Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 123 of 322
Found at i:40225310 original size:100 final size:100
Alignment explanation
Indices: 40225135--40225333 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
40225125 TTTAGAAAAT
40225135 CATTATAAATTGTACAAAAATGATTATAAAATAAAATTTATATGCTTAGAATCCTTAATGAGTCT
1 CATTATAAATTGTACAAAAATGATTATAAAATAAAATTTATATGCTTAGAATCCTTAATGAGTCT
40225200 AGTTTCAAATGAGATCAAATACAACACATTTTGAA
66 AGTTTCAAATGAGATCAAATACAACACATTTTGAA
*
40225235 CATTATAAATTGTACAAAAATGATTATAAAATAAAATTTATATGCTTAGACTCCTTAATGAGTCT
1 CATTATAAATTGTACAAAAATGATTATAAAATAAAATTTATATGCTTAGAATCCTTAATGAGTCT
*
40225300 AGTTTTAAATGAGATCAAATACAACACATTTTGA
66 AGTTTCAAATGAGATCAAATACAACACATTTTGA
40225334 CTTCTGTAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (100 bp):
CATTATAAATTGTACAAAAATGATTATAAAATAAAATTTATATGCTTAGAATCCTTAATGAGTCT
AGTTTCAAATGAGATCAAATACAACACATTTTGAA
Found at i:40226129 original size:40 final size:40
Alignment explanation
Indices: 40226070--40226257 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
40226060 GAGCACTGGA
* *
40226070 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
40226110 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
40226150 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
40226190 ATATATCCGGGTTAAGACCCGAAAGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
40226230 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
40226258 ATGTGTTTGC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:40243948 original size:40 final size:40
Alignment explanation
Indices: 40243904--40244167 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
40243894 GCTCCTCGTT
* *
40243904 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
40243944 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
40243984 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
40244024 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40244064 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
40244103 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
40244144 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40244168 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40250792 original size:10 final size:10
Alignment explanation
Indices: 40250767--40250839 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
40250757 TCGGTATTTG
40250767 ATGAATTTAT
1 ATGAATTTAT
40250777 -TGAATTTAT
1 ATGAATTTAT
*
40250786 ATGAATTGA-
1 ATGAATTTAT
*
40250795 ATTGAATTCAT
1 A-TGAATTTAT
*
40250806 ATGAATTGA-
1 ATGAATTTAT
*
40250815 ATTGAATTCAT
1 A-TGAATTTAT
* *
40250826 ATGTATATAT
1 ATGAATTTAT
40250836 ATGA
1 ATGA
40250840 TAATGTGATT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 11 0.22
10 37 0.74
11 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.44
Consensus pattern (10 bp):
ATGAATTTAT
Found at i:40250800 original size:20 final size:20
Alignment explanation
Indices: 40250775--40250828 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40250765 TGATGAATTT
*
40250775 ATTGAATTTATATGAATTGA
1 ATTGAATTCATATGAATTGA
40250795 ATTGAATTCATATGAATTGA
1 ATTGAATTCATATGAATTGA
40250815 ATTGAATTCATATG
1 ATTGAATTCATATG
40250829 TATATATATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
ATTGAATTCATATGAATTGA
Found at i:40252225 original size:12 final size:12
Alignment explanation
Indices: 40252208--40252238 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40252198 ATTTCGAAAG
*
40252208 GGCACACTGCTT
1 GGCACACTGCCT
40252220 GGCACACTGCCT
1 GGCACACTGCCT
40252232 GGCACAC
1 GGCACAC
40252239 GAGCGTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.39, G:0.26, T:0.16
Consensus pattern (12 bp):
GGCACACTGCCT
Found at i:40254068 original size:24 final size:24
Alignment explanation
Indices: 40254018--40254117 Score: 118
Period size: 24 Copynumber: 4.2 Consensus size: 24
40254008 CATGGTTGGC
40254018 AAGCTCCT-CTGAGCTGATAAACAGT
1 AAGCT-CTACTGAGCTGA-AAACAGT
*
40254043 AAGCTCTACTGAGCTGAAAACGGT
1 AAGCTCTACTGAGCTGAAAACAGT
*
40254067 AAGCTCTATTGAGCTGAAAAC-GAT
1 AAGCTCTACTGAGCTGAAAACAG-T
*
40254091 AAGCTCTATTGAGCT--AAACAGT
1 AAGCTCTACTGAGCTGAAAACAGT
40254113 AAGCT
1 AAGCT
40254118 ATTTCGAGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
22 10 0.14
23 2 0.03
24 44 0.63
25 14 0.20
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (24 bp):
AAGCTCTACTGAGCTGAAAACAGT
Found at i:40254115 original size:22 final size:22
Alignment explanation
Indices: 40254035--40254140 Score: 99
Period size: 24 Copynumber: 4.6 Consensus size: 22
40254025 TCTGAGCTGA
*
40254035 TAAACAGTAAGCTCTACTGAGC
1 TAAACAGTAAGCTCTATTGAGC
*
40254057 TGAAAACGGTAAGCTCTATTGAGC
1 T--AAACAGTAAGCTCTATTGAGC
40254081 TGAAA-ACGATAAGCTCTATTGAGC
1 T-AAACA-G-TAAGCTCTATTGAGC
*
40254105 TAAACAGTAAGCTAT-TTCGAGC
1 TAAACAGTAAGCTCTATT-GAGC
*
40254127 TAAATCGGTAAGCT
1 TAAA-CAGTAAGCT
40254141 TCAATGAGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.03
22 16 0.23
23 16 0.23
24 37 0.52
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (22 bp):
TAAACAGTAAGCTCTATTGAGC
Found at i:40254156 original size:46 final size:47
Alignment explanation
Indices: 40254027--40254156 Score: 126
Period size: 46 Copynumber: 2.8 Consensus size: 47
40254017 CAAGCTCCTC
* * *
40254027 TGAGCTGATAAAC-AGTAAGCTCTACTGAGCTGAAAACGGTAAGCTCTAT
1 TGAGCTGA-AAACGA-TAAGCTCTAATGAGCTG-AAACAGTAAGCTATAT
*
40254076 TGAGCTGAAAACGATAAGCTCTATTGAGCT-AAACAGTAAGCTAT-T
1 TGAGCTGAAAACGATAAGCTCTAATGAGCTGAAACAGTAAGCTATAT
* *
40254121 TCGAGCT-AAATCGGTAAGCT-TCAATGAGCTGAAACA
1 T-GAGCTGAAAACGATAAGCTCT-AATGAGCTGAAACA
40254157 ATAAACTCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
44 1 0.01
45 20 0.28
46 22 0.31
48 19 0.27
49 9 0.13
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (47 bp):
TGAGCTGAAAACGATAAGCTCTAATGAGCTGAAACAGTAAGCTATAT
Found at i:40256403 original size:45 final size:45
Alignment explanation
Indices: 40256352--40256442 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
40256342 AATTAAATTA
* *
40256352 ACCATTATTAGCAGGTTTAGA-TTCATTTAAGTCATGCATATATAT
1 ACCATTATTAGCAGGTTTA-ACTTCATTTAAATCAAGCATATATAT
40256397 ACCATTATTAGCAGGTTTAACTTCATTTAAATCAAGCATATATAT
1 ACCATTATTAGCAGGTTTAACTTCATTTAAATCAAGCATATATAT
40256442 A
1 A
40256443 TATTTATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (45 bp):
ACCATTATTAGCAGGTTTAACTTCATTTAAATCAAGCATATATAT
Found at i:40256523 original size:36 final size:36
Alignment explanation
Indices: 40256452--40256524 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
40256442 ATATTTATAT
* *
40256452 ATATTAATGCATATGTATACTGTTTAGCTTCATTTA
1 ATATTAATGCATATATATAATGTTTAGCTTCATTTA
* *
40256488 ATATTAATGCATATATATAAAT-TTTTGCTTTATTTA
1 ATATTAATGCATATATAT-AATGTTTAGCTTCATTTA
40256524 A
1 A
40256525 GTCATGTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (36 bp):
ATATTAATGCATATATATAATGTTTAGCTTCATTTA
Found at i:40256550 original size:58 final size:57
Alignment explanation
Indices: 40256488--40256608 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 57
40256478 GCTTCATTTA
* *
40256488 ATATTAATGCATATATA-TAAATTTTTGCTTTATTTAAGTCATGTGCATATATA-TATAT
1 ATATTAATGCATATATATTAAA-TTTAGCTTCATTTAAGTCA--TGCATATATACTATAT
**
40256546 ATATTAATGCATATATATTCCATTTAGCTTCATTTAAGTCATGCATATATACTATAT
1 ATATTAATGCATATATATTAAATTTAGCTTCATTTAAGTCATGCATATATACTATAT
40256603 ATATTA
1 ATATTA
40256609 TAAAAACCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 10 0.18
57 11 0.19
58 34 0.60
59 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (57 bp):
ATATTAATGCATATATATTAAATTTAGCTTCATTTAAGTCATGCATATATACTATAT
Found at i:40263856 original size:82 final size:82
Alignment explanation
Indices: 40263761--40264155 Score: 579
Period size: 82 Copynumber: 4.9 Consensus size: 82
40263751 AATCTGTCTA
*
40263761 TGTATAATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
1 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
40263826 TTTTTTAGGAGTGTGTG
66 TTTTTTAGGAGTGTGTG
*
40263843 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGC-A-G--TG
1 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
* * *
40263904 TTTTTTA--ATTTGTCTA
66 TTTTTTAGGA-GTGTGTG
* * * * *
40263920 TGTATGATTGTTGGTAGGGAT-GATCATATACTGTTGACTATTTTTTAATATGCATGCAATGACT
1 TGTATGATTGTTGGTGGGGTTAG-TTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACT
*
40263984 ATTTTTTAGGTGTGTGTG
65 ATTTTTTAGGAGTGTGTG
40264002 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
1 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
*
40264067 TTTTTTAGGTGTGTGTG
66 TTTTTTAGGAGTGTGTG
* * * *
40264084 TGTATGATTGTTGGTGGGGATGGTCACATGCTGTTGACTATTTTTTAATATGCATGCAGTGACTA
1 TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
40264149 TTTTTTA
66 TTTTTTA
40264156 ATAATATGCA
Statistics
Matches: 280, Mismatches: 24, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
76 2 0.01
77 54 0.19
78 9 0.03
79 1 0.00
80 1 0.00
81 9 0.03
82 203 0.73
83 1 0.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (82 bp):
TGTATGATTGTTGGTGGGGTTAGTTACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTA
TTTTTTAGGAGTGTGTG
