Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 45 of 185
Found at i:12674942 original size:59 final size:58
Alignment explanation
Indices: 12674664--12675067 Score: 264
Period size: 61 Copynumber: 6.8 Consensus size: 58
12674654 TTAATCATAT
* * * *
12674664 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT-TTAATAAAATTCTTAA
1 TTTAA-ATAATTATTATTAAATATAATTTAATAAAAATATATAATACT-ATAAAA-T-ATAA
* * * * * ** * * *
12674725 TAATCAAT-ATTATTATCTGAATTTACTAAAATAATAATATATGATACTATAAAATAT-T
1 T-TTAAATAATTATTAT-TAAATATAATTTAATAAAAATATATAATACTATAAAATATAA
* * *
12674783 TTTAACATAACTATTATTAAATATAATTTAATAAAAATATATAAT-TTAATAAAATTCTTAA
1 TTTAA-ATAATTATTATTAAATATAATTTAATAAAAATATATAATACT-ATAAAA-T-ATAA
* * * ** ** * *
12674844 TATTAAAT-ATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
1 T-TTAAATAATTATTAT-TAAATATAATTTAATAAAAATATATAATACTATAAAATATAA
* *
12674903 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAAT-TTAATAAAATTCTTAA
1 TTTAA-ATAATTATTATTAAATATAATTTAATAAAAATATATAATACT-ATAAAA-T-ATAA
* * * ** * * *
12674964 TATTAAAT-ATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATAA
1 T-TTAAATAATTATTAT-TAAATATAATTTAATAAAAATATATAATACTATAAAATATAA
12675023 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAAT
1 TTT-AAATAATTATTATTAAATATAATTTAATAAAAATATATAAT
12675068 TTAATAAAAT
Statistics
Matches: 255, Mismatches: 66, Indels: 46
0.69 0.18 0.13
Matches are distributed among these distances:
57 3 0.01
58 37 0.15
59 71 0.28
60 40 0.16
61 91 0.36
62 13 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (58 bp):
TTTAAATAATTATTATTAAATATAATTTAATAAAAATATATAATACTATAAAATATAA
Found at i:12674964 original size:120 final size:120
Alignment explanation
Indices: 12674664--12675141 Score: 805
Period size: 120 Copynumber: 4.0 Consensus size: 120
12674654 TTAATCATAT
* * *
12674664 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * * * * * *
12674729 CAATATTATTATCTGAATTTACTAAAATAATAATATATGATACTATAAAATAT-T
66 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
*
12674783 TTTAACATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
**
12674848 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
12674903 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
12674968 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATAA
66 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
*
12675023 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
12675088 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
66 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATA
12675142 GATTAATAGT
Statistics
Matches: 342, Mismatches: 16, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
119 108 0.32
120 234 0.68
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
Found at i:12675089 original size:18 final size:18
Alignment explanation
Indices: 12674923--12675076 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
12674913 TTATTATTAA
12674923 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
12674941 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* ****
12674959 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
12674978 ATATGAATTTAAT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
12674996 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* *
12675012 ATATAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
12675031 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
12675043 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
12675061 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
12675077 TTCTTAATAT
Statistics
Matches: 99, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 2 0.02
15 5 0.05
16 8 0.08
17 16 0.16
18 41 0.41
19 15 0.15
20 3 0.03
21 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:12679941 original size:14 final size:14
Alignment explanation
Indices: 12679918--12679965 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
12679908 TCCTCCCTGC
*
12679918 CTTCTTCATTTTCT
1 CTTCTACATTTTCT
*
12679932 CTTCTACATTTTCC
1 CTTCTACATTTTCT
*
12679946 CTTCGATCATTTTCT
1 CTTCTA-CATTTTCT
*
12679961 TTTCT
1 CTTCT
12679966 TTTTCCAGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.10, C:0.29, G:0.02, T:0.58
Consensus pattern (14 bp):
CTTCTACATTTTCT
Found at i:12686439 original size:16 final size:16
Alignment explanation
Indices: 12686418--12686450 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12686408 TTCGCTGTAT
12686418 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
12686434 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
12686450 T
1 T
12686451 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:12686712 original size:14 final size:15
Alignment explanation
Indices: 12686673--12686714 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12686663 TCTAAACATA
*
12686673 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12686688 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12686702 A-TATAATTTAATA
1 ATTATAATTAAATA
12686715 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12686807 original size:120 final size:120
Alignment explanation
Indices: 12686667--12686908 Score: 448
Period size: 120 Copynumber: 2.0 Consensus size: 120
12686657 ATCATATCTA
12686667 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
12686732 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
*
12686787 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* * *
12686852 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATTTT
66 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
12686907 AA
1 AA
12686909 TTAAAATTTA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
Found at i:12686823 original size:16 final size:16
Alignment explanation
Indices: 12686779--12686825 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
12686769 TACTATAAAA
*
12686779 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
12686795 TATTATT-AAATATAT
1 TATAATTAAAATATAT
12686810 TATAATTAAAATATAT
1 TATAATTAAAATATAT
12686826 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:12686910 original size:61 final size:61
Alignment explanation
Indices: 12686725--12686912 Score: 174
Period size: 61 Copynumber: 3.1 Consensus size: 61
12686715 AAATTCTTAA
* * *
12686725 TAATCAATATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATT
1 TAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATATTT
* * * * * * *
12686786 TAACATAATTATTATTAAAT--ATATTA-T-AATTAA-AATATATAAT-TTAATAAAAT-TCTTA
1 TAA-TTAA-TATTCTTATATGAAT-TTACTCAAATAATAATATATGATACT-ATAAAATATATT-
*
12686844 A
61 T
*
12686845 TAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATTT
1 TAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATATTT
12686906 TAATTAA
1 TAATTAA
12686913 AATTTATGAT
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 9 0.09
58 9 0.09
59 21 0.22
60 9 0.09
61 29 0.31
62 9 0.09
63 9 0.09
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
TAATTAATATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATATTT
Found at i:12686963 original size:120 final size:119
Alignment explanation
Indices: 12686667--12686955 Score: 370
Period size: 120 Copynumber: 2.4 Consensus size: 119
12686657 ATCATATCTA
* * * *
12686667 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACAAAATTATGATTAAATAAATTATAA-TAAAATATATAATCTAATAAAATTCTTAATAATCAA
12686732 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
65 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
* * * * *
12686787 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACAAAATTATGATTAAATAAATTATAA-TAAAATATATAATCTAATAAAATTCTTAATAATCAA
* * *
12686852 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATTTT
65 TATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
* *
12686907 AATTAAAATTTATGATTTAATAAAATT-TAA-AATAAT-TATAA-CTAATAAA
1 AA-CAAAA-TTATGATTAAAT-AAATTATAATAA-AATATATAATCTAATAAA
12686956 TTTTCTTATA
Statistics
Matches: 155, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
119 7 0.05
120 125 0.81
121 6 0.04
122 13 0.08
123 4 0.03
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (119 bp):
AACAAAATTATGATTAAATAAATTATAATAAAATATATAATCTAATAAAATTCTTAATAATCAAT
ATTCTTATATGAATTTACTCAAATAATAATATACGATACTATAAAATATAATTT
Found at i:12686992 original size:195 final size:185
Alignment explanation
Indices: 12686778--12687263 Score: 569
Period size: 182 Copynumber: 2.6 Consensus size: 185
12686768 ATACTATAAA
* *
12686778 ATATAATTTAACATAATTATTATTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTC
1 ATATAATTTAAAATAATTATTATTAAATATAATT-TAA-TAATAATATATAATTTCATAAAATTC
*
12686841 TTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATATT-
64 TTAATAATAAATATTCTTATATGAATTTACT-AAATCATAATATAT-A-A-T-T--AATATATTA
*
12686905 T-TAATTAAAATTTATGATTTAATAAAATTT-AAAATAATT-ATAACTAATAAATTTTCTTATAT
122 TATAATT-AAA-TAATGA--T-ATAAAATTTCAAAA-AATTCATAA-TAATAAATTTTCTTATAT
12686967 GAATTT
180 GAATTT
* *
12686973 GTATAATTTAAAATAATTATTATTGAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
* * * * *
12687038 GATAATAAATTTTTTTATATGAATTTA-TATAATC-TAA-A-ATAATTAATATGTTATATAATTT
66 AATAATAAATATTCTTATATGAATTTACTA-AATCATAATATATAATTAATATATTATATAATTA
* * * *
12687099 AATAATGATATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTT
130 AATAATGATATAAAATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTT
* *
12687155 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTT
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
*
12687220 AATAATAAAATGTTCTTATATGAATTTACTAAAATCATAATATA
66 AATAAT-AAATATTCTTATATGAATTTACT-AAATCATAATATA
12687264 ACTTGAGAAT
Statistics
Matches: 256, Mismatches: 22, Indels: 34
0.82 0.07 0.11
Matches are distributed among these distances:
182 102 0.40
183 25 0.10
184 5 0.02
185 16 0.06
186 4 0.02
187 7 0.03
188 1 0.00
