Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 31
Found at i:4942006 original size:14 final size:14
Alignment explanation
Indices: 4941974--4942036 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
4941964 AAGAAAAATG
* *
4941974 AAGAAAAAAGGAAA
1 AAGAAAAAAAGAGA
4941988 AAGAAAAAAAGAGA
1 AAGAAAAAAAGAGA
* *
4942002 CAGAAAAAGAGAG-
1 AAGAAAAAAAGAGA
* *
4942015 ACGAAAGAAAGAAGA
1 AAGAAAAAAAG-AGA
4942030 AAGAAAA
1 AAGAAAA
4942037 CAGATCTAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
13 7 0.19
14 25 0.68
15 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAGAGA
Found at i:4944021 original size:54 final size:54
Alignment explanation
Indices: 4943953--4944064 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
4943943 CCAAACAATA
* * * *
4943953 TGATGTTTTCAAATGAATTTT-GAAAGATGTTAAGCCTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTCAAAAGAAGCTAAGCCTAATTTT-AGGGGTTTCT
*
4944007 TGATGTTTTTAAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
4944061 TGAT
1 TGAT
4944065 AACTGTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCT
Found at i:4944090 original size:55 final size:55
Alignment explanation
Indices: 4943963--4944078 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 55
4943953 TGATGTTTTC
* * * * *** *
4943963 AAATGAATTTT-GAAAGATGTTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTT
1 AAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATAACTGT
4944017 AAATGAATTTTCAAAAGAAGCTAAGCCTAATTTT-AGGGGTTTCTTGATAACTGT
1 AAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATAACTGT
4944071 AAATGAAT
1 AAATGAAT
4944079 CTTTTTGAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (55 bp):
AAATGAATTTTCAAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATAACTGT
Found at i:4944959 original size:91 final size:90
Alignment explanation
Indices: 4944799--4945271 Score: 750
Period size: 91 Copynumber: 5.2 Consensus size: 90
4944789 GATAAACCGA
* *
4944799 TCAATATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
4944864 ATGAGAAGAACTTGTTCAACCTCGC
66 ATGAGAAGAACTTGTTCAACCTGGC
* * * *
4944889 TTCAACATTTCTAGT-TAGGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATAAGTTCA
1 -TCAACATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
4944953 TAATGAGAAGAACTTGTTCAACTTTGGC
64 TAATGAGAAGAACTTGTTCAAC-CTGGC
* * *
4944981 TCAATATTTCCAATGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
4945046 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACC-TGGC
*
4945072 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
4945137 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACC-TGGC
* *
4945163 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCAAACGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
4945228 ATGAGAAGAACTTGTTCAACCTAGGC
66 ATGAGAAGAACTTGTTCAACCT-GGC
4945254 TCAACATTTCCAAGTGGA
1 TCAACATTTCC-AGTGGA
4945272 TTGACATCCC
Statistics
Matches: 354, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
90 2 0.01
91 343 0.97
92 9 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (90 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTGGC
Found at i:4945459 original size:17 final size:17
Alignment explanation
Indices: 4945437--4945469 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4945427 GTAAACACCA
4945437 TTTTTTATTATTATTTG
1 TTTTTTATTATTATTTG
4945454 TTTTTTATTATTATTT
1 TTTTTTATTATTATTT
4945470 TATTAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTATTATTATTTG
Found at i:4945912 original size:11 final size:11
Alignment explanation
Indices: 4945896--4945929 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
4945886 GGTGGCATTG
4945896 GGGAGGAGAAA
1 GGGAGGAGAAA
4945907 GGGAGGAGAAA
1 GGGAGGAGAAA
*
4945918 AGGAGGAGAAA
1 GGGAGGAGAAA
4945929 G
1 G
4945930 AGTGAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (11 bp):
GGGAGGAGAAA
Found at i:4946688 original size:34 final size:34
Alignment explanation
Indices: 4946615--4946681 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
4946605 TTTATATTTA
* *
4946615 TTTTTATTTTTATTTTATGTTGTTTTTTTTACTG
1 TTTTTATTTTTATTTTATGTTGTTTGTTTTAATG
4946649 TTTTTACTTTTTATTATTAT-TTG-TTGTTTTAAT
1 TTTTTA-TTTTTATT-TTATGTTGTTTGTTTTAAT
4946682 TATTTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 14 0.48
35 11 0.38
36 4 0.14
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (34 bp):
TTTTTATTTTTATTTTATGTTGTTTGTTTTAATG
Found at i:4963431 original size:45 final size:45
Alignment explanation
Indices: 4963362--4963512 Score: 248
Period size: 45 Copynumber: 3.3 Consensus size: 45
4963352 TTTATTTTTG
*
4963362 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAAT-AA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
4963409 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
*
4963454 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
4963500 TTTTTGTGAATAA
1 TTTTT-TGAATAA
4963513 CAAAGCATGG
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
45 73 0.73
46 11 0.11
47 16 0.16
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
Found at i:4969650 original size:2 final size:2
Alignment explanation
Indices: 4969643--4969670 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4969633 AGATCATCCC
4969643 AT 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 AT
4969671 CTCCTCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4973089 original size:13 final size:13
Alignment explanation
Indices: 4973071--4973114 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
4973061 AAGAATAATG
4973071 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
4973084 AAAAAAAGA-AAA
1 AAAAAAAGAGAAA
4973096 AAAAAAA-AGAAA
1 AAAAAAAGAGAAA
*
4973108 AGAAAAA
1 AAAAAAA
4973115 TGAAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 1 0.03
12 19 0.66
13 9 0.31
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:4973095 original size:7 final size:7
Alignment explanation
Indices: 4973072--4973257 Score: 143
Period size: 7 Copynumber: 26.4 Consensus size: 7
4973062 AGAATAATGA
4973072 AAAAAAG
1 AAAAAAG
*
4973079 AGAAAA-
1 AAAAAAG
4973085 AAAAAAG
1 AAAAAAG
4973092 AAAAAA-
1 AAAAAAG
4973098 AAAAAAG
1 AAAAAAG
4973105 --AAAAG
1 AAAAAAG
*
4973110 AAAAATG
1 AAAAAAG
*
4973117 AAAAATG
1 AAAAAAG
*
4973124 AAAAATG
1 AAAAAAG
*
4973131 AAAAATG
1 AAAAAAG
*
4973138 AAAAATG
1 AAAAAAG
*
4973145 AAAAATG
1 AAAAAAG
*
4973152 AAAAATG
1 AAAAAAG
*
4973159 AAAAATG
1 AAAAAAG
*
4973166 AAAAATG
1 AAAAAAG
*
4973173 AAAAATG
1 AAAAAAG
4973180 AAAAAAATG
1 -AAAAAA-G
*
4973189 AAAAATG
1 AAAAAAG
4973196 AAAAAATG
1 AAAAAA-G
4973204 AAAAATA-
1 AAAAA-AG
4973211 AAAAGAAG
1 AAAA-AAG
4973219 AAAAAAG
1 AAAAAAG
4973226 AAAAAAG
1 AAAAAAG
4973233 AAGAAAA-
1 AA-AAAAG
4973240 AAGAAAA-
1 AA-AAAAG
4973247 ATAAAAAG
1 A-AAAAAG
4973255 AAA
1 AAA
4973258 TAAAATGAGG
Statistics
Matches: 160, Mismatches: 6, Indels: 26
0.83 0.03 0.14
Matches are distributed among these distances:
5 5 0.03
6 11 0.07
7 115 0.72
8 27 0.17
9 2 0.01
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (7 bp):
AAAAAAG
Found at i:4973120 original size:21 final size:21
Alignment explanation
Indices: 4973051--4973257 Score: 124
Period size: 21 Copynumber: 9.6 Consensus size: 21
4973041 ATTTCGCTTG
4973051 AAGAAAAATGAAGAATAATGAAAAA
1 AAGAAAAATG-A-AA-AAT-AAAAA
* *
4973076 AAGAGAAAA-AAAAAAGAAAAA
1 AAGA-AAAATGAAAAATAAAAA
*
4973097 AA-AAAAA-G-AAAA-GAAAA
1 AAGAAAAATGAAAAATAAAAA
* *
4973114 ATGAAAAATGAAAAATGAAAA
1 AAGAAAAATGAAAAATAAAAA
* *
4973135 ATGAAAAATGAAAAATGAAAA
1 AAGAAAAATGAAAAATAAAAA
*
4973156 ATGAAAAATGAAAAATGAAAAA
1 AAGAAAAATGAAAAAT-AAAAA
4973178 TGAA-AAAAATGAAAAATGAAAAA
1 --AAGAAAAATGAAAAAT-AAAAA
* *
4973201 ATGAAAAAT-AAAAAGAAGAAAA
1 AAGAAAAATGAAAAA-TA-AAAA
* *
4973223 AAGAAAAAAGAAGAAAAAAGAAA
1 AAGAAAAATGAA-AAATAA-AAA
*
4973246 AATAAAAA-GAAA
1 AAGAAAAATGAAA
4973258 TAAAATGAGG
Statistics
Matches: 156, Mismatches: 12, Indels: 32
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.03
18 9 0.06
19 5 0.03
20 5 0.03
21 57 0.37
22 27 0.17
23 35 0.22
24 5 0.03
25 4 0.03
26 4 0.03
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (21 bp):
AAGAAAAATGAAAAATAAAAA
Found at i:4973126 original size:14 final size:14
Alignment explanation
Indices: 4973105--4973230 Score: 182
Period size: 14 Copynumber: 8.8 Consensus size: 14
4973095 AAAAAAAAAG
4973105 AAAA-GAAAAATGA
1 AAAATGAAAAATGA
4973118 AAAATGAAAAATGA
1 AAAATGAAAAATGA
4973132 AAAATGAAAAATGA
1 AAAATGAAAAATGA
4973146 AAAATGAAAAATGA
1 AAAATGAAAAATGA
4973160 AAAATGAAAAATGA
1 AAAATGAAAAATGA
4973174 AAAATGAAAAAAATGA
1 AAAATG--AAAAATGA
4973190 AAAATGAAAAAATGA
1 AAAATG-AAAAATGA
* *
4973205 AAAATAAAAAGAAGA
1 AAAATGAAAA-ATGA
*
4973220 AAAAAGAAAAA
1 AAAATGAAAAA
4973231 AGAAGAAAAA
Statistics
Matches: 105, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
13 4 0.04
14 62 0.59
15 25 0.24
16 14 0.13
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (14 bp):
AAAATGAAAAATGA
Found at i:4973258 original size:10 final size:9
Alignment explanation
Indices: 4973210--4973262 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
4973200 AATGAAAAAT
4973210 AAAAAGAAGA
1 AAAAAGAA-A
4973220 AAAAAGAAA
1 AAAAAGAAA
4973229 AAAGAAGAAA
1 AAA-AAGAAA
4973239 AAAGAA-AAA
1 AAA-AAGAAA
4973248 TAAAAAGAAA
1 -AAAAAGAAA
4973258 TAAAA
1 -AAAA
4973263 TGAGGGTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.22
10 31 0.77
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:4974623 original size:36 final size:38
Alignment explanation
Indices: 4974534--4974643 Score: 163
Period size: 36 Copynumber: 3.0 Consensus size: 38
4974524 TTAAAACAGG
* * *
4974534 TCAATCTTAAGCCTTCATGAAAGAGCAGTGAAG-AAAT
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
*
4974571 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA-
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
4974608 TC-ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
4974644 CTTGTTTGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 33 0.49
37 31 0.46
38 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (38 bp):
TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
Found at i:4974740 original size:55 final size:54
Alignment explanation
Indices: 4974661--4975026 Score: 305
Period size: 55 Copynumber: 6.6 Consensus size: 54
4974651 GTTGAAGATT
* * * *** *
4974661 GAGTCATATACTCTCTGAAGGAATAGGGGGCAGACAATTTTATTGAAGATTGTTT
1 GAGTCTTATACTCTCT-AAAGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
* *
4974716 GAGTCTTATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCTCTAAA-GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
* * *
4974771 GAGT-TCTATACTCTCTGAAGGAATAGAGAGC-GTACCCGTTT-TATGAAGATTGTTT
1 GAGTCT-TATACTCTCT-AAAGAATAGGGAGCAG-ACCCGTTTAT-TGAAGATTGTTC
* *
4974826 GAGT-TCTATACTCTCTGAAAGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTC
1 GAGTCT-TATACTCTCT-AAAGAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTC
* * * * *
4974881 GAGT-TCTATACTCTCTGAAGAAATAGAGAGCGGACCCGTTTATTAAATATTGTTC
1 GAGTCT-TATACTCTCTAAAG-AATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
* ** * * *** *
4974936 GAGTCTTATACTCCCTGACTGAATAAGGAGCAGACACGTTTGCCGAAGATTATTC
1 GAGTCTTATACTCTCT-AAAGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
4974991 GAGTCTTATACTC-CTTGAAAGAATAGGGAGCAGACC
