Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 180 of 332
Found at i:59736508 original size:71 final size:71
Alignment explanation
Indices: 59736384--59736549 Score: 235
Period size: 71 Copynumber: 2.3 Consensus size: 71
59736374 GGAGGAAGTG
* * *
59736384 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTAATGCCCCAGTTATCAAAAGGGCTTATGCCGC
1 AAAAAGGGCTTATGCCCCAGTTATGAAAGGGCTAACGCCCCAGTTATCAAAAGGGCTTATGCCCC
*
59736449 AGTTGT
66 AGTTAT
* * *
59736455 CAAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTACGCCCCAGTTAT-TAAAGGGCTTATGCCC
1 AAAAAGGGCTTATGCCCCAGTTAT-GAAAGGGCTAACGCCCCAGTTATCAAAAGGGCTTATGCCC
59736519 CAGTTAT
65 CAGTTAT
* *
59736526 AAAAAGGGATTTTGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTAT
59736550 TAAAAGAGGC
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 64 0.76
72 20 0.24
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (71 bp):
AAAAAGGGCTTATGCCCCAGTTATGAAAGGGCTAACGCCCCAGTTATCAAAAGGGCTTATGCCCC
AGTTAT
Found at i:59736532 original size:47 final size:47
Alignment explanation
Indices: 59736384--59736575 Score: 242
Period size: 47 Copynumber: 4.0 Consensus size: 47
59736374 GGAGGAAGTG
*
59736384 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTAATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* * * *
59736431 CAAAAGGGCTTATGCCGCAGTTGTCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
** *
59736479 CGAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* * *
59736526 AAAAAGGGATTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
59736575 A
1 A
59736576 TGATAAAGCA
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
47 63 0.50
48 50 0.40
49 12 0.10
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (47 bp):
AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:59736803 original size:31 final size:31
Alignment explanation
Indices: 59736768--59736831 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
59736758 CGTTTACAGT
*
59736768 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
59736799 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
59736830 AA
1 AA
59736832 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:59738376 original size:40 final size:40
Alignment explanation
Indices: 59738314--59738466 Score: 211
Period size: 40 Copynumber: 3.9 Consensus size: 40
59738304 TATTTAGCAC
* * * *
59738314 AGCCTGCAGGTTTTTAA-CCCGGATGTC-ATTCCAGCATGA
1 AGCCTGCGGGTCTTTAAGCCCGGAT-ACAATTCCAGCACGA
* * * *
59738353 AGCCTGTGGATCTTTAGGCCCGGATACAATTCTAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
59738393 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
59738433 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
59738467 CATCAAATAA
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 13 0.13
40 87 0.87
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
Found at i:59743709 original size:40 final size:40
Alignment explanation
Indices: 59743672--59743897 Score: 228
Period size: 40 Copynumber: 5.7 Consensus size: 40
59743662 GCTACTCGTT
*
59743672 CAAATGCCTTCGGGA-TATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACT-TAACCCGGATT-TAGTAACTCGCA
59743712 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
59743752 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * *
59743792 CAAATGCCTTC-AGATCTTAGTCTGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
59743832 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
* *
59743873 CAAA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
59743898 CATCATTCAA
Statistics
Matches: 163, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
39 2 0.01
40 146 0.90
41 15 0.09
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:59743891 original size:80 final size:81
Alignment explanation
Indices: 59743665--59743897 Score: 262
Period size: 80 Copynumber: 2.9 Consensus size: 81
59743655 AGATATAGCT
* * * * *
59743665 ACTCGTTCAAATGCCTTCGGGAT-ATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGTACAAATGCCTTCGGGATCTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCAGGACT
*
59743729 TAACCCGGATTTAGTA
66 TAGCCCGGATTTAGTA
* * * *
59743745 ACTCGCACAAATGCCTTCGGGA-CTTAACCCAGATTTAGTAACTCA-CACAAATGCCTTCA-GAT
1 ACTCGTACAAATGCCTTCGGGATCTTAGCCCGGATATAGTAACT-AGCACAAATGCCTTCAGGA-
* *
59743807 CTTAGTCTGGATTTAGTA
64 CTTAGCCCGGATTTAGTA
* * *
59743825 ACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCACAAA-GCCTTCAGGAC
1 ACTCGTACAAATGCCTTCGGGATCTTAGCCCGGATATAGT-AACTAGCACAAATGCCTTCAGGAC
59743888 TTAGCCCGGA
65 TTAGCCCGGA
59743898 CATCATTCAA
Statistics
Matches: 125, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
79 5 0.04
80 109 0.87
81 11 0.09
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (81 bp):
ACTCGTACAAATGCCTTCGGGATCTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCAGGACT
TAGCCCGGATTTAGTA
Found at i:59750064 original size:37 final size:37
Alignment explanation
Indices: 59750014--59750093 Score: 160
Period size: 37 Copynumber: 2.2 Consensus size: 37
59750004 GGGCTTCACT
59750014 CAAATTCATTTGAATTAACTCTAGATTTCTCAAAACA
1 CAAATTCATTTGAATTAACTCTAGATTTCTCAAAACA
59750051 CAAATTCATTTGAATTAACTCTAGATTTCTCAAAACA
1 CAAATTCATTTGAATTAACTCTAGATTTCTCAAAACA
59750088 CAAATT
1 CAAATT
59750094 TGATCTTGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (37 bp):
CAAATTCATTTGAATTAACTCTAGATTTCTCAAAACA
Found at i:59751074 original size:19 final size:19
Alignment explanation
Indices: 59751024--59751076 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
59751014 AAACCCATAG
**
59751024 GCGAGGGTGCCAGATTGTG
1 GCGAGGGTGCCAGATTGCA
* ***
59751043 GCGAAGCCACCAGATTGCA
1 GCGAGGGTGCCAGATTGCA
59751062 GCGAGGGTGCCAGAT
1 GCGAGGGTGCCAGAT
59751077 ATTGTGACGA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.40, T:0.15
Consensus pattern (19 bp):
GCGAGGGTGCCAGATTGCA
Found at i:59762131 original size:30 final size:30
Alignment explanation
Indices: 59762097--59762165 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
59762087 TCCTCCAGTA
*
59762097 GCCAAAGCTAGTTTAAATCGCACACTTAGT
1 GCCAAAGCTAATTTAAATCGCACACTTAGT
**
59762127 GCCAAAATTAATTTAAATCGCACACTTAGT
1 GCCAAAGCTAATTTAAATCGCACACTTAGT
59762157 GCCAAAGCT
1 GCCAAAGCT
59762166 TCCGATTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (30 bp):
GCCAAAGCTAATTTAAATCGCACACTTAGT
Found at i:59765048 original size:6 final size:6
Alignment explanation
Indices: 59765037--59765061 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59765027 TGTTTTTCTC
59765037 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
59765062 GAAAGGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:59767753 original size:12 final size:12
Alignment explanation
Indices: 59767738--59767781 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
59767728 GTGATTAGTT
59767738 GAGAGATTTGAG
1 GAGAGATTTGAG
59767750 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
59767762 GAGGGATTTTAG
1 GAGAGATTTGAG
59767774 GAGAGATT
1 GAGAGATT
59767782 AGGGGAGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:59767788 original size:24 final size:24
Alignment explanation
Indices: 59767723--59767789 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
59767713 GTAGTTGAGG
* ** *
59767723 GAGGAGTGATTAGTTGAGAGATTT
1 GAGGAGAGATTAGAGGAGGGATTT
*
59767747 GAGGAGAGATTTGAGGAGGGATTT
1 GAGGAGAGATTAGAGGAGGGATTT
* *
59767771 TAGGAGAGATTAGGGGAGG
1 GAGGAGAGATTAGAGGAGG
59767790 AAAAAGTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.25
Consensus pattern (24 bp):
GAGGAGAGATTAGAGGAGGGATTT
Found at i:59769745 original size:31 final size:31
Alignment explanation
Indices: 59769708--59769778 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
59769698 TTACTGGGCT
*
59769708 GAAGCCTTTTCATAAATTATATCACTCGGCC
1 GAAGCCTTTTCATAAATCATATCACTCGGCC
* *
59769739 GAAGCCTTTTCATAAATCATATCATTGGGCC
1 GAAGCCTTTTCATAAATCATATCACTCGGCC
59769770 GAAGCCTTT
1 GAAGCCTTT
59769779 ACTGTAAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (31 bp):
GAAGCCTTTTCATAAATCATATCACTCGGCC
Found at i:59770029 original size:25 final size:26
Alignment explanation
Indices: 59769997--59770093 Score: 171
Period size: 25 Copynumber: 3.8 Consensus size: 26
59769987 CTCTTTTAAT
59769997 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
59770022 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
59770047 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
59770073 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
59770094 GCACTTCCTC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
25 35 0.50
26 35 0.50
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:59770067 original size:51 final size:51
Alignment explanation
Indices: 59769997--59770093 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
59769987 CTCTTTTAAT
*
59769997 AACTGGGGCAAAGCCCTTTTCGATAAACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
59770047 AACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCA-AAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
59770094 GCACTTCCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 10 0.23
51 24 0.55
52 10 0.23
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (51 bp):
AACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGATA
Found at i:59770921 original size:27 final size:27
Alignment explanation
Indices: 59770891--59770982 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
59770881 GGGCACATTC
*
59770891 GTCATTTTACTATACAGGGG-TATTACG
1 GTCATTTTACCATACAGGGGCT-TTACG
* * *
59770918 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
*
59770945 GTC-TCTTTACCCTACAGGGGCTTTACG
1 GTCAT-TTTACCATACAGGGGCTTTACG
*
59770972 GTCTTTTTACC
1 GTCATTTTACC
59770983 TAATAGGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCTTTACG
Found at i:59770990 original size:27 final size:27
Alignment explanation
Indices: 59770913--59770991 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
59770903 TACAGGGGTA
*
59770913 TTACGGTCACTTTACCCTATAGGGGCT
1 TTACGGTCTCTTTACCCTATAGGGGCT
*
59770940 TTACGGTCTCTTTACCCTACAGGGGCT
1 TTACGGTCTCTTTACCCTATAGGGGCT
*
59770967 TTACGGTCTTTTTA-CCTAATAGGGG
1 TTACGGTCTCTTTACCCT-ATAGGGG
59770992 TATTTTAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
26 3 0.06
27 44 0.94
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TTACGGTCTCTTTACCCTATAGGGGCT
Found at i:59771213 original size:81 final size:80
