Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 122 of 190
Found at i:19281560 original size:16 final size:17
Alignment explanation
Indices: 19281529--19281570 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19281519 TAACCTAAAG
19281529 TTTTATTTATTTATATA
1 TTTTATTTATTTATATA
*
19281546 TTTTATTTA-TTATATT
1 TTTTATTTATTTATATA
*
19281562 TTTTGTTTA
1 TTTTATTTA
19281571 ATCTCGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTATATA
Found at i:19282245 original size:8 final size:8
Alignment explanation
Indices: 19282232--19282256 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19282222 TTCTACTCTG
19282232 CTTTGCTT
1 CTTTGCTT
19282240 CTTTGCTT
1 CTTTGCTT
19282248 CTTTGCTT
1 CTTTGCTT
19282256 C
1 C
19282257 GTCGCTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.12, T:0.60
Consensus pattern (8 bp):
CTTTGCTT
Found at i:19282263 original size:16 final size:16
Alignment explanation
Indices: 19282232--19282265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19282222 TTCTACTCTG
* *
19282232 CTTTGCTTCTTTGCTT
1 CTTTGCTTCGTCGCTT
19282248 CTTTGCTTCGTCGCTT
1 CTTTGCTTCGTCGCTT
19282264 CT
1 CT
19282266 CCCCTTCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.15, T:0.56
Consensus pattern (16 bp):
CTTTGCTTCGTCGCTT
Found at i:19283118 original size:16 final size:15
Alignment explanation
Indices: 19283097--19283148 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
19283087 TTTATTATTT
19283097 TTTATTACTTAATATA
1 TTTATTA-TTAATATA
*
19283113 TTTATTTATTATTATA
1 TTTA-TTATTAATATA
* * *
19283129 TTTATTTTTTATATT
1 TTTATTATTAATATA
19283144 TTTAT
1 TTTAT
19283149 ATTCGTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 12 0.40
16 15 0.50
17 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTATTAATATA
Found at i:19283120 original size:20 final size:17
Alignment explanation
Indices: 19283075--19283140 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 17
19283065 CTCTTTTTAC
* *
19283075 ATTTATTTACTATTTATT
1 ATTT-TTTATTATTAATT
19283093 ATTTTTTATTACTTAATAT
1 ATTTTTTATTA-TTAAT-T
19283112 ATTTATTTATTATTATATTT
1 ATTT-TTTATTATTA-A-TT
19283132 ATTTTTTAT
1 ATTTTTTAT
19283141 ATTTTTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 13 0.32
20 13 0.32
21 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTATTATTAATT
Found at i:19283144 original size:13 final size:16
Alignment explanation
Indices: 19283085--19283140 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
19283075 ATTTATTTAC
19283085 TATTTATTATT-T-TT
1 TATTTATTATTATATT
*
19283099 TA-TTACTTAATATATT
1 TATTTA-TTATTATATT
19283115 TATTTATTATTATATT
1 TATTTATTATTATATT
*
19283131 TATTTTTTAT
1 TATTTATTAT
19283141 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 3 0.09
14 6 0.17
15 1 0.03
16 22 0.63
17 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTATTATATT
Found at i:19283150 original size:37 final size:37
Alignment explanation
Indices: 19283067--19283151 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
19283057 AGCTCTTTCT
*
19283067 CTTTTTACATTTATTTACTATTTATTATTTTTTATTA
1 CTTTTTATATTTATTTACTATTTATTATTTTTTATTA
** *
19283104 CTTAATATATTTATTTATTATTATATTTATTTTTTA-TA
1 CTTTTTATATTTATTTACTATT-TA-TTATTTTTTATTA
19283142 -TTTTTATATT
1 CTTTTTATATT
19283152 CGTTATTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 26 0.65
38 4 0.10
39 10 0.25
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (37 bp):
CTTTTTATATTTATTTACTATTTATTATTTTTTATTA
Found at i:19286331 original size:15 final size:15
Alignment explanation
Indices: 19286311--19286347 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
19286301 AAAGAGCAAT
19286311 CAACACCACTTGCAC
1 CAACACCACTTGCAC
19286326 CAACACCACTTGCAC
1 CAACACCACTTGCAC
19286341 CAACACC
1 CAACACC
19286348 CATGGCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.49, G:0.05, T:0.11
Consensus pattern (15 bp):
CAACACCACTTGCAC
Found at i:19303058 original size:14 final size:14
Alignment explanation
Indices: 19303039--19303066 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19303029 TAATTTGCTA
19303039 AGCATTAGTCTACT
1 AGCATTAGTCTACT
19303053 AGCATTAGTCTACT
1 AGCATTAGTCTACT
19303067 TTGTGACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
AGCATTAGTCTACT
Found at i:19304174 original size:3 final size:3
Alignment explanation
Indices: 19304166--19304215 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
19304156 AGGAAAGGAT
19304166 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
19304213 GAA
1 GAA
19304216 CCTTATGCAG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19326227 original size:22 final size:21
Alignment explanation
Indices: 19326201--19326242 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19326191 TTACCACAAT
*
19326201 ATTTCCTTAAAAATAAAAATA
1 ATTTTCTTAAAAATAAAAATA
* *
19326222 ATTTTCTTTAAAATAATAATA
1 ATTTTCTTAAAAATAAAAATA
19326243 TTAATGACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTTCTTAAAAATAAAAATA
Found at i:19326769 original size:26 final size:27
Alignment explanation
Indices: 19326740--19326800 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
19326730 TGAGATTTTA
* *
19326740 TTTAGGGTTTATGGTT-TTATTTAGGG-
1 TTTAGGGTTTA-GGTTCTCATCTAGGGT
*
19326766 TTTAGGATTTAGGTTCTCATCTAGGGT
1 TTTAGGGTTTAGGTTCTCATCTAGGGT
19326793 TTTAGGGT
1 TTTAGGGT
19326801 CTCACTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 18 0.62
27 7 0.24
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (27 bp):
TTTAGGGTTTAGGTTCTCATCTAGGGT
Found at i:19326798 original size:20 final size:20
Alignment explanation
Indices: 19326773--19326820 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
19326763 GGGTTTAGGA
*
19326773 TTTAGGTTCTCA-TCTAGGGT
1 TTTAGGGTCTCACT-TAGGGT
19326793 TTTAGGGTCTCACTTAGGGT
1 TTTAGGGTCTCACTTAGGGT
*
19326813 TTTGGGGT
1 TTTAGGGT
19326821 TTACCTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.44
Consensus pattern (20 bp):
TTTAGGGTCTCACTTAGGGT
Found at i:19327344 original size:33 final size:32
Alignment explanation
Indices: 19327271--19327354 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 32
19327261 TAAGATGCCA
*
19327271 CTAAGTTAGTAGCATTTGTCAAGACAAATACTG
1 CTAA-TTAGTGGCATTTGTCAAGACAAATACTG
* *
19327304 CTAAATTAGTGGCATTTGTAGCACGA-AAATGCTG
1 CT-AATTAGTGGCATTTGT--CAAGACAAATACTG
19327338 CTAATTAAGTGGCATTT
1 CTAATT-AGTGGCATTT
19327355 TTATGATAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 19 0.43
34 21 0.48
35 4 0.09
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (32 bp):
CTAATTAGTGGCATTTGTCAAGACAAATACTG
Found at i:19327857 original size:16 final size:17
Alignment explanation
Indices: 19327836--19327868 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19327826 GCTATTTTTT
19327836 ATATTTA-AAAATATAA
1 ATATTTACAAAATATAA
*
19327852 ATATTTACTAAATATAA
1 ATATTTACAAAATATAA
19327869 TACCTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTTACAAAATATAA
Found at i:19329052 original size:161 final size:160
Alignment explanation
Indices: 19328720--19329175 Score: 413
Period size: 161 Copynumber: 2.8 Consensus size: 160
19328710 TATTTTGGCC
* * * * * ** * *
19328720 TTTCACATATATCAATCATGGAAACCAAATTCAATTATTTGGACAAGTTTAATACCATGGATTG-
1 TTTCACACATATCAACCATAGAAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGT
* * ** * ** *
19328784 AAGCCATC-AAACTATTAAAAGCCGTCCAA-AAGT-TTAATTTGTATTTTTGCCTTTAAAAGGCA
66 AA-CTATCAAAACTATTAAAA-CAGAACAACAACTAACAATTTGTATTTTTACCTTT-AAAGGCA
* **
19328846 -AAAATAGTCCTAAATAGATGTAAATGACAACTT
128 CAAAA-AGTCCTAAATAGACGTAAACAACAACTT
**
19328879 TTTCACACATATCAACTGTAGAAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTG-
1 TTTCACACATATCAACCATAGAAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGT
* * *
19328943 AAGCTATCCAAACTATTAAAATAGAACAACAAC-AACAATTTTGTATTTTTACCTATTAACGGCA
66 AA-CTATCAAAACTATTAAAACAGAACAACAACTAACAA-TTTGTATTTTTACCT-TTAAAGGCA
*
19329007 CAAAAAGTCCTAAATAGACGTAAACAATAACTT
128 CAAAAAGTCCTAAATAGACGTAAACAACAACTT
* * * * * * ** * * *
19329040 TTTCATACATATCAACCATGGAAGCTAGGTTCAATACTTTGGATACGTTTGATATCATGTATTGT
1 TTTCACACATATCAACCATAGAAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGT
* ** * *
19329105 AACTATCAAAACTATTAAAACAGAACAATAACTATTAATTTGCATTTTTACCTTTTAATGGCACA
66 AACTATCAAAACTATTAAAACAGAACAACAACTAACAATTTGTATTTTTACC-TTTAAAGGCACA
19329170 AAAAGT
130 AAAAGT
19329176 TCATTCATTC
Statistics
Matches: 243, Mismatches: 45, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
159 64 0.26
160 16 0.07
161 151 0.62
162 12 0.05
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (160 bp):
TTTCACACATATCAACCATAGAAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGT
AACTATCAAAACTATTAAAACAGAACAACAACTAACAATTTGTATTTTTACCTTTAAAGGCACAA
AAAGTCCTAAATAGACGTAAACAACAACTT
Found at i:19336015 original size:91 final size:91
Alignment explanation
Indices: 19335914--19336097 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
19335904 GACTACAAAT
19335914 AGCTTCACTAATTCTCTCAAATTTTTTGAAATAATTTATTGAAGGCATTTTTAAACTAATACGCC
1 AGCTTCACTAATTCTCTCAAATTTTTTGAAATAATTTATTGAAGGCATTTTTAAACTAATACGCC
19335979 TTTAATAATCCTTTTGATTTTTATCA
66 TTTAATAATCCTTTTGATTTTTATCA
19336005 AGCTTCACTAATTCTCTCAAATTTTTTGAAATAATTTATTGAAGGCATTTTTAAACTAATACGCC
1 AGCTTCACTAATTCTCTCAAATTTTTTGAAATAATTTATTGAAGGCATTTTTAAACTAATACGCC
19336070 TTTAATAATCCTTTTGATTTTTATCA
66 TTTAATAATCCTTTTGATTTTTATCA
19336096 AG
1 AG
