Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 160 of 373
Found at i:53462366 original size:40 final size:40
Alignment explanation
Indices: 53462306--53462483 Score: 243
Period size: 40 Copynumber: 4.5 Consensus size: 40
53462296 TGGATGATAA
*
53462306 CCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53462346 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53462386 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * * *
53462426 CCGGGCTATGTCCCGAAGGTATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
53462466 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53462484 TACTTGGCTT
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 15 0.12
40 110 0.88
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53473441 original size:13 final size:13
Alignment explanation
Indices: 53473423--53473447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53473413 AACGAAGCAG
53473423 GACACGGCCGTGC
1 GACACGGCCGTGC
53473436 GACACGGCCGTG
1 GACACGGCCGTG
53473448 TGCACCAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.40, T:0.08
Consensus pattern (13 bp):
GACACGGCCGTGC
Found at i:53497702 original size:17 final size:19
Alignment explanation
Indices: 53497660--53497703 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53497650 ATGAAAAGTT
*
53497660 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53497679 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53497697 AA-TATTA
1 AATTATTA
53497704 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53498766 original size:15 final size:15
Alignment explanation
Indices: 53498745--53498809 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 15
53498735 CTACTTCCTT
53498745 TCTTCTTCTTCTTTC
1 TCTTCTTCTTCTTTC
*
53498760 CCTTCTT-TTCTTT-
1 TCTTCTTCTTCTTTC
53498773 TCTT-TTC-T-TTTC
1 TCTTCTTCTTCTTTC
* *
53498785 TCTTCATCTACTTTC
1 TCTTCTTCTTCTTTC
53498800 TCTTCTTCTT
1 TCTTCTTCTT
53498810 TTCCCCCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.08
12 7 0.18
13 5 0.13
14 6 0.15
15 18 0.46
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (15 bp):
TCTTCTTCTTCTTTC
Found at i:53499645 original size:20 final size:21
Alignment explanation
Indices: 53499608--53499646 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53499598 GCACGTCGGT
*
53499608 AATTGGGCCTCGATAGGCTAA
1 AATTGGGCCTCAATAGGCTAA
53499629 AATTGGGCC-CAATAGGCT
1 AATTGGGCCTCAATAGGCT
53499647 TGCGAGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (21 bp):
AATTGGGCCTCAATAGGCTAA
Found at i:53502531 original size:17 final size:19
Alignment explanation
Indices: 53502489--53502532 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53502479 ATGAAAAATT
*
53502489 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53502508 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53502526 AA-TATTA
1 AATTATTA
53502533 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53507806 original size:21 final size:19
Alignment explanation
Indices: 53507772--53507833 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
53507762 TAAGTTATAT
53507772 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
53507794 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
53507816 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
53507834 GTAATTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:53507881 original size:21 final size:21
Alignment explanation
Indices: 53507855--53507895 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53507845 TAAATATAGT
*
53507855 AAAATAAATAGTATAAAAAAC
1 AAAATAAATAATATAAAAAAC
*
53507876 AAAATAAATAATATACAAAA
1 AAAATAAATAATATAAAAAA
53507896 TATAAGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATAAATAATATAAAAAAC
Found at i:53508054 original size:51 final size:53
Alignment explanation
Indices: 53507997--53508110 Score: 151
Period size: 54 Copynumber: 2.2 Consensus size: 53
53507987 GGTATACGTA
* * * * *
53507997 TATTATAAAATAAAT-AGGATATGAGTAAT-TTTTTAAATGGAATATGGATAC
1 TATTATAAAATAAATAAGAAAAGGAGTAATATATATAAATGGAATATGGATAC
*
53508048 TATTATAAAATAAATAAAGAAAAGGTGTAATATATATAAATGGAATATGGATAC
1 TATTATAAAATAAAT-AAGAAAAGGAGTAATATATATAAATGGAATATGGATAC
53508102 TATTATAAA
1 TATTATAAA
53508111 TAAGGATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
51 15 0.28
53 10 0.19
54 29 0.54
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (53 bp):
TATTATAAAATAAATAAGAAAAGGAGTAATATATATAAATGGAATATGGATAC
Found at i:53508113 original size:27 final size:27
Alignment explanation
Indices: 53508030--53508113 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
53508020 AGTAATTTTT
53508030 TAAATGGAATATGGATACTATTATAAAA
1 TAAATGGAATATGGATACTATTAT-AAA
* * * * *
53508058 TAAATAAAGAA-AAGG-T-GTAATATATA
1 TAAAT--GGAATATGGATACTATTATAAA
53508084 TAAATGGAATATGGATACTATTATAAA
1 TAAATGGAATATGGATACTATTATAAA
53508111 TAA
1 TAA
53508114 GGATAATATA
Statistics
Matches: 41, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
24 3 0.07
25 3 0.07
26 8 0.20
27 15 0.37
28 6 0.15
29 3 0.07
30 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (27 bp):
TAAATGGAATATGGATACTATTATAAA
Found at i:53508229 original size:14 final size:14
Alignment explanation
Indices: 53508199--53508263 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
53508189 CAATTTTATA
53508199 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
53508211 GAAATATATAAAAT
1 AAAATATATAAAAT
*
53508225 AAAATATATAATAT
1 AAAATATATAAAAT
* * *
53508239 AATATAATTTATAGAT
1 AAAAT-ATATA-AAAT
53508255 AAAATATAT
1 AAAATATAT
53508264 GATAAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 8 0.20
13 3 0.07
14 16 0.39
15 7 0.17
16 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:53520646 original size:11 final size:11
Alignment explanation
Indices: 53520616--53520664 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
53520606 AGAGAATGAT
53520616 GAATGA-TGA-
1 GAATGATTGAG
53520625 GAATGGA-TGAG
1 GAAT-GATTGAG
53520636 GAATGATTGAG
1 GAATGATTGAG
* *
53520647 GGATGCTTGAG
1 GAATGATTGAG
53520658 GAATGAT
1 GAATGAT
53520665 GAATGAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 4 0.12
10 7 0.21
11 22 0.67
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (11 bp):
GAATGATTGAG
Found at i:53524760 original size:28 final size:27
Alignment explanation
Indices: 53524703--53524854 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
53524693 TAAATTGTGC
* *
53524703 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
53524730 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
53524758 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
53524785 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
53524813 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
53524840 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53524855 GACTTAATAT
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:53524768 original size:55 final size:55
Alignment explanation
Indices: 53524703--53524854 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
53524693 TAAATTGTGC
* *
53524703 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
53524758 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
53524813 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
53524855 GACTTAATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:53532924 original size:28 final size:27
Alignment explanation
Indices: 53532867--53533018 Score: 214
Period size: 27 Copynumber: 5.6 Consensus size: 27
53532857 TAAATTGTGC
* *
53532867 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
53532894 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
*
53532922 AGCACTAAGTGTGCGAGTTGACAATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
53532949 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
53532977 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
53533004 GGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53533019 GACTTAATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 64 0.56
28 51 0.44
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:53532932 original size:55 final size:55
Alignment explanation
Indices: 53532867--53533018 Score: 225
Period size: 55 Copynumber: 2.8 Consensus size: 55
53532857 TAAATTGTGC
* *
53532867 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
*
53532922 AGCACTAAGTGTGCGAGTTGACA-ATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGA-ATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * * *
53532977 AGCACTAAGTGTGCGAGTTGATTATATGGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
53533019 GACTTAATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
55 87 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:53541183 original size:10 final size:10
Alignment explanation
Indices: 53541154--53541189 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
53541144 AATGGACATG
53541154 AAAATAAATA
1 AAAATAAATA
53541164 AAAATGAAATA
1 AAAAT-AAATA
*
53541175 AGAATAAATA
1 AAAATAAATA
53541185 AAAAT
1 AAAAT
53541190 TATACAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:53541370 original size:24 final size:24
Alignment explanation
Indices: 53541341--53541388 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53541331 TTTCTAGAAG
* *
53541341 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
53541365 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
53541389 GTAATATTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:53541518 original size:11 final size:11
Alignment explanation
Indices: 53541502--53541528 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53541492 GCATGATTAT
53541502 GTGAAAATTTC
1 GTGAAAATTTC
53541513 GTGAAAATTTC
1 GTGAAAATTTC
53541524 GTGAA
1 GTGAA
53541529 GAAATTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (11 bp):
GTGAAAATTTC
Found at i:53549177 original size:22 final size:22
Alignment explanation
