Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 45 of 141
Found at i:13612937 original size:20 final size:20
Alignment explanation
Indices: 13612914--13612964 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
13612904 CCCCTGTATA
13612914 CACTTCAGTG-TCTCTATTTG
1 CACTTCAGTGCTC-CTATTTG
* *
13612934 CACTACTGTGCTCCTATTTG
1 CACTTCAGTGCTCCTATTTG
13612954 CACTTCAGTGC
1 CACTTCAGTGC
13612965 CCTTATATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (20 bp):
CACTTCAGTGCTCCTATTTG
Found at i:13613044 original size:20 final size:20
Alignment explanation
Indices: 13613021--13613059 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13613011 TCACACTTCG
*
13613021 GTGCCCCTGACTGCACGTAT
1 GTGCACCTGACTGCACGTAT
13613041 GTGCACCTGACTGCACGTA
1 GTGCACCTGACTGCACGTA
13613060 ATTACCCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (20 bp):
GTGCACCTGACTGCACGTAT
Found at i:13613069 original size:20 final size:20
Alignment explanation
Indices: 13613024--13613069 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13613014 CACTTCGGTG
*
13613024 CCCCTGACTGCACGTATGTG
1 CCCCTGACTGCACGTATGTA
*
13613044 CACCTGACTGCACGTAAT-TA
1 CCCCTGACTGCACGT-ATGTA
13613064 CCCCTG
1 CCCCTG
13613070 TTCTGCATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.24
Consensus pattern (20 bp):
CCCCTGACTGCACGTATGTA
Found at i:13619136 original size:11 final size:11
Alignment explanation
Indices: 13619120--13619171 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 11
13619110 AAAATTCAAA
13619120 TATTAAAAATT
1 TATTAAAAATT
13619131 TATTAAAAA-T
1 TATTAAAAATT
13619141 TA--AAAAATT
1 TATTAAAAATT
*
13619150 TA-TAAATA-T
1 TATTAAAAATT
13619159 T-TTAAAAATT
1 TATTAAAAATT
13619169 TAT
1 TAT
13619172 AAATGTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
8 5 0.15
9 10 0.29
10 9 0.26
11 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAAAATT
Found at i:13619144 original size:18 final size:20
Alignment explanation
Indices: 13619119--13619199 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 20
13619109 AAAAATTCAA
13619119 ATATTAAAAATTTATTAAA-
1 ATATTAAAAATTTATTAAAT
13619138 A-ATTAAAAAATTTA-TAAAT
1 ATATT-AAAAATTTATTAAAT
*
13619157 ATTTTAAAAATTTA-TAAAT
1 ATATTAAAAATTTATTAAAT
* ** *
13619176 GTCGTAAAAATTTATAAAAT
1 ATATTAAAAATTTATTAAAT
13619196 ATAT
1 ATAT
13619200 AGAAATATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 7 0.14
19 36 0.72
20 7 0.14
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATTAAAAATTTATTAAAT
Found at i:13619205 original size:19 final size:19
Alignment explanation
Indices: 13619121--13619231 Score: 63
Period size: 19 Copynumber: 5.9 Consensus size: 19
13619111 AAATTCAAAT
*
13619121 ATTA-AAAATTTATTAAAA
1 ATTATAAAATTTATAAAAA
* *
13619139 ATTAAAAAATTTAT-AAAT
1 ATTATAAAATTTATAAAAA
* *
13619157 ATTTTAAAAATTTAT-AAAT
1 ATTAT-AAAATTTATAAAAA
* *
13619176 GTCGTA-AAAATTTATAAAAT
1 AT--TATAAAATTTATAAAAA
*
13619196 A-TATAGAAATATA-AAAAA
1 ATTATA-AAATTTATAAAAA
13619214 ATTATAAAATTTTATAAA
1 ATTATAAAA-TTTATAAA
13619232 GTCATAAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.03
18 19 0.26
19 45 0.61
20 7 0.09
21 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTATAAAATTTATAAAAA
Found at i:13619498 original size:38 final size:37
Alignment explanation
Indices: 13619429--13619500 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
13619419 GGGTTATTAA
* * **
13619429 TTTTTTATGATTTTTATAAAATTTTACAATTTTTTAT
1 TTTTTTACGATTTTTAAAAAAAATTACAATTTTTTAT
*
13619466 TTTTTTACGATTTTTACAAAAAAATTATAATTTTT
1 TTTTTTACGATTTTTA-AAAAAAATTACAATTTTT
13619501 AACAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 15 0.52
38 14 0.48
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (37 bp):
TTTTTTACGATTTTTAAAAAAAATTACAATTTTTTAT
Found at i:13619555 original size:45 final size:45
Alignment explanation
Indices: 13619461--13619567 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 45
13619451 TTTACAATTT
*
13619461 TTTATTTTTTTACGATTTTTACAAAAAAATTATAATTTTTAACAAAA
1 TTTATTTTTTTA-TATTTTTACAAAAAAATTATAATTTTT-ACAAAA
** *
13619508 TTTATTTTTTTATATTTTTA-TTAAAATTTAATAATTTTT-CTAAAA
1 TTTATTTTTTTATATTTTTACAAAAAAATT-ATAATTTTTAC-AAAA
13619553 TTTATTATTTATTAT
1 TTTATT-TTT-TTAT
13619568 TTTCTAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
44 1 0.02
45 16 0.31
46 19 0.37
47 16 0.31
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (45 bp):
TTTATTTTTTTATATTTTTACAAAAAAATTATAATTTTTACAAAA
Found at i:13619751 original size:91 final size:89
Alignment explanation
Indices: 13619589--13619783 Score: 223
Period size: 91 Copynumber: 2.2 Consensus size: 89
13619579 TAATAAGAGC
* * * * *
13619589 AGGGGCTTAATTGC-TTTTTTGAAACAATTTGAGGGTCTTTTTTATGCATTTTGAAAGTTTAAGT
1 AGGGGCTTAATTGCTTTTTTTGAAACAACTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAGT
* ** *
13619653 ACCCAATTGAGTGGGGGAAAAAAAGT
66 ACCCAATTAAGT--GCAAAAAAAAGG
* *
13619679 AGGGGCTTAATTGCTTTTTTTGGAGA-AGCTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTT-GAAACAACTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAG
* *
13619743 TGCTCAATTAAGTGCAAAAAAAAGG
65 TACCCAATTAAGTGCAAAAAAAAGG
*
13619768 AGGGCCTTAATTGCTT
1 AGGGGCTTAATTGCTT
13619784 CTTCTTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
89 24 0.27
90 14 0.16
91 48 0.54
92 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTTGAAACAACTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAGT
ACCCAATTAAGTGCAAAAAAAAGG
Found at i:13626065 original size:51 final size:50
Alignment explanation
Indices: 13625902--13626083 Score: 145
Period size: 51 Copynumber: 3.6 Consensus size: 50
13625892 GAAGTTGCTA
* *
13625902 GGTCACGTGTGTAGTACTATGTGCAGGCTAATACATGTACTGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTAATACATGTAC-GG-ATGAAAAT
* * * *** ** ***
13625952 GGTCGCATGTCTAGTACTATGTGCAGGCTACTATGCGTACCAAAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTAATACATGTA-CGGATGAAAAT
* * *
13626002 CGATCACGTGTGTAGTACTATGTGCAGGCTATTACATGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTAATACATGTA-CGGATGAAAAT
*
13626054 GGTCACATGTGTAGTACTATGTGTAGGCTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTA
13626084 CTATGTGAAC
Statistics
Matches: 98, Mismatches: 29, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
49 2 0.02
50 32 0.33
51 62 0.63
52 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTAATACATGTACGGATGAAAAT
Found at i:13628960 original size:54 final size:54
Alignment explanation
Indices: 13628876--13629085 Score: 224
Period size: 54 Copynumber: 3.9 Consensus size: 54
13628866 AACACAGCCG
* * * * * * *
13628876 TGTGTTAGGCCCTATGCCAGACCGTGTAACTCTCTAACTTGAGTTAGACGGGTA
1 TGTGTCAGGCCATGTGCTAGACCGTGTAACTCTCTAACTTGAGTCACACGGGCA
* * * *
13628930 TGTGTCAGGCCATGTGCTAGACCGTATAACTCTTTGACTTGAGTCACACGAGCA
1 TGTGTCAGGCCATGTGCTAGACCGTGTAACTCTCTAACTTGAGTCACACGGGCA
* * * * * *
13628984 TGTGTCAGGCCGTGTGTTAGACTGTGTAACTCTTTGACTTGAGTCACACGGGCG
1 TGTGTCAGGCCATGTGCTAGACCGTGTAACTCTCTAACTTGAGTCACACGGGCA
** *
13629038 TGTGTCAGGCCATGTG-TCAGACTATCTAACTCTCTAACTTGAGTCACA
1 TGTGTCAGGCCATGTGCT-AGACCGTGTAACTCTCTAACTTGAGTCACA
13629086 TGACTATGTG
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 1 0.01
54 132 0.99
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (54 bp):
TGTGTCAGGCCATGTGCTAGACCGTGTAACTCTCTAACTTGAGTCACACGGGCA
Found at i:13629068 original size:108 final size:108
Alignment explanation
Indices: 13628894--13629107 Score: 270
Period size: 108 Copynumber: 2.0 Consensus size: 108
13628884 GCCCTATGCC
* * * *
13628894 AGACCGTGTAACTCTCTAACTTGAGTTAGACGGGTATGTGTCAGGCCATGTGCTAGACCGTATAA
1 AGACCGTGTAACTCTCTAACTTGAGTCACACGGGCATGTGTCAGGCCATGTGCTAGACCATATAA
* *
13628959 CTCTTTGACTTGAGTCACACGAGC-ATGTGTCAGGCCGTGTGTT
66 CTCTCTAACTTGAGTCACACGA-CTATGTGTCAGGCCGTGTGTT
* * * * * *
13629002 AGACTGTGTAACTCTTTGACTTGAGTCACACGGGCGTGTGTCAGGCCATGTG-TCAGACTATCTA
1 AGACCGTGTAACTCTCTAACTTGAGTCACACGGGCATGTGTCAGGCCATGTGCT-AGACCATATA
* *
13629066 ACTCTCTAACTTGAGTCACATGACTATGTGTTAGGCCGTGTG
65 ACTCTCTAACTTGAGTCACACGACTATGTGTCAGGCCGTGTG
13629108 ACAATCCGTG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 2 0.02
108 88 0.98
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (108 bp):
AGACCGTGTAACTCTCTAACTTGAGTCACACGGGCATGTGTCAGGCCATGTGCTAGACCATATAA
CTCTCTAACTTGAGTCACACGACTATGTGTCAGGCCGTGTGTT
Found at i:13629096 original size:54 final size:53
Alignment explanation
Indices: 13628893--13629107 Score: 189
Period size: 54 Copynumber: 4.0 Consensus size: 53
13628883 GGCCCTATGC
* * * * **
13628893 CAGACCGTGTAACTCTCTAACTTGAGTTAGACGGGTATGTGTCAGGCCATGTG-
1 CAGACTGTATAACTCTCTAACTTGAGTCACAC-GACATGTGTCAGGCCATGTGT
* * * *
13628946 CTAGACCGTATAACTCTTTGACTTGAGTCACACGAGCATGTGTCAGGCCGTGTGT
1 C-AGACTGTATAACTCTCTAACTTGAGTCACACGA-CATGTGTCAGGCCATGTGT
* * * * * *
13629001 TAGACTGTGTAACTCTTTGACTTGAGTCACACGGGCGTGTGTCAGGCCATGTGT
1 CAGACTGTATAACTCTCTAACTTGAGTCACAC-GACATGTGTCAGGCCATGTGT
* * * * *
13629055 CAGACTATCTAACTCTCTAACTTGAGTCACATGACTATGTGTTAGGCCGTGTG
1 CAGACTGTATAACTCTCTAACTTGAGTCACACGAC-ATGTGTCAGGCCATGTG
13629108 ACAATCCGTG
Statistics
Matches: 133, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
53 4 0.03
54 128 0.96
55 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (53 bp):
CAGACTGTATAACTCTCTAACTTGAGTCACACGACATGTGTCAGGCCATGTGT
Found at i:13639052 original size:54 final size:52