1 GAGTCTTATACTCTC-T-AAAGAATAGGGAGCAGACC
4975027 TGCCATTTGA
Statistics
Matches: 264, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
54 9 0.03
55 249 0.94
56 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (54 bp):
GAGTCTTATACTCTCTAAAGAATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
Found at i:4974836 original size:110 final size:110
Alignment explanation
Indices: 4974667--4975026 Score: 396
Period size: 110 Copynumber: 3.3 Consensus size: 110
4974657 GATTGAGTCA
* * **
4974667 TATACTCTCTGAAGGAATAGGGGGCAGA-CAATTTTATTGAAGATTGTTTGAGTCTTATACTCCC
1 TATACTCTCTGAAGGAATAGAGAGC-GACCCGTTTTATTGAAGATTGTTTGAGTCTTATACTCCC
4974731 TAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTC
65 TAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTC
*
4974777 TATACTCTCTGAAGGAATAGAGAGCGTACCCGTTTTA-TGAAGATTGTTTGAGT-TCTATACTCT
1 TATACTCTCTGAAGGAATAGAGAGCG-ACCCGTTTTATTGAAGATTGTTTGAGTCT-TATACTCC
* *
4974840 CTGAAA-GAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTTC
64 CT-AAACGAATAGGGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTTC
* * * *
4974887 TATACTCTCTGAAGAAATAGAGAGCGGACCCG-TTTATTAAATATTGTTCGAGTCTTATACTCCC
1 TATACTCTCTGAAGGAATAGAGAGC-GACCCGTTTTATTGAAGATTGTTTGAGTCTTATACTCCC
* * * ** *
4974951 T-GACTGAATAAGGAGCAGACACGTTTGCCGAAGATTATTCGAG-TC
65 TAAAC-GAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTC
* *
4974996 TTATACTC-CTTGAAAGAATAGGGAGCAGACC
1 -TATACTCTC-TGAAGGAATAGAGAGC-GACC
4975027 TGCCATTTGA
Statistics
Matches: 213, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
108 1 0.00
109 10 0.05
110 191 0.90
111 11 0.05
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (110 bp):
TATACTCTCTGAAGGAATAGAGAGCGACCCGTTTTATTGAAGATTGTTTGAGTCTTATACTCCCT
AAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTC
Found at i:4974986 original size:165 final size:166
Alignment explanation
Indices: 4974659--4975026 Score: 394
Period size: 165 Copynumber: 2.2 Consensus size: 166
4974649 TTGTTGAAGA
* * *
4974659 TTGAGTCATATACTCTCTGAAGGAATAGGGGGCAGA-CAATTTTATTGAAGATTGTTTGAGTCTT
1 TTGAGTCATATACTCTCTGAAAGAATAGGGAGCAGACCAATTTTATTGAAGATTGTTCGAGTCTT
* * * *
4974723 ATACTCCCTAAACGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTG
66 ATACTCCCTAAACGAATAGAGAGCAGACCCGTTTATTAAAGATTGTTCGAGTTCTATACTCCCTG
* * * *
4974788 AAGGAATAGAGAGCGTACCCGTTTTATGAAGATTGT
131 AAGGAATAGAGAGCGTACACGTTTGACGAAGATTAT
* * **
4974824 TTGAGTTC-TATACTCTCTGAAAGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTCGAGT-T
1 TTGAG-TCATATACTCTCTGAAAGAATAGGGAGCAGACCAATTTTATTGAAGATTGTTCGAGTCT
* * * *
4974886 CTATACTCTCTGAA-GAAATAGAGAGCGGACCCGTTTATTAAATATTGTTCGAG-TCTTATACTC
65 -TATACTCCCTAAACG-AATAGAGAGCAGACCCGTTTATTAAAGATTGTTCGAGTTC-TATACTC
** *
4974949 CCTGACTGAATA-AGGAGCAG-ACACGTTTGCCGAAGATTAT
127 CCTGAAGGAATAGA-GAGC-GTACACGTTTGACGAAGATTAT
* *
4974989 TCGAGTCTTATACTC-CTTGAAAGAATAGGGAGCAGACC
1 TTGAGTCATATACTCTC-TGAAAGAATAGGGAGCAGACC
4975027 TGCCATTTGA
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
164 8 0.05
165 152 0.90
166 9 0.05
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (166 bp):
TTGAGTCATATACTCTCTGAAAGAATAGGGAGCAGACCAATTTTATTGAAGATTGTTCGAGTCTT
ATACTCCCTAAACGAATAGAGAGCAGACCCGTTTATTAAAGATTGTTCGAGTTCTATACTCCCTG
AAGGAATAGAGAGCGTACACGTTTGACGAAGATTAT
Found at i:4981276 original size:60 final size:61
Alignment explanation
Indices: 4981171--4981342 Score: 206
Period size: 60 Copynumber: 2.9 Consensus size: 61
4981161 GGGGGATATT
* * * * *
4981171 ATTGGTATGTACAAAAGTTTGGGGACTAATTTAGAATAAGG-GTCATAGTTTGA-GGGTGAA
1 ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAAT-AGGAGTCATAGTTTGATGGATGAA
* *
4981231 TTTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAATGGGAGTCATAGTTT-ATGGATGAA
1 ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAATAGGAGTCATAGTTTGATGGATGAA
** * **
4981291 ATTAAAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAGTCATAGTTTG
1 ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAATAGGAGTCATAGTTTG
4981343 GGAATGTATG
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
59 3 0.03
60 92 0.97
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (61 bp):
ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAATAGGAGTCATAGTTTGATGGATGAA
Found at i:4981471 original size:2 final size:2
Alignment explanation
Indices: 4981464--4981541 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
4981454 GTATGGTTTC
*
4981464 AT AT AT AT TT AT AT AT 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 AT AT AT AT AT AT AT AT
4981506 AT AT AT AT AT 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 AT AT AT AT AT
4981542 CATTACCTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4984115 original size:13 final size:13
Alignment explanation
Indices: 4984099--4984123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4984089 ATCTTCGCTC
4984099 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
4984112 TTTTTCTTTTTC
1 TTTTTCTTTTTC
4984124 ATACTTTGTC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:4986296 original size:18 final size:18
Alignment explanation
Indices: 4986273--4986307 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4986263 GTTTTTAAGG
4986273 AGTGGTC-TTCTGGGACAT
1 AGTGGTCATTC-GGGACAT
4986291 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
4986308 AGTTTAAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:4996333 original size:20 final size:19
Alignment explanation
Indices: 4996307--4996364 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
4996297 ATCGATCCAC
* *
4996307 AATGATATAACAGGTAAAA
1 AATGATAAAACCGGTAAAA
*
4996326 ATATGATAAAACCGGTATCAA
1 A-ATGATAAAACCGGTA-AAA
4996347 AATGATAAAACCGGTAAA
1 AATGATAAAACCGGTAAA
4996365 GCGCTACCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 28 0.85
21 3 0.09
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (19 bp):
AATGATAAAACCGGTAAAA
Found at i:4996406 original size:180 final size:181
Alignment explanation
Indices: 4995948--4996406 Score: 635
Period size: 180 Copynumber: 2.5 Consensus size: 181
4995938 ACCCATATCA
* * * *
4995948 ATATAATAGGTAAAAATATCGATAAAACCGGTCA-CGAAAA-GACAATACCGGTAAATC-CTTAC
1 ATATAACAGGTAAAAATAT-GATAAAACCGGT-ATC-AAAATGATAAAACCGGTAAAGCGC-TAC
* **
4996010 CGGATATATTG-AACGTGTCGATACTTTAATATAAGGATTGACACTTTGTGAATTTAAAAGAGAA
62 CGGATATATTGAAAC-TGTCGATACTTT-ATATAAGTATCAACACTTTGTGAATTTAAAAGAGAA
*
4996074 GCAGTTTTAACGTCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAATG
125 GCAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAATG
* * * * * *
4996131 ATATAACAGGTAAATATATG--ACAACCGATATCAAAATGATAAAACCAGTAAAGAGCTACCCGA
1 ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
* * *
4996194 TATATTTAAAGTGTCGATACTTTAATATAAGTATCAACACTTTGTGAATTTAAAAGAGAAGTAGT
66 TATATTGAAACTGTCGATACTTT-ATATAAGTATCAACACTTTGTGAATTTAAAAGAGAAGCAGT
*
4996259 TTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAATG
130 TTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAATG
4996311 ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
1 ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
*
4996376 TATATTGAAACTGTCGATACTTT-CATAAGTA
66 TATATTGAAACTGTCGATACTTTATATAAGTA
4996407 CGTGTAATAA
Statistics
Matches: 243, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
179 5 0.02
180 158 0.65
181 3 0.01
182 60 0.25
183 17 0.07
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (181 bp):
ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
TATATTGAAACTGTCGATACTTTATATAAGTATCAACACTTTGTGAATTTAAAAGAGAAGCAGTT
TTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAATG
Found at i:4998605 original size:21 final size:21
Alignment explanation
Indices: 4998579--4998619 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4998569 AAGACAATCA
4998579 AGAGTCAAAGAGAAACTTGAT
1 AGAGTCAAAGAGAAACTTGAT
*
4998600 AGAGTCGAAGAGAAACTTGA
1 AGAGTCAAAGAGAAACTTGA
4998620 GAGAATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAT
Found at i:4998628 original size:21 final size:21
Alignment explanation
Indices: 4998586--4998643 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
4998576 TCAAGAGTCA
* *
4998586 AAGAGAAACTTGATAGAGTCG
1 AAGAGAAACTTGAGAGAATCG
4998607 AAGAGAAACTTGAGAGAATCG
1 AAGAGAAACTTGAGAGAATCG
* *
4998628 AAGATACACTTGAGAG
1 AAGAGAAACTTGAGAG
4998644 GCATTAGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAGAAACTTGAGAGAATCG
Found at i:4998969 original size:24 final size:21
Alignment explanation
Indices: 4998926--4998983 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
4998916 ACTGAAAAAT
4998926 ATGAAGAAGAAAATAGGGAGG
1 ATGAAGAAGAAAATAGGGAGG
4998947 ATGAAGAAGAAAATAGGGAGG
1 ATGAAGAAGAAAATAGGGAGG
*
4998968 AGGAAGAAGAAAATAG
1 ATGAAGAAGAAAATAG
4998984 AGAAGAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (21 bp):
ATGAAGAAGAAAATAGGGAGG
Found at i:5000421 original size:19 final size:19
Alignment explanation
Indices: 5000397--5000445 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
5000387 AATGTAGGGT
*
5000397 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
5000416 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
5000435 TAATTTTGTAT
1 TAATTTTGTAT
5000446 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5002537 original size:18 final size:18
Alignment explanation
Indices: 5002514--5002549 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5002504 ACTAAACGAT
5002514 CAATGAAGATGAAGATGA
1 CAATGAAGATGAAGATGA
*
5002532 CAATGAAGATGATGATGA
1 CAATGAAGATGAAGATGA
5002550 TGATCCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (18 bp):
CAATGAAGATGAAGATGA
Found at i:5004254 original size:252 final size:252
Alignment explanation
Indices: 5003850--5004305 Score: 702
Period size: 252 Copynumber: 1.8 Consensus size: 252
5003840 AACGATCCAA
* * *
5003850 AAAAATATCGAAACCCATAATTATAATGTAATGGGTAATTTTTCAATGTAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
* * * *
5003915 CCAGTTTTATGAAAAATATGTCTACAATATTTATCGACACTTATTAGTATTGTGTCGATACTTTT
66 CCAGTTTTATGAAAAATAGGTCTACAATATATATCGACACTTATTAATATTGTGTCGATAATTTT
* * *
5003980 TGTCTAGAATGGATGCCAAAAAGGGTGAAC-CTACAAAGTGTCGATACATTTTCATAGAGTGTCG
131 TGTCCAGAATGGATGCCAAAAAGGGTGAACGC-ACAAAGTGTCGATACATTTTCAAAAAGTGTCG
5004044 AT-CCAAAAATGGTTGCACGCATAAAGTTTTGATACATTTATTTAAAGTGTCGATTCC
195 ATCCCAAAAATGGTTGCACGCATAAAGTTTTGATACATTTATTTAAAGTGTCGATTCC
*
5004101 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACCGGTATACATAT
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCGGTATAAATAT
* * * *
5004165 ACCGGTTTTATGAGAGAATAGGTCTATAATATATATCGACACTTCTTAATATTGTGTCGATAATT
65 ACCAGTTTTATGA-AAAATAGGTCTACAATATATATCGACACTTATTAATATTGTGTCGATAATT
* * *
5004230 TTTGTCCAGAATGGATGTCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTTTC
129 TTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTC
5004295 GATCCCAAAAA
194 GATCCCAAAAA
5004306 CATTGAAACC
Statistics
Matches: 183, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
251 70 0.38
252 105 0.57
253 8 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (252 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
CCAGTTTTATGAAAAATAGGTCTACAATATATATCGACACTTATTAATATTGTGTCGATAATTTT
TGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGA
TCCCAAAAATGGTTGCACGCATAAAGTTTTGATACATTTATTTAAAGTGTCGATTCC
