAAGAGGAAGACACCAACGCTCCAAGGAAGA
66 ATAGCACCGTCCACATTTAGTTTGAAAAAGCCCAAAAGAGGAAGACACCAACGCTCCAAGGAAGA
589587 ACTGCCATTCTTAGTACTCACGGCAAAATCTGCTACTTTTGGATCACC
131 ACTGCCATTCTTAGTACTCACGGCAAAATCTGCTACTTTTGGATCACC
589635 CGAACATCACACCATCACTATCCCTTAACAAGCCGCCAATGCCTCCTCTTAACCACCTATTTACC
1 CGAACATCACACCATCACTATCCCTTAACAAGCCGCCAATGCCTCCTCTTAACCACCTATTTACC
589700 ATAGCACCGTCCACATTTAGTTTGAAAAAGCCCAAAAGAGGAAGACACCAACGCTCCAAGGAAGA
66 ATAGCACCGTCCACATTTAGTTTGAAAAAGCCCAAAAGAGGAAGACACCAACGCTCCAAGGAAGA
589765 ACTGCCATTCTTAGTACTCACGGCAAAATCTGCTACTTTTGGATCACC
131 ACTGCCATTCTTAGTACTCACGGCAAAATCTGCTACTTTTGGATCACC
589813 C
1 C
589814 ACAAGAGAAT
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 179 1.00
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.22
Consensus pattern (178 bp):
CGAACATCACACCATCACTATCCCTTAACAAGCCGCCAATGCCTCCTCTTAACCACCTATTTACC
ATAGCACCGTCCACATTTAGTTTGAAAAAGCCCAAAAGAGGAAGACACCAACGCTCCAAGGAAGA
ACTGCCATTCTTAGTACTCACGGCAAAATCTGCTACTTTTGGATCACC
Found at i:592037 original size:29 final size:29
Alignment explanation
Indices: 591995--592054 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
591985 CCGAAGTACA
591995 GATAAAACATTGTGACCTCTTCTTTTCTG
1 GATAAAACATTGTGACCTCTTCTTTTCTG
*
592024 GATAGAACATTGTGACCTCTTCTTTTCTG
1 GATAAAACATTGTGACCTCTTCTTTTCTG
592053 GA
1 GA
592055 AACTAAGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (29 bp):
GATAAAACATTGTGACCTCTTCTTTTCTG
Found at i:597887 original size:21 final size:21
Alignment explanation
Indices: 597861--597903 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
597851 CCGTTAGACA
* *
597861 GGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCTATACCCCCTG
597882 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTATACCCCCTG
597903 G
1 G
597904 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCTATACCCCCTG
Found at i:599349 original size:20 final size:20
Alignment explanation
Indices: 599324--599374 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
599314 TCTACATTAT
*
599324 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATCTCATTTTGA
599344 TTTTCAAAATCTCATTTTGA
1 TTTTCAAAATCTCATTTTGA
599364 TTTTCAAAATC
1 TTTTCAAAATC
599375 AACTTTTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGA
Found at i:599381 original size:20 final size:21
Alignment explanation
Indices: 599336--599395 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
599326 TTCAAAATTT
*
599336 CATTTTGATTTTCAAAATC-T
1 CATTTTGATTTTCAAAATCAA
599356 CATTTTGATTTTCAAAATCAA
1 CATTTTGATTTTCAAAATCAA
*
599377 C-TTTTG-CTTTCAAAATCAA
1 CATTTTGATTTTCAAAATCAA
599396 ATTATCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 12 0.32
20 24 0.65
21 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (21 bp):
CATTTTGATTTTCAAAATCAA
Found at i:601006 original size:21 final size:21
Alignment explanation
Indices: 600981--601022 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
600971 CGTTAGACAA
600981 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
601002 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
601023 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:607203 original size:21 final size:21
Alignment explanation
Indices: 607177--607216 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
607167 CAGAACCCCA
*
607177 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
607198 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
607217 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:607251 original size:20 final size:21
Alignment explanation
Indices: 607197--607259 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
607187 GATTCCCCTG
607197 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
607221 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
607241 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
607260 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:611108 original size:22 final size:21
Alignment explanation
Indices: 611066--611105 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
611056 GAGTTTGTTT
*
611066 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
611087 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
611106 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:614494 original size:24 final size:24
Alignment explanation
Indices: 614463--614521 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
614453 CGAAACTGAT
* *
614463 ACGTAGAATTTGCACCGAAGTGCC
1 ACGTAGAATTTGCAACAAAGTGCC
*
614487 ACGTAGAATATGCAACAAAGTGCC
1 ACGTAGAATTTGCAACAAAGTGCC
*
614511 ACATAG-ATTTG
1 ACGTAGAATTTG
614522 TCCTGAAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
ACGTAGAATTTGCAACAAAGTGCC
Found at i:614563 original size:23 final size:23
Alignment explanation
Indices: 614509--614566 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
614499 CAACAAAGTG
* *
614509 CCACATAGATTTGTCCTGAAGGA
1 CCACATAGAATTGTCCTGAAGAA
***
614532 CCTTGTAGAATTGTCCTGAAGAA
1 CCACATAGAATTGTCCTGAAGAA
614555 CCACATAGAATT
1 CCACATAGAATT
614567 ATCCCGAATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (23 bp):
CCACATAGAATTGTCCTGAAGAA
Found at i:615970 original size:23 final size:23
Alignment explanation
Indices: 615936--615996 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
615926 CTCATATAAA
*
615936 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
615959 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
615982 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
615997 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:617703 original size:21 final size:21
Alignment explanation
Indices: 617673--617717 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
617663 TTTTATTCGT
* *
617673 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
617694 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
617715 TTG
1 TTG
617718 CCTATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:629888 original size:2 final size:2
Alignment explanation
Indices: 629881--629925 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
629871 ATTAAAAGAA
629881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
629923 AT A
1 AT A
629926 AGCTTAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:633356 original size:2 final size:2
Alignment explanation
Indices: 633349--633387 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
633339 GTATTCATTA
633349 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
633388 CGATCATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:635230 original size:6 final size:6
Alignment explanation
Indices: 635074--635216 Score: 272
Period size: 6 Copynumber: 24.2 Consensus size: 6
635064 TGATTGGATG
635074 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
635122 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
635170 TATTTA TATTTA TATTTA TA-TTA TATTTA TATTTA TATTTA T-TTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
635216 T
1 T
635217 TTATGTTTAT
Statistics
Matches: 136, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.07
6 126 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:636240 original size:29 final size:29
Alignment explanation
Indices: 636153--636254 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
636143 TTTCATTTAA
*
636153 GTACCTAAAGTATTTTTTGATCAAAATAA
1 GTACCTAAAGTATTTTTTGATCAAAATAG
* *
636182 GTA-CTCAAAGTTATCTTTTGATCAATATAG
1 GTACCT-AAAG-TATTTTTTGATCAAAATAG
* *
636212 GTACTTAAAGTATTTTTTGGTCAAAATAG
1 GTACCTAAAGTATTTTTTGATCAAAATAG
*
636241 ATACCTAAAGTATT
1 GTACCTAAAGTATT
636255 CAATTTATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.03
