Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 84 of 325
Found at i:28518131 original size:86 final size:85
Alignment explanation
Indices: 28517915--28518233 Score: 383
Period size: 86 Copynumber: 3.7 Consensus size: 85
28517905 TCCTGTCCCT
* *
28517915 CTAAGTAGTAGGGTAATAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGATC
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCC-TAAGCAGTAGGGAAACAGATC
28517980 GAAGACGAAGGTCTTAAACCC
65 GAAGACGAAGGTCTTAAACCC
* * * * * * *
28518001 CTAAGCAGTAGGGAAACAGAC-CAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGAT
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAAC-CCCTAAGCAGTAG-GGAAACAGAT
* *
28518064 CGAAGACAAAGAGCCTTAAACCC
64 CGAAGACGAAG-GTCTTAAACCC
28518087 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGATCG
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGATCG
28518152 AAGACGAAGGGTCTTAAACCC
66 AAGACGAA-GGTCTTAAACCC
* * * * * * * * *
28518173 CTACGAAGTAGGGTAACAGAC-CAAATTGCAGATTTTATCTCCCTAAGCAGTAGGGTAACAG
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAAC-CCCTAAGCAGTAGGGAAACAG
28518234 GCTGAATTTC
Statistics
Matches: 197, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
85 55 0.28
86 127 0.64
87 15 0.08
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (85 bp):
CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGATCG
AAGACGAAGGTCTTAAACCC
Found at i:28518191 original size:44 final size:43
Alignment explanation
Indices: 28517948--28518321 Score: 236
Period size: 42 Copynumber: 8.7 Consensus size: 43
28517938 AATTTCCAGA
28517948 TCTT-AACCCCTTAAGCAGTAGGGAAACAGATCGAAGACGAAGG
1 TCTTAAACCCC-TAAGCAGTAGGGAAACAGATCGAAGACGAAGG
* * * *
28517991 TCTTAAACCCCTAAGCAGTAGGGAAACAGA-CCAA-ATTGCAGA
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGA-CGAAGG
* * *
28518033 TCTT-ATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGACAAAGAG
1 TCTTAAAC-CCCTAAGCAGTAG-GGAAACAGATCGAAGACGAAG-G
* * * ** * *
28518077 CCTTAAACCCCTAAGCAGTAGGGTAACAG-GCTGAATTTC-CAGA
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGATC-GAA-GACGAAGG
28518120 TCTT-AACCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGG
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGACGAA-GG
* * * * * * *
28518163 TCTTAAACCCCTACGAAGTAGGGTAACAGA-CCAA-ATTGCAGA
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGA-CGAAGG
* * * * ** * *
28518205 T-TTTATCTCCCTAAGCAGTAGGGTAACAG-GCTGAATTTC-CAGA
1 TCTTAAAC-CCCTAAGCAGTAGGGAAACAGATC-GAA-GACGAAGG
* *
28518248 TCTT-AACCCCTTAAGCAGTAGGGAAACAGATCGAATACAAAGGG
1 TCTTAAACCCC-TAAGCAGTAGGGAAACAGATCGAAGACGAA-GG
*
28518292 TCTTAAACCCTTAAGCAGTAGGGAAACAGA
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGA
28518322 CCAAATTGCA
Statistics
Matches: 257, Mismatches: 47, Indels: 53
0.72 0.13 0.15
Matches are distributed among these distances:
41 8 0.03
42 83 0.32
43 77 0.30
44 81 0.32
45 8 0.03
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (43 bp):
TCTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGG
Found at i:28518213 original size:172 final size:172
Alignment explanation
Indices: 28517915--28518225 Score: 552
Period size: 172 Copynumber: 1.8 Consensus size: 172
28517905 TCCTGTCCCT
* *
28517915 CTAAGTAGTAGGGTAATAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGATC
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGATC
*
28517980 GAAGACGAAGGTCTTAAACCCCTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTATCTCCCT
66 GAAGACGAAGGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCTCCCT
28518045 AAGCAGTAGTGGAGCAGATCGAAGACAAAGAGCCTTAAACCC
131 AAGCAGTAGTGGAGCAGATCGAAGACAAAGAGCCTTAAACCC
28518087 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCC-TAAGCAGTAGGGAAACAGATC
1 CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGATC
* * *
28518151 GAAGACGAAGGGTCTTAAACCCCTACGAAGTAGGGTAACAGACCAAATTGCAGATTTTATCTCCC
66 GAAGACGAA-GGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCTCCC
28518216 TAAGCAGTAG
130 TAAGCAGTAG
28518226 GGTAACAGGC
Statistics
Matches: 132, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
171 30 0.23
172 102 0.77
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (172 bp):
CTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGATC
GAAGACGAAGGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCTCCCT
AAGCAGTAGTGGAGCAGATCGAAGACAAAGAGCCTTAAACCC
Found at i:28518314 original size:129 final size:128
Alignment explanation
Indices: 28518085--28518354 Score: 468
Period size: 129 Copynumber: 2.1 Consensus size: 128
28518075 AGCCTTAAAC
28518085 CCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGAT
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGAT
* * * *
28518150 CGAAGACGAAGGGTCTTAAACCCCTACGAAGTAGGGTAACAGACCAAATTGCAGATTTTATCT
66 CGAAGACAAAGGGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCT
28518213 CCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTTAAGCAGTAGGGAAACAGA
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCC-TAAGCAGTAGGGAAACAGA
* * *
28518278 TCGAATACAAAGGGTCTTAAACCCTTAAGCAGTAGGGAAACAGACCAAATTGCAGATCTTATCT
65 TCGAAGACAAAGGGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCT
28518342 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
28518355 TGGAGCAGAT
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
128 45 0.34
129 89 0.66
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (128 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCTAAGCAGTAGGGAAACAGAT
CGAAGACAAAGGGTCTTAAACCCCTAAGAAGTAGGGAAACAGACCAAATTGCAGATCTTATCT
Found at i:28519239 original size:29 final size:30
Alignment explanation
Indices: 28519180--28519237 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28519170 TCCGAGCCTT
*
28519180 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28519210 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28519238 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28519467 original size:13 final size:13
Alignment explanation
Indices: 28519449--28519480 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28519439 TTTCTAGCAA
28519449 TTATGAATTTATT
1 TTATGAATTTATT
28519462 TTATGAATTTATT
1 TTATGAATTTATT
*
28519475 TGATGA
1 TTATGA
28519481 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28519703 original size:50 final size:50
Alignment explanation
Indices: 28519574--28519819 Score: 366
Period size: 50 Copynumber: 4.8 Consensus size: 50
28519564 ATTTGGGTAA
28519574 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT--G
28519626 AGGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 A-GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
28519677 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
28519727 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
28519777 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28519820 TGTTATTATC
Statistics
Matches: 178, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 93 0.52
51 36 0.20
52 1 0.01
53 48 0.27
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28523927 original size:19 final size:18
Alignment explanation
Indices: 28523896--28523931 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28523886 TTATATGCAG
28523896 TTTTAAATTTTATTTTAT
1 TTTTAAATTTTATTTTAT
*
28523914 TTTTGAATTATTATTTTA
1 TTTTAAATT-TTATTTTA
28523932 AGCTATTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTAAATTTTATTTTAT
Found at i:28526639 original size:15 final size:16
Alignment explanation
Indices: 28526614--28526643 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28526604 TATTTTTCCT
28526614 TTTTAACTTTTTATCC
1 TTTTAACTTTTTATCC
28526630 TTTTAA-TTTTTATC
1 TTTTAACTTTTTATC
28526644 TTTCCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAACTTTTTATCC
Found at i:28530655 original size:19 final size:19
Alignment explanation
Indices: 28530622--28530666 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28530612 AACTGTTGAT
*
28530622 TTTTTTTACTATTTTCTTG
1 TTTTTTTACCATTTTCTTG
* *
28530641 TTTTTTTACCGTTTTGTTG
1 TTTTTTTACCATTTTCTTG
28530660 TTATTTT
1 TT-TTTT
28530667 CTTGTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (19 bp):
TTTTTTTACCATTTTCTTG
Found at i:28531230 original size:17 final size:17
Alignment explanation
Indices: 28531208--28531240 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28531198 CCCGGTTAAA
*
28531208 GGTAATAGCAATCTAAG
1 GGTAATACCAATCTAAG
28531225 GGTAATACCAATCTAA
1 GGTAATACCAATCTAA
28531241 TCAAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (17 bp):
GGTAATACCAATCTAAG
Found at i:28532775 original size:29 final size:30
Alignment explanation
Indices: 28532729--28532787 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
28532719 TAATTAGATC
*
28532729 AAATTAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
* *
28532759 AAATCAAAATTT-ATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
28532788 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:28537093 original size:39 final size:41
Alignment explanation
Indices: 28537025--28537112 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 41
28537015 TAAAAATATC
*
28537025 TATATT-AAAAATAATACCATAAATATAATAATTATTTTAT
1 TATATTAAAAAATAATACAATAAATATAATAATTATTTTAT
