Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 136 of 221
Found at i:41915730 original size:112 final size:111
Alignment explanation
Indices: 41915472--41915796 Score: 421
Period size: 112 Copynumber: 3.0 Consensus size: 111
41915462 AAAATTCAAG
* * * * *
41915472 AGGATATTTGGCAATATGGTTAAACGAG--AAATCGAAACCCAGCACATTA-GGACACG-TTCCT
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGA-ACGTTTTCT
* * **
41915533 TGAATTTCCAAACGCAAAACATTACCTTATTTTGAAA--TTTTTGGA
65 CGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAA
*
41915578 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
41915643 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTT-AAA
* *
41915690 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
* * * ** *
41915755 GAATTTTCAAAAGC-TAATGTTGCCTTATTTAGAAATTTTTTT
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTT
41915797 TGAAGTATGG
Statistics
Matches: 193, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
106 24 0.12
108 24 0.12
109 41 0.21
111 29 0.15
112 75 0.39
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (111 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAA
Found at i:41915854 original size:20 final size:20
Alignment explanation
Indices: 41915818--41915855 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41915808 GTTAATATAC
*
41915818 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
41915838 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
41915856 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:41915930 original size:4 final size:4
Alignment explanation
Indices: 41915923--41915954 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
41915913 ACAAACAAAC
41915923 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
41915955 ACATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41915986 original size:12 final size:12
Alignment explanation
Indices: 41915923--41915988 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
41915913 ACAAACAAAC
*
41915923 AAATAAATAAAT
1 AAATAAATACAT
*
41915935 AAATAAATAAAT
1 AAATAAATACAT
41915947 AAACTAAA-ACAT
1 AAA-TAAATACAT
*
41915959 AAA-AAAGGACATAT
1 AAATAAA-TAC--AT
41915973 AAATAAATACAT
1 AAATAAATACAT
41915985 AAAT
1 AAAT
41915989 GAACATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 3 0.07
12 29 0.63
13 4 0.09
14 7 0.15
15 3 0.07
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (12 bp):
AAATAAATACAT
Found at i:41916142 original size:17 final size:18
Alignment explanation
Indices: 41916122--41916155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41916112 TATATGTTTT
41916122 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
41916139 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
41916156 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:41916163 original size:84 final size:88
Alignment explanation
Indices: 41916075--41916244 Score: 233
Period size: 90 Copynumber: 2.0 Consensus size: 88
41916065 ATATATATGT
*
41916075 ATGTATATACATAAAATTATAAAAATAT-G-AAAATA-TATATATG-TTTTAAGGA-TATTAAAT
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAA-AATTATTAAAT
41916135 ATAAAAGGTTATGTAAATATATAC
65 ATAAAAGGTTATGTAAATATATAC
* * *
41916159 ATGTATATATATATAATTATGAAAATATGGAAAAATATGTATATATGTATTTTAAAATTATTAAA
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATA-GTATATATG-ATTTTAAAATTATTAAA
*
41916224 TATAAAAGTTTATGTAAATAT
64 TATAAAAGGTTATGTAAATAT
41916245 GTATATGCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
84 25 0.34
85 1 0.01
86 6 0.08
88 8 0.11
89 1 0.01
90 33 0.45
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (88 bp):
ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAAAATTATTAAATA
TAAAAGGTTATGTAAATATATAC
Found at i:41917348 original size:12 final size:12
Alignment explanation
Indices: 41917309--41917349 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
41917299 TGCAGGTGCA
*
41917309 GGTGGCAGAGTT
1 GGTGGCTGAGTT
*
41917321 GGTAGCTGAGTT
1 GGTGGCTGAGTT
41917333 GGTGGCTGAGTT
1 GGTGGCTGAGTT
41917345 GGTGG
1 GGTGG
41917350 TGGCAGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.07, G:0.51, T:0.29
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:41918062 original size:98 final size:98
Alignment explanation
Indices: 41917893--41918188 Score: 472
Period size: 98 Copynumber: 3.0 Consensus size: 98
41917883 GAGATAAGAC
* * *
41917893 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT--TTGTGATTTTAATCCACTCCAC
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTT-T-ATTTTAATCCACTCCAC
* * * *
41917956 TGCAACTTCAGGGAGATAGGATTA-TCGGCTTCAAT
64 TGTAACTTCAGAGAGTTAGGATTACT-AGCTTCAAT
*
41917991 CTGATGTGATCTATTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
41918056 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
66 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
41918089 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
41918154 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
66 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
41918187 CT
1 CT
41918189 ACTCTATGGT
Statistics
Matches: 186, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
98 182 0.98
99 2 0.01
100 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (98 bp):
CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
Found at i:41918373 original size:131 final size:128
Alignment explanation
Indices: 41918181--41918654 Score: 433
Period size: 131 Copynumber: 3.6 Consensus size: 128
41918171 GATTACTAGC
* * *** * *
41918181 TTCAATCTACTCTA-TGGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTA
1 TTCAATCTACTCTACT-GTAACT-TCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTA
* *
41918244 ACCTCAGGGAGATAAGATCTGAAATTCTTCTGTCTACTCCACTGTAACCTCAGGGAGATAAGACC
64 ACTTCAGGGAGATAAGAT-T--AATTCTT-TGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
41918309 T-GA
125 TGGA
* * *
41918312 TTCAATCTACTCTGCTGTAACTTCAGAGAGATGAGATCCT-TTATTTTAATCCGCTCAACTGTAA
1 TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATTATTTTAATCCGCTCCACTGTAA
* * * *
41918376 CTTCAGGGAGATAGGA-TAGTGTCTTGGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
65 CTTCAGGGAGATAAGATTAAT-TCTTTG-TCTGCTCCACTGTAACCTCAGGGAGATAAGA-C-CT
*
41918440 GGC
126 GGA
* * * * * ** *
41918443 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAC
1 TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAAC
* * * * *
41918508 TTCAGGAAGAGATATGATTACTTCTTTCGTCTGCTCCACTGCAACTTCAGGAAGATAAGA-CTGG
66 TTCAGG--GAGATAAGATTAATTCTTT-GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGG
41918572 A
128 A
* * * * *
41918573 TACGATCTACTCTACTGCT-ACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCTCTGCAA
1 TTCAATCTACTCTACTG-TAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAA
*
41918637 CTTCAGGGA-ATAGGATTA
65 CTTCAGGGAGATAAGATTA
41918655 TCTGCTTCAA
Statistics
Matches: 283, Mismatches: 46, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
127 11 0.04
128 35 0.12
129 2 0.01
130 66 0.23
131 122 0.43
132 4 0.01
133 39 0.14
134 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (128 bp):
TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAAC
TTCAGGGAGATAAGATTAATTCTTTGTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGGA
Found at i:41918417 original size:43 final size:44
Alignment explanation
Indices: 41918110--41918567 Score: 269
Period size: 44 Copynumber: 10.4 Consensus size: 44
41918100 TACTCTATTA
* * * * **
41918110 TAACTTCAGAGAGATAAGATC-CTTTATTTTAATCCACTCCACTG
1 TAACTTCAGGGAGATAAGATCACTGT-CTTCAATCTGCTCCACTG
* * * * * *
41918154 TAACTTCAGAGAGTTAGGATTACTAG-CTTCAATCTACTCTA-TGG
1 TAACTTCAGGGAGATAAGATCACT-GTCTTCAATCTGCTCCACT-G
* *
41918198 TAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
1 TAACT-TCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* * ** *
41918242 TAACCTCAGGGAGATAAGATCTGAAAT-TCTTCTGTCTACTCCACTG
1 TAACTTCAGGGAGATAAGATC---ACTGTCTTCAATCTGCTCCACTG
* * * **
41918288 TAACCTCAGGGAGATAAGA-C-CTG-ATTCAATCTACTCTGCTG
1 TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* * * * * * *
41918329 TAACTTCAGAGAGATGAGATC-CTTTATTTTAATCCGCTCAACTG
1 TAACTTCAGGGAGATAAGATCACTGT-CTTCAATCTGCTCCACTG
* * **
41918373 TAACTTCAGGGAGATAGGAT-AGTGTCTTGGATCTGCTCCACTG
1 TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* *
41918416 TAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
1 TAACT-TCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* ** * *
41918460 TAACCTCAGGGAGATAAGATCTGTGGT-TTTAATCCGCTCCACTG
1 TAACTTCAGGGAGATAAGATCACT-GTCTTCAATCTGCTCCACTG
* * * *
41918504 CAACTTCAGGAAGAGATATGATTACT-TCTTTC-GTCTGCTCCACTG
1 TAACTTCAGG--GAGATAAGATCACTGTC-TTCAATCTGCTCCACTG
* *
41918549 CAACTTCAGGAAGATAAGA
1 TAACTTCAGGGAGATAAGA
41918568 CTGGATACGA
Statistics
Matches: 321, Mismatches: 70, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
41 30 0.09
42 4 0.01
43 40 0.12
44 174 0.54
45 26 0.08
46 46 0.14
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
Found at i:41924829 original size:112 final size:109
Alignment explanation
Indices: 41924579--41924872 Score: 409
Period size: 112 Copynumber: 2.7 Consensus size: 109
41924569 AAAATTCAAG
* * * * *
41924579 AGGATATTTGGCAATATGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGACACGTTCCTT-
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTT--TTC
**
41924641 A--AATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTGGA
64 ACGAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTAAA
41924685 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
* *
41924750 GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
66 GAATTTCCAAACGCAAAACATTACCTTATTTTG-AA-ATTTTT-AAA
*
41924797 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
*
41924862 GAATTTTCAAA
66 GAATTTCCAAA
41924873 AGCTAATGTT
Statistics
Matches: 169, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
106 26 0.15
107 1 0.01
108 29 0.17
109 30 0.18
110 2 0.01
111 6 0.04
112 75 0.44
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
GAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTAAA
Found at i:41924961 original size:20 final size:20
Alignment explanation
Indices: 41924925--41924962 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41924915 GTTAATATAC
*
41924925 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
41924945 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
41924963 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:41925112 original size:22 final size:21
Alignment explanation
Indices: 41925063--41925112 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
41925053 AGGACATATA
* *
41925063 AATAAATACATAAATGAACAT
1 AATAAAAACATAAATGAAAAT
*
41925084 AAAAAAAACAATAAATGAAAAT
1 AATAAAAAC-ATAAATGAAAAT
*
41925106 TATAAAA
1 AATAAAA
41925113 TATGAACATG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (21 bp):
