Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 7 of 259
Found at i:1914073 original size:27 final size:27
Alignment explanation
Indices: 1914030--1914133 Score: 127
Period size: 27 Copynumber: 3.9 Consensus size: 27
1914020 CAAGTTTAGA
* *
1914030 CCTGGTGAGCTGAGGTTCGCCAGTAGG
1 CCTGGTGAGCTGGGGTTCGCCAGTAAG
* * * *
1914057 CCTGGCGAGTTGGGGTTTGCTAGTAAG
1 CCTGGTGAGCTGGGGTTCGCCAGTAAG
* *
1914084 CCTGGTGAGCTGGGGTTCACTAGTAAG
1 CCTGGTGAGCTGGGGTTCGCCAGTAAG
*
1914111 CCTAGTGAGCTGGGGTTCGCCAG
1 CCTGGTGAGCTGGGGTTCGCCAG
1914134 AGGGTCTAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.15, C:0.20, G:0.39, T:0.25
Consensus pattern (27 bp):
CCTGGTGAGCTGGGGTTCGCCAGTAAG
Found at i:1916015 original size:27 final size:27
Alignment explanation
Indices: 1915984--1916035 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1915974 TTCTTCAAAA
1915984 TGGAGAAATGGAATCATTTGAAAATTT
1 TGGAGAAATGGAATCATTTGAAAATTT
1916011 TGGAGAAATGGAATCATTTGAAAAT
1 TGGAGAAATGGAATCATTTGAAAAT
1916036 GAATGTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (27 bp):
TGGAGAAATGGAATCATTTGAAAATTT
Found at i:1919317 original size:43 final size:43
Alignment explanation
Indices: 1919162--1919317 Score: 149
Period size: 43 Copynumber: 3.6 Consensus size: 43
1919152 TGTGTTATCG
**
1919162 TGTAAGACCACGTCTGGGACGTTTTCATCGAT-TTATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTACA
* * * * * * *
1919206 TGTAAGACCATGTCTGGGACATTGGTATC-TTATATGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
*
1919248 TGTAAGACC-CTGTGTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTACA
*
1919291 TGTAAGACCACGTCTGGCACGTTGGCA
1 TGTAAGACCACGTCTGGGACGTTGGCA
1919318 CTGTACGAGC
Statistics
Matches: 87, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
42 27 0.31
43 34 0.39
44 26 0.30
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
Found at i:1933355 original size:27 final size:27
Alignment explanation
Indices: 1933308--1933465 Score: 173
Period size: 27 Copynumber: 5.9 Consensus size: 27
1933298 CGAGGCTGCT
* *
1933308 AGATATTGTGACA-ACGTCACCAGATAC
1 AGATATTGTGGCAGA-GCCACCAGATAC
* *
1933335 AGATATTATGGTAGAGCCACCAGA-AC
1 AGATATTGTGGCAGAGCCACCAGATAC
1933361 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATAT-TGTGGCAGAGCCACCAGATAC
* *
1933388 AGATAATTGTGGCATAGCCACCAG-GAC
1 AGAT-ATTGTGGCAGAGCCACCAGATAC
1933415 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATAT-TGTGGCAGAGCCACCAGATAC
*
1933442 AGATAATTGTGGCATAGCCACCAG
1 AGAT-ATTGTGGCAGAGCCACCAG
1933466 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
26 10 0.09
27 97 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGATAC
Found at i:1933466 original size:54 final size:54
Alignment explanation
Indices: 1933325--1933468 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
1933315 GTGACAACGT
* * * *
1933325 CACCAGATACAGAT-ATTATGGTAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1933379 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1933433 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1933469 GCTTCCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 5 0.06
54 80 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:1935093 original size:26 final size:26
Alignment explanation
Indices: 1935062--1935169 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1935052 TGAAATGCCC
*
1935062 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1935088 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
1935114 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1935140 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1935166 ATCA
1 ATCA
1935170 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1938098 original size:19 final size:18
Alignment explanation
Indices: 1938074--1938116 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
1938064 TGAATTTGAG
1938074 CCTTTAACTCCACTAACT
1 CCTTTAACTCCACTAACT
1938092 CCCTTTAACTCCACTAACT
1 -CCTTTAACTCCACTAACT
1938111 CCTTTA
1 CCTTTA
1938117 GTGCCATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.35
Consensus pattern (18 bp):
CCTTTAACTCCACTAACT
Found at i:1940323 original size:27 final size:27
Alignment explanation
Indices: 1940275--1940433 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
1940265 ACGAGGCTGC
* *
1940275 CAGATATTGTGACA-ACGTCACCAGATA
1 CAGATATTGTGGCAGA-GCCACCAGATA
*
1940302 CAGATATTGTGGTAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
1940328 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
1940355 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
1940382 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
1940409 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
1940434 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:1940434 original size:54 final size:54
Alignment explanation
Indices: 1940293--1940436 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
1940283 GTGACAACGT
* * *
1940293 CACCAGATACAGAT-ATTGTGGTAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1940347 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
1940401 CACCAAATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1940437 GCTTCCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 5 0.06
54 80 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:1942061 original size:26 final size:26
Alignment explanation
Indices: 1942030--1942137 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
1942020 TGAAATGCCC
* *
1942030 ATCATGGAACATTTACTTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1942056 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
1942082 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1942108 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1942134 ATCA
1 ATCA
1942138 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1949155 original size:15 final size:16
Alignment explanation
Indices: 1949127--1949156 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1949117 ATACAAAAAT
1949127 AAATAAATACAATGAC
1 AAATAAATACAATGAC
1949143 AAATAAA-ACAATGA
1 AAATAAATACAATGA
1949157 GATCATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (16 bp):
AAATAAATACAATGAC
Found at i:1958978 original size:56 final size:56
Alignment explanation
Indices: 1958907--1959136 Score: 205
Period size: 55 Copynumber: 4.1 Consensus size: 56
1958897 TAGACGTGCT
* *
1958907 ACATAACAATTGATTTAAACATATAAACAATCGATTCAAAATAAAG-CAACATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAA-AAAGACAATATTCCA
*
1958963 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTC-AAA-AA-AAG--ACAATATTCCA
* * * * * * * * * *
1959024 CCATAAGAATCGATTTAAACATGTTAATAGTCAATTCAAAAGAAGTC-TTATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
* * * * * * *
1959079 ACATGACAATCGATTTAAACATATAGACAATTGATTTAAAAGAAGTC-GTATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
1959134 ACA
1 ACA
1959137 ATTAAGATGA
Statistics
Matches: 143, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
55 53 0.37
56 36 0.25
57 4 0.03
58 7 0.05
59 1 0.01
60 3 0.02
61 39 0.27
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (56 bp):
ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
Found at i:1958983 original size:18 final size:18
Alignment explanation
Indices: 1958907--1958985 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
1958897 TAGACGTGCT
* *
1958907 ACATAACAATTGATTTAA
1 ACATAACAATCGATTCAA
1958925 ACATATAAACAATCGATTCAA
1 AC--AT-AACAATCGATTCAA
*
1958946 A-ATAAAGCAA-C-ATTCCA
1 ACAT-AA-CAATCGATTCAA
*
1958963 ACATAACAATCGATTTAA
1 ACATAACAATCGATTCAA
1958981 ACATA
1 ACATA
1958986 TAAAAAATCG
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
16 3 0.06
17 9 0.18
18 19 0.39
19 3 0.06
20 2 0.04
21 13 0.27
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (18 bp):
ACATAACAATCGATTCAA
Found at i:1959045 original size:61 final size:58
Alignment explanation
Indices: 1958907--1959123 Score: 201
Period size: 61 Copynumber: 3.8 Consensus size: 58
1958897 TAGACGTGCT
* * *
1958907 ACATAACAATTGATTTAAACATATAAACAATCGATTCAAAA-TA-AAGCAACATTCCA
1 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGCAACATTCCA
*
1958963 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCA
1 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAG---CAACATTCCA
* * * * * * * * **
1959024 CCATAAGAATCGATTTAAACATGTTAATAGTCAATTCAAAAGAAG--TC-TTATTCCA
1 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGCAACATTCCA
* * * * *
1959079 ACATGACAATCGATTTAAACATATAGACAATTGATTTAAAAGAAG
1 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAG
1959124 TCGTATTCCA
Statistics
Matches: 132, Mismatches: 24, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
55 41 0.31
56 40 0.30
57 1 0.01
58 3 0.02
61 47 0.36
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (58 bp):
ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGCAACATTCCA
Found at i:1959396 original size:17 final size:17
Alignment explanation