*
28537065 TATATTAAAAAAT-ATA-AATAAATATAATAATTGTTTTAT
1 TATATTAAAAAATAATACAATAAATATAATAATTATTTTAT
*
28537104 TGTATTAAA
1 TATATTAAA
28537113 TATAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 29 0.66
40 9 0.20
41 6 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (41 bp):
TATATTAAAAAATAATACAATAAATATAATAATTATTTTAT
Found at i:28537551 original size:57 final size:55
Alignment explanation
Indices: 28537482--28537600 Score: 152
Period size: 55 Copynumber: 2.1 Consensus size: 55
28537472 ATTATTAGTA
*
28537482 AATATTTTTTTTGGT-TACCTAATTATAAAAAAATTATAAAAT-GATCACTCAACTATT
1 AATATTTTTTTT-GTCT-CCTAACTA-AAAAAAATTATAAAATAG-TCACTCAACTATT
* *
28537539 AATATTTTTTTTGTCTTCTAACTACAAAAAATTATAAAATAGTCACTCAACTATT
1 AATATTTTTTTTGTCTCCTAACTAAAAAAAATTATAAAATAGTCACTCAACTATT
*
28537594 AAAATTT
1 AATATTT
28537601 ATCTTTTTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
55 34 0.61
56 9 0.16
57 13 0.23
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (55 bp):
AATATTTTTTTTGTCTCCTAACTAAAAAAAATTATAAAATAGTCACTCAACTATT
Found at i:28538014 original size:30 final size:30
Alignment explanation
Indices: 28537980--28538046 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
28537970 TTAGACAGAA
*
28537980 TTAATTAGTATGTAATTATATATAT-GAATT
1 TTAATTAG-ATGTAATTATATATATAAAATT
* * *
28538010 TTAATTTGGTGTAATTATATATGTAAAATT
1 TTAATTAGATGTAATTATATATATAAAATT
28538040 TTAATTA
1 TTAATTA
28538047 TAGTTCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (30 bp):
TTAATTAGATGTAATTATATATATAAAATT
Found at i:28545039 original size:15 final size:15
Alignment explanation
Indices: 28545021--28545055 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28545011 CATGGTAACT
* *
28545021 ACATTTCTAGTAATC
1 ACATTTCAAGGAATC
28545036 ACATTTCAAGGAATC
1 ACATTTCAAGGAATC
28545051 ACATT
1 ACATT
28545056 CTACCAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (15 bp):
ACATTTCAAGGAATC
Found at i:28545347 original size:46 final size:45
Alignment explanation
Indices: 28545297--28545395 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
28545287 TTAATGTCAC
*
28545297 GTAAAATATTATGTGACATAA-TTTAAAA-TAAAAATTTTAAAGA-AAA
1 GTAAAATATTAT-TG-CATAATTTTAAAATTAAAAA--TTAAAAATAAA
*
28545343 GTAAAATGTTATTGCATAATTTTTAAAATTAAAAATTAAAAATAAA
1 GTAAAATATTATTGCATAA-TTTTAAAATTAAAAATTAAAAATAAA
28545389 GTAAAAT
1 GTAAAAT
28545396 TGGGAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
44 5 0.11
45 8 0.17
46 28 0.60
47 6 0.13
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (45 bp):
GTAAAATATTATTGCATAATTTTAAAATTAAAAATTAAAAATAAA
Found at i:28547803 original size:11 final size:11
Alignment explanation
Indices: 28547787--28547821 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
28547777 AGAAACAATG
28547787 ATGATTTTAAA
1 ATGATTTTAAA
28547798 ATGATTTTAAA
1 ATGATTTTAAA
*
28547809 ATAATTTTAAA
1 ATGATTTTAAA
28547820 AT
1 AT
28547822 TATCTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (11 bp):
ATGATTTTAAA
Found at i:28567552 original size:12 final size:12
Alignment explanation
Indices: 28567535--28567560 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28567525 CTAAAAATTT
28567535 TAAATATTTTTA
1 TAAATATTTTTA
28567547 TAAATATTTTTA
1 TAAATATTTTTA
28567559 TA
1 TA
28567561 TCCATTTTAC
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:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:28573446 original size:13 final size:13
Alignment explanation
Indices: 28573428--28573465 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
28573418 ATCAAAAATG
28573428 TATTTTTTATATA
1 TATTTTTTATATA
28573441 TATTTTTTA-A-A
1 TATTTTTTATATA
28573452 TATTTTTTATATA
1 TATTTTTTATATA
28573465 T
1 T
28573466 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTTTATATA
Found at i:28573454 original size:11 final size:11
Alignment explanation
Indices: 28573428--28573467 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
28573418 ATCAAAAATG
28573428 TATTTTTTATATA
1 TATTTTTTA-A-A
28573441 TATTTTTTAAA
1 TATTTTTTAAA
*
28573452 TATTTTTTATA
1 TATTTTTTAAA
28573463 TATTT
1 TATTT
28573468 AAAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 16 0.62
12 1 0.04
13 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:28577059 original size:22 final size:22
Alignment explanation
Indices: 28577034--28577076 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28577024 TGATTTCAAG
28577034 TTTAAATT-TGTATTAACTATTT
1 TTTAAATTATGT-TTAACTATTT
**
28577056 TTTATTTTATGTTTAACTATT
1 TTTAAATTATGTTTAACTATT
28577077 GTAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTAAATTATGTTTAACTATTT
Found at i:28582895 original size:39 final size:39
Alignment explanation
Indices: 28582812--28582908 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
28582802 TGAAACCAAT
* *
28582812 TACCAGTAC-AAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
28582850 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGG-CATAA
* *
28582889 TTCCAGCACGTAGCCTGCGG
1 TACCAGCACGAAGCCTGCGG
28582909 ACCTTAAGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 13 0.27
39 35 0.73
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.21
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:28582932 original size:39 final size:39
Alignment explanation
Indices: 28582889--28583002 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 39
28582879 CCGGACATAT
* *
28582889 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCAGTTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCAGATATAA
*
28582928 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCAGATATAA
*
28582967 TTCCAGCACATAGCCTGCGGACCCTAAGTCCAGATA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCAGATA
28583003 AACATTACTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCAGATATAA
Found at i:28591333 original size:18 final size:17
Alignment explanation
Indices: 28591290--28591333 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
28591280 AGCTCGGGCC
*
28591290 ATGTAATGTTTTATATT
1 ATGTAATTTTTTATATT
* *
28591307 ATATTATTTTTATATATT
1 ATGTAATTTTT-TATATT
28591325 ATGTAATTT
1 ATGTAATTT
28591334 ATATCACATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (17 bp):
ATGTAATTTTTTATATT
Found at i:28595314 original size:48 final size:47
Alignment explanation
Indices: 28595260--28595352 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 47
28595250 CTATTTGAGC
* * * *
28595260 TCGAGCTCAATTAAGTTCGTTTA-TCAATTTTTATACTTAAGCTCGAAT
1 TCGAGCTCAATTAAGCTCATTTACT-AAATTTCATAC-TAAGCTCGAAT
28595308 TCGAGCTCAATTAAGCTCATTTACTAAATTTCATACTAAGCTCGA
1 TCGAGCTCAATTAAGCTCATTTACTAAATTTCATACTAAGCTCGA
28595353 GCTCAACTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 9 0.22
48 30 0.75
49 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (47 bp):
TCGAGCTCAATTAAGCTCATTTACTAAATTTCATACTAAGCTCGAAT
Found at i:28598334 original size:23 final size:23
Alignment explanation
Indices: 28598303--28598348 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28598293 AATGGGAATT
*
28598303 TTAACATTTTAAAATCAAAATAA
1 TTAAAATTTTAAAATCAAAATAA
*
28598326 TTAAAATTTTAAAATTAAAATAA
1 TTAAAATTTTAAAATCAAAATAA
28598349 ACAACCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAATTTTAAAATCAAAATAA
Found at i:28603624 original size:53 final size:53
Alignment explanation
Indices: 28603468--28603633 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
28603458 GACGAAAAAT
* **
28603468 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
28603520 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
28603573 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
28603627 TATGTGA
1 -ATGTGA
28603634 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:28609992 original size:52 final size:53
Alignment explanation
Indices: 28609900--28610049 Score: 187
Period size: 52 Copynumber: 2.8 Consensus size: 53
28609890 ATAAGTGTGC
* **
28609900 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATATGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATATGACT
* *
28609953 CCGTATAAGACCATAGCTGGGCTATGG-ATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATATGACT
* * *
28610005 CTGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
28610050 ACCGTGTAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 1 0.01
52 44 0.52
53 33 0.39
54 1 0.01
55 6 0.07
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATATGACT
Found at i:28611573 original size:20 final size:22
Alignment explanation
Indices: 28611549--28611606 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
28611539 TTTATTTTCA
28611549 ATAATAATAATCATAATTT-AT
1 ATAATAATAATCATAATTTGAT
*
28611570 -TAAT-ATAAATTATAATTTGAT
1 ATAATAAT-AATCATAATTTGAT
* *
28611591 AGAATAATAATGATAA
1 ATAATAATAATCATAA
28611607 ATAATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 14 0.47
21 2 0.07
22 10 0.33
23 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
ATAATAATAATCATAATTTGAT
Found at i:28617286 original size:61 final size:60
Alignment explanation
Indices: 28617178--28617299 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 60
28617168 GACTGAGAAC
28617178 ATAGTGAAAGTGATTTGTGATCATTGAAAGTAGCCTCTAATAGACAAAAGTCTTATGCAT
