Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 105 of 168
Found at i:31061811 original size:44 final size:44
Alignment explanation
Indices: 31061760--31062133 Score: 152
Period size: 44 Copynumber: 8.1 Consensus size: 44
31061750 AGTGTAAGGA
* * *
31061760 AGCAGATTTAAGCCA-CAGGTCTTATCTCCCTGAGATTACAGCGG
1 AGCAGATTGAAGCCAGCA-ATCCTATCTCCCTGAGATTACAGCGG
* * *
31061804 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * * * * * *
31061848 AGCGGATTAAAATG-AAG-GAT-TTATCTCTCTGA-AGTTACAATAGAGTAG
1 AGCAGATT-GAA-GCCAGCAATCCTATCTCCCTGAGA-TTAC---AGCG--G
* * *
31061896 ATCGCATCAGATGGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGG
1 A--G---CAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * *
31061945 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
** *** * * *
31061989 AGTGGATT-AAAATAG-AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAG
1 AGCAGATTGAAGCCAGCA--ATCCTATCTCCCTGAGA-TTAC---AGCG--G
** *
31062038 ATCACGTCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGG
1 ---A-G-CAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * *
31062087 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
31062131 AGC
1 AGC
31062134 GGGTTAAAAT
Statistics
Matches: 251, Mismatches: 45, Indels: 68
0.69 0.12 0.19
Matches are distributed among these distances:
42 2 0.01
43 20 0.08
44 145 0.58
45 6 0.02
46 5 0.02
47 4 0.02
48 2 0.01
49 4 0.02
50 1 0.00
51 7 0.03
52 5 0.02
53 7 0.03
54 37 0.15
55 5 0.02
56 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
Found at i:31062101 original size:142 final size:142
Alignment explanation
Indices: 31061779--31062182 Score: 677
Period size: 142 Copynumber: 2.9 Consensus size: 142
31061769 AAGCCACAGG
31061779 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* *
31061844 GTGGAGCGGATTAAAAT-GAAGGAT-TTATCTCTCTGAAGTTACAATAGAGTAGATCGCATCAGA
66 GTGGAGCGGATTAAAATAG-AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGA
*
31061907 TGGAAGCCAGAAA
130 TGGAAGCCAAAAA
31061920 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* *
31061985 GTGGAGTGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACGTCAGAT
66 GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGAT
*
31062050 TGAAGCCAAAAA
131 GGAAGCCAAAAA
31062062 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* * * * * *
31062127 GTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAACTTATAGCAGAGTAGATC
66 GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
31062183 GCATTAGGTC
Statistics
Matches: 248, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
141 86 0.35
142 162 0.65
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (142 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGAT
GGAAGCCAAAAA
Found at i:31062126 original size:98 final size:97
Alignment explanation
Indices: 31061947--31062128 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
31061937 TACAGCGGAG
* ** * ** *
31061947 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAGAGGATCTT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAGA-GATCCT
*
31062012 ATCTCTCTGAAGTTACAGTAGAGTAGATCACGT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCACGT
* **
31062045 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA-ATCC
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAG-AGATCC
31062109 TATCTCCCTG-AGATTACAGT
64 TATCTCCCTGAAG-TTACAGT
31062129 GGAGCGGGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 2 0.03
98 62 0.89
99 5 0.07
100 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (97 bp):
CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAGAGATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCACGT
Found at i:31062157 original size:44 final size:44
Alignment explanation
Indices: 31062057--31062163 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
31062047 GATTGAAGCC
**
31062057 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
1 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
** * * * *
31062101 AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGGTT-AAAAT
1 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
*
31062144 AAAAGATCTTATCTCTCTGA
1 AAAA-ATCTTATCTCCCTGA
31062164 ACTTATAGCA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
43 5 0.10
44 45 0.90
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
Found at i:31065942 original size:20 final size:19
Alignment explanation
Indices: 31065917--31065955 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31065907 TCTACTATAC
31065917 TTACATATGTAATTTAATTT
1 TTACAT-TGTAATTTAATTT
* *
31065937 TTACATTTTAATTTCATTT
1 TTACATTGTAATTTAATTT
31065956 AATTTGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
TTACATTGTAATTTAATTT
Found at i:31066209 original size:50 final size:50
Alignment explanation
Indices: 31066153--31066258 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
31066143 CTTGAATTAA
31066153 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
1 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
31066203 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
1 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
31066253 TTAATA
1 TTAATA
31066259 GGCTTTGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (50 bp):
TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
Found at i:31066239 original size:27 final size:27
Alignment explanation
Indices: 31066159--31066241 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
31066149 TTAATTAATA
31066159 ATATTACGAAAATAGAAGAATCAAATC
1 ATATTACGAAAATAGAAGAATCAAATC
* * * * *
31066186 ATATT---AAATTGCGAAG-GT-TAATA
1 ATATTACGAAAAT-AGAAGAATCAAATC
31066209 ATATTACGAAAATAGAAGAATCAAATC
1 ATATTACGAAAATAGAAGAATCAAATC
31066236 ATATTA
1 ATATTA
31066242 AATTGCGAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 8 0.20
24 5 0.12
25 8 0.20
26 5 0.12
27 14 0.35
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (27 bp):
ATATTACGAAAATAGAAGAATCAAATC
Found at i:31068751 original size:20 final size:20
Alignment explanation
Indices: 31068726--31068780 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
31068716 AATTACAAAA
31068726 AAAATAATTTTAAAAAATTC
1 AAAATAATTTTAAAAAATTC
* *
31068746 AAAATAATTTT-TAAAATTT
1 AAAATAATTTTAAAAAATTC
31068765 AAAAT-ATTTATAAAAA
1 AAAATAATTT-TAAAAA
31068781 TCAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 14 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTAAAAAATTC
Found at i:31068763 original size:19 final size:19
Alignment explanation
Indices: 31068726--31068787 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
31068716 AATTACAAAA
*
31068726 AAAATAATTTTAAAAAATTC
1 AAAATAATTTT-TAAAATTC
*
31068746 AAAATAATTTTTAAAATTT
1 AAAATAATTTTTAAAATTC
* *
31068765 AAAAT-ATTTATAAAAATC
1 AAAATAATTTTTAAAATTC
31068783 AAAAT
1 AAAAT
31068788 TTTATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.41
19 11 0.30
20 11 0.30
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTC
Found at i:31068778 original size:18 final size:18
Alignment explanation
Indices: 31068734--31068815 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 18
31068724 AAAAAATAAT
* *
31068734 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTTAAAAT-A
*
31068753 TTTTTAAAATTTAAAATA
1 TTTATAAAATTTAAAATA
* *
31068771 TTTATAAAAATCAAAAT-
1 TTTATAAAATTTAAAATA
**
31068788 TTTAT-ATTTTTAAAA-A
1 TTTATAAAATTTAAAATA
*
31068804 ATTATAAAATTT
1 TTTATAAAATTT
31068816 TTCAAACAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
16 10 0.21
17 9 0.19
18 15 0.31
19 14 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATAAAATTTAAAATA
Found at i:31068826 original size:20 final size:19
Alignment explanation
Indices: 31068793--31068831 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
31068783 AAAATTTTAT
31068793 ATTTTTAAAAAATTATAAA
1 ATTTTTAAAAAATTATAAA
* *
31068812 ATTTTTCAAACAATTCTAAA
1 ATTTTT-AAAAAATTATAAA
31068832 GAATACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTTTAAAAAATTATAAA
Found at i:31074014 original size:34 final size:35
Alignment explanation
Indices: 31073947--31074068 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 35
31073937 TAAAGAGTGT
31073947 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
1 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
* * *
31073982 GCCCAGCGCTAGTCGGAT-AACTGAC-GATAGTTGT
1 GCCCAGCACTAGTCAGATAAACTGACAGA-AGTTGC
* * * *
31074016 GCCCAGTACTAATCAGATAAATTGACAGAAATTGC
1 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
**
31074051 GCCCAGTGCTAGTCAGAT
1 GCCCAGCACTAGTCAGAT
31074069 GAATCGACAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
33 2 0.03
34 26 0.36
35 42 0.58
36 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (35 bp):
GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
Found at i:31074148 original size:20 final size:21
Alignment explanation
Indices: 31074108--31074156 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
31074098 AGTCCATAAA
31074108 ATCACATTTCATAACCTCAAT
1 ATCACATTTCATAACCTCAAT
31074129 ATCACATTTCATAA-CTCAAT
1 ATCACATTTCATAACCTCAAT
31074149 ATCACATT
1 ATCACATT
31074157 CACTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.35
Consensus pattern (21 bp):
ATCACATTTCATAACCTCAAT
Found at i:31080885 original size:22 final size:22
Alignment explanation
Indices: 31080855--31080906 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
31080845 AATGGCTAAG
* * *
31080855 AGCCGTAAATAGGATAGCTATA
1 AGCCATAAATAGAATAGCTACA
* *
31080877 AGCTATAAATAGAATGGCTACA
1 AGCCATAAATAGAATAGCTACA
31080899 AGCCATAA
1 AGCCATAA
31080907 GTACAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (22 bp):
AGCCATAAATAGAATAGCTACA
Found at i:31080951 original size:32 final size:32
Alignment explanation
Indices: 31080913--31081033 Score: 140
Period size: 32 Copynumber: 3.8 Consensus size: 32
31080903 ATAAGTACAA
* * *
31080913 TAATATGATTGGCACAAAGCCATCAGTAGTAG
1 TAATATGATCGACACAAAGCCATCAGTAATAG
31080945 TAATATGATCGACACATAA-CCATCAGTAATAG
1 TAATATGATCGACACA-AAGCCATCAGTAATAG
* * *
31080977 TAGTATGATCAACACAAAGCCATCAGTAATGG
1 TAATATGATCGACACAAAGCCATCAGTAATAG
31081009 TAATATGATTCGGACAC--AGCCATCA
1 TAATATGA-TC-GACACAAAGCCATCA
31081034 ATAGTATCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.03
32 67 0.87
33 4 0.05
34 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (32 bp):
TAATATGATCGACACAAAGCCATCAGTAATAG
Found at i:31081256 original size:24 final size:25
Alignment explanation
Indices: 31081229--31081292 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
31081219 CAAATCACAA
* *
31081229 ACAAATCAGTCATTTACATCTC-GG
