Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 94 of 196
Found at i:27234262 original size:45 final size:44
Alignment explanation
Indices: 27234213--27234351 Score: 163
Period size: 44 Copynumber: 3.1 Consensus size: 44
27234203 CTCACTGAGG
* * *
27234213 TTGCAGTAGAGCAGACTAAAGATAGCAATCCTTATCTCCCTGAAA
1 TTGCAGTAGAGCAGATTAAAGATA-CAAACCTTATCTCCCTAAAA
* ** *
27234258 TTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCTCTAAAA
1 TTGCAGTAGAGCAGATTAAAGATACAAACCTTATCTCCCTAAAA
* *
27234302 TTGCAGTAGAGCAGGTTAAA-ATAACAAACCTTATCCCCCTAAAA
1 TTGCAGTAGAGCAGATTAAAGAT-ACAAACCTTATCTCCCTAAAA
*
27234346 TAGCAG
1 TTGCAG
27234352 CGAGGCAGGT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 59 0.75
45 20 0.25
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (44 bp):
TTGCAGTAGAGCAGATTAAAGATACAAACCTTATCTCCCTAAAA
Found at i:27234360 original size:44 final size:44
Alignment explanation
Indices: 27234281--27234367 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
27234271 GATTAAAGCC
* * * *
27234281 ACAAACCTTATCTCTCTAAAATTGCAGTAGAGCAGGTTAAAATA
1 ACAAACCTTATCCCCCTAAAATAGCAGGAGAGCAGGTTAAAATA
*
27234325 ACAAACCTTATCCCCCTAAAATAGCAGCGAG-GCAGGTTGAAAT
1 ACAAACCTTATCCCCCTAAAATAGCAG-GAGAGCAGGTTAAAAT
27234368 TATAAGTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (44 bp):
ACAAACCTTATCCCCCTAAAATAGCAGGAGAGCAGGTTAAAATA
Found at i:27234625 original size:44 final size:44
Alignment explanation
Indices: 27234509--27234629 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 44
27234499 CTTATCATAT
* * * *
27234509 CAAACCTTATCT-CTCTGAAGTTGCAGTAGAGTAGGTTGAAGTAA
1 CAAACCTTATCTCCT-TGAAGTTGCAGTGGGGCAGGTTAAAGTAA
* * *
27234553 CAAACCTCATC-CCCTAAAGTTGCAGTGGGGCAGGTTAAAG-ACA
1 CAAACCTTATCTCCTTGAAGTTGCAGTGGGGCAGGTTAAAGTA-A
27234596 CAAACCTTATCTCCTTGAAGTTGCAGTGGGGCAG
1 CAAACCTTATCTCCTTGAAGTTGCAGTGGGGCAG
27234630 ATTGAAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 32 0.50
44 31 0.48
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
CAAACCTTATCTCCTTGAAGTTGCAGTGGGGCAGGTTAAAGTAA
Found at i:27234649 original size:44 final size:44
Alignment explanation
Indices: 27234509--27234668 Score: 137
Period size: 44 Copynumber: 3.7 Consensus size: 44
27234499 CTTATCATAT
* * * * * * *
27234509 CAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAGTA-A
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAGATTAAAG-ACA
* *
27234553 CAAACCTCATC-CCCTAAAGTTGCAGTGGGGCAGGTTAAAGACA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAGATTAAAGACA
* * *
27234596 CAAACCTTATCTCCTTGAAGTTGCAGTGGGGCAGATTGAAA-ATA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAGATT-AAAGACA
* ** *
27234640 TAAGTCTTATCTCCCTAAAGTTGTAGTGG
1 CAAACCTTATCTCCCTAAAGTTGCAGTGG
27234669 AGCGAATTAA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.01
43 34 0.36
44 57 0.60
45 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
CAAACCTTATCTCCCTAAAGTTGCAGTGGGGCAGATTAAAGACA
Found at i:27236468 original size:4 final size:4
Alignment explanation
Indices: 27236461--27236502 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
27236451 ATATATATGT
*
27236461 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
27236503 TTTGATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:27248591 original size:72 final size:73
Alignment explanation
Indices: 27248505--27248707 Score: 291
Period size: 72 Copynumber: 2.7 Consensus size: 73
27248495 AATTATGCAT
27248505 TAATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATATTGAATGCTTGCTCAAAC
1 TAATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATATTGAATGCTTGCTCAAAC
27248570 GAG-CCAC
66 GAGTCCAC
* * * *
27248577 TAATTATACCGAATGCTTGCTCAAACGAGCATTATGCACTGATTGTACTGAATGCTTGCTCAAAC
1 TAATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATATTGAATGCTTGCTCAAAC
27248642 GAGCATTATCCAC
66 GAG-----TCCAC
* * *
27248655 TGATTATATTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATTTTGAAT
1 TAATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATATTGAAT
27248708 AAGATTTTCT
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 64 0.56
78 50 0.44
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (73 bp):
TAATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATATTGAATGCTTGCTCAAAC
GAGTCCAC
Found at i:27248676 original size:111 final size:112
Alignment explanation
Indices: 27248466--27248684 Score: 377
Period size: 111 Copynumber: 2.0 Consensus size: 112
27248456 ATGGAATTTC
* * *
27248466 AATTATACTGAATGATTTGCTCAAACGAGAATTATGCATTAATTATACTGAATGCTTGCTCAAAC
1 AATTATACCGAATGACTTGCTCAAACGAGAATTATGCACTAATTATACTGAATGCTTGCTCAAAC
27248531 GAGCATTATCCACTGATTATATTGAATGCTTGCTCAAACGAGCCACT
66 GAGCATTATCCACTGATTATATTGAATGCTTGCTCAAACGAGCCACT
* * *
27248578 AATTATACCGAATG-CTTGCTCAAACGAGCATTATGCACTGATTGTACTGAATGCTTGCTCAAAC
1 AATTATACCGAATGACTTGCTCAAACGAGAATTATGCACTAATTATACTGAATGCTTGCTCAAAC
27248642 GAGCATTATCCACTGATTATATTGAATGCTTGCTCAAACGAGC
66 GAGCATTATCCACTGATTATATTGAATGCTTGCTCAAACGAGC
27248685 ATTATCCACT
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
111 88 0.87
112 13 0.13
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (112 bp):
AATTATACCGAATGACTTGCTCAAACGAGAATTATGCACTAATTATACTGAATGCTTGCTCAAAC
GAGCATTATCCACTGATTATATTGAATGCTTGCTCAAACGAGCCACT
Found at i:27248707 original size:39 final size:39
Alignment explanation
Indices: 27248467--27248700 Score: 318
Period size: 39 Copynumber: 6.1 Consensus size: 39
27248457 TGGAATTTCA
* * * * *
27248467 ATTATACTGAATGATTTGCTCAAACGAGAATTATGCATTA
1 ATTATACTGAATG-CTTGCTCAAACGAGCATTATCCACTG
27248507 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* *
27248546 ATTATATTGAATGCTTGCTCAAACGAG------CCACTA
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* *
27248579 ATTATACCGAATGCTTGCTCAAACGAGCATTATGCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
*
27248618 ATTGTACTGAATGCTTGCTCAAACGAGCATTATCCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
*
27248657 ATTATATTGAATGCTTGCTCAAACGAGCATTATCCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
27248696 ATTAT
1 ATTAT
27248701 TTTGAATAAG
Statistics
Matches: 172, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.17
39 129 0.75
40 13 0.08
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (39 bp):
ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
Found at i:27252332 original size:23 final size:24
Alignment explanation
Indices: 27252306--27252353 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
27252296 TTCAGAATTT
27252306 GCCACAAAGG-TATCCCTTTTAGA
1 GCCACAAAGGCTATCCCTTTTAGA
* *
27252329 GCCACAAAGGCTATTCTTTTTAGA
1 GCCACAAAGGCTATCCCTTTTAGA
27252353 G
1 G
27252354 TTTGCCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
GCCACAAAGGCTATCCCTTTTAGA
Found at i:27257850 original size:42 final size:42
Alignment explanation
Indices: 27257803--27257885 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
27257793 AATATGTGTG
27257803 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
27257845 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
27257886 CTTTGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.39
Consensus pattern (42 bp):
AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
Found at i:27265815 original size:34 final size:34
Alignment explanation
Indices: 27265777--27265844 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
27265767 ATAAGAAATG
*
27265777 GCTATTGAGGGCATTAGTTTAAAATGGAGTTATA
1 GCTATTAAGGGCATTAGTTTAAAATGGAGTTATA
27265811 GCTATTAAGGGCATTAGTTTAAAATGGAGTTATA
1 GCTATTAAGGGCATTAGTTTAAAATGGAGTTATA
27265845 TAGGGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (34 bp):
GCTATTAAGGGCATTAGTTTAAAATGGAGTTATA
Found at i:27266534 original size:17 final size:18
Alignment explanation
Indices: 27266501--27266546 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
27266491 ATTTAAATTG
*
27266501 CGGTCGCGGTCGTGTTTT
1 CGGTCGCGGTCGCGTTTT
27266519 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
27266535 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
27266547 GACATAACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 3 0.12
17 5 0.19
18 7 0.27
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.30
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:27279229 original size:124 final size:124
Alignment explanation
Indices: 27278932--27279342 Score: 696
Period size: 124 Copynumber: 3.3 Consensus size: 124
27278922 ATTTATTAAG
*
27278932 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * * *
27278997 GTTTTTGAGAAAATAGTATAAAAACGTTTCAAGCAGTATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
*
27279056 GAAATCGCTCCCACGTGGACACGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * *
27279121 GTTTCTCAGCAAATAGTATAAAAAACGCTTGAAACAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
27279181 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAT
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
27279246 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
27279305 GAAATCGCTCCCACGTGGACGCGTTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAG
27279343 CATGTTTGGG
Statistics
Matches: 270, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
124 154 0.57
125 116 0.43
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:27282593 original size:49 final size:49
Alignment explanation
