Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 26
Found at i:4119794 original size:19 final size:20
Alignment explanation
Indices: 4119772--4119824 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
4119762 ATAATATGAA
4119772 AATATTTAATATAT-ATATT
1 AATATTTAATATATAATATT
4119791 AATATTTTAATAATATAATATT
1 AATA-TTTAAT-ATATAATATT
* *
4119813 ATTTTTTAATAT
1 AATATTTAATAT
4119825 TATTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
21 10 0.34
22 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATTTAATATATAATATT
Found at i:4119882 original size:26 final size:23
Alignment explanation
Indices: 4119853--4119901 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
4119843 TATATTATAA
*
4119853 TAATATATGATATAATATTATTATTT
1 TAATA-AT-ATATAATA-AATTATTT
4119879 TAATAATATATAATAAATTATTT
1 TAATAATATATAATAAATTATTT
4119902 AAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 8 0.36
25 2 0.09
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAATAATATATAATAAATTATTT
Found at i:4119911 original size:23 final size:24
Alignment explanation
Indices: 4119862--4119912 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4119852 ATAATATATG
* *
4119862 ATATAATATTATTATTTTAATAAT
1 ATATAATATAATTATTTTAAAAAT
4119886 ATATAATA-AATTA-TTTAAAAATT
1 ATATAATATAATTATTTTAAAAA-T
4119909 ATAT
1 ATAT
4119913 TATTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 9 0.38
24 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATAATATAATTATTTTAAAAAT
Found at i:4120946 original size:9 final size:9
Alignment explanation
Indices: 4120934--4120985 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
4120924 TAATATTTTG
4120934 TATTTAATT
1 TATTTAATT
*
4120943 TATTTAA-G
1 TATTTAATT
4120951 TATTTAATT
1 TATTTAATT
4120960 TATTTAA--
1 TATTTAATT
*
4120967 TATTTTATT
1 TATTTAATT
*
4120976 TAATTAATT
1 TATTTAATT
4120985 T
1 T
4120986 TTTGCATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:4120955 original size:17 final size:17
Alignment explanation
Indices: 4120933--4120982 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
4120923 TTAATATTTT
4120933 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
4120950 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
4120967 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
4120983 TTTTTTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:4123197 original size:13 final size:13
Alignment explanation
Indices: 4123177--4123223 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
4123167 TATTTAGTAC
*
4123177 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
4123190 TGTTTATTGGACT
1 TTTTTATTGTAAT
4123203 TTTTTATTGTAAT
1 TTTTTATTGTAAT
4123216 TTTTTATT
1 TTTTTATT
4123224 ACTTATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:4127333 original size:83 final size:83
Alignment explanation
Indices: 4127112--4127402 Score: 225
Period size: 83 Copynumber: 3.5 Consensus size: 83
4127102 GTTTATAGCT
* * * * * * * * ** * *
4127112 AAAATGCCGGAATAGATTTGTTTACAGTGGCATTTTTTCAATAAACGCCGCAATAGAGTAGTAAT
1 AAAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTTTACAAAAAACGACATAATAGATTAATAAT
* *
4127177 TTAGCGGCGTTTGTA-TA
66 TTAGCGACGTTTGTAGAA
* * * * * * * * * *
4127194 AAAATGCTGTAACAGGGTTGTTTATAGTGGCGTTTGTCCAACAAATGACATTATAGA-TAATTAA
1 AAAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTTTACAAAAAACGACATAATAGATTAA-TAA
*
4127258 TTTAGCGGCGCTTAT-TA-AA
65 TTTAGCGACG-TT-TGTAGAA
* * *
4127277 AAAACGTCGCAATAGGTTTGTTTATAGCGGCGTTTTTACAAAAAACGCCATAATAGATTAATAAT
1 AAAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTTTACAAAAAACGACATAATAGATTAATAAT
4127342 TTAGCGACGTTTGTAGAA
66 TTAGCGACGTTTGTAGAA
* * * *
4127360 CAAACGCCGCCATATGTTTGTTTATAGTGGTG-TTTTA-AAAAAA
1 AAAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTTTACAAAAAA
4127403 TACCGCAAAA
Statistics
Matches: 166, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
81 9 0.05
82 64 0.39
83 89 0.54
84 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (83 bp):
AAAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTTTACAAAAAACGACATAATAGATTAATAAT
TTAGCGACGTTTGTAGAA
Found at i:4130540 original size:132 final size:132
Alignment explanation
Indices: 4130296--4130543 Score: 347
Period size: 132 Copynumber: 1.9 Consensus size: 132
4130286 TTAGTCTTAT
* * *
4130296 GATAAGAAATGTTAAGTCTTAGGAGCCTTTGTACTCTATCTCTAGATAGAATTTTATATTTAGCA
1 GATAAGAAATGATAAGCCTTAGGAACCTTTGTACTCTATCTCTAGATAGAATTTTATATTTAGC-
*
4130361 AAAAAAAAATCCTATTACAAGTCAACAACTCAGTTTATTTAAACTATTGTATGTTTAGGAATCTA
65 -AAAAAAAATCCTATTACAAGTCAACAACTCAGTTTATTCAAACTATTGTATGTTTAGGAATCTA
4130426 TCAC
129 TCAC
* *
4130430 GATAAGAAA-GATAAGCCTTAGGAATCTTTGTAATCTCTATCTCTAGATAGAATTTTATCTTTAG
1 GATAAGAAATGATAAGCCTTAGGAACCTTTGT-A-CTCTATCTCTAGATAGAATTTTATATTTAG
* * * **
4130494 C-AAAAAAGTCCTATTAGAAGTTAACAACTTGGTTTATTCAAACTATTGTA
64 CAAAAAAAATCCTATTACAAGTCAACAACTCAGTTTATTCAAACTATTGTA
4130544 ATCTTCTAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
132 43 0.43
133 18 0.18
134 10 0.10
135 30 0.30
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (132 bp):
GATAAGAAATGATAAGCCTTAGGAACCTTTGTACTCTATCTCTAGATAGAATTTTATATTTAGCA
AAAAAAATCCTATTACAAGTCAACAACTCAGTTTATTCAAACTATTGTATGTTTAGGAATCTATC
AC
Found at i:4132755 original size:18 final size:18
Alignment explanation
Indices: 4132732--4132766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4132722 TAGCAAATAA
*
4132732 ATGTGAACTTAAATTATT
1 ATGTGAAATTAAATTATT
4132750 ATGTGAAATTAAATTAT
1 ATGTGAAATTAAATTAT
4132767 GCGTGCTTAT
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:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATGTGAAATTAAATTATT
Found at i:4136783 original size:17 final size:15
Alignment explanation
Indices: 4136752--4136785 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
4136742 TCATTACTTA
4136752 ATTCATTTTTTTATT
1 ATTCATTTTTTTATT
4136767 ATTCATGTTTGTTTATT
1 ATTCAT-TTT-TTTATT
4136784 AT
1 AT
4136786 AGATAGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (15 bp):
ATTCATTTTTTTATT
Found at i:4138287 original size:21 final size:21
Alignment explanation
Indices: 4138263--4138302 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4138253 TGAAGCAAGG
*
4138263 GAAGCAGAGAGAGCAGCAGTA
1 GAAGCAGACAGAGCAGCAGTA
*
4138284 GAAGCAGCCAGAGCAGCAG
1 GAAGCAGACAGAGCAGCAG
4138303 CGAAAGTAGA
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:0.40, C:0.20, G:0.38, T:0.03
Consensus pattern (21 bp):
GAAGCAGACAGAGCAGCAGTA
Found at i:4138341 original size:21 final size:21
Alignment explanation
Indices: 4138316--4138366 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4138306 AAGTAGAGAA
* *
4138316 AGAAGTAGTGGCAGCACAGAG
1 AGAAGCAGCGGCAGCACAGAG
4138337 AGAAGCAGCGGCAGCACAGAG
1 AGAAGCAGCGGCAGCACAGAG
4138358 AGAAGCAGC
1 AGAAGCAGC
4138367 ATATCAGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.37, T:0.04
Consensus pattern (21 bp):
AGAAGCAGCGGCAGCACAGAG
Found at i:4138778 original size:43 final size:42
Alignment explanation
Indices: 4138681--4138793 Score: 133
Period size: 41 Copynumber: 2.7 Consensus size: 42
4138671 ATTTTGTGTT
4138681 ATTTAGCGGCGTTTGT-TAAAAAACGCCGTAATATACCATAC
1 ATTTAGCGGCGTTTGTATAAAAAACGCCGTAATATACCATAC
* * *
4138722 ATTTAGCGGCGTTTGTATATTATAAATGCCGTGATATACCGA-AC
1 ATTTAGCGGCGTTTGTATA--AAAAACGCCGTAATATACC-ATAC
* *
4138766 -TTTAGCGGCGTTTGTATGATAAACGCCG
1 ATTTAGCGGCGTTTGTATAAAAAACGCCG
4138794 CTAAAGCTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
41 25 0.40
42 2 0.03
43 17 0.27
44 18 0.29
45 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
ATTTAGCGGCGTTTGTATAAAAAACGCCGTAATATACCATAC
Found at i:4138817 original size:43 final size:43
Alignment explanation
Indices: 4138770--4139140 Score: 190
Period size: 43 Copynumber: 8.6 Consensus size: 43
4138760 CCGAACTTTA
* * *
4138770 GCGGCGTTTGTATGATAAACGCCGCTAAAGCTCAACACTTATT
1 GCGGCGTTTGTATGACAAACGCCGCTAAATCTCAACACCTATT
* ** * * *
4138813 GCGGCGTTT-TCAAT-AAAAACGCTACTAATTGTCAAC-CATTATT
1 GCGGCGTTTGT--ATGACAAACGCCGCTAAATCTCAACAC-CTATT
* * ** * * *
4138856 GTGTCGTTT-TCGAT-ACAAACGCCGCTTTATCTGAAAACCTACT
1 GCGGCGTTTGT--ATGACAAACGCCGCTAAATCTCAACACCTATT
* ** *
4138899 GCGACGTTTGTGGGAGAAACGCCGCTAAA-CATCATA-ACCTATT
1 GCGGCGTTTGTATGACAAACGCCGCTAAATC-TCA-ACACCTATT
* * * *
4138942 GCGGCATTTGT-TGTA-ACAACGCCGCAAAATATCAACACCTACT
1 GCGGCGTTTGTATG-ACA-AACGCCGCTAAATCTCAACACCTATT
* * ** * *
4138985 GCGACGTTTGTAAGTTAAACGCCGCTAAATATCAACACCTACT
1 GCGGCGTTTGTATGACAAACGCCGCTAAATCTCAACACCTATT
* *
4139028 GCGGCGTTTGTAGGGA-AAACGCCGCTAAA-CATCAAAACCTATT
1 GCGGCGTTTGTA-TGACAAACGCCGCTAAATC-TCAACACCTATT
* * * * * **
4139071 ACGGCATTTTTGTGACAAACGCTGCTAAATAACAACACCTATT
1 GCGGCGTTTGTATGACAAACGCCGCTAAATCTCAACACCTATT
*
4139114 GCGGCATTTGT-TGAACAAACGCCGCTA
1 GCGGCGTTTGTATG-ACAAACGCCGCTA
4139141 TATGTTATTA
Statistics
Matches: 251, Mismatches: 58, Indels: 38
0.72 0.17 0.11
Matches are distributed among these distances:
42 10 0.04
43 233 0.93
44 8 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTGTATGACAAACGCCGCTAAATCTCAACACCTATT
Found at i:4138963 original size:86 final size:85
Alignment explanation
Indices: 4138873--4139139 Score: 243
Period size: 86 Copynumber: 3.1 Consensus size: 85
4138863 TTTCGATACA
* * * * *
4138873 AACGCCGCTTTATCTGAAAACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCATA-AC
1 AACGCCGCTTAATCTCAAAACCTACTGCGACGTTTGTGAGACAAACGCCGCTAAATATCA-ACAC
4138937 CTATTGCGGCATTTGTTGTAAC
65 CTATTGCGGCATTTGTTG-AAC
** * * * **
4138959 AACGCCGCAAAATATCAACACCTACTGCGACGTTTGTAAGTTAAACGCCGCTAAATATCAACACC
1 AACGCCGCTTAATCTCAAAACCTACTGCGACGTTTGTGAGACAAACGCCGCTAAATATCAACACC
* * *