189 1 0.00
190 1 0.00
191 2 0.01
192 1 0.00
193 4 0.02
194 8 0.03
195 76 0.30
196 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (185 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTT
AATAATAAATATTCTTATATGAATTTACTAAATCATAATATATAATTAATATATTATATAATTAA
ATAATGATATAAAATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTT
Found at i:12687045 original size:91 final size:91
Alignment explanation
Indices: 12686949--12687247 Score: 492
Period size: 91 Copynumber: 3.3 Consensus size: 91
12686939 TAATTATAAC
* *
12686949 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTGAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTGAATATAATTTAATAAT
*
12687014 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
* * *
12687040 TAATAAATTTTTTTATATGAATTTATATAATCTAAAATAATTAATA-TGTTATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTG-AATATAATTTAATAA
12687104 TGATATATAATTTCATAAAATTCTTGA
65 TGATATATAATTTCATAAAATTCTTGA
*
12687131 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTGAATATAATTTAATAAT
*
12687196 GATATATAATTTCATAAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
*
12687222 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
12687248 CTAAAATCAT
Statistics
Matches: 193, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
90 2 0.01
91 170 0.88
92 21 0.11
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTGAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:12687111 original size:44 final size:44
Alignment explanation
Indices: 12687063--12687207 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
12687053 TATATGAATT
*
12687063 TATATAATCTAAAATAATTAATATGTTATATAATTTAATAATGA
1 TATATAATTTAAAATAATTAATATGTTATATAATTTAATAATGA
* * * **
12687107 TATATAATTTCATAA-AATT-CT-TGATA-ATAAATTTTCTTATATGAA
1 TATATAATTT-AAAATAATTAATATGTTATAT-AA-TTTAATA-ATG-A
*
12687152 TTTATATAATTTAAAATAATTAATAT-TAAATATAATTTAATAATGA
1 --TATATAATTTAAAATAATTAATATGT-TATATAATTTAATAATGA
12687198 TATATAATTT
1 TATATAATTT
12687208 CATAAAATTC
Statistics
Matches: 77, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
41 2 0.03
42 6 0.08
43 6 0.08
44 26 0.34
45 4 0.05
46 4 0.05
47 17 0.22
48 6 0.08
49 4 0.05
50 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (44 bp):
TATATAATTTAAAATAATTAATATGTTATATAATTTAATAATGA
Found at i:12687112 original size:18 final size:18
Alignment explanation
Indices: 12687076--12687121 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
12687066 ATAATCTAAA
*
12687076 ATAA-TTAAT-ATGTTAT
1 ATAATTTAATAATGATAT
12687092 ATAATTTAATAATGATAT
1 ATAATTTAATAATGATAT
*
12687110 ATAATTTCATAA
1 ATAATTTAATAA
12687122 AATTCTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 17 0.65
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAATTTAATAATGATAT
Found at i:12687258 original size:47 final size:46
Alignment explanation
Indices: 12687025--12687259 Score: 126
Period size: 47 Copynumber: 5.1 Consensus size: 46
12687015 ATATATAATT
* * * *
12687025 TCATAAAATTCTTGATAAT-AAATTTTTTTATATGAATTTATATAA
1 TCATAAAATTCTTAATAATAAAATATTCTTATATGAATTTATAAAA
** * * * * * **
12687070 TC-TAAAATAATTAATATGTTATATAATT-TAATAATG-ATATATAATT
1 TCATAAAATTCTTAATA-ATAAAAT-ATTCTTAT-ATGAATTTATAAAA
* * *
12687116 TCATAAAATTCTTGATAAT-AAATTTTCTTATATGAATTTATATAA
1 TCATAAAATTCTTAATAATAAAATATTCTTATATGAATTTATAAAA
* ** * * * **
12687161 T-TTAAAATAATTAATATTAAATATAATT-TAATAATG-ATATATAATT
1 TCATAAAATTCTTAATAATAAA-AT-ATTCTTAT-ATGAATTTATAAAA
*
12687207 TCATAAAATTCTTAATAATAAAATGTTCTTATATGAATTTACTAAAA
1 TCATAAAATTCTTAATAATAAAATATTCTTATATGAATTTA-TAAAA
12687254 TCATAA
1 TCATAA
12687260 TATAACTTGA
Statistics
Matches: 133, Mismatches: 42, Indels: 28
0.66 0.21 0.14
Matches are distributed among these distances:
44 28 0.21
45 23 0.17
46 36 0.27
47 46 0.35
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (46 bp):
TCATAAAATTCTTAATAATAAAATATTCTTATATGAATTTATAAAA
Found at i:12688617 original size:20 final size:20
Alignment explanation
Indices: 12688592--12688637 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12688582 GTGCAGTTAG
* *
12688592 GGGCACAAAAGTGTAAATAA
1 GGGCACAAAAGTGCAAACAA
12688612 GGGCACAAAAGTGCAAACAA
1 GGGCACAAAAGTGCAAACAA
12688632 GGGCAC
1 GGGCAC
12688638 TTCGTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.28, T:0.09
Consensus pattern (20 bp):
GGGCACAAAAGTGCAAACAA
Found at i:12690676 original size:3 final size:3
Alignment explanation
Indices: 12690648--12690685 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
12690638 AGAAAGATGT
*
12690648 AGA AGA ATGA AGA AAA AGA A-A AGA AGA AGA AGA AGA AG
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12690686 CTATCATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:12690678 original size:17 final size:18
Alignment explanation
Indices: 12690650--12690684 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12690640 AAAGATGTAG
12690650 AAGAATGAAGAAAAAGAA
1 AAGAATGAAGAAAAAGAA
*
12690668 AAGAA-GAAGAAGAAGAA
1 AAGAATGAAGAAAAAGAA
12690685 GCTATCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (18 bp):
AAGAATGAAGAAAAAGAA
Found at i:12690678 original size:27 final size:25
Alignment explanation
Indices: 12690635--12690685 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
12690625 TAGATGTTTT
* *
12690635 AAAAGAAAGATGTAGAAGAATGAAGA
1 AAAAGAAAGAAGAAGAAGAA-GAAGA
12690661 AAAAGAAAAGAAGAAGAAGAAGAAG
1 AAAAG-AAAGAAGAAGAAGAAGAAG
12690686 CTATCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (25 bp):
AAAAGAAAGAAGAAGAAGAAGAAGA
Found at i:12691011 original size:24 final size:22
Alignment explanation
Indices: 12690983--12691033 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
12690973 AAATATTGTG
12690983 TATGAAAAATGTGTATTATGTAAA
1 TATGAAAAA--TGTATTATGTAAA
**
12691007 TATGATTAATGTATTATGTAAA
1 TATGAAAAATGTATTATGTAAA
12691029 TATGA
1 TATGA
12691034 TTAGTGCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
24 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (22 bp):
TATGAAAAATGTATTATGTAAA
Found at i:12691022 original size:22 final size:22
Alignment explanation
Indices: 12690994--12691036 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12690984 ATGAAAAATG
12690994 TGTATTATGTAAATATGATTAA
1 TGTATTATGTAAATATGATTAA
12691016 TGTATTATGTAAATATGATTA
1 TGTATTATGTAAATATGATTA
12691037 GTGCATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (22 bp):
TGTATTATGTAAATATGATTAA
Found at i:12693891 original size:27 final size:28
Alignment explanation
Indices: 12693856--12693908 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
12693846 CGAAATTCAG
*
12693856 ACTTTAATTA-TAAAATAGTTAATTTGA
1 ACTTAAATTATTAAAATAGTTAATTTGA
* *
12693883 ACTTAAATTATTAACATATTTAATTT
1 ACTTAAATTATTAAAATAGTTAATTT
12693909 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAGTTAATTTGA
Found at i:12695975 original size:24 final size:24
Alignment explanation
Indices: 12695959--12696004 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12695949 TAATCAATGT
12695959 AAAATATATTATGCTAATAAATTC
1 AAAATATATTATGCTAATAAATTC
* * *
12695983 TAAATATATTATACTACTAAAT
1 AAAATATATTATGCTAATAAAT
12696005 CTTTTAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (24 bp):
AAAATATATTATGCTAATAAATTC
Found at i:12696068 original size:35 final size:35
Alignment explanation
Indices: 12696020--12696091 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
12696010 AGAATGAAAA
*
12696020 TATATTTTTTTTAACTTAACTTGCAAGCAATCTCT
1 TATATTTTATTTAACTTAACTTGCAAGCAATCTCT
*
12696055 TATATTTTATTTAACTTGACTTGCAAGCAATCTCT
1 TATATTTTATTTAACTTAACTTGCAAGCAATCTCT
12696090 TA
1 TA
12696092 AAATTTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (35 bp):
TATATTTTATTTAACTTAACTTGCAAGCAATCTCT
Found at i:12704569 original size:5 final size:5
Alignment explanation
Indices: 12704559--12704584 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12704549 TGAGCATTTG
12704559 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
12704585 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:12704682 original size:5 final size:5
Alignment explanation
Indices: 12704674--12704699 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12704664 GAGATGGAAT
12704674 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
12704700 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:12704699 original size:26 final size:26
Alignment explanation
Indices: 12704648--12704699 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
12704638 TGAAGTTTTC
* * *
12704648 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
12704674 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
12704700 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:12705101 original size:19 final size:19
Alignment explanation
Indices: 12705068--12705115 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12705058 TAAACAATTC
12705068 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
12705085 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
12705104 AATAATATAAAT
1 AATAATATAAAT
12705116 AGTATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:12705630 original size:9 final size:9
Alignment explanation
Indices: 12705616--12705649 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
12705606 AGTTTGATAC
12705616 TCGAATTAT
1 TCGAATTAT
12705625 TCGAATTAT
1 TCGAATTAT
*
12705634 TCGAGTTAT
1 TCGAATTAT
12705643 TCGAATT
1 TCGAATT
12705650 CGAAAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (9 bp):
TCGAATTAT
Found at i:12705718 original size:9 final size:9
Alignment explanation
Indices: 12705701--12705731 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12705691 TCGAATTGAT
12705701 TCGAATAAC
1 TCGAATAAC
*
12705710 TCGATTAAC
1 TCGAATAAC
12705719 TCGAATAAC
1 TCGAATAAC
12705728 TCGA
1 TCGA