Indices: 27282540--27282807 Score: 473
Period size: 49 Copynumber: 5.5 Consensus size: 49
27282530 TAAGAATATT
* *
27282540 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * *
27282589 AACTATTTTGTATTTTATTAAATGAAATAATATTAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
27282638 AACTATTTTGTATTTTATTACATCAAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
27282687 AACTATTTTGTATTTTATTACATCAAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
27282736 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
27282785 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
27282808 TAATATAAAC
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 213 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:27282956 original size:21 final size:22
Alignment explanation
Indices: 27282932--27282986 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
27282922 AGCTTTCGAC
*
27282932 GGGGATTGTGGTTGC-TCCGGT-
1 GGGGATTCTGGTT-CATCCGGTA
27282953 GGGGATTCTGGTTCATCCGGTA
1 GGGGATTCTGGTTCATCCGGTA
27282975 GGGGA-TCTGGTT
1 GGGGATTCTGGTT
27282987 ATCGGTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.09, C:0.15, G:0.44, T:0.33
Consensus pattern (22 bp):
GGGGATTCTGGTTCATCCGGTA
Found at i:27288791 original size:24 final size:25
Alignment explanation
Indices: 27288762--27288815 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
27288752 TTTCTAGAAA
* *
27288762 ATTTAGTA-TTTATTAGTATAATAT
1 ATTTAGCATTTTATTAGCATAATAT
* *
27288786 ATTTAGCATTTTGTTAGCATAATTT
1 ATTTAGCATTTTATTAGCATAATAT
27288811 ATTTA
1 ATTTA
27288816 ACCTATGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (25 bp):
ATTTAGCATTTTATTAGCATAATAT
Found at i:27311812 original size:21 final size:21
Alignment explanation
Indices: 27311786--27311829 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27311776 TAATATTACT
* *
27311786 GCTACAATATCCAATCTCACC
1 GCTACAATAACAAATCTCACC
*
27311807 GCTACAGTAACAAATCTCACC
1 GCTACAATAACAAATCTCACC
27311828 GC
1 GC
27311830 CACCGCTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.20
Consensus pattern (21 bp):
GCTACAATAACAAATCTCACC
Found at i:27332601 original size:12 final size:12
Alignment explanation
Indices: 27332576--27332614 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27332566 ACTCGCTTCT
* *
27332576 TTACTTACTCAC
1 TTACTTGCTTAC
*
27332588 TTACTTGTTTAC
1 TTACTTGCTTAC
27332600 TTACTTGCTTAC
1 TTACTTGCTTAC
27332612 TTA
1 TTA
27332615 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:27332989 original size:30 final size:30
Alignment explanation
Indices: 27332955--27333012 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
27332945 CCTTGACTTG
27332955 AACTTTGGAAAAATTACGA-TTTTGCCCCTA
1 AACTTTGGAAAAATTAC-ACTTTTGCCCCTA
* * *
27332985 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGAAAAATTACACTTTTGCCCC
27333013 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:27336155 original size:17 final size:18
Alignment explanation
Indices: 27336116--27336156 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
27336106 TTGTCGGGGC
27336116 AAAAAGAAACCCAATCGT
1 AAAAAGAAACCCAATCGT
*
27336134 AAAAAGAAACCTAATCGT
1 AAAAAGAAACCCAATCGT
27336152 AAAAA
1 AAAAA
27336157 CCCTAGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAAAGAAACCCAATCGT
Found at i:27336281 original size:8 final size:8
Alignment explanation
Indices: 27336268--27336300 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
27336258 TTTAATGGTT
27336268 ATATTTAA
1 ATATTTAA
27336276 ATATTTAA
1 ATATTTAA
*
27336284 ATGTTTAA
1 ATATTTAA
27336292 ATATTTAA
1 ATATTTAA
27336300 A
1 A
27336301 ATATAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (8 bp):
ATATTTAA
Found at i:27336375 original size:30 final size:30
Alignment explanation
Indices: 27336336--27336392 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
27336326 ATTTATAAAT
27336336 AATTAATA-TTAAT-TGCTTAAAAATATTTAA
1 AATTAATATTTAATAT-CTT-AAAATATTTAA
*
27336366 AATTTATATTTAATATCTTAAAATATT
1 AATTAATATTTAATATCTTAAAATATT
27336393 AACAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.62
31 8 0.33
32 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (30 bp):
AATTAATATTTAATATCTTAAAATATTTAA
Found at i:27344240 original size:5 final size:5
Alignment explanation
Indices: 27344227--27344265 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
27344217 AATAAATTAG
*
27344227 TTATG TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
27344266 GAAATAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:27344585 original size:16 final size:17
Alignment explanation
Indices: 27344555--27344597 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
27344545 CATTTGTAAT
27344555 ATATTTATT-TAATTAG
1 ATATTTATTATAATTAG
*
27344571 ATATTTATTAT-ATTAT
1 ATATTTATTATAATTAG
*
27344587 ATTTTTATTAT
1 ATATTTATTAT
27344598 TATTGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTATTATAATTAG
Found at i:27345804 original size:23 final size:23
Alignment explanation
Indices: 27345777--27345845 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
27345767 GGCTTTGCCG
27345777 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
27345800 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * **
27345823 TTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
27345846 CAGGAACCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:27345848 original size:21 final size:21
Alignment explanation
Indices: 27345790--27345927 Score: 109
Period size: 21 Copynumber: 6.5 Consensus size: 21
27345780 AGGCACTTTA
* **
27345790 TGTGTCGTATATCAGGCACTTTA
1 TGTGTCG--TATCAGGCACCTCG
27345813 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
27345836 TGTGTCGTATCAGGAACCTCG
1 TGTGTCGTATCAGGCACCTCG
**
27345857 CAT-TCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
** *
27345877 CATGTCGTATCAGACACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * **
27345898 CGTGTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
27345918 TGTGTCGTAT
1 TGTGTCGTAT
27345928 ACTAATCAGG
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
20 29 0.30
21 43 0.44
23 25 0.26
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:27345871 original size:41 final size:42
Alignment explanation
Indices: 27345815--27345927 Score: 124
Period size: 41 Copynumber: 2.7 Consensus size: 42
27345805 GCACTTTATG
27345815 TGTCGTATTTCAGGCACCTCGTGTGTCGTATCAGGA-ACCTCGCA
1 TGTCGTA--TCAGGCACCTCGTGTGTCGTATCA-GACACCTCGCA
** *
27345859 T-TCGTATCAGGCACCTCGCATGTCGTATCAGACACCTCGCG
1 TGTCGTATCAGGCACCTCGTGTGTCGTATCAGACACCTCGCA
* **
27345900 TGTCGTTTCAGGCA-CTTATGTGTCGTAT
1 TGTCGTATCAGGCACCTCGTGTGTCGTAT
27345928 ACTAATCAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.03
41 40 0.68
42 11 0.19
43 5 0.08
44 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTCGTATCAGGCACCTCGTGTGTCGTATCAGACACCTCGCA
Found at i:27346301 original size:12 final size:12
Alignment explanation
Indices: 27346284--27346309 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27346274 ATAAAAGAAC
27346284 GAATTGATAATG
1 GAATTGATAATG
27346296 GAATTGATAATG
1 GAATTGATAATG
27346308 GA
1 GA
27346310 TGAGTTATTA
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:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (12 bp):
GAATTGATAATG
Found at i:27349635 original size:29 final size:29
Alignment explanation
Indices: 27349564--27349636 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
27349554 GTTCATGCTG
27349564 TATCAAGCACTATGTGCCAATGTTATATT
1 TATCAAGCACTATGTGCCAATGTTATATT
* * *** *
27349593 TATCAGGCATTATGTGCTGGTGTTATTTT
1 TATCAAGCACTATGTGCCAATGTTATATT
*
27349622 TATCAAGTACTATGT
1 TATCAAGCACTATGT
27349637 ACCGATGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (29 bp):
TATCAAGCACTATGTGCCAATGTTATATT
Found at i:27360154 original size:41 final size:41
Alignment explanation
Indices: 27360097--27360176 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
27360087 ATTTTCAGTT
27360097 GTTCTTTGTCAAGAGATCTAATTTGTGGAGATTATCAAATA
1 GTTCTTTGTCAAGAGATCTAATTTGTGGAGATTATCAAATA
27360138 GTTCTTTGTCAAGAGATCTAATTTGTGGAGATTATCAAA
1 GTTCTTTGTCAAGAGATCTAATTTGTGGAGATTATCAAA
27360177 CTTTATGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (41 bp):
GTTCTTTGTCAAGAGATCTAATTTGTGGAGATTATCAAATA
Found at i:27361003 original size:7 final size:7
Alignment explanation
Indices: 27360991--27361017 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27360981 AATAAATCAC
27360991 AATAAAG
1 AATAAAG
27360998 AATAAAG
1 AATAAAG
27361005 AATAAAG
1 AATAAAG
27361012 AATAAA
1 AATAAA
27361018 TTAGGAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:27369045 original size:42 final size:42
Alignment explanation
Indices: 27368997--27369079 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
27368987 TCCACACGAC
* *
27368997 CTGAGACACGGGCGTGTCTCTTGACCGTGTGAGATGCACGGT
1 CTGAGACACGGACGTGTCTCTTGACCGTGTGAGAAGCACGGT
*
27369039 CTGAGACACGGACGTGTCTCTTGACCGTGTTAGAAGCACGG
1 CTGAGACACGGACGTGTCTCTTGACCGTGTGAGAAGCACGG
27369080 CCTGGCCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (42 bp):
CTGAGACACGGACGTGTCTCTTGACCGTGTGAGAAGCACGGT
Found at i:27372615 original size:116 final size:117
Alignment explanation
Indices: 27372450--27372680 Score: 358
Period size: 116 Copynumber: 2.0 Consensus size: 117
27372440 GTTGATGCAT
*