Alignment explanation
Indices: 13638994--13639140 Score: 154
Period size: 52 Copynumber: 2.8 Consensus size: 52
13638984 CATGTGCTAG
* *
13638994 GCTGTGTGTCAAG-CCGTGTAACTCTCTGGCTTGAGTCACACAGATGTGTGTCAA
1 GCTGTGTG-CAAGACCGTGTAACTCTCTGACTTGAGTCACACA-A-GCGTGTCAA
* * * * *
13639048 GCTGTGCGCTAGACCGAGTAACTCTCTGACTGGAGTCCCACAAGCGTGTCAA
1 GCTGTGTGCAAGACCGTGTAACTCTCTGACTTGAGTCACACAAGCGTGTCAA
* * *
13639100 GCCT-TGTGCCAGACCGTGTAACTCTTTTACTTGAGTCACAC
1 G-CTGTGTGCAAGACCGTGTAACTCTCTGACTTGAGTCACAC
13639141 GACAATGTGA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
52 39 0.51
53 6 0.08
54 32 0.42
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (52 bp):
GCTGTGTGCAAGACCGTGTAACTCTCTGACTTGAGTCACACAAGCGTGTCAA
Found at i:13640751 original size:13 final size:13
Alignment explanation
Indices: 13640733--13640794 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
13640723 TTCTTCATTA
13640733 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
13640746 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
13640759 -TTGTAGAAAAGTA
1 CTT-TTGAAAAGTG
*
13640772 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
13640785 CTTTTGAAAA
1 CTTTTGAAAA
13640795 ATTTGAGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 2 0.05
13 37 0.90
14 2 0.05
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:13641046 original size:19 final size:19
Alignment explanation
Indices: 13641022--13641075 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
13641012 AATTATTTAT
13641022 TAAATT-TAATTAGAATATA
1 TAAATTATAATTA-AATATA
* *
13641041 TAAATTATATTTAAATATT
1 TAAATTATAATTAAATATA
13641060 TAAA-TAT--TTAAATATA
1 TAAATTATAATTAAATATA
13641076 ATAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.26
18 3 0.10
19 15 0.48
20 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAATTATAATTAAATATA
Found at i:13641060 original size:8 final size:8
Alignment explanation
Indices: 13641047--13641074 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
13641037 TATATAAATT
13641047 ATATTTAA
1 ATATTTAA
13641055 ATATTTAA
1 ATATTTAA
13641063 ATATTTAA
1 ATATTTAA
13641071 ATAT
1 ATAT
13641075 AATAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTTAA
Found at i:13641089 original size:29 final size:27
Alignment explanation
Indices: 13641035--13641089 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
13641025 ATTTAATTAG
*
13641035 AATATATAAATTATATTTAAATATTTA
1 AATATATAAATTATAATTAAATATTTA
*
13641062 AATATTTAAATATAATAATTAAATATTT
1 AATATATAAAT-T-ATAATTAAATATTT
13641090 GTAGTTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
29 13 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATATAAATTATAATTAAATATTTA
Found at i:13641937 original size:16 final size:16
Alignment explanation
Indices: 13641916--13641949 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
13641906 AAAACACTTG
13641916 CAATAAGGATGAGAAT
1 CAATAAGGATGAGAAT
13641932 CAATAAGGATGAGAAT
1 CAATAAGGATGAGAAT
13641948 CA
1 CA
13641950 CACAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.18
Consensus pattern (16 bp):
CAATAAGGATGAGAAT
Found at i:13643752 original size:29 final size:29
Alignment explanation
Indices: 13643719--13643775 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
13643709 CTCCAATTTC
*
13643719 ACCAGCAGAGGGGAAAGAACGTTTGGGGA
1 ACCAGCAGAGGGGAAAAAACGTTTGGGGA
13643748 ACCAGCAGAGGGGAAAAAACGTTTGGGG
1 ACCAGCAGAGGGGAAAAAACGTTTGGGG
13643776 GAGAAGACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.40, T:0.11
Consensus pattern (29 bp):
ACCAGCAGAGGGGAAAAAACGTTTGGGGA
Found at i:13651601 original size:23 final size:23
Alignment explanation
Indices: 13651571--13651614 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
13651561 ACTGCAGCGA
13651571 AGTGCCCCTAATTTATTTACTGG
1 AGTGCCCCTAATTTATTTACTGG
13651594 AGTGCCCCTAATTTATTTACT
1 AGTGCCCCTAATTTATTTACT
13651615 TTCTATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (23 bp):
AGTGCCCCTAATTTATTTACTGG
Found at i:13662691 original size:14 final size:15
Alignment explanation
Indices: 13662666--13662702 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
13662656 CCTATAGAAA
13662666 TTAAATTAAACTAAG
1 TTAAATTAAACTAAG
13662681 TTAAA-TAAACTAA-
1 TTAAATTAAACTAAG
*
13662694 TCAAATTAA
1 TTAAATTAA
13662703 TTAAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (15 bp):
TTAAATTAAACTAAG
Found at i:13664494 original size:26 final size:26
Alignment explanation
Indices: 13664439--13664494 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
13664429 CGAGAGGACA
* * * *
13664439 GCAAGGCGAGCTCGCAGGCCTTGCTT
1 GCAAAGCGAGCTCACAGGACTTGCTC
13664465 GCAAAGCGAGCTCACA-GACTTAGCTC
1 GCAAAGCGAGCTCACAGGACTT-GCTC
13664491 GCAA
1 GCAA
13664495 TGTAAGGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.25, C:0.30, G:0.29, T:0.16
Consensus pattern (26 bp):
GCAAAGCGAGCTCACAGGACTTGCTC
Found at i:13672555 original size:78 final size:78
Alignment explanation
Indices: 13672413--13672556 Score: 189
Period size: 78 Copynumber: 1.8 Consensus size: 78
13672403 GTGTTGCTAT
* * * *
13672413 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACCATTACGAATTCAGTCCTCATTAACCC
1 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTACAAATTCACTCCTCATCAACCC
13672478 CGAGTGTCACTGC
66 CGAGTGTCACTGC
* * * * * **
13672491 CTTATCAATGGAAGCTAAGCCAATTAAGTTAGAATCACAATTGCAAATTCACTCCTTGTCAACCC
1 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTACAAATTCACTCCTCATCAACCC
13672556 C
66 C
13672557 TTGGCTGATA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
78 55 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (78 bp):
CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTACAAATTCACTCCTCATCAACCC
CGAGTGTCACTGC
Found at i:13674057 original size:16 final size:16
Alignment explanation
Indices: 13674032--13674067 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
13674022 TTAAATTAAA
13674032 TTAA-ATTTTTTATTT
1 TTAATATTTTTTATTT
13674047 TTAATATTTTTTATTT
1 TTAATATTTTTTATTT
13674063 TTAAT
1 TTAAT
13674068 TTTCCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATATTTTTTATTT
Found at i:13677075 original size:21 final size:22
Alignment explanation
Indices: 13677049--13677091 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13677039 GAATTGAATT
13677049 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
13677070 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
13677092 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:13677090 original size:20 final size:21
Alignment explanation
Indices: 13677049--13677092 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
13677039 GAATTGAATT
*
13677049 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
13677070 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
13677090 TAA
1 TAA
13677093 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:13677119 original size:60 final size:62
Alignment explanation
Indices: 13677043--13677198 Score: 158
Period size: 65 Copynumber: 2.5 Consensus size: 62
13677033 TTTCATGAAT
* * * *
13677043 TGAATTTAAAGTTATGAATTATATATATAAAGTTTGAAT-G-TATGATA-T-AAGTTCTTTGAGC
1 TGAATTTAATG-TATGAATTACATACATAAAGTTCGAATAGATAT-ATATTCAAGTTC-TTGAGC
**
13677104 TGAATTTAATGTATGAATTTTACATACATATGGTTCGAATAGATATATATTTCAAGTTCTTGAGC
1 TGAATTTAATGTATGAA--TTACATACATAAAGTTCGAATAGATATATA-TTCAAGTTCTTGAGC
13677169 TGAATTTAATGTATGAATTTCACATACATA
1 TGAATTTAATGTATGAA-TT-ACATACATA
13677199 TGTGGTTCGA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
60 6 0.07
61 10 0.12
62 16 0.20
63 4 0.05
64 6 0.07
65 33 0.41
66 6 0.07
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (62 bp):
TGAATTTAATGTATGAATTACATACATAAAGTTCGAATAGATATATATTCAAGTTCTTGAGC
Found at i:13677242 original size:65 final size:63
Alignment explanation
Indices: 13677086--13677245 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 63
13677076 TTGAATGTAT
* *
13677086 GATAT-AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGGTTCGAATAGATA
1 GATATCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATATGGTTCGAATA-ATA
* *
13677149 TATATTTCAAGTTC-TTGAGCTGAATTTAATGTATGAATTTCACATACATATGTGGTTCGAAT-A
1 GATA--TCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATA--TGGTTCGAATAA
13677212 TA
62 TA
*
13677214 GGCTA-CAAATTCTTTGAGCTGAATTTTAATGT
1 -GATATCAAATTCTTTGAGCTGAA-TTTAATGT
13677246 TGTAAATTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 14
0.82 0.05 0.14
Matches are distributed among these distances:
63 9 0.11
64 10 0.12
65 47 0.56
66 8 0.10
67 10 0.12
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (63 bp):
GATATCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATATGGTTCGAATAATA
Found at i:13677445 original size:41 final size:41
Alignment explanation
Indices: 13677388--13677544 Score: 174
Period size: 41 Copynumber: 3.8 Consensus size: 41
13677378 TTTGAGATTT
* * * * *
13677388 TCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGGATTACA
1 TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
*
13677429 TCAGGCTTTATGCCTAGCAGGC-TCAGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTGA-TGCCGGTGAATTATA
* * * *
13677470 TCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTGAATTATA
* *
13677511 TCAGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
13677545 TTTTATACAA
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.04
41 92 0.95