Indices: 1959374--1959407 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1959364 ACAGAAGATG
1959374 AATTAATCTATTAACAA
1 AATTAATCTATTAACAA
1959391 AATTAATCTATTAACAA
1 AATTAATCTATTAACAA
1959408 GAAAATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAATCTATTAACAA
Found at i:1974763 original size:23 final size:23
Alignment explanation
Indices: 1974736--1974786 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1974726 ATTTATCTAC
1974736 AATATAAACATTAAATTTAATTT
1 AATATAAACATTAAATTTAATTT
1974759 AATATAAACATTAAATTTAATTT
1 AATATAAACATTAAATTTAATTT
1974782 AATAT
1 AATAT
1974787 TAAGATAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATAAACATTAAATTTAATTT
Found at i:1983098 original size:19 final size:20
Alignment explanation
Indices: 1983062--1983100 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1983052 ATTATTATTC
*
1983062 AATAACTTCTCTTTTGAGTT
1 AATAAATTCTCTTTTGAGTT
1983082 AATAAATTCTC-TTTGAGTT
1 AATAAATTCTCTTTTGAGTT
1983101 TTTCTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
AATAAATTCTCTTTTGAGTT
Found at i:1983359 original size:17 final size:19
Alignment explanation
Indices: 1983321--1983363 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1983311 TATTTTCTTT
1983321 TTTATTGTTCTAATACTTGA
1 TTTATTGTTCTAATA-TTGA
1983341 TTTATTGTTCT-AT-TTGA
1 TTTATTGTTCTAATATTGA
1983358 TTTATT
1 TTTATT
1983364 TATTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
19 2 0.09
20 11 0.48
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (19 bp):
TTTATTGTTCTAATATTGA
Found at i:1999695 original size:10 final size:10
Alignment explanation
Indices: 1999682--1999717 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1999672 AGAAACCTAC
1999682 TATTTTTTAT
1 TATTTTTTAT
**
1999692 TATTTTTTGC
1 TATTTTTTAT
1999702 TATTTTTTAT
1 TATTTTTTAT
1999712 TATTTT
1 TATTTT
1999718 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:1999819 original size:17 final size:19
Alignment explanation
Indices: 1999786--1999820 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1999776 ATTATTTGGA
1999786 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
1999805 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
1999821 ACTATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:2002767 original size:23 final size:23
Alignment explanation
Indices: 2002741--2002787 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2002731 AATTTTACAA
2002741 TCCAACCACAAATACTACATAGT
1 TCCAACCACAAATACTACATAGT
2002764 TCCAACCACAAATACTACATAGT
1 TCCAACCACAAATACTACATAGT
2002787 T
1 T
2002788 ATACATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.30, G:0.04, T:0.23
Consensus pattern (23 bp):
TCCAACCACAAATACTACATAGT
Found at i:2003546 original size:18 final size:17
Alignment explanation
Indices: 2003520--2003586 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 17
2003510 TGTATATTAC
*
2003520 TATGGATATTATGTATG
1 TATGTATATTATGTATG
2003537 TTATGTATATTATTGTTTATG
1 -TATGTATATTA-TG--TATG
* *
2003558 TATGCATATGATGTATG
1 TATGTATATTATGTATG
2003575 CTATGTATATTA
1 -TATGTATATTA
2003587 CAATTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 4 0.10
18 19 0.47
19 4 0.10
20 9 0.22
21 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (17 bp):
TATGTATATTATGTATG
Found at i:2003594 original size:38 final size:38
Alignment explanation
Indices: 2003520--2003594 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
2003510 TGTATATTAC
* * * ***
2003520 TATGGATATTATGTATGTTATGTATATTATTGTTTATG
1 TATGCATATGATGTATGCTATGTATATTACAATTTATG
2003558 TATGCATATGATGTATGCTATGTATATTACAATTTAT
1 TATGCATATGATGTATGCTATGTATATTACAATTTAT
2003595 ATTATGTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (38 bp):
TATGCATATGATGTATGCTATGTATATTACAATTTATG
Found at i:2008484 original size:104 final size:104
Alignment explanation
Indices: 2008304--2008527 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
2008294 TGTATATAAA
** * *
2008304 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
2008369 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
2008408 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
2008472 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
2008512 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
2008528 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:2008579 original size:71 final size:72
Alignment explanation
Indices: 2008446--2008597 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
2008436 TCATTGGTGG
* *
2008446 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
2008511 GAGGGGT
66 GAGGGGT
***
2008518 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
2008582 GAGGGGT
66 GAGGGGT
2008589 TGCTAAGTG
1 TGCTAAGTG
2008598 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:2016036 original size:104 final size:104
Alignment explanation
Indices: 2015856--2016079 Score: 369
Period size: 104 Copynumber: 2.2 Consensus size: 104
2015846 TGTATATAAA
** * *
2015856 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
*
2015921 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGAGTTGCTATGTGCTGATTCCCCCG
* *
2015960 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
2016024 TTGAAATGTGAAAGGGAGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGAGTTGCTATGTGCTGATTCCCCCG
2016064 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
2016080 GATATCCATT
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGAGTTGCTATGTGCTGATTCCCCCG
Found at i:2016132 original size:71 final size:72
Alignment explanation
Indices: 2015998--2016149 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
2015988 TCATTGGTGG
* *
2015998 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGAGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGAGTTGCTATGTGCTGATTCCCCC
2016063 GAGGGGT
66 GAGGGGT
*** *
2016070 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGAGTTGCTATGTGCTGATTCCCCC
2016134 GAGGGGT
66 GAGGGGT
2016141 TGCTAAGTG
1 TGCTAAGTG
2016150 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
71 44 0.59
72 30 0.41
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGAGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:2026082 original size:51 final size:50
Alignment explanation
Indices: 2026022--2026122 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 50
2026012 CAAGTACCAA
* *
2026022 GCAGATAAAACTAATAACATAGAAATATAGTTTAAAAAAAACAAAAGCTAC
1 GCAGATAAAACTAATAACATAAAAATATAATTT-AAAAAAACAAAAGCTAC
2026073 GCAGATAAAACTAATAACATAAAAATATAATTTAAAAAAACAAAAGCTAC
1 GCAGATAAAACTAATAACATAAAAATATAATTTAAAAAAACAAAAGCTAC
2026123 TAACCAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 17 0.35
51 31 0.65
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (50 bp):
GCAGATAAAACTAATAACATAAAAATATAATTTAAAAAAACAAAAGCTAC
Found at i:2030900 original size:20 final size:19
Alignment explanation
Indices: 2030854--2030906 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
2030844 TTTAAAACAT
2030854 TTTTAACTTTGATTGAAAAA
1 TTTTAAC-TTGATTGAAAAA
* * *
2030874 GTCTAACTCGATTGAAATAA
1 TTTTAACTTGATTGAAA-AA
2030894 TTTTAACTTGATT
1 TTTTAACTTGATT
2030907 AAAGGTTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTTAACTTGATTGAAAAA
Found at i:2033058 original size:22 final size:21
Alignment explanation
Indices: 2033011--2033060 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2033001 TTTGGAGCAA
*
2033011 AGATTTGGTGAAAAAGTGGGAG
1 AGATTT-GTGAAAAAGTAGGAG
*
2033033 -GATTTGTGAAAAAATTAGGAG
1 AGATTTGTG-AAAAAGTAGGAG
2033054 AGATTTG
1 AGATTTG
2033061 AGAGGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (21 bp):
AGATTTGTGAAAAAGTAGGAG
Found at i:2036451 original size:27 final size:27
Alignment explanation
Indices: 2036418--2036471 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2036408 TTATTTGGCA
2036418 TGCTCAATATGTCCTCAATACTCACAT
1 TGCTCAATATGTCCTCAATACTCACAT
2036445 TGCTCAATATGTCCTCAATACTCACAT
1 TGCTCAATATGTCCTCAATACTCACAT
2036472 ACTTTCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (27 bp):
TGCTCAATATGTCCTCAATACTCACAT
Found at i:2037501 original size:27 final size:27
Alignment explanation
Indices: 2037453--2037611 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
2037443 GCGAGGCTGC
* *
2037453 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
2037480 CAGATATTGTAGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
2037506 CAGATATATGTGGCAGAGCCACCAGGT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
2037533 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
2037560 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
2037587 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
2037612 GACGTTTTCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:2037555 original size:54 final size:54
Alignment explanation
Indices: 2037471--2037611 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
2037461 GTGACGAAGT
* * *
2037471 CACCAGATACAGAT-ATTGTAGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