AATAAAAACATAAATGAAAAT
Found at i:41925220 original size:17 final size:18
Alignment explanation
Indices: 41925200--41925233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41925190 TATATGTTTT
41925200 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
41925217 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
41925234 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:41925400 original size:29 final size:29
Alignment explanation
Indices: 41925333--41925421 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
41925323 GTATATGCAC
* * *
41925333 GTATATGTATACAAAATGTATATAAAAAT
1 GTATATATATAAAAAATATATATAAAAAT
* **
41925362 -TATAAAATATAAAAAATATATATAAGTAT
1 GTAT-ATATATAAAAAATATATATAAAAAT
*
41925391 GTATATATATAAATAAATAAATTATAAAAAT
1 GTATATATATAAA-AAATATA-TATAAAAAT
41925422 ATGAACGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 3 0.07
29 27 0.59
30 9 0.20
31 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (29 bp):
GTATATATATAAAAAATATATATAAAAAT
Found at i:41925897 original size:30 final size:30
Alignment explanation
Indices: 41925861--41925919 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41925851 GGCCCATTTT
41925861 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAG
*
41925891 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAA
41925920 TTAAAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAG
Found at i:41925900 original size:11 final size:10
Alignment explanation
Indices: 41925861--41925912 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
41925851 GGCCCATTTT
41925861 TATTTTAAAA
1 TATTTTAAAA
41925871 -ATTTTAAAA
1 TATTTTAAAA
* **
41925880 AATTAAAAAA
1 TATTTTAAAA
41925890 GTATTTTAAAAA
1 -TATTTT-AAAA
41925902 TATTTTAAAA
1 TATTTTAAAA
41925912 T
1 T
41925913 TAAAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.26
10 12 0.35
11 9 0.26
12 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:41925921 original size:38 final size:38
Alignment explanation
Indices: 41925874--41925957 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
41925864 TTTAAAAATT
* *
41925874 TTAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
41925912 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
41925950 TTAAAAAA
1 TTAAAAAA
41925958 AAAAATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (38 bp):
TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
Found at i:41926804 original size:12 final size:12
Alignment explanation
Indices: 41926773--41926813 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
41926763 TGCACGTACA
* *
41926773 GGTGGCAGATTT
1 GGTGGCTGAGTT
*
41926785 GGTAGCTGAGTT
1 GGTGGCTGAGTT
41926797 GGTGGCTGAGTT
1 GGTGGCTGAGTT
41926809 GGTGG
1 GGTGG
41926814 TGGCAGAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.49, T:0.32
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:41928021 original size:2 final size:2
Alignment explanation
Indices: 41928014--41928039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41928004 CCTACTATGC
41928014 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41928040 CTCAACCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41932291 original size:29 final size:29
Alignment explanation
Indices: 41932258--41932316 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41932248 ACTACTATGC
41932258 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
41932287 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
41932316 A
1 A
41932317 CGTAAGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
AAGTAGTATCAGCTATCACCACTAATGTA
Found at i:41932344 original size:29 final size:29
Alignment explanation
Indices: 41932312--41932369 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41932302 TCACCACTAA
41932312 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
41932341 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
41932370 AGTAGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (29 bp):
TGTAACGTAAGCAAGGTAAGTCTTAGTAC
Found at i:41936026 original size:34 final size:35
Alignment explanation
Indices: 41935986--41936054 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
41935976 CCTTCTTCAC
41935986 CCCTGCCCT-AAAATCACATTATTATAATAAGTCA
1 CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
***
41936020 CCCTGCCCTAAAAATTTTATTATTATAATAAGTCA
1 CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
41936055 AGTTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (35 bp):
CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
Found at i:41945593 original size:23 final size:24
Alignment explanation
Indices: 41945548--41945593 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
41945538 AAAAAAAGAA
* *
41945548 ACATTTGTATTTTTCAATTCTCAC
1 ACATTTGTATTTCTCAATACTCAC
41945572 ACATTTGT-TTTCTCAATACTCA
1 ACATTTGTATTTCTCAATACTCA
41945594 TATGTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (24 bp):
ACATTTGTATTTCTCAATACTCAC
Found at i:41946031 original size:21 final size:21
Alignment explanation
Indices: 41946005--41946116 Score: 81
Period size: 21 Copynumber: 5.5 Consensus size: 21
41945995 ATTTTTGGTA
41946005 AGTTGGGGCAGCTTGTTGATG
1 AGTTGGGGCAGCTTGTTGATG
*
41946026 AGTTGGGGCAGCTTG-TAACTG
1 AGTTGGGGCAGCTTGTTGA-TG
* *
41946047 AGTTAGGGCAGCCTG-T--TG
1 AGTTGGGGCAGCTTGTTGATG
* * *
41946065 AGTTGGGGTA-CTCTCTTGCTG
1 AGTTGGGGCAGCT-TGTTGATG
* * * *
41946086 ATTTGGGGTAGCCTGTTGCTG
1 AGTTGGGGCAGCTTGTTGATG
41946107 AGTTGGGGCA
1 AGTTGGGGCA
41946117 ACCACTTGGT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.01
18 11 0.15
19 1 0.01
20 2 0.03
21 57 0.78
22 1 0.01
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.32
Consensus pattern (21 bp):
AGTTGGGGCAGCTTGTTGATG
Found at i:41946866 original size:26 final size:25
Alignment explanation
Indices: 41946819--41946867 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
41946809 ACATGCATAT
**
41946819 TATTAAAAAATACTTATTGCATGCA
1 TATTAAAAAATACTTACAGCATGCA
*
41946844 TATTAAAAAATAGTTAACAGCATG
1 TATTAAAAAATACTT-ACAGCATG
41946868 TGACCATCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (25 bp):
TATTAAAAAATACTTACAGCATGCA
Found at i:41946932 original size:136 final size:135
Alignment explanation
Indices: 41946778--41947090 Score: 495
Period size: 136 Copynumber: 2.3 Consensus size: 135
41946768 ATCACACACA
* * *
41946778 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTATTAAAAAA-TACTTATTGCATG
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTA-CAAAAAATTACTCACTGCATG
* * *
41946842 CATATTAAAAAATAGTTAACAGCATGTGACCATCCCCACCAACAATTACTGCATGCATATTAAAA
65 CATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAA
41946907 AAACAGT
130 AAA-AGT
* * *
41946914 CACACACACACACTCCTAAATAATAATCACTACATGCATATTACAAAAAATTACTCACTGCATGC
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATGC
41946979 ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
66 ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
41947044 AAAGT
131 AAAGT
* *
41947049 CACACACACACACACCTAAAAAA-AGTCACTGCATACATATTA
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTA
41947091 AATAGTTATA
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 16 0.10
135 30 0.19
136 116 0.72
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (135 bp):
CACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATGC
ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
AAAGT
Found at i:41949112 original size:62 final size:62
Alignment explanation
Indices: 41948981--41949118 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 62
41948971 CCATTTCTGT
*
41948981 CAGACAATAACCAATACAAAAATAATTTAATACAAACGCAACCATTTAAGTCATGCACATGG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* * ** *
41949043 CAAACAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTCTGTCATGCACATTG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* *
41949105 TAGACAATAGCCAA
1 CAGACAATAACCAA
41949119 ACACTTTAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
Found at i:41949432 original size:16 final size:17
Alignment explanation
Indices: 41949413--41949448 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
41949403 ATAAAAATTG
41949413 AAATAACCCTAAAT-CA
1 AAATAACCCTAAATCCA
41949429 AAATAACCCTAAATCCA
1 AAATAACCCTAAATCCA
41949446 AAA
1 AAA
41949449 AATACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAACCCTAAATCCA
Found at i:41949449 original size:40 final size:39
Alignment explanation
Indices: 41949366--41949442 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
41949356 AATAAAACCC
**
41949366 AAAATTGAAATAACCCTAAATCAAAATCAAAGTCAAAATA
1 AAAATTGAAATAACCCTAAATCAAAAT-AAACCCAAAATA
*
41949406 AAAATTGAAATAACCCTAAATCAAAAT-AACCCTAAAT
1 AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAAT
41949443 CCAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 7 0.21
40 27 0.79
ACGTcount: A:0.58, C:0.17, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAATA
Found at i:41949884 original size:21 final size:21
Alignment explanation
Indices: 41949858--41949898 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41949848 CAACATCGTA
* *
41949858 AGTTAACTTTCCATATCAGCT
1 AGTTAACTTGCCACATCAGCT
41949879 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
41949899 AGTCCCGTTA
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:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:41949975 original size:30 final size:30
Alignment explanation
Indices: 41949935--41950000 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
41949925 TATTAATCAA
* *
41949935 TGACTATTTTGTCACTTTT-TATAACGTT-AG
1 TGACTGTTTTGTAACTTTTCTA-AA-GTTGAG
41949965 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
1 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
41949995 TGACTG
1 TGACTG
41950001 AAATGAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.09
30 27 0.84
31 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (30 bp):
TGACTGTTTTGTAACTTTTCTAAAGTTGAG
Found at i:41950676 original size:29 final size:31
Alignment explanation
Indices: 41950644--41950707 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
41950634 TTAATTTTAT
*
41950644 TATTAAATTT-AAA-TAAAATAATGTATTTC
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
* *
41950673 TATT--TTTTAAAAGGAAAATAATGTATTTT
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
41950702 TATTAA
1 TATTAA
41950708 TAACCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.11
28 3 0.11
29 22 0.79
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTAAATTTAAAAGGAAAATAATGTATTTC
Found at i:41953599 original size:22 final size:22
Alignment explanation
Indices: 41953560--41953601 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41953550 AGATCAACAC
41953560 AAATATAATCACATACATATTA
1 AAATATAATCACATACATATTA
*
41953582 AAATATCAATCTCA-ACATAT
1 AAATAT-AATCACATACATAT