Indices: 53549141--53549182 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53549131 AATACTTAAA
* * *
53549141 AGGGTTTTGATGTTTTAAATGG
1 AGGGTTTTAAGGTTTAAAATGG
53549163 AGGGTTTTAAGGTTTAAAAT
1 AGGGTTTTAAGGTTTAAAAT
53549183 CGATTAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (22 bp):
AGGGTTTTAAGGTTTAAAATGG
Found at i:53555905 original size:25 final size:25
Alignment explanation
Indices: 53555874--53555923 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
53555864 TAAAAGCAAT
53555874 ATGAATG-CATGAAACAGATAAAAAA
1 ATGAATGACATGAAA-AGATAAAAAA
*
53555899 ATGAATGATCATGAAAATATAAAAA
1 ATGAATGA-CATGAAAAGATAAAAA
53555924 TAAAAGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 8 0.36
27 7 0.32
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
ATGAATGACATGAAAAGATAAAAAA
Found at i:53562767 original size:20 final size:19
Alignment explanation
Indices: 53562691--53562780 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 19
53562681 GAATAAATGA
53562691 AATAGAAATAGATAAATAATAT
1 AATAG-AATA-ATAAAT-ATAT
53562713 AA-A-AATAATACTAATATAT
1 AATAGAATAATA--AATATAT
*
53562732 ATTAGAAT-AT--ATATAT
1 AATAGAATAATAAATATAT
53562748 AATAGAATAGATAAATATAT
1 AATAGAATA-ATAAATATAT
53562768 AATAGAATTAATA
1 AATAGAA-TAATA
53562781 TTCTAACATC
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
16 13 0.23
18 5 0.09
19 9 0.16
20 22 0.39
21 6 0.11
22 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (19 bp):
AATAGAATAATAAATATAT
Found at i:53576475 original size:49 final size:51
Alignment explanation
Indices: 53576328--53576463 Score: 215
Period size: 50 Copynumber: 2.7 Consensus size: 51
53576318 ATGATCTATT
*
53576328 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGA-TG
1 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG
* *
53576378 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACT-
1 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG
*
53576428 GT-TGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
53576464 TGCTTACCAG
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 31 0.39
50 47 0.59
51 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (51 bp):
GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG
Found at i:53578270 original size:46 final size:46
Alignment explanation
Indices: 53578217--53578392 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
53578207 TATTTGGGCA
53578217 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
53578263 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* * *
53578310 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
53578356 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53578393 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.61
47 31 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:53578372 original size:93 final size:93
Alignment explanation
Indices: 53578213--53578385 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
53578203 GGGATATTTG
* *
53578213 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
53578278 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
53578306 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
53578371 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
53578386 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:53583468 original size:41 final size:40
Alignment explanation
Indices: 53583423--53583583 Score: 159
Period size: 41 Copynumber: 4.0 Consensus size: 40
53583413 TTCTTAGCAT
53583423 TGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTAGACCAC
1 TGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTAGA-CAC
* * * *
53583464 TGGCTCAAAGGCCCTTTG-GAACTAAG-TCCGG-TTATGAAAC
1 TGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGATTA-GACAC
* * * *
53583504 TGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTATTAG-CAC
1 TGGCTCAAAAGCCCTTCGAGACCAAGCTCGG--ATTAGACAC
53583545 TGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTTAGAC
1 TGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA-TTAGAC
53583584 CCCGATTAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
39 1 0.01
40 35 0.36
41 57 0.59
42 1 0.01
43 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
TGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTAGACAC
Found at i:53590582 original size:40 final size:41
Alignment explanation
Indices: 53590525--53590676 Score: 163
Period size: 40 Copynumber: 3.8 Consensus size: 41
53590515 CGATTCTTAG
53590525 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGATTA-GAC
1 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGATTATGAC
* * *
53590565 CACTGGCTCAAAGGCCCTTCG-GAACTAAG-TCCGGTTATGA-
1 CACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGATTATGAC
* * * * * *
53590605 CACTGGCTC-TAAGCCCTTCGA-ACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGATTATGAC
53590644 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCG
1 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCG
53590677 GATTTAGACC
Statistics
Matches: 95, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
38 14 0.15
39 21 0.22
40 50 0.53
41 10 0.11
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (41 bp):
CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGATTATGAC
Found at i:53597630 original size:41 final size:41
Alignment explanation
Indices: 53597585--53597752 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 41
53597575 GCACAAACAT
* *
53597585 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53597626 CCTTC-GAGACCAAGCTCAGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * *
53597667 CCTTCGGAACTAAGTCCGGTTATGA-CACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
** * *
53597707 CCTTC-GAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
53597747 CCTTCG
1 CCTTCG
53597753 AGACCAAGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
39 17 0.16
40 44 0.42
41 37 0.35
42 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53597709 original size:40 final size:40
Alignment explanation
Indices: 53597611--53597753 Score: 173
Period size: 40 Copynumber: 3.5 Consensus size: 40
53597601 CGATTCTTAG
* * *
53597611 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGATTA-GAC
1 CACTGGCTCAAAAGCCCTTCGA-ACTAAG-TCCGGTTATGAC
*
53597652 CACTGGCTCAAAGGCCCTTCGGAACTAAGTCCGGTTATGA-
1 CACTGGCTCAAAAGCCCTTC-GAACTAAGTCCGGTTATGAC
* * * *
53597692 CACTGGCTCTAAAGCCCTTCGAACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGAACTAAGTCCGGTTATGAC
53597732 CACTGGCTCAAAAGCCCTTCGA
1 CACTGGCTCAAAAGCCCTTCGA
53597754 GACCAAGCTC
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 17 0.19
40 45 0.50
41 26 0.29
42 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (40 bp):
CACTGGCTCAAAAGCCCTTCGAACTAAGTCCGGTTATGAC
Found at i:53604761 original size:41 final size:41
Alignment explanation
Indices: 53604716--53604883 Score: 148
Period size: 40 Copynumber: 4.1 Consensus size: 41
53604706 GCACAAACAT
* *
53604716 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * *
53604757 CCTTC-GAGACCAAGCTCAGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * *
53604798 CCTTCGGAACTAAGTCCGGTTATGA-CACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
** * * *
53604838 CCTTC-GAACTAAGTTCGGTTATTAGCACTGGCGCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
53604878 CCTTCG
1 CCTTCG
53604884 AGACCAAGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
39 17 0.16
40 43 0.41
41 37 0.36
42 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53604840 original size:40 final size:40
Alignment explanation
Indices: 53604742--53604884 Score: 164
Period size: 40 Copynumber: 3.5 Consensus size: 40
53604732 CGATTCTTAG
* * *
53604742 CACTGGCTCAAAAGCCCTTCGAGACCAAGCTCAGATTA-GAC
1 CACTGGCTCAAAAGCCCTTCGA-ACTAAG-TCCGGTTATGAC
*
53604783 CACTGGCTCAAAGGCCCTTCGGAACTAAGTCCGGTTATGA-
1 CACTGGCTCAAAAGCCCTTC-GAACTAAGTCCGGTTATGAC
* * * *
53604823 CACTGGCTCTAAAGCCCTTCGAACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGAACTAAGTCCGGTTATGAC
*
53604863 CACTGGCGCAAAAGCCCTTCGA
1 CACTGGCTCAAAAGCCCTTCGA
53604885 GACCAAGCTC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 17 0.19
40 44 0.49
41 26 0.29
42 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CACTGGCTCAAAAGCCCTTCGAACTAAGTCCGGTTATGAC
Found at i:53608555 original size:53 final size:53
Alignment explanation
Indices: 53608475--53608580 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
53608465 GAAAATTTAG
53608475 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCAGTTGTGTGTCT
1 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCAGTTGTGTGTCT
* * * *
53608528 AAAATTTTTCAAAATACAAGGGACACACGCCTGTGTGGCCCGGTTGTGTGTCT
1 AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCAGTTGTGTGTCT
53608581 CACACGGCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (53 bp):
AAAATTTTTCAAAATACAAAGGACACACACCTGTATGGCCCAGTTGTGTGTCT
Found at i:53616695 original size:47 final size:47
Alignment explanation
Indices: 53616641--53617188 Score: 898
Period size: 47 Copynumber: 11.6 Consensus size: 47
53616631 TATTTGAATA
*
53616641 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATTTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
53616688 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGCTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53616735 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53616784 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53616831 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53616878 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53616927 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53616974 AATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53617021 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53617068 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * **
53617115 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACATGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53617162 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