27372450 TGAGCAAGAAATCGATGACTAATTTGAGAGCGATGTTCGCTAAGTAGAGTTTGACTGATG-GAGG
1 TGAGCAAAAAATCGATGACTAATTTGAGAGCGATGTTCGCTAAGTAGAGTTTGACTGATGAGAGG
*
27372514 TTTGCTTGCAAAGTTACAAGTGATACCTACCTTAGTGGATGGGGTTTGGAAC
66 TTTGCTTGCAAAGTTACAAGTGAGACCTACCTTAGTGGATGGGGTTTGGAAC
* *
27372566 TGAGCAAAAAA-CTGATGACTGATTTGAGAGCGATGTTTGCTAAGTAGAGTTTGACTGATGATAG
1 TGAGCAAAAAATC-GATGACTAATTTGAGAGCGATGTTCGCTAAGTAGAGTTTGACTGATG--AG
** *
27372630 AGGTTTGCTTGTGAAGTTACAAGTGAGACCTGCCTTAGTGGATGGGGTTTG
63 AGGTTTGCTTGCAAAGTTACAAGTGAGACCTACCTTAGTGGATGGGGTTTG
27372681 ATCAAAGCAA
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
115 1 0.01
116 55 0.53
119 48 0.46
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (117 bp):
TGAGCAAAAAATCGATGACTAATTTGAGAGCGATGTTCGCTAAGTAGAGTTTGACTGATGAGAGG
TTTGCTTGCAAAGTTACAAGTGAGACCTACCTTAGTGGATGGGGTTTGGAAC
Found at i:27381048 original size:29 final size:30
Alignment explanation
Indices: 27380997--27381063 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
27380987 AGAAAAGTTT
*
27380997 ATTGTGATTAATTTTTATGATTTGCCAATTG
1 ATTG-GATTAATTTTTATCATTTGCCAATTG
*
27381028 ATTGGATTAA-TTTTATCATTTTCCAATTG
1 ATTGGATTAATTTTTATCATTTGCCAATTG
27381057 ATTGGAT
1 ATTGGAT
27381064 GCATGTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 24 0.71
30 6 0.18
31 4 0.12
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (30 bp):
ATTGGATTAATTTTTATCATTTGCCAATTG
Found at i:27395203 original size:17 final size:19
Alignment explanation
Indices: 27395174--27395213 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
27395164 CATATTTATA
27395174 ACATGATACTATA-A-TCC
1 ACATGATACTATACATTCC
27395191 ACATGAT-CATATACATTCC
1 ACATGATAC-TATACATTCC
27395210 ACAT
1 ACAT
27395214 AATAATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 1 0.05
19 7 0.35
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (19 bp):
ACATGATACTATACATTCC
Found at i:27403530 original size:12 final size:12
Alignment explanation
Indices: 27403515--27403573 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
27403505 ACTTCCTTTG
27403515 GATCTTCCTCAA
1 GATCTTCCTCAA
* **
27403527 GATCTTCTTCGG
1 GATCTTCCTCAA
27403539 GATCTTCCTCAA
1 GATCTTCCTCAA
* **
27403551 GATCTTCTTCGT
1 GATCTTCCTCAA
27403563 GATCTTCCTCA
1 GATCTTCCTCA
27403574 TCTTTTGATT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.39
Consensus pattern (12 bp):
GATCTTCCTCAA
Found at i:27403541 original size:24 final size:24
Alignment explanation
Indices: 27403514--27403573 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
27403504 AACTTCCTTT
27403514 GGATCTTCCTCAAGATCTTCTTCG
1 GGATCTTCCTCAAGATCTTCTTCG
27403538 GGATCTTCCTCAAGATCTTCTTCG
1 GGATCTTCCTCAAGATCTTCTTCG
*
27403562 TGATCTTCCTCA
1 GGATCTTCCTCA
27403574 TCTTTTGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (24 bp):
GGATCTTCCTCAAGATCTTCTTCG
Found at i:27410770 original size:40 final size:40
Alignment explanation
Indices: 27410712--27410788 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
27410702 CATCATACAT
* *
27410712 GCCAATCTGGTTAGCAACT-ATCATGCCCT-ACTAGTGGCCC
1 GCCAACCTGGTTAACAACTAAT-ATG-CCTAACTAGTGGCCC
27410752 GCCAACCTGGTTAACAACTAATATGCCTAACTAGTGG
1 GCCAACCTGGTTAACAACTAATATGCCTAACTAGTGG
27410789 TCCATTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 3 0.09
40 28 0.85
41 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (40 bp):
GCCAACCTGGTTAACAACTAATATGCCTAACTAGTGGCCC
Found at i:27412577 original size:42 final size:42
Alignment explanation
Indices: 27412508--27412646 Score: 106
Period size: 42 Copynumber: 3.3 Consensus size: 42
27412498 TCGCTCACAC
* *
27412508 GAGCTTCTATTTAA-CTTATATGAGTTTCCATTCAGCTCTATT
1 GAGCTTCTATTTAACCCT-TATGGGTTTCCATTCAGCTCTATT
* * *
27412550 GAGCTTCTGTTTAACCCTTATGGGTTTCCGTTCTA-CTCT-TAC
1 GAGCTTCTATTTAACCCTTATGGGTTTCCATTC-AGCTCTAT-T
* ** * * * *
27412592 AAGCTTCCGTTCATCCCTTATGGGTTTCTATTTAGCTCTCA-T
1 GAGCTTCTATTTAACCCTTATGGGTTTCCATTCAGCTCT-ATT
27412634 GAGCTTCTATTTA
1 GAGCTTCTATTTA
27412647 GCCTTCGAGC
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
41 2 0.03
42 69 0.93
43 3 0.04
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (42 bp):
GAGCTTCTATTTAACCCTTATGGGTTTCCATTCAGCTCTATT
Found at i:27418821 original size:29 final size:29
Alignment explanation
Indices: 27418780--27418842 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
27418770 AAAACTTCTC
27418780 ACTC-TATTAACCAAGAAAGAATCACTAG
1 ACTCGTATTAACCAAGAAAGAATCACTAG
27418808 ACTCGTATTAACCAAGAAAGAATCACTAG
1 ACTCGTATTAACCAAGAAAGAATCACTAG
27418837 ACTCGT
1 ACTCGT
27418843 GAAAGATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (29 bp):
ACTCGTATTAACCAAGAAAGAATCACTAG
Found at i:27423144 original size:17 final size:17
Alignment explanation
Indices: 27423124--27423195 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
27423114 ATTTTAATCG
27423124 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
27423141 ATTTAATACTT--ATCTT-
1 ATTTAATA-TTAAAT-TTA
* * **
27423157 A-GTAGTATTTTA-TTA
1 ATTTAATATTAAATTTA
27423172 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
27423189 ATTTAAT
1 ATTTAAT
27423196 GTTTATCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 11 0.26
17 20 0.48
18 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:27423637 original size:45 final size:46
Alignment explanation
Indices: 27423568--27423685 Score: 213
Period size: 45 Copynumber: 2.6 Consensus size: 46
27423558 AAGATTACTC
27423568 GTTTGATTAAGTGTTTATTACTTTAGATGAATAAAAAAGGTAC-AT
1 GTTTGATTAAGTGTTTATTACTTTAGATGAATAAAAAAGGTACAAT
*
27423613 GTTTTATTAAGTGTTTATTACTTTAGATGAATAAAAAAGGTACAAT
1 GTTTGATTAAGTGTTTATTACTTTAGATGAATAAAAAAGGTACAAT
27423659 -TTTGATTAAGTGTTTATTACTTTAGAT
1 GTTTGATTAAGTGTTTATTACTTTAGAT
27423686 ATCATAACCA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
45 68 0.97
46 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (46 bp):
GTTTGATTAAGTGTTTATTACTTTAGATGAATAAAAAAGGTACAAT
Found at i:27428281 original size:48 final size:48
Alignment explanation
Indices: 27428222--27428416 Score: 210
Period size: 48 Copynumber: 4.1 Consensus size: 48
27428212 AACAAATTTC
* * * * * *
27428222 TCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCATAACAGATTA
* * * * * * *
27428270 TCGATGGCCTGCACATAGTTCGCGCCACCCTTGTATCTTAACAGGTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCATAACAGATTA
* * * *
27428318 TTGGTGGCCTGCACACAGTCCTTGCCACCCTTATATCATAATAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCATAACAGATTA
* * *
27428366 TCGGTGGCCTGCACACAGTTCGTGCCACCCTTATGTCATAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCATAACAGATTA
27428414 TCG
1 TCG
27428417 ATGCGCATAG
Statistics
Matches: 120, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 120 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCATAACAGATTA
Found at i:27428393 original size:96 final size:96
Alignment explanation
Indices: 27428224--27428397 Score: 240
Period size: 96 Copynumber: 1.8 Consensus size: 96
27428214 CAAATTTCTC
* * * * * *
27428224 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTCTCGATGGCCTGCACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTATATAATAACAGAATATCGATGGCCTGCACACAGT
27428289 TCGCGCCACCCTTGTATCTTAACAGGTTATT
66 TCGCGCCACCCTTGTATCTTAACAGGTTATT
* * * * *
27428320 GGTGGCCTGCACACAGTCCTTGCCACCCTTATATCATAATAGAATATCGGTGGCCTGCACACAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTATATAATAACAGAATATCGATGGCCTGCACACAGT
*
27428385 TCGTGCCACCCTT
66 TCGCGCCACCCTT
27428398 ATGTCATAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 66 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTATATAATAACAGAATATCGATGGCCTGCACACAGT
TCGCGCCACCCTTGTATCTTAACAGGTTATT
Found at i:27430383 original size:14 final size:14
Alignment explanation
Indices: 27430364--27430393 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27430354 GTGACTTGTA
27430364 TACTTTGATGTAAG
1 TACTTTGATGTAAG
27430378 TACTTTGATGTAAG
1 TACTTTGATGTAAG
27430392 TA
1 TA
27430394 AAAGCTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (14 bp):
TACTTTGATGTAAG
Found at i:27432353 original size:25 final size:25
Alignment explanation
Indices: 27432323--27432462 Score: 94
Period size: 25 Copynumber: 5.7 Consensus size: 25
27432313 GCACTCTCTT
*
27432323 GAGCCATATAATGGGAAGCTCATGT
1 GAGCCATATAATGGGAAGCTCATGA
* * * **
27432348 GAGCCATGTAATAGGAAGCTTATCC
1 GAGCCATATAATGGGAAGCTCATGA
** * *
27432373 GAGCTTTATAACGGGAAGCTCATAA
1 GAGCCATATAATGGGAAGCTCATGA
*
27432398 GAGTCATAT--TGAGGAAGCTCATGA
1 GAGCCATATAATG-GGAAGCTCATGA
* *
27432422 GAGCCA-AT-ATCGGGTAGCTTCA-AA
1 GAGCCATATAAT-GGGAAGC-TCATGA
27432446 GAGCCA-ATAATGGGAAG
1 GAGCCATATAATGGGAAG
27432463 ATCCGGATAG
Statistics
Matches: 88, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
23 3 0.03
24 36 0.41
25 49 0.56
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.22
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCATGA
Found at i:27433427 original size:17 final size:18
Alignment explanation
Indices: 27433405--27433439 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27433395 GACCTAATTG
27433405 TAAAAATTACAA-AAACA
1 TAAAAATTACAAGAAACA
*
27433422 TAAAAATTTCAAGAAACA
1 TAAAAATTACAAGAAACA
27433440 GGTAAGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAATTACAAGAAACA
Found at i:27451065 original size:20 final size:21
Alignment explanation
