Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 49 of 297
Found at i:17534252 original size:24 final size:25
Alignment explanation
Indices: 17534220--17534306 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
17534210 ATGCTAATCC
17534220 AAGCCTTTGTGGC-AAGTTATCTAT
1 AAGCCTTTGTGGCTAAGTTATCTAT
* * *
17534244 AAGCTTTTGTGGCTAGGTTATCTAGG
1 AAGCCTTTGTGGCTAAGTTATCTA-T
* * *
17534270 AAGCCTTTATGGCGAA-TTATCTTAA
1 AAGCCTTTGTGGCTAAGTTATC-TAT
*
17534295 AAGCCTATGTGG
1 AAGCCTTTGTGG
17534307 TGTATTGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 12 0.24
25 24 0.48
26 14 0.28
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (25 bp):
AAGCCTTTGTGGCTAAGTTATCTAT
Found at i:17537066 original size:30 final size:29
Alignment explanation
Indices: 17537021--17537079 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
17537011 ATTTAATACG
*
17537021 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTT-CCCCTA
* *
17537051 AACTTTTGCATAATTACACTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTCCCCTA
17537080 GGCCCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (29 bp):
AACTTTGGCAAAATTACACTTTTCCCCTA
Found at i:17544058 original size:30 final size:30
Alignment explanation
Indices: 17544022--17544082 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
17544012 CATTTAATAC
* *
17544022 AAACTTTAGCAAAATTACATTTTTGCCCCT
1 AAACTTTAGCAAAATTACACTTTTACCCCT
* *
17544052 AAACTTTTGCATAATTACACTTTTACCCCT
1 AAACTTTAGCAAAATTACACTTTTACCCCT
17544082 A
1 A
17544083 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AAACTTTAGCAAAATTACACTTTTACCCCT
Found at i:17556127 original size:40 final size:40
Alignment explanation
Indices: 17556068--17556500 Score: 668
Period size: 40 Copynumber: 10.8 Consensus size: 40
17556058 GAACATTGGA
* *
17556068 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556108 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556148 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556188 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556228 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556268 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17556308 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17556348 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17556388 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17556428 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17556468 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
17556501 TTTGCGGCTG
Statistics
Matches: 355, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 355 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:17556201 original size:80 final size:80
Alignment explanation
Indices: 17556068--17556500 Score: 776
Period size: 80 Copynumber: 5.4 Consensus size: 80
17556058 GAACATTGGA
17556068 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
17556133 CAATTATGCGAGATG
66 CAATTATGCGAGATG
17556148 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
17556213 CAATTATGCGAGATG
66 CAATTATGCGAGATG
17556228 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
17556293 CAATTATGCGAGATG
66 CAATTATGCGAGATG
17556308 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
*
17556373 CAATTATGCGAGTTG
66 CAATTATGCGAGATG
* * * *
17556388 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
* *
17556453 CAATTATGCGAGTTC
66 CAATTATGCGAGATG
* * *
17556468 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGTTATGACCCGAAGGCAATTATG
17556501 TTTGCGGCTG
Statistics
Matches: 343, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 343 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTGACATATCCGGGCTAAGACCCGAAGG
CAATTATGCGAGATG
Found at i:17558899 original size:25 final size:25
Alignment explanation
Indices: 17558865--17558993 Score: 134
Period size: 25 Copynumber: 5.2 Consensus size: 25
17558855 AAAGCAAACC
17558865 AAGCCTTTGTGGTGAATATTCTATA
1 AAGCCTTTGTGGTGAATATTCTATA
* * *
17558890 AAGCCTTTGTGGCGAATACTCTGTA
1 AAGCCTTTGTGGTGAATATTCTATA
* * * *
17558915 AAGCCATTATGGTAAATATTCTGTA
1 AAGCCTTTGTGGTGAATATTCTATA
* * *
17558940 AAGCATTTGTGGTGAA-CTCCTTATA
1 AAGCCTTTGTGGTGAATATTC-TATA
* *
17558965 AAGCCTTTCTGGTGAATATTATATA
1 AAGCCTTTGTGGTGAATATTCTATA
17558990 AAGC
1 AAGC
17558994 TTCAGTGGCA
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
24 2 0.02
25 79 0.96
26 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (25 bp):
AAGCCTTTGTGGTGAATATTCTATA
Found at i:17558967 original size:50 final size:50
Alignment explanation
Indices: 17558865--17558993 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
17558855 AAAGCAAACC
* * *
17558865 AAGCCTTTGTGGTGAATATTCTATAAAGCCTTTGTGGCGAATACTCTGTA
1 AAGCCTTTATGGTGAATATTCTATAAAGCATTTGTGGCGAATACTCTATA
* * * * *
17558915 AAGCCATTATGGTAAATATTCTGTAAAGCATTTGTGGTGAACTCCT-TATA
1 AAGCCTTTATGGTGAATATTCTATAAAGCATTTGTGGCGAA-TACTCTATA
* *
17558965 AAGCCTTTCTGGTGAATATTATATAAAGC
1 AAGCCTTTATGGTGAATATTCTATAAAGC
17558994 TTCAGTGGCA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 62 0.95
51 3 0.05
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (50 bp):
AAGCCTTTATGGTGAATATTCTATAAAGCATTTGTGGCGAATACTCTATA
Found at i:17564846 original size:15 final size:15
Alignment explanation
Indices: 17564814--17564869 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
17564804 GTATCTTGGG
**
17564814 TTTCTTTATTCTAAA
1 TTTCTTTATTCTGGA
17564829 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
17564844 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
17564859 TTTCTTTATTC
1 TTTCTTTATTC
17564870 GGTTTCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:17573895 original size:43 final size:42
Alignment explanation
Indices: 17573798--17573917 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 42
17573788 AGGGTTATTA
** *
17573798 AGATTACGTGTAAGACCATATTTGGGATATGGCATCGATATG
1 AGATTACGTGTAAGACCATAGCTGGGATATGGCATCGATACG
* *
17573840 AGACTT-CGTGTAAGACCATGGCTGGGCTATTGGCATCGATACG
1 AGA-TTACGTGTAAGACCATAGCTGGGATA-TGGCATCGATACG
* *
17573883 AGATTACATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATAGCTGGGATATGGCAT
17573918 TGGTACGGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
42 30 0.45
43 36 0.55
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATAGCTGGGATATGGCATCGATACG
Found at i:17581047 original size:26 final size:26
Alignment explanation
Indices: 17581010--17581061 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
17581000 TCATTTCAAT
* *
17581010 GTCGATGTCATGTCCCAGACATGGTC
1 GTCGATGCCATGTCCCAAACATGGTC
17581036 GTCGATGCCATGTCCCAAACATGGTC
1 GTCGATGCCATGTCCCAAACATGGTC
17581062 CTATACTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (26 bp):
GTCGATGCCATGTCCCAAACATGGTC
Found at i:17585544 original size:42 final size:42
Alignment explanation
Indices: 17585497--17585651 Score: 213
Period size: 42 Copynumber: 3.7 Consensus size: 42
17585487 ATAAGGTTAT
* * *
17585497 GTGTAAGACCATATATGGGATATGGAATCGACATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTC
*
17585539 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTC
* * *
17585581 GTGTAAGACCATAGCTGCGCTATTGGCATCGATATGAGA-TTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGACTT-C
*
17585624 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
17585652 TGGTACGGTA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
42 65 0.66
43 34 0.34
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTC
Found at i:17585629 original size:85 final size:84
Alignment explanation
Indices: 17585497--17585651 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 84
17585487 ATAAGGTTAT
* * *
17585497 GTGTAAGACCATATATGGGATATGGAATCGACATGAGACTTCGTGTAAGACCATATCTGGGATAT
1 GTGTAAGACCATAGATGCGATATGGAATCGACATGAGACTTCATGTAAGACCATATCTGGGATAT
17585562 GGCATCAATATGAGACTTC
66 GGCATCAATATGAGACTTC
* * * *
17585581 GTGTAAGACCATAGCTGCGCTATTGGCATCGATATGAGA-TTACATGTAAGACCATATCTGGGAT
1 GTGTAAGACCATAGATGCGATA-TGGAATCGACATGAGACTT-CATGTAAGACCATATCTGGGAT
17585645 ATGGCAT
64 ATGGCAT
17585652 TGGTACGGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 20 0.32
85 42 0.68
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (84 bp):
GTGTAAGACCATAGATGCGATATGGAATCGACATGAGACTTCATGTAAGACCATATCTGGGATAT
GGCATCAATATGAGACTTC
Found at i:17591734 original size:29 final size:30
Alignment explanation
Indices: 17591681--17591740 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
17591671 GATTCATACA
17591681 TGGAAAATAAAATAAAAAAAGGATGA-AAT
1 TGGAAAATAAAATAAAAAAAGGATGATAAT
*
17591710 TGGAAAGTGAAAA-AAATAAAA-GATGATAAT
1 TGGAAAAT-AAAATAAA-AAAAGGATGATAAT
17591740 T
1 T
17591741 AATTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (30 bp):
TGGAAAATAAAATAAAAAAAGGATGATAAT
Found at i:17592504 original size:42 final size:42
Alignment explanation
Indices: 17592426--17592505 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
17592416 GTGTAGGTTT
* *
17592426 CACATGGCCAAGACACACGCCCATGTTCTAGGCCGTGTAGCA
1 CACACGGCCAAGACACACGCCCATGTTCTAGCCCGTGTAGCA
* *
17592468 CACACGGCTAAGACACATGCCCATGTCTCTA-CCCGTGT
1 CACACGGCCAAGACACACGCCCATGT-TCTAGCCCGTGT
17592506 GCTCAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 29 0.88
43 4 0.12
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.19
Consensus pattern (42 bp):
CACACGGCCAAGACACACGCCCATGTTCTAGCCCGTGTAGCA
Found at i:17598108 original size:77 final size:77
Alignment explanation
Indices: 17597981--17598131 Score: 275
Period size: 77 Copynumber: 2.0 Consensus size: 77
17597971 ATACTCATTG
*
17597981 TTGGAAGTAACAATGAAATGGTAAAATATACCAAAGACATGTGAAATTCAAGATTGACATGAAAG
1 TTGGAAGTAACAATGAAATAGTAAAATATACCAAAGACATGTGAAATTCAAGATTGACATGAAAG
17598046 ATATAGGACTTC
66 ATATAGGACTTC
* *
17598058 TTGGAAGTAACAATGAAATAGTAAAATGTACCAAAGACATGTTAAATTCAAGATTGACATGAAAG
1 TTGGAAGTAACAATGAAATAGTAAAATATACCAAAGACATGTGAAATTCAAGATTGACATGAAAG
17598123 ATATAGGAC
66 ATATAGGAC
17598132 CAGTTATGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (77 bp):
TTGGAAGTAACAATGAAATAGTAAAATATACCAAAGACATGTGAAATTCAAGATTGACATGAAAG
ATATAGGACTTC
Found at i:17600314 original size:43 final size:43
Alignment explanation
Indices: 17600263--17600372 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 43