43 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
Found at i:13677558 original size:41 final size:40
Alignment explanation
Indices: 13677389--13677563 Score: 140
Period size: 41 Copynumber: 4.3 Consensus size: 40
13677379 TTGAGATTTT
* * * * *
13677389 CAGGCTTAATGCCTAGCAGACTTGATGTCGGTGGA-TTACA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGT-GATTTATA
* *
13677429 TCAGGCTTTATGCCTAGCAGGC-TCAGTGCCGGTGAATTATA
1 -CAGGCTTTATGCCTAGCAGGCTTTA-TGCCGGTGATTTATA
* * * *
13677470 TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTAT-
1 -CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG--ATTTATA
* *
13677512 CAGGCTTTGTGCCTAGCAGGCTTTATGCCGGTGTTTTATA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGATTTATA
*
13677552 CAAGGCTCTATG
1 C-AGGCTTTATG
13677564 TTCTATAAAT
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 4 0.04
40 5 0.05
41 94 0.87
42 1 0.01
43 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (40 bp):
CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGATTTATA
Found at i:13680007 original size:49 final size:49
Alignment explanation
Indices: 13679950--13680053 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
13679940 TCATGTGTTA
*** *
13679950 TAATTTTATAAAGTGTTGTGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
13679999 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
13680048 TAATTT
1 TAATTT
13680054 GTTTTTTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:13681478 original size:21 final size:21
Alignment explanation
Indices: 13681437--13681479 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
13681427 AATAAAGTAG
*
13681437 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
13681458 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
13681479 A
1 A
13681480 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:13681559 original size:26 final size:27
Alignment explanation
Indices: 13681496--13681688 Score: 88
Period size: 28 Copynumber: 6.7 Consensus size: 27
13681486 TATAAGAATA
* *
13681496 ATTATTTTAAATTTTATTAAATTATAT
1 ATTATTTTAAATTATATTTAATTATAT
*
13681523 ATTTTTATTAAATTATATTTAA-TA-AT
1 ATTATT-TTAAATTATATTTAATTATAT
13681549 GATTATTTTAAATTATATTTTATAGTATTATAT
1 -ATTATTTTAAATTATA--TT-TA--ATTATAT
* * * * * *
13681582 ATTATGATTT-TAGTAAATTCATATAAGAAT
1 ATTAT--TTTAAATTATATTTA-ATTA-TAT
* *
13681612 ATTTATTATTAAGAATTTTATTAAATTATAT
1 A-TTATT-TT-A-AATTATATTTAATTATAT
* *
13681643 ATTTTTATTAAATTATATTTAATAATA-
1 ATTATT-TTAAATTATATTTAATTATAT
*
13681670 ATTATGTTAAATTATATTT
1 ATTATTTTAAATTATATTT
13681689 TATAGTATTA
Statistics
Matches: 126, Mismatches: 23, Indels: 35
0.68 0.12 0.19
Matches are distributed among these distances:
26 25 0.20
27 16 0.13
28 29 0.23
29 8 0.06
30 13 0.10
31 10 0.08
32 10 0.08
33 12 0.10
34 3 0.02
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTATTTTAAATTATATTTAATTATAT
Found at i:13681581 original size:41 final size:41
Alignment explanation
Indices: 13681506--13681787 Score: 134
Period size: 38 Copynumber: 7.0 Consensus size: 41
13681496 ATTATTTTAA
* *
13681506 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATG
1 ATTTTATTAAATTATAT-TTTATAGT--ATTATATTTAATAATG
*
13681550 ATTATT-TTAAATTATATTTTATAGTATTATA--T-ATTATG
1 ATT-TTATTAAATTATATTTTATAGTATTATATTTAATAATG
* * * * *
13681588 ATTTTAGTAAATTCATA--TAAGAATATT-TA-TTATTAA-G
1 ATTTTATTAAATT-ATATTTTATAGTATTATATTTAATAATG
* * *
13681625 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
1 -ATTTTATTAAATTATAT-TTTATAGT--ATTATATTTAATAATG
* * *
13681670 ATTATGTTAAATTATATTTTATAGTATTATA--T-ATTATG
1 ATTTTATTAAATTATATTTTATAGTATTATATTTAATAATG
* *
13681708 ATTTTAGTAAATTCATA---TA-AG-A--ATATTTAATATTAAG
1 ATTTTATTAAATT-ATATTTTATAGTATTATATTTAATA--ATG
* *
13681745 AATTTTATTAAATTATATTTTTTATTAAATTATATTTAATAAT
1 -ATTTTATTAAATTATATTTTATAGT--ATTATATTTAATAAT
13681788 AATTATGTTA
Statistics
Matches: 177, Mismatches: 31, Indels: 60
0.66 0.12 0.22
Matches are distributed among these distances:
32 3 0.02
34 2 0.01
35 4 0.02
36 4 0.02
37 19 0.11
38 54 0.31
39 8 0.05
40 4 0.02
41 13 0.07
42 3 0.02
43 14 0.08
44 37 0.21
45 2 0.01
46 10 0.06
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (41 bp):
ATTTTATTAAATTATATTTTATAGTATTATATTTAATAATG
Found at i:13681583 original size:59 final size:61
Alignment explanation
Indices: 13681505--13681793 Score: 231
Period size: 59 Copynumber: 4.8 Consensus size: 61
13681495 AATTATTTTA
13681505 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTATTTTAAATT-A-
1 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTATTTTAAATTAAG
* * * * ** * * * * *
13681564 TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCATATAA-GAATA-TTTATTATTAAG
1 AATTTTATTA-AATTATATATTTTTATTAAATTATATTTA-ATAATGATTATTTTA-AATTAAG
* *
13681625 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATT-A-
1 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTATTTTAAATTAAG
* * * * ** * * * *
13681684 TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCATATAA-GAATA-TTTAATATTAAG
1 AATTTTATTA-AATTATATATTTTTATTAAATTATATTTA-ATAATGATTATTTTAA-ATTAAG
*
13681745 AATTTTATTAAATTATAT-TTTTTATTAAATTATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTAT
13681794 GTTACAATAT
Statistics
Matches: 167, Mismatches: 47, Indels: 30
0.68 0.19 0.12
Matches are distributed among these distances:
58 12 0.07
59 71 0.43
60 31 0.19
61 46 0.28
62 7 0.04
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (61 bp):
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTATTTTAAATTAAG
Found at i:13681633 original size:15 final size:16
Alignment explanation
Indices: 13681605--13681634 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13681595 TAAATTCATA
13681605 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
13681621 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
13681635 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:13681674 original size:120 final size:120
Alignment explanation
Indices: 13681444--13681797 Score: 637
Period size: 120 Copynumber: 3.0 Consensus size: 120
13681434 TAGATTATAT
*
13681444 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTATT-TT-A-
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
* *
13681505 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATGATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
13681560 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
13681625 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
*
13681680 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
13681745 AATTTTATTAAATTATAT-TTTTTATTAAATTATATTTAATAATAATTATGTTA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTA
13681798 CAATATGATT
Statistics
Matches: 230, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
116 5 0.02
117 52 0.23
118 2 0.01
119 36 0.16
120 135 0.59
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:13681767 original size:17 final size:17
Alignment explanation
Indices: 13681747--13681781 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13681737 ATATTAAGAA
13681747 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
13681764 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
13681781 T
1 T
13681782 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:13685219 original size:33 final size:33
Alignment explanation
Indices: 13685177--13685241 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
13685167 GTAGTAAATT
13685177 AAATATTTTAATATAATTTAATATAAAAATAAA
1 AAATATTTTAATATAATTTAATATAAAAATAAA
*
13685210 AAATCTTTTAATATAATTTAATATAAAAATAA
1 AAATATTTTAATATAATTTAATATAAAAATAA
13685242 TTATATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (33 bp):
AAATATTTTAATATAATTTAATATAAAAATAAA
Found at i:13685350 original size:61 final size:59
Alignment explanation
Indices: 13685215--13685362 Score: 158
Period size: 61 Copynumber: 2.5 Consensus size: 59
13685205 ATAAAAAATC
* * ***
13685215 TTTTAATATAATT-TAATATAAAAATAATTATATTAAGAATGTTATTAAATTATATATTAT
1 TTTTATTA-AATTATAAT-TAATAATAATTATATTAAGAATAAGATTAAATTATATATTAT
*
13685275 TTTTATTAAATTAT-ATGTAATAATAATTATATTAA-AATAAGATTAAATTATTTATTTTTAT
1 TTTTATTAAATTATAAT-TAATAATAATTATATTAAGAATAAGATTAAATTA--TA-TATTAT
*
13685336 TTTTATTAACTTATAATTAATAATAAT
1 TTTTATTAAATTATAATTAATAATAAT
13685363 GTTCTTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 12 0.16
59 23 0.31
60 10 0.13
61 28 0.37
62 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (59 bp):
TTTTATTAAATTATAATTAATAATAATTATATTAAGAATAAGATTAAATTATATATTAT
Found at i:13692227 original size:5 final size:5
Alignment explanation
Indices: 13692217--13692265 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
13692207 TTGCCCTATT
13692217 TTTTA TTTTA TTTTA TTTTA --TTA TTTTAA TTTTA -TTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA
13692264 TT
1 TT
13692266 CCTATGCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.08
4 8 0.20
5 24 0.60
6 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:13692242 original size:13 final size:13
Alignment explanation
Indices: 13692224--13692265 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
13692214 ATTTTTTATT
13692224 TTATTTTATTTTA
1 TTATTTTATTTTA
13692237 TTATTTTAATTTTA
1 TTATTTT-ATTTTA
13692251 TT-TATTTATTTTA
1 TTAT-TTTATTTTA
13692264 TT
1 TT
13692266 CCTATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:13692242 original size:18 final size:18