Indices: 27451030--27451069 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
27451020 AGTTATATTT
*
27451030 ATATTTAATTTAATTTTTAAA
1 ATATTTAATGTAATTTTTAAA
27451051 ATATTTAA-GTAATTTTTAA
1 ATATTTAATGTAATTTTTAA
27451070 TTTTTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATTTAATGTAATTTTTAAA
Found at i:27452055 original size:28 final size:28
Alignment explanation
Indices: 27452017--27452080 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
27452007 TATTTAATGA
27452017 TTTTTTATGTAAATAAAATTATAATGGT
1 TTTTTTATGTAAATAAAATTATAATGGT
*
27452045 TTTTTTATGTAAATAAAATTATAATGTT
1 TTTTTTATGTAAATAAAATTATAATGGT
27452073 TTTTTTAT
1 TTTTTTAT
27452081 TTTGCAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (28 bp):
TTTTTTATGTAAATAAAATTATAATGGT
Found at i:27455079 original size:21 final size:20
Alignment explanation
Indices: 27455041--27455093 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
27455031 AATCAAAATA
* *
27455041 CCTTTTTTTTTCTTCTTCTT
1 CCTTTTTTCTTCTGCTTCTT
27455061 CCTTTGTTTCTTCTGCTTCCTT
1 CCTTT-TTTCTTCTGCTT-CTT
*
27455083 -CTTATTTCTTC
1 CCTTTTTTCTTC
27455094 CGTTTCTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.43
21 13 0.46
22 3 0.11
ACGTcount: A:0.02, C:0.28, G:0.04, T:0.66
Consensus pattern (20 bp):
CCTTTTTTCTTCTGCTTCTT
Found at i:27455204 original size:27 final size:27
Alignment explanation
Indices: 27455165--27455260 Score: 113
Period size: 27 Copynumber: 3.5 Consensus size: 27
27455155 GACGCCTTTC
27455165 AATATGGCACCAATAATGGCTCCTCCCA
1 AATA-GGCACCAATAATGGCTCCTCCCA
27455193 AATAGGCACCAATAATGGCTCCTCCCA
1 AATAGGCACCAATAATGGCTCCTCCCA
* * ** * *
27455220 GATAGGCATCACCATTGGCTCCT-CTA
1 AATAGGCACCAATAATGGCTCCTCCCA
27455246 AGATAGGCACCAATA
1 A-ATAGGCACCAATA
27455261 CTATGTATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
26 2 0.04
27 51 0.89
28 4 0.07
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (27 bp):
AATAGGCACCAATAATGGCTCCTCCCA
Found at i:27458294 original size:2 final size:2
Alignment explanation
Indices: 27458287--27458335 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
27458277 CTCTGCAAAA
27458287 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27458329 AG AG AG A
1 AG AG AG A
27458336 AGCTTAAGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27458744 original size:24 final size:25
Alignment explanation
Indices: 27458696--27458744 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
27458686 TACACTAACA
*
27458696 CTAAATAAAAAATTTAATCTATATT
1 CTAAATAAAAAATTTAATATATATT
* *
27458721 CTAAA-AAAAACTTTAATATCTATT
1 CTAAATAAAAAATTTAATATATATT
27458745 TCATATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (25 bp):
CTAAATAAAAAATTTAATATATATT
Found at i:27462446 original size:14 final size:14
Alignment explanation
Indices: 27462436--27462474 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
27462426 TACTATATTT
27462436 TATTTATTATATCA
1 TATTTATTATATCA
*
27462450 TATTTATCATATCA
1 TATTTATTATATCA
27462464 TATTTATTATA
1 TATTTATTATA
27462475 ATTGGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTATTATATCA
Found at i:27466181 original size:43 final size:43
Alignment explanation
Indices: 27466132--27466440 Score: 388
Period size: 43 Copynumber: 7.2 Consensus size: 43
27466122 CGAAAAAAAT
* * *
27466132 GCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCCTACAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
27466175 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTACAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* ** *
27466218 GCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* * *
27466261 GCCGCTATAGACCACGACCTTTAGAGGCGCTTTT-CCAAAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
27466303 GCCGCTATAGATCACGACCTTTAGCAGCGTTTTTCCCACAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
27466346 GCCGCTATAGACCGCGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * * *
27466389 GCCACTAAAGATCACGACCTTTAGCAGCGCTTCTCGCTA-AAAC
1 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTC-CCACAAAC
27466432 GCCGCTAAA
1 GCCGCTAAA
27466441 AACATAACCT
Statistics
Matches: 235, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
42 37 0.16
43 196 0.83
44 2 0.01
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:27466417 original size:171 final size:171
Alignment explanation
Indices: 27466126--27466438 Score: 441
Period size: 171 Copynumber: 1.8 Consensus size: 171
27466116 AAGCGCCGAA
* * * *
27466126 AAAAATGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCCTACAAACGCCGCTAAAGACCAAG
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGACCAAG
* *
27466191 ACCTTTAGCGGCGCTTTTCCTACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTC-CC
66 ACCTTTAGCGGCGCTTTTCCCACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTCTCGCC
27466255 ACAAACGCCGCTATAGACCACGACCTTTAGAGGCGCTTTTCC
131 A-AAACGCCGCTATAGACCACGACCTTTAGAGGCGCTTTTCC
* * * * * **
27466297 AAAAACGCCGCTATAGATCACGACCTTTAGCAGCGTTTTTCCCACAAACGCCGCTATAGACCGCG
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGACCAAG
* **
27466362 ACCTTTAGCGGCGCTTTTCCCACAAACGCCA-CTAAAGATCACGACCTTTAGCAGCGCTTCTCGC
66 ACCTTTAGCGGCGCTTTTCCCACAAACG-CAGCTAAAGACCAAAACCTTTAGCAGCGCTTCTCGC
*
27466426 TAAAACGCCGCTA
130 CAAAACGCCGCTA
27466439 AAAACATAAC
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
171 119 0.97
172 4 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (171 bp):
AAAAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGACCAAG
ACCTTTAGCGGCGCTTTTCCCACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTCTCGCC
AAAACGCCGCTATAGACCACGACCTTTAGAGGCGCTTTTCC
Found at i:27466451 original size:128 final size:126
Alignment explanation
Indices: 27466136--27466453 Score: 368
Period size: 128 Copynumber: 2.5 Consensus size: 126
27466126 AAAAATGCCG
* * * * *
27466136 CTAAAGACCAAGACCTTTAGCGGTGCTTTTCCTACAAACGCCGCTAAAGACCAAGACCTTTAGCG
1 CTAAAGACCACGACCTTTAGCAGCGCTTTTCCTA-AAACGCCGCTAAA-AACAA-ACCTTTAGCA
* *
27466201 GCGCTTTTCCTACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTCCCACAAACGCCG
63 GCGCTTTTCCCACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTCCCACAAACGCCA
* * * * *
27466265 CTATAGACCACGACCTTTAG-AGGCGCTTTTCCAAAAACGCCGCTATAGATCACGACCTTTAGCA
1 CTAAAGACCACGACCTTTAGCA-GCGCTTTTCCTAAAACGCCGCTA-AAAACA-AACCTTTAGCA
* * * *** *
27466329 GCGTTTTTCCCACAAACGCCGCTATAGACCGCGACCTTTAGCGGCGCTTTTCCCACAAACGCCA
63 GCGCTTTTCCCACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTCCCACAAACGCCA
* *
27466393 CTAAAGATCACGACCTTTAGCAGCGCTTCTCGCTAAAACGCCGCTAAAAACATAACCTTTA
1 CTAAAGACCACGACCTTTAGCAGCGCTTTTC-CTAAAACGCCGCTAAAAACA-AACCTTTA
27466454 AAAAAATTAT
Statistics
Matches: 158, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
128 115 0.73
129 43 0.27
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (126 bp):
CTAAAGACCACGACCTTTAGCAGCGCTTTTCCTAAAACGCCGCTAAAAACAAACCTTTAGCAGCG
CTTTTCCCACAAACGCAGCTAAAGACCAAAACCTTTAGCAGCGCTTTTCCCACAAACGCCA
Found at i:27466567 original size:115 final size:116
Alignment explanation
Indices: 27466364--27466590 Score: 350
Period size: 115 Copynumber: 2.0 Consensus size: 116
27466354 AGACCGCGAC
* * * *
27466364 CTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGATCACGACCTTTAGCAGCGCTTCTCGCTAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACACAACCTTTAGCAGCACTTCTCGCAAA
*
27466429 AACGCCGCTAAAAACATAACCTTTAAAAAAATTATTTTAATCAAATACTAT
66 AACGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCAAATACTAT
* * * *
27466480 CTTTAGCGGTGTTTTTCCTACAAACGCCACTAAAGAACA-AACCTTTAGC-GACACTTCTTGCAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACACAACCTTTAGCAG-CACTTCTCGCAA
27466543 AAACGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCAAATA
65 AAACGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCAAATA
27466591 ATATTTACTT
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
114 1 0.01
115 65 0.64
116 35 0.35
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (116 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACACAACCTTTAGCAGCACTTCTCGCAAA
AACGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCAAATACTAT
Found at i:27471690 original size:10 final size:10
Alignment explanation
Indices: 27471666--27471728 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
27471656 AAAATAAAAG
27471666 TTTAAAATCTT
1 TTTAAAAT-TT
27471677 TTTAAAATTT
1 TTTAAAATTT
**
27471687 TTTAAAA-AA
1 TTTAAAATTT
* *
27471696 ATTAAAATCT
1 TTTAAAATTT
27471706 TTTAAAATTCAT
1 TTTAAAATT--T
27471718 TTTAAAATTT
1 TTTAAAATTT
27471728 T
1 T
27471729 AAATCACGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 6 0.14
10 18 0.43
11 8 0.19
12 10 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:27471703 original size:30 final size:30
Alignment explanation
Indices: 27471667--27471724 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
27471657 AAATAAAAGT
27471667 TTAAAATCTTTTTAAAATT-TTTTAAAAAAA
1 TTAAAATC-TTTTAAAATTATTTTAAAAAAA
27471697 TTAAAATCTTTTAAAATTCATTTTAAAA
1 TTAAAATCTTTTAAAATT-ATTTTAAAA
27471725 TTTTAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 10 0.38
30 8 0.31
31 8 0.31
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAAATCTTTTAAAATTATTTTAAAAAAA
Found at i:27471731 original size:30 final size:29
Alignment explanation
Indices: 27471660--27471731 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