1 ATAGTGAAAGTGATTTGTGATCATTGAAAGTAGCCTCTAATAGACAAAAGTCTTATGCAT
28617238 ATAGTGAAAGTGATTTGTGATCATCTGAAAGTAGCCTCTAATAGACAAAAGTCTTATGCAT
1 ATAGTGAAAGTGATTTGTGATCAT-TGAAAGTAGCCTCTAATAGACAAAAGTCTTATGCAT
28617299 A
1 A
28617300 CTTGAAAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 24 0.39
61 37 0.61
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (60 bp):
ATAGTGAAAGTGATTTGTGATCATTGAAAGTAGCCTCTAATAGACAAAAGTCTTATGCAT
Found at i:28618859 original size:23 final size:22
Alignment explanation
Indices: 28618832--28618880 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28618822 GACAGCAAAC
* *
28618832 AAAAATCAAAGAAGAATGAGAAA
1 AAAAAACAAAGAA-AAAGAGAAA
*
28618855 AAAAAAGAAAGAAAAAGAGAAA
1 AAAAAACAAAGAAAAAGAGAAA
28618877 AAAA
1 AAAA
28618881 TTGAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAAACAAAGAAAAAGAGAAA
Found at i:28621231 original size:39 final size:39
Alignment explanation
Indices: 28621160--28621301 Score: 187
Period size: 39 Copynumber: 3.6 Consensus size: 39
28621150 ACCAGCTCGA
* * * * *
28621160 AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGT
1 AGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCACAT
*
28621199 AGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
* *
28621238 AGCCTGCAGACCTTAAGTCCAGATATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
*
28621277 AGCCTGCGGACCCTAAGTCCGGATA
1 AGCCTGCGGACCTTAAGTCCGGATA
28621302 AACATCACTG
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
38 3 0.03
39 87 0.97
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.23
Consensus pattern (39 bp):
AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
Found at i:28623556 original size:17 final size:16
Alignment explanation
Indices: 28623530--28623563 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28623520 TTTATATTGA
28623530 TTTTTGAAAATATAATT
1 TTTTTGAAAAT-TAATT
*
28623547 TTTTTTAAAATTAATT
1 TTTTTGAAAATTAATT
28623563 T
1 T
28623564 AATGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTTGAAAATTAATT
Found at i:28625782 original size:70 final size:70
Alignment explanation
Indices: 28625662--28625792 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
28625652 GGAAAATCAC
*
28625662 ATACTTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGTAGAATTACTACCAATCTCCA
1 ATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGTAGAATTACTACCAATCTCCA
28625727 CACTT
66 CACTT
* *
28625732 ATACCTCGATGCTCACACAGAGCTACGGTAGTCCCCAACATATGTGGAATTACTACCAATC
1 ATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGTAGAATTACTACCAATC
28625793 ACTATATTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (70 bp):
ATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGTAGAATTACTACCAATCTCCA
CACTT
Found at i:28629267 original size:39 final size:39
Alignment explanation
Indices: 28629212--28629467 Score: 363
Period size: 39 Copynumber: 6.6 Consensus size: 39
28629202 TTCCAACCCA
* * *
28629212 AATGCCTTCGGAACTTAGCCCGGATATAACATCAGCATG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* *
28629251 AATGCCTTCAGGACTTAGCCCAGATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* *
28629290 AATGCCTTCGGGACTTAGCCCGGATATAATACCAGTACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* *
28629329 AATGCCTTCGGGACTTAACCCGAATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
28629368 AATGCCTTCGGGACTTAGCCCGTATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
28629407 AATGCCTTCGGGACTTAGCCCGGATATAAATCTCA-CAC-
1 AATGCCTTCGGGACTTAGCCCGGATAT-AATATCAGCACG
* * *
28629445 AAGGCCTGCGGGTCTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
28629468 TTAAAATCCT
Statistics
Matches: 196, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
38 20 0.10
39 170 0.87
40 6 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
Found at i:28632498 original size:22 final size:20
Alignment explanation
Indices: 28632454--28632503 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
28632444 ATATTCCAAC
28632454 TGTGTGTCGATGAGACACTA
1 TGTGTGTCGATGAGACACTA
28632474 TGTGTGTCGATGAGACACTA
1 TGTGTGTCGATGAGACACTA
**
28632494 CATGTGTCGA
1 TGTGTGTCGA
28632504 CTACTGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
TGTGTGTCGATGAGACACTA
Found at i:28632613 original size:6 final size:6
Alignment explanation
Indices: 28632598--28632630 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
28632588 GTACTTTGTG
*
28632598 TACTGC TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
28632631 CCTAACGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:28633726 original size:27 final size:27
Alignment explanation
Indices: 28633682--28634022 Score: 168
Period size: 27 Copynumber: 12.6 Consensus size: 27
28633672 TTAGTTTACC
* * *
28633682 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28633709 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** *
28633736 GAATTACCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* **** * * *
28633763 GAATTACCGTTTTTCCCTCAATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** * * **
28633790 GAATTACCATTTTACCATCAATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **** **
28633817 GAATTATCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** * *
28633844 GAATTACCATTTTACCCTCGATTAGAA
1 AAATTACCAAAATACCCTCGATTTGTA
*
28633871 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
28633898 AAATTACCAAAATACCCT-TAGTTTGTG
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
28633925 AAATTACCAAAATACTCCT-GATTTGTG
1 AAATTACCAAAATAC-CCTCGATTTGTA
*** * *
28633952 AAATTATTGATATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
28633979 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
28634006 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
28634023 CTGTAGGGTA
Statistics
Matches: 260, Mismatches: 48, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.02
27 251 0.97
28 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.34
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:28633768 original size:54 final size:54
Alignment explanation
Indices: 28633721--28633862 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
28633711 ATTACCAAAG
*
28633721 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTT
* * * * *
28633775 TTCCCTCAATTTATAGAATTACCATTTTACCATCAATTTACAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTT
*
28633829 TACCCTCGATTTACAGAATTACCATTTTACCCTC
1 TACCCTCGATTTATAGAATTACCATTTTACCCTC
28633863 GATTAGAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTT
Found at i:28633820 original size:81 final size:81
Alignment explanation
Indices: 28633696--28633886 Score: 222
Period size: 81 Copynumber: 2.4 Consensus size: 81
28633686 TACTAAAATG
* * * *
28633696 CCCTCAATTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTA
1 CCCTCAATTTATAAAATTACCAAAGTACCATCAATTTACAGAATTACCATTTTACCCTCGATTTA
* * *
28633761 TAGAATTACCGTTTTT
66 CAGAATTACCATTTTA
* *** * *
28633777 CCCTCAATTTATAGAATTACCATTTTACCATCAATTTACAGAATTATCGTTTTACCCTCGATTTA
1 CCCTCAATTTATAAAATTACCAAAGTACCATCAATTTACAGAATTACCATTTTACCCTCGATTTA
28633842 CAGAATTACCATTTTA
66 CAGAATTACCATTTTA
* * *
28633858 CCCTCGA-TTAGAAAAATTACCAAAATACC
1 CCCTCAATTTA-TAAAATTACCAAAGTACC
28633887 CCTGGTTTGT
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 3 0.03
81 87 0.97
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (81 bp):
CCCTCAATTTATAAAATTACCAAAGTACCATCAATTTACAGAATTACCATTTTACCCTCGATTTA
CAGAATTACCATTTTA
Found at i:28634021 original size:54 final size:53
Alignment explanation
Indices: 28633856--28634022 Score: 208
Period size: 54 Copynumber: 3.1 Consensus size: 53
28633846 ATTACCATTT
*
28633856 TACCCTCGATTAGAAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATT-GTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * * * * *** *
28633910 TACCCTTAGTTTGTGAAATTACCAAAATACTCCTGATTTGTGAAATTATTGATA
1 TACCC-TCGATTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
28633964 TACCCTCGACTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
28634018 TACCC
1 TACCC
28634023 CTGTAGGGTA
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
53 2 0.02
54 84 0.93
55 4 0.04
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (53 bp):
TACCCTCGATTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
Found at i:28634023 original size:27 final size:27
Alignment explanation
Indices: 28633870--28634025 Score: 188
Period size: 27 Copynumber: 5.8 Consensus size: 27
28633860 CTCGATTAGA
28633870 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
28633897 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
28633924 GAAATTACCAAAATACTCCTGATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *** * **
28633951 GAAATTATTGATATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
28633978 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
28634005 AAAATTACCAAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
28634026 TAGGGTAGAA
Statistics
Matches: 107, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.03
27 100 0.93
28 4 0.04
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:28634038 original size:54 final size:54
Alignment explanation
Indices: 28633872--28634148 Score: 205
