Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 62 of 235
Found at i:21059688 original size:25 final size:25
Alignment explanation
Indices: 21059660--21059710 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
21059650 CCCTTATAAT
* *
21059660 GTGAAAATGACCATTTTGCCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
21059685 GTGAAAATGACCATTATACCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
21059710 G
1 G
21059711 GATATGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (25 bp):
GTGAAAATGACCATTATACCCCTAG
Found at i:21059767 original size:10 final size:10
Alignment explanation
Indices: 21059752--21059789 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
21059742 GTATTGTACG
21059752 TGATATGCCA
1 TGATATGCCA
*
21059762 TGATATGCACT
1 TGATATGC-CA
21059773 TGATATGCCA
1 TGATATGCCA
21059783 TGATATG
1 TGATATG
21059790 TTCATATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (10 bp):
TGATATGCCA
Found at i:21060163 original size:31 final size:30
Alignment explanation
Indices: 21060125--21060208 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 30
21060115 CGTTTACAGT
21060125 AAAGGCTTCAGCCCAGTGATATGAAAAATGA
1 AAAGGCTTC-GCCCAGTGATATGAAAAATGA
*
21060156 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTC-GCCCAGTGATATGAAAAATGA
21060187 AAAGGCTTCGACCCAGT-ATATG
1 AAAGGCTTCG-CCCAGTGATATG
21060209 TTGAGACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 6 0.12
31 44 0.88
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (30 bp):
AAAGGCTTCGCCCAGTGATATGAAAAATGA
Found at i:21064566 original size:55 final size:55
Alignment explanation
Indices: 21064444--21064553 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
21064434 AAACTTAAAA
*
21064444 TTTATACTTAGCCATTTTAGCATGGTTTAATATATACACAACCTCAAAATCAAAC
1 TTTATACTTAGCCATTTTAGCATGGCTTAATATATACACAACCTCAAAATCAAAC
*
21064499 TTTATACTTAGCCATTTTTGCATGGCTTAATATATACACAACCTCAAAATCAAAC
1 TTTATACTTAGCCATTTTAGCATGGCTTAATATATACACAACCTCAAAATCAAAC
21064554 ATATTAACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (55 bp):
TTTATACTTAGCCATTTTAGCATGGCTTAATATATACACAACCTCAAAATCAAAC
Found at i:21076880 original size:40 final size:40
Alignment explanation
Indices: 21076782--21077044 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
21076772 TCCTCGTTCA
* * * ** *
21076782 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
21076821 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
21076861 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
21076901 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
21076941 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
21076981 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
21077021 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
21077045 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:21088920 original size:27 final size:27
Alignment explanation
Indices: 21088889--21089066 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21088879 TAAATTGTAC
21088889 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21088916 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21088942 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21088970 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21088998 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21089025 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21089052 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21089067 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21089003 original size:82 final size:81
Alignment explanation
Indices: 21088890--21089045 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21088880 AAATTGTACA
* *
21088890 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21088954 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21088971 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21089036 TGCGAGTTGA
65 TGCGAATTGA
21089046 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21089057 original size:82 final size:81
Alignment explanation
Indices: 21088886--21089066 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
21088876 GATTAAATTG
* *
21088886 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21088951 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21088967 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21089031 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21089049 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21089067 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21094413 original size:54 final size:54
Alignment explanation
Indices: 21094331--21094463 Score: 257
Period size: 54 Copynumber: 2.5 Consensus size: 54
21094321 TCTCTTGGCA
*
21094331 GGATTACCAGTCCAGGCTAAATCCCCCATATCATAAACTCATAAGGTGATGTTG
1 GGATTACCAGTCCAGGCTAAATCCCCCATATCATAAACTCATAAGGTGATGTCG
21094385 GGATTACCAGTCCAGGCTAAATCCCCCATATCATAAACTCATAAGGTGATGTCG
1 GGATTACCAGTCCAGGCTAAATCCCCCATATCATAAACTCATAAGGTGATGTCG
21094439 GGATTACCAGTCCAGGCTAAATCCC
1 GGATTACCAGTCCAGGCTAAATCCC
21094464 TTATAGCGAC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (54 bp):
GGATTACCAGTCCAGGCTAAATCCCCCATATCATAAACTCATAAGGTGATGTCG
Found at i:21103714 original size:40 final size:40
Alignment explanation
Indices: 21103645--21103929 Score: 389
Period size: 40 Copynumber: 7.2 Consensus size: 40
21103635 CAGATGATAA
* * *
21103645 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATA-TCCGGGCTAAGTCC
* * *
21103685 CGAAGGCATTTGTGCCAACTACTATTTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCC
*
21103725 CGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATA-TCCGGGCTAAGTCC
*
21103765 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCC
*
21103805 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCC
*
21103845 CGAAGGCATTTGTGCGAACTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCC
* * * *
21103885 CGAAGGCATTTGAGCG-AGTAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAATTA-CTATATCCGGGCTAAGTCC
21103924 CGAAGG
1 CGAAGG
21103930 TACTTGGTTT
Statistics
Matches: 226, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
39 17 0.08
40 208 0.92
41 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCC
Found at i:21103915 original size:80 final size:80
Alignment explanation
Indices: 21103645--21103903 Score: 439
Period size: 80 Copynumber: 3.2 Consensus size: 80
21103635 CAGATGATAA
* * *
21103645 CGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCCAACTACTAT
1 CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAT
*
21103710 TTCCGGGCTAAGTCC
66 ATCCGGGCTAAGTCC
**
21103725 CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
1 CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAT
21103790 ATCCGGGCTAAGTCC
66 ATCCGGGCTAAGTCC
21103805 CGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTA
1 CGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTA
21103869 TATCCGGGCTAAGTCC
65 TATCCGGGCTAAGTCC
*
21103885 CGAAGGCATTTGAGCGAGT
1 CGAAGGCATTTGTGCGAGT
21103904 AGCTATATCC
Statistics
Matches: 169, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
79 2 0.01
80 167 0.99
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (80 bp):
CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAT
ATCCGGGCTAAGTCC
Found at i:21111432 original size:40 final size:40
Alignment explanation
Indices: 21111377--21111566 Score: 294
Period size: 40 Copynumber: 4.8 Consensus size: 40
21111367 NNNNNNNNNN
21111377 TGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATT
1 TGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATT
*
21111417 TGTGCGAGTTACTAATTTCGGGCTAAGTCCCGAAGGCATT
1 TGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATT
* * *
21111457 TGTCCGAGTTACTATTTCCGGGCTAAGTCCCAAAGGCATT
1 TGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATT
21111497 TGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATT
1 TGTGCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATT
* *
21111537 GGTGCGAGTTACT-ATATCCGGGCTATGTCC
1 TGTGCGAGTTACTAAT-TCCGGGCTAAGTCC
21111567 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 138 0.99
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.29
Consensus pattern (40 bp):
TGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATT
Found at i:21112959 original size:13 final size:13
Alignment explanation
Indices: 21112941--21112973 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21112931 GGTTGTTTAT
21112941 TAAACTAATTAAC
1 TAAACTAATTAAC
21112954 TAAACTAATTAAC
1 TAAACTAATTAAC
21112967 T-AACTAA
1 TAAACTAA
21112974 ACTAAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:21114032 original size:12 final size:11
Alignment explanation
Indices: 21114006--21114033 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21113996 ATTTTGTCCC
21114006 TTTTTGGCTCG
1 TTTTTGGCTCG
21114017 TTTTTGGCTCG
1 TTTTTGGCTCG
21114028 TTTTTG
1 TTTTTG
21114034 ACTCTTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.25, T:0.61
Consensus pattern (11 bp):
TTTTTGGCTCG
Found at i:21115908 original size:6 final size:6
Alignment explanation
Indices: 21115884--21115948 Score: 105
Period size: 6 Copynumber: 10.8 Consensus size: 6
21115874 TATGTCTTTC
*
21115884 AAAAGT AAATAAT -AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
21115932 AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAA
21115949 GATAGGAGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
5 3 0.05
6 51 0.91
7 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:21117976 original size:39 final size:39
Alignment explanation