29 35 0.57
30 23 0.38
31 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
GTACCTAAAGTATTTTTTGATCAAAATAG
Found at i:636274 original size:23 final size:23
Alignment explanation
Indices: 636247--636299 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
636237 ATAGATACCT
**
636247 AAAGTATTCAATTTATTTTCATTC
1 AAAGTATTCAAAGT-TTTTCATTC
*
636271 -AAGTATTTAAAGTTTTTCATTC
1 AAAGTATTCAAAGTTTTTCATTC
636293 AAAGTAT
1 AAAGTAT
636300 CTAAAGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (23 bp):
AAAGTATTCAAAGTTTTTCATTC
Found at i:636290 original size:22 final size:23
Alignment explanation
Indices: 636262--636306 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
636252 ATTCAATTTA
*
636262 TTTTCATTC-AAGTATTTAAAGT
1 TTTTCATTCAAAGTATCTAAAGT
636284 TTTTCATTCAAAGTATCTAAAGT
1 TTTTCATTCAAAGTATCTAAAGT
636307 ATTATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTTCATTCAAAGTATCTAAAGT
Found at i:636668 original size:19 final size:19
Alignment explanation
Indices: 636632--636670 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
636622 GGATGGTGAG
* *
636632 TATCTGATTGGGTGGTGGA
1 TATCTAATTGGGTAGTGGA
*
636651 TATCTAATTGGTTAGTGGA
1 TATCTAATTGGGTAGTGGA
636670 T
1 T
636671 GTGAAGTGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (19 bp):
TATCTAATTGGGTAGTGGA
Found at i:637305 original size:21 final size:21
Alignment explanation
Indices: 637279--637526 Score: 392
Period size: 21 Copynumber: 11.9 Consensus size: 21
637269 CGCAACACAG
*
637279 TCTCCAAAATCGCAACGCAGT
1 TCTCCAAAATCGCAACGCGGT
637300 TCTCCAAAATCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
637321 TCTCCAAAATCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637342 TCT-CAAATTCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637362 TCTCAAAAATCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637383 TCTCCAAAATCGCAACGCGAT
1 TCTCCAAAATCGCAACGCGGT
*
637404 TCTCCAAATTCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
637425 TCTCCAAAATCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637446 TCT-CAAATTCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637466 TCTCCAAAATCGCAACGCGAT
1 TCTCCAAAATCGCAACGCGGT
* *
637487 TCTCTAAATTCGCAACGCGGT
1 TCTCCAAAATCGCAACGCGGT
*
637508 TCTCCAAAATCACAACGCG
1 TCTCCAAAATCGCAACGCG
637527 TTGCGAAAAT
Statistics
Matches: 207, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
20 38 0.18
21 169 0.82
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.21
Consensus pattern (21 bp):
TCTCCAAAATCGCAACGCGGT
Found at i:637389 original size:83 final size:83
Alignment explanation
Indices: 637283--637526 Score: 409
Period size: 83 Copynumber: 2.9 Consensus size: 83
637273 ACACAGTCTC
* * *
637283 CAAAATCGCAACGCAGTTCTCCAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGGTTCT-CA
1 CAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCCA
*
637347 AATTCGCAACGCGGTTCT
66 AAATCGCAACGCGGTTCT
637365 CAAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCC
1 C-AAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCC
637430 AAAATCGCAACGCGGTTCT
65 AAAATCGCAACGCGGTTCT
* *
637449 CAAATTCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCTAAATTCGCAACGCGGTTCTCCA
1 CAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCCA
*
637514 AAATCACAACGCG
66 AAATCGCAACGCG
637527 TTGCGAAAAT
Statistics
Matches: 153, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
82 1 0.01
83 132 0.86
84 20 0.13
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (83 bp):
CAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCCA
AAATCGCAACGCGGTTCT
Found at i:637421 original size:104 final size:104
Alignment explanation
Indices: 637279--637526 Score: 417
Period size: 104 Copynumber: 2.4 Consensus size: 104
637269 CGCAACACAG
637279 TCTCCAAAATCGCAACGC-AGTTCTCCAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGGTT
1 TCTCCAAAATCGCAACGCGA-TTCTCCAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGGTT
*
637343 CTCAAATTCGCAACGCGGTTCTCAAAAATCGCAACGCGGT
65 CTCAAATTCGCAACGCGGTTCTCAAAAATCGCAACGCGAT
*
637383 TCTCCAAAATCGCAACGCGATTCTCCAAATTCGCAACGCGGTTCTCCAAAATCGCAACGCGGTTC
1 TCTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGGTTC
*
637448 TCAAATTCGCAACGCGGTTCTCCAAAATCGCAACGCGAT
66 TCAAATTCGCAACGCGGTTCTCAAAAATCGCAACGCGAT
* * * *
637487 TCTCTAAATTCGCAACGCGGTTCTCCAAAATCACAACGCG
1 TCTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCG
637527 TTGCGAAAAT
Statistics
Matches: 135, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
104 134 0.99
105 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.21
Consensus pattern (104 bp):
TCTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCGGTTCTCCAAAATCGCAACGCGGTTC
TCAAATTCGCAACGCGGTTCTCAAAAATCGCAACGCGAT
Found at i:638051 original size:61 final size:61
Alignment explanation
Indices: 637956--638072 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
637946 TATGAAATAG
* *
637956 ATGAATTTCTGTGTCTACAAACAATACCCAATTCTCTTCT-TTAAAAATGTAATTAGAACAT
1 ATGAACTTCTGTGCCTACAAACAATACCCAATTCTCTT-TATTAAAAATGTAATTAGAACAT
638017 ATGAACTTCTGTGCCTACAAACAATACCCAATTCTCTTTATTAAAAATGTAATTAG
1 ATGAACTTCTGTGCCTACAAACAATACCCAATTCTCTTTATTAAAAATGTAATTAG
638073 GATAGAATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 1 0.02
61 52 0.98
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (61 bp):
ATGAACTTCTGTGCCTACAAACAATACCCAATTCTCTTTATTAAAAATGTAATTAGAACAT
Found at i:640759 original size:43 final size:45
Alignment explanation
Indices: 640730--640813 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
640720 TGCGAGGATG
640730 ATAATAATT-T-TTATTTTTAAAGAGTTAATTGTATTACACGTGT
1 ATAATAATTGTATTATTTTTAAAGAGTTAATTGTATTACACGTGT
* * *
640773 CTATTAATTGTATTATTTTTAAAGAGTTAATTATATTACAC
1 ATAATAATTGTATTATTTTTAAAGAGTTAATTGTATTACAC
640814 ATTTATGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 7 0.19
44 1 0.03
45 28 0.78
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (45 bp):
ATAATAATTGTATTATTTTTAAAGAGTTAATTGTATTACACGTGT
Found at i:641044 original size:3 final size:3
Alignment explanation
Indices: 641036--641060 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
641026 GGATTACATT
641036 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
641061 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:646975 original size:2 final size:2
Alignment explanation
Indices: 646968--646996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
646958 TATTTATCCT
646968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
646997 TTCTCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:648268 original size:17 final size:15
Alignment explanation
Indices: 648246--648279 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
648236 CCTTACTAAC
648246 TCTTTTCATTTATATTT
1 TCTTTT-ATTT-TATTT
648263 TCTTTTATTTTATTT
1 TCTTTTATTTTATTT
648278 TC
1 TC
648280 ATTATTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTATTTTATTT
Found at i:649870 original size:14 final size:14
Alignment explanation
Indices: 649853--649885 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
649843 CTGGAAGAAG
649853 AATTCATATGAAAT
1 AATTCATATGAAAT
649867 AATTCATATGAAAT
1 AATTCATATGAAAT
649881 AATTC
1 AATTC
649886 TATCTTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (14 bp):
AATTCATATGAAAT
Found at i:650233 original size:15 final size:16
Alignment explanation
Indices: 650208--650269 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 16
650198 AGATTCAATC
650208 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
650223 AAGAAGCAAAAAAGAAAA
1 AAGAAGCAAAAAAG--AA
