Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 89 of 198
Found at i:28679972 original size:36 final size:35
Alignment explanation
Indices: 28679930--28680021 Score: 121
Period size: 36 Copynumber: 2.6 Consensus size: 35
28679920 AATTGTGCCT
* *
28679930 TGCACTGGTCAAATAAACCAACGATGTTTTGCGCCC
1 TGCACTGGTCAGATAAACCAACGATGTTTTGC-ACC
* *
28679966 TGCACTGGTCAGATAAATCGACGATGTTTTGCACC
1 TGCACTGGTCAGATAAACCAACGATGTTTTGCACC
*
28680001 TAGCACTGGTCGGATAAACCA
1 T-GCACTGGTCAGATAAACCA
28680022 CAATAATTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 3 0.06
36 45 0.94
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (35 bp):
TGCACTGGTCAGATAAACCAACGATGTTTTGCACC
Found at i:28684064 original size:28 final size:28
Alignment explanation
Indices: 28684003--28684118 Score: 128
Period size: 28 Copynumber: 4.2 Consensus size: 28
28683993 GTGACAGTAT
* *
28684003 AGTGTGGGCCTT-CCCTAATATAGTAAC
1 AGTGTGGGCCTTACCCCAATACAGTAAC
*
28684030 AGTGTGGGCCTTACCCCAAAACAGTAAC
1 AGTGTGGGCCTTACCCCAATACAGTAAC
* * *
28684058 AATGTGGGCCTTAGCCCAATATAG-AATC
1 AGTGTGGGCCTTACCCCAATACAGTAA-C
* * *
28684086 AGTGTGGGCCTTAGCCCAATACAGAAAT
1 AGTGTGGGCCTTACCCCAATACAGTAAC
28684114 AGTGT
1 AGTGT
28684119 AGTGCAATAA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.18
28 60 0.79
29 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (28 bp):
AGTGTGGGCCTTACCCCAATACAGTAAC
Found at i:28684092 original size:56 final size:55
Alignment explanation
Indices: 28684005--28684109 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 55
28683995 GACAGTATAG
28684005 TGTGGGCCTTCCCTAATATAGTAACAGTGTGGGCCTTACCCCAAAACAGTAACAA
1 TGTGGGCCTTCCCTAATATAGTAACAGTGTGGGCCTTACCCCAAAACAGTAACAA
* *
28684060 TGTGGGCCTTAGCCC-AATATAG-AATCAGTGTGGGCCTTAGCCCAATACAG
1 TGTGGGCCTT--CCCTAATATAGTAA-CAGTGTGGGCCTTACCCCAAAACAG
28684110 AAATAGTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
55 12 0.27
56 30 0.67
57 3 0.07
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (55 bp):
TGTGGGCCTTCCCTAATATAGTAACAGTGTGGGCCTTACCCCAAAACAGTAACAA
Found at i:28684632 original size:80 final size:80
Alignment explanation
Indices: 28684533--28684864 Score: 384
Period size: 80 Copynumber: 4.1 Consensus size: 80
28684523 GGTATAACAT
* * *
28684533 TCATTTTACCTTATGGGGGTATTTCGGTCATTTTACTCTATGGGGGTATTTCAGTCATTTTACCT
1 TCATTTTACC-TATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCC
*
28684598 TAT-GGGATATTTCAG
65 TATAGGGATATTTCGG
* * *
28684613 TCATTTTACTCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCC
1 TCATTTTAC-CTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCC
*
28684678 TATAGGG-TATTTTGG
65 TATAGGGATATTTCGG
* * **
28684693 TCATTTTACCT-TATGAGGGTATTTCGGTTATTTTACCCTATGGGGATATTTTGGTCATTTTACC
1 TCATTTTACCTATA-G-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACC
* * *
28684757 CTATGGGGGTATTTCGA
64 CTATAGGGATATTTCGG
* * * * * *
28684774 TCATTTTACCATATCGAGGT-GTTCTAGTCATTTTACCCTATGAGGGTATTTCAATCATTTTACC
1 TCATTTTACC-TATAGGGGTATTTC-GGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACC
*
28684838 CTATAGCGATATTTCGG
64 CTATAGGGATATTTCGG
28684855 TCATTTTACC
1 TCATTTTACC
28684865 CTATTTTGGG
Statistics
Matches: 214, Mismatches: 30, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
78 2 0.01
79 3 0.01
80 128 0.60
81 78 0.36
82 2 0.01
83 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (80 bp):
TCATTTTACCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCT
ATAGGGATATTTCGG
Found at i:28684865 original size:27 final size:27
Alignment explanation
Indices: 28684533--28684868 Score: 369
Period size: 27 Copynumber: 12.5 Consensus size: 27
28684523 GGTATAACAT
* *
28684533 TCATTTTACCTTATGGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGG
* * *
28684560 TCATTTTACTCTATGGGGGTATTTCAG
1 TCATTTTACCCTATAGGGGTATTTCGG
* * *
28684587 TCATTTTACCTTAT-GGGATATTTCAG
1 TCATTTTACCCTATAGGGGTATTTCGG
* *
28684613 TCATTTTACTCTATAGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGG
28684640 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGG
*
28684667 TCATTTTACCCTATA-GGGTATTTTGG
1 TCATTTTACCCTATAGGGGTATTTCGG
*
28684693 TCATTTTACCTTAT-GAGGGTATTTCGG
1 TCATTTTACCCTATAG-GGGTATTTCGG
* *
28684720 TTATTTTACCCTAT-GGGGATATTTTGG
1 TCATTTTACCCTATAGGGG-TATTTCGG
* *
28684747 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGG
* * * * *
28684774 TCATTTTACCATATCGAGGT-GTTCTAG
1 TCATTTTACCCTATAGGGGTATTTC-GG
**
28684801 TCATTTTACCCTAT-GAGGGTATTTCAA
1 TCATTTTACCCTATAG-GGGTATTTCGG
* *
28684828 TCATTTTACCCTATAGCGATATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGG
28684855 TCATTTTACCCTAT
1 TCATTTTACCCTAT
28684869 TTTGGGGTCT
Statistics
Matches: 264, Mismatches: 36, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
26 53 0.20
27 203 0.77
28 8 0.03
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCGG
Found at i:28689772 original size:24 final size:25
Alignment explanation
Indices: 28689725--28689772 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
28689715 GCAGTATATA
*
28689725 AACATAAAAAATTAATAATCTAAAC
1 AACATAAAAAATTAACAATCTAAAC
* *
28689750 AACAT-AATAATTAACAATTTAAA
1 AACATAAAAAATTAACAATCTAAA
28689773 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.27
Consensus pattern (25 bp):
AACATAAAAAATTAACAATCTAAAC
Found at i:28690265 original size:83 final size:82
Alignment explanation
Indices: 28690118--28690275 Score: 178
Period size: 83 Copynumber: 1.9 Consensus size: 82
28690108 TAAAGGAAAG
* * *
28690118 CACGTCCTATAAGGCGCGTTTTCACGGATGTGGCAATGAAAATGTGCCTTGTAGGACGTGTTTTT
1 CACGTCCTATAAGGCGCATTTTCACGGATGTGGCAATGAAAATGTGCCCTGTAGAACGTGTTTTT
*
28690183 GTTTTTTTCTCCTCAAGA
66 -TTATTTTCTCCTCAAGA
** * * *
28690201 CACGTCCTATGTGGCGCATTTTCACTGATGTGG-AGGTGAAAACT-TGCCCTGTAGAATGCT-TT
1 CACGTCCTATAAGGCGCATTTTCACGGATGTGGCA-ATGAAAA-TGTGCCCTGTAGAACG-TGTT
28690263 TTTTTATTTTCTC
63 TTTTTATTTTCTC
28690276 TCTAAACTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
82 10 0.16
83 51 0.81
84 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (82 bp):
CACGTCCTATAAGGCGCATTTTCACGGATGTGGCAATGAAAATGTGCCCTGTAGAACGTGTTTTT
TTATTTTCTCCTCAAGA
Found at i:28700614 original size:31 final size:31
Alignment explanation
Indices: 28700574--28700650 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
28700564 CTGAGATTTT
*
28700574 GCCCAGGCCCGGCCCGTGGAAAAAATAAGAA
1 GCCCGGGCCCGGCCCGTGGAAAAAATAAGAA
28700605 GCCCGGGCCCGGCCCGTGGAAAAAATAAGAA
1 GCCCGGGCCCGGCCCGTGGAAAAAATAAGAA
28700636 GCCCGGGCCCGGCCC
1 GCCCGGGCCCGGCCC
28700651 ATTTTTTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.35, G:0.32, T:0.05
Consensus pattern (31 bp):
GCCCGGGCCCGGCCCGTGGAAAAAATAAGAA
Found at i:28703432 original size:43 final size:42
Alignment explanation
Indices: 28703379--28703498 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
28703369 CCCGAGGTGT
* *
28703379 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCCATATGC
1 GATTACGTGTAAGACCATATCTGGGACA-TGGCATCCATATGC
* ** *
28703422 GATTACGTGTAAGACCCTATCTGGGACAGTGGCATTGATATGT
1 GATTACGTGTAAGACCATATCTGGGACA-TGGCATCCATATGC
* * *
28703465 GATAACATGTAAGACCATATCTGGGATATGGCAT
1 GATTACGTGTAAGACCATATCTGGGACATGGCAT
28703499 TGTATGTGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 6 0.09
43 60 0.91
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (42 bp):
GATTACGTGTAAGACCATATCTGGGACATGGCATCCATATGC
Found at i:28706225 original size:28 final size:28
Alignment explanation
Indices: 28706172--28706227 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
28706162 CCTGAACATG
* *
28706172 CATGAATGTCTAGCCGAATTTAAGACAA
1 CATGAATGTCCAGCCGAACTTAAGACAA
*
28706200 CATGAATG-CCAGCCGAACCTTGAGACAA
1 CATGAATGTCCAGCCGAA-CTTAAGACAA
28706228 TCTGTAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (28 bp):
CATGAATGTCCAGCCGAACTTAAGACAA
Found at i:28706877 original size:39 final size:38
Alignment explanation
Indices: 28706822--28706920 Score: 135
Period size: 39 Copynumber: 2.6 Consensus size: 38
28706812 GAATATAATT
* * *
28706822 ATTATAATTACCATAATTATAATAATGTTTGAACGAAAA
1 ATTATAATTACAATAATTATAATAATATTCGAACG-AAA
* * *
28706861 ATTACAATTACAATAATTATAATAATATTCGATCGTAA
1 ATTATAATTACAATAATTATAATAATATTCGAACGAAA
28706899 ATTATAATTACAATAATTATAA
1 ATTATAATTACAATAATTATAA
28706921 CAAGGATTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 23 0.43
39 30 0.57
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (38 bp):
ATTATAATTACAATAATTATAATAATATTCGAACGAAA
Found at i:28719198 original size:28 final size:29
Alignment explanation
Indices: 28719142--28719198 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
28719132 ATTCTCTTAG
*
28719142 TTTTTATGGCTCAACTAAATCCCTATGAC
1 TTTTTATGGCTCAACTAAAACCCTATGAC
28719171 TTTTT-TGGCTCAACTAGAAACCCT-TGAC
1 TTTTTATGGCTCAACTA-AAACCCTATGAC
28719199 AATCTACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (29 bp):
TTTTTATGGCTCAACTAAAACCCTATGAC
Found at i:28732829 original size:35 final size:35
Alignment explanation
Indices: 28732790--28732858 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
28732780 TGTCTCGGTT
*
28732790 GGACTAGCTCTGATGAGCATTGGTGTGTTTCGGAA
1 GGACTAGCTCTGATGAGCATTGGTGTGTTCCGGAA
* * *
28732825 GGACTAGCTTTTATGAGTATTGGTGTGTTCCGGA
1 GGACTAGCTCTGATGAGCATTGGTGTGTTCCGGA
28732859 GGGATTGGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (35 bp):
GGACTAGCTCTGATGAGCATTGGTGTGTTCCGGAA
Found at i:28737169 original size:20 final size:20
Alignment explanation
Indices: 28737146--28737255 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
28737136 CATCACAGGA
*
28737146 GCACCGAAGTGCAGACAGAG
1 GCACCGAAGTGCAAACAGAG
* * * *
28737166 GCA-CAAATGTGTAAAAAGGG
1 GCACCGAA-GTGCAAACAGAG
* *
28737186 GCACCGTAGTGCGAACAG-G
1 GCACCGAAGTGCAAACAGAG
* * * *
28737205 ACACCGAAGTGTATACAAAG
1 GCACCGAAGTGCAAACAGAG
* *
28737225 GCGCTGAAGTGCAAACAGAG
1 GCACCGAAGTGCAAACAGAG
28737245 GCACCGAAGTG
1 GCACCGAAGTG
28737256 AAAATCCCAT
Statistics
Matches: 63, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
19 16 0.25
20 45 0.71
21 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.32, T:0.11
Consensus pattern (20 bp):
GCACCGAAGTGCAAACAGAG
Found at i:28740674 original size:10 final size:10
Alignment explanation
Indices: 28740659--28740683 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28740649 TTTATAATAA
28740659 ATTTTGATTT
1 ATTTTGATTT
28740669 ATTTTGATTT
1 ATTTTGATTT
28740679 ATTTT
1 ATTTT
28740684 CGACAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
ATTTTGATTT
Found at i:28748501 original size:35 final size:34
Alignment explanation
Indices: 28748462--28748542 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
28748452 TAATTACCCA
28748462 CAATTTAAAA-CATACCAAATTGATCAAATCCATAC
1 CAATTTAAAAGCAT--CAAATTGATCAAATCCATAC
* *
28748497 CAATTCTAAAAGCATTAAATTGATCATATCCATAC
1 CAATT-TAAAAGCATCAAATTGATCAAATCCATAC
28748532 CATATTTAAAA
1 CA-ATTTAAAA
28748543 ACCAAACACC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 30 0.73
36 8 0.20
37 3 0.07
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.30
Consensus pattern (34 bp):
CAATTTAAAAGCATCAAATTGATCAAATCCATAC
Found at i:28748980 original size:20 final size:20
Alignment explanation
Indices: 28748950--28749044 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
28748940 GGCACGTAAC
*
28748950 TACAATTAGGGGTACCGAAG
1 TACAATCAGGGGTACCGAAG
* *
28748970 TACAAACAGGGGCA-CGTAAG
1 TACAATCAGGGGTACCG-AAG
* * *
28748990 TGCAATCAAGGATACCGAAG
1 TACAATCAGGGGTACCGAAG
* **
28749010 TACAATCAGGGGCACATAAG
1 TACAATCAGGGGTACCGAAG
*
28749030 TGCAATCAGGGGTAC