19336098 GGAATATCAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (91 bp):
AGCTTCACTAATTCTCTCAAATTTTTTGAAATAATTTATTGAAGGCATTTTTAAACTAATACGCC
TTTAATAATCCTTTTGATTTTTATCA
Found at i:19336899 original size:28 final size:28
Alignment explanation
Indices: 19336831--19336900 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
19336821 TTAAATATTA
* *
19336831 TGGTTTGCTTAATGTTATTGTATGATAT
1 TGGTTTGCTGAATGATATTGTATGATAT
* *
19336859 TGTTTTGTTGAATGATATTGTATGATAT
1 TGGTTTGCTGAATGATATTGTATGATAT
*
19336887 TGGTTTGCAGAATG
1 TGGTTTGCTGAATG
19336901 GTTTATCGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.24, T:0.50
Consensus pattern (28 bp):
TGGTTTGCTGAATGATATTGTATGATAT
Found at i:19336926 original size:25 final size:25
Alignment explanation
Indices: 19336897--19336950 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
19336887 TGGTTTGCAG
*
19336897 AATGGTTTATCGAATGGTGTTTTTA
1 AATGGTTTATCGAATGGTATTTTTA
* * *
19336922 AATGGTTTCTTGAATGGTATTTTTG
1 AATGGTTTATCGAATGGTATTTTTA
19336947 AATG
1 AATG
19336951 ATTTGCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (25 bp):
AATGGTTTATCGAATGGTATTTTTA
Found at i:19336927 original size:13 final size:12
Alignment explanation
Indices: 19336896--19336950 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 12
19336886 TTGGTTTGCA
* *
19336896 GAATGGTTTATC
1 GAATGGTTTTTT
19336908 GAATGGTGTTTTT
1 GAATGGT-TTTTT
* *
19336921 AAATGGTTTCTT
1 GAATGGTTTTTT
19336933 GAATGGTATTTTT
1 GAATGGT-TTTTT
19336946 GAATG
1 GAATG
19336951 ATTTGCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (12 bp):
GAATGGTTTTTT
Found at i:19338640 original size:21 final size:22
Alignment explanation
Indices: 19338611--19338659 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
19338601 ATAAGTTTAA
*
19338611 TATTAATTTGTTTA-TTATATT
1 TATTAATTTGGTTACTTATATT
*
19338632 TATTGATTTGGTTACTTATATT
1 TATTAATTTGGTTACTTATATT
19338654 TCATTA
1 T-ATTA
19338660 TATATTGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 8 0.35
23 3 0.13
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.61
Consensus pattern (22 bp):
TATTAATTTGGTTACTTATATT
Found at i:19340397 original size:126 final size:125
Alignment explanation
Indices: 19340267--19340514 Score: 288
Period size: 126 Copynumber: 2.0 Consensus size: 125
19340257 TTTGAAGGCA
* * *
19340267 TTTTTT-ACTAAAACCGCCTTCAATAA-TCAAAT-ATAAATATTTATTGAGTGGTTTATTGAAGG
1 TTTTTTAACCAAAACCGCCTTCAATAATTC--ATCATAAAAATTTATTGAGTGGATTATTGAAGG
* * * * *
19340329 CA-TTTTGGGCCAAAAATGCCTTCAATAATCCATTCCAACTTTTTTGTATGGATTATTGAAGAT
64 CACCTTT-AGCCAAAAATGCCTTCAAGAAGCCATTCCAA-TTTTTTGTATAGATTATTGAAGAT
** * *
19340392 TTTTTTAACCAAAATTGCCTTCAATAATTCTTCATAAAAATTTATTGATTGGATTATTGAAGGCA
1 TTTTTTAACCAAAACCGCCTTCAATAATTCATCATAAAAATTTATTGAGTGGATTATTGAAGGCA
* ** *
19340457 CCTTTAGCCAAAAATGCTTTCAAGAAGCTGTTCCAATTTTTTTTATAGATTATTGAAG
66 CCTTTAGCCAAAAATGCCTTCAAGAAGCCATTCCAATTTTTTGTATAGATTATTGAAG
19340515 GCGTTTTTCT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
125 27 0.26
126 71 0.69
127 5 0.05
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (125 bp):
TTTTTTAACCAAAACCGCCTTCAATAATTCATCATAAAAATTTATTGAGTGGATTATTGAAGGCA
CCTTTAGCCAAAAATGCCTTCAAGAAGCCATTCCAATTTTTTGTATAGATTATTGAAGAT
Found at i:19340558 original size:126 final size:126
Alignment explanation
Indices: 19340300--19340581 Score: 277
Period size: 126 Copynumber: 2.2 Consensus size: 126
19340290 TAATCAAATA
* * * * * *
19340300 TAAATATTTATTGAGTGGTTTATTGAAGGCATTTTGGGCCAAAAATGCCTTCAATAATCCATTCC
1 TAAA-ATTTATTGAATGGATTATTGAAGGCACTTTGAGCCAAAAATGCCTTCAAGAAGCCATTCC
* *
19340365 AACTTTTTTGTATGGATTATTGAAGATTTTTTTAACCAAAATTGCCTTCAATAATTCTTCAT
65 AACTTTTTTGTATAGATTATTGAAGATTTTTCTAACCAAAATTGCCTTCAATAATTCTTCAT
* * * **
19340427 AAAAATTTATTGATTGGATTATTGAAGGCACCTTT-AGCCAAAAATGCTTTCAAGAAGCTGTTCC
1 TAAAATTTATTGAATGGATTATTGAAGGCA-CTTTGAGCCAAAAATGCCTTCAAGAAGCCATTCC
* * ** * *
19340491 AA-TTTTTTTTATAGATTATTGAAGGCGTTTTTCTGTCGAAAA-TGCCTTTAAT-ATTCTCTC-T
65 AACTTTTTTGTATAGATTATTGAA-G-ATTTTTCTAACCAAAATTGCCTTCAATAATTCT-TCAT
* * *
19340552 CTAAAATTTTTTAAATGGATTAGTGAAGGC
1 -TAAAATTTATTGAATGGATTATTGAAGGC
19340582 GTTTTTGCTC
Statistics
Matches: 127, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
125 25 0.20
126 85 0.67
127 17 0.13
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (126 bp):
TAAAATTTATTGAATGGATTATTGAAGGCACTTTGAGCCAAAAATGCCTTCAAGAAGCCATTCCA
ACTTTTTTGTATAGATTATTGAAGATTTTTCTAACCAAAATTGCCTTCAATAATTCTTCAT
Found at i:19340873 original size:63 final size:62
Alignment explanation
Indices: 19340800--19340934 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 62
19340790 ATTTCTTGCA
* * ** *
19340800 AAAAATGCCTTCAATAATCGCCTA-CATTTTTTTATGAGGAGATTATTCAAGGCGTTGTCTACC
1 AAAAACGCCTTCAATAATCGCCTACCATTTTTATAACA-G-GATTATACAAGGCGTTGTCTACC
* * * **
19340863 AAAAACGCCTTCAGTAATCTCCTATCCATTTTTATAACAGGATTATACAAGGCGTTTTCTGTC
1 AAAAACGCCTTCAATAATCGCCTA-CCATTTTTATAACAGGATTATACAAGGCGTTGTCTACC
19340926 AAAAACGCC
1 AAAAACGCC
19340935 AAAAAACGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 49 0.82
64 1 0.02
65 10 0.17
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (62 bp):
AAAAACGCCTTCAATAATCGCCTACCATTTTTATAACAGGATTATACAAGGCGTTGTCTACC
Found at i:19341915 original size:18 final size:18
Alignment explanation
Indices: 19341861--19341915 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
19341851 AAAACTAAAC
* *
19341861 CATGAAAAATTGAAGC-A
1 CATGAAAAATTAAAACAA
*
19341878 CATG-AAAATTAAAATAAA
1 CATGAAAAATTAAAA-CAA
*
19341896 CATGAAAAATTCAAACAA
1 CATGAAAAATTAAAACAA
19341914 CA
1 CA
19341916 AGGAAAAGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 8 0.27
17 4 0.13
18 9 0.30
19 9 0.30
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (18 bp):
CATGAAAAATTAAAACAA
Found at i:19342564 original size:17 final size:16
Alignment explanation
Indices: 19342535--19342577 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
19342525 TCTGTTACCG
*
19342535 TTTTTTGCTCCTAGTT
1 TTTTTTGCTCCTACTT
*
19342551 TTTTTTGTTGCCTACTT
1 TTTTTTGCT-CCTACTT
*
19342568 TCTTTTGCTC
1 TTTTTTGCTC
19342578 TTGGTACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.05, C:0.21, G:0.12, T:0.63
Consensus pattern (16 bp):
TTTTTTGCTCCTACTT
Found at i:19343422 original size:17 final size:18
Alignment explanation
Indices: 19343400--19343469 Score: 94
Period size: 17 Copynumber: 4.1 Consensus size: 18
19343390 TTCTCTTTTA
19343400 TTATTAT-TTTTTTAATT
1 TTATTATATTTTTTAATT
19343417 TTATTATATTTTTTAATT
1 TTATTATATTTTTTAATT
*
19343435 TTA-TAT-TTTTCTAATT
1 TTATTATATTTTTTAATT
*
19343451 TTATT-TGTTTTTTAATT
1 TTATTATATTTTTTAATT
19343468 TT
1 TT
19343470 TATTTTGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 13 0.27
17 22 0.46
18 13 0.27
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (18 bp):
TTATTATATTTTTTAATT
Found at i:19343435 original size:8 final size:8
Alignment explanation
Indices: 19343407--19343470 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
19343397 TTATTATTAT
19343407 TTTTTTAA
1 TTTTTTAA
19343415 TTTTATTATA
1 TTTT-TTA-A
19343425 TTTTTTAA
1 TTTTTTAA
*
19343433 TTTTAT-A
1 TTTTTTAA
19343440 TTTTTCTAA
1 TTTTT-TAA
**
19343449 TTTTATTTG
1 TTTT-TTAA
19343458 TTTTTTAA
1 TTTTTTAA
19343466 TTTTT
1 TTTTT
19343471 ATTTTGTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
7 5 0.11
8 18 0.40
9 16 0.36
10 6 0.13
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTTTTAA
Found at i:19343443 original size:34 final size:32
Alignment explanation
Indices: 19343395--19343475 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
19343385 AGCTTTTCTC
* *
19343395 TTTT-ATTATTATTTTTTTAATTTTATTATATT
1 TTTTAATTTTTATTTTTCTAATTTTATT-TATT
*
19343427 TTTTAATTTTATATTTTTCTAATTTTATTTGTT
1 TTTTAATTTT-TATTTTTCTAATTTTATTTATT
19343460 TTTTAATTTTTATTTT
1 TTTTAATTTTTATTTT
19343476 GTTGCTGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 10 0.23
33 17 0.39
34 17 0.39
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTTAATTTTTATTTTTCTAATTTTATTTATT
Found at i:19343470 original size:18 final size:16
Alignment explanation
Indices: 19343400--19343475 Score: 89
Period size: 18 Copynumber: 4.4 Consensus size: 16
19343390 TTCTCTTTTA
19343400 TTATTATTTTTTTAATT
1 TTATT-TTTTTTTAATT
19343417 TTATTATATTTTTTAATT
1 TTATT-T-TTTTTTAATT
* *
19343435 TTATATTTTTCTAATT
1 TTATTTTTTTTTAATT
19343451 TTATTTGTTTTTTAATTT
1 TTATTT-TTTTTTAA-TT
19343469 TTATTTT
1 TTATTTT
19343476 GTTGCTGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
16 14 0.27
17 16 0.31
18 22 0.42
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (16 bp):
TTATTTTTTTTTAATT
Found at i:19345322 original size:17 final size:17
Alignment explanation
Indices: 19345302--19345349 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
19345292 GGTTTTCAGT
19345302 TTTTCTCTTTTTTTTCC
1 TTTTCTCTTTTTTTTCC
*
19345319 TTTTC-CTTTTTTTTCT
1 TTTTCTCTTTTTTTTCC
*
19345335 TTTTTTCTTTTTTTT
1 TTTTCTCTTTTTTTT
19345350 TTTCTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTCTTTTTTTTCC
Found at i:19345327 original size:16 final size:17
Alignment explanation
Indices: 19345302--19345349 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
19345292 GGTTTTCAGT
19345302 TTTTCTCTTTTTTTTC-C
1 TTTTC-CTTTTTTTTCTC
*
19345319 TTTTCCTTTTTTTTCTT
1 TTTTCCTTTTTTTTCTC
*
19345336 TTTTTCTTTTTTTT
1 TTTTCCTTTTTTTT