4139024 TACTGCGGCGTTTGTAGGGAA-
66 TATTGCGGCATTTGT--TGAAC
* * * * * * * * *
4139045 AACGCCGC-TAAACATCAAAACCTATTACGGCATTTTTGTGACAAACGCTGCTAAATAACAACAC
1 AACGCCGCTTAATC-TCAAAACCTACTGCGACGTTTGTGAGACAAACGCCGCTAAATATCAACAC
4139109 CTATTGCGGCATTTGTTGAAC
65 CTATTGCGGCATTTGTTGAAC
4139130 AAACGCCGCT
1 -AACGCCGCT
4139140 ATATGTTATT
Statistics
Matches: 142, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
84 3 0.02
85 3 0.02
86 133 0.94
87 2 0.01
88 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (85 bp):
AACGCCGCTTAATCTCAAAACCTACTGCGACGTTTGTGAGACAAACGCCGCTAAATATCAACACC
TATTGCGGCATTTGTTGAAC
Found at i:4139124 original size:129 final size:129
Alignment explanation
Indices: 4138892--4139124 Score: 344
Period size: 129 Copynumber: 1.8 Consensus size: 129
4138882 TTATCTGAAA
* *
4138892 ACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCATAACCTATTGCGGCATTTGTTGTA
1 ACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCAAAACCTATTACGGCATTTGTTGTA
* *
4138957 ACAACGCCGCAAAATATCAACACCTACTGCGACGTTTGTAAGTTAAACGCCGCTAAATATCAAC
66 ACAACGCCGCAAAATAACAACACCTACTGCGACATTTGTAAGTTAAACGCCGCTAAATATCAAC
*
4139021 ACCTACTGCGGCGTTTGTAGGGA-AAACGCCGCTAAACATCAAAACCTATTACGGCATTT-TTGT
1 ACCTACTGCGACGTTTGT-GGGAGAAACGCCGCTAAACATCAAAACCTATTACGGCATTTGTTGT
* * * * *
4139084 GACAAACGCTGCTAAATAACAACACCTATTGCGGCATTTGT
65 AAC-AACGCCGCAAAATAACAACACCTACTGCGACATTTGT
4139125 TGAACAAACG
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
128 6 0.07
129 82 0.89
130 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (129 bp):
ACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCAAAACCTATTACGGCATTTGTTGTA
ACAACGCCGCAAAATAACAACACCTACTGCGACATTTGTAAGTTAAACGCCGCTAAATATCAAC
Found at i:4140961 original size:20 final size:20
Alignment explanation
Indices: 4140938--4140978 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4140928 TAAGGAGAGG
4140938 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
4140958 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
4140978 A
1 A
4140979 AATGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:4141086 original size:24 final size:24
Alignment explanation
Indices: 4141059--4141110 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4141049 ACCTTTAGAG
*
4141059 TGAAATGAAATAACTATTTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
** *
4141083 TGAAAAGACTTAATTATTTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
4141107 TGAA
1 TGAA
4141111 TAGTCATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (24 bp):
TGAAAAGAAATAACTATTTTTTCA
Found at i:4145342 original size:23 final size:24
Alignment explanation
Indices: 4145316--4145366 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
4145306 ACCTTTATAG
*
4145316 TGAAATGAAATAACTA-TTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
** *
4145339 TGAAAAGACTTAATTATTTTTTCA
1 TGAAAAGAAATAACTATTTTTTCA
4145363 TGAA
1 TGAA
4145367 TAGTCATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (24 bp):
TGAAAAGAAATAACTATTTTTTCA
Found at i:4146497 original size:131 final size:134
Alignment explanation
Indices: 4146328--4146578 Score: 382
Period size: 131 Copynumber: 1.9 Consensus size: 134
4146318 TAAAATAAGT
* *
4146328 TAATAGAATAATTTTAGGTTGGTAAAATGGTCGAGATAATGTCTTTGAGAAAAATAATTCCCAAA
1 TAATAGAATAATTTTAGGTTGGTAAAATAGTCGAGATAATGTCCTTGAGAAAAATAATTCCCAAA
* * * *
4146393 ATAAT-TC-AT-AGCATTATTTCCCAAATTAGGGCAATTGTTACGATGTAAAGGGGAAGATGTGA
66 ACAATCACTATGAGCATTATTTCCCAAAGTAGGGCAATTATTACGATGTAAAGGGGAAGATGTGA
4146455 GATA
131 GATA
**
4146459 TAATAGAATAATTTTAGGTTGGTAAAATAGTTTAGATAATGTCCTTGAGAAAAATAATTCCCAAA
1 TAATAGAATAATTTTAGGTTGGTAAAATAGTCGAGATAATGTCCTTGAGAAAAATAATTCCCAAA
* *
4146524 ACAATCCACTATGAGCATTATTTCCCATAGTAGGGCAATTATTACGGTGTAAAGG
66 ACAAT-CACTATGAGCATTATTTCCCAAAGTAGGGCAATTATTACGATGTAAAGG
4146579 AGAATACACG
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
131 65 0.61
133 1 0.01
134 2 0.02
135 38 0.36
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (134 bp):
TAATAGAATAATTTTAGGTTGGTAAAATAGTCGAGATAATGTCCTTGAGAAAAATAATTCCCAAA
ACAATCACTATGAGCATTATTTCCCAAAGTAGGGCAATTATTACGATGTAAAGGGGAAGATGTGA
GATA
Found at i:4149352 original size:33 final size:32
Alignment explanation
Indices: 4149283--4149371 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 32
4149273 CTGGTGACTT
** *
4149283 CACTTCGTCGGCCGATCT-TTCTTTCCCTCGC
1 CACTTCGTCGGCCGATCTCCCCTTTCCCTAGC
*
4149314 CACTTCGTCGGCCGATCTCCCCCTTTCCCTAGT
1 CACTTCGTCGGCCGATCT-CCCCTTTCCCTAGC
*
4149347 GACTTC-TACGGCCGATCTTCCCCTT
1 CACTTCGT-CGGCCGATC-TCCCCTT
4149372 CCGAGTTCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 18 0.37
32 1 0.02
33 29 0.59
34 1 0.02
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.33
Consensus pattern (32 bp):
CACTTCGTCGGCCGATCTCCCCTTTCCCTAGC
Found at i:4149491 original size:21 final size:19
Alignment explanation
Indices: 4149465--4149505 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4149455 GGTAGTAGCT
4149465 TCTGTAAACCAATTTTAACGG
1 TCTGT-AACCAATTTT-ACGG
*
4149486 TCTGTAATCAATTTTACGG
1 TCTGTAACCAATTTTACGG
4149505 T
1 T
4149506 TGCAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (19 bp):
TCTGTAACCAATTTTACGG
Found at i:4150078 original size:133 final size:133
Alignment explanation
Indices: 4149840--4150106 Score: 516
Period size: 133 Copynumber: 2.0 Consensus size: 133
4149830 ATTTGGTAGT
* *
4149840 GGGTAATTTTAGTTGCTTTTAAATTTCTACTTCTGGATGGGATGTACCTGAATGATAAATGCGAA
1 GGGTAATTTTAATTGCTTTTAAATTTCTACTTCTGGATGGGATGTACCTGAATGATAAATACGAA
4149905 ATTAGTGTTTCAAGTTTGATAAATGGTCTTCAATCTTGTTTGCAAACTGATGCATTTTAGGAAAA
66 ATTAGTGTTTCAAGTTTGATAAATGGTCTTCAATCTTGTTTGCAAACTGATGCATTTTAGGAAAA
4149970 ATA
131 ATA
4149973 GGGTAATTTTAATTGCTTTTAAATTTCTACTTCTGGATGGGATGTACCTGAATGATAAATACGAA
1 GGGTAATTTTAATTGCTTTTAAATTTCTACTTCTGGATGGGATGTACCTGAATGATAAATACGAA
4150038 ATTAGTGTTTCAAGTTTGATAAATGGTCTTCAATCTTGTTTGCAAACTGATGCATTTTAGGAAAA
66 ATTAGTGTTTCAAGTTTGATAAATGGTCTTCAATCTTGTTTGCAAACTGATGCATTTTAGGAAAA
4150103 ATA
131 ATA
4150106 G
1 G
4150107 TTACTAATTA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (133 bp):
GGGTAATTTTAATTGCTTTTAAATTTCTACTTCTGGATGGGATGTACCTGAATGATAAATACGAA
ATTAGTGTTTCAAGTTTGATAAATGGTCTTCAATCTTGTTTGCAAACTGATGCATTTTAGGAAAA
ATA
Found at i:4151064 original size:33 final size:32
Alignment explanation
Indices: 4151027--4151102 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 32
4151017 GCGGTATGTT
4151027 TATTTGTTTAATCGGTTTCTAATTTGTATCTTG
1 TATTT-TTTAATCGGTTTCTAATTTGTATCTTG
* *
4151060 TATTTATT--T-GGTTTCTAATTTGTATGTTG
1 TATTTTTTAATCGGTTTCTAATTTGTATCTTG
*
4151089 CATTTATTTCAATC
1 TATTT-TTT-AATC
4151103 TATTGGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
29 23 0.68
30 3 0.09
32 2 0.06
33 6 0.18
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (32 bp):
TATTTTTTAATCGGTTTCTAATTTGTATCTTG
Found at i:4151072 original size:29 final size:29
Alignment explanation
Indices: 4151040--4151097 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
4151030 TTGTTTAATC
*
4151040 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGCATTTATTT
*
4151069 GGTTTCTAATTTGTATGTTGCATTTATTT
1 GGTTTCTAATTTGTATCTTGCATTTATTT
4151098 CAATCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.17, C:0.07, G:0.16, T:0.60
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGCATTTATTT
Found at i:4151306 original size:59 final size:59
Alignment explanation
Indices: 4151235--4151352 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
4151225 AGCCGAATAA
4151235 TGAGGTACTTTAAACTTACATTTGCTAGTTAGGTACTAAATATAAGAACTAAATTGATT
1 TGAGGTACTTTAAACTTACATTTGCTAGTTAGGTACTAAATATAAGAACTAAATTGATT
4151294 TGAGGTACTTTAAACTTACATTTGCTAGTTAGGTACTAAATATAAGAACTAAATTGATT
1 TGAGGTACTTTAAACTTACATTTGCTAGTTAGGTACTAAATATAAGAACTAAATTGATT
4151353 CTAATTACTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (59 bp):
TGAGGTACTTTAAACTTACATTTGCTAGTTAGGTACTAAATATAAGAACTAAATTGATT
Found at i:4151330 original size:28 final size:28
Alignment explanation
Indices: 4151237--4151330 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
4151227 CCGAATAATG
4151237 AGGTACTTTAAACTTACATTTGCTAGTT
1 AGGTACTTTAAACTTACATTTGCTAGTT
* *
4151265 AGGTACTAAATATAAGAAC-TA-AATTG--ATTT
1 AGGTACT---T-T-A-AACTTACATTTGCTAGTT
4151295 GAGGTACTTTAAACTTACATTTGCTAGTT
1 -AGGTACTTTAAACTTACATTTGCTAGTT
4151324 AGGTACT
1 AGGTACT
4151331 AAATATAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 22
0.66 0.05 0.29
Matches are distributed among these distances:
25 3 0.06
26 3 0.06
27 5 0.10
28 15 0.29
29 3 0.06
30 3 0.06
31 8 0.16
32 5 0.10
33 3 0.06
34 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (28 bp):
AGGTACTTTAAACTTACATTTGCTAGTT
Found at i:4153908 original size:23 final size:23
Alignment explanation
Indices: 4153881--4153927 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4153871 ATATTCAAGA
*
4153881 TAGATAAGTGTATATCTTGAAAT
1 TAGATAAGTGCATATCTTGAAAT
4153904 TAGATAAGTGCATATCTTGAAAT
1 TAGATAAGTGCATATCTTGAAAT
4153927 T
1 T
4153928 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TAGATAAGTGCATATCTTGAAAT
Found at i:4155244 original size:31 final size:31
Alignment explanation
Indices: 4155187--4155344 Score: 139
Period size: 30 Copynumber: 5.2 Consensus size: 31
4155177 CAGAAACTTG
* *
4155187 AGGACCAAAATAGCAAAAACAT-AAACTCAA
1 AGGACTAAAATAGCAAAAACATAAAACTTAA
* *
4155217 AGTACTAAAATAACAAAAA-ATAGAAACTTAA
1 AGGACTAAAATAGCAAAAACATA-AAACTTAA
* * *
4155248 AGGGCTAAAATAGTAAAAA-A-AAGACATTTAA
1 AGGACTAAAATAGCAAAAACATAA-A-ACTTAA
*
4155279 AGGACTAAAATAACAAAAACA-AAAACTTAA
1 AGGACTAAAATAGCAAAAACATAAAACTTAA
* * * *
4155309 GGGACTAAAATAGCAAAAATAT-ACATTTAA