2037525 CACCAGGTCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
2037579 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATCGTGGCATAGCCACCAG
2037612 GACGTTTTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 5 0.06
54 75 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:2037778 original size:28 final size:26
Alignment explanation
Indices: 2037717--2037779 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
2037707 AAAGTAACCT
* * *
2037717 TAGGGGTATAATGGTAATTTTGCACC
1 TAGGGGTATAATAGTAATTTTCCACA
*
2037743 TAGGGGTATAGTAGTAATTTTCCATACA
1 TAGGGGTATAATAGTAATTTTCC--ACA
2037771 TAGGGGTAT
1 TAGGGGTAT
2037780 TCAAGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 20 0.65
28 11 0.35
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAATAGTAATTTTCCACA
Found at i:2039249 original size:26 final size:26
Alignment explanation
Indices: 2039219--2039300 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
2039209 TGAAATTCCC
2039219 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2039245 ATCATGAAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
2039271 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2039297 ATCA
1 ATCA
2039301 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2040917 original size:5 final size:6
Alignment explanation
Indices: 2040902--2040933 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2040892 ATCTTGTGGC
2040902 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
2040934 GAGATGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2042416 original size:18 final size:18
Alignment explanation
Indices: 2042377--2042420 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2042367 AGTATTAAAG
2042377 CAAAATAAAAATAAATCCC
1 CAAAATAAAAATAAAT-CC
*
2042396 CAAATTAAAAATAAAATCC
1 CAAAATAAAAAT-AAATCC
*
2042415 AAAAAT
1 CAAAAT
2042421 CCCTTATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (18 bp):
CAAAATAAAAATAAATCC
Found at i:2042420 original size:20 final size:19
Alignment explanation
Indices: 2042378--2042420 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2042368 GTATTAAAGC
*
2042378 AAAA-TAAAAATAAATCCC
1 AAAATTAAAAATAAATCCA
*
2042396 CAAATTAAAAATAAAATCCA
1 AAAATTAAAAAT-AAATCCA
2042416 AAAAT
1 AAAAT
2042421 CCCTTATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.15
19 7 0.35
20 10 0.50
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATTAAAAATAAATCCA
Found at i:2042711 original size:18 final size:17
Alignment explanation
Indices: 2042688--2042723 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
2042678 CTTGGCCCAT
2042688 TGCAGTAACAGTAATCAG
1 TGCAGTAACAGTAA-CAG
2042706 TGCAGTAACAGTAACAG
1 TGCAGTAACAGTAACAG
2042723 T
1 T
2042724 ACATATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (17 bp):
TGCAGTAACAGTAACAG
Found at i:2043346 original size:400 final size:394
Alignment explanation
Indices: 2042601--2043396 Score: 1265
Period size: 400 Copynumber: 2.0 Consensus size: 394
2042591 CCTGGGCCTA
* *
2042601 AGCCCTTTTTAGTAACAGTGACAATATGAGTTTGGGCTTTAGCCCATTTCAATACAGAAACAGTC
1 AGCCCTTTTTAGTAACAGTGACAATATCAGTTTGGGCTTTAGCCCATCTCAATACAGAAACAGTC
2042666 ATGTGTTTGGGCCTTGGCCCATTGCAGTAACAGTAATCAGTGCAGTAACAGTAACAGTACATATA
66 ATGTGTTTGGGCCTTGGCCCATTGCAGTAACAGTAATCAGTGCAGTAACAGTAACAGTACATATA
* *
2042731 TGCAATAAGAAATCCTACCCAACCAGCCTCTATACACCACTCCGTCCAGCCTTACACACCATGTA
131 TGCAATAAGAAATCCTACCCAACCAGCCTCTACACACCACTCCGTCCAGCCCTACACACCATGTA
** *
2042796 GGGATAAAATCAACCCACCAATCCCTACACACCAAAAATAGCACCGGTTACGGCACTAAATAGTA
196 GGGATAAAATCAACCCACCAATCCCTACACACCAAAAATAGCACCAATTACGGCACTAAACAGTA
*
2042861 TTTGCAGTAAAACTGCCAGTATAATAGGCTTAAAGCCAACAGTGATTTGCAGCAGAGCTGTCAGT
261 TTTGCAGTAAAACTGCCAGTATAATAGGCTTAAAGCCAACAGTGATTTGCAGCAGAGCTGCCAGT
* *
2042926 ACAGTACATTTCCTCCAATCATAACAAACCCATCCCCATGCAATGCATCATAGAGTCATATCATG
326 ACAGTACACTTCCTCCAATCATAACAAACCCA-----ATGCAATGCATCATACAGTCATATCATG
*
2042991 TCATATTAT
386 TCATATCAT
2043000 AGCCCTTTTTTAGTAACAGTGACAATATCAGTTTGGGCTTTAGCCCATCTCAATACAGAAACAGT
1 AGCCC-TTTTTAGTAACAGTGACAATATCAGTTTGGGCTTTAGCCCATCTCAATACAGAAACAGT
*
2043065 CATGTGTTTGGGCCTTGGCCCATTGCTGTAACAGTAATCAGTGCAGTAACAGTAACA-TA-ATAG
65 CATGTGTTTGGGCCTTGGCCCATTGCAGTAACAGTAATCAGTGCAGTAACAGTAACAGTACAT--
* *
2043128 ATATGTAATCAGAAATCCTACCCAACCAGCCTCTACACACCACTCCGTCCAGCCCTACACACCAT
128 ATATGCAATAAGAAATCCTACCCAACCAGCCTCTACACACCACTCCGTCCAGCCCTACACACCAT
* * * *
2043193 GTGGGGATAAAATCAACCCACCCATCCTTACACACCAAAAATAGCATCAATTACGGCACTAAACA
193 GTAGGGATAAAATCAACCCACCAATCCCTACACACCAAAAATAGCACCAATTACGGCACTAAACA
* * * * *
2043258 GTATTTGCAGTAGAGA-TGCCAGTATAATAGGCTTAGAGCCATCAGTGATTTGTAGTAGAGCTGC
258 GTATTTGCAGTA-AAACTGCCAGTATAATAGGCTTAAAGCCAACAGTGATTTGCAGCAGAGCTGC
* *
2043322 CAGTACAGTACACTTCCTCCAATCATAATAAACCCAATGCAATGCATCATACAGTCATGTCATGT
322 CAGTACAGTACACTTCCTCCAATCATAACAAACCCAATGCAATGCATCATACAGTCATATCATGT
2043387 CATATCAT
387 CATATCAT
2043395 AG
1 AG
2043397 AAATCATACA
Statistics
Matches: 368, Mismatches: 25, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
395 36 0.10
398 2 0.01
399 7 0.02
400 321 0.87
401 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (394 bp):
AGCCCTTTTTAGTAACAGTGACAATATCAGTTTGGGCTTTAGCCCATCTCAATACAGAAACAGTC
ATGTGTTTGGGCCTTGGCCCATTGCAGTAACAGTAATCAGTGCAGTAACAGTAACAGTACATATA
TGCAATAAGAAATCCTACCCAACCAGCCTCTACACACCACTCCGTCCAGCCCTACACACCATGTA
GGGATAAAATCAACCCACCAATCCCTACACACCAAAAATAGCACCAATTACGGCACTAAACAGTA
TTTGCAGTAAAACTGCCAGTATAATAGGCTTAAAGCCAACAGTGATTTGCAGCAGAGCTGCCAGT
ACAGTACACTTCCTCCAATCATAACAAACCCAATGCAATGCATCATACAGTCATATCATGTCATA
TCAT
Found at i:2043518 original size:27 final size:27
Alignment explanation
Indices: 2043488--2043550 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
2043478 AGGGGCAAAT
2043488 CAGTCATTTTACCACATAAGG-GAAAAA
1 CAGTCATTTTACCACAT-AGGAGAAAAA
* *
2043515 CAGTTATTTTACCACATAGGAGCAAAA
1 CAGTCATTTTACCACATAGGAGAAAAA
2043542 CAGTCATTT
1 CAGTCATTT
2043551 GTCAATTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (27 bp):
CAGTCATTTTACCACATAGGAGAAAAA
Found at i:2053637 original size:6 final size:6
Alignment explanation
Indices: 2053626--2053680 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
2053616 AAAAGAAAAT
2053626 AATAAA AATAAA AATAAA AATAAA AAT-AA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
2053673 AATAAA AA
1 AATAAA AA
2053681 GATAATTCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:2053660 original size:23 final size:23
Alignment explanation
Indices: 2053630--2053679 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2053620 GAAAATAATA
2053630 AAAATAAAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAATAAAAAT
2053653 AAAATAAAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAATAAAAAT
2053676 AAAA
1 AAAA
2053680 AGATAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAATAAAAATAAAAATAAAAAT
Found at i:2062908 original size:20 final size:20
Alignment explanation
Indices: 2062883--2062930 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2062873 AGTTGAAGTG
2062883 AATGTGATATTGAGTTATGA
1 AATGTGATATTGAGTTATGA
*
2062903 AATGTGATATTGGGTTATGA
1 AATGTGATATTGAGTTATGA
*
2062923 AATATGAT
1 AATGTGAT
2062931 TTTATGGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
AATGTGATATTGAGTTATGA
Found at i:2063091 original size:76 final size:75
Alignment explanation
Indices: 2062957--2063219 Score: 296
Period size: 76 Copynumber: 3.5 Consensus size: 75
2062947 TGAGTAATTG
*
2062957 ATAT-TGTCGGTTCATCCAACTAGCTCTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGTTAG
1 ATATCTGTCGGTTCAT-CAACTAGCTCTGGGCGCAACTTCTGTTAGTTTATCTGACTAGTGTTAG
*
2063021 GTACACTTTCT
65 GCACACTTTCT
* * * * * *
2063032 ATATCTGTTGGTTCATCAGACTGGCGCTGGCCGCAACTTCTATTAGTTTATCTGACTAGTGTTGG
1 ATATCTGTCGGTTCATCA-ACTAGCTCTGGGCGCAACTTCTGTTAGTTTATCTGACTAGTGTTAG
2063097 GCACACTTTCT
65 GCACACTTTCT
* * * * * *
2063108 ATATCTATCGGTTTATCTAACTAGCTTTGGGCACAACTTCTGTTAGTTTATTTGACTAGTGTTGG
1 ATATCTGTCGGTTCATC-AACTAGCTCTGGGCGCAACTTCTGTTAGTTTATCTGACTAGTGTTAG
*
2063173 GCACACCCTT-T
65 GCACA-CTTTCT
* * * *
2063184 ATATTTGTCAGTTCATCCGACTAGCACTGGGCGCAA
1 ATATCTGTCGGTTCAT-CAACTAGCTCTGGGCGCAA
2063220 AGTTTAGATA
Statistics
Matches: 156, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
75 6 0.04
76 145 0.93
77 5 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (75 bp):
ATATCTGTCGGTTCATCAACTAGCTCTGGGCGCAACTTCTGTTAGTTTATCTGACTAGTGTTAGG
CACACTTTCT
Found at i:2068425 original size:31 final size:31
Alignment explanation
Indices: 2068383--2068448 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
2068373 CTTGTTCCAA
2068383 CAAA-GTTTGGTTTTGAATTTTATTCTTTTT
1 CAAATGTTTGGTTTTGAATTTTATTCTTTTT
2068413 CAAATGTTTGGTTTTGAATTTTATTCTTTTT
1 CAAATGTTTGGTTTTGAATTTTATTCTTTTT
2068444 CAAAT
1 CAAAT
2068449 CATTTTGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (31 bp):
CAAATGTTTGGTTTTGAATTTTATTCTTTTT
Found at i:2068443 original size:16 final size:16