Alignment explanation
Indices: 13692213--13692265 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
13692203 CTCCTTGCCC
13692213 TATTTT-TTATTTTATTT
1 TATTTTATTATTTTATTT
13692230 TATTTTATTATTTTAATTT
1 TATTTTATTATTTT-ATTT
13692249 TA-TTTATTTATTTTATT
1 TATTTTA-TTATTTTATT
13692266 CCTATGCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.18
18 14 0.42
19 13 0.39
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTATTATTTTATTT
Found at i:13692248 original size:24 final size:21
Alignment explanation
Indices: 13692213--13692262 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
13692203 CTCCTTGCCC
13692213 TATTTTTTATTTTATTTTATTT
1 TATTTTTTATTTTA-TTTATTT
13692235 TATTATTTTAATTTTATTTA-TT
1 TATT-TTTT-ATTTTATTTATTT
13692257 TATTTT
1 TATTTT
13692263 ATTCCTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.08
22 10 0.38
23 8 0.31
24 6 0.23
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTTTATTTTATTTATTT
Found at i:13692250 original size:19 final size:19
Alignment explanation
Indices: 13692213--13692263 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
13692203 CTCCTTGCCC
13692213 TATTTT-TTATTTT-ATTT
1 TATTTTATTATTTTAATTT
13692230 TATTTTATTATTTTAATTT
1 TATTTTATTATTTTAATTT
13692249 TA-TTTATTTATTTTA
1 TATTTTA-TTATTTTA
13692264 TTCCTATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.19
18 11 0.35
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTATTATTTTAATTT
Found at i:13692423 original size:3 final size:3
Alignment explanation
Indices: 13692415--13692470 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
13692405 TTTTATCTGT
* * *
13692415 TTA TTA TTA CTA TTA TTA -TC TTA TTA TTA TT- TT- TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
13692460 TTA TGA TTA TT
1 TTA TTA TTA TT
13692471 TCATTATTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13694081 original size:6 final size:6
Alignment explanation
Indices: 13693998--13694086 Score: 72
Period size: 6 Copynumber: 14.5 Consensus size: 6
13693988 ATTTTATTTG
* * * * * *
13693998 TTTTCT TTTTAG TTTTAG TTTTAG TTTTAG TTTTA- TTTTAT GTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
13694045 GTTTAT GTTTAT TTTTAT TTTTAGTT GTTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT TTTTAT TTT
13694087 CTTAGGCTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
5 5 0.07
6 63 0.84
7 1 0.01
8 1 0.01
9 5 0.07
ACGTcount: A:0.15, C:0.01, G:0.10, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:13702855 original size:23 final size:24
Alignment explanation
Indices: 13702799--13702856 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
13702789 ACCACAATGT
* *
13702799 AATTCATTCTAGCACTTTGGTGCG
1 AATTCATTCTGGCACTATGGTGCG
* *
13702823 AATTCTTTCTGGCACTATGGTGTG
1 AATTCATTCTGGCACTATGGTGCG
13702847 -ATTCATTCTG
1 AATTCATTCTG
13702857 TGGAGTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (24 bp):
AATTCATTCTGGCACTATGGTGCG
Found at i:13706574 original size:16 final size:17
Alignment explanation
Indices: 13706553--13706584 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13706543 AAATATACTA
13706553 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
13706569 TCACATAACTTCATAT
1 TCACATAACTTCATAT
13706585 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:13706811 original size:43 final size:43
Alignment explanation
Indices: 13706745--13706915 Score: 208
Period size: 43 Copynumber: 4.0 Consensus size: 43
13706735 GAGTCGTACA
* * *
13706745 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
* *
13706788 ATGCC-ACTGTCCCAGACAG-GGTCTTACAC-AAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACATATCG
* * *
13706829 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATA-TCG
13706872 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
13706915 A
1 A
13706916 AATCCTATGT
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
41 27 0.25
42 16 0.15
43 64 0.59
44 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
Found at i:13706886 original size:84 final size:84
Alignment explanation
Indices: 13706745--13706900 Score: 228
Period size: 84 Copynumber: 1.9 Consensus size: 84
13706735 GAGTCGTACA
* * *
13706745 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGAC-GTGG
13706809 TCTTACACAAATCAAATACG
65 TCTTACACAAATCAAATACG
*
13706829 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ACTGTCCCAGACGTG
13706892 GTCTTACAC
64 GTCTTACAC
13706901 GAAAACACAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 61 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACGTGGT
CTTACACAAATCAAATACG
Found at i:13712576 original size:27 final size:26
Alignment explanation
Indices: 13712558--13712636 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 26
13712548 AAAATAACCA
13712558 AAATACCCCTATAGGGTAAAATGACTG
1 AAATACCCC-ATAGGGTAAAATGACTG
*
13712585 AAATACCTCCATAGGATAAAATGACTG
1 AAATACC-CCATAGGGTAAAATGACTG
*
13712612 AAACACCCCCATAGGGTAAAATGAC
1 AAATA-CCCCATAGGGTAAAATGAC
13712637 CGAATAACTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
27 43 0.91
28 4 0.09
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACTG
Found at i:13712687 original size:27 final size:27
Alignment explanation
Indices: 13712646--13712735 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
13712636 CCGAATAACT
* *
13712646 GAAATATCCCTATAAGGTAAAATGACC
1 GAAATACCCCCATAAGGTAAAATGACC
* **
13712673 TAAATACCCCCATAAGGTAAAATGATG
1 GAAATACCCCCATAAGGTAAAATGACC
* * * *
13712700 GGAATACCCTCTTAGGGTAAAATGACC
1 GAAATACCCCCATAAGGTAAAATGACC
13712727 GAAATACCC
1 GAAATACCC
13712736 TCAGGATAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (27 bp):
GAAATACCCCCATAAGGTAAAATGACC
Found at i:13712716 original size:89 final size:89
Alignment explanation
Indices: 13712558--13712729 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 89
13712548 AAAATAACCA
* *
13712558 AAATACCCCTATAGGGTAAAATGACTGAAATACCTCCATAGGATAAAATGACTGAAACACCCCCA
1 AAATACCCCTATAAGGTAAAATGACTGAAATACCCCCATAGGATAAAATGACTGAAACACCCCCA
13712623 TAGGGTAAAATGACCGAATAACTG
66 TAGGGTAAAATGACCGAATAACTG
* * *
13712647 AAATATCCCTATAAGGTAAAATGACCT-AAATACCCCCATAAGG-TAAAATGA-TGGGAATACCC
1 AAATACCCCTATAAGGTAAAATGA-CTGAAATACCCCCAT-AGGATAAAATGACT-GAAACACCC
* *
13712709 TCTTAGGGTAAAATGACCGAA
63 CCATAGGGTAAAATGACCGAA
13712730 ATACCCTCAG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
88 1 0.01
89 67 0.92
90 5 0.07
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (89 bp):
AAATACCCCTATAAGGTAAAATGACTGAAATACCCCCATAGGATAAAATGACTGAAACACCCCCA
TAGGGTAAAATGACCGAATAACTG
Found at i:13712736 original size:27 final size:26
Alignment explanation
Indices: 13712646--13712750 Score: 95
Period size: 27 Copynumber: 4.0 Consensus size: 26
13712636 CCGAATAACT
* *
13712646 GAAATATCCCTATAAGGTAAAATGACC
1 GAAATA-CCCTCTAGGGTAAAATGACC
* * * **
13712673 TAAATACCCCCATAAGGTAAAATGATG
1 GAAATACCCTC-TAGGGTAAAATGACC
*
13712700 GGAATACCCTCTTAGGGTAAAATGACC
1 GAAATACCCTC-TAGGGTAAAATGACC
*
13712727 GAAATACCCTC-AGGATAAAATGAC
1 GAAATACCCTCTAGGGTAAAATGAC
13712751 TGTTATACCC
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
25 12 0.19
26 3 0.05
27 48 0.76
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (26 bp):
GAAATACCCTCTAGGGTAAAATGACC
Found at i:13722092 original size:2 final size:2
Alignment explanation
Indices: 13722085--13722111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13722075 TACCCAGATA
13722085 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
13722112 ACCAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13723291 original size:17 final size:17
Alignment explanation
Indices: 13723271--13723303 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13723261 TATATATTTA
13723271 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
13723288 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
13723304 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:13723933 original size:26 final size:24
Alignment explanation
Indices: 13723902--13723951 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
13723892 TAACATACTT
13723902 TTTAATATTTACATTAATATAATAAA
1 TTTAATATTTACA-TAATAT-ATAAA
* *
13723928 TTTAATCTTTATATAATATATAAA
1 TTTAATATTTACATAATATATAAA
13723952 AATACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 11 0.50
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAATATTTACATAATATATAAA
Found at i:13724146 original size:31 final size:31
Alignment explanation
Indices: 13724106--13724176 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
13724096 TTTTTTTTTA
* *
13724106 AGTTAAATTT-AGCACTCAACTTTTTACAAAG
1 AGTTAAATTTGACCA-TCAACTTTTTAAAAAG
*
13724137 AGTTTAATTTGACCATCAACTTTTTAAAAAG
1 AGTTAAATTTGACCATCAACTTTTTAAAAAG
*
13724168 AGTCAAATT
1 AGTTAAATT
13724177 GTTGTTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (31 bp):
AGTTAAATTTGACCATCAACTTTTTAAAAAG
Found at i:13724332 original size:17 final size:17
Alignment explanation
Indices: 13724283--13724342 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
13724273 TTTAATTATA
13724283 AATTTATTTT-TATTTT
1 AATTTATTTTATATTTT
13724299 GAATTTATTTTAT-TTTT
1 -AATTTATTTTATATTTT
13724316 -ATTTATTTTATAATTTTT
1 AATTTATTTTAT-A-TTTT
*
13724334 AAGTTATTT
1 AATTTATTT
13724343 GTTGACATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
15 11 0.30
17 14 0.38
18 5 0.14