Found at i:40264013 original size:159 final size:157
Alignment explanation
Indices: 40263725--40264155 Score: 646
Period size: 159 Copynumber: 2.7 Consensus size: 157
40263715 CTAGTGCGTG
* * * *
40263725 TTTTTTAATATGCATGCAGTTTTTTTAATCTGTCTATGTATAATTGTTGGTGGGGTTAGTTACAT
1 TTTTTTAATATGCATGCAGTTTTTTTAATCTGTCTATGTATGATTGTTGGTGGGATGA-TCACAT
40263790 GCTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTAGGAGTGTGTGTGTATGATTGTT
65 GCTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTAGGAGTGTGTGTGTATGATTGTT
40263855 GGTGGGGTTAGTTACATGCTGTTGACTA
130 GGTGGGGTTAGTTACATGCTGTTGACTA
* *
40263883 TTTTTTAATATGCATGCAGTGTTTTTTAATTTGTCTATGTATGATTGTTGGTAGGGATGATCATA
1 TTTTTTAATATGCATGCAGT-TTTTTTAATCTGTCTATGTATGATTGTTGGT-GGGATGATCACA
* *
40263948 TACTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTAGGTGTGTGTGTGTATGATTGT
64 TGCTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTAGGAGTGTGTGTGTATGATTGT
40264013 TGGTGGGGTTAGTTACATGCTGTTGACTA
129 TGGTGGGGTTAGTTACATGCTGTTGACTA
* * * * *
40264042 TTTTTTAATATGCATGCAATGACTATTTTTTAGGTGTGTGTGTGTATGATTGTTGGTGGGGATGG
1 TTTTTTAATATGCATGC-A-G--T-TTTTTTA-ATCTGTCTATGTATGATTGTTGGT-GGGATGA
*
40264107 TCACATGCTGTTGACTATTTTTTAATATGCATGCAGTGACTATTTTTTA
59 TCACATGCTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTA
40264156 ATAATATGCA
Statistics
Matches: 248, Mismatches: 18, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
158 20 0.08
159 141 0.57
160 6 0.02
161 1 0.00
163 8 0.03
164 72 0.29
ACGTcount: A:0.21, C:0.08, G:0.24, T:0.47
Consensus pattern (157 bp):
TTTTTTAATATGCATGCAGTTTTTTTAATCTGTCTATGTATGATTGTTGGTGGGATGATCACATG
CTGTTGACTATTTTTTAATATGCATGCAATGACTATTTTTTAGGAGTGTGTGTGTATGATTGTTG
GTGGGGTTAGTTACATGCTGTTGACTA
Found at i:40264172 original size:28 final size:27
Alignment explanation
Indices: 40264118--40264183 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 27
40264108 CACATGCTGT
*
40264118 TGACTA-TTTTT-TAATATGCATGCAG
1 TGACTATTTTTTATAATATGCAAGCAG
*
40264143 TGACTATTTTTTAATAATATGCAAGTAG
1 TGACTATTTTTT-ATAATATGCAAGCAG
* *
40264171 TGATTGTTTTTTA
1 TGACTATTTTTTA
40264184 GGTATGTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 1 0.03
28 22 0.65
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (27 bp):
TGACTATTTTTTATAATATGCAAGCAG
Found at i:40267655 original size:9 final size:9
Alignment explanation
Indices: 40267639--40267690 Score: 86
Period size: 9 Copynumber: 5.8 Consensus size: 9
40267629 GGTATTTTTC
40267639 GGTAATTCG
1 GGTAATTCG
*
40267648 GTTAATTCG
1 GGTAATTCG
*
40267657 GTTAATTCG
1 GGTAATTCG
40267666 GGTAATTCG
1 GGTAATTCG
40267675 GGTAATTCG
1 GGTAATTCG
40267684 GGTAATT
1 GGTAATT
40267691 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:40267868 original size:12 final size:12
Alignment explanation
Indices: 40267851--40267875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40267841 AGTAATTTCG
40267851 GGTCGGTTAACC
1 GGTCGGTTAACC
40267863 GGTCGGTTAACC
1 GGTCGGTTAACC
40267875 G
1 G
40267876 AATAACACCC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:40267915 original size:27 final size:27
Alignment explanation
Indices: 40267877--40267932 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
40267867 GGTTAACCGA
40267877 ATAACACCCCTAAGTGTAATGTCCTTG
1 ATAACACCCCTAAGTGTAATGTCCTTG
40267904 ATAACACCCCTAAGTGTAATGTCCTTG
1 ATAACACCCCTAAGTGTAATGTCCTTG
40267931 AT
1 AT
40267933 GTGGGAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (27 bp):
ATAACACCCCTAAGTGTAATGTCCTTG
Found at i:40281061 original size:93 final size:93
Alignment explanation
Indices: 40280953--40281123 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40280943 GCCCATAAGT
* * * *
40280953 GAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40281018 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
40281046 GAACTCGGACTCAACTCAACGAATTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40281111 TGAGTTCGGATGC
66 CGAGTTCGGATGC
40281124 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40281120 original size:46 final size:46
Alignment explanation
Indices: 40280945--40281120 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
40280935 TGTAACCCGC
* * * *
40280945 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40280991 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * *
40281041 --TTCA-CGAACTCGGACTCAACTCAACGAATTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40281084 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40281121 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40281580 original size:30 final size:30
Alignment explanation
Indices: 40281546--40281605 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40281536 ATTTAATACG
40281546 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40281576 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40281606 GGCTCGGGAA
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:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40285914 original size:127 final size:127
Alignment explanation
Indices: 40285680--40285997 Score: 422
Period size: 127 Copynumber: 2.5 Consensus size: 127
40285670 CAATGAAAAA
* * ** * *
40285680 CGAAACCCAACACAATAGGGCATAATTCCTCAAATTTGCAAACATTG-ACATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGTTTTAG
* * *
40285744 AATTTATAAAATACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAATAAACCGGAAAT
66 AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCGGAAAT
* *
40285806 CGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACCTTGAACATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGTTTTAG
* * * * * * *
40285871 AATTTGGAAAACACGAGTGAAATTCTAAATGAATATTCGATTATTTTGAACAAACGGGAAAT
66 AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCGGAAAT
* * **
40285933 CGAAACCCAGCACGGTAGGGCACGATTTCTCGAATTTCCAAACATCAAACATTGCCTTCGTTTTA
1 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTT-GTTTTA
40285998 AGGAATTTTC
Statistics
Matches: 166, Mismatches: 24, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
126 39 0.23
127 121 0.73
128 6 0.04
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (127 bp):
CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGTTTTAG
AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCGGAAAT
Found at i:40286497 original size:23 final size:22
Alignment explanation
Indices: 40286467--40286517 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
40286457 TTAAAATAAC
40286467 ATATAAAAGGTCTAAAATAAATA
1 ATATAAAAGGT-TAAAATAAATA
* *
40286490 ATATAAAAATGTTAAAGTAAATA
1 ATAT-AAAAGGTTAAAATAAATA
40286513 ATATA
1 ATATA
40286518 CATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.72
24 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (22 bp):
ATATAAAAGGTTAAAATAAATA
Found at i:40287976 original size:8 final size:8
Alignment explanation
Indices: 40287959--40287994 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
40287949 TTTGTAATAG
40287959 AAAATAAA
1 AAAATAAA
40287967 AAAA-ATAA
1 AAAATA-AA
40287975 AAAATAAA
1 AAAATAAA
40287983 AAAATAAA
1 AAAATAAA
40287991 AAAA
1 AAAA
40287995 CGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 24 0.92
9 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:40287994 original size:16 final size:16
Alignment explanation
Indices: 40287954--40287993 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
40287944 ATAAATTTGT
*
40287954 AATAGAAAATAAAAAA
1 AATAAAAAATAAAAAA
40287970 AATAAAAAAT-AAAAA
1 AATAAAAAATAAAAAA
40287985 AATAAAAAA
1 AATAAAAAA
40287994 ACGAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (16 bp):
AATAAAAAATAAAAAA
Found at i:40288571 original size:15 final size:17
Alignment explanation
Indices: 40288537--40288577 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
40288527 TTAGCATTTT
40288537 TATTATTATTACAGTAC
1 TATTATTATTACAGTAC
*
40288554 TATTATTTTTA-A-TAC
1 TATTATTATTACAGTAC
40288569 TATTATTAT
1 TATTATTAT
40288578 AATTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTATTATTACAGTAC
Found at i:40290341 original size:20 final size:20
Alignment explanation
Indices: 40290318--40290357 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40290308 TATTCTAGAG
40290318 TAATCGTCCAAATTCAGGGT
1 TAATCGTCCAAATTCAGGGT
40290338 TAATCGTCCAAATTCAGGGT
1 TAATCGTCCAAATTCAGGGT
40290358 AGTTTCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
TAATCGTCCAAATTCAGGGT
Found at i:40291066 original size:28 final size:28
Alignment explanation
Indices: 40291026--40291085 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
40291016 TTAACCCTTA
*
40291026 ACCTAAGCCCCTTTACAACCTTATAAAG
1 ACCTAAGCCCCTTTACAACATTATAAAG
*
40291054 ACCTAAGGCCCTTTACAACATTATAAAG
1 ACCTAAGCCCCTTTACAACATTATAAAG
40291082 ACCT
1 ACCT
40291086 CTTGTAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (28 bp):
ACCTAAGCCCCTTTACAACATTATAAAG
Found at i:40293036 original size:30 final size:30
Alignment explanation
Indices: 40293002--40293059 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40292992 ACTTAACAAG
40293002 AAAATGCATCTAAAATAATAACAAAATTAA
1 AAAATGCATCTAAAATAATAACAAAATTAA
* * *
40293032 AAAATGCCTTTACAATAATAACAAAATT