*
650241 AACAAGAACAAAAAAGAA
1 AAGAAG--CAAAAAAGAA
650259 AAGAAGCAAAA
1 AAGAAGCAAAA
650270 TCAAAAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.12
16 13 0.32
18 14 0.35
20 8 0.20
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:650240 original size:21 final size:21
Alignment explanation
Indices: 650216--650263 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
650206 TCAAGAACAA
650216 AAAAGAA-AAGAAGCAAAAAAG
1 AAAAGAACAAGAA-CAAAAAAG
650237 AAAA-AACAAGAACAAAAAAG
1 AAAAGAACAAGAACAAAAAAG
650257 AAAAGAA
1 AAAAGAA
650264 GCAAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAGAACAAGAACAAAAAAG
Found at i:651842 original size:34 final size:34
Alignment explanation
Indices: 651757--651835 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
651747 AAGTTGGATT
651757 TCAACTTCACGACGAAGGATATCCAATTCCTGGC
1 TCAACTTCACGACGAAGGATATCCAATTCCTGGC
651791 TCAACTTCACGACGAAGGATATCCAATTCCTGGC
1 TCAACTTCACGACGAAGGATATCCAATTCCTGGC
651825 TCAACTTCACG
1 TCAACTTCACG
651836 GTGAAGGGGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCAATTCCTGGC
Found at i:651937 original size:36 final size:36
Alignment explanation
Indices: 651890--651996 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
651880 GTGCTCATCA
** *
651890 TTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
651926 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
651962 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAC
651997 CTTTAAAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:653393 original size:106 final size:106
Alignment explanation
Indices: 653243--653516 Score: 401
Period size: 106 Copynumber: 2.6 Consensus size: 106
653233 AAGGAGTGTC
* * *
653243 TGTCAACAAA-C-TTT-CCAGTTTTAGAGTCAATTTCTACTTCACAGCGAAGGATATTGGACTCG
1 TGTCAACAAACCATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
653305 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
66 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
* *
653346 TGTCAACAAACCATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCG
1 TGTCAACAAACCATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
* * *
653411 AGACAACACAAGTTTAACTTTACAACGAAGGGACGGCTGGT
66 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
* * * * * *
653452 TGTCAACAAACAATTTCCCAGTTCCATAACCAATTTCAACTTCACGGCGGAGGATATTGGACTCG
1 TGTCAACAAACCATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
653517 GAAGGGGTCA
Statistics
Matches: 152, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
103 10 0.07
104 1 0.01
105 3 0.02
106 138 0.91
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (106 bp):
TGTCAACAAACCATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
Found at i:653639 original size:394 final size:393
Alignment explanation
Indices: 652912--653698 Score: 1360
Period size: 394 Copynumber: 2.0 Consensus size: 393
652902 GCGCCATTTA
652912 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTCCCAATTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTCCCAATTTC
*
652977 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATACAAGTTCAACTTCACAA
66 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* *
653042 CGAAGGGACGGTTGGTTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGCG
131 CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGCG
* * *
653107 GAGGATATTGGACTCGGAAGGGGTCACCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCATA
196 GAGGATATTGGACTCGGAAGGGGTCACCCACGGTTTCAACTTCACGAAGAAGAGAATCGTGCACA
* * * * *
653172 CAAGCAGCATCCATCTTTAGATTGGATTTCAACTTCACGGCGAAGGATATTCAACTCAAAGAAGG
261 CAAGCAACATCCATCTTTAGAGTGGATTTCAACTACACGACGAAGGATATTCAAATCAAAGAAGG
* *
653237 AGTGTCTGTCAACAAACTTTCCAGTTTTAGAGTCAATTTCTACTTCACAGCGAAGGATATTGGAC
326 AGTGTCTGTCAACAAACTTTCCAGTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
653302 TCG
391 TCG
653305 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCA-TTCCCAATTT
* * *
653370 CAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTTAACTTTACA
65 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
*
653435 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCATAACCAATTTCAACTTCACGGC
130 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGC
*
653500 GGAGGATATTGGACTCGGAAGGGGTCACCCGCGGTTTCAACTTCACGAAGAAGAGAATCGTGCAC
195 GGAGGATATTGGACTCGGAAGGGGTCACCCACGGTTTCAACTTCACGAAGAAGAGAATCGTGCAC
*
653565 ACAAGCAACA-CCTATCTTTAGAGTGGATTTCAACTACACGACGAAGGATATTCAAATCAAATAA
260 ACAAGCAACATCC-ATCTTTAGAGTGGATTTCAACTACACGACGAAGGATATTCAAATCAAAGAA
*
653629 GGAGTGTCTGTCAACACACTTTCCAGTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
324 GGAGTGTCTGTCAACAAACTTTCCAGTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
*
653694 CCTCG
389 ACTCG
653699 TAACAACGCA
Statistics
Matches: 371, Mismatches: 21, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
393 56 0.15
394 315 0.85
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (393 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTCCCAATTTC
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGCG
GAGGATATTGGACTCGGAAGGGGTCACCCACGGTTTCAACTTCACGAAGAAGAGAATCGTGCACA
CAAGCAACATCCATCTTTAGAGTGGATTTCAACTACACGACGAAGGATATTCAAATCAAAGAAGG
AGTGTCTGTCAACAAACTTTCCAGTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
TCG
Found at i:655244 original size:2 final size:2
Alignment explanation
Indices: 655237--655265 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
655227 TATTTATCCT
655237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
655266 TTCTCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:655307 original size:8 final size:8
Alignment explanation
Indices: 655290--655336 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
655280 TTTATCTTAT
*
655290 TTTATTTA
1 TTTATATA
*
655298 TTTATGTA
1 TTTATATA
655306 TTTATATA
1 TTTATATA
*
655314 TATATATA
1 TTTATATA
*
655322 TATATATA
1 TTTATATA
655330 TTTATAT
1 TTTATAT
655337 TTCTTTCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:655309 original size:12 final size:12
Alignment explanation
Indices: 655292--655336 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
655282 TATCTTATTT
* *
655292 TATTTATTTATG
1 TATTTATATATA
655304 TATTTATATATA
1 TATTTATATATA
*
655316 TATATATATATA
1 TATTTATATATA
655328 TATTTATAT
1 TATTTATAT
655337 TTCTTTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TATTTATATATA
Found at i:655329 original size:65 final size:67
Alignment explanation
Indices: 655165--655334 Score: 197
Period size: 69 Copynumber: 2.5 Consensus size: 67
655155 ATATTTTTCC
* * * * *
655165 TTATTTATTTTTATATATATATATAT-TGT-TTTATTCATCATTTATTTTACTTTTATTTTCTTT
1 TTATTTATTTATATATATATATATATATATATTTATTCATCATTGATTTTACTCTTATTTTATTT
655228 AT
66 AT
*
655230 TTATCCTTATATATATATATATATATATATATATATTTCTCTC-TC-TTGATTTTA-TCTTATTT
1 TTAT--TTAT-T-TATATATATATATATATATATATTTAT-TCATCATTGATTTTACTCTTATTT
655292 TATTTAT
61 TATTTAT
*
655299 TTATGTATTTATATATATATATATATATATATTTAT
1 TTATTTATTTATATATATATATATATATATATTTAT
655335 ATTTCTTTCA
Statistics
Matches: 90, Mismatches: 8, Indels: 14
0.80 0.07 0.12
Matches are distributed among these distances:
65 30 0.33
66 1 0.01
67 7 0.08
68 1 0.01
69 33 0.37
70 10 0.11
71 6 0.07
72 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (67 bp):
TTATTTATTTATATATATATATATATATATATTTATTCATCATTGATTTTACTCTTATTTTATTT
AT
Found at i:655361 original size:71 final size:71
Alignment explanation
Indices: 655236--655369 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 71
655226 TTATTTATCC
* * *** *
655236 TTATATATATATATATATATATATATATATTTCTCTCTCTTGATTTTATCTTATTTTATTTATTT