1 ACAAATCAATCATTTACATCACAGG
*
31081253 ACAAATCATTCATTTACATCACAGG
1 ACAAATCAATCATTTACATCACAGG
31081278 A-AAATCAATCATTTA
1 ACAAATCAATCATTTA
31081293 ACCCCGAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 33 0.92
25 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (25 bp):
ACAAATCAATCATTTACATCACAGG
Found at i:31081342 original size:27 final size:27
Alignment explanation
Indices: 31081311--31081616 Score: 337
Period size: 27 Copynumber: 11.3 Consensus size: 27
31081301 GGGTAAAATA
* *
31081311 GTCATTTTACCCTACAAGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
31081338 ATCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
31081365 ATCTTTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
31081392 ATCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
31081419 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
31081446 GTCATTTTACCCTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
31081473 GTCATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* **
31081500 GTCATTTTACCCTATAGGGAAATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
31081527 GTCATTTTACCC-ATC-GAGGGTATTTCG
1 GTCATTTTACCCTA-CAG-GGGCATTACG
** * *
31081554 GTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * **
31081581 ATAATTTTACCCTTCAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
31081608 GTCATTTTA
1 GTCATTTTA
31081617 TCATTCGGTG
Statistics
Matches: 244, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 241 0.99
28 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:31081588 original size:54 final size:54
Alignment explanation
Indices: 31081339--31081671 Score: 192
Period size: 54 Copynumber: 6.2 Consensus size: 54
31081329 GACATTACGA
* * * ** * * *
31081339 TCATTTTACCCTATAGGGGCATTACGATCTTTTTACCCTAC-AGGGGTATTACGA
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
** * * * * * * * *
31081393 TCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTAC-AGGGGCATTACGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
** * * * * * ** * *
31081447 TCATTTTACCCTACAGAGGCATTACGGTCATTTTA-CCTTATAGGGGCATTACGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
* ** * * * *
31081501 TCATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGG
*
31081555 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTC-AGGGGTATTTTGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
* * * *
31081609 TCATTTTA-TCATTCGGTGGTATTTC-AGTAATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTTAGG-GGTATTTCGA-TAATTTTACCCTTCGAGGGTATTTCGG
*
31081663 TAATTTTAC
1 TCATTTTAC
31081672 AACCTTTTTG
Statistics
Matches: 239, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
53 10 0.04
54 224 0.94
55 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (54 bp):
TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGG
Found at i:31081630 original size:81 final size:81
Alignment explanation
Indices: 31081336--31081671 Score: 249
Period size: 81 Copynumber: 4.1 Consensus size: 81
31081326 AAGGACATTA
* ** * * * *
31081336 CGATCATTTTACCCTATAGGGGCATTACGATCTTTTTACCC-TAC-AGGGGTATTACGATCATTT
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCAT-CGA-GGGTATTTCGGTCATTT
** * * *
31081399 TACCCTACAAGGGCATTA
64 TACCCTTTAGGGGTATTT
* * * ** * *
31081417 CGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC-TAC-AGAGGCATTACGGTCATTT
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCAT-CGAG-GGTATTTCGGTCATTT
* *
31081480 TA-CCTTATAGGGGCATTA
64 TACCCTT-TAGGGGTATTT
* *
31081498 CGGTCATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
31081563 CCCTTTAGGGGTATTT
66 CCCTTTAGGGGTATTT
** ** * * *
31081579 CGATAATTTTACCCT-TCAGGGGTATTTTGGTCATTTTA-TCATTCG-GTGGTATTTCAGTAATT
1 CGATAATTTTACCCTAT-AGGGAAATTACGGTCATTTTACCCA-TCGAG-GGTATTTCGGTCATT
*
31081641 TTACCC-TTCGAGGGTATTT
63 TTACCCTTTAG-GGGTATTT
31081660 CGATAATTTTAC
1 CGATAATTTTAC
31081672 AACCTTTTTG
Statistics
Matches: 220, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
80 11 0.05
81 202 0.92
82 7 0.03
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (81 bp):
CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
CCCTTTAGGGGTATTT
Found at i:31081641 original size:27 final size:26
Alignment explanation
Indices: 31081530--31081671 Score: 142
Period size: 27 Copynumber: 5.3 Consensus size: 26
31081520 AATTACGGTC
* * *
31081530 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCTTCG-GGGTATTTCGATA
*
31081557 ATTTTACCCTTTAGGGGTATTTCGATA
1 ATTTTACCC-TTCGGGGTATTTCGATA
* * *
31081584 ATTTTACCCTTCAGGGGTATTTTGGTC
1 ATTTTACCCTTC-GGGGTATTTCGATA
* *
31081611 ATTTTATCATTCGGTGGTATTTC-AGTA
1 ATTTTACCCTTCGG-GGTATTTCGA-TA
31081638 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCG-GGGTATTTCGATA
31081665 ATTTTAC
1 ATTTTAC
31081672 AACCTTTTTG
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
26 4 0.04
27 86 0.91
28 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTTCGGGGTATTTCGATA
Found at i:31084656 original size:15 final size:15
Alignment explanation
Indices: 31084617--31084648 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31084607 TAGATACATC
31084617 AAGACAGAGTTTGTA
1 AAGACAGAGTTTGTA
*
31084632 AAGATAGAGTTTGTA
1 AAGACAGAGTTTGTA
31084647 AA
1 AA
31084649 AGCAGAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (15 bp):
AAGACAGAGTTTGTA
Found at i:31088612 original size:42 final size:42
Alignment explanation
Indices: 31088546--31088705 Score: 123
Period size: 42 Copynumber: 3.8 Consensus size: 42
31088536 AAACTCGTAC
* * *
31088546 AATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATC-AATAT
1 AATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* *
31088587 CGATGCCACTGTCCCAGACAAGGTCTTACACGAAATCAAATAT
1 -AATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* * * *
31088630 AATGTCGA-TGTCCCAGACATGGTCTTATACATAAATCTCAAAT-C
1 AATG-CCACTGTCCCAGACATGGTCTTACAC-GAAA--TCAAATAT
* *
31088674 GATGCCAAC-GTCCCAGACGTGGTCTTACACGA
1 AATGCC-ACTGTCCCAGACATGGTCTTACACGA
31088706 TAACACATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 51 0.54
43 12 0.13
44 23 0.24
45 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
AATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
Found at i:31097720 original size:6 final size:6
Alignment explanation
Indices: 31097709--31097742 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
31097699 TCTACTTTAT
*
31097709 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCT CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
31097743 ATTTGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CTTCCC
Found at i:31097771 original size:13 final size:13
Alignment explanation
Indices: 31097753--31097778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31097743 ATTTGCATGT
31097753 AGTTCCTTGGGAA
1 AGTTCCTTGGGAA
31097766 AGTTCCTTGGGAA
1 AGTTCCTTGGGAA
31097779 TAGGTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
AGTTCCTTGGGAA
Found at i:31103827 original size:2 final size:2
Alignment explanation
Indices: 31103820--31103854 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31103810 TGTGTTAAGT
31103820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31103855 GTTCGGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31104085 original size:42 final size:42
Alignment explanation
Indices: 31104024--31104280 Score: 408
Period size: 42 Copynumber: 6.1 Consensus size: 42
31104014 CAGTGCCTAT
* * *
31104024 CAGGTTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
31104066 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
31104108 CAGGCTTAATGCCGGTGAAACAATATCAGACTCTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
31104150 CAGGCTTAATGCTGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
31104192 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
31104234 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
31104275 CAGGCT
1 CAGGCT
31104281 AAGTGTCGGT
Statistics
Matches: 199, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
41 23 0.12
42 176 0.88
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:31108564 original size:40 final size:40
Alignment explanation
Indices: 31108520--31108681 Score: 179
Period size: 40 Copynumber: 4.2 Consensus size: 40
31108510 GTACCTAGCG
* * * *
31108520 CTAGTCAGACAAACTGACGATATCAAATGTGTGTCCAGCA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
*
31108560 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCATCA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
* * * * *
31108600 CTAGTCGGATAAACTGAC-A-AT-AAAT-TACGCCTAACA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
* * *
31108636 CTAGTCGGATAAACCGACGATATCAAATGTGTGCCCAGAA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
31108676 CTAGTC
1 CTAGTC
31108682 GGGTAAACTG
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
36 25 0.25
37 5 0.05
38 4 0.04
39 5 0.05
40 63 0.62
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (40 bp):
CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
Found at i:31113684 original size:24 final size:24
Alignment explanation
Indices: 31113657--31113704 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31113647 GATGAGATAC
* *
31113657 CGACCTTTTCGTTGATATCCTTTT
1 CGACCTTTTCATTGATATCATTTT
*
31113681 CGACCTTTTCATTTATATCATTTT
1 CGACCTTTTCATTGATATCATTTT
31113705 TAATCTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.52
Consensus pattern (24 bp):
CGACCTTTTCATTGATATCATTTT
Found at i:31113923 original size:40 final size:40
Alignment explanation
Indices: 31113873--31114008 Score: 113
Period size: 40 Copynumber: 3.5 Consensus size: 40
31113863 AGTTTCATGC
*
31113873 CCAGCGCTAGTCAGATAAACTGACGATATCAAATGTGTGT
1 CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
* * * ** * * *
31113913 CCAGCACTAGTCGGATAAATTGA-TA-AT--GTTTTGCGC
1 CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
*
31113949 CCGGCGA-TAGT-AGGATAAACTGACGATATCAAATGTGTGT
1 CCAGC-ACTAGTCA-GATAAACTGACGATATCAAATGTGTGT
*
31113989 CTAGCACTAGTCAGATAAAC
1 CCAGCACTAGTCAGATAAAC
31114009 CGACAATGAT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
36 21 0.31
37 2 0.03
38 4 0.06
39 2 0.03
40 38 0.56
41 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (40 bp):
CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
Found at i:31114202 original size:27 final size:27
Alignment explanation
Indices: 31114171--31114224 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31114161 ATATATTTCC
31114171 ATAGCATTACATTTAAAATACTAATCA
1 ATAGCATTACATTTAAAATACTAATCA
31114198 ATAGCATTACATTTAAAATACTAATCA
1 ATAGCATTACATTTAAAATACTAATCA