1 AAAATGCATCTAAAATAATAACAAAATT
40293060 GACAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AAAATGCATCTAAAATAATAACAAAATTAA
Found at i:40296351 original size:15 final size:15
Alignment explanation
Indices: 40296331--40296361 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40296321 ACCAAAATAA
40296331 AAGTGGATAAAGACC
1 AAGTGGATAAAGACC
40296346 AAGTGGATAAAGACC
1 AAGTGGATAAAGACC
40296361 A
1 A
40296362 TAGTCTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (15 bp):
AAGTGGATAAAGACC
Found at i:40308545 original size:43 final size:43
Alignment explanation
Indices: 40308493--40308604 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
40308483 ACATATTGGC
* * * * *
40308493 GCCACTGTCCCAGACAAGGTCTTACACGAAATC-GATTAACGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAATCTCAAT-ACAAT
*
40308536 GCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATACAAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAATCTCAATACAAT
*
40308579 GCCAATGTTCCAGACATGGTCTTACA
1 GCCAATGTCCCAGACATGGTCTTACA
40308605 TGTAATCACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 59 0.97
44 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACGAAATCTCAATACAAT
Found at i:40314159 original size:34 final size:34
Alignment explanation
Indices: 40314113--40314188 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
40314103 TGCACAGTCA
* *
40314113 AACAGTCTTAGGCCTAAGCCCCTTTCAGTATCAGT
1 AACAGT-TTAGGCCTAAGCCCATCTCAGTATCAGT
*
40314148 AACAGTTTAGGCCTTAGCCCATCTCAGTATCAGT
1 AACAGTTTAGGCCTAAGCCCATCTCAGTATCAGT
*
40314182 ATCAGTT
1 AACAGTT
40314189 ATGCAGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 31 0.84
35 6 0.16
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (34 bp):
AACAGTTTAGGCCTAAGCCCATCTCAGTATCAGT
Found at i:40321363 original size:8 final size:8
Alignment explanation
Indices: 40321350--40321376 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40321340 GTCCCTCTAT
40321350 TTTTAAAA
1 TTTTAAAA
40321358 TTTTAAAA
1 TTTTAAAA
40321366 TTTTAAAA
1 TTTTAAAA
40321374 TTT
1 TTT
40321377 AAGTCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:40339034 original size:19 final size:18
Alignment explanation
Indices: 40338998--40339036 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
40338988 GCTTTTTTGT
40338998 ATTCATCGCATTCATTGC
1 ATTCATCGCATTCATTGC
40339016 ATTCAT-GCATCTGCATTGC
1 ATTCATCGCAT-T-CATTGC
40339035 AT
1 AT
40339037 CATACGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTCATCGCATTCATTGC
Found at i:40347127 original size:44 final size:44
Alignment explanation
Indices: 40347073--40347317 Score: 272
Period size: 44 Copynumber: 5.7 Consensus size: 44
40347063 ATTCACAAGC
* *
40347073 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGATCGAAGATGAAGGGT
* * * *
40347117 CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAA-TTGCA-GAT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGATCGAAGATGAAGGGT
* *
40347159 CTT-ATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGATGAAGGGT
1 CTTAAAC-CCCTAAGCAGTAG-GGTAACAGATCGAAGATGAAGGGT
* * * *
40347203 CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAA-TTGCA-GAT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGATCGAAGATGAAGGGT
* *
40347245 CTT-ATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGATGAAGGGT
1 CTTAAAC-CCCTAAGCAGTAG-GGTAACAGATCGAAGATGAAGGGT
40347289 CTTAAACCCCTAAGCAGTAGGGTAACAGA
1 CTTAAACCCCTAAGCAGTAGGGTAACAGA
40347318 CCAAATTGCA
Statistics
Matches: 163, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
41 4 0.02
42 54 0.33
43 20 0.12
44 81 0.50
45 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGATCGAAGATGAAGGGT
Found at i:40347175 original size:42 final size:42
Alignment explanation
Indices: 40347080--40347401 Score: 285
Period size: 42 Copynumber: 7.5 Consensus size: 42
40347070 AGCCTTAACC
* * * * * *
40347080 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGTCTTAAAC-
1 CCCTAAGCAGTAGGGTAACAGACCGAA-TTGCA-GATCTT-ATCT
40347124 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
* * * * * *
40347166 CCCTAAGCAGTAGTGG-AGCAGATCGAAGATGAAGGGTCTTAAAC-
1 CCCTAAGCAGTAG-GGTAACAGACCGAA-TTGCA-GATCTT-ATCT
40347210 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
* * * * * *
40347252 CCCTAAGCAGTAGTGG-AGCAGATCGAAGATGAAGGGTCTTAAAC-
1 CCCTAAGCAGTAG-GGTAACAGACCGAA-TTGCA-GATCTT-ATCT
* * *
40347296 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATTT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
* * *
40347338 CCCTAAGCAGTAGAGTAACAGACCAAATTGCAAATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
*
40347380 CCCTAAGCAGTAGGGAAACAGA
1 CCCTAAGCAGTAGGGTAACAGA
40347402 TCAAAGGTGA
Statistics
Matches: 226, Mismatches: 39, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
41 5 0.02
42 116 0.51
43 23 0.10
44 78 0.35
45 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCT
Found at i:40347225 original size:86 final size:86
Alignment explanation
Indices: 40347080--40347350 Score: 490
Period size: 86 Copynumber: 3.2 Consensus size: 86
40347070 AGCCTTAACC
*
40347080 CCCTAAGCAGTAG-GGAAACAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACA
1 CCCTAAGCAGTAGTGG-AGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACA
40347144 GACCGAATTGCAGATCTTATCT
65 GACCGAATTGCAGATCTTATCT
40347166 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACAG
40347231 ACCGAATTGCAGATCTTATCT
66 ACCGAATTGCAGATCTTATCT
40347252 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACAG
* * *
40347317 ACCAAATTGCAGATATTATTT
66 ACCGAATTGCAGATCTTATCT
40347338 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
40347351 AGTAACAGAC
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
86 178 0.99
87 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (86 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGTCTTAAACCCCTAAGCAGTAGGGTAACAG
ACCGAATTGCAGATCTTATCT
Found at i:40347356 original size:128 final size:128
Alignment explanation
Indices: 40347210--40347444 Score: 357
Period size: 128 Copynumber: 1.8 Consensus size: 128
40347200 GGTCTTAAAC
* * * *
40347210 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGA
1 CCCTAAGCAGTAGAGTAACAGACCAAATTGCAAATCTTATCTCCCTAAGCAGTAG-GGAAACAGA
* * * *
40347274 TCGAAGATGA-AGGGTCTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATTT
65 TCAAAGATGACA-AGCCTTAAACCCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATTT
40347338 CCCTAAGCAGTAGAGTAACAGACCAAATTGCAAATCTTATCTCCCTAAGCAGTAGGGAAACAGAT
1 CCCTAAGCAGTAGAGTAACAGACCAAATTGCAAATCTTATCTCCCTAAGCAGTAGGGAAACAGAT
*
40347403 CAAAGGTGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAG
66 CAAAGATGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAG
40347445 GCTGAAGATT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
127 2 0.02
128 93 0.97
129 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (128 bp):
CCCTAAGCAGTAGAGTAACAGACCAAATTGCAAATCTTATCTCCCTAAGCAGTAGGGAAACAGAT
CAAAGATGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATTT
Found at i:40347478 original size:89 final size:88
Alignment explanation
Indices: 40347338--40347551 Score: 238
Period size: 89 Copynumber: 2.4 Consensus size: 88
40347328 GATATTATTT
* * * * *
40347338 CCCTAAGCAGTAGAGTAACAGAC-CAAATTG-CAAATCTTATCTCCCTAAGCAGTAGGGAAACAG
1 CCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAAATCTTAACCCCCTAAGCAGTAGGGAAACAG
*
40347401 ATCA-AAGGTGACAAGCCTTAAAC
66 AGCAGAA-GTGACAAGCCTTAAAC
* *
40347424 CCCTAAACAGTAGGGTAACAGGCTGAAGATTGACAAATCTTAACCCCCTAAGCAGTAGGGAAGCA
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-ATTGACAAATCTTAACCCCCTAAGCAGTAGGGAAACA
* ***
40347489 TAGCAGAAGTGATGGGCCTTAAAC
65 GAGCAGAAGTGACAAGCCTTAAAC
* * *
40347513 CCCTGAGCAATAGGGTCACAGGCTGGAAATT-ACAAATCT
1 CCCTAAGCAGTAGGGTAACAGGCT-GAAATTGACAAATCT
40347552 CTTCTCCTTG
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
86 20 0.19
87 2 0.02
88 12 0.11
89 68 0.64
90 5 0.05
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (88 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAAATCTTAACCCCCTAAGCAGTAGGGAAACAG
AGCAGAAGTGACAAGCCTTAAAC
Found at i:40349467 original size:15 final size:15
Alignment explanation
Indices: 40349447--40349476 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40349437 TTTAAATCAT
40349447 TCATTATTTGTATTA
1 TCATTATTTGTATTA
*
40349462 TCATTATTTTTATTA
1 TCATTATTTGTATTA
40349477 CTAACATATA
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:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (15 bp):
TCATTATTTGTATTA
Found at i:40355209 original size:4 final size:5
Alignment explanation
Indices: 40355187--40355225 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
40355177 AAGAAGAAGT
* *
40355187 AAATA AAATA AAATA AAATA AATATG AAATA ACATA AAA
1 AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAA
40355226 GAGAAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:40355218 original size:16 final size:15
Alignment explanation
Indices: 40355187--40355225 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40355177 AAGAAGAAGT
40355187 AAATAAAATAAAATA
1 AAATAAAATAAAATA
*