1 TTATATATATATATATATATATATATATATTTCTCTCACTTCACCATATCTTATTTTAATTATTT
655301 ATGTAT
66 ATGTAT
* * *
655307 TTATATATATATATATATATATATTTATATTTCTTTCACTTTCCCCATAT-TTATTTTAATTAT
1 TTATATATATATATATATATATATATATATTTCTCTCAC-TTCACCATATCTTATTTTAATTAT
655370 GCAATTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 48 0.91
72 5 0.09
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (71 bp):
TTATATATATATATATATATATATATATATTTCTCTCACTTCACCATATCTTATTTTAATTATTT
ATGTAT
Found at i:657902 original size:19 final size:19
Alignment explanation
Indices: 657874--657910 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
657864 TCGAATGCAA
*
657874 AAAGGGTATCGATACCATG
1 AAAGGATATCGATACCATG
657893 AAAGGATATCGATACCAT
1 AAAGGATATCGATACCAT
657911 AGTGCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (19 bp):
AAAGGATATCGATACCATG
Found at i:658200 original size:33 final size:33
Alignment explanation
Indices: 658163--658227 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
658153 GTAAATATTT
658163 TGGTTCTAGCTTAG-CC-TGCTAAAAGCTAGGGAA
1 TGGTTCTAGCTTAGCCCGTG-TAAAA-CTAGGGAA
*
658196 TGGTTCTAGTTTAGCCCGTGTAAAACTAGGGA
1 TGGTTCTAGCTTAGCCCGTGTAAAACTAGGGA
658228 GTTTGTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 20 0.69
34 7 0.24
35 2 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (33 bp):
TGGTTCTAGCTTAGCCCGTGTAAAACTAGGGAA
Found at i:659766 original size:19 final size:20
Alignment explanation
Indices: 659742--659779 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
659732 TAAAGATAAA
659742 TCGATTTTGAAAAT-AAAAG
1 TCGATTTTGAAAATCAAAAG
659761 TCGATTTTGAAAATCAAAA
1 TCGATTTTGAAAATCAAAA
659780 TGAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (20 bp):
TCGATTTTGAAAATCAAAAG
Found at i:660907 original size:21 final size:21
Alignment explanation
Indices: 660883--660924 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
660873 AACATTTTCA
* *
660883 TATTTTTTCAACAATTGGTAT
1 TATTTTGTCAACAATCGGTAT
660904 TATTTTGTCAACAATCGGTAT
1 TATTTTGTCAACAATCGGTAT
660925 CTTTTTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (21 bp):
TATTTTGTCAACAATCGGTAT
Found at i:660930 original size:21 final size:19
Alignment explanation
Indices: 660885--660932 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
660875 CATTTTCATA
*
660885 TTTTTTCAACAATTGGTAT
1 TTTTTTCAACAATCGGTAT
660904 TATTTTGTCAACAATCGGTAT
1 T-TTTT-TCAACAATCGGTAT
*
660925 CTTTTTCA
1 TTTTTTCA
660933 TTAAACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTTTTCAACAATCGGTAT
Found at i:661202 original size:19 final size:20
Alignment explanation
Indices: 661146--661202 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
661136 AATACTAAGA
* *
661146 AGTACCGATACCGCTTCATGT
1 AGTATCGATACC-CATCATGT
661167 AGTATCGATACCCATCATGT
1 AGTATCGATACCCATCATGT
661187 AGTATCGATA-CCATCA
1 AGTATCGATACCCATCA
661203 AGGTAGTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.18
20 17 0.50
21 11 0.32
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCCATCATGT
Found at i:661208 original size:20 final size:20
Alignment explanation
Indices: 661146--661210 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
661136 AATACTAAGA
* * *
661146 AGTACCGATACCGCTTCATGT
1 AGTATCGATACC-CATCAGGT
*
661167 AGTATCGATACCCATCATGT
1 AGTATCGATACCCATCAGGT
661187 AGTATCGATA-CCATCAAGGT
1 AGTATCGATACCCATC-AGGT
661207 AGTA
1 AGTA
661211 CCAATACTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 5 0.12
20 24 0.60
21 11 0.28
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCCATCAGGT
Found at i:674831 original size:14 final size:15
Alignment explanation
Indices: 674812--674844 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
674802 AACCACTCCT
674812 TTGTCTTCTTCAT-C
1 TTGTCTTCTTCATCC
*
674826 TTGTCTTTTTCATCC
1 TTGTCTTCTTCATCC
674841 TTGT
1 TTGT
674845 AAGAAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.06, C:0.24, G:0.09, T:0.61
Consensus pattern (15 bp):
TTGTCTTCTTCATCC
Found at i:679055 original size:15 final size:15
Alignment explanation
Indices: 679037--679085 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
679027 CCCGTTTTGA
* *
679037 ATCCATACGTTTCGC
1 ATCCATACGTTCCAC
679052 ATCCATACGTTCCAC
1 ATCCATACGTTCCAC
* *
679067 ATCCATATGTCCCAC
1 ATCCATACGTTCCAC
679082 ATCC
1 ATCC
679086 GTCCACCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.24, C:0.39, G:0.08, T:0.29
Consensus pattern (15 bp):
ATCCATACGTTCCAC
Found at i:680944 original size:16 final size:15
Alignment explanation
Indices: 680925--680974 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
680915 TATAAGGTAA
680925 TTTTTTTATAATATAT
1 TTTTTTTATAAT-TAT
*
680941 TTTTTATTATACTTAT
1 TTTTT-TTATAATTAT
*
680957 TGTTTTTTATGATTAT
1 T-TTTTTTATAATTAT
680973 TT
1 TT
680975 GAAAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.03
16 18 0.62
17 10 0.34
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTTTTTATAATTAT
Found at i:684459 original size:34 final size:33
Alignment explanation
Indices: 684421--684504 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
684411 GTAATAAACA
*
684421 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAACC-AAATAAATTAA-AATAAA-TCCAACC
684455 AAATTTAACCAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACCAAATAAATTAAAATAAATCCAACC
**
684489 AAATTAATGAAATAAA
1 AAATTAACCAAATAAA
684505 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 18 0.41
34 20 0.45
35 6 0.14
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACCAAATAAATTAAAATAAATCCAACC
Found at i:684504 original size:33 final size:34
Alignment explanation
Indices: 684417--684493 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
684407 AATGGTAATA
* *
684417 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAACC-AAATAAATTAACAAAAAGTCC
684452 AACAAATTTAACCAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACCAAATAAATTAACAA-AAAGTCC
684485 AACCAAATT
1 AA-CAAATT
684494 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 19 0.50
35 12 0.32
ACGTcount: A:0.60, C:0.18, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACCAAATAAATTAACAAAAAGTCC
Found at i:690441 original size:16 final size:16
Alignment explanation
Indices: 690420--690462 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
690410 GGTTTTTTAT
*
690420 ATTTTTTAAAAATAGA
1 ATTTTTTAAAAATAAA
*
690436 ATTTTTTCAAAAGTAAA
1 ATTTTTT-AAAAATAAA
690453 ATATTTTTAA
1 AT-TTTTTAA
690463 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (16 bp):
ATTTTTTAAAAATAAA
Found at i:705724 original size:20 final size:20
Alignment explanation
Indices: 705669--705990 Score: 404
Period size: 20 Copynumber: 16.2 Consensus size: 20
705659 CAATTCGCAT
705669 GCAACGCGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705689 GCAA-GTGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
**
705708 GCAACGCGTATGGGTAAATC
1 GCAACGCGTATCCGTAAATC
* *
705728 GCAATGCGTATCCGTATATC
1 GCAACGCGTATCCGTAAATC
705748 GCAACGCGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705768 GCAACGCGTATCCGTAAACC
1 GCAACGCGTATCCGTAAATC
*
705788 GCAACGTGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
705808 GCAACGCGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705828 GCAATGCGTATCCGTAAATC
1 GCAACGCGTATCCGTAAATC
705848 GCAACGCGTAT-CGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705867 GCAACG-ATAATCCGTAAATC
1 GCAACGCGT-ATCCGTAAATC
*
705887 GCAACGCG-ATCCGTTAATC
1 GCAACGCGTATCCGTAAATC
*
705906 GCAACG-ATAATCCGTAAATC
1 GCAACGCGT-ATCCGTAAATC
* * *
705926 GCAACGAGAATCTGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705946 GCAACG-ATAATCCGTAAATC
1 GCAACGCGT-ATCCGTAAATC