Found at i:5004407 original size:200 final size:199
Alignment explanation
Indices: 5004046--5004477 Score: 607
Period size: 200 Copynumber: 2.2 Consensus size: 199
5004036 GAGTGTCGAT
* * * * ** *
5004046 CCAAAAATGGTTGCACGCATAAAGTTTTGATACATTTATTTAAAGTGTCGATTCCAAAAACATCG
1 CCAAAAA-GGATGAACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCG
* ** *
5004111 AAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATACATATACCGGTTTTAT
65 AAACCCATAATTATAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTAT
* *
5004176 GAGAGAATAGGTCTATAATATATATCGACACTTCTT-AATATTGTGTCGATAATTTTTGTCCAGA
130 GAGAGAATAGGTCTATAACATATAGCGACACTTCTTAAAT-TTGTGTCGATAATTTTT-TCCAGA
5004240 ATGGATG
193 ATGGATG
* * * *
5004247 TCAAAAAGGGTGAACGCATAAAGTGTCGATACATTT-TCAAAAAGTTTCGATCCCAAAAACATTG
1 CCAAAAAGGATGAACGCATAAAGTGTCGATACATTTAT-AAAAAGTGTCGATCCCAAAAACATCG
*
5004311 AAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTAT
65 AAACCCATAATTATAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTAT
* * * *
5004376 GAGAGAATAGGTCTATAACATGTAGCGACACTTGTTAAATTTGTGTCGATACTTTTTTTCAGAAT
130 GAGAGAATAGGTCTATAACATATAGCGACACTTCTTAAATTTGTGTCGATAATTTTTTCCAGAAT
5004441 GGATG
195 GGATG
*
5004446 CCAAAAAGGATGAACGCACAAAGTGTCGATAC
1 CCAAAAAGGATGAACGCATAAAGTGTCGATAC
5004478 CGAAAATATC
Statistics
Matches: 205, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
199 42 0.20
200 154 0.75
201 9 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
CCAAAAAGGATGAACGCATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGA
AACCCATAATTATAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATG
AGAGAATAGGTCTATAACATATAGCGACACTTCTTAAATTTGTGTCGATAATTTTTTCCAGAATG
GATG
Found at i:5007570 original size:185 final size:186
Alignment explanation
Indices: 5007237--5007604 Score: 487
Period size: 185 Copynumber: 2.0 Consensus size: 186
5007227 AACATGTCAA
* * * * *
5007237 CATAATGTATCGACGCTTGTGTAATTTGTGTCGATACTTATTGTCCATGATGAATGCACAAACGA
1 CATAAAGTATCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCATGATGAATACACAAAAGA
* * *
5007302 GGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTTTCGATCCCAAAAACATCAAAACCGATA
66 GGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCCATA
* * *
5007367 ATTATAGTATATTAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTCAG
131 AGTATAATATAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTCAG
5007423 CATAAAGTATCGACACTTGCT-AAATTTGTGTCGATACTT-TTGGTCCA-GAATGAATACGA-AA
1 CATAAAGTATCGACACTTG-TGAAATTTGTGTCGATACTTATT-GTCCATG-ATGAATAC-ACAA
* *
5007484 AAG-GGTGCAAC-CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAAC
62 AAGAGGTGC-ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAAC
* * * * *
5007547 CCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACTGGTATAAATATACCTGTTT
126 CCATAAGTATAATATAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTT
5007605 TATGAGAGAA
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
185 105 0.66
186 52 0.33
187 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (186 bp):
CATAAAGTATCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCATGATGAATACACAAAAGA
GGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCCATA
AGTATAATATAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTCAG
Found at i:5007912 original size:64 final size:64
Alignment explanation
Indices: 5007844--5007963 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 64
5007834 TACCTATTAC
5007844 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCCTATTTT
1 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCCTATTTT
* *
5007908 ATTATATAAGCGCTGCCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATG
1 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATG
5007964 ATATAACATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (64 bp):
ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCCTATTTT
Found at i:5009893 original size:23 final size:19
Alignment explanation
Indices: 5009851--5009897 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5009841 AAAACATTTC
5009851 ATAATTATTTACTAATTAAA
1 ATAATTATTTACTAATT-AA
5009871 ATAATTATTTAAACATAATTAA
1 ATAATTATTT--AC-TAATTAA
5009893 ATAAT
1 ATAAT
5009898 AAGTTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATTATTTACTAATTAA
Found at i:5010418 original size:16 final size:16
Alignment explanation
Indices: 5010397--5010437 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5010387 TTTACTTCAT
5010397 AATGATTCAAATACTG
1 AATGATTCAAATACTG
*
5010413 AATGATTCAAATGCTG
1 AATGATTCAAATACTG
5010429 AATGATTCA
1 AATGATTCA
5010438 GAGACTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (16 bp):
AATGATTCAAATACTG
Found at i:5016434 original size:22 final size:22
Alignment explanation
Indices: 5016389--5016440 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
5016379 TCAAAAGGTC
***
5016389 GAAAACGTGTCAAAAGACTGAA
1 GAAAACGTGTCAAAAGAAAAAA
*
5016411 GAAAACGTGTCATAAGAAAAAA
1 GAAAACGTGTCAAAAGAAAAAA
5016433 GAAAACGT
1 GAAAACGT
5016441 ATAATACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.13
Consensus pattern (22 bp):
GAAAACGTGTCAAAAGAAAAAA
Found at i:5016496 original size:18 final size:18
Alignment explanation
Indices: 5016463--5016505 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5016453 TACTTATTGA
5016463 AAATAA-AAAAAAACAAT
1 AAATAATAAAAAAACAAT
*
5016480 AAATAATAAAAAGACAAT
1 AAATAATAAAAAAACAAT
5016498 AAATAATA
1 AAATAATA
5016506 TCAACGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (18 bp):
AAATAATAAAAAAACAAT
Found at i:5032785 original size:60 final size:61
Alignment explanation
Indices: 5032653--5032795 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 61
5032643 AACATAATGA
* * * * *
5032653 ATAG-TCAGGTGACCATTTTGTAACTTTTAATAGTCGAGAGAGTCAACAAAGCAACTCCGT
1 ATAGATCAGGGGACCATTTTGTAACTTTTAATAGTAGAAAAAGTAAACAAAGCAACTCCGT
* *
5032713 ATAGTTTA-GGGACCATTTTGTAACTTTTAATAGTAGAAAAAGTAAACAAAGCAGTA-TCC-T
1 ATAGATCAGGGGACCATTTTGTAACTTTTAATAGTAGAAAAAGTAAACAAAGCA--ACTCCGT
*
5032773 ATA-ATCAGGGGACAATTTGTGTA
1 ATAGATCAGGGGACCATTT-TGTA
5032796 TTTTACCCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
59 2 0.03
60 57 0.83
61 9 0.13
62 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (61 bp):
ATAGATCAGGGGACCATTTTGTAACTTTTAATAGTAGAAAAAGTAAACAAAGCAACTCCGT
Found at i:5033217 original size:12 final size:12
Alignment explanation
Indices: 5033202--5033226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5033192 CAACGGCAAC
5033202 GACAACGATAAT
1 GACAACGATAAT
5033214 GACAACGATAAT
1 GACAACGATAAT
5033226 G
1 G
5033227 GTAATGACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (12 bp):
GACAACGATAAT
Found at i:5033749 original size:36 final size:37
Alignment explanation
Indices: 5033685--5033759 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
5033675 AACAAATGAT
* *
5033685 AAATAAATATTAAATAAATCAAATGG-AAAAGGAAAA
1 AAATAAATATAAAATAAATCAAAGGGAAAAAGGAAAA
*
5033721 AAATAAA-ATAAAATAAATCAAAAGGGAAAAAGGGAAA
1 AAATAAATATAAAATAAATC-AAAGGGAAAAAGGAAAA
5033758 AA
1 AA
5033760 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 11 0.32
36 12 0.35
37 11 0.32
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (37 bp):
AAATAAATATAAAATAAATCAAAGGGAAAAAGGAAAA
Found at i:5033793 original size:17 final size:16
Alignment explanation
Indices: 5033765--5033802 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
5033755 AAAAATGAAG
*
5033765 AAAA-AAATAAAAGCA
1 AAAATAAATAAAAGAA
5033780 AAAATAAATCAAAAGAA
1 AAAATAAAT-AAAAGAA
5033797 AAAATA
1 AAAATA
5033803 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAATAAATAAAAGAA
Found at i:5033837 original size:28 final size:26
Alignment explanation
Indices: 5033795--5033862 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 26
5033785 AAATCAAAAG
*
5033795 AAAAAATATTAAATAAATGTGAAAACAA
1 AAAAAATA-AAAATAAATGT-AAAACAA
*
5033823 AAATAAATAAAAAT--ATGTATAACAA
1 AAA-AAATAAAAATAAATGTAAAACAA
*
5033848 AAAAAATAAAGATAA
1 AAAAAATAAAAATAA
5033863 GTGAAATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 9 0.26
25 9 0.26
26 4 0.12
28 7 0.21
29 5 0.15
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAAAATAAAAATAAATGTAAAACAA
Found at i:5033926 original size:33 final size:32
Alignment explanation
Indices: 5033876--5033965 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
5033866 AAATTGAGTA
*
5033876 AAAAAGATATAATAATAAAAAAAGAAAAAAAAT
1 AAAAAGAAATAA-AATAAAAAAAGAAAAAAAAT
* *
5033909 AAAAAGGAAATAAAATAAATAAAAGTAGAAAAAT
1 AAAAA-GAAATAAAATAAA-AAAAGAAAAAAAAT
* *
5033943 GAAATAGAATAAAAAATAAAAAA
1 -AAAAAGAA-ATAAAATAAAAAA
5033966 GGATAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
33 11 0.23
34 24 0.50
35 13 0.27
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (32 bp):
AAAAAGAAATAAAATAAAAAAAGAAAAAAAAT
Found at i:5035587 original size:84 final size:82
Alignment explanation
Indices: 5035441--5035594 Score: 220
Period size: 84 Copynumber: 1.9 Consensus size: 82
5035431 TGACATATAT
* * ** *
5035441 CCCTTCTTGCCTTATCTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCAAAGG
1 CCCTTCTAGCCTTATCTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAATCAAAATCAAAGG
5035506 TCTTTGGTTGGCAGATAA
66 T-TTTGGTTGGCAGATAA
*
5035524 CCCTTCTAGCCTTGAGT-TATGTTGTAAATGATATGCCTTTGAGCTGAGCGTAATCAAAATCAAA
1 CCCTTCTAGCCTT-A-TCTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAATCAAAATCAAA
5035588 GGTTTTG
64 GGTTTTG
5035595 TGTTTCAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
83 16 0.25
84 46 0.73
85 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (82 bp):
CCCTTCTAGCCTTATCTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAATCAAAATCAAAGG
TTTTGGTTGGCAGATAA
Found at i:5035632 original size:33 final size:33
Alignment explanation
Indices: 5035583--5035675 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
5035573 GTAATCAAAA
*
5035583 TCAAAGG--TTTTGTGTTTCAAGAGAAA-TATTT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGA-TT
5035614 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
*
5035647 TCAAAGGTTTTTTGTTTTTCAAGAGAAAC
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
5035676 TGTCTCAGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 7 0.12
33 49 0.86
34 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (33 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
Found at i:5035719 original size:69 final size:67
Alignment explanation
Indices: 5035623--5035766 Score: 161
Period size: 65 Copynumber: 2.1 Consensus size: 67
5035613 TTCAAAGGTT
* *
5035623 TTTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTTTTGTTTTTCAAGAGAAACTGTCTC-AGGGA
1 TTTTGT-TTTCAAGAGAAACGATTTCAAA-G-ATTTTG--TTTCAAGAGAAACTGTCTCAAGAGA
*
5035687 GGCAAAA
61 GACAAAA
* *
5035694 TTTTGTTTT-AAGAGAAA-TATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTTGTTTTCAAGAGAAACGAT-TTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
5035757 AAA
65 AAA
5035760 -TTTGTTT
1 TTTTGTTT
5035767 CAAAGGAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
65 25 0.38
66 10 0.15
67 5 0.08
68 3 0.05
69 14 0.21
70 3 0.05
71 6 0.09
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (67 bp):
TTTTGTTTTCAAGAGAAACGATTTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AA
Found at i:5035775 original size:36 final size:36