12705732 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:12708197 original size:48 final size:48
Alignment explanation
Indices: 12708099--12708194 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
12708089 TTTTTCTAAT
*
12708099 ATTATATATTATTTTTATTAGTTCATATTTTAATAATAATTATATTAA
1 ATTATATATTATTTTTATTAATTCATATTTTAATAATAATTATATTAA
* *
12708147 ATTATTTATTATTTTTATTAAATT-ATA-TTTAATTAA-AATTCTATTAA
1 ATTATATATTATTTTTATT-AATTCATATTTTAA-TAATAATTATATTAA
12708194 A
1 A
12708195 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 16 0.37
48 24 0.56
49 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (48 bp):
ATTATATATTATTTTTATTAATTCATATTTTAATAATAATTATATTAA
Found at i:12708357 original size:49 final size:49
Alignment explanation
Indices: 12708297--12708406 Score: 177
Period size: 49 Copynumber: 2.2 Consensus size: 49
12708287 ACATCTATTT
*
12708297 CATTCAACCAAAAGCAAGAATACTATTATAATTTTATTCTATTC-CATTC
1 CATTCAACCAAAAGCAAGAATACTATTATAATTCTATTCTA-TCACATTC
* *
12708346 CATTCAACCAAATGCAAGAATACTATTATAGTTCTATTCTATCACATTC
1 CATTCAACCAAAAGCAAGAATACTATTATAATTCTATTCTATCACATTC
12708395 CATTCAACCAAA
1 CATTCAACCAAA
12708407 CAATTGAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 2 0.04
49 55 0.96
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (49 bp):
CATTCAACCAAAAGCAAGAATACTATTATAATTCTATTCTATCACATTC
Found at i:12713198 original size:15 final size:14
Alignment explanation
Indices: 12713179--12713214 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
12713169 TTTTTATAAT
12713179 AATAAAATAAAAGA
1 AATAAAATAAAAGA
*
12713193 AGATAACATAAAAGA
1 A-ATAAAATAAAAGA
12713208 AATAAAA
1 AATAAAA
12713215 GTTCAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:12717907 original size:24 final size:24
Alignment explanation
Indices: 12717875--12717922 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12717865 AAAGAAAGAA
12717875 AGAAATTGCTTTGTATTCCCAATG
1 AGAAATTGCTTTGTATTCCCAATG
12717899 AGAAATTGCTTTGTATTCCCAATG
1 AGAAATTGCTTTGTATTCCCAATG
12717923 TCTTTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
AGAAATTGCTTTGTATTCCCAATG
Found at i:12719502 original size:15 final size:15
Alignment explanation
Indices: 12719479--12719516 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12719469 TTATATATAC
*
12719479 ATAATATTA-TTTCAA
1 ATAAAATTAGTTTC-A
12719494 ATAAAATTAGTTTCA
1 ATAAAATTAGTTTCA
12719509 ATAAAATT
1 ATAAAATT
12719517 TAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAAATTAGTTTCA
Found at i:12745027 original size:10 final size:10
Alignment explanation
Indices: 12744998--12745032 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
12744988 TTAATTTTTA
12744998 ATTTTTAATT
1 ATTTTTAATT
*
12745008 ATCATTTAATT
1 AT-TTTTAATT
12745019 ATTTTTAATT
1 ATTTTTAATT
12745029 ATTT
1 ATTT
12745033 ATTTAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTAATT
Found at i:12745044 original size:21 final size:20
Alignment explanation
Indices: 12744998--12745049 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
12744988 TTAATTTTTA
12744998 ATTTTTAATTATCATTTAATT
1 ATTTTTAATTATCATTTAA-T
*
12745019 ATTTTTAATTATTTATTTAA-
1 ATTTTTAATTA-TCATTTAAT
*
12745039 AGTTTTAATTA
1 ATTTTTAATTA
12745050 GGGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.36
21 11 0.39
22 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTTAATTATCATTTAAT
Found at i:12745711 original size:11 final size:12
Alignment explanation
Indices: 12745696--12745726 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
12745686 TAAATGATAT
12745696 TTTATTATTTTA
1 TTTATTATTTTA
12745708 -TTATTATTTTA
1 TTTATTATTTTA
12745719 TTTATTAT
1 TTTATTAT
12745727 ATATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:12751923 original size:12 final size:10
Alignment explanation
Indices: 12751851--12751921 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 10
12751841 ATTATTTAGA
12751851 TTTTATTTAGTT
1 TTTTATTT--TT
*
12751863 TTATATTTTAT
1 TTTTATTTT-T
*
12751874 GTTTTATTTCT
1 -TTTTATTTTT
12751885 TTTTATTTTT
1 TTTTATTTTT
*
12751895 TTTGCTATTTGT
1 TTT--TATTTTT
12751907 TTTTATTTTAT
1 TTTTATTTT-T
12751918 TTTT
1 TTTT
12751922 TAGACTTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
10 18 0.38
11 7 0.15
12 23 0.48
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:12754247 original size:21 final size:21
Alignment explanation
Indices: 12754200--12754249 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
12754190 GTCAAATCTA
*
12754200 ATCTTAGAAATATTCAATCGT
1 ATCTTGGAAATATTCAATCGT
12754221 ATCTTGGAAATATTCAATCGT
1 ATCTTGGAAATATTCAATCGT
12754242 ATCTTGGA
1 ATCTTGGA
12754250 CGGCCAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
ATCTTGGAAATATTCAATCGT
Found at i:12755409 original size:14 final size:14
Alignment explanation
Indices: 12755387--12755425 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
12755377 AGGAAATTCC
12755387 ATTAGATTAATTTA
1 ATTAGATTAATTTA
12755401 GATTA-ATTAATTTA
1 -ATTAGATTAATTTA
12755415 ATTAGATTAAT
1 ATTAGATTAAT
12755426 AAATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (14 bp):
ATTAGATTAATTTA
Found at i:12755424 original size:9 final size:9
Alignment explanation
Indices: 12755387--12755425 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
12755377 AGGAAATTCC
12755387 ATTAGATTA
1 ATTAGATTA
12755396 ATTTAGATTA
1 A-TTAGATTA
12755406 ATTA-ATTTA
1 ATTAGA-TTA
12755415 ATTAGATTA
1 ATTAGATTA
12755424 AT
1 AT
12755426 AAATATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 16 0.59
10 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (9 bp):
ATTAGATTA
Found at i:12759797 original size:3 final size:3
Alignment explanation
Indices: 12759789--12759839 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
12759779 AAGCATTTAA
* *
12759789 AAT AAT AAT AAT ATT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12759837 AAT
1 AAT
12759840 GAACATGTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12759927 original size:21 final size:22
Alignment explanation
Indices: 12759903--12759964 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
12759893 AAGAAAATAG
12759903 ATAAAAAT-TAT-TA-ATATAT
1 ATAAAAATATATGTATATATAT
12759922 ATATAAAATATATGTATATATAT
1 ATA-AAAATATATGTATATATAT
*
12759945 ATAAGAAATATATGTGTATA
1 ATAA-AAATATATGTATATA
12759965 ACAAAGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 3 0.08
22 3 0.08
23 23 0.62
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (22 bp):
ATAAAAATATATGTATATATAT
Found at i:12760121 original size:42 final size:43
Alignment explanation
Indices: 12760044--12760124 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
12760034 CTTGAAGTAA
* *
12760044 ATAATAAATAATAAAAATGATATAATTAGACAAATATACATAT
1 ATAAAAAATAATAAAAATGAAATAATTAGACAAATATACATAT
* *
12760087 ATAAAAAATAA-ACAAATGAAATAAATTATA-AAATATAC
1 ATAAAAAATAATAAAAATGAAAT-AATTAGACAAATATAC
12760125 TAATTCATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 17 0.52
43 16 0.48
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (43 bp):
ATAAAAAATAATAAAAATGAAATAATTAGACAAATATACATAT
Found at i:12762980 original size:20 final size:21
Alignment explanation
Indices: 12762942--12762981 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12762932 ATGTTTTTCT
**
12762942 ATTTTCTAAATAATTTTTAAA
1 ATTTTCTAAATAAAATTTAAA
12762963 ATTTTC-AAATAAAATTTAA
1 ATTTTCTAAATAAAATTTAA
12762982 TTTTTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTCTAAATAAAATTTAAA
Found at i:12763095 original size:15 final size:15
Alignment explanation
Indices: 12763075--12763104 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12763065 GAAATAACTG
*
12763075 AAAAAAGAAAGAAAA
1 AAAAAACAAAGAAAA
12763090 AAAAAACAAAGAAAA
1 AAAAAACAAAGAAAA
12763105 GAGTATTGTT
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:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAGAAAA
Found at i:12763736 original size:15 final size:15
Alignment explanation
Indices: 12763716--12763746 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12763706 GGTCGATTCC
12763716 TCTTCTAAGCTCATT
1 TCTTCTAAGCTCATT
12763731 TCTTCTAAGCTCATT
1 TCTTCTAAGCTCATT
12763746 T
1 T
12763747 GTATTTTCTA
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:0.19, C:0.26, G:0.06, T:0.48
Consensus pattern (15 bp):
TCTTCTAAGCTCATT
Found at i:12764402 original size:13 final size:13
Alignment explanation
Indices: 12764384--12764422 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12764374 CAATATATTT
12764384 ATTAATTAAAAAA
1 ATTAATTAAAAAA
12764397 ATTAATTAAAAATA
1 ATTAATTAAAAA-A
12764411 ATT--TTAAAAAA
1 ATTAATTAAAAAA
12764422 A
1 A
12764423 AAAGCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 7 0.28
13 12 0.48
14 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAATTAAAAAA
Found at i:12773017 original size:16 final size:18
Alignment explanation
Indices: 12772984--12773021 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12772974 TGCAATTTCG
12772984 ATTATAAAATAAATTTTA
1 ATTATAAAATAAATTTTA
* *
12773002 ATTA-AAAATATATTTAA
1 ATTATAAAATAAATTTTA
12773019 ATT
1 ATT
12773022 TGAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATAAAATAAATTTTA
Found at i:12774025 original size:26 final size:26
Alignment explanation
Indices: 12773989--12774065 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 26
12773979 GGCTTGGCCC
* *
12773989 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAATTAAAAAATT
*
12774015 ATTTTAAAAATAAAAAATAAAAAAAATT
1 ATTTTAAAAAT-AAAAAT-TAAAAAATT
*
12774043 ATTTTAAAAATAAAAAATAAAAA
1 ATTTTAAAAATAAAAATTAAAAA
12774066 TAAAAATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
26 15 0.34
27 10 0.23
28 19 0.43
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (26 bp):
ATTTTAAAAATAAAAATTAAAAAATT
Found at i:12774047 original size:28 final size:28
Alignment explanation