Indices: 21117927--21118181 Score: 395
Period size: 39 Copynumber: 6.5 Consensus size: 39
21117917 GTGTGAGATA
* * *
21117927 TATATCCGGGCTAATTCTCGAAGGCATTCGTGCTGGTGT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
21117966 TATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
21118005 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
21118044 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
21118083 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * * *
21118122 TATATCCGGGCTAAGTCCTGAAGGC-TTTGTGCTGGTAT
1 TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
21118160 TACATCCGGGCTTAAAGTCCCG
1 TATATACGGGC-T-AAGTCCCG
21118182 CATGCTTTGT
Statistics
Matches: 204, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
38 21 0.10
39 176 0.86
40 7 0.03
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (39 bp):
TATATACGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:21124838 original size:13 final size:13
Alignment explanation
Indices: 21124820--21124852 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21124810 GGTTGTTTAT
21124820 TAAACTAATTAAC
1 TAAACTAATTAAC
21124833 TAAACTAATTAAC
1 TAAACTAATTAAC
21124846 T-AACTAA
1 TAAACTAA
21124853 ACTAAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:21125912 original size:10 final size:11
Alignment explanation
Indices: 21125886--21125911 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21125876 GTTTTGTCCC
21125886 TTTTTGGCTCG
1 TTTTTGGCTCG
21125897 TTTTTGGCTCG
1 TTTTTGGCTCG
21125908 TTTT
1 TTTT
21125912 GACTCTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.23, T:0.62
Consensus pattern (11 bp):
TTTTTGGCTCG
Found at i:21130976 original size:42 final size:42
Alignment explanation
Indices: 21130782--21130983 Score: 172
Period size: 42 Copynumber: 4.6 Consensus size: 42
21130772 AGATGCCAAT
* *
21130782 GCCATATCCTAGATATGGTCTTACATGGGATCACATATCGAT
1 GCCATATCCCAGATATGGTCTTACATGGGATCACATATCGAG
* * *** * *
21130824 GCCAATAGCCCAGCTATGGTCTTACACAATG-TCTCATATCGAT
1 GCC-ATATCCCAGATATGGTCTTACA-TGGGATCACATATCGAG
* * * * ** *
21130867 GCCATGTCCCACACATGGTCTTACACGAAATCACATATTGATG
1 GCCATATCCCAGATATGGTCTTACATGGGATCACATATCGA-G
21130910 CTAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCGAG
1 -----GCCATATCCCAGATATGGTCTTACATGGGATCACATATCGAG
*
21130957 GTCATATCCCAGATATGGTCTTACATG
1 GCCATATCCCAGATATGGTCTTACATG
21130984 AAACCATACA
Statistics
Matches: 124, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
42 55 0.44
43 33 0.27
44 1 0.01
47 1 0.01
48 34 0.27
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACATGGGATCACATATCGAG
Found at i:21132175 original size:21 final size:19
Alignment explanation
Indices: 21132141--21132181 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
21132131 ACAAATATTT
*
21132141 TTACTTTGGATTTGTTGAAA
1 TTACTTTAGATTTGTT-AAA
21132161 TTACTTATAGATTTGTTAAA
1 TTACTT-TAGATTTGTTAAA
21132181 T
1 T
21132182 CAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (19 bp):
TTACTTTAGATTTGTTAAA
Found at i:21137526 original size:12 final size:12
Alignment explanation
Indices: 21137498--21137526 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
21137488 TATACCTATA
21137498 TGGTAGAATTTT
1 TGGTAGAATTTT
21137510 T-GTAGAATTTT
1 TGGTAGAATTTT
21137521 TGGTAG
1 TGGTAG
21137527 GGCCAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (12 bp):
TGGTAGAATTTT
Found at i:21151818 original size:13 final size:13
Alignment explanation
Indices: 21151800--21151825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21151790 CCTAAGGTTT
21151800 CCATAGAAATTTA
1 CCATAGAAATTTA
21151813 CCATAGAAATTTA
1 CCATAGAAATTTA
21151826 GGGAAGAAGA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CCATAGAAATTTA
Found at i:21158217 original size:58 final size:59
Alignment explanation
Indices: 21158168--21158283 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 59
21158158 ATCACATTAA
* *
21158168 TATTAAAATCATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAAGC
1 TATTAAAATAATAGAATACTTACTACAAGATAAATATTAGATTAAATTTAATATTAAA-C
* * *
21158226 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAAATAATAGAATACTTA-CTACAAGATAAATATTAGATTAAATTTAATATTAA
21158284 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 19 0.38
60 1 0.02
61 30 0.60
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (59 bp):
TATTAAAATAATAGAATACTTACTACAAGATAAATATTAGATTAAATTTAATATTAAAC
Found at i:21158322 original size:25 final size:25
Alignment explanation
Indices: 21158268--21158322 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
21158258 AAATATTAAA
*
21158268 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
21158293 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
21158317 TATTAA
1 T-TTAA
21158323 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:21195209 original size:28 final size:28
Alignment explanation
Indices: 21195177--21195304 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
21195167 ATAGTAAGTC
*
21195177 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
21195205 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
21195234 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
21195262 TGCACACTTAGTGCTATACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
21195291 CGCACGCTTAGTGC
1 CGCACACTTAGTGC
21195305 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:21195235 original size:29 final size:29
Alignment explanation
Indices: 21195177--21195304 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
21195167 ATAGTAAGTC
*
21195177 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
21195205 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
*
21195234 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * *
21195262 TGCACACTTAGTGCTATACA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
*
21195291 CGCACGCTTAGTGC
1 CGCACACTTAGTGC
21195305 CAATCTCATG
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
28 39 0.44
29 46 0.52
30 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:21195267 original size:57 final size:57
Alignment explanation
Indices: 21195176--21195304 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
21195166 TATAGTAAGT
*
21195176 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * *
21195233 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATACAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
*
21195290 CCGCACGCTTAGTGC
1 CCGCACACTTAGTGC
21195305 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 60 0.94
58 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:21197152 original size:107 final size:107
Alignment explanation
Indices: 21197018--21197229 Score: 379
Period size: 107 Copynumber: 2.0 Consensus size: 107
21197008 AAACATGCAT
* *
21197018 AGATTTTCAAGAATCATTCAATACATACCTCATTCTAGCCATCTTCCAAGCCAAAATCCAATAAC
1 AGATTTTCAAGAATCATTCAATACATACCTCATTCTAGCCATATTCCAAGCCAAAATCAAATAAC
*
21197083 CAAATCTCCCTTCCTTCTCCTTACTCACGGCAATAGCCAAAG
66 CAAATCTCCCTTCCTTCTCCTCACTCACGGCAATAGCCAAAG
21197125 AGATTTTCAAGAATCATTCAATACATACCTCATTCTAGCCATATTCCAAGCCAAAATCAAATAAC
1 AGATTTTCAAGAATCATTCAATACATACCTCATTCTAGCCATATTCCAAGCCAAAATCAAATAAC
* *
21197190 CAAGTCTCCCTTCCTTCTCCTCACTCACGGCAATTGCCAA
66 CAAATCTCCCTTCCTTCTCCTCACTCACGGCAATAGCCAA
21197230 GAAAAAAAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (107 bp):
AGATTTTCAAGAATCATTCAATACATACCTCATTCTAGCCATATTCCAAGCCAAAATCAAATAAC
CAAATCTCCCTTCCTTCTCCTCACTCACGGCAATAGCCAAAG
Found at i:21213178 original size:28 final size:28
Alignment explanation
Indices: 21213138--21213193 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
21213128 TGGTAAGATT
*
21213138 TTCGAGGACGAAAATCCTTAAAGGGGGG
1 TTCGAAGACGAAAATCCTTAAAGGGGGG
21213166 TTCGAAGACGAAAATCCTTAAAGGGGGG
1 TTCGAAGACGAAAATCCTTAAAGGGGGG
21213194 AGAGTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.18
Consensus pattern (28 bp):
TTCGAAGACGAAAATCCTTAAAGGGGGG
Found at i:21213999 original size:30 final size:30
Alignment explanation
Indices: 21213963--21214022 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
21213953 TTCCCGAGCC
*
21213963 TAGGGGCAAAAGTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAATGTAATTTTGCAAAAGTT
* *
21213993 TAGGGGCAAAAATGTAATTTTTCTAAAGTT
1 TAGGGGCAAAAATGTAATTTTGCAAAAGTT
21214023 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTTTGCAAAAGTT
Found at i:21229788 original size:24 final size:24
Alignment explanation
Indices: 21229756--21229814 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
21229746 GTCAATTAAA
21229756 TAAAGTAATTTCTATAAAAAAAAC
1 TAAAGTAATTTCTATAAAAAAAAC
21229780 TAAAGTAATTTCTATAAAAAAAAC
1 TAAAGTAATTTCTATAAAAAAAAC
21229804 TAAAGTAATTT
1 TAAAGTAATTT
21229815 AAAAGCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (24 bp):
TAAAGTAATTTCTATAAAAAAAAC
Found at i:21231027 original size:28 final size:30
Alignment explanation
Indices: 21230964--21231033 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
21230954 TGTAAATTTG
*
21230964 TGAAAAG-TGAAGAGTTAAATTGTAAAAAT
1 TGAAAAGTTGAAGAGTTAAATTGTAAAAAA
*
21230993 TCAAAAGTTGAAGAGTT-AA-T-TAAAAACA
1 TGAAAAGTTGAAGAGTTAAATTGTAAAAA-A
21231021 TGAAAAGTTGAAG
1 TGAAAAGTTGAAG
21231034 GACCAAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.17
28 13 0.36
29 8 0.22
30 9 0.25
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.26
Consensus pattern (30 bp):
TGAAAAGTTGAAGAGTTAAATTGTAAAAAA
Found at i:21231135 original size:20 final size:20
Alignment explanation
Indices: 21231110--21231180 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