Alignment explanation
Indices: 5035724--5035839 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
5035714 ATTCAAAGAT
5035724 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
5035760 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
5035796 TTTCTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
5035832 CTTTGTTT
1 -TTTGTTT
5035840 TGAGTAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 68 0.92
37 6 0.08
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:5035805 original size:21 final size:21
Alignment explanation
Indices: 5035745--5035806 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5035735 GGAAACTGTC
*
5035745 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTCTT
* *
5035766 TCAA-AG-G--AAACTGTC--
1 TCAAGAGAGACAAAATTTCTT
5035781 TCAAGAGAGACAAAATTTCTT
1 TCAAGAGAGACAAAATTTCTT
5035802 TCAAG
1 TCAAG
5035807 GGAAACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 4 0.13
16 2 0.07
17 6 0.20
19 7 0.23
20 2 0.07
21 9 0.30
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTCTT
Found at i:5036138 original size:116 final size:116
Alignment explanation
Indices: 5035925--5036157 Score: 360
Period size: 116 Copynumber: 2.0 Consensus size: 116
5035915 ATTCCTAAGG
* * * *
5035925 ATGAATGTTGTTGGTGGGTACGATTCCCTTCATAGTGAAGTTGAAACCGTGGATGGCCCATTCGT
1 ATGAATGTTGCTGGTGAGCACGATTCCCTTCATAGTGAAGTTGAAACCGTGGATGGCCCATTCAT
* *
5035990 TGTGAAGTTGAGCCTTGAATTGGATATTCTTCGCCGTGAAGTTGAAATCCA
66 TGTGAAGTTGAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCA
* *
5036041 ATGAATGTTGCTGGTGAGCACGATTCCCTTCGTTGTGAAGTTGAAACCGTGGATGGCCCATTCAT
1 ATGAATGTTGCTGGTGAGCACGATTCCCTTCATAGTGAAGTTGAAACCGTGGATGGCCCATTCAT
* *
5036106 TTTGAAGTTGAGCCTT-AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCA
66 TGTGAAGTTGAGCCTTGAA-TTGAATATCCTTCGCCGTGAAGTTGAAATCCA
5036157 A
1 A
5036158 GCTTGTATTG
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
115 2 0.02
116 104 0.98
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (116 bp):
ATGAATGTTGCTGGTGAGCACGATTCCCTTCATAGTGAAGTTGAAACCGTGGATGGCCCATTCAT
TGTGAAGTTGAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCA
Found at i:5036362 original size:43 final size:43
Alignment explanation
Indices: 5036299--5036381 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
5036289 CTTGTGTAGA
* * *
5036299 TGGGCATGATATCCTTCGTCGT-GAAGTTGAAATCGTGGATTTG
1 TGGGCACGATATCCTCCGTCGTAG-AGTCGAAATCGTGGATTTG
*
5036342 TGGGCACGATATCCTCCGTCGTAGAGTCGAAATTGTGGAT
1 TGGGCACGATATCCTCCGTCGTAGAGTCGAAATCGTGGAT
5036382 GGGCCCTTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 34 0.97
44 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
TGGGCACGATATCCTCCGTCGTAGAGTCGAAATCGTGGATTTG
Found at i:5040993 original size:31 final size:31
Alignment explanation
Indices: 5040922--5040986 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
5040912 AACAAATGAT
* *
5040922 AAATAAATATTAAATAAATCAAATGGAAAAGG
1 AAATAAA-ATAAAATAAATCAAATGAAAAAGG
5040954 AAATAAAATAAAATAAATCAAAAGTGAAAAAGG
1 AAATAAAATAAAATAAATC-AAA-TGAAAAAGG
5040987 GAAAAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 11 0.38
32 10 0.34
33 8 0.28
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.18
Consensus pattern (31 bp):
AAATAAAATAAAATAAATCAAATGAAAAAGG
Found at i:5041126 original size:17 final size:16
Alignment explanation
Indices: 5041113--5041148 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5041103 GTAAAAAAGG
5041113 AAATAATAATAAAAACA
1 AAATAATAA-AAAAACA
*
5041130 AAATAATAAAAAAATA
1 AAATAATAAAAAAACA
5041146 AAA
1 AAA
5041149 AGGAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAATAATAAAAAAACA
Found at i:5041132 original size:22 final size:20
Alignment explanation
Indices: 5041105--5041168 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
5041095 TAAATTGAGT
5041105 AAAAAAGGAAATAATAATAAA
1 AAAAAAGGAAATAA-AATAAA
*
5041126 AACAAAA--TAATAAAA-AAA
1 AA-AAAAGGAAATAAAATAAA
*
5041144 TAAAAAGGAAATAAAATAAA
1 AAAAAAGGAAATAAAATAAA
5041164 TAAAA
1 -AAAA
5041169 GTGAAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 9 0.26
20 8 0.24
21 5 0.15
22 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (20 bp):
AAAAAAGGAAATAAAATAAA
Found at i:5041149 original size:17 final size:17
Alignment explanation
Indices: 5041113--5041168 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
5041103 GTAAAAAAGG
*
5041113 AAATAATAATAAAAA-CA
1 AAATAATAA-AAAAATAA
5041130 AAATAATAAAAAAATAA
1 AAATAATAAAAAAATAA
*
5041147 AAAGGAAATAAAATAAATAA
1 AAA--TAATAAAA-AAATAA
5041167 AA
1 AA
5041169 GTGAAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 5 0.15
17 13 0.39
19 7 0.21
20 8 0.24
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (17 bp):
AAATAATAAAAAAATAA
Found at i:5041175 original size:27 final size:24
Alignment explanation
Indices: 5041120--5041202 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 24
5041110 AGGAAATAAT
5041120 AATAAAAACAAAAT--AATAAAAA
1 AATAAAAACAAAATAAAATAAAAA
**
5041142 AATAAAAAGGAAATAAAATAAATAA
1 AATAAAAACAAAATAAAATAAA-AA
*
5041167 AAGTGAAAAACAAAATAGAATAAACAA
1 AA-T-AAAAACAAAATAAAATAAA-AA
5041194 TAATAAAAA
1 -AATAAAAA
5041203 AAGGATAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 12 0.24
24 6 0.12
25 4 0.08
26 6 0.12
27 19 0.39
28 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (24 bp):
AATAAAAACAAAATAAAATAAAAA
Found at i:5042113 original size:3 final size:3
Alignment explanation
Indices: 5042093--5042144 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
5042083 ACAAAACATT
5042093 TTA TTA -TA TT- TTA TTTA TTA TTA TTA TTA TTA TTA TT- TT- TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5042135 TT- TTA TTA TT
1 TTA TTA TTA TT
5042145 TTTGTAGGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 10 0.23
3 31 0.70
4 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:5042145 original size:15 final size:15
Alignment explanation
Indices: 5042090--5042147 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
5042080 TCTACAAAAC
*
5042090 ATTTTATTATATTTT
1 ATTTTATTATTTTTT
*
5042105 A-TTTATTA-TTATT
1 ATTTTATTATTTTTT
5042118 ATTATTATTATTTTTT
1 ATT-TTATTATTTTTT
5042134 ATTTTATTATTTTT
1 ATTTTATTATTTTT
5042148 GTAGGCCCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.11
14 8 0.22
15 18 0.49
16 7 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTATTATTTTTT
Found at i:5042642 original size:27 final size:28
Alignment explanation
Indices: 5042603--5042663 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
5042593 TTACATTGTT
5042603 ATATATATATATATTTAAT-TTTTTTATTA
1 ATAT-TATATATA-TTAATATTTTTTATTA
5042632 ATATTAT-TATATTAATATTTTTTATTA
1 ATATTATATATATTAATATTTTTTATTA
*
5042659 TTATT
1 ATATT
5042664 TTCTATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.17
27 18 0.60
28 3 0.10
29 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATATTATATATATTAATATTTTTTATTA
Found at i:5042663 original size:13 final size:13
Alignment explanation
Indices: 5042617--5042665 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
5042607 ATATATATAT
5042617 TTAAT-TTTTTTA
1 TTAATATTTTTTA
*
5042629 TTAATATTATTATA
1 TTAATATT-TTTTA
5042643 TTAATATTTTTTA
1 TTAATATTTTTTA
*
5042656 TTATTATTTT
1 TTAATATTTT
5042666 CTATGTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 5 0.16
13 15 0.47
14 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATATTTTTTA
Found at i:5044372 original size:20 final size:20
Alignment explanation
Indices: 5044326--5044372 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5044316 CAGACGAAGG
* *
5044326 CAGAAGACTAGTCAACATGT
1 CAGAAGCCTAGTCAACATAT
5044346 CAGAAGCCTAGTCAACATAT
1 CAGAAGCCTAGTCAACATAT
5044366 CAGAAGC
1 CAGAAGC
5044373 TGTCAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
CAGAAGCCTAGTCAACATAT
Found at i:5046555 original size:103 final size:103
Alignment explanation
Indices: 5046370--5046658 Score: 393
Period size: 103 Copynumber: 2.8 Consensus size: 103
5046360 GATGGTGGTT
* * * * * *
5046370 GCTCAACTTCATAGCGAAGGGGCGACTGTCAGCAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAACGAAGAGGCGACTG--A-CTATCAACTTTTCAGTTTCATTCAGATTCAATT
5046435 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
63 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
5046476 GCTCAACTTCACAATGAAGGGGCGACTGACTATCAACCTTTT-AGTTTCATTCAGATTCAATTTC
1 GCTCAACTTCACAACGAAGAGGCGACTGACTATCAA-CTTTTCAGTTTCATTCAGATTCAATTTC
* *
5046540 AACTTCACAGTGAAGGATATTGGACTCGAGACAACACTA
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
5046579 GCTCAACTTCACAGCGAAGAGGTGGCTGACTGTCAACTTTTCAGTTTCATTCAGAGTT-AATTTC
1 GCTCAACTTCACAACGAAGAGGCGACTGACTATCAACTTTTCAGTTTCATTCAGA-TTCAATTTC
5046643 AACTTCACAGCGAAGG
65 AACTTCACAGCGAAGG
5046659 GGCGACTAAC
Statistics
Matches: 165, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
102 5 0.03
103 127 0.77
104 8 0.05
106 25 0.15
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (103 bp):
GCTCAACTTCACAACGAAGAGGCGACTGACTATCAACTTTTCAGTTTCATTCAGATTCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:5046674 original size:60 final size:61
Alignment explanation
Indices: 5046581--5046725 Score: 175
Period size: 67 Copynumber: 2.3 Consensus size: 61
5046571 CAACACTAGC
* * * * *
5046581 TCAACTTCACAGCGAAGAGGTGGCTGACTGT-CAACTTTTCAGTTTCATTCAGAGTTAATT
1 TCAACTTCACAGCGAAGGGGCGACTAACTGTACAACTTTTCAGTTTCATTCAGAGTCAATT
5046641 TCAACTTCACAGCGAAGGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTAACTGT------ACAACTTTTCAGTTTCATTCAGAGTCAA
5046706 TT
60 TT
*
5046708 TCAACTTCACAACGAAGG
1 TCAACTTCACAGCGAAGG
5046726 ATATTGGACT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
60 27 0.38
67 45 0.62
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (61 bp):
TCAACTTCACAGCGAAGGGGCGACTAACTGTACAACTTTTCAGTTTCATTCAGAGTCAATT
Found at i:5046785 original size:108 final size:107
Alignment explanation
Indices: 5046641--5046949 Score: 414
Period size: 108 Copynumber: 2.9 Consensus size: 107
5046631 AGAGTTAATT
*
5046641 TCAACTTCACAGCGAAGGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACA-CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCA-AGTCAA
*
5046706 TTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATACAAGC
64 TTTCAACTTCAC-ACGAAGGATATTGGACTCGAGACAACACAAGC
* * *
5046751 TCAACTTCAC-TGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGCTTCTTTCAAAGTCAAT
1 TCAACTTCACACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC-AAGTCAAT
*
5046815 TTCAACTTCACA-GAAGGATATTAGACTCGAGACAACACAAGC
65 TTCAACTTCACACGAAGGATATTGGACTCGAGACAACACAAGC
* * * * *
5046857 TCAACTTCACAGCGAAGGGGTGGCTGGCTGTTAACAAACAACTTTCCAGTTT-A-T--AGTCAAT
1 TCAACTTCACA-CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAGTCAAT
*
5046918 TTCAACTTCACGACGAAGGATATTGGCCTCGA
65 TTCAACTTCAC-ACGAAGGATATTGGACTCGA
5046950 AATAGCACAA
Statistics
Matches: 178, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
103 18 0.10
104 1 0.01
105 16 0.09
106 39 0.22
107 1 0.01
108 92 0.52
109 1 0.01
110 10 0.06
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (107 bp):
TCAACTTCACACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAGTCAATT
TCAACTTCACACGAAGGATATTGGACTCGAGACAACACAAGC
Found at i:5047301 original size:84 final size:81
Alignment explanation