40355202 AAATAAATATGAAATA
1 AAATAAA-ATAAAATA
*
40355218 ACATAAAA
1 AAATAAAA
40355226 GAGAAAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:40358915 original size:6 final size:6
Alignment explanation
Indices: 40358880--40358960 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
40358870 GAAAGCAAAG
* * * * * *
40358880 TAAACA TAAAAA GAAAAA TAAAAG TGAAAA TAAAAA T-AAAG TAAAAGC
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA-A
* * *
40358928 TAAAAAA TAAAGA TAAACA TAAACA TAAAAA TA
1 T-AAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
40358961 GTCGGACTCA
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
5 4 0.07
6 49 0.83
7 2 0.03
8 4 0.07
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:40358931 original size:18 final size:17
Alignment explanation
Indices: 40358893--40358950 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 17
40358883 ACATAAAAAG
40358893 AAAAATAAAAGTGAAAAT-
1 AAAAAT-AAAGT-AAAATA
40358911 AAAAATAAAGTAAAAGCTA
1 AAAAATAAAGTAAAA--TA
40358930 AAAAATAAAGATAAACATA
1 AAAAATAAAG-TAAA-ATA
40358949 AA
1 AA
40358951 CATAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 7 0.20
19 14 0.40
20 4 0.11
21 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAATAAAGTAAAATA
Found at i:40362741 original size:18 final size:18
Alignment explanation
Indices: 40362697--40362745 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40362687 TGTCAGAAGA
*
40362697 AAATAAAAGA-AAAATTAG
1 AAATAAAA-ATAAAAATAG
* *
40362715 TAATTAAAATAAAAATAG
1 AAATAAAAATAAAAATAG
40362733 AAATAAAAATAAA
1 AAATAAAAATAAA
40362746 TTTCAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAAATAAAAATAG
Found at i:40384026 original size:19 final size:20
Alignment explanation
Indices: 40384002--40384040 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40383992 TCAATGAATA
*
40384002 TTTTAAAAAA-ATAATTTTT
1 TTTTAAAAAACAAAATTTTT
40384021 TTTTAAAAAACAAAATTTTT
1 TTTTAAAAAACAAAATTTTT
40384041 ATAATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAAAACAAAATTTTT
Found at i:40384242 original size:31 final size:30
Alignment explanation
Indices: 40384174--40384249 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
40384164 TTAAGAAAGT
40384174 TATTT-AAAATT-ATTAAGAATTATAAAAA
1 TATTTAAAAATTAATTAAGAATTATAAAAA
* *
40384202 AACTCTAAAATATTAATTAA-AATTAATAAAAA
1 TA-TTTAAAA-ATTAATTAAGAATT-ATAAAAA
40384234 TATTTAAAAAATTAAT
1 TATTT-AAAAATTAAT
40384250 CTTCATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
28 1 0.03
29 2 0.05
30 3 0.08
31 15 0.39
32 17 0.45
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
TATTTAAAAATTAATTAAGAATTATAAAAA
Found at i:40384674 original size:21 final size:21
Alignment explanation
Indices: 40384644--40384691 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
40384634 TTTCTTATTG
40384644 TTTCTAATAATATTTTAAT-AT
1 TTTCTAATAAT-TTTTAATAAT
*
40384665 TTTCTTATAATTTTTAATAAT
1 TTTCTAATAATTTTTAATAAT
40384686 TTTCTA
1 TTTCTA
40384692 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTCTAATAATTTTTAATAAT
Found at i:40384677 original size:11 final size:11
Alignment explanation
Indices: 40384644--40384691 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
40384634 TTTCTTATTG
40384644 TTTCTAATAAT
1 TTTCTAATAAT
40384655 ATTT-TAAT-AT
1 -TTTCTAATAAT
*
40384665 TTTCTTATAAT
1 TTTCTAATAAT
40384676 TTT-TAATAAT
1 TTTCTAATAAT
40384686 TTTCTA
1 TTTCTA
40384692 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 3 0.10
10 14 0.45
11 11 0.35
12 3 0.10
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTCTAATAAT
Found at i:40384683 original size:31 final size:31
Alignment explanation
Indices: 40384624--40384697 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
40384614 TTTTATTGTA
**
40384624 ATTTTAA-ATATTTCTTATTGTTTCTAATAAT
1 ATTTTAATAT-TTTCTTATAATTTCTAATAAT
*
40384655 ATTTTAATATTTTCTTATAATTTTTAATAAT
1 ATTTTAATATTTTCTTATAATTTCTAATAAT
40384686 -TTTCT-ATATTTT
1 ATTT-TAATATTTT
40384698 AAATTGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 10 0.26
31 26 0.68
32 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (31 bp):
ATTTTAATATTTTCTTATAATTTCTAATAAT
Found at i:40384693 original size:20 final size:19
Alignment explanation
Indices: 40384644--40384697 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
40384634 TTTCTTATTG
40384644 TTTCTAATAATATTTTAATAT
1 TTTCT-ATAAT-TTTTAATAT
40384665 TTTCTTATAATTTTTAATAAT
1 TTTC-TATAATTTTTAAT-AT
40384686 TTTCTAT-ATTTT
1 TTTCTATAATTTT
40384698 AAATTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 15 0.48
22 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTCTATAATTTTTAATAT
Found at i:40386676 original size:25 final size:25
Alignment explanation
Indices: 40386635--40386703 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
40386625 ATACACCTTA
40386635 GCTC-TTATGAGCATTCCGATT-ATAG
1 GCTCTTTATGAGC-TTCCG-TTAATAG
*
40386660 GCTCTTTATGAGCTTCCCGTTAAATTG
1 GCTCTTTATGAGCTT-CCGTT-AATAG
*
40386687 GCTCTTTGTGAGCTTCC
1 GCTCTTTATGAGCTTCC
40386704 CGATAGTGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 8 0.21
26 13 0.34
27 17 0.45
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
GCTCTTTATGAGCTTCCGTTAATAG
Found at i:40389231 original size:12 final size:12
Alignment explanation
Indices: 40389216--40389241 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40389206 TAAAATAATG
40389216 AAAATAATAGTA
1 AAAATAATAGTA
40389228 AAAATAATAGTA
1 AAAATAATAGTA
40389240 AA
1 AA
40389242 GGGGAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAATAATAGTA
Found at i:40390194 original size:10 final size:10
Alignment explanation
Indices: 40390161--40390219 Score: 77
Period size: 10 Copynumber: 6.0 Consensus size: 10
40390151 TGAAATTCTA
40390161 AAAGATAAAT
1 AAAGATAAAT
40390171 ACAA-A-AAAT
1 A-AAGATAAAT
*
40390180 AAAGATAATT
1 AAAGATAAAT
40390190 AAAGATAAAT
1 AAAGATAAAT
40390200 AAAGATAAAT
1 AAAGATAAAT
*
40390210 AAAAATAAAT
1 AAAGATAAAT
40390220 CCTAAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
8 2 0.05
9 6 0.14
10 33 0.77
11 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40392944 original size:28 final size:27
Alignment explanation
Indices: 40392881--40392945 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
40392871 ACACGCCATG
*
40392881 TTCTATCTTTTATTTTCTTCTTTATTA
1 TTCTATCTTTGATTTTCTTCTTTATTA
40392908 TTCTAATCTTTGATTTATCGTTCTATT-TTA
1 TTCT-ATCTTTGATTT-TC-TTCT-TTATTA
40392938 TT-TATCTT
1 TTCTATCTT
40392946 AGTTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 4 0.12
28 15 0.45
29 3 0.09
30 9 0.27
31 2 0.06
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (27 bp):
TTCTATCTTTGATTTTCTTCTTTATTA
Found at i:40400458 original size:22 final size:22
Alignment explanation
Indices: 40400433--40400474 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40400423 GGACTAAATC
40400433 AAAAACATTT-AAAAATTTAAGG
1 AAAAA-ATTTAAAAAATTTAAGG
*
40400455 AAAAATTTTAAAAAATTTAA
1 AAAAAATTTAAAAAATTTAA
40400475 TTACAGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAAATTTAAAAAATTTAAGG
Found at i:40416949 original size:29 final size:30
Alignment explanation
Indices: 40416893--40416958 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
40416883 CGTATTTCGG
* *
40416893 TGATGGACGATTTAATTGATGGTTGTATTT
1 TGATGGACAATTTAATTGATGCTTGTATTT
40416923 TGATGGACAATTT-ATTGATGCTTGTATTT
1 TGATGGACAATTTAATTGATGCTTGTATTT
40416952 TGATGGA
1 TGATGGA
40416959 TGGTTCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (30 bp):
TGATGGACAATTTAATTGATGCTTGTATTT
Found at i:40421137 original size:17 final size:16
Alignment explanation
Indices: 40421100--40421138 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40421090 AACAAAAAAT
40421100 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
40421115 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
40421133 TAAATT
1 TAAATT
40421139 CGGGTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:40436422 original size:45 final size:46
Alignment explanation
Indices: 40436347--40436456 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
40436337 GATCGGAGGG
* ** * * *
40436347 TGCCATGGTGTCTTTCAACTGTGGCCTTATTTA-TTCTTGACTTGA
1 TGCCATAGTGTCTTTCAACCATGGCATTATTCATTTCTTGACGTGA
* * * *
40436392 TGCCATAGTGTCTTTCAACCATGGTATTATTCATTTTTTGCCGTGT
1 TGCCATAGTGTCTTTCAACCATGGCATTATTCATTTCTTGACGTGA
40436438 TGCCATAGTGTCTTTCAAC
1 TGCCATAGTGTCTTTCAAC
40436457 TATGTCTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 27 0.50
46 27 0.50
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGCATTATTCATTTCTTGACGTGA
Found at i:40436510 original size:45 final size:44
Alignment explanation
Indices: 40436433--40436588 Score: 154
Period size: 45 Copynumber: 3.5 Consensus size: 44
40436423 CATTTTTTGC
* ** * * * *
40436433 CGTGTTGCCATAGTGTCTTTCAACTATGTCTTATTCGTTTGATT
1 CGTGATGCCATAACGTCTTTCAACTATGTCTTAATCGATAGAAT
* *
40436477 CGTGATGTCATAACGTCGTTT-AGCTATGTTCTTAATCGATAGAAT
1 CGTGATGCCATAACGTC-TTTCAACTATG-TCTTAATCGATAGAAT
* *
40436522 CGTGATGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTAAAAT
1 CGTGATGCCATAACGTCTTTCAACTAT-GTCTTAATCGA-TAGAAT