21231100 GATGGAACTG
21231110 ATATATTATATTAAACATAA
1 ATATATTATATTAAACATAA
* * *
21231130 ATATATTTTA-TGAAGATGGAACTA
1 ATATATTATATTAAACAT---A--A
21231154 ATATATTATATTAAACATAA
1 ATATATTATATTAAACATAA
21231174 ATATATT
1 ATATATT
21231181 TACTGTGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 5 0.13
20 17 0.44
22 2 0.05
24 10 0.26
25 5 0.13
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (20 bp):
ATATATTATATTAAACATAA
Found at i:21231135 original size:22 final size:22
Alignment explanation
Indices: 21231110--21231179 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
21231100 GATGGAACTG
21231110 ATATATTATATTAAACATAAAT
1 ATATATTATATTAAACATAAAT
* * *
21231132 ATAT-TT-TA-TGAAGATGGAACT
1 ATATATTATATTAAACAT--AAAT
21231153 AATATATTATATTAAACATAAAT
1 -ATATATTATATTAAACATAAAT
21231176 ATAT
1 ATAT
21231180 TTACTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 5 0.14
20 2 0.06
21 5 0.14
22 12 0.33
23 5 0.14
24 2 0.06
25 5 0.14
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (22 bp):
ATATATTATATTAAACATAAAT
Found at i:21231158 original size:44 final size:44
Alignment explanation
Indices: 21231092--21231181 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
21231082 TTGATTTTGC
*
21231092 TTTATGAAGATGGAACTGATATATTATATTAAACATAAATATAT
1 TTTATGAAGATGGAACTAATATATTATATTAAACATAAATATAT
21231136 TTTATGAAGATGGAACTAATATATTATATTAAACATAAATATAT
1 TTTATGAAGATGGAACTAATATATTATATTAAACATAAATATAT
21231180 TT
1 TT
21231182 ACTGTGTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (44 bp):
TTTATGAAGATGGAACTAATATATTATATTAAACATAAATATAT
Found at i:21232520 original size:29 final size:28
Alignment explanation
Indices: 21232473--21232527 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
21232463 GTGAGTTATA
*
21232473 CTGATTTGGCTTTAAGCCATGAATATCGG
1 CTGATTTGGCTTCAAGCCATG-ATATCGG
**
21232502 CTGATTTGGCTTCGGGCCATGATATC
1 CTGATTTGGCTTCAAGCCATGATATC
21232528 AGTATTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (28 bp):
CTGATTTGGCTTCAAGCCATGATATCGG
Found at i:21232555 original size:77 final size:77
Alignment explanation
Indices: 21232426--21232570 Score: 195
Period size: 77 Copynumber: 1.9 Consensus size: 77
21232416 TAAGGAACAT
* * * *
21232426 TGATTTGGCTTCGGGCCATGATATTAGCATTTCAAGTGTGAGTTATACTGATTTGGCTTTAAGCC
1 TGATTTGGCTTCGGGCCATGATATCAGCATTTCAAGTATAAGTTATACTGATTTGGCTTCAAGCC
21232491 ATGAATATCGGC
66 ATGAATATCGGC
* * *
21232503 TGATTTGGCTTCGGGCCATGATATCAGTATTTCGAA-TATAAGTTA-CCTTGATTTGGCTTCGAG
1 TGATTTGGCTTCGGGCCATGATATCAGCATTTC-AAGTATAAGTTATAC-TGATTTGGCTTCAAG
21232566 CCATG
64 CCATG
21232571 GTATATGTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
76 1 0.02
77 56 0.95
78 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (77 bp):
TGATTTGGCTTCGGGCCATGATATCAGCATTTCAAGTATAAGTTATACTGATTTGGCTTCAAGCC
ATGAATATCGGC
Found at i:21235269 original size:18 final size:18
Alignment explanation
Indices: 21235246--21235284 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21235236 GAGACAAGGT
21235246 TAGAAAACATGATTTAGA
1 TAGAAAACATGATTTAGA
*
21235264 TAGAAAACATGATTTATA
1 TAGAAAACATGATTTAGA
21235282 TAG
1 TAG
21235285 TAGATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (18 bp):
TAGAAAACATGATTTAGA
Found at i:21241659 original size:23 final size:23
Alignment explanation
Indices: 21241633--21241703 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
21241623 TTCATTTAAC
21241633 TTAATCAAATATGTTCACGAACA
1 TTAATCAAATATGTTCACGAACA
* * *
21241656 TTAAACAAATATATTCATGAACA
1 TTAATCAAATATGTTCACGAACA
** * *
21241679 TATAATTGAACATGATCACGAACA
1 T-TAATCAAATATGTTCACGAACA
21241703 T
1 T
21241704 GTTAATAAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.30
Consensus pattern (23 bp):
TTAATCAAATATGTTCACGAACA
Found at i:21241743 original size:4 final size:4
Alignment explanation
Indices: 21241734--21241763 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
21241724 CGAAAATAAC
21241734 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
21241764 TATTGTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:21241945 original size:12 final size:12
Alignment explanation
Indices: 21241914--21241948 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21241904 GTCATTAATA
* *
21241914 AATAAACAAGTC
1 AATAAACGAGCC
21241926 AATAAACGAGCC
1 AATAAACGAGCC
21241938 AATAAACGAGC
1 AATAAACGAGC
21241949 TTTTTCGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.11
Consensus pattern (12 bp):
AATAAACGAGCC
Found at i:21244788 original size:39 final size:40
Alignment explanation
Indices: 21244674--21244858 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
21244664 GCTACTCGTT
*
21244674 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
21244714 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
21244754 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
21244793 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
21244834 CAAA-GCCTTCGAGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
21244859 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:21244842 original size:79 final size:80
Alignment explanation
Indices: 21244674--21244858 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 80
21244664 GCTACTCGTT
* * *
21244674 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCG
* *
21244738 GATTTAGTAACTCGCAC
64 GATATAGTAACTAGCAC
* **
21244755 CAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 CAAAGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* *
21244818 ATATGGTCACTTAGCA-
65 ATATAGTAAC-TAGCAC
*
21244834 CAAAGCCTTCGAGACTTAGCCCGGA
1 CAAAGCCTTCG-GGCTTAGCCCGGA
21244859 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 56 0.64
80 26 0.30
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGA
TATAGTAACTAGCAC
Found at i:21252376 original size:39 final size:40
Alignment explanation
Indices: 21252277--21252420 Score: 127
Period size: 40 Copynumber: 3.6 Consensus size: 40
21252267 CGAATGATGT
* * *
21252277 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
*** *
21252317 CCATACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
* *
21252357 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
21252396 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
21252421 AACGAGTAGC
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
39 33 0.39
40 40 0.48
41 10 0.12
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:21252427 original size:40 final size:39
Alignment explanation
Indices: 21252329--21252420 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 39
21252319 ATACTAAGAT
* *
21252329 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGC
* *
21252368 CCGAAGGCATTGGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-C
21252408 CCGAAGGCATTTG
1 CCGAAGGCATTTG
21252421 AACGAGTAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.04
39 31 0.67
40 13 0.28
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGC
Found at i:21252712 original size:47 final size:47
Alignment explanation
Indices: 21252643--21253899 Score: 2271
Period size: 47 Copynumber: 26.6 Consensus size: 47
21252633 AAGGGTTGGT
21252643 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21252690 AATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21252737 AATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21252784 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21252831 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21252880 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGGGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21252927 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21252974 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253021 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253068 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253115 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253162 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253209 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253256 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21253303 AATGTGAAATTGTATATATATGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21253350 AATGTGAAATTGTATATATATGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253399 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253446 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253493 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253540 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253587 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21253634 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGAGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21253683 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGGGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
21253732 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
21253779 AATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
21253826 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
21253873 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
21253900 TCCCGAAGGG
Statistics
Matches: 1175, Mismatches: 29, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
47 992 0.84
49 183 0.16
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:21254074 original size:37 final size:37
Alignment explanation
Indices: 21254018--21254096 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
21254008 CCGAGCTCTA
* * *
21254018 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
21254055 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