1 TACAATCAGGGGTAC
28749045 TAAAGTAAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.04
20 53 0.93
21 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (20 bp):
TACAATCAGGGGTACCGAAG
Found at i:28749006 original size:40 final size:40
Alignment explanation
Indices: 28748939--28749059 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
28748929 AATGTAAATA
* * *
28748939 GGGCACGTAACTACAATTAGGGGTACCGAAGTACAAACAG
1 GGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAACAG
* * *
28748979 GGGCACGTAAGTGCAATCAAGGATACCGAAGTACAATCAG
1 GGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAACAG
* **
28749019 GGGCACATAAGTGCAATCAGGGGTACTAAAGTA-AAACAG
1 GGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAACAG
28749058 GG
1 GG
28749060 TATAATTTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 7 0.10
40 62 0.90
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (40 bp):
GGGCACGTAAGTGCAATCAGGGGTACCGAAGTACAAACAG
Found at i:28760629 original size:14 final size:14
Alignment explanation
Indices: 28760610--28760638 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28760600 TCAAAACCAT
28760610 ATAAATGACACAAA
1 ATAAATGACACAAA
28760624 ATAAATGACACAAA
1 ATAAATGACACAAA
28760638 A
1 A
28760639 CTAACCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAATGACACAAA
Found at i:28763322 original size:21 final size:21
Alignment explanation
Indices: 28763298--28763348 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
28763288 ATTTTCTAAA
28763298 ACCACTTGACCTTAGGTTCTT
1 ACCACTTGACCTTAGGTTCTT
28763319 ACCACTTGACCTTAGGTTCTT
1 ACCACTTGACCTTAGGTTCTT
28763340 ACCACTTGA
1 ACCACTTGA
28763349 AATTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (21 bp):
ACCACTTGACCTTAGGTTCTT
Found at i:28764205 original size:6 final size:6
Alignment explanation
Indices: 28764194--28764268 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
28764184 AGATTGCAAG
* * * * *
28764194 TTTCCA TTTCCA TTTTCA TTTTCA TTTTCA TTTTCA TTTCCA CTTCCA
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
*
28764242 TTTCCA TTTCCA TTTTCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTT
28764269 TTGGAAACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTCCA
Found at i:28773193 original size:50 final size:49
Alignment explanation
Indices: 28773078--28773198 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
28773068 GTGCCAAATA
* * * * *
28773078 CATGTCCCAGACATGGCCTTACATGGGATGTTTCTTGTACTGCCAATGT
1 CATGTCCCAGACATGGTCTTACATGAGATGTTTCATATACTGCCAATGC
* * * *
28773127 CATATCCCAGATATGGTCTTACATGAGA-GTTCTCATATCAGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGAGATGTT-TCATAT-ACTGCCAATGC
28773177 CATGTCCCAGACATGGTCTTAC
1 CATGTCCCAGACATGGTCTTAC
28773199 GGGGGACCTC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 3 0.05
49 28 0.47
50 28 0.47
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (49 bp):
CATGTCCCAGACATGGTCTTACATGAGATGTTTCATATACTGCCAATGC
Found at i:28773211 original size:50 final size:50
Alignment explanation
Indices: 28773118--28773309 Score: 159
Period size: 50 Copynumber: 3.8 Consensus size: 50
28773108 TTTCTTGTAC
* * * * * * ** * *
28773118 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCAG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
28773168 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * * * *
28773218 TGCCAACGTCATGTCCGAAACATGGTCTTACATGGTACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * * * *
28773268 TGCTAATTCCATGTCCCATACATGTTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCT
28773310 TTACCAAAAT
Statistics
Matches: 113, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 113 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:28781107 original size:14 final size:14
Alignment explanation
Indices: 28781088--28781114 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28781078 AATAAGTTTC
28781088 TTCTATAAAATATT
1 TTCTATAAAATATT
28781102 TTCTATAAAATAT
1 TTCTATAAAATAT
28781115 AGCAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTCTATAAAATATT
Found at i:28785399 original size:25 final size:26
Alignment explanation
Indices: 28785361--28785416 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
28785351 ATTAAAAATT
*
28785361 ATAAAGTAATGTTAAGTTAAATTATA
1 ATAAAGTAAGGTTAAGTTAAATTATA
28785387 ATAAA-TAAGGTTAAGTTAAATTATA
1 ATAAAGTAAGGTTAAGTTAAATTATA
28785412 ATAAA
1 ATAAA
28785417 CAAAAGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.36
Consensus pattern (26 bp):
ATAAAGTAAGGTTAAGTTAAATTATA
Found at i:28787814 original size:19 final size:20
Alignment explanation
Indices: 28787787--28787830 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28787777 TCGAATGGTA
* *
28787787 CATGGTTTG-GCCACACAGC
1 CATGTTTTGAGCCACACAAC
28787806 CATGTTTTGAGCCACACAAC
1 CATGTTTTGAGCCACACAAC
28787826 CATGT
1 CATGT
28787831 GACCCCTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
CATGTTTTGAGCCACACAAC
Found at i:28798790 original size:12 final size:12
Alignment explanation
Indices: 28798775--28798799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28798765 TAAAAAAAAA
28798775 AAAAAGAAGAAG
1 AAAAAGAAGAAG
28798787 AAAAAGAAGAAG
1 AAAAAGAAGAAG
28798799 A
1 A
28798800 TAATATCTAC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:28799278 original size:48 final size:48
Alignment explanation
Indices: 28799202--28799296 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
28799192 TTTGCTTTTC
* *
28799202 ATTTATTACTAACTTATGAGATTTCTTGCGA-GAAATTCTATCAAGTGG
1 ATTTATTACCAACTTATGAGATTACTTGC-ATGAAATTCTATCAAGTGG
*
28799250 ATTTATTACCAACTTATGAGATTACTTGCATGAAATTCTATCTAGTG
1 ATTTATTACCAACTTATGAGATTACTTGCATGAAATTCTATCAAGTG
28799297 TTCATTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 1 0.02
48 42 0.98
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (48 bp):
ATTTATTACCAACTTATGAGATTACTTGCATGAAATTCTATCAAGTGG
Found at i:28815530 original size:12 final size:12
Alignment explanation
Indices: 28815513--28815540 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28815503 TAGTCGGGTA
28815513 TCCATTTTGGTC
1 TCCATTTTGGTC
28815525 TCCATTTTGGTC
1 TCCATTTTGGTC
28815537 TCCA
1 TCCA
28815541 ATTGCACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.29, G:0.14, T:0.46
Consensus pattern (12 bp):
TCCATTTTGGTC
Found at i:28826052 original size:20 final size:20
Alignment explanation
Indices: 28826027--28826066 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28826017 CGTAAAATGA
*
28826027 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28826047 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28826067 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28826056 original size:34 final size:35
Alignment explanation
Indices: 28826012--28826078 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28826002 CAGTAAAATA
*
28826012 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
28826046 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
28826079 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:28826082 original size:14 final size:15
Alignment explanation
Indices: 28826006--28826082 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28825996 GATTGCCAGT
* *
28826006 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
28826020 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
28826034 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
28826054 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
28826069 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
28826083 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:28828844 original size:14 final size:14
Alignment explanation
Indices: 28828825--28828852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28828815 CGGAAATTAA
28828825 GGAAAATATTTTCC
1 GGAAAATATTTTCC
28828839 GGAAAATATTTTCC
1 GGAAAATATTTTCC
28828853 ACCAAACAAA
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAAAATATTTTCC
Found at i:28831226 original size:113 final size:114
Alignment explanation
Indices: 28830957--28831248 Score: 340
Period size: 114 Copynumber: 2.6 Consensus size: 114
28830947 AAAATAAGCA
* * * *
28830957 TTAGCGGCGTTTTCCATAAAGCGCCGCAAAATACCTAATCCCAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTCAATAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * ** * *
28831022 TGGGGATTTAGCGGCGTTTTTTAAGAAATTGTCGCTAAGGCTCAGGCAT
66 CGGGGATTTAGCAGCGTTTTTTAAGAAAGCGCCGCTAACGCTCAGGCAT
* * * * *
28831071 TTAGCGGCGTTTTTAAAAAAGCGCCACAAAAAA-AGTAAGCCCAACGACGTC-ATTTCTGAGCTT
1 TTAGCGGCGTTTTCAATAAAGCGCCGCAAAAAACA-TAAGCCCAACGACGCCGTTTTCTGAGCTT
** *
28831134 TCGGGGATTTAGCAGCG-TTTTTGGGTAAGCGCCGCTAACGCTCAGGGC-T
65 TCGGGGATTTAGCAGCGTTTTTTAAGAAAGCGCCGCTAACGCTCA-GGCAT
* **
28831183 TTAGCGGCGTTTACGGTAAAGCGCCGCAAAGAAACATAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTCAATAAAGCGCCGCAAA-AAACATAAGCCCAACGACGCCGTTTTCTGAGCTT
28831248 T
65 T
28831249 TCACTGATTT
Statistics
Matches: 147, Mismatches: 26, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
112 45 0.31
113 47 0.32
114 55 0.37
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTCAATAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCAGCGTTTTTTAAGAAAGCGCCGCTAACGCTCAGGCAT
Found at i:28831304 original size:74 final size:73
Alignment explanation
Indices: 28831200--28831395 Score: 225
Period size: 73 Copynumber: 2.7 Consensus size: 73
28831190 CGTTTACGGT
* *
28831200 AAAGCGCCGCAAAGAA-ACATAAGCCCAACGACGCCGTTTTCTGAGCTTTTCACTGATTTAGCGG
1 AAAGCGCCACAAA-AATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTTCAC-GATTTAGCGG
28831264 CG-TTTTTAG
64 CGTTTTTTAG
* *** * * ** *
28831273 TTAAGCGTTGCAAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTTTTGGCGATTTAGTGGC
1 -AAAGCGCCACAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTTCACGATTTAGCGGC
28831338 GTTTTTTAG
65 GTTTTTTAG
* * *
28831347 AAAGCGCCACAAAAATACGTAAGCCCAACGATGCCGTTTTCGGAGCTTT
1 AAAGCGCCACAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
28831396 CGGGGGATTT
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
73 53 0.52
74 49 0.48
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (73 bp):
AAAGCGCCACAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTTCACGATTTAGCGGCG
TTTTTTAG
Found at i:28831371 original size:73 final size:74
Alignment explanation
Indices: 28831198--28831415 Score: 244
Period size: 74 Copynumber: 2.9 Consensus size: 74
28831188 GGCGTTTACG
** *
28831198 GTAAAGCGCCGCAAAGAA-ACATAAGCCCAACGACGCCGTTTTCTGAGCTTTTCACTGATTTAGC
1 GTAAAGCGCCGCAAA-AATACATAAGCCCAACGACGCCGTTTTCTGAGCTTTTGGC-GATTTAGT
28831262 GGCG-TTTTTA
64 GGCGTTTTTTA
* ** * * *
28831272 GTTAAGCGTTGCAAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTTTTGGCGATTTAGTGG
1 GTAAAGCGCCGCAAAAATACATAAGCCCAACGACGCCGTTTTCTGAGCTTTTGGCGATTTAGTGG
28831337 CGTTTTTTA
66 CGTTTTTTA
* * * * * *
28831346 G-AAAGCGCCACAAAAATACGTAAGCCCAACGATGCCGTTTTCGGAGCTTTCGGGGGATTTAGTG
1 GTAAAGCGCCGCAAAAATACATAAGCCCAACGACGCCGTTTTCTGAGCTTT-TGGCGATTTAGTG
*
28831410 ACGTTT
65 GCGTTT
28831416 ATGGGTAAGT
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
73 53 0.44
74 67 0.56
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (74 bp):
GTAAAGCGCCGCAAAAATACATAAGCCCAACGACGCCGTTTTCTGAGCTTTTGGCGATTTAGTGG
CGTTTTTTA
Found at i:28835412 original size:2 final size:2
Alignment explanation
Indices: 28835405--28835431 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28835395 CAAGCAAATC
28835405 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28835432 AACCTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28835816 original size:9 final size:9