41953602 CAATCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAATCACATACATATTA
Found at i:41958107 original size:3 final size:3
Alignment explanation
Indices: 41958101--41958126 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41958091 CCACCACCAT
41958101 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
41958127 TGCTCTCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:41966833 original size:42 final size:42
Alignment explanation
Indices: 41966780--41966897 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
41966770 TGATATGAGT
* *
41966780 TTCAGATTAACCCTTTTGGGTTTCAGTTTAGCTCTT-TTGAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTT-AGC
* ** * * * *
41966822 TTTAGTTTAACCCTAATGGGCTTCAATTTAGCTATTCTTAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
* *
41966864 TTCAAATTAACCCTTATGGGTTTCCGTTCAGCTC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTC
41966898 CAATGAGCTT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
42 57 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
Found at i:41966950 original size:42 final size:42
Alignment explanation
Indices: 41966872--41966975 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 42
41966862 GCTTCAAATT
* * * * *
41966872 AACCCTTATGGGTTTCCGTTCAGCTCCAATGAGCTTCCGTTC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
** * *
41966914 AACCCTTACGGGTTTCTGTTTAGCACTTATGTGCTTCTGTGC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
* *
41966956 -AGCCTT-CGGGCTTCTGTTTA
1 AACCCTTACGGGTTTCTGTTTA
41966976 CGATGTACTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 13 0.25
41 5 0.10
42 33 0.65
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (42 bp):
AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
Found at i:41977823 original size:19 final size:18
Alignment explanation
Indices: 41977799--41977834 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41977789 GCAAATGGAT
*
41977799 CATTTCTCATTTTCATTTC
1 CATTTCT-ATTTCCATTTC
41977818 CATTTCTATTTCCATTT
1 CATTTCTATTTCCATTT
41977835 TTTTAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (18 bp):
CATTTCTATTTCCATTTC
Found at i:41977828 original size:12 final size:12
Alignment explanation
Indices: 41977798--41977835 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
41977788 TGCAAATGGA
41977798 TCATTTCTCATTT
1 TCATTTC-CATTT
41977811 TCATTTCCA-TT
1 TCATTTCCATTT
41977822 TCTATTTCCATTT
1 TC-ATTTCCATTT
41977835 T
1 T
41977836 TTTAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 9 0.39
13 10 0.43
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:41984020 original size:33 final size:33
Alignment explanation
Indices: 41983978--41984045 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
41983968 TATTGACGTA
41983978 AATGATGACATGATCTTTTTTAATTGGTATAAT
1 AATGATGACATGATCTTTTTTAATTGGTATAAT
41984011 AATGATGACATGATCTTTTTTAATTGGTATAAT
1 AATGATGACATGATCTTTTTTAATTGGTATAAT
41984044 AA
1 AA
41984046 CACATTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (33 bp):
AATGATGACATGATCTTTTTTAATTGGTATAAT
Found at i:41985770 original size:14 final size:15
Alignment explanation
Indices: 41985753--41985785 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41985743 TCAAAACATC
*
41985753 AAAATCAATTAA-AT
1 AAAATCAAATAATAT
41985767 AAAATCAAATAATAT
1 AAAATCAAATAATAT
41985782 AAAA
1 AAAA
41985786 AATGGAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATCAAATAATAT
Found at i:41987415 original size:21 final size:22
Alignment explanation
Indices: 41987361--41987415 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
41987351 ATATTCTGAG
41987361 TTGACATTAT-TTCATATGAAAT
1 TTGA-ATTATATTCATATGAAAT
*
41987383 TT-AATTATTATT-ATATGATAT
1 TTGAATTA-TATTCATATGAAAT
41987404 TTGAATTATATT
1 TTGAATTATATT
41987416 TTGAGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGAATTATATTCATATGAAAT
Found at i:41987974 original size:20 final size:20
Alignment explanation
Indices: 41987951--41987989 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41987941 CTTAAATTAA
*
41987951 TTTTCTTTTAAATTTTAAAT
1 TTTTATTTTAAATTTTAAAT
*
41987971 TTTTATTTTATATTTTAAA
1 TTTTATTTTAAATTTTAAA
41987990 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTTTAAATTTTAAAT
Found at i:41988013 original size:19 final size:18
Alignment explanation
Indices: 41987987--41988022 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41987977 TTTATATTTT
*
41987987 AAAATTATTTTTAATAAA
1 AAAATTATATTTAATAAA
41988005 AAAATTTATATTTAATAA
1 AAAA-TTATATTTAATAA
41988023 TTATCTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTATATTTAATAAA
Found at i:41990311 original size:49 final size:49
Alignment explanation
Indices: 41990238--41990390 Score: 162
Period size: 49 Copynumber: 3.1 Consensus size: 49
41990228 AAGCTAGCCC
* * * *
41990238 GTGTTGTCCACACAGTCTACCCACATGGTTTGCACGATTTCACACAGTT
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
* * * **
41990287 GTGTGGTCTACACGGGCTACCCACACGGTCTGCACGATTTCAGACAGCC
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
* ** * * * *
41990336 GTGTGGTCCACATGGTTTACCTACATGGTCTGTATGATTTCACACGGTT
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
41990385 GTGTGG
1 GTGTGG
41990391 CACTGGGCAG
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 83 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (49 bp):
GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
Found at i:41997488 original size:36 final size:36
Alignment explanation
Indices: 41997444--41997515 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
41997434 AGCATAACTT
*
41997444 CACATCTTGGATTTCATTATCTC-AGTTTTCTTATCA
1 CACATCTTGGATTTCATTATCTCGA-TTTTCATATCA
41997480 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
1 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
41997516 TTCTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (36 bp):
CACATCTTGGATTTCATTATCTCGATTTTCATATCA
Found at i:41998661 original size:13 final size:13
Alignment explanation
Indices: 41998643--41998668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41998633 TTGGATCCGT
41998643 ACCAAAACAATCA
1 ACCAAAACAATCA
41998656 ACCAAAACAATCA
1 ACCAAAACAATCA
41998669 TGAAACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:42010172 original size:42 final size:42
Alignment explanation
Indices: 42010059--42010177 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
42010049 AAGAAAGCTC
* * * ***
42010059 ATACAATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAAACATGGTCTTACACAAAATCAA
* * * *
42010101 ATAATGATGCCACTGTCCCATAA-AAGGTCTTACACAAAATCAT
1 AT-ACGATGCCAATGTCCCA-AACATGGTCTTACACAAAATCAA
42010144 ATACGATGCCAATGTCCCAAACATGGTCTTACAC
1 ATACGATGCCAATGTCCCAAACATGGTCTTACAC
42010178 GTAAATCTCA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.03
42 28 0.46
43 29 0.48
44 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAAACATGGTCTTACACAAAATCAA
Found at i:42011336 original size:15 final size:13
Alignment explanation
Indices: 42011303--42011327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42011293 ACAAACGACA
42011303 AAATTTTCACACG
1 AAATTTTCACACG
42011316 AAATTTTCACAC
1 AAATTTTCACAC
42011328 ATATAATTTG
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:42021280 original size:49 final size:49
Alignment explanation
Indices: 42021222--42021380 Score: 141
Period size: 49 Copynumber: 3.2 Consensus size: 49
42021212 ATAATAAATA
* *
42021222 TTTTT-ATTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATATATT
1 TTTTTAATTTTTTTATTTTTATAATTTTAAAATACTTTTTAAATATATT
* * *
42021270 TTTTTAATTTTTTTAATTTTAAAATTTTTTTAAAAT--TTTTTAAA-ATACT
1 TTTTTAATTTTTTTATTTTTATAA---TTTTAAAATACTTTTTAAATATATT
* * * *
42021319 TTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAT-T-TT
1 TTTTTAATTTTTTTATTTT--TATAATTTTAAAATACTTTTTAAATATATT
42021368 TGTTTTAATTTTT
1 T-TTTTAATTTTT
42021381 AAAATAAATT
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
48 14 0.16
49 38 0.43
50 26 0.29
51 2 0.02
52 9 0.10
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (49 bp):
TTTTTAATTTTTTTATTTTTATAATTTTAAAATACTTTTTAAATATATT
Found at i:42021281 original size:9 final size:9
Alignment explanation
Indices: 42021267--42021337 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
42021257 TTTAAAATAT
42021267 ATTTTTTTA
1 ATTTTTTTA
42021276 ATTTTTTTA
1 ATTTTTTTA
**
42021285 A-TTTTAAA
1 ATTTTTTTA
42021293 ATTTTTTTAAA
1 ATTTTTTT--A
*
42021304 ATTTTTTAAA
1 ATTTTTT-TA
42021314 ATACTTTTTTA
1 AT--TTTTTTA
42021325 A-TTTTTTA
1 ATTTTTTTA
42021333 ATTTT
1 ATTTT
42021338 AAAATATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 14 0.29
9 17 0.35
10 3 0.06
11 10 0.20
12 5 0.10
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:42021300 original size:11 final size:11
Alignment explanation
Indices: 42021286--42021363 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 11
42021276 ATTTTTTTAA
42021286 TTTTAAAATTT
1 TTTTAAAATTT
42021297 TTTTAAAA-TT
1 TTTTAAAATTT
42021307 TTTTAAAATACTT
1 TTTTAAAAT--TT
**
42021320 TTTTAATTTTTT
1 TTTTAA-AATTT
*
42021332 AATTTTAAAATAT
1 --TTTTAAAATTT
42021345 TTTTAAAATACTT
1 TTTTAAAAT--TT
42021358 TTTTAA
1 TTTTAA
42021364 TTTTTGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 10 0.19
11 17 0.32
12 2 0.04
13 17 0.32
14 7 0.13
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:42021312 original size:21 final size:20
Alignment explanation
Indices: 42021278--42021368 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
42021268 TTTTTTTAAT
42021278 TTTTTTAA--TTTTAAAAT-
1 TTTTTTAATTTTTTAAAATA
42021295 TTTTTTAAAATTTTTTAAAATA
1 TTTTTT--AATTTTTTAAAATA
42021317 CTTTTTTAATTTTTT---A-A
1 -TTTTTTAATTTTTTAAAATA
**
42021334 TTTTAAAATATTTTTAAAATA
1 TTTTTTAAT-TTTTTAAAATA
42021355 CTTTTTTAATTTTT
1 -TTTTTTAATTTTT
42021369 GTTTTAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
16 7 0.12
17 12 0.21
18 1 0.02
19 2 0.03
20 1 0.02
21 22 0.38
22 7 0.12
23 6 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTAATTTTTTAAAATA
Found at i:42021338 original size:37 final size:38
Alignment explanation
Indices: 42021297--42021368 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
42021287 TTTAAAATTT
42021297 TTTTAAAAT-TTTTTAAAATACTTTTTTAATTTTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTAA
42021334 TTTTAAAATATTTTTAAAATACTTTTTTAATTTTT
1 TTTTAAAATATTTTTAAAATACTTTTTTAATTTTT
42021369 GTTTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTAA
Found at i:42022262 original size:25 final size:25
Alignment explanation
Indices: 42022232--42022280 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42022222 TTTCAACTCT
42022232 TATGAGCTTA-CTGTTACTCAGCTCA
1 TATGAGCTTATC-GTTACTCAGCTCA
*
42022257 TATGAGCTTATCGTTATTCAGCTC
1 TATGAGCTTATCGTTACTCAGCTC
42022281 GGAAGAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (25 bp):
TATGAGCTTATCGTTACTCAGCTCA