17600253 CAATGCTGAC
* *
17600263 GTCCCAGACGTGGTCTTACATGTAATTCAG-TATCAATGCCTCT
1 GTCCCAGACATGGTCTTACATGTAATTCAGATA-CAATGCCGCT
* * * *
17600306 GTCCCAGACAAGGTCTTACACG-AATTCAGATACGATGCCGGT
1 GTCCCAGACATGGTCTTACATGTAATTCAGATACAATGCCGCT
*
17600348 GTCCCAGACATGGTCTTACGTGTAA
1 GTCCCAGACATGGTCTTACATGTAA
17600373 ATCTCAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 33 0.59
43 23 0.41
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGTAATTCAGATACAATGCCGCT
Found at i:17601244 original size:75 final size:76
Alignment explanation
Indices: 17601111--17601262 Score: 225
Period size: 75 Copynumber: 2.0 Consensus size: 76
17601101 CGAAGCAACG
* * * * *
17601111 ATCATAGAAACGTATAAATTATAAAAAATAGACGAAAATTCATGCCTTAACCAAGGATTACCAAT
1 ATCATAGAAACATAGAAATTATAAAAAACAAACGAAAATTCATACCTTAACCAAGGATTACCAAT
*
17601176 GTCGAATATCA
66 GCCGAATATCA
* *
17601187 ATCATAGAAACATAGAAATTATCAAAAACAAATG-AAATTCATACCTTAACCAAGGATTACCAAT
1 ATCATAGAAACATAGAAATTATAAAAAACAAACGAAAATTCATACCTTAACCAAGGATTACCAAT
17601251 GCCGAATATCA
66 GCCGAATATCA
17601262 A
1 A
17601263 AACCCCATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
75 40 0.59
76 28 0.41
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.24
Consensus pattern (76 bp):
ATCATAGAAACATAGAAATTATAAAAAACAAACGAAAATTCATACCTTAACCAAGGATTACCAAT
GCCGAATATCA
Found at i:17602420 original size:17 final size:17
Alignment explanation
Indices: 17602398--17602433 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
17602388 TATTATAAGT
17602398 GAATTCAATCAAAGGTA
1 GAATTCAATCAAAGGTA
17602415 GAATTCAATCAAAGGTA
1 GAATTCAATCAAAGGTA
17602432 GA
1 GA
17602434 TATTGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (17 bp):
GAATTCAATCAAAGGTA
Found at i:17608492 original size:40 final size:40
Alignment explanation
Indices: 17608431--17608564 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
17608421 CCTGCAGAAC
* * *
17608431 TTTAAGCCCGGATAT--AGTACCAGCACTAAGCCTACGGGA
1 TTTAA-CCCGGATATACATTACCAGCACGAAGCCTGCGGGA
*
17608470 TTTGACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
1 TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
* *
17608510 TTTAACCCGGATATACGTTACCAGCACGAAGCCTGTGGGA
1 TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
*
17608550 TTTAACCCAGATATA
1 TTTAACCCGGATATA
17608565 TAATATATCG
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 9 0.11
39 4 0.05
40 72 0.85
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (40 bp):
TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
Found at i:17616492 original size:40 final size:40
Alignment explanation
Indices: 17616418--17616564 Score: 208
Period size: 40 Copynumber: 3.7 Consensus size: 40
17616408 TACTAGCTCA
* * *
17616418 AAGCCTGCGGAACTTTAAGCCCGGATAT--AGTACCAGCACT
1 AAGCCTGCGGGA-TTTAA-CCCGGATATACATTACCAGCACG
*
17616458 AAGCCTGCGGGATTTAACCTGGATATACATTACCAGCACG
1 AAGCCTGCGGGATTTAACCCGGATATACATTACCAGCACG
* *
17616498 AAGCCTGTGGGATTTAACCTGGATATACATTACCAGCACG
1 AAGCCTGCGGGATTTAACCCGGATATACATTACCAGCACG
17616538 AAGCCTGCGGGATTTAACCCGGATATA
1 AAGCCTGCGGGATTTAACCCGGATATA
17616565 TAATATATCG
Statistics
Matches: 98, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 8 0.08
39 5 0.05
40 85 0.87
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (40 bp):
AAGCCTGCGGGATTTAACCCGGATATACATTACCAGCACG
Found at i:17624415 original size:24 final size:25
Alignment explanation
Indices: 17624388--17624441 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
17624378 CAAATTTAAA
*
17624388 TTAAAT-AATTT-TAAAATATTGTAT
1 TTAAATGAATTTATAAAATATTAT-T
*
17624412 TTAAATGTATTTATAAAATATTATT
1 TTAAATGAATTTATAAAATATTATT
17624437 TTAAA
1 TTAAA
17624442 AACTAACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
25 10 0.38
26 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTAAATGAATTTATAAAATATTATT
Found at i:17624729 original size:54 final size:54
Alignment explanation
Indices: 17624648--17624763 Score: 207
Period size: 54 Copynumber: 2.2 Consensus size: 54
17624638 AAGAAAGGAA
* *
17624648 AGATAAGT-GAGGAAAAAAGTAAGGAGAGAAAAGAATTACCAATTATTTTGTTT
1 AGATAATTAGAGGAAAAAAGTAAGGAGAGAAAAGAATTACAAATTATTTTGTTT
17624701 AGATAATTAGAGGAAAAAAGTAAGGAGAGAAAAGAATTACAAATTATTTTGTTT
1 AGATAATTAGAGGAAAAAAGTAAGGAGAGAAAAGAATTACAAATTATTTTGTTT
17624755 AGATAATTA
1 AGATAATTA
17624764 AAAATTATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 7 0.12
54 53 0.88
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.28
Consensus pattern (54 bp):
AGATAATTAGAGGAAAAAAGTAAGGAGAGAAAAGAATTACAAATTATTTTGTTT
Found at i:17625846 original size:13 final size:14
Alignment explanation
Indices: 17625828--17625856 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17625818 ATAGTACGAT
17625828 AATTAAAATTG-AG
1 AATTAAAATTGTAG
17625841 AATTAAAATTGTAG
1 AATTAAAATTGTAG
17625855 AA
1 AA
17625857 AAAACTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (14 bp):
AATTAAAATTGTAG
Found at i:17637645 original size:28 final size:28
Alignment explanation
Indices: 17637605--17637662 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
17637595 GAATTTTAGG
17637605 TTGAAAATGACAATAATAAGATGATATT
1 TTGAAAATGACAATAATAAGATGATATT
*
17637633 TTGAAGATGACAATAATAAGATGATATT
1 TTGAAAATGACAATAATAAGATGATATT
17637661 TT
1 TT
17637663 CTTTTATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (28 bp):
TTGAAAATGACAATAATAAGATGATATT
Found at i:17638861 original size:6 final size:6
Alignment explanation
Indices: 17638843--17638950 Score: 62
Period size: 6 Copynumber: 17.3 Consensus size: 6
17638833 AAGAAACATT
* *
17638843 ATCAGA A-CTAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATCAGA ATCAGT
1 ATCAGA ATC-AGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA
* * * *
17638892 ATCAAGTA A-GAGA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA
1 ATC-AG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA
17638943 ATCAGA AT
1 ATCAGA AT
17638951 GTGAATGCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
5 6 0.08
6 55 0.71
7 14 0.18
8 3 0.04
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:17638878 original size:31 final size:31
Alignment explanation
Indices: 17638843--17638950 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
17638833 AAGAAACATT
* *
17638843 ATCAGAA-CTAGAATCAGAATCAGGTGACAGA
1 ATCAGAATC-AGAATCAGTATCAGGTAACAGA
* *
17638874 ATCAGAATCAGAATCAGTATCAAGTAAGAGA
1 ATCAGAATCAGAATCAGTATCAGGTAACAGA
*
17638905 ATCAAAATCAGAATCAGTATCAGGTAACAGA
1 ATCAGAATCAGAATCAGTATCAGGTAACAGA
*
17638936 ATCAAAAATCAGAAT
1 ATC-AGAATCAGAAT
17638951 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 56 0.82
32 12 0.18
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (31 bp):
ATCAGAATCAGAATCAGTATCAGGTAACAGA
Found at i:17639051 original size:38 final size:38
Alignment explanation
Indices: 17639007--17639096 Score: 162
Period size: 38 Copynumber: 2.4 Consensus size: 38
17638997 TCCACCCGTA
*
17639007 CCAGCCCTACACTCCATGTGGGGAATAGATCCACCCAC
1 CCAGCCCTACACTCCATGTGGGGAATAGATCAACCCAC
*
17639045 CCAGCCCTACACTCCATGTGGGGAATAGCTCAACCCAC
1 CCAGCCCTACACTCCATGTGGGGAATAGATCAACCCAC
17639083 CCAGCCCTACACTC
1 CCAGCCCTACACTC
17639097 AACAGTTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.42, G:0.17, T:0.16
Consensus pattern (38 bp):
CCAGCCCTACACTCCATGTGGGGAATAGATCAACCCAC
Found at i:17639224 original size:27 final size:27
Alignment explanation
Indices: 17639125--17639226 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
17639115 GCTCAGTTAT
* * *
17639125 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGAAA
*
17639152 CAGATATTGTGGCAGAGCTACCAG-AA
1 CAGATATTGTGGCAGAGCCACCAGAAA
* *
17639178 CAGGTATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAGAAA
* *
17639206 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
17639227 TTAACAGAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 6 0.10
27 50 0.79
28 7 0.11
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGAAA
Found at i:17639413 original size:22 final size:22
Alignment explanation
Indices: 17639385--17639449 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
17639375 GCAAATACGT
*
17639385 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
17639407 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
17639429 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
17639450 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:17639934 original size:27 final size:27
Alignment explanation
Indices: 17639904--17640124 Score: 255
Period size: 27 Copynumber: 8.2 Consensus size: 27
17639894 GGAATCTCGA
* **
17639904 TAATTCCACCCTACAGGGGTATTTTAG
1 TAATTCTACCCTACAGGGGTATTTCGG
*
17639931 TAATTCTACCCTACAGGGGTATTTCGT
1 TAATTCTACCCTACAGGGGTATTTCGG
* * ** *
17639958 TAATTCTACCCTATAAGGGTATAGCGA
1 TAATTCTACCCTACAGGGGTATTTCGG
*
17639985 TAATTCTACCCTATAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGG
17640012 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGG
17640039 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGG
* * * **
17640066 TATTTCTACCCAACAAGGGTATTTTAG
1 TAATTCTACCCTACAGGGGTATTTCGG
* ** *
17640093 TAATTTTA-CAAACCAGGGGTATTTTGG
1 TAATTCTACCCTA-CAGGGGTATTTCGG
17640120 TAATT
1 TAATT
17640125 TGGTAAACTA
Statistics
Matches: 169, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 3 0.02
27 166 0.98
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGG
Found at i:17640125 original size:27 final size:27
Alignment explanation
Indices: 17639876--17640125 Score: 173
Period size: 27 Copynumber: 9.3 Consensus size: 27
17639866 GGGGCAAAAT
* * * *
17639876 GGTAATTTTACCCCACA-AGGAATCTC
1 GGTAATTTTACCCAACAGGGGTATTTC
* ** * *
17639902 GATAATTCCACCCTACAGGGGTATTTT
1 GGTAATTTTACCCAACAGGGGTATTTC
* * *
17639929 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCAACAGGGGTATTTC
* * * * * **
17639956 GTTAATTCTACCCTATAAGGGTATAGC
1 GGTAATTTTACCCAACAGGGGTATTTC
* * * *
17639983 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTTTACCCAACAGGGGTATTTC
* *
17640010 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCAACAGGGGTATTTC
* *
17640037 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCAACAGGGGTATTTC
* *
17640064 GGT-ATTTCTACCCAACAAGGGTATTTT
1 GGTAATTT-TACCCAACAGGGGTATTTC