* * *
705966 GCAACGAGAATCTGTAAATC
1 GCAACGCGTATCCGTAAATC
*
705986 ACAAC
1 GCAAC
705991 ACTGAAATTT
Statistics
Matches: 262, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.00
19 50 0.19
20 211 0.81
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
GCAACGCGTATCCGTAAATC
Found at i:706950 original size:2 final size:2
Alignment explanation
Indices: 706943--706986 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
706933 TTTCATTATG
*
706943 AT AT AT AT -T CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
706984 AT A
1 AT A
706987 ATTGCTTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:707328 original size:165 final size:166
Alignment explanation
Indices: 707056--707386 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
707046 CTACAACCAC
707056 ACGATGTTGATTTACCAAATTACAGGAAAGTTTCCACCATCCGAGTTCATCGATGGATATCGGGT
1 ACGATGTTGATTTACCAAATTACAGGAAAGTTTCCACCATCCGAGTTCATCGATGGATATCGGGT
707121 ATGGATGACATGGTTGGAGTTCAAATTACAAGTGACGGTTGATTCTATTGAGAACGAGGTTATTT
66 ATGGATGACATGGTTGGAGTTCAAATTACAAGTGACGGTTGATTCTATTGAGAACGAGGTTATTT
707186 TTACGTCCCGAGCATATCTTCTTTAA-TGAACGGAG
131 TTACGTCCCGAGCATATCTTCTTTAATTGAACGGAG
707221 ACGATGTTGATTTACCAAATTACAGGAAAGTTTCCACCATCCGAGTTCATCGATGGATATCGGGT
1 ACGATGTTGATTTACCAAATTACAGGAAAGTTTCCACCATCCGAGTTCATCGATGGATATCGGGT
707286 ATGGATGACATGGTTGGAGTTCAAATTACAAGTGACGGTTGATTCTATTGAGAACGAGGTTATTT
66 ATGGATGACATGGTTGGAGTTCAAATTACAAGTGACGGTTGATTCTATTGAGAACGAGGTTATTT
707351 TTACGTCCCGAGCATATCTTCTTTAATTGAACGGAG
131 TTACGTCCCGAGCATATCTTCTTTAATTGAACGGAG
707387 GAGTATTATT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 156 0.95
166 9 0.05
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (166 bp):
ACGATGTTGATTTACCAAATTACAGGAAAGTTTCCACCATCCGAGTTCATCGATGGATATCGGGT
ATGGATGACATGGTTGGAGTTCAAATTACAAGTGACGGTTGATTCTATTGAGAACGAGGTTATTT
TTACGTCCCGAGCATATCTTCTTTAATTGAACGGAG
Found at i:710562 original size:21 final size:21
Alignment explanation
Indices: 710532--710585 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
710522 GAGTTTACTA
*
710532 TTTTTATATTTT-AAAATTAAT
1 TTTTTTTATTTTCAAAATT-AT
*
710553 TTTTTTTATTTTCACAATTAT
1 TTTTTTTATTTTCAAAATTAT
710574 TTTTGTTT-TTTT
1 TTTT-TTTATTTT
710586 GTGACTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTTATTTTCAAAATTAT
Found at i:716562 original size:28 final size:27
Alignment explanation
Indices: 716521--716575 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
716511 TCAAGGGGAC
*
716521 GAGTTTCACGTAATATTATTTTTTAATG
1 GAGTTTCACATAATATTA-TTTTTAATG
716549 GAGTTTCACATAATATTATTTTTAATG
1 GAGTTTCACATAATATTATTTTTAATG
716576 AACCCGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (27 bp):
GAGTTTCACATAATATTATTTTTAATG
Found at i:717280 original size:3 final size:3
Alignment explanation
Indices: 717274--717330 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
717264 TCATTTCATT
717274 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
717320 TTA TTA TTA TT
1 TTA TTA TTA TT
717331 TAACAAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:718065 original size:12 final size:12
Alignment explanation
Indices: 718047--718079 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
718037 TGGTCGACGG
718047 TGAATAGTGATCA
1 TGAATAGTGA-CA
718060 -GAATAGTGACA
1 TGAATAGTGACA
718071 TGAATAGTG
1 TGAATAGTG
718080 TCCGACGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 17 0.89
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (12 bp):
TGAATAGTGACA
Found at i:718635 original size:27 final size:28
Alignment explanation
Indices: 718605--718664 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
718595 AATAATCTAT
*
718605 ATTAGCTT-TTAAAATAAAATAA-AATAA
1 ATTAGATTATTAAAA-AAAATAATAATAA
*
718632 ATTA-ATTATTAAAAATAATAATAATAA
1 ATTAGATTATTAAAAAAAATAATAATAA
718659 ATTAGA
1 ATTAGA
718665 AAGAAAGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 8 0.29
27 19 0.68
28 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTAGATTATTAAAAAAAATAATAATAA
Found at i:723732 original size:75 final size:75
Alignment explanation
Indices: 723600--723769 Score: 222
Period size: 75 Copynumber: 2.3 Consensus size: 75
723590 ACAAGAAGTA
* *
723600 AATGATGGAGCATGCTGAAAGTCCATTTCAATCATGATCAAGAATATTGACACATTTTGAACGTT
1 AATGTTGGGGCATGCTGAAAGTCCATTTCAATCATGATCAAGAATATTGACACATTTTGAACGTT
*
723665 TGTATTAGCT
66 TGTATTAGCC
* ***
723675 AATGTTGGGGCATGCTGAAAG-CTTATTTCAATCA-GAATC-AGTAATATTGATGTATTTTGAAC
1 AATGTTGGGGCATGCTGAAAGTC-CATTTCAATCATG-ATCAAG-AATATTGACACATTTTGAAC
723737 GTTTGTATTAGCC
63 GTTTGTATTAGCC
723750 AATGTTGGGGCATGCT-AAAG
1 AATGTTGGGGCATGCTGAAAG
723770 GCCCATATCA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
74 8 0.09
75 77 0.91
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (75 bp):
AATGTTGGGGCATGCTGAAAGTCCATTTCAATCATGATCAAGAATATTGACACATTTTGAACGTT
TGTATTAGCC
Found at i:724728 original size:56 final size:57
Alignment explanation
Indices: 724642--724805 Score: 160
Period size: 54 Copynumber: 2.9 Consensus size: 57
724632 TTGACCAGAA
* *
724642 ATCTGTGCAGAAACCACAGAAAATGATGAATGT-TTGTTAAATATTTTATGAACATC
1 ATCTGTGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATACTTTATGAACATC
** * * *
724698 ATCTGTGCAGAAGTCACAGGAAATGATGAATGTGTTGTCAATTGCTTTATGAACAT-
1 ATCTGTGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATACTTTATGAACATC
* * * * *
724754 A--TG-GACAGAAATCACAAGAAAA-GATAAATATGTTGCCAAATATTTTATGAAC
1 ATCTGTG-CAGAAACCAC-AGAAAATGATGAATGTGTTGTCAAATACTTTATGAAC
724806 CAGTGATTAT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 35 0.39
55 5 0.06
56 31 0.34
57 18 0.20
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (57 bp):
ATCTGTGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATACTTTATGAACATC
Found at i:725082 original size:22 final size:22
Alignment explanation
Indices: 725050--725099 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
725040 ATCTACACAT
* * *
725050 TTCAAAGATGATAGATTTTCTC
1 TTCAAACATGATAAATTCTCTC
*
725072 TTCAAACATGATAAATTCTCTT
1 TTCAAACATGATAAATTCTCTC
725094 TTCAAA
1 TTCAAA
725100 GAGGAAAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (22 bp):
TTCAAACATGATAAATTCTCTC
Found at i:725745 original size:79 final size:80
Alignment explanation
Indices: 725613--725771 Score: 284
Period size: 79 Copynumber: 2.0 Consensus size: 80
725603 CCACAAAAGA
*
725613 AGTATTATTTTTGGGGCATGTTACCCAATCAAACAAGTTATTTCAATGAGAAAATGCTTTCCAAA
1 AGTATTATTTTTGGGGCATGTTACCCAATCAAACAAGTTATTTCAATGAGAAAACGCTTTCCAAA
725678 GTTTCTCATTTAATC
66 GTTTCTCATTTAATC
* *
725693 AGTATTA-TTTTGGGGCATGTTACCCAATCAAGCAAGTTATTTCAATGAGAAAACGCTTTCTAAA
1 AGTATTATTTTTGGGGCATGTTACCCAATCAAACAAGTTATTTCAATGAGAAAACGCTTTCCAAA
725757 GTTTCTCATTTAATC
66 GTTTCTCATTTAATC
725772 TTTTCTGAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 69 0.91
80 7 0.09
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (80 bp):
AGTATTATTTTTGGGGCATGTTACCCAATCAAACAAGTTATTTCAATGAGAAAACGCTTTCCAAA
GTTTCTCATTTAATC
Found at i:725922 original size:45 final size:45
Alignment explanation
Indices: 725861--726064 Score: 264
Period size: 45 Copynumber: 4.4 Consensus size: 45
725851 TAAGACCTTA
* *
725861 AGTGCATTATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGC
1 AGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGC
* * * *
725906 AGTGCATGATGTTTTCAAAAAAAGCCTTCGGGTCATCTGTAATCCCTTC
1 AGTGCATGATGCTTTC---AAAA-CCTTCGGGTCATCCGTAAGCCCTGC
* * *
725955 ATTGCATGATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTC
1 AGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGC
*
726000 AGTGCATGATGCTTTCAAAACCTTTGGGTCATCCGTAAGCCCTGC