21254092 AAGAC
1 AAGAC
21254097 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:21262763 original size:49 final size:49
Alignment explanation
Indices: 21262691--21262788 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
21262681 TTACTCATTA
*
21262691 CATGATTTCCCTATTCCATTTGATTAGTTAGAAGTGAATATTCATGGTT
1 CATGATTTCCCTACTCCATTTGATTAGTTAGAAGTGAATATTCATGGTT
21262740 CATGATTTCCCTACTCCATTTGATTAGTTAGAAGTGAATATTCATGGTT
1 CATGATTTCCCTACTCCATTTGATTAGTTAGAAGTGAATATTCATGGTT
21262789 AAGATAGTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (49 bp):
CATGATTTCCCTACTCCATTTGATTAGTTAGAAGTGAATATTCATGGTT
Found at i:21267579 original size:86 final size:86
Alignment explanation
Indices: 21267434--21267604 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
21267424 AACGGGGCTT
21267434 GGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGAGAAACCTTGAAATT
1 GGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGAGAAACCTTGAAATT
21267499 TCGGCCTAATGAAGAAGATGC
66 TCGGCCTAATGAAGAAGATGC
*
21267520 GGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGAGAACCCTTGAAATT
1 GGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGAGAAACCTTGAAATT
21267585 TCGGCCTAATGAAGAAGATG
66 TCGGCCTAATGAAGAAGATG
21267605 GACAAAAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (86 bp):
GGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGAGAAACCTTGAAATT
TCGGCCTAATGAAGAAGATGC
Found at i:21270594 original size:47 final size:47
Alignment explanation
Indices: 21270524--21270724 Score: 294
Period size: 47 Copynumber: 4.3 Consensus size: 47
21270514 CCCTTCGGGA
* * * *
21270524 CTTATCACATTTATATACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* *
21270571 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* *
21270618 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* * * *
21270665 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
21270712 CTTATCACATATA
1 CTTATCACATATA
21270725 CATATCTTGT
Statistics
Matches: 139, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 139 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
Found at i:21276711 original size:60 final size:60
Alignment explanation
Indices: 21276643--21276759 Score: 209
Period size: 60 Copynumber: 1.9 Consensus size: 60
21276633 ACAAAAAGTA
*
21276643 ATATACATCATTGAAGGTGGGATTTTATACCTT-TCTTGGTAGAATTTGTGTCAATTTTCC
1 ATATACATCATTGAAGGTGGGATTTTATACCTTCT-TTGGTAGAACTTGTGTCAATTTTCC
21276703 ATATACATCATTGAAGGTGGGATTTTATACCTTCTTTGGTAGAACTTGTGTCAATTT
1 ATATACATCATTGAAGGTGGGATTTTATACCTTCTTTGGTAGAACTTGTGTCAATTT
21276760 CCCCTACAGC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (60 bp):
ATATACATCATTGAAGGTGGGATTTTATACCTTCTTTGGTAGAACTTGTGTCAATTTTCC
Found at i:21279120 original size:54 final size:54
Alignment explanation
Indices: 21279056--21279163 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
21279046 CTAGCTCTAT
21279056 TAGGGGTGTAACCATTACAATGCTATTTTTTTTTTTTAGTTTCATTGTTACTAA
1 TAGGGGTGTAACCATTACAATGCTATTTTTTTTTTTTAGTTTCATTGTTACTAA
*
21279110 TAGGGGTGTAACCATTTCAATGCTATTTTTTTTTTTTAGTTTCATTGTTACTAA
1 TAGGGGTGTAACCATTACAATGCTATTTTTTTTTTTTAGTTTCATTGTTACTAA
21279164 GTGAGGTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (54 bp):
TAGGGGTGTAACCATTACAATGCTATTTTTTTTTTTTAGTTTCATTGTTACTAA
Found at i:21285155 original size:28 final size:28
Alignment explanation
Indices: 21285092--21285188 Score: 153
Period size: 27 Copynumber: 3.5 Consensus size: 28
21285082 ATATTAAGTC
* *
21285092 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
21285119 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
21285147 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
21285175 C-CACACTTAGTGCT
1 CGCACACTTAGTGCT
21285189 GCACAATTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
27 34 0.52
28 32 0.48
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:21285201 original size:28 final size:27
Alignment explanation
Indices: 21285092--21285213 Score: 108
Period size: 27 Copynumber: 4.4 Consensus size: 27
21285082 ATATTAAGTC
* * *
21285092 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCT-CACAATCAAACT
*
21285119 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCT-CACAATCAAACT
21285147 CGCACACTTAGTGCT-ACATAGTCAAACT
1 CGCACACTTAGTGCTCACA-A-TCAAACT
*
21285175 C-CACACTTAGTGCTGCACAATTTAAAC-
1 CGCACACTTAGTGCT-CACAA-TCAAACT
21285202 CTGCACACTTAG
1 C-GCACACTTAG
21285214 CGCCAATGCA
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.02
27 36 0.43
28 33 0.40
29 12 0.14
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCTCACAATCAAACT
Found at i:21285278 original size:128 final size:128
Alignment explanation
Indices: 21285093--21285348 Score: 453
Period size: 128 Copynumber: 2.0 Consensus size: 128
21285083 TATTAAGTCC
*
21285093 GCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAG
1 GCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAG
21285158 TGCTACATAGTCAAACTC-CACACTTAGTGCTGCACAATTTAAACCTGCACACTTAGCGCCAAT
66 TGCTACATAGTC-AACTCGCACACTTAGTGCTGCACAATTTAAACCTGCACACTTAGCGCCAAT
*
21285221 GCACACTTAGTGCTACATAAGTCAACTCGCACACTTAGTGCTACAT-ATCAAACTCGCACACTTA
1 GCACACTCAGTGCTACATAA-TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
*
21285285 GTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACCTGCACACTTAGCGCCAAT
65 GTGCTACATAGTCAACTCGCACACTTAGTGCTGCACAATTTAAACCTGCACACTTAGCGCCAAT
21285349 CTCATGGTCA
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
127 4 0.03
128 94 0.76
129 25 0.20
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (128 bp):
GCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAG
TGCTACATAGTCAACTCGCACACTTAGTGCTGCACAATTTAAACCTGCACACTTAGCGCCAAT
Found at i:21285282 original size:27 final size:27
Alignment explanation
Indices: 21285221--21285316 Score: 158
Period size: 27 Copynumber: 3.5 Consensus size: 27
21285211 TAGCGCCAAT
21285221 GCACACTTAGTGCTACATAAGTCAACTC
1 GCACACTTAGTGCTACAT-AGTCAACTC
21285249 GCACACTTAGTGCTACATA-TCAAACTC
1 GCACACTTAGTGCTACATAGTC-AACTC
*
21285276 GCACACTTAGTGCTACATAGTCAATTC
1 GCACACTTAGTGCTACATAGTCAACTC
21285303 GCACACTTAGTGCT
1 GCACACTTAGTGCT
21285317 GCACAATTTA
Statistics
Matches: 65, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
26 2 0.03
27 43 0.66
28 20 0.31
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAGTCAACTC
Found at i:21296117 original size:26 final size:26
Alignment explanation
Indices: 21296088--21296143 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
21296078 TGATAAAAAG
21296088 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
21296114 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
21296140 TGAT
1 TGAT
21296144 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:21297780 original size:27 final size:27
Alignment explanation
Indices: 21297740--21297879 Score: 146
Period size: 27 Copynumber: 5.2 Consensus size: 27
21297730 AGGAAGCGTC
*
21297740 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
21297767 CTGGTGGCTCTGCCAC-ATATATTTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
21297793 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* * *
21297821 TTGGTGGCTCTACCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
21297848 CT-GTGGCTCTGCTACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
21297874 CTGGTG
1 CTGGTG
21297880 ACTTCATCAC
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
25 6 0.06
26 19 0.20
27 65 0.70
28 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:21297819 original size:54 final size:54
Alignment explanation
Indices: 21297737--21297879 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
21297727 TGGAGGAAGC
* *
21297737 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATTT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
*
21297791 GTCCTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
* * *
21297845 GTTCT-GTGGCTCTGCTACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
21297880 ACTTCATCAC
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
52 6 0.07
53 20 0.25
54 55 0.68
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.36
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
Found at i:21300903 original size:14 final size:14
Alignment explanation
Indices: 21300884--21300921 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21300874 AAAAAGTAAG
21300884 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
**
21300898 TCATTTTCTTAAAA
1 TCATTTTCCAAAAA
21300912 TCA-TTTCCAA
1 TCATTTTCCAA
21300922 TGAAACAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:21301374 original size:38 final size:37
Alignment explanation
Indices: 21301331--21301406 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 37
21301321 ATCTCTTTGG
21301331 CATCTTTCAACAGCTTCACTATTGCCATCATCTTTCC
1 CATCTTTCAACAGCTTCACTATTGCCATCATCTTTCC
21301368 CNATCTTTCAACAGCTTCACTATTGCCATCATCTTTCC
1 C-ATCTTTCAACAGCTTCACTATTGCCATCATCTTTCC
21301406 C
1 C
21301407 TAGAGATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.37
Consensus pattern (37 bp):
CATCTTTCAACAGCTTCACTATTGCCATCATCTTTCC
Found at i:21311375 original size:15 final size:17
Alignment explanation
Indices: 21311350--21311381 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21311340 AACAAATAGA
21311350 AAACAACAT-AATTTAT
1 AAACAACATAAATTTAT
21311366 AAAC-ACATAAATTTAT
1 AAACAACATAAATTTAT
21311382 TCAATAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACAACATAAATTTAT
Found at i:21315335 original size:77 final size:77
Alignment explanation
Indices: 21315208--21315363 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