* * *
17640091 AGTAATTTTA-CAAACCAGGGGTATTTT
1 GGTAATTTTACCCAA-CAGGGGTATTTC
17640118 GGTAATTT
1 GGTAATTT
17640126 GGTAAACTAA
Statistics
Matches: 188, Mismatches: 32, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
26 19 0.10
27 165 0.88
28 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTTTACCCAACAGGGGTATTTC
Found at i:17640306 original size:122 final size:122
Alignment explanation
Indices: 17640089--17640333 Score: 418
Period size: 122 Copynumber: 2.0 Consensus size: 122
17640079 CAAGGGTATT
* *
17640089 TTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTAAAGTATTTTAAACCGAGAT
1 TTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTAAAGTATTCTAAACAGAGAT
*
17640154 AACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGGGCCCACATGCTCGTG
66 AACAATACGAATGGCCCTAAAGCCTATTCTCGACCCAAATGGGCCCACATGCTCGTG
* *
17640211 TTAGTAATTTTACAAACCATGGGTATTTTGGTAATTTGGTAAACTAAAGTATTCTAAACAGGGAT
1 TTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTAAAGTATTCTAAACAGAGAT
* * *
17640276 AACAATACGAATGGCCCTACAGCCTATTCTCGGCCTAAATGGGCCCACATGCTCGTG
66 AACAATACGAATGGCCCTAAAGCCTATTCTCGACCCAAATGGGCCCACATGCTCGTG
17640333 T
1 T
17640334 GGCTCTTTTA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (122 bp):
TTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACTAAAGTATTCTAAACAGAGAT
AACAATACGAATGGCCCTAAAGCCTATTCTCGACCCAAATGGGCCCACATGCTCGTG
Found at i:17642215 original size:6 final size:6
Alignment explanation
Indices: 17642197--17642287 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
17642187 AAGAAACATT
* * * * *
17642197 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAAA ATTAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
17642246 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAG
17642288 TATTAGGTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
5 4 0.06
6 54 0.83
7 5 0.08
8 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:17642252 original size:31 final size:31
Alignment explanation
Indices: 17642214--17642316 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 31
17642204 CTAGAATCAG
* * * *
17642214 AATCAGAATCAGAATTAGGTGACAAAATTAA
1 AATCAGAATCAGTATTAGGTAACAGAATAAA
* *
17642245 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGTATTAGGTAACAGAATAAA
17642276 AATCAGAATCAGTATTAGGTAACAGAATAAAA
1 AATCAGAATCAGTATTAGGTAACAGAAT-AAA
17642308 AATCAGAAT
1 AATCAGAAT
17642317 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 53 0.83
32 11 0.17
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGTATTAGGTAACAGAATAAA
Found at i:17642501 original size:27 final size:26
Alignment explanation
Indices: 17642455--17642553 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 26
17642445 TCAGTTATCT
* *
17642455 GATATTGTGACATAGTCACCAGATACA
1 GATATTGTGGCATAGCCACCAGA-ACA
*
17642482 GATATTGTGGCAGAGCCACCAGAACA
1 GATATTGTGGCATAGCCACCAGAACA
*
17642508 GATATTTGTGGCATAGCCACAAGAAACA
1 GATA-TTGTGGCATAGCCACCAG-AACA
* *
17642536 GATAATGTGGCAAAGCCA
1 GATATTGTGGCATAGCCA
17642554 ATTAACAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
26 7 0.11
27 48 0.76
28 8 0.13
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (26 bp):
GATATTGTGGCATAGCCACCAGAACA
Found at i:17643261 original size:27 final size:27
Alignment explanation
Indices: 17643231--17643451 Score: 220
Period size: 27 Copynumber: 8.2 Consensus size: 27
17643221 GGTATCTCGA
* *
17643231 TAATTCCACCCTACAGGGGTATTTTAG
1 TAATTCTACCCTACAGGGGTATTTTCG
17643258 TAATTCTACCCTACAGGGGTA-TTTCG
1 TAATTCTACCCTACAGGGGTATTTTCG
* **
17643284 TTAATTCTACCCTATAGGGGTA-TAGCG
1 -TAATTCTACCCTACAGGGGTATTTTCG
*
17643311 ATAATTCTACCCTATAGGGGTA-TTTCGG
1 -TAATTCTACCCTACAGGGGTATTTTC-G
*
17643339 TAATTCTACCCTAGAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTC-G
17643366 TAATTCTACCCTACAGGGGTA-TTTCG
1 TAATTCTACCCTACAGGGGTATTTTCG
* * *
17643392 ATATTTCTACCCTACAAGGGTATTTTAG
1 -TAATTCTACCCTACAGGGGTATTTTCG
* ** *
17643420 TAATTTTA-CAAACCAGGGGTATTTTGG
1 TAATTCTACCCTA-CAGGGGTATTTTCG
17643447 TAATT
1 TAATT
17643452 TGGTAAACTA
Statistics
Matches: 170, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.04
27 158 0.93
28 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTTCG
Found at i:17643330 original size:81 final size:81
Alignment explanation
Indices: 17643228--17643451 Score: 297
Period size: 81 Copynumber: 2.8 Consensus size: 81
17643218 CAAGGTATCT
* *
17643228 CGATAATTCCACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGTTAATTCTA
1 CGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA
*
17643293 CCCTATAGGGGTATAG
66 CCCTACAGGGGTATAG
* ** *
17643309 CGATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAGAGGGGTATTTCGGTAATTCTA
1 CGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA
**
17643374 CCCTACAGGGGTATTT
66 CCCTACAGGGGTATAG
* * * ** *
17643390 CGATATTTCTACCCTACAAGGGTATTTTAGTAATTTTA-CAAACCAGGGGTATTTTGGTAATT
1 CGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTA-CAGGGGTATTTCGGTAATT
17643452 TGGTAAACTA
Statistics
Matches: 123, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
80 2 0.02
81 121 0.98
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (81 bp):
CGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA
CCCTACAGGGGTATAG
Found at i:17643443 original size:54 final size:54
Alignment explanation
Indices: 17643204--17643424 Score: 266
Period size: 54 Copynumber: 4.1 Consensus size: 54
17643194 GGGCAAAATG
* * * * *
17643204 GTAATTTTACCCCACA-AGGTATCTCGATAATTCCACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTA
* * ***
17643257 GTAATTCTACCCTACAGGGGTATTTCGTTAATTCTACCCTATAGGGGTA-TAGC
1 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTA
* * * **
17643310 GATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAGAGGGGTATTTCG
1 G-TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTA
* *
17643365 GTAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTA
17643419 GTAATT
1 GTAATT
17643425 TTACAAACCA
Statistics
Matches: 142, Mismatches: 23, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
53 16 0.11
54 124 0.87
55 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTA
Found at i:17643671 original size:153 final size:153
Alignment explanation
Indices: 17643393--17643697 Score: 610
Period size: 153 Copynumber: 2.0 Consensus size: 153
17643383 GGTATTTCGA
17643393 TATTTCTACCCTACAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAA
1 TATTTCTACCCTACAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAA
17643458 ACTAAAGTATTTTAAACCGAGATAACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGG
66 ACTAAAGTATTTTAAACCGAGATAACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGG
17643523 GCCCACATGCTCGTGTGGCCCTG
131 GCCCACATGCTCGTGTGGCCCTG
17643546 TATTTCTACCCTACAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAA
1 TATTTCTACCCTACAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAA
17643611 ACTAAAGTATTTTAAACCGAGATAACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGG
66 ACTAAAGTATTTTAAACCGAGATAACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGG
17643676 GCCCACATGCTCGTGTGGCCCT
131 GCCCACATGCTCGTGTGGCCCT
17643698 TTTAGCCGAA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (153 bp):
TATTTCTACCCTACAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAA
ACTAAAGTATTTTAAACCGAGATAACAATACGAATGGCTCTAAAGCCTATTCTCGACCCAAATGG
GCCCACATGCTCGTGTGGCCCTG
Found at i:17649662 original size:40 final size:40
Alignment explanation
Indices: 17649625--17649725 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
17649615 CTACTCGCTT
*** *
17649625 AAATGCCTTCGGGACTTAGCCCGGTTTTAGTAGCTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCAC
17649665 AAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCAC
17649705 AAATGCCTTCGGGACTTAGCC
1 AAATGCCTTCGGGACTTAGCC
17649726 TGCTTATCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCAC
Found at i:17651113 original size:43 final size:43
Alignment explanation
Indices: 17651052--17651136 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
17651042 ACCATAGCCG
*
17651052 ATTTTCTCCAAGCTCTTTCCCTTCCTTTCTTTCCTCTATTCGT
1 ATTTTCTCCAAGCCCTTTCCCTTCCTTTCTTTCCTCTATTCGT
*
17651095 ATTTTCTCCAAGCCCTTTCCCTTCCTTTCTTTCTTCTATTCG
1 ATTTTCTCCAAGCCCTTTCCCTTCCTTTCTTTCCTCTATTCG
17651137 GCCAACTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.09, C:0.35, G:0.05, T:0.51
Consensus pattern (43 bp):
ATTTTCTCCAAGCCCTTTCCCTTCCTTTCTTTCCTCTATTCGT
Found at i:17656733 original size:47 final size:47
Alignment explanation
Indices: 17656542--17656735 Score: 262
Period size: 47 Copynumber: 4.1 Consensus size: 47
17656532 ATAGGATTTT
** * *
17656542 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
17656589 ATGCGATGAATGTGAACATGCATATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
17656636 ATGCGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
17656683 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
17656730 ATGTGA
1 ATGTGA
17656736 AATATGTATG
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:17657050 original size:37 final size:37
Alignment explanation
Indices: 17656942--17657050 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
17656932 GGAAATATAT
* *
17656942 TCCGGGTAAGACCCGATGTCTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
17656979 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
17657016 TCCGGGTAAGACCCGATGACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
17657051 CGTTTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:17658885 original size:40 final size:40
Alignment explanation
Indices: 17658848--17659072 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
17658838 GCTACTCGTT
* *
17658848 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
17658888 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17658928 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
17658968 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
17659007 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
17659048 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
17659073 CATCATTCAA
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 119 0.71