1 AGGACTAAAATAGCAAAAACATAAAACTTAA
4155339 AGGACT
1 AGGACT
4155345 GAACCATAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
29 3 0.03
30 52 0.50
31 45 0.44
32 3 0.03
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.17
Consensus pattern (31 bp):
AGGACTAAAATAGCAAAAACATAAAACTTAA
Found at i:4155266 original size:61 final size:60
Alignment explanation
Indices: 4155175--4155327 Score: 163
Period size: 61 Copynumber: 2.5 Consensus size: 60
4155165 AAATATGATT
* * * *
4155175 AACAGAAACTTGA-GGACCAAAATAGCAAAAACATAA-AC-TCAAAGTACTAAAATAACAAA
1 AACAAAAACTTAAGGGACTAAAATAGCAAAAA-A-AAGACATCAAAGGACTAAAATAACAAA
* *
4155234 AA-ATAGAAACTTAAAGGG-CTAAAATAGTAAAAAAAAGACATTTAAAGGACTAAAATAACAAA
1 AACA-A-AAACTT-AAGGGACTAAAATAGCAAAAAAAAGACA-TCAAAGGACTAAAATAACAAA
4155296 AACAAAAACTTAAGGGACTAAAATAGCAAAAA
1 AACAAAAACTTAAGGGACTAAAATAGCAAAAA
4155328 TATACATTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 14 0.18
61 34 0.44
62 24 0.31
63 1 0.01
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (60 bp):
AACAAAAACTTAAGGGACTAAAATAGCAAAAAAAAGACATCAAAGGACTAAAATAACAAA
Found at i:4155340 original size:60 final size:60
Alignment explanation
Indices: 4155175--4155344 Score: 184
Period size: 62 Copynumber: 2.8 Consensus size: 60
4155165 AAATATGATT
* * * * * * * *
4155175 AACAGAAACTTGA-GGACCAAAATAGCAAAAACATAAACTCAAAGTACTAAAATAACAAA
1 AACAAAAACTTAAGGGACTAAAATAGCAAAAAAATACATTTAAAGGACTAAAATAACAAA
* *
4155234 AA-ATAGAAACTTAAAGGG-CTAAAATAGTAAAAAAAAGACATTTAAAGGACTAAAATAACAAA
1 AACA-A-AAACTT-AAGGGACTAAAATAG-CAAAAAAATACATTTAAAGGACTAAAATAACAAA
*
4155296 AACAAAAACTTAAGGGACTAAAATAGCAAAAATATACATTTAAAGGACT
1 AACAAAAACTTAAGGGACTAAAATAGCAAAAAAATACATTTAAAGGACT
4155345 GAACCATAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 31 0.34
61 24 0.26
62 32 0.35
63 1 0.01
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (60 bp):
AACAAAAACTTAAGGGACTAAAATAGCAAAAAAATACATTTAAAGGACTAAAATAACAAA
Found at i:4156466 original size:2 final size:2
Alignment explanation
Indices: 4156459--4156528 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
4156449 TTTGATTTTG
4156459 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
4156501 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
4156529 TATTTTCTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4157723 original size:65 final size:66
Alignment explanation
Indices: 4157590--4157731 Score: 214
Period size: 65 Copynumber: 2.2 Consensus size: 66
4157580 AGAAGATGAT
* * * * * *
4157590 TCAAGAGAGACAAAATTCGTTTTAATGGAAACGATCTCAAAGATTGGTGTTTCATGAGAAACTGT
1 TCAAGAGAGACAAAATCCGTTTCAAGGGAAACGATCTCAAAGATAGGTGTTGCAAGAGAAACTGT
4157655 C
66 C
4157656 TCAAGAGAGACAAAATCCGTTTCAAGGGAAACGA-CTCAAAGATAGGTGTTGCAAGAGAAACTGT
1 TCAAGAGAGACAAAATCCGTTTCAAGGGAAACGATCTCAAAGATAGGTGTTGCAAGAGAAACTGT
4157720 C
66 C
*
4157721 TCAAAAGAGAC
1 TCAAGAGAGAC
4157732 TAAACTTTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 38 0.55
66 31 0.45
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (66 bp):
TCAAGAGAGACAAAATCCGTTTCAAGGGAAACGATCTCAAAGATAGGTGTTGCAAGAGAAACTGT
C
Found at i:4158112 original size:35 final size:36
Alignment explanation
Indices: 4158073--4158146 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
4158063 TTTTTGCAAG
*
4158073 AAATTGTCTTAAACGAGACAAAA-TTTGTTTTTAGA
1 AAATTGTCTCAAACGAGACAAAACTTTGTTTTTAGA
***
4158108 AAATTGTCTCATGTGAGACAAAACTTTGTTTTTAGA
1 AAATTGTCTCAAACGAGACAAAACTTTGTTTTTAGA
4158144 AAA
1 AAA
4158147 ACACCCTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 19 0.56
36 15 0.44
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (36 bp):
AAATTGTCTCAAACGAGACAAAACTTTGTTTTTAGA
Found at i:4163418 original size:29 final size:29
Alignment explanation
Indices: 4163368--4163536 Score: 106
Period size: 30 Copynumber: 5.7 Consensus size: 29
4163358 CACTTAAATA
** *
4163368 AAGGACCAAAATATG-ATTAACAGAAACTT
1 AAGGACCAAAATA-GCAAAAACATAAACTT
* *
4163397 GAGGACCAAAATAGCAAAAACATAAACTCA
1 AAGGACCAAAATAGCAAAAACATAAACT-T
* *
4163427 AAGTACTAAAATAGCAAAAACATAAACTT
1 AAGGACCAAAATAGCAAAAACATAAACTT
* * * * * *
4163456 AAAGGGCTAAAATAGCAAAAATAGACATTT
1 -AAGGACCAAAATAGCAAAAACATAAACTT
** * * *
4163486 AAAGGAATAAAATAACAAAAATAAAAACTT
1 -AAGGACCAAAATAGCAAAAACATAAACTT
* *
4163516 AAGGGACTAAAATACCAAAAA
1 AA-GGACCAAAATAGCAAAAA
4163537 TAAATATATA
Statistics
Matches: 113, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
28 1 0.01
29 24 0.21
30 88 0.78
ACGTcount: A:0.59, C:0.13, G:0.12, T:0.17
Consensus pattern (29 bp):
AAGGACCAAAATAGCAAAAACATAAACTT
Found at i:4163537 original size:30 final size:30
Alignment explanation
Indices: 4163398--4163540 Score: 151
Period size: 30 Copynumber: 4.8 Consensus size: 30
4163388 CAGAAACTTG
* * * *
4163398 AGGACCAAAATAGCAAAAACATAAACTCAA
1 AGGACTAAAATAGCAAAAATAAAAACTTAA
* * *
4163428 AGTACTAAAATAGCAAAAACATAAACTTAA
1 AGGACTAAAATAGCAAAAATAAAAACTTAA
* * * *
4163458 AGGGCTAAAATAGCAAAAATAGACATTTAA
1 AGGACTAAAATAGCAAAAATAAAAACTTAA
* *
4163488 AGGAATAAAATAACAAAAATAAAAACTTAA
1 AGGACTAAAATAGCAAAAATAAAAACTTAA
* *
4163518 GGGACTAAAATACCAAAAATAAA
1 AGGACTAAAATAGCAAAAATAAA
4163541 TATATATTTA
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (30 bp):
AGGACTAAAATAGCAAAAATAAAAACTTAA
Found at i:4166011 original size:18 final size:17
Alignment explanation
Indices: 4165966--4166012 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
4165956 TATGGAATTG
4165966 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
* * *
4165983 TATTACAATTCCTTTACA
1 GATTCCAATTCC-TGACA
4166001 GATTCCAATTCC
1 GATTCCAATTCC
4166013 CTCAGAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:4166097 original size:17 final size:17
Alignment explanation
Indices: 4166073--4166113 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
4166063 CGGGTCCTCC
4166073 TCCGGGTCGAGTCTGGA
1 TCCGGGTCGAGTCTGGA
*
4166090 TTCGGGTCGAGTCTGGA
1 TCCGGGTCGAGTCTGGA
4166107 TCCGGGT
1 TCCGGGT
4166114 TTGCTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.22, G:0.41, T:0.27
Consensus pattern (17 bp):
TCCGGGTCGAGTCTGGA
Found at i:4170040 original size:36 final size:36
Alignment explanation
Indices: 4169989--4170060 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
4169979 TAATTCAAAG
* * *
4169989 TCCATTAAAAGTGAATTTGAGCATAAAAATGGTTTT
1 TCCATTAAAAATGAATTTGAGCACAAAAATGATTTT
4170025 TCCATTAAAAATGAATTTGAGCACAAAAATGATTTT
1 TCCATTAAAAATGAATTTGAGCACAAAAATGATTTT
4170061 CACATATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (36 bp):
TCCATTAAAAATGAATTTGAGCACAAAAATGATTTT
Found at i:4178646 original size:15 final size:15
Alignment explanation
Indices: 4178628--4178657 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4178618 TTATTCGTTC
4178628 AAGTCTAATTCATTT
1 AAGTCTAATTCATTT
*
4178643 AAGTCTGATTCATTT
1 AAGTCTAATTCATTT
4178658 GCACTAATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (15 bp):
AAGTCTAATTCATTT
Found at i:4183714 original size:10 final size:10
Alignment explanation
Indices: 4183699--4183734 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
4183689 AAAATTTGGC
4183699 TTTTTTGTTT
1 TTTTTTGTTT
*
4183709 TTTTTTGTCT
1 TTTTTTGTTT
4183719 TTTTTTGTTT
1 TTTTTTGTTT
4183729 TTTTTT
1 TTTTTT
4183735 TTGAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:4183715 original size:19 final size:20
Alignment explanation
Indices: 4183693--4183734 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4183683 TTTCTGAAAA
4183693 TTTGGC-TTTTTTGTTTTTT
1 TTTGGCTTTTTTTGTTTTTT
*
4183712 TTTGTCTTTTTTTGTTTTTT
1 TTTGGCTTTTTTTGTTTTTT
4183732 TTT
1 TTT
4183735 TTGAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (20 bp):
TTTGGCTTTTTTTGTTTTTT
Found at i:4196976 original size:141 final size:143
Alignment explanation
Indices: 4196783--4197067 Score: 556
Period size: 141 Copynumber: 2.0 Consensus size: 143
4196773 TGGAAAATAT
4196783 TAGAAGGCTGAAATTACGTTTTTTTTTTTTTGTGTTGAAATGGAATTGAAAAGAAAATGAAATTT
1 TAGAAGGCTGAAATTACGTTTTTTTTTTTTTGTGTTGAAATGGAATTGAAAAGAAAATGAAATTT
4196848 TCCCACGCGGACCAACGGTATTTGTTCTCTCGTCTTTCTGCATTGTGTTGACGGGATGACAGATT
66 TCCCACGCGGACCAACGGTATTTGTTCTCTCGTCTTTCTGCATTGTGTTGACGGGATGACAGATT
4196913 TCTGCC-CGTGCA
131 TCTGCCACGTGCA
4196925 TAGAAGGCTGAAATTACG-TTTTTTTTTTTTGTGTTGAAATGGAATTGAAAAGAAAATGAAATTT
1 TAGAAGGCTGAAATTACGTTTTTTTTTTTTTGTGTTGAAATGGAATTGAAAAGAAAATGAAATTT
4196989 TCCCACGCGGACCAACGGTATTTGTTCTCTCGTCTTTCTGCATTGTGTTGACGGGATGACAGATT
66 TCCCACGCGGACCAACGGTATTTGTTCTCTCGTCTTTCTGCATTGTGTTGACGGGATGACAGATT
4197054 TCTGCCACGTGCA
131 TCTGCCACGTGCA
4197067 T
1 T
4197068 GCATGAGTGT
Statistics
Matches: 142, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 117 0.82
142 25 0.18
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (143 bp):
TAGAAGGCTGAAATTACGTTTTTTTTTTTTTGTGTTGAAATGGAATTGAAAAGAAAATGAAATTT
TCCCACGCGGACCAACGGTATTTGTTCTCTCGTCTTTCTGCATTGTGTTGACGGGATGACAGATT
TCTGCCACGTGCA
Found at i:4199264 original size:19 final size:19
Alignment explanation
Indices: 4199240--4199306 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4199230 ATGACCAACA
* *
4199240 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4199259 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
* *
4199278 AAATCGCAACACGATCTCC
1 AAATCGCAACGCGATCTCT
4199297 AATATCGCAA
1 AA-ATCGCAA
4199307 ATCAGTTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 36 0.84
20 7 0.16
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4199386 original size:21 final size:21
Alignment explanation
Indices: 4199340--4199393 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4199330 GATTTTGACT
*
4199340 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
4199361 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