Period size: 54 Copynumber: 5.1 Consensus size: 54
28633862 CGATTAGAAA
*
28633872 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATA-CCCT-TAGTTTGT-G
1 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGTAG--GGTAG
* * * *** * ** *
28633925 AAATTACCAAAATACTCCTGATTTGTGAAATTATTGATATA-CCCTCG-ACTTGTAA
1 -AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-GTA-GGGTAG
28633980 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAG
* * * *
28634034 AATTACCGAAATAACCCTCTAGG---GTAGAATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAAT-ACCC-CT-GGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAG
* * ** * *
28634088 AAATATCAAAATACCCCT-GTAGGGTAGAAA-TATCAAAATACCCCTGTATGGTAG
1 AATTACCAAAATACCCCTGGT-TTGTA-AAATTACCAAAATACCCCTGTAGGGTAG
28634142 AATTACC
1 AATTACC
28634149 GAGATACACT
Statistics
Matches: 176, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
50 1 0.01
52 2 0.01
53 4 0.02
54 153 0.87
55 12 0.07
56 2 0.01
57 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.28
Consensus pattern (54 bp):
AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAG
Found at i:28634038 original size:81 final size:81
Alignment explanation
Indices: 28633872--28634116 Score: 212
Period size: 81 Copynumber: 3.0 Consensus size: 81
28633862 CGATTAGAAA
* * * * * *
28633872 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTAGTTTGTGAAATTACCAAAA
1 AATTACCGAAATAACCCTCGATTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
* **
28633937 TACTCCTG-ATTTGT-G
66 TACCCCTGTA-GGGTAG
** * *
28633952 AAATTATTGATAT-ACCCTCGACTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
1 -AATTACCGAAATAACCCTCGA-TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
28634016 AATACCCCTGTAGGGTAG
64 AATACCCCTGTAGGGTAG
* ** * * * ** *
28634034 AATTACCGAAATAACCCTCTAGGGTAGAATTACCGAAATA-CCCTTGTAGGGTAGAAA-TATCAA
1 AATTACCGAAATAACCCTCGATTGTAAAATTACCAAAATACCCCTAGT-TTGTA-AAATTACCAA
28634097 AATACCCCTGTAGGGTAG
64 AATACCCCTGTAGGGTAG
28634115 AA
1 AA
28634117 ATATCAAAAT
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
80 11 0.08
81 110 0.83
82 12 0.09
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (81 bp):
AATTACCGAAATAACCCTCGATTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
TACCCCTGTAGGGTAG
Found at i:28634155 original size:27 final size:27
Alignment explanation
Indices: 28633980--28634148 Score: 205
Period size: 27 Copynumber: 6.3 Consensus size: 27
28633970 CGACTTGTAA
** *
28633980 AATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCAAAATACCCCT-GTAGGGTAG
28634007 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
28634034 AATTACCGAAATAACCCTCTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
28634061 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
28634088 AAATATCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
28634115 AAATATCAAAATACCCCTGTATGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
28634142 AATTACC
1 AATTACC
28634149 GAGATACACT
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
26 2 0.02
27 123 0.98
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGTAGGGTAG
Found at i:28634381 original size:24 final size:25
Alignment explanation
Indices: 28634305--28634374 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
28634295 AGGAAGTGCT
* *
28634305 AAAAGGGCTATGCCCCAGTTTACCGA
1 AAAAGGGCTTTGCCCCAGTTTATC-A
28634331 AAAA-GGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
28634355 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28634375 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.12
25 32 0.78
26 4 0.10
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:28634387 original size:24 final size:24
Alignment explanation
Indices: 28634304--28634399 Score: 86
Period size: 25 Copynumber: 3.9 Consensus size: 24
28634294 GAGGAAGTGC
* *
28634304 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAAGGCTATGCCCCAGTTTA-T
* *
28634329 GAAAAAGGCTTTGCCCCAGTTTAT
1 TAAAAAGGCTATGCCCCAGTTTAT
* *
28634353 CAAAAAGGGCTTTGCCCCAG-TTAT
1 TAAAAA-GGCTATGCCCCAGTTTAT
*
28634377 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAA-AGGCTATGCC-CCAGTT
28634400 ATATGATAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 20 0.34
25 38 0.64
26 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
TAAAAAGGCTATGCCCCAGTTTAT
Found at i:28634398 original size:50 final size:50
Alignment explanation
Indices: 28634305--28634399 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
28634295 AGGAAGTGCT
**
28634305 AAAAGGGCTATGCCCCAGTTTACCGAAAAAGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAAGGCTAGGCCCCAGTTTATCA
* **
28634355 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAA-AGGCTAGGCC-CCAGTT
28634400 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 4 0.11
49 11 0.29
50 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAAGGCTAGGCCCCAGTTTATCA
Found at i:28635303 original size:18 final size:18
Alignment explanation
Indices: 28635246--28635305 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
28635236 GACTGTCTGC
28635246 TACTGAATAATTGACTAT
1 TACTGAATAATTGACTAT
* **
28635264 TACAGAATAAACGACTGA-
1 TACTGAATAATTGACT-AT
*
28635282 TACTGAATAATTGAATAT
1 TACTGAATAATTGACTAT
28635300 TACTGA
1 TACTGA
28635306 TTAACCGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (18 bp):
TACTGAATAATTGACTAT
Found at i:28638240 original size:18 final size:18
Alignment explanation
Indices: 28638217--28638251 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28638207 ACCGTCGCCT
28638217 GCAAAGAAGAACAGACAC
1 GCAAAGAAGAACAGACAC
* *
28638235 GCAAAGCAGAAGAGACA
1 GCAAAGAAGAACAGACA
28638252 ACAAAGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.20, G:0.26, T:0.00
Consensus pattern (18 bp):
GCAAAGAAGAACAGACAC
Found at i:28639435 original size:29 final size:26
Alignment explanation
Indices: 28639367--28639436 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 26
28639357 ATTTTATTAT
28639367 TTATTTATTTATTTATTTTGTTTCAA
1 TTATTTATTTATTTATTTTGTTTCAA
* * *
28639393 TT-TTTAATTAATTTTTTATTGATATTCAC
1 TTATTT-ATTTATTTATT-TTG-T-TTCAA
28639422 TTATTTATTTATTTA
1 TTATTTATTTATTTA
28639437 CTTAATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.09
26 11 0.32
27 3 0.09
28 1 0.03
29 13 0.38
30 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (26 bp):
TTATTTATTTATTTATTTTGTTTCAA
Found at i:28644959 original size:21 final size:21
Alignment explanation
Indices: 28644934--28644977 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28644924 GGGTCTACAG
* *
28644934 GCCCATGTGGAGGCTACACAC
1 GCCCATGTGAAGGCCACACAC
*
28644955 GCCCATGTGAAGGCCCCACAC
1 GCCCATGTGAAGGCCACACAC
28644976 GC
1 GC
28644978 TCGTGTGAGT
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:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (21 bp):
GCCCATGTGAAGGCCACACAC
Found at i:28647867 original size:58 final size:57
Alignment explanation
Indices: 28647764--28647876 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 57
28647754 CTATTTTGGG
* * *
28647764 CCTAAACTTGACAACTATTCCTACATTGGGGCCTAAACTTTTTTTGTCCAAGTTAGGC
1 CCTAAACTTCACAACTATTCCCACATTGAGGCC-AAACTTTTTTTGTCCAAGTTAGGC
* * *
28647822 CCTAAACTTCACAATTGTTCCCACATTGAGGCC-AACTTTTCTTTTGTTCAAGTTA
1 CCTAAACTTCACAACTATTCCCACATTGAGGCCAAAC-TTT-TTTTGTCCAAGTTA
28647877 ATCCTTGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 3 0.06
57 3 0.06
58 41 0.87
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (57 bp):
CCTAAACTTCACAACTATTCCCACATTGAGGCCAAACTTTTTTTGTCCAAGTTAGGC
Found at i:28656619 original size:12 final size:12
Alignment explanation
Indices: 28656602--28656630 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28656592 ACAGGATTGG
28656602 CACGGCCTAGCA
1 CACGGCCTAGCA
28656614 CACGGCCTAGCA
1 CACGGCCTAGCA
28656626 CACGG
1 CACGG
28656631 GCGTGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.28, T:0.07
Consensus pattern (12 bp):
CACGGCCTAGCA
Found at i:28658588 original size:28 final size:28
Alignment explanation
Indices: 28658556--28658620 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28658546 ATTTACTAGA
*
28658556 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
28658584 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28658612 ATACCCCTA
1 ATACCCCTA
28658621 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28658784 original size:27 final size:27
Alignment explanation
Indices: 28658726--28658815 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
28658716 AGGAAGCGTC
28658726 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
28658754 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
28658781 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
28658810 CTGGTG
1 CTGGTG
28658816 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:28658834 original size:55 final size:56
Alignment explanation
Indices: 28658726--28658840 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
28658716 AGGAAGCGTC
* *
28658726 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
28658781 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28658837 CTGG
1 CTGG
28658841 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28665315 original size:12 final size:13
