Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 13 of 32
Found at i:1725530 original size:17 final size:17
Alignment explanation
Indices: 1725483--1725532 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1725473 TTATTATATT
1725483 ATTTTTATATTTAT-TA
1 ATTTTTATATTTATGTA
*
1725499 ATATATTATATTTATGTCA
1 AT-TTTTATATTTATGT-A
1725518 ATTTTTATA-TTATGT
1 ATTTTTATATTTATGT
1725533 TCAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 17 0.59
18 7 0.24
19 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
ATTTTTATATTTATGTA
Found at i:1727012 original size:14 final size:13
Alignment explanation
Indices: 1726986--1727034 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1726976 GCTAAGAAAA
1726986 AAAAAAGATAAATT
1 AAAAAA-ATAAATT
*
1727000 ATAAATAATAAATT
1 A-AAAAAATAAATT
*
1727014 AAAAAAAAAAATT
1 AAAAAAATAAATT
1727027 AAACAAAA
1 AAA-AAAA
1727035 ACCATAGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 13 0.43
14 13 0.43
15 4 0.13
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAAAAATAAATT
Found at i:1727828 original size:22 final size:21
Alignment explanation
Indices: 1727776--1727838 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
1727766 ATAGACTTAG
*
1727776 TTTATAAAAT-AATATAAATA
1 TTTATAAAATAAATATAAAAA
*
1727796 TTT-T-AATTAAATTATAAAAA
1 TTTATAAAATAAA-TATAAAAA
*
1727816 TTTATAAAATAAAAGATAAAAA
1 TTTATAAAAT-AAATATAAAAA
1727838 T
1 T
1727839 ATCATTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 13 0.38
21 1 0.03
22 11 0.32
23 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTATAAAATAAATATAAAAA
Found at i:1728077 original size:14 final size:15
Alignment explanation
Indices: 1728058--1728086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1728048 CATTTATCCA
1728058 TTTTTT-ATAAAAAT
1 TTTTTTAATAAAAAT
1728072 TTTTTTAATAAAAAT
1 TTTTTTAATAAAAAT
1728087 ATAAACGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTTAATAAAAAT
Found at i:1728174 original size:22 final size:20
Alignment explanation
Indices: 1728125--1728175 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1728115 AATATTTATT
* *
1728125 TAAATTTTAATATGTTAATA
1 TAAATATTAATATCTTAATA
*
1728145 TAATTATTAATATACTTACATA
1 TAAATATTAATAT-CTTA-ATA
1728167 TAAATATTA
1 TAAATATTA
1728176 TATTTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
21 3 0.12
22 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATATTAATATCTTAATA
Found at i:1728195 original size:5 final size:5
Alignment explanation
Indices: 1728170--1728225 Score: 55
Period size: 5 Copynumber: 11.8 Consensus size: 5
1728160 TTACATATAA
* * *
1728170 ATATT ATATT -TATA ATTTT ATATT ATATT ATATT ATATT -T-TT ATTTT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
*
1728217 TTATT ATAT
1 ATATT ATAT
1728226 AATTATTTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
3 2 0.05
4 5 0.12
5 34 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
ATATT
Found at i:1728205 original size:23 final size:23
Alignment explanation
Indices: 1728170--1728225 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1728160 TTACATATAA
1728170 ATATTATATTTATAATTTTATATT
1 ATATTATA-TTATAATTTTATATT
* *
1728194 ATATTATATTATATTTTTATTTT
1 ATATTATATTATAATTTTATATT
*
1728217 TTATTATAT
1 ATATTATAT
1728226 AATTATTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATATTATATTATAATTTTATATT
Found at i:1728232 original size:29 final size:29
Alignment explanation
Indices: 1728164--1728228 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
1728154 ATATACTTAC
1728164 ATATAAATATTATATTTATAATTTTATATT
1 ATAT-AATATTATATTTATAATTTTATATT
* * *
1728194 ATATTATATTATATTT-TTATTTTTTATT
1 ATATAATATTATATTTATAATTTTATATT
1728222 ATATAAT
1 ATATAAT
1728229 TATTTGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 16 0.52
29 11 0.35
30 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATATAATATTATATTTATAATTTTATATT
Found at i:1733876 original size:19 final size:19
Alignment explanation
Indices: 1733846--1733890 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1733836 AATAAAAAAT
1733846 TTAATTATAAAAAT-ATATA
1 TTAA-TATAAAAATAATATA
*
1733865 TTAATATAAAAATAATATC
1 TTAATATAAAAATAATATA
1733884 TTAATAT
1 TTAATAT
1733891 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATATAAAAATAATATA
Found at i:1737004 original size:30 final size:28
Alignment explanation
Indices: 1736970--1737045 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
1736960 TTAAGATAAA
1736970 TTTATATAATATTATTATCTTCATATTA-TT
1 TTTATATAATATTA-TAT-TTCA-ATTATTT
* *
1737000 TTTATATCATATTATATTTTAATTATTT
1 TTTATATAATATTATATTTCAATTATTT
*
1737028 TTTATATTATATTTATAT
1 TTTATATAATA-TTATAT
1737046 CATGTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 15 0.37
29 9 0.22
30 13 0.32
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTATATAATATTATATTTCAATTATTT
Found at i:1737361 original size:40 final size:38
Alignment explanation
Indices: 1737289--1737372 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
1737279 TATTATTATT
* * *
1737289 TTAAATAAATATATTTTTATTAATATTTATAA-TTAAA
1 TTAAATAAAAATATTTTTAATAATATTAATAATTTAAA
1737326 GTTAAATAAAAATATTTTTAATATATATATAATAATTTAAA
1 -TTAAATAAAAATATTTTTAATA-ATAT-TAATAATTTAAA
1737367 TTAAAT
1 TTAAAT
1737373 TTAACGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
38 20 0.50
39 4 0.10
40 11 0.28
41 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
TTAAATAAAAATATTTTTAATAATATTAATAATTTAAA
Found at i:1742686 original size:19 final size:19
Alignment explanation
Indices: 1742674--1742714 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1742664 AATTTTCAAT
1742674 ATAATAT-AAAATTATAAA
1 ATAATATGAAAATTATAAA
*
1742692 ATAATATGAAAATAATATAA
1 ATAATATGAAAATTATA-AA
1742712 ATA
1 ATA
1742715 TATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATATGAAAATTATAAA
Found at i:1742705 original size:11 final size:10
Alignment explanation
Indices: 1742674--1742720 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 10
1742664 AATTTTCAAT
1742674 ATAATATAAA
1 ATAATATAAA
1742684 AT--TATAAA
1 ATAATATAAA
1742692 ATAATATGAAA
1 ATAATAT-AAA
1742703 ATAATAT-AA
1 ATAATATAAA
1742712 AT-ATATAAA
1 ATAATATAAA
1742721 TTTATTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 12 0.36
9 6 0.18
10 5 0.15
11 10 0.30
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
ATAATATAAA
Found at i:1742773 original size:18 final size:17
Alignment explanation
Indices: 1742731--1742775 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1742721 TTTATTAAGA
1742731 TTTATAAAATA-TAAAT
1 TTTATAAAATATTAAAT
*
1742747 TAT-TAAAATATTAAAT
1 TTTATAAAATATTAAAT
1742763 TTTATATAAATAT
1 TTTATA-AAATAT
1742776 ATATTACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 2 0.08