53617189 TCCCGAAGGG
Statistics
Matches: 473, Mismatches: 24, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
47 383 0.81
49 90 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:53616800 original size:143 final size:143
Alignment explanation
Indices: 53616641--53617188 Score: 933
Period size: 143 Copynumber: 3.9 Consensus size: 143
53616631 TATTTGAATA
* *
53616641 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATTTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
*
53616706 TGTGATAAGGCCGAATGGCCAATGTGCTGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
53616771 GGCCGATGTGATG
131 GGCCGATGTGATG
53616784 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
*
53616849 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
53616914 GGCCGATGTGATG
131 GGCCGATGTGATG
53616927 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
53616992 TGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
53617055 GGCCGATGTGATG
131 GGCCGATGTGATG
* * *
53617068 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * ** *
53617133 TGTGATAGGGCCGAGTGGCCAACATGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
53617189 TCCCGAAGGG
Statistics
Matches: 386, Mismatches: 17, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
141 140 0.36
142 1 0.00
143 245 0.63
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
GGCCGATGTGATG
Found at i:53618939 original size:40 final size:40
Alignment explanation
Indices: 53618616--53618927 Score: 489
Period size: 40 Copynumber: 7.8 Consensus size: 40
53618606 GAGAATTGAG
53618616 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53618656 AGTGATGTATCCAGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53618696 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
53618736 AGTGATGTATCCGGGCTAAGTCTCAAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53618776 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
53618816 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * **
53618856 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
53618896 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
53618928 ATCATGCTGG
Statistics
Matches: 252, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 252 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:53623006 original size:47 final size:47
Alignment explanation
Indices: 53622952--53623450 Score: 838
Period size: 47 Copynumber: 10.6 Consensus size: 47
53622942 TATTTGAATA
53622952 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53622999 AATGTGAAAGTGTATATATGTGATAAGG-CTGAATGGCCAATGTGCTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
53623046 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53623095 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53623142 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53623189 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
53623236 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
53623283 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53623330 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
53623377 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
53623424 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
53623451 TCCCGAAGGG
Statistics
Matches: 430, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 2 0.00
47 384 0.89
49 42 0.10
50 2 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:53637726 original size:37 final size:37
Alignment explanation
Indices: 53637676--53637754 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
53637666 TTATTACGAA
* *
53637676 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
53637713 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
53637750 GTCTT
1 GTCTT
53637755 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:53637951 original size:47 final size:47
Alignment explanation
Indices: 53637873--53638363 Score: 784
Period size: 47 Copynumber: 10.4 Consensus size: 47
53637863 CTCTTCGGGA
* * * * * * *
53637873 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53637920 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCTTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53637967 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
53638014 CTTATTACATATATACACTTTCACATTAATCACATTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53638061 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53638108 CTTATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53638155 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53638202 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53638251 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53638298 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53638345 CTTATCACATATATACACT
1 CTTATCACATATATACACT
53638364 GTCTTGGCTG
Statistics
Matches: 413, Mismatches: 29, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
47 367 0.89
49 46 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53642221 original size:42 final size:42
Alignment explanation
Indices: 53642172--53642407 Score: 382
Period size: 42 Copynumber: 5.6 Consensus size: 42
53642162 GTGACACCGA
*
53642172 CATCGTATCTGATTTTGTGTAAGACCATGTCTGGGACATCGG
1 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
*
53642214 CATCGTATCTGATTTTGTGTAAGACCATGTCTGGGACATCGG
1 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
53642256 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
1 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
* * * *
53642298 CATCATATCAGATTTCGTGTAAGACCATGTCTGGAACATCGA
1 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
* *
53642340 CATCGTATCTGATTTCGTGTAAGACCCTGTCTGGGACATCGA
1 CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
* *
53642382 CATCATATCTAATTTCGTGTAAGACC
1 CATCGTATCTGATTTCGTGTAAGACC
53642408 CCGATACTGA
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 183 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
CATCGTATCTGATTTCGTGTAAGACCATGTCTGGGACATCGG
Found at i:53648795 original size:40 final size:40
Alignment explanation
Indices: 53648699--53648923 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
53648689 GCTCCTCGTT
* * * *
53648699 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
53648739 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
53648778 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
53648818 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
53648858 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
53648899 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53648924 CAGCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 39 0.24
40 108 0.67
41 15 0.09
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53648932 original size:41 final size:41
Alignment explanation
Indices: 53648855--53648932 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53648845 TTTGTATCTC
* * *
53648855 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53648896 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53648933 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:53655223 original size:39 final size:40
Alignment explanation
Indices: 53655178--53655402 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
53655168 GCTCCTCGTT
* * * *
53655178 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
53655218 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
53655257 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
53655297 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
53655337 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
53655378 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53655403 CAGCATTCAA
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
39 39 0.24
40 107 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53655411 original size:41 final size:41
Alignment explanation
Indices: 53655334--53655411 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53655324 TTTGTATCTC
* * *
53655334 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53655375 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53655412 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:53657412 original size:28 final size:28
Alignment explanation
Indices: 53657380--53657441 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
53657370 TAATTCATTC
53657380 TCTTTTGGACTCTTTACAAACCAGTTCA
1 TCTTTTGGACTCTTTACAAACCAGTTCA
*
53657408 TCTTTTGGACTCTTTACAAACCTGTTCA
1 TCTTTTGGACTCTTTACAAACCAGTTCA
53657436 TCTTTT
1 TCTTTT
53657442 TTTTTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (28 bp):
TCTTTTGGACTCTTTACAAACCAGTTCA
Found at i:53659087 original size:31 final size:31
Alignment explanation
Indices: 53659052--53659118 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
53659042 ACGTACTAAC
*
53659052 TGATATAATATGGTCACTAGTACATAGAACT
1 TGATATAATATAGTCACTAGTACATAGAACT
* *
53659083 TGATATAATATAGTCACTGGTACATAGTACT
1 TGATATAATATAGTCACTAGTACATAGAACT
53659114 TGATA
1 TGATA
53659119 CTTCAAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
TGATATAATATAGTCACTAGTACATAGAACT
Found at i:53662399 original size:43 final size:43
Alignment explanation
Indices: 53662274--53662436 Score: 149
Period size: 43 Copynumber: 3.8 Consensus size: 43
53662264 TGGAAAGCTC
* *
53662274 GTACAATGCTAACGTCCTAGACGTGGTCTTACA--TATAATCAA
1 GTACAATGCCAACGTCCCAGACGTGGTCTTACACGTA-AATCAA
* *
53662316 ATATCGATGCC-ACAGTCCCAGACAG-GGTCTTACACG-AAATCAA
1 GTA-CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAA
* *
53662359 GTACGATGCCAACGTCCCAGACGTGGTTTTACACGTAAATCATAA
1 GTACAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATC--AA
* * *
53662404 GT-CAACGCCAACGTCCTAGATGTGGTCTTACAC
1 GTACAATGCCAACGTCCCAGACGTGGTCTTACAC
53662437 AAAACACATA
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 37 0.37