Indices: 12774007--12774065 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
12773997 AATAAACATT
12774007 AAAAAATTATTTTAAAAATAAAAAATAA
1 AAAAAATTATTTTAAAAATAAAAAATAA
12774035 AAAAAATTATTTTAAAAATAAAAAATAA
1 AAAAAATTATTTTAAAAATAAAAAATAA
12774063 AAA
1 AAA
12774066 TAAAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAAATTATTTTAAAAATAAAAAATAA
Found at i:12781522 original size:43 final size:43
Alignment explanation
Indices: 12781470--12781892 Score: 515
Period size: 43 Copynumber: 9.8 Consensus size: 43
12781460 TTTTCTTTAC
* ***
12781470 AACGCCGCTATAGACCATGGTTTTTAGCGGCGCTTACCCCTGA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * *
12781513 AACGCCGCTATAGACCATGGCCTTTAGCGGCGCATACCAAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
*
12781556 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * *
12781599 AACGCCACTATAGACCATGGTCTTTTGCGCCGCTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * * ** *
12781642 AACGCTGCTATAGACCATGCTCTATAGCGGCGCTTAGACAAGA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * * *
12781685 GACGCCGCTATAGACCATGGTCTTTAACGGCGCTTACGCAAGA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
12781728 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * * * *
12781771 AACGCTGCTATAGACCGTGGTCTTTAGCAGCGCTTATCCAATA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* ** ** *
12781814 AACGCCGCTAAAGATAATGACCTTTAGCGGCGCTTACCGTGAA-A
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACC--CAACA
* *
12781858 AACACCGCTATAGACCATGGTCTTTAGCGGTGCTT
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTT
12781893 TTAGAAAAAC
Statistics
Matches: 321, Mismatches: 57, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
43 290 0.90
44 29 0.09
45 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (43 bp):
AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
Found at i:12782252 original size:21 final size:21
Alignment explanation
Indices: 12782207--12782255 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
12782197 TTTAAGTTGT
*
12782207 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCA
*
12782228 TCTGCTTCTCTCGCTGTC-GCA
1 TCTGCTTCCCTCGCTG-CAGCA
12782249 TCTGCTT
1 TCTGCTT
12782256 TAAGCTGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCA
Found at i:12782316 original size:87 final size:86
Alignment explanation
Indices: 12782210--12782407 Score: 283
Period size: 87 Copynumber: 2.3 Consensus size: 86
12782200 AAGTTGTTCT
* * * *
12782210 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCGCTGTCGCATCTGCTTTAAGCTGCT-GCTGGAGTT
1 GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTT
12782274 CTTCATA-CTTTCGTTGAACCTCA
65 CTTCATATCTTT--TTGAACCTCA
* *
12782297 GCTTCTCTCGTTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTC
12782362 TTCATATCTTTTTGAACCTCA
66 TTCATATCTTTTTGAACCTCA
* *
12782383 GCTTCTCTCGATGTTGCCTCCGCTT
1 GCTTCTCTCGATGCTGCCTCTGCTT
12782408 TAAGTTGTGT
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
86 33 0.33
87 64 0.63
88 4 0.04
ACGTcount: A:0.11, C:0.32, G:0.19, T:0.38
Consensus pattern (86 bp):
GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTC
TTCATATCTTTTTGAACCTCA
Found at i:12782321 original size:21 final size:21
Alignment explanation
Indices: 12782292--12782342 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
12782282 TTTCGTTGAA
* * *
12782292 CCTCAGCTTCTCTCGTTGCTG
1 CCTCTGCTTCTCTCGCTGCCG
12782313 CCTCTGCTTCTCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCCG
*
12782334 CATCTGCTT
1 CCTCTGCTT
12782343 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCCG
Found at i:12787922 original size:15 final size:15
Alignment explanation
Indices: 12787886--12787926 Score: 73
Period size: 16 Copynumber: 2.7 Consensus size: 15
12787876 CGTATTATGT
12787886 AAGTTATGTATTAAA
1 AAGTTATGTATTAAA
12787901 AATGTTATGTATTAAA
1 AA-GTTATGTATTAAA
12787917 AAGTTATGTA
1 AAGTTATGTA
12787927 AGTTACGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (15 bp):
AAGTTATGTATTAAA
Found at i:12787973 original size:18 final size:19
Alignment explanation
Indices: 12787950--12787985 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12787940 TTTAAAATAT
12787950 ATATTA-ATAAGTTATGTC
1 ATATTATATAAGTTATGTC
*
12787968 ATATTATGTAAGTTATGT
1 ATATTATATAAGTTATGT
12787986 ATTAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (19 bp):
ATATTATATAAGTTATGTC
Found at i:12788012 original size:50 final size:50
Alignment explanation
Indices: 12787951--12788106 Score: 184
Period size: 50 Copynumber: 3.3 Consensus size: 50
12787941 TTAAAATATA
12787951 TATTAATAAGTTATGTCATATTATGTAAGTTATGTATTAAAAATGTTATG
1 TATTAATAAGTTATGTCATATTATGTAAGTTATGTATTAAAAATGTTATG
* * * * *
12788001 TATTAATAAGTTATAT-A-AGGTATGT-A-TCAT-T-TT-AAAAT-ATATA
1 TATTAATAAGTTATGTCATA-TTATGTAAGTTATGTATTAAAAATGTTATG
* *
12788044 TATTAATAAGTTATGTCGTATTATATAAGTTATGTATTAAAAATGTTATG
1 TATTAATAAGTTATGTCATATTATGTAAGTTATGTATTAAAAATGTTATG
12788094 TATTAATAAGTTA
1 TATTAATAAGTTA
12788107 CGTAAGTTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
43 18 0.21
44 9 0.11
45 4 0.05
46 4 0.05
47 4 0.05
48 4 0.05
49 11 0.13
50 31 0.36
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (50 bp):
TATTAATAAGTTATGTCATATTATGTAAGTTATGTATTAAAAATGTTATG
Found at i:12788050 original size:43 final size:43
Alignment explanation
Indices: 12788001--12788163 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 43
12787991 AAATGTTATG
* *
12788001 TATTAATAAGTTATATAAGGTATGTATCATTTTAAAATATATA
1 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATATA
* * * * *
12788044 TATTAATAAGTTATGT-CGTATTATATAAGTTATGTATTAAAAATGTTATG
1 TATTAATAAGTTATGTAAG--TTATGT-A-TCAT-T-TT-AAAAT-ATATA
* *
12788094 TATTAATAAGTTACGTAAGTTATGTATCATTTTAAAAAATATA
1 TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATATA
12788137 TATTAATAAGTTATGTAA-TGTATGTAT
1 TATTAATAAGTTATGTAAGT-TATGTAT
12788164 TATAAATGAG
Statistics
Matches: 95, Mismatches: 15, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
42 2 0.02
43 42 0.44
44 8 0.08
45 3 0.03
46 4 0.04
47 4 0.04
48 3 0.03
49 10 0.11
50 18 0.19
51 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (43 bp):
TATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATATA
Found at i:12788082 original size:16 final size:15
Alignment explanation
Indices: 12788044--12788106 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 15
12788034 AAAATATATA
12788044 TATTAATAAGTTATGTCG
1 TATTAATAAGTTA--T-G
12788062 TATTATATAAGTTATG
1 TATTA-ATAAGTTATG
*
12788078 TATTAAAAATGTTATG
1 TATTAATAA-GTTATG
12788094 TATTAATAAGTTA
1 TATTAATAAGTTA
12788107 CGTAAGTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.17
16 20 0.49
17 1 0.02
18 5 0.12
19 8 0.20
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.46
Consensus pattern (15 bp):
TATTAATAAGTTATG
Found at i:12788097 original size:93 final size:92
Alignment explanation
Indices: 12787870--12788152 Score: 478
Period size: 93 Copynumber: 3.1 Consensus size: 92
12787860 ATTTATGTTA
* *
12787870 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAAAAAGTTATGTAAGTTACGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
12787935 ATCATTTT-AAAATATATATTAATAAG
66 ATCATTTTAAAAATATATATTAATAAG
* * *
12787961 TTATGTCATATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATATAAGGTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
12788026 ATCATTTTAAAATATATATATTAATAAG
66 ATCATTTTAAAA-ATATATATTAATAAG
* *
12788054 TTATGTCGTATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTACGTAAGTTATGT
1 TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
12788119 ATCATTTTAAAAAATATATATTAATAAG
66 ATCATTTT-AAAAATATATATTAATAAG
12788147 TTATGT
1 TTATGT
12788153 AATGTATGTA
Statistics
Matches: 179, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
91 68 0.38
92 3 0.02
93 104 0.58
94 4 0.02
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (92 bp):
TTATGTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGT
ATCATTTTAAAAATATATATTAATAAG
Found at i:12788795 original size:15 final size:15
Alignment explanation
Indices: 12788767--12788802 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12788757 TTAATAAAAG
*
12788767 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
12788781 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
12788796 GAAAACA
1 GAAAACA
12788803 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:12790650 original size:13 final size:14
Alignment explanation
Indices: 12790624--12790659 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
12790614 AATTCAGTTC
12790624 TTATAATATTTTAT
1 TTATAATATTTTAT
12790638 TTATAAT-TTTTAT
1 TTATAATATTTTAT
*
12790651 TTTTAATAT
1 TTATAATAT
12790660 ATTTCTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATATTTTAT
Found at i:12791821 original size:74 final size:73
Alignment explanation
Indices: 12791652--12791899 Score: 424
Period size: 73 Copynumber: 3.4 Consensus size: 73
12791642 ATAACTATCA
*
12791652 TTTGCGGCGTTTGTACCAGAAACGCCGTTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
12791717 GTTAAACT
66 GTTAAACT
* *
12791725 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACTAATAAACAGTATACAAAACGAAGTCATTTT
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATA-AAAACGAAGTCGTTTT
12791790 GGTTAAACT
65 GGTTAAACT
*
12791799 TTTGCGGCGTTTTTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
1 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
12791864 GTTAAACT
66 GTTAAACT
* * *
12791872 TTTGCGGCGTTTTTACAATAAACGCCGC
1 TTTGCGGCGTTTGTACCAGAAACGCCGC
12791900 AAATTCGTGC
Statistics
Matches: 166, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
73 96 0.58
74 70 0.42
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (73 bp):
TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCGTTTTG
GTTAAACT
