Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 145 of 228
Found at i:43698634 original size:19 final size:19
Alignment explanation
Indices: 43698587--43698665 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
43698577 AAATTAAATC
*
43698587 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
43698607 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
43698629 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
43698650 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
43698666 CTTGAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:43698647 original size:21 final size:21
Alignment explanation
Indices: 43698621--43698664 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
43698611 CTAAGATTAC
43698621 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
43698642 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
43698663 AT
1 AT
43698665 CCTTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:43700387 original size:43 final size:43
Alignment explanation
Indices: 43700325--43700664 Score: 554
Period size: 43 Copynumber: 7.9 Consensus size: 43
43700315 TTACAATGCT
* *
43700325 ACTATAGACCATGGTCTTTAGCGGCGCTTACCCAACAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
* * *
43700368 GCTATAAACCATGGTCTTTAGTGGCGCTTAGCCAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
* *
43700411 GCTATAGATCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
*
43700454 GCTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
43700497 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
** *
43700540 ACTATAGACCATTCTCTTTAGCGGCGCTTAGGCAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
**
43700583 ACTATAGACCATGGTCTTTAGCGGCGCTTAGGAAAAAAACGCC
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
*
43700626 ACTATAGACCATGGTCTTTAGCGGCGCTTACCCAAAAAA
1 ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAA
43700665 TGCCGCTAAT
Statistics
Matches: 278, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 278 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (43 bp):
ACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCC
Found at i:43701005 original size:21 final size:21
Alignment explanation
Indices: 43700979--43701033 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
43700969 AGCTGTTCTG
*
43700979 CTTCCCTCGCTGTAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTA
*
43701000 CTTCCCTCGCTGCAGCCTCTG
1 CTTCCCTCGCTGCAGCCTCTA
* *
43701021 TTTCTCTCGCTGC
1 CTTCCCTCGCTGC
43701034 CACATCTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.44, G:0.16, T:0.35
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTA
Found at i:43701120 original size:21 final size:21
Alignment explanation
Indices: 43701080--43701120 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43701070 CTTTCGTTGA
**
43701080 ACCTCAGCTTCTCTTGCTGCT
1 ACCTCAGCTTCTCTCACTGCT
*
43701101 ACCTCTGCTTCTCTCACTGC
1 ACCTCAGCTTCTCTCACTGC
43701121 CGCATCTGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.41, G:0.12, T:0.37
Consensus pattern (21 bp):
ACCTCAGCTTCTCTCACTGCT
Found at i:43701127 original size:87 final size:87
Alignment explanation
Indices: 43701015--43701180 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
43701005 CTCGCTGCAG
* *
43701015 CCTCTGTTTCTCTCGCTGCCACATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCTGCTTCTCTCACTGCCACATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
43701078 GAACCTCAGCTTCTCTTGCTGCTA
64 GAACCTCAGCTTCTCTTGCTGCTA
* * *
43701102 CCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCTGCTTCTCTCACTGCCACATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
43701167 ACCTCAGCTTCTCT
66 ACCTCAGCTTCTCT
43701181 CGATATTGCC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 1 0.01
87 67 0.93
88 4 0.06
ACGTcount: A:0.13, C:0.30, G:0.16, T:0.40
Consensus pattern (87 bp):
CCTCTGCTTCTCTCACTGCCACATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
ACCTCAGCTTCTCTTGCTGCTA
Found at i:43706746 original size:15 final size:15
Alignment explanation
Indices: 43706707--43706748 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
43706697 TCGTATTATG
43706707 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
*
43706722 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
43706738 TAAGTTATGTA
1 TAAGTTATGTA
43706749 AGTTATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TAAGTTATGTATTAA
Found at i:43706878 original size:19 final size:17
Alignment explanation
Indices: 43706849--43707223 Score: 111
Period size: 16 Copynumber: 23.9 Consensus size: 17
43706839 AAATATATAT
43706849 ATTA-ATAAGTTATGTC
1 ATTATATAAGTTATGTC
*
43706865 GTATTATGTAAGTTATG-C
1 --ATTATATAAGTTATGTC
43706883 ATTATATAAGTTATGT-
1 ATTATATAAGTTATGTC
43706899 ATTA-ATAAGTTATGT-
1 ATTATATAAGTTATGTC
* *
43706914 A--AGATATG-TA--TC
1 ATTATATAAGTTATGTC
* * *
43706926 ATTTTA-AAATATATAT-
1 ATTATATAAGT-TATGTC
43706942 ATTA-ATAAGTTATGTC
1 ATTATATAAGTTATGTC
* *
43706958 GTATTATGTAACTTATGT-
1 --ATTATATAAGTTATGTC
*
43706976 ATTATATAAGTCATGT-
1 ATTATATAAGTTATGTC
43706992 ATTA-ATAAGTTATGT-
1 ATTATATAAGTTATGTC
*
43707007 ATTA-AAAATGTTATGT-
1 ATTATATAA-GTTATGTC
* *
43707023 ATTA-ATAAGTTGTGTA
1 ATTATATAAGTTATGTC
*
43707039 AGT-TAT--G-TA--TC
1 ATTATATAAGTTATGTC
* * *
43707050 ATTTTA-AAATATATAT-
1 ATTATATAAGT-TATGTC
43707066 ATTA-ATAAGTTATGTC
1 ATTATATAAGTTATGTC
*
43707082 GTATTATGTAAGTTATGT-
1 --ATTATATAAGTTATGTC
43707100 ATTATATAAGTTATGT-
1 ATTATATAAGTTATGTC
43707116 ATTA-ATAAGTTATGT-
1 ATTATATAAGTTATGTC
* *
43707131 A--AGATATG-TA--TC
1 ATTATATAAGTTATGTC
* * *
43707143 ATTTTA-AAATATATAT-
1 ATTATATAAGT-TATGTC
43707159 ATTA-ATAAGTTATGTC
1 ATTATATAAGTTATGTC
43707175 GTATTATATAAGTTATGT-
1 --ATTATATAAGTTATGTC
*
43707193 ATTA-AAAATGTTATGT-
1 ATTATATAA-GTTATGTC
43707209 ATTA-ATAAGTTATGT
1 ATTATATAAGTTATGT
43707224 AAGTTATGTA
Statistics
Matches: 274, Mismatches: 39, Indels: 91
0.68 0.10 0.23
Matches are distributed among these distances:
11 5 0.02
12 4 0.01
13 9 0.03
14 11 0.04
15 78 0.28
16 108 0.39
17 3 0.01
18 17 0.06
19 39 0.14
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (17 bp):
ATTATATAAGTTATGTC
Found at i:43706911 original size:50 final size:50
Alignment explanation
Indices: 43706848--43707006 Score: 174
Period size: 50 Copynumber: 3.3 Consensus size: 50
43706838 AAAATATATA
43706848 TATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATG
1 TATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATG
* * * *
43706898 TATTAATAAGTTA--T-GTA--A-GATATG-TAT-CATTTTA-AAATATATA
1 TATTAATAAGTTATGTCGTATTATG-TAAGTTATGCATTATATAAGT-TATG
* * *
43706941 TATTAATAAGTTATGTCGTATTATGTAACTTATGTATTATATAAGTCATG
1 TATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATG
43706991 TATTAATAAGTTATGT
1 TATTAATAAGTTATGT
43707007 ATTAAAAATG
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
42 3 0.03
43 22 0.25
44 4 0.05
45 5 0.06
46 3 0.03
47 3 0.03
48 4 0.05
49 4 0.05
50 36 0.41
51 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (50 bp):
TATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATG
Found at i:43706913 original size:40 final size:41
Alignment explanation
Indices: 43706868--43707080 Score: 109
Period size: 43 Copynumber: 5.1 Consensus size: 41
43706858 TTATGTCGTA
* * *
43706868 TTATGTAAGTTATG-CATTATATAAGT-TATGTATTAATAAG
1 TTATGTAAGATATGTCATTATA-AAATATATATATTAATAAG
*
43706908 TTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAG
1 TTATGTAAGATATG--TCATTATAAAATATATATATTAATAAG
* * ** * * * *
43706951 TTATGT-CGTATTATGTAACTTATGTATTATATA-AGTCATGTA-
1 TTATGTAAG-A-TATGTCA-TTATAAAATATATATATTAAT-AAG
* * * *
43706993 TTA-ATAAGTTATGT-ATTA-AAAATGTTATGTATTAATAAG
1 TTATGTAAGATATGTCATTATAAAAT-ATATATATTAATAAG
* * *
43707032 TTGTGTAAGTTATGTATCATTTTAAAATATATATATTAATAAG
1 TTATGTAAGATATG--TCATTATAAAATATATATATTAATAAG
43707075 TTATGT
1 TTATGT
43707081 CGTATTATGT
Statistics
Matches: 126, Mismatches: 30, Indels: 31
0.67 0.16 0.17
Matches are distributed among these distances:
37 2 0.02
38 7 0.06
39 7 0.06
40 27 0.21
41 1 0.01
42 15 0.12
43 58 0.46
44 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (41 bp):
TTATGTAAGATATGTCATTATAAAATATATATATTAATAAG
Found at i:43706933 original size:93 final size:93
Alignment explanation
Indices: 43706792--43707007 Score: 364
Period size: 93 Copynumber: 2.3 Consensus size: 93
43706782 GTTATGTCGT
** *
43706792 ATTATATAAGTTATGTATTAATAAG--GGGAAAGATATGTATCATTTTAAAATATATATATTAAT
1 ATTATATAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAAT
*
43706855 AAGTTATGTCGTATTATGTAAGTTATGC
66 AAGTTATGTCGTATTATGTAACTTATGC
43706883 ATTATATAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAAT
1 ATTATATAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAAT
*
43706948 AAGTTATGTCGTATTATGTAACTTATGT
66 AAGTTATGTCGTATTATGTAACTTATGC
*
43706976 ATTATATAAGTCATGTATTAATAAGTTATGTA
1 ATTATATAAGTTATGTATTAATAAGTTATGTA
43707008 TTAAAAATGT
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
91 25 0.21
93 92 0.79
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.44
Consensus pattern (93 bp):
ATTATATAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAAT
AAGTTATGTCGTATTATGTAACTTATGC
Found at i:43707028 original size:124 final size:124
Alignment explanation
Indices: 43706873--43707131 Score: 448
Period size: 124 Copynumber: 2.1 Consensus size: 124
43706863 TCGTATTATG
* *
43706873 TAAGTTATGCATTATATAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATAT
1 TAAGTTATGTATTATAAAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATAT
43706938 ATATATTAATAAGTTATGTCGTATTATGTAACTTATGTATTATATAAGTCATGTATTAA
66 ATATATTAATAAGTTATGTCGTATTATGTAACTTATGTATTATATAAGTCATGTATTAA
* *
43706997 TAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTGTGTAAGTTATGTATCATTTTAAAATA
1 TAAGTTATGTATTATAAAA-GTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATA
* *
43707061 TATATATTAATAAGTTATGTCGTATTATGTAAGTTATGTATTATATAAGTTATGTATTAA
65 TATATATTAATAAGTTATGTCGTATTATGTAACTTATGTATTATATAAGTCATGTATTAA
43707121 TAAGTTATGTA
1 TAAGTTATGTA
43707132 AGATATGTAT
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
123 3 0.02
124 125 0.98
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (124 bp):
TAAGTTATGTATTATAAAAGTTATGTATTAATAAGTTATGTAAGATATGTATCATTTTAAAATAT
ATATATTAATAAGTTATGTCGTATTATGTAACTTATGTATTATATAAGTCATGTATTAA
Found at i:43707064 original size:217 final size:215
Alignment explanation
Indices: 43706773--43707224 Score: 746
Period size: 217 Copynumber: 2.1 Consensus size: 215
43706763 TTAAAATATA
*
43706773 TATTAATAAGTTATGTCGTATTATATAAGTTATGTATTAATAAGGGGAAAGATATGTATCATTTT
1 TATTAATAAGTTA--T-GTATTATAAAAGTTATGTATTAATAAGGGGAAAGATATGTATCATTTT
43706838 AAAATATATATATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATGTATTA
63 AAAATATATATATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATGTATTA
*
43706903 ATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATGTA
128 ATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATATA
*
43706968 ACTTATGTATTATATAA-GTCATG
193 ACTTATGTATTA-AAAATGTCATG
* * *
43706991 TATTAATAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTGTGTAAGTTATGTATCATTTT
1 TATTAATAAGTTATGTATTATAAAA-GTTATGTATTAATAAG--GGGAAAGATATGTATCATTTT
*