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:17659032 original size:119 final size:120
Alignment explanation
Indices: 17658848--17659072 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 120
17658838 GCTACTCGTT
*
17658848 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
17658913 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
17658968 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
17659030 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
17659073 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.72
120 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:17666291 original size:39 final size:40
Alignment explanation
Indices: 17666174--17666358 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
17666164 GCTACTCGTT
*
17666174 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGATT-TAGTAACTCGCA
* *
17666214 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
* *
17666254 CAAATGCCTTCGGG-CATAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
* * * * * *
17666293 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAGCCCGGATTTAGTAAC-TCGCA
*
17666334 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAGCCCGGA
17666359 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
Found at i:17666291 original size:79 final size:82
Alignment explanation
Indices: 17666174--17666358 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
17666164 GCTACTCGTT
* *
17666174 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACATAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
17666237 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
17666254 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
17666317 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
*
17666334 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAGCCCGGA
17666359 CATCATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.61
80 33 0.36
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACATAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:17667554 original size:56 final size:56
Alignment explanation
Indices: 17667487--17667606 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
17667477 TATTAGTTTA
17667487 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
17667543 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
17667599 TTGCCCAT
1 TTGCCCAT
17667607 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:17682815 original size:42 final size:41
Alignment explanation
Indices: 17682710--17682849 Score: 131
Period size: 44 Copynumber: 3.3 Consensus size: 41
17682700 AGATGTGTTA
* *
17682710 TCGTGTAAGACCACGTTTGGGACATTGGCATCG-ATTTGGGATT
1 TCGTGTAAGACTA-GTCTGGGACATTGGCATCGTATTT--GATT
*
17682753 TACGTGTAAGACTATGTCTGGGACATTGGCATCGTATATGATT
1 T-CGTGTAAGACTA-GTCTGGGACATTGGCATCGTATTTGATT
* * *
17682796 TTGTGTAAGATCCTA-TCTGGGACAGTAGCATCGATATTTGATT
1 TCGTGTAAGA--CTAGTCTGGGACATTGGCATCG-TATTTGATT
*
17682839 TCATGTAAGAC
1 TCGTGTAAGAC
17682850 CACGTCTAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 24 0.29
43 22 0.27
44 32 0.39
45 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (41 bp):
TCGTGTAAGACTAGTCTGGGACATTGGCATCGTATTTGATT
Found at i:17686766 original size:21 final size:21
Alignment explanation
Indices: 17686740--17686791 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
17686730 CACGGCCTAC
17686740 CCACACGGGCGTGTCCCAAAG
1 CCACACGGGCGTGTCCCAAAG
17686761 CCACACGGGCGTGTCCCAAAG
1 CCACACGGGCGTGTCCCAAAG
17686782 CCACACGGGC
1 CCACACGGGC
17686792 ATGTGACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.40, G:0.29, T:0.08
Consensus pattern (21 bp):
CCACACGGGCGTGTCCCAAAG
Found at i:17690478 original size:37 final size:37
Alignment explanation
Indices: 17690428--17690501 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
17690418 TTACATTACT
17690428 CCTCATTAATCAACTCAAAAAGTATCCATAGTAAATC
1 CCTCATTAATCAACTCAAAAAGTATCCATAGTAAATC
17690465 CCTCATTAATCAACTCAAAAAGTATCCATAGTAAATC
1 CCTCATTAATCAACTCAAAAAGTATCCATAGTAAATC
17690502 ATTCTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.27
Consensus pattern (37 bp):
CCTCATTAATCAACTCAAAAAGTATCCATAGTAAATC
Found at i:17693996 original size:5 final size:5
Alignment explanation
Indices: 17693986--17694011 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17693976 TATATAAAAT
17693986 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
17694012 AATTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:17694014 original size:17 final size:17
Alignment explanation
Indices: 17693968--17694006 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17693958 TGATTTCTTT
* *
17693968 TAAAAAATTATATAAAA
1 TAAAAAATAAAATAAAA
*
17693985 TATAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA
17694002 TAAAA
1 TAAAA
17694007 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAATAAAATAAAA
Found at i:17695403 original size:22 final size:23
Alignment explanation
Indices: 17695378--17695425 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
17695368 GAAAATAATA
*
17695378 TTTTAATTCTAAATTTA-ATTTT
1 TTTTAATTCTAAATTTATACTTT
*
17695400 TTTTAATTTTAAATTTATACTTT
1 TTTTAATTCTAAATTTATACTTT
17695423 TTT
1 TTT
17695426 ATCAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTAATTCTAAATTTATACTTT
Found at i:17695584 original size:18 final size:18
Alignment explanation
Indices: 17695563--17695600 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17695553 TTTTTAAGTG
* *
17695563 TTAAAAAATTAAAATTAT
1 TTAAAAAATAAAAAATAT
17695581 TTAAAAAATAAAAAATAT
1 TTAAAAAATAAAAAATAT
17695599 TT
1 TT
17695601 TGAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAAAATAAAAAATAT
Found at i:17700653 original size:27 final size:28
Alignment explanation
Indices: 17700544--17700666 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
17700534 GAGATTGGCG
* * * *
17700544 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
17700573 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
17700601 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
17700629 CTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
17700656 CTGAGTGTGCG
1 CTAAGTGTGCG
17700667 GACTTAATAT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 23 0.27
28 47 0.55
29 15 0.18
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:17700656 original size:55 final size:57
Alignment explanation
Indices: 17700544--17700666 Score: 169
Period size: 55 Copynumber: 2.2 Consensus size: 57
17700534 GAGATTGGCG
* * * *
17700544 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
* *
17700601 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
*
17700656 CTGAGTGTGCG
1 CTAAGTGTGCG
17700667 GACTTAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 23 0.39
56 21 0.36
57 15 0.25
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (57 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
Found at i:17700677 original size:27 final size:27
Alignment explanation
Indices: 17700569--17700679 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 27
17700559 TAAATTGTAC
** * *
17700569 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGC-AACTTGAATATAT
** *
17700597 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGC-AACTTGAATATAT
* *
17700625 AGCACTAAGTGTGCAAGTTGATTATAT
1 AGCACTAAGTGTGCAACTTGAATATAT
* *
17700652 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-AACTTGAATATAT
17700679 A
1 A
17700680 CTTTTGAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 31 0.41
28 44 0.59
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCAACTTGAATATAT
Found at i:17707595 original size:46 final size:46
Alignment explanation
Indices: 17707545--17708076 Score: 983
Period size: 46 Copynumber: 11.6 Consensus size: 46
17707535 TTGAGCATCC
17707545 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707591 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707637 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707683 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707729 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707775 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707821 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707867 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17707913 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
*** *** *
17707959 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTTGAGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
* *
17708005 GAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17708051 GAACTCGTTGAGTTGAGTCCGAGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC
17708077 GTGAGATGTA
Statistics
Matches: 472, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 472 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
Found at i:17711427 original size:15 final size:15
Alignment explanation
Indices: 17711388--17711467 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
17711378 GTATCTTGGG
*
17711388 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
17711403 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
17711418 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
17711433 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
17711448 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
17711462 TTTCTT
1 TTTCTT
17711468 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:17711457 original size:30 final size:30
Alignment explanation
Indices: 17711379--17711466 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
17711369 CATAGTGTCG
* * *
17711379 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
17711409 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
17711439 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
17711467 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:17713919 original size:46 final size:46
Alignment explanation
Indices: 17713869--17714676 Score: 1553
Period size: 46 Copynumber: 17.6 Consensus size: 46
17713859 TTGAGCATCC