Alignment explanation
Indices: 28835791--28836112 Score: 383
Period size: 9 Copynumber: 36.7 Consensus size: 9
28835781 TAATAACATA
*
28835791 ATAACTAAC
1 ATAACTTAC
28835800 ATAA--TAC
1 ATAACTTAC
*
28835807 ATAACCTAC
1 ATAACTTAC
28835816 ATAACTTAC
1 ATAACTTAC
28835825 ATAACTTAC
1 ATAACTTAC
28835834 ATAACTTAC
1 ATAACTTAC
* *
28835843 ATAAATTAA
1 ATAACTTAC
28835852 ATAACTTAC
1 ATAACTTAC
28835861 ATAACTTAC
1 ATAACTTAC
*
28835870 ATAACTTAA
1 ATAACTTAC
28835879 ATAACTTAC
1 ATAACTTAC
28835888 ATAA--TAC
1 ATAACTTAC
28835895 ATAAACTT-C
1 AT-AACTTAC
*
28835904 CTAACTTAC
1 ATAACTTAC
* *
28835913 ATTATTTAC
1 ATAACTTAC
28835922 ATAA--TAC
1 ATAACTTAC
** *
28835929 ATTGCCTAC
1 ATAACTTAC
28835938 ATAACTTAC
1 ATAACTTAC
* *
28835947 ATAAATTAA
1 ATAACTTAC
28835956 ATAACTTAC
1 ATAACTTAC
*
28835965 TTAACTTAC
1 ATAACTTAC
28835974 ATAACTTAC
1 ATAACTTAC
* *
28835983 ATAAATTAA
1 ATAACTTAC
28835992 ATAACTTAC
1 ATAACTTAC
28836001 ATAACTTAC
1 ATAACTTAC
28836010 ATAACTTAC
1 ATAACTTAC
* *
28836019 ATAAATTAA
1 ATAACTTAC
28836028 ATAACTTAC
1 ATAACTTAC
28836037 ATAACTTAC
1 ATAACTTAC
* *
28836046 ATAAATTAA
1 ATAACTTAC
28836055 ATAACTTAC
1 ATAACTTAC
*
28836064 ATAACTTAA
1 ATAACTTAC
28836073 ATAACTTAC
1 ATAACTTAC
28836082 ATAACTTAC
1 ATAACTTAC
28836091 ATAA--TAC
1 ATAACTTAC
28836098 ATAACTTAC
1 ATAACTTAC
28836107 ATAACT
1 ATAACT
28836113 CATTTATGGT
Statistics
Matches: 265, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
7 23 0.09
8 7 0.03
9 234 0.88
10 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28841617 original size:21 final size:21
Alignment explanation
Indices: 28841593--28841649 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
28841583 GATGTGGCAA
*
28841593 CGAGGGAAGCAGAGGCTACAG
1 CGAGAGAAGCAGAGGCTACAG
*
28841614 CGAGAGAAGCAGAGGCTATAG
1 CGAGAGAAGCAGAGGCTACAG
28841635 CGAGAGAAGCAGAGG
1 CGAGAGAAGCAGAGG
28841650 TTCAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.42, T:0.05
Consensus pattern (21 bp):
CGAGAGAAGCAGAGGCTACAG
Found at i:28842110 original size:42 final size:42
Alignment explanation
Indices: 28842037--28842245 Score: 197
Period size: 42 Copynumber: 5.0 Consensus size: 42
28842027 TTTTTTAAGA
* * * *
28842037 AAGCGCCGCTAAAGAACAT-TTCTTTTTGCGGCGTTTTTGTGT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTCTCT
* * * *
28842079 AAGCGTCGCTAAAAAATATGATCTTTAGCGGCGTTTTTCTCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
* * * *
28842121 ATA-CGCCGCTAAAGAACAAGATCTCTAGCGGCGTCTTTTTTTT
1 A-AGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTCTCT
* * * *
28842164 AAGCGCCGCTAAAGAACATGACCTTTAGTGGCGTTTTTTTCG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
** * *
28842206 AAATGCCACTAAAGAACATGACCTTTAGCGGCGTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCT
28842246 TTGTAAACGC
Statistics
Matches: 136, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
42 100 0.74
43 36 0.26
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
Found at i:28842197 original size:85 final size:84
Alignment explanation
Indices: 28842064--28842243 Score: 216
Period size: 85 Copynumber: 2.1 Consensus size: 84
28842054 ATTTCTTTTT
* * * * *
28842064 GCGGCGTTTTTGTGTAAGCGTCGCTAAAAAATATGATCTTTAGCGGCGTTTTTCTCCATACGCCG
1 GCGGCGTTTTTGTGTAAGCGCCGCTAAAAAACATGACCTTTAGCGGCGTTTTTCTCCAAACGCCA
*
28842129 CTAAAGAACAAGATCTCTA
66 CTAAAGAACAAGACCTCTA
* * * * * * *
28842148 GCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGACCTTTAGTGGCGTTTTTTTCGAAATGCC
1 GCGGCGT-TTTTGTGTAAGCGCCGCTAAAAAACATGACCTTTAGCGGCGTTTTTCTCCAAACGCC
* *
28842213 ACTAAAGAACATGACCTTTA
65 ACTAAAGAACAAGACCTCTA
28842233 GCGGCGTTTTT
1 GCGGCGTTTTT
28842244 CTTTGTAAAC
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
84 11 0.14
85 69 0.86
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (84 bp):
GCGGCGTTTTTGTGTAAGCGCCGCTAAAAAACATGACCTTTAGCGGCGTTTTTCTCCAAACGCCA
CTAAAGAACAAGACCTCTA
Found at i:28848554 original size:553 final size:553
Alignment explanation
Indices: 28846217--28850076 Score: 5998
Period size: 553 Copynumber: 7.0 Consensus size: 553
28846207 CAAAAATCAG
* * *
28846217 TCATAATTCATGATTAAACTGAAGCCACCAAAACCGAAAACAGTCCAATTCAAACCTTCATCACT
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
* * * * * * *
28846282 TACCCTAACACTACAAACAATTTCGATTACGATTCCATGATAAGAGAGCTCCTTTCTTCCC-AGT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGA-T
* * * *
28846346 TCACTGCTGCCAAAACTCGAAATCAAAAATGGAAAGAAAAGAATAGCATCGATTTGAGCAGTTAA
130 TCACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAA
* ** * * * **
28846411 AACGATTACTACAACCCACACGAAAACACCCTTTACACTTACCAAACTGCGCAAGAAAAGTAAAG
195 AACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAG
* * * *
28846476 AACTGAAAAC-CAGAATTGAATGACAGAATTGCGATGGAATATCAAAAGTGAGGAAACAAAAAGA
260 AACTGAAAACTGA-AATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGA
*
28846540 ATTTTGCCAGAACAC-AAAAAATGAATGT-AAAAATTTTAGGAGTTTCTAGAGAGAGAAAAA-A-
324 ATTTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATAT
* *
28846601 ATATCAAAACGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCCACTAACCCAC
389 ATATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
**
28846666 TAACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAATTGAGCAAAAATTA
454 TAACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTA
28846731 ACACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
519 ACACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* * *
28846766 TCATTATTCATGACTAAACCGAAACCACCAAAATCGACAACAGTCCAATTCAAACCTTCATCACT
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
28846831 TACCCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGAT
66 TA-CCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGAT
* * **
28846896 TCACTACTGCCAAAACTCGAAATCAACAATGGAAAGAAAAGAATAATATTGATTTGAACAGTTAA
130 TCACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAA
* *
28846961 AACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCACGTAAGGACAGCGAAG
195 AACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAG
* *
28847026 AACTAAAAACTGAAATTGAATGATAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAA
260 AACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAA
* * *
28847091 TTTTCCCAGAACACAAAAAAATGAATGTCAAAAATTTTGGGAGTTTTTAGAGAGAGAAAAATATA
325 TTTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATATA
* *
28847156 TATCAAAAAGAAAAAAAATAATATGATTATACCCAAATCCCTCGAATTGCTCCCCACTAACCCAC
390 TATCAAAAAG-AAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
* *
28847221 TAACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACGGAGCAAAAACTA
454 TAACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTA
* *
28847286 ACACCCTCGCTCCCGTAGAGATTCAAACAGAGGAA
519 ACACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* * * *
28847321 TCATAATTCATGATTAAACCGACACCACAAAAACTGACAACAGTCCAATTCAAACCTTCATCACA
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
* * *
28847386 TACCCCAACACTCCGAACGATTTCAATTACAATTCCATGAGAGGAGAGCCTCTTTCTTCCCGATT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
* * *
28847451 CACTACTGCCAAAACTTGAAATCAACAATGGAAAGAAAAGAATAGCATTGACTTGAACAGTTAAA
131 CACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAAA
* *
28847516 ACGGTTACCCCAACCCACACGAAAACACCCTTTACATTTACCAAACCGCGCAAGGACATCGAAGA
196 ACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAGA
* * * * **
28847581 ACTGAAAACTAAAATTGAATGATAAAATTGAGATGGAATTTCAAAAGTAAATAAACAAAAAGAAT
261 ACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAAT
* * *
28847646 TTTGCCAGAACACAAAACAATGAATGTCAAAAATTTTGGGAGTTTCTAGAGGGAGAAAAA-A-AT
326 TTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATATAT
28847709 AT-AAAACAG-AAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACT
391 ATCAAAA-AGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACT
* * *
28847772 AACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAATACACAACGGAGCAAAAATCAA
455 AACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTAA
* * * *
28847837 TACCCTCACTCCTGTAGAGATTCGAACACAAGAA
520 CACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* * * *
28847871 TCATAATTCATGATTAAACCGAAACCACCAAAATCGACAAAAGTCTAATTCAAACCTTCATCACA
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
* * *
28847936 TACCCCAACACTCCGAAAGATTTCGATTATGATTCCAGGAGAGGAGAGCCCCTTTCTTCCCGATT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
* **
28848001 CACTGCTGCCAAAACTAGAAATCAACAATAGAAAGAAAAGAATAGCATTGATTTGAGTAGTTAAA
131 CACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAAA
*
28848066 ACGGTTACCCCAACCCACACGAAAACACCTTTTACACTTACCAAACCGCGCAAGGACAGCGAAGA
196 ACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAGA
*
28848131 ACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAAGGAAACAAAAAGAAT
261 ACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAAT
*
28848196 TTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGTGAGAAAAATATAT
326 TTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATATAT
28848261 ATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACTA
391 ATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACTA
* **
28848326 ACAAACCACTTACTCAGAATCTCAACTTCTTTAAAACTCTAACACACAACCGAGCAAAAATTAAC
456 ACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTAAC
*
28848391 ACCCTCGCTCCCGTAGAGATTTGAACACAGGAA
521 ACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* * * * * *
28848424 TCATAATTCATGATCAAACCAAAACCACCAAAACCGACAATAGTCTAATTCAAACTTTCAACACT
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
*
28848489 TACCCCAACACTCCGAACGATTTCGATTACGATTCCACGAGAGGAGAGCCCCTTTCTTCCCGATT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
*
28848554 CACTGCTGCCAAAACTCA-AAATCAACAATGGAAAGAAAAGAATCGCATTGATTTGAACAGTTAA
131 CACTGCTGCCAAAACT-AGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAA
* *
28848618 AACGGTTACCCCAACCCACACGAAAAAACCCTTTACACTTACCAAACCGCGAAAGGACAGCGAAG
195 AACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAG
28848683 AACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAAGA
260 AACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAAC-AAAAAGA
* *
28848748 ATTTTGCCAGAGCAC-AAAAAATGAATGTAAAAAATTTTAGGAGTTTCTAGAGAGAGAAAAATAT
324 ATTTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATAT
28848812 ATATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
389 ATATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
* **
28848877 TAACAAACCACTTACTCAGAATCTCAAC-CACCCTAAAACTCTAATACACAATTGAGCAAAAATT
454 TAACAAACCACTTACTCAGAATCTCAACTC-CCCTAAAACTCTAACACACAACCGAGCAAAAATT
* *
28848941 AACACCCTCACTCCCGTAGAGATTCGAACACAAGAA
518 AACACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* * *
28848977 TCATAATTCATGATTAAACCGAAACCACCAAAACTGACAATAGTCCAATTCAAACTTTCATCACT
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
* * * * *
28849042 TACCCCGACACTCGGAATGATTTCGATTACGATTCCATGATAGGAGAGCCCCTTTCTACCCGATT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
28849107 CACTGCTGCCAAAACTCA-AAATCAACAATGGAAAGAAAAGAATAGCATTGATTT-AACAGTTAA
131 CACTGCTGCCAAAACT-AGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAA
* * *
28849170 AACGGTTACCCCAACCCACATGAAAACACCTTTTACACTTAGCAAACCGCGCAAGGACAG-GAAA
195 AACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCG-AA
*
28849234 GAACTGAAAACTGAAATTGAATGATAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGA
259 GAACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGA
*
28849299 ATTTTGCCAGAACACAAAAAAATAAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATAT
324 ATTTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATAT
28849364 ATATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
389 ATATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCAC
* * *
28849429 TAACAAACCACTTACTTAGAATTTGAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTA
454 TAACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTA
*
28849494 ACACCCTCGCTCCCGTAGAGATTCGAACACAAGAA
519 ACACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
* *
28849529 TCATAATTCATGATTAAACCGAAACCATCAAAATCGACAACAGTCCAATTCAAACCTTCATCACT
1 TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
** * * *
28849594 TACCCCAACACTCCGAATAATTTCAATTACGATTCCACGAGAAGAGAGCCCCTTTCTTCCCGATT
66 TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
* * * * *
28849659 CACTACTACCAAAACTCGAAATCAACAACGGAAAGAAAAGAATAGCATTGATTTGAACAATTAAA
131 CACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAAA
* * * *
28849724 ACGATTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAAGACATCGGAGA
196 ACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAGA
* * * * * * * *
28849789 ACTAAAAACCGGAATTAAATTACAAAATTGTGATGGAATTTCAAAAGTAAGGAAACAAAAAGAAT
261 ACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAAT
* * *
28849854 TTTACCAGAACACAAAAAAATTAACGTAAAAAATTTTGGGAGTTT-TCA-A-AGAGAAAAA-A-A
326 TTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCT-AGAGAGAGAAAAATATA
* * *
28849914 TATCAAAAAGAAAAAAATAATATGATTATACCTAAATCCCTCGAAGTTCTCCCCACTAACCCACT
390 TATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACT
* *
28849979 AACAAACCACTTACTTAGAATCTGAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTAA
455 AACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTAA
* *
28850044 CACCCTCACTCCCATAGAGATTCGAACACAGGA
520 CACCCTCGCTCCCGTAGAGATTCGAACACAGGA
28850077 CCTCCAACAT
Statistics
Matches: 3061, Mismatches: 227, Indels: 46
0.92 0.07 0.01
Matches are distributed among these distances:
549 218 0.07
550 735 0.24
551 51 0.02
552 536 0.18
553 983 0.32
554 330 0.11
555 208 0.07
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (553 bp):
TCATAATTCATGATTAAACCGAAACCACCAAAACCGACAACAGTCCAATTCAAACCTTCATCACT
TACCCCAACACTCCGAACGATTTCGATTACGATTCCATGAGAGGAGAGCCCCTTTCTTCCCGATT
CACTGCTGCCAAAACTAGAAATCAACAATGGAAAGAAAAGAATAGCATTGATTTGAACAGTTAAA
ACGGTTACCCCAACCCACACGAAAACACCCTTTACACTTACCAAACCGCGCAAGGACAGCGAAGA
ACTGAAAACTGAAATTGAATGACAGAATTGCGATGGAATTTCAAAAGTAACGAAACAAAAAGAAT
TTTGCCAGAACACAAAAAAATGAATGTAAAAAATTTTGGGAGTTTCTAGAGAGAGAAAAATATAT
ATCAAAAAGAAAAAAATAATATGATTATACCCAAATCCCTCGAATTTCTCCCAACTAACCCACTA
ACAAACCACTTACTCAGAATCTCAACTCCCCTAAAACTCTAACACACAACCGAGCAAAAATTAAC
ACCCTCGCTCCCGTAGAGATTCGAACACAGGAA
Found at i:28849925 original size:17 final size:17
Alignment explanation
Indices: 28849899--28849932 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28849889 TTGGGAGTTT
*
28849899 TCAAAGAGAAAAAAATA
1 TCAAAAAGAAAAAAATA
28849916 TCAAAAAGAAAAAAATA
1 TCAAAAAGAAAAAAATA
28849933 ATATGATTAT
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:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (17 bp):
TCAAAAAGAAAAAAATA
Found at i:28856901 original size:22 final size:21
Alignment explanation
Indices: 28856861--28856901 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28856851 TGGGAGTTTC
* *
28856861 CAAAGAGAGAAAAATATATAT
1 CAAAAAGAAAAAAATATATAT
28856882 CAAAAAGAAAAAAATA-ATAT
1 CAAAAAGAAAAAAATATATAT
28856902 GATTATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (21 bp):
CAAAAAGAAAAAAATATATAT
Found at i:28862188 original size:24 final size:26
Alignment explanation
Indices: 28862159--28862216 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
28862149 TTGTATAACG
28862159 GGAAGCTCATAAGAGCC-ATAT-TCA
1 GGAAGCTCATAAGAGCCAATATGTCA
*
28862183 GGAAGCTCATACGAGCCAATATGTCA
1 GGAAGCTCATAAGAGCCAATATGTCA
28862209 GGAAGCTC
1 GGAAGCTC
28862217 TAGATAGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 16 0.52
25 4 0.13
26 11 0.35
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
GGAAGCTCATAAGAGCCAATATGTCA
Found at i:28862225 original size:26 final size:26
Alignment explanation
Indices: 28862159--28862241 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
28862149 TTGTATAACG
*
28862159 GGAAGCTCATA-AGAGCC-ATATTCA
1 GGAAGCTCATAGATAGCCAATATTCA
28862183 GGAAGCTCATACG--AGCCAATATGTCA
1 GGAAGCTCATA-GATAGCCAATAT-TCA
* * *
28862209 GGAAGCTC-TAGATAGCCATTAATCG
1 GGAAGCTCATAGATAGCCAATATTCA
28862234 GGAAGCTC
1 GGAAGCTC
28862242 CAGATAGGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
24 16 0.32
25 16 0.32
26 18 0.36
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
GGAAGCTCATAGATAGCCAATATTCA
Found at i:28862246 original size:25 final size:25
Alignment explanation
Indices: 28862209--28862312 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
28862199 CAATATGTCA
*
28862209 GGAAGCTCTAGATAGCCATTAATCG
1 GGAAGCTCCAGATAGCCATTAATCG
*
28862234 GGAAGCTCCAGATAGGCA-TATATCG
1 GGAAGCTCCAGATAGCCATTA-ATCG
* * ** *
28862259 GGAAGTTCAAGCGAGCCAAT-ATCG
1 GGAAGCTCCAGATAGCCATTAATCG
* *
28862283 GAAAGCTCCAGAAAGCCATTAATCG
1 GGAAGCTCCAGATAGCCATTAATCG
28862308 GGAAG
1 GGAAG
28862313 TTCCGAAGAA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
24 20 0.32
25 41 0.66
26 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
GGAAGCTCCAGATAGCCATTAATCG
Found at i:28862328 original size:74 final size:74
Alignment explanation
Indices: 28862157--28862348 Score: 196
Period size: 74 Copynumber: 2.6 Consensus size: 74
28862147 GGTTGTATAA
* * *
28862157 CGGGAAGCTCATAAGAGCCATAT-TCAGGAAGCTCATACGAGCCAATATGTCAGGAAGCTCTAGA
1 CGGGAAGCTC-CAAGAACCATATATCAGGAAGCTCATACGAGCCAATA-GTCAGGAAGCTCCAGA
*
28862221 TAGCCATTAAT
64 AAGCCATTAAT
* * *
28862232 CGGGAAGCTCC-AGATAGGCATATATCGGGAAGTTCA-AGCGAGCCAATA-TC-GGAAAGCTCCA
1 CGGGAAGCTCCAAGA-A-CCATATATCAGGAAGCTCATA-CGAGCCAATAGTCAGG-AAGCTCCA
28862293 GAAAGCCATTAAT
62 GAAAGCCATTAAT
* * *
28862306 CGGGAAGTTCCGAAGAACCATATATCAGGACGCTCATAAGAGC
1 CGGGAAGCTCC-AAGAACCATATATCAGGAAGCTCATACGAGC
28862349 TGCGACATGT
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
73 5 0.05
74 50 0.52
75 18 0.19
76 23 0.24
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (74 bp):
CGGGAAGCTCCAAGAACCATATATCAGGAAGCTCATACGAGCCAATAGTCAGGAAGCTCCAGAAA
GCCATTAAT
Found at i:28865506 original size:17 final size:17
Alignment explanation
Indices: 28865484--28865517 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28865474 ATAAACTCGC
*
28865484 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
28865501 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
28865518 AATATACGAA
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:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:28871499 original size:58 final size:58
Alignment explanation
Indices: 28871437--28871591 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 58
28871427 GTGTTTATTG
*
28871437 TTTTTTAAGAAAAAATCA-ATTA-AATTAGGGTCTAAGGTTACTTGAGTAATTTAATTAA
1 TTTTTTAA-AAAAAATCAGATTAGAATTAGAGT-TAAGGTTACTTGAGTAATTTAATTAA
* * ** *
28871495 TTTTTTTAAAAAAATTAGATTAGGGTTTAGAGTTAGGGTTACTTGAGTAATTTAATTAA
1 TTTTTTAAAAAAAATCAGATTA-GAATTAGAGTTAAGGTTACTTGAGTAATTTAATTAA
**
28871554 TTTTTTAAAAAAAATCAGATTAGGGTTTAGAGTTAAGG
1 TTTTTTAAAAAAAATCAGATTA-GAATTAGAGTTAAGG
28871592 GTTTTTATGA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 8 0.09
58 11 0.13
59 60 0.71
60 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (58 bp):
TTTTTTAAAAAAAATCAGATTAGAATTAGAGTTAAGGTTACTTGAGTAATTTAATTAA
Found at i:28871535 original size:59 final size:60
Alignment explanation
Indices: 28871472--28871594 Score: 221
Period size: 59 Copynumber: 2.1 Consensus size: 60
28871462 TAGGGTCTAA
* *
28871472 GGTTACTTGAGTAATTTAATTAATTTTTTTAAAAAAATTAGATTAGGGTTTAGAGTT-AG
1 GGTTACTTGAGTAATTTAATTAATTTTTTAAAAAAAATCAGATTAGGGTTTAGAGTTAAG
28871531 GGTTACTTGAGTAATTTAATTAATTTTTTAAAAAAAATCAGATTAGGGTTTAGAGTTAAG
1 GGTTACTTGAGTAATTTAATTAATTTTTTAAAAAAAATCAGATTAGGGTTTAGAGTTAAG
28871591 GGTT
1 GGTT
28871595 TTTATGAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 55 0.90
60 6 0.10
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (60 bp):
GGTTACTTGAGTAATTTAATTAATTTTTTAAAAAAAATCAGATTAGGGTTTAGAGTTAAG
Found at i:28871597 original size:96 final size:94
Alignment explanation
Indices: 28871521--28871716 Score: 252
Period size: 96 Copynumber: 2.0 Consensus size: 94
28871511 AGATTAGGGT
* **
28871521 TTAGAGTT-AGGGTTACTTGAGTAATTTAATTA-ATTTTTTAAAAAAAATCAGATTAGGGTTTAG
1 TTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTT-AAAAAAATCAGATTAGGGTTTAG
28871584 AGTTAAGGGTTTTTATGAAAAAATCAAATAAA
65 AGTTAAGGGTTTTTA--AAAAAATCAAATAAA
* * * *
28871616 TTAGGGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTTAGATTAGGGTTTAGT
1 TTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATCAGATTAGGGTTTAGA
*
28871681 GTTTAGGGTTTTTAAGTAAAAACTCAAATAAA
66 GTTAAGGGTTTTTAA--AAAAA-TCAAATAAA
28871713 TTAG
1 TTAG
28871717 GGTTTGAGGT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
94 1 0.01
95 7 0.08
96 62 0.70
97 18 0.20
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (94 bp):
TTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATCAGATTAGGGTTTAGA
GTTAAGGGTTTTTAAAAAAATCAAATAAA
Found at i:28873655 original size:7 final size:7
Alignment explanation
Indices: 28873645--28873684 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
28873635 TTATATACAT
28873645 AATACTA
1 AATACTA
28873652 AATACTA
1 AATACTA
28873659 AATACTA
1 AATACTA
28873666 AATACTA
1 AATACTA
28873673 AATACTA
1 AATACTA
28873680 AATAC
1 AATAC
28873685 CAATCGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28874893 original size:22 final size:21
Alignment explanation
Indices: 28874855--28874895 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28874845 AATAAGAATT
*
28874855 TTAGAGGAATTTGAGAGAAGA
1 TTAGAGGAAATTGAGAGAAGA
28874876 TTAGAGAGAAATTGAGAGAA
1 TTAGAG-GAAATTGAGAGAA
28874896 AGGATTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (21 bp):
TTAGAGGAAATTGAGAGAAGA
Found at i:28881996 original size:6 final size:6
Alignment explanation
Indices: 28881963--28881990 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28881953 ATCTCCTCCA
28881963 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
28881991 GAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:28882492 original size:7 final size:7
Alignment explanation
Indices: 28882443--28882543 Score: 69
Period size: 7 Copynumber: 14.1 Consensus size: 7
28882433 TTAAGTGTTG
28882443 GGGTTTA
1 GGGTTTA
*
28882450 AGGTTTA
1 GGGTTTA
*
28882457 GGGGTTA
1 GGGTTTA
*
28882464 GGGGTTA
1 GGGTTTA
*
28882471 GGGGTTA
1 GGGTTTA
28882478 GGGATTTA
1 GGG-TTTA
28882486 GGGTTTA
1 GGGTTTA
* *
28882493 TGTTTTA
1 GGGTTTA
* *
28882500 TGATTTA
1 GGGTTTA
*
28882507 AGGTTTA
1 GGGTTTA
*
28882514 GGAG-ATA
1 GG-GTTTA
*
28882521 GGGGTTA
1 GGGTTTA
28882528 GGGGTTTA
1 -GGGTTTA
28882536 GGGTTTA
1 GGGTTTA
28882543 G
1 G
28882544 ATTAATTAGT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
6 1 0.01
7 63 0.82
8 13 0.17
ACGTcount: A:0.20, C:0.00, G:0.42, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:28887408 original size:43 final size:43
Alignment explanation
Indices: 28887285--28887698 Score: 544
Period size: 43 Copynumber: 9.6 Consensus size: 43
28887275 TGATAAAAGT
* * *
28887285 CCGCTAAAGATCATGTTCTTTAGCGGTGTTTGTGGGTAAATCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
28887328 CCGCTAAAGGTCAT-TTTTTTAGCGGCGTTCT-TGGGTAAAGCA
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTT-TGTGGGTAAAGCG