18 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATAAAATATTAAAT
Found at i:1742774 original size:33 final size:32
Alignment explanation
Indices: 1742705--1742791 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 32
1742695 ATATGAAAAT
*
1742705 AATATAAA-TATATAAATTTATTAAGATTTATAA
1 AATATAAATTAT-TAAA-ATATTAAGATTTATAA
1742738 AATATAAATTATTAAAATATTAA-ATTTTATATA
1 AATATAAATTATTAAAATATTAAGA-TTTATA-A
* *
1742771 AATATATATTACTTTAAATAT
1 AATATAAATTA-TTAAAATAT
1742792 ATTATAATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 1 0.02
32 12 0.26
33 23 0.49
34 11 0.23
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (32 bp):
AATATAAATTATTAAAATATTAAGATTTATAA
Found at i:1743441 original size:2 final size:2
Alignment explanation
Indices: 1743434--1743475 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1743424 TCTGTGGAAT
* *
1743434 TC TC TC TC TC TC TC TC TC TC TG TC TC GC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1743476 CCATGGCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.48, G:0.05, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1744981 original size:37 final size:36
Alignment explanation
Indices: 1744939--1745039 Score: 157
Period size: 37 Copynumber: 2.7 Consensus size: 36
1744929 TCCAACCCCA
*
1744939 TGAAAGACAGAAAGAAAATTGGGGTGGCGGCTCCATG
1 TGAAAGA-AGAAAGAAAATTGGGGTGGCGGCCCCATG
*
1744976 TGAAAGAAGGAAAGAAAATTAGGGTGGCGGCCCCATG
1 TGAAAGAA-GAAAGAAAATTGGGGTGGCGGCCCCATG
1745013 TGAAAGAAAGAAAGAAAATTGGGGTGG
1 TGAAAG-AAGAAAGAAAATTGGGGTGG
1745040 TGCAGCCTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
36 1 0.02
37 56 0.95
38 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.36, T:0.15
Consensus pattern (36 bp):
TGAAAGAAGAAAGAAAATTGGGGTGGCGGCCCCATG
Found at i:1745111 original size:27 final size:27
Alignment explanation
Indices: 1745081--1745133 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1745071 CTGTGCCGCC
*
1745081 AATTTTGAAATTCAATTTAAAACAGTA
1 AATTATGAAATTCAATTTAAAACAGTA
*
1745108 AATTATGAAATTCAATTTGAAACAGT
1 AATTATGAAATTCAATTTAAAACAGT
1745134 GAAGGTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (27 bp):
AATTATGAAATTCAATTTAAAACAGTA
Found at i:1745811 original size:44 final size:45
Alignment explanation
Indices: 1745747--1745832 Score: 156
Period size: 44 Copynumber: 1.9 Consensus size: 45
1745737 TAATTGTTAG
*
1745747 AATTTGGGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGC
1 AATTTGGGTGGCTATGCCAATCCACGAAAAAATAAATAAATATGC
1745792 AATTT-GGTGGCTATGCCAATCCACGAAAAAATAAATAAATA
1 AATTTGGGTGGCTATGCCAATCCACGAAAAAATAAATAAATA
1745833 AAAACACCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 35 0.88
45 5 0.12
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (45 bp):
AATTTGGGTGGCTATGCCAATCCACGAAAAAATAAATAAATATGC
Found at i:1746226 original size:27 final size:27
Alignment explanation
Indices: 1746188--1746240 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1746178 TGCAACCTTC
* *
1746188 ACTGTTTTAAATTGAATTTCATAATTT
1 ACTGTTTCAAATTGAATTTCAAAATTT
1746215 ACTGTTTCAAATTGAATTTCAAAATT
1 ACTGTTTCAAATTGAATTTCAAAATT
1746241 GGCGGCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTT
Found at i:1746321 original size:37 final size:37
Alignment explanation
Indices: 1746280--1746382 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