31114225 TTTGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (27 bp):
ATAGCATTACATTTAAAATACTAATCA
Found at i:31119189 original size:40 final size:40
Alignment explanation
Indices: 31118993--31119190 Score: 146
Period size: 40 Copynumber: 5.2 Consensus size: 40
31118983 CGATTAATCC
*
31118993 GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCC
1 GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
* ** * * ** *
31119033 GACTAGCGCAGGGCGCAAATATT----T-GTCATTTAATCT
1 GACTAGTGTTGGGCACACAT-TTAACATCGTCGGTTCATCT
* * *
31119069 AAGTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCC
1 GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
* * * * * *
31119109 GACTAGTGCTGGGCACA-A-AT-A-GTTGACGGTTAAT-T
1 GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
31119144 CGACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
1 -GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
31119185 GACTAG
1 GACTAG
31119191 CGCTGGACGC
Statistics
Matches: 111, Mismatches: 35, Indels: 24
0.65 0.21 0.14
Matches are distributed among these distances:
35 2 0.02
36 46 0.41
37 3 0.03
38 2 0.02
39 3 0.03
40 52 0.47
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (40 bp):
GACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCT
Found at i:31119279 original size:76 final size:76
Alignment explanation
Indices: 31118971--31119267 Score: 386
Period size: 76 Copynumber: 3.9 Consensus size: 76
31118961 TTCTTGGCGA
* *
31118971 GCAAATATTTGTCGATTAATCCGACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
1 GCAAATATTTGTCGATTAATTCGACAAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
*
31119036 TAGCGCAGGGC
66 TAGCGCTGGGC
*
31119047 GCAAATATTTGTC-ATTTAA-TCTA-AGTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCC
1 GCAAATATTTGTCGA-TTAATTCGACA--AGTGTTGGGCACACATTTAACATCGTCGGTTCATCC
*
31119109 GACTAGTGCTGGGC
63 GACTAGCGCTGGGC
* * * * * *
31119123 ACAAATAGTTGACGGTTAATTCGACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCTGAC
1 GCAAATATTTGTCGATTAATTCGACAAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
*
31119188 TAGCGCTGGAC
66 TAGCGCTGGGC
* * * *
31119199 GCAAATCTTTGTCGATTAATTCGACAAGTGTTGGGCACAC-TTTTACTATCGTCGGTTTATCCAA
1 GCAAATATTTGTCGATTAATTCGACAAGTGTTGGGCACACATTTAAC-ATCGTCGGTTCATCCGA
31119263 CTAGC
65 CTAGC
31119268 ACTGAGTGCA
Statistics
Matches: 190, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
75 8 0.04
76 179 0.94
77 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (76 bp):
GCAAATATTTGTCGATTAATTCGACAAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
TAGCGCTGGGC
Found at i:31126680 original size:19 final size:18
Alignment explanation
Indices: 31126651--31126700 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
31126641 GTATATGTTT
31126651 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
31126669 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
*
31126688 TAAGTTTTATTTA
1 TAA-ATTTATTTA
31126701 TATTCTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 23 0.79
20 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:31128007 original size:31 final size:31
Alignment explanation
Indices: 31127972--31128147 Score: 239
Period size: 31 Copynumber: 5.7 Consensus size: 31
31127962 GTATATATTT
*
31127972 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
31128003 TATACATTGCCGAATTTGATTTATATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
31128034 TATACATTGTCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
31128065 TATACATTGCCGAA-TTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
31128095 TATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
31128126 TATATATTTCTGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
31128148 GGCATTGGAT
Statistics
Matches: 126, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
30 35 0.28
31 91 0.72
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATGGA
Found at i:31128113 original size:61 final size:61
Alignment explanation
Indices: 31127972--31128147 Score: 244
Period size: 61 Copynumber: 2.9 Consensus size: 61
31127962 GTATATATTT
* * * *
31127972 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTATATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTGTATATAGA
* * *
31128034 TATACATTGTCAAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGA
* * * *
31128095 TATACATTGCCGAATTTGATTCGTATATGGATATATATTTCTGAATTGATTTG
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTG
31128148 GGCATTGGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 59 0.58
62 42 0.42
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (61 bp):
TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGA
Found at i:31128376 original size:44 final size:44
Alignment explanation
Indices: 31128265--31128376 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 44
31128255 TCCGAGGTGT
* **
31128265 GATTTCATGTAAGACCATAGT-TGAGCTATTGGCATCAATTTGA
1 GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
* * * *
31128308 CATTTCGTGTAAGACCATAG-CTGGGCTATTGTCATCGATACGA
1 GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
31128351 GATTTCCATGTAAGACCAT-GTCTGGG
1 GATTT-CATGTAAGACCATAGTCTGGG
31128377 ACATGGCATT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 40 0.70
44 17 0.30
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
Found at i:31130490 original size:50 final size:50
Alignment explanation
Indices: 31130389--31130525 Score: 130
Period size: 50 Copynumber: 2.7 Consensus size: 50
31130379 TGAGGTTATT
* * * * *
31130389 AGAGGTCCCAGGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
* * * *
31130439 AGAGGTCCCCCGTAAGACCATGTTTAGGACATGGCATGGGCACTGATATG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
** * * * * *
31130489 AGAACTCTCATGTAAGACCATATCTGGGATATGGCAT
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCAT
31130526 TTCCAGTACA
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATG
Found at i:31130807 original size:20 final size:20
Alignment explanation
Indices: 31130782--31130820 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31130772 TGAGTTATTT
31130782 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
31130802 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
31130821 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:31135571 original size:23 final size:23
Alignment explanation
Indices: 31135539--31135586 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
31135529 CCTATTTATC
*
31135539 CTTAATTTCGTCATGTTTTGATA
1 CTTAAATTCGTCATGTTTTGATA
31135562 CTTAAATTCGTCATGTTTTGATA
1 CTTAAATTCGTCATGTTTTGATA
31135585 CT
1 CT
31135587 GATGTCGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (23 bp):
CTTAAATTCGTCATGTTTTGATA
Found at i:31137548 original size:45 final size:45
Alignment explanation
Indices: 31137484--31137580 Score: 187
Period size: 45 Copynumber: 2.2 Consensus size: 45
31137474 CCTATCCCAA
31137484 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
1 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
31137529 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
1 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
31137574 AC-ATTGA
1 ACAATTGA
31137581 CTCACTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 5 0.10
45 47 0.90
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (45 bp):
ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
Found at i:31137603 original size:14 final size:14
Alignment explanation
Indices: 31137584--31137612 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31137574 ACATTGACTC
31137584 ACTAATCCCCTATT
1 ACTAATCCCCTATT
31137598 ACTAATCCCCTATT
1 ACTAATCCCCTATT
31137612 A
1 A
31137613 AGAGGATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ACTAATCCCCTATT
Found at i:31146582 original size:20 final size:20
Alignment explanation
Indices: 31146557--31146596 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31146547 TCATACATTT
31146557 TTATAATATATATTTACGTA
1 TTATAATATATATTTACGTA
31146577 TTATAATATATATTTACGTA
1 TTATAATATATATTTACGTA
31146597 CATACTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATAATATATATTTACGTA
Found at i:31146639 original size:7 final size:7
Alignment explanation
Indices: 31146627--31146656 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
31146617 AACATATACT
31146627 TTTTATA
1 TTTTATA
31146634 TTTTATA
1 TTTTATA
*
31146641 TTTCATA
1 TTTTATA
31146648 TTTTATA
1 TTTTATA
31146655 TT
1 TT
31146657 CTTTATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:31149213 original size:23 final size:23
Alignment explanation
Indices: 31149187--31149231 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
31149177 CAAATTGATG
31149187 AATAA-AAAATAAAACATTTTCAA
1 AATAACAAAA-AAAACATTTTCAA
*
31149210 AATAAGCAAAAAAAATATTTTC
1 AATAA-CAAAAAAAACATTTTC
31149232 TTTTCCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAACAAAAAAAACATTTTCAA
Found at i:31160549 original size:3 final size:3
Alignment explanation
Indices: 31160541--31160605 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
31160531 ATATTGCATC
31160541 ATT ATT ATT A-T ATT A-T ATT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
31160585 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
31160606 TCTATACATA
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31164293 original size:120 final size:120
Alignment explanation
Indices: 31164169--31164395 Score: 321
Period size: 120 Copynumber: 1.9 Consensus size: 120
31164159 ATAAATTTTT
* * *
31164169 AAAAATTATTTATAACAAATTTTAAAATAATTGTCTTTTAAATTAAA-AATTTTATCTATTAATT
1 AAAAATCATTTATAACAAATTTTAAAAGAATTATCTTTTAAATTAAATAA-TTTATCTATTAATT
* * *
31164233 AAATTTTAATATTATTTTTAAATAACTTCACAATAACTATTATATATTTTTTCAAA
65 AAATTTTAATACTAATTTCAAATAACTTCACAATAACTATTATATATTTTTTCAAA
* ** *
31164289 AAAAATCATTTATTACAGTTTTTAAAAGAATTATTTTTTAAATTAAATAATTTATCTATTAATTA
1 AAAAATCATTTATAACAAATTTTAAAAGAATTATCTTTTAAATTAAATAATTTATCTATTAATTA
* * *
31164354 AATTTTAATACTAATTTCAAATCACTTCATAATAATTATTAT
66 AATTTTAATACTAATTTCAAATAACTTCACAATAACTATTAT
31164396 GTACTTAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
120 91 0.98
121 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (120 bp):
AAAAATCATTTATAACAAATTTTAAAAGAATTATCTTTTAAATTAAATAATTTATCTATTAATTA
AATTTTAATACTAATTTCAAATAACTTCACAATAACTATTATATATTTTTTCAAA
Found at i:31172009 original size:46 final size:46
Alignment explanation
Indices: 31171953--31172521 Score: 405
Period size: 46 Copynumber: 12.4 Consensus size: 46
31171943 GATTTTTTAT
* * * * * * *