Alignment explanation
Indices: 2068393--2068443 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2068383 CAAAGTTTGG
2068393 TTTTGAATTTTATTCT
1 TTTTGAATTTTATTCT
* * * **
2068409 TTTTCAAATGT-TTGG
1 TTTTGAATTTTATTCT
2068424 TTTTGAATTTTATTCT
1 TTTTGAATTTTATTCT
2068440 TTTT
1 TTTT
2068444 CAAATCATTT
Statistics
Matches: 24, Mismatches: 10, Indels: 2
0.67 0.28 0.06
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.67
Consensus pattern (16 bp):
TTTTGAATTTTATTCT
Found at i:2069433 original size:13 final size:13
Alignment explanation
Indices: 2069415--2069442 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2069405 ATAAAATTGG
2069415 AAAGATGATAAAT
1 AAAGATGATAAAT
2069428 AAAGATGATAAAT
1 AAAGATGATAAAT
2069441 AA
1 AA
2069443 TAAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:2070095 original size:26 final size:26
Alignment explanation
Indices: 2070066--2070117 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2070056 GGTAAAGAAA
2070066 AAGTAATGGATTAGTAGTATACGAGT
1 AAGTAATGGATTAGTAGTATACGAGT
2070092 AAGTAATGGATTAGTAGTATACGAGT
1 AAGTAATGGATTAGTAGTATACGAGT
2070118 TCACGAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (26 bp):
AAGTAATGGATTAGTAGTATACGAGT
Found at i:2070718 original size:50 final size:50
Alignment explanation
Indices: 2070662--2070766 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
2070652 GAGTTTCCTG
*
2070662 TTATACAGCTCGGAAAAGCTTCCCGTTACTTGGCTCATATGAGCTTCCCA
1 TTATACAGCTCGGAAAAGCTTCCCGTTACATGGCTCATATGAGCTTCCCA
* *
2070712 TTATACAGTTCGGATAAGCTTCCCGTTACATGGCTCATATGAGCTTCCCA
1 TTATACAGCTCGGAAAAGCTTCCCGTTACATGGCTCATATGAGCTTCCCA
2070762 TTATA
1 TTATA
2070767 TGGCTTGAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (50 bp):
TTATACAGCTCGGAAAAGCTTCCCGTTACATGGCTCATATGAGCTTCCCA
Found at i:2070769 original size:25 final size:25
Alignment explanation
Indices: 2070678--2070771 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
2070668 AGCTCGGAAA
*
2070678 AGCTTCCCGTTACT-TGGCTCATATG
1 AGCTTCCCATTA-TATGGCTCATATG
** * ** *
2070703 AGCTTCCCATTATACAGTTCGGATA
1 AGCTTCCCATTATATGGCTCATATG
* *
2070728 AGCTTCCCGTTACATGGCTCATATG
1 AGCTTCCCATTATATGGCTCATATG
2070753 AGCTTCCCATTATATGGCT
1 AGCTTCCCATTATATGGCT
2070772 TGAGAGAAGG
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
24 1 0.02
25 50 0.98
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (25 bp):
AGCTTCCCATTATATGGCTCATATG
Found at i:2071982 original size:30 final size:30
Alignment explanation
Indices: 2071922--2071987 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2071912 GTATGGACAT
2071922 GGCCAGGTGCCCAAATATGAATGTCCACAC
1 GGCCAGGTGCCCAAATATGAATGTCCACAC
* * *
2071952 GGCCATGTGCCCAAATTTGAATG-CATACAC
1 GGCCAGGTGCCCAAATATGAATGTC-CACAC
2071982 GGCCAG
1 GGCCAG
2071988 AGACATGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (30 bp):
GGCCAGGTGCCCAAATATGAATGTCCACAC
Found at i:2086118 original size:46 final size:46
Alignment explanation
Indices: 2086058--2086323 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
2086048 TTTGACATGA
* * * * * *
2086058 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
2086104 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
2086150 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
2086196 TGCCATGGTATCTTTCAACCATGGGCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2086242 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2086280 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
2086324 AGAGCACACT
Statistics
Matches: 196, Mismatches: 15, Indels: 18
0.86 0.07 0.08
Matches are distributed among these distances:
38 33 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 149 0.76
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:2086288 original size:38 final size:38
Alignment explanation
Indices: 2086237--2086312 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2086227 CATTTCATAT
2086237 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2086275 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2086313 TTTCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:2097168 original size:18 final size:18
Alignment explanation
Indices: 2097137--2097172 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2097127 AGGATAATGA
2097137 CTTTTATTTTGAAAAATT
1 CTTTTATTTTGAAAAATT
2097155 CTTTT-TTTTAGAAAAATT
1 CTTTTATTTT-GAAAAATT
2097173 GACGTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
CTTTTATTTTGAAAAATT
Found at i:2098724 original size:23 final size:21
Alignment explanation
Indices: 2098690--2098732 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2098680 GATTTTACAC
2098690 ACAAACGAGATTTTCCTAAAATT
1 ACAAACGAGA-TTT-CTAAAATT
2098713 ACAAATCG-GATTTCTAAAAT
1 ACAAA-CGAGATTTCTAAAAT
2098733 CTATTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 7 0.37
24 2 0.11
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (21 bp):
ACAAACGAGATTTCTAAAATT
Found at i:2106484 original size:15 final size:15
Alignment explanation
Indices: 2106448--2106498 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
2106438 ATAATTTATA
*
2106448 AGACATTTTAGATAT
1 AGACATTTTAGAAAT
*
2106463 AGA-ATTTTTGAAAT
1 AGACATTTTAGAAAT
*
2106477 AGACATTTTA-AATT
1 AGACATTTTAGAAAT
2106491 AGAC-TTTT
1 AGACATTTT
2106499 TTAATTTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 4 0.13
14 19 0.61
15 8 0.26
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (15 bp):
AGACATTTTAGAAAT
Found at i:2113544 original size:21 final size:21
Alignment explanation
Indices: 2113520--2113571 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
2113510 GATATTTGGC
2113520 TTTGCGTTTAGGAGCTTTTCT
1 TTTGCGTTTAGGAGCTTTTCT
* * *
2113541 TTTG-GCTTAAGGTGGTTTTCT
1 TTTGCG-TTTAGGAGCTTTTCT
2113562 TTTGCTGTTT
1 TTTGC-GTTT
2113572 GGTTTTGGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 2 0.08
23 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.56
Consensus pattern (21 bp):
TTTGCGTTTAGGAGCTTTTCT
Found at i:2115932 original size:31 final size:31
Alignment explanation
Indices: 2115895--2115965 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2115885 TAAACAGACA
* *
2115895 ACTTTTGAAGTTAGAAGTGCTTTT-GAAAAGC
1 ACTTTTGAAGTCAGAAGTG-TTTTCCAAAAGC
*
2115926 ACTTTTGGAGTCAGAAGTGTTTTCCAAAAGC
1 ACTTTTGAAGTCAGAAGTGTTTTCCAAAAGC
2115957 ACTTTTGAA
1 ACTTTTGAA
2115966 CCCAAAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (31 bp):
ACTTTTGAAGTCAGAAGTGTTTTCCAAAAGC
Found at i:2127552 original size:20 final size:20
Alignment explanation
Indices: 2127527--2127566 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2127517 CCATTACACC
* *
2127527 ATTCAAAATTTGGTATCACT
1 ATTCAAAATATGATATCACT
*
2127547 ATTCAATATATGATATCACT
1 ATTCAAAATATGATATCACT
2127567 TCTGTATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTCAAAATATGATATCACT
Found at i:2128400 original size:31 final size:30
Alignment explanation
Indices: 2128328--2128401 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
2128318 TTAACAAACT
* *
2128328 AATACTTTATATAAAAAATTTTAAATAATTT
1 AATA-TTTAAATAAAAAATTTTAAATAATTC
*
2128359 AATAACTTAAATAAAAAATTTTCAAATAATTC
1 AAT-ATTTAAATAAAAAATTTT-AAATAATTC
2128391 AATATTTAAAT
1 AATATTTAAAT
2128402 TATTAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
AATATTTAAATAAAAAATTTTAAATAATTC
Found at i:2132631 original size:49 final size:49
Alignment explanation
Indices: 2132572--2132669 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
2132562 TGTTTACCCC
2132572 AAATGCATTCTTTTATAATTAGTGTCTGAAGTATTTTAAAAAAAAATAG
1 AAATGCATTCTTTTATAATTAGTGTCTGAAGTATTTTAAAAAAAAATAG
*
2132621 AAATGCATTCTTTTATAATTAGTGTCTGAAGTATTTTAAAAAGAAATAG
1 AAATGCATTCTTTTATAATTAGTGTCTGAAGTATTTTAAAAAAAAATAG
2132670 TTAATTGAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (49 bp):
AAATGCATTCTTTTATAATTAGTGTCTGAAGTATTTTAAAAAAAAATAG
Found at i:2136503 original size:66 final size:66
Alignment explanation
Indices: 2136397--2136538 Score: 275
Period size: 66 Copynumber: 2.2 Consensus size: 66
2136387 TATTCTATCG
2136397 ATCTCTTTCTCTCCTTTCCTTCAACTGGTACTTTGGTTGAATATTAGTAGGGTATCTCTACCTCT
1 ATCTCTTTCTCTCCTTTCCTTCAACTGGTACTTTGGTTGAATATTAGTAGGGTATCTCTACCTCT
2136462 C
66 C
*
2136463 ATCTCTTTCTCTCCTTTCCTTCAACTGGTACTTTGGTTGAATATTAGTAGGGTATCTCTACCTGT
1 ATCTCTTTCTCTCCTTTCCTTCAACTGGTACTTTGGTTGAATATTAGTAGGGTATCTCTACCTCT
2136528 C
66 C
2136529 ATCTCTTTCT
1 ATCTCTTTCT
2136539 TTCCCTACTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 75 1.00
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.45
Consensus pattern (66 bp):
ATCTCTTTCTCTCCTTTCCTTCAACTGGTACTTTGGTTGAATATTAGTAGGGTATCTCTACCTCT
C
Found at i:2139225 original size:12 final size:12
Alignment explanation
Indices: 2139205--2139248 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
2139195 CAAGTCACAA
2139205 GCCGTGTGCTAG
1 GCCGTGTGCTAG
*
2139217 GCTGTGTGCTAG
1 GCCGTGTGCTAG
2139229 GCCGTGTGCTAG
1 GCCGTGTGCTAG
*
2139241 GTCGTGTG
1 GCCGTGTG