Found at i:12793069 original size:41 final size:41
Alignment explanation
Indices: 12792980--12793073 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
12792970 GCTAGCTACA
*
12792980 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAT
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
** * *
12793021 ATGCGCCGCTAATGCTGCGGTTTTTAGCGGCGCTTTT-TAAG
1 AAACGCCGCTAATGCTCCGGTCTTTAGCGGCG-TTTTCTAAG
12793062 AAACGCCGCTAA
1 AAACGCCGCTAA
12793074 AGACCTAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTCTAAG
Found at i:12793089 original size:41 final size:41
Alignment explanation
Indices: 12793044--12793351 Score: 336
Period size: 41 Copynumber: 7.5 Consensus size: 41
12793034 GCTGCGGTTT
* *
12793044 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTAAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* * *
12793085 TTAGCGGCGC-TTGTTAAGAAATGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTG-TAAAAAACGCCGCTAAAGACCTAAGCA
* *
12793126 TTAGCGGCGCTTGGTAAAAAATGCCGCTAAAAGACCGT-AGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCT-AAAGACC-TAAGCA
*
12793168 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTCAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
** * * * *
12793209 TTAGCAACGCTTTGTAAAGAACGCCGCGAAAGACATAAGTA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* *
12793250 TTAGCGGCGCTTTGTAAAAAACGTCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
* * * * *
12793291 TTAGCGGTGCATAT-TAGAAAACGCCGCGAAAGA-CTGTAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACCT-AAGCA
*
12793332 TTAGCGGCGATTATGTAAAA
1 TTAGCGGCGCTT-TGTAAAA
12793352 GCACCGCTAA
Statistics
Matches: 226, Mismatches: 32, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
40 6 0.03
41 174 0.77
42 45 0.20
43 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAAGCA
Found at i:12793210 original size:124 final size:122
Alignment explanation
Indices: 12793044--12793350 Score: 350
Period size: 124 Copynumber: 2.5 Consensus size: 122
12793034 GCTGCGGTTT
* * *
12793044 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTAAGCATTAGCGGCGC-TTGTTAAGAAATG
1 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAG-AACG
* * * *
12793108 CCGCTAAAGACCTGAGCATTAGCGGCGCTTGGTAAAAAATGCCGCTAAAAGACC-GTAGCA
64 CCGCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCT-AAAGACCTG-AGCA
* **
12793168 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTCAGCATTAGCAACGCTTTGTAAAGAACGC
1 TTAGCGGCGCTTT-TAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAGAACGC
* * *
12793233 CGCGAAAGACATAAGTATTAGCGGCGCTTTGTAAAAAACGTCGCTAAAGACCTGAGCA
65 CGCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGACCTGAGCA
* * * * * *
12793291 TTAGCGGTGCATATTAGAAAACGCCGCGAAAGA-CTGTAGCATTAGCGGCGATTATGTAAA
1 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAGACCT-AAGCATTAGCGGCGCTT-TGTAAA
12793351 AGCACCGCTA
Statistics
Matches: 156, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
122 2 0.01
123 53 0.34
124 94 0.60
125 7 0.04
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (122 bp):
TTAGCGGCGCTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTTGTAAAGAACGCC
GCGAAAGACATAAGCATTAGCGGCGCTTGGTAAAAAACGCCGCTAAAGACCTGAGCA
Found at i:12793554 original size:41 final size:41
Alignment explanation
Indices: 12793465--12793555 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
12793455 TTACATATAT
12793465 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
1 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
* * * * *
12793506 CGTCGCTAATGCTCG-ATTTTTTGTGGCGTTTTTTGTCCAAA-
1 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGT--AAAG
12793547 CGCCGCTAA
1 CGCCGCTAA
12793556 AAGCGCCGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
40 17 0.40
41 22 0.52
42 3 0.07
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (41 bp):
CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAG
Found at i:12793564 original size:12 final size:12
Alignment explanation
Indices: 12793547--12793571 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12793537 TTTGTCCAAA
12793547 CGCCGCTAAAAG
1 CGCCGCTAAAAG
12793559 CGCCGCTAAAAG
1 CGCCGCTAAAAG
12793571 C
1 C
12793572 CTGTTTTGGT
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:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CGCCGCTAAAAG
Found at i:12801983 original size:31 final size:32
Alignment explanation
Indices: 12801909--12801984 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 32
12801899 GTAAAAGTTA
* *
12801909 ATTTCAAATTTTTAATATTATTTAATATTTTT
1 ATTTCAATTTTTTAATATTAATTAATATTTTT
12801941 ATTTCAATTTTTTAAT-TTAATTAATATTTTT
1 ATTTCAATTTTTTAATATTAATTAATATTTTT
12801972 -TTAT-AATTTTTTA
1 ATT-TCAATTTTTTA
12801985 TAACAGTCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 11 0.27
31 15 0.37
32 15 0.37
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTCAATTTTTTAATATTAATTAATATTTTT
Found at i:12803946 original size:59 final size:59
Alignment explanation
Indices: 12803784--12803958 Score: 255
Period size: 58 Copynumber: 3.0 Consensus size: 59
12803774 ATTGATTTAT
* * *
12803784 TTTTGAATATATTTGTACAAATTGTTTTTATATTGTTTCATTTAATAAAACAAAAGTTC
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
*
12803843 TTTTGAA-ATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
** * *
12803901 TTTTGAATATGCTTGTACAAATTATTTTT-TCATTGTTTCATTTAATAAATTAGGAGTT
1 TTTTGAATATATTTGTACAAATTATTTTTAT-ATTGTTTCATTTAATAAAATAGAAGTT
12803959 ATTTCGATTT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 55 0.52
59 51 0.48
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (59 bp):
TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:12806247 original size:22 final size:22
Alignment explanation
Indices: 12806222--12806272 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
12806212 CTTATATTTC
12806222 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
12806244 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
12806266 CTCTCAA
1 CTCTCAA
12806273 ATCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:12807460 original size:7 final size:7
Alignment explanation
Indices: 12807448--12807472 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12807438 AGTTGATTGA
12807448 TATTTAG
1 TATTTAG
12807455 TATTTAG
1 TATTTAG
12807462 TATTTAG
1 TATTTAG
12807469 TATT
1 TATT
12807473 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:12808624 original size:25 final size:25
Alignment explanation
Indices: 12808590--12808710 Score: 110
Period size: 25 Copynumber: 5.0 Consensus size: 25
12808580 TATTTTGAAG
12808590 TTTATTTGATGTAAAAAAATAGAAT
1 TTTATTTGATGTAAAAAAATAGAAT
12808615 TTTATTTGATGTAATAAAAATAGAAAT
1 TTTATTTGATGTAA-AAAAATAG-AAT
* ** *
12808642 TTT-TTTGA-GT---TATTTTG-AT
1 TTTATTTGATGTAAAAAAATAGAAT
* * *
12808661 ATTATTTGATGTAATAAAATAGAAG
1 TTTATTTGATGTAAAAAAATAGAAT
*
12808686 TTTATTTGATGTAATAAAATAGAAT
1 TTTATTTGATGTAAAAAAATAGAAT
12808711 ATTTTGAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.05
20 5 0.07
21 5 0.07
24 3 0.04
25 40 0.53
26 13 0.17
27 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (25 bp):
TTTATTTGATGTAAAAAAATAGAAT
Found at i:12808669 original size:71 final size:67
Alignment explanation
Indices: 12808569--12808736 Score: 239
Period size: 71 Copynumber: 2.4 Consensus size: 67
12808559 TATTTGTACA
*
12808569 AATATTTTGAGTATTTTGA-AGTTTATTTGATGTAAAAAAATAGAATTTTATTTGATGTAATAAA
1 AATATTTTGAGTATTTTGATA--TTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAAT-AA
12808633 AATAG
63 AATAG
* *
12808638 AAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAA
1 -AA-TATTTTGAG-TATTTTGATATTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAATAA
12808703 AATAG
63 AATAG
*
12808708 AATATTTTGAATATTTTGATATTATTTGA
1 AATATTTTGAGTATTTTGATATTATTTGA
12808737 GAATTCTACT
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
67 18 0.20
68 7 0.08
69 2 0.02
70 9 0.10
71 45 0.50
72 8 0.09
73 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (67 bp):
AATATTTTGAGTATTTTGATATTATTTGATGTAAAAAAATAGAAGTTTATTTGATGTAATAAAAT
AG
Found at i:12808783 original size:23 final size:23
Alignment explanation
Indices: 12808757--12809436 Score: 616
Period size: 23 Copynumber: 28.0 Consensus size: 23
12808747 AACCTAATTA
*
12808757 AATTGAAA-AGAAAACCCTAACGT
1 AATT-AAATAGAAAACCCTAACCT
*
12808780 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12808803 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12808826 AATTAAAAAGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
****
12808849 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12808872 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
* *
12808900 ACTTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
12808923 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
**** *
12808946 AATTAAACCCTAAATCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12808969 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
****
12808997 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12809020 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12809048 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
* *
12809076 AATTAAATTGAAAATCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
* *
12809099 AGTTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12809122 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12809150 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
**
12809173 AATTAAATTGAAAAGAAAACTTTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
*
12809201 AATTAAATTGAAAAACCCTAACCT
1 AATTAAATAG-AAAACCCTAACCT
*
12809225 AATTAAATTGAAAAACCCTAACCT
1 AATTAAATAG-AAAACCCTAACCT
*
12809249 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
****
12809272 AATTAAACCCTAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