27471650 ATTATAAAAA
*
27471660 TAAAAGTTTAAAATCTTTTTAAAATTTTT
1 TAAAAATTTAAAATCTTTTTAAAATTTTT
*
27471689 TAAAAAAATTAAAATC-TTTTAAAATTCATTT
1 T-AAAAATTTAAAATCTTTTTAAAATT--TTT
*
27471720 TAAAATTTTAAA
1 TAAAAATTTAAA
27471732 TCACGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 11 0.31
30 21 0.58
31 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (29 bp):
TAAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:27471732 original size:29 final size:28
Alignment explanation
Indices: 27471660--27471733 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
27471650 ATTATAAAAA
27471660 TAAAAGTTTAAAATCTTTTTAAAATTTTT
1 TAAAA-TTTAAAATCTTTTTAAAATTTTT
*
27471689 TAAAAAAATTAAAATC-TTTTAAAATTCATTT
1 T--AAAATTTAAAATCTTTTTAAAATT--TTT
*
27471720 TAAAATTTTAAATC
1 TAAAATTTAAAATC
27471734 ACGAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 22 0.58
30 8 0.21
31 8 0.21
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:27473300 original size:41 final size:41
Alignment explanation
Indices: 27473240--27473423 Score: 264
Period size: 41 Copynumber: 4.5 Consensus size: 41
27473230 AGATTTTATT
* *
27473240 ATTAGCGGCGTTTTTTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
* * *
27473281 ATTAGCGGTGCTTTCTCAAAAACACTGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
*
27473322 ATTAGTGGCGC-TTCTTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTC-TCAAAAACGCCGCTAAAGGCACGAGC
* *
27473363 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
*
27473404 ATTAGCGGCGC-TCCTCAAAA
1 ATTAGCGGCGCTTTCTCAAAA
27473424 CTTTGAAAAC
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 11 0.09
41 114 0.89
42 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
Found at i:27473608 original size:12 final size:12
Alignment explanation
Indices: 27473591--27473616 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27473581 TTTTTTGTCC
27473591 AAACGCCGCTAA
1 AAACGCCGCTAA
27473603 AAACGCCGCTAA
1 AAACGCCGCTAA
27473615 AA
1 AA
27473617 CCCTGTTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:27474160 original size:19 final size:19
Alignment explanation
Indices: 27474129--27474181 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
27474119 AAATTTAAAA
27474129 AATACTACTTTTATAAATTT
1 AATACT-CTTTTATAAATTT
* * *
27474149 TATACTCTTTTATCAGTTT
1 AATACTCTTTTATAAATTT
27474168 AATACT-TTTTATAA
1 AATACTCTTTTATAA
27474182 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 7 0.25
19 16 0.57
20 5 0.18
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (19 bp):
AATACTCTTTTATAAATTT
Found at i:27492156 original size:21 final size:21
Alignment explanation
Indices: 27492117--27492156 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27492107 AGAATACAAT
*
27492117 TTTGTGCTATTTTACATTAAA
1 TTTGTGCTAATTTACATTAAA
27492138 TTTGTGCATAATTTA-ATTA
1 TTTGTGC-TAATTTACATTA
27492157 TTTTATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTGTGCTAATTTACATTAAA
Found at i:27499385 original size:71 final size:71
Alignment explanation
Indices: 27499303--27499540 Score: 413
Period size: 71 Copynumber: 3.4 Consensus size: 71
27499293 ATGAATTTCC
* *
27499303 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAGGTATTAATAATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
27499368 GTCATA
66 GTCATA
* * * *
27499374 ATCCAATTAATACGTGAACCTAATTCCTTAAGCATTCACATGTGCTAATAATAGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
27499439 GTCATA
66 GTCATA
*
27499445 ATCCAATTAATACGTGAACCTTATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
27499510 GTCATA
66 GTCATA
27499516 ATCCAATTAATACGTGAACCTAATT
1 ATCCAATTAATACGTGAACCTAATT
27499541 TATGCTTGAT
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 156 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (71 bp):
ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
GTCATA
Found at i:27500703 original size:16 final size:17
Alignment explanation
Indices: 27500682--27500716 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27500672 AATTGATTTA
*
27500682 AATTAATTAATTTT-TC
1 AATTAAATAATTTTCTC
27500698 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
27500715 AA
1 AA
27500717 CCCAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:27511308 original size:18 final size:18
Alignment explanation
Indices: 27511285--27511344 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
27511275 ATAGAGATTA
*
27511285 GATATGAAGTTTTGTTAT
1 GATATGAAGTTTTGATAT
* * * *
27511303 GATATGAAGATCTAATCT
1 GATATGAAGTTTTGATAT
27511321 GATATTG-AGTTTTGATAT
1 GATA-TGAAGTTTTGATAT
27511339 GATATG
1 GATATG
27511345 GAATTTTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (18 bp):
GATATGAAGTTTTGATAT
Found at i:27530390 original size:7 final size:7
Alignment explanation
Indices: 27530378--27530412 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
27530368 TTTGATAACT
27530378 CTAAACC
1 CTAAACC
27530385 CTAAACC
1 CTAAACC
27530392 CTAAACC
1 CTAAACC
27530399 CTAAACC
1 CTAAACC
27530406 CTAAACC
1 CTAAACC
27530413 TCCCCACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CTAAACC
Found at i:27532720 original size:50 final size:50
Alignment explanation
Indices: 27532665--27532796 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
27532655 TATTGAGGTT
* * *
27532665 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCAAG
* * *
27532715 ATGAGAGGTCCC-TCGTAAGACCATGTCTAGGACATAGCATGGGCACCGAT
1 ATGAGAGGTCCCAT-GTAAGACCATGTCTGGGACATAGCATGGGCACCAAG
** *
27532765 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGA
27532797 TATGACATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 68 0.97
51 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCAAG
Found at i:27533220 original size:14 final size:14
Alignment explanation
Indices: 27533203--27533240 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
27533193 TTTACGCTTA
27533203 CTTCTTTTATTTTC
1 CTTCTTTTATTTTC
27533217 CTTCTTTTTTATTTTC
1 CTTC--TTTTATTTTC
27533233 CTTCTTTT
1 CTTCTTTT
27533241 TTATAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTCTTTTATTTTC
Found at i:27533228 original size:16 final size:16
Alignment explanation
Indices: 27533207--27533244 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
27533197 CGCTTACTTC
27533207 TTTTATTTTCCTTCTT
1 TTTTATTTTCCTTCTT
27533223 TTTTATTTTCCTTCTT
1 TTTTATTTTCCTTCTT
27533239 TTTTAT
1 TTTTAT
27533245 AGTATTGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTTCCTTCTT
Found at i:27540502 original size:50 final size:50
Alignment explanation
Indices: 27540407--27540512 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
27540397 TATTGAGGTT
* * * *
27540407 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCCAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACACGGCATGGGCACCCAG
* * * * *
27540457 ATGAGGGGTCCCCCGTAGGACCATGTCTGGGACACGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACACGGCATGGGCACCCAG
27540507 ATGAGA
1 ATGAGA
27540513 ACTCCCATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.24, C:0.25, G:0.34, T:0.18
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACACGGCATGGGCACCCAG
Found at i:27540828 original size:20 final size:20
Alignment explanation
Indices: 27540803--27540851 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27540793 TGAGTTATTT
*
27540803 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAC
*
27540823 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
27540843 AAG-AAGCAA
1 AAGTAAGCAA
27540852 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:27546085 original size:43 final size:43
Alignment explanation
Indices: 27545979--27546086 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
27545969 CCAACAAATA
* * *
27545979 TATGGACAAAGCCACCAAATTTGTAGACAAGCTATCATGTAGGT
1 TATGGACAAAGCCA-CAAATTTGCAGACAAGCTACCATGTAAGT
* * *
27546023 TATGGATAAA-CTACAAAATTTGCAGACAAGCTGCCATGTAAGT
1 TATGGACAAAGCCAC-AAATTTGCAGACAAGCTACCATGTAAGT
*
27546066 T-TGGACGAAGCCAGCAAATTT
1 TATGGACAAAGCCA-CAAATTT
27546087 CTAGAGAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
42 7 0.13
43 35 0.67
44 10 0.19
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (43 bp):
TATGGACAAAGCCACAAATTTGCAGACAAGCTACCATGTAAGT
Found at i:27549094 original size:44 final size:43
Alignment explanation
Indices: 27549046--27549425 Score: 465
Period size: 44 Copynumber: 8.6 Consensus size: 43
27549036 TTCGATCTGC
* *
27549046 TCCACTACTGCTT-AGGGAGACAGGATCTACAATCTTCAACCTAT
1 TCCACTGCTG-TTCAGGGAGATAGGA-CTACAATCTTCAACCTAT
* * *
27549090 TCCACTACTATTCAGGGAGATAGGACTTATAATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGAC-TACAATCTTCAACCTAT
** * **
27549134 TCCACTATTGTTCAGGGAGATAGAACTTGTAATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGAC-TACAATCTTCAACCTAT
* **
27549178 TCCACTGCTGTTCAGGGAGATAGGAATTGTAATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGG-ACTACAATCTTCAACCTAT
* * *
27549222 TCCAACTGCTGTTCAGGGAGATAAGACATGCAATCTTCCACCTAT
1 TCC-ACTGCTGTTCAGGGAGATAGGAC-TACAATCTTCAACCTAT
*
27549267 TCCACTGCTGTTCAGGGAGATAGGATATACAATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGA-CTACAATCTTCAACCTAT
* *
27549311 TCCACTGCTGTTCAGGGAGATAGGACTTGCTATCTTCAACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGAC-TACAATCTTCAACCTAT
* *
27549355 TCCACTGTTGTTCAGGGAGATAGGACATACAATCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGATAGGAC-TACAATCTTCAACCTAT