4199382 ATCGCAATGCGA
1 ATCGCATTGCGA
4199394 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:4199405 original size:20 final size:20
Alignment explanation
Indices: 4199380--4199418 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4199370 CGATTTTAGA
*
4199380 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
4199400 AAATCGCAACGCGATTATG
1 AAATCGCAACGCGAATATG
4199419 ACTATTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:4199598 original size:17 final size:17
Alignment explanation
Indices: 4199576--4199613 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4199566 CGACATTCGT
*
4199576 TCCTATATCCAACGACA
1 TCCTATATCCAACAACA
4199593 TCCTATATCCAACAACA
1 TCCTATATCCAACAACA
4199610 TCCT
1 TCCT
4199614 TCCCCATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACAACA
Found at i:4200318 original size:24 final size:24
Alignment explanation
Indices: 4200261--4200320 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4200251 TAGTCAGTAT
*
4200261 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* *
4200285 -CCAGACTTTGATATTGGTCAATAC
1 TCGA-AATTTGATATTGGTCAATAC
*
4200309 TCGAATTTTGAT
1 TCGAAATTTGAT
4200321 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.07
24 25 0.86
25 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:4202785 original size:20 final size:20
Alignment explanation
Indices: 4202760--4202822 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
4202750 TTACACATTC
* *
4202760 ATTTGAATATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
4202780 ATTTGACTATCGAAATGCGA
1 ATTTGACTATCGCAACGCGA
*
4202800 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
4202820 ATT
1 ATT
4202823 GGCTTTCGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:4202846 original size:20 final size:20
Alignment explanation
Indices: 4202821--4202883 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
4202811 GCAACACGAA
*
4202821 TTGGCTTTCGCGTTGCGATT
1 TTGGCTTTCGCATTGCGATT
4202841 TTGGCTTTCGCATTGCGATT
1 TTGGCTTTCGCATTGCGATT
* *
4202861 TTGACTTTCGTATTGCGATT
1 TTGGCTTTCGCATTGCGATT
4202881 TTG
1 TTG
4202884 AGTTTAGCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (20 bp):
TTGGCTTTCGCATTGCGATT
Found at i:4202884 original size:20 final size:20
Alignment explanation
Indices: 4202825--4202898 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
4202815 CACGAATTGG
* *
4202825 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGA
4202845 CTTTCGCATTGCGATTTTGA
1 CTTTCGCATTGCGATTTTGA
*
4202865 CTTTCGTATTGCGATTTTGA
1 CTTTCGCATTGCGATTTTGA
* * *
4202885 GTTTAGCGTTGCGA
1 CTTTCGCATTGCGA
4202899 AAGTGTGCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.12, C:0.18, G:0.26, T:0.45
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGA
Found at i:4203062 original size:67 final size:66
Alignment explanation
Indices: 4202950--4203119 Score: 186
Period size: 71 Copynumber: 2.5 Consensus size: 66
4202940 GATTGAAATC
*
4202950 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-TTATTTAC-ACATCA
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATTTATTTACTACATCA
4203013 ATTA
63 ATTA
* * *
4203017 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAATAATAATAATAATTCTTATTTTCTTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGC--A-AA-AATAAGAA-T-TTATTTACTACA
4203081 TCAATTA
60 TCAATTA
*
4203088 AACAAATCAACTTTTA-AGAATCAATTAAACAA
1 AACAAATCAACTTTTACATAATCAATTAAACAA
4203120 TAAAAAAAAG
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
63 16 0.18
65 1 0.01
66 1 0.01
67 25 0.28
70 8 0.09
71 39 0.43
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.31
Consensus pattern (66 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATTTATTTACTACATCAATT
A
Found at i:4203201 original size:16 final size:16
Alignment explanation
Indices: 4203180--4203210 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4203170 CACGCAGCTT
4203180 ACTTCAGGATTAACCC
1 ACTTCAGGATTAACCC
4203196 ACTTCAGGATTAACC
1 ACTTCAGGATTAACC
4203211 TACAGAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (16 bp):
ACTTCAGGATTAACCC
Found at i:4204477 original size:21 final size:21
Alignment explanation
Indices: 4204453--4204554 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
4204443 GTGTGAGGGA
*
4204453 CCTCTTCAACGATGACAGAGG
1 CCTCTTGAACGATGACAGAGG
* ** *
4204474 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGAGG
* *
4204495 ACTCTTGAAGGATGACA-AGGG
1 CCTCTTGAACGATGACAGA-GG
*
4204516 CCTCTTGAATGATAGA-AGAGG
1 CCTCTTGAACGAT-GACAGAGG
4204537 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
4204555 GTGAGTCAGG
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.92
22 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGAGG
Found at i:4204493 original size:42 final size:42
Alignment explanation
Indices: 4204433--4204524 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
4204423 GTGAATCGGG
* *
4204433 CTCTTGAATGGTGTGA-GGGACCTCTTCAACGATGAC-AGAGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAAG-GGC
* *
4204475 CTCTTGAACGGTGGGAGGGGACTCTTGAAGGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAAGGGC
4204517 CTCTTGAA
1 CTCTTGAA
4204525 TGATAGAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 38 0.86
43 6 0.14
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAAGGGC
Found at i:4205142 original size:19 final size:19
Alignment explanation
Indices: 4205038--4205176 Score: 89
Period size: 19 Copynumber: 7.1 Consensus size: 19
4205028 TCTGAAACTT
* *
4205038 AAAATCGCAACACGAAACTT
1 AAAATCGCAACGCGAAA-TA
* *
4205058 AAAATCGCAACGCTAAAATG
1 AAAATCGCAACGC-GAAATA
** *
4205078 ACTATCGCAACGCGAAAATG
1 AAAATCGCAACGCG-AAATA
** * * *
4205098 AGTATTGCAACGCGAATTT
1 AAAATCGCAACGCGAAATA
** *
4205117 ACTATCGCAATGCGAAATA
1 AAAATCGCAACGCGAAATA
**
4205136 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
4205155 AAAATCGCAACGCGAAACTA
1 AAAATCGCAACGCGAAA-TA
4205175 AA
1 AA
4205177 TTCGCGTTGC
Statistics
Matches: 94, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
19 48 0.51
20 43 0.46
21 3 0.03
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4205181 original size:19 final size:19
Alignment explanation
Indices: 4205031--4205181 Score: 106
Period size: 20 Copynumber: 7.7 Consensus size: 19
4205021 AATAGTTTCT
*
4205031 GAAACTTAAAATCGCAACAC
1 GAAAC-TAAAATCGCAACGC
4205051 GAAACTTAAAATCGCAACGC
1 GAAAC-TAAAATCGCAACGC
* * **
4205071 TAAAATGACTATCGCAACGC
1 GAAACT-AAAATCGCAACGC
* ** *
4205091 GAAAATGAGTATTGCAACGC
1 GAAACT-AAAATCGCAACGC
** ** *
4205111 GAATTTACTATCGCAATGC
1 GAAACTAAAATCGCAACGC
4205130 GAAA-TAAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
*
4205149 GAAACCAAAATCGCAACGC
1 GAAACTAAAATCGCAACGC
*
4205168 GAAACTAAATTCGC
1 GAAACTAAAATCGC
4205182 GTTGCGATTT
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
18 1 0.01
19 53 0.49
20 54 0.50
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:4205253 original size:20 final size:20
Alignment explanation
Indices: 4205228--4205296 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
4205218 ACGATTATCC
* *
4205228 CGTTGCGATATTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
4205248 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
4205268 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
4205288 CGTTGCGAT
1 CGTTGCGAT
4205297 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:4207204 original size:20 final size:20
Alignment explanation
Indices: 4207181--4207236 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
4207171 TCTGAAACTT
4207181 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
4207201 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
4207221 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
4207237 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:4207242 original size:20 final size:20
Alignment explanation
Indices: 4207184--4207252 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
4207174 GAAACTTAAA
* **
4207184 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
4207204 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
4207224 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4207244 ATCGCAACG
1 ATCGCAACG
4207253 AGATAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4207889 original size:20 final size:19
Alignment explanation
Indices: 4207864--4207937 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
4207854 ATTTTGTATT
4207864 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGT-AGA
* **
4207884 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGA
*
4207905 ATCGCGTTGTGATAGTTAGA
1 ATCGCGTTGCGATAG-TAGA
4207925 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
4207938 TTACATATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.60
21 12 0.28
22 3 0.07
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGA
Found at i:4207906 original size:41 final size:41
Alignment explanation
Indices: 4207849--4207939 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
4207839 TTTGAAAGCA
4207849 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
* *
4207890 TTGCGATTTTGTATTATCGCGTTGTGATAGTTAGAATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
4207931 TTGCGATTT
1 TTGCGATTT
4207940 ACATATTCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.41
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
Found at i:4208019 original size:41 final size:41
Alignment explanation
Indices: 4207864--4208078 Score: 125
Period size: 41 Copynumber: 5.3 Consensus size: 41
4207854 ATTTTGTATT
* * * * **
4207864 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
* * * * ** *