Alignment explanation
Indices: 28665287--28665319 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28665277 TTATTTCTTT
28665287 TTCTCCATCTACC
1 TTCTCCATCTACC
*
28665300 TTCTCC-TCTTCC
1 TTCTCCATCTACC
28665312 TTCTCCAT
1 TTCTCCAT
28665320 AGCTGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:28666418 original size:28 final size:28
Alignment explanation
Indices: 28666386--28666450 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
28666376 ATTTACTAGA
*
28666386 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
** * *
28666414 ATACCTTTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28666442 ATACCCCTA
1 ATACCCCTA
28666451 GGGTTAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28666597 original size:28 final size:29
Alignment explanation
Indices: 28666556--28666618 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
28666546 AGGAAGCGTC
*
28666556 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
28666584 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
28666613 CTGGTG
1 CTGGTG
28666619 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:28666629 original size:29 final size:28
Alignment explanation
Indices: 28666566--28666629 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
28666556 CTGGTGGCTA
* *
28666566 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28666594 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
28666623 TGTCACA
1 TGCCACA
28666630 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:28672254 original size:43 final size:43
Alignment explanation
Indices: 28672153--28672258 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 43
28672143 TTATCGAGAG
* *
28672153 GTGATTACATGTAAGACCATGTCTGGGACATTGGAATCAATAT
1 GTGATTACATGTAAGACCATGTCTGGGACAGTGGAATCAATAC
* * * * * * *
28672196 ATGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCGATAC
1 GTGATTACATGTAAGACCATGTCTGGGACAGTGGAATCAATAC
*
28672239 GTGATAACATGTAAGACCAT
1 GTGATTACATGTAAGACCAT
28672259 ATCCGGGATA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (43 bp):
GTGATTACATGTAAGACCATGTCTGGGACAGTGGAATCAATAC
Found at i:28674634 original size:8 final size:8
Alignment explanation
Indices: 28674623--28674647 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28674613 TTTAATAAGA
28674623 TATTTTAT
1 TATTTTAT
28674631 TATTTTAT
1 TATTTTAT
28674639 TATTTTAT
1 TATTTTAT
28674647 T
1 T
28674648 TAGTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:28674668 original size:2 final size:2
Alignment explanation
Indices: 28674663--28674690 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28674653 TATATATATA
28674663 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28674691 GAAAAAAACA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28677346 original size:5 final size:5
Alignment explanation
Indices: 28677336--28677376 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
28677326 AAAGTGAACA
* * *
28677336 TGAAT TGAAT TGAAT TGAAT TGAAT GGAAT GGAAT GGAAT T
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT T
28677377 ATGATCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (5 bp):
TGAAT
Found at i:28677872 original size:57 final size:57
Alignment explanation
Indices: 28677781--28678090 Score: 336
Period size: 57 Copynumber: 5.2 Consensus size: 57
28677771 TTATATGCTG
* * * * **
28677781 GTTACTATTACCGCTACTGCTACTATGACCGATTCGGCACTTTGTGTGTCGAATATT
1 GTTACTGTTACTGCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTCGAATATT
*
28677838 GTTACTGTTACTGCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTTGAATATT
1 GTTACTGTTACTGCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTCGAATATT
28677895 GTTACTGTTATTGCTACTGCTACTGCTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 GTTACTG----T--TACTGCTACTGCTACTGTTA----TA--GATTCGGCACTTTGTGTGTCGAA
28677960 TATT
54 TATT
* * * *
28677964 GTTACTGTTACCGCTATTGTTACTGTTACT-GATTCGGCATTTTGTGTGTCGAATATT
1 GTTACTGTTACTGCTACTGCTACTGTTA-TAGATTCGGCACTTTGTGTGTCGAATATT
** * **
28678021 GTTACTGTTA-TCGCTACTGCTACTGTTACCGATTCGGCACTTTCTGTGTAAAATATT
1 GTTACTGTTACT-GCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTCGAATATT
28678078 GTTACTGTTACTG
1 GTTACTGTTACTG
28678091 TTACCGATTC
Statistics
Matches: 217, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
57 141 0.65
58 1 0.00
60 1 0.00
61 1 0.00
63 37 0.17
65 1 0.00
67 2 0.01
69 33 0.15
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (57 bp):
GTTACTGTTACTGCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTCGAATATT
Found at i:28677930 original size:12 final size:12
Alignment explanation
Indices: 28677897--28677931 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28677887 TGAATATTGT
*
28677897 TACTGTTATTGC
1 TACTGTTACTGC
*
28677909 TACTGCTACTGC
1 TACTGTTACTGC
28677921 TACTGTTACTG
1 TACTGTTACTG
28677932 TTACCGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (12 bp):
TACTGTTACTGC
Found at i:28677942 original size:69 final size:69
Alignment explanation
Indices: 28677834--28678045 Score: 259
Period size: 69 Copynumber: 3.2 Consensus size: 69
28677824 GTGTGTCGAA
* * * * *
28677834 TATTGTTACTGTTACTGCTACTGCTACTGTTATAGATTCGGCACTTTGTGTGTTGAATATTGTTA
1 TATTGCTACTGCTACTGCTACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATATTGTTA
28677899 CTGT
66 CTGT
*
28677903 TATTGCTACTGCTACTGCTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTA
1 TATTGCTACTGCTACTGCTACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATATTGTTA
28677968 CTGT
66 CTGT
* *
28677972 TA---C--C-GCTA----T--TGTTACTGTTACTGATTCGGCATTTTGTGTGTCGAATATTGTTA
1 TATTGCTACTGCTACTGCTACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATATTGTTA
28678025 CTGT
66 CTGT
*
28678029 TATCGCTACTGCTACTG
1 TATTGCTACTGCTACTG
28678046 TTACCGATTC
Statistics
Matches: 126, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
57 48 0.38
59 1 0.01
60 1 0.01
62 1 0.01
63 8 0.06
64 1 0.01
66 1 0.01
69 65 0.52
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (69 bp):
TATTGCTACTGCTACTGCTACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATATTGTTA
CTGT
Found at i:28678012 original size:126 final size:126
Alignment explanation
Indices: 28677793--28678045 Score: 409
Period size: 126 Copynumber: 2.0 Consensus size: 126
28677783 TACTATTACC
*
28677793 GCTACTGCTACTATGACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACTGCTACTGC
1 GCTACTGCTACTATGACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCGCTACTGC
* *
28677858 TACTGTTATAGATTCGGCACTTTGTGTGTTGAATATTGTTACTGTTATTGCTACTGCTACT
66 TACTGTTATAGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTATCGCTACTGCTACT
* * * * *
28677919 GCTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCGCTATTGT
1 GCTACTGCTACTATGACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCGCTACTGC
*
28677984 TACTGTTACT-GATTCGGCATTTTGTGTGTCGAATATTGTTACTGTTATCGCTACTGCTACT
66 TACTGTTA-TAGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTATCGCTACTGCTACT
28678045 G
1 G
28678046 TTACCGATTC
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
126 116 0.99
127 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (126 bp):
GCTACTGCTACTATGACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCGCTACTGC
TACTGTTATAGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTATCGCTACTGCTACT
Found at i:28678099 original size:45 final size:45
Alignment explanation
Indices: 28678035--28678184 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
28678025 CTGTTATCGC
* * *
28678035 TACTGCTACTGTTACCGATTCGGCACTTTCTGTGTAAAATATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTAAAATACTGT
* **
28678080 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTAAAATACTGT
* * * * **
28678125 TACCGTTACTGTTTCAGATTCAGCACTTTGTGTGTTCAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTAAAATACTGT
*
28678170 TACTGTTACTATTAC
1 TACTGTTACTGTTAC
28678185 TGCTACTGTT
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTAAAATACTGT
Found at i:28678175 original size:6 final size:6
Alignment explanation
Indices: 28678164--28678207 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
28678154 GTGTGTTCAA
* * *
28678164 TACTGT TACTGT TACTAT TACTGC TACTGT TATTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
28678208 CTGGTACTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:28678191 original size:18 final size:19
Alignment explanation
Indices: 28678164--28678205 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
28678154 GTGTGTTCAA
*
28678164 TACTGTTACTGTTACT-AT
1 TACTGCTACTGTTACTGAT
*
28678182 TACTGCTACTGTTATTGAT
1 TACTGCTACTGTTACTGAT
28678201 TACTG
1 TACTG
28678206 TTCTGGTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (19 bp):
TACTGCTACTGTTACTGAT
Found at i:28679328 original size:74 final size:71
Alignment explanation
Indices: 28679235--28679383 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 71
28679225 TGGGCCTCTT
*
28679235 ATAAAAAGGGAAATTTTCGTTATAAGGTATGTTCGCAATATTGAATTAAAAATAAATTGTGAAAT
1 ATAAAAAGGGAAATTTTCGTTATAAGGTATATTCGCAATATTGAATTAAAAATAAATTGTGAAAT
28679300 GAAAGG
66 GAAAGG
28679306 ATAAAAAGGGAAGCAATTTTCGTTATAAGGTATATTCGCAATATTGAATTAAAAATAAATTGTGA