Found at i:42022288 original size:25 final size:25
Alignment explanation
Indices: 42022260--42022317 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
42022250 CAGCTCATAT
* *
42022260 GAGCTTATCGTTATTCAGCTCGGAA
1 GAGCTTACCATTATTCAGCTCGGAA
* *
42022285 GAGCTTACCATTATTCAGCTTGGAG
1 GAGCTTACCATTATTCAGCTCGGAA
42022310 GAGCTTAC
1 GAGCTTAC
42022318 GGTTTATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (25 bp):
GAGCTTACCATTATTCAGCTCGGAA
Found at i:42027406 original size:20 final size:19
Alignment explanation
Indices: 42027373--42027420 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
42027363 TCGTATTCGT
* *
42027373 ATTTT-ATTTTATTTTTAT
1 ATTTTAATTTAATTTTTAC
42027391 ATTTTTAATTTAATTTTTAC
1 A-TTTTAATTTAATTTTTAC
42027411 ATTTTAATTT
1 ATTTTAATTT
42027421 TTCTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTTAATTTTTAC
Found at i:42027416 original size:14 final size:13
Alignment explanation
Indices: 42027379--42027422 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
42027369 TCGTATTTTA
*
42027379 TTTTATTTTTATAT
1 TTTTAATTTTA-AT
42027393 TTTTAA-TTTAAT
1 TTTTAATTTTAAT
42027405 TTTTACATTTTAAT
1 TTTTA-ATTTTAAT
42027419 TTTT
1 TTTT
42027423 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 5 0.19
14 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:42031270 original size:3 final size:3
Alignment explanation
Indices: 42031262--42031304 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
42031252 CCTATTCTTT
*
42031262 TTA TTA TTA TTA TTA TTA TT- TTCA TTA TTA TTTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA -TTA TTA TTA TTA
42031305 AATCTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:42033417 original size:50 final size:50
Alignment explanation
Indices: 42033225--42033416 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 50
42033215 ATTTGGGTAA
* *
42033225 AGAGGTCCCATGTAAGACCATGTCTGGGACATGTCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
42033275 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
42033325 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
42033375 AGAACAT-CCATGTAAGACCATGTTTGGGGCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42033417 TGTTATTATC
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
50 120 0.98
51 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:42035589 original size:6 final size:6
Alignment explanation
Indices: 42035578--42035635 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
42035568 TTTTCAGCTC
* **
42035578 TATTTT TATTTT TATTATT T-TTAT TATTTT TATTATT T-TAGT TA-TTT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATT-TT TATTTT TATTTT
42035625 TATTTT TATTT
1 TATTTT TATTT
42035636 CTTAGACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
5 7 0.17
6 28 0.68
7 6 0.15
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:42035626 original size:9 final size:9
Alignment explanation
Indices: 42035583--42035625 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
42035573 AGCTCTATTT
42035583 TTATTTTTA
1 TTATTTTTA
42035592 TTATTTTTA
1 TTATTTTTA
42035601 TTATTTTTA
1 TTATTTTTA
42035610 TTA-TTTTA
1 TTATTTTTA
42035618 GTTATTTT
1 -TTATTTT
42035626 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 5 0.16
9 24 0.75
10 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:42040578 original size:18 final size:18
Alignment explanation
Indices: 42040557--42040595 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42040547 AATTCTGTAA
42040557 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
42040575 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
42040593 TTA
1 TTA
42040596 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:42040820 original size:7 final size:7
Alignment explanation
Indices: 42040808--42040843 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
42040798 ACCTTCCAAG
42040808 CCCTTTC
1 CCCTTTC
42040815 CCCTTTC
1 CCCTTTC
*
42040822 CTCTTTC
1 CCCTTTC
42040829 CCCTTTC
1 CCCTTTC
*
42040836 CACTTTC
1 CCCTTTC
42040843 C
1 C
42040844 ATAATTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (7 bp):
CCCTTTC
Found at i:42044613 original size:77 final size:77
Alignment explanation
Indices: 42044486--42044646 Score: 304
Period size: 77 Copynumber: 2.1 Consensus size: 77
42044476 AAAAATTTAC
*
42044486 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGGTATAAGTATGTGTGTATATCTATA
1 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
42044551 CATAGACAATCA
66 CATAGACAATCA
*
42044563 TTTTAATCTAGATGAATCATGATGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
1 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
42044628 CATAGACAATCA
66 CATAGACAATCA
42044640 TTTTAAT
1 TTTTAAT
42044647 TTGTTCTTCC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (77 bp):
TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
CATAGACAATCA
Found at i:42045629 original size:11 final size:11
Alignment explanation
Indices: 42045613--42045650 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
42045603 TTATAAAATG
42045613 ACAATATCTCA
1 ACAATATCTCA
42045624 ACAATATCTCA
1 ACAATATCTCA
42045635 ACAATATCTCA
1 ACAATATCTCA
42045646 ACAAT
1 ACAAT
42045651 TGATAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:42048676 original size:92 final size:91
Alignment explanation
Indices: 42048519--42048727 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
42048509 TTGATTTTAG
* * *
42048519 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
42048584 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
42048611 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
42048675 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
42048703 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
42048728 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:42048690 original size:24 final size:25
Alignment explanation
Indices: 42048655--42048702 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
42048645 TTATGAAATT
42048655 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
42048679 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
42048703 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:42048952 original size:120 final size:120
Alignment explanation
Indices: 42048746--42049154 Score: 682
Period size: 120 Copynumber: 3.4 Consensus size: 120
42048736 TATTTTAAAA
* * * *
42048746 TTTATTAAATCATATATTTTAAA-TAAAATATA-TTAATATTAATTAT-TTCAAATTTA-AATTT
1 TTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATAATTATGTT--AATTTATATTTT
*
42048807 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
63 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
42048865 TTTATTAAATTATATATTTAAATTATAAGATATTTAATAATAATTATGTTAATTTATATTTTACA
1 TTTATTAAATTATATATTTAAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACA
42048930 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
42048985 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACA
1 TTTATTAAATTATATATTTAAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACA
*
42049050 GTATCATATATTATGATTTGAGTAAATTCAAATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
*
42049105 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTTATTAAATTATATATTTAAATTATAATATATTTAATAATAATTATGTT
42049155 TAAATATGAT
Statistics
Matches: 277, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
118 6 0.02
119 28 0.10
120 241 0.87
121 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
TTTATTAAATTATATATTTAAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACA
GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAAT
Found at i:42048976 original size:66 final size:66
Alignment explanation
Indices: 42048900--42049097 Score: 199
Period size: 66 Copynumber: 3.2 Consensus size: 66
42048890 TAAGATATTT
42048900 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
42048965 G
66 G
* * * * *
42048966 AATATTAATTAT-TAAGAATTT-TA--TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT
1 AATAATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAT
**
42049018 -TT
64 AAG
*
42049020 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCAAATAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
42049085 G
66 G
*
42049086 AATATTAATTAT
1 AATAATAATTAT
42049098 TAAGAATTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 32
0.68 0.11 0.22
Matches are distributed among these distances:
53 5 0.05
54 13 0.13
55 5 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 4 0.04
66 24 0.24
67 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (66 bp):
AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
G
Found at i:42049022 original size:15 final size:15
Alignment explanation
Indices: 42048987--42049038 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42048977 TTAAGAATTT
*
42048987 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42049001 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42049015 TATTTAATAATAAT-
1 TATTTAATTATAATA
42049029 TATGTTAATT
1 TAT-TTAATT
42049039 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42049137 original size:16 final size:16
Alignment explanation
Indices: 42049116--42049157 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42049106 TTATTAAATT
*
42049116 ATATATTTTAATTATA
1 ATATATTTTAATAATA
42049132 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
42049147 AT-TATGTTTAA
1 ATATAT-TTTAA
42049158 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:42049142 original size:15 final size:15
Alignment explanation
Indices: 42049107--42049148 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42049097 TTAAGAATTT
*
42049107 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42049121 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42049135 TATTTAATAATAAT
1 TATTTAATTATAAT
42049149 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42049248 original size:153 final size:153
Alignment explanation
Indices: 42049091--42049377 Score: 502
Period size: 153 Copynumber: 1.9 Consensus size: 153
42049081 ATAAGAATAT
* * *
42049091 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* *
42049156 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
42049221 TAATTACCAAAACAAATATCTGC
131 TAATTACCAAAACAAATATCTGC
* * *
42049244 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTTTAATAATATTTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
42049309 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
42049374 TAAT
131 TAAT
42049378 CATTTACCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 126 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (153 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATTACCAAAACAAATATCTGC
Found at i:42049250 original size:240 final size:235
Alignment explanation
Indices: 42048772--42049250 Score: 544
Period size: 240 Copynumber: 2.0 Consensus size: 235
42048762 TTTTAAATAA