1 AGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGC
* *
726045 AGTGCAGGATGTTTTCAAAA
1 AGTGCATGATGCTTTCAAAA
726065 AAAGCCTTCG
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
45 97 0.69
46 4 0.03
48 4 0.03
49 35 0.25
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (45 bp):
AGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGC
Found at i:726006 original size:94 final size:94
Alignment explanation
Indices: 725845--726019 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 94
725835 CAATTTCCTA
*
725845 CATCTGTAAGACCTTAAGTGCATTATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTG
1 CATCTGTAAGACCTTAAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTG
*
725910 CATGATGTTTTCAAAAAAAGCCTTCGGGT
66 CATGATGCTTTCAAAAAAAGCCTTCGGGT
** * * * * *
725939 CATCTGTAATCCCTTCATTGCATGATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGACCTTAAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTG
726004 CATGATGCTTTCAAAA
66 CATGATGCTTTCAAAA
726020 CCTTTGGGTC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 72 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (94 bp):
CATCTGTAAGACCTTAAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTG
CATGATGCTTTCAAAAAAAGCCTTCGGGT
Found at i:726076 original size:94 final size:92
Alignment explanation
Indices: 725869--726064 Score: 261
Period size: 94 Copynumber: 2.1 Consensus size: 92
725859 TAAGTGCATT
*
725869 ATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTGCATGATGTTTTCAAAAAAAGCCTT
1 ATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTGCATGATGCTTTC--AAAAAGCCTT
* * * * *
725934 CGGGTCATCTGTAATCCCTTCATTGCATG
64 CGGGTCATCCGTAAGCCCTGCAGTGCAGG
* * * *
725963 ATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTC-AAAA-CCTTTG
1 ATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTGCATGATGCTTTCAAAAAGCCTTCG
726026 GGTCATCCGTAAGCCCTGCAGTGCAGG
66 GGTCATCCGTAAGCCCTGCAGTGCAGG
*
726053 ATGTTTTCAAAA
1 ATGCTTTCAAAA
726065 AAAGCCTTCG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
90 38 0.42
91 4 0.04
94 49 0.54
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (92 bp):
ATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCATGCAGTGCATGATGCTTTCAAAAAGCCTTCG
GGTCATCCGTAAGCCCTGCAGTGCAGG
Found at i:726138 original size:45 final size:44
Alignment explanation
Indices: 726089--726240 Score: 196
Period size: 45 Copynumber: 3.3 Consensus size: 44
726079 CTTTTGATAT
* *
726089 TTTCAAAGCCTTCGGTTAATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCGG-TCATCTGTAAGCCCTTCAGTGCATGATGC
726134 TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGC
** * * *
726179 TTTCAAAACCTTCGGGTCATCCATAAGCCCTGCAGTGCAGGATGT
1 TTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGC
726224 TTTCAAAAAGCCTTCGG
1 TTTC-AAAA-CCTTCGG
726241 GAGCTTTTTG
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
45 83 0.86
46 8 0.08
47 5 0.05
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (44 bp):
TTTCAAAACCTTCGGTCATCTGTAAGCCCTTCAGTGCATGATGC
Found at i:726184 original size:122 final size:122
Alignment explanation
Indices: 725967--726186 Score: 359
Period size: 122 Copynumber: 1.8 Consensus size: 122
725957 TGCATGATGC
* **
725967 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTGGGTCAT
1 TTTCAAAACCTTCGGGTAATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGTCAT
*
726032 CCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAAAGCCTTCGGGAGCTTTTGATAT
66 CCGTAAGCCCTGCAGTGCAGGATGCTTTCAAAAAAAGCCTTCGGGAGCTTTTGATAT
* *
726089 TTTCAAAGCCTTCGGTTAATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGTCAT
1 TTTCAAAACCTTCGGGTAATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGTCAT
* * *
726154 CTGTAAGCCCTTCAGTGCATGATGCTTTCAAAA
66 CCGTAAGCCCTGCAGTGCAGGATGCTTTCAAAA
726187 CCTTCGGGTC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
122 89 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (122 bp):
TTTCAAAACCTTCGGGTAATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGTCAT
CCGTAAGCCCTGCAGTGCAGGATGCTTTCAAAAAAAGCCTTCGGGAGCTTTTGATAT
Found at i:726208 original size:167 final size:165
Alignment explanation
Indices: 725926--726352 Score: 694
Period size: 167 Copynumber: 2.6 Consensus size: 165
725916 GTTTTCAAAA
* *
725926 AAAGCCTTCGGGTCATCTGTAATCCCTTCATTGCATGATGCTTTCAAAACCTTCGGGTCATCTGT
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTC-GGTCATCTGT
* *
725991 AAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTGGGTCATCCGTAAGCCCTGCAGTGCAGGATG
65 AAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTGCAGTGCAGGATG
*
726056 TTTTCAAAAAAAGCCTTCGGGAGC-TTTTGATATTTTC
130 TTTTC--AAAAAGCCTTCGGGAGCTTTTTGATACTTTC
* *
726093 AAAGCCTTCGGTTAATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGTCATCTGT
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTC-GGTCATCTGT
726158 AAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTGCAGTGCAGGATG
65 AAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTGCAGTGCAGGATG
726223 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTC
130 TTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTC
* *
726259 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCATCCGT
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG-GTCATCTGT
* * *
726324 AAGCCCTGCAGTGCAGGATGTTTTCAAAA
65 AAGCCCTTCAGTGCATGATGCTTTCAAAA
726353 AGCCTTTGGG
Statistics
Matches: 243, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
165 18 0.07
166 97 0.40
167 128 0.53
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (165 bp):
AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGTCATCTGTA
AGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGCCCTGCAGTGCAGGATGT
TTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTC
Found at i:726278 original size:121 final size:121
Alignment explanation
Indices: 726128--726593 Score: 702
Period size: 121 Copynumber: 3.9 Consensus size: 121
726118 CTTCAGTGCA
* *
726128 TGATGCTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
726193 GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
66 GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
726249 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
* * *
726314 AGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
66 GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* * * * *
726370 TGATATTTTCAAAGCCTTCTGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCT
1 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
* * *
726435 GGTCATCCATAAGACATGCAGTGTAGG--GTTTTCAAAAAAGCCTTCGGGAGCTTTT
66 GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGAGCTTTT
* * * *
726490 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
*** * * *
726555 GGTCATCTGCAAGTCCTTCAGTGCATGATGTTTTCAAAA
66 GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTCAAAA
726594 CCTTCAGGTC
Statistics
Matches: 315, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
119 6 0.02
120 101 0.32
121 202 0.64
122 6 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (121 bp):
TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
GGTCATCCATAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:726303 original size:45 final size:45
Alignment explanation
Indices: 726249--726352 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
726239 GGGAGCTTTT
* * * *
726249 TGATACTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGCTTTCAAAACCTTCGAGTCATCCGTAAGCCCTGCAGTGCA
726294 TGATGCTTTCAAAACCTTCGAGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGCTTTCAAAACCTTCGAGTCATCCGTAAGCCCTGCAGTGCA
* *
726339 GGATGTTTTCAAAA