4207905 ATCGCGTTGTGATAGTTAGAATCGCGTTGCG-ATTTACATA
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
* ** ****
4207945 TTCGCATTGCGATTTTCTAAAATCGTAACGCGAATTTGGAAA
1 ATCGCATTGCGATAGTC-AAAATCGCGTTGCGAATTTGGAAA
*
4207987 ATCGCAATGCGATAGTCAAAATCGCGTTGCGAATTTGG-AA
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
* * ** * * *
4208027 ATTG-ATTTGCGATACTGGAGATCGCGTTGCG-ATTTAG-AG
1 ATCGCA-TTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
4208066 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4208079 TTTGTTGGTC
Statistics
Matches: 133, Mismatches: 37, Indels: 10
0.74 0.21 0.06
Matches are distributed among these distances:
39 17 0.13
40 42 0.32
41 55 0.41
42 19 0.14
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
Found at i:4208028 original size:20 final size:19
Alignment explanation
Indices: 4208005--4208080 Score: 62
Period size: 20 Copynumber: 3.9 Consensus size: 19
4207995 GCGATAGTCA
4208005 AAATCGCGTTGCGAATTTGG
1 AAATCGCGTTGCG-ATTTGG
* ** *
4208025 AAATTGATTTGCGATACTGG
1 AAATCGCGTTGCGAT-TTGG
* *
4208045 AGATCGCGTTGCGATTTAG
1 AAATCGCGTTGCGATTTGG
* *
4208064 AGATCGCATTGCGATTT
1 AAATCGCGTTGCGATTT
4208081 TGTTGGTCAT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 20 0.45
20 24 0.55
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (19 bp):
AAATCGCGTTGCGATTTGG
Found at i:4208068 original size:19 final size:19
Alignment explanation
Indices: 4208044--4208080 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4208034 TGCGATACTG
*
4208044 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
4208063 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
4208081 TGTTGGTCAT
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:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:4211921 original size:22 final size:22
Alignment explanation
Indices: 4211892--4211945 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4211882 AAACATTAAA
4211892 AGTTAAAATACTTAAAAA-ATG
1 AGTTAAAATACTTAAAAATATG
4211913 AGTTTAAAATACTTAAAAATATG
1 AG-TTAAAATACTTAAAAATATG
4211936 AGTTAAAATA
1 AGTTAAAATA
4211946 ATTATTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.06
22 24 0.77
23 5 0.16
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (22 bp):
AGTTAAAATACTTAAAAATATG
Found at i:4214634 original size:2 final size:2
Alignment explanation
Indices: 4214627--4214666 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4214617 GAATCTTATC
4214627 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
4214667 GAGTTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4223793 original size:34 final size:33
Alignment explanation
Indices: 4223754--4223841 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 33
4223744 AATGGTAATA
*
4223754 AACAAAATTATCAAAATAAA-TTAACAAAAAGTCC
1 AACAAAATTAACAAAATAAATTTAA-AAAAA-TCC
* **
4223788 AACAAAATAAACAAAATAAAATTTAAAATTATCC
1 AACAAAATTAACAAAAT-AAATTTAAAAAAATCC
* *
4223822 AACCAAATTACCAAAATAAA
1 AACAAAATTAACAAAATAAA
4223842 GTAAGTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.07
34 32 0.71
35 6 0.13
36 4 0.09
ACGTcount: A:0.64, C:0.15, G:0.01, T:0.20
Consensus pattern (33 bp):
AACAAAATTAACAAAATAAATTTAAAAAAATCC
Found at i:4226136 original size:17 final size:18
Alignment explanation
Indices: 4226118--4226150 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4226108 TAATTAAATA
4226118 AAATA-TTAAA-AAATTT
1 AAATACTTAAATAAATTT
4226134 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
4226151 ACTAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATACTTAAATAAATTT
Found at i:4226774 original size:38 final size:38
Alignment explanation
Indices: 4226732--4226808 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
4226722 ATTATCTCAT
* *
4226732 TCAAAATATTATATTAGAAAATTTAATAAATAATGATA
1 TCAAAATATTATATTAGAAAAATTAATAAATAATAATA
4226770 TCAAAATATTATATTAGAAAAATTAATAAATAATAATA
1 TCAAAATATTATATTAGAAAAATTAATAAATAATAATA
4226808 T
1 T
4226809 TATTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (38 bp):
TCAAAATATTATATTAGAAAAATTAATAAATAATAATA
Found at i:4229530 original size:130 final size:130
Alignment explanation
Indices: 4229297--4229557 Score: 504
Period size: 130 Copynumber: 2.0 Consensus size: 130
4229287 ACATCTCCCA
4229297 AAACCTTTGTCAGAAATATATGCAACACTGTTAGTTCAATTATTACCGCAAATAGCCGGTCATCC
1 AAACCTTTGTCAGAAATATATGCAACACTGTTAGTTCAATTATTACCGCAAATAGCCGGTCATCC
*
4229362 TCCGGTTTTCTCGAAACCCTATGATCACCAGGCTTTCCTAATGGTCATAGCCAGAGAGAAACATC
66 TCCGGTTTTCTCAAAACCCTATGATCACCAGGCTTTCCTAATGGTCATAGCCAGAGAGAAACATC
*
4229427 AAACCTTTGTCAGAAATATCTGCAACACTGTTAGTTCAATTATTACCGCAAATAGCCGGTCATCC
1 AAACCTTTGTCAGAAATATATGCAACACTGTTAGTTCAATTATTACCGCAAATAGCCGGTCATCC
4229492 TCCGGTTTTCTCAAAACCCTATGATCACCAGGCTTTCCTAATGGTCATAGCCAGAGAGAAACATC
66 TCCGGTTTTCTCAAAACCCTATGATCACCAGGCTTTCCTAATGGTCATAGCCAGAGAGAAACATC
4229557 A
1 A
4229558 CAGAGAAAGT
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (130 bp):
AAACCTTTGTCAGAAATATATGCAACACTGTTAGTTCAATTATTACCGCAAATAGCCGGTCATCC
TCCGGTTTTCTCAAAACCCTATGATCACCAGGCTTTCCTAATGGTCATAGCCAGAGAGAAACATC
Found at i:4242968 original size:169 final size:170
Alignment explanation
Indices: 4242676--4243018 Score: 645
Period size: 169 Copynumber: 2.0 Consensus size: 170
4242666 ATCTGTCAAG
*
4242676 CCAAAGGCGCCATCCCACTGCAGGGAAACTATGGAGGCTTTTCCATTGGTTGGTTCGGCAAAATT
1 CCAAAGGCGCCATCCCACTGCAGGGAAACTATGGAGCCTTTTCCATTGGTTGGTTCGGCAAAATT
4242741 AGCCATCCAAACAACTGTTTTCTTCATCGATGGTGTCCGAATTACGGTTTCAATTGACAAATAGT
66 AGCCATCCAAACAACTGTTTTCTTCATCGATGGTGTCCGAATTACGGTTTCAATTGACAAATAGT
4242806 TCATTATTCTTGATGGTACTAAGAAAGATGGTTCCAAACC
131 TCATTATTCTTGATGGTACTAAGAAAGATGGTTCCAAACC
4242846 CCAAAGGCGCCATCCCACTGCAGGGAAACTATGGAGCCTTTTCCATTGGTTGGTTCGGC-AAATT
1 CCAAAGGCGCCATCCCACTGCAGGGAAACTATGGAGCCTTTTCCATTGGTTGGTTCGGCAAAATT
*
4242910 AGCCATCCAAACAACTGTTTTCTTCGTCGATGGTGTCC-AGATTACGGTTTCAATTGACAAATAG
66 AGCCATCCAAACAACTGTTTTCTTCATCGATGGTGTCCGA-ATTACGGTTTCAATTGACAAATAG
4242974 TTCATTATTCTTGATGGTACTAAGAAAGATGGTTCCAAACC
130 TTCATTATTCTTGATGGTACTAAGAAAGATGGTTCCAAACC
4243015 CCAA
1 CCAA
4243019 GGACAGGAGC
Statistics
Matches: 170, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
168 1 0.01
169 111 0.65
170 58 0.34
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (170 bp):
CCAAAGGCGCCATCCCACTGCAGGGAAACTATGGAGCCTTTTCCATTGGTTGGTTCGGCAAAATT
AGCCATCCAAACAACTGTTTTCTTCATCGATGGTGTCCGAATTACGGTTTCAATTGACAAATAGT
TCATTATTCTTGATGGTACTAAGAAAGATGGTTCCAAACC
Found at i:4249447 original size:71 final size:71
Alignment explanation
Indices: 4249372--4249512 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
4249362 TGAAGGGGAC
* *
4249372 AAAGCTTAGTTTGATCGATATTTAAAGTAATAGGGACCTAAAATGTCATTTGAC-AAAAAATTGA
1 AAAGCTTAATTTGATCAATATTTAAAGTAATAGGGACCTAAAATGTCATTTGACAAAAAAATTGA
4249436 GAGAGGT
66 G-GAGGT
* *
4249443 AAAGCTTAATTTGATCAATATTTAAAGTAATAGGGATCTAAAGTGTCATTTGACAAAAAAATTGA
1 AAAGCTTAATTTGATCAATATTTAAAGTAATAGGGACCTAAAATGTCATTTGACAAAAAAATTGA
4249508 GGAGG
66 GGAGG
4249513 GCAAGAGTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 54 0.83
72 11 0.17
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.30
Consensus pattern (71 bp):
AAAGCTTAATTTGATCAATATTTAAAGTAATAGGGACCTAAAATGTCATTTGACAAAAAAATTGA
GGAGGT
Found at i:4250496 original size:21 final size:22
Alignment explanation
Indices: 4250455--4250507 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
4250445 AATTATTATC
*
4250455 TCTTTTTATTTTGATAATC-AA
1 TCTTTTAATTTTGATAATCAAA
*
4250476 TCTTTTAATTTTG-TCATTCAAA
1 TCTTTTAATTTTGAT-AATCAAA
*
4250498 TCATTTAATT
1 TCTTTTAATT
4250508 ATCTATGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 11 0.41
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (22 bp):
TCTTTTAATTTTGATAATCAAA
Found at i:4259690 original size:82 final size:83
Alignment explanation
Indices: 4259584--4259751 Score: 320
Period size: 82 Copynumber: 2.0 Consensus size: 83
4259574 AGGCCAATAG
*
4259584 ACCCTAACTTAAACCCCAAATAACCCAAGCCCAAATAAAAATCAAACCCGTTGACCCGAGTACAA
1 ACCCTAACTAAAACCCCAAATAACCCAAGCCCAAATAAAAATCAAACCCGTTGACCCGAGTACAA
4259649 GCACAAACCCGGATACTA
66 GCACAAACCCGGATACTA
4259667 ACCC-AACTAAAACCCCAAATAACCCAAGCCCAAATAAAAATCAAACCCGTTGACCCGAGTACAA
1 ACCCTAACTAAAACCCCAAATAACCCAAGCCCAAATAAAAATCAAACCCGTTGACCCGAGTACAA
4259731 GCACAAACCCGGATACTA
66 GCACAAACCCGGATACTA
4259749 ACC
1 ACC
4259752 TAAACCTAAT
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 80 0.95
83 4 0.05
ACGTcount: A:0.44, C:0.35, G:0.10, T:0.12
Consensus pattern (83 bp):
ACCCTAACTAAAACCCCAAATAACCCAAGCCCAAATAAAAATCAAACCCGTTGACCCGAGTACAA
GCACAAACCCGGATACTA
Found at i:4266095 original size:64 final size:65
Alignment explanation
Indices: 4266020--4266146 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 65
4266010 AATAGAAGAG
*
4266020 CTAAGCCGTATCTATAGAAGTGAAATATTATGTAATG-AAACTTTTTGTT-TCAAAGGAAGTTGA
1 CTAAGCCGTATCTATAGAAATGAAATATTATGTAATGAAAACTTTTTGTTAT-AAAGGAAGTTGA
4266083 A
65 A
* * * *
4266084 CTAAGTCGTATCTGTAGAAATGAACTATTATGTAATGAAAACTTTTTGTTATAATGGAAGTTG
1 CTAAGCCGTATCTATAGAAATGAAATATTATGTAATGAAAACTTTTTGTTATAAAGGAAGTTG
4266147 TTCTATGACA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 33 0.59
65 22 0.39
66 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (65 bp):
CTAAGCCGTATCTATAGAAATGAAATATTATGTAATGAAAACTTTTTGTTATAAAGGAAGTTGAA
Found at i:4271979 original size:162 final size:162
Alignment explanation
Indices: 4271712--4272025 Score: 628
Period size: 162 Copynumber: 1.9 Consensus size: 162
4271702 AACCAAAAAG
4271712 CAATCAAAGGGAATGCCATAGCAGATTTCCTTGCAAGTCGTGCCTCGGATGATTATGAGTCCTTA
1 CAATCAAAGGGAATGCCATAGCAGATTTCCTTGCAAGTCGTGCCTCGGATGATTATGAGTCCTTA