19345350 TTTCTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCCTTTTTTTTCTC
Found at i:19345349 original size:18 final size:18
Alignment explanation
Indices: 19345301--19345375 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
19345291 GGGTTTTCAG
19345301 TTTTTCTCTTTTTTTTC--
1 TTTTTCT-TTTTTTTTCTT
* *
19345318 CTTTTCCTTTTTTTTCTT
1 TTTTTCTTTTTTTTTCTT
19345336 TTTTTCTTTTTTTTTTTCTT
1 TTTTTC--TTTTTTTTTCTT
* *
19345356 ATTCTTCTTTTCTTTTCTT
1 -TTTTTCTTTTTTTTTCTT
19345375 T
1 T
19345376 GATTTTTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
16 9 0.19
17 5 0.11
18 6 0.13
19 11 0.23
20 11 0.23
21 5 0.11
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTCTT
Found at i:19345360 original size:26 final size:24
Alignment explanation
Indices: 19345309--19345372 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
19345299 AGTTTTTCTC
*
19345309 TTTTTTTTCCTTTTCCTTTTTTT-
1 TTTTTTTTTCTTTTCCTTTTTTTA
* **
19345332 TCTTTTTTTCTTTTTTTTTTTCTTA
1 TTTTTTTTTCTTTTCCTTTTT-TTA
*
19345357 TTCTTCTTTTCTTTTC
1 TT-TTTTTTTCTTTTC
19345373 TTTGATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 17 0.55
24 2 0.06
25 1 0.03
26 11 0.35
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTTTTCTTTTCCTTTTTTTA
Found at i:19352798 original size:3 final size:3
Alignment explanation
Indices: 19352792--19352833 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
19352782 TATTATTATG
19352792 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
19352834 ATTATTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:19354200 original size:24 final size:24
Alignment explanation
Indices: 19354173--19354220 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19354163 CTTTAAAAAG
*
19354173 AATGCCATCCATTGTCCCTTTGTC
1 AATGCCATCCATTATCCCTTTGTC
19354197 AATGCCATCCATTATCCCTTTGTC
1 AATGCCATCCATTATCCCTTTGTC
19354221 CAATCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (24 bp):
AATGCCATCCATTATCCCTTTGTC
Found at i:19356581 original size:19 final size:17
Alignment explanation
Indices: 19356544--19356582 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19356534 AGCTAACTGC
19356544 AAACATAAATTAAAAAT
1 AAACATAAATTAAAAAT
*
19356561 AAACATATATATAAGAAAT
1 AAACATAAAT-TAA-AAAT
19356580 AAA
1 AAA
19356583 TGGAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
AAACATAAATTAAAAAT
Found at i:19357019 original size:20 final size:20
Alignment explanation
Indices: 19356976--19357022 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19356966 GTTCTCATAG
*
19356976 AGGGTTTTAGGGTCTCACTC
1 AGGGTTTTAAGGTCTCACTC
* * *
19356996 AGGGTTTTAAGGTTTCATTT
1 AGGGTTTTAAGGTCTCACTC
19357016 AGGGTTT
1 AGGGTTT
19357023 CAAAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.43
Consensus pattern (20 bp):
AGGGTTTTAAGGTCTCACTC
Found at i:19357476 original size:12 final size:12
Alignment explanation
Indices: 19357459--19357493 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
19357449 ACAGCATGCT
19357459 TAATAACAATAG
1 TAATAACAATAG
*
19357471 TAATAATAATAG
1 TAATAACAATAG
*
19357483 TAAGAACAATA
1 TAATAACAATA
19357494 ATGATGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (12 bp):
TAATAACAATAG
Found at i:19357835 original size:51 final size:51
Alignment explanation
Indices: 19357773--19357869 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
19357763 TATTATTATT
* *
19357773 TTTTATTAAAAAAAGACTTATTAGTATTATTATCTTATATTTTATTCTTAA
1 TTTTATTAAAAAAAGACTTATTAATATTACTATCTTATATTTTATTCTTAA
* *
19357824 TTTTATTAAAAAAAGACTTGTTAATATTACTATCTTTTATTTTATT
1 TTTTATTAAAAAAAGACTTATTAATATTACTATCTTATATTTTATT
19357870 AAAAGTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (51 bp):
TTTTATTAAAAAAAGACTTATTAATATTACTATCTTATATTTTATTCTTAA
Found at i:19358595 original size:18 final size:19
Alignment explanation
Indices: 19358574--19358610 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
19358564 TCTGTTACCG
19358574 TTTTTGCTTCTGGT-TTTT
1 TTTTTGCTTCTGGTATTTT
19358592 TTTTTGCTTCTGGTATTTT
1 TTTTTGCTTCTGGTATTTT
19358611 GTTCTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.03, C:0.11, G:0.16, T:0.70
Consensus pattern (19 bp):
TTTTTGCTTCTGGTATTTT
Found at i:19359380 original size:11 final size:11
Alignment explanation
Indices: 19359364--19359395 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19359354 AAGCTTATCC
19359364 TTTTTATTATT
1 TTTTTATTATT
19359375 TTTTTATTATT
1 TTTTTATTATT
*
19359386 TTTTTTTTAT
1 TTTTTATTAT
19359396 ATTTACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:19359390 original size:14 final size:14
Alignment explanation
Indices: 19359367--19359399 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19359357 CTTATCCTTT
*
19359367 TTATTATTTTTTTA
1 TTATTTTTTTTTTA
19359381 TTATTTTTTTTTTA
1 TTATTTTTTTTTTA
19359395 -TATTT
1 TTATTT
19359400 ACTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TTATTTTTTTTTTA
Found at i:19359405 original size:23 final size:22
Alignment explanation
Indices: 19359379--19359421 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
19359369 ATTATTTTTT
* *
19359379 TATTATTTTTTTTTTATATTTAC
1 TATTATATATTTTTTA-ATTTAC
19359402 TATTATATATTTTTTAATTT
1 TATTATATATTTTTTAATTT
19359422 TTAACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTATATATTTTTTAATTTAC
Found at i:19369595 original size:97 final size:97
Alignment explanation
Indices: 19369467--19369803 Score: 408
Period size: 97 Copynumber: 3.5 Consensus size: 97
19369457 AATAGTAATG
** * ** * *
19369467 AGATTTAATTATGATATTTAAATAATCTAATAGTTTGGTAGGATTTTTAGTCAAAATTTATTTTT
1 AGATTTAATTACAAAATTTAAATTCTTTAATAGTTTGGTAGGATTTTTATTCAAAATTTATTTTT
* *
19369532 AAAAAATCATTAAATATTATAATAGTTTGGTA
66 AAAAAATCATTAAATCTTCTAATAGTTTGGTA
* * **
19369564 AAATTTAATTACAAAATTTAAATCCTTTAATAGTTTGGTAAAATTTTTATTCAAAATTTA--TTT
1 AGATTTAATTACAAAATTTAAATTCTTTAATAGTTTGGTAGGATTTTTATTCAAAATTTATTTTT
*
19369627 AAAAACCATCATTAAATCTTCTAGTAGTTTGGTA
66 AAAAA--ATCATTAAATCTTCTAATAGTTTGGTA
* * * * *
19369661 AGATTGAATTACAAATTTTAAATTTTTTAAAAGTTTGGTAGGATTTTTATTCAGAATTTATTTTT
1 AGATTTAATTACAAAATTTAAATTCTTTAATAGTTTGGTAGGATTTTTATTCAAAATTTATTTTT
* *
19369726 AAAAAAATCATTAAATCTCCTAATAATTTGGTA
66 -AAAAAATCATTAAATCTTCTAATAGTTTGGTA
* * * *
19369759 AGATTTAATTATAAGATTTAAATTCTCTAATAGTTTGGTTGGATT
1 AGATTTAATTACAAAATTTAAATTCTTTAATAGTTTGGTAGGATT
19369804 ATAAAATTAT
Statistics
Matches: 202, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
95 8 0.04
97 125 0.62
98 61 0.30
99 3 0.01
100 5 0.02
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (97 bp):
AGATTTAATTACAAAATTTAAATTCTTTAATAGTTTGGTAGGATTTTTATTCAAAATTTATTTTT
AAAAAATCATTAAATCTTCTAATAGTTTGGTA
Found at i:19370680 original size:42 final size:42
Alignment explanation
Indices: 19370606--19370693 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
19370596 GTGCATAACT
* * * *
19370606 TTAAGATTTGAGAAAGATTCCTCTATATAGAGGCACACAACA
1 TTAAGATTTGAAAAAGACTCCTCTAAAAAGAGGCACACAACA
* * * *
19370648 TTAAGATTTGAAAAAGACTCTTTTAAAAAGAGGCACTCAACT
1 TTAAGATTTGAAAAAGACTCCTCTAAAAAGAGGCACACAACA
19370690 TTAA
1 TTAA
19370694 AATGTGAAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (42 bp):
TTAAGATTTGAAAAAGACTCCTCTAAAAAGAGGCACACAACA
Found at i:19370791 original size:42 final size:42
Alignment explanation
Indices: 19370746--19371026 Score: 217
Period size: 42 Copynumber: 6.9 Consensus size: 42
19370736 AAGGTTCATT
* * *
19370746 TAAACAGAGGCACATAACTTTAAATTTTGAAAAATGCTTTTT
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTTTTC
* * **
19370788 TAAATAGAGG----C-AC----AATTTTAAAAAAGG-TGCCTC
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCT-TTTC
* * * * *
19370821 TAAGCAAAGGCACACAAATTTAAAGTTTGAGAAAGG-TTATTC
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTT-TTC
19370863 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTTTTC
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTTTTC
* * * * *
19370905 TAAATAAAGGCACACAACTTTAAAATTTGAAAAAGGGTCCTT-
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCT-TTTC
* * * * * *
19370947 TAAATAAAGGCACCCAACTTTAAAATTTGAACAAGGCTATTC
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTTTTC
* * *
19370989 TAAAAAGAGGCATACAACTTTAAATTTTTAAAAAGGCT
1 TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCT
19371027 CCTTTAAACA
Statistics
Matches: 188, Mismatches: 37, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
32 1 0.01
33 20 0.11
37 3 0.02
38 1 0.01
41 2 0.01
42 157 0.84
43 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (42 bp):
TAAACAGAGGCACACAACTTTAAATTTTGAAAAAGGCTTTTC
Found at i:19370958 original size:84 final size:83
Alignment explanation
Indices: 19370826--19371040 Score: 261
Period size: 84 Copynumber: 2.6 Consensus size: 83
19370816 GCCTCTAAGC
* * * ** * *
19370826 AAAGGCACACAAATTTAAAGTTTGAGAAA-GGTTATTCTAAACAGAGGCACACAACTTTAAATTT
1 AAAGGCACACAACTTTAAAATTTGAAAAAGGGTCCTT-TAAACAAAGGCACACAACTTTAAAATT
*
19370890 TGAAAAAGGCTTTTCTAAA
65 TGAAAAAGGCTATTCTAAA
* *
19370909 TAAAGGCACACAACTTTAAAATTTGAAAAAGGGTCCTTTAAATAAAGGCACCCAACTTTAAAATT
1 -AAAGGCACACAACTTTAAAATTTGAAAAAGGGTCCTTTAAACAAAGGCACACAACTTTAAAATT
*
19370974 TGAACAAGGCTATTCTAAA
65 TGAAAAAGGCTATTCTAAA
* * * *
19370993 AAGAGGCATACAACTTTAAATTTTTAAAAAGGCTCCTTTAAACAAAGG
1 AA-AGGCACACAACTTTAAAATTTGAAAAAGGGTCCTTTAAACAAAGG
19371041 GACAAAACCT
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.02
84 106 0.94
85 5 0.04
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (83 bp):