*
40436567 CATGATGCCATAACGTCTTTCA
1 CGTGATGCCATAACGTCTTTCA
40436589 GTTATGGTCT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
44 23 0.25
45 69 0.74
46 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (44 bp):
CGTGATGCCATAACGTCTTTCAACTATGTCTTAATCGATAGAAT
Found at i:40436595 original size:45 final size:45
Alignment explanation
Indices: 40436479--40436602 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
40436469 GTTTGATTCG
* * * * *
40436479 TGATGTCATAACGTCGTTT-AGCTATGTTCTTAATCGATAGAATCG
1 TGATGCCATAACGTC-TTTCAGCTATGGTCTTACTCGATAAAATCA
*
40436524 TGATGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTAAAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGA-TAAAATCA
*
40436569 TGATGCCATAACGTCTTTCAGTTATGGTCTTACT
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACT
40436603 TATTTCTGGT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 4 0.06
45 65 0.94
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCGATAAAATCA
Found at i:40436600 original size:90 final size:89
Alignment explanation
Indices: 40436433--40436600 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 89
40436423 CATTTTTTGC
* ** * * ** * * *
40436433 CGTGTTGCCATAGTGTCTTTCAACTATGTCTTATTCGTTTGATTCGTGATGTCATAACGTCGTTT
1 CGTGATGCCATAACGTCTTTCAACTATGTCTTACTCATTAAAATCATGATGCCATAACGTCGTTT
*
40436498 AGCTATGTTCTTAATCGATAGAAT
66 AGCTATGGTCTTAATCGATAGAAT
40436522 CGTGATGCCATAACGTCTTTCAACTATGGTCTTACTCATTAAAATCATGATGCCATAACGTC-TT
1 CGTGATGCCATAACGTCTTTCAACTAT-GTCTTACTCATTAAAATCATGATGCCATAACGTCGTT
*
40436586 TCAGTTATGGTCTTA
65 T-AGCTATGGTCTTA
40436601 CTTATTTCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
89 27 0.42
90 38 0.58
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (89 bp):
CGTGATGCCATAACGTCTTTCAACTATGTCTTACTCATTAAAATCATGATGCCATAACGTCGTTT
AGCTATGGTCTTAATCGATAGAAT
Found at i:40446982 original size:16 final size:17
Alignment explanation
Indices: 40446958--40446999 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
40446948 CTTCAACAAG
40446958 AAAAA-AAAATATAAC-
1 AAAAAGAAAATATAACT
* *
40446973 AAAAAGAAAATCTATCT
1 AAAAAGAAAATATAACT
40446990 AAAAAGAAAA
1 AAAAAGAAAA
40447000 GAAAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 10 0.43
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAAGAAAATATAACT
Found at i:40449744 original size:29 final size:29
Alignment explanation
Indices: 40449708--40449805 Score: 169
Period size: 29 Copynumber: 3.4 Consensus size: 29
40449698 TTTGTGTACC
* *
40449708 ATGTGAAAAGGGATAGCTTTGGCTATTGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
40449737 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
40449766 ATGTGGAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
40449795 ATGTGAAAAGG
1 ATGTGAAAAGG
40449806 TTAGGTATAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.32, C:0.10, G:0.33, T:0.26
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCGA
Found at i:40449840 original size:33 final size:32
Alignment explanation
Indices: 40449798--40449987 Score: 222
Period size: 32 Copynumber: 5.9 Consensus size: 32
40449788 CTATCGAATG
* *
40449798 TGAAAAGGTTAGGTATACTTTGTGTATACCACA
1 TGAAAAGGTTAGGTACACTTTGTGTGTA-CACA
* *
40449831 TGAAAAGGTTATGTACACTTTGTGTGTACACT
1 TGAAAAGGTTAGGTACACTTTGTGTGTACACA
*
40449863 TGAAAAGGTTATGTACACTTTGTGTGTACACA
1 TGAAAAGGTTAGGTACACTTTGTGTGTACACA
*
40449895 TGAAAAGGTTATGTACACTTTGTGTGTACA-A
1 TGAAAAGGTTAGGTACACTTTGTGTGTACACA
* * * *
40449926 TTGAAAAGG-AAGGTATACTTTGTGTATACCATA
1 -TGAAAAGGTTAGGTACACTTTGTGTGTA-CACA
** *
40449959 TGAAAAGGAAAGGTATACTTTGTGTGTAC
1 TGAAAAGGTTAGGTACACTTTGTGTGTAC
40449988 CAATCAGAAA
Statistics
Matches: 143, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.11
32 83 0.58
33 44 0.31
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (32 bp):
TGAAAAGGTTAGGTACACTTTGTGTGTACACA
Found at i:40449910 original size:64 final size:65
Alignment explanation
Indices: 40449798--40449987 Score: 276
Period size: 64 Copynumber: 3.0 Consensus size: 65
40449788 CTATCGAATG
*
40449798 TGAAAAGGTTAGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTACACT
1 TGAAAAGGTTAGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTACAAT
* * *
40449863 TGAAAAGGTTATGTACACTTTGTGTGTA-CACATGAAAAGGTTATGTACACTTTGTGTGTACAAT
1 TGAAAAGGTTAGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTACAAT
* * ** * *
40449927 TGAAAAGG-AAGGTATACTTTGTGTATACCATATGAAAAGGAAAGGTATACTTTGTGTGTAC
1 TGAAAAGGTTAGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTAC
40449988 CAATCAGAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
63 15 0.14
64 71 0.64
65 25 0.23
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (65 bp):
TGAAAAGGTTAGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTACAAT
Found at i:40454097 original size:138 final size:138
Alignment explanation
Indices: 40453769--40454193 Score: 634
Period size: 138 Copynumber: 3.1 Consensus size: 138
40453759 AGAGAACATA
* *
40453769 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
1 AATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTAT
* * *
40453834 TAATATAAACAATTATATTAATTAATTTTGGTCAAAAATATAAAAGAAATGAAAAATTAATATTT
66 TAATATAAACAGTTATATTAATTAATTTTGGTC-AAAATATAAAAGAAATG-GAAATTAATATTA
40453899 TTTTGGAAAG
129 TTTTGGAAAG
* *
40453909 AATATAATTAATATATTAATTTGATTCATACAAAATATTAATTGTGTATATTTTACAGAATTTAT
1 AATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTAT
* * * * *
40453974 TAATATAAACTGTTACATTAATTAATTTCGGTCAAAATATTAAAGATATGGAAATTAATATTATT
66 TAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGGAAATTAATATTATT
*
40454039 TTAGAAAG
131 TTGGAAAG
* *
40454047 AATATAATTAATATATAAATTTTATTCATACAAAATATTAATTGTATATATTTTACTGAATTTAT
1 AATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTAT
* * ** * *
40454112 TAATATAAACAGTTATATTAATTAATTTTAGTTAAAATATAAAAGGCATGGACATTAATATTCTT
66 TAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGGAAATTAATATTATT
*
40454177 TTGGAAAT
131 TTGGAAAG
40454185 AATATAATT
1 AATATAATT
40454194 CATTTTTCTA
Statistics
Matches: 257, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
138 151 0.59
139 15 0.06
140 91 0.35
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (138 bp):
AATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTAT
TAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGGAAATTAATATTATT
TTGGAAAG
Found at i:40454375 original size:75 final size:74
Alignment explanation
Indices: 40454211--40454377 Score: 210
Period size: 75 Copynumber: 2.2 Consensus size: 74
40454201 CTAACTTTCC
*
40454211 ATTAATAAA-GGAATAATCCTATTTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCCATT
1 ATTAA-AAAGGGAATAATCCTATTTCTTTTGAAAAGAATATAATTCTTTTTTCTAACTTTCCATT
** *
40454275 TGTTTTCTCT
65 TGCCTTCTCA
* ** * * * *
40454285 ATTCATTAGGAAATAATCTTGTATTCTTTTGAAAAGAATATAATTCTTTTTTCTAACTTTTCATT
1 ATTAAAAAGGGAATAATCCTAT-TTCTTTTGAAAAGAATATAATTCTTTTTTCTAACTTTCCATT
40454350 TGCCTTCTCA
65 TGCCTTCTCA
40454360 ATTAAAAAGGGAATAATC
1 ATTAAAAAGGGAATAATC
40454378 ATGGTTTTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
73 1 0.01
74 14 0.18
75 61 0.80
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (74 bp):
ATTAAAAAGGGAATAATCCTATTTCTTTTGAAAAGAATATAATTCTTTTTTCTAACTTTCCATTT
GCCTTCTCA
Found at i:40458887 original size:51 final size:51
Alignment explanation
Indices: 40458806--40458907 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
40458796 GTAGCATGTG
* *
40458806 AAACTAGTGATAAAGTTATGGAGGGTATTATTGTGCTATGATGGGATATGA
1 AAACTAGTGATAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
*
40458857 AAACTAGTGGTAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
1 AAACTAGTGATAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
40458908 CTAGCCTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.32
Consensus pattern (51 bp):
AAACTAGTGATAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
Found at i:40460009 original size:62 final size:61
Alignment explanation
Indices: 40459912--40460037 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 61
40459902 TGAGAAATCG
* *
40459912 ACATGGCCTAGACTTCCGTACACGGGTAGATCACACGCCCGTGCCTATTCAACAGACTCTAA
1 ACATGACCTAGACTTCCGTACACGGGTAGACCACACGCCCGTGCCTATTCAACAGACTC-AA
* * * *
40459974 ACATGACCTGGACTTCC-TCACATGGGTAGACCACACGCCCGTGTCTATTTAACAGACTCAA
1 ACATGACCTAGACTTCCGT-ACACGGGTAGACCACACGCCCGTGCCTATTCAACAGACTCAA
40460035 ACA
1 ACA
40460038 CGATTTGAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 6 0.11
62 51 0.89
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (61 bp):
ACATGACCTAGACTTCCGTACACGGGTAGACCACACGCCCGTGCCTATTCAACAGACTCAA
Found at i:40466472 original size:16 final size:17
Alignment explanation
Indices: 40466451--40466483 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40466441 ACTACTTTTT
40466451 ATTTTATTTTT-CTTTA
1 ATTTTATTTTTACTTTA
40466467 ATTTTATTTTTACTTTA
1 ATTTTATTTTTACTTTA
40466484 TCCTTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTATTTTTACTTTA
Found at i:40473682 original size:40 final size:40
Alignment explanation
Indices: 40473601--40473818 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