Indices: 5047068--5047497 Score: 386
Period size: 84 Copynumber: 5.3 Consensus size: 81
5047058 TCGTACCCAC
* * * * * * *
5047068 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA-GTG
1 CAAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCG
5047132 A-ATGAGGGCTATCTGC-
66 AGA--AGGGCTATCTGCT
* * * * * *
5047148 CAAA-ACCCTCGAGTTTGATTACACTCAGCTTCGAGGGTACATCATTTGCAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCA-CCTCCAAGGCACATCATTTGCAGCATAACTCAAGGC
* *
5047212 TAGAAGGGTTATCTGCT
65 GAGAAGGGCTATCTGCT
* *
5047229 AACAAAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGCACATCATTTGCAGCATATCTTAAG
1 --C-AAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGCACATCATTTGCAGCATAACTCAAG
*
5047294 TCGAGAAGGGCTATCTGC-
63 GCGAGAAGGGCTATCTGCT
* * * * * *
5047312 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCA-CCTCCAAGGCACATCATTTGCAGCATAACTCAAGGC
* * * *
5047377 TAGAAGGGTTATATGTCAA
65 GAGAAGGGCTATCTG-C-T
* * * * * * *
5047396 CAAAGACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCTCCATCATTTGCAACATAGCTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGC-ACATCATTTGCAGCATAACTCAAGGC
* * *
5047461 AATAAGGGCTATCTTC-
65 GAGAAGGGCTATCTGCT
5047477 CAAAGACCTTCGAGTTCGATT
1 CAAAGACCTTCGAGTTCGATT
5047498 CGATTCAGCT
Statistics
Matches: 285, Mismatches: 52, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
79 20 0.07
80 67 0.24
81 63 0.22
82 2 0.01
83 8 0.03
84 104 0.36
85 21 0.07
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (81 bp):
CAAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCG
AGAAGGGCTATCTGCT
Found at i:5047403 original size:164 final size:163
Alignment explanation
Indices: 5047068--5047513 Score: 605
Period size: 165 Copynumber: 2.7 Consensus size: 163
5047058 TCGTACCCAC
* *
5047068 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT-G
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
* * *
5047132 AATGAGGGCTATCTGCCAAA-ACCCTCGAGTTTGATTACACTCAGCTTCGAGGGTACATCATTTG
66 AA--AGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
* *
5047196 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCTAA
129 CAACATAACTCAAGGCTAGAAGGGTTATATGCTAA
* * *
5047231 CAAAAGACCTTCGAGTTCGATTACACTCACCTCCAAGGCACATCATTTGCAGCATATCTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
5047296 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
65 GA-AAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
5047361 CAACATAACTCAAGGCTAGAAGGGTTATATG-TCAA
129 CAACATAACTCAAGGCTAGAAGGGTTATATGCT-AA
* * * * * *
5047396 CAAAGACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCTCCATCATTTGCAACATAGCTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGC-ACATCATTTGCAGCATAGCTTAAGTC
* * * *
5047461 AATAAGGGCTATCTTCCAAAGACCTTCGAGTTCGATT-CGATTCAGC-TCGAGGG
65 GA-AAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC-ACTCAGCTTCGAGGG
5047514 TGTATCAACC
Statistics
Matches: 252, Mismatches: 24, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
163 1 0.00
164 115 0.46
165 135 0.54
166 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (163 bp):
CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
AAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
ACATAACTCAAGGCTAGAAGGGTTATATGCTAA
Found at i:5047894 original size:27 final size:24
Alignment explanation
Indices: 5047837--5047898 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
5047827 CTACAAAAAC
5047837 ATTTTATTA-TATTTTATTTATTT
1 ATTTTATTATTATTTTATTTATTT
*
5047860 ATTATTATTATTATTGTTAATATTTTTT
1 ATT-TTATTATTATT-TT-AT-TTATTT
5047888 ATTTTATTATT
1 ATTTTATTATT
5047899 TTTGCAAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 4 0.12
26 2 0.06
27 10 0.30
28 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (24 bp):
ATTTTATTATTATTTTATTTATTT
Found at i:5047901 original size:9 final size:9
Alignment explanation
Indices: 5047838--5047901 Score: 55
Period size: 9 Copynumber: 7.4 Consensus size: 9
5047828 TACAAAAACA
5047838 TTTTATTAT
1 TTTTATTAT
5047847 ATTTTATT-T
1 -TTTTATTAT
*
5047856 ATTTATTAT
1 TTTTATTAT
*
5047865 TATTATTAT
1 TTTTATTAT
* *
5047874 TGTTAATA-
1 TTTTATTAT
5047882 TTTT-TTA-
1 TTTTATTAT
5047889 TTTTATTAT
1 TTTTATTAT
5047898 TTTT
1 TTTT
5047902 GCAAGCCCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.14
8 12 0.27
9 19 0.43
10 7 0.16
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTATTAT
Found at i:5048836 original size:18 final size:18
Alignment explanation
Indices: 5048815--5048850 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5048805 ACAACAACAG
* *
5048815 TAGTGACGACAATGATAA
1 TAGTAACGACAACGATAA
5048833 TAGTAACGACAACGATAA
1 TAGTAACGACAACGATAA
5048851 CGGCATGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.19
Consensus pattern (18 bp):
TAGTAACGACAACGATAA
Found at i:5049192 original size:24 final size:24
Alignment explanation
Indices: 5049156--5049212 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5049146 CAATGATAAC
* *
5049156 GACAACAATGGTAATGGAAACAGA-
1 GACAATAACGGTAATGGAAACA-AT
5049180 GACAATAACGGTAATGGAAACAAT
1 GACAATAACGGTAATGGAAACAAT
5049204 GACAATAAC
1 GACAATAAC
5049213 AACGGCGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (24 bp):
GACAATAACGGTAATGGAAACAAT
Found at i:5052958 original size:31 final size:31
Alignment explanation
Indices: 5052922--5052999 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
5052912 AACTAACTCG
* *
5052922 TTTCTTTTTGTTTGGTTTCTACTAACATTGA
1 TTTCTTTTTGTCTAGTTTCTACTAACATTGA
5052953 TTTCTTTTTGTCTAGTTTCTACTAACATTGA
1 TTTCTTTTTGTCTAGTTTCTACTAACATTGA
5052984 TTTCTTTTTGTCTAGT
1 TTTCTTTTTGTCTAGT
5053000 CTTGTTGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.15, C:0.14, G:0.12, T:0.59
Consensus pattern (31 bp):
TTTCTTTTTGTCTAGTTTCTACTAACATTGA
Found at i:5055745 original size:58 final size:56
Alignment explanation
Indices: 5055668--5055875 Score: 221
Period size: 57 Copynumber: 3.7 Consensus size: 56
5055658 TTCTAAAGAG
* *
5055668 TTTTAAAAGAAACTAAGCCTGATTTTCAGGAGTTTCTTGATTATGATTTTCAATGAA
1 TTTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGA-TATGATTTTCAATGAA
* *
5055725 TTTTTAAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTTG--ATG-TTTTCAAATGAG
1 TTTTT-AAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATATGATTTTC-AATGAA
* * * * * *
5055780 TTTTT--AGAAACTCAGCCTGATTTTCAGGGGTTTCTTGATGATTATTTCCAAAGAA
1 TTTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGAT-ATGATTTTCAATGAA
* *
5055835 TTTTTTAAGAAACTAAGCCTAATTTTTA-GAGGTTTCTTGAT
1 TTTTTAAAGAAACTAAGCCTAATTTTCAGGA-GTTTCTTGAT
5055876 GATAACTTAA
Statistics
Matches: 126, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
52 28 0.22
54 5 0.04
55 24 0.19
56 5 0.04
57 32 0.25
58 32 0.25
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (56 bp):
TTTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATATGATTTTCAATGAA
Found at i:5056450 original size:135 final size:137
Alignment explanation
Indices: 5056192--5056494 Score: 396
Period size: 135 Copynumber: 2.2 Consensus size: 137
5056182 TTCTTTAAGC
* * * * *
5056192 CAACTACGCCTCGCTTGAGGGATTAACATTTTCAAATGGAGAGTTCATAATGATAAGAACTCATC
1 CAACGACGCCTCGCTTAAGGGATTAACATCTTCAAATGAAGAGTTCATAATGAGAAGAACTCATC
* *
5056257 CGACAGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTTGACCTATCACTCGATTCATGACAT
66 CGACAGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTTGACCTATCACTCAATTCACGACAT
*
5056322 TTTGAAT
131 TTCGAAT
5056329 CAACGACGCCTCGCTTAAGGGATTAACA-CTTCAAA-GAAGAGTTCATAATGAGAAGAACTCATC
1 CAACGACGCCTCGCTTAAGGGATTAACATCTTCAAATGAAGAGTTCATAATGAGAAGAACTCATC
* * * * * * *
5056392 TGATAGAGGGAGAATAAGTTCATAATGAGAAGAGCTTGTTTGACCTATCGCTTAATTCACGACAT
66 CGACAGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTTGACCTATCACTCAATTCACGACAT
5056457 TTCGAAT
131 TTCGAAT
* * * * *
5056464 TAGCGACACCTCACTTGAA-GGATCAACATCT
1 CAACGACGCCTCGCTT-AAGGGATTAACATCT
5056495 CGCTTGAGAT
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
135 108 0.75
136 10 0.07
137 26 0.18
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (137 bp):
CAACGACGCCTCGCTTAAGGGATTAACATCTTCAAATGAAGAGTTCATAATGAGAAGAACTCATC
CGACAGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTTGACCTATCACTCAATTCACGACAT
TTCGAAT
Found at i:5056534 original size:39 final size:39
Alignment explanation
Indices: 5056491--5056854 Score: 508
Period size: 39 Copynumber: 9.5 Consensus size: 39
5056481 AAGGATCAAC
5056491 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
5056530 ATCTCGCTTGAGATTGTTTGACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
5056569 ATCTTGCTTGAGATAGTTTCACTCAAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
5056608 ATCTCGCTTGAGATAGTTTCACTCGAAACTGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
5056646 ATCTCGCTTGAGATAGTTTCACTTGAAACATAACATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
5056685 ATCTCGCTT--G--AG-TTCACTCGAAAAAGAAGACTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
5056719 ATCTCGCTTGAGATAGTTTTACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
5056758 ATCTCACTTGAGATAGTTTCACTCAAAACAGAAGAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG-ATTTT
* * *
5056798 ATCTCGCTTAAGGTAGTTTCACTCGAAACATAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
5056836 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
5056855 TTCTTAAAAC
Statistics
Matches: 285, Mismatches: 33, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
34 26 0.09
35 2 0.01
36 1 0.00
37 1 0.00
38 54 0.19
39 167 0.59
40 34 0.12
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:5056729 original size:189 final size:190
Alignment explanation
Indices: 5056508--5056854 Score: 581
Period size: 189 Copynumber: 1.8 Consensus size: 190
5056498 TTGAGATAGT
* * *
5056508 TTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATTGTTTGACTCGAAACAGAAGATTTTATCT
1 TTCACTCGAAAAAGAAGACTTTATCTCGCTTGAGATAGTTTGACTCGAAACAGAAGATTTTATCT
** *
5056573 TGCTTGAGATAGTTTCACTCAAAACAGAAG-ATTTTATCTCGCTTGAGATAGTTTCACTCGAAAC
66 CACTTGAGATAGTTTCACTCAAAACAGAAGAATTTTATCTCGCTTAAGATAGTTTCACTCGAAAC
*
5056637 -TGAAGATTTATCTCGCTTGAGATAGTTTCACTTGAAACATAACATTTTATCTCGCTTGAG
131 AT-AAGATTTATCTCACTTGAGATAGTTTCACTTGAAACATAACATTTTATCTCGCTTGAG
*
5056697 TTCACTCGAAAAAGAAGACTTTATCTCGCTTGAGATAGTTTTACTCGAAACAGAAGATTTTATCT
1 TTCACTCGAAAAAGAAGACTTTATCTCGCTTGAGATAGTTTGACTCGAAACAGAAGATTTTATCT
*
5056762 CACTTGAGATAGTTTCACTCAAAACAGAAGAATTTTATCTCGCTTAAGGTAGTTTCACTCGAAAC
66 CACTTGAGATAGTTTCACTCAAAACAGAAGAATTTTATCTCGCTTAAGATAGTTTCACTCGAAAC
*
5056827 ATAAGATTTATCTCACTTGAGATTGTTT
131 ATAAGATTTATCTCACTTGAGATAGTTT
5056855 TTCTTAAAAC
Statistics
Matches: 146, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
189 89 0.61
190 56 0.38
191 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (190 bp):
TTCACTCGAAAAAGAAGACTTTATCTCGCTTGAGATAGTTTGACTCGAAACAGAAGATTTTATCT
CACTTGAGATAGTTTCACTCAAAACAGAAGAATTTTATCTCGCTTAAGATAGTTTCACTCGAAAC
ATAAGATTTATCTCACTTGAGATAGTTTCACTTGAAACATAACATTTTATCTCGCTTGAG
Found at i:5056739 original size:20 final size:20
Alignment explanation
Indices: 5056716--5056776 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
5056706 AAAAGAAGAC
5056716 TTTATCTCGCTTGAGATAGT
1 TTTATCTCGCTTGAGATAGT
****
5056736 TTTA-CTCGAAACAGA-AGAT
1 TTTATCTCGCTTGAGATAG-T
*
5056755 TTTATCTCACTTGAGATAGT