AAAGGCACACAACTTTAAAATTTGAAAAAGGGTCCTTTAAACAAAGGCACACAACTTTAAAATTT
GAAAAAGGCTATTCTAAA
Found at i:19371102 original size:42 final size:41
Alignment explanation
Indices: 19371055--19371212 Score: 172
Period size: 42 Copynumber: 3.8 Consensus size: 41
19371045 AAACCTTTTC
* *
19371055 ACAAAGGTATGCAAATTTAAAATTTGAAAAAGGTTCCTCTAA
1 ACAAAGGTATGCAACTTTAAAATTTGAAAAAGCTT-CTCTAA
*
19371097 ACAAAGGTACGCAACTTTAAAATTTGAGAAAAGCTTCTCTAA
1 ACAAAGGTATGCAACTTTAAAATTTGA-AAAAGCTTCTCTAA
* * * *
19371139 ACAAAGGCATACAACTTTAAAATTTGAAAAAGACTTTTGTAA
1 ACAAAGGTATGCAACTTTAAAATTTGAAAAAG-CTTCTCTAA
* * * * * *
19371181 ATAAAAGCATACTACTTTCAAATTTGAAAAAG
1 ACAAAGGTATGCAACTTTAAAATTTGAAAAAG
19371213 GCATACTACT
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 5 0.05
42 90 0.88
43 7 0.07
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (41 bp):
ACAAAGGTATGCAACTTTAAAATTTGAAAAAGCTTCTCTAA
Found at i:19371217 original size:26 final size:26
Alignment explanation
Indices: 19371183--19371238 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
19371173 TTTTGTAAAT
*
19371183 AAAAGCATACTAC-TTTCAAATTTGA
1 AAAAGCATACTACTTTTAAAATTTGA
*
19371208 AAAAGGCATACTACTTTTAAAATTTGG
1 AAAA-GCATACTACTTTTAAAATTTGA
19371235 AAAA
1 AAAA
19371239 TGTTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 9 0.33
27 14 0.52
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (26 bp):
AAAAGCATACTACTTTTAAAATTTGA
Found at i:19371267 original size:69 final size:68
Alignment explanation
Indices: 19371141--19371280 Score: 165
Period size: 69 Copynumber: 2.0 Consensus size: 68
19371131 TTCTCTAAAC
* **
19371141 AAAGGCATACAACTTTAAAATTTGAAAAAGACTTTTGTAAATAAAAGCATACTACTTTCAAATTT
1 AAAGGCATACAACTTTAAAATTTGAAAAAGACTTTTGTAAACAAAAGCATAAAACTTTCAAATTT
19371206 GAA
66 GAA
* * * * * * *
19371209 AAAGGCATACTACTTTTAAAATTTGGAAAATG-TTTTTGTAAACAGAGGGATAAAACTTTCAATT
1 AAAGGCATACAAC-TTTAAAATTT-GAAAAAGACTTTTGTAAACAAAAGCATAAAACTTTCAAAT
19371273 TTGAA
64 TTGAA
19371278 AAA
1 AAA
19371281 AGGTTTTTCT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
68 12 0.20
69 42 0.70
70 6 0.10
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (68 bp):
AAAGGCATACAACTTTAAAATTTGAAAAAGACTTTTGTAAACAAAAGCATAAAACTTTCAAATTT
GAA
Found at i:19373746 original size:65 final size:65
Alignment explanation
Indices: 19373669--19373804 Score: 227
Period size: 65 Copynumber: 2.1 Consensus size: 65
19373659 AACAGGAACC
*
19373669 AAAATTATATAAATCAATTATGCAATAACCAAATGTAACCTAAACCAATTAACATGCAAAGTATA
1 AAAATTAAATAAATCAATTATGCAATAACCAAATGTAACCTAAACCAATTAACATGCAAAGTATA
* * * *
19373734 AAAATTAAATAAATCAATTATGCAATAATCGAATGTAACCTAAACCAATTAACATTCAAAGTATG
1 AAAATTAAATAAATCAATTATGCAATAACCAAATGTAACCTAAACCAATTAACATGCAAAGTATA
19373799 AAAATT
1 AAAATT
19373805 GAACTTAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (65 bp):
AAAATTAAATAAATCAATTATGCAATAACCAAATGTAACCTAAACCAATTAACATGCAAAGTATA
Found at i:19373783 original size:31 final size:31
Alignment explanation
Indices: 19373678--19373784 Score: 85
Period size: 31 Copynumber: 3.4 Consensus size: 31
19373668 CAAAATTATA
* *
19373678 TAAATCAATTATGCAATAACCAAATGTAACC
1 TAAACCAATTATGCAATAATCAAATGTAACC
* *
19373709 TAAACCAATTAACATGCAA-AGTATAAAAAT-TAA-A
1 TAAACCAATT---ATGCAATA--AT-CAAATGTAACC
* *
19373743 TAAATCAATTATGCAATAATCGAATGTAACC
1 TAAACCAATTATGCAATAATCAAATGTAACC
19373774 TAAACCAATTA
1 TAAACCAATTA
19373785 ACATTCAAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
29 3 0.05
30 5 0.09
31 25 0.43
32 1 0.02
33 1 0.02
34 15 0.26
35 4 0.07
36 4 0.07
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (31 bp):
TAAACCAATTATGCAATAATCAAATGTAACC
Found at i:19373819 original size:44 final size:43
Alignment explanation
Indices: 19373770--19373907 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 43
19373760 AATCGAATGT
*
19373770 AACCTAAACCAATTAACATTCAAAGTATGAAAATTGAACTTAGC
1 AACCTAAACCAATTAACATTCAAAGTATGAAAATT-AACTTAAC
* * *
19373814 AACCTAAA-CATATTAA-ACTAACAAG-A-GATAAA--ACCTTAAC
1 AACCTAAACCA-ATTAACATTCA-AAGTATGA-AAATTAACTTAAC
*
19373854 TAACCTAAACCAATTAACATTCAAAGTATGAAAATTAAACTTACC
1 -AACCTAAACCAATTAACATTCAAAGTATGAAAATT-AACTTAAC
19373899 AACCTAAAC
1 AACCTAAAC
19373908 TTATTAAACT
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
40 6 0.08
41 16 0.21
42 11 0.15
43 11 0.15
44 25 0.33
45 6 0.08
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (43 bp):
AACCTAAACCAATTAACATTCAAAGTATGAAAATTAACTTAAC
Found at i:19373870 original size:41 final size:41
Alignment explanation
Indices: 19373814--19373944 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
19373804 TGAACTTAGC
19373814 AACCTAAA-CATATTAAACTAACAAGAGATAAAACCTTAACT
1 AACCTAAACCA-ATTAAACTAACAAGAGATAAAACCTTAACT
* * * * *
19373855 AACCTAAACCAATTAACATTCA-AAGTATGAAAATTAAACTT-ACC
1 AACCTAAACCAATTAA-ACTAACAAG-A-GATAA--AACCTTAACT
** *
19373899 AACCTAAACTTATTAAACTAACAAGAGATAAAGCCTTAACT
1 AACCTAAACCAATTAAACTAACAAGAGATAAAACCTTAACT
19373940 AACCT
1 AACCT
19373945 GTATTAACCC
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
40 4 0.06
41 23 0.33
42 10 0.14
43 8 0.12
44 19 0.28
45 5 0.07
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (41 bp):
AACCTAAACCAATTAAACTAACAAGAGATAAAACCTTAACT
Found at i:19373913 original size:85 final size:85
Alignment explanation
Indices: 19373769--19373944 Score: 316
Period size: 85 Copynumber: 2.1 Consensus size: 85
19373759 TAATCGAATG
* *
19373769 TAACCTAAACCAATTAACATTCAAAGTATGAAAATTGAACTTAGCAACCTAAACATATTAAACTA
1 TAACCTAAACCAATTAACATTCAAAGTATGAAAATTAAACTTACCAACCTAAACATATTAAACTA
19373834 ACAAGAGATAAAACCTTAAC
66 ACAAGAGATAAAACCTTAAC
*
19373854 TAACCTAAACCAATTAACATTCAAAGTATGAAAATTAAACTTACCAACCTAAACTTATTAAACTA
1 TAACCTAAACCAATTAACATTCAAAGTATGAAAATTAAACTTACCAACCTAAACATATTAAACTA
*
19373919 ACAAGAGATAAAGCCTTAAC
66 ACAAGAGATAAAACCTTAAC
19373939 TAACCT
1 TAACCT
19373945 GTATTAACCC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.24
Consensus pattern (85 bp):
TAACCTAAACCAATTAACATTCAAAGTATGAAAATTAAACTTACCAACCTAAACATATTAAACTA
ACAAGAGATAAAACCTTAAC
Found at i:19385371 original size:16 final size:16
Alignment explanation
Indices: 19385350--19385381 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19385340 ATTACTAAGG
19385350 ATCTACACTTTTGAGA
1 ATCTACACTTTTGAGA
*
19385366 ATCTACAGTTTTGAGA
1 ATCTACACTTTTGAGA
19385382 GAGCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (16 bp):
ATCTACACTTTTGAGA
Found at i:19399044 original size:14 final size:14
Alignment explanation
Indices: 19399016--19399079 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
19399006 TGTTAAAACT
*
19399016 TTAAAATT-TAAAA
1 TTAAAATTAAAAAA
*
19399029 TTAAATTTAAAAAA
1 TTAAAATTAAAAAA
19399043 TTAATAAAATTAAAAAA
1 -T--TAAAATTAAAAAA
* *
19399060 TTAAAACTAATAAA
1 TTAAAATTAAAAAA
19399074 TTAAAA
1 TTAAAA
19399080 AATAAATGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 7 0.17
14 21 0.50
15 1 0.02
16 1 0.02
17 12 0.29
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATTAAAAAA
Found at i:19399059 original size:8 final size:8
Alignment explanation
Indices: 19399035--19399082 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
19399025 AAAATTAAAT
19399035 TTAAAAAA
1 TTAAAAAA
19399043 TTAATAAAA
1 TTAA-AAAA
19399052 TTAAAAAA
1 TTAAAAAA
19399060 TT--AAAA
1 TTAAAAAA
* *
19399066 CTAATAAA
1 TTAAAAAA
19399074 TTAAAAAA
1 TTAAAAAA
19399082 T
1 T
19399083 AAATGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.15
8 20 0.61
9 8 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:19399063 original size:31 final size:30
Alignment explanation
Indices: 19399017--19399082 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
19399007 GTTAAAACTT
* **
19399017 TAAAATTTAAAATTAAATTTAAAAAATTAA
1 TAAAATTAAAAATTAAAACTAAAAAATTAA
*
19399047 TAAAATTAAAAAATTAAAACTAATAAATTAA
1 TAAAATT-AAAAATTAAAACTAAAAAATTAA
19399078 -AAAAT
1 TAAAAT
19399083 AAATGCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
TAAAATTAAAAATTAAAACTAAAAAATTAA
Found at i:19399065 original size:23 final size:22
Alignment explanation
Indices: 19399039--19399082 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19399029 TTAAATTTAA
*
19399039 AAAATTAATAAAATTAAAAAATT
1 AAAACTAAT-AAATTAAAAAATT
19399062 AAAACTAATAAATTAAAAAAT
1 AAAACTAATAAATTAAAAAAT
19399083 AAATGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAACTAATAAATTAAAAAATT
Found at i:19399073 original size:17 final size:17
Alignment explanation
Indices: 19399030--19399063 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19399020 AATTTAAAAT
*
19399030 TAAATTTAAAAAATTAA
1 TAAAATTAAAAAATTAA
19399047 TAAAATTAAAAAATTAA
1 TAAAATTAAAAAATTAA
19399064 AACTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATTAAAAAATTAA
Found at i:19400959 original size:16 final size:16
Alignment explanation
Indices: 19400938--19400974 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
19400928 TCATTTTGGA
19400938 TCATGATATATGGTGG
1 TCATGATATATGGTGG
19400954 TCATGATATATGGTGG
1 TCATGATATATGGTGG
19400970 TCATG
1 TCATG
19400975 TTCTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (16 bp):
TCATGATATATGGTGG
Found at i:19401243 original size:13 final size:13
Alignment explanation
Indices: 19401223--19401365 Score: 65
Period size: 13 Copynumber: 10.8 Consensus size: 13
19401213 CGTAAATTCG
19401223 TAAAACCCTAAAA
1 TAAAACCCTAAAA
* *
19401236 TGAAACCCTAAGAT
1 TAAAACCCTAA-AA
* *