* * * *
28887370 CCGCTAAGGGTCATGTTCTTTAGCGGCGTTTTTTGGTAAAGCA
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* * *
28887413 CCGCTAAAGGTCTTGTTCTTTAGCGACATTTGTGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* * *
28887456 TCGCTTAAGGTCATGTTCTTTAGCGGCGTTTATGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* * * *
28887499 TCGCTTAAGGTCATGTTTTTTAGTGGCGTTTGTGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
28887542 TCGCTTAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
28887585 CCGCTAAAAGGTCATGTTCTTTAGCGGCATTTTTGGGTAAAGCG
1 CCGCT-AAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* * *
28887629 CCGCTAAATGTCATGTTCTTTAGTGGCGTTTCTGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
28887672 CCACTAAAGATCATGTTCTTTAGCGGC
1 CCGCTAAAGGTCATGTTCTTTAGCGGC
28887699 ATTTTTTTAC
Statistics
Matches: 329, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
42 36 0.11
43 253 0.77
44 40 0.12
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (43 bp):
CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
Found at i:28889134 original size:14 final size:14
Alignment explanation
Indices: 28889115--28889149 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28889105 AACAATATAA
*
28889115 AAAACTTGTGTGAT
1 AAAACTTGTATGAT
*
28889129 AAAACTTGTATGTT
1 AAAACTTGTATGAT
28889143 AAAACTT
1 AAAACTT
28889150 ATGTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (14 bp):
AAAACTTGTATGAT
Found at i:28894503 original size:25 final size:25
Alignment explanation
Indices: 28894456--28894530 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
28894446 TCTAAGCTAA
* * **
28894456 AATAACGGTAAGCTCCTCCGAGCTG
1 AATAATGGTAAGCTCATAAGAGCTG
*
28894481 AATAATGGTAAGCTCATATGAGCTG
1 AATAATGGTAAGCTCATAAGAGCTG
* *
28894506 AGT-ATCGGTAAACTCATAAGAGCTG
1 AATAAT-GGTAAGCTCATAAGAGCTG
28894531 GTATCGTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (25 bp):
AATAATGGTAAGCTCATAAGAGCTG
Found at i:28907231 original size:9 final size:9
Alignment explanation
Indices: 28907217--28907295 Score: 83
Period size: 9 Copynumber: 9.0 Consensus size: 9
28907207 TACAGATTAG
28907217 CATAACTTA
1 CATAACTTA
*
28907226 CATAACTCA
1 CATAACTTA
28907235 CATAACTTA
1 CATAACTTA
28907244 CATAACTTA
1 CATAACTTA
28907253 CATAA-TT-
1 CATAACTTA
*
28907260 CATAA-ATA
1 CATAACTTA
* * *
28907268 TATATCATA
1 CATAACTTA
28907277 TCATAACTTA
1 -CATAACTTA
28907287 CATAACTTA
1 CATAACTTA
28907296 ATTATACTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
7 6 0.10
8 5 0.08
9 42 0.71
10 6 0.10
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:28910342 original size:2 final size:2
Alignment explanation
Indices: 28910335--28910360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28910325 GCATGGCTTT
28910335 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28910361 CATGCCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28912629 original size:175 final size:175
Alignment explanation
Indices: 28912332--28912694 Score: 663
Period size: 175 Copynumber: 2.1 Consensus size: 175
28912322 TATTTTTGCA
28912332 ATGTCGAAGAAAGAGAAGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCATATGCA
1 ATGTC-AAGAAAGAGAAGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCATATGCA
*
28912397 TCAAATATATTTCAATGTGTGAGTCTTAGAGATCGAAGACTATATTCCTTAAAATCACATGATTA
65 TCAAATATATCTCAATGTGTGAGTCTTAGAGATCGAAGACTATATTCCTTAAAATCACATGATTA
* *
28912462 TCACATCTTCATGCAAGATTTACTGCCAATTGCTTTACGGTGTTGT
130 TCACATCTTCATGCAAGATTTACTACCAATTGCTTTACGATGTTGT
*
28912508 ATGTCAAGAAAGAGAAGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCGTATGCAT
1 ATGTCAAGAAAGAGAAGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCATATGCAT
28912573 CAAATATATCTCAATGTGTGAGTCTTAGAGATCGAAGACTATATTCCTTAAAATCACATGATTAT
66 CAAATATATCTCAATGTGTGAGTCTTAGAGATCGAAGACTATATTCCTTAAAATCACATGATTAT
*
28912638 CACATCTTCATGCAAGATTTACTACCAGTTGCTTTACGATGTTGT
131 CACATCTTCATGCAAGATTTACTACCAATTGCTTTACGATGTTGT
*
28912683 ATGTCAAAAAAG
1 ATGTCAAGAAAG
28912695 TTGACGTCTT
Statistics
Matches: 181, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
175 176 0.97
176 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (175 bp):
ATGTCAAGAAAGAGAAGTGTTCTGCATGGTGTTGAAGGATATAAAGGTCCCAGATGCATATGCAT
CAAATATATCTCAATGTGTGAGTCTTAGAGATCGAAGACTATATTCCTTAAAATCACATGATTAT
CACATCTTCATGCAAGATTTACTACCAATTGCTTTACGATGTTGT
Found at i:28916578 original size:133 final size:133
Alignment explanation
Indices: 28916339--28916618 Score: 479
Period size: 133 Copynumber: 2.1 Consensus size: 133
28916329 GCGCTTAAGA
*
28916339 TAAAAGCGCCGCTAAAGGTCATGCTCTATAGCAGCGTTTATGTGAAGAAAACGTCGCAAAATTTA
1 TAAAAGCGCCGCTAAAGGTCATGCTCTATAGCAGCGTTTATGTGAAGAAAACGCCGCAAAATTTA
* ** *
28916404 GCGACATTATTTATAGCGGCGTTTTTTGCGGCGCTTTTGAAAGCACCGCAAATACTTTTAGCGAC
66 GCGACATTATCTATAGCGGCGTTTTTTGCAACGCTTGTGAAAGCACCGCAAATACTTTTAGCGAC
28916469 ACC
131 ACC
28916472 TAAAAGCGCCGCTAAAGGTCATGCTCTATAGCAGCGTTTATGTGAAGAAAACGCCGCAAAATTTA
1 TAAAAGCGCCGCTAAAGGTCATGCTCTATAGCAGCGTTTATGTGAAGAAAACGCCGCAAAATTTA
* * *
28916537 GCGACATTGTCTATAGCGGTGTTTTTTGCAACGCTTGTGAAAGCACTGCAAATACTTTTAGCGAC
66 GCGACATTATCTATAGCGGCGTTTTTTGCAACGCTTGTGAAAGCACCGCAAATACTTTTAGCGAC
*
28916602 GCC
131 ACC
28916605 TAAAAGCGCCGCTA
1 TAAAAGCGCCGCTA
28916619 TAGGCCTAAA
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 138 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (133 bp):
TAAAAGCGCCGCTAAAGGTCATGCTCTATAGCAGCGTTTATGTGAAGAAAACGCCGCAAAATTTA
GCGACATTATCTATAGCGGCGTTTTTTGCAACGCTTGTGAAAGCACCGCAAATACTTTTAGCGAC
ACC
Found at i:28917956 original size:16 final size:15
Alignment explanation
Indices: 28917934--28917976 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
28917924 TACTATTAAT
28917934 TTAAAATTTTATAAA
1 TTAAAATTTTATAAA
** *
28917949 TTATAAATGGTCTAAA
1 TTA-AAATTTTATAAA
28917965 TTAAAATTTTAT
1 TTAAAATTTTAT
28917977 CATTTTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (15 bp):
TTAAAATTTTATAAA
Found at i:28927402 original size:41 final size:41
Alignment explanation
Indices: 28927333--28927509 Score: 150
Period size: 40 Copynumber: 4.3 Consensus size: 41
28927323 CTCAATGTTT
* **
28927333 CGCACACTAAATGCCATCGCATAGCCGAAGCTATTAT-AATCC
1 CGCACACTAAGTGCC-TTACATAGCCGAAGCTA-TATCAATCC
* *
28927375 CGCACACTAAGTGCCTTACATAGCCGAAGCTATATCAGTCT
1 CGCACACTAAGTGCCTTACATAGCCGAAGCTATATCAATCC
* *
28927416 CGCACACTAAGTGCCATATATAGCCGAAGCTA-ATCCCAAT--
1 CGCACACTAAGTGCCTTACATAGCCGAAGCTATAT--CAATCC
* * * * *
28927456 CGCACACTAAGTGCCATAAATAGCGGGAGCTATCTCAAAT--
1 CGCACACTAAGTGCCTTACATAGCCGAAGCTATATC-AATCC
*
28927496 CTCACACTAAGTGC
1 CGCACACTAAGTGC
28927510 TAAACATAGT
Statistics
Matches: 117, Mismatches: 13, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
39 1 0.01
40 50 0.43
41 49 0.42
42 17 0.15
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.21
Consensus pattern (41 bp):
CGCACACTAAGTGCCTTACATAGCCGAAGCTATATCAATCC
Found at i:28934200 original size:40 final size:40
Alignment explanation
Indices: 28934105--28934239 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
28934095 ATTATAATCC
* * ** **
28934105 CGCACACTAAGTGCCTTACATAGCTGAAGCTA-CATCAGTCT
1 CGCACACTAAGTGCCATAAATAGCCAAAGCTATC-TCA-AAT
* *
28934146 CGCACACTAAGTGCCATATATAGCCAAAGCTAT-TCCCAAT
1 CGCACACTAAGTGCCATAAATAGCCAAAGCTATCT-CAAAT
**
28934186 CGCACACTAAGTGCCATAAATAGCGGAAGCTATCTCAAAT
1 CGCACACTAAGTGCCATAAATAGCCAAAGCTATCTCAAAT
*
28934226 CACACACTAAGTGC
1 CGCACACTAAGTGC
28934240 TAAACATAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 49 0.62
41 30 0.38
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (40 bp):
CGCACACTAAGTGCCATAAATAGCCAAAGCTATCTCAAAT
Found at i:28936183 original size:24 final size:25
Alignment explanation
Indices: 28936149--28936202 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
28936139 ATTCTTTGTC
** *
28936149 CTTTTTCATTTTTTTTCTTTTTAA-
1 CTTTTTCATTTACTTACTTTTTAAG
*
28936173 CTTTTTTATTTACTTACTTTTTAAG
1 CTTTTTCATTTACTTACTTTTTAAG
28936198 CTTTT
1 CTTTT
28936203 CTTTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (25 bp):
CTTTTTCATTTACTTACTTTTTAAG
Found at i:28936309 original size:22 final size:23
Alignment explanation
Indices: 28936271--28936316 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
28936261 ACTAGAAATG
28936271 TTTTATAATATGATTTTTTAAAA
1 TTTTATAATATGATTTTTTAAAA
28936294 TTTTA-AATAT-ATTTTTTAAAA
1 TTTTATAATATGATTTTTTAAAA
28936315 TT
1 TT
28936317 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.57
22 5 0.22
23 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATAATATGATTTTTTAAAA
Found at i:28936366 original size:19 final size:19
Alignment explanation
Indices: 28936342--28936383 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28936332 TTTAAATGTC
*
28936342 ATTTTTAA-AATTATAAATA
1 ATTTTTAATAA-TATAAAAA
28936361 ATTTTTAATAATATAAAAA
1 ATTTTTAATAATATAAAAA
28936380 ATTT
1 ATTT
28936384 AAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTTAATAATATAAAAA
Found at i:28936389 original size:19 final size:18
Alignment explanation
Indices: 28936345--28936392 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
28936335 AAATGTCATT
*
28936345 TTTAAAAT-TATAAATAA
1 TTTAAAATATATAAAAAA
**
28936362 TTTTTAATAATATAAAAAA
1 TTTAAAAT-ATATAAAAAA
28936381 TTTAAAATATAT
1 TTTAAAATATAT
28936393 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAATATATAAAAAA
Found at i:28936495 original size:22 final size:20
Alignment explanation
Indices: 28936467--28936510 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
28936457 AAAATTTTAA
28936467 AATTTTAAATATATATTTATTT
1 AATTTTAAATATA-ATTT-TTT
28936489 AATTTTAAATATAATTTTTT
1 AATTTTAAATATAATTTTTT
28936509 AA
1 AA
28936511 ATTATGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTAAATATAATTTTTT
Found at i:28936498 original size:29 final size:29
Alignment explanation
Indices: 28936423--28936498 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
28936413 TTCAAATTTA
* *
28936423 TTATTTATTTTATAATATTTTAAATGTATAT
1 TTATTTAATTT-TAA-ATTTTAAATATATAT
**
28936454 TT-TAAAATTTTAAAATTTTAAATATATAT
1 TTATTTAATTTT-AAATTTTAAATATATAT
28936483 TTATTTAATTTTAAAT
1 TTATTTAATTTTAAAT
28936499 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 21 0.57
30 14 0.38
31 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (29 bp):
TTATTTAATTTTAAATTTTAAATATATAT
Found at i:28936500 original size:20 final size:22
Alignment explanation
Indices: 28936467--28936510 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
28936457 AAAATTTTAA
28936467 AATTTTAAATATAT-ATTTATTT
1 AATTTTAAATATATAATTT-TTT
28936489 AATTTT-AA-ATATAATTTTTT
1 AATTTTAAATATATAATTTTTT
28936509 AA
1 AA
28936511 ATTATGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTAAATATATAATTTTTT
Found at i:28936522 original size:15 final size:15
Alignment explanation
Indices: 28936491--28936530 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
28936481 ATTTATTTAA
28936491 TTTTAAA-TATAATT
1 TTTTAAATTATAATT
*
28936505 TTTTAAATTATGATT
1 TTTTAAATTATAATT
28936520 TTTTAAATTAT
1 TTTTAAATTAT
28936531 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTTAAATTATAATT
Found at i:28936534 original size:12 final size:14
Alignment explanation
Indices: 28936491--28936541 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 14
28936481 ATTTATTTAA
28936491 TTTTAAATATAATT
1 TTTTAAATATAATT
*
28936505 TTTTAAATTATGATT
1 TTTTAAA-TATAATT
28936520 TTTTAAAT-T-A-T
1 TTTTAAATATAATT
28936531 TTTTAAATATA
1 TTTTAAATATA