2139249 GAGCATACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.07, C:0.20, G:0.43, T:0.30
Consensus pattern (12 bp):
GCCGTGTGCTAG
Found at i:2157223 original size:12 final size:12
Alignment explanation
Indices: 2157206--2157230 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2157196 TATATTCAAA
2157206 ATTAACTTATTT
1 ATTAACTTATTT
2157218 ATTAACTTATTT
1 ATTAACTTATTT
2157230 A
1 A
2157231 ATCATATCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAACTTATTT
Found at i:2159904 original size:36 final size:36
Alignment explanation
Indices: 2159863--2159935 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
2159853 CGAAAGGGGA
2159863 AAATAAGCTGAAAGGTATTCTGGAAAATATGAAAGC
1 AAATAAGCTGAAAGGTATTCTGGAAAATATGAAAGC
2159899 AAATAAGCTGAAAGGTATTCTGGAAAATATGAAAGC
1 AAATAAGCTGAAAGGTATTCTGGAAAATATGAAAGC
2159935 A
1 A
2159936 TTTCGGGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (36 bp):
AAATAAGCTGAAAGGTATTCTGGAAAATATGAAAGC
Found at i:2164079 original size:13 final size:13
Alignment explanation
Indices: 2164061--2164085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2164051 TCGGCAGGGA
2164061 CACGCCCGTGTGC
1 CACGCCCGTGTGC
2164074 CACGCCCGTGTG
1 CACGCCCGTGTG
2164086 ACATGATTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.44, G:0.32, T:0.16
Consensus pattern (13 bp):
CACGCCCGTGTGC
Found at i:2164279 original size:11 final size:11
Alignment explanation
Indices: 2164263--2164287 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2164253 GTTTTGTCCC
2164263 TTTTTGGCTCA
1 TTTTTGGCTCA
2164274 TTTTTGGCTCA
1 TTTTTGGCTCA
2164285 TTT
1 TTT
2164288 CGCTCTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTTGGCTCA
Found at i:2164599 original size:42 final size:42
Alignment explanation
Indices: 2164528--2164638 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
2164518 ATAAGTGCTA
* ** * * *
2164528 AACGGAAACCCGTAAGGGTTAAACAGAAGCTTATAATAGCTG
1 AACGGAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGCTG
2164570 AACGGAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGCTG
1 AACGGAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGCTG
** * *
2164612 AACTAAAACCTAAAAGGGTTAAATTGA
1 AACGGAAACCCATAAGGGTTAAATTGA
2164639 GACTCATATG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (42 bp):
AACGGAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGCTG
Found at i:2172357 original size:21 final size:21
Alignment explanation
Indices: 2172331--2172371 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2172321 ATCTGCTCAA
* *
2172331 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2172352 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2172372 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2178559 original size:19 final size:19
Alignment explanation
Indices: 2178535--2178651 Score: 121
Period size: 19 Copynumber: 6.7 Consensus size: 19
2178525 ATTATACATA
2178535 ATAATAAATAATAAATAAT
1 ATAATAAATAATAAATAAT
*
2178554 ATAATAAATAATATAT-A-
1 ATAATAAATAATAAATAAT
2178571 AT-A-AAAT-ATAAATAAT
1 ATAATAAATAATAAATAAT
*
2178587 ATAATGAATAAT--AT-AT
1 ATAATAAATAATAAATAAT
2178603 ATAATAAA-ATATAAATAAT
1 ATAATAAATA-ATAAATAAT
*
2178622 ATAATAAATAATACATAA-
1 ATAATAAATAATAAATAAT
2178640 ATAA-AAATAATA
1 ATAATAAATAATA
2178652 TATATAATAA
Statistics
Matches: 83, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.06
15 6 0.07
16 14 0.17
17 13 0.16
18 10 0.12
19 34 0.41
20 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.32
Consensus pattern (19 bp):
ATAATAAATAATAAATAAT
Found at i:2178572 original size:33 final size:33
Alignment explanation
Indices: 2178535--2178661 Score: 170
Period size: 33 Copynumber: 3.8 Consensus size: 33
2178525 ATTATACATA
2178535 ATAAT-AAATAATAAATAATATAATAAATAATAT
1 ATAATAAAAT-ATAAATAATATAATAAATAATAT
*
2178568 ATAATAAAATATAAATAATATAATGAATAATATAT
1 ATAATAAAATATAAATAATATAATAAAT-A-ATAT
*
2178603 ATAATAAAATATAAATAATATAATAAATAATAC
1 ATAATAAAATATAAATAATATAATAAATAATAT
2178636 ATAAATAAAA-AT-AATATATATAATAA
1 AT-AATAAAATATAAATA-ATATAATAA
2178662 TTTTTTACAT
Statistics
Matches: 86, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
32 4 0.05
33 38 0.44
34 13 0.15
35 31 0.36
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (33 bp):
ATAATAAAATATAAATAATATAATAAATAATAT
Found at i:2178678 original size:68 final size:69
Alignment explanation
Indices: 2178527--2178659 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 69
2178517 TTTTTAAAAT
*
2178527 TATACATAATAATAAATAATAAATAATATAATAAATAATATATAATAAAATATAAATAATATAAT
1 TATACATAAT-A-AAATAATAAATAATATAATAAATAATACATAATAAAATATAAATAATATAAT
2178592 GAATAA
64 GAATAA
*
2178598 TATATATAATAAAAT-ATAAATAATATAATAAATAATACATAAATAAAA-AT-AATATATATAAT
1 TATACATAATAAAATAATAAATAATATAATAAATAATACAT-AATAAAATATAAATA-ATATAAT
2178660 AATTTTTTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
67 4 0.07
68 33 0.57
69 11 0.19
70 1 0.02
71 9 0.16
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.33
Consensus pattern (69 bp):
TATACATAATAAAATAATAAATAATATAATAAATAATACATAATAAAATATAAATAATATAATGA
ATAA
Found at i:2178687 original size:19 final size:21
Alignment explanation
Indices: 2178649--2178687 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2178639 AATAAAAATA
*
2178649 ATATATATAATAATTTTTTAC
1 ATATATATAATAATTGTTTAC
2178670 ATATATA-AATAA-TGTTTA
1 ATATATATAATAATTGTTTA
2178688 TAGTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
ATATATATAATAATTGTTTAC
Found at i:2178730 original size:30 final size:30
Alignment explanation
Indices: 2178694--2178752 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2178684 TTTATAGTAA
*
2178694 AAATAAA-TACTATATAAAATATTTTAAAAT
1 AAATAAATTA-TATATAAAATATTTAAAAAT
2178724 AAATAAATTATATATAAAATATTTAAAAA
1 AAATAAATTATATATAAAATATTTAAAAA
2178753 GGATTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAAATTATATATAAAATATTTAAAAAT
Found at i:2178943 original size:30 final size:30
Alignment explanation
Indices: 2178907--2178965 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2178897 TATAATGGAT
* *
2178907 ATTAGGGCTAAAGTGAAACAAAAATAAAAG
1 ATTAGGGCCAAAGTAAAACAAAAATAAAAG
* *
2178937 ATTAGGGCCAAATTAAAATAAAAATAAAA
1 ATTAGGGCCAAAGTAAAACAAAAATAAAA
2178966 TGAAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (30 bp):
ATTAGGGCCAAAGTAAAACAAAAATAAAAG
Found at i:2179986 original size:17 final size:17
Alignment explanation
Indices: 2179945--2179977 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2179935 AACATTTAAT
*
2179945 TATTTTGGTTTTTTGTG
1 TATTTTGGTTTATTGTG
2179962 TATTTTGGTTTATTGT
1 TATTTTGGTTTATTGT
2179978 TTTTTTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (17 bp):
TATTTTGGTTTATTGTG
Found at i:2180243 original size:45 final size:45
Alignment explanation
Indices: 2180188--2180644 Score: 301
Period size: 45 Copynumber: 10.2 Consensus size: 45
2180178 GAGACGCCAA
* * *
2180188 ATCTGTTATCTTCGATTTGCTTCGATGTAAACACGCAAATGTCAG
1 ATCTGCTATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
* * * * * * * * *
2180233 ATCTGCTATCTTTGATCTGCTCCCCG-TCT-AATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCT--TCGATGTAAACACACAAATGTCAG
*
2180278 ATCTG-TCATCTTCGATCTGCTTCAATGTAAACACACAAATGTCAG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
* * * * * *
2180323 ATCTGCTATCTTCGATCTGCTCCCCG-T-TTAATACAGAGATGCCA-
1 ATCTGCTATCTTCGATCTGCT--TCGATGTAAACACACAAATGTCAG
* *
2180367 ACTCTG-TCATTTTCGATCTACTTCGATGTAAACACACAAATGTCAG
1 A-TCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
* ** * * * * * *
2180413 ATCTGCTATCTTCAATCTGC-TCCCTGTCTAATATAGAGAA-GCCAA
1 ATCTGCTATCTTCGATCTGCTTCGATGT-AAACACACA-AATGTCAG
* * * *
2180458 ATCT-ATCATCTTCAATCTGTTTCGATGTAAACACACAAATGTCTG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
* * * * * * * *
2180503 ATCTGCTATCTTCGATCTGCTCCCCG-T-TTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCT--TCGATGTAAACACACAAATGTCAG
*
2180548 ATCTG-TCATCTTCGATCTGCTTTGATGTAAACACACAAATGTCAG
1 ATCTGCT-ATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
* *
2180593 ATCTGCTATCTTCGATCTGCTTTGATGTAAACACACGAATGTCAG
1 ATCTGCTATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
2180638 ATCTGCT
1 ATCTGCT
2180645 CCGCGTCTAA
Statistics
Matches: 305, Mismatches: 81, Indels: 52
0.70 0.18 0.12
Matches are distributed among these distances:
43 4 0.01
44 16 0.05
45 264 0.87
46 16 0.05
47 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTTCGATGTAAACACACAAATGTCAG
Found at i:2180269 original size:90 final size:90
Alignment explanation
Indices: 2180167--2180613 Score: 714
Period size: 90 Copynumber: 5.0 Consensus size: 90
2180157 ACCTGTTTTT
* * *
2180167 CGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATTTGCTTCGATGTAAACACGCAAATGTCA
1 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
*
2180232 GATCTGCTATCTTTGATCTGCTCCC
66 GATCTGCTATCTTCGATCTGCTCCC
*
2180257 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCAATGTAAACACACAAATGTCA
1 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
2180322 GATCTGCTATCTTCGATCTGCTCCC
66 GATCTGCTATCTTCGATCTGCTCCC
* * * * *
2180347 CGTTTAATACAGAGATGCCAACTCTGTCATTTTCGATCTACTTCGATGTAAACACACAAATGTCA
1 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
*
2180412 GATCTGCTATCTTCAATCTGCTCCC
66 GATCTGCTATCTTCGATCTGCTCCC
* * * * * * *
2180437 TGTCTAATATAGAGAAGCCAAATCTATCATCTTCAATCTGTTTCGATGTAAACACACAAATGTCT
1 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
2180502 GATCTGCTATCTTCGATCTGCTCCC
66 GATCTGCTATCTTCGATCTGCTCCC
* *
2180527 CGTTTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACACACAAATGTCA
1 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
2180592 GATCTGCTATCTTCGATCTGCT
66 GATCTGCTATCTTCGATCTGCT
2180614 TTGATGTAAA
Statistics
Matches: 324, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 324 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (90 bp):
CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACACACAAATGTCA
GATCTGCTATCTTCGATCTGCTCCC
Found at i:2180701 original size:211 final size:211
Alignment explanation
Indices: 2180427--2180821 Score: 630
Period size: 211 Copynumber: 1.9 Consensus size: 211
2180417 GCTATCTTCA
* *
2180427 ATCTGCTCCCTGTCTAATATAGAGAAGCCAAATCTATCATCTTCAATCTGTTTCGATGTAAACAC
1 ATCTGCTCCCTGTCTAATACAGAGAAGCCAAATCTATCATCTTCAATCTGCTTCGATGTAAACAC
* * * *
2180492 ACAAATGTCTGATCTGCTATCTTCGATCTGCTCCCCGTTTAATACAGAGACGCCAAATCTGTCAT
66 ACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCAT
*
2180557 CTTCGATCTGCTTTGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTGCTTTGATGTA
131 CTTCGATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTGCTTTGATGTA
2180622 AACACACGAATGTCAG
196 AACACACGAATGTCAG
* * *
2180638 ATCTGCTCCGC-GTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 ATCTGCTCC-CTGTCTAATACAGAGAAGCCAAATCTATCATCTTCAATCTGCTTCGATGTAAACA
* *
2180702 CACGAATGTCAGATCTTCTATCTTCAATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCA
65 CACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCA
** * *
2180767 TCTTCGATCTGCTTCGATGTAAACACATGAATGTCAGATTTGCTATCTTTGATCT
130 TCTTCGATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCT
2180822 ACTCCCCGTC
Statistics
Matches: 167, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
211 166 0.99
212 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (211 bp):
ATCTGCTCCCTGTCTAATACAGAGAAGCCAAATCTATCATCTTCAATCTGCTTCGATGTAAACAC
ACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCAT
CTTCGATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTGCTTTGATGTA
AACACACGAATGTCAG
Found at i:2180763 original size:121 final size:121
Alignment explanation
Indices: 2180517--2180736 Score: 314
Period size: 121 Copynumber: 1.8 Consensus size: 121
2180507 GCTATCTTCG
* *
2180517 ATCTGCTCCCCGTTTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
* * ** * * * *
2180582 ACAAATGTCAGATCTGCTATCTTCGATCTGCTTTGATGTAAACACACGAATGTCAG
66 ACAAATGTCAGATCTGCTATCTTCAATCTACTCCGATCTAAACACACGAACGCCAA
* *
2180638 ATCTGCTCCGCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
* *
2180703 ACGAATGTCAGATCTTCTATCTTCAATCTACTCC
66 ACAAATGTCAGATCTGCTATCTTCAATCTACTCC
2180737 CCGTCTAATA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 89 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (121 bp):
ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
ACAAATGTCAGATCTGCTATCTTCAATCTACTCCGATCTAAACACACGAACGCCAA
Found at i:2180850 original size:301 final size:301
Alignment explanation
Indices: 2180336--2180911 Score: 909
Period size: 301 Copynumber: 1.9 Consensus size: 301
2180326 TGCTATCTTC
* * *
2180336 GATCTGCTCCCCGTTTAATACAGAGATGCCAACTCTGTCATTTTCGATCTACTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
* * *
2180401 CACAAATGTCAGATCTGCTATCTTCAATCTGCTCCCTGTCTAATATAGAGAAGCCAAATCTATCA
66 CACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGAAGCCAAATCTATCA
* * * *
2180466 TCTTCAATCTGTTTCGATGTAAACACACAAATGTCTGATCTGCTATCTTCGATCTGCTCCCCGTT
131 TCTTCAATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTACTCCCCGTC
* *
2180531 TAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACACACAAATGTCAGATC
196 AAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACACACAAATGCCAGATC
2180596 TGCTATCTTCGATCTGCTTTGATGTAAACACACGAATGTCA
261 TGCTATCTTCGATCTGCTTTGATGTAAACACACGAATGTCA
* *
2180637 GATCTGCTCCGCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
* * * *
2180702 CACGAATGTCAGATCTTCTATCTTCAATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCA
66 CACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGAAGCCAAATCTATCA
* ** * *
2180767 TCTTCGATCTGCTTCGATGTAAACACATGAATGTCAGATTTGCTATCTTTGATCTACTCCCCGTC
131 TCTTCAATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTACTCCCCGTC
* * * *
2180832 AAATATAGAGATGCCAAATTTGTCATCTTCGATCTGCTTTGATGTAAACACACGAATGCCAGATC
196 AAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACACACAAATGCCAGATC
2180897 TGCTATCTTCGATCT
261 TGCTATCTTCGATCT
2180912 ACTCCTCGTC
Statistics
Matches: 248, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
301 248 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (301 bp):
GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
CACAAATGTCAGATCTGCTATCTTCAATCTACTCCCCGTCTAATACAGAGAAGCCAAATCTATCA
TCTTCAATCTGCTTCGATGTAAACACACAAATGTCAGATCTGCTATCTTCGATCTACTCCCCGTC
AAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTTGATGTAAACACACAAATGCCAGATC
TGCTATCTTCGATCTGCTTTGATGTAAACACACGAATGTCA
Found at i:2180944 original size:45 final size:46
Alignment explanation
Indices: 2180637--2180945 Score: 180
Period size: 45 Copynumber: 6.8 Consensus size: 46
2180627 ACGAATGTCA
*
2180637 GATCTGCTCCGCGTCTAATACAGAGATGCCAAATCTG-TCATCTTC
1 GATCTGCTCCTCGTCTAATACAGAGATGCCAAATCTGCTCATCTTC
* * * * *
2180682 GATCTGCT--TCGATGTAA-ACACACGAATGTCAGATCTTCT-ATCTTC
1 GATCTGCTCCTCG-TCTAATACAGA-G-ATGCCAAATCTGCTCATCTTC
* * * *
2180727 AATCTACTCCCCGTCTAATACAGAGACGCCAAATCTG-TCATCTTC
1 GATCTGCTCCTCGTCTAATACAGAGATGCCAAATCTGCTCATCTTC
* * * * * *
2180772 GATCTGCT--TCGATGTAA-ACACATGAATGTCAGATTTGCT-ATCTTT
1 GATCTGCTCCTCG-TCTAATACAGA-G-ATGCCAAATCTGCTCATCTTC
* * * * *
2180817 GATCTACTCCCCGTCAAATATAGAGATGCCAAATTTG-TCATCTTC
1 GATCTGCTCCTCGTCTAATACAGAGATGCCAAATCTGCTCATCTTC
* * * *
2180862 GATCTGCT--TTGATGTAA-ACACACGAATGCCAGATCTGCT-ATCTTC
1 GATCTGCTCCTCG-TCTAATACAGA-G-ATGCCAAATCTGCTCATCTTC
* * *
2180907 GATCTACTCCTCGTCTAATACAGAGACGTCAAATCTGCT
1 GATCTGCTCCTCGTCTAATACAGAGATGCCAAATCTGCT
2180946 TCCGGTGATC
Statistics
Matches: 191, Mismatches: 50, Indels: 46
0.67 0.17 0.16
Matches are distributed among these distances:
43 16 0.08
44 16 0.08
45 125 0.65
46 17 0.09
47 17 0.09
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (46 bp):
GATCTGCTCCTCGTCTAATACAGAGATGCCAAATCTGCTCATCTTC
Found at i:2180956 original size:90 final size:90
Alignment explanation
Indices: 2180637--2180943 Score: 470
Period size: 90 Copynumber: 3.4 Consensus size: 90
2180627 ACGAATGTCA
* * *
2180637 GATCTGCTCCGCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 GATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
2180702 CACGAATGTCAGATCTTCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
*
2180727 AATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 GATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
* * *
2180792 CATGAATGTCAGATTTGCTATCTTT
66 CACGAATGTCAGATCTGCTATCTTC
* * * * *
2180817 GATCTACTCCCCGTCAAATATAGAGATGCCAAATTTGTCATCTTCGATCTGCTTTGATGTAAACA
1 GATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
2180882 CACGAATGCCAGATCTGCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* *
2180907 GATCTACTCCTCGTCTAATACAGAGACGTCAAATCTG
1 GATCTACTCCCCGTCTAATACAGAGACGCCAAATCTG
2180944 CTTCCGGTGA
Statistics
Matches: 193, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 193 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (90 bp):
GATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
CACGAATGTCAGATCTGCTATCTTC
Found at i:2189315 original size:34 final size:34
Alignment explanation
Indices: 2189206--2189317 Score: 102
Period size: 34 Copynumber: 3.2 Consensus size: 34
2189196 ATAAAAACGC
2189206 TTTTAAATACAATATAAATATAATTTATCAAATG
1 TTTTAAATACAATATAAATATAATTTATCAAATG
* * * ** * *
2189240 TTTT--ATGCATTTTAAACTAAATAACTAAATAAAACG
1 TTTTAAATACAATATAAA-T--ATAA-TTTATCAAATG
2189276 CTTTTAAATACAATATAAATATAATTTATCAAATG
1 -TTTTAAATACAATATAAATATAATTTATCAAATG
2189311 TTTTAAA
1 TTTTAAA
2189318 CAACTAAATA
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
32 9 0.16
33 1 0.02
34 11 0.19
35 11 0.19
36 11 0.19
37 4 0.07
38 1 0.02
39 9 0.16
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (34 bp):
TTTTAAATACAATATAAATATAATTTATCAAATG
Found at i:2191150 original size:21 final size:20
Alignment explanation
Indices: 2191122--2191163 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
2191112 TTTTTTAAAG
*
2191122 TTTTAAAACTAATTTTA-ATT
1 TTTTAAAAAT-ATTTTATATT