19 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
AATTTATTTTATATTTT
Found at i:13726521 original size:46 final size:46
Alignment explanation
Indices: 13726454--13726545 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
13726444 AAAGGTTTAG
13726454 CTATACATGCTCACCGTAAAGAAAATTAACATAGCAATGGAAAACA
1 CTATACATGCTCACCGTAAAGAAAATTAACATAGCAATGGAAAACA
13726500 CTATACATGCTCACCGTAAAGAAAATTAACATAGCAATGGAAAACA
1 CTATACATGCTCACCGTAAAGAAAATTAACATAGCAATGGAAAACA
13726546 ATATGAAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (46 bp):
CTATACATGCTCACCGTAAAGAAAATTAACATAGCAATGGAAAACA
Found at i:13728609 original size:22 final size:23
Alignment explanation
Indices: 13728579--13728622 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13728569 CAACCAATCC
**
13728579 ATTTCAACATATTTTCAAGATAG
1 ATTTCAACATATTCACAAGATAG
13728602 ATTT-AACATATTCACAAGATA
1 ATTTCAACATATTCACAAGATA
13728623 ACCTCATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTTCAACATATTCACAAGATAG
Found at i:13729560 original size:115 final size:115
Alignment explanation
Indices: 13729353--13729580 Score: 357
Period size: 115 Copynumber: 2.0 Consensus size: 115
13729343 GCTAAATTCA
*
13729353 GACCCTAATTCGGATTACCAATCCGGGCAAAATCCATTTTCCACATATTCTTCGGGAGGGCTATA
1 GACCCTAATTCGGATTACCAATCCAGGCAAAATCCATTTTCCACATATTCTTCGGGAGGGCTATA
* *
13729418 TCAGAATAGGATCACCCGTCCGAGCTAGATCATTTTTACCGTCAATTCCT
66 TCAGAATAAGATCACCCATCCGAGCTAGATCATTTTTACCGTCAATTCCT
** * *
13729468 GACCCTAATTCGGATTACCCGTCCAGGCTAAATCCATTTTCCACATATTCTTTGGGAGGGCTATA
1 GACCCTAATTCGGATTACCAATCCAGGCAAAATCCATTTTCCACATATTCTTCGGGAGGGCTATA
* * * *
13729533 TCAGGATAAGATCACCCATCCGGGCTAGATCCTTTTTACCGTTAATTC
66 TCAGAATAAGATCACCCATCCGAGCTAGATCATTTTTACCGTCAATTC
13729581 ATTTTCAGAG
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 102 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (115 bp):
GACCCTAATTCGGATTACCAATCCAGGCAAAATCCATTTTCCACATATTCTTCGGGAGGGCTATA
TCAGAATAAGATCACCCATCCGAGCTAGATCATTTTTACCGTCAATTCCT
Found at i:13743034 original size:3 final size:3
Alignment explanation
Indices: 13743026--13743086 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
13743016 AATTGTTTTC
* * * * * *
13743026 ATT ATT ATT GTT ATT ATT ATT AAT GTT ATT ATA ACT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13743074 ATT -TAT ATT ATT A
1 ATT AT-T ATT ATT A
13743087 CTTTAAGTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:13743035 original size:15 final size:15
Alignment explanation
Indices: 13743017--13743076 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
13743007 TAATTACTCA
13743017 ATTGTT-TTCATTATT
1 ATTGTTATT-ATTATT
13743032 ATTGTTATTATTATT
1 ATTGTTATTATTATT
* * *
13743047 AATGTTATTATAACT
1 ATTGTTATTATTATT
13743062 ATTAG-TATTATTATT
1 ATT-GTTATTATTATT
13743077 TATATTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 34 0.92
16 3 0.08
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (15 bp):
ATTGTTATTATTATT
Found at i:13743427 original size:28 final size:27
Alignment explanation
Indices: 13743373--13743434 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
13743363 ACCGTATTTT
13743373 TAATTTATTTCAAATTTTGATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
13743401 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
13743429 TAATTT
1 TAATTT
13743435 CCTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:13745310 original size:30 final size:31
Alignment explanation
Indices: 13745276--13745352 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
13745266 TTAAGATGAT
*
13745276 ATATTATTAATGTAAA-ACAAAAAATTTAAA
1 ATATTATTAATATAAATACAAAAAATTTAAA
* * *
13745306 ATATT-TTAAAATAAATATAAATAATTTAAA
1 ATATTATTAATATAAATACAAAAAATTTAAA
*
13745336 AAATATATTAATTATAA
1 ATAT-TATTAA-TATAA
13745353 CTATTAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 8 0.22
30 20 0.54
31 1 0.03
32 4 0.11
33 4 0.11
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (31 bp):
ATATTATTAATATAAATACAAAAAATTTAAA
Found at i:13745343 original size:20 final size:20
Alignment explanation
Indices: 13745294--13745343 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
13745284 AATGTAAAAC
* *
13745294 AAAAAATTTA-AAATATTTT
1 AAAAAATATATAAATAATTT
13745313 AAAATAA-ATATAAATAATTT
1 AAAA-AATATATAAATAATTT
13745333 AAAAAATATAT
1 AAAAAATATAT
13745344 TAATTATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATATATAAATAATTT
Found at i:13747789 original size:25 final size:25
Alignment explanation
Indices: 13747761--13747817 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
13747751 ATCATTTTTT
13747761 TATTTTTTGAATAT-TTGGAACTTTG
1 TATTTTTT-AATATATTGGAACTTTG
* *
13747786 TA-TTTTTAATATATTTGAATTTTG
1 TATTTTTTAATATATTGGAACTTTG
13747810 -ATTTTTTA
1 TATTTTTTA
13747818 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
24 20 0.71
25 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (25 bp):
TATTTTTTAATATATTGGAACTTTG
Found at i:13755677 original size:44 final size:44
Alignment explanation
Indices: 13755614--13755703 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
13755604 AGAACATGCT
13755614 AACCACCAATTTTTCCTCTCGTAGCTAGTCCAGATACGACCTGC
1 AACCACCAATTTTTCCTCTCGTAGCTAGTCCAGATACGACCTGC
13755658 AACCACCAATTTTTCCTCTCGTAGCTAGTCCAGATACGACCTGC
1 AACCACCAATTTTTCCTCTCGTAGCTAGTCCAGATACGACCTGC
13755702 AA
1 AA
13755704 ACCAACCCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (44 bp):
AACCACCAATTTTTCCTCTCGTAGCTAGTCCAGATACGACCTGC
Found at i:13760423 original size:12 final size:12
Alignment explanation
Indices: 13760408--13760441 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13760398 ATAAATAAAT
*
13760408 AAATAAAATTAG
1 AAATTAAATTAG
*
13760420 AAATTAAATTGG
1 AAATTAAATTAG
13760432 AAATTAAATT
1 AAATTAAATT
13760442 CAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (12 bp):
AAATTAAATTAG
Found at i:13765565 original size:39 final size:39
Alignment explanation
Indices: 13765439--13765600 Score: 153
Period size: 40 Copynumber: 4.1 Consensus size: 39
13765429 AAACAAACGT
* * * ** * *
13765439 CGCTATAGGTTGAGCATTAGCGACGTTTTTTAAAAAACGC
1 CGCTATAGATCGAGCATTAGCGGC-ACTTTTCAAAAATGC
* * * *
13765479 CGCTATAGATTGATCATTAGCGGCACTTTTTGAAAAATGA
1 CGCTATAGATCGAGCATTAGCGGCAC-TTTTCAAAAATGC
* *
13765519 CGCTATAGATCAAGCATTAGTGGCACTTTTCAAAAATGC
1 CGCTATAGATCGAGCATTAGCGGCACTTTTCAAAAATGC
* * *
13765558 CGCTATAGATCGAGCATTAGCGACGCTTTTCAGAGAATGC
1 CGCTATAGATCGAGCATTAGCGGCACTTTTCA-AAAATGC
13765598 CGC
1 CGC
13765601 AAAACACATT
Statistics
Matches: 101, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
39 39 0.39
40 62 0.61
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (39 bp):
CGCTATAGATCGAGCATTAGCGGCACTTTTCAAAAATGC
Found at i:13767032 original size:24 final size:24
Alignment explanation
Indices: 13767005--13767140 Score: 70
Period size: 25 Copynumber: 5.7 Consensus size: 24
13766995 TTTTTGCAAT
13767005 TATTTTTATTTATATATATATGTA
1 TATTTTTATTTATATATATATGTA
* * * * * *
13767029 TATTTGTTGTTTTTATGTACATATT
1 TATTT-TTATTTATATATATATGTA
* *
13767054 TATTTATATTT-T-TA-A-ATGAA
1 TATTTTTATTTATATATATATGTA
13767074 TATTTTTATATTCATATATATATGTA
1 TATTTTTAT-TT-ATATATATATGTA
* *
13767100 T-TTTTATTTTTATTTATAATAT-TA
1 TATTTT-TATTTATATAT-ATATGTA
*
13767124 TAATTATTATTTA-ATAT
1 T-ATTTTTATTTATATAT
13767141 TTTTTTCTAT
Statistics
Matches: 82, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
20 10 0.12
21 3 0.04
22 1 0.01
23 2 0.02
24 22 0.27
25 34 0.41
26 10 0.12
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (24 bp):
TATTTTTATTTATATATATATGTA
Found at i:13768527 original size:40 final size:39
Alignment explanation
Indices: 13768425--13768630 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 39
13768415 AGCTTTAATG
* *
13768425 GCATTAGTAGCGCTTTTTAAAAAACGCCGCAATAGATCGA
1 GCATTAGCAGCGC-TTTTGAAAAACGCCGCAATAGATCGA
* * *
13768465 GGATTAG--GCGCTTGTTGAAAAACACCGCTATAGATCGA
1 GCATTAGCAGCGCTT-TTGAAAAACGCCGCAATAGATCGA
*
13768503 GCATTAGCAGCGCTTTTCAGAAAACGCCGCAATAGATCGA
1 GCATTAGCAGCGCTTTTGA-AAAACGCCGCAATAGATCGA
* * * *
13768543 GAATTAGCGGCGCTTTTTAGAAAACGCCACAATAGATCGA
1 GCATTAGCAGCGCTTTTGA-AAAACGCCGCAATAGATCGA
* * * *
13768583 GAATTAGCGGCGCTTGTTGAAAAACGCCACTATAGATCGA
1 GCATTAGCAGCGCTT-TTGAAAAACGCCGCAATAGATCGA
13768623 GCATTAGC
1 GCATTAGC
13768631 TACACTTTTA
Statistics
Matches: 146, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
37 2 0.01
38 31 0.21
39 3 0.02
40 107 0.73
41 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (39 bp):
GCATTAGCAGCGCTTTTGAAAAACGCCGCAATAGATCGA
Found at i:13768639 original size:120 final size:118
Alignment explanation
Indices: 13768434--13768654 Score: 329
Period size: 120 Copynumber: 1.9 Consensus size: 118
13768424 GGCATTAGTA
* * *
13768434 GCGCTTTTTAAAAAACGCCGCAATAGATCGAGGATTAGGCGCTTGTTGAAAAACACCGCTATAGA
1 GCGCTTTTTAAAAAACGCCACAATAGATCGAGAATTAGGCGCTTGTTGAAAAACACCACTATAGA
*
13768499 TCGAGCATTAGCAGCGCTTTTCAG-AAAACGCCGCAATAGATCGAGAATTAGCG
66 TCGAGCATTAGCAGCACTTTT-AGCAAAACGCCGCAATAGATCGAGAATTAGCG
* *
13768552 GCGCTTTTTAGAAAACGCCACAATAGATCGAGAATTAGCGGCGCTTGTTGAAAAACGCCACTATA
1 GCGCTTTTTAAAAAACGCCACAATAGATCGAGAATTA--GGCGCTTGTTGAAAAACACCACTATA
*
13768617 GATCGAGCATTAGCTA-CACTTTTAGCAAAATGCCGCAA
64 GATCGAGCATTAGC-AGCACTTTTAGCAAAACGCCGCAA
13768655 AAAAGTTGAG
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
118 34 0.37
119 2 0.02