28936542 TTCAAACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 9 0.27
12 2 0.06
13 1 0.03
14 8 0.24
15 13 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTTAAATATAATT
Found at i:28936543 original size:12 final size:12
Alignment explanation
Indices: 28936469--28936543 Score: 57
Period size: 15 Copynumber: 6.1 Consensus size: 12
28936459 AATTTTAAAA
28936469 TTTTAAATATAT
1 TTTTAAATATAT
* * *
28936481 ATTT--ATTTAA
1 TTTTAAATATAT
28936491 TTTTAAATATAATT
1 TTTTAAATAT-A-T
28936505 TTTTAAATTATGATT
1 TTTTAAA-TAT-A-T
28936520 TTTTAAAT-TAT
1 TTTTAAATATAT
28936531 TTTTAAATATAT
1 TTTTAAATATAT
28936543 T
1 T
28936544 CAAACTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
10 7 0.14
11 9 0.18
12 11 0.22
13 2 0.04
14 8 0.16
15 13 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
TTTTAAATATAT
Found at i:28936670 original size:18 final size:19
Alignment explanation
Indices: 28936629--28936671 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
28936619 AAAAAAAATA
*
28936629 AAAAAAGGATTTATTTGTT
1 AAAAAAGGATTTAGTTGTT
28936648 AAAAAAGGATTTAGTTGTT
1 AAAAAAGGATTTAGTTGTT
28936667 AAAAA
1 AAAAA
28936672 TATGGCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (19 bp):
AAAAAAGGATTTAGTTGTT
Found at i:28936721 original size:21 final size:21
Alignment explanation
Indices: 28936686--28936743 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28936676 GCTTTTTTAA
28936686 AAAAATATATATATTAAAAAAGT
1 AAAAAT-T-TATATTAAAAAAGT
* *
28936709 AAAAATTTATATTAAAATATT
1 AAAAATTTATATTAAAAAAGT
*
28936730 AAAAATATATATTA
1 AAAAATTTATATTA
28936744 TAACTGATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 25 0.78
22 1 0.03
23 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTTATATTAAAAAAGT
Found at i:28936993 original size:22 final size:22
Alignment explanation
Indices: 28936959--28937020 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
28936949 GGCCCGGCCC
*
28936959 ATTTTTAATTAAAATTAAAATTA
1 ATTTTTAA-TAAAATTAAAACTA
*
28936982 TTTTTTAATAAAATTAAAACTA
1 ATTTTTAATAAAATTAAAACTA
* *
28937004 ATTGTTATTAAAATTAA
1 ATTTTTAATAAAATTAA
28937021 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTTTAATAAAATTAAAACTA
Found at i:28937033 original size:16 final size:16
Alignment explanation
Indices: 28936996--28937035 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
28936986 TTAATAAAAT
* *
28936996 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
28937012 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
28937028 TAAAATTA
1 TAAAATTA
28937036 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:28937113 original size:66 final size:59
Alignment explanation
Indices: 28937038--28937157 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
28937028 TAAAATTATC
* * *
28937038 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAATA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAATA
* *
28937096 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAATA
28937155 AAA
1 AAA
28937158 CAAACTTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
58 6 0.11
59 49 0.89
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAATA
Found at i:28937263 original size:22 final size:24
Alignment explanation
Indices: 28937223--28937266 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28937213 AAATAAACTT
28937223 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
28937247 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
28937267 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:28938751 original size:13 final size:13
Alignment explanation
Indices: 28938733--28938759 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28938723 TTAATTTATA
28938733 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28938746 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28938759 T
1 T
28938760 ATCGTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:28939907 original size:44 final size:44
Alignment explanation
Indices: 28939844--28939981 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 44
28939834 TATGATATCA
* *
28939844 TGTAAGACCACGTCTGGGACATTGGCATTGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATTTGAGATTTACG
* * * *
28939888 TGTAAGACCATGTTTGGGACATCGGCATCG-TAT-ATGATTT-TG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATTTGA-GATTTACG
* * * *
28939930 TGTAAGACCCTGTCAGGGACAGTGGCATCGATATTG-GA-TTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGAT-TTGAGATTTACG
28939973 TGTAAGACC
1 TGTAAGACC
28939982 TCGTTTGGGA
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
42 29 0.39
43 19 0.25
44 27 0.36
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATTTGAGATTTACG
Found at i:28949467 original size:120 final size:120
Alignment explanation
Indices: 28949254--28949589 Score: 618
Period size: 120 Copynumber: 2.8 Consensus size: 120
28949244 TTCTTTTTAC
** * * *
28949254 ATGATTTTATTAAATTCATATAAGAATATTTAATATTACGAATTGTATTAAATTATATATTATTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
28949319 TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
66 TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
*
28949374 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTC
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
28949439 TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
66 TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
28949494 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
28949559 TTAAATTATATTTAATAATAATTATGTTAAA
66 TTAAATTATATTTAATAATAATTATGTTAAA
28949590 ATATGATTAA
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 209 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (120 bp):
ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
Found at i:28949549 original size:54 final size:54
Alignment explanation
Indices: 28949371--28949549 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 54
28949361 AGTATTATAT
28949371 ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* *** * * **
28949425 ATTATATATTTTTCTTAAATTATATTTAATAATAATTATGTTAA-ATTATA-TTTTATAGTATTA
1 ATTAT-GA-TTTTAGAAAATT-CA--T-ATAAGAA-TAT-TTAATATTA-AGAATT-T--TATTA
28949488 TA
54 -A
28949490 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 -ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
28949545 ATTAT
1 ATTAT
28949550 ATATTTTTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
54 10 0.11
55 2 0.02
56 14 0.15
57 1 0.01
58 6 0.06
59 10 0.11
60 12 0.13
61 10 0.11
62 6 0.06
63 1 0.01
64 14 0.15
65 2 0.02
66 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (54 bp):
ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:28949827 original size:16 final size:16
Alignment explanation
Indices: 28949802--28949855 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
28949792 TTGATTTGCT
*
28949802 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
28949818 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
28949834 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
28949850 AATACA
1 ATTACA
28949856 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:28949906 original size:21 final size:20
Alignment explanation
Indices: 28949882--28949936 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
28949872 GTTAATTTTT
28949882 AAAAATTTAAATATAATTTAA
1 AAAAATTTAAATAT-ATTTAA
* *
28949903 AAAAATGTTTGAATATCTTTAA
1 AAAAA--TTTAAATATATTTAA
28949925 AAATAATTTAAA
1 AAA-AATTTAAA
28949937 AAATTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 10 0.36
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAATTTAAATATATTTAA
Found at i:28949965 original size:16 final size:18
Alignment explanation
Indices: 28949926--28949969 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
28949916 TATCTTTAAA
28949926 AATAATTT--AAAAAATT
1 AATAATTTAAAAAAAATT
28949942 AATAATTTAAAAAAAATT
1 AATAATTTAAAAAAAATT
28949960 -AT-ATTTAAAA
1 AATAATTTAAAA
28949970 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 16 0.62
17 2 0.08
18 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAATTTAAAAAAAATT
Found at i:28950215 original size:24 final size:23
Alignment explanation
Indices: 28950155--28950217 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
28950145 ATAAATAAAG
28950155 GAAAAATAAAAAAAACTTAAAAA
1 GAAAAATAAAAAAAACTTAAAAA
*
28950178 -ATAAATAAATAAAAAACTTAAAAA
1 GAAAAAT-AA-AAAAAACTTAAAAA
*
28950202 GAAAAACACAAAAAAA
1 GAAAAATA-AAAAAAA
28950218 GGGAAAGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 2 0.06
24 21 0.64
25 5 0.15
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.13
Consensus pattern (23 bp):
GAAAAATAAAAAAAACTTAAAAA
Found at i:28950297 original size:8 final size:8
Alignment explanation
Indices: 28950280--28950318 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
28950270 TACCTGTTTC
28950280 AATAGGCA
1 AATAGGCA
*
28950288 AATAGACA
1 AATAGGCA
28950296 AATAGGCA
1 AATAGGCA
*
28950304 GATAGGCA
1 AATAGGCA
28950312 AATAGGC
1 AATAGGC
28950319 TACAGTCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.49, C:0.13, G:0.26, T:0.13
Consensus pattern (8 bp):
AATAGGCA
Found at i:28950873 original size:9 final size:9
Alignment explanation
Indices: 28950859--28950885 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28950849 TTGATGATAT
28950859 GCAGAGGCG
1 GCAGAGGCG
28950868 GCAGAGGCG
1 GCAGAGGCG
28950877 GCAGAGGCG
1 GCAGAGGCG
28950886 ACGGAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.56, T:0.00
Consensus pattern (9 bp):
GCAGAGGCG
Found at i:28952362 original size:16 final size:16
Alignment explanation
Indices: 28952341--28952371 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28952331 TTATAATATA
28952341 AAATATAATAATAGTT
1 AAATATAATAATAGTT
*
28952357 AAATATAATAGTAGT
1 AAATATAATAATAGT
28952372 ACATTATACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAATATAATAATAGTT
Found at i:28952936 original size:113 final size:114
Alignment explanation
Indices: 28952776--28953071 Score: 339
Period size: 113 Copynumber: 2.6 Consensus size: 114
28952766 TTACGATCCT
* * *
28952776 GCGCCGCAAAATCTCA-AGACCAAAACGCATCGTTTTTGTCTTGATGTATACTAGAATTAGTGGC
1 GCGCCGCAAAATATCATA-ACCAAAACGCATCGTTTTGGTCTTGATGTATATTAGAATTAGTGGC
* * ** * * ** **
28952840 GATTATGAGCAA-ACGCCGCTAAAGCAAGTATTAGCGGCGCATTGTGGGAA
65 GCTTATCAAAAACACGCCACTAAAACAAGTATTAGCGGCGC-TTACGAAAA
* * * * *
28952890 GCGCCGCAAAA-ATCTTAACGAAAACGCATCGTTTTGGTATCGATGTATATTAGAATTAATGGCG
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCG
*
28952954 CTTA-CAAAAACACGCCACTAAAACAAGTCTTAGCGGCGCTTACGAAAA
66 CTTATCAAAAACACGCCACTAAAACAAGTATTAGCGGCGCTTACGAAAA
* ** *
28953002 GCGCCGCAAAATATGATAACCAAAACGCAAAGTTTTGATCTTGATGTATATTAGAATTAGTGGCG
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCG
28953067 CTTAT
66 CTTAT
28953072 TAGAAGTGCC
Statistics
Matches: 150, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
112 19 0.13
113 119 0.79
114 12 0.08
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCG
CTTATCAAAAACACGCCACTAAAACAAGTATTAGCGGCGCTTACGAAAA
Found at i:28953442 original size:115 final size:112
Alignment explanation
Indices: 28953093--28953689 Score: 501
Period size: 115 Copynumber: 5.2 Consensus size: 112
28953083 CAAAAAATCT
* ** * * * **
28953093 TAACCAAAACGCAGCGTTTTGGTCTCAATGTATAATACAATTAGTGGAG-TTA-GGGAAAAACGC
1 TAACCAAAACGCAGAG-TTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACTAG-AAAACGC
** ** *
28953156 C-CTAAAGCATAAC-ATTAGCGGCGATTTTTTAGAAGCGCCGCAAAATATCT
64 CGCTAAAGCAT-ACTATTAGCGGCGCGTTTGGAGAAGCGCCGC-AAATAT-G
* ***
28953206 TAACCAAAACGCAGAGTTTGGTCTTGAAGTATACTAGAATTAGTGGCGAAAAC-AGAAAACGCCG
1 TAACCAAAACGCAGAGTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACTAGAAAACGCCG
* *
28953270 CTAAAGCGTACTATTAGCGGCGCGTTTGGAGAAGCGCCGCTAAATTTTG
66 CTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGC-AAA-TATG
* * * *
28953319 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGCTTACTAGAAAATGC
1 -TAACCAAAACGCAGAG-TTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACTAGAAAACGC
** * *
28953384 CGCTAAATAATAGTATTAGCGGCGC-TTTGCGATAAGCGCCGCAAGATATG
64 CGCTAAAGCATACTATTAGCGGCGCGTTTG-GAGAAGCGCCGCAA-ATATG
* * * * *
28953434 CACACCAAAAAGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA-TGGGAAAACGC
1 TA-ACCAAAACGCAGAGTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACT-AGAAAACGC
* * ** *
28953498 CGCTATAGCATACTATTAGCGTCGCGTTTTTAGAAGCGCCGCAAAATATAT
64 CGCTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGC-AAATAT-G
** * * * * *
28953549 TAACCAAAACGTTGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCG-TTCACGAGAAATCGC
1 TAACCAAAACGCAGAGTTT-GGTCTTGATGTATACTAGAATTAGTGGCGCTT-ACTAGAAAACGC
* * * *
28953613 CGCTAAAGCGTATTATTAGCGGCGCTTTTTGG-GAAGCGCCGCAAAATATCT
64 CGCTAAAGCATACTATTAGCGGCGC-GTTTGGAGAAGCGCCGC-AAATAT-G
*
28953664 TAACCAAAACGCACAGTTTTGGTCTT
1 TAACCAAAACGCAGAG-TTTGGTCTT
28953690 AACCATGCAT
Statistics
Matches: 389, Mismatches: 75, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
112 36 0.09
113 53 0.14
114 106 0.27
115 147 0.38
116 47 0.12
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
TAACCAAAACGCAGAGTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACTAGAAAACGCCG
CTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAATATG
Found at i:28953554 original size:229 final size:226
Alignment explanation
Indices: 28953057--28953689 Score: 648
Period size: 229 Copynumber: 2.8 Consensus size: 226
28953047 GTATATTAGA
* * * * * * **
28953057 ATTAGTGGCGC-TTATTAGAAGTGCCGCAAAAAATCTTAACCAAAACGCAGCGTTTTGGTCTCAA
1 ATTAGCGGCGCGTTTTTAGAAGCGCCGCAAAATATATTAACCAAAACTCAGCGTTTTGGTCTTGA
* * * * * * *
28953121 TGTATAATACAATTAGTGGAGTTA-GGGAAAAACGCC-CTAAAGCATAACATTAGCGGCGATTTT
66 TGTATACTACAATTAGTGGCGTTACGAG-AAAATGCCGCTAAAGCATAATATTAGCGGCGCTTTG
** *
28953184 TTAGAAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAAGTATACTAGAATTAG
130 CGAGAAGCGCCGCAAAATATC-TAACCAAAAAGCAGAGTTTGGTCTTGAAGTATACTAGAATTAG
*
28953249 TGGCGAAAACAGAAAACGCCGCTAAAGCGTACT
194 TGGCGAAAACAGAAAACGCCGCTAAAGCATACT
** * * *
28953282 ATTAGCGGCGCGTTTGGAGAAGCGCCGCTAAATTTTGTTAACCAAAACTCAGCGTTTTGGTCTTG
1 ATTAGCGGCGCGTTTTTAGAAGCGCCGC-AAAATATATTAACCAAAACTCAGCGTTTTGGTCTTG
* * ** *
28953347 ATGTATACTATAATTAGTGGCGCTTACTAGAAAATGCCGCTAAATAATAGTATTAGCGGCGCTTT
65 ATGTATACTACAATTAGTGGCG-TTACGAGAAAATGCCGCTAAAGCATAATATTAGCGGCGCTTT
* * * *
28953412 GCGATAAGCGCCGCAAGATATGC-ACACCAAAAAGCAGAGTTTGGTCTTGAGGTATATTAGAATT
129 GCGAGAAGCGCCGCAAAATAT-CTA-ACCAAAAAGCAGAGTTTGGTCTTGAAGTATACTAGAATT
** *** *
28953476 AGTGGCGCTTATGGGAAAACGCCGCTATAGCATACT
192 AGTGGCG-AAAACAGAAAACGCCGCTAAAGCATACT
* * **
28953512 ATTAGCGTCGCGTTTTTAGAAGCGCCGCAAAATATATTAACCAAAACGT-TGCGTTTAAGTCTTG
1 ATTAGCGGCGCGTTTTTAGAAGCGCCGCAAAATATATTAACCAAAAC-TCAGCGTTTTGGTCTTG
** * *
28953576 ATGTATACTGGAATTAGTGGCGTTCACGAG-AAATCGCCGCTAAAGCGTATTATTAGCGGCGCTT
65 ATGTATACTACAATTAGTGGCGTT-ACGAGAAAAT-GCCGCTAAAGCATAATATTAGCGGCGCTT
** * * *
28953640 TTTGGGAAGCGCCGCAAAATATCTTAACCAAAACGCACAGTTTTGGTCTT
128 TGCGAGAAGCGCCGCAAAATATC-TAACCAAAAAGCAGAG-TTTGGTCTT
28953690 AACCATGCAT
Statistics
Matches: 333, Mismatches: 61, Indels: 23
0.80 0.15 0.06
Matches are distributed among these distances:
225 10 0.03
226 12 0.04
227 48 0.14
228 18 0.05
229 187 0.56
230 58 0.17
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (226 bp):
ATTAGCGGCGCGTTTTTAGAAGCGCCGCAAAATATATTAACCAAAACTCAGCGTTTTGGTCTTGA
TGTATACTACAATTAGTGGCGTTACGAGAAAATGCCGCTAAAGCATAATATTAGCGGCGCTTTGC
GAGAAGCGCCGCAAAATATCTAACCAAAAAGCAGAGTTTGGTCTTGAAGTATACTAGAATTAGTG
GCGAAAACAGAAAACGCCGCTAAAGCATACT
Found at i:28955995 original size:22 final size:22
Alignment explanation
Indices: 28955965--28956007 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28955955 ACAACAAAAC
*
28955965 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
28955987 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
28956008 AGCGCCGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:28956166 original size:43 final size:42
Alignment explanation
Indices: 28956101--28956501 Score: 464
Period size: 43 Copynumber: 9.3 Consensus size: 42
28956091 TTCCAGTAAA
* *
28956101 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCC-ACAC
** *
28956144 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTTATAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
* * *
28956187 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCATAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
*
28956230 AAACGCCGCTAAAGACCAATACCTTTAGCGGCGCTTCCAACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCC-ACAC
* * * ** *
28956273 AAACGCTGCCAAAAGGCCAAGACCTTTAGCGGCGCTTTTAATAC
1 AAACGCCG-CTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
* *
28956317 AAACGTCGCTAAAGACTAAGACCTTTAGCGGCGCTTTCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCACAC
* *
28956360 AAATGCCGCTATAGACCAAGACCTTTAGCGGCGCTTACCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCACAC
*
28956403 AAACGCCGCTAAAGA-CAACGACCATTTAGCGGCGCTTACACGAC
1 AAACGCCGCTAAAGACCAA-GACC-TTTAGCGGCGCTTCCAC-AC
* * *
28956447 AAACGCCGCTAAAGATCGAGACCTTTAGCGGCGCTTTTCC-CAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC--TTCCACAC
28956490 AAACGCCGCTAA
1 AAACGCCGCTAA
28956502 TTTTGGCAGA
Statistics
Matches: 311, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
42 8 0.03
43 227 0.73
44 69 0.22
45 7 0.02
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCACAC
Found at i:28956338 original size:130 final size:129
Alignment explanation
Indices: 28956101--28956501 Score: 538
Period size: 130 Copynumber: 3.1 Consensus size: 129
28956091 TTCCAGTAAA
* * *
28956101 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGGCCAAGAC
* * * *
28956166 CTTTAGCGGCGCTTTTTATACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCATAC
66 CTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTCACAC
* * *
28956230 AAACGCCGCTAAAGACCAATACCTTTAGCGGCGCTTCCAACACAAACGCTGCCAAAAGGCCAAGA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCG-CTAAAGGCCAAGA
* *
28956295 CCTTTAGCGGCGCTTTTAATACAAACGTCGCTAAAGACTAAGACCTTTAGCGGCGCTTTCCACAC
65 CCTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTCACAC
* * *
28956360 AAATGCCGCTATAGACCAAGACCTTTAGCGGCGCTTACC-ACACAAACGCCGCTAAA-GACAACG
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-CCAACACAAACGCCGCTAAAGGCCAA-G
** ** * *
28956423 ACCATTTAGCGGCGCTTACACGACAAACGCCGCTAAAGA-TCGAGACCTTTAGCGGCGCTTTTCC
64 ACC-TTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACT-AAGACCTTTAGCGGCGCTTTTCA
*
28956487 CAA
127 CAC
28956490 AAACGCCGCTAA
1 AAACGCCGCTAA
28956502 TTTTGGCAGA
Statistics
Matches: 238, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
128 4 0.02
129 56 0.24
130 176 0.74
131 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (129 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGGCCAAGAC
CTTTAGCGGCGCTTTTAATACAAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTCACAC
Found at i:28956483 original size:173 final size:172
Alignment explanation
Indices: 28956101--28956501 Score: 536
Period size: 173 Copynumber: 2.3 Consensus size: 172
28956091 TTCCAGTAAA
**
28956101 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTCCAACACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGACCAAGAC
** * ** *
28956166 CTTTAGCGGCGCTTTTTATACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCATACA
66 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTACCACACA
* *
28956231 AACGCCGCTAAAGACCAATACCTTTAGCGGCGCTTCCAACAC
131 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTACAACAC
* * * * * *
28956273 AAACGCTGCCAAAAGGCCAAGACCTTTAGCGGCGCTTTTAATACAAACGTCGCTAAAGACTAAGA
1 AAACGCCG-CTAAAGGCCGAGACCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGACCAAGA
* * *
28956338 CCTTTAGCGGCGCTTTCCACACAAATGCCGCTATAGACCAAGACCTTTAGCGGCGCTTACCACAC
65 CCTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTACCACAC
28956403 AAACGCCGCTAAAGA-CAACGACCATTTAGCGGCGCTTAC-ACGAC
130 AAACGCCGCTAAAGACCAA-GACC-TTTAGCGGCGCTTACAAC-AC
** ** *
28956447 AAACGCCGCTAAAGATCGAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAA
1 AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTTTAACACAAACGCCGCTAA
28956502 TTTTGGCAGA
Statistics
Matches: 196, Mismatches: 29, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
172 10 0.05
173 163 0.83
174 23 0.12
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (172 bp):
AAACGCCGCTAAAGGCCGAGACCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTACCACACA
AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTACAACAC
Found at i:28956761 original size:9 final size:9
Alignment explanation
Indices: 28956747--28956801 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
28956737 GTCTCAGAAG
*
28956747 GCGGCTGTT
1 GCGGCTGCT
28956756 GCGGCTGCT
1 GCGGCTGCT
*
28956765 GCAGCTGCT
1 GCGGCTGCT
*
28956774 GCGGCTGTT
1 GCGGCTGCT
28956783 GCGGCTGCT
1 GCGGCTGCT
*
28956792 GCGACTGCT
1 GCGGCTGCT
28956801 G
1 G
28956802 AAACATATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.04, C:0.29, G:0.42, T:0.25
Consensus pattern (9 bp):
GCGGCTGCT
Found at i:28956785 original size:27 final size:27
Alignment explanation
Indices: 28956747--28956801 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
28956737 GTCTCAGAAG
28956747 GCGGCTGTTGCGGCTGCTGC-AGCTGCT
1 GCGGCTGTTGCGGCTGCTGCGA-CTGCT
28956774 GCGGCTGTTGCGGCTGCTGCGACTGCT
1 GCGGCTGTTGCGGCTGCTGCGACTGCT
28956801 G
1 G
28956802 AAACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.04, C:0.29, G:0.42, T:0.25
Consensus pattern (27 bp):
GCGGCTGTTGCGGCTGCTGCGACTGCT
Found at i:28964539 original size:19 final size:20
Alignment explanation
Indices: 28964512--28964552 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
28964502 AAAATTTTAA
28964512 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
28964531 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
28964551 TT
1 TT
28964553 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:28964999 original size:17 final size:17
Alignment explanation
Indices: 28964970--28965018 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
28964960 GACACCCTAA
28964970 CCCCTAAATCCCTAAATC
1 CCCCTAAA-CCCTAAATC
*
28964988 CCCCTAACCCCTAAATC
1 CCCCTAAACCCTAAATC
28965005 CCCCTAAACCCTAA
1 CCCCTAAACCCTAA
28965019 CCCCTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (17 bp):
CCCCTAAACCCTAAATC
Found at i:28965058 original size:22 final size:21
Alignment explanation
Indices: 28965027--28965073 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
28965017 AACCCCTAAT
28965027 TAAATCACTAACCCCTAACCCC
1 TAAATCACTAA-CCCTAACCCC
*
28965049 TAAATTACTAACCCTAACCCC
1 TAAATCACTAACCCTAACCCC
28965070 TAAA
1 TAAA
28965074 CCTTAATCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAATCACTAACCCTAACCCC
Found at i:28965826 original size:41 final size:39
Alignment explanation
Indices: 28965715--28965871 Score: 113
Period size: 42 Copynumber: 3.8 Consensus size: 39
28965705 CGTTTCCATC
*
28965715 AAAACGCCGCTAAAACTCC-AACATTAGCGGCGCTTTACAA
1 AAAACGCCGCTAAAAC-CCTAA-ATTAGCGGCGCATTACAA
* * *
28965755 ACAAACGCCACTAAAAACCTTAACTATAGCGGCGCATTATC-A