1 TGATGCTTTCAAAA
726353 AGCCTTTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
TGATGCTTTCAAAACCTTCGAGTCATCCGTAAGCCCTGCAGTGCA
Found at i:726457 original size:45 final size:45
Alignment explanation
Indices: 726370--726457 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
726360 GGGAGCTTTT
* ** * * *
726370 TGATATTTTCAAAGCCTTCTGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCTGGTCATCCATAAGACATGCAGTGCA
*
726415 TGATGTTTTCAAAACCTTCTGGTCATCCATAAGACATGCAGTG
1 TGATATTTTCAAAACCTTCTGGTCATCCATAAGACATGCAGTG
726458 TAGGGTTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCTGGTCATCCATAAGACATGCAGTGCA
Found at i:726546 original size:45 final size:45
Alignment explanation
Indices: 726490--726680 Score: 280
Period size: 45 Copynumber: 4.3 Consensus size: 45
726480 GGGAGCTTTT
* *
726490 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
726535 TGATGTTTTCAAAACCTTCGGGTCATCTGCAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
726580 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
726625 TGATGTTTTCAAAACCTTCGGGTCAT-TCATAAGA-CTTCTAG-GCA
1 TGATGTTTTCAAAACCTTCGGGTCATCT-GTAAGACCTTC-AGTGCA
*
726669 TAATGTTTTCAA
1 TGATGTTTTCAA
726681 CATTTCTATC
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
44 19 0.14
45 115 0.86
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:726579 original size:241 final size:241
Alignment explanation
Indices: 726134--726593 Score: 742
Period size: 241 Copynumber: 1.9 Consensus size: 241
726124 TGCATGATGC
726134 TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCAT
1 TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCAT
* *
726199 CCATAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAAAAC
66 CCATAAGACATGCAGTGCAGGA-GTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAAAAC
* *
726264 CTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCATCCGTAAGCC
130 CTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCATCCGCAAGCC
726329 CTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATAT
195 CTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATAT
* * * *
726376 TTTCAAAGCCTTCTGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCTGGTCAT
1 TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCAT
* * *
726441 CCATAAGACATGCAGTGTAGG-GTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGC
66 CCATAAGACATGCAGTGCAGGAGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATACTTTCAAAAC
* * * *
726505 CTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGCAAGTC
130 CTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCATCCGCAAGCC
* *
726570 CTTCAGTGCATGATGTTTTCAAAA
195 CTGCAGTGCAGGATGTTTTCAAAA
726594 CCTTCAGGTC
Statistics
Matches: 200, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
240 6 0.03
241 115 0.57
242 79 0.40
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (241 bp):
TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCAT
CCATAAGACATGCAGTGCAGGAGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAAAACC
TTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCATCCGCAAGCCC
TGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATAT
Found at i:726815 original size:3 final size:3
Alignment explanation
Indices: 726807--726879 Score: 101
Period size: 3 Copynumber: 23.7 Consensus size: 3
726797 TCATTTCATT
**
726807 TTA TTA TTA TTA TTA AAA 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
*
726855 TTA TATA TATG TTA TTA TTA TTA TT
1 TTA T-TA T-TA TTA TTA TTA TTA TT
726880 TAACAAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:727614 original size:12 final size:12
Alignment explanation
Indices: 727591--727628 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
727581 AATAGTGGCC
727591 GACGATGAATAGT
1 GACG-TGAATAGT
727604 GATCG-GAATAGT
1 GA-CGTGAATAGT
727616 GACGTGAATAGT
1 GACGTGAATAGT
727628 G
1 G
727629 TCCGACGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.09
12 17 0.74
13 2 0.09
14 2 0.09
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.24
Consensus pattern (12 bp):
GACGTGAATAGT
Found at i:728579 original size:9 final size:9
Alignment explanation
Indices: 728565--728598 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
728555 ATATCTTATG
728565 TTAATTAAT
1 TTAATTAAT
728574 TTAATTAAT
1 TTAATTAAT
*
728583 TTTA-TAAT
1 TTAATTAAT
728591 TTAATTAA
1 TTAATTAA
728599 ATAATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:736541 original size:27 final size:27
Alignment explanation
Indices: 736510--736568 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
736500 TTAAAAAAAT
*
736510 TATTACAAATAAGAATATAATAAATAA
1 TATTACAAATAAGAAAATAATAAATAA
** * * *
736537 TATTATTAATTAGAAAATAATTAATAT
1 TATTACAAATAAGAAAATAATAAATAA
736564 TATTA
1 TATTA
736569 TTTTTCAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (27 bp):
TATTACAAATAAGAAAATAATAAATAA
Found at i:737154 original size:14 final size:15
Alignment explanation
Indices: 737137--737165 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
737127 AAATATTAAG
737137 ATTAATAT-ATTTTT
1 ATTAATATAATTTTT
737151 ATTAATATAATTTTT
1 ATTAATATAATTTTT
737166 TTTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTAATATAATTTTT
Found at i:737198 original size:26 final size:26
Alignment explanation
Indices: 737169--737226 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
737159 AATTTTTTTT
*
737169 TAAATTATATTA-ATTATTTATTATCA
1 TAAATTATATTATATTATTAATTAT-A
*
737195 TAAA-AATATTATATTATTAATTATA
1 TAAATTATATTATATTATTAATTATA
*
737220 TTAATTA
1 TAAATTA
737227 CTTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TAAATTATATTATATTATTAATTATA
Found at i:737219 original size:42 final size:43
Alignment explanation
Indices: 737171--737266 Score: 124
Period size: 42 Copynumber: 2.2 Consensus size: 43
737161 TTTTTTTTTA
**
737171 AATTATATTAATTA-TTTATTATCATAAAAATATTA-TATTATT
1 AATTATATTAATTACTTT-TTAAAATAAAAATATTATTATTATT
*
737213 AATTATATTAATTACTTTTTAAAATAAAATTATTATTATTATT
1 AATTATATTAATTACTTTTTAAAATAAAAATATTATTATTATT
*
737256 ATATTAAATTA
1 A-ATTATATTA
737267 TAATAATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 28 0.60
43 11 0.23
44 8 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (43 bp):
AATTATATTAATTACTTTTTAAAATAAAAATATTATTATTATT
Found at i:737313 original size:22 final size:22
Alignment explanation
Indices: 737239--737313 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
737229 TTTTAAAATA
* *
737239 AAATTATT-ATTATTATTATATT
1 AAATTATTAATTAATA-TATTTT
737261 AAATTA-TAATAATACACTATATTTT
1 AAATTATTAAT--TA-A-TATATTTT
737286 CGAAATTATTAATTAATATATTTT
1 --AAATTATTAATTAATATATTTT
737310 AAAT
1 AAAT
737314 ATTTAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
21 1 0.02
22 12 0.28
24 10 0.23
25 6 0.14
26 4 0.09
27 6 0.14
28 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATTATTAATTAATATATTTT
Found at i:737364 original size:29 final size:29
Alignment explanation
Indices: 737342--737404 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
737332 ATTATAACAT
737342 TAAAAATATAATATAATTTATTATATAAA
1 TAAAAATATAATATAATTTATTATATAAA
*
737371 TAAAAATATAATATCATTTATTATTATAATA
1 TAAAAATATAATATAATTTATTA-TATAA-A
737402 TAA
1 TAA
737405 TTCAATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 22 0.71
30 5 0.16
31 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAAAATATAATATAATTTATTATATAAA
Found at i:739206 original size:17 final size:18
Alignment explanation
Indices: 739171--739207 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
739161 TTATGAGGTG
*
739171 AAAATGTTATTATTGTAA
1 AAAATGTAATTATTGTAA
739189 AAAATGTAATTATT-TAA