19401250 TAAGACCCTAAAT
1 TAAAACCCTAAAA
* * *
19401263 TAAAATCGTAAAG
1 TAAAACCCTAAAA
* *
19401276 TCAAACCCTAAAT
1 TAAAACCCTAAAA
19401289 TAAAACCCGT-AAA
1 TAAAACCC-TAAAA
* * *
19401302 TCGAAATCCTAAAT
1 T-AAAACCCTAAAA
** *
19401316 TGGAACCCCAAAA
1 TAAAACCCTAAAA
*
19401329 TAAAACCCT-ACA
1 TAAAACCCTAAAA
** *
19401341 TGCAACCTTAAAA
1 TAAAACCCTAAAA
19401354 TCAAAACCCTAA
1 T-AAAACCCTAA
19401366 GGGCAACCCA
Statistics
Matches: 92, Mismatches: 32, Indels: 11
0.68 0.24 0.08
Matches are distributed among these distances:
12 8 0.09
13 58 0.63
14 26 0.28
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (13 bp):
TAAAACCCTAAAA
Found at i:19401323 original size:27 final size:27
Alignment explanation
Indices: 19401254--19401316 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
19401244 TAAGATTAAG
*
19401254 ACCCTAAATTAAAA-TCGTAAAGTCAA
1 ACCCTAAATTAAAACCCGTAAAGTCAA
19401280 ACCCTAAATTAAAACCCGTAAA-TCGAA
1 ACCCTAAATTAAAACCCGTAAAGTC-AA
*
19401307 ATCCTAAATT
1 ACCCTAAATT
19401317 GGAACCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (27 bp):
ACCCTAAATTAAAACCCGTAAAGTCAA
Found at i:19401323 original size:40 final size:39
Alignment explanation
Indices: 19401224--19401338 Score: 113
Period size: 40 Copynumber: 2.9 Consensus size: 39
19401214 GTAAATTCGT
* * *
19401224 AAAACCCTAAAATGAAACCCTAAGATTAAGACCCTAAATT
1 AAAATCCTAAAATGAAACCCTAA-ATTAAAACCCTAAATC
* * *
19401264 AAAATCGTAAAGTCAAACCCTAAATTAAAACCCGTAAATC
1 AAAATCCTAAAATGAAACCCTAAATTAAAACCC-TAAATC
* * * * *
19401304 GAAATCCTAAATTGGAACCCCAAAATAAAACCCTA
1 AAAATCCTAAAATGAAACCCTAAATTAAAACCCTA
19401339 CATGCAACCT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 11 0.18
40 50 0.82
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (39 bp):
AAAATCCTAAAATGAAACCCTAAATTAAAACCCTAAATC
Found at i:19401371 original size:26 final size:25
Alignment explanation
Indices: 19401325--19401373 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
19401315 TTGGAACCCC
*
19401325 AAAATAAAACCCTACATGCAACCTT
1 AAAATAAAACCCTACAGGCAACCTT
19401350 AAAATCAAAACCCTA-AGGGCAACC
1 AAAAT-AAAACCCTACA-GGCAACC
19401374 CAAAACCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.49, C:0.29, G:0.08, T:0.14
Consensus pattern (25 bp):
AAAATAAAACCCTACAGGCAACCTT
Found at i:19408062 original size:16 final size:16
Alignment explanation
Indices: 19408041--19408085 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
19408031 TGAATCCACT
19408041 AAAAAAAATGAGAA-TG
1 AAAAAAAA-GAGAAGTG
*
19408057 AAAAAAAAGAAAAGTG
1 AAAAAAAAGAGAAGTG
19408073 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
19408086 AAGATGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
AAAAAAAAGAGAAGTG
Found at i:19408078 original size:18 final size:19
Alignment explanation
Indices: 19408057--19408106 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
19408047 AATGAGAATG
19408057 AAAAAAAAGAAAAG-TGAA
1 AAAAAAAAGAAAAGATGAA
*
19408075 AAAAAAGAGAAAAGATGAA
1 AAAAAAAAGAAAAGATGAA
*
19408094 AGAAGAAAAGAAA
1 A-AAAAAAAGAAA
19408107 TAAATAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 13 0.48
19 5 0.19
20 9 0.33
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAAAGATGAA
Found at i:19408141 original size:9 final size:9
Alignment explanation
Indices: 19408127--19408157 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
19408117 CAAAGGAAGA
19408127 GAAAGAAAT
1 GAAAGAAAT
19408136 GAAAGAAAT
1 GAAAGAAAT
19408145 GAAATGAAAT
1 GAAA-GAAAT
19408155 GAA
1 GAA
19408158 TGGGTAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.13
Consensus pattern (9 bp):
GAAAGAAAT
Found at i:19408159 original size:14 final size:14
Alignment explanation
Indices: 19408100--19408157 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
19408090 TGAAAGAAGA
*
19408100 AAAGAAAT-AAATA
1 AAAGAAATGAAATG
*
19408113 AAAGCAAAGGAAGA-G
1 AAAG-AAATGAA-ATG
19408128 AAAGAAATGAAA-G
1 AAAGAAATGAAATG
19408141 AAATGAAATGAAATG
1 AAA-GAAATGAAATG
19408156 AA
1 AA
19408158 TGGGTAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.24
14 18 0.49
15 9 0.24
16 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.10
Consensus pattern (14 bp):
AAAGAAATGAAATG
Found at i:19408520 original size:20 final size:20
Alignment explanation
Indices: 19408495--19408537 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19408485 TCAGTCAATT
*
19408495 AAAAAAA-AAGAGAACAAAA
1 AAAAAAACAAAAGAACAAAA
*
19408514 AAAAAAACAAAAGAATAAAA
1 AAAAAAACAAAAGAACAAAA
19408534 AAAA
1 AAAA
19408538 TGAATGTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.86, C:0.05, G:0.07, T:0.02
Consensus pattern (20 bp):
AAAAAAACAAAAGAACAAAA
Found at i:19409191 original size:33 final size:32
Alignment explanation
Indices: 19409113--19409191 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 32
19409103 CATTTATGAA
* *
19409113 AAGATTTAAGCCCAATTTAGTTGGCACCAATG
1 AAGATTTAAGCCCAAATTAGTTAGCACCAATG
*
19409145 AAGATTTATGCCCAAATTA-TCTAGCACCTAATAG
1 AAGATTTAAGCCCAAATTAGT-TAGCACC-AAT-G
19409179 AA-ATTTAAGCCCA
1 AAGATTTAAGCCCA
19409192 GTTTAACTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.03
32 23 0.57
33 13 0.32
34 3 0.08
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (32 bp):
AAGATTTAAGCCCAAATTAGTTAGCACCAATG
Found at i:19409299 original size:35 final size:34
Alignment explanation
Indices: 19409210--19409356 Score: 124
Period size: 34 Copynumber: 4.4 Consensus size: 34
19409200 GACATCCTAT
* * *
19409210 AAAAATTTAAGCCCTGA-TTAGTTGGCACCCCATG
1 AAAAATTTAAGCTC-AACTTAGTTGGCACCCAATG
* *
19409244 AAAAATTTAAGCTCAGCTTAGTTGGCACTCAATG
1 AAAAATTTAAGCTCAACTTAGTTGGCACCCAATG
* * * *
19409278 AAAAATTTTAAGCTTAACTTAGCTGGCACCTAAAG
1 AAAAA-TTTAAGCTCAACTTAGTTGGCACCCAATG
* *
19409313 -AAAATTTAAGCTCAGA-TTAGCTGACA-CCAAGTG
1 AAAAATTTAAGCTCA-ACTTAGTTGGCACCCAA-TG
19409346 -AAAATTTAAGC
1 AAAAATTTAAGC
19409357 CCAGTCCAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
32 3 0.03
33 30 0.32
34 38 0.40
35 23 0.24
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (34 bp):
AAAAATTTAAGCTCAACTTAGTTGGCACCCAATG
Found at i:19409333 original size:33 final size:33
Alignment explanation
Indices: 19409116--19409588 Score: 192
Period size: 33 Copynumber: 14.4 Consensus size: 33
19409106 TTATGAAAAG
* *
19409116 ATTTAAGCCCA-ATTTAGTTGGCACC-AATGAAG
1 ATTTAAGCCCAGA-TTAGCTGGCACCTAATGAAA
* * * *
19409148 ATTTATGCCCAAATTATCTAGCACCTAAT-AGAA
1 ATTTAAGCCCAGATTAGCTGGCACCTAATGA-AA
* * * *
19409181 ATTTAAGCCCAGTTTAACTGACATCCT-ATAAAA
1 ATTTAAGCCCAGATTAGCTGGCA-CCTAATGAAA
* * **
19409214 ATTTAAGCCCTGATTAGTTGGCACCCCATGAAAA
1 ATTTAAGCCCAGATTAGCTGGCACCTAATG-AAA
* * *
19409248 ATTTAAGCTCAGCTTAGTTGGCA-CTCAATGAAAA
1 ATTTAAGCCCAGATTAGCTGGCACCT-AATG-AAA
** *
19409282 ATTTTAAGCTTA-ACTTAGCTGGCACCTAAAGAAA
1 A-TTTAAGCCCAGA-TTAGCTGGCACCTAATGAAA
* *
19409316 ATTTAAGCTCAGATTAGCTGACACC-AAGTGAAA
1 ATTTAAGCCCAGATTAGCTGGCACCTAA-TGAAA
* * *
19409349 ATTTAAGCCCAG-TCCAACTGGC-TCTAAATG-AA
1 ATTTAAGCCCAGAT-TAGCTGGCACCT-AATGAAA
* * * *
19409381 ATTCAAGCCTAG-TTAGCTAGCA-CTTATGAAAA
1 ATTTAAGCCCAGATTAGCTGGCACCTAATG-AAA
*
19409413 GATTTAAGCCTAGATTAGCTGGCA-CTAAT-AAA
1 -ATTTAAGCCCAGATTAGCTGGCACCTAATGAAA
* * ** * * *
19409445 GATTTAAGCCTAGTTTATTTAGTACCCAATGAAA
1 -ATTTAAGCCCAGATTAGCTGGCACCTAATGAAA
* * * * *
19409479 TTTTAAG-CCAAACTTATCTAGCA-CTCATGAAAA
1 ATTTAAGCCCAGA-TTAGCTGGCACCTAATG-AAA
*
19409512 GATTTAAGCCCA-ATTTAGCTGGCA-TTAAT-AAA
1 -ATTTAAGCCCAGA-TTAGCTGGCACCTAATGAAA
* * ** * * *
19409544 GTTTAAGCCTAGATTATTTGGCACCCAATTAAG
1 ATTTAAGCCCAGATTAGCTGGCACCTAATGAAA
*
19409577 ATATAAGCCCAG
1 ATTTAAGCCCAG
19409589 TCTATCTAGT
Statistics
Matches: 337, Mismatches: 74, Indels: 59
0.72 0.16 0.13
Matches are distributed among these distances:
30 3 0.01
31 24 0.07
32 76 0.23
33 132 0.39
34 76 0.23
35 24 0.07
36 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (33 bp):
ATTTAAGCCCAGATTAGCTGGCACCTAATGAAA
Found at i:19409350 original size:135 final size:133
Alignment explanation
Indices: 19409108--19409358 Score: 301
Period size: 135 Copynumber: 1.9 Consensus size: 133
19409098 ATCAGCATTT
* * * *
19409108 ATGAAAAGATTTAAGCCCAATTTAGTTGGCACCAATGAAGATTTATGCCCAAATTATCTAGCACC
1 ATGAAAAGATTTAAGCCCAACTTAGTTGGCACCAATGAAAATTTAAGCCCAAATTAGCTAGCACC
* *
19409173 TAATAGAAATTTAAGCCCAGTTTAACTGACATCCTATAAAAATTTAAGCCCTGATTAGTTGGCAC
66 TAATAGAAATTTAAGCCCAGATTAACTGACATCCAATAAAAATTTAAGCCCTGATTAGTTGGCAC
19409238 CCC
131 CCC
* * ** * *
19409241 ATGAAAA-ATTTAAGCTCAGCTTAGTTGGCACTCAATGAAAAATTTTAAGCTTAACTTAGCTGGC
1 ATGAAAAGATTTAAGCCCAACTTAGTTGGCAC-CAATG-AAAA-TTTAAGCCCAAATTAGCTAGC
* * *
19409305 ACCTAA-AGAAAATTTAAGCTCAGATTAGCTGACA-CCAAGTGAAAATTTAAGCCC
63 ACCTAATAG-AAATTTAAGCCCAGATTAACTGACATCCAA-TAAAAATTTAAGCCC
19409359 AGTCCAACTG
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
132 21 0.21
133 12 0.12
134 8 0.08
135 57 0.58
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (133 bp):
ATGAAAAGATTTAAGCCCAACTTAGTTGGCACCAATGAAAATTTAAGCCCAAATTAGCTAGCACC
TAATAGAAATTTAAGCCCAGATTAACTGACATCCAATAAAAATTTAAGCCCTGATTAGTTGGCAC
CCC
Found at i:19409438 original size:34 final size:31
Alignment explanation
Indices: 19409385--19409459 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 31
19409375 AATGAAATTC
*
19409385 AAGCCTAGTTAGCTAGCACTTATGAAAAGATTT
1 AAGCCTAGTTAGCTAGCACTAAT--AAAGATTT
*
19409418 AAGCCTAGATTAGCTGGCACTAATAAAGATTT
1 AAGCCTAG-TTAGCTAGCACTAATAAAGATTT
19409450 AAGCCTAGTT
1 AAGCCTAGTT