12809295 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12809318 AATTAAATTGAAAAGAAAACCATAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
12809346 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
12809369 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
12809392 AATTAAAAAGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
12809415 AATTAAATTGAAAACCCTAACC
1 AATTAAATAGAAAACCCTAACC
12809437 CTAAACCCTT
Statistics
Matches: 565, Mismatches: 56, Indels: 72
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.01
23 361 0.64
24 49 0.09
27 5 0.01
28 145 0.26
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (23 bp):
AATTAAATAGAAAACCCTAACCT
Found at i:12808820 original size:46 final size:46
Alignment explanation
Indices: 12808767--12809436 Score: 712
Period size: 51 Copynumber: 13.8 Consensus size: 46
12808757 AATTGAAAAG
*
12808767 AAAACCCTAACGTAATTAAATTGAAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
** ***
12808813 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
* * *
12808859 TAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTACTTAAATTG
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
***
12808910 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
* * ***
12808956 TAAATCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAACCC
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
*
12809007 TAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAATTGAAAA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATT----A
* * *
12809062 GAAAACCCTAACCTAATTAAATTGAAAATCCTAACCTAGTTAAATTG
1 -AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
12809109 AAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
**
12809160 AAAACCCTAACCTAATTAAATTGAAAAGAAAACTTTAACCTAATTAAATTGA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATT-A
*
12809212 AAAACCCTAACCTAATTAAATTGAAAAACCCTAACCTAATTAAATTG
1 AAAACCCTAACCTAATTAAATTG-AAAACCCTAACCTAATTAAATTA
****
12809259 AAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
*
12809305 AAAACCCTAACCTAATTAAATTGAAAAGAAAACCATAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATT-----GAAAACCCTAACCTAATTAAATTA
* *
12809356 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAA-AA
1 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
12809401 GAAAACCCTAACCTAATTAAATTGAAAACCCTAACC
1 -AAAACCCTAACCTAATTAAATTGAAAACCCTAACC
12809437 CTAAACCCTT
Statistics
Matches: 546, Mismatches: 50, Indels: 56
0.84 0.08 0.09
Matches are distributed among these distances:
45 1 0.00
46 215 0.39
47 21 0.04
48 20 0.04
51 245 0.45
52 23 0.04
56 21 0.04
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (46 bp):
AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTA
Found at i:12809372 original size:18 final size:20
Alignment explanation
Indices: 12809349--12809459 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 20
12809339 ATAACCTAAT
12809349 TAAATTAAAAACCCTAACCTAA
1 TAAATTAAAAACCCTAACC--A
12809371 TTAAATTAAAAACCCTAACCTAA
1 -TAAATTAAAAACCCTAACC--A
*
12809394 TTAAA-AAGAAAACCCTAACCTAA
1 -TAAATTA-AAAACCCTAACC--A
* *
12809417 TTAAATTGAAAACCCTAACCC
1 -TAAATTAAAAACCCTAACCA
12809438 TAAACCCTTAAAAACCCTAACC
1 TAAA---TTAAAAACCCTAACC
12809460 CTTAATATTC
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.05
22 1 0.01
23 73 0.94
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAATTAAAAACCCTAACCA
Found at i:12809449 original size:74 final size:69
Alignment explanation
Indices: 12808766--12809436 Score: 678
Period size: 74 Copynumber: 9.2 Consensus size: 69
12808756 AAATTGAAAA
* * *
12808766 GAAAACCCTAACGTAATTAAATTGAAAACCCTAACCTAATTAAATTA-AAAACCCTAACCTAATT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAA-AAGAAAACCCTAACCTAATT
**
12808830 AAAAA
65 AAATT
****
12808835 GAAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCTAACCT
*
12808900 ACTTAAATT
61 AATTAAATT
* **** *
12808909 GAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAACCCTAAATCCTAACCTAATTA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
12808974 AATT
66 AATT
****
12808978 GAAAAGAAAACCCTAACCTAATTAAACCCTAAACCCTAACCTAATTAAATTGAAAAGAAAACCCT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCT
12809043 AACCTAATTAAATT
56 AACCTAATTAAATT
* * * **
12809057 GAAAAGAAAACCCTAACCTAATTAAATTGAAAATCCTAACCTAGTTAAATTGAAAACCCTAACCT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCT
12809122 AATTAAATT
61 AATTAAATT
**
12809131 GAAAAGAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACTTT
1 -----GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCT
12809196 AACCTAATTAAATT
56 AACCTAATTAAATT
**
12809210 GAAAAACCCTAACCTAATTAAATTGAAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAAT
1 G-AAAACCCTAACCTAATTAAATT-AAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAAT
**
12809275 TAAACC
64 TAAATT
** *
12809281 CTAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACCATAACCT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATT--A---AAAAGAAAACCCTAACCT
12809346 AATTAAATT
61 AATTAAATT
*
12809355 AAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
12809420 AATT
66 AATT
12809424 GAAAACCCTAACC
1 GAAAACCCTAACC
12809437 CTAAACCCTT
Statistics
Matches: 514, Mismatches: 60, Indels: 56
0.82 0.10 0.09
Matches are distributed among these distances:
69 113 0.22
70 21 0.04
71 23 0.04
72 2 0.00
73 1 0.00
74 226 0.44
75 22 0.04
76 20 0.04
77 1 0.00
79 85 0.17
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (69 bp):
GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTA
AATT
Found at i:12809461 original size:16 final size:17
Alignment explanation
Indices: 12809433--12809464 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12809423 TGAAAACCCT
12809433 AACCCTAAACCCTTAAA
1 AACCCTAAACCCTTAAA
12809450 AACCCT-AACCCTTAA
1 AACCCTAAACCCTTAA
12809465 TATTCACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (17 bp):
AACCCTAAACCCTTAAA
Found at i:12809689 original size:115 final size:115
Alignment explanation
Indices: 12809478--12809693 Score: 330
Period size: 115 Copynumber: 1.9 Consensus size: 115
12809468 TCACATAATG
* * *
12809478 TTAGATTTGGAAAAATGTTTTTTCCTCGTACTAACAATTAATAATTTTATATAATTTGATAATTT
1 TTAGATTTGGAAAAATG-TTTTTCCTAGTACTAACAAATAATAATTTTATATAAATTGATAATTT
*
12809543 TACTAACAATTAATACAATTTATCGGATAATAATTTTACATTCACGTAACC
65 TACTAACAATTAATACAATTTATCGAATAATAATTTTACATTCACGTAACC
12809594 TTAGATTTGGAAAAATG-TTTTCACTAGTACTAACAAATAATAATTTTATATAAATTGA-AATTT
1 TTAGATTTGGAAAAATGTTTTTC-CTAGTACTAACAAATAATAATTTTATATAAATTGATAA-TT
*
12809657 TTACTAACCATTAATACAATTTATC-AATTAATAATTT
64 TTACTAACAATTAATACAATTTATCGAA-TAATAATTT
12809694 CACAAACTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
114 8 0.09
115 67 0.73
116 17 0.18
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (115 bp):
TTAGATTTGGAAAAATGTTTTTCCTAGTACTAACAAATAATAATTTTATATAAATTGATAATTTT
ACTAACAATTAATACAATTTATCGAATAATAATTTTACATTCACGTAACC
Found at i:12812831 original size:124 final size:124
Alignment explanation
Indices: 12812610--12812973 Score: 568
Period size: 123 Copynumber: 2.9 Consensus size: 124
12812600 CCCAAACATG
* *
12812610 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCTTA
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCTTG
12812675 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
12812735 CTACTGTAGCAAAAGCGCGTCTACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
* * *
12812800 TAAAAGTGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTTATCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
12812858 CTACTGTAGCAAAAACGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
* * **
12812923 TAGAAGCGATTTTATACTATTTGATTAGAAACGTCAACTCAAAATTATTTC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTC
12812974 TTCCCGGACC
Statistics
Matches: 216, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
123 112 0.52
124 58 0.27
125 46 0.21
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
Found at i:12818043 original size:22 final size:20
Alignment explanation
Indices: 12818015--12818071 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
12818005 TAAAATTTAG
12818015 GATAATTATAATTTAATAAA
1 GATAATTATAATTTAATAAA
*
12818035 GTGATAATTACATATTT-A-AAA
1 --GATAATTATA-ATTTAATAAA
12818056 -ATAATTATAATTTAAT
1 GATAATTATAATTTAAT
12818072 TTTCAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
21 3 0.10
22 10 0.33
23 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (20 bp):
GATAATTATAATTTAATAAA
Found at i:12818117 original size:20 final size:20
Alignment explanation
Indices: 12818092--12818132 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12818082 TAACTAAAAA
*
12818092 TTTTAATATAAAAATATATT
1 TTTTAATATAAAAATAAATT
* *
12818112 TTTTAATTTTAAAATAAATT
1 TTTTAATATAAAAATAAATT
12818132 T
1 T
12818133 ATTACATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAATATAAAAATAAATT
Found at i:12818263 original size:14 final size:15
Alignment explanation
Indices: 12818244--12818280 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
12818234 CCTTATTATA
12818244 AAAAAAATTGAT-GT
1 AAAAAAATTGATAGT
12818258 -AAAAAATTGATAGT
1 AAAAAAATTGATAGT
12818272 AAAAAAATT
1 AAAAAAATT
12818281 CAGCTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
AAAAAAATTGATAGT
Found at i:12818731 original size:4 final size:4
Alignment explanation
Indices: 12818724--12818796 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
12818714 TTTATTTATT
12818724 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12818772 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
12818797 GTTATTTGTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:12820710 original size:16 final size:16
Alignment explanation
Indices: 12820685--12820715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12820675 TGAGAGTAAA