43707055 AAAATATATATATTAATAAGTTATGTCGTATTATGTAAGTTATGTATTATATAAGTTATGTATTA
63 AAAATATATATATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATGTATTA
43707120 ATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATATA
128 ATAAGTTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATATA
* *
43707185 AGTTATGTATTAAAAATGTTATG
193 ACTTATGTATTAAAAATGTCATG
43707208 TATTAATAAGTTATGTA
1 TATTAATAAGTTATGTA
43707225 AGTTATGTAT
Statistics
Matches: 221, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
214 3 0.01
215 22 0.10
216 4 0.02
217 179 0.81
218 13 0.06
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (215 bp):
TATTAATAAGTTATGTATTATAAAAGTTATGTATTAATAAGGGGAAAGATATGTATCATTTTAAA
ATATATATATTAATAAGTTATGTCGTATTATGTAAGTTATGCATTATATAAGTTATGTATTAATA
AGTTATGTAAGATATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATATAACT
TATGTATTAAAAATGTCATG
Found at i:43707094 original size:93 final size:93
Alignment explanation
Indices: 43706990--43707264 Score: 477
Period size: 93 Copynumber: 3.0 Consensus size: 93
43706980 TATAAGTCAT
*
43706990 GTATTA-ATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTGTGTAAGTTATGTATCATTT
1 GTATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTT
43707054 TAAAATATATATATTAATAAGTTATGTC
66 TAAAATATATATATTAATAAGTTATGTC
* * *
43707082 GTATTATGTAAGTTATGTATTATATAA-GTTATGTATTAATAAGTTATGTAAGATATGTATCATT
1 GTATTATATAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATT
43707146 TTAAAATATATATATTAATAAGTTATGTC
65 TTAAAATATATATATTAATAAGTTATGTC
43707175 GTATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTT
1 GTATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTT
43707240 T-AAA-ATATATATTAATAAGTTATGT
66 TAAAATATATATATTAATAAGTTATGT
43707265 AATGTATGTA
Statistics
Matches: 173, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
91 21 0.12
92 12 0.07
93 137 0.79
94 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (93 bp):
GTATTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTT
TAAAATATATATATTAATAAGTTATGTC
Found at i:43707097 original size:53 final size:53
Alignment explanation
Indices: 43707035--43707194 Score: 184
Period size: 53 Copynumber: 3.3 Consensus size: 53
43707025 TAATAAGTTG
43707035 TGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
1 TGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
* * * *
43707088 TGTAAGTTATGTATTA-TAT-AAGT-TATGTATTAATAAGTTA--T-GTA--A
1 TGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
43707133 -G--A--TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
1 TGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
*
43707181 TATAAGTTATGTAT
1 TGTAAGTTATGTAT
43707195 TAAAAATGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
40 8 0.09
41 2 0.02
42 4 0.05
43 16 0.19
44 1 0.01
45 2 0.02
46 3 0.04
47 3 0.04
48 2 0.02
50 16 0.19
51 4 0.05
52 2 0.02
53 22 0.26
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (53 bp):
TGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTA
Found at i:43707099 original size:9 final size:9
Alignment explanation
Indices: 43707085--43707140 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
43707075 TTATGTCGTA
43707085 TTATGTAAG
1 TTATGTAAG
43707094 TTATGT-A-
1 TTATGTAAG
*
43707101 TTATATAAG
1 TTATGTAAG
43707110 TTATGT-A-
1 TTATGTAAG
*
43707117 TTA-ATAAG
1 TTATGTAAG
43707125 TTATGTAAG
1 TTATGTAAG
*
43707134 ATATGTA
1 TTATGTA
43707141 TCATTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 6 0.16
9 21 0.57
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:43707130 original size:31 final size:30
Alignment explanation
Indices: 43706848--43707224 Score: 189
Period size: 31 Copynumber: 12.1 Consensus size: 30
43706838 AAAATATATA
*
43706848 TATTAATAAGTTATGTCGTATTATGTAAGTTATG
1 TATTAATAAGTTA--T-GTATTA-ATAAGTTATG
*
43706882 CATTATATAAGTTATGTATTAATAAGTTATG
1 TATTA-ATAAGTTATGTATTAATAAGTTATG
* *
43706913 TA--AGATATGTATCAT-T-TTAA-AA-TATATA
1 TATTA-ATAAGT-T-ATGTATTAATAAGT-TATG
* *
43706941 TATTAATAAGTTATGTCGTATTATGTAACTTATG
1 TATTAATAAGTTA--T-GTATTA-ATAAGTTATG
*
43706975 TATTATATAAGTCATGTATTAATAAGTTATG
1 TATTA-ATAAGTTATGTATTAATAAGTTATG
* *
43707006 TATTAAAAATGTTATGTATTAATAAGTTGTG
1 TATTAATAA-GTTATGTATTAATAAGTTATG
*
43707037 TAAGTT-AT--GTATCAT-T-TTAA-AA-TATATA
1 T-A-TTAATAAGT-T-ATGTATTAATAAGT-TATG
*
43707065 TATTAATAAGTTATGTCGTATTATGTAAGTTATG
1 TATTAATAAGTTA--T-GTATTA-ATAAGTTATG
43707099 TATTATATAAGTTATGTATTAATAAGTTATG
1 TATTA-ATAAGTTATGTATTAATAAGTTATG
* *
43707130 TA--AGATATGTATCAT-T-TTAA-AA-TATATA
1 TATTA-ATAAGT-T-ATGTATTAATAAGT-TATG
43707158 TATTAATAAGTTATGTCGTATTATATAAGTTATG
1 TATTAATAAGTTA--T-GTATTA-ATAAGTTATG
*
43707192 TATTAAAAATGTTATGTATTAATAAGTTATG
1 TATTAATAA-GTTATGTATTAATAAGTTATG
43707223 TA
1 TA
43707225 AGTTATGTAT
Statistics
Matches: 269, Mismatches: 27, Indels: 97
0.68 0.07 0.25
Matches are distributed among these distances:
26 2 0.01
27 9 0.03
28 22 0.08
29 41 0.15
30 11 0.04
31 75 0.28
32 35 0.13
33 7 0.03
34 37 0.14
35 30 0.11
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (30 bp):
TATTAATAAGTTATGTATTAATAAGTTATG
Found at i:43707907 original size:15 final size:15
Alignment explanation
Indices: 43707879--43707914 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
43707869 TTAATAAAAG
*
43707879 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
43707893 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
43707908 GAAAACA
1 GAAAACA
43707915 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:43709782 original size:24 final size:24
Alignment explanation
Indices: 43709734--43709783 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43709724 AATTCAGTTC
* *
43709734 TTATAATATTTTATTTCTTTTTAT
1 TTATAATATTTTATTTCTATATAT
43709758 TTATAAT-TTTTATTTCTAATATAT
1 TTATAATATTTTATTTCT-ATATAT
43709782 TT
1 TT
43709784 CTGACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATAATATTTTATTTCTATATAT
Found at i:43710896 original size:74 final size:73
Alignment explanation
Indices: 43710775--43710945 Score: 279
Period size: 73 Copynumber: 2.3 Consensus size: 73
43710765 CTATCATTTA
* *
43710775 CGGCATTTGTACCAGAAACGCCACTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTTGGTT
1 CGGCATTTGTACCAGAAACGCCGCTAATACCAATAAACAGTAT-AAAAACGAAGTCATTTTGGTT
43710840 AAACTTTTG
65 AAACTTTTG
43710849 CGGCATTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTGGTTA
1 CGGCATTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTGGTTA
43710914 AACTTTTG
66 AACTTTTG
* * * *
43710922 CGGCGTTTTTACAATAAACGCCGC
1 CGGCATTTGTACCAGAAACGCCGC
43710946 AAATTCATGC
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 49 0.54
74 42 0.46
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (73 bp):
CGGCATTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATAAAAACGAAGTCATTTTGGTTA
AACTTTTG
Found at i:43712174 original size:82 final size:81
Alignment explanation
Indices: 43712022--43712218 Score: 195
Period size: 82 Copynumber: 2.4 Consensus size: 81
43712012 CGCTAGCTAC
* * ** * * **
43712022 AAAACGCCGCTAAAGACCGGAGCATTAGCGGCGTTTTCTAATATGCGCCGCTAATGCTGCGGTTT
1 AAAACGCCGCTAAAGACC-GAGCATTAGCGGCGTCTTCTAAAAAACGCCGCTAAAGCTGCAGCAT
* *
43712087 GTAGCGGCGCTTTTTA-
65 GTAGCGGCGCATATTAG
43712103 AGAAACGCCGCTAAAGACCTGAGCATTAGCGGCG-CTTCGTAAAAAACGCCGCTAAAGACCTG-A
1 A-AAACGCCGCTAAAGACC-GAGCATTAGCGGCGTCTTC-TAAAAAACGCCGCTAAAG--CTGCA
43712166 GCAT-TAGCGGCGCATATTAG
61 GCATGTAGCGGCGCATATTAG
* *
43712186 AAAACGCCGCGAAAGACCGCACCATTAGCGGCG
1 AAAACGCCGCTAAAGACCG-AGCATTAGCGGCG
43712219 ATTATGTAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
81 5 0.05
82 86 0.89
83 3 0.03
84 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (81 bp):
AAAACGCCGCTAAAGACCGAGCATTAGCGGCGTCTTCTAAAAAACGCCGCTAAAGCTGCAGCATG
TAGCGGCGCATATTAG
Found at i:43712235 original size:41 final size:41
Alignment explanation
Indices: 43712022--43712239 Score: 164
Period size: 41 Copynumber: 5.3 Consensus size: 41
43712012 CGCTAGCTAC
* * *
43712022 AAAACGCCGCTAAAGACCGGAGCATTAGCGGCG-TTTTCTA
1 AAAACGCCGCTAAAGACCTGAGCATTAGCGGCGATTATGTA
** * * ** * *
43712062 ATATGCGCCGCTAATG--CTGCGGTTTGTAGCGGCGCTT-TTTA
1 A-AAACGCCGCTAAAGACCTG-AGCAT-TAGCGGCGATTATGTA
* *
43712103 AGAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-CGTAA
1 A-AAACGCCGCTAAAGACCTGAGCATTAGCGGCGATTATGT-A
43712145 AAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCA-TAT-TA
1 AAAACGCCGCTAAAGACCTGAGCATTAGCGGCG-ATTATGTA
* *
43712185 GAAAACGCCGCGAAAGACC-GCACCATTAGCGGCGATTATGTA
1 -AAAACGCCGCTAAAGACCTG-AGCATTAGCGGCGATTATGTA
*
43712227 AAAGCGCCGCTAA
1 AAAACGCCGCTAA
43712240 GGGCCCCAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.01
40 6 0.04
41 123 0.87
42 8 0.06
43 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAGACCTGAGCATTAGCGGCGATTATGTA
Found at i:43712235 original size:82 final size:82
Alignment explanation
Indices: 43712088--43712239 Score: 193
Period size: 82 Copynumber: 1.9 Consensus size: 82
43712078 CTGCGGTTTG
* * * * *
43712088 TAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTCGTAAAAAACGCC
1 TAGCGGCGCATATTAAGAAACGCCGCGAAAGACCTGACCATTAGCGGCGATTCGTAAAAAACGCC
43712153 GCTAAAGACCTGAGCAT
66 GCTAAAGACCTGAGCAT
* *
43712170 TAGCGGCGCATATT-AGAAAACGCCGCGAAAGACC-GCACCATTAGCGGCGATTATGT-AAAAGC
1 TAGCGGCGCATATTAAG-AAACGCCGCGAAAGACCTG-ACCATTAGCGGCGATT-CGTAAAAAAC
43712232 GCCGCTAA
63 GCCGCTAA
43712240 GGGCCCCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 3 0.05
82 55 0.92
83 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.18
Consensus pattern (82 bp):
TAGCGGCGCATATTAAGAAACGCCGCGAAAGACCTGACCATTAGCGGCGATTCGTAAAAAACGCC
GCTAAAGACCTGAGCAT
Found at i:43712388 original size:41 final size:40
Alignment explanation
Indices: 43712343--43712433 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 40
43712333 TTACACATAT
43712343 CGCCGCTAATGCTCGTATCTTTGGCGGCGTTTTTTGT-AAA
1 CGCCGCTAATGCTCG-ATCTTTGGCGGCGTTTTTTGTCAAA
* * *
43712383 GCGCCGCTAATGCTCGATTTTTTGTGGCGTTTTTTGTCCAAA
1 -CGCCGCTAATGCTCGATCTTTGGCGGCGTTTTTTGT-CAAA
43712425 CGCCGCTAA
1 CGCCGCTAA
43712434 AAGCGCCGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 18 0.40
41 24 0.53
42 3 0.07
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATCTTTGGCGGCGTTTTTTGTCAAA
Found at i:43712442 original size:12 final size:12
Alignment explanation
Indices: 43712425--43712449 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43712415 TTTGTCCAAA
43712425 CGCCGCTAAAAG
1 CGCCGCTAAAAG
43712437 CGCCGCTAAAAG
1 CGCCGCTAAAAG
43712449 C
1 C
43712450 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:43712700 original size:33 final size:33
Alignment explanation
Indices: 43712662--43712725 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
43712652 TTTTTACATG
43712662 TGTATCAAAATCAAGATAGGATTCTAAGATTTT
1 TGTATCAAAATCAAGATAGGATTCTAAGATTTT
43712695 TGTATCAAAATCAAGATAGGATTCTAAGATT
1 TGTATCAAAATCAAGATAGGATTCTAAGATT
43712726 GTTTTTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (33 bp):
TGTATCAAAATCAAGATAGGATTCTAAGATTTT
Found at i:43714860 original size:11 final size:11
Alignment explanation
Indices: 43714844--43714904 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
43714834 TTTTTGGTAT
43714844 TAAAATTTCTA
1 TAAAATTTCTA
*
43714855 TAAAATTTCTG