* *
42048772 AATATATTAATATTAATTATTTCAAATTTAAATTTATAGTATCATATATTATGATTTGAGTAAAT
1 AATATATTAATAATAATTATTT-AAATTTAAATTTACAGTATCATATATTATGATTTGAGTAAAT
*
42048837 TCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTAAATTATAAGATATTTAA
65 TCAAATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTAAATTATAAGATATTTAA
* *
42048902 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
130 TAATAATTATGTTAA--TATATATTACAG-ATCATATATTATGATTTGAATAAATTCATATAAGA
* * * * ** ** * *
42048967 ATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAT
192 ATATTAATCAATAACAATATTACCAAAACAAATATTCTAATTAT
*
42049011 AATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAA
1 AATATA-TTAATAATAATTAT-TTAAATTTA-AATTTACAGTATCATATATTATGATTTGAGTAA
* *
42049075 ATTCAAATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
63 ATTCAAATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTAAATTATAAGATATTT
* * *
42049140 AATAATAATTATGTTTAA-ATATGATTA-A-ATTATTTATTATTGATATT-AAT-AA-TCTTATT
128 AATAATAATTATG-TTAATATAT-ATTACAGATCATATATTA-TGAT-TTGAATAAATTCATA-T
42049199 AA-AAT-TTAAATAACAATAACAATAATTACCAAAACAAATATCTGCTAATTAT
188 AAGAATATT-AAT--CAATAACAAT-ATTACCAAAACAAATAT-T-CTAATTAT
42049251 TAAGAATTTT
Statistics
Matches: 205, Mismatches: 21, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
234 2 0.01
235 10 0.05
236 14 0.07
237 13 0.06
238 18 0.09
239 16 0.08
240 126 0.61
241 6 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (235 bp):
AATATATTAATAATAATTATTTAAATTTAAATTTACAGTATCATATATTATGATTTGAGTAAATT
CAAATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTAAATTATAAGATATTTAAT
AATAATTATGTTAATATATATTACAGATCATATATTATGATTTGAATAAATTCATATAAGAATAT
TAATCAATAACAATATTACCAAAACAAATATTCTAATTAT
Found at i:42049547 original size:16 final size:16
Alignment explanation
Indices: 42049526--42049561 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
42049516 GATTTGCTAT
42049526 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42049542 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42049558 TACA
1 TACA
42049562 ACGAACCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42052367 original size:25 final size:25
Alignment explanation
Indices: 42052317--42052368 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
42052307 TAACACATCC
* * * *
42052317 TCTGCTTTGTTCTGTTCTGTTCTAT
1 TCTGCTTTGCTCTGCTCTGCTATAT
42052342 TCTGCTTTGCTCTGCTCTGCTATAT
1 TCTGCTTTGCTCTGCTCTGCTATAT
42052367 TC
1 TC
42052369 AGTTCAGTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.06, C:0.25, G:0.15, T:0.54
Consensus pattern (25 bp):
TCTGCTTTGCTCTGCTCTGCTATAT
Found at i:42052940 original size:17 final size:18
Alignment explanation
Indices: 42052907--42052941 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42052897 AAAAGTCTAC
42052907 ATAAAATAAAATATAAAT
1 ATAAAATAAAATATAAAT
*
42052925 ATAAAA-AAATTATAAAT
1 ATAAAATAAAATATAAAT
42052942 TATGCTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAATAAAATATAAAT
Found at i:42055870 original size:21 final size:20
Alignment explanation
Indices: 42055845--42055907 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
42055835 AATGGGTTTC
*
42055845 CTTTTAGCTCTTTTGAGCTT
1 CTTTTAGCTCTTATGAGCTT
* * *
42055865 CATTTTAACCCTTATGAGTTT
1 C-TTTTAGCTCTTATGAGCTT
*
42055886 CTGTTCAGCTCTTATGAGCTT
1 CT-TTTAGCTCTTATGAGCTT
42055907 C
1 C
42055908 CATTAAACCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (20 bp):
CTTTTAGCTCTTATGAGCTT
Found at i:42055896 original size:42 final size:42
Alignment explanation
Indices: 42055850--42055949 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
42055840 GTTTCCTTTT
* *
42055850 AGCTCTTTTGAGCTT-CATTTTAACCCTTATGAGTTTCTGTTC
1 AGCTCTTATGAGCTTCCA-TTAAACCCTTATGAGTTTCTGTTC
* *
42055892 AGCTCTTATGAGCTTCCATTAAACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCCATTAAACCCTTATGAGTTTCTGTTC
* *
42055934 AGCACTTATGTGCTTC
1 AGCTCTTATGAGCTTC
42055950 TATGCAACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCCATTAAACCCTTATGAGTTTCTGTTC
Found at i:42059698 original size:32 final size:32
Alignment explanation
Indices: 42059661--42059870 Score: 182
Period size: 32 Copynumber: 6.7 Consensus size: 32
42059651 AATCAAATTA
* *
42059661 GCAATATATAAATACATATACAAATCAATTCG
1 GCAATATATATATACATATACAATTCAATTCG
* ** * *
42059693 CCAATAGGTGTATACTTATACAA-TCAATTCG
1 GCAATATATATATACATATACAATTCAATTCG
*
42059724 GCAATATA-AGTAT--ATATACAATTCAAATCG
1 GCAATATATA-TATACATATACAATTCAATTCG
*
42059754 GCAATATA-AGTATATATATACAATTCAATTCG
1 GCAATATATA-TATACATATACAATTCAATTCG
* * * *
42059786 GCAATATGTGTATACCTATACAATTCAAATCG
1 GCAATATATATATACATATACAATTCAATTCG
* *
42059818 GCAATATA-AGTATATATATACAATTCAATTCA
1 GCAATATATA-TATACATATACAATTCAATTCG
* * *
42059850 ACAGTATATA-AAACATATACA
1 GCAATATATATATACATATACA
42059871 TTTAAATTTA
Statistics
Matches: 143, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
29 7 0.05
30 20 0.14
31 25 0.17
32 90 0.63
33 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (32 bp):
GCAATATATATATACATATACAATTCAATTCG
Found at i:42059821 original size:64 final size:62
Alignment explanation
Indices: 42059709--42059848 Score: 237
Period size: 64 Copynumber: 2.2 Consensus size: 62
42059699 GGTGTATACT
42059709 TATACAA-TCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
1 TATACAATTCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
**
42059770 TATACAATTCAATTCGGCAATATGTGTATACCTATACAATTCAAATCGGCAATATAAGTATATA
1 TATACAATTCAATTCGGCAATATAAGTATA--TATACAATTCAAATCGGCAATATAAGTATATA
42059834 TATACAATTCAATTC
1 TATACAATTCAATTC
42059849 AACAGTATAT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
61 7 0.09
62 20 0.27
64 47 0.64
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (62 bp):
TATACAATTCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
Found at i:42077745 original size:43 final size:44
Alignment explanation
Indices: 42077650--42077796 Score: 149
Period size: 43 Copynumber: 3.4 Consensus size: 44
42077640 CAAGATTACG
* * * *
42077650 TGTAAGACCATATCTGGGA-TA-TGGCATCGATATGAGAATTCA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
* *
42077692 TTTAAGACCATGTCTGGGAC-ATTGATATCGATATGTGATTTCA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
* * * * * *
42077735 TGTAATACCATGGCT-TGACTATTGGCATCGATACGTGATTACA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
*
42077778 TGTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
42077797 TATGGCATTG
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
42 21 0.25
43 60 0.72
44 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
Found at i:42080603 original size:23 final size:23
Alignment explanation
Indices: 42080577--42080629 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
42080567 ATAAGTGCCA
42080577 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42080600 CACTTGA-ATGTAGCTGAAGCTAC
1 CAC-TGATATGTAGCCGAAGCTAC
42080623 CACTGAT
1 CACTGAT
42080630 CAATAACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42090454 original size:26 final size:26
Alignment explanation
Indices: 42090390--42090455 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
42090380 TTCGACCTAT
* *
42090390 AGCTCGTGTGAGAAGGCCTATTTCAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
*
42090416 AGCTCGTGTGAGCAGGCCCATTTTAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
42090442 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
42090456 ATGATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGGCCCATTTCAC
Found at i:42091779 original size:96 final size:96
Alignment explanation
Indices: 42091615--42091803 Score: 378
Period size: 96 Copynumber: 2.0 Consensus size: 96
42091605 GCATATGGCT
42091615 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
1 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
42091680 GTGTGTCTTATCCATGTGAGTCACACGGGCA
66 GTGTGTCTTATCCATGTGAGTCACACGGGCA
42091711 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
1 TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
42091776 GTGTGTCTTATCCATGTGAGTCACACGG
66 GTGTGTCTTATCCATGTGAGTCACACGG
42091804 CCTAGCCACA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (96 bp):
TGGATACGGGCTAGGACACGAACGTATGTCCTTATTTCGATTGTTATATAGCCTGAGACATGGGT
GTGTGTCTTATCCATGTGAGTCACACGGGCA
Found at i:42093785 original size:28 final size:28
Alignment explanation
Indices: 42093751--42093820 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
42093741 GTGAGCAGCC
** *
42093751 CAAATATCACAGGTTGTGTGAGCAAATT
1 CAAATATCACAACTTGTGTGAGCAAACT
42093779 CAAATATCACAACTTGTGTGAGCAAACT
1 CAAATATCACAACTTGTGTGAGCAAACT
*
42093807 CAAATATCATAACT
1 CAAATATCACAACT
42093821 CGTATGAGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTTGTGTGAGCAAACT
Found at i:42093828 original size:28 final size:28
Alignment explanation
Indices: 42093751--42093828 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
42093741 GTGAGCAGCC
** * * *
42093751 CAAATATCACAGGTTGTGTGAGCAAATT
1 CAAATATCACAACTCGTATGAGCAAACT
* *
42093779 CAAATATCACAACTTGTGTGAGCAAACT
1 CAAATATCACAACTCGTATGAGCAAACT
*
42093807 CAAATATCATAACTCGTATGAG
1 CAAATATCACAACTCGTATGAG
42093829 ACAATCGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTCGTATGAGCAAACT
Found at i:42095265 original size:16 final size:15
Alignment explanation
Indices: 42095244--42095273 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42095234 AATTAAATAC
42095244 AACAACATTCATTAAT
1 AACAACATT-ATTAAT
42095260 AACAACATTATTAA
1 AACAACATTATTAA
42095274 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AACAACATTATTAAT
Found at i:42097723 original size:49 final size:49
Alignment explanation
Indices: 42097656--42097792 Score: 211
Period size: 49 Copynumber: 2.8 Consensus size: 49
42097646 TATTTTCTCA
* *
42097656 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATACCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
* *
42097705 ATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATTCCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
* * *
42097754 ATGCCATATCCTAGCTATGGTCTTACACGGAATCACATA
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
42097793 TCACTTATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (49 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCG
Found at i:42098990 original size:23 final size:23
Alignment explanation
Indices: 42098964--42099062 Score: 135
Period size: 23 Copynumber: 4.3 Consensus size: 23
42098954 ATAAGTGCCA
42098964 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
42098987 CACTAATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
42099010 TATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42099033 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42099056 CACTGAT
1 CACTGAT
42099063 CAATAACACT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42103108 original size:20 final size:18
Alignment explanation