*
12820685 AGAGTTTTAGTGTGTG
1 AGAGTATTAGTGTGTG
12820701 AGAGTATTAGTGTGT
1 AGAGTATTAGTGTGT
12820716 AAATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (16 bp):
AGAGTATTAGTGTGTG
Found at i:12821354 original size:21 final size:20
Alignment explanation
Indices: 12821326--12821364 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12821316 TCCAACAATA
12821326 TATTATTATTTTTCACTTAG
1 TATTATTATTTTTCACTTAG
*
12821346 TATTAATTATTTTTTACTT
1 TATT-ATTATTTTTCACTT
12821365 TGCATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTATTATTTTTCACTTAG
Found at i:12821824 original size:37 final size:35
Alignment explanation
Indices: 12821783--12821872 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 35
12821773 ATTTAAATTG
**
12821783 TTAAATATATTAATATATATTAATTATATT-TAATAAT
1 TTAAATATATTAA-AT-TAAAAATTA-ATTATAATAAT
12821820 TTAAATA-A-TAAATTAAAAATTAATTATAATAAT
1 TTAAATATATTAAATTAAAAATTAATTATAATAAT
* *
12821853 TAAAATATATT-ATTTAAAAA
1 TTAAATATATTAAATTAAAAA
12821873 ATAAACATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 3 0.07
33 20 0.43
34 11 0.24
35 4 0.09
36 1 0.02
37 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TTAAATATATTAAATTAAAAATTAATTATAATAAT
Found at i:12822730 original size:4 final size:4
Alignment explanation
Indices: 12822721--12822765 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
12822711 TATTTGGAAA
12822721 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T
12822766 CTGCACTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:12825016 original size:19 final size:19
Alignment explanation
Indices: 12824994--12825045 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
12824984 AAACAAAATA
*
12824994 GAAAATTTTGGGAAAACTT
1 GAAAATTTTGGAAAAACTT
12825013 GAAAATTTTGGAAAAACTT
1 GAAAATTTTGGAAAAACTT
12825032 GAAAATTTTGGAAA
1 GAAAATTTTGGAAA
12825046 CAAGGGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (19 bp):
GAAAATTTTGGAAAAACTT
Found at i:12831118 original size:15 final size:15
Alignment explanation
Indices: 12831071--12831119 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
12831061 TATGATTCTT
*
12831071 TTATTTTAA-TGTTA
1 TTATTTTAATTTTTA
12831085 TTATTTTAACCTTTATTA
1 TTATTTTAA--TTT-TTA
12831103 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
12831118 TT
1 TT
12831120 TAATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 3 0.10
17 1 0.03
18 12 0.40
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTAATTTTTA
Found at i:12836314 original size:42 final size:42
Alignment explanation
Indices: 12836179--12836404 Score: 289
Period size: 42 Copynumber: 5.4 Consensus size: 42
12836169 TTTAAACAGA
* * * *
12836179 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGAT-TCAG-
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGT
* * * * * *
12836220 TACACTGGCATTTAGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
*
12836261 TTCACCGGCATTAAGCATGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* *
12836303 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
12836345 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
12836387 TTCACCGGCATTAAGCCT
1 TTCACCGGCATTAAGCCT
12836405 AATAGGCACT
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
40 3 0.02
41 59 0.36
42 101 0.62
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:12836926 original size:2 final size:2
Alignment explanation
Indices: 12836919--12836955 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12836909 AATCTTAAGT
12836919 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12836956 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12838396 original size:25 final size:24
Alignment explanation
Indices: 12838343--12838431 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 24
12838333 CCGTTATTTA
*
12838343 GCTCTCATGAGCTTCCCGATTA-ATT
1 GCTCTCATGAGCTTCTC-ATTATA-T
*
12838368 GCTCTCTTGAGCTTCTCATTATAT
1 GCTCTCATGAGCTTCTCATTATAT
* **
12838392 GGCTCTCACGAGCTTCTCGGTATAT
1 -GCTCTCATGAGCTTCTCATTATAT
12838417 GCTCTCATGAGCTTC
1 GCTCTCATGAGCTTC
12838432 CTATTTATGG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
24 19 0.35
25 36 0.65
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (24 bp):
GCTCTCATGAGCTTCTCATTATAT
Found at i:12857757 original size:22 final size:22
Alignment explanation
Indices: 12857726--12857855 Score: 133
Period size: 22 Copynumber: 5.9 Consensus size: 22
12857716 TTTATGGTGT
* *
12857726 ATTCTAATTTGGCATTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
12857748 ATTCTGATTTGGCCTTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
12857770 ATTCTGATTTGGCCTTTATGGC
1 ATTCTGATTTGGCCTTTATGGC
* *
12857792 ATTCTG-TTATGGCTTTTGTGGC
1 ATTCTGATT-TGGCCTTTATGGC
* * *
12857814 ATT-TTA-TTAGCCTTTGTGGTC
1 ATTCTGATTTGGCCTTTATGG-C
12857835 TAATT-TGATTTGGCCTTTATG
1 --ATTCTGATTTGGCCTTTATG
12857856 ACATATTCTG
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.11
21 5 0.05
22 62 0.67
23 5 0.05
24 10 0.11
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (22 bp):
ATTCTGATTTGGCCTTTATGGC
Found at i:12857844 original size:66 final size:67
Alignment explanation
Indices: 12857774--12857900 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 67
12857764 TATGGCATTC
* * *
12857774 TGATTTGGCCTTTATGGC-ATTCTGTTATGGCTTT-TGTG-GCATTTTATTAGCCTTTGTGGTCT
1 TGATTTGGCCTTTATGACAATTCTGTTA-GCCTTTATG-GAACATTTTATTAGCCTTTGTGGTCT
12857836 AATT
64 AATT
*
12857840 TGATTTGGCCTTTATGACATATTCTGTTAGCCTTTATGGAACATTTTGTTAGCCTTTGTGG
1 TGATTTGGCCTTTATGACA-ATTCTGTTAGCCTTTATGGAACATTTTATTAGCCTTTGTGG
12857901 CATTCTGCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
66 17 0.32
67 6 0.11
68 30 0.57
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (67 bp):
TGATTTGGCCTTTATGACAATTCTGTTAGCCTTTATGGAACATTTTATTAGCCTTTGTGGTCTAA
TT
Found at i:12857874 original size:22 final size:22
Alignment explanation
Indices: 12857847--12857896 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
12857837 ATTTGATTTG
12857847 GCCTTTAT-G-ACATATTCTGTTA
1 GCCTTTATGGAACAT-TT-TGTTA
12857869 GCCTTTATGGAACATTTTGTTA
1 GCCTTTATGGAACATTTTGTTA
12857891 GCCTTT
1 GCCTTT
12857897 GTGGCATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.73
23 3 0.12
24 4 0.15
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (22 bp):
GCCTTTATGGAACATTTTGTTA
Found at i:12857912 original size:20 final size:21
Alignment explanation
Indices: 12857860--12857920 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
12857850 TTTATGACAT
*
12857860 ATTCTGTTAGCCTTTATGGAAC
1 ATTCTGTTAGCCTTTGTGG-AC
*
12857882 ATTTTGTTAGCCTTTGTGG-C
1 ATTCTGTTAGCCTTTGTGGAC
* *
12857902 ATTCTGCTAGCCTTAGTGG
1 ATTCTGTTAGCCTTTGTGG
12857921 TGTACTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
22 17 0.50
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (21 bp):
ATTCTGTTAGCCTTTGTGGAC
Found at i:12857913 original size:88 final size:86
Alignment explanation
Indices: 12857752--12857921 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
12857742 TATGGCATTC
* * *
12857752 TGATTTGGCCTTTATGGCATTCTGATTTGGCCTTTATGGCATTCTGTTATGGCTTTTGTGGCATT
1 TGATTTGGCCTTTATGACATTCTGA-TTAGCCTTTATGGCATTCTGTTA-GGCCTTTGTGGCATT
* * *
12857817 TTATTAGCCTTTGTGGTCTAATT
64 CTACTAGCCTTAGTGGTCTAATT
*
12857840 TGATTTGGCCTTTATGACATATTCTG-TTAGCCTTTATGGAACATTTTGTTA-GCCTTTGTGGCA
1 TGATTTGGCCTTTATGAC--ATTCTGATTAGCCTTTATGG--CATTCTGTTAGGCCTTTGTGGCA
*
12857903 TTCTGCTAGCCTTAGTGGT
62 TTCTACTAGCCTTAGTGGT
12857922 GTACTCTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 55 0.79
90 15 0.21
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.46
Consensus pattern (86 bp):
TGATTTGGCCTTTATGACATTCTGATTAGCCTTTATGGCATTCTGTTAGGCCTTTGTGGCATTCT
ACTAGCCTTAGTGGTCTAATT
Found at i:12860235 original size:67 final size:63
Alignment explanation
Indices: 12860068--12860539 Score: 224
Period size: 64 Copynumber: 7.2 Consensus size: 63
12860058 TAAGATTGTA
* * * *
12860068 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTAATTTAAGATCGCAACCTAAGTTC
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
* * * * *
12860131 ACTCAATTTAAGATCATGAAC-AATTTTATT-TGAGTTAGCTGATTTAAGATCGCAACTTCGAAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC--C-AA-
12860194 AGCTT-
59 AG-TTC
* *
12860199 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGTTGATTTAAGATCG-AAGCCTAAGTTC
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAA-CCAAAGTTC
** * * * * * * *
12860262 ATTCGATTTAAGATCATGAAC-AATTTTGTT-TGAGATAGCTAATTTAATATCGCAACTCTGAAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC-C--AA-
**
12860325 AAATC
59 AGTTC
* * * * * *
12860330 GCTGATTTAAGATCACAATTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACCAAAGTTT
1 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
** * * * * *
12860393 ATTCGATTTAAGATCATGAAC-AATTTTATT-CGAGTTAGTTGATTTAAGATCGTAACTCTACAC
1 GCT-GATTTAAGATCA-AAACTAATATTATTAAG-GTTAGCTGATTTAAGATCGCAAC-C-A-A-
*
12860456 AGCTC
59 AGTTC
* * * * ** * * * *
12860461 ACTAAGTTAAGGTC-GCAGTCGATATTATTAAGGTTAGCTGATTTAAGATCCCAACCTAAGTTC
1 GCTGATTTAAGATCAAAACT-AATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
**
12860524 ATTTGATTTAAGATCA
1 -GCTGATTTAAGATCA
12860540 TGAAAAATTT
Statistics
Matches: 301, Mismatches: 74, Indels: 66
0.68 0.17 0.15
Matches are distributed among these distances:
62 2 0.01
63 15 0.05
64 128 0.43
65 15 0.05
66 11 0.04
67 112 0.37
68 16 0.05
69 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (63 bp):
GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGCTGATTTAAGATCGCAACCAAAGTTC
Found at i:12860245 original size:131 final size:131
Alignment explanation
Indices: 12860068--12860808 Score: 877
Period size: 131 Copynumber: 5.7 Consensus size: 131
12860058 TAAGATTGTA
* *
12860068 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTAATTTAAGATCGCAACCTAAGTTCAC