Alignment explanation
Indices: 59771099--59771359 Score: 323
Period size: 81 Copynumber: 3.2 Consensus size: 80
59771089 TAGAAAGTCA
* *
59771099 AGGGTATTTTCGTAACTTTGTA-AATC-AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
1 AGGGTATTTTAGTAA-TTT-TACAAACTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
*
59771162 CGGTAATTTCATAAACC
64 CGGTAATTTTATAAACC
* * *
59771179 AGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAATTGAGGGTATTTC
1 AG-GGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTC
*
59771244 GGTAATTTTACAAACC
65 GGTAATTTTATAAACC
* * **
59771260 AAGGGTATTTTAGCAATTTTACAGACTA-GGGTATTTTGGTAATTTTACTGA-TATAGGGTATTT
1 -AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTA-AGGGTATTT
* *
59771323 TGGTAATTTTATAAACTG
64 CGGTAATTTTATAAAC-C
59771341 AGGGTATTTTAGTAATTTT
1 AGGGTATTTTAGTAATTTT
59771360 GTAAATCGAG
Statistics
Matches: 158, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
79 3 0.02
80 69 0.44
81 84 0.53
82 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (80 bp):
AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCG
GTAATTTTATAAACC
Found at i:59771364 original size:27 final size:26
Alignment explanation
Indices: 59771127--59771359 Score: 252
Period size: 27 Copynumber: 8.7 Consensus size: 26
59771117 TGTAAATCAG
*
59771127 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTTACAAACT-A
* * * *
59771154 GGGTATTTCGGTAATTTCATAAACCA
1 GGGTATTTTGGTAATTTTACAAACTA
59771180 GTGGTATTTTGGTAATTTTACAAACTA
1 G-GGTATTTTGGTAATTTTACAAACTA
* *
59771207 GGGGTATTTTGATAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAACT-A
* *
59771235 GGGTATTTCGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAA-CTA
* * *
59771262 GGGTATTTTAGCAATTTTACAGACTA
1 GGGTATTTTGGTAATTTTACAAACTA
*
59771288 GGGTATTTTGGTAATTTTACTGATA-TA
1 GGGTATTTTGGTAATTTTAC--AAACTA
*
59771315 GGGTATTTTGGTAATTTTATAAACTGA
1 GGGTATTTTGGTAATTTTACAAACT-A
*
59771342 GGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
59771360 GTAAATCGAG
Statistics
Matches: 172, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.01
26 23 0.13
27 143 0.83
28 4 0.02
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACTA
Found at i:59771370 original size:27 final size:27
Alignment explanation
Indices: 59771013--59771520 Score: 236
Period size: 27 Copynumber: 18.7 Consensus size: 27
59771003 GTTCATCCTA
* * * * *
59771013 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * *
59771040 CAAGGGTATTTCAGTAATTTTGTTAAAC
1 CAAGGGTATTTTGGTAATTTT-ATAAAT
* *** *
59771068 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTATAAA-T
* * *
59771097 CAAGGGTATTTTCGTAACTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
59771124 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * *
59771151 TAAGGGTATTTCGGTAATTTCATAAA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
59771177 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTATAAAT
* * *
59771204 CTAGGGGTATTTTGATAATTTTACAAAT
1 C-AAGGGTATTTTGGTAATTTTATAAAT
** * * *
59771232 TGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * * *
59771259 CAAGGGTATTTTAGCAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
59771285 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTA-TAAAT
59771312 -ATAGGGTATTTTGGTAATTTTATAAA-
1 CA-AGGGTATTTTGGTAATTTTATAAAT
* * *
59771338 CTGAGGGTATTTTAGTAATTTTGTAAAT
1 C-AAGGGTATTTTGGTAATTTTATAAAT
* ****** *
59771366 CGAGGGTAAAACAATAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* ***** *
59771393 TAAGGGTAAAACAGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* ****
59771420 CGAGGGTAAAACGGTAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* **** *
59771447 CGAGGGTAAAACGGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * * *
59771474 CGAGGGTACTTTGGTAATTTTACAATT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* **
59771501 TAAGGGTATTTCAGTAATTT
1 CAAGGGTATTTTGGTAATTT
59771521 GGTAAACTAA
Statistics
Matches: 383, Mismatches: 85, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
26 24 0.06
27 312 0.81
28 29 0.08
29 18 0.05
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAT
Found at i:59771372 original size:54 final size:54
Alignment explanation
Indices: 59771015--59771373 Score: 280
Period size: 54 Copynumber: 6.6 Consensus size: 54
59771005 TCATCCTACA
* * * * ** *
59771015 AGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTTAAAC-C
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTT-ATAAACTC
* *** * * * *
59771069 AATGGTATTTCCATAATTTTTAGAAAGTCAAGGGTATTTTCGTAACTTTGTAAA-TC
1 -AGGGTATTTTGGTAA-TTTTACAAA-TCAAGGGTATTTTGGTAATTTTATAAACTC
* * *
59771125 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCATAAAC-C
1 A-GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACTC
* * * * *
59771179 AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGATAATTTTACAAATTG
1 AG-GGTATTTTGGTAATTTTACAAATC-AAGGGTATTTTGGTAATTTTATAAACTC
* * * * * *
59771234 AGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGACT-
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACTC
** *
59771287 AGGGTATTTTGGTAATTTTACTGAT-ATAGGGTATTTTGGTAATTTTATAAACTG
1 AGGGTATTTTGGTAATTTTACAAATCA-AGGGTATTTTGGTAATTTTATAAACTC
* ** *
59771341 AGGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTA
59771374 AAACAATAAT
Statistics
Matches: 239, Mismatches: 53, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
52 1 0.00
53 44 0.18
54 133 0.56
55 22 0.09
56 21 0.09
57 18 0.08
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTATAAACTC
Found at i:59771385 original size:107 final size:107
Alignment explanation
Indices: 59771182--59771386 Score: 234
Period size: 107 Copynumber: 1.9 Consensus size: 107
59771172 ATAAACCAGT
* *
59771182 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAATTGAGGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCAGT
**** *
59771247 AATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGACTAG
66 AATTTTACAAACCAAGGGTAAAACAACAATTTTACAGACTAG
* * * *
59771289 GGTATTTTGGTAATTTTACTGATA-TA-GGGTATTTTGGTAATTTTATAAACTGAGGGTATTTTA
1 GGTATTTTGGTAATTTTAC--AAACTAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCA
** * * *
59771352 GTAATTTTGTAAATCGAGGGTAAAACAATAATTTT
64 GTAATTTTACAAACCAAGGGTAAAACAACAATTTT
59771387 GTAAATTAAG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
107 76 0.95
108 2 0.03
109 2 0.03
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (107 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCAGT
AATTTTACAAACCAAGGGTAAAACAACAATTTTACAGACTAG
Found at i:59777548 original size:19 final size:20
Alignment explanation
Indices: 59777513--59777550 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59777503 CATTTCATGT
*
59777513 TTATTTTATTATTTTACTAA
1 TTATTTTACTATTTTACTAA
59777533 TTATTTTACT-TTTTACTA
1 TTATTTTACTATTTTACTA
59777551 TTTTAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTACTATTTTACTAA
Found at i:59780556 original size:49 final size:49
Alignment explanation
Indices: 59780500--59780597 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
59780490 ACTCAGTGTA
*
59780500 CAACCCCCTATCAGTCAATTGGTATACAACATACAGTAACAGACTGGGC
1 CAACCCCCTATCAGTCAATTGGTATACAACATACAGTAAAAGACTGGGC
59780549 CAACCCCCTATCAGTCAATTGGTATACAACATACAGTAAAAGACTGGGC
1 CAACCCCCTATCAGTCAATTGGTATACAACATACAGTAAAAGACTGGGC
59780598 TTGAGCCTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (49 bp):
CAACCCCCTATCAGTCAATTGGTATACAACATACAGTAAAAGACTGGGC
Found at i:59794534 original size:20 final size:20
Alignment explanation
Indices: 59794509--59794561 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
59794499 TAATCGCGTA
*
59794509 AATTGTAAAAGTGGCTAGCT
1 AATTGTTAAAGTGGCTAGCT
59794529 AATTGTTAAAGTGGCTAGCT
1 AATTGTTAAAGTGGCTAGCT
59794549 AATTGTTAAAGTG
1 AATTGTTAAAGTG
59794562 CTACATTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (20 bp):
AATTGTTAAAGTGGCTAGCT
Found at i:59794706 original size:19 final size:20
Alignment explanation
Indices: 59794682--59794719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59794672 AAGGTTAAAA
*
59794682 TAGTAAAA-AGTAAAATAAT
1 TAGTAAAATAATAAAATAAT
59794701 TAGTAAAATAATAAAATAA
1 TAGTAAAATAATAAAATAA
59794720 ACATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
TAGTAAAATAATAAAATAAT
Found at i:59799710 original size:27 final size:27
Alignment explanation
Indices: 59799652--59800045 Score: 240
Period size: 27 Copynumber: 14.6 Consensus size: 27
59799642 TTAATTCACC
** * * *
59799652 AAATTACTGAAATACCCTCAAATTGTA
1 AAATTACCAAAATACCCTCGATTTATA
*
59799679 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
59799706 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* ****
59799733 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* ***** *
59799760 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
***** * *
59799787 AAATTACTGTTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
59799814 AAATTACTAAAATACCTTC-AGTTTATA
1 AAATTACCAAAATACCCTCGA-TTTATA
*
59799841 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* * *
59799868 AATTTACCAAAATACCCTAG-TCTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * * * *
59799894 AAATTGCTAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
59799921 AAATTACCAAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
59799948 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * * *
59799975 AAATTACCAAATTACCACT-GGTTTGTG
1 AAATTACCAAAATACC-CTCGATTTATA
** *
59800002 AAATTACCAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
59800029 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
59800046 CTAATTTACA
Statistics
Matches: 307, Mismatches: 51, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
26 25 0.08
27 280 0.91
28 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:59799857 original size:54 final size:54
Alignment explanation
Indices: 59799799--59800086 Score: 280
Period size: 54 Copynumber: 5.3 Consensus size: 54
59799789 ATTACTGTTT
** * *
59799799 TACCCTTGATTTACAAAATTACTAAAATACCTTCAGTTTATAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* ** * * * *
59799853 TACCCTCGATCAGTAAATTTACCAAAATACCCT-AGTCTATAAAATTGCTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* * *
59799906 TACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* * * * *