1 TTTATCTCGCTTGAGATAGT
5056775 TT
1 TT
5056777 CACTCAAAAC
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
18 2 0.07
19 12 0.41
20 13 0.45
21 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (20 bp):
TTTATCTCGCTTGAGATAGT
Found at i:5056963 original size:59 final size:59
Alignment explanation
Indices: 5056866--5056989 Score: 176
Period size: 59 Copynumber: 2.1 Consensus size: 59
5056856 TCTTAAAACG
* *
5056866 AACAACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCATAACCCTTCGAATC
1 AACAACGCCCCACCAGAGGGGATAACATTTCCTTTGCTCGATTCATAACACTTCGAATC
* * * * * *
5056925 AACATCGCCCTACTAGAGGGGATCACATTTCTTTTGCTCGATTCATAACACTTCTAATC
1 AACAACGCCCCACCAGAGGGGATAACATTTCCTTTGCTCGATTCATAACACTTCGAATC
5056984 AACAAC
1 AACAAC
5056990 AATCACTCGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (59 bp):
AACAACGCCCCACCAGAGGGGATAACATTTCCTTTGCTCGATTCATAACACTTCGAATC
Found at i:5058732 original size:7 final size:7
Alignment explanation
Indices: 5058720--5058760 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
5058710 ATTTTATGTT
5058720 TATTTTA
1 TATTTTA
5058727 TATTTTA
1 TATTTTA
5058734 CT-TTTTA
1 -TATTTTA
5058741 TATTTTA
1 TATTTTA
5058748 TATTTTA
1 TATTTTA
5058755 T-TTTTA
1 TATTTTA
5058761 AATTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 25 0.78
8 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:5058746 original size:21 final size:20
Alignment explanation
Indices: 5058720--5058760 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
5058710 ATTTTATGTT
5058720 TATTTTATATTTTACTTTTTA
1 TATTTTATATTTTA-TTTTTA
5058741 TATTTTATATTTTATTTTTA
1 TATTTTATATTTTATTTTTA
5058761 AATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTATATTTTATTTTTA
Found at i:5061353 original size:45 final size:45
Alignment explanation
Indices: 5061276--5061362 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
5061266 TGGCCGCACT
*
5061276 TGGTAATAGAGTTTGGGAGTCGATTAAAAACTTTAAAAAAATCAG
1 TGGTAATAGAGTTTGGGAGTCAATTAAAAACTTTAAAAAAATCAG
* * *
5061321 TGGTAATAGAGTTTGGGGGTCAATTTAGAACTTTAAAAAAAT
1 TGGTAATAGAGTTTGGGAGTCAATTAAAAACTTTAAAAAAAT
5061363 TTGAAGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (45 bp):
TGGTAATAGAGTTTGGGAGTCAATTAAAAACTTTAAAAAAATCAG
Found at i:5062379 original size:200 final size:198
Alignment explanation
Indices: 5061902--5062486 Score: 739
Period size: 199 Copynumber: 2.9 Consensus size: 198
5061892 TTCTATACAC
* * * * * * * * * * * *
5061902 ATGTTCGAGTGCTATTTTCGGGGTGTAAATTGCAAAATTTTCGTAAAT-TATAAACGTGGAGGCA
1 ATGTTCGAGTGTTATCTTCCGGTTGTAAATAGGAGAGTTTTCGT-AATCTATAAGCTTAGAGGCG
* * * * *
5061966 TAGTATTGCAACATATCTTTAAGTTGATCCTAATATCGACACATTCGAGACATTATAAGCGGGTT
65 TAGTATTGCAACTTATCTTTAAGTTGAGCCTAATATCGCCACATTCGAGACATTCTAAGCGGGTA
* * * *
5062031 AAAAT-GCCCTGAAAATGGTTCAAAAGTATGGTTTTGTGCATAAAAAACAAGGTAAAATGGCTTC
130 AAAATCGCCCTGAAAAT-GTTCGAAAGTATGGTTTTGTGCAT-CAAAACAATGTAAAAAGGCTTC
5062095 ATAGGT
193 ATAGGT
*
5062101 ATGTTCGAGTGTTATTTTCCGGTTGTAAATAGGAGAGTTTTCGTAATCTATAAGCTTAGAGGCGT
1 ATGTTCGAGTGTTATCTTCCGGTTGTAAATAGGAGAGTTTTCGTAATCTATAAGCTTAGAGGCGT
5062166 AGTATTGCAACTTATCTTTAAGTTGAGCCTAATATCGCCACATTCGAGACATTCTAAGCGGGGTA
66 AGTATTGCAACTTATCTTTAAGTTGAGCCTAATATCGCCACATTCGAGACATTCTAAGC-GGGT-
** *
5062231 AAAAATCGCATTGAAAATGTTTTGAAAGTATGGTTTTGTGCATCAAGAACAATGTAAAAAGGCTT
129 AAAAATCGCCCTGAAAATG-TTCGAAAGTATGGTTTTGTGCATCAA-AACAATGTAAAAAGGCTT
5062296 CATA-G-
192 CATAGGT
* * *
5062301 ATGTTCTAGTGTTA-CTTCCGGGTTGTAAATAGGAGAGTTTTCGTAATTTATAAGCTTAGAGGTG
1 ATGTTCGAGTGTTATCTTCC-GGTTGTAAATAGGAGAGTTTTCGTAATCTATAAGCTTAGAGGCG
* * * *
5062365 TATTATTACAACTTATCTTTAAGTTGAGCCTAATATCGCCACAATCAAGACATTCTAAGCGGGTT
65 TAGTATTGCAACTTATCTTTAAGTTGAGCCTAATATCGCCACATTCGAGACATTCTAAGCGGG-T
*
5062430 AAAAATCGCCCTGAAAATAGTTCGAAAGCATGGTTTTGTGCATCAAATACAATGTAA
129 AAAAATCGCCCTGAAAAT-GTTCGAAAGTATGGTTTTGTGCATCAAA-ACAATGTAA
5062487 GATTAGAGCA
Statistics
Matches: 341, Mismatches: 35, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
198 4 0.01
199 161 0.47
200 117 0.34
201 9 0.03
202 50 0.15
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (198 bp):
ATGTTCGAGTGTTATCTTCCGGTTGTAAATAGGAGAGTTTTCGTAATCTATAAGCTTAGAGGCGT
AGTATTGCAACTTATCTTTAAGTTGAGCCTAATATCGCCACATTCGAGACATTCTAAGCGGGTAA
AAATCGCCCTGAAAATGTTCGAAAGTATGGTTTTGTGCATCAAAACAATGTAAAAAGGCTTCATA
GGT
Found at i:5064066 original size:42 final size:42
Alignment explanation
Indices: 5064014--5064093 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
5064004 TCCAAGAATG
* *
5064014 GATGGAATTCAATTCTCTTGTTGGAAGGAATTGAAATTAATA
1 GATGAAATTCAATTCCCTTGTTGGAAGGAATTGAAATTAATA
5064056 GATGAAATTCAATTCCCTTGTTGGAAGGAATTGAAATT
1 GATGAAATTCAATTCCCTTGTTGGAAGGAATTGAAATT
5064094 TGACCATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (42 bp):
GATGAAATTCAATTCCCTTGTTGGAAGGAATTGAAATTAATA
Found at i:5065179 original size:44 final size:44
Alignment explanation
Indices: 5065094--5065212 Score: 213
Period size: 44 Copynumber: 2.7 Consensus size: 44
5065084 TGTCTACAAG
* *
5065094 CCAAACAGAATATGGAATTGGA-TCCAATTCTATTTCCTGCCAA
1 CCAAACAGAATATGGAATTGGATTCCAATTCCATTTCATGCCAA
5065137 CCAAACAGAATATGGAATTGGATTCCAATTCCATTTCATGCCAA
1 CCAAACAGAATATGGAATTGGATTCCAATTCCATTTCATGCCAA
5065181 CCAAACAGAATATGGAATTGGATTCCAATTCC
1 CCAAACAGAATATGGAATTGGATTCCAATTCC
5065213 TACAGATTCT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 22 0.30
44 51 0.70
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (44 bp):
CCAAACAGAATATGGAATTGGATTCCAATTCCATTTCATGCCAA
Found at i:5065237 original size:18 final size:16
Alignment explanation
Indices: 5065201--5065246 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
5065191 TATGGAATTG
5065201 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
5065217 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
5065235 GATTTCAATTCC
1 GATTCCAATTCC
5065247 CTCAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:5067715 original size:21 final size:21
Alignment explanation
Indices: 5067690--5067806 Score: 105
Period size: 21 Copynumber: 5.4 Consensus size: 21
5067680 CAATAAAGTG
*
5067690 CCACATAATTGTCCCGTAGGA
1 CCACATAATTGTCCCGAAGGA
* *
5067711 CCACATAGGTT-TGCACCGAAGTA
1 CCACATA-ATTGT-C-CCGAAGGA
5067734 CCACATAAGTT-TGCACCGAAGTG-
1 CCACATAA-TTGT-C-CCGAAG-GA
*
5067757 CCACATATTTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
5067778 CCACATAATTGTCCCGGAGGA
1 CCACATAATTGTCCCGAAGGA
5067799 CCACATAA
1 CCACATAA
5067807 AACCCTCGAC
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
20 1 0.01
21 41 0.51
22 6 0.07
23 33 0.41
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:5067740 original size:23 final size:22
Alignment explanation
Indices: 5067710--5067784 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
5067700 GTCCCGTAGG
5067710 ACCACATAGGTTTGCACCGAAGT
1 ACCACATA-GTTTGCACCGAAGT
5067733 ACCACATAAGTTTGCACCGAAGT
1 ACCACAT-AGTTTGCACCGAAGT
* *
5067756 GCCACATA-TTTGTC-CCGAAGG
1 ACCACATAGTTTG-CACCGAAGT
5067777 ACCACATA
1 ACCACATA
5067785 ATTGTCCCGG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 17 0.36
22 2 0.04
23 27 0.57
24 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (22 bp):
ACCACATAGTTTGCACCGAAGT
Found at i:5073463 original size:21 final size:21
Alignment explanation
Indices: 5073439--5073488 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5073429 CACTGAAGTG
* *
5073439 CCACATATTTGTCCCGAAGGA
1 CCACATAATTATCCCGAAGGA
* *
5073460 CCACATAATTATCCTGGAGGA
1 CCACATAATTATCCCGAAGGA
5073481 CCACATAA
1 CCACATAA
5073489 AACCCTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGGA
Found at i:5074557 original size:22 final size:20
Alignment explanation
Indices: 5074508--5074583 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
5074498 GAATGCTCGA
* * *
5074508 ATGGTACCGATACCCCCCAT
1 ATGGTATCGATACCCCTCAG
5074528 A-GGTATCGATATCCCCATGCA-
1 ATGGTATCGATA-CCCC-T-CAG
5074549 ATGGTATCGATACCCCTCAG
1 ATGGTATCGATACCCCTCAG
*
5074569 ATGGTACCGATACCC
1 ATGGTATCGATACCC
5074584 TAAGGTATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 11 0.23
20 20 0.42
21 5 0.10
22 12 0.25
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (20 bp):
ATGGTATCGATACCCCTCAG
Found at i:5074934 original size:17 final size:17
Alignment explanation
Indices: 5074912--5074945 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5074902 ATCATCTTTG
5074912 AGTGTTCTTATCTTGTT
1 AGTGTTCTTATCTTGTT
5074929 AGTGTTCTTATCTTGTT
1 AGTGTTCTTATCTTGTT
5074946 CTAGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (17 bp):
AGTGTTCTTATCTTGTT
Found at i:5080387 original size:20 final size:19
Alignment explanation
Indices: 5080321--5080396 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
5080311 GAATGCTCGA
* *
5080321 ATGGTACCGATACCCCC-C
1 ATGGTATCGATACCCCCAG
5080339 ATAGGTATCGATACCCCCATG
1 AT-GGTATCGATACCCCCA-G
5080360 CAATGGTATCGATACCCCTCAG
1 --ATGGTATCGATACCCC-CAG
5080382 ATGGTA-CTGATACCC
1 ATGGTATC-GATACCC
5080397 TAAGGCATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
20 13 0.27
22 15 0.31
23 4 0.08
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (19 bp):
ATGGTATCGATACCCCCAG
Found at i:5083179 original size:16 final size:16
Alignment explanation
Indices: 5083155--5083196 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5083145 ATGGAATTTT
*
5083155 ATTATTTTAACAATAC
1 ATTAGTTTAACAATAC
*
5083171 ATTAGTTTAAACAATGC
1 ATTAGTTT-AACAATAC
5083188 -TTAGTTTAA
1 ATTAGTTTAA
5083197 ATGAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 14 0.61
17 7 0.30
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTAGTTTAACAATAC
Found at i:5083185 original size:17 final size:16
Alignment explanation
Indices: 5083163--5083197 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5083153 TTATTATTTT
5083163 AACAATACATTAGTTTA
1 AACAATAC-TTAGTTTA
*
5083180 AACAATGCTTAGTTTA
1 AACAATACTTAGTTTA
5083196 AA
1 AA
5083198 TGAATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (16 bp):
AACAATACTTAGTTTA
Found at i:5088540 original size:44 final size:44
Alignment explanation
Indices: 5088454--5088546 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
5088444 TGATCATATC
** * *
5088454 GATACTACTTTACATAGTAGTATCGATACTCCTTGTACGGTATA
1 GATACTACTACACATAGTAGTACCGATACTCCTTGTAAGGTATA
* *
5088498 GATACTACTACACATAGTAGTCCCGATACTCCTTG-AGAGGTATC
1 GATACTACTACACATAGTAGTACCGATACTCCTTGTA-AGGTATA
5088542 GATAC
1 GATAC
5088547 CGTTGAATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (44 bp):
GATACTACTACACATAGTAGTACCGATACTCCTTGTAAGGTATA
Found at i:5092670 original size:18 final size:18
Alignment explanation
Indices: 5092647--5092682 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5092637 TGTCTTTCAG
5092647 TATTAAAGAAATAATGAA
1 TATTAAAGAAATAATGAA
*
5092665 TATTAAAGAACTAATGAA
1 TATTAAAGAAATAATGAA
5092683 CATTCCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (18 bp):
TATTAAAGAAATAATGAA
Found at i:5096078 original size:45 final size:45
Alignment explanation
Indices: 5096026--5096303 Score: 287
Period size: 45 Copynumber: 6.2 Consensus size: 45
5096016 AATACATCAT
* ** *
5096026 TATGCATTTTAAACTCTAACAT-CTTTTTTGTTGATAATGCACCCA
1 TATGCA-TTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * *
5096071 TATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * *
5096116 TATACATCTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCGA
1 TATGCATTTCAACTC-TAGTATACTTTTCTGTTGATAATGCACCCA
* **
5096161 TATACATTTCAACTCTAACATACTTTTCTGTTGATAATATGCA-CCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGAT-A-ATGCACCCA
5096207 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCA-CCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * ***
5096251 TATGCATATCAACTCTGGTAT-CCTTTCATGCCAATAATGCACCCA
1 TATGCATTTCAACTCTAGTATACTTTTC-TGTTGATAATGCACCCA
*
5096296 TCTGCATT
1 TATGCATT
5096304 ATTCTTTTAT
Statistics
Matches: 199, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
43 5 0.03
44 48 0.24
45 106 0.53
46 36 0.18
47 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:5096917 original size:21 final size:22
Alignment explanation
Indices: 5096891--5096963 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 22
5096881 TGTGGTCCAA
* *
5096891 TATCGATACCTTTACCATA-GG
1 TATCGATACCATTACAATATGG
* *
5096912 TATCGATACAATTATAATATGG
1 TATCGATACCATTACAATATGG
* *
5096934 TATCGATACC---CCTATATGG
1 TATCGATACCATTACAATATGG
5096953 TATCGATACCA
1 TATCGATACCA
5096964 AAATTAGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 16 0.38
21 15 0.36
22 11 0.26
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (22 bp):
TATCGATACCATTACAATATGG
Found at i:5098955 original size:24 final size:24
Alignment explanation
Indices: 5098927--5098976 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5098917 TGGTGGTTGA
5098927 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
5098951 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
5098975 TT
1 TT
5098977 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:5105857 original size:19 final size:21
Alignment explanation
Indices: 5105820--5105862 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5105810 TAACTTTTTC
*
5105820 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
5105840 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
5105860 TTT
1 TTT
5105863 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:5110962 original size:21 final size:21
Alignment explanation
Indices: 5110936--5110975 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5110926 AGTACAGGTA
*
5110936 GTATCGGTAC-TCTCTTTATGG
1 GTATCGATACTTC-CTTTATGG
5110957 GTATCGATACTTCCTTTAT
1 GTATCGATACTTCCTTTAT
5110976 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
GTATCGATACTTCCTTTATGG
Found at i:5111221 original size:20 final size:20
Alignment explanation
Indices: 5111180--5111222 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5111170 CGCATGACAA
* *
5111180 TATTGATACTGTTCATATAG
1 TATTGATACTGTTCAAACAG
5111200 TATTGATACTG-TCAGAACAG
1 TATTGATACTGTTCA-AACAG
5111220 TAT
1 TAT
5111223 CGGTACTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (20 bp):
TATTGATACTGTTCAAACAG
Found at i:5111376 original size:14 final size:15
Alignment explanation
Indices: 5111357--5111390 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5111347 ACATAATACA
5111357 AGTTAAAAA-AACAT
1 AGTTAAAAATAACAT
*
5111371 AGTTAAAAATGACAT
1 AGTTAAAAATAACAT
5111386 AGTTA
1 AGTTA
5111391 CAATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (15 bp):
AGTTAAAAATAACAT
Found at i:5113099 original size:20 final size:21
Alignment explanation
Indices: 5113069--5113108 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5113059 AGCCGTTGGG
*
5113069 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCAATACTAT
5113090 GCCT-ATGGTATCAATACTA
1 GCCTGATGGTATCAATACTA
5113109 CTAAACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:5114579 original size:19 final size:20
Alignment explanation
Indices: 5114537--5114584 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5114527 CTAAATCATT
* *
5114537 TTTCAAAATATCATTTTGAT
1 TTTCAAAATATAATTTTGAC
*
5114557 TTTCAAAAT-TAATTTTTAC
1 TTTCAAAATATAATTTTGAC
5114576 TTTCAAAAT
1 TTTCAAAAT
5114585 CAAATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTCAAAATATAATTTTGAC
Found at i:5115256 original size:19 final size:21
Alignment explanation
Indices: 5115232--5115270 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
5115222 AATTTTACAC
5115232 TTAGGGA-ACCGA-TTCCCCA
1 TTAGGGATACCGATTTCCCCA
5115251 TTAGGGATACCGATTTCCCC
1 TTAGGGATACCGATTTCCCC
5115271 CACGCTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (21 bp):
TTAGGGATACCGATTTCCCCA
Found at i:5120454 original size:18 final size:19
Alignment explanation
Indices: 5120413--5120454 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5120403 CCCCCTTTGA
*
5120413 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
5120432 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
5120451 -GGGG
1 AGGGG
5120455 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:5125472 original size:19 final size:21
Alignment explanation
Indices: 5125443--5125481 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
5125433 AGCCTTTGGG
5125443 GCCTGATGGTATCGA-ACTAT
1 GCCTGATGGTATCGATACTAT
5125463 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
5125482 CTATACATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:5134744 original size:12 final size:12
Alignment explanation
Indices: 5134727--5134752 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5134717 AGATCCATAA
5134727 ATATTTTTCAGG
1 ATATTTTTCAGG
5134739 ATATTTTTCAGG
1 ATATTTTTCAGG
5134751 AT
1 AT
5134753 GAACACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (12 bp):
ATATTTTTCAGG
Found at i:5135774 original size:31 final size:30
Alignment explanation
Indices: 5135723--5135797 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
5135713 TAGTAATTCA
* ** *
5135723 ATTTTTTATTTCTAATATTTATTTTTATAAT
1 ATTTTTTATTT-TTATATTTAAATTTAAAAT
5135754 ATTTGTTTATTTTTATATTTAAATTTAAAAT
1 ATTT-TTTATTTTTATATTTAAATTTAAAAT
*
5135785 AATTTTTATTTTT
1 ATTTTTTATTTTT
5135798 TAAAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 9 0.24
31 22 0.58
32 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (30 bp):
ATTTTTTATTTTTATATTTAAATTTAAAAT
Found at i:5135798 original size:31 final size:31
Alignment explanation
Indices: 5135725--5135808 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
5135715 GTAATTCAAT
* * ** * *
5135725 TTTTTATTTCTAATATTTATTTTTATAATAT
1 TTTTTATTTTTTATATTTAAATTTAAAATAA
5135756 TTGTTTA-TTTTTATATTTAAATTTAAAATAA
1 TT-TTTATTTTTTATATTTAAATTTAAAATAA
* *
5135787 TTTTTATTTTTTAAAATTAAAT
1 TTTTTATTTTTTATATTTAAAT
5135809 AAACGTGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 4 0.09
31 35 0.81
32 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (31 bp):
TTTTTATTTTTTATATTTAAATTTAAAATAA
Found at i:5143953 original size:81 final size:81
Alignment explanation
Indices: 5143868--5144287 Score: 277
Period size: 81 Copynumber: 5.2 Consensus size: 81
5143858 AAATATTGAA
*
5143868 CTTTAGTGGTGTTTTTGTACAAACGCCACTCAATTCTAGTATTTAGCGGCGTTTATATAAAAATG
1 CTTTAGTGGTGTTTTTGTACAAACGCCACTCAATTCTAGTATTTAGTGGCGTTTATATAAAAATG
*
5143933 ACACTAAAGTACGAGT
66 CCACTAAAGTACGAGT
* * * * * *
5143949 CTTTAGTGGCG--TTTGTACAAAAACACCACTAAAATCTCA-TACTTTAGTGGCATTTTTATATA
1 CTTTAGTGGTGTTTTTGTAC--AAACGCCACTCAATTCT-AGTA-TTTAGTGGCGTTTATATA-A
* * *
5144011 AACT-CCACTAAA-TACTATT
61 AAATGCCACTAAAGTACGAGT
* * * * **
5144030 ATTTACTGGAGTTTGTGCTTA-AAACGCCACTCAATAATAGTATTTAGTGGCGTTTATATAAAAA
1 CTTTAGTGGTGTTTTTG--TACAAACGCCACTCAATTCTAGTATTTAGTGGCGTTTATATAAAAA
*
5144094 TGCCACTAAAGTATGAGAT
64 TGCCACTAAAGTACGAG-T
* ** * * * * * *
5144113 -TTTAGTGGTGTTTTTGTACAAACGCCACTAAAGACTCGTACTTTAGTGTCATTTTTATATAAAC
1 CTTTAGTGGTGTTTTTGTACAAACGCCACTCAATTCTAGTA-TTTAGTGGCGTTTATATAAAAAT
* * *
5144177 GCCGCTAAA-TACTAGA
65 GCCACTAAAGTACGAGT
* * * * * * *
5144193 ATTGAGTGGCG--TTTGTACAAAAACACCACTAAAGTTC-AATATTTAGCGGCGTTTATATAAAA
1 CTTTAGTGGTGTTTTTGTAC--AAACGCCACTCAA-TTCTAGTATTTAGTGGCGTTTATATAAAA
* *
5144255 AAGCTACTAAAGTACGAGT
63 ATGCCACTAAAGTACGAGT
* * *
5144274 ATTTACTGGAGTTT
1 CTTTAGTGGTGTTT
5144288 GTTCAAAAAA
Statistics
Matches: 255, Mismatches: 62, Indels: 42
0.71 0.17 0.12
Matches are distributed among these distances:
79 14 0.05
80 30 0.12
81 120 0.47
82 80 0.31
83 9 0.04
85 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (81 bp):
CTTTAGTGGTGTTTTTGTACAAACGCCACTCAATTCTAGTATTTAGTGGCGTTTATATAAAAATG
CCACTAAAGTACGAGT
Found at i:5143979 original size:41 final size:41
Alignment explanation
Indices: 5143881--5144296 Score: 230
Period size: 41 Copynumber: 10.3 Consensus size: 41
5143871 TAGTGGTGTT
* * *
5143881 TTTGTAC--AAACGCCACTCAA-TTCTAGTATTTAGCGGCG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * * * * *
5143919 TTTATATAAAAATGACACTAAAGTACGAGTCTTTAGTGGCG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * *
5143960 TTTGTACAAAAACACCACTAAAAT-CTCA-TACTTTAGTGGCA
1 TTTGTACAAAAACGCCACTAAAGTACT-AGTA-TTTAGTGGCG
* * * * * * *
5144001 TTTTTATATAAACTCCACTAAA-TACTATTATTTACTGGAG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * * *
5144041 TTTGTGCTTAAAACGCCACTCAA-TAATAGTATTTAGTGGCG
1 TTTGTAC-AAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * * *
5144082 TTTATATAAAAATGCCACTAAAGTA-TGAG-ATTTTAGTGGTG
1 TTTGTACAAAAACGCCACTAAAGTACT-AGTA-TTTAGTGGCG
* * *
5144123 TTTTTGTAC--AAACGCCACTAAAG-ACTCGTACTTTAGTGTCA
1 --TTTGTACAAAAACGCCACTAAAGTACTAGTA-TTTAGTGGCG
* * * * * *
5144164 TTTTTATATAAACGCCGCTAAA-TACTAGAATTGAGTGGCG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * * *
5144204 TTTGTACAAAAACACCACTAAAGTTC-AATATTTAGCGGCG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
* * * * * * *
5144244 TTTATATAAAAAAGCTACTAAAGTACGAGTATTTACTGGAG
1 TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
*
5144285 TTTGTTCAAAAA
1 TTTGTACAAAAA
5144297 ACGTCGATAA
Statistics
Matches: 276, Mismatches: 82, Indels: 37
0.70 0.21 0.09
Matches are distributed among these distances:
38 5 0.02
39 5 0.02
40 95 0.34
41 166 0.60
43 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (41 bp):
TTTGTACAAAAACGCCACTAAAGTACTAGTATTTAGTGGCG
Found at i:5144095 original size:163 final size:160
Alignment explanation
Indices: 5143807--5144296 Score: 474
Period size: 163 Copynumber: 3.0 Consensus size: 160
5143797 TTTTTTGAAC
* * * * * * * *
5143807 AAACTCCAGTAAATACTCGTACTTTAGTAGCTTTTTTATATAAACGCCGCTAAATA-TTGAACTT
1 AAACACCACTAAAGACTCATACTTTAGTGGCATTTTTATATAAACGCCACTAAATACTAGAA-TT
* * * **
5143871 TAGTGGTGTTTTTGTAC--AAACGCCACTCAATTCTAGTATTTAGCGGCGTTTATATAAAAATGA
65 GACTGGAG--TTTGTACAAAAACGCCACTCAATAATAGTATTTAGCGGCGTTTATATAAAAATG-
*
5143934 CACTAAAGTACGAGTCTTTAGTGGCGTTTGTACAA
127 CACTAAAGTACGAGT-TTTAGTGGAGTTTGTACAA
* **
5143969 AAACACCACTAAA-ATCTCATACTTTAGTGGCATTTTTATATAAACTCCACTAAATACTATTATT
1 AAACACCACTAAAGA-CTCATACTTTAGTGGCATTTTTATATAAACGCCACTAAATACTAGAATT
* * * *
5144033 TACTGGAGTTTGTGCTTAAAACGCCACTCAATAATAGTATTTAGTGGCGTTTATATAAAAATGCC
65 GACTGGAGTTTGTAC-AAAAACGCCACTCAATAATAGTATTTAGCGGCGTTTATATAAAAATG-C
* *
5144098 ACTAAAGTATGAGATTTTAGTGGTGTTTTTGTAC--
128 ACTAAAGTACGAG-TTTTAGTGGAG--TTTGTACAA
* * * *
5144132 AAACGCCACTAAAGACTCGTACTTTAGTGTCATTTTTATATAAACGCCGCTAAATACTAGAATTG
1 AAACACCACTAAAGACTCATACTTTAGTGGCATTTTTATATAAACGCCACTAAATACTAGAATTG
* * * * * *
5144197 AGTGGCGTTTGTACAAAAACACCACT-AA-AGTTCAATATTTAGCGGCGTTTATATAAAAAAGCT
66 ACTGGAGTTTGTACAAAAACGCCACTCAATA-AT-AGTATTTAGCGGCGTTTATATAAAAATGC-
* *
5144260 ACTAAAGTACGAGTATTTACTGGAGTTTGTTCAA