44 28 0.28
45 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
GTACAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAA
Found at i:53670023 original size:186 final size:180
Alignment explanation
Indices: 53669669--53670028 Score: 445
Period size: 186 Copynumber: 2.0 Consensus size: 180
53669659 ATGTTCACAA
* * *
53669669 AGGTACATGTACGTACCTTTCATTCTCAACATAGTGTACAATTTAAACGTACTTGAATAGGATAC
1 AGGTACATGTACGTACCTTTCATTCTCAACATAGTATACAATTCAAACGTACCTGAATAGGATAC
* * * * *
53669734 ACATTTTAGATACTCATTTGTATCTCAAAATGCCCTGTTCGGAATCATAAGGATACGCGGATAAC
66 ACATTTCAGATAATCATTGGTATCTCAAAATGCCCTGTTCAGAATCATAAGGATACACGGATAAC
* * * * *
53669799 TTGGAAAGCTCGTACAATGCTAACATCCTAGACGTGGTCGTACACATTTT
131 TCGAAAAGCTCATACAATGCCAACATCCCAGACGTGGTCGTACACATTTT
* *
53669849 AGGTACATGTACTTACCTTTTATTCTCAACATAGTATACAATTCAAA-GTACCTGAATCA-GATA
1 AGGTACATGTACGTACCTTTCATTCTCAACATAGTATACAATTCAAACGTACCTGAAT-AGGATA
* * *
53669912 CACATTTCAGATAATCATTGGTATCTCGAAATGCTCGTTGAACCATTCAGAATCATAAGGATATA
65 CACATTTCAGATAATCATTGGTATCTCAAAATGC-C-CTG-----TTCAGAATCATAAGGATACA
* * *
53669977 CGGATAACTCGAAAAGCTCATACGATGCCAACGTCCCAGACGTGGTCTTACA
123 CGGATAACTCGAAAAGCTCATACAATGCCAACATCCCAGACGTGGTCGTACA
53670029 TGTAATCAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
179 43 0.28
180 45 0.30
181 2 0.01
186 61 0.40
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (180 bp):
AGGTACATGTACGTACCTTTCATTCTCAACATAGTATACAATTCAAACGTACCTGAATAGGATAC
ACATTTCAGATAATCATTGGTATCTCAAAATGCCCTGTTCAGAATCATAAGGATACACGGATAAC
TCGAAAAGCTCATACAATGCCAACATCCCAGACGTGGTCGTACACATTTT
Found at i:53670067 original size:43 final size:43
Alignment explanation
Indices: 53669999--53670157 Score: 200
Period size: 43 Copynumber: 3.7 Consensus size: 43
53669989 AAAGCTCATA
*
53669999 CGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CGATGCCAACGTCCCAGACGTGGTCTTACAAGTAATCAAATAT
* * *
53670042 TGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAAGTA-
1 CGATGCCAAC-GTCCCAGAC-GTGGTCTTACAAGTAATCAAATAT
* *
53670084 CGATGCCAACGTCCCAGATGTGGTCTTACAAGTAAATCATAA-GT
1 CGATGCCAACGTCCCAGACGTGGTCTTACAAGT-AATCA-AATAT
53670128 CGATGCCAACGTCCCAGACGTGGTCTTACA
1 CGATGCCAACGTCCCAGACGTGGTCTTACA
53670158 CGATAACACA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.27
43 41 0.41
44 31 0.31
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (43 bp):
CGATGCCAACGTCCCAGACGTGGTCTTACAAGTAATCAAATAT
Found at i:53684347 original size:38 final size:33
Alignment explanation
Indices: 53684270--53684335 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
53684260 GTACCGGTTG
53684270 CGGCACTAAATAGTAGTTACAGCAGAGCTGCCA
1 CGGCACTAAATAGTAGTTACAGCAGAGCTGCCA
*
53684303 CGGCACTAAATAGTAGTTACAGTAGAGCTGCCA
1 CGGCACTAAATAGTAGTTACAGCAGAGCTGCCA
53684336 GTACAGTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (33 bp):
CGGCACTAAATAGTAGTTACAGCAGAGCTGCCA
Found at i:53686983 original size:20 final size:19
Alignment explanation
Indices: 53686951--53686991 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
53686941 AATTAGATGA
* *
53686951 TTGTTTATTTATAAGTTAT
1 TTGTTTATATATAAGATAT
53686970 TTGTATTATATATAAGATAT
1 TTGT-TTATATATAAGATAT
53686990 TT
1 TT
53686992 TTTGCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TTGTTTATATATAAGATAT
Found at i:53687432 original size:43 final size:43
Alignment explanation
Indices: 53687331--53687569 Score: 349
Period size: 43 Copynumber: 5.6 Consensus size: 43
53687321 ATGTGTGCGA
*
53687331 GTAAGACCACGTCTGGGACGTTGGCATCGACATGTGATTA-GT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
*
53687373 GTAAGACCACGTCTGGGATGTTGGCATCGATATGTGATTACGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
53687416 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
* * *
53687459 GTAAGACCACGTCTGGGATGTTGGCATCGATATGTGTTTACGA
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
* * * *
53687502 GTAAGACTC-TGTTTGGGACAG-TAGCATCGATATGTGATTACAT
1 GTAAGAC-CACGTCTGGGAC-GTTGGCATCGATATGTGATTACGT
*
53687545 GTAAGACCACGTCTGAGACGTTGGC
1 GTAAGACCACGTCTGGGACGTTGGC
53687570 TTTGTACGAT
Statistics
Matches: 175, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
42 40 0.23
43 133 0.76
44 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (43 bp):
GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
Found at i:53700421 original size:30 final size:30
Alignment explanation
Indices: 53700364--53700424 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
53700354 GCTAAGTCCC
* *
53700364 GAAGGCATTTATGCTAGTGATTTTATCCGG
1 GAAGGCATTTATGCGAGTGATTATATCCGG
*
53700394 GAAGGCATTTGTGCGAGTTGA-TATATCCGG
1 GAAGGCATTTATGCGAG-TGATTATATCCGG
53700424 G
1 G
53700425 CTAAGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (30 bp):
GAAGGCATTTATGCGAGTGATTATATCCGG
Found at i:53700449 original size:40 final size:40
Alignment explanation
Indices: 53700394--53700487 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
53700384 TTTTATCCGG
*
53700394 GAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCC
1 GAAGGCATTTGTGCGAGTTGATATACCCGGGCTAAGACCC
* *
53700434 GAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCC
1 GAAGGCATTTGTGCGAGTTGATATACCCGGGCTAAGACCC
*
53700474 GAAGGCAATTGTGC
1 GAAGGCATTTGTGC
53700488 TTGTGGTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (40 bp):
GAAGGCATTTGTGCGAGTTGATATACCCGGGCTAAGACCC
Found at i:53706611 original size:53 final size:53
Alignment explanation
Indices: 53706524--53706736 Score: 232
Period size: 53 Copynumber: 4.0 Consensus size: 53
53706514 TCATGGCACT
*
53706524 GAAGAACCATATCATGTAAGA-TCGTAACTAGTGGGTTATGACATCATAT-GAGAA
1 GAAG-ACCATATAATGTAAGACT-GTAACTAGTGGGTTATGACATCATATGGA-AA
** * *
53706578 GAAGACCATATCGTGTAAGACTGTAATTGGTGGGTTATGACATCATATGGAAA
1 GAAGACCATATAATGTAAGACTGTAACTAGTGGGTTATGACATCATATGGAAA
* * * *
53706631 GAAGACCATATAGTGTAAGACTATAACTAGTGGATTATGGCATCATATGGAAA
1 GAAGACCATATAATGTAAGACTGTAACTAGTGGGTTATGACATCATATGGAAA
* * * * * * * *
53706684 GAATATCGTATAATGTAAGACCGTAATTGGTGGGTCATAACATCATATGGAAA
1 GAAGACCATATAATGTAAGACTGTAACTAGTGGGTTATGACATCATATGGAAA
53706737 ATTTTAGGAA
Statistics
Matches: 136, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
53 129 0.95
54 7 0.05
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (53 bp):
GAAGACCATATAATGTAAGACTGTAACTAGTGGGTTATGACATCATATGGAAA
Found at i:53709208 original size:30 final size:30
Alignment explanation
Indices: 53709173--53709231 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53709163 CATAAATCAT
* *
53709173 ACTTTTTCAAATTTAC-ATTTTGACCCCTAA
1 ACTTTTACAAATTTACGATTTAG-CCCCTAA
*
53709203 ACTTTTACATATTTACGATTTAGCCCCTA
1 ACTTTTACAAATTTACGATTTAGCCCCTA
53709232 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (30 bp):
ACTTTTACAAATTTACGATTTAGCCCCTAA
Found at i:53722317 original size:6 final size:6
Alignment explanation
Indices: 53722306--53722367 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
53722296 TCCTCCTATC
53722306 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
53722354 TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TT
53722368 ATTTCCTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:53726536 original size:29 final size:28
Alignment explanation
Indices: 53726500--53726577 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
53726490 TCATGAGATT
53726500 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
53726530 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
53726557 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
53726578 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:53726795 original size:174 final size:174
Alignment explanation
Indices: 53726530--53726857 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
53726520 AAATTGTACA
* *
53726530 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
53726595 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTACGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
53726660 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53726704 GCACTAAGTGTGTGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
53726769 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
53726834 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
53726858 ACCTTGAGTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:53729624 original size:40 final size:40
Alignment explanation
Indices: 53729526--53729828 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
53729516 TCGTCGTTCA
* * * * *
53729526 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
53729565 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
53729605 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53729645 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53729685 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
53729725 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
53729765 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
53729805 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53729829 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:53737612 original size:40 final size:40
Alignment explanation
Indices: 53737514--53737816 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
53737504 TCCTCGTTCA
* * * * *
53737514 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
53737553 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
53737593 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53737633 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53737673 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
53737713 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
53737753 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
53737793 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53737817 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:53739762 original size:27 final size:27
Alignment explanation