59799960 TACCCCT-AGTTTGTAAAATTACCAAATTACCACT-GGTTTGTGAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAATACC-CTCAGTTTATAAAATTACCAAAA
* * * *
59800014 TACCCTTAATTTGTAAAATTACCAAAATACCC-CTAATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTC-AGTTTATAAAATTACCA-AAA
*
59800068 TACCCTTGACTTTCTAAAA
1 TACCCTTGA-TTTGTAAAA
59800087 ATTATGGAAA
Statistics
Matches: 189, Mismatches: 37, Indels: 15
0.78 0.15 0.06
Matches are distributed among these distances:
53 48 0.25
54 130 0.69
55 11 0.06
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
Found at i:59800006 original size:81 final size:81
Alignment explanation
Indices: 59799813--59800075 Score: 309
Period size: 81 Copynumber: 3.3 Consensus size: 81
59799803 CTTGATTTAC
* * * * ** *
59799813 AAAATTACTAAAATA-CCTTCAGTTTATAAAATTACCAAAATACCCTCGATCAGTAAATTTACCA
1 AAAATTACCAAAATACCCTT-GGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
59799877 AAATA-CCCTAGTCTAT
65 AAATACCCCTAGTCTAT
* *
59799893 AAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
* *
59799958 AATACCCCTAGTTTGT
66 AATACCCCTAGTCTAT
* * *
59799974 AAAATTACCAAATTACCAC-TGGTTTGTGAAATTACCAAAATACCCTTAATTTGTAAAATTACCA
1 AAAATTACCAAAATACC-CTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
* * *
59800038 AAATACCCCTAATTTAC
65 AAATACCCCTAGTCTAT
*
59800055 AAAGTTA-CAGAAATACCCTTG
1 AAAATTACCA-AAATACCCTTG
59800076 ACTTTCTAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
80 60 0.38
81 98 0.62
82 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
AATACCCCTAGTCTAT
Found at i:59800068 original size:27 final size:27
Alignment explanation
Indices: 59799807--59800072 Score: 139
Period size: 27 Copynumber: 9.9 Consensus size: 27
59799797 TTTACCCTTG
* *
59799807 ATTTACAAAATTACTAAAATA-CCTTCA
1 ATTTACAAAATTACCAAAATACCCCT-A
* * *
59799834 GTTTATAAAATTACCAAAATA-CCCTCG
1 ATTTACAAAATTACCAAAATACCCCT-A
* * *
59799861 A-TCAGTAAATTTACCAAAATA-CCCTA
1 ATTTA-CAAAATTACCAAAATACCCCTA
* * * * * * *
59799887 GTCTATAAAATTGCTAAAATACCCTTG
1 ATTTACAAAATTACCAAAATACCCCTA
* **
59799914 GTTTGTAAAATTACCAAAATA-CCCTCA
1 ATTTACAAAATTACCAAAATACCCCT-A
**
59799941 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTACAAAATTACCAAAATACCCCTA
* ** * * *
59799968 GTTTGTAAAATTACCAAATTACCACTG
1 ATTTACAAAATTACCAAAATACCCCTA
* *** *
59799995 GTTTGTGAAATTACCAAAATACCCTTA
1 ATTTACAAAATTACCAAAATACCCCTA
**
59800022 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTACAAAATTACCAAAATACCCCTA
*
59800049 ATTTACAAAGTTA-CAGAAATACCC
1 ATTTACAAAATTACCA-AAATACCC
59800073 TTGACTTTCT
Statistics
Matches: 194, Mismatches: 39, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
26 20 0.10
27 170 0.88
28 4 0.02
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTTACAAAATTACCAAAATACCCCTA
Found at i:59800124 original size:28 final size:27
Alignment explanation
Indices: 59800049--59800128 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
59800039 AATACCCCTA
* * *
59800049 ATTTACAAAGTTACAGAAATACCCTTG
1 ATTTACAAAATTACTGAAATACCATTG
59800076 ACTTT-CTAAAAATTA-TGGAAATACCATTG
1 A-TTTAC--AAAATTACT-GAAATACCATTG
59800105 ATTTAACAAAATTACTGAAATACC
1 ATTT-ACAAAATTACTGAAATACC
59800129 CTTGGTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
27 2 0.05
28 21 0.49
29 19 0.44
30 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (27 bp):
ATTTACAAAATTACTGAAATACCATTG
Found at i:59800280 original size:27 final size:26
Alignment explanation
Indices: 59800190--59800280 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 26
59800180 ACCCCTATTA
*
59800190 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAA-CCCCTGTAG
*
59800217 GGT-AAATAGACCGTAAGCCCCTGTAG
1 GGTAAAAT-GACCGTAAACCCCTGTAG
* *
59800243 GGTAAAGTGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAA-ACCCCTGTAG
59800270 GGTAAAATGAC
1 GGTAAAATGAC
59800281 GAATGTGCCC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 23 0.42
27 32 0.58
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (26 bp):
GGTAAAATGACCGTAAACCCCTGTAG
Found at i:59801213 original size:24 final size:25
Alignment explanation
Indices: 59801079--59801200 Score: 174
Period size: 26 Copynumber: 4.8 Consensus size: 25
59801069 GAGGAAGTGC
*
59801079 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTATCG
* *
59801105 AAAAGGGCTTTTGCCCCAATTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTATCG
*
59801131 AAATGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTT-TGCCCCAGTTTATCG
59801157 AAAAGGGCTTTG-CCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCG
59801181 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
59801201 ATTGAAAGAG
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.28
25 11 0.13
26 49 0.57
27 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCG
Found at i:59801496 original size:31 final size:31
Alignment explanation
Indices: 59801419--59801531 Score: 144
Period size: 31 Copynumber: 3.7 Consensus size: 31
59801409 CATTTACAGT
*
59801419 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
59801450 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* ** *
59801481 AAAGGCTTCAGCCCAGT-A-ACCATTAAATG-
1 AAAGGCTTCGGCCCAGTGATATGATT-TATGA
59801510 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
59801532 TCAAGACTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.29
30 5 0.07
31 46 0.64
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:59802691 original size:27 final size:27
Alignment explanation
Indices: 59802669--59802773 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 27
59802659 AACAAAATAG
**
59802669 TAATTTTACCTTATAAGGGCAAAACAA
1 TAATTTTACCACATAAGGGCAAAACAA
* *
59802696 TAATTTTACCACATAAAGGCAAAACAT
1 TAATTTTACCACATAAGGGCAAAACAA
* * *
59802723 TCATTTCACCTCATAAGGGCAAAACAA
1 TAATTTTACCACATAAGGGCAAAACAA
* *
59802750 TCATTTTACCACAAAAGGGCAAAA
1 TAATTTTACCACATAAGGGCAAAA
59802774 TAGTTATTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (27 bp):
TAATTTTACCACATAAGGGCAAAACAA
Found at i:59802705 original size:54 final size:52
Alignment explanation
Indices: 59802647--59802784 Score: 141
Period size: 54 Copynumber: 2.5 Consensus size: 52
59802637 AACAGTCATC
* *
59802647 TTACCATGAAAGAACAAAATAGTAATTTTACCTTATAAGGGCAAAACAATAATT
1 TTACCAT-AAAG-GCAAAATAGTAATTTTACCTCATAAGGGCAAAACAATAATT
* * * * *
59802701 TTACCACATAAAGGCAAAACATTCATTTCACCTCATAAGGGCAAAACAATCATT
1 TTA-C-CATAAAGGCAAAATAGTAATTTTACCTCATAAGGGCAAAACAATAATT
* *
59802755 TTACCACAAAAGGGCAAAATAGTTATTTTA
1 TTACCA-TAAA-GGCAAAATAGTAATTTTA
59802785 TCGATTAAGG
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
52 2 0.03
53 4 0.06
54 54 0.79
55 5 0.07
56 3 0.04
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (52 bp):
TTACCATAAAGGCAAAATAGTAATTTTACCTCATAAGGGCAAAACAATAATT
Found at i:59803780 original size:12 final size:12
Alignment explanation
Indices: 59803765--59803808 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
59803755 TTCCTCCCCT
*
59803765 AATCTCTCCTAA
1 AATCTCTCCTCA
*
59803777 AATCCCTCCTCA
1 AATCTCTCCTCA
59803789 AATCTCTCCTCA
1 AATCTCTCCTCA
59803801 AATCTCTC
1 AATCTCTC
59803809 AACTAATCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.41, G:0.00, T:0.32
Consensus pattern (12 bp):
AATCTCTCCTCA
Found at i:59803816 original size:24 final size:24
Alignment explanation
Indices: 59803763--59803823 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
59803753 TTTTCCTCCC
* **
59803763 CTAATCTCTCCTAAAATCCCTCCT
1 CTAATCTCTCCTCAAATCCCTCAA
* *
59803787 CAAATCTCTCCTCAAATCTCTCAA
1 CTAATCTCTCCTCAAATCCCTCAA
*
59803811 CTAATCACTCCTC
1 CTAATCTCTCCTC
59803824 CCTCAACTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (24 bp):
CTAATCTCTCCTCAAATCCCTCAA
Found at i:59809733 original size:30 final size:30
Alignment explanation
Indices: 59809666--59809734 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
59809656 ATGAATCGGA
* *
59809666 AACTTTGGCACTAAGTGTGTGATTTAAATT
1 AACTTTGGCACTAAGTGTGCGATTTAAACT
* *
59809696 AATTTTGGCACTAAGTGTGCGGTTTAAACT
1 AACTTTGGCACTAAGTGTGCGATTTAAACT
*
59809726 AGCTTTGGC
1 AACTTTGGC
59809735 TACTGGAGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (30 bp):
AACTTTGGCACTAAGTGTGCGATTTAAACT
Found at i:59811993 original size:46 final size:46
Alignment explanation
Indices: 59811943--59812118 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
59811933 TGATTGAGCA
59811943 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59811989 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
59812034 CATCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
59812082 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59812119 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:59812099 original size:93 final size:93
Alignment explanation
Indices: 59811940--59812111 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
59811930 GGATGATTGA
* *
59811940 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
59812005 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
59812033 GCATCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
59812097 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
59812112 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59818556 original size:29 final size:27
Alignment explanation
Indices: 59818533--59818592 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
59818523 CGCCACATAT
59818533 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGGCCTAGCCACA
* * * *
59818559 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGGCCTAGCCACA
59818586 ATATCTG
1 ATATCTG
59818593 GCAACCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGGCCTAGCCACA
Found at i:59821541 original size:93 final size:93
Alignment explanation
Indices: 59821382--59821552 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
59821372 GGATGGTTGA
* *
59821382 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCCGAACTCGTTGAGT
59821447 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
59821475 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCCGAACTCGTTGAGT
59821540 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
59821553 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59821555 original size:46 final size:46
Alignment explanation
Indices: 59821385--59821557 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
59821375 TGGTTGAGCA
* * *
59821385 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
59821431 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