31171953 TGCTGTAAATTGAGGTGTATAAACGTTGTTAACTGAGATGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
*
31171999 TGCTGCAAATTGAAGTGTTTAAATATTGTAAATTGA-AGTGTTTAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * ** * * * * *
31172045 TACTGCAAGTTGAAGTGTTTAGTTGCTGGAAATTAAGATGTTTTAC
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
** * * ** * * * *
31172091 TGCTTTAAATTGAGGTGTATAAACATTATTAATTGAGATGTTAAAA
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * *
31172137 TGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTGA-AGTGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
** *
31172183 CACTGCAAATTGAAGTGTTTCAATGTTGTAAATTGA-AGTGTTTAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * ** * * *
31172229 TACTACAAATTGAAGTG-TTAGTTGTTGGAAATTGAGATGTTTTAT
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
** * * * * *
31172274 TGCTATAAATTGAGGTGTATAAACGTTGTTAATTGAGATGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * *
31172320 TGTTGCGAATTGAAGTGTTTAAATGTTGTAAATT-AAAGTGTTTAAC
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * * * * * * *
31172366 TACTACAAATTGAACTGTTTAATTGCTGGAAATTGAGATGTTTTAT
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * * * *
31172412 TGTTGTAAATTAAAGTGTATAAACGTTGTTAATTGAGATG-TTACAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTA-AG
* * *
31172458 TGCTGCAAAATGAAGTGTTTAAATATTGTAAATTGA-AGTGTTTGAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
*
31172504 TGCTGCAAATTGAGGTGT
1 TGCTGCAAATTGAAGTGT
31172522 ACAAATGAGT
Statistics
Matches: 391, Mismatches: 122, Indels: 20
0.73 0.23 0.04
Matches are distributed among these distances:
45 41 0.10
46 345 0.88
47 5 0.01
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (46 bp):
TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
Found at i:31172017 original size:23 final size:23
Alignment explanation
Indices: 31171953--31172521 Score: 140
Period size: 23 Copynumber: 24.8 Consensus size: 23
31171943 GATTTTTTAT
*
31171953 TGCTGTAAATTGAGGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
* *
31171978 T--TGTTAACTG-AGATGTTAAAG
1 TGCTGTAAATTGAAG-TGTTAAAG
*
31171999 TGCTGCAAATTGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
** *
31172022 TATTGTAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGAAGTGTTAAAG
* * * *
31172045 TACTGCAAGTTGAAGTGTT-TAG
1 TGCTGTAAATTGAAGTGTTAAAG
* ** *
31172067 TTGCTGGAAATT-AAGATGTTTTAC
1 -TGCTGTAAATTGAAG-TGTTAAAG
* * *
31172091 TGCTTTAAATTGAGGTGTATAAACA
1 TGCTGTAAATTGAAGTGT-TAAA-G
* * *
31172116 T--TATTAATTG-AGATGTTAAAA
1 TGCTGTAAATTGAAG-TGTTAAAG
* * *
31172137 TGTTGCAAAATGAAGTGCTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
*
31172160 TGTTGTAAATTGAAGTGTTAAAG
1 TGCTGTAAATTGAAGTGTTAAAG
** * *
31172183 CACTGCAAATTGAAGTGTTTCAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
* *
31172206 TGTTGTAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGAAGTGTTAAAG
* **
31172229 TACTACAAATTGAAGTGTT--AG
1 TGCTGTAAATTGAAGTGTTAAAG
* * ** *
31172250 TTGTTGGAAATTG-AGATGTTTTAT
1 -TGCTGTAAATTGAAG-TGTTAAAG
* *
31172274 TGCTATAAATTGAGGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
*
31172299 T--TGTTAATTG-AGATGTTAAAG
1 TGCTGTAAATTGAAG-TGTTAAAG
* **
31172320 TGTTGCGAATTGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
* * * *
31172343 TGTTGTAAATTAAAGTGTTTAAC
1 TGCTGTAAATTGAAGTGTTAAAG
* ** * * *
31172366 TACTACAAATTGAACTGTTTAAT
1 TGCTGTAAATTGAAGTGTTAAAG
* ** *
31172389 TGCTGGAAATTG-AGATGTTTTAT
1 TGCTGTAAATTGAAG-TGTTAAAG
* *
31172412 TGTTGTAAATTAAAGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
* *
31172437 T--TGTTAATTG-AGATGTTACAG
1 TGCTGTAAATTGAAG-TGTTAAAG
* *
31172458 TGCTGCAAAATGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
** **
31172481 TATTGTAAATTGAAGTGTTTGAG
1 TGCTGTAAATTGAAGTGTTAAAG
* *
31172504 TGCTGCAAATTGAGGTGT
1 TGCTGTAAATTGAAGTGT
31172522 ACAAATGAGT
Statistics
Matches: 398, Mismatches: 103, Indels: 88
0.68 0.17 0.15
Matches are distributed among these distances:
21 12 0.03
22 58 0.15
23 279 0.70
24 45 0.11
25 4 0.01
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
TGCTGTAAATTGAAGTGTTAAAG
Found at i:31172151 original size:138 final size:138
Alignment explanation
Indices: 31171901--31172202 Score: 417
Period size: 138 Copynumber: 2.2 Consensus size: 138
31171891 TAATGCCCTA
* ** * *
31171901 TTTAAATACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGGTGATTTTTTATTGCTGTAAATTGA
1 TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGAAGATGTTTTACTGCTGTAAATTGA
* * * * *
31171966 GGTGTATAAACGTTGTTAACTGAGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATATTGTAAA
66 GGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAAA
31172031 TTGAAGTG
131 TTGAAGTG
* * * *
31172039 TTTAAGTACTGCAAGTTGAAGTGTTTAGTTGCTGGAAA-TTAAGATGTTTTACTGCTTTAAATTG
1 TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCT-AAAAGTGAAGATGTTTTACTGCTGTAAATTG
* * *
31172103 AGGTGTATAAACATTATTAATTGAGATGTTAAAATGTTGCAAAATGAAGTGCTTAAATGTTGTAA
65 AGGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAA
31172168 ATTGAAGTG
130 ATTGAAGTG
* *
31172177 TTAAAGCACTGCAAATTGAAGTGTTT
1 TTTAAGTACTGCAAATTGAAGTGTTT
31172203 CAATGTTGTA
Statistics
Matches: 143, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
138 140 0.98
139 3 0.02
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (138 bp):
TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGAAGATGTTTTACTGCTGTAAATTGA
GGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAAA
TTGAAGTG
Found at i:31172239 original size:138 final size:138
Alignment explanation
Indices: 31171959--31172522 Score: 499
Period size: 138 Copynumber: 4.1 Consensus size: 138
31171949 TTATTGCTGT
** * * * **
31171959 AAATTGAGGTGTATAAACGTTGTTAACTGAGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATA
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* * ** * *
31172024 TTGTAAATTGA-AGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTTGCTGGAAATT-AAGATGTT
66 TTGTAAATTGAGA-TGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAG-TGTT
* * **
31172087 TTACTGCTTT
129 TAACTACTAC
* *** * * * *
31172097 AAATTGAGGTGTATAAACATTATTAATTGAGATGTTAAAATGTTGCAAAATGAAGTGCT-TAAAT
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTG-TATAAAC
* *
31172161 GTTGTAAATTGA-AGTGTTAAAGCACTGCAAATTGAAGTGTTTCAATGTTGTAAATTGAAGTGTT
65 GTTGTAAATTGAGA-TGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTT
*
31172225 TAAGTACTAC
129 TAACTACTAC
* *** ** ** *
31172235 AAATTGAAGTGT-TAGTTGTTGGAAATTGAGATGTTTTATTGCTATAAATTGAGGTGTATAAACG
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* ** * *
31172299 TTGTTAATTGAGATGTTAAAGTGTTGCGAATTGAAGTGTTTAAATGTTGTAAATTAAAGTGTTTA
66 TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
31172364 ACTACTAC
131 ACTACTAC
** * ** * ** * * *
31172372 AAATTGAACTGTTTAATTGCTGGAAATTGAGATGTTTTATTGTTGTAAATTAAAGTGTATAAACG
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* * * * * *
31172437 TTGTTAATTGAGATGTTACAGTGCTGCAAAATGAAGTGTTTAAATATTGTAAATTGAAGTGTTTG
66 TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
* * *
31172502 AGTGCTGC
131 ACTACTAC
31172510 AAATTGAGGTGTA
1 AAATTGAGGTGTA
31172523 CAAATGAGTC
Statistics
Matches: 356, Mismatches: 65, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
136 1 0.00
137 108 0.30
138 243 0.68
139 4 0.01
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (138 bp):
AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
ACTACTAC
Found at i:31172248 original size:69 final size:68
Alignment explanation
Indices: 31172005--31172521 Score: 252
Period size: 69 Copynumber: 7.5 Consensus size: 68
31171995 AAAGTGCTGC
* * * * * **
31172005 AAATTGAAGTGTTTAAATATTGTAAATTGAAGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTTG
1 AAATTGAAGTGTTT-AATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
* *
31172070 CTGG
65 TTGT
* * ***
31172074 AAATT-AAGATGTTT--TACTGCTTTAAATTGAGGTGTATAAACAT--TATTAATTG-AGATGTT
1 AAATTGAAG-TGTTTAATACTGC---AAATTGAAGTGT-TAAA-GTGCTGCAAATTGAAG-TGTT
* *
31172133 AAAATGTTGC
59 TAAATGTTGT
* * ** * ** *
31172143 AAAATGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGCACTGCAAATTGAAGTGTTTCAATG
1 AAATTGAAGTG-TTTAATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
31172208 TTGT
65 TTGT
* * * * *
31172212 AAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTT--AGTTGTTGGAAATTG-AGATGTTTTAT
1 AAATTGAAGTGTTTAA-TACTGCAAATTGAAGTGTTAAAG-TGCTGCAAATTGAAG-TGTTTAAA
* *
31172274 TGCTAT
63 TGTTGT
* * ** * *
31172280 AAATTGAGGTGTATAA-ACGTTGTTAATTG-AGATGTTAAAGTGTTGCGAATTGAAGTGTTTAAA
1 AAATTGAAGTGTTTAATAC--TGCAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
31172343 TGTTGT
63 TGTTGT
* * * * * * * *
31172349 AAATTAAAGTGTTTAACTACTACAAATTGAACTGTTTAATTGCTGGAAATTG-AGATGTTTTATT
1 AAATTGAAGTGTTTAA-TACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAG-TGTTTAAAT
31172413 GTTGT
64 GTTGT
* * ** * *
31172418 AAATTAAAGTGTATAA-ACGTTGTTAATTG-AGATGTTACAGTGCTGCAAAATGAAGTGTTTAAA
1 AAATTGAAGTGTTTAATAC--TGCAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
*
31172481 TATTGT
63 TGTTGT
* * *
31172487 AAATTGAAGTGTTTGAGTGCTGCAAATTGAGGTGT
1 AAATTGAAGTGTTT-AATACTGCAAATTGAAGTGT
31172522 ACAAATGAGT
Statistics
Matches: 327, Mismatches: 87, Indels: 68
0.68 0.18 0.14
Matches are distributed among these distances:
66 6 0.02
67 8 0.02
68 58 0.18
69 229 0.70
70 19 0.06
71 4 0.01
72 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (68 bp):
AAATTGAAGTGTTTAATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGT
TGT
Found at i:31172401 original size:183 final size:183
Alignment explanation
Indices: 31172004--31172388 Score: 576
Period size: 183 Copynumber: 2.1 Consensus size: 183
31171994 TAAAGTGCTG
* * *
31172004 CAAATTGAAGTGTTTAAATATTGTAAATTGAAGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTT
1 CAAATTGAAGTGTTT-AATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTT
*
31172069 GCTGGAAATTAAGATGTTTTACTGCTTTAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
65 GCTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
* *
31172134 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGCACTG
130 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGCACTA
31172188 CAAATTGAAGTGTTTCAATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTG-TTAGTT
1 CAAATTGAAGTGTTT-AATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTT
* * * * *
31172252 GTTGGAAATTGAGATGTTTTATTGCTATAAATTGAGGTGTATAAACGTTGTTAATTGAGATGTTA
65 GCTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
* * * * *