21315198 CCCACAAGTT
21315208 AGTGTGTTAGAAAAATTGTTGAGAAATATTGAAGCTTAACAAGCCTTGGTTATGATGTATCAAAT
1 AGTGTGTTAGAAAAATTGTTGAGAAATATTGAAGCTTAACAAGCCTTGGTTATGATGTATCAAAT
21315273 TGACTAATAATG
66 TGACTAATAATG
21315285 AGTGTGTTAGAAAAATTGTTGAGAAATATTGAAGCTTAACAAGCCTTGGTTATGATGTATCAAAT
1 AGTGTGTTAGAAAAATTGTTGAGAAATATTGAAGCTTAACAAGCCTTGGTTATGATGTATCAAAT
21315350 TGACTAATAATG
66 TGACTAATAATG
21315362 AG
1 AG
21315364 GTATGATATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (77 bp):
AGTGTGTTAGAAAAATTGTTGAGAAATATTGAAGCTTAACAAGCCTTGGTTATGATGTATCAAAT
TGACTAATAATG
Found at i:21317333 original size:18 final size:17
Alignment explanation
Indices: 21317310--21317343 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
21317300 TTTGCTAAGA
21317310 AAAAAAAATAGAAGAAAG
1 AAAAAAAAT-GAAGAAAG
21317328 AAAAAAAATGAAGAAA
1 AAAAAAAATGAAGAAA
21317344 TGTAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAAAATGAAGAAAG
Found at i:21326864 original size:42 final size:42
Alignment explanation
Indices: 21326784--21326900 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
21326774 GCTCCAGTTA
* * * * * *
21326784 CTTATGAGTTTTAGTTCAACCC-TATTGGGTTTCTGTTCAGCT
1 CTTATGAGCTTCAATTCAACCCTTA-TAGGTTTCCGTTCAACT
*
21326826 CTTCTGAGCTTCAACTT-AACCCTTATAGGTTTCCGTTCAACT
1 CTTATGAGCTTCAA-TTCAACCCTTATAGGTTTCCGTTCAACT
* *
21326868 CTTATGAGCTTCCATTCAACCCTTATGGGTTTC
1 CTTATGAGCTTCAATTCAACCCTTATAGGTTTC
21326901 TATTTAGCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.03
42 56 0.90
43 4 0.06
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (42 bp):
CTTATGAGCTTCAATTCAACCCTTATAGGTTTCCGTTCAACT
Found at i:21327871 original size:52 final size:53
Alignment explanation
Indices: 21327751--21327897 Score: 217
Period size: 53 Copynumber: 2.8 Consensus size: 53
21327741 CAGGTTTTTG
* * *
21327751 CACATGGCCTAGCACGCGGGTGTGTGGCTTGGCCGAGTGACCCTTGAACCTTT
1 CACACGGCCTAGCACACGGGTGTGTGGCTTGGCCGTGTGACCCTTGAACCTTT
* *
21327804 CACACGGCCTAGCACATGGGTGTGTGGCTTAGCCGTGTGACCC-TGAACCTTT
1 CACACGGCCTAGCACACGGGTGTGTGGCTTGGCCGTGTGACCCTTGAACCTTT
* *
21327856 CACACGGCTTAGCACACAGGTGTGTGG-TTGGCCGTGTGACCC
1 CACACGGCCTAGCACACGGGTGTGTGGCTTGGCCGTGTGACCC
21327898 AAGTCAGAGA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 14 0.16
52 33 0.39
53 38 0.45
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.24
Consensus pattern (53 bp):
CACACGGCCTAGCACACGGGTGTGTGGCTTGGCCGTGTGACCCTTGAACCTTT
Found at i:21329398 original size:8 final size:8
Alignment explanation
Indices: 21329385--21329410 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21329375 TGGCTAAGGT
21329385 TTCCAAGC
1 TTCCAAGC
21329393 TTCCAAGC
1 TTCCAAGC
21329401 TTCCAAGC
1 TTCCAAGC
21329409 TT
1 TT
21329411 GATTATGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.31
Consensus pattern (8 bp):
TTCCAAGC
Found at i:21330087 original size:28 final size:28
Alignment explanation
Indices: 21330056--21330139 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
21330046 AACTGTGATC
21330056 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
21330084 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
*
21330106 ACGTGTGTAATACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
21330134 ACGTGT
1 ACGTGT
21330140 ACCGGATAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
21 1 0.02
22 8 0.20
23 2 0.05
24 3 0.07
25 6 0.15
26 3 0.07
27 2 0.05
28 14 0.34
29 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:21330174 original size:49 final size:49
Alignment explanation
Indices: 21330001--21330246 Score: 303
Period size: 49 Copynumber: 5.0 Consensus size: 49
21329991 TATATTGTGA
* * * * *
21330001 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCTGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GGATAGT-T
* * * * *
21330052 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTT
* *
21330101 AGGTCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCGGATAGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTT
*
21330151 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTT
* * * * *
21330200 GGTCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACCAGATAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAG
21330247 CTTTGGCTAC
Statistics
Matches: 170, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 88 0.52
50 46 0.27
51 36 0.21
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTT
Found at i:21333315 original size:306 final size:306
Alignment explanation
Indices: 21332762--21333376 Score: 1221
Period size: 306 Copynumber: 2.0 Consensus size: 306
21332752 TAACTTAATT
21332762 AAACAAAGTATAGAAAAGTAGTGTCGATCCCACAAGGACTGGGACTCCTAATATCGTTTCTACGT
1 AAACAAAGTATAGAAAAGTAGTGTCGATCCCACAAGGACTGGGACTCCTAATATCGTTTCTACGT
21332827 GACCAGATTCCAAGGTCGTGGCAACTATCATGCCCACAACTTATCGTGTGCTGAAATGAAAAATA
66 GACCAGATTCCAAGGTCGTGGCAACTATCATGCCCACAACTTATCGTGTGCTGAAATGAAAAATA
21332892 AATAAAAGGGGATTTTAGTTGATAAATGTTAAAATAATAAAATGAATAGAACGAAATAATAACAG
131 AATAAAAGGGGATTTTAGTTGATAAATGTTAAAATAATAAAATGAATAGAACGAAATAATAACAG
21332957 AACGATAATTGCAAATAAAATTAAATTGGTAAATCAAATATGCGAATCCTTAGCCTTAGACTTGG
196 AACGATAATTGCAAATAAAATTAAATTGGTAAATCAAATATGCGAATCCTTAGCCTTAGACTTGG
*
21333022 TAAATTCCAGTCTTGAATCGATCCTTAAAATTGAATATTTCCTTTC
261 TAAATTCCAGTCTTGAATCGATCCTTAAAAGTGAATATTTCCTTTC
21333068 AAACAAAGTATAGAAAAGTAGTGTCGATCCCACAAGGACTGGGACTCCTAATATCGTTTCTACGT
1 AAACAAAGTATAGAAAAGTAGTGTCGATCCCACAAGGACTGGGACTCCTAATATCGTTTCTACGT
21333133 GACCAGATTCCAAGGTCGTGGCAACTATCATGCCCACAACTTATCGTGTGCTGAAATGAAAAATA
66 GACCAGATTCCAAGGTCGTGGCAACTATCATGCCCACAACTTATCGTGTGCTGAAATGAAAAATA
21333198 AATAAAAGGGGATTTTAGTTGATAAATGTTAAAATAATAAAATGAATAGAACGAAATAATAACAG
131 AATAAAAGGGGATTTTAGTTGATAAATGTTAAAATAATAAAATGAATAGAACGAAATAATAACAG
21333263 AACGATAATTGCAAATAAAATTAAATTGGTAAATCAAATATGCGAATCCTTAGCCTTAGACTTGG
196 AACGATAATTGCAAATAAAATTAAATTGGTAAATCAAATATGCGAATCCTTAGCCTTAGACTTGG
21333328 TAAATTCCAGTCTTGAATCGATCCTTAAAAGTGAATATTTCCTTTC
261 TAAATTCCAGTCTTGAATCGATCCTTAAAAGTGAATATTTCCTTTC
21333374 AAA
1 AAA
21333377 TGATAAGTTG
Statistics
Matches: 308, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
306 308 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (306 bp):
AAACAAAGTATAGAAAAGTAGTGTCGATCCCACAAGGACTGGGACTCCTAATATCGTTTCTACGT
GACCAGATTCCAAGGTCGTGGCAACTATCATGCCCACAACTTATCGTGTGCTGAAATGAAAAATA
AATAAAAGGGGATTTTAGTTGATAAATGTTAAAATAATAAAATGAATAGAACGAAATAATAACAG
AACGATAATTGCAAATAAAATTAAATTGGTAAATCAAATATGCGAATCCTTAGCCTTAGACTTGG
TAAATTCCAGTCTTGAATCGATCCTTAAAAGTGAATATTTCCTTTC
Found at i:21334369 original size:69 final size:69
Alignment explanation
Indices: 21334288--21334426 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
21334278 TCCTTGATAA
21334288 AATTTAAGCAAGAAATAACAAGCTTATTAGTATTCTATTAAAAAATTTATCAAAATAGGTACATT
1 AATTTAAGCAAGAAATAACAAGCTTATTAGTATTCTATTAAAAAATTTATCAAAATAGGTACATT
21334353 AAGC
66 AAGC
*
21334357 AATTTAAGCAAGAAATAACAAGCTTATTAGTATTCTATTAAAAAATTTATCAAAATAGGTACTTT
1 AATTTAAGCAAGAAATAACAAGCTTATTAGTATTCTATTAAAAAATTTATCAAAATAGGTACATT
21334422 AAGC
66 AAGC
21334426 A
1 A
21334427 CACGAAATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (69 bp):
AATTTAAGCAAGAAATAACAAGCTTATTAGTATTCTATTAAAAAATTTATCAAAATAGGTACATT
AAGC
Found at i:21335403 original size:48 final size:48
Alignment explanation
Indices: 21335310--21335406 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
21335300 AAGGAAAGAT
* * **
21335310 TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGATGTATGTTATGTA
1 TTGAAAAGAGTAAATTAATATGACTCTGTATGTGATATACATTATGTA
* * * *
21335358 TTGAAAAGAGTAAATTAATATGACTTTGTCTTTGTTATACATTATGTA
1 TTGAAAAGAGTAAATTAATATGACTCTGTATGTGATATACATTATGTA
21335406 T
1 T
21335407 AATTGCTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (48 bp):
TTGAAAAGAGTAAATTAATATGACTCTGTATGTGATATACATTATGTA
Found at i:21339769 original size:25 final size:25
Alignment explanation
Indices: 21339731--21339778 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21339721 ATTTTTAATT
*
21339731 AATTATGAAAATAATTTAATTTAAA
1 AATTATGAAAATAAATTAATTTAAA
* * *
21339756 AATTATGTATATAAATTATTTTA
1 AATTATGAAAATAAATTAATTTA
21339779 TTTTTATAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
AATTATGAAAATAAATTAATTTAAA
Found at i:21340601 original size:20 final size:20
Alignment explanation
Indices: 21340565--21340612 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
21340555 GTCTAATTTG
* *
21340565 ATTAAATAAATTATT-AAAA
1 ATTAAAAAAAATATTAAAAA
21340584 ATTAAAAAAAATATTTAAAAA
1 ATTAAAAAAAATA-TTAAAAA
21340605 ATTAAAAA
1 ATTAAAAA
21340613 CCTGGTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 2 0.08
21 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAAAAAAAATATTAAAAA
Found at i:21353069 original size:20 final size:20
Alignment explanation
Indices: 21353041--21353079 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21353031 AAAATTTTAA
*
21353041 AAAACAAAAGTAAAAATAAT
1 AAAACAAAACTAAAAATAAT
* *
21353061 AAAATAAAACTTAAAATAA
1 AAAACAAAACTAAAAATAA
21353080 ATAATGACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAACAAAACTAAAAATAAT
Found at i:21353465 original size:63 final size:62
Alignment explanation
Indices: 21353393--21353533 Score: 187
Period size: 63 Copynumber: 2.3 Consensus size: 62
21353383 GAATTGGAGG
* * *
21353393 CACACGGGCTAGGGACACAG-GGGTGTGTCTAGGCCGTGTAACTTACTATTTGTACTGTTT-GGT
1 CACACGGGCTAGGGACA-AGAGGGTGTGTCCAGGCCGTGTAACTCACTATTTGTA-T-TTTAGGC
* * *
21353456 CACATGGGCTAGGGACATGAGTGTGTGTCCAGGCCGTGTAACTCACTATTTGTATTTTAGGC
1 CACACGGGCTAGGGACAAGAGGGTGTGTCCAGGCCGTGTAACTCACTATTTGTATTTTAGGC