17713869 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17713915 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17713961 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714007 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714053 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714099 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714145 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714191 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714237 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714283 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714329 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714375 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714421 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714467 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714513 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
*** *** *
17714559 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTTGAGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714605 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
17714651 GAACTCGTTGAGTTGAGTCCGAGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC
17714677 GTGAGATGTA
Statistics
Matches: 748, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 748 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCT
Found at i:17716592 original size:46 final size:45
Alignment explanation
Indices: 17716478--17716609 Score: 147
Period size: 46 Copynumber: 2.9 Consensus size: 45
17716468 AGACTATTTG
* * * **
17716478 TTGTGTAGGTTCAACCCTAACGAGTGACCAGACACTATTATTTTAT
1 TTGTGTAGGTTCAA-CCTAATGGGTGACCAAACACTATTATTCGAT
* *
17716524 TTATGTAGGTTCAACCCCAATGGGTGACCAAACACTATTATTCGAT
1 TTGTGTAGGTTCAA-CCTAATGGGTGACCAAACACTATTATTCGAT
* * *
17716570 TTGTGTAGGTTTAACCTAAATGGGTAACCAAAAACTATTA
1 TTGTGTAGGTTCAACCT-AATGGGTGACCAAACACTATTA
17716610 CTTTCACCTG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 2 0.03
46 71 0.97
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (45 bp):
TTGTGTAGGTTCAACCTAATGGGTGACCAAACACTATTATTCGAT
Found at i:17719689 original size:40 final size:40
Alignment explanation
Indices: 17719595--17719779 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 40
17719585 TATTCGAATG
* *
17719595 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* * * *
17719636 ATAACTGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCTGGGCTAAG-TCCCGAAGGCATTTGTGCTAG-TGACT
* *
17719676 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
17719716 ATATCTGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
17719756 ACATCCGGGCTAAGACTCGAAGGC
1 ATATCTGGGCTAAGTCCCGAAGGC
17719780 CTTGTGCAAG
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 90 0.75
41 28 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:17727276 original size:40 final size:40
Alignment explanation
Indices: 17727216--17727321 Score: 160
Period size: 40 Copynumber: 2.6 Consensus size: 40
17727206 NNNNNNNNNN
17727216 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTCAAA-CCGGGC
* *
17727256 TAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAACCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTCAAACCGGGC
* *
17727296 TATGTCCCGAAGGCATTTGAGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGT
17727322 AGCTATATCC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 58 0.97
41 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTCAAACCGGGC
Found at i:17735638 original size:56 final size:54
Alignment explanation
Indices: 17735514--17735665 Score: 223
Period size: 56 Copynumber: 2.8 Consensus size: 54
17735504 ATGTATATGA
* ** *
17735514 GGCATCGATATGTGATTCTAATATATGTATGCGAGTAAGACCACTTTATACGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACTTTATACGTT
*
17735568 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCAC--TTTATACGTT
* *
17735624 GGCATTGATATGTGACTTCGATATATGTGTGCGAGTAAGACC
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACC
17735666 CTGTCTGGGA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 40 0.45
56 49 0.55
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (54 bp):
GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACTTTATACGTT
Found at i:17735683 original size:56 final size:56
Alignment explanation
Indices: 17735514--17735694 Score: 192
Period size: 56 Copynumber: 3.3 Consensus size: 56
17735504 ATGTATATGA
* ** * * * *
17735514 GGCATCGATATGTGATTCTAATATATGTATGCGAGTAAGACCAC-TT-TATACGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTGGACATGTT
** *
17735568 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTGGACATGTT
* *
17735624 GGCATTGATATGTGACTTCGATATATGTGTGCGAGTAAGACC-CTGTCTGGGACA-G-T
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCAC-GT-T-GGACATGTT
17735680 GGCATCGATATGTGA
1 GGCATCGATATGTGA
17735695 TTACATGTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
54 40 0.36
55 3 0.03
56 64 0.58
57 2 0.02
58 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (56 bp):
GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTGGACATGTT
Found at i:17738552 original size:48 final size:48
Alignment explanation
Indices: 17738501--17738713 Score: 363
Period size: 48 Copynumber: 4.4 Consensus size: 48
17738491 GCCGAATCAC
* * *
17738501 TAGCCATTTGGCTTTACCACATATACATATCTCATACATAGTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
17738549 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
**
17738597 TAGCCATTCGGCTTTACTGCATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
17738645 TAACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
17738693 TAGCCATTCGGCTTTACCACA
1 TAGCCATTCGGCTTTACCACA
17738714 CACATATATA
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 154 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
Found at i:17742058 original size:28 final size:27
Alignment explanation
Indices: 17741971--17742066 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
17741961 CTGATTTCGT
*
17741971 ACACATAGCGCTC-GATTAAAGAACTCGC
1 ACACATAGTGCTCAG-TT-AAGAACTCGC
* **
17741999 ACACATAGTGCCTCAATTACCAATCTCGC
1 ACACATAGTG-CTCAGTTAAGAA-CTCGC
*
17742028 ACACATAGTGCTCAGTTGAAGAACTTGC
1 ACACATAGTGCTCAGTT-AAGAACTCGC
*
17742056 ACACACAGTGC
1 ACACATAGTGC
17742067 CTCATAACTC
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
28 32 0.58
29 23 0.42
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (27 bp):
ACACATAGTGCTCAGTTAAGAACTCGC
Found at i:17742142 original size:40 final size:40
Alignment explanation
Indices: 17742098--17742225 Score: 229
Period size: 40 Copynumber: 3.2 Consensus size: 40
17742088 CCTTCGAGGT
* *
17742098 TTAGCCTGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
17742138 TTAGCCCGGATACATTACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
17742178 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
17742218 TTAGCCCG
1 TTAGCCCG
17742226 ACTATATAAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:17743928 original size:38 final size:38
Alignment explanation
Indices: 17743873--17743993 Score: 163
Period size: 38 Copynumber: 3.2 Consensus size: 38
17743863 TGGACCTGCC
* * *
17743873 ATGGTCTTTACATTTTATCACAATACCAGAGCCCAGCT
1 ATGGTCTTTACACTTTATCACAATGCCATAGCCCAGCT
*
17743911 ATGGTCTTTACACTTTATCACAATGCCATAGCTCAGCT
1 ATGGTCTTTACACTTTATCACAATGCCATAGCCCAGCT
* * *
17743949 ATGGTC-TTACACTTTAATTACGATGCCATAACCCAGCT
1 ATGGTCTTTACACTTT-ATCACAATGCCATAGCCCAGCT
17743987 ATGGTCT
1 ATGGTCT
17743994 ACACGTACAC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
37 9 0.12
38 64 0.88
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (38 bp):
ATGGTCTTTACACTTTATCACAATGCCATAGCCCAGCT
Found at i:17756372 original size:46 final size:48
Alignment explanation
Indices: 17756228--17756590 Score: 223
Period size: 46 Copynumber: 7.7 Consensus size: 48
17756218 TTTGTGTGCT
* * * **
17756228 AGTGTAAGA-CATGTCTGGTACA-GGCATCAGCCACATTATG-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAAATGTA-AGCC
* * * * ** * * *
17756274 AGTGTAAGATCATGTCTGAGATATGGCATCGGCATTGAGACG-AGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAAATGTA-AGCC
*
17756322 AGTGTAAGA-CATGTATGGGACAT-GCATCGGCCTCAAAATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAAATGTAAGCC
* * * *
17756368 AGTGTAAGA-CATGTTTGGGACAT-GCATCGG-CTACGAGATGT--GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CAAAATGTAAGCC
* * * *
17756412 AGTGTAAGACCATGTCTGGGACATGGCATC-GACACAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCA-AAATGT-A-AGCC
* ** ** ** **
17756462 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTTGATTTCAATAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAAATGTA-AGCC
* * * **
17756511 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATG--AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCA-AAATGTAAGCC
17756558 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
17756591 AGTATACCCT
Statistics
Matches: 250, Mismatches: 53, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
44 11 0.04
45 17 0.07
46 70 0.28
47 56 0.22
48 24 0.10
49 36 0.14
50 34 0.14
51 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAAATGTAAGCC
Found at i:17756524 original size:99 final size:96
Alignment explanation
Indices: 17756227--17756590 Score: 283
Period size: 94 Copynumber: 3.8 Consensus size: 96
17756217 GTTTGTGTGC
* * * *
17756227 TAGTGTAAGA-CATGTCTGGTACA-GGCATC-AGCCACAT-TATGAGAGCCAGTGTAAGATCATG
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGA-CCAGATGGAT--GAGCCAGTGTAAGACCATG
* * * ** * * *
17756288 TCTGAGATATGGCATCGGCATTGA-GACGAGAGC
63 TCTGGGACATGGCATCGGCCTTGATTTCAATAGT
* * * *
17756321 TAGTGTAAGA-CATGTATGGGACAT-GCATCGGCCTCAAAAT-G-TAAGCCAGTGTAAGA-CATG
1 TAGTGTAAGACCATGTCTGGGACATGGCATC-GAC-C-AGATGGATGAGCCAGTGTAAGACCATG
* * ** *
17756381 TTTGGGACAT-GCATCGG-CTACGAGAT--GT-GT
63 TCTGGGACATGGCATCGGCCT-TGATTTCAATAGT
* *
17756411 CAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATGTGA-GAGCTAGTGTAAGACCAT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CAG--ATG-GATGAGCCAGTGTAAGACCAT
*
17756475 GTCTGGGACATGGCGTCGGCCTTGATTTCAATAGT
62 GTCTGGGACATGGCATCGGCCTTGATTTCAATAGT
**
17756510 TAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGCCAGTGTAAGACCATGTCT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACCAGATGGATGAGCCAGTGTAAGACCATGTCT
17756575 GGGACATGGCATCGGC
66 GGGACATGGCATCGGC
17756591 AGTATACCCT
Statistics