31172317 AAGTGTTGCGAATTGAAGTGTTTAAATGTTGTAAATTAAAGTGTTTAA-CTACTA
130 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGC-ACTA
*
31172371 CAAATTGAACTGTTTAAT
1 CAAATTGAAGTGTTTAAT
31172389 TGCTGGAAAT
Statistics
Matches: 182, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
182 4 0.02
183 124 0.68
184 54 0.30
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (183 bp):
CAAATTGAAGTGTTTAATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTTG
CTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTAA
AATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGCACTA
Found at i:31177317 original size:11 final size:11
Alignment explanation
Indices: 31177301--31177330 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31177291 TATATATACT
31177301 TAAAAATTATA
1 TAAAAATTATA
*
31177312 TAAAAATAATA
1 TAAAAATTATA
31177323 TAAAAATT
1 TAAAAATT
31177331 TAATATGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:31180578 original size:32 final size:32
Alignment explanation
Indices: 31180542--31180602 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
31180532 AAATAAACAC
31180542 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
31180574 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
31180603 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:31181842 original size:30 final size:29
Alignment explanation
Indices: 31181804--31181862 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
31181794 GAGGTGGGAT
*
31181804 GTGAAGGGAATAAAAGTTTTAGGGAAAAA
1 GTGAAGGGAATAAAAATTTTAGGGAAAAA
* * *
31181833 GTGAGAGGGAGTAAAAATTTTGGGGGAAAA
1 GTGA-AGGGAATAAAAATTTTAGGGAAAAA
31181863 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (29 bp):
GTGAAGGGAATAAAAATTTTAGGGAAAAA
Found at i:31190307 original size:3 final size:3
Alignment explanation
Indices: 31190299--31190350 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
31190289 CAAATGGAAT
31190299 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31190347 TAA T
1 TAA T
31190351 GATGATGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31192074 original size:15 final size:15
Alignment explanation
Indices: 31192050--31192093 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
31192040 AAGTAGCCTA
*
31192050 TCTTTTTTCCTTCTT
1 TCTTTCTTCCTTCTT
31192065 TCTTTCTTCCTTCCTT
1 TCTTTCTTCCTT-CTT
31192081 TC-TTCTT-CTTCTT
1 TCTTTCTTCCTTCTT
31192094 CTTGTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 3 0.11
15 16 0.59
16 5 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTTCTTCCTTCTT
Found at i:31211805 original size:232 final size:232
Alignment explanation
Indices: 31211436--31211881 Score: 614
Period size: 232 Copynumber: 1.9 Consensus size: 232
31211426 TAACCGTGAA
*
31211436 TAAACCTCACAGCAGCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTTCAAAAAAAGAC
1 TAAACCTCACAG-AGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAACTTCAAAAAAAGAC
* * * * * *
31211501 TAAAACTTGCATAGTTTTTTGTACAGATACCCTAATTCAACCAAATTTCTAGAACCTCGCATCTA
65 GAAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTAGAAACTCGCATCTA
* * * *
31211566 ATTACGAACTAACTTCCTCTAAGAAAGCGATTTCA-AG-AAAGAGGTTTATGACGCCCAATTAAA
130 ATTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAATTAAA
*
31211629 ACCCAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCAAG
195 ACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
*
31211667 TAAACCTCACAG-GCTAGGAAGCTCGCTCAAATTAAGTAATTCAATTGAACTTTCAGAAAACAAA
1 TAAACCTCACAGAGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAAC-TTC--AAAA-AAA
* *
31211731 TACGGAAACTTACAAAG-TTCTTGTACACATACCCTAATTCAACCAAATTTC-AGGAAACTCGCA
62 GACGAAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTA-GAAACTCGCA
** * **
31211794 TCTAATTACGAACTAACTTCCTCTGGGAAAGCAAATTCATAGAAAAGAGGTTCATGATACCCTTT
126 TCTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAAT
*
31211859 TAAAACCTAAAATACTAAGGAAA
191 TAAAACCCAAAATACTAAGGAAA
31211882 CACAAAAAAG
Statistics
Matches: 187, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
229 36 0.19
230 3 0.02
231 13 0.07
232 80 0.43
233 17 0.09
234 38 0.20
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (232 bp):
TAAACCTCACAGAGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAACTTCAAAAAAAGACG
AAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTAGAAACTCGCATCTAA
TTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAATTAAAA
CCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
Found at i:31213275 original size:30 final size:31
Alignment explanation
Indices: 31213227--31213285 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
31213217 GAATTATTCA
31213227 AAAGTTTTCATGCAAGTCACT-GGACTATTTG
1 AAAGTTTTCATGCAAGTCACTAGG-CTATTTG
*
31213258 AAAGTTTT-ATTCAAGTCACTAGGCTATT
1 AAAGTTTTCATGCAAGTCACTAGGCTATT
31213286 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (31 bp):
AAAGTTTTCATGCAAGTCACTAGGCTATTTG
Found at i:31213751 original size:17 final size:18
Alignment explanation
Indices: 31213731--31213766 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31213721 TTAGAAGTTA
31213731 AATC-TATTACTAAATTC
1 AATCATATTACTAAATTC
31213748 AATCATATTACTAAATTC
1 AATCATATTACTAAATTC
31213766 A
1 A
31213767 CATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
AATCATATTACTAAATTC
Found at i:31214586 original size:4 final size:4
Alignment explanation
Indices: 31214577--31214601 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31214567 TTGCAATGAT
31214577 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
31214602 AAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31218449 original size:24 final size:24
Alignment explanation
Indices: 31218399--31218452 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
31218389 TTTGTAGGTC
* * **
31218399 AAATAAATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
31218423 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
31218447 AAATAT
1 AAATAT
31218453 TCTAGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:31222444 original size:24 final size:24
Alignment explanation
Indices: 31222412--31222475 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
31222402 TACTTTTTTT
* * *
31222412 TAAAATTATAATGTATTTTTATTA
1 TAAATTTATTATGTATTATTATTA
* * *
31222436 TAAGTTTATTACGTATTATTATTT
1 TAAATTTATTATGTATTATTATTA
31222460 TAAATTTATTATGTAT
1 TAAATTTATTATGTAT
31222476 CACTACTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
TAAATTTATTATGTATTATTATTA
Found at i:31223980 original size:14 final size:14
Alignment explanation
Indices: 31223951--31223979 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31223941 TAAAGAATAT
31223951 AATAAATTATTAAA
1 AATAAATTATTAAA
31223965 AATAAA-TATTAAA
1 AATAAATTATTAAA
31223978 AA
1 AA
31223980 AAGACATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATTATTAAA
Found at i:31225984 original size:2 final size:2
Alignment explanation
Indices: 31225977--31226015 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31225967 GGTCATCATG
31225977 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
31226016 TGTGTGTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31228043 original size:22 final size:22
Alignment explanation
Indices: 31228000--31228042 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31227990 AGGACAAAAA
31228000 AATGCTATTTTTTTGTTGTTTT
1 AATGCTATTTTTTTGTTGTTTT
31228022 AATGCT-TTTTCTTT-TTGTTTT
1 AATGCTATTTT-TTTGTTGTTTT
31228043 TTTCCCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.70
Consensus pattern (22 bp):
AATGCTATTTTTTTGTTGTTTT
Found at i:31232180 original size:20 final size:22
Alignment explanation
Indices: 31232138--31232182 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
31232128 GACCAAGGAT
*
31232138 TCCCTTTAGTGGTATCGCGATA
1 TCCCTTTAGTGGTATCGCAATA
*
31232160 TCCCTTT-G-GGTATGGCAATA
1 TCCCTTTAGTGGTATCGCAATA
31232180 TCC
1 TCC
31232183 ACCTCTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (22 bp):
TCCCTTTAGTGGTATCGCAATA
Found at i:31234174 original size:2 final size:2
Alignment explanation
Indices: 31234167--31234201 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31234157 TGTTACACAA
31234167 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31234202 AAGGGTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31235554 original size:65 final size:63
Alignment explanation
Indices: 31235466--31235602 Score: 188
Period size: 65 Copynumber: 2.2 Consensus size: 63
31235456 GTTCAACTAT
* * *
31235466 TATTAAATTTAATTACTTCAATATTAAATTAATATAATACATATCAGGATAAGTGATTAAATTTA
1 TATTAAATATAATTACTTCAATATTAAATTAATAAAATAC-TATCAAGATAAGT-ATTAAA-TTA
31235531 A
63 A
* *
31235532 TATTAAA-ATAATTACTTTAATATTAAATTAATAAAATACTATTAAGATAAGTATTAAATTAA
1 TATTAAATATAATTACTTCAATATTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAA
31235594 -ATTAAATAT
1 TATTAAATAT
31235603 TAAATTTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
61 6 0.09
62 6 0.09
63 6 0.09
64 11 0.17
65 29 0.45
66 7 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (63 bp):
TATTAAATATAATTACTTCAATATTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAA
Found at i:31235618 original size:17 final size:17
Alignment explanation
Indices: 31235521--31235608 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
31235511 AGGATAAGTG
*
31235521 ATTAAATTTAATATTAA
1 ATTAAATTAAATATTAA
* *
31235538 AATAATTACTTTAATATTAA
1 ATTAA--A-TTAAATATTAA
* *
31235558 ATT-AATAAAATACT--
1 ATTAAATTAAATATTAA
*
31235572 ATTAAGA-TAAGTATTAA
1 ATTAA-ATTAAATATTAA
31235589 ATTAAATTAAATATTAA
1 ATTAAATTAAATATTAA
31235606 ATT
1 ATT
31235609 TATTAAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
14 3 0.06
15 6 0.11
16 8 0.15
17 22 0.41
19 2 0.04
20 13 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTAAATTAAATATTAA
Found at i:31235621 original size:68 final size:65
Alignment explanation
Indices: 31235485--31235624 Score: 149
Period size: 68 Copynumber: 2.1 Consensus size: 65
31235475 TAATTACTTC
* * ***
31235485 AATATTAAATTAATATAATACATATCAGGATAAGTGATTAAATTTAATATTAAAATAATTACTTT
1 AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAATTTAATATTAAAATAATTAAAAT
* * *
31235550 AATATTAAATTAATAAAATAC-TATTAAGATAAGT-ATTAAATTAAATTAAATATTAAATTTATT
1 AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAA-T---TT-AATATTAAAATAATT
31235613 AAAAT
61 AAAAT
31235618 AATATTA
1 AATATTA
31235625 TTTTTAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
63 6 0.10
64 12 0.19
65 20 0.32
67 2 0.03
68 22 0.35
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (65 bp):
AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAATTTAATATTAAAATAATTAAAAT
Found at i:31237750 original size:5 final size:5
Alignment explanation
Indices: 31237740--31237766 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31237730 AAAAGGACAT
31237740 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
31237767 CAAAGGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:31238335 original size:46 final size:46
Alignment explanation
Indices: 31238276--31238384 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 46
31238266 AATTTTAGAC
* * *
31238276 TCATTTGTA-CACCTTAATGTGTAGCACTTAAACACTTCAATTTACA
1 TCATTTG-AGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
*
31238322 TCATTTGAGCACCTCAATTTGCAGCAATTAAACACTTCAATTTACA
1 TCATTTGAGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
* *
31238368 GCATTTAAGCACCTCAA
1 TCATTTGAGCACCTCAA
31238385 CTGACAACAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.02
46 55 0.98
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (46 bp):
TCATTTGAGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
Found at i:31238361 original size:23 final size:23
Alignment explanation
Indices: 31238298--31239006 Score: 325
Period size: 23 Copynumber: 30.8 Consensus size: 23
31238288 CTTAATGTGT
*
31238298 AGCACTTAAACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * * *
31238321 ATCATTTGAGCACCTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238344 AGCAATTAAACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * *
31238367 AGCATTTAAGCACCTCAACTGAC
1 AGCATTTAAACACTTCAATTTAC
* * *
31238390 AACACTTT-AACA-TCCCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* * * *
31238413 AACAGTTATACACCTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
* *
31238435 ATAG-A-TAAAACA-TCTCAATTTCC
1 --AGCATTTAAACACT-TCAATTTAC
* ** *
31238458 TGCAACTAAACAATTCAATTTGA-
1 AGCATTTAAACACTTCAATTT-AC
* * * *
31238481 TGTAATTAAAACACTTCAATTCAC
1 AG-CATTTAAACACTTCAATTTAC
* *
31238505 AACATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
31238528 AGCACTTTAAA-ACTTCAATTCT-C
1 AGCA-TTTAAACACTTCAATT-TAC
* * *
31238551 AACATTTAAACACCTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238574 AACACTTT-AACACTTCAATTTAC
1 AGCA-TTTAAACACTTCAATTTAC
*
31238597 AGCATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
* *
31238620 AGAACTTT-AACA-TCTCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* ** * *
31238643 AACATTTATGCACCTCAA-TTAT
1 AGCATTTAAACACTTCAATTTAC
* *
31238665 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ATTTAAACACT-TCAATTTAC
** *
31238688 AGCAACTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238711 AGCATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238734 AGCACTTT-AACACTTCAATTCAC
1 AGCA-TTTAAACACTTCAATTTAC
* * * *
31238757 AACATTTAAATAGTACTTCAATGTGC
1 AGCATTT-AA-A-CACTTCAATTTAC
*
31238783 AACACTTT-AACACTTCAATTTAC
1 AGCA-TTTAAACACTTCAATTTAC
* * *
31238806 AACATTTAAGCACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238829 AGCACTTT-AACATCTT-AATTAAC
1 AGCA-TTTAAACA-CTTCAATTTAC
* * *
31238852 AACATTTATACACCTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
* *
31238874 AGCGA-TAAAACATCTT-AATTTCC
1 AGC-ATTTAAACA-CTTCAATTTAC
** *
31238897 AGCAACTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
31238920 AGCACTTT-AACA-TGTCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* * *
31238943 AACGTTTATACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * *
31238966 AGAAATAAAACA-TCTCAATTTGC
1 AGCATTTAAACACT-TCAATTTAC
**
31238989 AGCAACTAAACACTTCAA
1 AGCATTTAAACACTTCAA
31239007 ATTGCAGTAC
Statistics
Matches: 511, Mismatches: 124, Indels: 102
0.69 0.17 0.14
Matches are distributed among these distances:
21 1 0.00
22 74 0.14
23 372 0.73
24 46 0.09
25 2 0.00
26 13 0.03
27 3 0.01
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (23 bp):
AGCATTTAAACACTTCAATTTAC
Found at i:31238707 original size:230 final size:227
Alignment explanation
Indices: 31238298--31238838 Score: 619
Period size: 230 Copynumber: 2.3 Consensus size: 227
31238288 CTTAATGTGT
* * * *
31238298 AGCAC-TTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTGCAGCAATTAAACACTTCAA
1 AGCACTTTAAACACTTCAATTT-CAACATTT-AACACCTCAATTTGCAAC-ATTTAACACTTCAA
*
31238362 TTTACAGCATTTAAGCACCTCAACTGACAACACTTTAACATCCCAATTAACAACAGTTATACACC
63 TTTACAGCATTTAAACACCTCAACTGACAACACTTTAACATCCCAATTAACAACAGTTATACACC
* *
31238427 TCAATTACATAGATAAAACATCTCAATTTCCTGCAACTAAACAATTCAATTTG-ATGTAATTAAA
128 TCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCA-G-AATTAAA
**
31238491 ACACTTCAATTCACAACA-TTTAAACACTTCAATTTGC
191 ACACTTCAATTCACAACACTTT-AACACTTCAATTCAC
31238528 AGCACTTTAAA-ACTTCAATTCTCAACATTTAAACACCTCAATTTGCAACACTTTAACACTTCAA
1 AGCACTTTAAACACTTCAATT-TCAACATTT-AACACCTCAATTTGCAACA-TTTAACACTTCAA
* * * * *
31238592 TTTACAGCATTTAAACACTTCAATTTG-CAGA-ACTTTAACATCTCAATTAACAACATTTATGCA
63 TTTACAGCATTTAAACACCTCAA-CTGACA-ACACTTTAACATCCCAATTAACAACAGTTATACA
* * * * *
31238655 CCTCAATTATAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCATTTAA
126 CCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGAATTAAA
** *
31238720 ACACTTCAATTTGCAGCACTTTAACACTTCAATTCAC
191 ACACTTCAATTCACAACACTTTAACACTTCAATTCAC
* * * * *
31238757 AACA-TTTAAATAGTACTTCAATGTGCAACACTTTAACACTTCAATTTACAACATTTAAGCACTT
1 AGCACTTT-AA-A-CACTTCAAT-TTCAACA-TTTAACACCTCAATTTGCAACATTTAA-CACTT
*
31238821 CAATTTGCAGCACTTTAA
60 CAATTTACAGCA-TTTAA
31238839 CATCTTAATT
Statistics
Matches: 268, Mismatches: 28, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
228 3 0.01
229 39 0.15
230 156 0.58
231 15 0.06
232 46 0.17
233 9 0.03
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.31
Consensus pattern (227 bp):
AGCACTTTAAACACTTCAATTTCAACATTTAACACCTCAATTTGCAACATTTAACACTTCAATTT
ACAGCATTTAAACACCTCAACTGACAACACTTTAACATCCCAATTAACAACAGTTATACACCTCA
ATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGCAGAATTAAAACACT
TCAATTCACAACACTTTAACACTTCAATTCAC
Found at i:31238851 original size:209 final size:206
Alignment explanation
Indices: 31238489--31238929 Score: 711
Period size: 209 Copynumber: 2.1 Consensus size: 206
31238479 GATGTAATTA
** * *
31238489 AAACACTTCAATTCACAACATTTAAACACTTCAATTTGCAGCACTTTAAAACTTCAATTCTCAAC
1 AAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTTTAAAACTTCAATTCACAAC
* *
31238554 ATTTAAACACCTCAATTTGCAACACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTG
66 ATTTAAACACCTCAATGTGCAACACTTTAACACTTCAATTTACAACATTTAAACACTTCAATTTG
* *
31238619 CAGAACTTTAACATCTCAATTAACAACATTTATGCACCTCAATTATAGCGATAAAACATCTCAAT
131 CAGAACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAAT
31238684 TTCCAGCAACT
196 TTCCAGCAACT
*
31238695 AAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAAC
1 AAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTTTAAAACTTCAATTCACAAC
* * *
31238760 ATTTAAATAGTACTTCAATGTGCAACACTTTAACACTTCAATTTACAACATTTAAGCACTTCAAT
66 ATTT-AA-A-CACCTCAATGTGCAACACTTTAACACTTCAATTTACAACATTTAAACACTTCAAT
* * *
31238825 TTGCAGCACTTTAACATCTTAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTT
128 TTGCAGAACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTC
31238890 AATTTCCAGCAACT
193 AATTTCCAGCAACT
31238904 AAACACTTCAATTTGCAGCACTTTAA
1 AAACACTTCAATTTGCAGCA-TTTAA
31238930 CATGTCAATT
Statistics
Matches: 216, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
206 64 0.30
207 2 0.01
208 1 0.00
209 144 0.67
210 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (206 bp):
AAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTTTAAAACTTCAATTCACAAC
ATTTAAACACCTCAATGTGCAACACTTTAACACTTCAATTTACAACATTTAAACACTTCAATTTG
CAGAACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAAT
TTCCAGCAACT
Found at i:31239527 original size:15 final size:15
Alignment explanation
Indices: 31239507--31239540 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
31239497 AATGTTTTAA
31239507 TACAACATAAATACT
1 TACAACATAAATACT
*
31239522 TACAACATGAATACT
1 TACAACATAAATACT
31239537 TACA
1 TACA
31239541 TTTTAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (15 bp):
TACAACATAAATACT
Found at i:31245451 original size:16 final size:16
Alignment explanation
Indices: 31245430--31245461 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31245420 ATCTGTACAT
31245430 AAAATGCGTATAAGAC
1 AAAATGCGTATAAGAC
31245446 AAAATGCGTATAAGAC
1 AAAATGCGTATAAGAC
31245462 TGTACATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATGCGTATAAGAC
Found at i:31248166 original size:21 final size:23
Alignment explanation
Indices: 31248142--31248196 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 23
31248132 TGACTTGAAA
31248142 ATTAATTTTAA-AATTT-TTAAT
1 ATTAATTTTAATAATTTATTAAT
31248163 ATTAATTTTAATTAATTTCATTAAT
1 ATTAATTTTAA-TAATTT-ATTAAT
31248188 -TTAATTTTA
1 ATTAATTTTA
31248197 CTTGATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.37
23 5 0.17
24 9 0.30
25 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTAATTTTAATAATTTATTAAT
Found at i:31249859 original size:50 final size:50
Alignment explanation
Indices: 31249781--31250070 Score: 339
Period size: 50 Copynumber: 5.7 Consensus size: 50
31249771 TCTTGTACTA
* * * * ** * *
31249781 CCAATGTCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATAGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* **
31249831 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * *
31249881 CCAACGCCATGTCCTAGACAAGGTCTTACATGAGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
31249931 CCAACGCCATGTCCCAGACAAGGTCTTACATGAGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
31249981 CCAATGCCATGTCCCAGACATGGTCTTACATGGTACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTG
31250037 CCAATGCCATGTCCCAGACATGGTCTTACA-GGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31250071 TCTATTTACC
Statistics
Matches: 209, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
50 168 0.80
53 5 0.02
55 3 0.01
56 33 0.16
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:31272458 original size:29 final size:29
Alignment explanation
Indices: 31272391--31272465 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
31272381 TGTTAATAGT
*
31272391 TGGATTAAATTTTAAAATATGAAAAGTAA
1 TGGATTAAATTCTAAAATATGAAAAGTAA
* *
31272420 AGTGACTAAATTCCTAAAA-AT-AAAAGTACA
1 TG-GATTAAATT-CTAAAATATGAAAAGTA-A
31272450 TGGATTAAATTCTAAA
1 TGGATTAAATTCTAAA
31272466 TTTTTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 12 0.32
31 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGATTAAATTCTAAAATATGAAAAGTAA
Found at i:31275112 original size:14 final size:14
Alignment explanation