21353518 CACACGGGCTAGGGAC
1 CACACGGGCTAGGGAC
21353534 GGGCTTGGGT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 3 0.04
62 19 0.28
63 47 0.68
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (62 bp):
CACACGGGCTAGGGACAAGAGGGTGTGTCCAGGCCGTGTAACTCACTATTTGTATTTTAGGC
Found at i:21353879 original size:20 final size:20
Alignment explanation
Indices: 21353851--21353891 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21353841 TAAACTAGTG
* *
21353851 AGTAGTTGCATTCTTTATCA
1 AGTAATTGCATTCTCTATCA
21353871 AGTAATTGCATTCTCTATCA
1 AGTAATTGCATTCTCTATCA
21353891 A
1 A
21353892 CTAAGTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
AGTAATTGCATTCTCTATCA
Found at i:21355948 original size:15 final size:16
Alignment explanation
Indices: 21355901--21355993 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 16
21355891 TCCATTTCTT
21355901 TATTATTA-A-ATTAA
1 TATTATTATATATTAA
*
21355915 TTATTTTTAATATTATTTAA
1 -TATTATT-ATA-TA-TTAA
*
21355935 TATTATTATAT-TTAC
1 TATTATTATATATTAA
*
21355950 TATTATT-TATATTAT
1 TATTATTATATATTAA
*
21355965 TCTTATTATCATTATTAA
1 TATTATTAT-A-TATTAA
*
21355983 TATTAGTATAT
1 TATTATTATAT
21355994 GTTTTATTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
14 3 0.05
15 25 0.41
16 3 0.05
17 4 0.07
18 15 0.25
19 7 0.11
20 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (16 bp):
TATTATTATATATTAA
Found at i:21355962 original size:34 final size:34
Alignment explanation
Indices: 21355901--21355965 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
21355891 TCCATTTCTT
*
21355901 TATTATTAAATTAATTATTTTTAATATTATTTAA
1 TATTATTAAATTAACTATTTTTAATATTATTTAA
* *
21355935 TATTATTATATTTACTATTATTT-ATATTATT
1 TATTATTAAATTAACTATT-TTTAATATTATT
21355966 CTTATTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATTAAATTAACTATTTTTAATATTATTTAA
Found at i:21356020 original size:21 final size:21
Alignment explanation
Indices: 21355971--21356038 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
21355961 TTATTCTTAT
*
21355971 TATCATTATTA-ATAT-TAGTA
1 TATCTTTATTATATATGTA-TA
*
21355991 TATGTTTTATTATATATGTATA
1 TAT-CTTTATTATATATGTATA
21356013 TATCTTTAATATATATATGTATA
1 TATCTTT-AT-TATATATGTATA
21356036 TAT
1 TAT
21356039 TTATGTAGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.08
21 9 0.22
22 11 0.28
23 17 0.43
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (21 bp):
TATCTTTATTATATATGTATA
Found at i:21356124 original size:24 final size:23
Alignment explanation
Indices: 21356082--21356142 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
21356072 TCTAATATGC
* *
21356082 ATATATTATGTAAATATTT-TAAT
1 ATATATTATGTATACATTTAT-AT
21356105 ACTATATTATGTATACATTTATAT
1 A-TATATTATGTATACATTTATAT
*
21356129 ATATATTACGTATA
1 ATATATTATGTATA
21356143 TATATCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 13 0.39
24 19 0.58
25 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATATTATGTATACATTTATAT
Found at i:21356214 original size:15 final size:14
Alignment explanation
Indices: 21356116--21356219 Score: 67
Period size: 15 Copynumber: 7.6 Consensus size: 14
21356106 CTATATTATG
*
21356116 TATACATTTATATA
1 TATATATTTATATA
**
21356130 TATATTACGTATATA
1 TATA-TATTTATATA
* *
21356145 TATCT-TTTAAATA
1 TATATATTTATATA
21356158 T-TATATTT-T-TA
1 TATATATTTATATA
* *
21356169 TATATA-TCATGTA
1 TATATATTTATATA
*
21356182 TATATTTTTA-ATA
1 TATATATTTATATA
21356195 CTATATTATTTATATA
1 -TATA-TATTTATATA
21356211 TATATATTT
1 TATATATTT
21356220 TACATATTAT
Statistics
Matches: 67, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
11 4 0.06
12 7 0.10
13 18 0.27
14 16 0.24
15 19 0.28
16 3 0.04
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:21356216 original size:17 final size:17
Alignment explanation
Indices: 21356107--21356218 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
21356097 ATTTTAATAC
* * *
21356107 TATATTATGTATACATT
1 TATATTATTTATATATA
**
21356124 TATATATATATTACGTATA
1 TATAT-TAT-TTATATATA
*
21356143 TATATCT-TTTAAATAT-
1 TATAT-TATTTATATATA
21356159 TATATT-TTTATATATA
1 TATATTATTTATATATA
*
21356175 TCATGTATATATTTTTA-ATA
1 T-A--TAT-TATTTATATATA
21356195 CTATATTATTTATATATA
1 -TATATTATTTATATATA
21356213 TATATT
1 TATATT
21356219 TTACATATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
15 9 0.12
16 6 0.08
17 25 0.34
18 10 0.14
19 13 0.18
20 5 0.07
21 6 0.08
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (17 bp):
TATATTATTTATATATA
Found at i:21356218 original size:31 final size:32
Alignment explanation
Indices: 21356180--21356265 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 32
21356170 ATATATCATG
21356180 TATATATTTTTAATACTATATTAT--T-TATA
1 TATATATTTTTAATACTATATTATCGTATATA
* *
21356209 TATATATATTT--TAC-ATATTATCGTATGTA
1 TATATATTTTTAATACTATATTATCGTATATA
21356238 TATAT-TTTTTAATAACTATATTAT-GTAT
1 TATATATTTTTAAT-ACTATATTATCGTAT
21356266 GTATTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
26 7 0.15
27 3 0.06
28 5 0.11
29 18 0.38
30 1 0.02
31 6 0.13
32 7 0.15
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (32 bp):
TATATATTTTTAATACTATATTATCGTATATA
Found at i:21356239 original size:27 final size:27
Alignment explanation
Indices: 21356177--21356269 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 27
21356167 TATATATATC
*
21356177 ATGTATATATTTTTAATACTATATTATTT
1 ATGTATATATTTTT--TACTATATTATGT
* *
21356206 ATATATATATATTTTAC-ATATTATCGT
1 ATGTATATATTTTTTACTATATTAT-GT
21356233 ATGTATATATTTTTTAATAACTATATTATGT
1 ATGTATATA-TTTTT--T-ACTATATTATGT
21356264 ATGTAT
1 ATGTAT
21356270 TTTTAATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
26 7 0.13
27 12 0.23
28 4 0.08
29 12 0.23
30 1 0.02
31 10 0.19
32 7 0.13
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.55
Consensus pattern (27 bp):
ATGTATATATTTTTTACTATATTATGT
Found at i:21356266 original size:31 final size:29
Alignment explanation
Indices: 21356177--21356289 Score: 114
Period size: 26 Copynumber: 4.0 Consensus size: 29
21356167 TATATATATC
*
21356177 ATGTATATATTTTTAATACTATATTATTT
1 ATGTATATATTTTTAATACTATATTATGT
* *
21356206 ATATATATATATTT--TAC-ATATTATCGT
1 ATGTATATATTTTTAATACTATATTAT-GT
21356233 ATGTATATATTTTTTAATAACTATATTATGT
1 ATGTATATA-TTTTTAAT-ACTATATTATGT
*
21356264 ATG----TATTTTTAATGCTATATTATGT
1 ATGTATATATTTTTAATACTATATTATGT
21356289 A
1 A
21356290 CATATTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
25 12 0.17
26 15 0.21
27 14 0.19
28 4 0.06
29 12 0.17
30 1 0.01
31 7 0.10
32 7 0.10
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (29 bp):
ATGTATATATTTTTAATACTATATTATGT
Found at i:21356270 original size:27 final size:25
Alignment explanation
Indices: 21356159--21356365 Score: 157
Period size: 25 Copynumber: 8.3 Consensus size: 25
21356149 TTTTAAATAT
*
21356159 TATATTTTT-ATA-TATATCATGTA
1 TATATTTTTAATACTATATTATGTA
*
21356182 TATATTTTTAATACTATATTATTTA
1 TATATTTTTAATACTATATTATGTA
*
21356207 TATATATATATT-TTACATATTATCGTATGTA
1 TATAT-T-T-TTAATAC-TA-TAT--TATGTA
21356238 TATATTTTTTAATAACTATATTATGTA
1 TATA-TTTTTAAT-ACTATATTATGTA
* *
21356265 TGTATTTTTAATGCTATATTATGTA
1 TATATTTTTAATACTATATTATGTA
*
21356290 CATATTTTTAATAC-----TATGTA
1 TATATTTTTAATACTATATTATGTA
* * *
21356310 TATACTTTTTATTCCTATTATTACGTA
1 TATA-TTTTTAATACTA-TATTATGTA
21356337 TATA-TTTTAATAC-ATA-TATGTA
1 TATATTTTTAATACTATATTATGTA
21356359 TATATTT
1 TATATTT
21356366 ATATATCGTT
Statistics
Matches: 147, Mismatches: 17, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
20 9 0.06
21 8 0.05
22 9 0.06
23 13 0.09
24 4 0.03
25 44 0.30
26 9 0.06
27 22 0.15
28 4 0.03
29 8 0.05
30 4 0.03
31 12 0.08
32 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (25 bp):
TATATTTTTAATACTATATTATGTA
Found at i:21356332 original size:72 final size:69
Alignment explanation
Indices: 21356232--21356365 Score: 162
Period size: 72 Copynumber: 1.9 Consensus size: 69
21356222 CATATTATCG
* * * *
21356232 TATGTATATATTTTTTAATAACTATATTATGTATGTATTTTTAATGCTATATTATGTACATATTT
1 TATGTATATACTTTTTAATAACTATATTACGTATATA-TTTTAATAC-ATA-TATGTACATATTT
21356297 TTAATAC
63 TTAATAC
** *
21356304 TATGTATATACTTTTT-ATTCCTATTATTACGTATATATTTTAATACATATATGTATATATTT
1 TATGTATATACTTTTTAATAACTA-TATTACGTATATATTTTAATACATATATGTACATATTT
21356366 ATATATCGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
69 12 0.22
70 3 0.06
71 13 0.24
72 26 0.48
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (69 bp):
TATGTATATACTTTTTAATAACTATATTACGTATATATTTTAATACATATATGTACATATTTTTA
ATAC
Found at i:21356342 original size:47 final size:44
Alignment explanation
Indices: 21356259--21356365 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 44
21356249 ATAACTATAT
* * *
21356259 TATGTATGTATTTTTAATGCTATATTATGTACATATTTTTAATAC
1 TATGTATATATTTTTAATCCTATATTACGTACATA-TTTTAATAC
* *
21356304 TATGTATATACTTTTTATTCCTATTATTACGTATATATTTTAATAC
1 TATGTATATA-TTTTTAATCCTA-TATTACGTACATATTTTAATAC
21356350 ATATATGTATATATTT
1 ---TATGTATATATTT
21356366 ATATATCGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
45 9 0.17
46 19 0.37
47 11 0.21
48 3 0.06
49 10 0.19
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (44 bp):
TATGTATATATTTTTAATCCTATATTACGTACATATTTTAATAC
Found at i:21360032 original size:14 final size:14
Alignment explanation
Indices: 21360010--21360054 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
21360000 TTAAAGAAGC
21360010 AACTCATTAAATTA
1 AACTCATTAAATTA
*
21360024 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
21360037 AACTCATTTAATTA
1 AACTCATTAAATTA
21360051 AACT
1 AACT