1 ATAAAAAGGG-A--AATTTTCGTTATAAGGTATATTCGCAATATTGAATTAAAAATAAATTGTGA
28679371 AATGAAAGG
63 AATGAAAGG
28679380 ATAA
1 ATAA
28679384 GGAATGGATA
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
71 10 0.14
72 1 0.01
74 63 0.85
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (71 bp):
ATAAAAAGGGAAATTTTCGTTATAAGGTATATTCGCAATATTGAATTAAAAATAAATTGTGAAAT
GAAAGG
Found at i:28679613 original size:30 final size:30
Alignment explanation
Indices: 28679579--28679638 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
28679569 AAAGGAAATA
28679579 AAGTGACAAGAAGAGGAAAATTGAGTTATG
1 AAGTGACAAGAAGAGGAAAATTGAGTTATG
28679609 AAGTGACAAGAAGAGGAAAATTGAGTTATG
1 AAGTGACAAGAAGAGGAAAATTGAGTTATG
28679639 TCACTAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (30 bp):
AAGTGACAAGAAGAGGAAAATTGAGTTATG
Found at i:28680516 original size:13 final size:13
Alignment explanation
Indices: 28680473--28680519 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
28680463 CTTGATATGT
28680473 TAGTGAAGAGAAA
1 TAGTGAAGAGAAA
28680486 -A-T-AAGAG-AA
1 TAGTGAAGAGAAA
28680495 -AGTGAAGAGAAA
1 TAGTGAAGAGAAA
*
28680507 TAGTGTAGAGAAA
1 TAGTGAAGAGAAA
28680520 GATGATAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
9 3 0.10
10 6 0.21
11 6 0.21
12 3 0.10
13 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (13 bp):
TAGTGAAGAGAAA
Found at i:28682327 original size:43 final size:43
Alignment explanation
Indices: 28682280--28682361 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
28682270 ACAATGAAAT
28682280 GCTTGTATATGGTTATAAATTTAATTTTGAACATATTATGAAG
1 GCTTGTATATGGTTATAAATTTAATTTTGAACATATTATGAAG
28682323 GCTTGTATATGGTTATAAATTTAATTTTGAACATATTAT
1 GCTTGTATATGGTTATAAATTTAATTTTGAACATATTAT
28682362 TGATGTGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (43 bp):
GCTTGTATATGGTTATAAATTTAATTTTGAACATATTATGAAG
Found at i:28686714 original size:22 final size:22
Alignment explanation
Indices: 28686685--28686727 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28686675 AGATCACATG
*
28686685 AAATTTC-ATTTTTTTTATTTT
1 AAATTTCAATTTTATTTATTTT
28686706 AAATGTTCAATTTTATTTATTT
1 AAAT-TTCAATTTTATTTATTT
28686728 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
AAATTTCAATTTTATTTATTTT
Found at i:28687816 original size:30 final size:30
Alignment explanation
Indices: 28687780--28687839 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28687770 AGTCAAGACT
28687780 TTTATTTATAAAATTTATTACATTTATACC
1 TTTATTTATAAAATTTATTACATTTATACC
*
28687810 TTTATTTATAAGATTTATTACATTTATACC
1 TTTATTTATAAAATTTATTACATTTATACC
28687840 AATATAGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTATTTATAAAATTTATTACATTTATACC
Found at i:28687818 original size:21 final size:22
Alignment explanation
Indices: 28687792--28687836 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28687782 TATTTATAAA
* *
28687792 ATTTATTACATTTA-TACCTTT
1 ATTTATAACATTTATTACATTT
*
28687813 ATTTATAAGATTTATTACATTT
1 ATTTATAACATTTATTACATTT
28687835 AT
1 AT
28687837 ACCAATATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATAACATTTATTACATTT
Found at i:28688016 original size:35 final size:36
Alignment explanation
Indices: 28687977--28688044 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
28687967 TAACTGTTTT
*
28687977 TATTTAATTAAA-TTTTATAAAATCTATTTAAAAAC
1 TATTTAATTAAATTTTTATAAAATATATTTAAAAAC
* *
28688012 TATTTCATTAAATTTTTATAATATATATTTAAA
1 TATTTAATTAAATTTTTATAAAATATATTTAAA
28688045 TATTTATCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.38
36 18 0.62
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (36 bp):
TATTTAATTAAATTTTTATAAAATATATTTAAAAAC
Found at i:28688942 original size:19 final size:19
Alignment explanation
Indices: 28688890--28688942 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
28688880 ATATATCAAA
28688890 CTTTTATAGTTTATACAATCC
1 CTTTTATAG-TT-TACAATCC
* *
28688911 CTTTAATAATTTACAATCC
1 CTTTTATAGTTTACAATCC
28688930 CTTTTATAGTTTA
1 CTTTTATAGTTTA
28688943 ATTTACAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 19 0.68
20 2 0.07
21 7 0.25
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (19 bp):
CTTTTATAGTTTACAATCC
Found at i:28689032 original size:16 final size:15
Alignment explanation
Indices: 28689011--28689053 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
28689001 TAATATATTT
28689011 TAATTATATTTATTAA
1 TAATTAT-TTTATTAA
*
28689027 TAATTATTTTGAATAA
1 TAATTATTTT-ATTAA
28689043 T-ATTATTTTAT
1 TAATTATTTTAT
28689054 ATTAATTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 11 0.46
16 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TAATTATTTTATTAA
Found at i:28689059 original size:16 final size:18
Alignment explanation
Indices: 28689021--28689059 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
28689011 TAATTATATT
28689021 TATTAATAATTATTTTGA
1 TATTAATAATTATTTTGA
28689039 -A-TAAT-ATTATTTT-A
1 TATTAATAATTATTTTGA
28689053 TATTAAT
1 TATTAAT
28689060 TACATAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.05
15 9 0.47
16 8 0.42
17 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTAATAATTATTTTGA
Found at i:28691841 original size:42 final size:42
Alignment explanation
Indices: 28691794--28691881 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
28691784 GGTGATCTTC
* *
28691794 GTAATTTTATATGTTGATGATATTCTACTCATTGGGAATGAT
1 GTAATTTTATATGTTGATGACATTCTACTCATTCGGAATGAT
28691836 GTAATTTTATATGTTGATGACATTCTACTCATTCGGAATGAT
1 GTAATTTTATATGTTGATGACATTCTACTCATTCGGAATGAT
28691878 GTAA
1 GTAA
28691882 GGACATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (42 bp):
GTAATTTTATATGTTGATGACATTCTACTCATTCGGAATGAT
Found at i:28694175 original size:18 final size:17
Alignment explanation
Indices: 28694142--28694175 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28694132 AATTGTATTA
*
28694142 AGAAAATAATTTAATTG
1 AGAAAATAAATTAATTG
28694159 AGAAAATTAAATTAATT
1 AGAAAA-TAAATTAATT
28694176 AATTAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
AGAAAATAAATTAATTG
Found at i:28696880 original size:16 final size:16
Alignment explanation
Indices: 28696859--28696908 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
28696849 GTAACCTAAT
28696859 CTATGAGATTGTGATC
1 CTATGAGATTGTGATC
28696875 CTATGA-ATTAG-G-T-
1 CTATGAGATT-GTGATC
28696888 -TATGAGATTGTGATC
1 CTATGAGATTGTGATC
28696903 CTATGA
1 CTATGA
28696909 ATTAGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 2 0.07
15 4 0.14
16 12 0.43
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (16 bp):
CTATGAGATTGTGATC
Found at i:28696900 original size:28 final size:28
Alignment explanation
Indices: 28696860--28696916 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28696850 TAACCTAATC
28696860 TATGAGATTGTGATCCTATGAATTAGGT
1 TATGAGATTGTGATCCTATGAATTAGGT
28696888 TATGAGATTGTGATCCTATGAATTAGGT
1 TATGAGATTGTGATCCTATGAATTAGGT
28696916 T
1 T
28696917 CATATGACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (28 bp):
TATGAGATTGTGATCCTATGAATTAGGT
Found at i:28704614 original size:18 final size:20
Alignment explanation
Indices: 28704591--28704629 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
28704581 AATATTTATC
*
28704591 TTGATGT-TTTTA-ATATTT
1 TTGATGTATTATATATATTT
28704609 TTGATGTATTATATATATTT
1 TTGATGTATTATATATATTT
28704629 T
1 T
28704630 AAAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
TTGATGTATTATATATATTT
Found at i:28704894 original size:14 final size:14
Alignment explanation
Indices: 28704875--28704906 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28704865 AGGTCATTTA
28704875 GCCCAACCAAACTG
1 GCCCAACCAAACTG
28704889 GCCCAACCAAACTG
1 GCCCAACCAAACTG
28704903 GCCC
1 GCCC
28704907 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:28710012 original size:14 final size:14
Alignment explanation
Indices: 28709993--28710024 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28709983 AGGTCATTTA
28709993 GCCCAACCAAACTG
1 GCCCAACCAAACTG
28710007 GCCCAACCAAACTG
1 GCCCAACCAAACTG
28710021 GCCC
1 GCCC
28710025 GGTGATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:28710917 original size:20 final size:20
Alignment explanation
Indices: 28710881--28710919 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28710871 TTGTATATTT
*
28710881 TTTAAAAATACGTAAAAAGC
1 TTTAAAAATACGAAAAAAGC
28710901 TTTAAAAATATC-AAAAAAG
1 TTTAAAAATA-CGAAAAAAG
28710920 TTATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (20 bp):
TTTAAAAATACGAAAAAAGC
Found at i:28713221 original size:27 final size:28
Alignment explanation
Indices: 28713179--28713234 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
28713169 AAAGATTCCA
*
28713179 TTGATGAATATGTATGAGT-TTTGATGT
1 TTGATGAATATGTATGAATATTTGATGT
28713206 TTGATGATATAT-TATGAATATTTGATGT
1 TTGATGA-ATATGTATGAATATTTGATGT
28713234 T
1 T
28713235 AGTTAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (28 bp):
TTGATGAATATGTATGAATATTTGATGT
Found at i:28731283 original size:14 final size:12
Alignment explanation
Indices: 28731264--28731313 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
28731254 TAACTAAAGT
28731264 GAATAAAAGAAACA
1 GAAT-AAAGAAA-A
28731278 GAATAAAGAAAA
1 GAATAAAGAAAA
*
28731290 GAA-ACA-AAAA