4271777 AACTTTAATTTTCCCGGAGAAGATCTGATGTGCATCACAACTGAGGATGAAATAATTTCAGATGA
66 AACTTTAATTTTCCCGGAGAAGATCTGATGTGCATCACAACTGAGGATGAAATAATTTCAGATGA
4271842 TAAGTCTTGGAGGTTGTATTTTGGGGTATCCA
131 TAAGTCTTGGAGGTTGTATTTTGGGGTATCCA
4271874 CAATCAAAGGGAATGCCATAGCAGATTTCCTTGCAAGTCGTGCCTCGGATGATTATGAGTCCTTA
1 CAATCAAAGGGAATGCCATAGCAGATTTCCTTGCAAGTCGTGCCTCGGATGATTATGAGTCCTTA
4271939 AACTTTAATTTTCCCGGAGAAGATCTGATGTGCATCACAACTGAGGATGAAATAATTTCAGATGA
66 AACTTTAATTTTCCCGGAGAAGATCTGATGTGCATCACAACTGAGGATGAAATAATTTCAGATGA
4272004 TAAGTCTTGGAGGTTGTATTTT
131 TAAGTCTTGGAGGTTGTATTTT
4272026 TATGGGGTAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 152 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (162 bp):
CAATCAAAGGGAATGCCATAGCAGATTTCCTTGCAAGTCGTGCCTCGGATGATTATGAGTCCTTA
AACTTTAATTTTCCCGGAGAAGATCTGATGTGCATCACAACTGAGGATGAAATAATTTCAGATGA
TAAGTCTTGGAGGTTGTATTTTGGGGTATCCA
Found at i:4273157 original size:18 final size:18
Alignment explanation
Indices: 4273134--4273176 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
4273124 TTTCTCAAAT
*
4273134 GACCACTATGTCCTGAAG
1 GACCACTATGTCCCGAAG
4273152 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
4273170 GACCACT
1 GACCACT
4273177 GATAATCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (18 bp):
GACCACTATGTCCCGAAG
Found at i:4280733 original size:21 final size:22
Alignment explanation
Indices: 4280704--4280744 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4280694 TTATTTATTT
4280704 AAGAGTGCATCGATACACATTG
1 AAGAGTGCATCGATACACATTG
*
4280726 AAGA-TGCATCGATGCACAT
1 AAGAGTGCATCGATACACAT
4280745 AACCCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGAGTGCATCGATACACATTG
Found at i:4282710 original size:28 final size:28
Alignment explanation
Indices: 4282679--4282746 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
4282669 TATGCTTGAA
4282679 GAAAAAAGAAA-GAAAGAATAAAAAAAAT
1 GAAAAAAGAAAGGAAA-AATAAAAAAAAT
* **
4282707 GAAAAAATAAAGGAAAAATATGAAAAAT
1 GAAAAAAGAAAGGAAAAATAAAAAAAAT
4282735 GAAAAAATGAAA
1 GAAAAAA-GAAA
4282747 AAGGAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 27 0.79
29 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (28 bp):
GAAAAAAGAAAGGAAAAATAAAAAAAAT
Found at i:4282789 original size:17 final size:17
Alignment explanation
Indices: 4282719--4282790 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
4282709 AAAAATAAAG
*
4282719 GAAAA-ATATGAAAAAT
1 GAAAAGATATAAAAAAT
* *
4282735 GAAAA-A-ATGAAAAAG
1 GAAAAGATATAAAAAAT
*
4282750 GAAAAGAAATAAAGAGAA-
1 GAAAAGATATAAA-A-AAT
4282768 -AAAAGATATAAAAAAT
1 GAAAAGATATAAAAAAT
4282784 GAAAAGA
1 GAAAAGA
4282791 AAATAAGGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
15 15 0.32
16 8 0.17
17 21 0.45
18 1 0.02
19 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (17 bp):
GAAAAGATATAAAAAAT
Found at i:4284147 original size:64 final size:65
Alignment explanation
Indices: 4284076--4284209 Score: 198
Period size: 65 Copynumber: 2.1 Consensus size: 65
4284066 ACAAATCTAC
* *
4284076 TTCGATGTTTCAAAATA-GCCAGGGTGCATCGATGCATGTCTTGTGCATCGGTGCACTGAATGCA
1 TTCGATGTTTCAAAATATGCCAGGGTGCATCGATGCATGGCTTGTACATCGGTGCACTGAATGCA
**** *
4284140 TTCGATGTTTCAAAATATTTTGGGGTGCATCTATGCATGGCTTGTACATCGGTGCACTGAATGCA
1 TTCGATGTTTCAAAATATGCCAGGGTGCATCGATGCATGGCTTGTACATCGGTGCACTGAATGCA
4284205 TTCGA
1 TTCGA
4284210 AATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 17 0.27
65 45 0.73
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (65 bp):
TTCGATGTTTCAAAATATGCCAGGGTGCATCGATGCATGGCTTGTACATCGGTGCACTGAATGCA
Found at i:4284255 original size:65 final size:65
Alignment explanation
Indices: 4284099--4284255 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 65
4284089 AATAGCCAGG
* ** * ** *
4284099 GTGCATCGATGCATGTCTTGTGCATCGGTGCACTGAATGCATTCGATGTTTCAAAATATTTTGGG
1 GTGCATCGATGCATGACTTGTGCATCGGTGCACTGAATGCATTCGATAATTCAAAATAATTAAGA
* * * **
4284164 GTGCATCTATGCATGGCTTGTACATCGGTGCACTGAATGCATTCGA-AATTCAATTTAATTAAGA
1 GTGCATCGATGCATGACTTGTGCATCGGTGCACTGAATGCATTCGATAATTCAAAATAATTAAGA
* *
4284228 GTGTATCGATGCATGAACTAGTGCATCG
1 GTGCATCGATGCATG-ACTTGTGCATCG
4284256 ATTCATTCAT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
64 23 0.31
65 52 0.69
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATGACTTGTGCATCGGTGCACTGAATGCATTCGATAATTCAAAATAATTAAGA
Found at i:4286891 original size:23 final size:23
Alignment explanation
Indices: 4286861--4286943 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
4286851 ATGCATAGCA
4286861 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
*
4286884 GAGTGCATC-AGTGCACCTTCAA-
1 GAGTGCATCGA-TGCACATTCAAG
* *
4286906 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
4286929 GA-TGCATCGATGCAC
1 GAGTGCATCGATGCAC
4286944 TGTTTAGTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
21 13 0.27
22 5 0.10
23 31 0.63
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:4293653 original size:105 final size:104
Alignment explanation
Indices: 4293519--4294121 Score: 901
Period size: 105 Copynumber: 5.8 Consensus size: 104
4293509 ACCGCAAAAG
* * *
4293519 GAGGTGAACAAACATTTCCAGAAGAGTTCATAATGAGAAGAACTTGTCTTAAAGGAGAAAGTTCA
1 GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCA
4293584 TAATGAGAAGAACTTGTTCCTTTCAAATCCATCGTATAAA
66 TAATGAGAAGAACTTGTTCCTTTCAAATCCA-CGTATAAA
*
4293624 GAGGTAAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCA
1 GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCA
* * *
4293689 TAATGAGAAGAACATGTTCCTTTCAAATCCAC-CACAGAA
66 TAATGAGAAGAACTTGTTCCTTTCAAATCCACGTATA-AA
*
4293728 GAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACT--CATTAAAGGAGAAAGTTC
1 G-AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTC
*
4293791 ATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGTATAAT
65 ATAATGAGAAGAACTTGTTCCTTTCAAATCCA-CGTATAAA
* * * * *
4293832 GAGGTGAACCAACATTTCCAGAAGAGTTCATAATAAGAATAAGTCACCTTAAAGGAGAAAGTTCG
1 GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCA
* * *
4293897 TAATGAGAAGAACATGTTCCTTTCAAATCCAC-CACAGAA
66 TAATGAGAAGAACTTGTTCCTTTCAAATCCACGTATA-AA
* * *
4293936 GGAGGTGAACCAACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGTCTTAAAGGAGAAAGTTC
1 -GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTC
*
4294001 ATAATGAGAAGAACTTGTTCCTTTCAAATCCACCTCAT-AA
65 ATAATGAGAAGAACTTGTTCCTTTCAAATCCACGT-ATAAA
*
4294041 GAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGGAAGTTC
1 G-AGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTC
4294106 ATAATGAGAAGAACTT
65 ATAATGAGAAGAACTT
4294122 ACTCAACTTT
Statistics
Matches: 450, Mismatches: 37, Indels: 22
0.88 0.07 0.04
Matches are distributed among these distances:
103 92 0.20
104 10 0.02
105 347 0.77
107 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (104 bp):
GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCA
TAATGAGAAGAACTTGTTCCTTTCAAATCCACGTATAAA
Found at i:4293799 original size:15 final size:16
Alignment explanation
Indices: 4293748--4293802 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
4293738 CAACATTTCC
4293748 AGAAGAGTTCATAATG
1 AGAAGAGTTCATAATG
** *
4293764 AGAAGAACTCATTAAAGG
1 AGAAGAGTTCA-T-AATG
4293782 AGAA-AGTTCATAATG
1 AGAAGAGTTCATAATG
4293797 AGAAGA
1 AGAAGA
4293803 ACTTGTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.23
16 11 0.37
17 5 0.17
18 7 0.23
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.20
Consensus pattern (16 bp):
AGAAGAGTTCATAATG
Found at i:4293865 original size:208 final size:207
Alignment explanation
Indices: 4293505--4294119 Score: 1018
Period size: 208 Copynumber: 2.9 Consensus size: 207
4293495 AAGAACTATG
* * *
4293505 ATCCACCGCAAAAGGAGGTGAACAAACATTTCCAGAAGAGTTCATAATGAGAAGAACTTGTCTTA
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAAC--GTCTTA
* *
4293570 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCATCGTATAAAGAGGTAAACCA
64 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGTAT-AAGAGGTGAACCA
4293635 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
128 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
4293700 ACATGTTCCTTTCAA
193 ACATGTTCCTTTCAA
*
4293715 ATCCACCACAGAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAAC-TCATTAA
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACGTC-TTAA
4293779 AGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGTATAATGAGGTGAACCAA
65 AGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGTATAA-GAGGTGAACCAA
* * * * *
4293844 CATTTCCAGAAGAGTTCATAATAAGAATAAGTCACCTTAAAGGAGAAAGTTCGTAATGAGAAGAA
129 CATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAGAA
4293909 CATGTTCCTTTCAA
194 CATGTTCCTTTCAA
*
4293923 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGTCTTA
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAG-A-ACGTCTTA
4293988 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACC-TCATAAGAAGGTGAACC
64 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGT-ATAAG-AGGTGAACC
*
4294052 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGGAAGTTCATAATGAGAAG
127 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAG
4294117 AAC
192 AAC
4294120 TTACTCAACT
Statistics
Matches: 379, Mismatches: 19, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
207 4 0.01
208 190 0.50
209 3 0.01
210 180 0.47
211 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (207 bp):
ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACGTCTTAAA
GGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCGTATAAGAGGTGAACCAACA
TTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAGAACA
TGTTCCTTTCAA
Found at i:4294073 original size:313 final size:314
Alignment explanation