21360055 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:21360095 original size:42 final size:42
Alignment explanation
Indices: 21360037--21360142 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
21360027 TCATTAAATA
* * *
21360037 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACTAGT
1 AACTCATTT-ATTAAACTAAGATAAGTTGTATTAATGACCAGC
*
21360080 AACTCATCTATTAAACTAAGATAAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATAAGTTGTATTAATGACCAGC
21360122 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
21360143 GGCTTAAATG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 50 0.86
43 8 0.14
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATAAGTTGTATTAATGACCAGC
Found at i:21360111 original size:20 final size:20
Alignment explanation
Indices: 21360047--21360113 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
21360037 AACTCATTTA
*
21360047 ATTAAACTAAGATGAGTTGT
1 ATTAAACTAAGATAAGTTGT
* *
21360067 ATTAATGACT-AG-TAACTCATCT
1 ATTAA--ACTAAGATAAGT--TGT
21360089 ATTAAACTAAGATAAGTTGT
1 ATTAAACTAAGATAAGTTGT
21360109 ATTAA
1 ATTAA
21360114 TGACCAGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 18 0.50
21 4 0.11
22 14 0.39
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
ATTAAACTAAGATAAGTTGT
Found at i:21370159 original size:77 final size:74
Alignment explanation
Indices: 21370030--21370412 Score: 432
Period size: 77 Copynumber: 5.1 Consensus size: 74
21370020 TGCTCTGATG
* *
21370030 TTTT-AATTTCTGTCTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGCTCACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCACA
21370094 CGCTGAGGTA
65 CGCTGAGGTA
* * * *
21370104 TTTACAATTTCTGTTTTTCAAAAATATCAACTCATATTGCGATAGATGAGTTGAGCCTCAGTTCA
1 TTTTCAATTTCTGTTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCA
21370169 CACGCTGAGGTA
63 CACGCTGAGGTA
* * * *
21370181 TTTTCAATTCCTGTTTTTTAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACA
21370244 CGCTGAGGTA
65 CGCTGAGGTA
* * * *
21370254 TTTTTAATTTCTGTTTTTCAAAAATCAACTCATACTGTGAGAGGTGAGTTGAGCCTCGAATCACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GTCACA
*
21370319 CG-TGATGTA
65 CGCTGAGGTA
* * * * *
21370328 TTTTCTATTTCCGCTTTTTATAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAA
1 TTTTCAATTTCTG--TTTT-T---CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G
*
21370393 GTCACACACTGAGGTA
59 GTCACACGCTGAGGTA
21370409 TTTT
1 TTTT
21370413 TAGTTTTTTA
Statistics
Matches: 261, Mismatches: 33, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
72 1 0.00
73 63 0.24
74 19 0.07
75 50 0.19
76 12 0.05
77 64 0.25
78 1 0.00
80 41 0.16
81 10 0.04
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (74 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACAC
GCTGAGGTA
Found at i:21370603 original size:44 final size:45
Alignment explanation
Indices: 21370522--21370616 Score: 156
Period size: 44 Copynumber: 2.1 Consensus size: 45
21370512 GAATAAAGGC
* *
21370522 TGGAGCTGATCGAAGACACCAGATTTTTCCTCCCTGAAGTTGCAG
1 TGGAGCTGATCGAAGACACCAGATTCTGCCTCCCTGAAGTTGCAG
*
21370567 TGGAGCTGATCGAAGATA-CAGATTCTGCCTCCCTGAAGTTGCAG
1 TGGAGCTGATCGAAGACACCAGATTCTGCCTCCCTGAAGTTGCAG
21370611 TGGAGC
1 TGGAGC
21370617 AGGTTGAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 30 0.64
45 17 0.36
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (45 bp):
TGGAGCTGATCGAAGACACCAGATTCTGCCTCCCTGAAGTTGCAG
Found at i:21370695 original size:45 final size:43
Alignment explanation
Indices: 21370555--21370699 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 43
21370545 TTTTTCCTCC
* * *
21370555 CTGAAGTTGCAGTGGAGCTGATCGAAGATACAGATTC-TGCCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATACAGATTCAT--CTCT
* * *
21370599 CTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTTTCATCT-T
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AGATTCATCTCT
* *
21370642 CCTGAAGTTGTAGCGGAGCAGATTGAAGATACTAGATCTCATCTCT
1 -CTGAAGTTGCAGTGGAGCAGATTGAAGATAC-AGAT-TCATCTCT
21370688 CTGAAGTTGCAG
1 CTGAAGTTGCAG
21370700 AAAAACAGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
44 59 0.71
45 22 0.27
46 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
CTGAAGTTGCAGTGGAGCAGATTGAAGATACAGATTCATCTCT
Found at i:21372261 original size:3 final size:3
Alignment explanation
Indices: 21372253--21372343 Score: 53
Period size: 3 Copynumber: 30.0 Consensus size: 3
21372243 TTCCATTTCT
* * * *
21372253 TTA TTA TTA -AA TTAA TTA TTT TTA ATA TTA TTTA ATA TTA TTA -TA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
21372298 TTTA CTA TTA TT- TATA TTA TTC TTA TTC TTA TTA TTA TTA ATA TTA
1 -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21372344 GTATATGTTT
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
2 4 0.06
3 52 0.80
4 9 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:21372315 original size:34 final size:34
Alignment explanation
Indices: 21372254--21372318 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
21372244 TCCATTTCTT
*
21372254 TATTATTAAATTAATTATTTTTAATATTATTTAA
1 TATTATTAAATTAACTATTTTTAATATTATTTAA
* *
21372288 TATTATTATATTTACTATTATTT-ATATTATT
1 TATTATTAAATTAACTATT-TTTAATATTATT
21372319 CTTATTCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATTAAATTAACTATTTTTAATATTATTTAA
Found at i:21372342 original size:9 final size:9
Alignment explanation
Indices: 21372263--21372343 Score: 60
Period size: 9 Copynumber: 9.1 Consensus size: 9
21372253 TTATTATTAA
21372263 ATTAATTATT
1 ATTAA-TATT
*
21372273 TTTAATATT
1 ATTAATATT
21372282 ATTTAATATT
1 A-TTAATATT
21372292 ATT-ATA-T
1 ATTAATATT
*
21372299 -TTACTATT
1 ATTAATATT
*
21372307 ATTTATATT
1 ATTAATATT
**
21372316 ATTCTTATT
1 ATTAATATT
* *
21372325 CTTATTATT
1 ATTAATATT
21372334 ATTAATATT
1 ATTAATATT
21372343 A
1 A
21372344 GTATATGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
6 2 0.04
7 3 0.05
8 4 0.07
9 34 0.61
10 13 0.23
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTAATATT
Found at i:21372376 original size:21 final size:22
Alignment explanation
Indices: 21372344--21372396 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
21372334 ATTAATATTA
*
21372344 GTATATGTTTT-AT-TATATAT
1 GTATATATTTTAATATATATAT
21372364 GTATATATCTTTAATATATATAT
1 GTATATAT-TTTAATATATATAT
21372387 GTATATATTT
1 GTATATATTT
21372397 ATGTAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (22 bp):
GTATATATTTTAATATATATAT
Found at i:21372567 original size:25 final size:25
Alignment explanation
Indices: 21372518--21372717 Score: 163
Period size: 25 Copynumber: 8.3 Consensus size: 25
21372508 TTTTAAATAT
*
21372518 TATATTTTT-ATA-TATATCATGTA
1 TATATTTTTAATACTATATTATGTA
21372541 TATATTTTTAATACTATATTA--TA
1 TATATTTTTAATACTATATTATGTA
* * *
21372564 TATATATTTACATATTATCTTATGTA
1 TATATTTTTA-ATACTATATTATGTA
21372590 TATATTTTTTAATAACTATATTATGTA
1 TATA-TTTTTAAT-ACTATATTATGTA
* ** *
21372617 TGTATTTTTAACGCTATACTATGTA
1 TATATTTTTAATACTATATTATGTA
*
21372642 CATATTTTTAATAC-----TATGTA
1 TATATTTTTAATACTATATTATGTA
* * *
21372662 TATACTTTTTATTCCTATTGTTATGTA
1 TATA-TTTTTAATACTA-TATTATGTA
21372689 TATA-TTTTAATAC-ATA-TATGTA
1 TATATTTTTAATACTATATTATGTA
21372711 TATATTT
1 TATATTT
21372718 ATATATCGTT
Statistics
Matches: 141, Mismatches: 21, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.06
21 8 0.06
22 10 0.07
23 23 0.16
24 13 0.09
25 34 0.24
26 15 0.11
27 29 0.21
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (25 bp):
TATATTTTTAATACTATATTATGTA
Found at i:21372657 original size:20 final size:21
Alignment explanation
Indices: 21372632--21372672 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
21372622 TTTTAACGCT
21372632 ATACTATGTACATA-TTTTTA
1 ATACTATGTACATACTTTTTA
*
21372652 ATACTATGTATATACTTTTTA
1 ATACTATGTACATACTTTTTA
21372673 TTCCTATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (21 bp):
ATACTATGTACATACTTTTTA
Found at i:21387602 original size:30 final size:30
Alignment explanation
Indices: 21387566--21387639 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
21387556 TCATCGACCA
***
21387566 ATGAAAAGGGATAGCTTTTGCTATCAAATT
1 ATGAAAAGGGATAGCTTCAACTATCAAATT
21387596 ATGAAAAGGGATAGCTTCAACTATCAAATT
1 ATGAAAAGGGATAGCTTCAACTATCAAATT
21387626 ATGAAAAGGGATAG
1 ATGAAAAGGGATAG
21387640 TGACGACCTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCAACTATCAAATT
Found at i:21388787 original size:44 final size:44
Alignment explanation
Indices: 21388724--21388810 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
21388714 GGTAATAGAC
21388724 TTGTGTTATATGATTTTTATATTATTTCATTAAAGTTAATTTAG
1 TTGTGTTATATGATTTTTATATTATTTCATTAAAGTTAATTTAG
21388768 TTGTGTTATATGATTTTTATATTATTTCATTAAAGTTAATTTA
1 TTGTGTTATATGATTTTTATATTATTTCATTAAAGTTAATTTA
21388811 ATAAACTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.57
Consensus pattern (44 bp):
TTGTGTTATATGATTTTTATATTATTTCATTAAAGTTAATTTAG
Found at i:21392380 original size:50 final size:50
Alignment explanation
Indices: 21392321--21392419 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
21392311 GTAGTGGCCT
*
21392321 GCCAAGGTGATGGATAGTTGATAATGTATGCATTTTAGCATTTTAATAGG
1 GCCAAGGTGATGGATAGTTGATAAAGTATGCATTTTAGCATTTTAATAGG
21392371 GCCAAGGTGATGGATAGTTGATAAAGTATGCATTTTAGCATTTTAATAG
1 GCCAAGGTGATGGATAGTTGATAAAGTATGCATTTTAGCATTTTAATAG
21392420 TTAATGGATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (50 bp):
GCCAAGGTGATGGATAGTTGATAAAGTATGCATTTTAGCATTTTAATAGG
Found at i:21392441 original size:32 final size:32
Alignment explanation
Indices: 21392405--21392465 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
21392395 AGTATGCATT