Indices: 53739732--53739909 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
53739722 ATATTGAGCC
* * **
53739732 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
53739759 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
53739786 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
* ** ** *
53739814 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
53739841 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
53739868 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
53739895 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
53739910 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:53739871 original size:82 final size:81
Alignment explanation
Indices: 53739758--53739908 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
53739748 TATAATCATC
* * *
53739758 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACTCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACCCTT
53739823 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
53739840 TCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
1 TCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
53739904 AGTGC
65 AGTGC
53739909 TGTACAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTTA
GTGCCGCATGGTCAAT
Found at i:53747615 original size:27 final size:27
Alignment explanation
Indices: 53747585--53747762 Score: 151
Period size: 27 Copynumber: 6.6 Consensus size: 27
53747575 ATATTGAGCC
* * **
53747585 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
53747612 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
53747639 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-AAT
* ** ** *
53747667 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
53747694 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
53747721 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
53747748 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
53747763 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:53747724 original size:82 final size:81
Alignment explanation
Indices: 53747611--53747761 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
53747601 TATAATCATC
* * * *
53747611 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCACTCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCACCCTT
53747676 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
53747693 TCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
1 TCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
53747757 AGTGC
65 AGTGC
53747762 TGTACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 17 0.28
82 44 0.72
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTTA
GTGCCGCATGGTCAAT
Found at i:53751484 original size:49 final size:48
Alignment explanation
Indices: 53751412--53751686 Score: 290
Period size: 49 Copynumber: 5.7 Consensus size: 48
53751402 TCTATTGTGA
*
53751412 GGTCACATATGTAGTACTAAGTGCAGGCTACTACGTGTGCTGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGT-CTGGATAATT
* *
53751461 GGTCATATGTGTATTACTAAGTGCAGGCTACTACGTGTGCTGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGT-CTGGATAATT
* *
53751510 GGTCATATGTGTAGTACTAAGTGCAGGCTACTAC----C-CGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTCTGGATAA-TT
* * * * * **
53751554 CGATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTCT-GGATAATT
** **
53751604 AGGTCATGTGTGTAGTACTAAGTATAGGCTACTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGT-CTGGATAATT
* *
53751654 GGTCGCATGTGTAGTACTAAGTCCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
53751687 TGCGTACCAG
Statistics
Matches: 191, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
43 5 0.03
44 3 0.02
45 30 0.16
49 107 0.56
50 42 0.22
51 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (48 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTCTGGATAATT
Found at i:53751681 original size:144 final size:143
Alignment explanation
Indices: 53751421--53751686 Score: 390
Period size: 144 Copynumber: 1.9 Consensus size: 143
53751411 AGGTCACATA
* * *
53751421 TGTAGTACTAAGTGCAGGCTACTACGTGTGCTGGATAATTGGTCATATGTGTATTACTAAGTGCA
1 TGTAGTACTAAGTGCAGGCTACTACGTGTGCTAGATAATTGGTCATATGTGTAGTACTAAGTACA
* * *
53751486 GGCTACTACGTGTGCTGGATAATTGGTCATATGTGTAGTACTAAGTGCAGGCTACTACCCGATAA
66 GGCTACTACGTGTACTGGATAATTGGTCACATGTGTAGTACTAAGTCCAGGCTACTACCCGATAA
53751551 CTTCGATCACGTG
131 CTTCGATCACGTG
* * ** *
53751564 TGTAGTACTAAGTGTAGGCTACTACGTGT-ATCAGATGGTTAGGTCATGTGTGTAGTACTAAGTA
1 TGTAGTACTAAGTGCAGGCTACTACGTGTGCT-AGATAATT-GGTCATATGTGTAGTACTAAGTA
* *
53751628 TAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACTAAGTCCAGGCTACTA
64 CAGGCTACTACGTGTACTGGATAATTGGTCACATGTGTAGTACTAAGTCCAGGCTACTA
53751687 TGCGTACCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
142 1 0.01
143 33 0.31
144 74 0.69
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (143 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTGCTAGATAATTGGTCATATGTGTAGTACTAAGTACA
GGCTACTACGTGTACTGGATAATTGGTCACATGTGTAGTACTAAGTCCAGGCTACTACCCGATAA
CTTCGATCACGTG
Found at i:53760183 original size:49 final size:47
Alignment explanation
Indices: 53759937--53760304 Score: 628
Period size: 47 Copynumber: 7.7 Consensus size: 47
53759927 ATGATAGTAT
* *
53759937 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
*
53759984 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
* *
53760031 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
53760078 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
53760125 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATTTGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA--TGTGATAG
53760174 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAG
53760223 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAG
53760272 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
53760305 CCCGAAGGGC
Statistics
Matches: 312, Mismatches: 4, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
47 176 0.56
49 126 0.40
50 4 0.01
51 6 0.02
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
Found at i:53760478 original size:37 final size:37
Alignment explanation
Indices: 53760422--53760500 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53760412 CCGAGCTCTA
* * *
53760422 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53760459 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53760496 AAGAC
1 AAGAC
53760501 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53762442 original size:29 final size:29
Alignment explanation
Indices: 53762407--53762487 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
53762397 GTTGTGAGAT
* *
53762407 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
53762436 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
53762465 TGGCACTAAGTGTGCGAGGTTGA
1 TGGCACTAAGTGTGCGA-GTTGA
53762488 TTATTAAGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 5 0.11
29 37 0.80
30 4 0.09
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:53762848 original size:40 final size:40
Alignment explanation
Indices: 53762791--53762987 Score: 202
Period size: 40 Copynumber: 4.9 Consensus size: 40
53762781 TTGAATGATG
* * * *
53762791 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCT-AGTGA-TATA
*
53762831 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
53762871 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
*** * *
53762911 TCCGTG-CTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCG-GACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * * * * *
53762951 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGAT
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
53762988 GTGTATTCGG
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 120 0.88
41 8 0.06
42 7 0.05
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:53766745 original size:49 final size:47
Alignment explanation
Indices: 53766499--53766817 Score: 548
Period size: 47 Copynumber: 6.7 Consensus size: 47
53766489 ATGATAGTAT
*
53766499 GGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
53766546 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
53766593 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
53766640 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
53766687 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
*
53766736 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
53766785 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
53766818 CCCGAAGGGC
Statistics
Matches: 265, Mismatches: 4, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
47 170 0.64
49 91 0.34
50 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:53766991 original size:37 final size:37
Alignment explanation
Indices: 53766935--53767013 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53766925 CCGAGCTCTA
* * * *
53766935 AAGACTCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53766972 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53767009 AAGAC
1 AAGAC
53767014 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53768829 original size:27 final size:27
Alignment explanation
Indices: 53768799--53768977 Score: 191
Period size: 27 Copynumber: 6.6 Consensus size: 27
53768789 ATATTGAGCC
* * *
53768799 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCATAT
* *
53768826 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCATAT
* *
53768853 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCATA-T
** **
53768881 CGCACACTTAGTGCCGCATGGTCA-ATT
1 CGCACACTTAGTGCTACATAATCATA-T
* *
53768908 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCATAT
*
53768935 CGCACACTTAGTGCAACATAATCATAT
1 CGCACACTTAGTGCTACATAATCATAT
53768962 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
53768978 TACAATTTAA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCATAT
Found at i:53768938 original size:82 final size:81
Alignment explanation
Indices: 53768825--53768975 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