1 TAAAATTTCTA
*
43714866 TAAAA--TCAA
1 TAAAATTTCTA
*
43714875 TCAATCAATTTCTG
1 T-AA--AATTTCTA
43714889 TAAAATTTCTA
1 TAAAATTTCTA
43714900 TAAAA
1 TAAAA
43714905 ATAAAACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.08
10 2 0.05
11 27 0.69
12 2 0.05
13 2 0.05
14 3 0.08
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.39
Consensus pattern (11 bp):
TAAAATTTCTA
Found at i:43716992 original size:7 final size:7
Alignment explanation
Indices: 43716977--43717016 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
43716967 TCTTTAATAA
*
43716977 TAAATCC
1 TAAACCC
43716984 TAAACCC
1 TAAACCC
*
43716991 TAAACTC
1 TAAACCC
*
43716998 TAAACCA
1 TAAACCC
43717005 TAAACCC
1 TAAACCC
43717012 TAAAC
1 TAAAC
43717017 TCAAAACTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:43717008 original size:21 final size:21
Alignment explanation
Indices: 43716984--43717023 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43716974 TAATAAATCC
*
43716984 TAAACCCTAAACTCTAAACCA
1 TAAACCCTAAACTCAAAACCA
43717005 TAAACCCTAAACTCAAAAC
1 TAAACCCTAAACTCAAAAC
43717024 TCTAATCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACTCAAAACCA
Found at i:43718149 original size:185 final size:185
Alignment explanation
Indices: 43717837--43718211 Score: 687
Period size: 185 Copynumber: 2.0 Consensus size: 185
43717827 TTTTATTGTA
* *
43717837 TTTTCAGCCTTTAATTCAACTTTTACCTACCCAAGCCATTCACCCTCTTCCTCTCCTCTTTTCTC
1 TTTTCAGCATTTAATTCAAATTTTACCTACCCAAGCCATTCACCCTCTTCCTCTCCTCTTTTCTC
*
43717902 TTCAATTTTCTTTCTTTCTCCCATTGTTGTCGTCACCTACACCTAGTTTTACCATCTCTTTCTTC
66 TTCAATTTTCTTTCTTTCTCCCATTATTGTCGTCACCTACACCTAGTTTTACCATCTCTTTCTTC
* *
43717967 TTTTTCTTTTTGCCACAAGATTTGTTAACATATTTTCCATCATATTGCTGTTATT
131 TTTTTCTTTTTGCCACAAGATTTGTTAACATATTCTCCACCATATTGCTGTTATT
*
43718022 TTTTCAGCATTTAATTCAAATTTTACCTACCCAAGCCGTTCACCCTCTTCCTCTCCTCTTTTCTC
1 TTTTCAGCATTTAATTCAAATTTTACCTACCCAAGCCATTCACCCTCTTCCTCTCCTCTTTTCTC
*
43718087 TTCAATTTTCTTTCTTTCTCCCATTATTGTCGTCACCTACTCCTAGTTTTACCATCTCTTTCTTC
66 TTCAATTTTCTTTCTTTCTCCCATTATTGTCGTCACCTACACCTAGTTTTACCATCTCTTTCTTC
43718152 TTTTTCTTTTTGCCACAAGATTTGTTAACATATTCTCCACCATATTGCTGTTATT
131 TTTTTCTTTTTGCCACAAGATTTGTTAACATATTCTCCACCATATTGCTGTTATT
43718207 TTTTC
1 TTTTC
43718212 CTCATTAAAA
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
185 183 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (185 bp):
TTTTCAGCATTTAATTCAAATTTTACCTACCCAAGCCATTCACCCTCTTCCTCTCCTCTTTTCTC
TTCAATTTTCTTTCTTTCTCCCATTATTGTCGTCACCTACACCTAGTTTTACCATCTCTTTCTTC
TTTTTCTTTTTGCCACAAGATTTGTTAACATATTCTCCACCATATTGCTGTTATT
Found at i:43722272 original size:42 final size:42
Alignment explanation
Indices: 43722221--43722338 Score: 191
Period size: 42 Copynumber: 2.8 Consensus size: 42
43722211 GTTTACAAAC
*
43722221 AAAAACGCCGCTAAAGACCATGTTCTTCAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
43722263 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
43722305 AAAAACACCGCTAAAGATCATGTTCTTTAGCGGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
43722339 TTTTTCTCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:43722362 original size:42 final size:41
Alignment explanation
Indices: 43722312--43722526 Score: 281
Period size: 42 Copynumber: 5.1 Consensus size: 41
43722302 GAGAAAAACA
* *
43722312 CCGCTAAAGATCATGTTCTTTAGCGGCTTTTTCTCTTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCTTTTTCTC-TAAGCG
* *
43722354 CCGTTAAAGAACATGGTCTTTAGCGGCATTTTTTTCTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTCTCTAAGCG
* *
43722396 CCTCTGAAGAACATGGTCTTTAGCGGCCTTTTT-TCTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGG-CTTTTTCTCTAAGCG
*
43722437 CCGCTAAAGAACATGGTCTTTAGCGG-TGTTTCTTTCTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCT-TTT-TCTCTAAGCG
* *
43722479 CCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTCTCTAAGCG
43722521 CCGCTA
1 CCGCTA
43722527 TACAAAAACG
Statistics
Matches: 156, Mismatches: 10, Indels: 14
0.87 0.06 0.08
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 33 0.21
42 107 0.69
43 11 0.07
44 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (41 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCTTTTTCTCTAAGCG
Found at i:43722449 original size:83 final size:83
Alignment explanation
Indices: 43722312--43722526 Score: 306
Period size: 83 Copynumber: 2.6 Consensus size: 83
43722302 GAGAAAAACA
* * *
43722312 CCGCTAAAGATCATGTTCTTTAGCGG-CTTTTTCTCTTAAGCGCCGTTAAAGAACATGGTCTTTA
1 CCGCTAAAGAACATGGTCTTTAGCGGCCTTTTT-TC-TAAGCGCCGCTAAAGAACATGGTCTTTA
*
43722376 GCGGCATTTTTTTCTAAGCG
64 GCGGCATTTCTTTCTAAGCG
* *
43722396 CCTCTGAAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGC
1 CCGCTAAAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGC
**
43722461 GGTGTTTCTTTCTAAGCG
66 GGCATTTCTTTCTAAGCG
* *
43722479 CCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAGCGCCGCTA
1 CCGCTAAAGAACATGGTCTTTAGCGGC-CTTTTTTCTAAGCGCCGCTA
43722527 TACAAAAACG
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 68 0.58
84 43 0.37
85 6 0.05
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (83 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCCTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGC
GGCATTTCTTTCTAAGCG
Found at i:43724397 original size:28 final size:28
Alignment explanation
Indices: 43724331--43724385 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
43724321 AATATATAGT
* *
43724331 ACTAATAATTATAAATTTTAGTGTTTTC
1 ACTAATATTTTTAAATTTTAGTGTTTTC
43724359 ACTAATATTTTTAAATTTTAGTGTTTT
1 ACTAATATTTTTAAATTTTAGTGTTTT
43724386 TATTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTAATATTTTTAAATTTTAGTGTTTTC
Found at i:43725900 original size:23 final size:23
Alignment explanation
Indices: 43725857--43725900 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
43725847 CTTAAATTAT
* *
43725857 ACATATTTTACAATTACATAAGA
1 ACATATTTTAAAATTAAATAAGA
43725880 ACATA-TTTAAAATATAAATAA
1 ACATATTTTAAAAT-TAAATAA
43725901 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ACATATTTTAAAATTAAATAAGA
Found at i:43725995 original size:391 final size:390
Alignment explanation
Indices: 43725158--43726092 Score: 1349
Period size: 391 Copynumber: 2.4 Consensus size: 390
43725148 TTGGTCCTCT
* * * *
43725158 CCTAAACCCTAAATTCCTCAGTCTTAATCACTAACATCTAACCCCTAAACCCCTAACCCCTAAAT
1 CCTAAA-CCTAAATCCCTAAGTCTTAACCACTAACATCTAACCCCTAAACCCCT--CCCCTAAAC
* * *
43725223 CTCAAAT-CTCGGCCAACCCTTAATTAAGCATAATCCATAATCTATAATCCCTAAATCCACATAT
63 CTTAAATCCT-GGCCAACCCTTAATTAAGCATAATCCATAATCTATAATCCCTAAATTCACTTAT
* *
43725287 ATATAGTACTCCCTAAACATTAAAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAGTTAAA
127 ATATAGTACTCCCTAACCATTAAAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAATTAAA
*
43725352 CCTTAATCTTATTAAACCCGCCTAAATTAACCATTGAAGGGATATAAATATTTAAGTATTCTATC
192 CCTTAATCTTATTAAACCCGCCTAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATC
* * *
43725417 TATTATATATATATATCTCTCAAGGCATAATTTAAACCCTAATTTATACATCTTTTACAATTACA
257 TATTATATATATATATCTCTAAAGGCATAATTTAAACCCTAAATTATACATATTTTACAATTACA
*
43725482 TAAGAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAATTATAACCAGACCCCTG
322 TAAGAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAATCATAACCAGACCCCTG
43725547 AAAC
387 AAAC
*
43725551 CCTAAACCTTAAATCCCTAAGTCTTAACAACTAACATCTAACCCCTAAACCCCTCCCCTAAACCT
1 CCTAAACC-TAAATCCCTAAGTCTTAACCACTAACATCTAACCCCTAAACCCCTCCCCTAAACCT
*
43725616 TAAATCCTGGCCAACCCTTAGTTAAGCATAATCCATAATCTATAATCCCTAAATTCACTTATATA
65 TAAATCCTGGCCAACCCTTAATTAAGCATAATCCATAATCTATAATCCCTAAATTCACTTATATA
43725681 TAGTACTCCCTAACCATTAAAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAATTAAACCT
130 TAGTACTCCCTAACCATTAAAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAATTAAACCT
*
43725746 TAATCTTATTAAACCCGCCTAAATTAACCATTGAA-GGATATAAATAATTTTCTA-TACTCTATC
195 TAATCTTATTAAACCCGCCTAAATTAACCATTGAAGGGATATAAAT-A-TTT-AAGTACTCTATC
* *
43725809 TA-T-TATATATATCTCTCTAAAGGCATAATTAATTAAACCTTAAATTATACATATTTTACAATT
257 TATTATATATATATATCTCTAAAGGCATAA-T--TTAAACCCTAAATTATACATATTTTACAATT
* *
43725872 ACATAAGAACATATTTAAAATATAAATAAAAAAATTAATCTAAA-CCAAAATCGTAACCCGACCC
319 ACATAAGAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAATCATAACCAGACCC
43725936 CTGAAAC
384 CTGAAAC
*
43725943 CCTAAACACAAAATCCCTAAGTCTTAACCACTAACATCTAACCCCT-AA-----CCCCTAAACCT
1 CCTAAAC-CTAAATCCCTAAGTCTTAACCACTAACATCTAACCCCTAAACCCCTCCCCTAAACCT
* * * * * * *
43726002 TAAATCCCGGCCAATCCTTAATTAAGCAAAACCCCTAATCTATAATCCATATATAAATC-CATAT
65 TAAATCCTGGCCAACCCTTAATTAAGCATAATCCATAATCTATAATCC--CTA-AATTCAC-T-T
43726066 ATATATAGTACTCCCTAAACC-TTAAAA
125 ATATATAGTACTCCCT-AACCATTAAAA
43726093 TTATATGAAC
Statistics
Matches: 496, Mismatches: 31, Indels: 33
0.89 0.06 0.06
Matches are distributed among these distances:
386 53 0.11
388 3 0.01
389 5 0.01
390 56 0.11
391 175 0.35
392 83 0.17
393 121 0.24
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.30
Consensus pattern (390 bp):
CCTAAACCTAAATCCCTAAGTCTTAACCACTAACATCTAACCCCTAAACCCCTCCCCTAAACCTT
AAATCCTGGCCAACCCTTAATTAAGCATAATCCATAATCTATAATCCCTAAATTCACTTATATAT
AGTACTCCCTAACCATTAAAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAATTAAACCTT
AATCTTATTAAACCCGCCTAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATT
ATATATATATATCTCTAAAGGCATAATTTAAACCCTAAATTATACATATTTTACAATTACATAAG
AACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAATCATAACCAGACCCCTGAAAC
Found at i:43726811 original size:114 final size:114
Alignment explanation
Indices: 43726628--43726891 Score: 379
Period size: 113 Copynumber: 2.3 Consensus size: 114
43726618 TTTATTTTTT
* * ** * * *
43726628 GCGGCGCTATACCAAAAATGCCACTAGGGCCACTGAAGGCCATTAAACGACGCCGTTGTATTTTA
1 GCGGCGCTAAACCAAAAACGCCACTAACGCCACCGTAGGCCACTAAACGACGCCGTTGTATTTTA
* * *
43726693 TTTTTTGCGGCGTT-TATCCTGAAAACGCCGCTAAAAACACAGACCATTA
66 TTTTTTGCGGCGTTCT-TCCTAAAAACACCACTAAAAACACAGACCATTA
*
43726742 GCGGCGCCAAACCAAAAACGCCACTAACGCCACCGTA-GCCACTAAACGACGCCGTTGTATTTTA
1 GCGGCGCTAAACCAAAAACGCCACTAACGCCACCGTAGGCCACTAAACGACGCCGTTGTATTTTA
43726806 TTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAACACAGACCATTA
66 TTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAACACAGACCATTA
* *
43726855 GCGGCGCTAGACCAAAAACGCCACTAAACGACACCGT
1 GCGGCGCTAAACCAAAAACGCCACT-AACGCCACCGT
43726892 TGTATTTTAT
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
113 93 0.69
114 41 0.31
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (114 bp):
GCGGCGCTAAACCAAAAACGCCACTAACGCCACCGTAGGCCACTAAACGACGCCGTTGTATTTTA
TTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAACACAGACCATTA
Found at i:43726895 original size:95 final size:95
Alignment explanation
Indices: 43726779--43726976 Score: 315
Period size: 95 Copynumber: 2.1 Consensus size: 95
43726769 CGCCACCGTA
*
43726779 GCCACTAAACGACGCCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAAC
1 GCCACTAAACGACACCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAAC
* * *
43726844 ACAGACCATTAGCGGCGCTAGACCAAAAAC
66 ACAGACCATTAGCAGCGCAAGACAAAAAAC
* * * * *
43726874 GCCACTAAACGACACCGTTGTATTTTATTTTTTGCGGCGTTTTTTCTGAAAACGCCGCTAAAAAC
1 GCCACTAAACGACACCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAAC
43726939 ACAGACCATTAGCAGCGCAAGACAAAAAAC