2191142 TTTTAAAAAATATTTTATATT
1 TTTT-AAAAATATTTTATATT
2191163 T
1 T
2191164 AATGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAAAATATTTTATATT
Found at i:2191281 original size:12 final size:11
Alignment explanation
Indices: 2191258--2191290 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2191248 CGTGAAATTC
2191258 TATTTTTAAAA
1 TATTTTTAAAA
*
2191269 TATTTTTATAA
1 TATTTTTAAAA
2191280 -ATTTTTAAAA
1 TATTTTTAAAA
2191290 T
1 T
2191291 TTAAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:2191297 original size:28 final size:27
Alignment explanation
Indices: 2191262--2191328 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
2191252 AAATTCTATT
*
2191262 TTTAAAATATTTTTATAAATTTTTAAAA
1 TTTAAAATATTTTTAT-AATTTTCAAAA
* *
2191290 TTTAAAATACTATTTATAATTTTCATAA
1 TTTAAAATA-TTTTTATAATTTTCAAAA
2191318 --TAAAATATTTT
1 TTTAAAATATTTT
2191329 GAACAACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.09
26 7 0.21
28 18 0.53
29 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAAAATATTTTTATAATTTTCAAAA
Found at i:2192062 original size:15 final size:15
Alignment explanation
Indices: 2192042--2192095 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
2192032 ATACTACAAA
2192042 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
2192057 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
2192074 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
2192091 ATATT
1 ATATT
2192096 AACATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:2192159 original size:16 final size:16
Alignment explanation
Indices: 2192128--2192164 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2192118 ATGTGAATAA
2192128 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
2192144 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
2192160 TATTA
1 TATTA
2192165 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:2192494 original size:19 final size:19
Alignment explanation
Indices: 2192458--2192495 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2192448 ACCTGTAAGT
*
2192458 TATTTTCTGTTGATCAAAC
1 TATTTTCTGTTGAACAAAC
2192477 TATTTTCTG-TGAAACAAAC
1 TATTTTCTGTTG-AACAAAC
2192496 ACAGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TATTTTCTGTTGAACAAAC
Found at i:2192973 original size:17 final size:16
Alignment explanation
Indices: 2192953--2192985 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2192943 TATTTCATAT
2192953 TAATTAAATAAAATAAA
1 TAATTAAAT-AAATAAA
2192970 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
2192986 AGAAAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:2193041 original size:24 final size:23
Alignment explanation
Indices: 2193014--2193058 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2193004 TGATGATGAT
*
2193014 ATACAAATGTAATAATATATATGG
1 ATACAAATGTAA-AATAAATATGG
2193038 ATACAAATGTAAAATAAATAT
1 ATACAAATGTAAAATAAATAT
2193059 TTGTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (23 bp):
ATACAAATGTAAAATAAATATGG
Found at i:2193076 original size:18 final size:18
Alignment explanation
Indices: 2193049--2193083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2193039 TACAAATGTA
*
2193049 AAATAAATATTTGTTATT
1 AAATAAATATTTATTATT
*
2193067 AAATAGATATTTATTAT
1 AAATAAATATTTATTAT
2193084 AGTTATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
AAATAAATATTTATTATT
Found at i:2193088 original size:24 final size:24
Alignment explanation
Indices: 2193061--2193114 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
2193051 ATAAATATTT
2193061 GTTATTAAATAGATATTTATTATA
1 GTTATTAAATAGATATTTATTATA
2193085 GTTATTAAATAGATATTTATTATA
1 GTTATTAAATAGATATTTATTATA
2193109 GTTATT
1 GTTATT
2193115 CTTATTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (24 bp):
GTTATTAAATAGATATTTATTATA
Found at i:2193161 original size:14 final size:13
Alignment explanation
Indices: 2193142--2193198 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
2193132 ATATATATAT
2193142 AAATAAAATAAAAG
1 AAATAAAA-AAAAG
*
2193156 AAATAAAAGAAAGG
1 AAATAAAA-AAAAG
*
2193170 AAA-AAAAAAGAG
1 AAATAAAAAAAAG
*
2193182 AAATAAAGAAAACG
1 AAATAAA-AAAAAG
2193196 AAA
1 AAA
2193199 CAGAGAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 6 0.17
13 7 0.20
14 22 0.63
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (13 bp):
AAATAAAAAAAAG
Found at i:2193198 original size:26 final size:25
Alignment explanation
Indices: 2193146--2193198 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2193136 ATATATAAAT
* *
2193146 AAAATAAAAGAAATAAAAGAAAGGA
1 AAAAAAAAAGAAATAAAAGAAACGA
2193171 AAAAAAAAGAGAAAT-AAAGAAAACGA
1 AAAAAAAA-AGAAATAAAAG-AAACGA
2193197 AA
1 AA
2193199 CAGAGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (25 bp):
AAAAAAAAAGAAATAAAAGAAACGA
Found at i:2194087 original size:15 final size:16
Alignment explanation
Indices: 2194067--2194097 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2194057 TAATGTAAAG
2194067 TGAATTG-AAATATAT
1 TGAATTGAAAATATAT
2194082 TGAATTGAAAATATAT
1 TGAATTGAAAATATAT
2194098 ATGATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TGAATTGAAAATATAT
Found at i:2195880 original size:21 final size:21
Alignment explanation
Indices: 2195847--2195888 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2195837 TTCTTGAAAT
*
2195847 AAATTCAAAAAATTAGGAAAAA
1 AAATTCAAAAAATCA-GAAAAA
*
2195869 AAATT-AACAAATCAGAAAAA
1 AAATTCAAAAAATCAGAAAAA
2195889 TATGGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATTCAAAAAATCAGAAAAA
Found at i:2197010 original size:34 final size:33
Alignment explanation
Indices: 2196963--2197337 Score: 389
Period size: 34 Copynumber: 11.1 Consensus size: 33
2196953 GAAACAGGCA
* * * *
2196963 AACCCTATTTTATATTA-TATGACTTAGTATGTG
1 AACCCCATGTTATA-TAGTATGACATAGTATGCG
*
2196996 AACCCCATTGTTATATAGTATGACATAGTATAC-
1 AACCCCA-TGTTATATAGTATGACATAGTATGCG
* *
2197029 AACCCCTCATGTTATATAATATGACATAGTATGTG
1 AA-CCC-CATGTTATATAGTATGACATAGTATGCG
*
2197064 AACCCCCATGTTATATAGTATGACATAGCATG-G
1 AA-CCCCATGTTATATAGTATGACATAGTATGCG
* * *
2197097 AACCCCATGTCATATAGAATGACATAGTATGCA
1 AACCCCATGTTATATAGTATGACATAGTATGCG
* *
2197130 AACCCCCATGTTATATCA-TATGACATAATATGCA
1 AA-CCCCATGTTATAT-AGTATGACATAGTATGCG
** *
2197164 AACCCTCACATTATATAGTATGACATAGTATGCA
1 AACCC-CATGTTATATAGTATGACATAGTATGCG
* * *
2197198 AACTCCCATGTTACATAGAATGACATAGTATACG
1 AAC-CCCATGTTATATAGTATGACATAGTATGCG
* * *
2197232 AGCCCTCATGTTATATAGTATGACAAAGTATGTG
1 AACCC-CATGTTATATAGTATGACATAGTATGCG
2197266 AACCCCAATGTTATATAGTATGACATAGTATGCG
1 AACCCC-ATGTTATATAGTATGACATAGTATGCG
** *
2197300 AACACCCACATTATATAGTATGACATAGTATGTG
1 AAC-CCCATGTTATATAGTATGACATAGTATGCG
2197334 AACC
1 AACC
2197338 TGATCTTCCA
Statistics
Matches: 290, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
32 26 0.09
33 23 0.08
34 227 0.78
35 14 0.05
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (33 bp):
AACCCCATGTTATATAGTATGACATAGTATGCG
Found at i:2198858 original size:34 final size:34
Alignment explanation
Indices: 2198808--2198890 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
2198798 TCAGGACCCT
** **
2198808 ATGTTATATAAAATGACATTATATGCGAA-CCATC
1 ATGTTATATAGTATGACACAATATGCGAATCC-TC
*
2198842 ATGTTATATAGTATGACACAATATGTGAATCCTC
1 ATGTTATATAGTATGACACAATATGCGAATCCTC
*
2198876 ATCTTATATAGTATG
1 ATGTTATATAGTATG
2198891 TGATTTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 40 0.95
35 2 0.05
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (34 bp):
ATGTTATATAGTATGACACAATATGCGAATCCTC
Found at i:2198918 original size:15 final size:15
Alignment explanation
Indices: 2198898--2198963 Score: 87
Period size: 15 Copynumber: 4.4 Consensus size: 15
2198888 ATGTGATTTA
2198898 ATATGTGCAAACCCT
1 ATATGTGCAAACCCT
* *
2198913 ATATGTACAAACCTT
1 ATATGTGCAAACCCT
* *
2198928 ATATGTGCGAACCTT
1 ATATGTGCAAACCCT
*
2198943 TTATGTGCAAACCCT
1 ATATGTGCAAACCCT
2198958 ATATGT
1 ATATGT
2198964 AAACTTGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (15 bp):
ATATGTGCAAACCCT
Found at i:2204950 original size:5 final size:5
Alignment explanation
Indices: 2204940--2204968 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2204930 CTTATACTTG
2204940 CTATA CTATA CTATA CTATA CTATA CTAT
1 CTATA CTATA CTATA CTATA CTATA CTAT
2204969 TCCTTGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:2207244 original size:7 final size:6
Alignment explanation
Indices: 2207210--2207243 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2207200 TCCTTAGTTC
2207210 TTTTC- TTTTCTT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTT
2207244 TTATTATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:2208432 original size:22 final size:23
Alignment explanation
Indices: 2208381--2208432 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
2208371 TCTTAAGCTT
*
2208381 TATTTT-CATGGTTGCCTTAGTTT
1 TATTTTCCATGGTTG-CTTAGTTG
2208404 TCA-TTTCCATGGTTG-TTAGTTG
1 T-ATTTTCCATGGTTGCTTAGTTG
2208426 TATTTTC
1 TATTTTC