120 55 0.60
121 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (118 bp):
GCGCTTTTTAAAAAACGCCACAATAGATCGAGAATTAGGCGCTTGTTGAAAAACACCACTATAGA
TCGAGCATTAGCAGCACTTTTAGCAAAACGCCGCAATAGATCGAGAATTAGCG
Found at i:13769181 original size:22 final size:22
Alignment explanation
Indices: 13769127--13769188 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
13769117 TAGGGTATAA
* *
13769127 GTTTATGGTTTAGTGTTT-AGG
1 GTTTAGGGTTTAATGTTTAAGG
*
13769148 GTTTAGGATTTAATGTTTAAGG
1 GTTTAGGGTTTAATGTTTAAGG
*
13769170 G-TTAGGGGTTTAAGGTTTA
1 GTTTA-GGGTTTAATGTTTA
13769189 TAGTTTTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (22 bp):
GTTTAGGGTTTAATGTTTAAGG
Found at i:13769230 original size:29 final size:28
Alignment explanation
Indices: 13769115--13769231 Score: 93
Period size: 29 Copynumber: 4.1 Consensus size: 28
13769105 ATGCTTACGA
13769115 TTTA-GGGTATAA-GTTTATGGTTTAGTG
1 TTTAGGGGT-TAAGGTTTATGGTTTAGTG
*
13769142 TTTA-GGGTTTAGGATTTAAT-GTTTAAG-G
1 TTTAGGGGTTAAGG-TTT-ATGGTTT-AGTG
* * *
13769170 GTTAGGGGTTTAAGGTTTATAGTTT-TTAG
1 TTTAGGGG-TTAAGGTTTATGGTTTAGT-G
13769199 TTTAGGGGCTTAAGGTTTATGGTTTAGTG
1 TTTAGGGG-TTAAGGTTTATGGTTTAGTG
13769228 TTTA
1 TTTA
13769232 AGGTCTGATT
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
26 2 0.03
27 9 0.12
28 13 0.18
29 42 0.58
30 6 0.08
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (28 bp):
TTTAGGGGTTAAGGTTTATGGTTTAGTG
Found at i:13769722 original size:20 final size:20
Alignment explanation
Indices: 13769699--13769748 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
13769689 TACATAAACA
13769699 TTATATAAAAATTTTAAAAT
1 TTATATAAAAATTTTAAAAT
* ***
13769719 TTATCTAATTCTTTTAAAAT
1 TTATATAAAAATTTTAAAAT
*
13769739 TTATTTAAAA
1 TTATATAAAA
13769749 TTGATATGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAAAAATTTTAAAAT
Found at i:13781046 original size:9 final size:9
Alignment explanation
Indices: 13781032--13781096 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
13781022 TCGGGAATTT
13781032 TTCGGTTAA
1 TTCGGTTAA
13781041 TTCGGTTAA
1 TTCGGTTAA
13781050 TTCGGTTAA
1 TTCGGTTAA
***
13781059 TTTTTTTAA
1 TTCGGTTAA
* *
13781068 TTTGGGTAA
1 TTCGGTTAA
*
13781077 TTCGGGTAA
1 TTCGGTTAA
*
13781086 TTCGGGTAA
1 TTCGGTTAA
13781095 TT
1 TT
13781097 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.48
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:13781273 original size:12 final size:12
Alignment explanation
Indices: 13781256--13781280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13781246 AGTAATTTCG
13781256 GGTCGGTTAACC
1 GGTCGGTTAACC
13781268 GGTCGGTTAACC
1 GGTCGGTTAACC
13781280 G
1 G
13781281 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:13782536 original size:50 final size:50
Alignment explanation
Indices: 13782458--13782591 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
13782448 ATTTGGGTAA
* * * *
13782458 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATG
* * *
13782508 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATG
** * *
13782558 AGAACATCCTATGTAAGACCATGTCTGGGACATG
1 AG-AGGTCCCACGTAAGACCATGTCTGGGACATG
13782592 ACTTTGGCAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
50 45 0.64
51 25 0.36
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATG
Found at i:13786462 original size:40 final size:40
Alignment explanation
Indices: 13786362--13786626 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
13786352 GCTCCTCGTT
* * * *
13786362 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
13786402 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
13786441 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
13786481 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
13786521 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
13786561 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
13786602 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
13786627 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:13786586 original size:80 final size:80
Alignment explanation
Indices: 13786329--13786626 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
13786319 AAATCACGTA
* ** * * *
13786329 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
13786391 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
13786407 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
13786470 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
13786487 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
13786551 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
13786567 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
13786627 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:13786635 original size:41 final size:41
Alignment explanation
Indices: 13786558--13786635 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
13786548 TTTGTATCTC
* * *
13786558 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
13786599 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
13786636 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:13796045 original size:14 final size:14
Alignment explanation
Indices: 13796026--13796052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13796016 ACCAAAAAAT
13796026 AAAAATAAATAAAC
1 AAAAATAAATAAAC
13796040 AAAAATAAATAAA
1 AAAAATAAATAAA
13796053 AAGGTCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAATAAAC
Found at i:13809538 original size:44 final size:44
Alignment explanation
Indices: 13809356--13809520 Score: 109
Period size: 44 Copynumber: 3.6 Consensus size: 44
13809346 TACAGTAGCG
* * * * * *
13809356 AATCTTATCTCCTTGAAGATGTAATGGAGTAAGATGAAGCTACA
1 AATCCTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAACTACA
* * * * *
13809400 AATCCTACATCCCTGAAGTTGTACTAGATCGGATTG-AA-ATTATAACAACG
1 AATCCTATATCCTTGAAGTTG---TAG-T-GGA--GCAAGATGA-AACTACA
* * * *
13809450 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAAGATTAAGCTACA
1 AATCCTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAACTACA
13809494 AATCCTATATCCTTGAAGTTGTAGTGG
1 AATCCTATATCCTTGAAGTTGTAGTGG
13809521 GATGAATCGA
Statistics
Matches: 92, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
43 1 0.01
44 47 0.51
45 7 0.08
46 1 0.01
47 5 0.05
48 1 0.01
49 6 0.07
50 23 0.25
51 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCCTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAACTACA
Found at i:13809570 original size:94 final size:94
Alignment explanation
Indices: 13809356--13809578 Score: 259
Period size: 94 Copynumber: 2.4 Consensus size: 94
13809346 TACAGTAGCG
*
13809356 AATCTTATCTCCTTGAAGATGTAATGGAGTAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGATGTAGTGGAGTAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
* * * * *
13809421 TACTAGATCGGATTGAAATTATAACAACG
66 TACTAGATCGAATCGAAACTACAACAACA
* * * * *
13809450 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAAGATTAAGCTACAAATCCTATATCCTTGAAGTTG
1 AATCTTATCTCCTTGAAGATGTAGTGGAGTAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
* * **
13809515 TAGTGGGAT-GAATCGAAACTACAATGACA
66 TACT-AGATCGAATCGAAACTACAACAACA
* * **
13809544 AATCTCATCTCCCTGAAGATACAGTGGAGTAAGAT
1 AATCTTATCTCCTTGAAGATGTAGTGGAGTAAGAT
13809579 AAAGTTATAA
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
94 104 0.97
95 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (94 bp):
AATCTTATCTCCTTGAAGATGTAGTGGAGTAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
TACTAGATCGAATCGAAACTACAACAACA
Found at i:13812296 original size:24 final size:24
Alignment explanation
Indices: 13812248--13812294 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13812238 TGTGGTCATA
*
13812248 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
13812272 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
13812295 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:13813074 original size:27 final size:27
Alignment explanation
Indices: 13812963--13813105 Score: 162
Period size: 27 Copynumber: 5.3 Consensus size: 27
13812953 CGAGAGGTCA
*
13812963 TAAAATGATCGAATTACCTCTACAGGG
1 TAAAATGATCGAATTACCCCTACAGGG
* *
13812990 TAAAATGA-CTAAATTACCCTTACAGGG
1 TAAAATGATC-GAATTACCCCTACAGGG
*
13813017 TAAAATGATCGAATTACCCTTACAGGG
1 TAAAATGATCGAATTACCCCTACAGGG
* * *
13813044 TAAAATGATCGAATTACCCCCACATGA
1 TAAAATGATCGAATTACCCCTACAGGG
* * * * *
13813071 TAAAATGACCGAAATACCCCCATATGG
1 TAAAATGATCGAATTACCCCTACAGGG
13813098 TAAAATGA
1 TAAAATGA
13813106 CTATTATACC
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 100 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (27 bp):
TAAAATGATCGAATTACCCCTACAGGG
Found at i:13813511 original size:28 final size:28
Alignment explanation
Indices: 13813471--13813526 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
13813461 ACTATACCGA
* *
13813471 TACTGTATTGGGCTAAGGCCCATATTGT
1 TACTATATTGGGCTAAGGCCCACATTGT
13813499 TACTATATTGGGCTAAGGCCCACATTGT
1 TACTATATTGGGCTAAGGCCCACATTGT
13813527 ACTGTTACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (28 bp):
TACTATATTGGGCTAAGGCCCACATTGT
Found at i:13821498 original size:20 final size:20
Alignment explanation
Indices: 13821466--13821538 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
13821456 CTCAGGGGTT
*
13821466 AAAT-ATTTCATTTATAAAA
1 AAATAATTTTATTTATAAAA
13821485 AAATAATTTTATTTATATTAAA
1 AAATAATTTTATTTATA--AAA
* *