66 ACAGACCATTAGCAGCGCAAGACAAAAAAC
43726969 GCCACTAA
1 GCCACTAA
43726977 GGCCACTGAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (95 bp):
GCCACTAAACGACACCGTTGTATTTTATTTTTTGCGGCGTTCTTCCTAAAAACACCACTAAAAAC
ACAGACCATTAGCAGCGCAAGACAAAAAAC
Found at i:43733941 original size:140 final size:140
Alignment explanation
Indices: 43733522--43733942 Score: 707
Period size: 140 Copynumber: 3.0 Consensus size: 140
43733512 GAATAAATGT
*
43733522 TGCATACTTCGAAAACTTGTCCACCACAACAAAAATGCTTGCAAACCTATCAGATTTAGGCAAAC
1 TGCATACTTCGAAAACTTGTCCACCACAACAAAAATGCTTGCAAACCCATCAGATTTAGGCAAAC
* *
43733587 CCACAATAAAGTCCATGGATAAACTCTCCCATGGACGCTCTGGAATGGGTAAAGGTTGTAACAAA
66 CCACAATAAAGTCCATGGATAAACTCTCCCATGGACGCTCCGGAATGGGCAAAGGTTGTAACAAA
*
43733652 CCGGCAGCAA
131 CCGGCAGCAG
* *
43733662 TGCATACTTCGAAAACTTGTCCACCACAACATAAATGCTTGCAAACCCATCAGATTTAGGAAAAC
1 TGCATACTTCGAAAACTTGTCCACCACAACAAAAATGCTTGCAAACCCATCAGATTTAGGCAAAC
* *
43733727 CCACAATAAAGTCCATGGATAAACTCTCCTATGGACGCTCCGAAATGGGCAAAGGTTGTAACAAA
66 CCACAATAAAGTCCATGGATAAACTCTCCCATGGACGCTCCGGAATGGGCAAAGGTTGTAACAAA
*
43733792 TCGGCAGCAG
131 CCGGCAGCAG
* * *
43733802 TGCATACTTCAAAAACTTGTCCACCACAACAAAAATGCTTGTAAACCCATCAAATTTAGGCAAAC
1 TGCATACTTCGAAAACTTGTCCACCACAACAAAAATGCTTGCAAACCCATCAGATTTAGGCAAAC
* * *
43733867 CCACAATAAAGTTCATGGATAAACTCTCCCATGGACGCTCCGGAATAGGCAAAGGTTGCAACAAA
66 CCACAATAAAGTCCATGGATAAACTCTCCCATGGACGCTCCGGAATGGGCAAAGGTTGTAACAAA
43733932 CCGGCAGCAG
131 CCGGCAGCAG
43733942 T
1 T
43733943 CTTCAACTCG
Statistics
Matches: 261, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 261 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (140 bp):
TGCATACTTCGAAAACTTGTCCACCACAACAAAAATGCTTGCAAACCCATCAGATTTAGGCAAAC
CCACAATAAAGTCCATGGATAAACTCTCCCATGGACGCTCCGGAATGGGCAAAGGTTGTAACAAA
CCGGCAGCAG
Found at i:43736624 original size:15 final size:15
Alignment explanation
Indices: 43736599--43736633 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
43736589 GACTCTATTT
*
43736599 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
43736613 TAATTAATATTAAGA
1 TAATTAATATTAAGA
43736628 TAATTA
1 TAATTA
43736634 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:43740585 original size:23 final size:23
Alignment explanation
Indices: 43740542--43740600 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
43740532 AAAAGCTATC
*
43740542 TACAAATCAAATC-TCTAAGA-T
1 TACAAATCATATCTTCTAAGATT
43740563 TACAAAATCATATCTTCTAAGATT
1 TAC-AAATCATATCTTCTAAGATT
43740587 TACAAATCATATCT
1 TACAAATCATATCT
43740601 AAGATTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.09
22 9 0.26
23 18 0.53
24 4 0.12
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (23 bp):
TACAAATCATATCTTCTAAGATT
Found at i:43742600 original size:20 final size:20
Alignment explanation
Indices: 43742565--43742610 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
43742555 TTGACTTATT
* *
43742565 TTAAAAACAATTTAAC-TGA
1 TTAAAAAAAATCTAACTTGA
43742584 TTGAAAAAAAATCTAACTTGA
1 TT-AAAAAAAATCTAACTTGA
43742605 TTAAAA
1 TTAAAA
43742611 TCATTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 16 0.70
21 5 0.22
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAAAAAATCTAACTTGA
Found at i:43750118 original size:15 final size:16
Alignment explanation
Indices: 43750089--43750118 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43750079 CAAACATGTT
43750089 TTAACACATTATCAAA
1 TTAACACATTATCAAA
43750105 TTAACACA-TATCAA
1 TTAACACATTATCAA
43750119 CAAGGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:43757660 original size:40 final size:40
Alignment explanation
Indices: 43757560--43757824 Score: 277
Period size: 40 Copynumber: 6.7 Consensus size: 40
43757550 GCTCCTCGTT
* * * *
43757560 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
43757600 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
43757639 CGAATGCCTCCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
43757679 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
43757719 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * * *
43757759 CAAATGCCTTC-GGATCTTAGTCCGGGTATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
43757800 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
43757825 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 141 0.72
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:43761637 original size:45 final size:45
Alignment explanation
Indices: 43761573--43761661 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
43761563 AACAGATACT
* *
43761573 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
43761618 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
43761662 TTGGTTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:43761730 original size:51 final size:52
Alignment explanation
Indices: 43761672--43761807 Score: 179
Period size: 50 Copynumber: 2.7 Consensus size: 52
43761662 TTGGTTCACA
* *
43761672 TAGTAGCCTACACATAGTACTACACATGTGACCATTACCA-TCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
* * ** *
43761723 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTTTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
*
43761773 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
43761808 CACTTTCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.05
50 38 0.52
51 31 0.42
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
Found at i:43764400 original size:41 final size:40
Alignment explanation
Indices: 43764343--43764503 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 40
43764333 TAAACAGATT
* * *
43764343 CACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATT-AGTA
* * * *
43764384 CACCGGCACTTAGCCTGCTAGACATATAGTCTGA-AATGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTA-GTA
* *
43764424 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTGAATTACTT
1 -CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTAGTA
* * *
43764466 CACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTA
43764504 TATTCAATCA
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 92 0.93
42 2 0.02
43 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTAGTA
Found at i:43771689 original size:30 final size:30
Alignment explanation
Indices: 43771653--43771711 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
43771643 TTTATACCTG
43771653 AATACCTAGGTAACACATACATTCGAAATT
1 AATACCTAGGTAACACATACATTCGAAATT
43771683 AATACCTAGGTAACACATACATTCGAAAT
1 AATACCTAGGTAACACATACATTCGAAAT
43771712 ACACACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.25
Consensus pattern (30 bp):
AATACCTAGGTAACACATACATTCGAAATT
Found at i:43771986 original size:41 final size:40
Alignment explanation
Indices: 43771927--43772087 Score: 144
Period size: 41 Copynumber: 3.9 Consensus size: 40
43771917 TAAACAGATT
* * * * *
43771927 CACCGGCATTTTGTCTGCTAGGCTTAGAGCCTGATTCAGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATT-AGTA
* * * *
43771968 CACCGGCACTTAGCCTGCTAGACATATAGTCTGA-AATGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTA-GTA
* *
43772008 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTGAATTACTT
1 -CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTAGTA
* * *
43772050 CACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTA
43772088 TATTCAATCA
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 91 0.93
42 2 0.02
43 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTAGTA
Found at i:43775462 original size:16 final size:15
Alignment explanation
Indices: 43775431--43775464 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43775421 GCAATAAAAA
*
43775431 TTCAGTACTTAATTT
1 TTCAGCACTTAATTT
*
43775446 TTCAGCACTTAAATT
1 TTCAGCACTTAATTT
43775461 TTCA
1 TTCA
43775465 AATTATCAAA
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:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (15 bp):
TTCAGCACTTAATTT
Found at i:43776567 original size:13 final size:13
Alignment explanation
Indices: 43776549--43776595 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
43776539 TGATCATATT
*
43776549 TAAAAATATTAAA
1 TAAAAATATTACA
*
43776562 TAAAAATATTTTCA
1 TAAAAATA-TTACA
43776576 -AAAAATATTACA
1 TAAAAATATTACA
43776588 TAAAAATA
1 TAAAAATA
43776596 AAAAGGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.14
13 22 0.76
14 3 0.10
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATATTACA
Found at i:43776893 original size:20 final size:20
Alignment explanation
Indices: 43776851--43776894 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43776841 TCATATATGA
* *
43776851 AATTTAAGAAAATAACTCTT
1 AATTTAAGAAAATAACACGT
43776871 AATTTAAAGAAAATAA-ACGT
1 AATTT-AAGAAAATAACACGT
43776891 AATT
1 AATT
43776895 ATCTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (20 bp):
AATTTAAGAAAATAACACGT
Found at i:43781208 original size:21 final size:21
Alignment explanation
Indices: 43781167--43781208 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43781157 AATGTTTTGA
*
43781167 CATGTTTTGAGCTTGTTTAAT
1 CATGTTTTGAGCTTGTATAAT
43781188 CATGTTTTGAG-TTGGTATAAT
1 CATGTTTTGAGCTT-GTATAAT
43781209 TGATGGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (21 bp):
CATGTTTTGAGCTTGTATAAT
Found at i:43784145 original size:22 final size:22
Alignment explanation
Indices: 43784114--43784157 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43784104 AGAAAGAATG
*
43784114 TCCTTCTGAACAGTCGGACTAA
1 TCCTTCTGAACAATCGGACTAA
* *
43784136 TCCTTGTGAACAATCGGGCTAA
1 TCCTTCTGAACAATCGGACTAA
43784158 CATACTATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (22 bp):
TCCTTCTGAACAATCGGACTAA
Found at i:43785571 original size:20 final size:20
Alignment explanation
Indices: 43785540--43785598 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
43785530 CATCAGTAAT
*
43785540 AACAGAAACTTATCCATATC
1 AACAGTAACTTATCCATATC
* * *
43785560 AATAGTAACTTATACATACC
1 AACAGTAACTTATCCATATC
43785580 AACAGTAA-TTCATCCATAT
1 AACAGTAACTT-ATCCATAT
43785599 AATTACATAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (20 bp):
AACAGTAACTTATCCATATC
Found at i:43785813 original size:23 final size:24
Alignment explanation
Indices: 43785787--43785861 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
43785777 AATCTCTATC
*
43785787 GAGCTGAAACGGTAAGCTCCGT-A
1 GAGCTGAAACGGTAAGCTCCATAA
* *
43785810 GAGCTGAAACAGTAAACT-CATAA
1 GAGCTGAAACGGTAAGCTCCATAA
* * *
43785833 GAGTTGAAATGGTAAGCT-CATAC
1 GAGCTGAAACGGTAAGCTCCATAA
43785856 GAGCTG
1 GAGCTG
43785862 TGGTGAGTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (24 bp):
GAGCTGAAACGGTAAGCTCCATAA
Found at i:43792924 original size:14 final size:14
Alignment explanation
Indices: 43792880--43792926 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
43792870 AAATTCATTC
43792880 ATCAATTCATGTAA
1 ATCAATTCATGTAA
*
43792894 ATCATATATCAT-AAA
1 ATCA-AT-TCATGTAA
43792909 ATCAATTCATGTAA
1 ATCAATTCATGTAA
43792923 ATCA
1 ATCA
43792927 TGTATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 8 0.29
16 4 0.14
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (14 bp):
ATCAATTCATGTAA
Found at i:43793054 original size:20 final size:19
Alignment explanation
Indices: 43793004--43793054 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
43792994 AATAACGGAA