Indices: 42103085--42103118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42103075 GCGCCGCGCT
42103085 CCTCC-CACGTGTGCCTG
1 CCTCCTCACGTGTGCCTG
42103102 CCTCCTCACGTGTGCCT
1 CCTCCTCACGTGTGCCT
42103119 CCGTACCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.47, G:0.21, T:0.26
Consensus pattern (18 bp):
CCTCCTCACGTGTGCCTG
Found at i:42109159 original size:27 final size:26
Alignment explanation
Indices: 42109122--42109172 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
42109112 AAAAAGGAGC
**
42109122 AAAAGAAAAAAATCAAAATCAAAACA
1 AAAAGAAAAAAAGAAAAATCAAAACA
42109148 AAAAGAAGAAAAAGAAAAATCAAAA
1 AAAAGAA-AAAAAGAAAAATCAAAA
42109173 ATCAAGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAAAATCAAAACA
Found at i:42109198 original size:13 final size:12
Alignment explanation
Indices: 42109182--42109230 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
42109172 AATCAAGGTC
*
42109182 AAAATGAAAATGA
1 AAAAAGAAAA-GA
*
42109195 AAAATAGAGAAGAA
1 AAAA-AGAAAAG-A
42109209 AAAAAGAAAAGA
1 AAAAAGAAAAGA
42109221 AAAAAGAAAA
1 AAAAAGAAAA
42109231 AGAGAAGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 11 0.35
13 11 0.35
14 9 0.29
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:42111583 original size:88 final size:87
Alignment explanation
Indices: 42111319--42111892 Score: 735
Period size: 88 Copynumber: 6.6 Consensus size: 87
42111309 CAGATCAGTG
* * *
42111319 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCATATCGAAAACA-AAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
42111383 ATCGATTGCATTGGAGCTGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
* * * * *
42111406 AAGACAACAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
42111470 ATTGGTTGCAGTGGAGC-GGATTA
65 ATCGGTTGCAGTGGAGCAGG-TTA
** * *
42111493 AAGATATTAGATTTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
42111558 ATCGGTTGCAGTGGAGCAGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
* * *
42111581 AAGATAGCAGATCTTGCCTTCCTACACT-ACAGCGAAGCAGATCGAAGATACCAACCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
42111645 CTCGGTTGCAGTGGAGCAGGTTA
65 ATCGGTTGCAGTGGAGCAGGTTA
*
42111668 AAGATAGCAGATCTTGCCCTCCTACGC-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCT--GCATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
*
42111732 CCTCGGTTGCAGTGGAGCAGGTTA
64 CATCGGTTGCAGTGGAGCAGGTTA
* * *
42111756 AAGATAGCAGATCTTGCCCTCCTGCGCTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGC-ATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
42111821 CTCGGTTGTAGTGGAGCAGGTTG
65 ATCGGTTGCAGTGGAGCAGGTTA
* * * * *
42111844 AAGATAGCAGATCTTACCTTTCTGCATCGACAGTGAAGTAGATCAAAGA
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGA
42111893 TTACAAGTCC
Statistics
Matches: 437, Mismatches: 39, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
86 5 0.01
87 198 0.45
88 230 0.53
89 4 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCAGGTTA
Found at i:42111644 original size:175 final size:174
Alignment explanation
Indices: 42111319--42111892 Score: 744
Period size: 175 Copynumber: 3.3 Consensus size: 174
42111309 CAGATCAGTG
* * **
42111319 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCATATCGAA-AACAAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCA-TGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
* * * * * * *
42111383 ATCGATTGCATTGGAGCTGGTTAAAGACAACAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGA
65 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGA
* * *
42111448 TCGAA-AACAAAGCCTTGCCTCCATTGGTTGCAGTGGAGC-GGATTA
130 TCGAAGAACCAA-CCTTGCCTCCCTCGGTTGCAGTGGAGCAGG-TTA
** *
42111493 AAGATATTAGATTTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCC
*
42111558 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTACACT-ACAGCGAAGCAGA
65 ATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGA
42111622 TCGAAGATACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
130 TCGAAGA-ACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
* *
42111668 AAGATAGCAGATCTTGCCCTCCTACGC-TGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCT--GCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTC
* * * *
42111732 CCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCCTCCTGCGCTGACAACGAAGCAG
64 CATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAG
* * *
42111797 ATCGAAGACACCAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTG
129 ATCGAAGA-ACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
* * * * *
42111844 AAGATAGCAGATCTTACCTTTCTGCATCGACAGTGAAGTAGATCAAAGA
1 AAGATAGCAGATCTTGCCTTCCTGCAT-GACAGCGAAGCAGATCGAAGA
42111893 TTACAAGTCC
Statistics
Matches: 352, Mismatches: 38, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
173 1 0.00
174 61 0.17
175 189 0.54
176 99 0.28
177 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (174 bp):
AAGATAGCAGATCTTGCCTTCCTGCATGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGAT
CGAAGAACCAACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTA
Found at i:42112094 original size:44 final size:45
Alignment explanation
Indices: 42112026--42112236 Score: 137
Period size: 44 Copynumber: 4.6 Consensus size: 45
42112016 TGAAGCCAGT
*
42112026 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* * * * * *
42112070 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTACAGT-G-G-AG--CGGATTAAAAT-AA---AGA
* * ** *
42112124 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGA
*
42112168 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
* *
42112212 GATCTTATCTCTCTGA-AGTTACAGT
1 AATCTTATCTCCCTGAGA-TTACAGT
42112237 AGAGTAGATC
Statistics
Matches: 125, Mismatches: 26, Indels: 32
0.68 0.14 0.17
Matches are distributed among these distances:
43 5 0.04
44 74 0.59
45 2 0.02
46 1 0.01
47 2 0.02
49 10 0.08
50 4 0.03
51 2 0.02
52 1 0.01
53 3 0.02
54 20 0.16
55 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGA
Found at i:42112190 original size:98 final size:97
Alignment explanation
Indices: 42112012--42112192 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 97
42112002 GTAATGAAGT
* * * * *
42112012 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCTA
*
42112077 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATC
65 TCTCCCTGAAGTTACAGTAGAGTAGATCGCATC
* **
42112110 AGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCCT
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATCCT
42112174 ATCTCCCTG-AGATTACAGT
64 ATCTCCCTGAAG-TTACAGT
42112193 GGAGCGGATT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.90
99 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (97 bp):
AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTAT
CTCCCTGAAGTTACAGTAGAGTAGATCGCATC
Found at i:42112268 original size:142 final size:142
Alignment explanation
Indices: 42112012--42112278 Score: 507
Period size: 142 Copynumber: 1.9 Consensus size: 142
42112002 GTAATGAAGT
*
42112012 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
*
42112077 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCCTGAGA
42112142 TTACAGCGGAGC
131 TTACAGCGGAGC
*
42112154 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
42112219 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCC
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCC
42112279 AAGCGATGCA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 122 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTCCCTGAGA
TTACAGCGGAGC
Found at i:42112354 original size:50 final size:50
Alignment explanation
Indices: 42112285--42112571 Score: 340
Period size: 50 Copynumber: 5.7 Consensus size: 50
42112275 TCCCAAGCGA
*
42112285 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* ** * * * * * **
42112335 TGCGGTTCAAAAGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* * * *
42112385 TGCAGTAGAGCAGATTAAAGCCACAACAGTGAATCTTGCCTCCCTGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* * * *
42112435 TGCAGTGGAGCATATTAAAGCCACAACAGTGAATCTTGCCTCCCTGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
* *
42112485 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
** * **
42112535 TGCAGTTAAAAAGATTAAAGCCACAATGGCGAATCTT
1 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTT
42112572 ACTTTCCAAA
Statistics
Matches: 200, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 200 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (50 bp):
TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCCGACAT
Found at i:42112452 original size:100 final size:100
Alignment explanation
Indices: 42112266--42112573 Score: 384
Period size: 100 Copynumber: 3.1 Consensus size: 100
42112256 TGAAGCCAGA
* *
42112266 AATCTTATCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
1 AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
* * *
42112331 ACATTGCGGTTCAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
* * * * * *
42112366 AATCTTACCTCCCAGGCGGTGCAGTAGAGCAGATTAAAGCCACAACAGTGAATCTTGCCTCCCTG
1 AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
* ** * *
42112431 ACATTGCAGTGGAGCATATTAAAGCCACAACAGTG
66 ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
* * * *
42112466 AATCTTGCCTCCCTGAC-ATTGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCC
1 AATCTTACCTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCC
** **
42112530 GACATTGCAGTTAAAAAGATTAAAGCCACAATGGCG
65 GACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
42112566 AATCTTAC
1 AATCTTAC
42112574 TTTCCAAAAG
Statistics
Matches: 172, Mismatches: 35, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
100 172 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (100 bp):
AATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCG
ACATTGCAGTGCAAAAGATTAAAGCCACAACAGCG
Found at i:42113997 original size:23 final size:23
Alignment explanation
Indices: 42113971--42114015 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42113961 CACGCATTTT
*
42113971 TTTATATAGTATAGACATATTCC
1 TTTATATAATATAGACATATTCC
* *
42113994 TTTATATAATATATATATATTC
1 TTTATATAATATAGACATATTC
42114016 TTAAACTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTATATAATATAGACATATTCC
Found at i:42118345 original size:36 final size:36
Alignment explanation
Indices: 42118305--42118384 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
42118295 GACAAGAAGG
* * *
42118305 AAGGAAAAATAAAAGAAAGAAATGAAAAAGAAAA-AT
1 AAGGAAAAACAAAA-AAACAAATGAAAAAGAAAAGAA
* **
42118341 AAGGAAGAACAAAAAAACAAATGATTAAGAAAAGAA
1 AAGGAAAAACAAAAAAACAAATGAAAAAGAAAAGAA
42118377 AAGGAAAA
1 AAGGAAAA
42118385 CGTTAATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 16 0.44
36 20 0.56
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (36 bp):
AAGGAAAAACAAAAAAACAAATGAAAAAGAAAAGAA
Found at i:42127559 original size:54 final size:54
Alignment explanation
Indices: 42127477--42127601 Score: 232