Indices: 4293505--4294121 Score: 984
Period size: 313 Copynumber: 2.0 Consensus size: 314
4293495 AAGAACTATG
* ***
4293505 ATCCACCGCAAAAGGAGGTGAACAAACATTTCCAGAAGAGTTCATAATGAGAAGAACTTGTCTTA
1 ATCCACCGCAAAAGGAGGTGAACAAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCACCTTA
* * ** *
4293570 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCATCGTATAAAGAGGTAAACCA
66 AAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAAGAGGTAAACCA
* *
4293635 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
131 ACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
4293700 ACATGTTCCTTTCAAATCCACCACAGAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGA
196 ACATGTTCCTTTCAAATCCACCACAGAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGA
4293765 GAAGAACT-CATTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
261 GAAGAACTCCATTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * * * *
4293818 ATCCACCGTATAATGAGGTGAACCAACATTTCCAGAAGAGTTCATAATAAGAATAAGTCACCTTA
1 ATCCACCGCAAAAGGAGGTGAACAAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCACCTTA
* * *
4293883 AAGGAGAAAGTTCGTAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCA
66 AAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAAGAGGTAAACCA
*
4293948 ACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGTCTTAAAGGAGAAAGTTCATAATGAGAAGA
131 ACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
* * *
4294013 ACTTGTTCCTTTCAAATCCACCTCATAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGA
196 ACATGTTCCTTTCAAATCCACCACAGAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGA
* *
4294078 GAAGAACTCGCCTTAAAGGAGGAAGTTCATAATGAGAAGAACTT
261 GAAGAACTC-CATTAAAGGAGAAAGTTCATAATGAGAAGAACTT
4294122 ACTCAACTTT
Statistics
Matches: 276, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
313 244 0.88
315 32 0.12
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (314 bp):
ATCCACCGCAAAAGGAGGTGAACAAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCACCTTA
AAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAAGAGGTAAACCA
ACATTTCCAGAAGAGTTCAAAATGAGAAGAACACGCCTTAAAGGAGAAAGTTCATAATGAGAAGA
ACATGTTCCTTTCAAATCCACCACAGAAGAAGGTGAACCAACATTTCCAGAAGAGTTCATAATGA
GAAGAACTCCATTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
Found at i:4295903 original size:19 final size:19
Alignment explanation
Indices: 4295840--4295903 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
4295830 CTTTGTACAT
*
4295840 AATATTATAGTTT-GATATA
1 AATATTATATTTTAGA-ATA
* * *
4295859 AATATTTTATTTTA-CATT
1 AATATTATATTTTAGAATA
**
4295877 TTTATTATATTTTAGAATA
1 AATATTATATTTTAGAATA
4295896 AATATTAT
1 AATATTAT
4295904 GTTCTATGTT
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 13 0.41
19 19 0.59
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
AATATTATATTTTAGAATA
Found at i:4305593 original size:32 final size:32
Alignment explanation
Indices: 4305552--4305622 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
4305542 CCCATGATTA
* *
4305552 ACCCAAGAAAGTGACAT-GGGGCCTGAGAGCCT
1 ACCCAAGAAAGTGAC-TCGAGGCCTCAGAGCCT
**
4305584 ACCCAAGAAAGTTTCTCGAGGCCTCAGAGCCT
1 ACCCAAGAAAGTGACTCGAGGCCTCAGAGCCT
4305616 ACCCAAG
1 ACCCAAG
4305623 GGTCACCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.14
Consensus pattern (32 bp):
ACCCAAGAAAGTGACTCGAGGCCTCAGAGCCT
Found at i:4306834 original size:27 final size:27
Alignment explanation
Indices: 4306804--4306861 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
4306794 TTATTCCATG
*
4306804 ACTTGA-ATATATTTTAGGTCATTTTAC
1 ACTTGAGAGATATTTT-GGTCATTTTAC
* * *
4306831 ACTTTAGGGGTATTTTGGTCATTTTAC
1 ACTTGAGAGATATTTTGGTCATTTTAC
4306858 ACTT
1 ACTT
4306862 TAGGGCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (27 bp):
ACTTGAGAGATATTTTGGTCATTTTAC
Found at i:4306862 original size:27 final size:28
Alignment explanation
Indices: 4306813--4306866 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
4306803 GACTTGAATA
4306813 TATTTTAGGTCATTTTACACTTTAGGGG
1 TATTTTAGGTCATTTTACACTTTAGGGG
4306841 TATTTT-GGTCATTTTACACTTTAGGG
1 TATTTTAGGTCATTTTACACTTTAGGG
4306867 CAATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (28 bp):
TATTTTAGGTCATTTTACACTTTAGGGG
Found at i:4311764 original size:20 final size:20
Alignment explanation
Indices: 4311727--4311764 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4311717 CTTAAACTTC
*
4311727 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
4311747 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
4311765 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:4311947 original size:23 final size:23
Alignment explanation
Indices: 4311921--4311989 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
4311911 CACCACAGCT
*
4311921 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
4311944 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
4311967 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4311990 TATAATATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4316441 original size:20 final size:20
Alignment explanation
Indices: 4316404--4316441 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4316394 CTTAAACTTC
*
4316404 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
4316424 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
4316442 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:4316639 original size:23 final size:23
Alignment explanation
Indices: 4316605--4316673 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
4316595 CACCACATCT
* *
4316605 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
4316628 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
4316651 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4316674 TATAATATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4320401 original size:22 final size:20
Alignment explanation
Indices: 4320376--4320447 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
4320366 CGGGATATAT
4320376 GGACATATACCTATGTCCTTCG
1 GGACATATA--TATGTCCTTCG
* *
4320398 GGACATATGAATAGGTCATTCG
1 GGACATAT--ATATGTCCTTCG
* *
4320420 GGACATAGATGTCGTCCTTCG
1 GGACATATATAT-GTCCTTCG
4320441 GGACATA
1 GGACATA
4320448 GATTTCATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.05
21 14 0.34
22 24 0.59
24 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
GGACATATATATGTCCTTCG
Found at i:4320442 original size:21 final size:20
Alignment explanation
Indices: 4320390--4320450 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 20
4320380 ATATACCTAT
4320390 GTCCTTCGGGACATATGAATAG
1 GTCCTTCGGGACATA-G-ATAG
*
4320412 GTCATTCGGGACATAGAT-G
1 GTCCTTCGGGACATAGATAG
4320431 TCGTCCTTCGGGACATAGAT
1 --GTCCTTCGGGACATAGAT
4320451 TTCATATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 18 0.51
22 14 0.40
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
GTCCTTCGGGACATAGATAG
Found at i:4325790 original size:13 final size:13
Alignment explanation
Indices: 4325772--4325796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4325762 AAAAGAATTA
4325772 ATGATAATAATAT
1 ATGATAATAATAT
4325785 ATGATAATAATA
1 ATGATAATAATA
4325797 AAAATGTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
ATGATAATAATAT
Found at i:4327644 original size:21 final size:21
Alignment explanation
Indices: 4327602--4327644 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4327592 TTTCTGGGCT
* *
4327602 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
4327623 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
4327644 A
1 A
4327645 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:4328331 original size:23 final size:23
Alignment explanation
Indices: 4328299--4328388 Score: 144
Period size: 23 Copynumber: 3.9 Consensus size: 23
4328289 TTATTATATA
*
4328299 GCACTACGGTGCAATTCTACGCG
1 GCACTCCGGTGCAATTCTACGCG
*
4328322 GCACTCCGGTGCAATTCTATGCG
1 GCACTCCGGTGCAATTCTACGCG
4328345 GCACTCCGGTGCAATTCTACGCG
1 GCACTCCGGTGCAATTCTACGCG
* *
4328368 GCACTTCGGTGCAATTATACG
1 GCACTCCGGTGCAATTCTACG
4328389 AGCTGTGGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.24
Consensus pattern (23 bp):
GCACTCCGGTGCAATTCTACGCG
Found at i:4333689 original size:9 final size:9
Alignment explanation
Indices: 4333675--4333705 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
4333665 CCTTACTGTT
4333675 AATTTTTAA
1 AATTTTTAA
4333684 AATTTTTAA
1 AATTTTTAA
4333693 AATTTTTAA
1 AATTTTTAA
4333702 AATT
1 AATT
4333706 GATTTAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:4340756 original size:227 final size:227
Alignment explanation
Indices: 4340345--4340830 Score: 659
Period size: 227 Copynumber: 2.1 Consensus size: 227
4340335 CTTATTCATA
*
4340345 TATTGAATAAAAAT-A-TTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
* *
4340408 TCGGGTCGGTCGGTGTTTTTAAGTGTGATATTCGAGTCGGGTCGAGTTCGAGTTTAGGGTGAAAA
66 TCGGGTCGG-CGGTG---TAAACTGTGATATTCGAGTCGGGTCGAGTTCGAGTTTAGGGTGAAAA
* * *
4340473 ATACCCGACCCGAAAATATATATAATTTTACCTTATATTTTTAGGGATAATTACAATAATACCCC
127 ATACCCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
*
4340538 TCTATATATA-ATTTTTTTCAATTAAGTCACTGTTTT
192 TCTATATATATA-TTTTTTCAATTAAGTCACTATTTT
4340574 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCT-ATTCATATATTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
* * * *
4340638 TCGGGTC-G-GGTG-AAACT-TTAT-TTTG-GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATAC
66 TCGGGTCGGCGGTGTAAACTGTGATATTCGAGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATAC
4340697 CCGACCCAACCCAAAAATATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
131 CCG-----ACCC-AAAA-ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
* *