*
43793004 AATTATCCATATCAATAGT
1 AATTATCCATACCAATAGT
*
43793023 AACTTATACATACCAATAGT
1 AA-TTATCCATACCAATAGT
43793043 AATTCATCCATA
1 AATT-ATCCATA
43793055 TAATTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (19 bp):
AATTATCCATACCAATAGT
Found at i:43793309 original size:23 final size:23
Alignment explanation
Indices: 43793231--43793311 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
43793221 GCTAATGAAT
* *
43793231 GGTAAGCTC-TATCGAGCTAAAAC
1 GGTAAGCTCATA-AGAGCTGAAAC
* *
43793254 GGTAAGCTCCGT-AGAGCTGAAAT
1 GGTAAGCT-CATAAGAGCTGAAAC
* *
43793277 AGTAAACTCATAAGAGCTGAAAC
1 GGTAAGCTCATAAGAGCTGAAAC
43793300 GGTAAGCTCATA
1 GGTAAGCTCATA
43793312 CAAGCTGTGG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.04
23 42 0.91
24 1 0.02
25 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (23 bp):
GGTAAGCTCATAAGAGCTGAAAC
Found at i:43793830 original size:125 final size:125
Alignment explanation
Indices: 43793608--43793945 Score: 516
Period size: 125 Copynumber: 2.7 Consensus size: 125
43793598 TAAGAGACGC
* *
43793608 CGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGTTTATCTACAAACGCCAGTAAAGATCTAGCA
1 CGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGCCGGTAAAGATCTAGCA
*
43793673 TTTGCGACGCTTATCAAAAAACGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGT
66 TTTGCGACGCTTATCAAAAAACGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCAGT
* ** * *
43793733 CGTTTAACTTTGACTTATAGTGGCACTAGCGGCGTTTATCTGGAAATGCCGGTAAAGATCTAGCT
1 CGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGCCGGTAAAGATCTAGCA
*
43793798 TTTGC-AGCGCTTATCAAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCAGT
66 TTTGCGA-CGCTTATCAAAAAACGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCAGT
* * *
43793858 CGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGTCGGTAAAGATCTATCA
1 CGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGCCGGTAAAGATCTAGCA
* * * *
43793923 TTTGTGGCTCTTATCCAAAAACG
66 TTTGCGACGCTTATCAAAAAACG
43793946 TTGCTAAAGA
Statistics
Matches: 190, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.01
125 189 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (125 bp):
CGTTTAACTTTGACTTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGCCGGTAAAGATCTAGCA
TTTGCGACGCTTATCAAAAAACGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCAGT
Found at i:43793998 original size:166 final size:163
Alignment explanation
Indices: 43793801--43794436 Score: 699
Period size: 166 Copynumber: 3.9 Consensus size: 163
43793791 TCTAGCTTTT
* *
43793801 GCAGCGCTTATCAAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCAGTCGTTTAAC
1 GCAGCGC-TAACAAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGTCGTTTAAC
* * **
43793866 TTTGACCTGTAGTGGCACTAGCGGCGTTTATCTAAAAACGTCGGTAAAGATCTATCATTTGTGGC
65 TTTGACCTGTAGTGACACTAGCGGCGTTTATCTAAAAAC--CGGTAAAGATCTAGCATTTGCAGC
* ** *
43793931 TCTTATCCAAAAACGTTGCTAAAGATCGGTATATTA
128 TCTTATCAAAAAACGCCGCTAAAGATCGGTACATTA
* * **
43793967 GCAGCGCTAACAGAAAAATGCCACTAATGCTCCGTAAATAATTGAGCAGAACATCGTCGTTTAAC
1 GCAGCGCTAACA-AAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGTCGTTTAAC
*
43794032 TTTGACCTGTAGTGACACTAGCGGCGTTTATCTGAAAACATCGGTAAAGATCTAGCATTTGCAGC
65 TTTGACCTGTAGTGACACTAGCGGCGTTTATCT-AAAA-ACCGGTAAAGATCTAGCATTTGCAGC
* * * *
43794097 GCTTATCAAAAAATGCCGCTAGAGATTGGTACATTA
128 TCTTATCAAAAAACGCCGCTAAAGATCGGTACATTA
* * * *
43794133 GCGGCGCTAACAGAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCATTGTTTAAA
1 GCAGCGCTAACA-AAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGTCGTTTAAC
* * * * *
43794198 TTTGA----TA---ATATTAG-TG-G--TA-GTAAAACACCGATAAAGATCTAGCATTTGCAG-T
65 TTTGACCTGTAGTGACACTAGCGGCGTTTATCTAAAA-ACCGGTAAAGATCTAGCATTTGCAGCT
*
43794250 GCTTATCAAAAAATGCCGCTAAAGATCGGTACATTA
129 -CTTATCAAAAAACGCCGCTAAAGATCGGTACATTA
* * * * *
43794286 GCAGCGCTAGA-AAAAAATGCCACTATTGCTCCGCAAATAATTAAGTAGAATGTCGTCATTTAAC
1 GCAGCGCTA-ACAAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGTCGTTTAAC
* * * *
43794350 TTTGACCTGTAGTGACACTAGCGGCATTTATATGGAAATACCGGTAAAGATCTAGCATTTGCGGC
65 TTTGACCTGTAGTGACACTAGCGGCGTTTATCT--AAAAACCGGTAAAGATCTAGCATTTGCAGC
*
43794415 GT-TTATCAAAAAACGCCACTAA
128 -TCTTATCAAAAAACGCCGCTAA
43794437 TCCTCGATCT
Statistics
Matches: 394, Mismatches: 55, Indels: 43
0.80 0.11 0.09
Matches are distributed among these distances:
152 49 0.12
153 70 0.18
154 2 0.01
155 2 0.01
156 2 0.01
157 1 0.00
158 1 0.00
159 10 0.03
160 1 0.00
162 2 0.01
163 2 0.01
164 1 0.00
165 45 0.11
166 200 0.51
167 5 0.01
168 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (163 bp):
GCAGCGCTAACAAAAAATGCCACTAATGCTCCGCAAATAATTAAGCAGAACGCCGTCGTTTAACT
TTGACCTGTAGTGACACTAGCGGCGTTTATCTAAAAACCGGTAAAGATCTAGCATTTGCAGCTCT
TATCAAAAAACGCCGCTAAAGATCGGTACATTA
Found at i:43794591 original size:40 final size:39
Alignment explanation
Indices: 43794539--43794614 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
43794529 CTTTTTTGGA
* * *
43794539 AAACGCCGTAATTGCTCA-ACTATAGCGGCGTTTTTTTAC
1 AAACGCCGTAATTCCCCATA-TATAGCGGCATTTTTTTAC
43794578 AAACGCCGCTAATTCCCCATATATAGCGGCATTTTTT
1 AAACGCCG-TAATTCCCCATATATAGCGGCATTTTTT
43794615 GCCAAATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.25
40 23 0.72
41 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (39 bp):
AAACGCCGTAATTCCCCATATATAGCGGCATTTTTTTAC
Found at i:43795075 original size:13 final size:13
Alignment explanation
Indices: 43795057--43795099 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
43795047 GTGTTTACGA
43795057 TTTATGGTGTAGG
1 TTTATGGTGTAGG
* *
43795070 TTTATGATTTAGTG
1 TTTATGGTGTAG-G
*
43795084 TTTATGGTGTACG
1 TTTATGGTGTAGG
43795097 TTT
1 TTT
43795100 TCAATTTACA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.53
Consensus pattern (13 bp):
TTTATGGTGTAGG
Found at i:43795180 original size:22 final size:22
Alignment explanation
Indices: 43795121--43795180 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
43795111 GTTGAGTGTT
* *
43795121 TAGGGGTGAG-GGCTTAGGGTT
1 TAGGGGTTAGTGGCTTAGGGTC
*
43795142 TAGGGGTTA-TAGACTTAGGGTC
1 TAGGGGTTAGT-GGCTTAGGGTC
43795164 TAGGGGTTAGTGGCTTA
1 TAGGGGTTAGTGGCTTA
43795181 AGGTTACAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.25
22 23 0.72
23 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (22 bp):
TAGGGGTTAGTGGCTTAGGGTC
Found at i:43795207 original size:7 final size:7
Alignment explanation
Indices: 43795178--43795229 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
43795168 GGTTAGTGGC
43795178 TTAAGG-
1 TTAAGGT
43795184 TTACAGGT
1 TTA-AGGT
43795192 TTAAGGGT
1 TTAA-GGT
43795200 TTAAGGT
1 TTAAGGT
43795207 TTAAGGT
1 TTAAGGT
* *
43795214 ATAGAAGT
1 TTA-AGGT
43795222 TTAAGGT
1 TTAAGGT
43795229 T
1 T
43795230 ATGGGCTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 3 0.08
7 20 0.53
8 15 0.39
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (7 bp):
TTAAGGT
Found at i:43799330 original size:21 final size:21
Alignment explanation
Indices: 43799304--43799353 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
43799294 CTACAACTTA
*
43799304 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGGG
*
43799325 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGGG
43799346 AAGCAGAG
1 AAGCAGAG
43799354 CAGAGCAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.46, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGGG
Found at i:43799799 original size:43 final size:42
Alignment explanation
Indices: 43799708--43799943 Score: 265
Period size: 43 Copynumber: 5.4 Consensus size: 42
43799698 CATTTATAGA
* ** * * *
43799708 AAAAGCGCCGCTAAAAGTCACCAAACAATAGTGGCGTTTGTGG
1 AAAAGCGTCGCTAAAAGTCA-TGATCTATAGCGGCGTTTGTGG
* *
43799751 AAAAAGCGTCGCTAAAAGTCATGATCTATAGTGGCGTTTGTGAT
1 -AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTGTG-G
43799795 AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGG
1 AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGG
**
43799837 AAAAGCGTCGCTAAAGGTCATGAGTCATGATCTATAGCGATGTTTGTGG
1 AAAAGCGTCGCT-AA----A--AGTCATGATCTATAGCGGCGTTTGTGG
*
43799886 AAAAGCGTCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
1 AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTGT-GG
*
43799929 ATAAGCGTCGCTAAA
1 AAAAGCGTCGCTAAA
43799944 GAACATGACC
Statistics
Matches: 169, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
42 34 0.20
43 75 0.44
44 20 0.12
47 1 0.01
48 2 0.01
49 37 0.22
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (42 bp):
AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGG
Found at i:43799882 original size:49 final size:49
Alignment explanation
Indices: 43799810--43799908 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
43799800 CGTCGCTAAA
*
43799810 AGTCATGATCTATAGCGGCGTTTGTGGAAAAGCGTCGCTAAAGGTCATG
1 AGTCATGATCTATAGCGACGTTTGTGGAAAAGCGTCGCTAAAGGTCATG
*
43799859 AGTCATGATCTATAGCGATGTTTGTGGAAAAGCGTCGCTAAAGGTCATG
1 AGTCATGATCTATAGCGACGTTTGTGGAAAAGCGTCGCTAAAGGTCATG
43799908 A
1 A
43799909 TCTATAGCGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (49 bp):
AGTCATGATCTATAGCGACGTTTGTGGAAAAGCGTCGCTAAAGGTCATG
Found at i:43799908 original size:91 final size:93
Alignment explanation
Indices: 43799767--43799944 Score: 288
Period size: 92 Copynumber: 1.9 Consensus size: 93
43799757 CGTCGCTAAA
* * *
43799767 AGTCATGATCTATAGTGGCGTTTGTGATAAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTT
1 AGTCATGATCTATAGCGACGTTTGTGAGAAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTT
43799832 TGT-GGAAAAGCGTCGCTAAAGGTCATG
66 TGTGGGAAAAGCGTCGCTAAAGGTCATG
* *
43799859 AGTCATGATCTATAGCGATGTTTGTG-GAAAAGCGTCGCTAAAGGTCATGATCTATAGCGGCGTT
1 AGTCATGATCTATAGCGACGTTTGTGAGAAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTT
*
43799923 TGTGGGATAAGCGTCGCTAAAG
66 TGTGGGAAAAGCGTCGCTAAAG
43799945 AACATGACCT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 39 0.49
92 40 0.51
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (93 bp):
AGTCATGATCTATAGCGACGTTTGTGAGAAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTT
TGTGGGAAAAGCGTCGCTAAAGGTCATG
Found at i:43799960 original size:43 final size:42
Alignment explanation
Indices: 43799862--43799960 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 42
43799852 GGTCATGAGT
* ** **
43799862 CATGATCTATAGCGATGTTTGTGGAAAAGCGTCGCTAAAGGT
1 CATGACCTATAGCGGCGTTTGTGGAAAAGCGTCGCTAAAGAA
* *
43799904 CATGATCTATAGCGGCGTTTGTGGGATAAGCGTCGCTAAAGAA
1 CATGACCTATAGCGGCGTTTGT-GGAAAAGCGTCGCTAAAGAA
*
43799947 CATGACCTTTAGCG
1 CATGACCTATAGCG
43799961 ACATTTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 20 0.41
43 29 0.59
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
CATGACCTATAGCGGCGTTTGTGGAAAAGCGTCGCTAAAGAA
Found at i:43801547 original size:30 final size:30
Alignment explanation
Indices: 43801486--43801548 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
43801476 CTTCTTGGGA
* *
43801486 TTGAGAAGACCTGATATCTCATTCAATAGC
1 TTGAGAAGACCTGATATCGCATTCAAGAGC
* *
43801516 TTGAGAAGA-CTCGATATCGCGTTCAGGAGC
1 TTGAGAAGACCT-GATATCGCATTCAAGAGC
43801546 TTG
1 TTG
43801549 GGATTGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (30 bp):
TTGAGAAGACCTGATATCGCATTCAAGAGC
Found at i:43801549 original size:66 final size:66
Alignment explanation