*
27549399 TCCACTGCTGATCAGGGAGATAGGACT
1 TCCACTGCTGTTCAGGGAGATAGGACT
27549426 GGCAGCTTAA
Statistics
Matches: 300, Mismatches: 29, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
43 4 0.01
44 257 0.86
45 39 0.13
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
TCCACTGCTGTTCAGGGAGATAGGACTACAATCTTCAACCTAT
Found at i:27549355 original size:177 final size:176
Alignment explanation
Indices: 27549075--27549420 Score: 527
Period size: 177 Copynumber: 2.0 Consensus size: 176
27549065 ACAGGATCTA
*
27549075 CAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGACTTATAATCTTCAACCTATTCCACT
1 CAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
*
27549140 ATTGTTCAGGGAGATAGAACTTGTAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGA-A
66 ACTGTTCAGGGAGATAGAACTTGTAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACA
** *
27549204 TTGTAATCTTCAACCTATTCCAACTGCTGTTCAGGGAGATAAGACATG
131 -TACAATCTTCAACCTATTCC-ACTGCTGATCAGGGAGATAAGACATG
* * *
27549252 CAATCTTCCACCTATTCCACTGCTGTTCAGGGAGATAGGA-TATACAATCTTCAACCTATTCCAC
1 CAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGACT-TACAATCTTCAACCTATTCCAC
* * *
27549316 TGCTGTTCAGGGAGATAGGACTTGCT-ATCTTCAACCTATTCCACTGTTGTTCAGGGAGATAGGA
65 TACTGTTCAGGGAGATAGAACTTG-TAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGA
*
27549380 CATACAATCTTCCACCTATTCCACTGCTGATCAGGGAGATA
129 CATACAATCTTCAACCTATTCCACTGCTGATCAGGGAGATA
27549421 GGACTGGCAG
Statistics
Matches: 154, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
176 19 0.12
177 133 0.86
178 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (176 bp):
CAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
ACTGTTCAGGGAGATAGAACTTGTAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACA
TACAATCTTCAACCTATTCCACTGCTGATCAGGGAGATAAGACATG
Found at i:27550474 original size:22 final size:22
Alignment explanation
Indices: 27550449--27550521 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
27550439 GATTGGGAAG
27550449 GTGTATCTTGGAAAAGAATGAA
1 GTGTATCTTGGAAAAGAATGAA
*** * *
27550471 GTGT-TCCACGAAATTGATTGGGAA
1 GTGTATCTTGGAAA-AGAAT--GAA
27550495 TGTGTATCTTGGAAAAGAATGAA
1 -GTGTATCTTGGAAAAGAATGAA
27550518 GTGT
1 GTGT
27550522 TCCAAGAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 3 0.08
24 3 0.08
25 7 0.19
26 6 0.17
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (22 bp):
GTGTATCTTGGAAAAGAATGAA
Found at i:27550487 original size:47 final size:47
Alignment explanation
Indices: 27550433--27550525 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
27550423 AGATAACAAA
27550433 GAAATTGATTGGGAAGGTGTATCTTGGAAAAGAATGAAGTGTTCCAC
1 GAAATTGATTGGGAAGGTGTATCTTGGAAAAGAATGAAGTGTTCCAC
*
27550480 GAAATTGATTGGGAATGTGTATCTTGGAAAAGAATGAAGTGTTCCA
1 GAAATTGATTGGGAAGGTGTATCTTGGAAAAGAATGAAGTGTTCCA
27550526 AGAATAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
GAAATTGATTGGGAAGGTGTATCTTGGAAAAGAATGAAGTGTTCCAC
Found at i:27562129 original size:39 final size:38
Alignment explanation
Indices: 27562086--27562163 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
27562076 ATTTACACAT
* *
27562086 ATAATCACCTAACATACAAGTAGATATCACAATACTCAA
1 ATAATCACATAACATACAAGCAGATATC-CAATACTCAA
** *
27562125 ATAATCACATAACATTTAAGCATATATCCAATACTCAA
1 ATAATCACATAACATACAAGCAGATATCCAATACTCAA
27562163 A
1 A
27562164 AACATCTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 11 0.32
39 23 0.68
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.26
Consensus pattern (38 bp):
ATAATCACATAACATACAAGCAGATATCCAATACTCAA
Found at i:27568332 original size:23 final size:23
Alignment explanation
Indices: 27568302--27568426 Score: 76
Period size: 23 Copynumber: 5.3 Consensus size: 23
27568292 TGTACAAAAA
27568302 TGGACAGCATTTAAGCACCAATT
1 TGGACAGCATTTAAGCACCAATT
* *
27568325 TGGACAGCATTAATATACTCAACAA--
1 TGGACAGCATT--TA-A-GCACCAATT
* *
27568350 TGGACAGCAATTAAGCATCAATT
1 TGGACAGCATTTAAGCACCAATT
* * * **
27568373 TGGATAGCATTAATATGCTA-AAAAA
1 TGGACAGCATT--TAAGC-ACCAATT
*
27568398 TGGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACCAATT
27568421 TGGACA
1 TGGACA
27568427 ACATCTTATC
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
21 5 0.07
22 2 0.03
23 34 0.45
25 28 0.37
26 2 0.03
27 5 0.07
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACCAATT
Found at i:27568352 original size:48 final size:48
Alignment explanation
Indices: 27568297--27568426 Score: 197
Period size: 48 Copynumber: 2.7 Consensus size: 48
27568287 TGATTTGTAC
*
27568297 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTC
1 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTA
* * * * *
27568345 AACAATGGACAGCAATTAAGCATCAATTTGGATAGCATTAATATGCTA
1 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTA
*
27568393 AAAAATGGACAGCATTTAAGCACTAATTTGGACA
1 AAAAATGGACAGCATTTAAGCACCAATTTGGACA
27568427 ACATCTTATC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (48 bp):
AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTA
Found at i:27570332 original size:56 final size:56
Alignment explanation
Indices: 27570266--27570378 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
27570256 GTTCTAAAAC
27570266 CACTGTTCTGATTTAACTAAAATCGGGTTGTTACAACTCTCCCCCTTAGGGATTTT
1 CACTGTTCTGATTTAACTAAAATCGGGTTGTTACAACTCTCCCCCTTAGGGATTTT
27570322 CACTGTTCTGATTTAACTAAAATCGGGTTGTTACAACTCTCCCCCTTAGGGATTTT
1 CACTGTTCTGATTTAACTAAAATCGGGTTGTTACAACTCTCCCCCTTAGGGATTTT
27570378 C
1 C
27570379 GTCCCCAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (56 bp):
CACTGTTCTGATTTAACTAAAATCGGGTTGTTACAACTCTCCCCCTTAGGGATTTT
Found at i:27573895 original size:20 final size:20
Alignment explanation
Indices: 27573870--27573908 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27573860 TTCTGGGTGT
27573870 TCTACCTCTAACTGCAGTGG
1 TCTACCTCTAACTGCAGTGG
27573890 TCTACCTCTAACTGCAGTG
1 TCTACCTCTAACTGCAGTG
27573909 TTACTCGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.31
Consensus pattern (20 bp):
TCTACCTCTAACTGCAGTGG
Found at i:27576186 original size:23 final size:23
Alignment explanation
Indices: 27576160--27576265 Score: 99
Period size: 23 Copynumber: 4.5 Consensus size: 23
27576150 TGTACAAAAA
*
27576160 TGGACAACATTTAAGCACCAATT
1 TGGACAGCATTTAAGCACCAATT
* *
27576183 TGGACAGCATTAATATACTCAACAA--
1 TGGACAGCATT--TA-A-GCACCAATT
* *
27576208 TGGACAGCAATTAAGCATCAATT
1 TGGACAGCATTTAAGCACCAATT
*
27576231 TGGACAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACCAATT
*
27576254 TGGACAACATTT
1 TGGACAGCATTT
27576266 TATCATCACA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
21 5 0.07
22 1 0.01
23 43 0.64
25 12 0.18
26 1 0.01
27 5 0.07
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACCAATT
Found at i:27576903 original size:42 final size:41
Alignment explanation
Indices: 27576841--27576919 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
27576831 ATGTTATAAT
* *
27576841 ATATCGATGCCATTATCCCAGACAGGGTTTTACACAAAATC
1 ATATCGATGCCAATATCCCAGACAGGGTCTTACACAAAATC
* *
27576882 ATATGCGATGCCAATGTCCCAGACATGGTCTTACACAA
1 ATAT-CGATGCCAATATCCCAGACAGGGTCTTACACAA
27576920 CATACGTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
ATATCGATGCCAATATCCCAGACAGGGTCTTACACAAAATC
Found at i:27578409 original size:9 final size:9
Alignment explanation
Indices: 27578395--27578425 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27578385 GTTAGACAAA
27578395 TCGAGTTAT
1 TCGAGTTAT
*
27578404 TCGAGTTAA
1 TCGAGTTAT
27578413 TCGAGTTAT
1 TCGAGTTAT
27578422 TCGA
1 TCGA
27578426 ATTAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:27578416 original size:18 final size:18
Alignment explanation
Indices: 27578393--27578435 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
27578383 GAGTTAGACA
*
27578393 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAATT
27578411 AATCGAGTTATTCGAATT
1 AATCGAGTTATTCGAATT
27578429 AACTCGA
1 AA-TCGA
27578436 TTTTTTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAATT
Found at i:27578500 original size:9 final size:9
Alignment explanation
Indices: 27578476--27578512 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27578466 TGAGTTTTCG
*
27578476 AATTCAAAT
1 AATTCGAAT
*
27578485 AACTCGAAT
1 AATTCGAAT
27578494 AATTCGAAT
1 AATTCGAAT
27578503 AATTCGAAT
1 AATTCGAAT
27578512 A
1 A
27578513 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27579436 original size:5 final size:5
Alignment explanation
Indices: 27579426--27579451 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27579416 GAACAAATAT
27579426 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
27579452 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:27584536 original size:89 final size:89
Alignment explanation
Indices: 27584430--27584607 Score: 320
Period size: 89 Copynumber: 2.0 Consensus size: 89
27584420 CTTTATTAAA
*
27584430 AAATTTATAGAAACTTTATGGTTAACATTTCTCAATAAAAGCACAATTTACATGGCTCTTTTCTA
1 AAATTGATAGAAACTTTATGGTTAACATTTCTCAATAAAAGCACAATTTACATGGCTCTTTTCTA
*
27584495 GTGGATGAAACGGACGGTGGCTGC
66 GTGGATAAAACGGACGGTGGCTGC
*
27584519 AAATTGATAGAAACTTTATGGTTACCATTTCTCAATAAAAGCACAATTTACATGGCTCTTTTCTA
1 AAATTGATAGAAACTTTATGGTTAACATTTCTCAATAAAAGCACAATTTACATGGCTCTTTTCTA
*
27584584 GTGGATAAAATGGACGGTGGCTGC
66 GTGGATAAAACGGACGGTGGCTGC