40473591 AAACCAAGTA
* * * * *
40473601 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAATTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
40473640 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40473680 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40473720 CCTTCTGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40473760 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAACG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
40473800 CTTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40473819 TTATCATCCG
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.09
40 145 0.91
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40478984 original size:26 final size:25
Alignment explanation
Indices: 40478950--40479011 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
40478940 TTAATTATTT
*
40478950 CTGTTAAAAATTTC-ATTCATCTCTA
1 CTGTTAAAAACTTCAATT-ATCTCTA
40478975 CTGTTAAAAACTTCAATTATCTCTA
1 CTGTTAAAAACTTCAATTATCTCTA
*
40479000 TTGTTAAAAACT
1 CTGTTAAAAACT
40479012 GGTGTGGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 31 0.91
26 3 0.09
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (25 bp):
CTGTTAAAAACTTCAATTATCTCTA
Found at i:40479429 original size:7 final size:7
Alignment explanation
Indices: 40479390--40479443 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
40479380 TTAGCAAACA
40479390 AAAATTT
1 AAAATTT
40479397 AATAATATT
1 AA-AAT-TT
40479406 AATAA-TT
1 AA-AATTT
*
40479413 GAAA-TT
1 AAAATTT
40479419 AAAATTT
1 AAAATTT
40479426 AAAATTT
1 AAAATTT
40479433 AAAATTT
1 AAAATTT
40479440 AAAA
1 AAAA
40479444 AGCTATGGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 7 0.17
7 25 0.60
8 3 0.07
9 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:40487388 original size:30 final size:29
Alignment explanation
Indices: 40487348--40487442 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 29
40487338 GTTAATAATT
40487348 TATAAGAATTGAATC-AAATCAAAATTTCATG
1 TATAA-AATTGAA-CAAAATCAAAA-TTCATG
*
40487379 TATAAAATTGCACAAAATCAAAATTCATG
1 TATAAAATTGAACAAAATCAAAATTCATG
* * * *
40487408 TATACAATTGCACTTTAAATCATAATTCATG
1 TATAAAATTGAAC--AAAATCAAAATTCATG
40487439 TATA
1 TATA
40487443 GTTTTGGGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 19 0.33
30 15 0.26
31 23 0.40
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (29 bp):
TATAAAATTGAACAAAATCAAAATTCATG
Found at i:40487406 original size:29 final size:30
Alignment explanation
Indices: 40487363--40487442 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
40487353 GAATTGAATC
40487363 AAATCAAAATTTCATGTATAAAATTGCAC-A
1 AAATCAAAA-TTCATGTATAAAATTGCACTA
* *
40487393 AAATCAAAATTCATGTATACAATTGCACTTT
1 AAATCAAAATTCATGTATAAAATTGCAC-TA
*
40487424 AAATCATAATTCATGTATA
1 AAATCAAAATTCATGTATA
40487443 GTTTTGGGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.40
30 9 0.20
31 18 0.40
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTGCACTA
Found at i:40488074 original size:24 final size:24
Alignment explanation
Indices: 40488042--40488095 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
40488032 CCTATTGCCT
*
40488042 ACTATAAAGGTGGCGACACCACCA
1 ACTATAAAGGTGGCAACACCACCA
40488066 ACTATAAAGGTGGCAACACCACCA
1 ACTATAAAGGTGGCAACACCACCA
40488090 ACTATA
1 ACTATA
40488096 TATACTCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.15
Consensus pattern (24 bp):
ACTATAAAGGTGGCAACACCACCA
Found at i:40488485 original size:50 final size:52
Alignment explanation
Indices: 40488431--40488539 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
40488421 ATGAAAGAAA
40488431 GCGGCACCAAAAAACAATT-TTT-GTTTATTTTGATGCCTCCAAATAATGTG
1 GCGGCACCAAAAAACAATTGTTTAGTTTATTTTGATGCCTCCAAATAATGTG
* * * * *
40488481 GCGGCACCAAAAAATAATTGTTTATTTTATTTTGGTTCCTTCAAATAATGTG
1 GCGGCACCAAAAAACAATTGTTTAGTTTATTTTGATGCCTCCAAATAATGTG
40488533 GCGGCAC
1 GCGGCAC
40488540 TATAAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 18 0.35
51 3 0.06
52 31 0.60
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
GCGGCACCAAAAAACAATTGTTTAGTTTATTTTGATGCCTCCAAATAATGTG
Found at i:40490797 original size:56 final size:56
Alignment explanation
Indices: 40490711--40490819 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
40490701 TTTCGAGGCA
* *
40490711 ACAAATCTGATGAGTAAGTTCATAAATATTACTTATGAATATTTATGAGTCAAACC
1 ACAAATCCGATGAGCAAGTTCATAAATATTACTTATGAATATTTATGAGTCAAACC
* *
40490767 ACAAATCCGATGAGCAAGTTCGTAAATATTATTTATGAATATTTATGAGTCAA
1 ACAAATCCGATGAGCAAGTTCATAAATATTACTTATGAATATTTATGAGTCAA
40490820 TTATGGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (56 bp):
ACAAATCCGATGAGCAAGTTCATAAATATTACTTATGAATATTTATGAGTCAAACC
Found at i:40493139 original size:20 final size:20
Alignment explanation
Indices: 40493087--40493139 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
40493077 TATTTAAGCT
* *
40493087 AAAGTAAGTAAACGCAATGG
1 AAAGTAAGTAAATGCAATGA
*
40493107 AAAGTAAGTAAATGCTATGA
1 AAAGTAAGTAAATGCAATGA
40493127 AAAGTAAGTAAAT
1 AAAGTAAGTAAAT
40493140 AGAAGGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAGTAAGTAAATGCAATGA
Found at i:40496475 original size:42 final size:41
Alignment explanation
Indices: 40496348--40496476 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 41
40496338 CACAAGGTAC
* * * *
40496348 CATACCAATGCCATATTCCAGATATGGTCTTACATGGGATCT
1 CATATCAATG-CATATCCCAGATATGGTCTTACATGAGAACT
* * * * * *
40496390 CATATCAATGCAAATAGCTCAGCTATAGTCTTACACGAAAACT
1 CATATCAATGC--ATATCCCAGATATGGTCTTACATGAGAACT
*
40496433 CATATCGATGTCATATCCCAGATATGGTCTTACATGAGAACT
1 CATATCAATG-CATATCCCAGATATGGTCTTACATGAGAACT
40496475 CA
1 CA
40496477 AATAACCCTA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 35 0.52
43 30 0.45
44 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (41 bp):
CATATCAATGCATATCCCAGATATGGTCTTACATGAGAACT
Found at i:40499243 original size:18 final size:18
Alignment explanation
Indices: 40499216--40499272 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
40499206 ATACACAGAA
*
40499216 TAAGCTTTGAAAGCTTAG
1 TAAGCCTTGAAAGCTTAG
40499234 TAAGCCTTGAAAGCTTAG
1 TAAGCCTTGAAAGCTTAG
*
40499252 TAAGCCTTAAAAGCTTAG
1 TAAGCCTTGAAAGCTTAG
40499270 TAA
1 TAA
40499273 TCCATAAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (18 bp):
TAAGCCTTGAAAGCTTAG
Found at i:40499926 original size:43 final size:43
Alignment explanation
Indices: 40499858--40500031 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 43
40499848 AAAACTCATA
*
40499858 CGATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATAT
1 CGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAAATAT
* *
40499901 CGATGCCACTGTCCTAGACAGGGTCTTACACGAAATCAAATAT
1 CGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATAT
* * *
40499944 -GATGCTGA-TGTCCCAGACATGGTCTTACACGTAAATCATAA-GT
1 CGATGC-CACTGTCCCAGACAGGGTCTTACACGT-AATCA-AATAT
* * *
40499987 CGATGCTAAC-GTCCCAGAC-GTGGTCTTACACGAAATCACATAT
1 CGATGC-CACTGTCCCAGACAG-GGTCTTACACGTAATCAAATAT
40500030 CG
1 CG
40500032 GATCCTATGT
Statistics
Matches: 109, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 29 0.27
43 50 0.46
44 30 0.28
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
CGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATAT
Found at i:40500014 original size:86 final size:85
Alignment explanation
Indices: 40499868--40500029 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 85
40499858 CGATGCCAAC
* * * *
40499868 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCTAGACAGGGTCTTACACG
1 GTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCAACTGTCCCAGACAGGGTCTTACACG
40499933 AAATCAAATATGATGCTGAT
66 AAATCAAATATGATGCTGAT
*
40499953 GTCCCAGACATGGTCTTACACGTAAATCATAA-GTCGATGCTAAC-GTCCCAGAC-GTGGTCTTA
1 GTCCCAGACATGGTCTTACACGT-AATCA-AATATCGATGC-AACTGTCCCAGACAG-GGTCTTA
*
40500015 CACGAAATCACATAT
62 CACGAAATCAAATAT
40500030 CGGATCCTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
85 22 0.33
86 41 0.61
87 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (85 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCAACTGTCCCAGACAGGGTCTTACACG
AAATCAAATATGATGCTGAT
Found at i:40502910 original size:4 final size:4
Alignment explanation
Indices: 40502901--40502938 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
40502891 AATTTTCCCT
*
40502901 TTTC TTTC TTTGT TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC T
40502939 CCCCTGTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:40502918 original size:13 final size:12
Alignment explanation
Indices: 40502900--40502936 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
40502890 CAATTTTCCC
40502900 TTTTCTTTCTTT
1 TTTTCTTTCTTT
40502912 GTTTTCTTTCTTT
1 -TTTTCTTTCTTT
*
40502925 CTTTCTTTCTTT
1 TTTTCTTTCTTT
40502937 CTCCCCTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:40503082 original size:19 final size:19
Alignment explanation
Indices: 40503058--40503096 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40503048 AATACTTATT
*
40503058 TATTATT-TATACATGTGTA
1 TATTATTAT-TACATATGTA
40503077 TATTATTATTACATATGTA
1 TATTATTATTACATATGTA
40503096 T
1 T