128 ACTAAAGTACGAGT-TTTAGTGGAGTTTGTACAA
5144294 AAA
1 AAA
5144297 ACGTCGATAA
Statistics
Matches: 273, Mismatches: 40, Indels: 30
0.80 0.12 0.09
Matches are distributed among these distances:
160 13 0.05
161 6 0.02
162 113 0.41
163 132 0.48
164 2 0.01
165 7 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (160 bp):
AAACACCACTAAAGACTCATACTTTAGTGGCATTTTTATATAAACGCCACTAAATACTAGAATTG
ACTGGAGTTTGTACAAAAACGCCACTCAATAATAGTATTTAGCGGCGTTTATATAAAAATGCACT
AAAGTACGAGTTTTAGTGGAGTTTGTACAA
Found at i:5147130 original size:3 final size:3
Alignment explanation
Indices: 5147122--5147183 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
5147112 TTCCTGTTTT
* *
5147122 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTT ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
5147168 AT- ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
5147184 TAACGGTTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:5149676 original size:655 final size:662
Alignment explanation
Indices: 5148393--5149714 Score: 2410
Period size: 655 Copynumber: 2.0 Consensus size: 662
5148383 GATTTTTGAT
5148393 TTAAACTTTTTTGAATATAACTACTTTTTTGTGAAAAATCTAATTTTGATTGTTTCTTTACTATT
1 TTAAACTTTTTTGAATATAACTACTTTTTTGTGAAAAATCTAATTTTGATTGTTTCTTTACTATT
5148458 TACTTAGTTAGGTTTTTTTTTCTTTCATTTAATTTTTATTTAGCATGATTTTCTTAAATTTTTTT
66 TACTTAGTTAGGTTTTTTTTTCTTTCATTTAATTTTTATTTAGCATGATTTTCTTAAATTTTTTT
5148523 GTAAAATCTAATATTTTTTCTTCATACTTAAAATTTTATGTCTTTTAGGGATTAAGTGAAATTTT
131 GTAAAATCTAATATTTTTTCTTCATACTTAAAATTTTATGTCTTTTAGGGATTAAGTGAAATTTT
5148588 TAGGGATTTAATTTTTGCATTTGTAAAGATTTATGCTTTTTTAGGTTGAACTGGAAATAATTTTC
196 TAGGGATTTAATTTTTGCATTTGTAAAGATTTATGCTTTTTTAGGTTGAACTGGAAATAATTTTC
5148653 AGGGATTTCATTTTTTTTGTTCAATGTGTTTTTTATTTTTAGTAATAAATTTAGGGTATTTTCAA
261 AGGGATTTCATTTTTTTTGTTCAATGTGTTTTTTATTTTTAGTAATAAATTTAGGGTATTTTCAA
5148718 ATCGAGTTGGGTCGAAATCAAGTTTTTATTTTAATTTTAGAGTCGGAGTCAGATCAAATTAAATA
326 ATCGAGTTGGGTCGAAATCAAGTTTTTATTTTAATTTTAGAGTCGGAGTCAGATCAAATTAAATA
5148783 GTATTAAAATTAGAGTCCGGTTAGAGTCGAGTTACAATTTTATATATTCAATCATAATCAAAGAA
391 GTATTAAAATTAGAGTCCGGTTAGAGTCGAGTTACAATTTTATATATTCAATCATAATCAAAGAA
5148848 ACCCTATTATAATCCCTAGTCAAATGTGCTTTCTCCTATAAATTTTAAGCATGATTGATTGATTT
456 ACCCTATTATAATCCCTAGTCAAATGTGCTTTCTCCTATAAATTTTAAGCATGATTGATTGATTT
5148913 GTATTTGATGTAATACGAGCCTATAATAACATCCGCAATACCGGGTTGTATATCCCAAACTATGG
521 GTATTTGATGTAATACGAGCCTATAATAACATCCGCAATACCGGGTTGTATATCCCAAACTATGG
5148978 GTTAGTGACTTAATTGTAAAGTTTTAGAATTGGTGATTAAAGTAGAAGAATGGATTAGTTCAATG
586 GTTAGTGACTTAATTGTAAAGTTTTAGAATTGGTGATTAAAGTAGAAGAATGGATTAGTTCAATG
5149043 ATTTATCTGGAA
651 ATTTATCTGGAA
5149055 TTAAACTTTTTTGAATATAACTACTTTTTTTTGTGAAAAATCTAATTTTGATTGTTT-TTTACTA
1 TTAAACTTTTTTGAATATAACTAC--TTTTTTGTGAAAAATCTAATTTTGATTGTTTCTTTACTA
5149119 TTTTACTTAGTTAGG-TTTTTTTT-TTTCATTTAATTTTTATTTAGCATGATTTTCTTAAA-TTT
64 -TTTACTTAGTTAGGTTTTTTTTTCTTTCATTTAATTTTTATTTAGCATGATTTTCTTAAATTTT
5149181 TTTGTAAAAATCTAATATTTTTTCTTCATACTT-AAA-TTTATGTTCTTTTAGGGATTAAGTGAA
128 TTTGT-AAAATCTAATATTTTTTCTTCATACTTAAAATTTTATG-TCTTTTAGGGATTAAGTGAA
5149244 A-TTTTAGGGATTTAA-TTTTGCATTTGTAAAGATTTATGCTTTTTTAGGTTGAACTGGAAATAA
191 ATTTTTAGGGATTTAATTTTTGCATTTGTAAAGATTTATGCTTTTTTAGGTTGAACTGGAAATAA
5149307 -TTTCAGGGATTTCATTTTTTTTGTTCAATGTGTTTTTTATTTTTAGTAATAAATTTAGGGTATT
256 TTTTCAGGGATTTCATTTTTTTTGTTCAATGTGTTTTTTATTTTTAGTAATAAATTTAGGGTATT
5149371 TTCAAATCGAGTTGGGTCGAAATCAAG-TTTTATTTTAATTTT-GAGTCGGAGTCAGATC-AATT
321 TTCAAATCGAGTTGGGTCGAAATCAAGTTTTTATTTTAATTTTAGAGTCGGAGTCAGATCAAATT
5149433 AAATAGTATTAAAATTAGAGTCCGGTTAGAGTCGAGTTACAATTTTATATTATTCAATCA-AATC
386 AAATAGTATTAAAATTAGAGTCCGGTTAGAGTCGAGTTACAATTTTATA-TATTCAATCATAATC
5149497 -AAGAAACCCTATTATAATCCCTAGTCAAATGTGCTTTCTCCTATAAATTTTTAAGCATGATTGA
450 AAAGAAACCCTATTATAATCCCTAGTCAAATGTGCTTTCTCCTATAAA-TTTTAAGCATGATTGA
5149561 -TGA-TTGTA-TTGATGTAATACGAGCCTATAATGTAACATCCGCAATACCGGGTTGTAATATCC
514 TTGATTTGTATTTGATGTAATACGAGCCTATAA--TAACATCCGCAATACCGGGTTGT-ATATCC
5149623 CAAACTATGGGTTAGTGACTTAA-TGTAAAGTTTTAGAATTTGGTGATTAAAGTAGAAGAATGGA
576 CAAACTATGGGTTAGTGACTTAATTGTAAAGTTTTAGAA-TTGGTGATTAAAGTAGAAGAATGGA
5149687 TTAGTTCAATGATTTATCTGGAA
640 TTAGTTCAATGATTTATCTGGAA
*
5149710 ATAAA
1 TTAAA
5149715 TCCTTAAAGT
Statistics
Matches: 648, Mismatches: 1, Indels: 29
0.96 0.00 0.04
Matches are distributed among these distances:
652 22 0.03
653 5 0.01
654 88 0.14
655 154 0.24
656 26 0.04
657 15 0.02
658 91 0.14
659 48 0.07
660 20 0.03
661 32 0.05
662 87 0.13
663 15 0.02
664 45 0.07
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (662 bp):
TTAAACTTTTTTGAATATAACTACTTTTTTGTGAAAAATCTAATTTTGATTGTTTCTTTACTATT
TACTTAGTTAGGTTTTTTTTTCTTTCATTTAATTTTTATTTAGCATGATTTTCTTAAATTTTTTT
GTAAAATCTAATATTTTTTCTTCATACTTAAAATTTTATGTCTTTTAGGGATTAAGTGAAATTTT
TAGGGATTTAATTTTTGCATTTGTAAAGATTTATGCTTTTTTAGGTTGAACTGGAAATAATTTTC
AGGGATTTCATTTTTTTTGTTCAATGTGTTTTTTATTTTTAGTAATAAATTTAGGGTATTTTCAA
ATCGAGTTGGGTCGAAATCAAGTTTTTATTTTAATTTTAGAGTCGGAGTCAGATCAAATTAAATA
GTATTAAAATTAGAGTCCGGTTAGAGTCGAGTTACAATTTTATATATTCAATCATAATCAAAGAA
ACCCTATTATAATCCCTAGTCAAATGTGCTTTCTCCTATAAATTTTAAGCATGATTGATTGATTT
GTATTTGATGTAATACGAGCCTATAATAACATCCGCAATACCGGGTTGTATATCCCAAACTATGG
GTTAGTGACTTAATTGTAAAGTTTTAGAATTGGTGATTAAAGTAGAAGAATGGATTAGTTCAATG
ATTTATCTGGAA
Found at i:5150533 original size:56 final size:56
Alignment explanation
Indices: 5150430--5150538 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
5150420 TAATTCGTGC
* ** *
5150430 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCA
1 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATGAAACATCGAATGCA
*
5150486 ATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAAT-ACAACATCGAAT
1 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATGA-AACATCGAAT
5150539 ACTTTATGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (56 bp):
ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATGAAACATCGAATGCA
Found at i:5151279 original size:30 final size:30
Alignment explanation
Indices: 5151220--5151312 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 30
5151210 AAGGGTCGAG
5151220 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGAC-TATGGACT
5151251 GTTTACCTATGTTCTTCGGGACTATGGACT
1 GTTTACCTATGTTCTTCGGGACTATGGACT
* *
5151281 GTTTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGA-CTATGGACT
5151312 G
1 G
5151313 GTTTTTCGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 27 0.46
31 32 0.54
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGGACTATGGACT
Found at i:5152792 original size:62 final size:60
Alignment explanation
Indices: 5152722--5152874 Score: 184
Period size: 60 Copynumber: 2.5 Consensus size: 60
5152712 TTCAGTGTGT
* * *
5152722 ATCGATGCATAGGGAGTGCAT-GATGCACCCATTAAAATGGAAACATCGAATGCGATTGGTGC
1 ATCGATGCATAGGGAGTGCATCGATGCACCC--TAAAAT-CAAACATCGAATGAGATTGATGC
* *
5152784 ATCGATGCATAAGGAGTGCATCGATG-ATCCCTAAAATCAAACATCGAATGAGATTTATGC
1 ATCGATGCATAGGGAGTGCATCGATGCA-CCCTAAAATCAAACATCGAATGAGATTGATGC
* **
5152844 ACCGATGCATAGATAGTGCATCGATGCACCC
1 ATCGATGCATAGGGAGTGCATCGATGCACCC
5152875 GTTCTAGGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
60 44 0.56
61 7 0.09
62 21 0.27
63 7 0.09
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (60 bp):
ATCGATGCATAGGGAGTGCATCGATGCACCCTAAAATCAAACATCGAATGAGATTGATGC
Found at i:5153706 original size:57 final size:59
Alignment explanation
Indices: 5153609--5153722 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 59
5153599 GAGGGTTTAC
* * * *
5153609 CTATGTTCTACGGAAATATGGCCAATTTTACCTATGTCTTTCGAGA-CTATGGACAGTAT
1 CTATGTTCTAAGGAAATATGGACAAGTTTACCTAGGTCTTT-GAGACCTATGGACAGTAT
*
5153668 CTATGTT-TAAGGAAATATGGAC-AGTTTA-CTAGGTTCTTTGGGACCTATGGACAGT
1 CTATGTTCTAAGGAAATATGGACAAGTTTACCTAGG-TCTTTGAGACCTATGGACAGT
5153723 TGTCGAGGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
56 7 0.15
57 21 0.44
58 13 0.27
59 7 0.15
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (59 bp):
CTATGTTCTAAGGAAATATGGACAAGTTTACCTAGGTCTTTGAGACCTATGGACAGTAT
Found at i:5153743 original size:30 final size:30
Alignment explanation
Indices: 5153683--5153753 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
5153673 TTTAAGGAAA
* *
5153683 TATGGACAGTTTACTAGGTTCTTTGGGACC
1 TATGGACAGTTTACGAGGTTCTTTAGGACC
*
5153713 TATGGACAGTTGT-CGAGGTTCTTTATGACC
1 TATGGACAGTT-TACGAGGTTCTTTAGGACC
* *
5153743 TCTGGATAGTT
1 TATGGACAGTT
5153754 ACGGGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (30 bp):
TATGGACAGTTTACGAGGTTCTTTAGGACC
Found at i:5163813 original size:185 final size:185
Alignment explanation
Indices: 5163476--5163846 Score: 708
Period size: 185 Copynumber: 2.0 Consensus size: 185
5163466 CTCGAGTTTT
*
5163476 AGTACATTTAGGTATCTGGTCGTAGATCCCAAACAAAGAACACACTTCAACGGAGAGTAACATAT
1 AGTACATTTAGGTATCTGGTCGTAGATCCCAAACAAAGAACACACGTCAACGGAGAGTAACATAT
5163541 CTCAACTGCATAATAATCAGGACGGTAAAAGTGACAAAAATTGGAGCTATTTAGAGTGAGTTTTA
66 CTCAACTGCATAATAATCAGGACGGTAAAAGTGACAAAAATTGGAGCTATTTAGAGTGAGTTTTA
*
5163606 ATTTGATTTTCATGACTTTGGGTTGTTTCATGTAGATTTAATCGAATGCTTGAAA
131 ATTTGATTTTCATGACTTTGGGTTGTTTCATGTAGATTAAATCGAATGCTTGAAA
5163661 AGTACATTTAGGTATCTGGTCGTAGATCCCAAACAAAGAACACACGTCAACGGAGAGTAACATAT
1 AGTACATTTAGGTATCTGGTCGTAGATCCCAAACAAAGAACACACGTCAACGGAGAGTAACATAT
5163726 CTCAACTGCATAATAATC-GGACGGTAAAAGTGACAAAAATTGGAGCTATTTAGAGTGAGTTTTA
66 CTCAACTGCATAATAATCAGGACGGTAAAAGTGACAAAAATTGGAGCTATTTAGAGTGAGTTTTA
5163790 ATTTGATTTTCATGACTTTTGGGTTGTTTCATGTAGATTAAATCGAATGCTTGAAA
131 ATTTGATTTTCATGAC-TTTGGGTTGTTTCATGTAGATTAAATCGAATGCTTGAAA
5163846 A
1 A
5163847 CGAAGAGAAA
Statistics
Matches: 183, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 62 0.34
185 121 0.66
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (185 bp):
AGTACATTTAGGTATCTGGTCGTAGATCCCAAACAAAGAACACACGTCAACGGAGAGTAACATAT
CTCAACTGCATAATAATCAGGACGGTAAAAGTGACAAAAATTGGAGCTATTTAGAGTGAGTTTTA
ATTTGATTTTCATGACTTTGGGTTGTTTCATGTAGATTAAATCGAATGCTTGAAA
Found at i:5169009 original size:165 final size:167
Alignment explanation
Indices: 5168815--5169126 Score: 569
Period size: 165 Copynumber: 1.9 Consensus size: 167
5168805 TTTCCTTGTA
*
5168815 TGGTATTTGCATGATCGAGAGGCAAGTTTTGGTTATAGGAAAACGTCCTCATTAGTGTTTAGTTT
1 TGGTATTTGCATGATCGAGAGGCAAGTTTTGGTTATAGGAAAACGTCCTAATTAGTGTTTAGTTT
5168880 ACGCTTATGGTTGT-AGTCTTTCATTGTAATTTGGATATTT-C-CTCTCTTTTTAGTAAGGCTTA
66 ACGCTTATGGTTGTAAGTCTTTCATTGTAATTTGGATATTTCCTCTCTCTTTTTAGTAAGGCTTA
5168942 CG-CTTCTATTCGCATATCCGAATTGTTAAAAAAATG
131 CGCCTTCTATTCGCATATCCGAATTGTTAAAAAAATG
5168978 TGGTATTTGCATGATCTCGAGAGGCAAGTTTTGGTTATAGGAAAACGTCCTAATTAGTGTTTAGT
1 TGGTATTTGCATGA--TCGAGAGGCAAGTTTTGGTTATAGGAAAACGTCCTAATTAGTGTTTAGT
5169043 TTACGCTTATGGTTGTAAGTCTTTCATTGTAATTTGGATATTTCCTCTCTCTTTTTAGTAAGGCT
64 TTACGCTTATGGTTGTAAGTCTTTCATTGTAATTTGGATATTTCCTCTCTCTTTTTAGTAAGGCT
5169108 TACGCCTTCTATTCGCATA
129 TACGCCTTCTATTCGCATA
5169127 AAAAAAGTTT
Statistics
Matches: 142, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
163 14 0.10
165 64 0.45
166 26 0.18
167 1 0.01
168 23 0.16
169 14 0.10
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (167 bp):
TGGTATTTGCATGATCGAGAGGCAAGTTTTGGTTATAGGAAAACGTCCTAATTAGTGTTTAGTTT
ACGCTTATGGTTGTAAGTCTTTCATTGTAATTTGGATATTTCCTCTCTCTTTTTAGTAAGGCTTA
CGCCTTCTATTCGCATATCCGAATTGTTAAAAAAATG
Done.