Indices: 31275056--31275112 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
31275046 TTCGACAATG
* * *
31275056 ATATTGCAACGATT
1 ATATTGTAACGGTC
31275070 ATATTGTAACGGTC
1 ATATTGTAACGGTC
* **
31275084 AGATTCCAACGGTC
1 ATATTGTAACGGTC
*
31275098 ATATTGTAACAGTC
1 ATATTGTAACGGTC
31275112 A
1 A
31275113 GATTTTTGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (14 bp):
ATATTGTAACGGTC
Found at i:31276280 original size:67 final size:67
Alignment explanation
Indices: 31276172--31276303 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
31276162 TTTCCAATTC
**
31276172 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
31276237 CA
66 CA
*
31276239 AGAGAGCACACTCCCGTGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
31276304 TAATATAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:31278116 original size:12 final size:11
Alignment explanation
Indices: 31278087--31278130 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
31278077 AATCATTTAA
*
31278087 TAATAAAATAA
1 TAATAAAATAT
*
31278098 TACTAAAAATAT
1 TAAT-AAAATAT
31278110 TAATAAAATAT
1 TAATAAAATAT
*
31278121 TAATTAAATA
1 TAATAAAATA
31278131 ACATTTATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:31285059 original size:29 final size:29
Alignment explanation
Indices: 31285007--31285065 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
31284997 ATTAGACGTA
** *
31285007 TATGACTAATTAGGTGAATGAAATTTGTT
1 TATGACTAATTAGGTGAACAAAATTCGTT
31285036 TATGACTAATTAGGTGAACAAAATTCGTT
1 TATGACTAATTAGGTGAACAAAATTCGTT
31285065 T
1 T
31285066 TAGGTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (29 bp):
TATGACTAATTAGGTGAACAAAATTCGTT
Found at i:31285981 original size:27 final size:27
Alignment explanation
Indices: 31285943--31285997 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31285933 TCACTAGAAG
31285943 TAAGAATTATGTAATCGTACTTATAAA
1 TAAGAATTATGTAATCGTACTTATAAA
*
31285970 TAAGAATTATGTAATCGTATTTATAAA
1 TAAGAATTATGTAATCGTACTTATAAA
31285997 T
1 T
31285998 TGTTGTCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (27 bp):
TAAGAATTATGTAATCGTACTTATAAA
Found at i:31286183 original size:18 final size:18
Alignment explanation
Indices: 31286160--31286200 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
31286150 TAATTTTGTG
31286160 TTATTCTATAGGTGTTCT
1 TTATTCTATAGGTGTTCT
*
31286178 TTATTCTGTAGGTGTTCT
1 TTATTCTATAGGTGTTCT
31286196 TTATT
1 TTATT
31286201 TACGTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (18 bp):
TTATTCTATAGGTGTTCT
Found at i:31287635 original size:27 final size:28
Alignment explanation
Indices: 31287604--31287660 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
31287594 TTCTTGTCGA
31287604 AAAATATAATATA-ATTA-TAAAATAATT
1 AAAATATAAT-TACATTATTAAAATAATT
*
31287631 AAAATATAATTACATTATTAAAATATTT
1 AAAATATAATTACATTATTAAAATAATT
31287659 AA
1 AA
31287661 TTTTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.07
27 14 0.52
28 11 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAATATAATTACATTATTAAAATAATT
Found at i:31293777 original size:42 final size:43
Alignment explanation
Indices: 31293716--31293833 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
31293706 GATTTGAGAT
** *
31293716 TTACGTGTAAGACAATGTCTGGGACATTGGCGTCG-TATATGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
* *
31293758 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
* *
31293801 TTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 TTACGTGTAAGACC-CTGTCTGGGACATTGGCAT
31293834 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 31 0.47
43 34 0.52
44 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
Found at i:31295521 original size:13 final size:15
Alignment explanation
Indices: 31295489--31295525 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
31295479 AGTAATATTC
*
31295489 ATATATTTATGCTTT
1 ATATATATATGCTTT
31295504 ATATATATATGCTTT
1 ATATATATATGCTTT
31295519 ATATATA
1 ATATATA
31295526 ACATCAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (15 bp):
ATATATATATGCTTT
Found at i:31298157 original size:22 final size:19
Alignment explanation
Indices: 31298132--31298173 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
31298122 TGATAATAAC
31298132 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
31298154 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
31298173 T
1 T
31298174 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:31298164 original size:16 final size:15
Alignment explanation
Indices: 31298132--31298170 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
31298122 TGATAATAAC
31298132 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
31298148 TTATTATAATATATAT
1 TAATTATAAT-TATAT
31298164 TAATTAT
1 TAATTAT
31298171 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:31298942 original size:25 final size:26
Alignment explanation
Indices: 31298888--31298943 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
31298878 TTTCTCCTAA
* *
31298888 ATTTTAAATTTATTTAGTTAATTAAT
1 ATTTTAAATTTATTAAATTAATTAAT
*
31298914 -TTTTCAATTTATTAAATT-ATTAAT
1 ATTTTAAATTTATTAAATTAATTAAT
31298938 ATTTTA
1 ATTTTA
31298944 TACAAATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTAAATTTATTAAATTAATTAAT
Found at i:31301790 original size:20 final size:21
Alignment explanation
Indices: 31301742--31301782 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31301732 TATCACATTT
*
31301742 AATTTTAATTAATTTTATAATA
1 AATTTTCA-TAATTTTATAATA
31301764 AATTTTCATAATTTT-TAAT
1 AATTTTCATAATTTTATAAT
31301783 TTATTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTCATAATTTTATAATA
Found at i:31305514 original size:28 final size:29
Alignment explanation
Indices: 31305483--31305618 Score: 106
Period size: 28 Copynumber: 4.8 Consensus size: 29
31305473 TGTAATAATT
*
31305483 AGATTCCAACAACTATATTGTAACGA-AA
1 AGATTCCAACTACTATATTGTAACGATAA
* * * *
31305511 AGATTCCAACGGT-C-ACATTATAATGATCA
1 AGATTCCAAC--TACTATATTGTAACGATAA
*
31305540 AG-TTCCAACTACTATATTGTAACGA-AG
1 AGATTCCAACTACTATATTGTAACGATAA
* * * *
31305567 AGATTCCAACGA-TCATATTATAATGATCA
1 AGATTCCAACTACT-ATATTGTAACGATAA
31305596 AG-TTCCAACTACTATATTGTAAC
1 AGATTCCAACTACTATATTGTAAC
31305619 AGTCATTTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
26 1 0.01
27 4 0.05
28 69 0.85
29 7 0.09
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (29 bp):
AGATTCCAACTACTATATTGTAACGATAA
Found at i:31305560 original size:56 final size:56
Alignment explanation
Indices: 31305486--31305618 Score: 230
Period size: 56 Copynumber: 2.4 Consensus size: 56
31305476 AATAATTAGA
* *
31305486 TTCCAACAACTATATTGTAACGAAAAGATTCCAACGGTCACATTATAATGATCAAG
1 TTCCAACTACTATATTGTAACGAAAAGATTCCAACGATCACATTATAATGATCAAG
* *
31305542 TTCCAACTACTATATTGTAACGAAGAGATTCCAACGATCATATTATAATGATCAAG
1 TTCCAACTACTATATTGTAACGAAAAGATTCCAACGATCACATTATAATGATCAAG
31305598 TTCCAACTACTATATTGTAAC
1 TTCCAACTACTATATTGTAAC
31305619 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (56 bp):
TTCCAACTACTATATTGTAACGAAAAGATTCCAACGATCACATTATAATGATCAAG
Found at i:31316002 original size:24 final size:24
Alignment explanation
Indices: 31315970--31316016 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31315960 AAAGAAACAA
*
31315970 CAAAGATTTTATACTAATAAATAT
1 CAAAGATTTAATACTAATAAATAT
* *
31315994 CAAATATTTAATGCTAATAAATA
1 CAAAGATTTAATACTAATAAATA
31316017 CTAAATCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (24 bp):
CAAAGATTTAATACTAATAAATAT
Found at i:31320907 original size:10 final size:10
Alignment explanation
Indices: 31320894--31320929 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
31320884 ATATTGCATG
*
31320894 ATATAATGAT
1 ATATAATAAT
31320904 ATATAATAAT
1 ATATAATAAT
31320914 ATATAATAAT
1 ATATAATAAT
31320924 ATATAA
1 ATATAA
31320930 ATATTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATAATAAT
Found at i:31322477 original size:2 final size:2
Alignment explanation
Indices: 31322472--31322506 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31322462 AAATTTTTTA
31322472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31322507 AACTCGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31328157 original size:14 final size:14
Alignment explanation
Indices: 31328138--31328167 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31328128 CAACCTTCAT
31328138 CTCCACCAATCCAC
1 CTCCACCAATCCAC
*
31328152 CTCCACCGATCCAC
1 CTCCACCAATCCAC
31328166 CT
1 CT
31328168 TCGGTCCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.57, G:0.03, T:0.17
Consensus pattern (14 bp):
CTCCACCAATCCAC
Found at i:31329434 original size:2 final size:2
Alignment explanation
Indices: 31329427--31329477 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
31329417 AAGCAACTTT
*
31329427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31329469 TA TG TA TA T
1 TA TA TA TA T
31329478 CTTTACCGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31331439 original size:12 final size:12
Alignment explanation
Indices: 31331422--31331446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31331412 TCCTCAGAAG
31331422 TTTGATCTTAAA
1 TTTGATCTTAAA
31331434 TTTGATCTTAAA
1 TTTGATCTTAAA
31331446 T
1 T
31331447 GCCTTAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTGATCTTAAA
Found at i:31332963 original size:2 final size:2
Alignment explanation
Indices: 31332958--31332996 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31332948 AAAATTAACA
31332958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31332997 ATTGAGTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31334299 original size:14 final size:14
Alignment explanation
Indices: 31334280--31334306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31334270 CAGCTCATTT
31334280 TAGGACCCCACTAC
1 TAGGACCCCACTAC
31334294 TAGGACCCCACTA
1 TAGGACCCCACTA
31334307 TTTTGTCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (14 bp):
TAGGACCCCACTAC
Found at i:31337974 original size:71 final size:71
Alignment explanation
Indices: 31337604--31337971 Score: 366
Period size: 71 Copynumber: 5.2 Consensus size: 71
31337594 TTAATTCGCG
* *
31337604 AGCCTTAATATGACAGTTGAGAGTTTGTAACTCTCGCTAACTGTGTTGGAGGCTGTGGTTTTTCA
1 AGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGTGGTTTTTCA
31337669 C--GCA
66 CTTGCA
* * * **
31337673 CGAGCCTTAATATGATAG-TAAGGAGTTTGTAACTCTCACTAACTATGTTGGAGGCTGCAGTTTT
1 --AGCCTTAATATGACAGCTGA-GAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGTGGTTTT
* * *
31337737 TCCCCTGCG
63 TCACTTGCA
** * * * * * *
31337746 AGCCTTAATACAACAGCTGGGAGTTTGTAACTCTCACCAATTATATTAGAGGCTGTGGGTTTTT-