1746270 ACAAAGGCTA
* *
1746280 CGCCACCCCAATTTTCTTTCTTTCTTTCACAT-GAGGC
1 CGCCACCTCAATTTTCTTTCTTTATTTCACATGGA-GC
* *
1746317 CGCCACTTTAATTTTCTTTCTTTATTTCACATGGAGC
1 CGCCACCTCAATTTTCTTTCTTTATTTCACATGGAGC
*
1746354 CGCCACCTCAATTTTCTTTCTTTTTTTCA
1 CGCCACCTCAATTTTCTTTCTTTATTTCA
1746383 TGGGGCTGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 56 0.97
38 2 0.03
ACGTcount: A:0.17, C:0.30, G:0.09, T:0.45
Consensus pattern (37 bp):
CGCCACCTCAATTTTCTTTCTTTATTTCACATGGAGC
Found at i:1748222 original size:84 final size:83
Alignment explanation
Indices: 1748122--1748281 Score: 259
Period size: 84 Copynumber: 1.9 Consensus size: 83
1748112 CATTAGGGTG
**
1748122 ACCTTGGATTAAAAAACTCAACTCAGTCTATTG-GGGATGATCACTTTGAAATGTATTTCTGGTA
1 ACCTTGGATTAAAAAACTCAACTCAGTCTATTGTGGG-TGATCACTTTGAAATGTATTTCCAGTA
*
1748186 TATGGTCAGTTTTAAGTTTC
65 TATGATCA-TTTTAAGTTTC
*
1748206 ACCTTGGATTAAAAAACTCAACTCAGTCTATTGTGGGTGATCATTTTGAAATGTATTTCCAGTAT
1 ACCTTGGATTAAAAAACTCAACTCAGTCTATTGTGGGTGATCACTTTGAAATGTATTTCCAGTAT
1748271 ATGATCATTTT
66 ATGATCATTTT
1748282 GAAATGTATT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
83 4 0.06
84 64 0.90
85 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (83 bp):
ACCTTGGATTAAAAAACTCAACTCAGTCTATTGTGGGTGATCACTTTGAAATGTATTTCCAGTAT
ATGATCATTTTAAGTTTC
Found at i:1748285 original size:29 final size:29
Alignment explanation
Indices: 1748243--1748310 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
1748233 CTATTGTGGG
1748243 TGATCATTTTGAAATGTATTTCCAGTATA
1 TGATCATTTTGAAATGTATTTCCAGTATA
1748272 TGATCATTTTGAAATGTATTTCCAGTATA
1 TGATCATTTTGAAATGTATTTCCAGTATA
1748301 TGATCATTTT
1 TGATCATTTT
1748311 TAAGTTTCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.47
Consensus pattern (29 bp):
TGATCATTTTGAAATGTATTTCCAGTATA
Found at i:1758314 original size:259 final size:259
Alignment explanation
Indices: 1757855--1758379 Score: 1050
Period size: 259 Copynumber: 2.0 Consensus size: 259
1757845 GATAATATAT
1757855 TCCAAAATTTCCATCCACAGTTTTACTTATTTCGGTTCAGATAAAACAGTTTTCTTAACATAAAA
1 TCCAAAATTTCCATCCACAGTTTTACTTATTTCGGTTCAGATAAAACAGTTTTCTTAACATAAAA
1757920 CTTCACTTAATTCTACGTCAAGCCAAAAGCCAACTTTTCATTCTCAGCTTCTTGACGCAGAAATA
66 CTTCACTTAATTCTACGTCAAGCCAAAAGCCAACTTTTCATTCTCAGCTTCTTGACGCAGAAATA
1757985 CTGGCAAAGTAACCAACTTAAAGTACAGGCTCAAAATTAAGCACAAGATAATCTGAATGCACTAT
131 CTGGCAAAGTAACCAACTTAAAGTACAGGCTCAAAATTAAGCACAAGATAATCTGAATGCACTAT
1758050 AGCACTAGCATGAACCTATATAATTTCATAGGCTCGGTATTTAAAAAAAAGTATATCATCAATC
196 AGCACTAGCATGAACCTATATAATTTCATAGGCTCGGTATTTAAAAAAAAGTATATCATCAATC
1758114 TCCAAAATTTCCATCCACAGTTTTACTTATTTCGGTTCAGATAAAACAGTTTTCTTAACATAAAA
1 TCCAAAATTTCCATCCACAGTTTTACTTATTTCGGTTCAGATAAAACAGTTTTCTTAACATAAAA
1758179 CTTCACTTAATTCTACGTCAAGCCAAAAGCCAACTTTTCATTCTCAGCTTCTTGACGCAGAAATA
66 CTTCACTTAATTCTACGTCAAGCCAAAAGCCAACTTTTCATTCTCAGCTTCTTGACGCAGAAATA
1758244 CTGGCAAAGTAACCAACTTAAAGTACAGGCTCAAAATTAAGCACAAGATAATCTGAATGCACTAT
131 CTGGCAAAGTAACCAACTTAAAGTACAGGCTCAAAATTAAGCACAAGATAATCTGAATGCACTAT
1758309 AGCACTAGCATGAACCTATATAATTTCATAGGCTCGGTATTTAAAAAAAAGTATATCATCAATC
196 AGCACTAGCATGAACCTATATAATTTCATAGGCTCGGTATTTAAAAAAAAGTATATCATCAATC
1758373 TCCAAAA
1 TCCAAAA
1758380 AAAAAAAATT
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
259 266 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (259 bp):