1 GAATAAAGAAAA
*
28731300 GAATAGAGAAAA
1 GAATAAAGAAAA
28731312 GA
1 GA
28731314 GAACAGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 4 0.12
12 10 0.31
13 7 0.22
14 4 0.12
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
GAATAAAGAAAA
Found at i:28731303 original size:22 final size:23
Alignment explanation
Indices: 28731277--28731323 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
28731267 TAAAAGAAAC
28731277 AGAATAAAGAAAAGA-AACAAAA
1 AGAATAAAGAAAAGAGAACAAAA
* *
28731299 AGAATAGAGAAAAGAGAACAGAA
1 AGAATAAAGAAAAGAGAACAAAA
28731322 AG
1 AG
28731324 CATTCGAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (23 bp):
AGAATAAAGAAAAGAGAACAAAA
Found at i:28732879 original size:23 final size:23
Alignment explanation
Indices: 28732849--28732935 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
28732839 GCTTTACTGA
* *
28732849 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
28732872 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
28732893 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
28732915 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
28732936 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:28733814 original size:8 final size:8
Alignment explanation
Indices: 28733797--28733829 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
28733787 AAATTTTTGT
28733797 AAAAAT-A
1 AAAAATAA
28733804 AAAAATAA
1 AAAAATAA
28733812 AAAAATAA
1 AAAAATAA
28733820 AAAAATAA
1 AAAAATAA
28733828 AA
1 AA
28733830 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:28739270 original size:23 final size:21
Alignment explanation
Indices: 28739225--28739272 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
28739215 TATGTATGCA
28739225 TGATAAATTATGCATGATGAC
1 TGATAAATTATGCATGATGAC
* *
28739246 TGATATATGTATGCATATATGAC
1 TGATAAAT-TATGCAT-GATGAC
28739269 TGAT
1 TGAT
28739273 GGTTGCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (21 bp):
TGATAAATTATGCATGATGAC
Found at i:28739573 original size:34 final size:34
Alignment explanation
Indices: 28739535--28739599 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
28739525 ATATTTGATG
* *
28739535 CTGAAATTGGAATGGGCTAAGGCCCAAACTGCTA
1 CTGAAACTGAAATGGGCTAAGGCCCAAACTGCTA
* *
28739569 CTGAAACTGAAATGGGCTTAGGCCCAGACTG
1 CTGAAACTGAAATGGGCTAAGGCCCAAACTG
28739600 TATTTGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.20
Consensus pattern (34 bp):
CTGAAACTGAAATGGGCTAAGGCCCAAACTGCTA
Found at i:28742299 original size:18 final size:18
Alignment explanation
Indices: 28742264--28742300 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28742254 AATATGATAC
**
28742264 TTTTCTCTCTTTCTTTTT
1 TTTTCTCTCTTTAGTTTT
28742282 TTTTCTCTCTTTAGTTTT
1 TTTTCTCTCTTTAGTTTT
28742300 T
1 T
28742301 ATGTTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTCTCTCTTTAGTTTT
Found at i:28746822 original size:32 final size:32
Alignment explanation
Indices: 28746736--28746833 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 32
28746726 AATTTTAATA
* *
28746736 AATTACTAAAT-CTTATCAAAATATTGATACTT
1 AATTACTAAATAATTATAAAAATATT-ATACTT
* * *
28746768 -ATT-C-AATATATTTATTAAAATATTTTACTT
1 AATTACTAA-ATAATTATAAAAATATTATACTT
*
28746798 AATTACTAAATAATTATAAAAATATTATACCT
1 AATTACTAAATAATTATAAAAATATTATACTT
28746830 AATT
1 AATT
28746834 TAAAAGCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.04
30 8 0.15
31 18 0.33
32 24 0.44
33 2 0.04
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (32 bp):
AATTACTAAATAATTATAAAAATATTATACTT
Found at i:28747259 original size:14 final size:14
Alignment explanation
Indices: 28747240--28747271 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28747230 GAATTAATTG
28747240 ATTAATAAAAAAAT
1 ATTAATAAAAAAAT
*
28747254 ATTAATAATAAAAT
1 ATTAATAAAAAAAT
28747268 ATTA
1 ATTA
28747272 TAGGCCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAATAAAAAAAT
Found at i:28751600 original size:3 final size:3
Alignment explanation
Indices: 28751594--28751624 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28751584 GTATTATTTT
28751594 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28751625 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28751629 original size:3 final size:3
Alignment explanation
Indices: 28751623--28751792 Score: 60
Period size: 3 Copynumber: 55.3 Consensus size: 3
28751613 ATAATAATAA
* * * * *
28751623 TAT TAT TAT TAT TTT TAT TTT TAA TACT T-T TAC TAT TAT T-C TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * * * * *
28751667 ATAC TAT TAT TGT T-T TCT TTT TAT TAT TAT TAT TAGT AACG TAA TAG
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT
* * * *
28751714 TAT TTT TAT TAT TAT T-T TAT TAT TTT TACCT TTT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT
* * *
28751760 TAT TAACC TAT TAT TAT TAT TTT TAT TAA TAT T
1 TAT T-A-T TAT TAT TAT TAT TAT TAT TAT TAT T
28751793 GTGTTATTTT
Statistics
Matches: 120, Mismatches: 36, Indels: 22
0.67 0.20 0.12
Matches are distributed among these distances:
2 7 0.06
3 102 0.85
4 8 0.07
5 3 0.03
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28751955 original size:3 final size:3
Alignment explanation
Indices: 28751947--28751979 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28751937 AATCAATTTA
28751947 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28751980 ATTTTTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28752105 original size:26 final size:25
Alignment explanation
Indices: 28752047--28752106 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
28752037 TCTATTTTAT
28752047 TTATTTATTTCAGATTTTTACATAA
1 TTATTTATTTCAGATTTTTACATAA
*
28752072 -TATCTATTTCCA-ACTTTTATACA-AA
1 TTATTTATTT-CAGA-TTTT-TACATAA
28752097 TTATTTATTT
1 TTATTTATTT
28752107 TAAATGTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 9 0.31
25 8 0.28
26 12 0.41
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATTTATTTCAGATTTTTACATAA
Found at i:28752259 original size:27 final size:28
Alignment explanation
Indices: 28752202--28752259 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
28752192 CATTTTGTAT
* * *
28752202 ATTATTGATTTTCGGATTCTTTTCTTAC
1 ATTATTGATTTTCGAATTCATTTATTAC
28752230 ATTATT-ATTTT-GAATTCATTTATTATC
1 ATTATTGATTTTCGAATTCATTTATTA-C
28752257 ATT
1 ATT
28752260 TTCAAATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 11 0.42
27 9 0.35
28 6 0.23
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (28 bp):
ATTATTGATTTTCGAATTCATTTATTAC
Found at i:28758389 original size:88 final size:88
Alignment explanation
Indices: 28758235--28758893 Score: 883
Period size: 88 Copynumber: 7.5 Consensus size: 88
28758225 AATCTCCACT
* * * * * * * *
28758235 AGCCTTAACTCCCTAAACAGTAAGGCAACAGGCTGGAAATTACAGATCTTATCTCCTTAAGTAGT
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
28758300 AGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
28758323 AGCCTTATGCCCCTAAGTAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
28758388 AGTGGAGCAGATCGAAGACAGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * * * *
28758411 AACCTTAACCCCCTAAGCAGTAGGGCAACAGGATGAAGATTACAGATCTTATCTCCCTGAGCAGT
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* *
28758476 AGTGGAGCGGGTCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * *
28758499 AGCTTTAACCCCCTAAGCAATAGGGAAACAGG-TTAAAGATTACAGATCTTATCT-CCTAAGCAG
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAA-ATTACAGATCTTATCTCCCTAAGCAG
* *
28758562 TAGTGGAGCAAATCAAAGGA-GGTG
65 TAGTGGAGCAGATCGAA-GACGGTG
*
28758586 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* * * *
28758651 AGTGAAACAGATTGAAGACGATG
66 AGTGGAGCAGATCGAAGACGGTG
* * * *
28758674 AGCCTTATTCCCCTAAACAGTAGGGAAACAGGCTAAAAATTACAGATCTTATCTCCCTAAGCAAT
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
**
28758739 AGTGGAGTGGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* ** * *
28758762 AGCCTTATCCCCCTAAGCAGTAGGGAAACATGCCAAAAATTACAGATCTTATCTCCCTAAGTAGC
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
28758827 AGTGGAGCAGATCGAAGATGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
28758850 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGATTACA
1 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACA
28758894 AATCATAAGC
Statistics
Matches: 496, Mismatches: 70, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
87 75 0.15
88 421 0.85
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (88 bp):
AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGTG
Found at i:28758637 original size:44 final size:43
Alignment explanation
Indices: 28758326--28758736 Score: 175
Period size: 44 Copynumber: 9.4 Consensus size: 43
28758316 GACGGTGAGC
* * *
28758326 CTTATGCCCCTAAGTAGTAGGGAAACAGGCTGAAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGATG-AAATTACAGAT
* * * *
28758370 CTTATCTCCCTAAGCAGTAGTGG-AGCA-GATCG-AA-GACAGTGAAC
1 CTTATCCCCCTAAGCAGTAG-GGAAACAGGAT-GAAATTACA--G-AT
* *
28758414 CTTAACCCCCTAAGCAGTAGGGCAACAGGATGAAGATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGATGAA-ATTACAGAT
* * * * * * *
28758458 CTTATCTCCCTGAGCAGTAGTGG-AGC-GGGTCG-AA-GACGGTGAG
1 CTTATCCCCCTAAGCAGTAG-GGAAACAGGAT-GAAATTAC--AGAT
* * * *