19409460 TATTTAGTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 2 0.05
32 16 0.41
33 8 0.21
34 13 0.33
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (31 bp):
AAGCCTAGTTAGCTAGCACTAATAAAGATTT
Found at i:19409608 original size:99 final size:99
Alignment explanation
Indices: 19409046--19409585 Score: 250
Period size: 98 Copynumber: 5.5 Consensus size: 99
19409036 ATTATCAATG
* * * * * ***
19409046 AAGATTTTAAGCCTAGTTTATCTAGCACCCAACGAAATTTTAAGCTC-AGCTTATC-AGCATTTA
1 AAGA-TTTAAGCCTAGATTATTTAGCACCCAATGAAATTATAAGC-CAAACTTATCTAGCACCCA
* * *
19409109 TGAAAAGATTTAAGCCCA-ATTTAGTTGGCACCAATG
64 TGAAAAGATTTAAGCCCAGA-TTAGCTGGCACTAATA
* * * * * * ** * *
19409145 AAGATTTATGCCCAAATTATCTAGCACCTAATAGAAATT-TAAGCCCAGTTTAACT-GACATCCT
1 AAGATTTAAGCCTAGATTATTTAGCACCCAAT-GAAATTATAAGCCAAACTTATCTAG-CA-CCC
* * **
19409208 AT-AAAA-ATTTAAGCCCTGATTAGTTGGCACCCCATGA
63 ATGAAAAGATTTAAGCCCAGATTAGCTGGCA-CTAAT-A
* * * * * * ** * *
19409245 AAAATTTAAG-CTCAGCTTAGTTGGCACTCAATGAAAAATTTTAAGCTTAACTTAGCTGGCA-CC
1 AAGATTTAAGCCT-AGATTATTTAGCACCCAATG--AAATTATAAGCCAAACTTATCTAGCACCC
* * * * *
19409308 -TAAAGAAAATTTAAGCTCAGATTAGCTGACACCAAGTGA
63 ATGAA-AAGATTTAAGCCCAGATTAGCTGGCACTAA-T-A
* * ** * * ** * * * * **
19409347 AA-ATTTAAGCCCAG-TCCAACTGGCTCTAAATGAAATT-CAAGCC-TAGTTAGCTAGCACTTAT
1 AAGATTTAAGCCTAGAT-TATTTAGCACCCAATGAAATTATAAGCCAAACTTATCTAGCACCCAT
*
19409408 GAAAAGATTTAAGCCTAGATTAGCTGGCACTAATA
65 GAAAAGATTTAAGCCCAGATTAGCTGGCACTAATA
* * * *
19409443 AAGATTTAAGCCTAGTTTATTTAGTACCCAATGAAATTTTAAGCCAAACTTATCTAGCACTCATG
1 AAGATTTAAGCCTAGATTATTTAGCACCCAATGAAATTATAAGCCAAACTTATCTAGCACCCATG
*
19409508 AAAAGATTTAAGCCCA-ATTTAGCTGGCATTAATA
66 AAAAGATTTAAGCCCAGA-TTAGCTGGCACTAATA
* *
19409542 AAG-TTTAAGCCTAGATTATTTGGCACCCAATTAAGA-TATAAGCC
1 AAGATTTAAGCCTAGATTATTTAGCACCCAATGAA-ATTATAAGCC
19409586 CAGTCTATCT
Statistics
Matches: 340, Mismatches: 74, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
96 3 0.01
97 36 0.11
98 124 0.36
99 81 0.24
100 27 0.08
101 30 0.09
102 38 0.11
103 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (99 bp):
AAGATTTAAGCCTAGATTATTTAGCACCCAATGAAATTATAAGCCAAACTTATCTAGCACCCATG
AAAAGATTTAAGCCCAGATTAGCTGGCACTAATA
Found at i:19409698 original size:33 final size:33
Alignment explanation
Indices: 19409649--19409864 Score: 162
Period size: 33 Copynumber: 6.7 Consensus size: 33
19409639 AGTTTAGCTT
*
19409649 GCACC-AATGAAGATTTAAGCCTAAATTATCTG
1 GCACCTAATGAAAATTTAAGCCTAAATTATCTG
* * *
19409681 GTACCTGATGAAAATTTAAGCCTAAATTATTTG
1 GCACCTAATGAAAATTTAAGCCTAAATTATCTG
** ** *
19409714 GCACCCGATGAAAATTTTGGGCCT---TTATCTA
1 GCACCTAATGAAAA-TTTAAGCCTAAATTATCTG
* * * * * *
19409745 GCACTTAATGAAAAATTAAGCCCAACTTAGCTA
1 GCACCTAATGAAAATTTAAGCCTAAATTATCTG
* *
19409778 GCA-TTCAATGAAAATTTAAGCCTAAATTATTTG
1 GCACCT-AATGAAAATTTAAGCCTAAATTATCTG
*
19409811 GTACC-AATG-AAATTTAAG-CTCAAATTATCTG
1 GCACCTAATGAAAATTTAAGCCT-AAATTATCTG
**
19409842 GCACCCGATG-AAATTTAAGCCTA
1 GCACCTAATGAAAATTTAAGCCTA
19409865 GCTTAGTTGG
Statistics
Matches: 145, Mismatches: 29, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
30 7 0.05
31 38 0.26
32 23 0.16
33 70 0.48
34 7 0.05
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
GCACCTAATGAAAATTTAAGCCTAAATTATCTG
Found at i:19410780 original size:66 final size:65
Alignment explanation
Indices: 19410651--19410791 Score: 158
Period size: 66 Copynumber: 2.2 Consensus size: 65
19410641 CAACCTTGGT
* * * * * *
19410651 TTTAAGCCCAATTTAGCCGGCACCCAATGAAAATTTAAGCTCAGATTATCTAATACTCGATGAAA
1 TTTAAGCCCAACTTAGCCAGCACCCAATGAAAATTCAAGCTCAGATTAGCTAACACTCAATG-AA
19410716 A
65 A
* * * * *
19410717 TTTAAGCCCAACTTAGCTAGCACCTAATTAAGATTCAAGC-CTAGCTTAGCTAACACTCAATGAA
1 TTTAAGCCCAACTTAGCCAGCACCCAATGAAAATTCAAGCTC-AGATTAGCTAACACTCAATGAA
19410781 A
65 A
19410782 TTTAAGCCCA
1 TTTAAGCCCA
19410792 GTTTAGTTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 14 0.22
66 49 0.78
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (65 bp):
TTTAAGCCCAACTTAGCCAGCACCCAATGAAAATTCAAGCTCAGATTAGCTAACACTCAATGAAA
Found at i:19410803 original size:32 final size:32
Alignment explanation
Indices: 19410675--19410896 Score: 132
Period size: 33 Copynumber: 6.8 Consensus size: 32
19410665 AGCCGGCACC
* * *
19410675 CAATGAAAATTTAAGCTCAGATTA-TCTAATACT
1 CAATG-AAATTTAAGCCCAGCTTAGT-TAACACT
* * * *
19410708 CGATGAAAATTTAAGCCCAACTTAGCTAGCAC-
1 CAATG-AAATTTAAGCCCAGCTTAGTTAACACT
* * * *
19410740 CTAATTAAGATTCAAGCCTAGCTTAGCTAACACT
1 C-AATGAA-ATTTAAGCCCAGCTTAGTTAACACT
*
19410774 CAATGAAATTTAAGCCCAGTTTAGTTAACACT
1 CAATGAAATTTAAGCCCAGCTTAGTTAACACT
* * *
19410806 CAATGAAGTTTTAAGCCCAACTTA-TCAACA-T
1 CAATGAA-ATTTAAGCCCAGCTTAGTTAACACT
* ** *
19410837 CCAATGAAATTTAAGCCTAG-TGTAACTAGCACT
1 -CAATGAAATTTAAGCCCAGCT-TAGTTAACACT
* *
19410870 CAAT-AAAGTTTTAGCCCAGTTTAGTTA
1 CAATGAAA-TTTAAGCCCAGCTTAGTTA
19410897 GCATCTAGTA
Statistics
Matches: 146, Mismatches: 32, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
30 1 0.01
31 15 0.10
32 63 0.43
33 66 0.45
34 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (32 bp):
CAATGAAATTTAAGCCCAGCTTAGTTAACACT
Found at i:19410886 original size:96 final size:98
Alignment explanation
Indices: 19410675--19410896 Score: 240
Period size: 98 Copynumber: 2.3 Consensus size: 98
19410665 AGCCGGCACC
* * * * ** *
19410675 CAATGAAAATTTAAGCTCAGATTA-TCTAATACTCGATGAAAATTTAAGCCCAACTTAGCTAGCA
1 CAATG-AAATTTAAGCCCAGTTTAGT-TAACACTCAATGAAGTTTTAAGCCCAACTTAGCTAACA
* *
19410739 CCTAATTAAGATTCAAGCCTAGCTTAGCTAACACT
64 CCTAATGAAGATTCAAGCCTAGCTTAACTAACACT
*
19410774 CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATGAAGTTTTAAGCCCAACTTATC-AACATC
1 CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATGAAGTTTTAAGCCCAACTTAGCTAACA-C
* *
19410838 C-AATGAA-ATTTAAGCCTAG-TGTAACTAGCACT
65 CTAATGAAGATTCAAGCCTAGCT-TAACTAACACT
*
19410870 CAAT-AAAGTTTTAGCCCAGTTTAGTTA
1 CAATGAAA-TTTAAGCCCAGTTTAGTTA
19410897 GCATCTAGTA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
95 4 0.04
96 42 0.40
97 8 0.08
98 46 0.43
99 6 0.06
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (98 bp):
CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATGAAGTTTTAAGCCCAACTTAGCTAACACC
TAATGAAGATTCAAGCCTAGCTTAACTAACACT
Found at i:19410915 original size:96 final size:98
Alignment explanation
Indices: 19410675--19410917 Score: 230
Period size: 96 Copynumber: 2.5 Consensus size: 98
19410665 AGCCGGCACC
* * * * * *
19410675 CAATGAAAATTTAAGCTCAGATTA-TCTAATACTCGATGAAAATTTAAGCCCAACTTAGCTAGCA
1 CAATG-AAATTTAAGCCCAGTTTAGT-TAACACTCAATAAAAATTTAAGCCCAACTTAGCTAACA
* *
19410739 CCTAATTAAGATTCAAGCCTAGCTTAGCTAACACT
64 CCTAATGAAGATTCAAGCCTAGCTTAACTAACACT
* ** *
19410774 CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATGAAGTTTTAAGCCCAACTTATC-AACATC
1 CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATAAAAATTTAAGCCCAACTTAGCTAACA-C
* *
19410838 C-AATGAA-ATTTAAGCCTAG-TGTAACTAGCACT
65 CTAATGAAGATTCAAGCCTAGCT-TAACTAACACT
* * *
19410870 CAAT-AAAGTTTTAGCCCAGTTTAGTTAGCA-TCTAGTAAAAATTTAAGC
1 CAATGAAA-TTTAAGCCCAGTTTAGTTAACACTC-AATAAAAATTTAAGC
19410918 TCGATTTAGT
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
95 6 0.05
96 55 0.45
97 8 0.07
98 46 0.38
99 6 0.05
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (98 bp):
CAATGAAATTTAAGCCCAGTTTAGTTAACACTCAATAAAAATTTAAGCCCAACTTAGCTAACACC
TAATGAAGATTCAAGCCTAGCTTAACTAACACT
Found at i:19411398 original size:18 final size:19
Alignment explanation
Indices: 19411365--19411404 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
19411355 CATTAAATAT
19411365 ATAAAAAAAATAAATAACA
1 ATAAAAAAAATAAATAACA
*
19411384 ATAAAAATAAT-AATAACA
1 ATAAAAAAAATAAATAACA
19411402 ATA
1 ATA
19411405 TTAAAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (19 bp):
ATAAAAAAAATAAATAACA
Found at i:19411468 original size:26 final size:23
Alignment explanation
Indices: 19411439--19411503 Score: 60
Period size: 26 Copynumber: 2.7 Consensus size: 23
19411429 TTTAAAATTT
*
19411439 TAAATTAAATTAAAGATTATTCAAAC
1 TAAA-TAAATTAAA-AATATT-AAAC
*
19411465 TAAAAAAAATTTAAAAATATTAAAC
1 T-AAATAAA-TTAAAAATATTAAAC
19411490 T-AATAAATTAAAAA
1 TAAATAAATTAAAAA
19411504 ATAAATACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
25 5 0.15
26 9 0.26
27 8 0.24
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAATAAATTAAAAATATTAAAC
Found at i:19413692 original size:13 final size:13
Alignment explanation
Indices: 19413622--19413754 Score: 70
Period size: 13 Copynumber: 10.0 Consensus size: 13
19413612 CATAAATTCA
*
19413622 TAAAACCCTAAAG
1 TAAAACCCTAAAT
* *
19413635 TGAACCCCTAAGAT
1 TAAAACCCTAA-AT
* *
19413649 TAAGACCCAAAAT
1 TAAAACCCTAAAT
**
19413662 TAAAATCCAAAAAT
1 TAAAA-CCCTAAAT
*
19413676 TAAAACCCTAAAG
1 TAAAACCCTAAAT
**
19413689 TAAAGTCCTAAAT
1 TAAAACCCTAAAT
*
19413702 TGAAACCCTTAAAT
1 TAAAACCC-TAAAT
**
19413716 CGAAA-CCTAAAT
1 TAAAACCCTAAAT
* * *
19413728 TGGAACCCCAAAAT
1 T-AAAACCCTAAAT
*
19413742 TGAAACCCTAAAT
1 TAAAACCCTAAAT
19413755 GCAACCTTAA
Statistics
Matches: 91, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
12 5 0.05
13 50 0.55
14 36 0.40
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.20
Consensus pattern (13 bp):
TAAAACCCTAAAT
Found at i:19413720 original size:14 final size:14
Alignment explanation
Indices: 19413697--19413754 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
19413687 AGTAAAGTCC
19413697 TAAATTGAAACCCT
1 TAAATTGAAACCCT