Period size: 54 Copynumber: 2.3 Consensus size: 54
42127467 ATCACGGTCT
42127477 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
* *
42127531 CGGGTGCGGGTGCTTCAATCGGTGGGTCGGCCTTCTCTTCTTCCTTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
42127585 CGGGTGCGGGTGCTTCA
1 CGGGTGCGGGTGCTTCA
42127602 GTTTCGACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.09, C:0.29, G:0.32, T:0.30
Consensus pattern (54 bp):
CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
Found at i:42139604 original size:27 final size:27
Alignment explanation
Indices: 42139371--42139593 Score: 259
Period size: 27 Copynumber: 8.3 Consensus size: 27
42139361 AGAGGTCGAT
* *
42139371 AAATGATCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
42139398 AACTGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
42139425 AAATGACCGAAATACCCCTGTAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
42139452 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
42139479 GAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
42139506 AAATTG-TCGAAATACCTTCATAGGGTA
1 AAA-TGACCGAAATACCCCCATAGGGTA
** * *
42139533 AAATGACTAAAATACTCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
**
42139560 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
42139587 AAATGAC
1 AAATGAC
42139594 TATTATACCC
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 164 0.98
28 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:42139618 original size:81 final size:78
Alignment explanation
Indices: 42139380--42139621 Score: 236
Period size: 81 Copynumber: 3.0 Consensus size: 78
42139370 TAAATGATCG
* *
42139380 AAATACCCCCATAGGATAAACTGACCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCT-
1 AAATA-CCCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGA-CGAAATACCCCTA
* **
42139444 GTAAGGTAAAATGACCG
64 G-GA-GTAAAATGACTA
* * * * *
42139461 AAATACCCCTATAGGGTAGAATGACCGAAATACCCCCATAAGGTAAAATTGTCGAAATACCTTCA
1 AAATACCCC-ATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAA-TGACGAAATACC--CC
42139526 TAGG-GTAAAATGACTA
62 TAGGAGTAAAATGACTA
** * *
42139542 AAATACTCCCATAGGATAAAATGACTAAAATACCCCCATAGGGTAAAATGACTATTATACCCCTA
1 AAATAC-CCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACGA-AATACCCCTA
*
42139607 GGAGATGAAATGACT
64 GGAG-TAAAATGACT
42139622 GTTATGGCTT
Statistics
Matches: 132, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
79 5 0.04
80 9 0.07
81 110 0.83
82 5 0.04
83 2 0.02
84 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (78 bp):
AAATACCCCATAGGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACGAAATACCCCTAGG
AGTAAAATGACTA
Found at i:42144786 original size:35 final size:35
Alignment explanation
Indices: 42144740--42144811 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
42144730 TTCAGAAATA
*
42144740 TCTCGCCTGCTTAGATAAAGAGTCGAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
42144775 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
42144810 TC
1 TC
42144812 ATGCTGTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (35 bp):
TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
Found at i:42156297 original size:50 final size:53
Alignment explanation
Indices: 42156212--42156319 Score: 143
Period size: 50 Copynumber: 2.1 Consensus size: 53
42156202 TGATTCAAGA
*
42156212 ATGTTTATGAAGGAGGATGTGTAGCCTTCAGGCTTGACACAT-AGTGCCTAGGC
1 ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACAC-TCAGTGCCTAGGC
* **
42156265 ATGTTTCTGAA-G-GGATGT-TAGCCTTCAAGCTTGGTACTCAGTGCCTAGGC
1 ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACACTCAGTGCCTAGGC
42156315 ATGTT
1 ATGTT
42156320 CTTGGTTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
49 1 0.02
50 32 0.64
51 6 0.12
52 1 0.02
53 10 0.20
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (53 bp):
ATGTTTATGAAGGAGGATGTGTAGCCTTCAAGCTTGACACTCAGTGCCTAGGC
Found at i:42160043 original size:11 final size:11
Alignment explanation
Indices: 42160029--42160104 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
42160019 GATAATCACT
42160029 TTAATATTAAA
1 TTAATATTAAA
42160040 TTAATA--AAA
1 TTAATATTAAA
*
42160049 -TATTATTAAA
1 TTAATATTAAA
*
42160059 ATAAGTATTAAA
1 TTAA-TATTAAA
42160071 TTAA-ATTTAATA
1 TTAATA-TTAA-A
42160083 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
42160096 ATAATATTA
1 TTAATATTA
42160105 TTTTTTTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:42165855 original size:13 final size:13
Alignment explanation
Indices: 42165837--42165863 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42165827 TTCAACACTA
42165837 ACAGATTATCATG
1 ACAGATTATCATG
42165850 ACAGATTATCATG
1 ACAGATTATCATG
42165863 A
1 A
42165864 TACTATCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAGATTATCATG
Found at i:42177491 original size:516 final size:511
Alignment explanation
Indices: 42175161--42177647 Score: 4361
Period size: 511 Copynumber: 4.9 Consensus size: 511
42175151 TTGGGACGAA
* * **
42175161 AGTCGTCTACAAGCAAAGAAAAGGGAAAAGCGAAG-TTTGTTTAAAGCTTTCAACAAACCGGTGA
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTT-TTTAAAGCTTTCAATAAACTAGTGA
* *
42175225 GTG-TTTGGGGTTCGCTGCTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTTTA
65 GTGTTTTGGGGTT-GCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTA
* * **
42175289 AAACACCTAATCTAATTCCCGAGTGTAAGTTTCTTACTTTAACTTTTGTATTTTGTGATAAATGT
129 AAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAAT-T
* * * * *
42175354 -TTGTGTTATATTATAAGAAGTTCACACATGCGAACCATAGTTCGCATATGTAGTTTAGTCGAGT
193 CTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGT
* * * *
42175418 ATAGGATCGCAGACATCATGCTGCAAAGTATGTGACTGTGATATGTGTTAAATATGAAAATTAAT
258 ATAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAAT
42175483 ATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCAT
323 ATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCAT
*
42175548 AGGATTGTGAGTACTAACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAA
388 AGGATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAA
42175613 AATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
453 AATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
42175672 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
42175737 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
*
42175802 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
* *
42175867 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
196 GTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
* *
42175932 GGATCGCAGACATTATATTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAACTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
* *
42175997 AGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAACTGGATATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
42176062 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
42176127 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
*
42176183 AGTCATCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
*
42176248 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAATGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
42176313 ACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
*
42176378 GTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGTCGAGTATA
196 GTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
*
42176443 GGATCGCAGACATTATACTGCGAAGTATGAGATTGTGATATGTGTTAAATATGAAAATTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
42176508 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
42176573 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
42176638 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
* *
42176694 AGTCGTTTACATGTAAAGAAAAGGGAAAAGCGAAGC-TTTTTAAAGCTTTCAATAAACTAGTGAG
1 AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
*
42176758 TGTTTTGGGGTTGCTACTAGTACGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
66 TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
*
42176823 ACACCTAATCTAAGTCCTGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
131 ACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
* * * *
42176888 GTGTTATGTTATAAGGAGTTCATACACGTGAACCATAGTTTGCATATATAGTGTAGCCGAGTATA
196 GTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
*
42176953 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAACTAATATC
261 GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
* * * *
42177018 AGTAATTGTGGCTATTTTGGTACTACGATATTTGAAACAACTGGACATTGTTGGCATGCCATAGG
326 TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
42177083 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
391 ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
* * *
42177148 ATTATGTTTCGTCTATTAGTAACTTGATTATATTTGTGAAGTTGTGAACCTAATAG
456 AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
* *
42177204 AGTCGTCTACATGCAAAAAAAGAGAGAGGGAAAAACGAAGCTTTTTTAAAGCTTTCAATAAACTA
1 AGTCGTCTACATGC----AAAGA-AAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTA
* * ** *
42177269 GTGAGTGTTTTGGGGTTACTGCTAGTATGAGCAAACCATTGTGTTAAACAAGAGCTTAGGTTGGT
61 GTGAGTGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGT
42177334 CTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAA
126 CTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAA
42177399 TTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGA
191 TTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGA
*
42177464 GTATAGGATCGCAGACATTATACTGCGAAGTATGAGATTGTGATATGTGTTAAATATGAAAATTA
256 GTATAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTA
42177529 ATATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCC
321 ATATCTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCC
* *
42177594 ATAGGATTGTGAGTACTTACCTTTGTGTTTTATGATTTGGGCGAAAGGCCCTAG
386 ATAGGATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAG
42177648 TGTCACGGGA
Statistics
Matches: 1886, Mismatches: 81, Indels: 13
0.95 0.04 0.01
Matches are distributed among these distances:
510 470 0.25
511 1001 0.53
512 12 0.01
514 5 0.00
515 15 0.01
516 383 0.20
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (511 bp):
AGTCGTCTACATGCAAAGAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCAATAAACTAGTGAG
TGTTTTGGGGTTGCTACTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAA
ACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTT
GTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATA
GGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATC
TGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGG
ATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCAAAAGGCCCTAGGACAGGTTAGGAAAAT
AATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTGTGAACCTAATAG
Found at i:42179003 original size:513 final size:513
Alignment explanation
Indices: 42178284--42181378 Score: 5387
Period size: 512 Copynumber: 6.0 Consensus size: 513
42178274 CCCCGTGACA
* *