Indices: 43801441--43801591 Score: 221
Period size: 66 Copynumber: 2.3 Consensus size: 66
43801431 TACGAGGACG
* **
43801441 TTCAAGAGCTTGGGAAGACTCGATATCTCGTTCAGCTTCTTGGGATTGAGAAGACCTGATATCTC
1 TTCAAGAGCTTGGGAAGACTCGATATCGCGTTCAGCAGCTTGGGATTGAGAAGACCTGATATCTC
43801506 A
66 A
* * * *
43801507 TTCAATAGCTTGAGAAGACTCGATATCGCGTTCAGGAGCTTGGGATTGAGAAGACTTGATATCTC
1 TTCAAGAGCTTGGGAAGACTCGATATCGCGTTCAGCAGCTTGGGATTGAGAAGACCTGATATCTC
*
43801572 G
66 A
*
43801573 TTCAAGATCTTGGGAAGAC
1 TTCAAGAGCTTGGGAAGAC
43801592 CAAATATTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (66 bp):
TTCAAGAGCTTGGGAAGACTCGATATCGCGTTCAGCAGCTTGGGATTGAGAAGACCTGATATCTC
A
Found at i:43801585 original size:36 final size:35
Alignment explanation
Indices: 43801454--43801587 Score: 127
Period size: 36 Copynumber: 3.9 Consensus size: 35
43801444 AAGAGCTTGG
*
43801454 GAAGACTCGATATCTCGTTCAGCTTCTTGGGATTGA
1 GAAGACTCGATATCTCGTTCAG-ATCTTGGGATTGA
* * *
43801490 GAAGAC-CTGATATCTCATTCA-A---T-AGCTTGA
1 GAAGACTC-GATATCTCGTTCAGATCTTGGGATTGA
* *
43801520 GAAGACTCGATATCGCGTTCAGGAGCTTGGGATTGA
1 GAAGACTCGATATCTCGTTCA-GATCTTGGGATTGA
*
43801556 GAAGACTTGATATCTCGTTCAAGATCTTGGGA
1 GAAGACTCGATATCTCGTTC-AGATCTTGGGA
43801588 AGACCAAATA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
30 22 0.28
31 2 0.03
32 1 0.01
35 2 0.03
36 50 0.64
37 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (35 bp):
GAAGACTCGATATCTCGTTCAGATCTTGGGATTGA
Found at i:43812574 original size:22 final size:22
Alignment explanation
Indices: 43812546--43812611 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
43812536 GGGATGTCTA
* * *
43812546 AGAGCCCTTTATGGTACGTTTG
1 AGAGCCCTTTAGGGGACGTATG
43812568 AGAGCCCTTTAGGGGACGTATG
1 AGAGCCCTTTAGGGGACGTATG
* * *
43812590 CGAGCCCTCTAGGGGATGTATG
1 AGAGCCCTTTAGGGGACGTATG
43812612 GAAGTCCATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (22 bp):
AGAGCCCTTTAGGGGACGTATG
Found at i:43812683 original size:27 final size:27
Alignment explanation
Indices: 43812653--43812783 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 27
43812643 TGGCAGTCCA
43812653 CCAAGACAATCTAAATGTGGCAA-TCTG
1 CCAAGACAATCTAAATGTGG-AAGTCTG
** *
43812680 CCAAGATGATCT-AATGTGGAAGTTTG
1 CCAAGACAATCTAAATGTGGAAGTCTG
* * * **
43812706 TCAGGACAATATAAATGTGGAAGTCCA
1 CCAAGACAATCTAAATGTGGAAGTCTG
* * * * *
43812733 CGAGGACGATGT-AATGTGGAAGTTTG
1 CCAAGACAATCTAAATGTGGAAGTCTG
* **
43812759 TCAAGATGATCTAAATGTGGAAGTC
1 CCAAGACAATCTAAATGTGGAAGTC
43812784 CATCAGGATT
Statistics
Matches: 77, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
25 2 0.03
26 35 0.45
27 40 0.52
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (27 bp):
CCAAGACAATCTAAATGTGGAAGTCTG
Found at i:43818419 original size:43 final size:42
Alignment explanation
Indices: 43818328--43818439 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
43818318 TGTGATTTTG
* * * ** *
43818328 TGTAAGACCATGTTTGGGACATTGGCATCGTATATGATTTCG
1 TGTAAGACCATATTTGGGACAATGGCATCATATATGATAACA
* *
43818370 TGTAAGACCCTATTTGGGACAATGGCATCAATATATTATAACA
1 TGTAAGACCATATTTGGGACAATGGCATC-ATATATGATAACA
* *
43818413 TGTAAGACCATATCTGGGA-TATGGCAT
1 TGTAAGACCATATTTGGGACAATGGCAT
43818440 TGCACGAGCT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 33 0.57
43 25 0.43
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATATTTGGGACAATGGCATCATATATGATAACA
Found at i:43826799 original size:30 final size:30
Alignment explanation
Indices: 43826765--43826831 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 30
43826755 GTGACTCAGC
43826765 CGTGTGTGAGACAC-AGCTTGGCGACACAGT
1 CGTGTGTGAGACACGA-CTTGGCGACACAGT
43826795 CGTGTGTGAGACACGACTTGGCGACACAGT
1 CGTGTGTGAGACACGACTTGGCGACACAGT
43826825 CGTGTGT
1 CGTGTGT
43826832 CCCCTGTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (30 bp):
CGTGTGTGAGACACGACTTGGCGACACAGT
Found at i:43830802 original size:6 final size:6
Alignment explanation
Indices: 43830793--43830869 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
43830783 TATAAATCTA
* * * **
43830793 AAAAAT -AAAAT -AAAA- ACAAAT AACAAT AAAAAT AAAAGT ACGAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
43830838 AAAAAT AAAAAT --AAAT AAAATAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAA
43830870 TGAAATCACT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 34 0.61
7 6 0.11
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:43830822 original size:16 final size:15
Alignment explanation
Indices: 43830768--43830824 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
43830758 GTGTATAATA
43830768 AAATAAAAT-AAAAC
1 AAATAAAATAAAAAC
* **
43830782 ATAT-AAATCTAAA-
1 AAATAAAATAAAAAC
43830795 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
43830810 AAATAACAATAAAAA
1 AAATAA-AATAAAAA
43830825 TAAAAGTACG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 7 0.21
14 13 0.38
15 6 0.18
16 8 0.24
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:43830823 original size:27 final size:27
Alignment explanation
Indices: 43830761--43830829 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
43830751 AAAAAAAGTG
*
43830761 TATAATAAAATAAAATAAAACATATAAA
1 TATAA-AAAATAAAATAAAACAAATAAA
*
43830789 TCTAAAAAATAAAATAAAAACAAATAACA
1 TATAAAAAATAAAAT-AAAACAAATAA-A
43830818 -AT-AAAAATAAAA
1 TATAAAAAATAAAA
43830830 GTACGAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 20 0.56
28 15 0.42
29 1 0.03
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (27 bp):
TATAAAAAATAAAATAAAACAAATAAA
Found at i:43830828 original size:40 final size:41
Alignment explanation
Indices: 43830768--43830870 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 41
43830758 GTGTATAATA
43830768 AAATAAAATA-AAACATATAAATCTAAAAA-ATAAAATAAAAAC
1 AAATAAAATATAAA-A-ATAAATCTAAAAATA-AAAATAAAAAC
* ** ** *
43830810 AAATAACA-ATAAAAATAAAAGTACGAATAAAAATAAAAAT
1 AAATAAAATATAAAAATAAATCTAAAAATAAAAATAAAAAC
43830850 AAATAAAATATAAAAATAAAT
1 AAATAAAATATAAAAATAAAT
43830871 GAAATCACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
40 26 0.52
41 14 0.28
42 10 0.20
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (41 bp):
AAATAAAATATAAAAATAAATCTAAAAATAAAAATAAAAAC
Found at i:43830844 original size:24 final size:22
Alignment explanation
Indices: 43830793--43830869 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 22
43830783 TATAAATCTA
43830793 AAAAAT-AAAATAAAAACAAAT
1 AAAAATAAAAATAAAAACAAAT
* *
43830814 AACAATAAAAATAAAAGTACGAAT
1 AAAAATAAAAATAAAA--ACAAAT
43830838 AAAAATAAAAATAAATAA-AATAT
1 AAAAATAAAAATAAA-AACAA-AT
43830861 AAAAATAAA
1 AAAAATAAA
43830870 TGAAATCACT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
21 5 0.11
22 10 0.21
23 12 0.26
24 19 0.40
25 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:43830864 original size:17 final size:16
Alignment explanation
Indices: 43830793--43830870 Score: 77
Period size: 16 Copynumber: 4.6 Consensus size: 16
43830783 TATAAATCTA
*
43830793 AAAAATAAAATAAAAAC
1 AAAAAT-AAATAAAAAT
*
43830810 AAATAA-CAATAAAAAT
1 AAA-AATAAATAAAAAT
*
43830826 AAAAGTACGAATAAAAAT
1 AAAAATA--AATAAAAAT
43830844 AAAAATAAATAAAATAT
1 AAAAATAAATAAAA-AT
43830861 AAAAATAAAT
1 AAAAATAAAT
43830871 GAAATCACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 18 0.35
17 15 0.29
18 17 0.33
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:43830870 original size:12 final size:11
Alignment explanation
Indices: 43830767--43830869 Score: 66
Period size: 12 Copynumber: 8.7 Consensus size: 11
43830757 AGTGTATAAT
43830767 AAAATAAAATA
1 AAAATAAAATA
43830778 AAACATATAAATCTAA
1 AAA-ATA-AAA--T-A
43830794 AAAATAAAATA
1 AAAATAAAATA
*
43830805 AAAA-CAAATA
1 AAAATAAAATA
*
43830815 ACAATAAAAATA
1 AAAAT-AAAATA
* *
43830827 AAAGTACGAATA
1 AAAATA-AAATA
43830839 AAAATAAAAATA
1 AAAAT-AAAATA
*
43830851 AATAA-AATATA
1 AA-AATAAAATA
43830862 AAAATAAA
1 AAAATAAA
43830870 TGAAATCACT
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
10 10 0.14
11 18 0.25
12 26 0.37
13 6 0.08
14 3 0.04
15 4 0.06
16 4 0.06
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:43830875 original size:17 final size:17
Alignment explanation
Indices: 43830817--43830875 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
43830807 AACAAATAAC
*
43830817 AATAAAA-ATAAAAGTA
1 AATAAAATATAAAAATA
43830833 CGAATAAAA-ATAAAAATA
1 --AATAAAATATAAAAATA
43830851 AATAAAATATAAAAATA
1 AATAAAATATAAAAATA
*
43830868 AATGAAAT
1 AATAAAAT
43830876 CACTTCTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 7 0.18
17 16 0.42
18 15 0.39
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (17 bp):
AATAAAATATAAAAATA
Found at i:43831348 original size:21 final size:22
Alignment explanation
Indices: 43831324--43831366 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43831314 TTTTCAAAAC
* *
43831324 GTTTTAGAT-TTTTTCCTTTTT
1 GTTTTAAATCTTTTTCATTTTT
43831345 GTTTTAAATCTTTTTCATTTTT
1 GTTTTAAATCTTTTTCATTTTT
43831367 TAAGTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (22 bp):
GTTTTAAATCTTTTTCATTTTT
Found at i:43834578 original size:33 final size:33
Alignment explanation
Indices: 43834519--43834630 Score: 136
Period size: 33 Copynumber: 3.4 Consensus size: 33
43834509 CTATGGCCTC
* * *
43834519 AATAGAGTAAGTCTACCA-AGAGAGTAAACACAA
1 AATAGAGTAAGTCCA-TAGAGACAGTAAACACAA
* * *
43834552 AATAGAGTAGGTCCATAGGGACAGTAAACACAT
1 AATAGAGTAAGTCCATAGAGACAGTAAACACAA
*
43834585 AATAGAGTAAGTCCATCGAGACAGTAAACACAA
1 AATAGAGTAAGTCCATAGAGACAGTAAACACAA
*
43834618 AATAAAGTAAGTC
1 AATAGAGTAAGTC
43834631 TACTAGACTA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
32 1 0.01
33 66 0.99
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (33 bp):
AATAGAGTAAGTCCATAGAGACAGTAAACACAA
Found at i:43834644 original size:33 final size:33
Alignment explanation
Indices: 43834519--43834649 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 33
43834509 CTATGGCCTC
* * *
43834519 AATAGAGTAAGTCTACCAAGAGAGTAAACACAA
1 AATAGAGTAAGTCCACCTAGACAGTAAACACAA
* *
43834552 AATAGAGTAGGTCCA--TAGGGACAGTAAACACAT
1 AATAGAGTAAGTCCACCTA--GACAGTAAACACAA
* *
43834585 AATAGAGTAAGTCCATCGAGACAGTAAACACAA
1 AATAGAGTAAGTCCACCTAGACAGTAAACACAA
* *
43834618 AATAAAGTAAGTCTA-CTAGACTAGTAAACACA
1 AATAGAGTAAGTCCACCTAGAC-AGTAAACACA
43834650 GAACAGAGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
31 1 0.01
32 5 0.06
33 75 0.91
35 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (33 bp):
AATAGAGTAAGTCCACCTAGACAGTAAACACAA
Found at i:43834644 original size:66 final size:65
Alignment explanation
Indices: 43834519--43834649 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 65
43834509 CTATGGCCTC
* * * *
43834519 AATAGAGTAAGTCTACCAAGAGAGTAAACACAAAATAGAGTAGGTCCATAGGGACAGTAAACACA
1 AATAGAGTAAGTCCACCAAGACAGTAAACACAAAATAAAGTAAGTCCATA-GGACAGTAAACACA
43834584 T
65 T
* * *
43834585 AATAGAGTAAGTCCATCGAGACAGTAAACACAAAATAAAGTAAGTCTACTA-GACTAGTAAACAC
1 AATAGAGTAAGTCCACCAAGACAGTAAACACAAAATAAAGTAAGTCCA-TAGGAC-AGTAAACAC
43834649 A
64 A
43834650 GAACAGAGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 3 0.05
66 51 0.91
67 2 0.04
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (65 bp):
AATAGAGTAAGTCCACCAAGACAGTAAACACAAAATAAAGTAAGTCCATAGGACAGTAAACACAT
Found at i:43834679 original size:66 final size:65
Alignment explanation