53768815 TATAATCATC
* * *
53768825 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAATCAAA-TCGCACACTT
53768890 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* ** *
53768907 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAATCATATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAATCAAATCGCACACTT
53768971 AGTGC
65 AGTGC
53768976 TATACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 16 0.26
82 45 0.74
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAATCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:53769541 original size:13 final size:13
Alignment explanation
Indices: 53769523--53769547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53769513 TACTAAATTT
53769523 TCATGGATTCAAG
1 TCATGGATTCAAG
53769536 TCATGGATTCAA
1 TCATGGATTCAA
53769548 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:53779752 original size:30 final size:30
Alignment explanation
Indices: 53779718--53779814 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
53779708 TAAACTAAAA
53779718 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53779748 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
53779778 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
53779808 TGAGCTA
1 TGAGCTA
53779815 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53782265 original size:30 final size:30
Alignment explanation
Indices: 53782231--53782327 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53782221 AGCTCACTCC
53782231 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
53782261 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
53782291 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
53782321 TAGCTCA
1 TAGCTCA
53782328 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:53790233 original size:28 final size:30
Alignment explanation
Indices: 53790174--53790306 Score: 107
Period size: 29 Copynumber: 4.6 Consensus size: 30
53790164 CATACATGTG
* * *
53790174 TATGGCCCAT-TGGCCCAA--TCTCATTTA
1 TATGGCCCATCAGGCCCAATTTCACATTCA
* *
53790201 TATGGCCCATC-GGCTCGA-TTCACATTCA
1 TATGGCCCATCAGGCCCAATTTCACATTCA
*
53790229 TATGGCCCATCAGGCCCAATTTCATATTCA
1 TATGGCCCATCAGGCCCAATTTCACATTCA
* * * * *
53790259 TATGGCCCATTAGGCCTAA-ATCACCTTTA
1 TATGGCCCATCAGGCCCAATTTCACATTCA
* *
53790288 TTTGGCCCATTAGGCCCAA
1 TATGGCCCATCAGGCCCAA
53790307 ATCACCTTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
27 15 0.17
28 18 0.21
29 28 0.32
30 26 0.30
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (30 bp):
TATGGCCCATCAGGCCCAATTTCACATTCA
Found at i:53790260 original size:30 final size:30
Alignment explanation
Indices: 53790174--53790274 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 30
53790164 CATACATGTG
* *
53790174 TATGGCCCAT-TGGCCCAATCTCAT-TT-A
1 TATGGCCCATCAGGCCCAATTTCATATTCA
* * *
53790201 TATGGCCCATC-GGCTCGA-TTCACATTCA
1 TATGGCCCATCAGGCCCAATTTCATATTCA
53790229 TATGGCCCATCAGGCCCAATTTCATATTCA
1 TATGGCCCATCAGGCCCAATTTCATATTCA
*
53790259 TATGGCCCATTAGGCC
1 TATGGCCCATCAGGCC
53790275 TAAATCACCT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.05
27 17 0.28
28 12 0.20
29 5 0.08
30 24 0.39
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (30 bp):
TATGGCCCATCAGGCCCAATTTCATATTCA
Found at i:53790298 original size:29 final size:30
Alignment explanation
Indices: 53790261--53790319 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
53790251 CATATTCATA
*
53790261 TGGCCCATTAGGCCTAAATCACCTT-TATT
1 TGGCCCATTAGGCCCAAATCACCTTATATT
53790290 TGGCCCATTAGGCCCAAATCACCTTATATT
1 TGGCCCATTAGGCCCAAATCACCTTATATT
53790320 CATGCTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (30 bp):
TGGCCCATTAGGCCCAAATCACCTTATATT
Found at i:53793095 original size:40 final size:40
Alignment explanation
Indices: 53793049--53793193 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
53793039 CTCGCACAAG
* * * * *
53793049 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* *
53793089 GCCTTCGAGACTTAGCCCAGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
53793129 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
53793170 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
53793194 CATTCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 56 0.64
41 27 0.31
42 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:53797989 original size:28 final size:30
Alignment explanation
Indices: 53797958--53798035 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
53797948 GATCTTATTT
53797958 ATATGGCCCATC-GGCCCAA-TTCACATTC
1 ATATGGCCCATCAGGCCCAATTTCACATTC
*
53797986 ATATGGCCCATCAGGCCCAATTTCATATTC
1 ATATGGCCCATCAGGCCCAATTTCACATTC
* *
53798016 ATATGGCCCGTTAGGCCCAA
1 ATATGGCCCATCAGGCCCAA
53798036 ATCACCTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 12 0.27
29 7 0.16
30 26 0.58
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (30 bp):
ATATGGCCCATCAGGCCCAATTTCACATTC
Found at i:53798919 original size:22 final size:25
Alignment explanation
Indices: 53798880--53798924 Score: 60
Period size: 22 Copynumber: 1.9 Consensus size: 25
53798870 AAACCTGAGT
*
53798880 AGAAGAAGAATAGAAAATCAGCACA
1 AGAAGAAGAATAGAAAATAAGCACA
53798905 AGAAG-AGAA-AG-AAATAAGCA
1 AGAAGAAGAATAGAAAATAAGCA
53798925 AGGGTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 4 0.21
25 5 0.26
ACGTcount: A:0.62, C:0.09, G:0.22, T:0.07
Consensus pattern (25 bp):
AGAAGAAGAATAGAAAATAAGCACA
Found at i:53804220 original size:35 final size:35
Alignment explanation
Indices: 53804108--53804221 Score: 140
Period size: 35 Copynumber: 3.3 Consensus size: 35
53804098 CATAGGTAAG
* * *
53804108 TACATGTGAGCTTATATTTAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAACTTGTATATTTGGT
* * * *
53804143 TACAGGTGAGGTTATATTGAACTTG-AGTACTTGAT
1 TACATGTGAGCTTATATTGAACTTGTA-TATTTGGT
53804178 TACATGTGAGCTTATATTGAACTTGTATATTTGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTTGGT
*
53804213 TATATGTGA
1 TACATGTGA
53804222 ATTTATCTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.97
36 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTTGGT
Found at i:53808276 original size:28 final size:28
Alignment explanation
Indices: 53808233--53808297 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
53808223 ATGAAAATTT
* * *
53808233 CACTAAGCGTGCGAGTTTGGTTAAT-GAG
1 CACTAAGTGCGCGAGTTTGATT-ATCGAG
*
53808261 CATTAAGTGCGCGAGTTTGATTATCGAG
1 CACTAAGTGCGCGAGTTTGATTATCGAG
53808289 CACTAAGTG
1 CACTAAGTG
53808298 TGTGAAGGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTAAGTGCGCGAGTTTGATTATCGAG
Found at i:53816081 original size:28 final size:28
Alignment explanation
Indices: 53816040--53816104 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
53816030 TGAAAATTTT
* * *
53816040 ACTAAGAGTGCGAGTTTGGTTAAT-GAGC
1 ACTAAGTGTACGAGTTTGATT-ATCGAGC
53816068 ACTAAGTGTACGAGTTTGATTATCGAGC
1 ACTAAGTGTACGAGTTTGATTATCGAGC
53816096 ACTAAGTGT
1 ACTAAGTGT
53816105 GTGAAGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 2 0.06
28 31 0.94
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (28 bp):
ACTAAGTGTACGAGTTTGATTATCGAGC
Found at i:53830505 original size:43 final size:44
Alignment explanation
Indices: 53830439--53830595 Score: 166
Period size: 43 Copynumber: 3.7 Consensus size: 44
53830429 AGCTCATACA
* *
53830439 ATGCCAAC-GTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATATCG
* * *
53830482 ATGCC-ACTATCCCAGACAGGGTCTTACATGAAATCAAATA-CG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATATCG
* * *
53830524 ATGCCGA-TGTCCCAGACATGTTCTTACACGTAAATCATAAGT-T-G
1 ATGCCAACTGTCCCAGACATGGTCTTACATGT-AATCA-AA-TATCG
53830568 ATGCCAAC-GTCCCAGACATGGTCTTACA
1 ATGCCAACTGTCCCAGACATGGTCTTACA
53830596 CGAAAACACA
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
42 28 0.29
43 38 0.40
44 28 0.29
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATATCG
Found at i:53832268 original size:12 final size:12
Alignment explanation
Indices: 53832251--53832281 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53832241 TTCCACGAGG
53832251 ACACTTTCAAAA
1 ACACTTTCAAAA
53832263 ACACTTTCAAAA
1 ACACTTTCAAAA
53832275 ACACTTT
1 ACACTTT
53832282 ATTGCCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (12 bp):
ACACTTTCAAAA
Found at i:53835766 original size:39 final size:40
Alignment explanation
Indices: 53835682--53835766 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
53835672 ACTTAATTTA
* * *
53835682 CCAGCATTAAGCCTGCGGGACTTTAAACCCGGATACAATC
1 CCAGCATAAAGCCAGCGGGACTCTAAACCCGGATACAATC
*
53835722 CCAGCATAAAGCCAGCGGGTCTCT-AACCCGGATACAATC
1 CCAGCATAAAGCCAGCGGGACTCTAAACCCGGATACAATC
*
53835761 TCAGCA
1 CCAGCA
53835767 CAATTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 20 0.50
40 20 0.50
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.18
Consensus pattern (40 bp):
CCAGCATAAAGCCAGCGGGACTCTAAACCCGGATACAATC
Found at i:53835935 original size:47 final size:45
Alignment explanation
Indices: 53835848--53835992 Score: 175
Period size: 47 Copynumber: 3.1 Consensus size: 45
53835838 CACAATTGGT
* * *
53835848 CATTCGGCCTTATCACATATTCACTTACACATAT-ATCACATTAAC
1 CATTCGGCCTTATCACATATACACTTTCACAT-TCATCACATTGAC
* *
53835893 CATTCGGCCTTATCACACGTATGCACTTTCACATTCATCACATTGCC
1 CATTCGGCCTTATCACA--TATACACTTTCACATTCATCACATTGAC
* *
53835940 CATTCGGCCTTATCACATATAAAAACTTTCACATTCATCACATTGGC
1 CATTCGGCCTTATCACATAT--ACACTTTCACATTCATCACATTGAC
53835987 CATTCG
1 CATTCG
53835993 ATCTTAAGCT
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
45 20 0.23
46 1 0.01
47 67 0.76
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (45 bp):
CATTCGGCCTTATCACATATACACTTTCACATTCATCACATTGAC
Found at i:53839751 original size:40 final size:40
Alignment explanation
Indices: 53839696--53840011 Score: 452
Period size: 40 Copynumber: 7.9 Consensus size: 40
53839686 AAATACACAT
* * *
53839696 CACCAGCATGAATGCTCTTCGGGACCTAGACCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * **
53839736 CACCAGCACGAATGCTCTTCAGGACTTAACCCTAATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
53839776 CTCCATCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
53839816 CACCAGCACGAATGCTCTTCGGGACTTAGCCCAGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
53839856 CACCAACACGAATGCTCTTCGAGACTTAGCCCAGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
53839896 CACCAGCAGGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
53839936 CACCAGTACGTATGCTCTTCGGGACTTAGCCCGAATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
53839976 CTCCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
53840012 CATCGGCGAG
Statistics
Matches: 244, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 244 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:53842720 original size:47 final size:46
Alignment explanation
Indices: 53842632--53842776 Score: 186
Period size: 47 Copynumber: 3.1 Consensus size: 46
53842622 CACAATTGGT
* * *
53842632 CATTCGGCCTTATCACA-TATTCACTTACACATAT-ATCACATTAAC
1 CATTCGGCCTTATCACATTATACACTTTCACAT-TCATCACATTGAC
* *
53842677 CATTCGGCCTTATCACATGTATGCACTTTCACATTCATCACATTGCC
1 CATTCGGCCTTATCACAT-TATACACTTTCACATTCATCACATTGAC
* *
53842724 CATTCGGCCTTATCACATATACACACTTTCACATTCATCACATTGGC
1 CATTCGGCCTTATCACAT-TATACACTTTCACATTCATCACATTGAC
53842771 CATTCG
1 CATTCG
53842777 ATCTTAAGCT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 17 0.19
46 1 0.01
47 71 0.80
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (46 bp):
CATTCGGCCTTATCACATTATACACTTTCACATTCATCACATTGAC
Found at i:53849683 original size:42 final size:43
Alignment explanation
Indices: 53849625--53849736 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 43
53849615 TCAATGCCAC
* *
53849625 TGTCCCAGACAGGGTCTTACACGAAATCA-AA-TACGATG-TCGA
1 TGTCCCAGACATGGTCTTACACGAAATCATAAGT-CGATGCT-AA
53849667 TGTCCCAGACATGGTCTTACACGTAAATCATAAGTCGATGCTAA
1 TGTCCCAGACATGGTCTTACACG-AAATCATAAGTCGATGCTAA
*
53849711 CGTCCCAGACATGGTCTTACACGAAA
1 TGTCCCAGACATGGTCTTACACGAAA
53849737 ACACATATTG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
42 22 0.35
43 9 0.14
44 30 0.48
45 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (43 bp):
TGTCCCAGACATGGTCTTACACGAAATCATAAGTCGATGCTAA
Found at i:53853870 original size:29 final size:27
Alignment explanation
Indices: 53853828--53853882 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
53853818 TTTTTCATTT
*
53853828 ATTTCACATTTTAACTACTAACTTTACAA
1 ATTTCACAATTTAA-TACTAA-TTTACAA
*
53853857 ATTTCACAATTTAATCCTAATTTACA
1 ATTTCACAATTTAATACTAATTTACA
53853883 TTTTCACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 5 0.21
29 13 0.54
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTTCACAATTTAATACTAATTTACAA
Found at i:53860326 original size:42 final size:41
Alignment explanation
Indices: 53860165--53860318 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 41
53860155 ATGAGTTTAT
*
53860165 GTGTAAGACCATATCTGGGATATGGTATC-ATTATGA-AATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGA-TATGAGAA--TC
* *
53860207 GTGTAAGACCATGTCTGGGACATGGCATCGATATGAGAATC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATC
* * * *
53860248 GTGTAAGACCATAGCTGGGCTATTGGTATCGATATGAGACTCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGAAT-C
* *
53860291 ATGTAAGACCATATCTAGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
53860319 TGGTATGATT
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 20 0.21
42 52 0.55
43 22 0.23
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATC
Found at i:53860326 original size:84 final size:83
Alignment explanation
Indices: 53860165--53860318 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 83
53860155 ATGAGTTTAT
* * * * * *
53860165 GTGTAAGACCATATCTGGGATATGGTATCATTATGAAATTTCGTGTAAGACCATGTCTGGGACAT
1 GTGTAAGACCATAGCTGGGATATGGTATCATTATGAAACTCCATGTAAGACCATATCTAGGACAT
53860230 GGCATCGATATGAGAATC
66 GGCATCGATATGAGAATC
* * *
53860248 GTGTAAGACCATAGCTGGGCTATTGGTATCGA-TATGAGACTCCATGTAAGACCATATCTAGGAT
1 GTGTAAGACCATAGCTGGGATA-TGGTATC-ATTATGAAACTCCATGTAAGACCATATCTAGGAC
53860312 ATGGCAT
64 ATGGCAT
53860319 TGGTATGATT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
83 20 0.33
84 39 0.65
85 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (83 bp):
GTGTAAGACCATAGCTGGGATATGGTATCATTATGAAACTCCATGTAAGACCATATCTAGGACAT
GGCATCGATATGAGAATC
Found at i:53865671 original size:18 final size:18
Alignment explanation
Indices: 53865645--53865686 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
53865635 TTACTATAGA
*
53865645 TTTTGTATCTAAAATTAT
1 TTTTATATCTAAAATTAT
*
53865663 TTTTATATCTGAAATTAT
1 TTTTATATCTAAAATTAT
53865681 TTTTAT
1 TTTTAT
53865687 CTCCGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTATATCTAAAATTAT
Found at i:53865694 original size:18 final size:18
Alignment explanation
Indices: 53865656--53865694 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
53865646 TTTGTATCTA
*
53865656 AAATTATTTTTATATCTG
1 AAATTATTTTTATATCCG
*
53865674 AAATTATTTTTATCTCCG
1 AAATTATTTTTATATCCG
53865692 AAA
1 AAA
53865695 AGGAAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (18 bp):
AAATTATTTTTATATCCG
Found at i:53867353 original size:42 final size:42
Alignment explanation
Indices: 53867295--53867459 Score: 167
Period size: 42 Copynumber: 3.9 Consensus size: 42
53867285 ACATTAGGGT
*
53867295 TATGAG-TTTACGTGTAAGACCATATCTGGGATATGGTATC-A
1 TATGAGATTT-CGTGTAAGACCATATCTGGGATATGGCATCGA
* *
53867336 TTATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGA
1 -TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGA
* * * *
53867379 TATGAGA-ATCGTGAAAGAACATAGT-TGGGCTATTGGCATCGA
1 TATGAGATTTCGTGTAAGACCATA-TCTGGGATA-TGGCATCGA
* * * *
53867421 TATGAGACTCCATGTAAGACCATATCTAGGATATGGCAT
1 TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCAT
53867460 TGGTATGATT
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
41 17 0.17
42 64 0.63
43 20 0.20
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:53872049 original size:34 final size:33
Alignment explanation
Indices: 53871984--53872049 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
53871974 CTGTTATTGT
* *
53871984 TACTGAATTGGGCTAGGCCCACACTATTACTGA
1 TACTGAATTAGGCTAGGCCCACACTAATACTGA
*
53872017 TACTGTATTAGGCTAAGGCCCTA-ACTAATACTG
1 TACTGAATTAGGCT-AGGCCC-ACACTAATACTG
53872050 GACTATCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.43
34 15 0.54
35 1 0.04
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (33 bp):
TACTGAATTAGGCTAGGCCCACACTAATACTGA
Found at i:53878066 original size:34 final size:34
Alignment explanation
Indices: 53878018--53878082 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
53878008 TGGATGACAT
*
53878018 CTGTTACTGTTACTGAATTGGGCTAAGGCCCACA
1 CTGTTACTGATACTGAATTGGGCTAAGGCCCACA
*
53878052 CTGTTACTGATACTGTATTGGGCTAAGGCCC
1 CTGTTACTGATACTGAATTGGGCTAAGGCCC
53878083 TAACTGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (34 bp):
CTGTTACTGATACTGAATTGGGCTAAGGCCCACA
Found at i:53880827 original size:28 final size:29
Alignment explanation
Indices: 53880793--53880853 Score: 99
Period size: 28 Copynumber: 2.1 Consensus size: 29
53880783 CACATACCTG
53880793 TATATGGCCCA-CTAGGCCCAA-TCACATT
1 TATATGGCCCATC-AGGCCCAATTCACATT
53880821 TATATGGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCATCAGGCCCAATTCACATT
53880850 TATA
1 TATA
53880854 GTCATGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (29 bp):
TATATGGCCCATCAGGCCCAATTCACATT
Found at i:53881086 original size:16 final size:16
Alignment explanation
Indices: 53881065--53881099 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53881055 GTAGTCAAAC
53881065 TTTTAGCTTTTCAGCA
1 TTTTAGCTTTTCAGCA
*
53881081 TTTTAGCTTTTCGGCA
1 TTTTAGCTTTTCAGCA
53881097 TTT
1 TTT
53881100 CGACTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.54
Consensus pattern (16 bp):
TTTTAGCTTTTCAGCA
Found at i:53891075 original size:52 final size:52
Alignment explanation
Indices: 53890898--53891103 Score: 180
Period size: 52 Copynumber: 3.8 Consensus size: 52
53890888 ATTAGGGTTT
* * * *
53890898 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTC-TACGAGTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT-GTAAGTTCATA--AGGC
* * * * * * * *
53890952 AAGGAAATCATGGAAGACCATGTCAAGAAATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATG-T-AAGTTC-ATAAGGC
* * * *
53891007 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGTAAGTTCATAAGGC
* *
53891059 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT-GTAAGTT
53891104 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
52 39 0.33
53 10 0.08
54 32 0.27
55 36 0.30
57 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.20
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGTAAGTTCATAAGGC
Found at i:53893697 original size:20 final size:20
Alignment explanation
Indices: 53893660--53893697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53893650 CCTATATTTT
*
53893660 GTAAAAATTTTCTAAGTTTC
1 GTAAAAATTTCCTAAGTTTC
*
53893680 GTAAAAATTTCCTGAGTT
1 GTAAAAATTTCCTAAGTT
53893698 ATCGGTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
GTAAAAATTTCCTAAGTTTC
Found at i:53895615 original size:20 final size:20
Alignment explanation
Indices: 53895592--53895629 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53895582 ATTCGAAGCA
53895592 TTACATTAGCCACTGAAGTG
1 TTACATTAGCCACTGAAGTG
53895612 TTACATTAGCCACTGAAG
1 TTACATTAGCCACTGAAG
53895630 CGACTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (20 bp):
TTACATTAGCCACTGAAGTG
Found at i:53901053 original size:49 final size:49
Alignment explanation
Indices: 53900980--53901210 Score: 248
Period size: 49 Copynumber: 4.7 Consensus size: 49
53900970 CTAGTACGCA
* *
53900980 TAGTAGCCTGCA-TTAATACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* * *** * *