13821507 TAATAATTTAATATTT-TAAAT
1 AAATAATTT--TATTTATAAAA
*
13821528 AAATAAATTTA
1 AAATAATTTTA
13821539 AAATTAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.14
20 11 0.25
21 9 0.20
22 11 0.25
23 2 0.05
24 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTTTATTTATAAAA
Found at i:13821536 original size:22 final size:22
Alignment explanation
Indices: 13821475--13821539 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
13821465 TAAATATTTC
* * *
13821475 ATTTATAAAAAAATAATTTTATTT
1 ATTT-TAAATAAATAAATTTA-AT
*
13821499 ATATTAAAT-AAT-AATTTAAT
1 ATTTTAAATAAATAAATTTAAT
13821519 ATTTTAAATAAATAAATTTAA
1 ATTTTAAATAAATAAATTTAA
13821540 AATTAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 9 0.26
21 8 0.24
22 10 0.29
23 4 0.12
24 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTTAAATAAATAAATTTAAT
Found at i:13822138 original size:27 final size:26
Alignment explanation
Indices: 13822097--13822147 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
13822087 TAAAGTACAC
*
13822097 TCTTTATTGCTTTCATATTTTCTTTAT
1 TCTTTATTGCTTTCAT-TTCTCTTTAT
13822124 TCTTTATT-CTCTTCATTTCTCTTT
1 TCTTTATTGCT-TTCATTTCTCTTT
13822148 GTTTTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.67
Consensus pattern (26 bp):
TCTTTATTGCTTTCATTTCTCTTTAT
Found at i:13826401 original size:73 final size:73
Alignment explanation
Indices: 13826317--13826468 Score: 261
Period size: 73 Copynumber: 2.1 Consensus size: 73
13826307 GACTATATAA
* *
13826317 CGGGAAGCTCATAAGATCCATATTCAAGAAGCTCATGCGAGCTTATAACAGGTAGCGT-CGAAGA
1 CGGGAAACTCATAAGATCCATATTCAAGAAGCTCATGCGAGCTTATAACAGGTAGC-TCCAAAGA
13826381 GCCATTAAT
65 GCCATTAAT
*
13826390 CGGGAAACTCATAAGATCCATATTCAAGAATCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
1 CGGGAAACTCATAAGATCCATATTCAAGAAGCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
13826455 CCATTAAT
66 CCATTAAT
13826463 CGGGAA
1 CGGGAA
13826469 GCTCCGGATA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
72 1 0.01
73 74 0.99
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (73 bp):
CGGGAAACTCATAAGATCCATATTCAAGAAGCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
CCATTAAT
Found at i:13826471 original size:25 final size:24
Alignment explanation
Indices: 13826443--13826580 Score: 77
Period size: 25 Copynumber: 5.5 Consensus size: 24
13826433 TATAACAGGT
13826443 AGCTCCAAAGAGCCATTAATCGGGA
1 AGCTCCAAAGAGCCA-TAATCGGGA
** * *
13826468 AGCTCCGGATAGCCATATATCGGAA
1 AGCTCCAAAGAGCCATA-ATCGGGA
* * *
13826493 AG-TTCAAGCGAGCCAT-ATCAGGA
1 AGCTCCAA-AGAGCCATAATCGGGA
13826516 AGCTCACAAAGAGCCAGTTAAT-GGGA
1 AGCTC-CAAAGAGCCA--TAATCGGGA
* *
13826542 AGCTCACGAAGAGTCATATATCGGGA
1 AGCTC-CAAAGAGCCATA-ATCGGGA
*
13826568 TGCT-CATAAGAGC
1 AGCTCCA-AAGAGC
13826581 TAAGGTGTGT
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
23 7 0.08
24 14 0.17
25 36 0.43
26 25 0.30
27 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (24 bp):
AGCTCCAAAGAGCCATAATCGGGA
Found at i:13826484 original size:73 final size:73
Alignment explanation
Indices: 13826317--13826560 Score: 246
Period size: 73 Copynumber: 3.3 Consensus size: 73
13826307 GACTATATAA
* * * *
13826317 CGGGAAGCTCATAAGATCCATATTCAAGAAGCTCATGCGAGCTTATAACAGGTAGCGT-CGAAGA
1 CGGGAAGCTCAGAAGAGCCATATTCAAGAATCTCATGCGAGCTTATAACAGGTAGC-TCCAAAGA
13826381 GCCATTAAT
65 GCCATTAAT
* * *
13826390 CGGGAAACTCATAAGATCCATATTCAAGAATCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
1 CGGGAAGCTCAGAAGAGCCATATTCAAGAATCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
13826455 CCATTAAT
66 CCATTAAT
* * * * * * * *
13826463 CGGGAAGCTCCGGATAGCCATATATCGGAA-AGT-TCAAGCGAGC-CATATCAGGAAGCTCACAA
1 CGGGAAGCTCAGAAGAGCCATAT-TC--AAGAATCTCATGCGAGCTTATAACAGGTAGCTC-CAA
13826525 AGAGCCAGTTAAT
62 AGAGCCA-TTAAT
*
13826538 -GGGAAGCTCACGAAGAGTCATAT
1 CGGGAAGCTCA-GAAGAGCCATAT
13826561 ATCGGGATGC
Statistics
Matches: 146, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
72 1 0.01
73 97 0.66
74 30 0.21
75 16 0.11
76 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (73 bp):
CGGGAAGCTCAGAAGAGCCATATTCAAGAATCTCATGCGAGCTTATAACAGGTAGCTCCAAAGAG
CCATTAAT
Found at i:13832774 original size:9 final size:9
Alignment explanation
Indices: 13832762--13832804 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
13832752 AAAATTATTA
13832762 AAAAATCAT
1 AAAAATCAT
13832771 AAAAAATCAT
1 -AAAAATCAT
**
13832781 AAAAATTTT
1 AAAAATCAT
13832790 AAAAATCAT
1 AAAAATCAT
13832799 AAAAAT
1 AAAAAT
13832805 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATCAT
Found at i:13832817 original size:17 final size:18
Alignment explanation
Indices: 13832772--13832811 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
13832762 AAAAATCATA
13832772 AAAAATCATAAAAATTTT
1 AAAAATCATAAAAATTTT
13832790 AAAAATCATAAAAATTTT
1 AAAAATCATAAAAATTTT
13832808 AAAA
1 AAAA
13832812 TTATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATCATAAAAATTTT
Found at i:13834624 original size:23 final size:23
Alignment explanation
Indices: 13834594--13834642 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
13834584 TTTAAATGAA
13834594 ATAAACACAACATAACCATTTTC
1 ATAAACACAACATAACCATTTTC
*
13834617 ATAAACACAACATAAGCATTTTC
1 ATAAACACAACATAACCATTTTC
13834640 ATA
1 ATA
13834643 TAAAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAACACAACATAACCATTTTC
Found at i:13834651 original size:23 final size:23
Alignment explanation
Indices: 13834594--13834651 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
13834584 TTTAAATGAA
*
13834594 ATAAACACAACATAACCATTTTC
1 ATAAACAAAACATAACCATTTTC
* *
13834617 ATAAACACAACATAAGCATTTTC
1 ATAAACAAAACATAACCATTTTC
13834640 ATATAA-AAAACA
1 ATA-AACAAAACA
13834652 ATTCTTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.24
Consensus pattern (23 bp):
ATAAACAAAACATAACCATTTTC
Found at i:13834888 original size:3 final size:3
Alignment explanation
Indices: 13834880--13834911 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13834870 AGAAACAAAT
13834880 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
13834912 AACAACCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:13841128 original size:98 final size:98
Alignment explanation
Indices: 13840959--13841155 Score: 333
Period size: 98 Copynumber: 2.0 Consensus size: 98
13840949 GTGCAATAAA
13840959 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
* *
13841024 CCTCTAAAATC-CTAAACTTGAAATATTTCTTTT
66 CCTCTAAAATCTC-AAACTGGAAATATTTCCTTT
* *
13841057 ACTTTAAAAGAACATCTACTTATCCAAGATTTAAGAAATTACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
13841122 CCTCTAAAATCTCAAACTGGGAATATTTCCTTT
66 CCTCTAAAATCTCAAACTGGAAATATTTCCTTT
13841155 A
1 A
13841156 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 92 0.99
99 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCTCAAACTGGAAATATTTCCTTT
Found at i:13843536 original size:37 final size:37
Alignment explanation
Indices: 13843479--13843584 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
13843469 TATGATCACT
*
13843479 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
13843514 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
13843551 TATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
13843585 GAAGCTATCA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 54 0.84
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:13843626 original size:52 final size:52
Alignment explanation
Indices: 13843547--13843711 Score: 243
Period size: 46 Copynumber: 3.2 Consensus size: 52
13843537 TAAGTGTAGC
* *
13843547 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
13843600 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
13843652 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
13843698 CACTTTGTCACTTG
1 CACTTT-TCACTTG
13843712 ATCAGAAGTA
Statistics
Matches: 101, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
46 44 0.44
49 1 0.01
50 1 0.01
52 43 0.43
53 12 0.12
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:13844645 original size:124 final size:124
Alignment explanation
Indices: 13844328--13844951 Score: 1023
Period size: 124 Copynumber: 5.0 Consensus size: 124
13844318 TTGTAGCTTC
* * **
13844328 AACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCTTACTATCTTG
1 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
** * * * * *
13844393 GAAAGATACGATTCGCTGTCTTCTATCTGCTCCACTACTGCTTAAGGAGATAAGATCTACAATCT
66 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAG-TCT---A---
13844458 T
124 T
*
13844459 CAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTT
1 -AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTT
13844524 GGAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
65 GGAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
13844584 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
13844649 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
66 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
13844708 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
13844773 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
66 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
13844832 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
1 AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
* * **
13844897 GAAAGATAATATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAG
66 GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTT-AGGGAGATAAG
13844952 ACTACTGGTT
Statistics
Matches: 476, Mismatches: 15, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
124 351 0.74
125 12 0.03
128 1 0.00
131 3 0.01
132 109 0.23
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (124 bp):
AACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
GAAAGATAAAATTTGCCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGTCTAT
Found at i:13848462 original size:504 final size:504
Alignment explanation
Indices: 13847515--13848523 Score: 2018
Period size: 504 Copynumber: 2.0 Consensus size: 504
13847505 TCGATCAATC
13847515 CAAAAACCAATCTCCGGTAACAGATCAATTTAGGATCCTTCGTCTCCCATTCCCTTCTTAGCTGG
1 CAAAAACCAATCTCCGGTAACAGATCAATTTAGGATCCTTCGTCTCCCATTCCCTTCTTAGCTGG
13847580 TATATTACCAATGCTGAGTCTCCGTACACCTCTAATGTCTTGATTTTCCATTCTATGGCTGCCTG
66 TATATTACCAATGCTGAGTCTCCGTACACCTCTAATGTCTTGATTTTCCATTCTATGGCTGCCTG
13847645 TATACCCATGATGCAAGCTTCATACTCAGCCATGTTATTAGTGCAATCAAAGTCTAATTTACTGG
131 TATACCCATGATGCAAGCTTCATACTCAGCCATGTTATTAGTGCAATCAAAGTCTAATTTACTGG
13847710 TGAAAGGATGATAATCTCCATTCGGAGACACCAGGACTGCCCCAATCCCATTGCCTAATGCATTC
196 TGAAAGGATGATAATCTCCATTCGGAGACACCAGGACTGCCCCAATCCCATTGCCTAATGCATTC
13847775 GATGCTCCGTCAAAGTTTAATCTCCAAGAATGATTCTCTTGGGGATCCTCTTCAGCATTCGCCAC
261 GATGCTCCGTCAAAGTTTAATCTCCAAGAATGATTCTCTTGGGGATCCTCTTCAGCATTCGCCAC
13847840 ATACATCAAATCTTCATTCGAGAAATCAAAGTCAAGAGGCTCATATTCTTCCAGAGCCCTGCTAG
326 ATACATCAAATCTTCATTCGAGAAATCAAAGTCAAGAGGCTCATATTCTTCCAGAGCCCTGCTAG
13847905 CCAAGAAATCTGCTATCGCACTTCCCTTGACGGCCTTCTGACTTACGTATACGATATCAAACTCA
391 CCAAGAAATCTGCTATCGCACTTCCCTTGACGGCCTTCTGACTTACGTATACGATATCAAACTCA
13847970 GAGAGCAAGATTTGCCATCTAGTCATTCTTCCATTCAATGCTGTTGACT
456 GAGAGCAAGATTTGCCATCTAGTCATTCTTCCATTCAATGCTGTTGACT
13848019 CAAAAACCAATCTCCGGTAACAGATCAATTTAGGATCCTTCGTCTCCCATTCCCTTCTTAGCTGG
1 CAAAAACCAATCTCCGGTAACAGATCAATTTAGGATCCTTCGTCTCCCATTCCCTTCTTAGCTGG
13848084 TATATTACCAATGCTGAGTCTCCGTACACCTCTAATGTCTTGATTTTCCATTCTATGGCTGCCTG
66 TATATTACCAATGCTGAGTCTCCGTACACCTCTAATGTCTTGATTTTCCATTCTATGGCTGCCTG
13848149 TATACCCATGATGCAAGCTTCATACTCAGCCATGTTATTAGTGCAATCAAAGTCTAATTTACTGG
131 TATACCCATGATGCAAGCTTCATACTCAGCCATGTTATTAGTGCAATCAAAGTCTAATTTACTGG
13848214 TGAAAGGATGATAATCTCCATTCGGAGACACCAGGACTGCCCCAATCCCATTGCCTAATGCATTC
196 TGAAAGGATGATAATCTCCATTCGGAGACACCAGGACTGCCCCAATCCCATTGCCTAATGCATTC
13848279 GATGCTCCGTCAAAGTTTAATCTCCAAGAATGATTCTCTTGGGGATCCTCTTCAGCATTCGCCAC
261 GATGCTCCGTCAAAGTTTAATCTCCAAGAATGATTCTCTTGGGGATCCTCTTCAGCATTCGCCAC
13848344 ATACATCAAATCTTCATTCGAGAAATCAAAGTCAAGAGGCTCATATTCTTCCAGAGCCCTGCTAG
326 ATACATCAAATCTTCATTCGAGAAATCAAAGTCAAGAGGCTCATATTCTTCCAGAGCCCTGCTAG
13848409 CCAAGAAATCTGCTATCGCACTTCCCTTGACGGCCTTCTGACTTACGTATACGATATCAAACTCA
391 CCAAGAAATCTGCTATCGCACTTCCCTTGACGGCCTTCTGACTTACGTATACGATATCAAACTCA
13848474 GAGAGCAAGATTTGCCATCTAGTCATTCTTCCATTCAATGCTGTTGACT
456 GAGAGCAAGATTTGCCATCTAGTCATTCTTCCATTCAATGCTGTTGACT
13848523 C
1 C
13848524 CATCATATAC
Statistics
Matches: 505, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
504 505 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (504 bp):
CAAAAACCAATCTCCGGTAACAGATCAATTTAGGATCCTTCGTCTCCCATTCCCTTCTTAGCTGG
TATATTACCAATGCTGAGTCTCCGTACACCTCTAATGTCTTGATTTTCCATTCTATGGCTGCCTG
TATACCCATGATGCAAGCTTCATACTCAGCCATGTTATTAGTGCAATCAAAGTCTAATTTACTGG
TGAAAGGATGATAATCTCCATTCGGAGACACCAGGACTGCCCCAATCCCATTGCCTAATGCATTC
GATGCTCCGTCAAAGTTTAATCTCCAAGAATGATTCTCTTGGGGATCCTCTTCAGCATTCGCCAC
ATACATCAAATCTTCATTCGAGAAATCAAAGTCAAGAGGCTCATATTCTTCCAGAGCCCTGCTAG
CCAAGAAATCTGCTATCGCACTTCCCTTGACGGCCTTCTGACTTACGTATACGATATCAAACTCA
GAGAGCAAGATTTGCCATCTAGTCATTCTTCCATTCAATGCTGTTGACT
Found at i:13857713 original size:15 final size:13
Alignment explanation
Indices: 13857684--13857709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13857674 AATGGAAAAT
13857684 AATTTAAAAAACA
1 AATTTAAAAAACA
13857697 AATTTAAAAAACA
1 AATTTAAAAAACA
13857710 CAAAAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
AATTTAAAAAACA
Found at i:13860075 original size:39 final size:39
Alignment explanation
Indices: 13860025--13860120 Score: 165
Period size: 39 Copynumber: 2.5 Consensus size: 39
13860015 TGAGTTGTAA
*
13860025 GTGATTATTCATCTACATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
13860064 GTGACTATTCATCTACATCACTTAAATGTTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
*
13860103 GTGACTATTCATATACAT
1 GTGACTATTCATCTACAT
13860121 GCATGTATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:13878030 original size:16 final size:17
Alignment explanation
Indices: 13878000--13878032 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13877990 ATAAACGAAG
*
13878000 ATATGGTTTGTTTGTTT
1 ATATGGTTTGCTTGTTT
13878017 ATAT-GTTTGCTTGTTT
1 ATATGGTTTGCTTGTTT
13878033 TTTATGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.03, G:0.21, T:0.64
Consensus pattern (17 bp):
ATATGGTTTGCTTGTTT
Found at i:13879008 original size:33 final size:32
Alignment explanation
Indices: 13878955--13879112 Score: 111
Period size: 33 Copynumber: 4.8 Consensus size: 32
13878945 TTCGTAGTGA
* *
13878955 CATAACCCAATTATGGTCTTATCATCAGAATGC
1 CATAGCCCAACTATGGTCTTA-CATCAGAATGC
* * *
13878988 CATAGCCCAGCTATGGTCTTACATATAAACACTGC
1 CATAGCCCAACTATGGTCTTACAT-CAGA-A-TGC
* * * * *
13879023 CAT-GATCCAACCATGGTCTTACGTTCATAGTGC
1 CATAG-CCCAACTATGGTCTTAC-ATCAGAATGC
* *
13879056 CATAACCCAATTATGGTCTTATCATCAGAATGC
1 CATAGCCCAACTATGGTCTTA-CATCAGAATGC
* * *
13879089 CATAGTCCAGCTATAGTCTTACAT
1 CATAGCCCAACTATGGTCTTACAT
13879113 ATAAACACTG
Statistics
Matches: 94, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
32 6 0.06
33 62 0.66
34 3 0.03
35 22 0.23
36 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (32 bp):
CATAGCCCAACTATGGTCTTACATCAGAATGC
Found at i:13883156 original size:6 final size:6
Alignment explanation
Indices: 13883141--13883179 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
13883131 GGATTGCAAG
* *
13883141 TTTCCA TTTTCA TTTTCA TTTCCA TTTCCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
13883180 TTGGAAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCCA
Found at i:13883292 original size:10 final size:10
Alignment explanation
Indices: 13883267--13883295 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
13883257 CATTTCTCAT
13883267 TTTCTATTCA
1 TTTCTATTCA
13883277 -TTCTATTCA
1 TTTCTATTCA
13883286 TTTCTATTCA
1 TTTCTATTCA
13883296 AACACGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:13892264 original size:15 final size:15
Alignment explanation
Indices: 13892246--13892276 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13892236 GTCATTTTCC
*
13892246 TATTTTTTATTTATT
1 TATTTATTATTTATT
13892261 TATTTATTATTTATT
1 TATTTATTATTTATT
13892276 T
1 T
13892277 TATAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTATTATTTATT
Found at i:13892475 original size:9 final size:10
Alignment explanation
Indices: 13892453--13892486 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
13892443 TTGAATAAAC
13892453 AAATATTATA
1 AAATATTATA
13892463 AAATATT-TA
1 AAATATTATA
13892472 AAATATTATA
1 AAATATTATA
13892482 AAATA
1 AAATA
13892487 AATAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATTATA
Found at i:13892596 original size:22 final size:22
Alignment explanation
Indices: 13892548--13892597 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
13892538 AACAAATATT
*
13892548 ATAAAACATTTAAAATATAAAT
1 ATAAAACATTTAAAATATAAAA
* *
13892570 TTAAAATATTATAAAATA-AAAA
1 ATAAAACATT-TAAAATATAAAA
13892592 ATAAAA
1 ATAAAA
13892598 ACAGGAAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAACATTTAAAATATAAAA
Found at i:13892598 original size:23 final size:22
Alignment explanation
Indices: 13892550--13892600 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
13892540 CAAATATTAT
* * *
13892550 AAAACATTTAAAATATAAATTT
1 AAAACATTTAAAATAAAAAATA
*
13892572 AAAATATTATAAAATAAAAAATA
1 AAAACATT-TAAAATAAAAAATA
13892595 AAAACA
1 AAAACA
13892601 GGAAAAGGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAACATTTAAAATAAAAAATA
Found at i:13898919 original size:30 final size:30
Alignment explanation
Indices: 13898884--13898952 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
13898874 ATTTTGACAA
13898884 AAAACTCTCAAACCTCTCCCTAAATTTCTC
1 AAAACTCTCAAACCTCTCCCTAAATTTCTC
** *
13898914 AAAACTCTCAAATTTCTCCTTAAATTTCTC
1 AAAACTCTCAAACCTCTCCCTAAATTTCTC
*
13898944 AAAGCTCTC
1 AAAACTCTC
13898953 TTTAATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.33
Consensus pattern (30 bp):
AAAACTCTCAAACCTCTCCCTAAATTTCTC
Found at i:13900713 original size:18 final size:18
Alignment explanation
Indices: 13900690--13900726 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13900680 GTCAGGTGCA
* *
13900690 TATCCTAGCCTTTATATG
1 TATCCTAACCCTTATATG
13900708 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
13900726 T
1 T
13900727 TTTCTTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:13901167 original size:24 final size:25
Alignment explanation
Indices: 13901133--13901180 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13901123 TTTAATAAAA
13901133 TAAATT-TTTTTACTA-TTTTAATAG
1 TAAATTATTTTTA-TATTTTTAATAG
13901157 TAAATTATTTTTATATTTTTAATA
1 TAAATTATTTTTATATTTTTAATA
13901181 AAATAGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TAAATTATTTTTATATTTTTAATAG
Done.