1 AGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGT-GGTTTTTC
*
31337810 ACTTGTA
65 ACTTGCA
* * * * * ** *
31337817 AGCCTTAATATGACAGTTGGGAATTTGTAACTCTCAATAACTGTATCAGAGGCTGTGATTTTTCA
1 AGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGTGGTTTTTCA
* *
31337882 TTTACA
66 CTTGCA
* * ** *
31337888 AGCCTTAATATGATAGCTGAGAGTTTGGAACTCTTGCTAACTGTGTTGGAGGCTGTGGTCTTTCA
1 AGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGTGGTTTTTCA
31337953 CTTGCA
66 CTTGCA
31337959 AGCCTTAATATGA
1 AGCCTTAATATGA
31337972 TAGTTTGGTG
Statistics
Matches: 240, Mismatches: 51, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
70 8 0.03
71 223 0.93
72 7 0.03
73 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (71 bp):
AGCCTTAATATGACAGCTGAGAGTTTGTAACTCTCACTAACTGTGTTGGAGGCTGTGGTTTTTCA
CTTGCA
Found at i:31345865 original size:15 final size:15
Alignment explanation
Indices: 31345845--31345881 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
31345835 TCTGGTTGCC
31345845 CTGTGACACGCCAAT
1 CTGTGACACGCCAAT
31345860 CTGTGACACGCCAAT
1 CTGTGACACGCCAAT
31345875 CTGTGAC
1 CTGTGAC
31345882 TGGTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (15 bp):
CTGTGACACGCCAAT
Found at i:31346845 original size:24 final size:24
Alignment explanation
Indices: 31346818--31346887 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 24
31346808 AAAAATCTGG
31346818 TGGCTATTCTGTGAGAGGCTGGAA
1 TGGCTATTCTGTGAGAGGCTGGAA
* * *
31346842 TGGCTATTCTTTGATGGTAGTCTTGAA
1 TGGCTATTCTGTGA--G-AGGCTGGAA
31346869 TGGCTATT-TCGTGAGAGGC
1 TGGCTATTCT-GTGAGAGGC
31346888 CGTAATGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
24 16 0.43
25 1 0.03
26 2 0.05
27 18 0.49
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.36
Consensus pattern (24 bp):
TGGCTATTCTGTGAGAGGCTGGAA
Found at i:31347958 original size:43 final size:43
Alignment explanation
Indices: 31347741--31347950 Score: 323
Period size: 43 Copynumber: 4.9 Consensus size: 43
31347731 TACAAAAAAA
*
31347741 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
31347784 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
31347827 AAACGCCGCTAAAGATCAAAACCTTTAGCGGCGCTTCTCCCA-
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
31347869 AAATCGCCGCTAAAGACCAAGACCTTTAGCGGCACTTCTCTCAC
1 AAA-CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* * * *
31347913 AAACGCCGTTAAAAACTAGGACCTTTAGCGGCGCTTCT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCT
31347951 ATTACAAATG
Statistics
Matches: 153, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 3 0.02
43 147 0.96
44 3 0.02
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
Found at i:31348565 original size:2 final size:2
Alignment explanation
Indices: 31348558--31348592 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31348548 GTTAGAAATA
31348558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31348593 GCCATTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31349927 original size:5 final size:5
Alignment explanation
Indices: 31349883--31349909 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31349873 TATTCGATTC
31349883 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
31349910 GGTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:31354103 original size:28 final size:30
Alignment explanation
Indices: 31354037--31354105 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
31354027 ACACTGGATC
* * *
31354037 CATAAACCTTAAATCCCTAACTCTTAACCT
1 CATAAACCTTAAACCCCTAACCCCTAACCT
* *
31354067 C-TAACCCTT-GACCCCTAACCCCTAA-CT
1 CATAAACCTTAAACCCCTAACCCCTAACCT
31354094 CATAAACCTTAA
1 CATAAACCTTAA
31354106 TCACAACCCT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
27 3 0.10
28 19 0.63
29 7 0.23
30 1 0.03
ACGTcount: A:0.35, C:0.38, G:0.01, T:0.26
Consensus pattern (30 bp):
CATAAACCTTAAACCCCTAACCCCTAACCT
Found at i:31354141 original size:14 final size:15
Alignment explanation
Indices: 31354124--31354156 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
31354114 CTTAAATCAG
31354124 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
31354138 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
31354153 AATC
1 AATC
31354157 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:31354620 original size:41 final size:41
Alignment explanation
Indices: 31354563--31354673 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
31354553 AAATGTTTTT
* *
31354563 GCGGCGCTTTTCCAAAAACACCGCTAAAGAACTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTAAGCATTA
*
31354604 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTAAGCATTA
*
31354645 GCGGCGCTTTCCCAAAAACGCCGCTAAAG
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG
31354674 CCCCTAAAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTAAGCATTA
Found at i:31354760 original size:40 final size:40
Alignment explanation
Indices: 31354705--31354841 Score: 161
Period size: 40 Copynumber: 3.4 Consensus size: 40
31354695 GGGCTTAGGG
* * *
31354705 TTTTTTGCGGCGTTTTTCCAAGAAACACCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTTCGAA-AAACGCCGCTAATGCTCGA
*
31354745 TTTTTAGCGGCGTTTTT-GAAAAAGCGCCTCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCGAAAAA-CGCCGCTAATGCTCGA
* * * * *
31354785 TCTTTAGTGGCGTTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCGAAAAACGCCGCTAATGCTCGA
31354825 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
31354842 TTGTCCAAAC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 3 0.04
39 14 0.17
40 60 0.74
41 4 0.05
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCGAAAAACGCCGCTAATGCTCGA
Found at i:31357374 original size:27 final size:27
Alignment explanation
Indices: 31357344--31357402 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
31357334 GATGGAACGA
*
31357344 AAACAGACAGCGTTGAAAATGAAGCTG
1 AAACAGACAGCGTTGAAAACGAAGCTG
* * *
31357371 AAACAGACGGCGTTGAAGACGGAGCTG
1 AAACAGACAGCGTTGAAAACGAAGCTG
31357398 AAACA
1 AAACA
31357403 TTTAGTGAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.17, G:0.29, T:0.12
Consensus pattern (27 bp):
AAACAGACAGCGTTGAAAACGAAGCTG
Found at i:31360366 original size:39 final size:39
Alignment explanation
Indices: 31360323--31360397 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
31360313 AAGTTGGGAA
*
31360323 AACAAATATAATATATGAACTAAATCATTATATAAGTTT
1 AACAAATATAATATATGAACTAAATCATGATATAAGTTT
31360362 AACAAATATAATATATGAACTAAATCATGATATAAG
1 AACAAATATAATATATGAACTAAATCATGATATAAG
31360398 GATTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (39 bp):
AACAAATATAATATATGAACTAAATCATGATATAAGTTT
Found at i:31361918 original size:323 final size:323
Alignment explanation
Indices: 31361330--31361985 Score: 972
Period size: 323 Copynumber: 2.0 Consensus size: 323
31361320 AACTAGATGA
* * *
31361330 AAACCCAAACTCTTTGAGGCGTTTTCACCTTCCAAACCAGCCTTCAAATATTAGCATGCCCTATT
1 AAACCCAAACTCTTTGAGGCGTTTTCACCTTCCAAACCAGCCTCCAAATATTAGCAGGCCCAATT
*** * * *
31361395 CCTGGTGATACATATTTCTAAACCTTTTCGCTGTGGAAAAAACATCTTTCTTCATCCATTTTCAA
66 CCCCCTGATACATATTTCTAAACCTTTTCGCTATGGAAAAAACATCTTTCTTCATCCATCTCCAA
* *
31361460 GCTAACCAATCCTAACTTACATCACTAGAAAAATGCACAATAGATGCTATTTATATAACAATATT
131 GCTAACCAATCCTAACCTACATCACTAGAAAAAGGCACAATAGATGCTATTTATATAACAATATT
* * * * *
31361525 AATCGATAATAGCGAGAATAGATGAGGCCAGTCCCAACAACCATTTTCGTCTACCAAATCACATA
196 AACCGATAATAGCGAGAATAGATGAGACCAATCCCAACAAACATTTCCGTCTACCAAATCACATA
* * *
31361590 CTCTTAAAGC-ATCATCTAGCTGACAGCGACCTGTATAAAACCCTTGAAGAGGACCAATCTACC
261 CTCTTAAA-CTATCATCTAGCTGACAGCGACCTATATAAAACCCTCGAAGAGAACCAATCTACC
* * *
31361653 AAACCCAAACTCTTTGAGGTGTTTTCACCTTCCAAATCAGCCTCCAAATATTAGTAGGCCCAATT
1 AAACCCAAACTCTTTGAGGCGTTTTCACCTTCCAAACCAGCCTCCAAATATTAGCAGGCCCAATT
* * *
31361718 CCCCCTGATACATATTTTTAAACCTTTTCGCTATGGAAAAATCGTCTTTCTTCATCCATCTCCAA
66 CCCCCTGATACATATTTCTAAACCTTTTCGCTATGGAAAAAACATCTTTCTTCATCCATCTCCAA
* * * ** * *
31361783 GCTAACCAGTCCTGACCTACATCACTGGAAAGGGGCACAATAGATGCTATTTGTGTAACAATATT
131 GCTAACCAATCCTAACCTACATCACTAGAAAAAGGCACAATAGATGCTATTTATATAACAATATT
*
31361848 AACCGATAATAGCGAGAATAGATGAGACCAATCCCAACAAACATTTCCGTTTACCAAATCACATA
196 AACCGATAATAGCGAGAATAGATGAGACCAATCCCAACAAACATTTCCGTCTACCAAATCACATA
* * *
31361913 CTCTTAAACTATCATCTGGTTGACTGCGACCTATATAAAACCCTCGAAGAGAACCAATCTACC
261 CTCTTAAACTATCATCTAGCTGACAGCGACCTATATAAAACCCTCGAAGAGAACCAATCTACC
31361976 AAACCCAAAC
1 AAACCCAAAC
31361986 GTCATTCCAA
Statistics
Matches: 296, Mismatches: 36, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
322 1 0.00
323 295 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.27
Consensus pattern (323 bp):
AAACCCAAACTCTTTGAGGCGTTTTCACCTTCCAAACCAGCCTCCAAATATTAGCAGGCCCAATT
CCCCCTGATACATATTTCTAAACCTTTTCGCTATGGAAAAAACATCTTTCTTCATCCATCTCCAA
GCTAACCAATCCTAACCTACATCACTAGAAAAAGGCACAATAGATGCTATTTATATAACAATATT
AACCGATAATAGCGAGAATAGATGAGACCAATCCCAACAAACATTTCCGTCTACCAAATCACATA
CTCTTAAACTATCATCTAGCTGACAGCGACCTATATAAAACCCTCGAAGAGAACCAATCTACC
Found at i:31371753 original size:93 final size:93
Alignment explanation
Indices: 31371594--31371779 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
31371584 CTTGCTTGTT
*
31371594 TCACTCAATATAATATTTGGAGGTTTTTTTGGTGAAGCATTTCTTCTTCAGCTACATACGTATTC
1 TCACTCAATATAATATTTGGAGGTTTTTTTGGTGAAGCATTTCTCCTTCAGCTACATACGTATTC
31371659 TCCTCATTGTCACCCTTATGCAAATTTC
66 TCCTCATTGTCACCCTTATGCAAATTTC
31371687 TCACTCAATATAATATTTGGAGGTTTTTTTGGTGAAGCATTTCTCCTTCAGCTACATACGTATTC
1 TCACTCAATATAATATTTGGAGGTTTTTTTGGTGAAGCATTTCTCCTTCAGCTACATACGTATTC
31371752 TCCTCATTGTCACCCTTATGCAAATTTC
66 TCCTCATTGTCACCCTTATGCAAATTTC
31371780 CAAACCGAAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (93 bp):
TCACTCAATATAATATTTGGAGGTTTTTTTGGTGAAGCATTTCTCCTTCAGCTACATACGTATTC
TCCTCATTGTCACCCTTATGCAAATTTC
Found at i:31383673 original size:14 final size:14
Alignment explanation
Indices: 31383638--31383684 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
31383628 CTGCACAATT
* *
31383638 AATAACATGATTAT
1 AATAACATGAATAA
*
31383652 AATGACATGAATAA
1 AATAACATGAATAA
31383666 AATAACAT-AACTAA
1 AATAACATGAA-TAA
31383680 AATAA
1 AATAA
31383685 TTACATGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 2 0.07
14 26 0.93
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAACATGAATAA
Found at i:31385011 original size:2 final size:2
Alignment explanation
Indices: 31385004--31385048 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31384994 TATTAAGAAA
31385004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31385046 AT A
1 AT A
31385049 AACATAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.