TCCAAAATTTCCATCCACAGTTTTACTTATTTCGGTTCAGATAAAACAGTTTTCTTAACATAAAA
CTTCACTTAATTCTACGTCAAGCCAAAAGCCAACTTTTCATTCTCAGCTTCTTGACGCAGAAATA
CTGGCAAAGTAACCAACTTAAAGTACAGGCTCAAAATTAAGCACAAGATAATCTGAATGCACTAT
AGCACTAGCATGAACCTATATAATTTCATAGGCTCGGTATTTAAAAAAAAGTATATCATCAATC
Found at i:1759591 original size:17 final size:18
Alignment explanation
Indices: 1759569--1759608 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1759559 TAACCAACCA
1759569 ACTTAGTAGTAAGTGA-T
1 ACTTAGTAGTAAGTGATT
1759586 ACTTAGTAGTAAGTGATT
1 ACTTAGTAGTAAGTGATT
1759604 ACTTA
1 ACTTA
1759609 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (18 bp):
ACTTAGTAGTAAGTGATT
Found at i:1762044 original size:26 final size:26
Alignment explanation
Indices: 1762015--1762064 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1762005 TTGCTGCACG
*
1762015 AACAAA-ATCAAATCAAATAAAAAAAA
1 AACAAATATCAAAAC-AATAAAAAAAA
*
1762041 AACAAATATTAAAACAATAAAAAA
1 AACAAATATCAAAACAATAAAAAA
1762065 CAAGCGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (26 bp):
AACAAATATCAAAACAATAAAAAAAA
Found at i:1762850 original size:21 final size:21
Alignment explanation
Indices: 1762826--1762871 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1762816 AAAAATAACA
*
1762826 ATAATAAAAAAATTAATTATT
1 ATAATAAAAAAATTAAATATT
**
1762847 ATAATATTAAAATTAAATATT
1 ATAATAAAAAAATTAAATATT
1762868 ATAA
1 ATAA
1762872 CGATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATAAAAAAATTAAATATT
Found at i:1762878 original size:21 final size:21
Alignment explanation
Indices: 1762834--1762888 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1762824 CAATAATAAA
* *
1762834 AAAATTAATTATTATAATATT
1 AAAATTAAATATTATAAGATT
1762855 AAAATTAAATATTATAACGA-T
1 AAAATTAAATATTATAA-GATT
*
1762876 AAAA-TAAAAATTA
1 AAAATTAAATATTA
1762889 ATAATGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.27
21 21 0.70
22 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATTAAATATTATAAGATT
Found at i:1763165 original size:36 final size:35
Alignment explanation
Indices: 1763067--1763207 Score: 127
Period size: 33 Copynumber: 4.1 Consensus size: 35
1763057 TATTGAATGA
* * * *
1763067 TAAAGTTATATTCATAATAAATAATAAAAT-AAA-
1 TAAAATTATATTTATATTAAATAATAAATTAAAAT
* **
1763100 TAAAATTATATTCATGCTAAATAAT-AATTAAAAT
1 TAAAATTATATTTATATTAAATAATAAATTAAAAT
1763134 TATTAAATTATATTTATATTAAA-AATAAATT---AT
1 TA--AAATTATATTTATATTAAATAATAAATTAAAAT
1763167 TAAAATTATATTTATATTAAATAATTAAA-TAAATAT
1 TAAAATTATATTTATATTAAATAA-TAAATTAAA-AT
1763203 TAAAA
1 TAAAA
1763208 ACTAAAAATT
Statistics
Matches: 90, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
31 19 0.21
32 6 0.07
33 33 0.37
34 2 0.02
35 3 0.03
36 27 0.30
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (35 bp):
TAAAATTATATTTATATTAAATAATAAATTAAAAT
Found at i:1763168 original size:25 final size:25
Alignment explanation
Indices: 1763139--1763235 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
1763129 AAAATTATTA
*
1763139 AATTATATTTATATTAAAAATAAAT
1 AATTAAATTTATATTAAAAATAAAT
* * * * *
1763164 TATTAAAATTATATTTATATTAAAT
1 AATTAAATTTATATTAAAAATAAAT
**
1763189 AATTAAATAAATATTAAAAACTAAA-
1 AATTAAATTTATATTAAAAA-TAAAT
*
1763214 AATTATATTTATATTATAAAAT
1 AATTAAATTTATATTA-AAAAT
1763236 TATTAAAATA
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
25 46 0.85