Matches: 215, Mismatches: 34, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
90 11 0.05
91 17 0.08
92 16 0.07
93 11 0.05
94 52 0.24
95 16 0.07
96 50 0.23
97 5 0.02
98 2 0.01
99 35 0.16
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (96 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGACCAGATGGATGAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGGCCTTGATTTCAATAGT
Found at i:17769695 original size:23 final size:23
Alignment explanation
Indices: 17769669--17769712 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17769659 TCTCACCTGC
17769669 TTTAGAACTTACAAAAAAGAAGA
1 TTTAGAACTTACAAAAAAGAAGA
*
17769692 TTTAGAACTTACAAAGAAGAA
1 TTTAGAACTTACAAAAAAGAA
17769713 CATAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.23
Consensus pattern (23 bp):
TTTAGAACTTACAAAAAAGAAGA
Found at i:17770671 original size:20 final size:22
Alignment explanation
Indices: 17770646--17770698 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
17770636 AATTTGTTTC
*
17770646 ATGCGAACCCTAG-GTT-AAAT
1 ATGCGAACCCTAGTATTCAAAT
*
17770666 ATGCGAATCCT-GTATTCAAAT
1 ATGCGAACCCTAGTATTCAAAT
17770687 ATGCGAACCCTA
1 ATGCGAACCCTA
17770699 TATATATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 14 0.52
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (22 bp):
ATGCGAACCCTAGTATTCAAAT
Found at i:17770751 original size:24 final size:22
Alignment explanation
Indices: 17770718--17770763 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
17770708 CATGTGAATT
17770718 CTATACATGAGTTATATGCAAACC
1 CTATACATGA--TATATGCAAACC
*
17770742 CTATATATGATATATGCAAACC
1 CTATACATGATATATGCAAACC
17770764 ATTGAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (22 bp):
CTATACATGATATATGCAAACC
Found at i:17779552 original size:29 final size:30
Alignment explanation
Indices: 17779489--17779549 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
17779479 ATATAGTAAA
*
17779489 TTAAATT--TTTTTATTAACATAGAATGTT
1 TTAAATTGATTTTTATTAACATAGAAAGTT
*
17779517 TTAAATTGATTTTTGTT-ACAT-GAAAGTT
1 TTAAATTGATTTTTATTAACATAGAAAGTT
17779545 TTAAA
1 TTAAA
17779550 ATTTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 18 0.62
29 4 0.14
30 7 0.24
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (30 bp):
TTAAATTGATTTTTATTAACATAGAAAGTT
Found at i:17782964 original size:47 final size:48
Alignment explanation
Indices: 17782895--17783118 Score: 180
Period size: 47 Copynumber: 4.8 Consensus size: 48
17782885 AAGGTGCCGG
* *
17782895 TGCCATGTCCCAGACACGGTCTTACACTAGCTCAT-ATCTCATGTCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATGCCAA
*
17782942 TGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTAGCCAA
1 TGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTCAT-GCCAA
* * * * * * *
17782990 TG-CGTGTCCTAGACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-ATGCCAA
* * * ***
17783036 TG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTTGATGTTGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATC-TCATGCCAA
* *
17783082 TGCCATGTCCTAGACATGGTCTTACACTGGCTC-TCAT
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTCATCAT
17783119 AATGTGGCTG
Statistics
Matches: 145, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
46 60 0.41
47 63 0.43
48 22 0.15
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
TGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATGCCAA
Found at i:17783072 original size:46 final size:46
Alignment explanation
Indices: 17782898--17783158 Score: 167
Period size: 46 Copynumber: 5.6 Consensus size: 46
17782888 GTGCCGGTGC
* * * * *
17782898 CATGTCCCAGACACGGTCTTACACTAGCTCAT-ATCTC-ATGTCAATG
1 CATGTCCCAGACA-TGTCTTACACTAGCAC-TCATCTCGAGGCCGATG
*
17782944 CCATGTCCCAGACATGGTCTTACACT-G-ACTATCATCTCGTA-GCCAATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCAC--TCATCTCG-AGGCCGATG
* * * * *
17782992 CGTGTCCTAGACATGTCTTACACTGGC-TTACGTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCACT-CATCTCGAGGCCGATG
* * * **
17783038 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTTGATGTTGATG
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCGAGGCCGATG
* * * * * *
17783084 CCATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCACTCAT-CTCGAGGCCGATG
*
17783132 CATGTCCCAAACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
17783159 CCATAATAAT
Statistics
Matches: 174, Mismatches: 27, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
45 3 0.02
46 73 0.42
47 67 0.39
48 29 0.17
49 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCATCTCGAGGCCGATG
Found at i:17783150 original size:140 final size:140
Alignment explanation
Indices: 17782898--17783155 Score: 324
Period size: 140 Copynumber: 1.8 Consensus size: 140
17782888 GTGCCGGTGC
17782898 CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTCAATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTCAATGCCATGTCCCAGACATGGTC
* * * *
17782963 TTACACTGACTATCATCTCGTAGCCAATGCGTGTCCTAGACATGTCTTACACTGGCTTACGTCTC
66 TTACACTGACTATCATATCGTAGCCAATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTC
17783028 GAGGCCGATG
131 GAGGCCGATG
* * * * ** *
17783038 CATGTCCCAGACA-TGTCTTACACTAGCAC-TCGTCTTGATGTTGATGCCATGTCCTAGACATGG
1 CATGTCCCAGACACGGTCTTACACTAGCTCAT-ATC-TCATGTCAATGCCATGTCCCAGACATGG
* * * **
17783101 TCTTACACTGGCTCTCATAAT-GTGGCTGATGCATGTCCCAAACATGTCTTACACT
64 TCTTACACTGACTATCAT-ATCGTAGCCAATGCATGTCCCAAACATGTCTTACACT
17783156 AGCCCATAAT
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
138 1 0.01
139 16 0.16
140 81 0.82
141 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTCAATGCCATGTCCCAGACATGGTC
TTACACTGACTATCATATCGTAGCCAATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTC
GAGGCCGATG
Found at i:17783168 original size:47 final size:43
Alignment explanation
Indices: 17783034--17783160 Score: 128
Period size: 47 Copynumber: 2.8 Consensus size: 43
17783024 TCTCGAGGCC
* *
17783034 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTTGATGTT
1 GATGCATGTCCCAGACATGTCTTACACTAGC-C-C-TCATAATGTT
* * *
17783080 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCATAATGT---T
*
17783128 GATGCATGTCCCAAACATGTCTTACACTAGCCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCC
17783161 ATAATAATCC
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
45 7 0.10
46 18 0.27
47 25 0.37
48 17 0.25
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (43 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATAATGTT
Found at i:17784913 original size:30 final size:30
Alignment explanation
Indices: 17784877--17784950 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
17784867 CATGGGTTGT
17784877 CACACGGTCGTGTGCCACACACAACCATAC
1 CACACGGTCGTGTGCCACACACAACCATAC
*
17784907 CACACGGTCGTGTGCCACACACAACTATAC
1 CACACGGTCGTGTGCCACACACAACCATAC
*
17784937 CACACGATCGTGTG
1 CACACGGTCGTGTG
17784951 GCCTACTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.16
Consensus pattern (30 bp):
CACACGGTCGTGTGCCACACACAACCATAC
Found at i:17786308 original size:21 final size:21
Alignment explanation
Indices: 17786264--17786308 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17786254 AAACTTAAGC
*
17786264 TTATTTGACATAATTATTAAA
1 TTATTTGACATAATCATTAAA
* *
17786285 TTATTTGACATAATCCTTAGA
1 TTATTTGACATAATCATTAAA
17786306 TTA
1 TTA
17786309 GCACATTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (21 bp):
TTATTTGACATAATCATTAAA
Found at i:17786512 original size:32 final size:32
Alignment explanation
Indices: 17786476--17786536 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
17786466 TCAATAATTA
17786476 CACTAATTTAATG-TTAAACAAATTATAGAATC
1 CACTAATTTAATGTTTAAA-AAATTATAGAATC
* *
17786508 CACTAATTTAGTGTTTAAAAAATTCTAGA
1 CACTAATTTAATGTTTAAAAAATTATAGA
17786537 TAGGAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (32 bp):
CACTAATTTAATGTTTAAAAAATTATAGAATC
Found at i:17787557 original size:10 final size:10
Alignment explanation
Indices: 17787542--17787566 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17787532 CAATCCATAT
17787542 TATTTTTTAA
1 TATTTTTTAA
17787552 TATTTTTTAA
1 TATTTTTTAA
17787562 TATTT
1 TATTT
17787567 ATATTATTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:17787582 original size:16 final size:17
Alignment explanation
Indices: 17787547--17787589 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
17787537 CATATTATTT
17787547 TTTAATATTTTTTAATA
1 TTTAATATTTTTTAATA
17787564 TTT-ATATTATTTTAA-A
1 TTTAATATT-TTTTAATA
17787580 TTTAATATTT
1 TTTAATATTT
17787590 AATATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATTTTTTAATA
Found at i:17787606 original size:10 final size:9
Alignment explanation
Indices: 17787545--17787608 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 9
17787535 TCCATATTAT
17787545 TTTTTAATA
1 TTTTTAATA
17787554 TTTTTTAATA
1 -TTTTTAATA
* *
17787564 TTTATATTA
1 TTTTTAATA
17787573 -TTTTAA-A
1 TTTTTAATA
17787580 --TTTAATA
1 TTTTTAATA
17787587 --TTTAATA
1 TTTTTAATA
17787594 TTTTTATATA
1 TTTTTA-ATA
17787604 TTTTT
1 TTTTT
17787609 CTATTTATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 5 0.11
7 9 0.20
8 4 0.09
9 11 0.24
10 17 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTAATA
Found at i:17792360 original size:21 final size:21
Alignment explanation
Indices: 17792334--17792389 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
17792324 AATAGCGGTG
*
17792334 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
17792355 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
17792376 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
17792390 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:17795953 original size:32 final size:32
Alignment explanation
Indices: 17795913--17796065 Score: 225
Period size: 32 Copynumber: 4.8 Consensus size: 32
17795903 AAAAAATATG
* *
17795913 ATACATTAGGTTTACGTATAAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* *
17795945 ATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* *
17795977 ATACATTAGGTTCACATATAAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* * *
17796009 ATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
17796041 ATACATTAGTTTTACATATAAAAAA
1 ATACATTAGTTTTACATATAAAAAA
17796066 CTAGCATAGT