42178284 CTAGGACAGGTTAGGAGAAATAATATGTTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
42178349 TGAACCTAACAGAGTCGTCTACAGGC-AAAAAAAAGGGAAAAACGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
42178413 ATAAACTAGTGAGTGGTTTGAGGTTGCTGCTAGTATGAGTGAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
*
42178478 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGATGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
42178543 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
42178608 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* *
42178673 GAAAATTAATATCTGTAATTGTGGTTATTTTGGTACTATGATCTTTCAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
42178738 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
* *
42178796 CTAGGACAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
42178861 TGAACCTAGCAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
42178926 ATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCAAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
* *
42178991 AAGTTGGTCTAAAACACCTAATCTAAGTCCCAGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
*
42179056 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
*
42179121 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGAGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* * * * *
42179186 GACAATTAATATTTGTAATTGTGGCTATTTTGGTACTACGATCTTTGAAATAATTGGAAATTTGT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATA-TTGT
* *
42179251 AGGCATGCCGTAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
455 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
42179310 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
*
42179375 TGAACCTAACAGAGTCGTCTACAAGCAAAAAAAAAAGGG---AGCGAAGCTTTTTTAAAGCTTTC
66 TGAACCTAACAGAGTCGTCTACAGGC-AAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTC
* *
42179437 AATAAACTAGTGAGTGGTTTAGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACAAGAGCT
130 AATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCT
42179502 TAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTT
195 TAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTT
*
42179567 TGTGGTAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAG
260 TGTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAG
* *
42179632 TTTAGCCGAGTATAGGATCGCAGACATTATGTTGCGAAGAATGTGATTGTGATATGTGTTAAATA
325 TTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATA
**
42179697 TGAAAATTAATATCTGTAATTGTGTTTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGT
390 TGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGT
42179762 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
455 TGGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
*
42179821 CTAGGATAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
42179886 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
* *
42179951 ATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAACGAACCATTGTGTTAAACGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
*
42180016 AAGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
42180081 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
* *
42180146 TTAGCCGAGTATAGGATCGCAGACATTATGTTGCGAAGAATGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
42180211 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
*
42180276 GGCATGCCATAGAATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
*
42180334 CTAGGATAGGTTAGCAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
42180399 TGAACCTAACAGAGTCGTCTACAGGC-AAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
66 TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
*
42180463 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAATGAGAGCTT
131 ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
42180528 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
196 AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
* * *
42180593 GTGATAAATTCTTGTGTTATGTTATAAGGAGTTCATACATCTGAACCATAGTTTGCATATGTAGT
261 GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
*
42180658 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTTTGTGATTGTGATATGTGTTAAATAT
326 TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
* *
42180723 GAAAATTAATATCTGTAATGGTGGCTATTTTGGTACTACGATCTTTGAAACAATTGGATATTGTT
391 GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
*
42180788 GGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATGATTTGGGCGAAAGGCC
456 GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
* *
42180846 CTTGGACAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
1 CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
* *
42180911 TGAACCTAACGGAGTCGTCTACAGGCAAAAAGAAAAAAAAGGGAAAAGTGAAGCTTTTTTAAAGC
66 TGAACCTAACAGAGTCGTCTACAGGC----A-AAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGC
*
42180976 TTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAG
126 TTTCAATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAG
42181041 AGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCAT
191 AGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCAT
*
42181106 ATTTTGTGATAAATTCTTGTGTTATGTTATAAGACGTTCACACATGTGAACCATAGTTTGCATAT
256 ATTTTGTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATAT
* *
42181171 GTAGTTTAGCCGAGTGTAGGATCGCAGACATTATACTGCGAAGTATGTGATTGTGATATGTGTTA
321 GTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTA
* ** *
42181236 AATATG-TAATTAATATGAGTAATTGTGGCTATTTTGGT-GT-TGCAATCTTTGAAA-AAGTTGG
386 AATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATG--ATCTTTGAAACAA-TTGG
* * *
42181297 ATATTGTTGGCATG---T--CA-TG-GAGTACTCACCTTTGTGGTTTT-TGATTTGGGCGAGAGG
448 ATATTGTTGGCATGCCATAGGATTGTGAGTACTCACGTTTGT-GTTTTATGATTTGGGCGAAAGG
42181354 CC
512 CC
* *
42181356 ATGGGATAGGTTAGGAGAAATAA
1 CTAGGATAGGTTAGGAGAAATAA
42181379 GGGAATGATG
Statistics
Matches: 2471, Mismatches: 96, Indels: 34
0.95 0.04 0.01
Matches are distributed among these distances:
510 65 0.03
511 157 0.06
512 909 0.37
513 830 0.34
514 149 0.06
515 13 0.01
516 3 0.00
517 56 0.02
518 289 0.12
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (513 bp):
CTAGGATAGGTTAGGAGAAATAATATGCTTCGTCTATTAGTAACTTGAGTATATTTGTGAAGTTG
TGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAGGGAAAAGCGAAGCTTTTTTAAAGCTTTCA
ATAAACTAGTGAGTGGTTTGGGGTTGCTGCTAGTATGAGCGAACCATTGTGTTAAACGAGAGCTT
AGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTTTCTTACTTTAACTTTCATATTTT
GTGATAAATTCTTGTGTTATGTTATAAGGCGTTCACACATGTGAACCATAGTTTGCATATGTAGT
TTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATGTGATTGTGATATGTGTTAAATAT
GAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTATGATCTTTGAAACAATTGGATATTGTT
GGCATGCCATAGGATTGTGAGTACTCACGTTTGTGTTTTATGATTTGGGCGAAAGGCC
Found at i:42185656 original size:14 final size:14
Alignment explanation
Indices: 42185625--42185674 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
42185615 CCCCGAATCT
42185625 TTAAACCCTC-AA-C
1 TTAAA-CCTCAAACC
**
42185638 TTAAACCTTGAACC
1 TTAAACCTCAAACC
42185652 TTAAACCTCAAACC
1 TTAAACCTCAAACC
*
42185666 CTAAACCTC
1 TTAAACCTC
42185675 GAGGTTCAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 21 0.68
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (14 bp):
TTAAACCTCAAACC
Found at i:42186241 original size:26 final size:27
Alignment explanation
Indices: 42186189--42186251 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
42186179 TAAAAAAATA
42186189 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
42186216 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
42186242 ACCAAAATAT
1 ACCAAAATAT
42186252 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAATTTTTTTTATTT
Found at i:42186279 original size:19 final size:19
Alignment explanation
Indices: 42186244--42186281 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42186234 TTTTATTTAC
*
42186244 CAAAATATACAAAAAAAAA
1 CAAAAAATACAAAAAAAAA
42186263 CAAAAAATA-AAAGAAAAAA
1 CAAAAAATACAAA-AAAAAA
42186282 AAACCTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
CAAAAAATACAAAAAAAAA
Found at i:42186698 original size:19 final size:19
Alignment explanation
Indices: 42186674--42186739 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
42186664 ATTAAAATAG
42186674 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
42186693 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
42186711 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
42186730 TTTAATTTAA
1 TTTAATTTAA
42186740 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:42186918 original size:82 final size:81
Alignment explanation
Indices: 42186829--42186984 Score: 294
Period size: 82 Copynumber: 1.9 Consensus size: 81
42186819 AAAAATAACA
*
42186829 GAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAACA
1 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAA-A
42186894 TGTTAGACTAAATAATG
65 TGTTAGACTAAATAATG
42186911 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAT
1 GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAT
42186976 GTTAGACTA
66 GTTAGACTA
42186985 TTTTAATTAA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
81 11 0.15
82 62 0.85
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (81 bp):
GAAACATAAACTATTTTATCTATTTATAAACTTAATATATTCTTAATAGACTTATAACATAAAAT
GTTAGACTAAATAATG
Found at i:42187092 original size:18 final size:19
Alignment explanation
Indices: 42187053--42187148 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
42187043 ATTTTATATT
42187053 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
42187072 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
42187090 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
42187109 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
42187127 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
42187146 TTA
1 TTA
42187149 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:42187094 original size:37 final size:37
Alignment explanation
Indices: 42187053--42187148 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
42187043 ATTTTATATT
*
42187053 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
42187090 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
42187127 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
42187149 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:42187834 original size:30 final size:28
Alignment explanation
Indices: 42187786--42187847 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
42187776 TTTTTGGAGT
*
42187786 ATATTTTAATAAAT--AAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAATTATA
42187812 ATATTTTGATAAATAAAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAATTATA
42187840 ATATTTTG
1 ATATTTTG
42187848 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 13 0.39
28 20 0.61
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAAAATTATA
Done.