40503097 CCATAGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TATTATTATTACATATGTA
Found at i:40508819 original size:39 final size:38
Alignment explanation
Indices: 40508735--40508820 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
40508725 ATGAGATTGG
* * *
40508735 AAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAATATCCAGACATAAGATCCGCAGGCTACATGCTAGA
* * * *
40508773 AATATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGGA
1 AA-ATATCCAGACATAAGATCCGCAGGCTACATGCT-AGA
40508813 AAATATCC
1 AAATATCC
40508821 GGGTTAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.05
39 33 0.85
40 4 0.10
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (38 bp):
AAATATCCAGACATAAGATCCGCAGGCTACATGCTAGA
Found at i:40515252 original size:3 final size:3
Alignment explanation
Indices: 40515236--40515417 Score: 76
Period size: 3 Copynumber: 60.3 Consensus size: 3
40515226 ACGTTTAGAG
* * * *
40515236 TAT TAT TACA TAT TAT TAT TAT TATT TAT TAT TAC TAT TAC TCT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
** ** * *
40515283 TATT TAT TAT TAT CGT TGC TAT T-T CTAT TAT TGT T-T T-T CTAT TAC
1 TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT
* * *
40515328 TAT T-T ATAT TAT TGT TGT CAT TAT TCAT TA- TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* *
40515373 T-T TAT TAT T-T T-T CTGT TAT TGT TAT TAT TAGT CTA- TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA-T -TAT TAT TAT TAT
40515417 T
1 T
40515418 CCTATTAATG
Statistics
Matches: 138, Mismatches: 24, Indels: 34
0.70 0.12 0.17
Matches are distributed among these distances:
2 14 0.10
3 106 0.77
4 16 0.12
5 2 0.01
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40515254 original size:13 final size:12
Alignment explanation
Indices: 40515236--40515294 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
40515226 ACGTTTAGAG
40515236 TATTATTACATAT
1 TATTATTAC-TAT
*
40515249 TATTATTATTATT
1 TATTATTACTA-T
40515262 TATTATTACTAT
1 TATTATTACTAT
* * *
40515274 TACTCTTATTATT
1 TATTATTACTA-T
40515287 TATTATTA
1 TATTATTA
40515295 TCGTTGCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 11 0.30
13 26 0.70
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:40515257 original size:16 final size:15
Alignment explanation
Indices: 40515236--40515291 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
40515226 ACGTTTAGAG
40515236 TATTATTACATATTAT
1 TATTATTAC-TATTAT
*
40515252 TATTATTATTTATTAT
1 TATTATTA-CTATTAT
* *
40515268 TACTATTACTCTTAT
1 TATTATTACTATTAT
40515283 TATTTATTA
1 TA-TTATTA
40515292 TTATCGTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 7 0.21
16 26 0.79
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:40515548 original size:3 final size:3
Alignment explanation
Indices: 40515540--40515573 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
40515530 ACTCGCGTCG
*
40515540 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40515574 ACTATTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40515555 original size:9 final size:9
Alignment explanation
Indices: 40515541--40515580 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
40515531 CTCGCGTCGT
40515541 TATTATTAC
1 TATTATTAC
*
40515550 TATTATTAT
1 TATTATTAC
*
40515559 TATTATTAT
1 TATTATTAC
40515568 TATTA-TAC
1 TATTATTAC
40515576 TATTA
1 TATTA
40515581 AACTGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:40515747 original size:24 final size:25
Alignment explanation
Indices: 40515719--40515775 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
40515709 ATACTTTCAA
* *
40515719 ATTTTATATTATTTATTTTTATT-AT
1 ATTTTATAATA-TTATTGTTATTAAT
40515744 -TTTTACTAATATTATTGTTATTAAT
1 ATTTTA-TAATATTATTGTTATTAAT
40515769 ATTTTAT
1 ATTTTAT
40515776 GTTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 15 0.56
25 7 0.26
26 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTTATAATATTATTGTTATTAAT
Found at i:40515756 original size:15 final size:15
Alignment explanation
Indices: 40515738--40515771 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40515728 TATTTATTTT
*
40515738 TATTATTTTTACTAA
1 TATTATTGTTACTAA
*
40515753 TATTATTGTTATTAA
1 TATTATTGTTACTAA
40515768 TATT
1 TATT
40515772 TTATGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATTGTTACTAA
Found at i:40552894 original size:17 final size:16
Alignment explanation
Indices: 40552862--40552895 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40552852 AAATTTAGGT
*
40552862 AAAAAATTAAACCTAA
1 AAAAAATTAAAACTAA
40552878 AAAAAATTAAATACTAA
1 AAAAAATTAAA-ACTAA
40552895 A
1 A
40552896 CTATTCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATTAAAACTAA
Found at i:40554069 original size:14 final size:15
Alignment explanation
Indices: 40554037--40554070 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40554027 ATATTATTAT
*
40554037 TATTTATCTAATTTT
1 TATTTATCTAATTTA
40554052 TATTTATC-AATTTA
1 TATTTATCTAATTTA
40554066 TATTT
1 TATTT
40554071 CTACTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATCTAATTTA
Found at i:40554254 original size:3 final size:3
Alignment explanation
Indices: 40554246--40554280 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40554236 TTTAAAACTT
40554246 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40554281 TTCCTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40554336 original size:18 final size:17
Alignment explanation
Indices: 40554309--40554374 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
40554299 TATTCATTTT
*
40554309 ATTTCCATTTTTTTACTA
1 ATTTCTATTTTTTTA-TA
*
40554327 ATTTCTATTTTATTTATTT
1 ATTTCTATTTT-TTTA-TA
* *
40554346 ATTTCAGATTTTTATATA
1 ATTTC-TATTTTTTTATA
*
40554364 ATATCTATTTT
1 ATTTCTATTTT
40554375 CAACTCTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
17 5 0.13
18 15 0.39
19 13 0.34
20 5 0.13
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTCTATTTTTTTATA
Found at i:40554341 original size:23 final size:22
Alignment explanation
Indices: 40554285--40554346 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
40554275 ATTATTTTCC
* *
40554285 TTTA-TTTATTTATTTATTCAT
1 TTTATTTTATTTATTTACTAAT
* *
40554306 TTTATTTCCATTTTTTTACTAAT
1 TTTATTT-TATTTATTTACTAAT
40554329 TTCTATTTTATTTATTTA
1 TT-TATTTTATTTATTTA
40554347 TTTCAGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 21 0.66
24 5 0.16
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTTTATTTATTTACTAAT
Found at i:40554374 original size:37 final size:38
Alignment explanation
Indices: 40554297--40554374 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
40554287 TATTTATTTA
* *
40554297 TTTATTCATTTTATTTCCATTTTTTTACTAATTTCTAT
1 TTTATTCATTTTATTTCCATTTTTATACTAATATCTAT
* *
40554335 TTTATTTA-TTTATTTCAGATTTTTATA-TAATATCTAT
1 TTTATTCATTTTATTTC-CATTTTTATACTAATATCTAT
40554372 TTT
1 TTT
40554375 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.65
Consensus pattern (38 bp):
TTTATTCATTTTATTTCCATTTTTATACTAATATCTAT
Found at i:40555272 original size:14 final size:14
Alignment explanation
Indices: 40555253--40555281 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40555243 GCTGATATTT
40555253 ACATTTTCTCTTTC
1 ACATTTTCTCTTTC
40555267 ACATTTTCTCTTTC
1 ACATTTTCTCTTTC
40555281 A
1 A
40555282 AAGTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (14 bp):
ACATTTTCTCTTTC
Found at i:40555418 original size:8 final size:8
Alignment explanation
Indices: 40555405--40555432 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40555395 TTTAATGATT
40555405 ATATTTAA
1 ATATTTAA
40555413 ATATTTAA
1 ATATTTAA
40555421 ATATTTAA
1 ATATTTAA
40555429 ATAT
1 ATAT
40555433 AGTTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTTAA
Found at i:40557589 original size:163 final size:163
Alignment explanation
Indices: 40557319--40557646 Score: 656
Period size: 163 Copynumber: 2.0 Consensus size: 163
40557309 TAAATAGGTG
40557319 CGGAAATTTGAGTAGACTTCCAAAGTCTATTCATAAGCTTCAGAGCTTGCTGACATTGAGATTAC
1 CGGAAATTTGAGTAGACTTCCAAAGTCTATTCATAAGCTTCAGAGCTTGCTGACATTGAGATTAC
40557384 TTTATCTTCCAAAGATTCAAATTCGTGACCAACTGCAAAGAATCGTCAATCTCAAATTTCTAGAG
66 TTTATCTTCCAAAGATTCAAATTCGTGACCAACTGCAAAGAATCGTCAATCTCAAATTTCTAGAG
40557449 ATAACTACGGCTGACACGCAATTAAGGGAGATT
131 ATAACTACGGCTGACACGCAATTAAGGGAGATT
40557482 CGGAAATTTGAGTAGACTTCCAAAGTCTATTCATAAGCTTCAGAGCTTGCTGACATTGAGATTAC
1 CGGAAATTTGAGTAGACTTCCAAAGTCTATTCATAAGCTTCAGAGCTTGCTGACATTGAGATTAC
40557547 TTTATCTTCCAAAGATTCAAATTCGTGACCAACTGCAAAGAATCGTCAATCTCAAATTTCTAGAG
66 TTTATCTTCCAAAGATTCAAATTCGTGACCAACTGCAAAGAATCGTCAATCTCAAATTTCTAGAG
40557612 ATAACTACGGCTGACACGCAATTAAGGGAGATT
131 ATAACTACGGCTGACACGCAATTAAGGGAGATT
40557645 CG
1 CG
40557647 ACCTAGTAAT
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 165 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (163 bp):
CGGAAATTTGAGTAGACTTCCAAAGTCTATTCATAAGCTTCAGAGCTTGCTGACATTGAGATTAC
TTTATCTTCCAAAGATTCAAATTCGTGACCAACTGCAAAGAATCGTCAATCTCAAATTTCTAGAG
ATAACTACGGCTGACACGCAATTAAGGGAGATT
Found at i:40560847 original size:10 final size:9
Alignment explanation
Indices: 40560833--40560909 Score: 68
Period size: 10 Copynumber: 8.4 Consensus size: 9