28758501 CTTTAACCCCCTAAGCAATAGGGAAACAGGTTAAAGATTACAGAT
1 C-TTATCCCCCTAAGCAGTAGGGAAACAGGATGAA-ATTACAGAT
* * * * ** ** *
28758546 CTTAT-CTCCTAAGCAGTAGTGG-AGCA-AATCAAAGGAGGTGAGC
1 CTTATCCCCCTAAGCAGTAG-GGAAACAGGATGAAATTA-CAGA-T
*
28758589 CTTATCCCCCTAAGCAGTAGGGAAACAGGCTGGAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGAT-GAAATTACAGAT
* * * *
28758633 CTTATCTCCCTAAGCAGTAGTGAAACA-GATTG-AA-GACGATGAGC
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGA-TGAAATTAC-A-GA-T
* * * *
28758677 CTTATTCCCCTAAACAGTAGGGAAACAGGCTAAAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGGAAACAGGAT-GAAATTACAGAT
*
28758721 CTTATCTCCCTAAGCA
1 CTTATCCCCCTAAGCA
28758737 ATAGTGGAGT
Statistics
Matches: 264, Mismatches: 68, Indels: 70
0.66 0.17 0.17
Matches are distributed among these distances:
41 9 0.03
42 11 0.04
43 40 0.15
44 166 0.63
45 22 0.08
46 9 0.03
47 7 0.03
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (43 bp):
CTTATCCCCCTAAGCAGTAGGGAAACAGGATGAAATTACAGAT
Found at i:28758878 original size:351 final size:351
Alignment explanation
Indices: 28758235--28758893 Score: 967
Period size: 351 Copynumber: 1.9 Consensus size: 351
28758225 AATCTCCACT
* * * *
28758235 AGCCTTAACTCCCTAAACAGTAAGGCAACAGGCTGGAAATTACAGATCTTATCTCCTTAAGTAGT
1 AGCCTTAACCCCCTAAACAGTAAGGAAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* * * ** *
28758300 AGTGGAGCAGATCGAAGACGGTGAGCCTTATGCCCCTAAGTAGTAGGGAAACAGGCTGAAAATTA
66 AGTGAAACAGATCGAAGACGATGAGCCTTATGCCCCTAAACAGTAGGGAAACAGGCTAAAAATTA
*
28758365 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTGAACCTTAACCCCCTAAGCA
131 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGTGAACCTTAACCCCCTAAGCA
* ** * * * * *
28758430 GTAGGGCAACAGGATGAAGATTACAGATCTTATCTCCCTGAGCAGTAGTGGAGCGGGTCGAAGAC
196 GTAGGGAAACAGGACAAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGAC
* *
28758495 GGTGAGCTTTAACCCCCTAAGCAATAGGGAAACAGGTTAAAGATTACAGATCTTATCTCCTAAGC
261 GGTGAGCCTTAACCCCCTAAGCAATAGGGAAACAGGCTAAAGATTACAGATCTTATCTCCTAAGC
28758560 AGTAGTGGAGCAAATCAAAGGAGGTG
326 AGTAGTGGAGCAAATCAAAGGAGGTG
* * *
28758586 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAACAGTAAGGAAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* *
28758651 AGTGAAACAGATTGAAGACGATGAGCCTTATTCCCCTAAACAGTAGGGAAACAGGCTAAAAATTA
66 AGTGAAACAGATCGAAGACGATGAGCCTTATGCCCCTAAACAGTAGGGAAACAGGCTAAAAATTA
** * * *
28758716 CAGATCTTATCTCCCTAAGCAATAGTGGAGTGGATCGAAGACGGTGAGCCTTATCCCCCTAAGCA
131 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGTGAACCTTAACCCCCTAAGCA
* * * *
28758781 GTAGGGAAACATGCCAAAAATTACAGATCTTATCTCCCTAAGTAGCAGTGGAGCAGATCGAAGAT
196 GTAGGGAAACAGGACAAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGAC
* * * *
28758846 GGTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGATTACA
261 GGTGAGCCTTAACCCCCTAAGCAATAGGGAAACAGGCTAAAGATTACA
28758894 AATCATAAGC
Statistics
Matches: 269, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
351 269 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (351 bp):
AGCCTTAACCCCCTAAACAGTAAGGAAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGAAACAGATCGAAGACGATGAGCCTTATGCCCCTAAACAGTAGGGAAACAGGCTAAAAATTA
CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGTGAACCTTAACCCCCTAAGCA
GTAGGGAAACAGGACAAAAATTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGAC
GGTGAGCCTTAACCCCCTAAGCAATAGGGAAACAGGCTAAAGATTACAGATCTTATCTCCTAAGC
AGTAGTGGAGCAAATCAAAGGAGGTG
Found at i:28758888 original size:44 final size:43
Alignment explanation
Indices: 28758583--28758889 Score: 116
Period size: 44 Copynumber: 7.0 Consensus size: 43
28758573 ATCAAAGGAG
*
28758583 GTGAGCCTTATCCCCCTAAGCAGTAGGGAAACAGGCTGGAA-AT
1 GTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCT-GAAGAT
* * * ** *
28758626 -TACAGATCTTAT-CTCCCTAAGCAGTAGTGAAACAGATTGAAGAC
1 GT-GAG-CCTTATCCT-CCTAAGCAGTAGGGAAACAGGCTGAAGAT
* * *
28758670 GATGAGCCTTATTCC-CCTAAACAGTAGGGAAACAGGCTAAAAAT
1 G-TGAGCCTTA-TCCTCCTAAGCAGTAGGGAAACAGGCTGAAGAT
* * * ** * *
28758714 -TACAGATCTTAT-CTCCCTAAGCAATAGTGG--AGTGGATCGAAGACG
1 GT-GAG-CCTTATCCT-CCTAAGCAGTAG-GGAAACAGGCT-GAAGA-T
* * ** *
28758759 GTGAGCCTTATCCCCCTAAGCAGTAGGGAAACATGCCAAAAAT
1 GTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGAT
* * * * * *
28758802 -TACAGATCTTAT-CTCCCTAAGTAGCAGTGG-AGCA-GATCGAAGAT
1 GT-GAG-CCTTATCCT-CCTAAGCAGTAG-GGAAACAGGCT-GAAGAT
28758846 GGTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGAT
1 -GTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGAT
28758890 TACAAATCAT
Statistics
Matches: 181, Mismatches: 54, Indels: 57
0.62 0.18 0.20
Matches are distributed among these distances:
42 4 0.02
43 21 0.12
44 134 0.74
45 18 0.10
46 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (43 bp):
GTGAGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAGAT
Found at i:28759172 original size:13 final size:13
Alignment explanation
Indices: 28759154--28759234 Score: 85
Period size: 13 Copynumber: 6.0 Consensus size: 13
28759144 CAACCCAAAT
28759154 ACCACCCCACTAA
1 ACCACCCCACTAA
28759167 ACCACCCCACTAA
1 ACCACCCCACTAA
*
28759180 CTCCAACACCCCACTAA
1 ----ACCACCCCACTAA
28759197 ACCGA--CCACTAA
1 ACC-ACCCCACTAA
28759209 ACCACCCCACTAA
1 ACCACCCCACTAA
*
28759222 ACCACCTCACTAA
1 ACCACCCCACTAA
28759235 CTCCATCACC
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
11 1 0.02
12 10 0.17
13 34 0.59
14 1 0.02
17 12 0.21
ACGTcount: A:0.38, C:0.51, G:0.01, T:0.10
Consensus pattern (13 bp):
ACCACCCCACTAA
Found at i:28759192 original size:30 final size:30
Alignment explanation
Indices: 28759156--28759249 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
28759146 ACCCAAATAC
28759156 CACCCCACTAAACCACCCCACTAACTCCAA
1 CACCCCACTAAACCACCCCACTAACTCCAA
*
28759186 CACCCCACTAAACCGA--CCACTAA----AC
1 CACCCCACTAAACC-ACCCCACTAACTCCAA
* *
28759211 CACCCCACTAAACCACCTCACTAACTCCAT
1 CACCCCACTAAACCACCCCACTAACTCCAA
28759241 CACCCCACT
1 CACCCCACT
28759250 TGATTGTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
24 1 0.02
25 15 0.28
26 6 0.11
29 7 0.13
30 24 0.44
31 1 0.02
ACGTcount: A:0.35, C:0.52, G:0.01, T:0.12
Consensus pattern (30 bp):
CACCCCACTAAACCACCCCACTAACTCCAA
Found at i:28759633 original size:3 final size:3
Alignment explanation
Indices: 28759627--28759657 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28759617 TATTATTTTA
*
28759627 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28759658 TTATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28759963 original size:3 final size:3
Alignment explanation
Indices: 28759955--28759996 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28759945 AATCAATTTA
28759955 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28759997 ATTTTTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28760029 original size:20 final size:21
Alignment explanation
Indices: 28759991--28760029 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28759981 TTATTATTAT
* *
28759991 TATTATATTTTTTCTTTTTTG
1 TATTATATTTATTCATTTTTG
28760012 TATT-TATTTATTCATTTT
1 TATTATATTTATTCATTTT
28760030 ATTTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (21 bp):
TATTATATTTATTCATTTTTG
Found at i:28760068 original size:37 final size:38
Alignment explanation
Indices: 28760018--28760094 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
28760008 TTTGTATTTA
** *
28760018 TTTATTCATTTTATTTTCATTTTTTTACA-AATCTCTAT
1 TTTATTCATTTTA-TTTCAGATTTTTACATAATATCTAT
*
28760056 TTTATTTA-TTTATTTCAGATTTTTACATAATATCTAT
1 TTTATTCATTTTATTTCAGATTTTTACATAATATCTAT
28760093 TT
1 TT
28760095 CCAACTCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 13 0.38
37 14 0.41
38 7 0.21
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.62
Consensus pattern (38 bp):
TTTATTCATTTTATTTCAGATTTTTACATAATATCTAT
Found at i:28765536 original size:21 final size:20
Alignment explanation
Indices: 28765510--28765548 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28765500 TAAATTTTAA
28765510 AAAAATTTAAAAAATATTTCT
1 AAAAA-TTAAAAAATATTTCT
*
28765531 AAAAATTAAAAATTATTT
1 AAAAATTAAAAAATATTT
28765549 AAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTAAAAAATATTTCT
Found at i:28766543 original size:45 final size:43
Alignment explanation
Indices: 28766455--28766544 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 43
28766445 AATATAAAGA
* *
28766455 ATTATAATTCTTTAGATATGTTTAGTTGATATAGTGTAATTAC
1 ATTATAATTCTTTAGATATGTTTAGTAGATAAAGTGTAATTAC
* * *
28766498 ATTATAATTTTTTATATTATGTTTAGTAGTATAAATTGTAATTAC
1 ATTATAATTCTTTAGA-TATGTTTAGTAG-ATAAAGTGTAATTAC
28766543 AT
1 AT
28766545 AGTTACATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 14 0.35
44 11 0.28
45 15 0.38
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (43 bp):
ATTATAATTCTTTAGATATGTTTAGTAGATAAAGTGTAATTAC
Found at i:28766605 original size:19 final size:20
Alignment explanation
Indices: 28766564--28766612 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28766554 ATTTATATTT
* * *
28766564 TAAAAAAATATTAATTACTA
1 TAAAAAATTATTAAGTACGA
28766584 TAAAAAATTATT-AGTACGA
1 TAAAAAATTATTAAGTACGA
28766603 TAAAATAATT
1 TAAAA-AATT
28766613 TCTAAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAAAAATTATTAAGTACGA
Done.