59821478 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
59821524 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59821558 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 5 0.05
45 2 0.02
46 62 0.58
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:59828489 original size:93 final size:93
Alignment explanation
Indices: 59828330--59828500 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
59828320 GGATGGTTGA
*
59828330 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
59828395 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
59828423 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
59828488 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
59828501 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:59828503 original size:46 final size:46
Alignment explanation
Indices: 59828334--59828505 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
59828324 GGTTGAGCAT
* *
59828334 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * *
59828380 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
59828425 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
*
59828473 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59828506 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 60 0.56
47 28 0.26
48 4 0.04
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:59833422 original size:40 final size:40
Alignment explanation
Indices: 59833378--59833607 Score: 388
Period size: 40 Copynumber: 5.7 Consensus size: 40
59833368 GCTACTTGCT
* *
59833378 CAAATGCCTTTGGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
59833418 CAAATGCCTTCGGGACTTAGCTCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
59833458 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
59833498 CAAATGCCTTCGGGACTTAGCCCGGTTATTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
59833538 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
59833578 CAAATGCCTTCAGGACCTTAGCCCAGTTAT
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTAT
59833608 CATCCGAATA
Statistics
Matches: 181, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 168 0.93
41 13 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:59838086 original size:21 final size:21
Alignment explanation
Indices: 59838029--59838080 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
59838019 ACCCCTATCC
59838029 GTCAACTCTTGCAACTGAGCT
1 GTCAACTCTTGCAACTGAGCT
59838050 GTCAACTCTTGCAACTGAGCT
1 GTCAACTCTTGCAACTGAGCT
*
59838071 TTCAACTCTT
1 GTCAACTCTT
59838081 TTAACTCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (21 bp):
GTCAACTCTTGCAACTGAGCT
Found at i:59841405 original size:40 final size:40
Alignment explanation
Indices: 59841361--59841509 Score: 271
Period size: 40 Copynumber: 3.7 Consensus size: 40
59841351 GCTACTTGCT
*
59841361 CAAATGCCTTCGGGACTTAGCCTGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
59841401 CAAATGCCTTCTGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
59841441 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
59841481 CAAATGCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
59841510 CATCCGAATA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:59846197 original size:27 final size:27
Alignment explanation
Indices: 59846152--59846207 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
59846142 TGGATAAGTT
* * *
59846152 GTAGAATTACTGAAATACCTCTGTAGG
1 GTAGAACTACTGAAATACCCCTGGAGG
**
59846179 GTAGAACTACTGATTTACCCCTGGAGG
1 GTAGAACTACTGAAATACCCCTGGAGG
59846206 GT
1 GT
59846208 GAAATGACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (27 bp):
GTAGAACTACTGAAATACCCCTGGAGG
Found at i:59846884 original size:27 final size:26
Alignment explanation
Indices: 59846840--59846891 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
59846830 CTCACTGCAA
*
59846840 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
59846867 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
59846892 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:59847228 original size:88 final size:89
Alignment explanation
Indices: 59847062--59847240 Score: 326
Period size: 88 Copynumber: 2.0 Consensus size: 89
59847052 ACAGCCCAAA
59847062 ATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAGTCGTAAAAATAATTGACCGTCA
1 ATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAGTCGTAAAAATAATTGACCGTCA
*
59847127 TATTTGATGTTTCTTATATGTATAT
66 TATTTGATGTTTCTT-TATGTAAAT
59847152 ATTGACCCTAGTCGGGAAGTGGTTTCGGGA-CGCTAAACCGAGTCGT-AAAATAATTGACCGTCA
1 ATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAGTCGTAAAAATAATTGACCGTCA
59847215 TATTTGATGTTTCTTTATGTAAAT
66 TATTTGATGTTTCTTTATGTAAAT
59847239 AT
1 AT
59847241 GCATGTGTGA
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
87 10 0.11
88 32 0.36
89 16 0.18
90 30 0.34
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (89 bp):
ATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAGTCGTAAAAATAATTGACCGTCA
TATTTGATGTTTCTTTATGTAAAT
Found at i:59847506 original size:16 final size:16
Alignment explanation
Indices: 59847485--59847515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59847475 AAAGAGAGGA
*
59847485 AATAAATAAAAGAAAG
1 AATAAAAAAAAGAAAG
59847501 AATAAAAAAAAGAAA
1 AATAAAAAAAAGAAA
59847516 AAGTAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AATAAAAAAAAGAAAG
Found at i:59849378 original size:79 final size:80
Alignment explanation
Indices: 59849247--59849474 Score: 318
Period size: 79 Copynumber: 2.9 Consensus size: 80
59849237 ATTTGAATAC
* * * *
59849247 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTTATCCGGGCTAAGA-CCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGA-TATATCCGGGCTAAGACCCGAAGGCAT
*
59849310 TTGTGCAAGTTGATAT
65 TTGTGCAAGATGATAT
59849326 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
*
59849391 TGTGCGAGATGATAT
66 TGTGCAAGATGATAT
* * * * * *
59849406 ATCCGGGCTAAGACCCGAAGGCA-TCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
59849470 TGTGC
66 TGTGC
59849475 TTGTGGTTAT
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 85 0.63
80 50 0.37
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGATGATAT
Found at i:59849451 original size:39 final size:40
Alignment explanation
Indices: 59849247--59849474 Score: 318
Period size: 40 Copynumber: 5.8 Consensus size: 40
59849237 ATTTGAATAC
* * * *
59849247 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGA-TAT
59849287 ATCCGGGCTAAGA-CCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
59849326 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
59849366 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
59849406 ATCCGGGCTAAGACCCGAAGGCA-TCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
59849445 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
59849475 TTGTGGTTAT
Statistics
Matches: 173, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 66 0.38
40 107 0.62
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:59849458 original size:119 final size:119
Alignment explanation
Indices: 59849247--59849474 Score: 334
Period size: 119 Copynumber: 1.9 Consensus size: 119
59849237 ATTTGAATAC
* * * *
59849247 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCGAAGGCATTT
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCGAAGGCATTC
* *
59849312 GTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 GTGCAAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
*
59849366 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGA-TATATCCGGGCTAAGACCCGAAGGCA-
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGA-CCGAAGGCAT
* * *
59849429 TCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
64 TCGTGCAAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGC
59849475 TTGTGGTTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
119 85 0.88
120 12 0.12
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (119 bp):
ATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCGAAGGCATTC
GTGCAAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
Found at i:59857851 original size:40 final size:40
Alignment explanation
Indices: 59857794--59858023 Score: 302
Period size: 40 Copynumber: 5.8 Consensus size: 40
59857784 ATTTGAATAC
* * * *
59857794 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGA-TAT
59857834 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGATAT
*
59857874 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGATAT
* *
59857914 ATCCGGGCTAAGACCCGAAGGCATTTGTGTGAA-ATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTG-CAAGCTGATAT
* * * *
59857954 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGATAT
* * *
59857994 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
59858024 TTGTGGTTAT
Statistics
Matches: 171, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 165 0.96
41 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGCTGATAT
Found at i:59866041 original size:43 final size:42
Alignment explanation
Indices: 59865984--59866105 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
59865974 AATGCTGACA
* **
59865984 TCCCAGACATGGTCTTACATGTAATTCAG-TATCAATGCCTCTG
1 TCCCAGACATGGTCTTACATG-AAATCAGATA-CAATGCCGATG
* * *
59866027 TCCCAAACAGGGTCTTACATGAAATCAGATACGATGCCGATG
1 TCCCAGACATGGTCTTACATGAAATCAGATACAATGCCGATG
*
59866069 TCCCAGACATGGTCTTACACGACATATCAGAT-CAATG
1 TCCCAGACATGGTCTTACATGA-A-ATCAGATACAATG
59866106 TTCACATTCC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 33 0.50
43 26 0.39
44 7 0.11
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACATGAAATCAGATACAATGCCGATG
Found at i:59868873 original size:40 final size:40
Alignment explanation
Indices: 59868808--59868941 Score: 232
Period size: 40 Copynumber: 3.4 Consensus size: 40
59868798 AAAACATGTT
*
59868808 CTTCGTGCTAGAATTGTATCCGGGCTTAAAGACCCGCAGG
1 CTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGG
*
59868848 CTTCATGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGG
1 CTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGG
* *
59868888 CTTTGTGCTGGAATTGTATCCGGGCTTAAAGATCCGCAGG
1 CTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGG
59868928 CTTCGTGCTGGAAT
1 CTTCGTGCTGGAAT
59868942 GACATCCAGG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (40 bp):
CTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGG
Found at i:59870194 original size:21 final size:23
Alignment explanation
Indices: 59870165--59870206 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
59870155 TTTAGCAAGA
*
59870165 ACAACATT-AATCATAGAAACAG
1 ACAACATTAAATCACAGAAACAG
59870187 ACAA-ATTAAATCACAGAAAC
1 ACAACATTAAATCACAGAAAC
59870207 TTCACAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (23 bp):
ACAACATTAAATCACAGAAACAG
Found at i:59876485 original size:18 final size:18
Alignment explanation
Indices: 59876456--59876506 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
59876446 AGTCTAGGAA
* *
59876456 AACACGAGTTTTCAAAAT
1 AACACGATTTTTCAAAAG
* *
59876474 AGCACGATTTTTCTAAAG
1 AACACGATTTTTCAAAAG
*
59876492 AACACGATCTTTCAA
1 AACACGATTTTTCAA
59876507 CAACAAAGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (18 bp):
AACACGATTTTTCAAAAG
Found at i:59881684 original size:41 final size:41
Alignment explanation
Indices: 59881513--59881672 Score: 177
Period size: 41 Copynumber: 3.9 Consensus size: 41
59881503 GGGTCTAAAT
59881513 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
* * * * *
59881554 CCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTG-TCATAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
* * *
59881594 CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGTGGTCTAAT--
1 CCGAG-CTTGGTCT-CGAAGGGCTTTTGAGCCAGT-G-CTAATAA
59881635 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
59881673 GAATTAGGCT
Statistics
Matches: 100, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
39 5 0.05
40 33 0.33
41 57 0.57
42 2 0.02
43 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (41 bp):
CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
Found at i:59890011 original size:41 final size:41
Alignment explanation
Indices: 59889954--59890050 Score: 176
Period size: 41 Copynumber: 2.4 Consensus size: 41
59889944 GGTACTTGGT
59889954 AGCTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGAC
1 AGCTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGAC
*
59889995 AGCTTGTGTGAGCAGCACCGTGTAGCTGCGTCTTGACTGAC
1 AGCTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGAC
*
59890036 AGCTTGCGTGAGCAG
1 AGCTTGTGTGAGCAG
59890051 GCCCATTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.26
Consensus pattern (41 bp):
AGCTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGAC
Found at i:59894084 original size:49 final size:49
Alignment explanation
Indices: 59894023--59894150 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 49
59894013 ACACATTAAT
* * *
59894023 CGATG-CAGTGTCCTAGACAGGTCTTACACTGACTTTCATATATCGAG-GC
1 CGATGCCA-TGTCCCAGACAGCTCTTACACTGACTCTCATATATC-AGTGC
* * * *
59894072 CGATGCCATGTCCCAGATAGCTCTTACACTGGCTCTCATCTATCAGTGT
1 CGATGCCATGTCCCAGACAGCTCTTACACTGACTCTCATATATCAGTGC
* *
59894121 CAATGCCATGTCCCAGACAGTTCTTACACT
1 CGATGCCATGTCCCAGACAGCTCTTACACT
59894151 AACACACAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.03
49 63 0.94
50 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGCTCTTACACTGACTCTCATATATCAGTGC
Found at i:59896284 original size:27 final size:27
Alignment explanation
Indices: 59896255--59896389 Score: 171
Period size: 27 Copynumber: 5.0 Consensus size: 27
59896245 AGAATTATTG
*
59896255 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCA
*
59896282 AAATACCCCTGTAAGGTAGAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCA
* *
59896309 AAATACCCCTATAGGATAGAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCA
* **
59896336 AAATACCCCGGTAGGGTAGAATTATTA
1 AAATACCCCTGTAGGGTAGAATTACCA
* * * *
59896363 AGATACCCTTGTGGGGTAAAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCA
59896390 TTTTTCCCCT
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCA
Found at i:59899612 original size:28 final size:28
Alignment explanation
Indices: 59899546--59899703 Score: 217
Period size: 29 Copynumber: 5.5 Consensus size: 28
59899536 CATGAGATTG
* * **
59899546 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
59899575 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
59899603 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
*
59899632 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
59899661 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
59899689 ACACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
59899704 ACTTACTATA
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
28 46 0.39
29 73 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:59899635 original size:57 final size:58
Alignment explanation
Indices: 59899546--59899701 Score: 219
Period size: 57 Copynumber: 2.7 Consensus size: 58
59899536 CATGAGATTG
* * * *
59899546 GCACTAAGTGTGCGGGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATAT-A
1 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCAAGTTTGATTATATAA
* *
59899603 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA
*
59899661 GCACTAAGTGTGCGAGTTTGATTATATAA-CACTAAGTGTGC
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGC
59899702 GAACTTACTA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 58 0.64
58 32 0.36
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATAA
Found at i:59899694 original size:86 final size:86
Alignment explanation
Indices: 59899546--59899703 Score: 246
Period size: 86 Copynumber: 1.8 Consensus size: 86
59899536 CATGAGATTG
* *
59899546 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATAGCACTAAG
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATAACACTAAG
59899611 TGTGCGAGTTTGATTATGTAA
66 TGTGCGAGTTTGATTATGTAA
* * * *
59899632 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATAACACTAA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATAACACTAA
59899696 GTGTGCGA
65 GTGTGCGA
59899704 ACTTACTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
86 62 0.95
87 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (86 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATAACACTAAG
TGTGCGAGTTTGATTATGTAA
Found at i:59901957 original size:39 final size:39
Alignment explanation
Indices: 59901900--59902090 Score: 319
Period size: 39 Copynumber: 4.9 Consensus size: 39
59901890 ATGTATGAGA
*
59901900 CTAGAAATATATCCGGACATGAGGTCTGCAGGCTATATG
1 CTAGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
*
59901939 CTGGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
1 CTAGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
* *
59901978 CTAGAAATATATCTGGACATGAGGTCCGTAGGCTATATG
1 CTAGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
*
59902017 CTGGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
1 CTAGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
* *
59902056 CTAGAAATATATCCAGACTTGAGGTCCGCAGGCTA
1 CTAGAAATATATCCGGACATGAGGTCCGCAGGCTA
59902091 CGTGCTGAAA
Statistics
Matches: 141, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 141 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (39 bp):
CTAGAAATATATCCGGACATGAGGTCCGCAGGCTATATG
Found at i:59902124 original size:78 final size:78
Alignment explanation
Indices: 59901900--59902136 Score: 244
Period size: 78 Copynumber: 3.1 Consensus size: 78
59901890 ATGTATGAGA
* * * * * * * **
59901900 CTAGAAATATATCCGGACATGAGGTCTGCAGGCTATATGCTGGAAATATATCCGGACATGAGGTC
1 CTAGAAATATATCCAGACATGAGGTCCGCAGGCTACATGCTGAAAAAAAATCCGGACATAAGACC
59901965 CGCAGGCTATATG
66 CGCAGGCTATATG
** * * * * * * **
59901978 CTAGAAATATATCTGGACATGAGGTCCGTAGGCTATATGCTGGAAATATATCCGGACATGAGGTC
1 CTAGAAATATATCCAGACATGAGGTCCGCAGGCTACATGCTGAAAAAAAATCCGGACATAAGACC
59902043 CGCAGGCTATATG
66 CGCAGGCTATATG
* * **
59902056 CTAGAAATATATCCAGACTTGAGGTCCGCAGGCTACGTGCTGAAAAAAAATCCGG-GTTAAAGAC
1 CTAGAAATATATCCAGACATGAGGTCCGCAGGCTACATGCTGAAAAAAAATCCGGACAT-AAGAC
59902120 CCGCAGGCT-TATG
65 CCGCAGGCTATATG
59902133 CTAG
1 CTAG
59902137 TAATGTATTC
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
77 9 0.06
78 132 0.94
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (78 bp):
CTAGAAATATATCCAGACATGAGGTCCGCAGGCTACATGCTGAAAAAAAATCCGGACATAAGACC
CGCAGGCTATATG
Found at i:59902128 original size:117 final size:116
Alignment explanation
Indices: 59901903--59902134 Score: 288
Period size: 117 Copynumber: 2.0 Consensus size: 116
59901893 TATGAGACTA
* * *
59901903 GAAATATATCCGGACATGAGGTCTGCAGGCTATATGCTGGAAATATATCCGGACATGAGGTCCGC
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAGAAATATATCCAGACATGAGGTCCGC
* * * * * ** *
59901968 AGGCTATATGCTAGAAATATATCTGGACATGAGGTCCGTAGGCTATATGCTG
66 AGGCTACATGCTAGAAAAAAATCGGGACATAAGACCCGCAGGCT-TATGCTG
*
59902020 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAGAAATATATCCAGACTTGAGGTCCGC
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAGAAATATATCCAGACATGAGGTCCGC
* **
59902085 AGGCTACGTGCT-GAAAAAAAATCCGGGTTA-AAGACCCGCAGGCTTATGCT
66 AGGCTACATGCTAG-AAAAAAAT-CGGGACATAAGACCCGCAGGCTTATGCT
59902135 AGTAATGTAT
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
116 7 0.07
117 87 0.89
118 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (116 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAGAAATATATCCAGACATGAGGTCCGC
AGGCTACATGCTAGAAAAAAATCGGGACATAAGACCCGCAGGCTTATGCTG
Found at i:59906048 original size:25 final size:25
Alignment explanation
Indices: 59906020--59906095 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
59906010 AAACCCCTTT
59906020 TATTTTTATTAAAGAAATAAAATTA
1 TATTTTTATTAAAGAAATAAAATTA
59906045 TATTTTTATTAAAGAAATAAAATTA
1 TATTTTTATTAAAGAAATAAAATTA
*
59906070 TATTTTTAATAAAGAAATAAAATTA
1 TATTTTTATTAAAGAAATAAAATTA
59906095 T
1 T
59906096 CATTGCTCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TATTTTTATTAAAGAAATAAAATTA
Found at i:59909224 original size:19 final size:19
Alignment explanation
Indices: 59909178--59909223 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
59909168 TCTCTCTACT
*
59909178 TCTCGTTTTATCGCTTTTC
1 TCTCGTTTTATCACTTTTC
*
59909197 TCTCGTTTTATCATTTTTC
1 TCTCGTTTTATCACTTTTC
59909216 TCTC-TTTT
1 TCTCGTTTT
59909224 TGAGGTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.63
Consensus pattern (19 bp):
TCTCGTTTTATCACTTTTC
Found at i:59910504 original size:27 final size:27
Alignment explanation
Indices: 59910463--59910522 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
59910453 GTACCTAGTC
59910463 CCCCTAGTTGATAAAATGACTATTATG
1 CCCCTAGTTGATAAAATGACTATTATG
*
59910490 CCCCTAGTTGGTAAAATGACTATTATG