Indices: 43834543--43834691 Score: 149
Period size: 66 Copynumber: 2.3 Consensus size: 65
43834533 ACCAAGAGAG
* * * * *
43834543 TAAACACAAAATAGAGTAGGTCCATAGGGACAGTAAACACATAATAGAGTAAGTCCATCGAGACA
1 TAAACACAAAATAAAGTAAGTCCATA-GGACAGTAAACACAGAACAGAGTAAGTACATCGAGACA
*
43834608 G
65 A
* * *
43834609 TAAACACAAAATAAAGTAAGTCTACTA-GACTAGTAAACACAGAACAGAG-ATAGTACATTGGGA
1 TAAACACAAAATAAAGTAAGTCCA-TAGGAC-AGTAAACACAGAACAGAGTA-AGTACATCGAGA
43834672 CAA
63 CAA
* *
43834675 TAAACACGAGATAAAGT
1 TAAACACAAAATAAAGT
43834692 CTACCGAGAC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
65 4 0.06
66 63 0.91
67 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.17
Consensus pattern (65 bp):
TAAACACAAAATAAAGTAAGTCCATAGGACAGTAAACACAGAACAGAGTAAGTACATCGAGACAA
Found at i:43842799 original size:29 final size:29
Alignment explanation
Indices: 43842763--43842824 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
43842753 TGGTTATACC
*
43842763 ATCCCTTTCCAT-AATTCGATAGCCGAAGCT
1 ATCCTTTTCCATGAA-TCGATAGCCG-AGCT
* *
43842793 ATCCTTTTTCATGAATCGATAGTCGAGCT
1 ATCCTTTTCCATGAATCGATAGCCGAGCT
43842822 ATC
1 ATC
43842825 TATATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.25
30 19 0.68
31 2 0.07
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (29 bp):
ATCCTTTTCCATGAATCGATAGCCGAGCT
Found at i:43842913 original size:29 final size:29
Alignment explanation
Indices: 43842760--43843157 Score: 232
Period size: 29 Copynumber: 13.5 Consensus size: 29
43842750 TGATGGTTAT
* *
43842760 ACCATCCCTTTCCATAATTCGATAGCCGAA
1 ACCATCCCTTTTCAT-ATTCGATAGTCGAA
* * * *
43842790 GCTATCCTTTTTCATGAATCGATAGTCG-A
1 ACCATCCCTTTTCAT-ATTCGATAGTCGAA
* * ** * * * **
43842819 GCTATCTATATTCATAATTTTGATGGTCGTC
1 ACCATCCCTTTTCAT-A-TTCGATAGTCGAA
* * **
43842850 ACCATCCCTTTTCATAATTTTGATGGTCGTC
1 ACCATCCCTTTTCAT-A-TTCGATAGTCGAA
* *
43842881 ACCATCCCTTTTCATATTCGATGGTCAAA
1 ACCATCCCTTTTCATATTCGATAGTCGAA
*
43842910 ACCATCCCTTTTCATATTCGATAGCCGAA
1 ACCATCCCTTTTCATATTCGATAGTCGAA
* * * **
43842939 GCTATCCCTCTTT-ATATTCGATGGTCGTC
1 ACCATCCCT-TTTCATATTCGATAGTCGAA
* * * * *
43842968 ACCATCCATTTTCGTAGTT-AATGGTC-ATC
1 ACCATCCCTTTTCATA-TTCGATAGTCGA-A
** *
43842997 ACCATCCCTTTTCATAAGCGATAGCCGAA
1 ACCATCCCTTTTCATATTCGATAGTCGAA
* *
43843026 GCTATCCCTTTTCATATTCGATAGTC-AA
1 ACCATCCCTTTTCATATTCGATAGTCGAA
* *
43843054 AGCTATCCCTTTTCATATTCGATAG-CTAA
1 A-CCATCCCTTTTCATATTCGATAGTCGAA
* **
43843083 AGCTATCCCTTTTCATATTCGATAGTCGTC
1 A-CCATCCCTTTTCATATTCGATAGTCGAA
* * *
43843113 ACCATCCATTTTCATTGTTCGATAGTTGAA
1 ACCATCCCTTTTCA-TATTCGATAGTCGAA
*
43843143 ACTATCCCTTTTCAT
1 ACCATCCCTTTTCAT
43843158 TAGTAGATGA
Statistics
Matches: 292, Mismatches: 64, Indels: 25
0.77 0.17 0.07
Matches are distributed among these distances:
28 6 0.02
29 184 0.63
30 61 0.21
31 41 0.14
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATAGTCGAA
Found at i:43842970 original size:87 final size:87
Alignment explanation
Indices: 43842853--43843107 Score: 293
Period size: 87 Copynumber: 2.9 Consensus size: 87
43842843 GGTCGTCACC
*
43842853 ATCCCTTTTCATAATTTTGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCAAAACCATCCC
1 ATCCCTTTTCAT-A-TTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCAAAACCATCCC
43842918 TTTTCATATTCGATAGCCGAAGCT
64 TTTTCATATTCGATAGCCGAAGCT
* * * **
43842942 ATCCCTCTTT-ATATTCGATGGTCGTCACCATCCATTTTCGTAGTT-AATGGTCATCACCATCCC
1 ATCCCT-TTTCATATTCGATGGTCGTCACCATCCCTTTTCATA-TTCGATGGTCAAAACCATCCC
**
43843005 TTTTCATAAGCGATAGCCGAAGCT
64 TTTTCATATTCGATAGCCGAAGCT
* ** * * * *
43843029 ATCCCTTTTCATATTCGATAGTC-AAAGCTATCCCTTTTCATATTCGATAG-CTAAAGCTATCCC
1 ATCCCTTTTCATATTCGATGGTCGTCA-CCATCCCTTTTCATATTCGATGGTC-AAAACCATCCC
43843092 TTTTCATATTCGATAG
64 TTTTCATATTCGATAG
43843108 TCGTCACCAT
Statistics
Matches: 138, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
86 7 0.05
87 117 0.85
88 3 0.02
89 8 0.06
90 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (87 bp):
ATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCAAAACCATCCCTT
TTCATATTCGATAGCCGAAGCT
Found at i:43862095 original size:68 final size:70
Alignment explanation
Indices: 43862023--43862156 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 70
43862013 TTTAATAATT
* * *
43862023 TTAATATTAAATTTAATTTATTACTTATC-AAAAT-AGTATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAATTAAATTTAATACTTATCTAAAATAAATATTTTATTAATTTAATATTAAAGTGA
43862086 TTATC
66 TTATC
* *
43862091 TTAATATTAAATTAAATTTAATATTTATCTTTGAAATAAATATTTTATTAATTTAATATTAAAGT
1 TTAATATTAAATTAAATTTAATACTTATC--TAAAATAAATATTTTATTAATTTAATATTAAAGT
43862156 G
64 G
43862157 TGTGTTAGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 26 0.46
71 4 0.07
72 27 0.47
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (70 bp):
TTAATATTAAATTAAATTTAATACTTATCTAAAATAAATATTTTATTAATTTAATATTAAAGTGA
TTATC
Found at i:43863802 original size:4 final size:4
Alignment explanation
Indices: 43863793--43863820 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
43863783 TTAAACTAAG
43863793 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
43863821 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:43865226 original size:23 final size:22
Alignment explanation
Indices: 43865174--43865226 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
43865164 TCCACGTCTT
*
43865174 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
43865196 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
43865219 TTTCTTTT
1 TTTCTTTT
43865227 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:43876204 original size:43 final size:43
Alignment explanation
Indices: 43876151--43876452 Score: 365
Period size: 43 Copynumber: 6.9 Consensus size: 43
43876141 TTTTAGAACT
* * * *
43876151 AACGCTGCTAAAGGTCATGACCTTTAGCGGCGCTTTTTCCACA
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
* * * * *
43876194 AACGCCGCTAAAGATCATGACTTTTAACAGCGCTTTTCCCTCA
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
* *
43876237 AATGACGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
*
43876280 AACGCCGCTATAGATCATGACTTTTAGCAGTGC-CTTTCT-CACA
1 AACGCCGCTATAGATCATGACTTTTAGC-G-GCGCTTTTTCCACA
* *
43876323 AACGCCGCTATAGATCATGACTTTTAGCGACACTTTTTCCACA
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
* * *
43876366 AACGCCGCTATAGATCATGATCATGACTTTTAGCGGTGCCTTTCCCACA
1 AACGCCGC--T--AT-A-GATCATGACTTTTAGCGGCGCTTTTTCCACA
43876415 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTT
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTT
43876453 TTATAAAAGC
Statistics
Matches: 222, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.00
42 6 0.03
43 165 0.74
44 7 0.03
45 5 0.02
47 3 0.01
48 1 0.00
49 34 0.15
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (43 bp):
AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACA
Found at i:43876263 original size:86 final size:86
Alignment explanation
Indices: 43876151--43876452 Score: 415
Period size: 86 Copynumber: 3.4 Consensus size: 86
43876141 TTTTAGAACT
* * * *
43876151 AACGCTGCTAAAGGTCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGACT
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGACT
* * * *
43876216 TTTAACAGCGCTTTTCCCTCA
66 TTTAGCAGTGCCTTTCCCACA
* * *
43876237 AATGACGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGATCATGACT
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGACT
*
43876302 TTTAGCAGTGCCTTTCTCACA
66 TTTAGCAGTGCCTTTCCCACA
* *
43876323 AACGCCGCTATAGATCATGACTTTTAGCGACACTTTTTCCACAAACGCCGCTATAGATCATGATC
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCGC--TA-A--A-GATC
*
43876388 ATGACTTTTAGCGGTGCCTTTCCCACA
60 ATGACTTTTAGCAGTGCCTTTCCCACA
43876415 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTT
1 AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTT
43876453 TTATAAAAGC
Statistics
Matches: 189, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
86 121 0.64
88 2 0.01
91 1 0.01
92 65 0.34
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (86 bp):
AACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGACT
TTTAGCAGTGCCTTTCCCACA
Found at i:43876840 original size:9 final size:9
Alignment explanation
Indices: 43876826--43877062 Score: 80
Period size: 9 Copynumber: 27.7 Consensus size: 9
43876816 GCATTAGCTT
43876826 TAAGTTATG
1 TAAGTTATG
*
43876835 TAAGTTATA
1 TAAGTTATG
*
43876844 T-A-TTAAG
1 TAAGTTATG
*
43876851 TAAATTATG
1 TAAGTTATG
43876860 TAAG-T-TG
1 TAAGTTATG
* *
43876867 T--CTTATA
1 TAAGTTATG
43876874 TAAGTTATG
1 TAAGTTATG
43876883 T-A-TTATG
1 TAAGTTATG
43876890 TAAGTTATG
1 TAAGTTATG
43876899 TATA-TATCATAG
1 TA-AGT-T-AT-G
43876911 T-A-TTATG
1 TAAGTTATG
**
43876918 TATTTTATG
1 TAAGTTATG
43876927 TAAGTTATG
1 TAAGTTATG
*
43876936 T--CTTATG
1 TAAGTTATG
*
43876943 TAGGTTATG
1 TAAGTTATG
43876952 TAAGTTATG
1 TAAGTTATG
43876961 T-A-TTATG
1 TAAGTTATG
*
43876968 TAAGTTATA
1 TAAGTTATG
* *
43876977 TAAATATTTG
1 TAAGT-TATG
** *
43876987 T-CTTTGTG
1 TAAGTTATG
43876995 T-A-TTATG
1 TAAGTTATG
* *
43877002 TAACTTATA
1 TAAGTTATG
*
43877011 TAATTTATG
1 TAAGTTATG
*
43877020 TAGGTTATG
1 TAAGTTATG
43877029 TATTA-TTATG
1 TA--AGTTATG
*
43877039 TAAGTTTTG
1 TAAGTTATG
**
43877048 TCGGTTATG
1 TAAGTTATG
43877057 TAAGTT
1 TAAGTT
43877063 GTAATATGAT
Statistics
Matches: 168, Mismatches: 36, Indels: 48
0.67 0.14 0.19
Matches are distributed among these distances:
6 1 0.01
7 34 0.20
8 15 0.09
9 100 0.60
10 14 0.08
11 2 0.01
12 2 0.01
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (9 bp):
TAAGTTATG
Found at i:43876893 original size:16 final size:16
Alignment explanation
Indices: 43876854--43877150 Score: 93
Period size: 16 Copynumber: 18.1 Consensus size: 16
43876844 TATTAAGTAA
43876854 ATTATGTAAG-T-TGT
1 ATTATGTAAGTTATGT
* *
43876868 CTTATATAAGTTATGT
1 ATTATGTAAGTTATGT
43876884 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* *
43876900 A-TATATCA--TA-GT
1 ATTATGTAAGTTATGT
**
43876912 ATTATGTATTTTATGT
1 ATTATGTAAGTTATGT
*
43876928 AAGTTATGT--CTTATGT
1 -A-TTATGTAAGTTATGT
43876944 AGGTTATGTAAGTTATGT
1 A--TTATGTAAGTTATGT
*
43876962 ATTATGTAAGTTATAT
1 ATTATGTAAGTTATGT
* ** *
43876978 AAATATTTGT-CTTTGTGT
1 --AT-TATGTAAGTTATGT
* *
43876996 ATTATGTAACTTATAT
1 ATTATGTAAGTTATGT
*
43877012 AATTTATGTAGGTTATGTATT
1 -A-TTATGTAAGTTATG---T
*
43877033 ATTATGTAAGTTTTGT
1 ATTATGTAAGTTATGT
*
43877049 CGGTTATGTAAG-T-TGT
1 --ATTATGTAAGTTATGT
* *
43877065 AATATGATTAA--TATTT
1 ATTATG--TAAGTTATGT
43877081 ATGTATGTAAGTTATGAT
1 AT-TATGTAAGTTATG-T
* *
43877099 ATGATTGATAAGTT-T-C
1 ATTA-TG-TAAGTTATGT
*
43877115 AGTTATATAAGTTATGT
1 A-TTATGTAAGTTATGT
43877132 ATTATGTAAGTTTATGT
1 ATTATGTAAG-TTATGT
43877149 AT
1 AT
43877151 GTAGGTTATG
Statistics
Matches: 209, Mismatches: 39, Indels: 67
0.66 0.12 0.21
Matches are distributed among these distances:
12 3 0.01
13 6 0.03
14 12 0.06
15 23 0.11
16 74 0.35
17 22 0.11
18 45 0.22
19 22 0.11
20 1 0.00
21 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:43876950 original size:25 final size:25
Alignment explanation
Indices: 43876869--43876975 Score: 126
Period size: 25 Copynumber: 4.2 Consensus size: 25
43876859 GTAAGTTGTC
*
43876869 TTATATAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
**
43876894 TTATGTATA-TATCATAGTATTATGTATT