*
19413711 TAAATCGAAA-CC-
1 TAAATTGAAACCCT
* *
19413723 TAAATTGGAACCCC
1 TAAATTGAAACCCT
*
19413737 AAAATTGAAACCC-
1 TAAATTGAAACCCT
19413750 TAAAT
1 TAAAT
19413755 GCAACCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 8 0.22
13 8 0.22
14 20 0.56
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (14 bp):
TAAATTGAAACCCT
Found at i:19413724 original size:26 final size:27
Alignment explanation
Indices: 19413695--19413778 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 27
19413685 AAAGTAAAGT
**
19413695 CCTAAATTGAAACCCTTAAATCGAAA-
1 CCTAAATTGAAACCCCAAAATCGAAAC
* *
19413721 CCTAAATTGGAACCCCAAAATTGAAAC
1 CCTAAATTGAAACCCCAAAATCGAAAC
* ** *
19413748 CCTAAA-TGCAACCTTAAAATCAAAAC
1 CCTAAATTGAAACCCCAAAATCGAAAC
19413774 CCTAA
1 CCTAA
19413779 GGGAAACCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
26 42 0.88
27 6 0.12
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.20
Consensus pattern (27 bp):
CCTAAATTGAAACCCCAAAATCGAAAC
Found at i:19414044 original size:10 final size:10
Alignment explanation
Indices: 19414009--19414052 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
19413999 TTGTTTTGTT
19414009 AAAATAATAA
1 AAAATAATAA
* *
19414019 ATATAAAAATAT
1 A-A-AATAATAA
19414031 AAAATAATAA
1 AAAATAATAA
19414041 AAAATAATAA
1 AAAATAATAA
19414051 AA
1 AA
19414053 TGAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 19 0.68
11 2 0.07
12 7 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATAATAA
Found at i:19414044 original size:18 final size:18
Alignment explanation
Indices: 19414009--19414053 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 18
19413999 TTGTTTTGTT
19414009 AAAATAAT-AAAT-AT-A
1 AAAATAATAAAATAATAA
19414024 AAAAT-ATAAAATAATAA
1 AAAATAATAAAATAATAA
19414041 AAAATAATAAAAT
1 AAAATAATAAAAT
19414054 GAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 9 0.35
16 2 0.08
17 6 0.23
18 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAATAAAATAATAA
Found at i:19415826 original size:41 final size:41
Alignment explanation
Indices: 19415742--19415828 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
19415732 CCATTACTTG
* * *
19415742 AATGTGAATGTCTTTCTTTTGATGAAAATGCAAGAAATGCA
1 AATGCGAATGTCTTTCTTCTGATGAAAATGCAAGAAATACA
* *
19415783 AATGCGAATGTCATTT-TTCTGATGCAAATGCAA-ATGATACA
1 AATGCGAATGTC-TTTCTTCTGATGAAAATGCAAGA-AATACA
19415824 AATGC
1 AATGC
19415829 CTCTTTGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 1 0.03
41 35 0.90
42 3 0.08
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (41 bp):
AATGCGAATGTCTTTCTTCTGATGAAAATGCAAGAAATACA
Found at i:19417775 original size:14 final size:14
Alignment explanation
Indices: 19417756--19417785 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19417746 CCTTCTAAGG
*
19417756 TTTCTTTTTTTCTT
1 TTTCTTTTTTTATT
19417770 TTTCTTTTTTTATT
1 TTTCTTTTTTTATT
19417784 TT
1 TT
19417786 CCACATTTGC
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:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTTTATT
Found at i:19427013 original size:10 final size:9
Alignment explanation
Indices: 19426991--19427024 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
19426981 ATTAAAACTA
19426991 TTTTTTTC-
1 TTTTTTTCT
19426999 TTTTTTTCT
1 TTTTTTTCT
19427008 TGTTTTTTCT
1 T-TTTTTTCT
19427018 TTTTTTT
1 TTTTTTT
19427025 TTCATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:19430715 original size:35 final size:36
Alignment explanation
Indices: 19430641--19430715 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
19430631 TATACTTGTA
* ** * * *
19430641 GATTTGTCATATCAATTTTTTGGTGCCGTTGTTGGG
1 GATTTGTCATATCAAATTTTTGGCACCATTATTGAG
19430677 GATTTGTC-TATCAAATTTTTGGCACCATTATTGAG
1 GATTTGTCATATCAAATTTTTGGCACCATTATTGAG
19430712 GATT
1 GATT
19430716 GGTTCCTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (36 bp):
GATTTGTCATATCAAATTTTTGGCACCATTATTGAG
Found at i:19433316 original size:7 final size:7
Alignment explanation
Indices: 19433306--19433424 Score: 67
Period size: 7 Copynumber: 18.0 Consensus size: 7
19433296 GGGGTTCAAG
19433306 TTAGGGT
1 TTAGGGT
*
19433313 TTAGGAT
1 TTAGGGT
*
19433320 TTAGAG-
1 TTAGGGT
**
19433326 TTAAAGT
1 TTAGGGT
19433333 TTAGGGTT
1 TTAGGG-T
19433341 TTA--GT
1 TTAGGGT
*
19433346 TTAGAGT
1 TTAGGGT
*
19433353 TTA-GGA
1 TTAGGGT
**
19433359 TTAATGT
1 TTAGGGT
19433366 TTAGGGT
1 TTAGGGT
19433373 TTAGGGT
1 TTAGGGT
19433380 TTAGGG-
1 TTAGGGT
19433386 TTAGGG-
1 TTAGGGT
*
19433392 TT-GGAT
1 TTAGGGT
*
19433398 TTAAGGT
1 TTAGGGT
19433405 TATAGGG-
1 T-TAGGGT
19433412 TTAGGG-
1 TTAGGGT
19433418 TTAGGGT
1 TTAGGGT
19433425 GTTTGAATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
5 6 0.07
6 31 0.36
7 42 0.48
8 8 0.09
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:19433327 original size:20 final size:20
Alignment explanation
Indices: 19433304--19433393 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
19433294 TAGGGGTTCA
19433304 AGTTAGGGTTTAGGATTTAG
1 AGTTAGGGTTTAGGATTTAG
** *
19433324 AGTTAAAGTTTAGGGTTTTAG
1 AGTTAGGGTTTA-GGATTTAG
* *
19433345 -TTTAGAGTTTAGGA-TTA-
1 AGTTAGGGTTTAGGATTTAG
*
19433362 ATGTTTAGGGTTTAGGGTTTAG
1 A-G-TTAGGGTTTAGGATTTAG
*
19433384 GGTTAGGGTT
1 AGTTAGGGTT
19433394 GGATTTAAGG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
18 3 0.06
19 2 0.04
20 38 0.70
21 11 0.20
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (20 bp):
AGTTAGGGTTTAGGATTTAG
Found at i:19433356 original size:33 final size:33
Alignment explanation
Indices: 19433311--19433374 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
19433301 TCAAGTTAGG
19433311 GTTTAGGATTTA-GAGTTAAAGTTTAGGGTTTTA
1 GTTTAGGATTTAGGA-TTAAAGTTTAGGGTTTTA
*
19433344 GTTTA-GAGTTTAGGATTAATGTTTAGGGTTT
1 GTTTAGGA-TTTAGGATTAAAGTTTAGGGTTT
19433375 AGGGTTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.07
33 24 0.86
34 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (33 bp):
GTTTAGGATTTAGGATTAAAGTTTAGGGTTTTA
Found at i:19436227 original size:45 final size:46
Alignment explanation
Indices: 19436047--19436317 Score: 228
Period size: 45 Copynumber: 5.7 Consensus size: 46
19436037 GTAGGTAACG
* *
19436047 AACTTTAAGAAAATCTGTCTGGAAAAGGCTCATATAAAATAGGCATCA
1 AACTTT-A-AAAATATGTCTAGAAAAGGCTCATATAAAATAGGCATCA
* * **
19436095 AACTTTTAAAA-A--TCTAGAAAATGACTCATATAAAATAGATATCA
1 AACTTTAAAAATATGTCTAGAAAA-GGCTCATATAAAATAGGCATCA
* * * *
19436139 AACTTAAAAAAAATCTGTCTAGAAAAAGGCTCTTATGAAATAGGCATCA
1 AACTT--TAAAAATATGTCTAG-AAAAGGCTCATATAAAATAGGCATCA
* **
19436188 AACTTTAAAAATATGTCTTG-AAAGGCTTTTATAAAATAGGCATCA
1 AACTTTAAAAATATGTCTAGAAAAGGCTCATATAAAATAGGCATCA
* * * * *
19436233 AACTTTAAAAATCTATCTAGAAAGGGCTCCA-ATGAAATAAGCATCA
1 AACTTTAAAAATATGTCTAGAAAAGGCT-CATATAAAATAGGCATCA
*
19436279 AACTTTTTTTAAAAAATATGTCTAGAAAAGGCTAATATA
1 AAC----TTT-AAAAATATGTCTAGAAAAGGCTCATATA
19436318 TCTTGGAAAA
Statistics
Matches: 176, Mismatches: 32, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
43 8 0.05
44 24 0.14
45 40 0.23
46 30 0.17
47 12 0.07
48 6 0.03
49 27 0.15
50 8 0.05
51 21 0.12
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (46 bp):
AACTTTAAAAATATGTCTAGAAAAGGCTCATATAAAATAGGCATCA
Found at i:19436243 original size:92 final size:90
Alignment explanation
Indices: 19436047--19436284 Score: 248
Period size: 93 Copynumber: 2.6 Consensus size: 90
19436037 GTAGGTAACG
* * *
19436047 AACTTTAAGAAAATCTGTCTGGAAAAGGCTCATATAAAATAGGCATCAAACTTTTAAAAATCTAG
1 AACTTT-A-AAAATCTGTCTAGAAAAGGCTCATATGAAATAGGCATCAAACTTTAAAAAATCTAG
*
19436112 AAAATGACTCATATAAAATAGATATCA
64 AAAATGACTCATATAAAATAGACATCA
* *
19436139 AACTTAAAAAAAATCTGTCTAGAAAAAGGCTCTTATGAAATAGGCATCAAACTTTAAAAATATGT
1 AACTT--TAAAAATCTGTCTAG-AAAAGGCTCATATGAAATAGGCATCAAACTTTAAAAA-A--T
* * ** *
19436204 CTTG-AAA-GGCTTTTATAAAATAGGCATCA
60 CTAGAAAATGACTCATATAAAATAGACATCA
* * *
19436233 AACTTTAAAAATCTATCTAGAAAGGGCTCCA-ATGAAATAAGCATCAAACTTT
1 AACTTTAAAAATCTGTCTAGAAAAGGCT-CATATGAAATAGGCATCAAACTTT
19436285 TTTTAAAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
91 27 0.22
92 31 0.25
93 35 0.28
94 23 0.19
95 3 0.02
96 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (90 bp):
AACTTTAAAAATCTGTCTAGAAAAGGCTCATATGAAATAGGCATCAAACTTTAAAAAATCTAGAA
AATGACTCATATAAAATAGACATCA
Found at i:19437093 original size:26 final size:26
Alignment explanation
Indices: 19437047--19437098 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
19437037 TTTTCCAATT
* *
19437047 AATGATGAACAAATGGTTTGAATGAA
1 AATGATGAAAAAAAGGTTTGAATGAA
*
19437073 AATGAT-AAAAAAAGGTATTGATTGAA
1 AATGATGAAAAAAAGGT-TTGAATGAA
19437099 GTTATGGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.27
Consensus pattern (26 bp):
AATGATGAAAAAAAGGTTTGAATGAA
Found at i:19437548 original size:12 final size:12
Alignment explanation
Indices: 19437531--19437601 Score: 72
Period size: 12 Copynumber: 5.7 Consensus size: 12
19437521 GATCTTCCCC
19437531 TTTTTTTCTTCT
1 TTTTTTTCTTCT
*
19437543 TTTTTTTCTTCA
1 TTTTTTTCTTCT
19437555 TTTTTTTCTT-T
1 TTTTTTTCTTCT
*
19437566 TTTCTTTTTTTCCT
1 TTT-TTTTCTT-CT
*
19437580 TCTTCTTTCTTTCT
1 T-TTTTTTC-TTCT
19437594 TTTTTTTC
1 TTTTTTTC
19437602 AAGCATAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
11 3 0.06
12 27 0.56
13 6 0.12
14 8 0.17
15 4 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:19437558 original size:24 final size:24
Alignment explanation
Indices: 19437531--19437601 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