1 CCCCTAGTTGATAAAATGACTATTATG
59910517 CCCCTA
1 CCCCTA
59910523 TGAGATGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (27 bp):
CCCCTAGTTGATAAAATGACTATTATG
Found at i:59917996 original size:26 final size:26
Alignment explanation
Indices: 59917951--59918014 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
59917941 GTGCCTAGAC
*
59917951 CCCCTAGTTGATAAAATGACTA-TTATG
1 CCCCTAG-TGAGAAAATGAC-AGTTATG
59917978 CCCCTAGTGAGAAAATGACAGTTATG
1 CCCCTAGTGAGAAAATGACAGTTATG
59918004 CCCCTA-TGAGA
1 CCCCTAGTGAGA
59918015 TGTATGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 6 0.17
26 22 0.63
27 7 0.20
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (26 bp):
CCCCTAGTGAGAAAATGACAGTTATG
Found at i:59921740 original size:24 final size:24
Alignment explanation
Indices: 59921701--59921790 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
59921691 TACCGATATA
* *
59921701 TCAGCTCATAAGAGCTTACTATTT
1 TCAGCTCGTAAAAGCTTACTATTT
** *
59921725 TCAGCTCGTTGAAGCTTACT-GTT
1 TCAGCTCGTAAAAGCTTACTATTT
*
59921748 TCAGCTCATAAAAGCTTACTATTT
1 TCAGCTCGTAAAAGCTTACTATTT
* *
59921772 TTAGCTCGTAAGAGCTTAC
1 TCAGCTCGTAAAAGCTTAC
59921791 CGTTTCAGCT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.36
24 34 0.64
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (24 bp):
TCAGCTCGTAAAAGCTTACTATTT
Found at i:59921753 original size:23 final size:24
Alignment explanation
Indices: 59921713--59921801 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
59921703 AGCTCATAAG
* *
59921713 AGCTTACTATTTTCAGCTCGTTGA
1 AGCTTACTAGTTTCAGCTCGTTAA
* *
59921737 AGCTTACT-GTTTCAGCTCATAAA
1 AGCTTACTAGTTTCAGCTCGTTAA
* *
59921760 AGCTTACTATTTTTAGCTCG-TAA
1 AGCTTACTAGTTTCAGCTCGTTAA
*
59921783 GAGCTTAC-CGTTTCAGCTC
1 -AGCTTACTAGTTTCAGCTC
59921802 AATAGAGCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
23 29 0.56
24 23 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (24 bp):
AGCTTACTAGTTTCAGCTCGTTAA
Found at i:59921811 original size:47 final size:47
Alignment explanation
Indices: 59921676--59921814 Score: 167
Period size: 47 Copynumber: 2.9 Consensus size: 47
59921666 GGACTCACCG
59921676 CAGCTCG-AACGAGCTTACCGATATATCAGCTCATAAGAGCTTACTATTTT
1 CAGCTCGTAA-GAGCTTACCG-T-T-TCAGCTCATAAGAGCTTACTATTTT
* * *
59921726 CAGCTCGT-TGAAGCTTACTGTTTCAGCTCATAAAAGCTTACTATTTT
1 CAGCTCGTAAG-AGCTTACCGTTTCAGCTCATAAGAGCTTACTATTTT
*
59921773 TAGCTCGTAAGAGCTTACCGTTTCAGCTCA-ATAGAGCTTACT
1 CAGCTCGTAAGAGCTTACCGTTTCAGCTCATA-AGAGCTTACT
59921815 GTTCATAGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
46 1 0.01
47 58 0.74
48 2 0.03
49 2 0.03
50 15 0.19
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (47 bp):
CAGCTCGTAAGAGCTTACCGTTTCAGCTCATAAGAGCTTACTATTTT
Found at i:59921832 original size:47 final size:47
Alignment explanation
Indices: 59921737--59921833 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 47
59921727 AGCTCGTTGA
* ** * *
59921737 AGCTTACTGTTTCAGCTCATAAAAGCTTACTATTTTTAGCTCGTAAG
1 AGCTTACCGTTTCAGCTCATAAAAGCTTACTATTCATAGCTAGAAAG
* *
59921784 AGCTTACCGTTTCAGCTCA-ATAGAGCTTACTGTTCATAGCTAGAAAG
1 AGCTTACCGTTTCAGCTCATA-AAAGCTTACTATTCATAGCTAGAAAG
59921831 AGC
1 AGC
59921834 GGAAAATGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 1 0.02
47 41 0.98
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (47 bp):
AGCTTACCGTTTCAGCTCATAAAAGCTTACTATTCATAGCTAGAAAG
Found at i:59923003 original size:76 final size:76
Alignment explanation
Indices: 59922917--59923071 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
59922907 ATTAACAATC
* *
59922917 AAAGTACATGTATATACGTACACATAATTATCAGTTTTTCAAAAATGTATATAATGCTCATGGTG
1 AAAGTACATGTATATACGTACACATAATTATCAATTTTTCAAAAATGCATATAATGCTCATGGTG
59922982 TACTATTACAT
66 TACTATTACAT
* *
59922993 AAAGTACATGTATATATGTACACATAATTATCAATTTTTCAAAAATGCATATAATGGTCATGGTG
1 AAAGTACATGTATATACGTACACATAATTATCAATTTTTCAAAAATGCATATAATGCTCATGGTG
59923058 TACTATTACAT
66 TACTATTACAT
59923069 AAA
1 AAA
59923072 ATCACTATTC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (76 bp):
AAAGTACATGTATATACGTACACATAATTATCAATTTTTCAAAAATGCATATAATGCTCATGGTG
TACTATTACAT
Found at i:59924914 original size:11 final size:11
Alignment explanation
Indices: 59924878--59924933 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
59924868 CATGGTATGT
59924878 ATGATATGCAC
1 ATGATATGCAC
* *
59924889 ATGACATG--T
1 ATGATATGCAC
59924898 ATGATATGCAC
1 ATGATATGCAC
*
59924909 ATGATATG--T
1 ATGATATGCAC
59924918 ATGATATGCAC
1 ATGATATGCAC
59924929 ATGAT
1 ATGAT
59924934 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:59924933 original size:20 final size:20
Alignment explanation
Indices: 59924867--59924933 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
59924857 ATTTTGATAA
*
59924867 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59924887 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
59924907 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
59924927 ACATGAT
1 ACATGAT
59924934 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:59925011 original size:25 final size:25
Alignment explanation
Indices: 59924983--59925111 Score: 158
Period size: 25 Copynumber: 5.2 Consensus size: 25
59924973 AGGAAGTGTA
*
59924983 AAAGGGCTTATGCCCTAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
59925008 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
59925033 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
*
59925057 AAAGGGCTT-TGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
*
59925080 AAAGAGGC-TAGGCCTCCAGTTATATGAT
1 AAAG-GGCTTATGCC-CCAG-T-TATGAT
59925108 AAAG
1 AAAG
59925112 CAGCTATGCT
Statistics
Matches: 94, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.20
24 15 0.16
25 51 0.54
26 1 0.01
27 4 0.04
28 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:59929069 original size:46 final size:45
Alignment explanation
Indices: 59929002--59929164 Score: 184
Period size: 46 Copynumber: 3.5 Consensus size: 45
59928992 CGCCCCTAAG
59929002 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCATCCATAAA
* * * * **
59929048 TGAACTCGGACTCAACTCAACGAGTTCGGTTGCCTAG-ATACATCTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCATCCAT-AAA
* * * *
59929095 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCATCCATAAA
59929141 TGAACTCGGACTCAACTCAACGAG
1 TGAACTCGGACTCAACTCAACGAG
59929165 TTTGGATGCT
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 57 0.61
47 34 0.36
48 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCATCCATAAA
Found at i:59934025 original size:29 final size:29
Alignment explanation
Indices: 59933986--59934073 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
59933976 CAAAGATAAC
*
59933986 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
59934015 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
59934044 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
59934074 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:59934044 original size:15 final size:15
Alignment explanation
Indices: 59933986--59934064 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
59933976 CAAAGATAAC
*
59933986 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
59934000 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
59934015 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
59934029 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
59934044 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
59934059 AAGAAA
1 AAGAAA
59934065 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:59934073 original size:15 final size:15
Alignment explanation
Indices: 59933997--59934073 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
59933987 AGAAAACCGA
59933997 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
59934012 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
59934026 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
59934040 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
59934056 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
59934071 ATA
1 ATA
59934074 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:59942272 original size:39 final size:40
Alignment explanation
Indices: 59942155--59942339 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
59942145 GCTACTCGTT
*
59942155 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
59942195 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
59942235 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
59942274 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
59942315 -ACAA-GCCTTCGGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGACTTAGCCCGGA
59942340 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 80 0.63
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:59942299 original size:79 final size:82
Alignment explanation
Indices: 59942155--59942339 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 82
59942145 GCTACTCGTT
* *
59942155 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
59942219 GATTTAGTAAC-TCGCA
66 GATATAGTAACTTAGCA
* **
59942235 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
59942297 GGATATGGTCACTTAGCA
65 GGATATAGTAACTTAGCA
59942315 -ACAA-GCCTTCGGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGACTTAGCCCGGA
59942340 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 56 0.62
80 32 0.35
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GATATAGTAACTTAGCA
Found at i:59948945 original size:20 final size:20
Alignment explanation
Indices: 59948922--59948960 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
59948912 TAAACATGGT
*
59948922 ATGTATGATATGCGCATGAC
1 ATGTATGATATGCACATGAC
59948942 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
59948961 TGTATTCATA
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:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:59949072 original size:23 final size:24
Alignment explanation
Indices: 59949010--59949105 Score: 117
Period size: 24 Copynumber: 4.0 Consensus size: 24
59949000 GGAGGAAGTG
*
59949010 TAAAAGGGCTTATGCCCCAATTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
59949034 GATAAA-GGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
59949058 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
59949081 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
59949106 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