53901028 TAGTAGCCTACACTTAGTACTACACACGTGACCTAGCCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCCGGTACACG
* * * * * *
53901078 TAGTAGCCTGCACTTAATACTACACACGTGATCGAAATTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAATTATCCGGTACACG
* * * *
53901129 AAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
*
53901178 TAGTAGCCTGCATTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
53901211 TCACAATAGA
Statistics
Matches: 146, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
48 11 0.08
49 58 0.40
50 41 0.28
51 36 0.25
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:53901125 original size:101 final size:97
Alignment explanation
Indices: 53900980--53901209 Score: 262
Period size: 101 Copynumber: 2.3 Consensus size: 97
53900970 CTAGTACGCA
* * ** *
53900980 TAGTAGCCTGCATTAATACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTACACTTAG
1 TAGTAGCCTGCATTAATACTACACATGTGACAAATTATCCGGTACACAAAATAGCCTACACTTAG
* * * *
53901045 TACTACACACGTGACCTAGCCATCTGATACACG
66 TACTACACACGCGACC-AACAATCCGATACACG
* * * *
53901078 TAGTAGCCTGCACTTAATACTACACACGTGATCGAAATTATCGGGTACGCAAAATAGCCTGCACT
1 TAGTAGCCTGCA-TTAATACTACACATGTGA-C-AAATTATCCGGTACACAAAATAGCCTACACT
* * *
53901143 TAGTACTACACATGCGACCAATAATCCGGTACACG
63 TAGTACTACACACGCGACCAACAATCCGATACACG
*
53901178 TAGTAGCCTGCATTTAGTACTACACATGTGAC
1 TAGTAGCCTGCA-TTAATACTACACATGTGAC
53901210 CTCACAATAG
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
98 12 0.11
99 17 0.15
100 40 0.36
101 41 0.37
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (97 bp):
TAGTAGCCTGCATTAATACTACACATGTGACAAATTATCCGGTACACAAAATAGCCTACACTTAG
TACTACACACGCGACCAACAATCCGATACACG
Found at i:53903264 original size:40 final size:40
Alignment explanation
Indices: 53903169--53903386 Score: 302
Period size: 40 Copynumber: 5.5 Consensus size: 40
53903159 TGGATGATAA
*
53903169 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
53903210 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53903250 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53903290 CCGGGCTAAGTCCCGAAGGCATTGGTGGGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53903330 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
53903369 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53903387 TACTTGGCTT
Statistics
Matches: 164, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
38 15 0.09
39 15 0.09
40 106 0.65
41 24 0.15
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53911478 original size:36 final size:40
Alignment explanation
Indices: 53911267--53911480 Score: 284
Period size: 40 Copynumber: 5.5 Consensus size: 40
53911257 TGGATGATAA
*
53911267 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
53911308 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53911348 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53911388 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53911428 CC-GGCTATGT-CCGAAGGCA-TTG-GCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53911464 CC-GGTTAA-TCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53911481 TACTTTGGGA
Statistics
Matches: 161, Mismatches: 8, Indels: 13
0.88 0.04 0.07
Matches are distributed among these distances:
35 3 0.02
36 24 0.15
37 2 0.01
38 9 0.06
39 8 0.05
40 87 0.54
41 24 0.15
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53911845 original size:38 final size:39
Alignment explanation
Indices: 53911735--53911933 Score: 239
Period size: 38 Copynumber: 5.1 Consensus size: 39
53911725 TGGATGATAA
* * *
53911735 CCGGGCTAAGTCCCGAAGGCATTTTGAGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCA--TTGTGCGAGTTACTA-TAT
*
53911776 CCGGACTAAGTCCCGAAGGCATT-TGGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGT-GCGAGTTACTATAT
*
53911815 CCGGGCTAAGT-CCGAAGGCATTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
53911853 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTATAT
* *
53911893 CCGGGCTATGT-CCG-AGGCATTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTA-CTATAT
53911930 CCGG
1 CCGG
53911934 TTAAATCCGA
Statistics
Matches: 143, Mismatches: 9, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
36 2 0.01
37 16 0.11
38 43 0.30
39 37 0.26
40 25 0.17
41 20 0.14
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:53911865 original size:77 final size:78
Alignment explanation
Indices: 53911735--53911933 Score: 253
Period size: 77 Copynumber: 2.5 Consensus size: 78
53911725 TGGATGATAA
* *
53911735 CCGGGCTAAGTCCCGAAGGCATTTTGAGCTAGTGACTAGT-TCCGGACTAAGTCCCGAAGGCATT
1 CCGGGCTAAGT-CCGAAGGCATTGTGAG--AGTTACTA-TATCCGGACTAAGTCCCGAAGGCATT
*
53911799 TG-GCGAGTTACTATAT
62 GGTGCGAGTTACTATAT
* *
53911815 CCGGGCTAAGTCCGAAGGCATTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTG
1 CCGGGCTAAGTCCGAAGGCATTGTGAGAGTTACTATATCCGGACTAAGTCCCGAAGGCATTGGTG
53911880 CGAGTTACTATAT
66 CGAGTTACTATAT
* * *
53911893 CCGGGCTATGTCCG-AGGCATTGAGCGAG-TAGCTATATCCGG
1 CCGGGCTAAGTCCGAAGGCATTGTGAGAGTTA-CTATATCCGG
53911934 TTAAATCCGA
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
76 3 0.03
77 53 0.49
78 27 0.25
79 14 0.13
80 11 0.10
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (78 bp):
CCGGGCTAAGTCCGAAGGCATTGTGAGAGTTACTATATCCGGACTAAGTCCCGAAGGCATTGGTG
CGAGTTACTATAT
Found at i:53928097 original size:39 final size:39
Alignment explanation
Indices: 53928014--53928106 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 39
53928004 TGAAACCAAT
*
53928014 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
53928052 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGG-CATAA
* *
53928091 TTCCAGCACGTAGCCT
1 TACCAGCACGAAGCCT
53928107 ACGAACCTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
38 14 0.31
39 31 0.69
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:53928173 original size:39 final size:38
Alignment explanation
Indices: 53928081--53928193 Score: 163
Period size: 39 Copynumber: 2.9 Consensus size: 38
53928071 GGACTTTAGC
* * * * *
53928081 CCGGACATATTTCCAGCACGTAGCCTACGAACCTTAAG
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAG
53928119 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAG
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAG
*
53928157 TCCGGATATAATTCCAGCACATAGCCTGCGGACCCTA
1 -CCGGATATAATTCCAGCACATAGCCTACGGACCCTA
53928194 TGTAACACCC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
38 33 0.49
39 35 0.51
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (38 bp):
CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAG
Found at i:53929719 original size:119 final size:120
Alignment explanation
Indices: 53929537--53929759 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
53929527 TCCTCGTTCA
*
53929537 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
53929602 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * * **
53929657 AATGCTTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTT-TGGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
53929719 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
53929760 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 65 0.74
120 19 0.22
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:53929759 original size:40 final size:40
Alignment explanation
Indices: 53929535--53929759 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
53929525 GCTCCTCGTT
* *
53929535 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
53929575 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
53929615 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
53929655 CCAATGCTTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
53929694 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
53929735 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53929760 CATCATTCAA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 29 0.18
40 117 0.73
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:53932788 original size:6 final size:6
Alignment explanation
Indices: 53932770--53932860 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
53932760 AAGAAACATT
* * * *
53932770 ATCAGA A-CTAGA ATCAGA ATCATA ATCAGA ATTAG- GTGACAAA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
53932819 ATCAGA ATCAGT ATCAGGTA A-CAAA ATCAAA ATCAGA ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAG
53932861 TATTAGGTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
5 4 0.06
6 54 0.83
7 5 0.08
8 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:53932788 original size:24 final size:24
Alignment explanation
Indices: 53932755--53932800 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53932745 AACCCATTAC
*
53932755 AGAATAAGAAACATTATCAGAACT
1 AGAATAAGAAACATAATCAGAACT
* *
53932779 AGAATCAGAATCATAATCAGAA
1 AGAATAAGAAACATAATCAGAA
53932801 TTAGGTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (24 bp):
AGAATAAGAAACATAATCAGAACT
Found at i:53932817 original size:31 final size:31
Alignment explanation
Indices: 53932781--53932872 Score: 139
Period size: 31 Copynumber: 3.0 Consensus size: 31
53932771 TCAGAACTAG
* * *
53932781 AATCAGAATCATAATCAGAATTAGGTGACAA
1 AATCAGAATCAGAATCAGTATTAGGTAACAA
*
53932812 AATCAGAATCAGAATCAGTATCAGGTAACAA
1 AATCAGAATCAGAATCAGTATTAGGTAACAA
*
53932843 AATCAAAATCAGAATCAGTATTAGGTAACA
1 AATCAGAATCAGAATCAGTATTAGGTAACA
53932873 TAATAAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGTATTAGGTAACAA
Found at i:53933056 original size:27 final size:26
Alignment explanation
Indices: 53933026--53933085 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
53933016 GCTCAATTAT
*
53933026 CAGATATTGTGAC-AGAGTCACCAGATA
1 CAGATATTGTGACTAG-GCCACCAGA-A
*
53933053 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACTAGGCCACCAGAA
53933079 CAGATAT
1 CAGATAT
53933086 ATATATGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 8 0.27
27 20 0.67
28 2 0.07
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACTAGGCCACCAGAA
Done.