1 TTATGTA-AGT-T-AT-GTATTATGTAAG
* *
43876922 TTATGTAAGTTATGTCTTATGTAGG
1 TTATGTAAGTTATGTATTATGTAAG
43876947 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
43876972 TTAT
1 TTAT
43876976 ATAAATATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
25 43 0.62
26 4 0.06
27 4 0.06
28 18 0.26
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:43877031 original size:34 final size:36
Alignment explanation
Indices: 43876947--43877034 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 36
43876937 CTTATGTAGG
*
43876947 TTATGTAAGTTATGTATTATGTAAGTTATATAAATA
1 TTATGTAAGTTATGTATTATGTAACTTATATAAATA
** *
43876983 TT-TGT-CTTTGTGTATTATGTAACTTATAT-AAT-
1 TTATGTAAGTTATGTATTATGTAACTTATATAAATA
*
43877015 TTATGTAGGTTATGTATTAT
1 TTATGTAAGTTATGTATTAT
43877035 TATGTAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
32 2 0.05
33 6 0.14
34 30 0.70
35 3 0.07
36 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (36 bp):
TTATGTAAGTTATGTATTATGTAACTTATATAAATA
Found at i:43877161 original size:23 final size:23
Alignment explanation
Indices: 43877133--43877176 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
43877123 AAGTTATGTA
43877133 TTATGTAAGTTTATGT-ATGTAGG
1 TTATGTAAG-TTATGTAATGTAGG
43877156 TTATGTAAGTTATGTAATGTA
1 TTATGTAAGTTATGTAATGTA
43877177 TCAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
TTATGTAAGTTATGTAATGTAGG
Found at i:43877239 original size:19 final size:18
Alignment explanation
Indices: 43877187--43877240 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
43877177 TCAATTTTTA
*
43877187 AAAATATATATAAATTTT
1 AAAATATATATAAATATT
*
43877205 AAAA-ATATAT--ACATT
1 AAAATATATATAAATATT
43877220 AAAACTATATATAAATATT
1 AAAA-TATATATAAATATT
43877239 AA
1 AA
43877241 TAAGTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 7 0.24
17 12 0.41
18 4 0.14
19 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATATATATAAATATT
Found at i:43877445 original size:21 final size:21
Alignment explanation
Indices: 43877421--43877560 Score: 101
Period size: 21 Copynumber: 6.5 Consensus size: 21
43877411 TTTATATTGA
**
43877421 AAATATATATATTAATAAGTT
1 AAATATATATATTAATATTTT
* *
43877442 AAAT-TAAATTTTAAAATTATATTT
1 AAATATATATATT--AA-TAT-TTT
43877466 AAA-ATATATATTAA-ATTTT
1 AAATATATATATTAATATTTT
* *
43877485 AAAAATATATATACTAATTTTTTT
1 --AAATATATATATTAA-TATTTT
43877509 AAAATATATATATTAA-ATTTT
1 -AAATATATATATTAATATTTT
*
43877530 AAAATATATATATTAA-ATCTT
1 -AAATATATATATTAATATTTT
43877551 AAATATATAT
1 AAATATATAT
43877561 TAATAAGTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 21
0.75 0.08 0.16
Matches are distributed among these distances:
19 3 0.03
20 18 0.18
21 31 0.32
22 14 0.14
23 17 0.17
24 15 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
AAATATATATATTAATATTTT
Found at i:43877463 original size:31 final size:30
Alignment explanation
Indices: 43877427--43877494 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
43877417 TTGAAAATAT
43877427 ATATATTAATAAGT-TAAATTAAATTTTAAAA
1 ATATATTAA-AA-TATAAATTAAATTTTAAAA
* *
43877458 TTATATTTAAAATATATATTAAATTTTAAAA
1 ATATA-TTAAAATATAAATTAAATTTTAAAA
43877489 ATATAT
1 ATATAT
43877495 ATACTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.06
31 26 0.81
32 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATATTAAAATATAAATTAAATTTTAAAA
Found at i:43878713 original size:19 final size:19
Alignment explanation
Indices: 43878689--43878729 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
43878679 AGGTTAAGAC
43878689 ATATATAAATCTTCATTGA
1 ATATATAAATCTTCATTGA
*
43878708 ATATATATATCTTCATTGA
1 ATATATAAATCTTCATTGA
43878727 ATA
1 ATA
43878730 ACATATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATATAAATCTTCATTGA
Found at i:43879554 original size:14 final size:14
Alignment explanation
Indices: 43879535--43879567 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
43879525 AAGTTACAGT
43879535 TCCTACACTTTGAC
1 TCCTACACTTTGAC
43879549 TCCTACACTTTGAC
1 TCCTACACTTTGAC
43879563 TCCTA
1 TCCTA
43879568 TCCAGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (14 bp):
TCCTACACTTTGAC
Found at i:43879840 original size:28 final size:28
Alignment explanation
Indices: 43879800--43879857 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
43879790 GTGATTGAAG
*
43879800 TTGGTATCTAAACCCTAAATTCCCAAAT
1 TTGGTATCTAAACCCCAAATTCCCAAAT
43879828 TTGGTATCTAAACCCCAAATTCCCAAAT
1 TTGGTATCTAAACCCCAAATTCCCAAAT
43879856 TT
1 TT
43879858 CACTAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (28 bp):
TTGGTATCTAAACCCCAAATTCCCAAAT
Found at i:43880066 original size:18 final size:20
Alignment explanation
Indices: 43880037--43880078 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
43880027 CGTTTCTAAT
43880037 TTCTGATTTCCTCCTTTG-C
1 TTCTGATTTCCTCCTTTGCC
*
43880056 TTCTG-TTTCCTTCTTTGCC
1 TTCTGATTTCCTCCTTTGCC
43880075 TTCT
1 TTCT
43880079 AGGATTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.02, C:0.31, G:0.10, T:0.57
Consensus pattern (20 bp):
TTCTGATTTCCTCCTTTGCC
Found at i:43880819 original size:40 final size:40
Alignment explanation
Indices: 43880753--43880828 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
43880743 CATTTTTCCC
* *
43880753 AAAAATGCCACAAATGCCTATTTTTAGCGGC-ATTTTTAA
1 AAAAATGCCACAAATGCCGATCTTTAGCGGCGATTTTTAA
* *
43880792 AAAAATGCCACTAATTCTCGATCTTTAGCGGCGATTT
1 AAAAATGCCACAAATGC-CGATCTTTAGCGGCGATTT
43880829 CCATAAAGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 15 0.48
40 12 0.39
41 4 0.13
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (40 bp):
AAAAATGCCACAAATGCCGATCTTTAGCGGCGATTTTTAA
Found at i:43888334 original size:17 final size:18
Alignment explanation
Indices: 43888312--43888348 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43888302 AAGTTTTATA
*
43888312 ATTTTTAGTATAT-TTTT
1 ATTTTTAATATATATTTT
43888329 ATTTTTAATATATATTTT
1 ATTTTTAATATATATTTT
43888347 AT
1 AT
43888349 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTAATATATATTTT
Found at i:43896677 original size:22 final size:23
Alignment explanation
Indices: 43896633--43896682 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
43896623 GAAGAATTCT
*
43896633 GAAGTTAAATGAGAGGTTTTGCAG
1 GAAGTTAAACGAGA-GTTTTGCAG
43896657 GAAGTTAAACGAGA-TTTTGCAG
1 GAAGTTAAACGAGAGTTTTGCAG
43896679 GAAG
1 GAAG
43896683 CTCACTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.36, C:0.06, G:0.32, T:0.26
Consensus pattern (23 bp):
GAAGTTAAACGAGAGTTTTGCAG
Found at i:43901768 original size:19 final size:18
Alignment explanation
Indices: 43901732--43901774 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
43901722 AAAATTTAGA
43901732 AAATAT-TTAAAAATTTT
1 AAATATATTAAAAATTTT
*
43901749 AAATATATTAAATATATTT
1 AAATATATTAAAAAT-TTT
*
43901768 ATATATA
1 AAATATA
43901775 AATGGAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATATTAAAAATTTT
Found at i:43902717 original size:14 final size:14
Alignment explanation
Indices: 43902695--43902724 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43902685 TAAACAAAAA
*
43902695 TTAATATATATATT
1 TTAAAATATATATT
43902709 TTAAAATATATATT
1 TTAAAATATATATT
43902723 TT
1 TT
43902725 GTTAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAAATATATATT
Found at i:43911566 original size:55 final size:55
Alignment explanation
Indices: 43911507--43911830 Score: 409
Period size: 55 Copynumber: 5.9 Consensus size: 55
43911497 ACATTCTTAA
* * * *
43911507 ATGTGGAAAGTCCGCCAAGACAATCTTATGTGGAAGTCCATAAGGACTATCTGAT
1 ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * * *
43911562 ATGTGGAAAGTTCGCTAGGACTATCTTATGTGGAAGTCTGTGTGGACTATCTGAT
1 ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * * *
43911617 ATG-GAGAAAGTCCACCATGACTATCTTATATGGAAGTCCATGAGGACTATCTGAT
1 ATGTG-GAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * * *
43911672 ATGTGGAAAGTCGGTCAGGACTCTCTTATGTGGAAGTCCGTAAGGACTATCTGAT
1 ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * *
43911727 ATGAGGAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGGT
1 ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * ** *
43911782 ATG-GGGAATTCCGTTAGGACTATCTTATGTAGAAGTCCGTGAGGACTAT
1 ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTAT
43911831 TTGGTATAGG
Statistics
Matches: 230, Mismatches: 37, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
54 41 0.18
55 188 0.82
56 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (55 bp):
ATGTGGAAAGTCCGCCAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
Found at i:43911671 original size:110 final size:110
Alignment explanation
Indices: 43911511--43911847 Score: 450
Period size: 110 Copynumber: 3.1 Consensus size: 110
43911501 TCTTAAATGT
* *
43911511 GGAAAGTCCGCCAAGACAATCTTATGTGGAAGTCCATAAGGACTATCTGATATGTGGAAAGTTCG
1 GGAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCATGAGGACTATCTGATATGTGGAAAGTTCG
* *
43911576 CTAGGACTATCTTATGTGGAAGTCTGTGTGGACTATCTGATATG-
66 CTAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGA
* * *
43911620 GAGAAAGTCCACCATGACTATCTTATATGGAAGTCCATGAGGACTATCTGATATGTGGAAAG-TC
1 G-GAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCATGAGGACTATCTGATATGTGGAAAGTTC
* * *
43911684 GGTCAGGACTCTCTTATGTGGAAGTCCGTAAGGACTATCTGATATGA
65 GCT-AGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGA
* * *
43911731 GGAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGGTATG-GGGAA-TTCC
1 GGAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCATGAGGACTATCTGATATGTGGAAAGTT-C
* * * *
43911794 GTTAGGACTATCTTATGTAGAAGTCCGTGAGGACTATTTGGTAT-A
65 GCTAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGA
*
43911839 GGGAAGTCC
1 GGAAAGTCC
43911848 ATCAGGACTA
Statistics
Matches: 200, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
108 9 0.05
109 46 0.23
110 144 0.72
111 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (110 bp):
GGAAAGTCCGCCAAGACTATCTTATGTGGAAGTCCATGAGGACTATCTGATATGTGGAAAGTTCG
CTAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGA
Found at i:43913997 original size:30 final size:30
Alignment explanation
Indices: 43913946--43914002 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
43913936 CATAAATATT
*
43913946 AAATTATTATAATAATTATAAAGTAGAGTC
1 AAATTATTATAATAATAATAAAGTAGAGTC
* *
43913976 AAATTATTA-AATTATCAATAAATTAGA
1 AAATTATTATAATAAT-AATAAAGTAGA
43914003 CTAAAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (30 bp):
AAATTATTATAATAATAATAAAGTAGAGTC
Found at i:43917359 original size:4 final size:4
Alignment explanation
Indices: 43917338--43917372 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
43917328 GTTGTAAAGT
*
43917338 TTTA TTTT TTTA -TTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
43917373 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:43921957 original size:25 final size:23
Alignment explanation
Indices: 43921929--43921978 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
43921919 GAACAAAAAG
43921929 AAAATAT-TTTATGTTTAAAATATTT
1 AAAATATATTT-T-TTTAAAA-ATTT
43921954 AAAATATATTTTTTTAAAAATTT
1 AAAATATATTTTTTTAAAAATTT
43921977 AA
1 AA
43921979 TTAATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 7 0.29
25 8 0.33
26 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATATATTTTTTTAAAAATTT
Done.