23 22 0.35
24 30 0.48
25 11 0.17
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:59950734 original size:13 final size:13
Alignment explanation
Indices: 59950716--59950740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59950706 TAATGGTATA
59950716 TTGAATCCATGAT
1 TTGAATCCATGAT
59950729 TTGAATCCATGA
1 TTGAATCCATGA
59950741 AAATTTAGTA
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:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:59951797 original size:47 final size:47
Alignment explanation
Indices: 59951665--59951969 Score: 466
Period size: 47 Copynumber: 6.4 Consensus size: 47
59951655 AAATCATTAT
* *
59951665 AAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
59951712 AAAGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
59951761 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
59951808 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
59951855 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* * * * * * * *
59951902 AAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTA
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
59951949 AAAGTGTATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
59951970 TCCCGAAGGG
Statistics
Matches: 239, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 195 0.82
49 44 0.18
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:59958932 original size:38 final size:38
Alignment explanation
Indices: 59958879--59958955 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
59958869 TTGTATAACT
59958879 ATCATCAAACATCAAAACACATGCTTATTCAACAACGG
1 ATCATCAAACATCAAAACACATGCTTATTCAACAACGG
* *
59958917 ATCATCACACTTCAAAACACATGCTTATTCAACAACGG
1 ATCATCAAACATCAAAACACATGCTTATTCAACAACGG
59958955 A
1 A
59958956 AACATTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (38 bp):
ATCATCAAACATCAAAACACATGCTTATTCAACAACGG
Found at i:59961650 original size:32 final size:32
Alignment explanation
Indices: 59961609--59961687 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
59961599 TGATATTGAA
*
59961609 ATGGGCTAGGCCCAACTGATACTAG-TTCTGAT
1 ATGGGCTAGGCCCAACTGATA-TAGATTCTGAG
* *
59961641 ATGGGCTAGGCCCAACTGATATTGATTTTGAG
1 ATGGGCTAGGCCCAACTGATATAGATTCTGAG
*
59961673 ATAGGCTAGGCCCAA
1 ATGGGCTAGGCCCAA
59961688 TTAAGACTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (32 bp):
ATGGGCTAGGCCCAACTGATATAGATTCTGAG
Found at i:59963609 original size:26 final size:26
Alignment explanation
Indices: 59963573--59963626 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
59963563 CAGAGTAAGC
59963573 TATAAAGCTTAGTAAGCTCGTATGAT
1 TATAAAGCTTAGTAAGCTCGTATGAT
59963599 TATAAAGCTTAGTAAGCTCGTATGAT
1 TATAAAGCTTAGTAAGCTCGTATGAT
59963625 TA
1 TA
59963627 AAGTAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (26 bp):
TATAAAGCTTAGTAAGCTCGTATGAT
Found at i:59963672 original size:33 final size:33
Alignment explanation
Indices: 59963630--59963698 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
59963620 ATGATTAAAG
59963630 TAAAACTTACCATATATACACAATTTAAGCAAT
1 TAAAACTTACCATATATACACAATTTAAGCAAT
59963663 TAAAACTTACCATATATACACAATTTAAGCAAT
1 TAAAACTTACCATATATACACAATTTAAGCAAT
59963696 TAA
1 TAA
59963699 CATGTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.30
Consensus pattern (33 bp):
TAAAACTTACCATATATACACAATTTAAGCAAT
Found at i:59967682 original size:27 final size:27
Alignment explanation
Indices: 59967645--59967810 Score: 82
Period size: 27 Copynumber: 6.1 Consensus size: 27
59967635 ACATAGGCGT
* *
59967645 AAAATAGTCATCTTACCATAAAAGGGC
1 AAAATAATCATCTTACCACAAAAGGGC
* * *
59967672 AAAATAATCATTTTACCACATAAGGGT
1 AAAATAATCATCTTACCACAAAAGGGC
* ** * *
59967699 AAAACAATCAAT-TTACCTTATAAGGGT
1 AAAATAATC-ATCTTACCACAAAAGGGC
* * * * * *
59967726 AAAACAGTCATTTTCCCCCATAAGGGC
1 AAAATAATCATCTTACCACAAAAGGGC
* * * * *
59967753 AAAACAATCATTTTACCTCATAAGAGC
1 AAAATAATCATCTTACCACAAAAGGGC
* * * * *
59967780 AAAACAGTCATTTTACCTCATAAGGGC
1 AAAATAATCATCTTACCACAAAAGGGC
59967807 AAAA
1 AAAA
59967811 CAGTCATTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.02
27 114 0.97
28 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (27 bp):
AAAATAATCATCTTACCACAAAAGGGC
Found at i:59967811 original size:27 final size:27
Alignment explanation
Indices: 59967666--59967848 Score: 231
Period size: 27 Copynumber: 6.8 Consensus size: 27
59967656 CTTACCATAA
* * *
59967666 AAGGGCAAAATAATCATTTTACCACAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
* * * *
59967693 AAGGGTAAAACAATCAATTTACCTTAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
* * *
59967720 AAGGGTAAAACAGTCATTTTCCCCCAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
*
59967747 AAGGGCAAAACAATCATTTTACCTCAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
*
59967774 AAGAGCAAAACAGTCATTTTACCTCAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
59967801 AAGGGCAAAACAGTCATTTTACCTCAT
1 AAGGGCAAAACAGTCATTTTACCTCAT
* * *
59967828 AATGGAAAAATAGTCATTTTA
1 AAGGGCAAAACAGTCATTTTA
59967849 TTGATTAAGG
Statistics
Matches: 136, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (27 bp):
AAGGGCAAAACAGTCATTTTACCTCAT
Found at i:59969596 original size:9 final size:10
Alignment explanation
Indices: 59969557--59969603 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
59969547 GGGGCTGTTC
59969557 TGGGCCTCAA
1 TGGGCCTCAA
59969567 TGGGCCTCGAA
1 TGGGCCTC-AA
*
59969578 -GGGCC-AAA
1 TGGGCCTCAA
59969586 TGGGCCT-AA
1 TGGGCCTCAA
59969595 TGGGCCTCA
1 TGGGCCTCA
59969604 GGGCCCACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
8 2 0.06
9 14 0.44
10 14 0.44
11 2 0.06
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (10 bp):
TGGGCCTCAA
Found at i:59971156 original size:44 final size:43
Alignment explanation
Indices: 59971060--59971180 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 43
59971050 TCGATGCTTC
* * *** * *
59971060 TGTCCCAGACAGGGTCTTACATGAAATAAGATAT-GATGCCTA
1 TGTCCCAGACACGGTCTTACACGAAATCTCAAATCGAGGCCTA
** *
59971102 TGTCTTAGACATGGTCTTACACGTAAATCTCAAATCGAGGCCTA
1 TGTCCCAGACACGGTCTTACACG-AAATCTCAAATCGAGGCCTA
* * *
59971146 TGTCCCAGACACGGTGTTACATGATATCTCAAATC
1 TGTCCCAGACACGGTCTTACACGAAATCTCAAATC
59971181 AACGTCAACG
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 19 0.31
43 18 0.29
44 25 0.40
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
TGTCCCAGACACGGTCTTACACGAAATCTCAAATCGAGGCCTA
Found at i:59972648 original size:22 final size:22
Alignment explanation
Indices: 59972620--59972673 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
59972610 AAATTATATG
59972620 CGAAGGATCGGATTTGTATCTT
1 CGAAGGATCGGATTTGTATCTT
59972642 CGAAGGATCGGATTTGTATCTT
1 CGAAGGATCGGATTTGTATCTT
* *
59972664 TGAAGCATCG
1 CGAAGGATCG
59972674 ATACATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (22 bp):
CGAAGGATCGGATTTGTATCTT
Found at i:59975352 original size:22 final size:22
Alignment explanation
Indices: 59975324--59975369 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
59975314 CACGACTGTG
*
59975324 CAACATAGCTATGTGTCATACA
1 CAACATAGCTATGTGTCACACA
*
59975346 CAACATAGCTGTGTGTCACACA
1 CAACATAGCTATGTGTCACACA
59975368 CA
1 CA
59975370 GTTGAGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (22 bp):
CAACATAGCTATGTGTCACACA
Found at i:59975470 original size:15 final size:15
Alignment explanation
Indices: 59975450--59975484 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
59975440 CCAATTAGGT
59975450 CAAACCTACAAGTAC
1 CAAACCTACAAGTAC
59975465 CAAACCTACAAGTAC
1 CAAACCTACAAGTAC
59975480 CAAAC
1 CAAAC
59975485 AAAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.34, G:0.06, T:0.11
Consensus pattern (15 bp):
CAAACCTACAAGTAC
Found at i:59977714 original size:43 final size:42
Alignment explanation
Indices: 59977661--59977750 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
59977651 ATCACGTATC
* * *
59977661 ACATGTAATCAAACATCGATGCC-ACTGTCCCAGATAGGGTCTT
1 ACATGAAATCAAACA-CGATACCGA-TGTCCCAGACAGGGTCTT
* * *
59977704 ACATGAAATCAGATACGATACCGATGTCCCAGACATGGTCTT
1 ACATGAAATCAAACACGATACCGATGTCCCAGACAGGGTCTT
59977746 ACATG
1 ACATG
59977751 TAAAATAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.68
43 13 0.32
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (42 bp):
ACATGAAATCAAACACGATACCGATGTCCCAGACAGGGTCTT
Found at i:59994034 original size:49 final size:49
Alignment explanation
Indices: 59993962--59994059 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
59993952 TAAGGCTCAT
*
59993962 GCCCAGTCTGTTACTGTATGTTGTCTACCAATTGACTGATAGGGGGTTG
1 GCCCAGTCTGTTACTGTATGTTGTATACCAATTGACTGATAGGGGGTTG
*
59994011 GCCCAGTCTGTTACTGTATGTTGTATACCAATTGGCTGATAGGGGGTTG
1 GCCCAGTCTGTTACTGTATGTTGTATACCAATTGACTGATAGGGGGTTG
59994060 TACACTGAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (49 bp):
GCCCAGTCTGTTACTGTATGTTGTATACCAATTGACTGATAGGGGGTTG
Found at i:59996870 original size:20 final size:20
Alignment explanation
Indices: 59996845--59996897 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
59996835 TAATCGCGTA
*
59996845 AATTGTAAAAGTGGCTAGCT
1 AATTGTTAAAGTGGCTAGCT
59996865 AATTGTTAAAGTGGCTAGCT
1 AATTGTTAAAGTGGCTAGCT
59996885 AATTGTTAAAGTG
1 AATTGTTAAAGTG
59996898 CTACATTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (20 bp):
AATTGTTAAAGTGGCTAGCT
Found at i:59997042 original size:19 final size:20
Alignment explanation
Indices: 59997018--59997055 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59997008 AAGGTTAAAA
*
59997018 TAGTAAAA-AGTAAAATAAT
1 TAGTAAAATAATAAAATAAT
59997037 TAGTAAAATAATAAAATAA
1 TAGTAAAATAATAAAATAA
59997056 ACATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
TAGTAAAATAATAAAATAAT
Found at i:60002044 original size:27 final size:27
Alignment explanation
Indices: 60001986--60002379 Score: 240
Period size: 27 Copynumber: 14.6 Consensus size: 27
60001976 TTAATTCACC
** * * *
60001986 AAATTACTGAAATACCCTCAAATTGTA
1 AAATTACCAAAATACCCTCGATTTATA
*
60002013 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
60002040 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* ****
60002067 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* ***** *
60002094 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
***** * *
60002121 AAATTACTGTTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
60002148 AAATTACTAAAATACCTTC-AGTTTATA
1 AAATTACCAAAATACCCTCGA-TTTATA
*
60002175 AAATTACCAAAATACCCTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* * *
60002202 AATTTACCAAAATACCCTAG-TCTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * * * *
60002228 AAATTGCTAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
60002255 AAATTACCAAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
60002282 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * * *
60002309 AAATTACCAAATTACCACT-GGTTTGTG
1 AAATTACCAAAATACC-CTCGATTTATA
** *
60002336 AAATTACCAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
60002363 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
60002380 CTAATTTACA
Statistics
Matches: 307, Mismatches: 51, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
26 25 0.08
27 280 0.91
28 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:60002191 original size:54 final size:54
Alignment explanation
Indices: 60002133--60002420 Score: 280
Period size: 54 Copynumber: 5.3 Consensus size: 54
60002123 ATTACTGTTT
** * *
60002133 TACCCTTGATTTACAAAATTACTAAAATACCTTCAGTTTATAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* ** * * * *
60002187 TACCCTCGATCAGTAAATTTACCAAAATACCCT-AGTCTATAAAATTGCTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* * *
60002240 TACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
* * * * *
60002294 TACCCCT-AGTTTGTAAAATTACCAAATTACCACT-GGTTTGTGAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAATACC-CTCAGTTTATAAAATTACCAAAA
* * * *
60002348 TACCCTTAATTTGTAAAATTACCAAAATACCC-CTAATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTGTAAAATTACCAAAATACCCTC-AGTTTATAAAATTACCA-AAA
*
60002402 TACCCTTGACTTTCTAAAA
1 TACCCTTGA-TTTGTAAAA
60002421 ATTATGGAAA
Statistics
Matches: 189, Mismatches: 37, Indels: 15
0.78 0.15 0.06
Matches are distributed among these distances:
53 48 0.25
54 130 0.69
55 11 0.06
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
TACCCTTGATTTGTAAAATTACCAAAATACCCTCAGTTTATAAAATTACCAAAA
Found at i:60002340 original size:81 final size:81
Alignment explanation
Indices: 60002147--60002409 Score: 309
Period size: 81 Copynumber: 3.3 Consensus size: 81
60002137 CTTGATTTAC
* * * * ** *
60002147 AAAATTACTAAAATA-CCTTCAGTTTATAAAATTACCAAAATACCCTCGATCAGTAAATTTACCA
1 AAAATTACCAAAATACCCTT-GGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
60002211 AAATA-CCCTAGTCTAT
65 AAATACCCCTAGTCTAT
* *
60002227 AAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
* *
60002292 AATACCCCTAGTTTGT
66 AATACCCCTAGTCTAT
* * *
60002308 AAAATTACCAAATTACCAC-TGGTTTGTGAAATTACCAAAATACCCTTAATTTGTAAAATTACCA
1 AAAATTACCAAAATACC-CTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
* * *
60002372 AAATACCCCTAATTTAC
65 AAATACCCCTAGTCTAT
*
60002389 AAAGTTA-CAGAAATACCCTTG
1 AAAATTACCA-AAATACCCTTG
60002410 ACTTTCTAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
80 60 0.38
81 98 0.62
82 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
AATACCCCTAGTCTAT
Found at i:60002402 original size:27 final size:27
Alignment explanation
Indices: 60002141--60002406 Score: 139
Period size: 27 Copynumber: 9.9 Consensus size: 27
60002131 TTTACCCTTG
* *
60002141 ATTTACAAAATTACTAAAATA-CCTTCA
1 ATTTACAAAATTACCAAAATACCCCT-A
* * *
60002168 GTTTATAAAATTACCAAAATA-CCCTCG
1 ATTTACAAAATTACCAAAATACCCCT-A
* * *
60002195 A-TCAGTAAATTTACCAAAATA-CCCTA
1 ATTTA-CAAAATTACCAAAATACCCCTA
* * * * * * *
60002221 GTCTATAAAATTGCTAAAATACCCTTG
1 ATTTACAAAATTACCAAAATACCCCTA
* **
60002248 GTTTGTAAAATTACCAAAATA-CCCTCA
1 ATTTACAAAATTACCAAAATACCCCT-A
**
60002275 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTACAAAATTACCAAAATACCCCTA
* ** * * *
60002302 GTTTGTAAAATTACCAAATTACCACTG
1 ATTTACAAAATTACCAAAATACCCCTA
* *** *
60002329 GTTTGTGAAATTACCAAAATACCCTTA
1 ATTTACAAAATTACCAAAATACCCCTA
**
60002356 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTACAAAATTACCAAAATACCCCTA
*
60002383 ATTTACAAAGTTA-CAGAAATACCC
1 ATTTACAAAATTACCA-AAATACCC
60002407 TTGACTTTCT
Statistics
Matches: 194, Mismatches: 39, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
26 20 0.10
27 170 0.88
28 4 0.02
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTTACAAAATTACCAAAATACCCCTA
Found at i:60002458 original size:28 final size:27
Alignment explanation
Indices: 60002383--60002462 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
60002373 AATACCCCTA
* * *
60002383 ATTTACAAAGTTACAGAAATACCCTTG
1 ATTTACAAAATTACTGAAATACCATTG
60002410 ACTTT-CTAAAAATTA-TGGAAATACCATTG
1 A-TTTAC--AAAATTACT-GAAATACCATTG
60002439 ATTTAACAAAATTACTGAAATACC
1 ATTT-ACAAAATTACTGAAATACC
60002463 CTTGGTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
27 2 0.05
28 21 0.49
29 19 0.44
30 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (27 bp):
ATTTACAAAATTACTGAAATACCATTG
Found at i:60002614 original size:27 final size:26
Alignment explanation
Indices: 60002524--60002614 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 26
60002514 ACCCCTATTA
*
60002524 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAA-CCCCTGTAG
*
60002551 GGT-AAATAGACCGTAAGCCCCTGTAG
1 GGTAAAAT-GACCGTAAACCCCTGTAG
* *
60002577 GGTAAAGTGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAA-ACCCCTGTAG
60002604 GGTAAAATGAC
1 GGTAAAATGAC
60002615 GAATGTGCCC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 23 0.42
27 32 0.58
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (26 bp):
GGTAAAATGACCGTAAACCCCTGTAG
Found at i:60003546 original size:24 final size:25
Alignment explanation
Indices: 60003412--60003533 Score: 174
Period size: 26 Copynumber: 4.8 Consensus size: 25
60003402 GAGGAAGTGC
*
60003412 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTATCG
* *
60003438 AAAAGGGCTTTTGCCCCAATTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTATCG
*
60003464 AAATGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTT-TGCCCCAGTTTATCG
60003490 AAAAGGGCTTTG-CCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCG
60003514 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
60003534 ATTGAAAGAG
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.28
25 11 0.13
26 49 0.57
27 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCG
Found at i:60003829 original size:31 final size:31
Alignment explanation
Indices: 60003752--60003864 Score: 144
Period size: 31 Copynumber: 3.7 Consensus size: 31
60003742 CATTTACAGT
*
60003752 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
60003783 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* ** *
60003814 AAAGGCTTCAGCCCAGT-A-ACCATTAAATG-
1 AAAGGCTTCGGCCCAGTGATATGATT-TATGA
60003843 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
60003865 TCAAGACTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.29
30 5 0.07
31 46 0.64
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:60087556 original size:37 final size:37
Alignment explanation
Indices: 60087506--60087584 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
60087496 TTATTACGAA
* * *
60087506 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
60087543 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
60087580 GTCTT
1 GTCTT
60087585 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:60087781 original size:47 final size:47
Alignment explanation
Indices: 60087703--60088111 Score: 714
Period size: 47 Copynumber: 8.7 Consensus size: 47
60087693 CCCTTCGGGA
* * * * * *
60087703 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
60087750 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60087797 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60087844 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60087891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60087938 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60087985 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
60088032 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
60088079 CTTATCTCATATAT-CA-TTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
60088112 AGAATCCTAA
Statistics
Matches: 350, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
45 16 0.05
46 2 0.01
47 332 0.95
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:60091926 original size:40 final size:40
Alignment explanation
Indices: 60091773--60092413 Score: 988
Period size: 40 Copynumber: 16.1 Consensus size: 40
60091763 CGAATACACG
* * * *
60091773 TCACTAGCATGATTGCTCTTC-AAGACCTAGCCC-GATATA
1 TCACTAGCACGAATGCTCTTCGGA-ACTTAGCCCGGATATA
* * ** *
60091812 ACACCAGCACGAATGCTC-TCGG-GTTTAGCACGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60091850 TCACTAGCACGAATGCTCCTCGG-ACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* * *
60091889 TCACTAGCACAAATGCTCCTCGGGACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
60091929 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGAATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60091969 TCACTAGCACGAATGCTCTTCGGAACTTAGCTCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
60092009 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
60092049 TCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
* *
60092089 TCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60092129 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60092169 TCACTAGCACGAATGCTCTTTGGAACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
60092209 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
60092249 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60092289 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
*
60092329 TCACTAGCACGAATGCTCCTT-GGGACTTAGCCCGGATATA
1 TCACTAGCACGAATGCT-CTTCGGAACTTAGCCCGGATATA
* *
60092369 TCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
60092409 TCACT
1 TCACT
60092414 CTCAATTCTC
Statistics
Matches: 556, Mismatches: 40, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
37 5 0.01
38 24 0.04
39 55 0.10
40 469 0.84
41 3 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA
Found at i:60093675 original size:37 final size:37
Alignment explanation
Indices: 60093625--60093703 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
60093615 TTATTACGAA
* * *
60093625 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
60093662 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
60093699 GTCTT
1 GTCTT
60093704 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Done.