1 A-AAACGCCGCT-AAAACCCTAAAT-TAGCGGCGCATTA-CAA
* *
28965797 AAAACGCCGCTAAAATCCCTAAAGTTAGCGGCGC-TCAGAAAA
1 AAAACGCCGCTAAAA-CCCTAAA-TTAGCGGCGCAT--TACAA
* *
28965839 AAAACGCCACTAAAAACCATAACATTAGCGGCG
1 AAAACGCCGCT-AAAACCCTAA-ATTAGCGGCG
28965872 TTTGTTTAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
40 6 0.06
41 34 0.36
42 48 0.51
43 6 0.06
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.16
Consensus pattern (39 bp):
AAAACGCCGCTAAAACCCTAAATTAGCGGCGCATTACAA
Found at i:28965883 original size:42 final size:41
Alignment explanation
Indices: 28965734--28965892 Score: 144
Period size: 42 Copynumber: 3.8 Consensus size: 41
28965724 CTAAAACTCC
* *
28965734 AACATTAGCGGCGCTTTACAAACAAACGCCACTAAAAACCTT
1 AACATTAGCGGCGCTTTATAAA-AAACGCCACTAAAAACCAT
* * * * *
28965776 AAC-TATAGCGGCGCATTATCAAAAACGCCGCTAAAATCCCT
1 AACAT-TAGCGGCGCTTTATAAAAAACGCCACTAAAAACCAT
** *
28965817 AA-AGTTAGCGGCGCTCAGAAAAAAAACGCCACTAAAAACCAT
1 AACA-TTAGCGGCGCT-TTATAAAAAACGCCACTAAAAACCAT
* *
28965859 AACATTAGCGGCG-TTTGTTTAAAAACGCCACTAA
1 AACATTAGCGGCGCTTT-ATAAAAAACGCCACTAA
28965893 GGCCCTCTGA
Statistics
Matches: 92, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
41 43 0.47
42 48 0.52
43 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (41 bp):
AACATTAGCGGCGCTTTATAAAAAACGCCACTAAAAACCAT
Found at i:28965887 original size:83 final size:82
Alignment explanation
Indices: 28965715--28965871 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 82
28965705 CGTTTCCATC
* * * *
28965715 AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTTACAAACAAACGCCACTAAAAACCTTAACT
1 AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTCAAAAAAAAACGCCACTAAAAACCATAACT
28965780 ATAGCGGCGCATTATCA
66 ATAGCGGCGCATTATCA
28965797 AAAACGCCGCTAAAA-TCCCTAA-AGTTAGCGGCGC-TCAGAAAAAAAACGCCACTAAAAACCAT
1 AAAACGCCGCTAAAACT-CC-AACA-TTAGCGGCGCTTCA-AAAAAAAACGCCACTAAAAACCAT
28965859 AAC-ATTAGCGGCG
62 AACTA-TAGCGGCG
28965872 TTTGTTTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
81 1 0.02
82 21 0.32
83 44 0.67
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.16
Consensus pattern (82 bp):
AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTCAAAAAAAAACGCCACTAAAAACCATAACT
ATAGCGGCGCATTATCA
Found at i:28967214 original size:18 final size:19
Alignment explanation
Indices: 28967193--28967230 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28967183 TCTGTAACCT
28967193 ATATTAA-ATGTG-TAAATA
1 ATATTAACATG-GATAAATA
28967211 ATATTAACATGGATAAATA
1 ATATTAACATGGATAAATA
28967230 A
1 A
28967231 ATTGGTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (19 bp):
ATATTAACATGGATAAATA
Found at i:28967396 original size:19 final size:19
Alignment explanation
Indices: 28967372--28967433 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
28967362 TTTAAAGTTA
28967372 TATTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
** *
28967391 TATTTT-AATCA--CGAATT
1 TATTTTAAAT-ATTTTATTT
28967408 T-TTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
28967426 TATTTTAA
1 TATTTTAA
28967434 TCACGAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 7 0.22
19 13 0.41
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTAAATATTTTATTT
Found at i:28967418 original size:35 final size:35
Alignment explanation
Indices: 28967374--28967468 Score: 163
Period size: 35 Copynumber: 2.7 Consensus size: 35
28967364 TAAAGTTATA
*
28967374 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
28967409 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
* *
28967444 TTTTAAATATTTAATTTTTTTTTAA
1 TTTTAAATATTTTATTTTATTTTAA
28967469 AGTTCAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTTAATCACGAATAT
Found at i:28967507 original size:9 final size:9
Alignment explanation
Indices: 28967480--28967560 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
28967470 GTTCAAATTT
28967480 CATAACTTA
1 CATAACTTA
* *
28967489 CGTAATTTA
1 CATAACTTA
28967498 CATAACTTA
1 CATAACTTA
28967507 CATAA-TT-
1 CATAACTTA
28967514 CATAACTTA
1 CATAACTTA
*
28967523 CATAATTTA
1 CATAACTTA
* *
28967532 AATTTATA-ATA
1 CA--TA-ACTTA
28967543 CATAACTTA
1 CATAACTTA
28967552 CATAACTTA
1 CATAACTTA
28967561 TTAATATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 41 0.72
11 5 0.09
12 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.38
Consensus pattern (9 bp):
CATAACTTA
Found at i:28967519 original size:16 final size:16
Alignment explanation
Indices: 28967478--28967556 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
28967468 AAGTTCAAAT
*
28967478 TTCATAACTTACGTAA
1 TTCATAACTTACATAA
28967494 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
28967512 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
28967528 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
28967541 TACATAACTTACATAA
1 TTCATAACTTACATAA
28967557 CTTATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.38
17 4 0.08
18 13 0.25
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.39
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:28967620 original size:19 final size:19
Alignment explanation
Indices: 28967561--28967623 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
28967551 ACATAACTTA
* *
28967561 TTAATATTTATATATAGTT
1 TTAAAATTTATATATATTT
* * *
28967580 TTAATATATATATATATAT
1 TTAAAATTTATATATATTT
28967599 TTAAAATTTATATATATTT
1 TTAAAATTTATATATATTT
28967618 TTAAAA
1 TTAAAA
28967624 ATTGATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAAAATTTATATATATTT
Found at i:28967776 original size:12 final size:12
Alignment explanation
Indices: 28967759--28967898 Score: 83
Period size: 12 Copynumber: 11.8 Consensus size: 12
28967749 TACACAACCA
*
28967759 ACATAATGACTT
1 ACATAATAACTT
*
28967771 ACATAATAACCT
1 ACATAATAACTT
28967783 ACATAATAACTT
1 ACATAATAACTT
28967795 ACATAATAA--T
1 ACATAATAACTT
* *
28967805 ACATAACATACAT
1 ACATAATA-ACTT
* *
28967818 AAATTAAATAAGTT
1 ACA-T-AATAACTT
* **
28967832 ACATAGTACACAA
1 ACATAATA-ACTT
* * *
28967845 AAACAAAAACTT
1 ACATAATAACTT
28967857 AC---ATAACTT
1 ACATAATAACTT
* *
28967866 ACATAATATCCT
1 ACATAATAACTT
28967878 ACATAATAACTT
1 ACATAATAACTT
28967890 ACATAATAA
1 ACATAATAA
28967899 TACATACTTA
Statistics
Matches: 94, Mismatches: 25, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
9 8 0.09
10 8 0.09
11 1 0.01
12 60 0.64
13 9 0.10
14 5 0.05
15 3 0.03
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:28967817 original size:95 final size:95
Alignment explanation
Indices: 28967758--28968015 Score: 330
Period size: 94 Copynumber: 2.8 Consensus size: 95
28967748 TTACACAACC
* *
28967758 AACATA-ATGACTTACATAATAACCTACATAATAACTTACATAATAATACATAACATACATAAAT
1 AACATACATAACTTACATAATAACCTACATAATAACTTACATAATAATACATAACTTACATAAAT
*
28967822 TAAATAAGTTACATAGTACACAAAAACAAA
66 TAAATAAGTAACATAGTACACAAAAACAAA
* *
28967852 AACTTACATAACTTACATAATATCCTACATAATAACTTACATAATAATACAT-ACTTACATAAAT
1 AACATACATAACTTACATAATAACCTACATAATAACTTACATAATAATACATAACTTACATAAAT
* * *
28967916 TAAAAAAGTTACATAATACACAAAAACAAA
66 TAAATAAGTAACATAGTACACAAAAACAAA
* * * *
28967946 AACTTACATAACTTACATAAT-ACATAACTTACATAACCTAC-T--TAATACATAACTTACATAA
1 AACATACATAACTTACATAATAACCT-ACATA-ATAACTTACATAATAATACATAACTTACATAA
* *
28968007 CTTACATAA
64 ATTAAATAA
28968016 TACACAACTT
Statistics
Matches: 147, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
92 8 0.05
93 18 0.12
94 70 0.48
95 51 0.35
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.28
Consensus pattern (95 bp):
AACATACATAACTTACATAATAACCTACATAATAACTTACATAATAATACATAACTTACATAAAT
TAAATAAGTAACATAGTACACAAAAACAAA
Found at i:28967860 original size:43 final size:43
Alignment explanation
Indices: 28967813--28967972 Score: 144
Period size: 43 Copynumber: 3.6 Consensus size: 43
28967803 ATACATAACA
*
28967813 TACATAAATTAAATAAGTTACATAGTACACAAAAACAAAAACT
1 TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
* * * * * *
28967856 TACATAACTTACATAATATCCTACATAATAACTTACATAATAATACATACT
1 TACATAAATTAAATAA-GT--TACATAAT-AC--ACA-AA-AACAAAAACT
*
28967907 TACATAAATTAAAAAAGTTACATAATACACAAAAACAAAAACT
1 TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
* *
28967950 TACATAACTTACATAA--TACATAA
1 TACATAAATTAAATAAGTTACATAA
28967973 CTTACATAAC
Statistics
Matches: 92, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
41 7 0.08
43 34 0.37
44 3 0.03
45 3 0.03
46 7 0.08
47 4 0.04
48 8 0.09
49 3 0.03
50 3 0.03
51 20 0.22
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (43 bp):
TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
Found at i:28967866 original size:9 final size:9
Alignment explanation
Indices: 28967852--28968078 Score: 137
Period size: 9 Copynumber: 26.7 Consensus size: 9
28967842 CAAAAACAAA
28967852 AACTTACAT
1 AACTTACAT
28967861 AACTTACAT
1 AACTTACAT
*
28967870 AA--TATCCT
1 AACTTA-CAT
*
28967878 -ACATA-AT
1 AACTTACAT
28967885 AACTTACAT
1 AACTTACAT
28967894 AA-TAATACAT
1 AACT--TACAT
28967904 -ACTTACAT
1 AACTTACAT
* * *
28967912 AAATTAAAA
1 AACTTACAT
*
28967921 AAGTTACAT
1 AACTTACAT
*
28967930 AA--TACAC
1 AACTTACAT
** *
28967937 AA-AAACAA
1 AACTTACAT
28967945 AAACTTACAT
1 A-ACTTACAT
28967955 AACTTACAT
1 AACTTACAT
28967964 AA--TACAT
1 AACTTACAT
28967971 AACTTACAT
1 AACTTACAT
* *
28967980 AACCTACTT
1 AACTTACAT
28967989 AA--TACAT
1 AACTTACAT
28967996 AACTTACAT
1 AACTTACAT
28968005 AACTTACAT
1 AACTTACAT
*
28968014 AA--TACAC
1 AACTTACAT
28968021 AACTTACAT
1 AACTTACAT
* *
28968030 AAGTTTCAT
1 AACTTACAT
* *
28968039 AA--TCCAC
1 AACTTACAT
*
28968046 AACTTACAC
1 AACTTACAT
28968055 AACTTACAT
1 AACTTACAT
28968064 AACTTACAT
1 AACTTACAT
28968073 AACTTA
1 AACTTA
28968079 TTCCTAAATC
Statistics
Matches: 172, Mismatches: 26, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
7 34 0.20
8 16 0.09
9 112 0.65
10 10 0.06
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:28967950 original size:94 final size:95
Alignment explanation
Indices: 28967767--28967967 Score: 359
Period size: 94 Copynumber: 2.1 Consensus size: 95
28967757 CAACATAATG
*
28967767 ACTTACATAATAACCTACATAATAACTTACATAATAATACATAACATACATAAATTAAATAAGTT
1 ACTTACATAATAACCTACATAATAACTTACATAATAATACATAACATACATAAATTAAAAAAGTT
*
28967832 ACATAGTACACAAAAACAAAAACTTACATA
66 ACATAATACACAAAAACAAAAACTTACATA
* *
28967862 ACTTACATAATATCCTACATAATAACTTACATAATAATACAT-ACTTACATAAATTAAAAAAGTT
1 ACTTACATAATAACCTACATAATAACTTACATAATAATACATAACATACATAAATTAAAAAAGTT
28967926 ACATAATACACAAAAACAAAAACTTACATA
66 ACATAATACACAAAAACAAAAACTTACATA
28967956 ACTTACATAATA
1 ACTTACATAATA
28967968 CATAACTTAC
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 61 0.60
95 41 0.40
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.27
Consensus pattern (95 bp):
ACTTACATAATAACCTACATAATAACTTACATAATAATACATAACATACATAAATTAAAAAAGTT
ACATAATACACAAAAACAAAAACTTACATA
Found at i:28967971 original size:16 final size:17
Alignment explanation
Indices: 28967950--28968078 Score: 108
Period size: 16 Copynumber: 7.6 Consensus size: 17
28967940 AACAAAAACT
28967950 TACATAACTTACATAA-
1 TACATAACTTACATAAC
28967966 TACATAACTTACATAACC
1 TACATAACTTACATAA-C
*
28967984 TACTTAA--TACATAAC
1 TACATAACTTACATAAC
28967999 TTACATAACTTACATAA-
1 -TACATAACTTACATAAC
* *
28968016 TACACAACTTACATAAGT
1 TACATAACTTACATAA-C
* * *
28968034 TTCATAA--TCCACAAC
1 TACATAACTTACATAAC
*
28968049 TTACACAACTTACATAAC
1 -TACATAACTTACATAAC
28968067 TTACATAACTTA
1 -TACATAACTTA
28968079 TTCCTAAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
15 1 0.01
16 54 0.60
18 35 0.39
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (17 bp):
TACATAACTTACATAAC
Done.