4340762 CCCTCTCTCTATATATTTTTTCAATTAAGTCACTATTTT
189 CCCTCTATATATATATTTTTTCAATTAAGTCACTATTTT
* *
4340801 TATTAAATAAAAATATTTTTTTTATTATTT
1 TATTGAATAAAAATAATTTTTTTATTATTT
4340831 TTAGGTCGGG
Statistics
Matches: 232, Mismatches: 15, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
220 35 0.15
221 3 0.01
222 3 0.01
223 3 0.01
225 4 0.02
226 3 0.01
227 111 0.48
228 1 0.00
229 15 0.06
230 23 0.10
231 31 0.13
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (227 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
TCGGGTCGGCGGTGTAAACTGTGATATTCGAGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATAC
CCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTA
TATATATATTTTTTCAATTAAGTCACTATTTT
Found at i:4349868 original size:16 final size:16
Alignment explanation
Indices: 4349847--4349880 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4349837 TTACTATTCA
*
4349847 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
4349863 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
4349879 CG
1 CG
4349881 GTCGGCGATA
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:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:4359213 original size:23 final size:23
Alignment explanation
Indices: 4359176--4359240 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
4359166 CAGCTCGTAT
*
4359176 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACTGAAGTGCCATGTAG
* * **
4359199 AATTGCACTGTAGTGCCGCGTAG
1 AAATGCACTGAAGTGCCATGTAG
4359222 AAATGCACTGAAGTGCCAT
1 AAATGCACTGAAGTGCCAT
4359241 ATAATAATGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
AAATGCACTGAAGTGCCATGTAG
Found at i:4360624 original size:21 final size:21
Alignment explanation
Indices: 4360600--4360645 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4360590 TTTTGTTCGT
* *
4360600 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
4360621 TTGAATGGGTACCGATTCCTC
1 TTGAAGGGGTACCGATTCCCC
4360642 TTGA
1 TTGA
4360646 CCAGAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4361178 original size:23 final size:23
Alignment explanation
Indices: 4361152--4361198 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4361142 CTCCTATCCC
4361152 ACGTTTTTATATCCCTTAAAAAG
1 ACGTTTTTATATCCCTTAAAAAG
4361175 ACGTTTTTATATCCCTTAAAAAG
1 ACGTTTTTATATCCCTTAAAAAG
4361198 A
1 A
4361199 GAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
ACGTTTTTATATCCCTTAAAAAG
Found at i:4361788 original size:16 final size:18
Alignment explanation
Indices: 4361749--4361793 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
4361739 ATTCTTTAAA
4361749 CTTT-TTCCATTCATTTC
1 CTTTATTCCATTCATTTC
4361766 C-TTATTCCATT-A-TTC
1 CTTTATTCCATTCATTTC
4361781 CTTTATT-CATTCA
1 CTTTATTCCATTCA
4361794 AAAATCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.32
16 9 0.36
17 8 0.32
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
CTTTATTCCATTCATTTC
Found at i:4365792 original size:20 final size:22
Alignment explanation
Indices: 4365767--4365807 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4365757 CCTTGCCCAG
4365767 AAATCA-T-ATTTTTAGCTCGA
1 AAATCACTCATTTTTAGCTCGA
4365787 AAATCACTTCATTTTTAGCTC
1 AAATCAC-TCATTTTTAGCTC
4365808 AACACTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATCACTCATTTTTAGCTCGA
Found at i:4366920 original size:2 final size:2
Alignment explanation
Indices: 4366913--4366937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4366903 CTTTTAAAAC
4366913 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4366938 AACACTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4367174 original size:24 final size:24
Alignment explanation
Indices: 4367120--4367179 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
4367110 AAACATAATT
4367120 CAGGTCAAGTATCAGATCAAAAAC
1 CAGGTCAAGTATCAGATCAAAAAC
* * ** * *
4367144 TATGTCAAGTATCATTTCAGAATC
1 CAGGTCAAGTATCAGATCAAAAAC
4367168 CAGGTCAAGTAT
1 CAGGTCAAGTAT
4367180 AATAACAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAAAAAC
Found at i:4369932 original size:20 final size:20
Alignment explanation
Indices: 4369909--4369947 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4369899 CTGAAATTAA
4369909 CGACGAACGACGTCGATTCT
1 CGACGAACGACGTCGATTCT
4369929 CGACGAACGACGTCGATTC
1 CGACGAACGACGTCGATTC
4369948 AGGACGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (20 bp):
CGACGAACGACGTCGATTCT
Found at i:4369953 original size:20 final size:20
Alignment explanation
Indices: 4369908--4369954 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4369898 ACTGAAATTA
4369908 ACGACGAACGACGTCGATTC
1 ACGACGAACGACGTCGATTC
*
4369928 TCGACGAACGACGTCGATTC
1 ACGACGAACGACGTCGATTC
*
4369948 AGGACGA
1 ACGACGA
4369955 GAGGCTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (20 bp):
ACGACGAACGACGTCGATTC
Found at i:4371527 original size:19 final size:20
Alignment explanation
Indices: 4371473--4371528 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
4371463 TTCAACTTTA
4371473 ATTAATCACGTTTTTACATT
1 ATTAATCACGTTTTTACATT
4371493 ATTAGCA-CATACGTTTTTACATT
1 ATTA--ATC--ACGTTTTTACATT
4371516 A-TAATCACGTTTT
1 ATTAATCACGTTTT
4371529 CTTTTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
19 7 0.23
20 5 0.16
21 2 0.06
22 3 0.10
23 14 0.45
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (20 bp):
ATTAATCACGTTTTTACATT
Found at i:4373105 original size:12 final size:12
Alignment explanation
Indices: 4373088--4373112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4373078 TAATGTTCTG
4373088 AAAGAAGAAGAA
1 AAAGAAGAAGAA
4373100 AAAGAAGAAGAA
1 AAAGAAGAAGAA
4373112 A
1 A
4373113 GTTGTGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAGAA
Found at i:4376248 original size:2 final size:2
Alignment explanation
Indices: 4376241--4376272 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4376231 TGACATGATA
4376241 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
4376273 GGCCACCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4376976 original size:13 final size:13
Alignment explanation
Indices: 4376958--4376983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4376948 TTTTTAGCCT
4376958 AAAAATATTTAAA
1 AAAAATATTTAAA
4376971 AAAAATATTTAAA
1 AAAAATATTTAAA
4376984 TTATACGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATTTAAA
Found at i:4378689 original size:25 final size:25
Alignment explanation
Indices: 4378660--4378715 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
4378650 CTCCGCTTGT
*
4378660 CTGTTGCCGTTGATTGAGGCCAGAG
1 CTGTTGCCATTGATTGAGGCCAGAG
* * *
4378685 CTGTTTCCATTGATTGTGGCCGGAG
1 CTGTTGCCATTGATTGAGGCCAGAG
4378710 CTGTTG
1 CTGTTG
4378716 TTCTCTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.20, G:0.34, T:0.34
Consensus pattern (25 bp):
CTGTTGCCATTGATTGAGGCCAGAG
Found at i:4388495 original size:36 final size:36
Alignment explanation
Indices: 4388448--4388798 Score: 438
Period size: 36 Copynumber: 9.8 Consensus size: 36
4388438 ACGAACACTA
*
4388448 GAATCGAAAGTGCCGATGCTTCCTTCCGATCGACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* *
4388484 GAATCGAAAGTGTCGATG-TCTCCTTCCATTCGACTT
1 GAATCGAAAGTGCCGATGCT-TCCTTCCGTTCGACTT
* * *
4388520 GAATCGGAAGTGCCGATGCTTCCTTCCATTCGATTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* * *
4388556 CAATCGAAAATGTCGATGCTTCCTTCCGTTCGACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* * * * *
4388592 GAATCGGAAGTGTCGATGCCTCCTTTCGTTCGACTA
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* * *
4388628 AAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
*
4388664 GAATCGGAAA-TGCCGATGCTTCCTTTCGTTCGACTT
1 GAATC-GAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* * *
4388700 GAATCGGAAGTGTCGATGCCTCCTTCCGTTCGACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
* *
4388736 GAATC-AGAAGTGCTGATGCTTCTTTCCGTTCGACTT
1 GAATCGA-AAGTGCCGATGCTTCCTTCCGTTCGACTT
*
4388772 GAATCGGAAGTGCCGATGCTTCCTTCC
1 GAATCGAAAGTGCCGATGCTTCCTTCC
4388799 ATTCTTCTTA
Statistics
Matches: 269, Mismatches: 40, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
35 4 0.01
36 261 0.97
37 4 0.01
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (36 bp):
GAATCGAAAGTGCCGATGCTTCCTTCCGTTCGACTT
Found at i:4388595 original size:108 final size:108
Alignment explanation
Indices: 4388448--4388798 Score: 531
Period size: 108 Copynumber: 3.2 Consensus size: 108
4388438 ACGAACACTA
* * * * *
4388448 GAATCGAAAGTGCCGATGCTTCCTTCCGATCGACTTGAATCGAAAGTGTCGATGTCTCCTTCCAT
1 GAATCGAAAATGCCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTCCGT
* * *
4388513 TCGACTTGAATCGGAAGTGCCGATGCTTCCTTCCATTCGATTT
66 TCGACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
* * *
4388556 CAATCGAAAATGTCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTTCGT
1 GAATCGAAAATGCCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTCCGT
**
4388621 TCGACTAAAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
66 TCGACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
* *
4388664 GAATCGGAAATGCCGATGCTTCCTTTCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTCCGT
1 GAATCGAAAATGCCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTCCGT
* *
4388729 TCGACTTGAATCAGAAGTGCTGATGCTTCTTTCCGTTCGACTT
66 TCGACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
* *
4388772 GAATCGGAAGTGCCGATGCTTCCTTCC
1 GAATCGAAAATGCCGATGCTTCCTTCC
4388799 ATTCTTCTTA
Statistics
Matches: 219, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 219 1.00
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (108 bp):
GAATCGAAAATGCCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTCCGT
TCGACTTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGACTT
Done.