27584608 CCCTAATTAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (89 bp):
AAATTGATAGAAACTTTATGGTTAACATTTCTCAATAAAAGCACAATTTACATGGCTCTTTTCTA
GTGGATAAAACGGACGGTGGCTGC
Found at i:27592966 original size:20 final size:20
Alignment explanation
Indices: 27592941--27592981 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27592931 GTAAATGTAA
27592941 AAATAT-TTTTAAGATTTTTT
1 AAATATATTTT-AGATTTTTT
*
27592961 AAATATATTTTATATTTTTT
1 AAATATATTTTAGATTTTTT
27592981 A
1 A
27592982 GAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AAATATATTTTAGATTTTTT
Found at i:27599073 original size:20 final size:22
Alignment explanation
Indices: 27599050--27599094 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
27599040 TAAAAAGTAA
*
27599050 AAATTAGAAA-ATAAA-AAAAT
1 AAATTAGAAAGAAAAATAAAAT
*
27599070 AAATTTGAAAGAAAAATAAAAT
1 AAATTAGAAAGAAAAATAAAAT
27599092 AAA
1 AAA
27599095 AAGTTCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATTAGAAAGAAAAATAAAAT
Found at i:27611803 original size:18 final size:18
Alignment explanation
Indices: 27611754--27611830 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
27611744 TTGTCCCTTA
*
27611754 TTCCTCACCTACATCTTC
1 TTCCTCACCTATATCTTC
* * *
27611772 TTCATCGATC-ATATCTTG
1 TTCCTC-ACCTATATCTTC
*
27611790 TTCCTCACCTATATCTTT
1 TTCCTCACCTATATCTTC
* *
27611808 TTCATCAGCC-ACATCTTC
1 TTCCTCA-CCTATATCTTC
27611826 TTCCT
1 TTCCT
27611831 TATTTGCGCT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
17 2 0.04
18 39 0.87
19 4 0.09
ACGTcount: A:0.18, C:0.35, G:0.04, T:0.43
Consensus pattern (18 bp):
TTCCTCACCTATATCTTC
Found at i:27611824 original size:36 final size:36
Alignment explanation
Indices: 27611754--27611830 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
27611744 TTGTCCCTTA
* * *
27611754 TTCCTCACCTACATCTTCTTCATCGATCATATCTTG
1 TTCCTCACCTACATCTTCTTCATCGACCACATCTTC
* *
27611790 TTCCTCACCTATATCTTTTTCATC-AGCCACATCTTC
1 TTCCTCACCTACATCTTCTTCATCGA-CCACATCTTC
27611826 TTCCT
1 TTCCT
27611831 TATTTGCGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.18, C:0.35, G:0.04, T:0.43
Consensus pattern (36 bp):
TTCCTCACCTACATCTTCTTCATCGACCACATCTTC
Found at i:27618214 original size:20 final size:20
Alignment explanation
Indices: 27618189--27618229 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27618179 GCGTTTACTT
27618189 AAAGGTCAAGTCCCTTCAAA
1 AAAGGTCAAGTCCCTTCAAA
27618209 AAAGGTCAAGTCCCTTCAAA
1 AAAGGTCAAGTCCCTTCAAA
27618229 A
1 A
27618230 GCTCGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAGGTCAAGTCCCTTCAAA
Found at i:27625556 original size:32 final size:32
Alignment explanation
Indices: 27625520--27625581 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
27625510 GCATCCTAAG
27625520 GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
1 GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
*
27625552 GCCTTTGTGACTTGTATCAGTTGGTAATGC
1 GCCTTTGTGACTCGTATCAGTTGGTAATGC
27625582 CTTGATTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.39
Consensus pattern (32 bp):
GCCTTTGTGACTCGTATCAGTTGGTAATGCAT
Found at i:27631762 original size:17 final size:17
Alignment explanation
Indices: 27631740--27631776 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
27631730 AACTTAAGTT
*
27631740 AAATAATAAGAAAAAGA
1 AAATAAAAAGAAAAAGA
27631757 AAATAAAAAGAAAAAGA
1 AAATAAAAAGAAAAAGA
27631774 AAA
1 AAA
27631777 GGAATTAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (17 bp):
AAATAAAAAGAAAAAGA
Found at i:27639010 original size:359 final size:359
Alignment explanation
Indices: 27638351--27639071 Score: 1361
Period size: 359 Copynumber: 2.0 Consensus size: 359
27638341 CACTCAAGAA
* *
27638351 CTTGACTTACTAGGATTTTTTCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
1 CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
* *
27638416 TCTGGTCTCTTACTGAAACTTCTAGGGCCCATGAATAGACTGCTCTGTGCTTGCTTCTATCTTGG
66 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
*
27638481 AGGGACAATCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCTCAGAACGTCTCCAA
131 AGGGACAATCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
27638546 CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
196 CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
27638611 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACACCTGAAACTCGTAGGCTATGAAT
261 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACACCTGAAACTCGTAGGCTATGAAT
*
27638676 CTCTTCTTGAAGTTTAAAATGTTTGATATTTGAG
326 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
*
27638710 CTTGACTTACTAGAATTTTTCCTTAGTGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
1 CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
27638775 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
66 TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
*
27638840 AGGGACAATCCTTAATCAACTGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
131 AGGGACAATCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
27638905 CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
196 CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
*
27638970 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACGCCTGAAACTCGTAGGCTATGAAT
261 AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACACCTGAAACTCGTAGGCTATGAAT
27639035 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
326 CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
27639069 CTT
1 CTT
27639072 CTTAAAACTT
Statistics
Matches: 353, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
359 353 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (359 bp):
CTTGACTTACTAGAATTTTTCCTTAATGCTCCTTGCATTGAGCCAGACTTTGTTGCCACTCCAGA
TCTGGTCTCTTACTGAAACTTCTAAGGCCCATGAATAGACTGCTCTATGCTTGCTTCTATCTTGG
AGGGACAATCCTTAATCAAATGATCCTTGGATCCATATCCGAAACATGCCCCAGAACGTCTCCAA
CATTCTCCTCCATGGCTTCTACCGAAGTGTTCATAGTTAACATTTCTTATTACTCTAGACCCTCT
AGAGCTTGCCATAAAAATAGTTGATCTACTAAATCCTTCACACCTGAAACTCGTAGGCTATGAAT
CTCTTCTTGAAGTTGAAAATGTTTGATATTTGAG
Found at i:27640905 original size:24 final size:24
Alignment explanation
Indices: 27640878--27640938 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
27640868 ATAAGTTAGT
27640878 ATAAAAAAAAAGAAATGAAGAAAG
1 ATAAAAAAAAAGAAATGAAGAAAG
* * * *
27640902 ATAAAAACATACAAATTAAGAAAG
1 ATAAAAAAAAAGAAATGAAGAAAG
*
27640926 --AACAAAAAAGAAA
1 ATAAAAAAAAAGAAA
27640939 AAGAGAAAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 9 0.31
24 20 0.69
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.10
Consensus pattern (24 bp):
ATAAAAAAAAAGAAATGAAGAAAG
Found at i:27643535 original size:25 final size:25
Alignment explanation
Indices: 27643470--27643549 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
27643460 ATGTTCATAT
**
27643470 GAGCTATGAATCGAAAAGCTCACAC
1 GAGCTATGAATCGGTAAGCTCACAC
* *
27643495 GAGCTGA-GAATTGGTAAGCTCTCAC
1 GAGCT-ATGAATCGGTAAGCTCACAC
* * * *
27643520 GAGCTATAAATCGGTATGCTTATAC
1 GAGCTATGAATCGGTAAGCTCACAC
27643545 GAGCT
1 GAGCT
27643550 GTGGTATGTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 1 0.02
25 41 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GAGCTATGAATCGGTAAGCTCACAC
Found at i:27647650 original size:31 final size:31
Alignment explanation
Indices: 27647608--27647700 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
27647598 GGCTGTTACA
* *
27647608 CCTATACTTTTTAAATCGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
* *
27647639 CTTTTACTTTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
27647670 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
27647701 TTGACCCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (31 bp):
CCTATACTTTTTGAATTGGTCAAGTTTAGTC
Found at i:27654731 original size:31 final size:31
Alignment explanation
Indices: 27654696--27654764 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
27654686 CAACAAAACG
*
27654696 GTCATTGAACTATTCAAAAGATTTCACTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
*
27654727 GTCATTGAACTATTCAAAACATTTCATTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
27654758 GTCATTG
1 GTCATTG
27654765 GACAATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAACATTTCACTTAA
Found at i:27656703 original size:11 final size:11
Alignment explanation
Indices: 27656687--27656717 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
27656677 TTTTTTTGCA
27656687 ATTTGATTTTT
1 ATTTGATTTTT
27656698 ATTTGATTTTT
1 ATTTGATTTTT
*
27656709 ATTTAATTT
1 ATTTGATTT
27656718 CTAACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTGATTTTT
Found at i:27659966 original size:18 final size:17
Alignment explanation
Indices: 27659922--27659969 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
27659912 AACTTTAAAA
* *
27659922 ATTTTATTTTCATTTTT
1 ATTTTATTTTAATATTT
27659939 ATTTT-TTTTAATATTT
1 ATTTTATTTTAATATTT
27659955 ATTTTATGTTTAATA
1 ATTTTAT-TTTAATA
27659970 AGGGGGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 6 0.22
18 7 0.26
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTATTTTAATATTT
Found at i:27664493 original size:25 final size:25
Alignment explanation
Indices: 27664459--27664507 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
27664449 AACGGCAAGT
*
27664459 ACTCCTCCCAATTGCCTCGGAAATC
1 ACTCCTCCCAATTGCCTCGAAAATC
27664484 ACTCCTCCCAATTGCCTCGAAAAT
1 ACTCCTCCCAATTGCCTCGAAAAT
27664508 TAATAACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.39, G:0.10, T:0.24