19437521 GATCTTCCCC
19437531 TTTTTTTCTTCTTTTTTTTCTTCA
1 TTTTTTTCTTCTTTTTTTTCTTCA
* *
19437555 TTTTTTTCTT-TTTTCTTTTTTTCC
1 TTTTTTTCTTCTTTT-TTTTCTTCA
19437579 TTCTTCTTTCTTTCTTTTTTTTC
1 TT-TT-TTTC-TTCTTTTTTTTC
19437602 AAGCATAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.10
24 19 0.49
25 2 0.05
26 4 0.10
27 6 0.15
28 4 0.10
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTCTTCTTTTTTTTCTTCA
Found at i:19437567 original size:31 final size:30
Alignment explanation
Indices: 19437532--19437598 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
19437522 ATCTTCCCCT
* *
19437532 TTTTTTCTTCTTTTT-TTTCTTCATTTTTTTC
1 TTTTTTCTT-TTTTTCCTTCTTC-TTTCTTTC
19437563 TTTTTTCTTTTTTTCCTTCTTCTTTCTTTC
1 TTTTTTCTTTTTTTCCTTCTTCTTTCTTTC
19437593 TTTTTT
1 TTTTTT
19437599 TTCAAGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTTTTCTTTTTTTCCTTCTTCTTTCTTTC
Found at i:19437568 original size:19 final size:18
Alignment explanation
Indices: 19437544--19437599 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
19437534 TTTTCTTCTT
19437544 TTTTTTCTTCATTTTTTTC
1 TTTTTTCTTC-TTTTTTTC
19437563 TTTTTTCTT-TTTTTCCTTC
1 TTTTTTCTTCTTTTT--TTC
*
19437582 TTCTTTCTTTCTTTTTTT
1 TTTTTTC-TTCTTTTTTT
19437600 TCAAGCATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 5 0.16
19 20 0.62
20 2 0.06
21 5 0.16
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTCTTTTTTTC
Found at i:19437577 original size:15 final size:15
Alignment explanation
Indices: 19437532--19437598 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
19437522 ATCTTCCCCT
19437532 TTTTTTCTTCTTTTT-
1 TTTTTTCTT-TTTTTC
*
19437547 TTTCTTCATTTTTTTC
1 TTTTTTC-TTTTTTTC
19437563 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* * *
19437578 CTTCTTCTTTCTTTC
1 TTTTTTCTTTTTTTC
19437593 TTTTTT
1 TTTTTT
19437599 TTCAAGCATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 35 0.81
16 8 0.19
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:19437599 original size:31 final size:32
Alignment explanation
Indices: 19437530--19437599 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
19437520 AGATCTTCCC
* *
19437530 CTTTTTTTCTTCTTTTTTTTCTTCATTTTTTT
1 CTTTTTTTCTTCTTTTTCTTCTTCATTTCTTT
19437562 C-TTTTTTCTT-TTTTTCCTTCTTC-TTTCTTT
1 CTTTTTTTCTTCTTTTT-CTTCTTCATTTCTTT
19437592 CTTTTTTT
1 CTTTTTTT
19437600 TCAAGCATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 12 0.35
31 21 0.62
32 1 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (32 bp):
CTTTTTTTCTTCTTTTTCTTCTTCATTTCTTT
Found at i:19437841 original size:11 final size:10
Alignment explanation
Indices: 19437830--19437876 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
19437820 TTAAACAATA
*
19437830 AATAATATAT
1 AATAATAAAT
19437840 AATATATAAAT
1 AATA-ATAAAT
19437851 AATAATGAAAT
1 AATAAT-AAAT
19437862 AATAA-AAAT
1 AATAATAAAT
19437871 AA-AATA
1 AATAATA
19437877 TATATAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 2 0.06
9 7 0.21
10 6 0.18
11 18 0.55
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AATAATAAAT
Found at i:19437865 original size:14 final size:13
Alignment explanation
Indices: 19437826--19437873 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
19437816 CTCATTAAAC
19437826 AATAAATAATATAT
1 AATAAATAATA-AT
*
19437840 AATATATAAATAAT
1 AATAAAT-AATAAT
*
19437854 AATGAAATAATAAA
1 AAT-AAATAATAAT
19437868 AATAAA
1 AATAAA
19437874 ATATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 3 0.10
14 19 0.66
15 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:19439009 original size:17 final size:18
Alignment explanation
Indices: 19438970--19439009 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
19438960 TAAACAAAAA
19438970 GGAAAACTGGCAGCAAAC
1 GGAAAACTGGCAGCAAAC
* *
19438988 AGAAAATTGGCAG-AAAC
1 GGAAAACTGGCAGCAAAC
19439005 GGAAA
1 GGAAA
19439010 GCAGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.15, G:0.28, T:0.07
Consensus pattern (18 bp):
GGAAAACTGGCAGCAAAC
Found at i:19439786 original size:3 final size:3
Alignment explanation
Indices: 19439771--19439817 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
19439761 CCTTTTACAA
* * * *
19439771 TAT TAT TAG TAT TAT TAA TAT TAT CAT TAT TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19439818 CCATTATATG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19439799 original size:12 final size:12
Alignment explanation
Indices: 19439772--19439824 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
19439762 CTTTTACAAT
* *
19439772 ATTATTAGTATT
1 ATTATTATTATC
*
19439784 ATTAATATTATC
1 ATTATTATTATC
* *
19439796 ATTATTATTGTT
1 ATTATTATTATC
*
19439808 ATTATTATTACC
1 ATTATTATTATC
19439820 ATTAT
1 ATTAT
19439825 ATGATTATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:19440112 original size:14 final size:13
Alignment explanation
Indices: 19440079--19440117 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
19440069 GAAAAATTAT
19440079 TAAATAATAAAAA
1 TAAATAATAAAAA
19440092 TAAAAATAATAAAAGA
1 T--AAATAATAAAA-A
19440108 TAAATAATAA
1 TAAATAATAA
19440118 TGATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 11 0.48
16 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:19440114 original size:20 final size:20
Alignment explanation
Indices: 19440089--19440126 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19440079 TAAATAATAA
19440089 AAATAAAAATAATAAAAGAT
1 AAATAAAAATAATAAAAGAT
* *
19440109 AAATAATAATGATAAAAG
1 AAATAAAAATAATAAAAG
19440127 TTTTAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATAAAAATAATAAAAGAT
Found at i:19440278 original size:13 final size:13
Alignment explanation
Indices: 19440260--19440309 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
19440250 CTAAGACCCA
19440260 AAAACCCTAAAAT
1 AAAACCCTAAAAT
*
19440273 AAAACCCTAAAGT
1 AAAACCCTAAAAT
*
19440286 AAAACCCTAAAAC
1 AAAACCCTAAAAT
*
19440299 GAAACCCTAAA
1 AAAACCCTAAA
19440310 CACTCAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.58, C:0.26, G:0.04, T:0.12
Consensus pattern (13 bp):
AAAACCCTAAAAT
Found at i:19440295 original size:26 final size:26
Alignment explanation
Indices: 19440260--19440309 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
19440250 CTAAGACCCA
*
19440260 AAAACCCTAAAATAAAACCCTAAAGT
1 AAAACCCTAAAACAAAACCCTAAAGT
*
19440286 AAAACCCTAAAACGAAACCCTAAA
1 AAAACCCTAAAACAAAACCCTAAA
19440310 CACTCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.58, C:0.26, G:0.04, T:0.12
Consensus pattern (26 bp):
AAAACCCTAAAACAAAACCCTAAAGT
Found at i:19440451 original size:19 final size:18
Alignment explanation
Indices: 19440427--19440472 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
19440417 CTAAAAAAAC
19440427 CCTAAATCCTAGGTGAAAT
1 CCTAAA-CCTAGGTGAAAT
*
19440446 CCTAAACCTTAGGTGGAAT
1 CCTAAACC-TAGGTGAAAT
*
19440465 CCAAAACC
1 CCTAAACC
19440473 CTAAGTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (18 bp):
CCTAAACCTAGGTGAAAT
Found at i:19440686 original size:27 final size:28
Alignment explanation
Indices: 19440638--19440697 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
19440628 TCCATATTTT
* *
19440638 AAAATAAAAATAATTAAATTAAAAATTA
1 AAAATAAAAATAATGAAATTAAAAATAA
** *
19440666 AAAATAAAAAT-ATGATTTTAAATATAA
1 AAAATAAAAATAATGAAATTAAAAATAA
19440693 AAAAT
1 AAAAT
19440698 CACACCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATAAAAATAATGAAATTAAAAATAA
Found at i:19448932 original size:9 final size:8
Alignment explanation
Indices: 19448916--19448972 Score: 87
Period size: 8 Copynumber: 7.0 Consensus size: 8
19448906 AATATATAAA
*
19448916 TTAAAATT
1 TTAAAAAT
19448924 TTAAAAAT
1 TTAAAAAT
19448932 TTAAAAAAT
1 TT-AAAAAT
19448941 TTAAAAAT
1 TTAAAAAT
19448949 TTAAAAAT
1 TTAAAAAT
19448957 TTAAAAAT
1 TTAAAAAT
*
19448965 ATAAAAAT
1 TTAAAAAT
19448973 ATATAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
8 38 0.83
9 8 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TTAAAAAT
Found at i:19448945 original size:25 final size:25
Alignment explanation
Indices: 19448916--19448981 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
19448906 AATATATAAA
*
19448916 TTAAAATTTTAAAAATTTAAAAAAT
1 TTAAAAATTTAAAAATTTAAAAAAT
19448941 TTAAAAATTTAAAAATTT-AAAAAT
1 TTAAAAATTTAAAAATTTAAAAAAT
*
19448965 ATAAAAATATATAAAAA
1 TTAAAAAT-T-TAAAAA
19448982 ATACAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 13 0.35
25 18 0.49
26 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TTAAAAATTTAAAAATTTAAAAAAT
Found at i:19448973 original size:8 final size:8
Alignment explanation
Indices: 19448900--19449033 Score: 80
Period size: 8 Copynumber: 16.8 Consensus size: 8
19448890 AATAATAGTA
19448900 ATAATAAAT
1 ATAA-AAAT
*
19448909 ATATAAAT
1 ATAAAAAT
*
19448917 -TAAAATT
1 ATAAAAAT
*
19448924 TTAAAAAT
1 ATAAAAAT
*
19448932 TTAAAAAAT
1 AT-AAAAAT
*
19448941 TTAAAAAT
1 ATAAAAAT
*
19448949 TTAAAAAT
1 ATAAAAAT
*
19448957 TTAAAAAT
1 ATAAAAAT
19448965 ATAAAAAT
1 ATAAAAAT
*
19448973 ATATAAAAA
1 ATA-AAAAT
19448982 ATACAAAAT
1 ATA-AAAAT
*
19448991 -TCAAAAT
1 ATAAAAAT
*
19448998 -TCAAAAT
1 ATAAAAAT
*
19449005 ATAAAAAA
1 ATAAAAAT
*
19449013 ATTCAAAAT
1 A-TAAAAAT
19449022 -T-AAAAT
1 ATAAAAAT
19449028 ATAAAA
1 ATAAAA
19449034 CAATAACAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
6 5 0.05
7 19 0.18
8 54 0.51
9 27 0.26
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAAAAAT
Done.