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 105 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (32 bp):
ATACATTAGTTTTACATATAAAAAAGTAGATC
Found at i:17795998 original size:64 final size:64
Alignment explanation
Indices: 17795913--17796065 Score: 252
Period size: 64 Copynumber: 2.4 Consensus size: 64
17795903 AAAAAATATG
* *
17795913 ATACATTAGGTTTACGTATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
* * *
17795977 ATACATTAGGTTCACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
*
17796041 ATACATTAGTTTTACATATAAAAAA
1 ATACATTAGGTTTACATATAAAAAA
17796066 CTAGCATAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 82 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (64 bp):
ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
Found at i:17797306 original size:18 final size:18
Alignment explanation
Indices: 17797283--17797318 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17797273 ATAACACAAG
17797283 TGTAAGCATAAATCAGTA
1 TGTAAGCATAAATCAGTA
17797301 TGTAAGCATAAATCAGTA
1 TGTAAGCATAAATCAGTA
17797319 ATACAATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TGTAAGCATAAATCAGTA
Found at i:17798393 original size:18 final size:19
Alignment explanation
Indices: 17798358--17798393 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17798348 ATGATATTAA
17798358 TGATATACCTACAAGGTAG
1 TGATATACCTACAAGGTAG
17798377 TGATATACCTA-AAGGTA
1 TGATATACCTACAAGGTA
17798394 TAAAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (19 bp):
TGATATACCTACAAGGTAG
Found at i:17801031 original size:40 final size:40
Alignment explanation
Indices: 17800976--17801087 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
17800966 TATTCGGATG
17800976 ATATCCAGGCTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCAGGCTAAGATCCGAAGGCATTTGTGCTAGTTACT
* * *
17801016 ATATCCAGACTAAGATCCGAAGGCAATTGTGCTAGTTATT
1 ATATCCAGGCTAAGATCCGAAGGCATTTGTGCTAGTTACT
* * *
17801056 ATAACCAGGTTAAG-TCCCGAAGGCATTCGTGC
1 ATATCCAGGCTAAGAT-CCGAAGGCATTTGTGC
17801088 GGGTTATTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 62 0.98
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (40 bp):
ATATCCAGGCTAAGATCCGAAGGCATTTGTGCTAGTTACT
Found at i:17801094 original size:40 final size:40
Alignment explanation
Indices: 17800992--17801172 Score: 213
Period size: 40 Copynumber: 4.5 Consensus size: 40
17800982 AGGCTAAGAT
* * * * **
17800992 CCGAAGGCATTTGTGCTAGTTACTATATCCAGACTAAGAT-
1 CCGAAGGCATTCGTGCTGGTTATTATAACCAGGTTAAG-TC
*
17801032 CCGAAGGCAATT-GTGCTAGTTATTATAACCAGGTTAAGTC
1 CCGAAGGC-ATTCGTGCTGGTTATTATAACCAGGTTAAGTC
* **
17801072 CCGAAGGCATTCGTGCGGGTTATTATAACTGGGTTAAGTC
1 CCGAAGGCATTCGTGCTGGTTATTATAACCAGGTTAAGTC
* * *
17801112 CCGAAGGTATTCGTGCGGGTTATTATAACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCTGGTTATTATAACCAGGTTAAGTC
17801152 CCGAAGGCATTCGTGCTGGTT
1 CCGAAGGCATTCGTGCTGGTT
17801173 GTTACATCCG
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 4 0.03
40 119 0.94
41 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCTGGTTATTATAACCAGGTTAAGTC
Found at i:17805722 original size:65 final size:65
Alignment explanation
Indices: 17805649--17805798 Score: 162
Period size: 66 Copynumber: 2.3 Consensus size: 65
17805639 TATATGCGTA
* * * *
17805649 AAGTTTTTAGTCTA-TTTGTGTTGCAATTATATTTTCT-AATCCCACAATGTCCTATTATCATGG
1 AAGTTTTTAGT-TAGATTATGTTGCAATTATATTTT-TGAATCCCACAATGTCCTATCATCAAGG
17805712 GT
64 GT
* * * * *
17805714 AAGTTTTTAGTTAGGATTATGTTGTAATTATATTTTTGAGTCCCATAGTGTTCTATCATCAAGGG
1 AAGTTTTTAGTTA-GATTATGTTGCAATTATATTTTTGAATCCCACAATGTCCTATCATCAAGGG
17805779 T
65 T
17805780 AAG-TTTTAGTTAGGATTAT
1 AAGTTTTTAGTTA-GATTAT
17805799 TTTAGTTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 2 0.03
65 28 0.38
66 43 0.59
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (65 bp):
AAGTTTTTAGTTAGATTATGTTGCAATTATATTTTTGAATCCCACAATGTCCTATCATCAAGGGT
Found at i:17805743 original size:66 final size:65
Alignment explanation
Indices: 17805667--17805798 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 65
17805657 AGTCTATTTG
* *
17805667 TGTTGCAATTATATTTTCT-AATCCCACAATGTCCTATTATCATGGGTAAGTTTTTAGTTAGGAT
1 TGTTGCAATTATATTTT-TGAATCCCACAATGTCCTATCATCAAGGGTAAG-TTTTAGTTAGGAT
17805731 TA
64 TA
* * * * *
17805733 TGTTGTAATTATATTTTTGAGTCCCATAGTGTTCTATCATCAAGGGTAAGTTTTAGTTAGGATTA
1 TGTTGCAATTATATTTTTGAATCCCACAATGTCCTATCATCAAGGGTAAGTTTTAGTTAGGATTA
17805798 T
1 T
17805799 TTTAGTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
65 17 0.29
66 41 0.71
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (65 bp):
TGTTGCAATTATATTTTTGAATCCCACAATGTCCTATCATCAAGGGTAAGTTTTAGTTAGGATTA
Found at i:17811851 original size:41 final size:41
Alignment explanation
Indices: 17811786--17811866 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
17811776 CCAGGTTTTT
* * *
17811786 GGACATGGGCGATGACACGAGCGTGT-CTAGGCCGTGTGAG
1 GGACATGGGCAATAACACGAGCGTGTGCTAGGCCATGTGAG
* *
17811826 GGACATGGGCCAATAACACGGGCGTGTGCTTGGCCATGTGA
1 GGACATGGG-CAATAACACGAGCGTGTGCTAGGCCATGTGA
17811867 AAACCCCTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 9 0.26
41 14 0.41
42 11 0.32
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (41 bp):
GGACATGGGCAATAACACGAGCGTGTGCTAGGCCATGTGAG
Found at i:17815611 original size:11 final size:11
Alignment explanation
Indices: 17815595--17815624 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17815585 TCCATTGCTG
17815595 AAAATAAAAGA
1 AAAATAAAAGA
*
17815606 AAAATAAAATA
1 AAAATAAAAGA
17815617 AAAATAAA
1 AAAATAAA
17815625 GAATAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAATAAAAGA
Found at i:17819500 original size:46 final size:45
Alignment explanation
Indices: 17819450--17819811 Score: 373
Period size: 46 Copynumber: 7.8 Consensus size: 45
17819440 TGGTTGAGCA
17819450 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
17819496 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
17819541 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
17819589 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
17819634 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
17819682 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* *
17819727 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* *
17819775 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17819812 GCGGGTTACA
Statistics
Matches: 267, Mismatches: 22, Indels: 54
0.78 0.06 0.16
Matches are distributed among these distances:
42 6 0.02
43 15 0.06
45 9 0.03
46 121 0.45
47 87 0.33
48 9 0.03
50 14 0.05
51 6 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:17819606 original size:93 final size:93
Alignment explanation
Indices: 17819447--17819803 Score: 669
Period size: 93 Copynumber: 3.8 Consensus size: 93
17819437 GGATGGTTGA
17819447 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
17819512 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
17819540 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
17819605 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
17819633 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
17819698 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * *
17819726 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
17819791 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
17819804 ACTTATGGGC
Statistics
Matches: 259, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 259 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17819761 original size:24 final size:24
Alignment explanation
Indices: 17819734--17819806 Score: 57
Period size: 24 Copynumber: 3.1 Consensus size: 24
17819724 AGGCATCCGA
17819734 ACTCGTTGAGTTGAGTCCGAGTTC
1 ACTCGTTGAGTTGAGTCCGAGTTC
* * *
17819758 ACTCATGGA-TGTGAACGCCCGAG---
1 ACTCGTTGAGT-TG-A-GTCCGAGTTC
17819781 -CTCGTTGAGTTGAGTCCGAGTTC
1 ACTCGTTGAGTTGAGTCCGAGTTC
17819804 ACT
1 ACT
17819807 TATGGGCGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 8 0.23
23 2 0.06
24 11 0.31
25 1 0.03
26 6 0.17
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (24 bp):
ACTCGTTGAGTTGAGTCCGAGTTC
Found at i:17829055 original size:151 final size:151
Alignment explanation
Indices: 17828781--17829081 Score: 602
Period size: 151 Copynumber: 2.0 Consensus size: 151
17828771 AGGATCTATT
17828781 GTGCATGTAATCAAAAGGGTGGACTTGCATGTCAATTTTCCCCCCTAATTAGTAGTGGCCGGCCA
1 GTGCATGTAATCAAAAGGGTGGACTTGCATGTCAATTTTCCCCCCTAATTAGTAGTGGCCGGCCA
17828846 TGAGCATGAGGGTGGACAAAATGTTATGGCTAAAAAACATGTCATGAACATGTTGGGTTAATGCT
66 TGAGCATGAGGGTGGACAAAATGTTATGGCTAAAAAACATGTCATGAACATGTTGGGTTAATGCT
17828911 TTACGTTAGGAAAAATAAAAA
131 TTACGTTAGGAAAAATAAAAA
17828932 GTGCATGTAATCAAAAGGGTGGACTTGCATGTCAATTTTCCCCCCTAATTAGTAGTGGCCGGCCA
1 GTGCATGTAATCAAAAGGGTGGACTTGCATGTCAATTTTCCCCCCTAATTAGTAGTGGCCGGCCA
17828997 TGAGCATGAGGGTGGACAAAATGTTATGGCTAAAAAACATGTCATGAACATGTTGGGTTAATGCT
66 TGAGCATGAGGGTGGACAAAATGTTATGGCTAAAAAACATGTCATGAACATGTTGGGTTAATGCT
17829062 TTACGTTAGGAAAAATAAAA
131 TTACGTTAGGAAAAATAAAA
17829082 TAAGGAGTAT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (151 bp):
GTGCATGTAATCAAAAGGGTGGACTTGCATGTCAATTTTCCCCCCTAATTAGTAGTGGCCGGCCA
TGAGCATGAGGGTGGACAAAATGTTATGGCTAAAAAACATGTCATGAACATGTTGGGTTAATGCT
TTACGTTAGGAAAAATAAAAA
Found at i:17829218 original size:53 final size:54
Alignment explanation
Indices: 17829134--17829256 Score: 203
Period size: 53 Copynumber: 2.3 Consensus size: 54
17829124 TGATGAAAAA
*
17829134 AAAAAGAAAGAAAGAAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAG
1 AAAAAGAAAGAAA-AAAAGAAGCTCTCATGTTGTTCTTGACCGAATAGAAGAAAG
17829189 AAAAAGAAAGAAAAAAA-AAGCTCTCATGTTGTTCTTGACCGAATAGAAGAAAG
1 AAAAAGAAAGAAAAAAAGAAGCTCTCATGTTGTTCTTGACCGAATAGAAGAAAG
* *
17829242 AAAATGAAGGAAAAA
1 AAAAAGAAAGAAAAA
17829257 GAGCTTTGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
53 48 0.74
54 4 0.06
55 13 0.20
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (54 bp):
AAAAAGAAAGAAAAAAAGAAGCTCTCATGTTGTTCTTGACCGAATAGAAGAAAG
Found at i:17834098 original size:78 final size:78
Alignment explanation
Indices: 17834002--17834157 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
17833992 GTTTCTCACC
17834002 TTGGGGTGCACCAGTATTGTTTGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATCGACTATC
1 TTGGGGTGCACCAGTATTGTTTGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATCGACTATC
17834067 GTCAGCTGAATAA
66 GTCAGCTGAATAA
17834080 TTGGGGTGCACCAGTATTGTTTGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATCGACTATC
1 TTGGGGTGCACCAGTATTGTTTGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATCGACTATC
17834145 GTCAGCTGAATAA
66 GTCAGCTGAATAA
17834158 GGTGACAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (78 bp):
TTGGGGTGCACCAGTATTGTTTGTGAAAAAGAAGGACGGAACCATGAGGTTGTGCATCGACTATC
GTCAGCTGAATAA
Found at i:17837268 original size:52 final size:53
Alignment explanation
Indices: 17837180--17837301 Score: 201
Period size: 52 Copynumber: 2.3 Consensus size: 53
17837170 TGATGATGAA
17837180 AAAAAGAAAGAAAGAAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAG
1 AAAAAGAAAG-AA-AAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAG
*
17837235 AAAAAGAAAGAAAAAA-AAGCTCTCATGTTGTTCTTGGCCGAATAGAAGATAG
1 AAAAAGAAAGAAAAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAG
*
17837287 AAAAAGAAGGAAAAA
1 AAAAAGAAAGAAAAA
17837302 GAGCTTTGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
52 49 0.75
53 4 0.06
54 2 0.03
55 10 0.15
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (53 bp):
AAAAAGAAAGAAAAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAG
Found at i:17839730 original size:79 final size:81
Alignment explanation
Indices: 17839594--17839776 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
17839584 TCAAATGATG
* *
17839594 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
17839658 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
17839673 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
17839735 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
17839753 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
17839777 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:17839792 original size:40 final size:40
Alignment explanation
Indices: 17839595--17839778 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
17839585 CAAATGATGT
* * * *
17839595 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
17839635 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
17839675 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
17839713 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
17839754 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
17839779 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:17839800 original size:79 final size:79
Alignment explanation
Indices: 17839647--17839801 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
17839637 GGACTAAGAT
* **
17839647 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
17839712 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
17839726 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
17839789 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
17839802 ATTTCGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.61
80 24 0.36
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:17844632 original size:40 final size:42
Alignment explanation
Indices: 17844588--17844681 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 42
17844578 ACAGTGCTTA
* *
17844588 GCACTAAGTGTGCG-GTTTAATATAGCTTCGGCTATA-A-ATG
1 GCACTAAGTGTGCGAG-TTAACATAGCTTCGGCTATATATAAG
* ** *
17844628 GCACTACGTGTGCGAGTTGGCATAGCTTTGGCTATATATAAG
1 GCACTAAGTGTGCGAGTTAACATAGCTTCGGCTATATATAAG
17844670 GCACTAAGTGTG
1 GCACTAAGTGTG
17844682 TGATACTGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 29 0.66
41 2 0.05
42 13 0.30
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (42 bp):
GCACTAAGTGTGCGAGTTAACATAGCTTCGGCTATATATAAG
Found at i:17850302 original size:48 final size:47
Alignment explanation
Indices: 17850250--17850454 Score: 188
Period size: 48 Copynumber: 4.4 Consensus size: 47
17850240 TATCCCGAAT
*
17850250 ATGGTCTTACATGGGATCACATATCGACGACAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATCGATG-CAATGCCATGTCCCAGAC
** * * *
17850298 ATGGTCTTACATGGGATCGTAGATCGATGCTAATGTCATGTCCTAGAC
1 ATGGTCTTACATGGGATCACATATCGATGC-AATGCCATGTCCCAGAC
* *
17850346 ATGGTCTTACATGGAATCACATATCGATG---T-CGATAG-CCCAG-C
1 ATGGTCTTACATGGGATCACATATCGATGCAATGCCAT-GTCCCAGAC
* * ** * *
17850388 TATAGTCTTACACGAAATTACATATCGATGCCAAAGCCATGTCCCAGAC
1 -ATGGTCTTACATGGGATCACATATCGATG-CAATGCCATGTCCCAGAC
*
17850437 ATGGTATTACATGGGATC
1 ATGGTCTTACATGGGATC
17850455 GCACAAAACC
Statistics
Matches: 122, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
42 1 0.01
43 31 0.25
44 2 0.02
47 2 0.02
48 85 0.70
49 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
ATGGTCTTACATGGGATCACATATCGATGCAATGCCATGTCCCAGAC
Found at i:17858552 original size:27 final size:28
Alignment explanation
Indices: 17858468--17858565 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
17858458 CATGAGATTG
* * * *
17858468 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
17858497 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
17858525 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
17858552 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
17858566 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:17858576 original size:27 final size:27
Alignment explanation
Indices: 17858496--17858578 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
17858486 TAAATTGTAC
* *
17858496 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
17858524 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
17858551 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
17858578 A
1 A
17858579 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:17858579 original size:29 final size:27
Alignment explanation
Indices: 17858468--17858579 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
17858458 CATGAGATTG
** * *
17858468 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
17858497 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
17858525 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
17858552 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
17858580 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:17864086 original size:116 final size:116
Alignment explanation
Indices: 17863954--17864416 Score: 926
Period size: 116 Copynumber: 4.0 Consensus size: 116
17863944 TAACAATAAT
17863954 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
1 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
17864019 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
66 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
17864070 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
1 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
17864135 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
66 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
17864186 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
1 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
17864251 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
66 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
17864302 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
1 CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
17864367 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATT
66 CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATT
17864417 TCATTCCCCT
Statistics
Matches: 347, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 347 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (116 bp):
CATCTACTTAAATTTTTTTTATTAAGGGTACTTTGGTCATTTAAATATTTTTCCTTATGCTATTA
CAACATCTATTTCATTCAACCAAACACAAGAATACTATTACAACCCTATTC
Found at i:17864595 original size:18 final size:18
Alignment explanation
Indices: 17864572--17864607 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17864562 TATAATAATT
*
17864572 TATATTATGTTATTTTTA
1 TATATTATGTAATTTTTA
17864590 TATATTATGTAATTTTTA
1 TATATTATGTAATTTTTA
17864608 ATACATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TATATTATGTAATTTTTA
Found at i:17864615 original size:19 final size:18
Alignment explanation
Indices: 17864575--17864615 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
17864565 AATAATTTAT
* *
17864575 ATTATGTTATTTTTATAT
1 ATTATGTAATTTTTATAC
17864593 ATTATGTAATTTTTAATAC
1 ATTATGTAATTTTT-ATAC
17864612 ATTA
1 ATTA
17864616 AAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTATGTAATTTTTATAC
Found at i:17866001 original size:11 final size:10
Alignment explanation
Indices: 17865955--17866015 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
17865945 TAAAAAATAA
* *
17865955 TATTATATTA
1 TATTTTATTT
* *
17865965 TATTATATTA
1 TATTTTATTT
* *
17865975 TATTATATTA
1 TATTTTATTT
*
17865985 TATTTTGTTTT
1 TATTTT-ATTT
17865996 TATTTTATTT
1 TATTTTATTT
17866006 TATTTTATTT
1 TATTTTATTT
17866016 AATTAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
10 38 0.83
11 8 0.17
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TATTTTATTT
Found at i:17866004 original size:16 final size:15
Alignment explanation
Indices: 17865955--17866015 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
17865945 TAAAAAATAA
* * *
17865955 TATTATATTATATTA
1 TATTTTATTTTATTT
* * *
17865970 TATTATATTATATTA
1 TATTTTATTTTATTT
*
17865985 TATTTTGTTTTTATTT
1 TATTTT-ATTTTATTT
17866001 TATTTTATTTTATTT
1 TATTTTATTTTATTT
17866016 AATTAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 28 0.70
16 12 0.30
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TATTTTATTTTATTT
Found at i:17866008 original size:5 final size:5
Alignment explanation
Indices: 17865954--17865988 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
17865944 ATAAAAAATA
17865954 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
17865989 TTGTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:17868282 original size:20 final size:20
Alignment explanation
Indices: 17868259--17868310 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
17868249 AAATTCAAAT
*
17868259 TAAAATACTGAAATTTAGGA
1 TAAAATACTGAAATTTAGAA
* *
17868279 TAAAATCCTAAAATTTAGAA
1 TAAAATACTGAAATTTAGAA
17868299 TAAGAATACTGA
1 TAA-AATACTGA
17868311 TGTGGCATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29
Consensus pattern (20 bp):
TAAAATACTGAAATTTAGAA
Done.