1 AAAATGTAATTATTGTAA
739206 AA
1 AA
739208 TAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
AAAATGTAATTATTGTAA
Found at i:739772 original size:15 final size:16
Alignment explanation
Indices: 739734--739766 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
739724 TATATATAAA
*
739734 TTTAAAATTTGTAGAT
1 TTTAAATTTTGTAGAT
739750 TTTAAATTTTGT-GAT
1 TTTAAATTTTGTAGAT
739765 TT
1 TT
739767 GTAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTAAATTTTGTAGAT
Found at i:744288 original size:30 final size:31
Alignment explanation
Indices: 744235--744293 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
744225 AACTTAAAAG
*
744235 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
744266 AGTTTTACAATACT-AAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
744294 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:744804 original size:20 final size:20
Alignment explanation
Indices: 744756--744816 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
744746 AACTTAAATC
*
744756 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
744776 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
744794 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
744813 AAAA
1 AAAA
744817 CTAAATATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 5 0.14
18 13 0.36
19 10 0.28
20 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:744867 original size:23 final size:23
Alignment explanation
Indices: 744836--745014 Score: 349
Period size: 23 Copynumber: 7.8 Consensus size: 23
744826 TATAATATAA
*
744836 TATTAAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744859 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744882 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744905 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744928 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744951 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744974 TATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
744997 TATTTAAAAATTAATATT
1 TATTTAAAAATTAATATT
745015 AAAATTAATA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
23 155 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAAAAATTAATATTTAATT
Found at i:744893 original size:46 final size:46
Alignment explanation
Indices: 744836--745078 Score: 354
Period size: 46 Copynumber: 5.4 Consensus size: 46
744826 TATAATATAA
*
744836 TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
744882 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
744928 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
* *
744974 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAAT
1 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
* *** * *
745020 TA-ATATCTA-TAATA--TAA--TATTAAAAAATTATTATTTAATT
1 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
745060 TATTTAAAAAATTAATATT
1 TATTT-AAAAATTAATATT
745079 AAAATTAAAA
Statistics
Matches: 177, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
40 21 0.12
41 1 0.01
42 5 0.03
43 5 0.03
44 5 0.03
45 3 0.02
46 137 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (46 bp):
TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATT
Found at i:744924 original size:69 final size:69
Alignment explanation
Indices: 744836--745078 Score: 354
Period size: 69 Copynumber: 3.6 Consensus size: 69
744826 TATAATATAA
744836 TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
1 TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
744901 AATT
66 AATT
*
744905 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
1 TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
744970 AATT
66 AATT
* * * * ***
744974 TATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTA-ATATCTA-TAATA--T
1 TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
745035 AA--
66 AATT
*
745037 TATTAAAAAATTATTATTTAATTTATTTAAAAAATTAATATT
1 TATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATATT
745079 AAAATTAAAA
Statistics
Matches: 164, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
63 26 0.16
64 13 0.08
65 3 0.02
67 5 0.03
68 3 0.02
69 114 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (69 bp):
TATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTTAATTTATTTAAAAATTAATATTT
AATT
Found at i:745112 original size:12 final size:12
Alignment explanation
Indices: 745067--745117 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
745057 ATTTATTTAA
745067 AAAATT-AATATT
1 AAAATTAAATA-T
745079 AAAATTAAA-AT
1 AAAATTAAATAT
*
745090 CAAA-TATAATAT
1 AAAATTA-AATAT
745102 AAAATTAAATAT
1 AAAATTAAATAT
745114 AAAA
1 AAAA
745118 CCTATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:746047 original size:15 final size:16
Alignment explanation
Indices: 746027--746056 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
746017 TTGACCATGA
746027 ATATTTT-AATGGAAG
1 ATATTTTCAATGGAAG
746042 ATATTTTCAATGGAA
1 ATATTTTCAATGGAA
746057 AAATGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (16 bp):
ATATTTTCAATGGAAG
Found at i:750050 original size:23 final size:23
Alignment explanation
Indices: 750024--750075 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
750014 ATAGCACTAT
*
750024 GGTGTAATTCTACGCGGCACTTC
1 GGTGCAATTCTACGCGGCACTTC
*
750047 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTCTACGCGGCACTTC
750070 GGTGCA
1 GGTGCA
750076 TTTATACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTTC
Found at i:750083 original size:23 final size:23
Alignment explanation
Indices: 750024--750083 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
750014 ATAGCACTAT
* *
750024 GGTGTAATTCTACGCGGCACTTC
1 GGTGCAATTATACGCGGCACTTC
* *
750047 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTATACGCGGCACTTC
*
750070 GGTGCATTTATACG
1 GGTGCAATTATACG
750084 AGATGTGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCAATTATACGCGGCACTTC
Found at i:750419 original size:16 final size:15
Alignment explanation
Indices: 750395--750437 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
750385 GAGTAAACGA
*
750395 ATAAATATAAGAGAAT
1 ATAATTATAAGA-AAT
*
750411 ATAATTATAAGATAT
1 ATAATTATAAGAAAT
750426 A-AATTATAAGAA
1 ATAATTATAAGAA
750438 TATTGATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (15 bp):
ATAATTATAAGAAAT
Found at i:750430 original size:14 final size:15
Alignment explanation
Indices: 750393--750436 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
750383 TTGAGTAAAC
750393 GAATAAA-TATAAGA
1 GAATAAATTATAAGA
750407 GAATATAATTATAAGA
1 GAATA-AATTATAAGA
*
750423 -TATAAATTATAAGA
1 GAATAAATTATAAGA
750437 ATATTGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 15 0.56
15 5 0.19
16 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (15 bp):
GAATAAATTATAAGA
Found at i:755294 original size:23 final size:23
Alignment explanation
Indices: 755262--755320 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
755252 ATCTTATATA
* *
755262 GCACTACGGTGTAATCCTACGCG
1 GCACTTCGGTGCAATCCTACGCG
* *
755285 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATCCTACGCG
755308 GCACTTCGGTGCA
1 GCACTTCGGTGCA
755321 TTTATACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATCCTACGCG
Found at i:755328 original size:23 final size:23
Alignment explanation
Indices: 755279--755328 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
755269 GGTGTAATCC
*
755279 TACGCGGCACTTCGGTGCAATTC
1 TACGCGGCACTTCGGTGCAATTA
* *
755302 TACGTGGCACTTCGGTGCATTTA
1 TACGCGGCACTTCGGTGCAATTA
755325 TACG
1 TACG
755329 AGATGTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TACGCGGCACTTCGGTGCAATTA
Done.