2208433 AGTATGGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 11 0.44
23 4 0.16
24 9 0.36
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.56
Consensus pattern (23 bp):
TATTTTCCATGGTTGCTTAGTTG
Found at i:2210773 original size:40 final size:40
Alignment explanation
Indices: 2210591--2210813 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
2210581 TCCTCGTTCA
* * * * *
2210591 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2210630 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2210670 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2210710 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
2210750 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2210790 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2210814 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2210822 original size:41 final size:41
Alignment explanation
Indices: 2210745--2210822 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2210735 TTAGTATCTC
* * *
2210745 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2210786 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2210823 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2218665 original size:40 final size:40
Alignment explanation
Indices: 2218483--2218705 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
2218473 TCCTCGTTCA
* * * * *
2218483 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2218522 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
2218562 AATGCCTTCGGGACTTAACCCGAATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2218602 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
2218642 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2218682 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2218706 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2218714 original size:41 final size:41
Alignment explanation
Indices: 2218637--2218714 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2218627 TTAGTATCTC
* * *
2218637 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2218678 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2218715 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2226379 original size:23 final size:22
Alignment explanation
Indices: 2226348--2226390 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2226338 TTGTGAATCA
* *
2226348 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGCATGA-TTTGGCT
2226371 TATGATTTGGCATGATTTGG
1 TATGATTTGGCATGATTTGG
2226391 TATGGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.16, C:0.07, G:0.28, T:0.49
Consensus pattern (22 bp):
TATGATTTGGCATGATTTGGCT
Found at i:2233268 original size:42 final size:43
Alignment explanation
Indices: 2233207--2233311 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
2233197 GATTTGAGGT
* *
2233207 TTACGTGTAAGACCATGTCTGGGAC-G-TCAGTATC-ATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGTTC--CATCAATATTTGA
* *
2233249 TTTCATGTAAGACCCTGTCTGGGACAGTTCCATCAATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGTTCCATCAATATTTGA
*
2233292 TTACATGTAAGACCACGTCT
1 TTACATGTAAGACCATGTCT
2233312 AGGATGTTGC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
42 25 0.47
43 26 0.49
44 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGGACAGTTCCATCAATATTTGA
Found at i:2234072 original size:23 final size:22
Alignment explanation
Indices: 2234041--2234083 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2234031 TTGTGAATCA
* *
2234041 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGCATGA-TTTGGCT
2234064 TATGATTTGGCATGATTTGG
1 TATGATTTGGCATGATTTGG
2234084 TATGGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.16, C:0.07, G:0.28, T:0.49
Consensus pattern (22 bp):
TATGATTTGGCATGATTTGGCT
Found at i:2237578 original size:5 final size:5
Alignment explanation
Indices: 2237568--2237599 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2237558 ATAGAGACTA
*
2237568 AATAG AATAG AATAG AATAA AATAG AATAG AA
1 AATAG AATAG AATAG AATAG AATAG AATAG AA
2237600 AGTTGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (5 bp):
AATAG
Found at i:2240988 original size:48 final size:47
Alignment explanation
Indices: 2240885--2241012 Score: 143
Period size: 48 Copynumber: 2.6 Consensus size: 47
2240875 AAATAAAGTA
* *
2240885 CCAATGCCATGTCCCAGACATGGTCTTTC-ATGAATCCACATATCTTCG
1 CCAATGCCATGTCCCAGACATGGTCTTACAATG-A-CCACATATATTCG
* *
2240933 CCAATGCCATGTCCCAGACATGGTCTTACAATG-GCACATATATAATTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAATGACCACATATAT--TCG
*
2240981 CCGATGCCATGTCCCGCAGACATGGTCTTACA
1 CCAATGCCATGT-CC-CAGACATGGTCTTACA
2241013 CTGTAATAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
46 8 0.11
48 41 0.59
49 5 0.07
50 16 0.23
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (47 bp):
CCAATGCCATGTCCCAGACATGGTCTTACAATGACCACATATATTCG
Found at i:2242664 original size:68 final size:67
Alignment explanation
Indices: 2242592--2242777 Score: 177
Period size: 67 Copynumber: 2.8 Consensus size: 67
2242582 CATCATGTGT
* * *
2242592 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACC
2242654 ATGTAG
62 ATGTAG
** * * *
2242660 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCATGT
2242725 AG
66 AG
* * *
2242727 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGG-TACTAAGTG
1 ACAAGAGAGCTACGACATATA-TGTAGCTAGGTCGCATGGGTGGATAC-AAGTG
2242778 TTCACCATGT
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
64 20 0.20
65 9 0.09
66 25 0.25
67 31 0.31
68 15 0.15
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:2242697 original size:64 final size:64
Alignment explanation
Indices: 2242616--2242799 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
2242606 AGACATTATG
* *
2242616 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
2242680 ATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
2242745 AA
63 AA
* * * *
2242747 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
2242800 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:2244654 original size:48 final size:48
Alignment explanation
Indices: 2244580--2244884 Score: 423
Period size: 48 Copynumber: 6.4 Consensus size: 48
2244570 GAGTGTTACA
* * * *
2244580 TACACAGGCACATATATCGTCGCCGATGCAATGTCCCAGACATGCTCT
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
* * * *
2244628 TACATAGGCACATATATTATCACCGATGCCATGTCCCAGGCATAGTCT
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
* * *
2244676 TACACAGGCACATATATCATCGCTGATGCCATGTCCCAGACTTGGTCT
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
* *
2244724 CACACAGGTACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
* * *
2244772 CACACAAGCACATATATCATCACCAATGCCATGTCCCAGACATGGTCT
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
* * *
2244820 TACACAGGCACATCTATCATCACCGATGCCATGCCCCA-ATCATGGTCA
1 TACACAGGCACATATATCATCACCGATGCCATGTCCCAGA-CATGGTCT
2244868 TACACAGGCACATATAT
1 TACACAGGCACATATAT
2244885 TGTAACAACC
Statistics
Matches: 226, Mismatches: 30, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
47 1 0.00
48 225 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (48 bp):
TACACAGGCACATATATCATCACCGATGCCATGTCCCAGACATGGTCT
Found at i:2256246 original size:55 final size:54
Alignment explanation
Indices: 2256159--2256413 Score: 251
Period size: 55 Copynumber: 4.8 Consensus size: 54
2256149 ATTAGGGTTT
* *
2256159 AAGGATACCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
2256214 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
2256269 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
* *
2256322 AAGGATACCATGTAAGACAATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * * *
2256371 AAGGATACCACGTAAGACCATGACAAGTCATGG-AAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
2256414 GTACCCGTGT
Statistics
Matches: 168, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
48 2 0.01
49 36 0.21
52 7 0.04
53 40 0.24
54 12 0.07
55 67 0.40
56 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:2256365 original size:108 final size:110
Alignment explanation
Indices: 2256166--2256366 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
2256156 TTTAAGGATA
*
2256166 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* *
2256231 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CAATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
2256276 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
2256338 ACAATGTCAAGACATGGCAATGGTAAGTT
65 ACAATGTCAAGACATGGCAATGATAAGTT
2256367 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CAATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:2256479 original size:5 final size:5
Alignment explanation
Indices: 2256471--2256499 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2256461 AATAGAATAT
2256471 TAAGG TAAGG TAAGG TAAGG TAAGG TAAG
1 TAAGG TAAGG TAAGG TAAGG TAAGG TAAG
2256500 ACGAGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (5 bp):
TAAGG
Done.