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
* * * *
12860133 TCAATTTAAGATCATGAACAATTTTATTTGAGTTAGCTGATTTAAGATCGCAACT-TCGAACAGC
66 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCT-GAACAGC
*
12860197 TT
130 TC
* * *
12860199 GCTGATTTAAGATCAAAACTAATATTATTAAGGTTAGTTGATTTAAGATCG-AAGCCTAAGTTCA
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAA-CCTAAGTTCA
* * * * **
12860263 TTCGATTTAAGATCATGAACAATTTTGTTTGAGATAGCTAATTTAATATCGCAACTCTGAACAAA
65 TTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGC
12860328 TC
130 TC
* * * * *
12860330 GCTGATTTAAGATCACAATTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACCAAAGTTTAT
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
* * * *
12860395 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGTTGATTTAAGATCGTAACTCT-ACACAGC
66 TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGA-ACAGC
12860459 TC
130 TC
* * * * * * *
12860461 ACTAAGTTAAGGTCGC-AGTCGATATTATTAAGGTTAGCTGATTTAAGATCCCAACCTAAGTTCA
1 GCTGATTTAAGATCACAACT-GATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCA
* * *
12860525 TTTGATTTAAGATCATGAAAAATTTTATTCGAGTTAGCTAATTTAAAATTGCAACTCTGAACAGC
65 TTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGC
12860590 TC
130 TC
* * * * * *
12860592 ACTAAGTTAAGGTCGC-AGTCGATATTATTAAGGTTAGCTGATTTAAGATC-CTAACCTAAGTTC
1 GCTGATTTAAGATCACAACT-GATATTATTAAGGTTAGCTGATTTAAGATCGC-AACCTAAGTTC
* * * *
12860655 ATTCGATTTAAGATCATGAAAAATTTTATTCGAGTTAGCTAATTTAAAATTGCAACTCTAAACAA
64 ATTCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAG
12860720 CT-
129 CTC
* * ** * * ** *
12860722 TCTGATTTAAGATCGCAGTTGATATTATCAAGGTTAGCTGATTCAAGATCATAACCGAAGTTCAC
1 GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCA-
12860787 TT-GATTTAAGATCATGAACAAT
65 TTCGATTTAAGATCATGAACAAT
12860809 CTCACTTGTG
Statistics
Matches: 540, Mismatches: 60, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
130 76 0.14
131 460 0.85
132 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (131 bp):
GCTGATTTAAGATCACAACTGATATTATTAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTCAT
TCGATTTAAGATCATGAACAATTTTATTCGAGTTAGCTAATTTAAAATCGCAACTCTGAACAGCT
C
Found at i:12866790 original size:15 final size:15
Alignment explanation
Indices: 12866766--12866798 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12866756 CACTATGAGT
*
12866766 TCGCATGTAAGGCAC
1 TCGCACGTAAGGCAC
12866781 TCGCACGTAAGGCAC
1 TCGCACGTAAGGCAC
12866796 TCG
1 TCG
12866799 TACCCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.18
Consensus pattern (15 bp):
TCGCACGTAAGGCAC
Found at i:12869532 original size:17 final size:18
Alignment explanation
Indices: 12869512--12869545 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12869502 CAAATTACAT
12869512 AATTAACCGAA-TTAATC
1 AATTAACCGAAGTTAATC
*
12869529 AATTAACTGAAGTTAAT
1 AATTAACCGAAGTTAAT
12869546 AATCTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (18 bp):
AATTAACCGAAGTTAATC
Found at i:12875800 original size:5 final size:5
Alignment explanation
Indices: 12875792--12875825 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
12875782 ATTAGTAACT
12875792 TAAAA TAAAA TAAAA TAAAA TAAAA TAAATA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA-A TAA
12875826 CTAATATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:12881032 original size:19 final size:20
Alignment explanation
Indices: 12880986--12881034 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
12880976 ATTAAGTGTA
12880986 AATTCTTTTAAATCAACAACT
1 AATT-TTTTAAATCAACAACT
*
12881007 AATTTTTTAAATCCACAACT
1 AATTTTTTAAATCAACAACT
12881027 AATTTTTT
1 AATTTTTT
12881035 CTAGTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTTTAAATCAACAACT
Found at i:12882895 original size:58 final size:58
Alignment explanation
Indices: 12882809--12882926 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 58
12882799 TAAAATGAAA
* *
12882809 CTTAAAATATTAAAAACTAAAAATGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
1 CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
* * *
12882867 CTTAAACTACTAAAAACTGAAAACGTAATAAAAACATATAAAAGAGTTAGAAAACAAG
1 CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
12882925 CT
1 CT
12882927 CGTTAAACGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (58 bp):
CTTAAAATACTAAAAACTAAAAACGTAATAAAAACATATAAAAGAGTTAGAAAAAAAG
Found at i:12886004 original size:12 final size:12
Alignment explanation
Indices: 12885987--12886011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12885977 CAAAGTGAGT
12885987 AGAAAGAAAAAA
1 AGAAAGAAAAAA
12885999 AGAAAGAAAAAA
1 AGAAAGAAAAAA
12886011 A
1 A
12886012 TAAAAAAATA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:12886055 original size:13 final size:13
Alignment explanation
Indices: 12886037--12886061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12886027 TTTTGCACAA
12886037 AAAAATAAAATAG
1 AAAAATAAAATAG
12886050 AAAAATAAAATA
1 AAAAATAAAATA
12886062 AAATAAAATA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAG
Found at i:12892172 original size:23 final size:23
Alignment explanation
Indices: 12892146--12892192 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12892136 GTAATTATAA
*
12892146 ATACCTGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
12892169 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
12892192 A
1 A
12892193 CAGACTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:12893228 original size:25 final size:25
Alignment explanation
Indices: 12893200--12893309 Score: 108
Period size: 22 Copynumber: 4.6 Consensus size: 25
12893190 AATTTAGCGC
*
12893200 GCTCTATGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
12893225 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACATCAGT
*
12893250 GCTCTCTG--T-TTAGCACATCTGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
12893272 GCTCTC--AGTATT-GCACTTCAGT
1 GCTCTCTGATTATTAGCACATCAGT
12893294 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
12893310 TGCATAACAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
22 31 0.45
23 4 0.06
24 3 0.04
25 31 0.45
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.37
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:12893256 original size:27 final size:25
Alignment explanation
Indices: 12893200--12893276 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
12893190 AATTTAGCGC
*
12893200 GCTCTATGATTATTAGCACATCAGT
1 GCTCTATGATTACTAGCACATCAGT
* *
12893225 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTATGATTACTAGCACATCAGT
* *
12893250 GCTCTCTG-TT--TAGCACATCTGT
1 GCTCTATGATTACTAGCACATCAGT
12893272 GCTCT
1 GCTCT
12893277 CAGTATTGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
22 15 0.32
24 2 0.04
25 30 0.64
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCTATGATTACTAGCACATCAGT
Found at i:12896298 original size:16 final size:18
Alignment explanation
Indices: 12896277--12896309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12896267 ATTGACCTGT
12896277 AAAC-AACA-CAAAAAAG
1 AAACAAACAGCAAAAAAG
12896293 AAACAAACAGCAAAAAA
1 AAACAAACAGCAAAAAA
12896310 TGGAATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (18 bp):
AAACAAACAGCAAAAAAG
Found at i:12898789 original size:26 final size:26
Alignment explanation
Indices: 12898753--12898807 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12898743 TATCAGGTCA
12898753 GTTCTAATCAGGAAATGTTATTATGG
1 GTTCTAATCAGGAAATGTTATTATGG
12898779 GTTCTAATCAGGAAATGTTATTATGG
1 GTTCTAATCAGGAAATGTTATTATGG
12898805 GTT
1 GTT
12898808 AAAGTCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (26 bp):
GTTCTAATCAGGAAATGTTATTATGG
Found at i:12899615 original size:23 final size:23
Alignment explanation
Indices: 12899589--12899635 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12899579 GTAATTATAA
12899589 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
12899612 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
12899635 A
1 A
12899636 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:12899785 original size:26 final size:27
Alignment explanation
Indices: 12899726--12899790 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
12899716 GAATGGAAAC
*
12899726 AGAATAGAAAAACGAAAACAGGGGAGAA
1 AGAA-AGAAAAACGAAAACAGGGAAGAA
12899754 AGGAAAGAAAAA-GAAAA-AGGGAAGGAA
1 A-GAAAGAAAAACGAAAACAGGGAA-GAA
12899781 AGAAAGAAAA
1 AGAAAGAAAA
12899791 TTTGGGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 14 0.41
27 9 0.26
28 8 0.24
29 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (27 bp):
AGAAAGAAAAACGAAAACAGGGAAGAA
Found at i:12902361 original size:16 final size:16
Alignment explanation
Indices: 12902336--12902370 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12902326 TTGTGTTTTG
*
12902336 TTTTGGCTGCATGACA
1 TTTTGACTGCATGACA
*
12902352 TTTTGACTGCATGGCA
1 TTTTGACTGCATGACA
12902368 TTT
1 TTT
12902371 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:12904962 original size:6 final size:6
Alignment explanation
Indices: 12904953--12905003 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
12904943 AAAAATCAAA
*
12904953 AAAATG AAAATG AAAATG AAAATG ATGGAAA-G AAAAAG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG A---AAATG AAAATG AAAATG AAAATG
12905003 A
1 A
12905004 GAGGCCAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 3 0.08
6 32 0.80
8 2 0.05
9 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:12906269 original size:6 final size:7
Alignment explanation
Indices: 12906242--12906267 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12906232 AATCAATTCT
12906242 TTTTTTA
1 TTTTTTA
12906249 TTTTTTA
1 TTTTTTA
12906256 TTTTTTA
1 TTTTTTA
12906263 TTTTT
1 TTTTT
12906268 ATATATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Done.