Consensus pattern (25 bp):
ACTCCTCCCAATTGCCTCGAAAATC
Found at i:27670269 original size:37 final size:37
Alignment explanation
Indices: 27670206--27670293 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
27670196 ACACAAGTAG
* *
27670206 TCCAACCAA-AACACGCCAAACGCTCATAAGAGCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
* *
27670242 TCCAACCAATAACATGCCAAACACTCATGAGACCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
27670279 TCCAACCAATAACAC
1 TCCAACCAATAACAC
27670294 ACCTTGACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 9 0.20
37 37 0.80
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (37 bp):
TCCAACCAATAACACGCCAAACACTCATAAGACCTAA
Found at i:27679259 original size:12 final size:13
Alignment explanation
Indices: 27679235--27679263 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
27679225 AACTAATAGA
27679235 AACTAATTTTTCC
1 AACTAATTTTTCC
27679248 AACTAA-TTTTCC
1 AACTAATTTTTCC
27679260 AACT
1 AACT
27679264 TTTATGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
AACTAATTTTTCC
Found at i:27681556 original size:64 final size:64
Alignment explanation
Indices: 27681380--27681566 Score: 232
Period size: 64 Copynumber: 2.9 Consensus size: 64
27681370 CATAAATACA
* * * * *
27681380 ATAATATGATTGGCACAAAGCCATCAATAGCAGTGATATGATCGGCACATAACCATCAATAACG
1 ATAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACAAAACCATCAGTAACG
* * * * *
27681444 GTAATATGATCGGCACAAAGCCATCAGTAGA-AATGATATTATCGGCACACAGCCATCAGTAACG
1 ATAATATGATCGGCACAAAGCCATCAGTA-ACAGTGATATGATCGGCACAAAACCATCAGTAACG
* * * *
27681508 ATAATATGATCGGCACAAAGTCATCAGTAACGGTAATATGATCAGCACAAAACCATCAG
1 ATAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACAAAACCATCAG
27681567 CAACATCCCA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
63 1 0.01
64 102 0.99
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (64 bp):
ATAATATGATCGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACAAAACCATCAGTAACG
Found at i:27681566 original size:32 final size:32
Alignment explanation
Indices: 27681381--27681566 Score: 205
Period size: 32 Copynumber: 5.8 Consensus size: 32
27681371 ATAAATACAA
* * * *
27681381 TAATATGATTGGCACAAAGCCATCAATAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
* *
27681413 TGATATGATCGGCACATAA-CCATCAATAACGG
1 TAATATGATCGGCACA-AAGCCATCAGTAACGG
**
27681445 TAATATGATCGGCACAAAGCCATCAGTAGA-AA
1 TAATATGATCGGCACAAAGCCATCAGTA-ACGG
* * * *
27681477 TGATATTATCGGCACACAGCCATCAGTAACGA
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
*
27681509 TAATATGATCGGCACAAAGTCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACGG
* *
27681541 TAATATGATCAGCACAAAACCATCAG
1 TAATATGATCGGCACAAAGCCATCAG
27681567 CAACATCCCA
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
31 3 0.02
32 124 0.95
33 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACGG
Found at i:27681751 original size:24 final size:24
Alignment explanation
Indices: 27681687--27681772 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 24
27681677 CCATGCTCAG
** *
27681687 AATCAGTCATACAATTCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
27681711 AAACAGTCGTTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* **
27681735 AATCAGTCATTTTAATCATGGACA
1 AATCAGTCATTTAAATCACAGACA
* *
27681759 AATCAATCGTTTAA
1 AATCAGTCATTTAA
27681773 CCTCGATGGG
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:27681849 original size:27 final size:26
Alignment explanation
Indices: 27681819--27681992 Score: 129
Period size: 27 Copynumber: 6.5 Consensus size: 26
27681809 CACTACGGTT
*
27681819 ATTTTA-CCTTACAGTGGTATTTTGGTC
1 ATTTTACCCTT-CAG-GGTAATTTGGTC
** *
27681846 ATTTTACCCTAAGAGGGT-ATCTTAGTC
1 ATTTTACCCT-TCAGGGTAAT-TTGGTC
* *
27681873 ATTTTACCCTTCAGGGATAATTCGATC
1 ATTTTACCCTTCAGGG-TAATTTGGTC
* * *
27681900 ATGTTACCTTTTCAGGGTAATTTGATC
1 ATTTTACC-CTTCAGGGTAATTTGGTC
*
27681927 ATTTTACCCTTCAGGGGTAATTTAGTC
1 ATTTTACCCTTCA-GGGTAATTTGGTC
* *
27681954 ATTTTATCCTTCGAGGGT-ATTTCGGTA
1 ATTTTACCCTTC-AGGGTAATTT-GGTC
*
27681981 ATATTACCCTTC
1 ATTTTACCCTTC
27681993 GAGAGTATTT
Statistics
Matches: 117, Mismatches: 21, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
26 13 0.11
27 89 0.76
28 15 0.13
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.42
Consensus pattern (26 bp):
ATTTTACCCTTCAGGGTAATTTGGTC
Found at i:27681988 original size:81 final size:81
Alignment explanation
Indices: 27681834--27681988 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 81
27681824 ACCTTACAGT
* *
27681834 GGTATTTTGGTCATTTTACCCTAAGAGGGTATCTTAGTCATTTTACCCTTCAGGGATAATTCGAT
1 GGTAATTTGATCATTTTACCCTAAGAGGGTATCTTAGTCATTTTACCCTTCAGGGATAATTCGAT
* *
27681899 CATGTTACCTTTTCAG
66 AATATTACCTTTTCAG
* * *
27681915 GGTAATTTGATCATTTTACCCTTCAG-GGGTAAT-TTAGTCATTTTATCCTTCGAGGG-TATTTC
1 GGTAATTTGATCATTTTACCC-TAAGAGGGT-ATCTTAGTCATTTTACCCTTC-AGGGATAATTC
*
27681977 GGTAATATTACC
63 GATAATATTACC
27681989 CTTCGAGAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 54 0.86
82 9 0.14
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (81 bp):
GGTAATTTGATCATTTTACCCTAAGAGGGTATCTTAGTCATTTTACCCTTCAGGGATAATTCGAT
AATATTACCTTTTCAG
Found at i:27681993 original size:27 final size:27
Alignment explanation
Indices: 27681927--27682254 Score: 279
Period size: 27 Copynumber: 12.1 Consensus size: 27
27681917 TAATTTGATC
* *
27681927 ATTTTACCCTTC-AGGGGTAATTT-AGTC
1 ATTTTACCCATCGA-GGGT-ATTTCAGTA
* * *
27681954 ATTTTATCCTTCGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* * * *
27681981 ATATTACCCTTCGAGAGTATTTCAGAA
1 ATTTTACCCATCGAGGGTATTTCAGTA
** *
27682008 ATTTTATTCATTGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* * *
27682035 ACTTTACCCATCAAGGGAATTTC-GATA
1 ATTTTACCCATCGAGGGTATTTCAG-TA
* *
27682062 ATTTTACCAATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* *
27682089 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* *
27682116 GTTTTACCCATCG-GGGCTATTTTAGTA
1 ATTTTACCCATCGAGGG-TATTTCAGTA
* * *
27682143 ATTTTACCCTTCGAGGGTATCTCGGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* *** *
27682170 ACTTTACCCATCGACATTATTT-TGATA
1 ATTTTACCCATCGAGGGTATTTCAG-TA
* *
27682197 ATTTTACCCATCGACGATATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
* *
27682224 ATTTTACCCATCGAGGGCATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCAGTA
27682251 ATTT
1 ATTT
27682255 GCCTATGAAT
Statistics
Matches: 241, Mismatches: 52, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
26 9 0.04
27 227 0.94
28 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCAGTA
Found at i:27683365 original size:20 final size:20
Alignment explanation
Indices: 27683340--27683378 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27683330 CCCATTTTCC
27683340 TCCTTGATTTGCTCTACAAT
1 TCCTTGATTTGCTCTACAAT
27683360 TCCTTGATTTGCTCTACAA
1 TCCTTGATTTGCTCTACAA
27683379 CACCCTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.44
Consensus pattern (20 bp):
TCCTTGATTTGCTCTACAAT
Found at i:27683439 original size:91 final size:91
Alignment explanation
Indices: 27683284--27683453 Score: 331
Period size: 91 Copynumber: 1.9 Consensus size: 91
27683274 TCAATCAGCC
*
27683284 ACAACACCCTACCAACCTCTTATTTTCAAATTTCCTTGATTTTCTCCCCATTTTCCTCCTTGATT
1 ACAACACCCTACCAACCTCCTATTTTCAAATTTCCTTGATTTTCTCCCCATTTTCCTCCTTGATT
27683349 TGCTCTACAATTCCTTGATTTGCTCT
66 TGCTCTACAATTCCTTGATTTGCTCT
27683375 ACAACACCCTACCAACCTCCTATTTTCAAATTTCCTTGATTTTCTCCCCATTTTCCTCCTTGATT
1 ACAACACCCTACCAACCTCCTATTTTCAAATTTCCTTGATTTTCTCCCCATTTTCCTCCTTGATT
27683440 TGCTCTACAATTCC
66 TGCTCTACAATTCC
27683454 ATCCAAAACC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.21, C:0.34, G:0.05, T:0.41
Consensus pattern (91 bp):
ACAACACCCTACCAACCTCCTATTTTCAAATTTCCTTGATTTTCTCCCCATTTTCCTCCTTGATT
TGCTCTACAATTCCTTGATTTGCTCT
Found at i:27685275 original size:27 final size:26
Alignment explanation
Indices: 27685245--27685304 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
27685235 TTATCTCCTA
*
27685245 GGGGTATAACAGTCATTTTATCCTATG
1 GGGGTAT-ACAGTCATTTTACCCTATG
***
27685272 GGGGTATTTGGTCATTTTACCCTATG
1 GGGGTATACAGTCATTTTACCCTATG
*
27685298 AGGGTAT
1 GGGGTAT
27685305 TTTGGTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (26 bp):
GGGGTATACAGTCATTTTACCCTATG
Found at i:27685285 original size:26 final size:26
Alignment explanation
Indices: 27685256--27685340 Score: 107
Period size: 27 Copynumber: 3.2 Consensus size: 26
27685246 GGGTATAACA
*
27685256 GTCATTTTATCCTATGGGGGTATTTG
1 GTCATTTTACCCTATGGGGGTATTTG
*
27685282 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* * *
27685309 GTTATTCTACCCTATGGGGGTGTTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
27685336 GTCAT
1 GTCAT
27685341 AACAGTATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.46
27 27 0.54
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:27704985 original size:3 final size:3
Alignment explanation
Indices: 27704963--27705023 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
27704953 TTTGCTGAGA
* * * * * * *
27704963 TTG TTG CTG TTG TTG CTG TTG TTG CTG CTG CTG CTG CTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
27705011 TTG TTG TTG TTG T
1 TTG TTG TTG TTG T
27705024 CGGTGATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.11, G:0.33, T:0.56
Consensus pattern (3 bp):
TTG
Done.