40560823 ATTTTTCAAA
40560833 TTTTATAAT
1 TTTTATAAT
40560842 ATTTTAT-AT
1 -TTTTATAAT
*
40560851 TTTAATAAT
1 TTTTATAAT
*
40560860 TTATATAAT
1 TTTTATAAT
*
40560869 TTTT-TATT
1 TTTTATAAT
40560877 TTTTATAACT
1 TTTTATAA-T
*
40560887 TTTAATAAT
1 TTTTATAAT
*
40560896 TTCTAATAAT
1 TT-TTATAAT
40560906 TTTT
1 TTTT
40560910 TTCAAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
8 12 0.22
9 20 0.36
10 23 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40560866 original size:17 final size:18
Alignment explanation
Indices: 40560831--40560871 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
40560821 GTATTTTTCA
*
40560831 AATTTTATAATATTTTAT
1 AATTTTATAATATTATAT
40560849 -ATTTTAATAAT-TTATAT
1 AATTTT-ATAATATTATAT
40560866 AATTTT
1 AATTTT
40560872 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTATAATATTATAT
Found at i:40560874 original size:27 final size:25
Alignment explanation
Indices: 40560822--40560897 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 25
40560812 ATAAAAGTGG
* *
40560822 TATTTTTCA-AATTTTATAATATTT
1 TATTTTTAATAATTTTATAATTTTT
40560846 TATATTTTAATAATTTATATAATTTTT
1 TAT-TTTTAATAATTT-TATAATTTTT
*
40560873 TATTTTTTATAACTTTTAATAATTT
1 TATTTTTAATAA-TTTT-ATAATTT
40560898 CTAATAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 3 0.07
25 5 0.11
26 14 0.32
27 22 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTTAATAATTTTATAATTTTT
Found at i:40560892 original size:36 final size:35
Alignment explanation
Indices: 40560843--40560910 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
40560833 TTTTATAATA
40560843 TTTTATATTTTAATAATTTAT-ATAATTTTTTATT
1 TTTTATATTTTAATAATTTATAATAATTTTTTATT
*
40560877 TTTTATAACTTTTAATAATTTCTAATAATTTTTT
1 TTTTAT-A-TTTTAATAATTTATAATAATTTTTT
40560911 TCAAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 6 0.20
35 1 0.03
36 13 0.43
37 10 0.33
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (35 bp):
TTTTATATTTTAATAATTTATAATAATTTTTTATT
Found at i:40561453 original size:28 final size:28
Alignment explanation
Indices: 40561417--40561485 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
40561407 AAATGTTTAA
*
40561417 AAAAACAATAGAA-CCTCATAAAATAATT
1 AAAAACAATA-AATCCTCACAAAATAATT
*
40561445 AAAAACAATTAAATCCTCACAACATAATT
1 AAAAACAA-TAAATCCTCACAAAATAATT
40561474 AAAAA-AATAAAT
1 AAAAACAATAAAT
40561486 TAATCCCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.14
28 12 0.32
29 20 0.54
ACGTcount: A:0.62, C:0.14, G:0.01, T:0.22
Consensus pattern (28 bp):
AAAAACAATAAATCCTCACAAAATAATT
Found at i:40562185 original size:22 final size:22
Alignment explanation
Indices: 40562157--40562199 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40562147 ACTACTACTG
40562157 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
40562179 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
40562200 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:40567452 original size:17 final size:16
Alignment explanation
Indices: 40567430--40567469 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40567420 ATTAAGGTGC
*
40567430 TTTTTATTTCTATTTTA
1 TTTTTATTTAT-TTTTA
40567447 TTTTTATTTATTTTTA
1 TTTTTATTTATTTTTA
40567463 TCTTTTA
1 T-TTTTA
40567470 GTTCGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATTTATTTTTA
Found at i:40568545 original size:25 final size:25
Alignment explanation
Indices: 40568517--40568689 Score: 84
Period size: 25 Copynumber: 6.8 Consensus size: 25
40568507 TTTTAAACTC
40568517 TTTTTTATATATTATCTATTTAAAA
1 TTTTTTATATATTATCTATTTAAAA
* * * * *
40568542 -TTTTTATATGTTATTTAGTTATAC
1 TTTTTTATATATTATCTATTTAAAA
* * *
40568566 TATTTTATATGTTAATC-GTTTAAAA
1 TTTTTTATATATT-ATCTATTTAAAA
*
40568591 CTCATTTTTAT-TATTATTTACTTT-AAA
1 -T--TTTTTATATATTATCTA-TTTAAAA
** * *
40568618 CCTTTCATATATTATTTATTTTAAAA
1 TTTTTTATATATTATCTA-TTTAAAA
* * *
40568644 TATTTTTATATATTCTCTATTTTAGA
1 T-TTTTTATATATTATCTATTTAAAA
* *
40568670 TTATTTCATATGTTATCTAT
1 TT-TTTTATATATTATCTAT
40568690 CCGAAATTTT
Statistics
Matches: 108, Mismatches: 29, Indels: 21
0.68 0.18 0.13
Matches are distributed among these distances:
24 24 0.22
25 28 0.26
26 28 0.26
27 19 0.18
28 9 0.08
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTTTATATATTATCTATTTAAAA
Found at i:40568615 original size:28 final size:29
Alignment explanation
Indices: 40568584--40568657 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 29
40568574 ATGTTAATCG
40568584 TTTAAAACTCATTTTTAT-TATTATTTAC
1 TTTAAAACTCATTTTTATATATTATTTAC
* *
40568612 TTT-AAAC-C--TTTCATATATTATTTAT
1 TTTAAAACTCATTTTTATATATTATTTAC
40568637 TTTAAAA-T-ATTTTTATATATT
1 TTTAAAACTCATTTTTATATATT
40568658 CTCTATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
24 5 0.13
25 12 0.32
26 4 0.11
27 14 0.37
28 3 0.08
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAAAACTCATTTTTATATATTATTTAC
Found at i:40574991 original size:14 final size:14
Alignment explanation
Indices: 40574972--40574998 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40574962 TATTAAAGTA
40574972 ATAATTAAGAACAC
1 ATAATTAAGAACAC
40574986 ATAATTAAGAACA
1 ATAATTAAGAACA
40574999 AATCAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:40580582 original size:46 final size:49
Alignment explanation
Indices: 40580476--40580591 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 49
40580466 TGTCTTCGAC
** * *
40580476 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATATCTAAT
* * *
40580526 ATGGGCTTACATGGCTCATTCTTGTCTCCAAAGCC-ATATAT-T-TGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATCTAAT
40580572 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
40580592 TATGTCCTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 22 0.38
47 1 0.02
48 6 0.10
50 29 0.50
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATCTAAT
Found at i:40585594 original size:33 final size:33
Alignment explanation
Indices: 40585551--40585712 Score: 175
Period size: 33 Copynumber: 4.9 Consensus size: 33
40585541 TCTTTCTGAG
* *
40585551 TGGTACACACAAAGTATACCTTTCCTTTTCGTA
1 TGGTATACACAAAGTATACCTTTCCTTTTCATA
40585584 TGGTATACACAAAGTATACCTTTCCTTTTCATA
1 TGGTATACACAAAGTATACCTTTCCTTTTCATA
* * *
40585617 TGGCATACATAAAGTATACATTTCCTTTTCA-A
1 TGGTATACACAAAGTATACCTTTCCTTTTCATA
* * * ** *
40585649 -GTGTACACACAAAGTGTACATAACCTTTTCATG
1 TG-GTATACACAAAGTATACCTTTCCTTTTCATA
* **
40585682 TGGTATAAACAAAGTATACCTAACCTTTTCA
1 TGGTATACACAAAGTATACCTTTCCTTTTCA
40585713 CATTTGATAG
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.01
32 24 0.22
33 84 0.76
34 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (33 bp):
TGGTATACACAAAGTATACCTTTCCTTTTCATA
Found at i:40585696 original size:65 final size:66
Alignment explanation
Indices: 40585550--40585700 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 66
40585540 TTCTTTCTGA
* * * * * **
40585550 GTGGTACACACAAAGTATACCTTTCCTTTTCGTATGGTATACACAAAGTATACCTTTCCTTTTCA
1 GTGGTATACACAAAGTATACATTTCCTTTTCGAATGGTACACACAAAGTATACATAACCTTTTCA
40585615 T
66 T
* * * *
40585616 ATGGCATACATAAAGTATACATTTCCTTTTC-AA-GTGTACACACAAAGTGTACATAACCTTTTC
1 GTGGTATACACAAAGTATACATTTCCTTTTCGAATG-GTACACACAAAGTATACATAACCTTTTC
40585679 AT
65 AT
*
40585681 GTGGTATAAACAAAGTATAC
1 GTGGTATACACAAAGTATAC
40585701 CTAACCTTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
64 1 0.01
65 42 0.61
66 26 0.38
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (66 bp):
GTGGTATACACAAAGTATACATTTCCTTTTCGAATGGTACACACAAAGTATACATAACCTTTTCA
T
Found at i:40585747 original size:29 final size:29
Alignment explanation
Indices: 40585705--40585802 Score: 178
Period size: 29 Copynumber: 3.4 Consensus size: 29
40585695 GTATACCTAA
40585705 CCTTTTCACATTTGATAGCCAAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
40585734 CCTTTTCACATTTGATAGCCAAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
* *
40585763 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
40585792 CCTTTTCACAT
1 CCTTTTCACAT
40585803 GGTACACACA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.35
Consensus pattern (29 bp):
CCTTTTCACATTTGATAGCCAAAGCTATC
Found at i:40590333 original size:27 final size:27
Alignment explanation
Indices: 40590290--40590355 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
40590280 CCACCAAGAC
40590290 AGTAAACACGGGATAGTCTATTGG-AAT
1 AGTAAACACGGGATAGT-TATTGGAAAT
* *
40590317 AGTAAACACATGG-TAGTTCTTGGAAAT
1 AGTAAACAC-GGGATAGTTATTGGAAAT
*
40590344 AATAAACACGGG
1 AGTAAACACGGG
40590356 GATTACGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 7 0.21
27 24 0.73
28 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
AGTAAACACGGGATAGTTATTGGAAAT
Found at i:40592012 original size:18 final size:18
Alignment explanation
Indices: 40591986--40592038 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
40591976 GCTTAATTCT
*
40591986 AAATTAATAAAAAAATAA
1 AAATAAATAAAAAAATAA
*
40592004 AAATAAATAATAAAACTAA
1 AAATAAATAA-AAAAATAA
* *
40592023 ATA-AAATAAAATAATA
1 AAATAAATAAAAAAATA
40592039 TCTTCTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 9 0.31
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAAAATAA
Done.