21392405 TTAGCATTTTAATAGTTAATGGATGATGGACA
1 TTAGCATTTTAATAGTTAATGGATGATGGACA
21392437 TTAGCATTTTAATAGTTAATGGATGATGG
1 TTAGCATTTTAATAGTTAATGGATGATGG
21392466 GCATGGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGACA
Found at i:21395624 original size:12 final size:12
Alignment explanation
Indices: 21395604--21395634 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21395594 ACTTGGGGAA
21395604 GAGGCCGTGGTC
1 GAGGCCGTGGTC
*
21395616 GAGGTCGTGGTC
1 GAGGCCGTGGTC
21395628 GAGGCCG
1 GAGGCCG
21395635 AGGTAGTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.52, T:0.16
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:21405202 original size:13 final size:13
Alignment explanation
Indices: 21405184--21405208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21405174 TCGAGCACAC
21405184 GCCCGTGTCCCTA
1 GCCCGTGTCCCTA
21405197 GCCCGTGTCCCT
1 GCCCGTGTCCCT
21405209 TACACGGCCT
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:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTA
Found at i:21411232 original size:46 final size:46
Alignment explanation
Indices: 21411179--21411351 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
21411169 TTGAGCATCT
*
21411179 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
*** * * ** *
21411225 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACGTCC
* * *
21411272 GAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
** *
21411318 GAGTTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21411352 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
46 65 0.64
47 36 0.36
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:21411332 original size:93 final size:93
Alignment explanation
Indices: 21411173--21411344 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
21411163 GGATTGTTGA
* * * *
21411173 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
21411238 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* **
21411266 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGTTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
21411331 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
21411345 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:21420548 original size:34 final size:34
Alignment explanation
Indices: 21420465--21420550 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
21420455 GATTCTTTTT
*
21420465 CTGCATACTG-TACTGATATGGGCTAAGGCCCAGA
1 CTGC-TACTGTTACTGAAATGGGCTAAGGCCCAGA
** * * *
21420499 CTGCTTTTATCACTGAAATGGGCTAAGGCCTAGA
1 CTGCTACTGTTACTGAAATGGGCTAAGGCCCAGA
21420533 CTGCTACTGTTACTGAAA
1 CTGCTACTGTTACTGAAA
21420551 AGGGGGTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
33 2 0.05
34 39 0.95
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (34 bp):
CTGCTACTGTTACTGAAATGGGCTAAGGCCCAGA
Found at i:21422083 original size:21 final size:21
Alignment explanation
Indices: 21422057--21422100 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21422047 AAGTGTACCG
*
21422057 TACTGG-TAGCTCTCCTGCAAT
1 TACTGGAT-GCTCTCCTACAAT
*
21422078 TACTGGATGCTCTTCTACAAT
1 TACTGGATGCTCTCCTACAAT
21422099 TA
1 TA
21422101 TTGAATAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (21 bp):
TACTGGATGCTCTCCTACAAT
Found at i:21422195 original size:22 final size:23
Alignment explanation
Indices: 21422167--21422209 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
21422157 TTATCCCCAC
*
21422167 ATGGAGTGTAG-GGCTGGATGGA
1 ATGGAGTGTAGAGGATGGATGGA
21422189 ATGGAGTGTAGAGGATGGATG
1 ATGGAGTGTAGAGGATGGATG
21422210 TGTAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.26, C:0.02, G:0.49, T:0.23
Consensus pattern (23 bp):
ATGGAGTGTAGAGGATGGATGGA
Found at i:21422614 original size:172 final size:173
Alignment explanation
Indices: 21422321--21422643 Score: 594
Period size: 172 Copynumber: 1.9 Consensus size: 173
21422311 GCCTACGGAT
21422321 TGTTTGATTTGTTGTTGGGGATTACACACTGAGTTTTCGTAAACTCACACCGTTTCTAACTGTGC
1 TGTTTGATTTGTTGTTGGGGATTACACACTGAGTTTTCGTAAACTCACACCGTTTCTAACTGTGC
*
21422386 AGGTAATCCCTAAGCTTAGATGGTTTGGAGCTGCGAGGGACTCGGAGATGGCCACACTACTATTT
66 AGGTAATCCCTAAGCTTAGATGGTTTGGAGCTGCGAGGGACTCGAAGATGGCCACACTACTATTT
21422451 CTGTTTCTTTTAATTGCAATATGTAGCTCACTGTGTTAGTCAC
131 CTGTTTCTTTTAATTGCAATATGTAGCTCACTGTGTTAGTCAC
* *
21422494 TGTTTG-TTTGTTGTTGGGGATTACACACTGAGTTTTCGTAAACTCACCCCGTTTTTAACTGTGC
1 TGTTTGATTTGTTGTTGGGGATTACACACTGAGTTTTCGTAAACTCACACCGTTTCTAACTGTGC
*
21422558 AGGTAATCCCTAAGCTTAGATGGTTTGGAGCTGCGAGGGACTCGAAGATGGCCACACTACTGTTT
66 AGGTAATCCCTAAGCTTAGATGGTTTGGAGCTGCGAGGGACTCGAAGATGGCCACACTACTATTT
*
21422623 CTGTTTTTTTTAATTGCAATA
131 CTGTTTCTTTTAATTGCAATA
21422644 AGTAACCGGT
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
172 139 0.96
173 6 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (173 bp):
TGTTTGATTTGTTGTTGGGGATTACACACTGAGTTTTCGTAAACTCACACCGTTTCTAACTGTGC
AGGTAATCCCTAAGCTTAGATGGTTTGGAGCTGCGAGGGACTCGAAGATGGCCACACTACTATTT
CTGTTTCTTTTAATTGCAATATGTAGCTCACTGTGTTAGTCAC
Found at i:21424998 original size:17 final size:17
Alignment explanation
Indices: 21424976--21425012 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
21424966 TAACAACTTC
21424976 CTGGACTTACCCAAGAA
1 CTGGACTTACCCAAGAA
21424993 CTGGACTTACCCAAGAA
1 CTGGACTTACCCAAGAA
21425010 CTG
1 CTG
21425013 TCAGAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (17 bp):
CTGGACTTACCCAAGAA
Found at i:21428200 original size:25 final size:25
Alignment explanation
Indices: 21428154--21428205 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
21428144 CCTCGATTTA
* *
21428154 TAGAATTATTATTTTAACCTTGTTT
1 TAGAATTACTATTTTAACCTTGATT
*
21428179 TAGAATTACTGTTTT-ACGCTTGATT
1 TAGAATTACTATTTTAAC-CTTGATT
21428204 TA
1 TA
21428206 CAAAATTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (25 bp):
TAGAATTACTATTTTAACCTTGATT
Found at i:21428292 original size:27 final size:27
Alignment explanation
Indices: 21428262--21428360 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
21428252 TATAGGCTAT
21428262 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
21428289 AATTACCAAAATACCACTGGTTTATGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
21428316 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
21428343 AATTACCAAAATACCCCT
1 AATTACCAAAATACCCCT
21428361 GATTTACACA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.05
27 52 0.88
28 4 0.07
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:21428301 original size:54 final size:54
Alignment explanation
Indices: 21428229--21428360 Score: 137
Period size: 54 Copynumber: 2.4 Consensus size: 54
21428219 TTACCCTTGA
* ** *
21428229 TTGTGAAATTACTGAAATACCCCTATAGG-CTAT-AATTACCAAAATACCC-CTAGT
1 TTGTAAAATTACCAAAATACCCCT-T-GGTCTATAAATTACCAAAATACCCTC-AAT
* * *
21428283 TTGTAAAATTACCAAAATACCAC-TGGTTTATGAAATTACCGAAATACCCTCAAT
1 TTGTAAAATTACCAAAATACCCCTTGGTCTAT-AAATTACCAAAATACCCTCAAT
21428337 TTGTAAAATTACCAAAATACCCCT
1 TTGTAAAATTACCAAAATACCCCT
21428361 GATTTACACA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
51 2 0.03
52 4 0.06
54 58 0.89
55 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (54 bp):
TTGTAAAATTACCAAAATACCCCTTGGTCTATAAATTACCAAAATACCCTCAAT
Found at i:21428374 original size:54 final size:55
Alignment explanation
Indices: 21428262--21428442 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 55
21428252 TATAGGCTAT
* * * *
21428262 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTATGA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTATCA
*
21428316 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTGATTTA-CA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTATCA
** * * * * *
21428369 CAATTATAGAAATACCCT-TGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTA-CAA
1 -AATTACCGAAATACCCTCT-AATTTGT-AAAATTACCA-AAATACCACTGATTTATC-A
*
21428426 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
21428443 TGGTTTGTAG
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 7 0.07
56 36 0.34
57 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (55 bp):
AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTATCA
Found at i:21428445 original size:27 final size:27
Alignment explanation
Indices: 21428262--21428448 Score: 108
Period size: 27 Copynumber: 6.9 Consensus size: 27
21428252 TATAGGCTAT
* * * **
21428262 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCGAAATACCCTTGGTTTACAA
* **
21428289 AATTACCAAAATACCAC-TGGTTTATGA
1 AATTACCGAAATACC-CTTGGTTTACAA
*** **
21428316 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCGAAATACCCTTGGTTTACAA
* * * *
21428343 AATTACCAAAATACCCCTGATTTACAC
1 AATTACCGAAATACCCTTGGTTTACAA
** *
21428370 AATTATAGAAATACCCTTGACTTT-CTAAA
1 AATTACCGAAATACCCTTG-GTTTAC--AA
** *
21428399 AATTATAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCCTTGGTTTACAA
*
21428426 AATTACTGAAATACCCTTGGTTT
1 AATTACCGAAATACCCTTGGTTT
21428449 GTAGATTTAC
Statistics
Matches: 127, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
26 1 0.01
27 99 0.78
28 7 0.06
29 20 0.16
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGGTTTACAA
Found at i:21429378 original size:25 final size:25
Alignment explanation
Indices: 21429350--21429418 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
21429340 GGAAGTGCTG
* *
21429350 AAAGGGCTATACCCCAGTTGACCGA
1 AAAGGGCTTTACCCCAGTTGACCAA
* * * *
21429375 AAAGGGCTTTGCCTCAGTTTATCAA
1 AAAGGGCTTTACCCCAGTTGACCAA
*
21429400 AAAGGGCTTTTCCCCAGTT
1 AAAGGGCTTTACCCCAGTT
21429419 ATTAAAAGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (25 bp):
AAAGGGCTTTACCCCAGTTGACCAA
Done.