26 8 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTAAATTTATATTAAAAATAAAT
Found at i:1763176 original size:31 final size:32
Alignment explanation
Indices: 1762986--1763196 Score: 118
Period size: 31 Copynumber: 6.6 Consensus size: 32
1762976 AACCTGTATA
*
1762986 TATAATAAATAATTAAATTTATTAAATATATATT
1 TATATTAAATAATTAAA-TTATTAAAT-TATATT
* * * *
1763020 TATAGTAAATAA-CAGAA-TA-TAAA-TAAAAT
1 TATATTAAATAATTA-AATTATTAAATTATATT
* *
1763049 TATAATT--AT-ATTGAATGA-TAAAGTTATATT
1 TAT-ATTAAATAATTAAATTATTAAA-TTATATT
* * * * *
1763079 CATAATAAATAATAAAATAAATAAAATTATATT
1 TATATTAAATAATTAAAT-TATTAAATTATATT
* * *
1763112 CATGCTAAATAATAATTAAAATTATTAAATTATATT
1 TAT-AT-TA-AATAATT-AAATTATTAAATTATATT
1763148 TATATTAAA-AA-TAAATTATTAAAATTATATT
1 TATATTAAATAATTAAATTATT-AAATTATATT
1763179 TATATTAAATAATTAAAT
1 TATATTAAATAATTAAAT
1763197 AAATATTAAA
Statistics
Matches: 134, Mismatches: 25, Indels: 37
0.68 0.13 0.19
Matches are distributed among these distances:
27 3 0.02
28 7 0.05
29 9 0.07
30 16 0.12
31 26 0.19
32 11 0.08
33 19 0.14
34 17 0.13
35 2 0.01
36 20 0.15
37 4 0.03
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (32 bp):
TATATTAAATAATTAAATTATTAAATTATATT
Found at i:1763221 original size:19 final size:21
Alignment explanation
Indices: 1763178--1763222 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
1763168 AAAATTATAT
*
1763178 TTATATTAAATAATTAAATAA
1 TTATATTAAATAACTAAATAA
1763199 --ATATTAAA-AACTAAA-AA
1 TTATATTAAATAACTAAATAA
1763216 TTATATT
1 TTATATT
1763223 TATATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 2 0.10
18 6 0.29
19 13 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATATTAAATAACTAAATAA
Found at i:1765107 original size:11 final size:11
Alignment explanation
Indices: 1765091--1765115 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1765081 ATCAATCTCA
1765091 AAAAAAAAAAG
1 AAAAAAAAAAG
1765102 AAAAAAAAAAG
1 AAAAAAAAAAG
1765113 AAA
1 AAA
1765116 CTTTAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1771958 original size:2 final size:2
Alignment explanation
Indices: 1771953--1771985 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1771943 TGTGTGATTC
1771953 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 T
1771986 TAATGCAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1772467 original size:22 final size:23
Alignment explanation
Indices: 1772424--1772467 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1772414 TTTATATATT
* *
1772424 TAAAAATTTTATTTTTTATTTAA
1 TAAAAATTTAATATTTTATTTAA
1772447 TAAAAATTTAATATTTT-TTTA
1 TAAAAATTTAATATTTTATTTA
1772468 TCAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAAAAATTTAATATTTTATTTAA
Found at i:1774067 original size:10 final size:9
Alignment explanation
Indices: 1774051--1774081 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1774041 AAATATATTT
1774051 AAATTTTTA
1 AAATTTTTA
1774060 AAATTTTTA
1 AAATTTTTA
1774069 AAATATTTTA
1 AAAT-TTTTA
1774079 AAA
1 AAA
1774082 AATTTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AAATTTTTA
Found at i:1775657 original size:5 final size:5
Alignment explanation
Indices: 1775639--1775667 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1775629 GGATTTTTTT
1775639 AAAGA AAA-A AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1775668 TGCTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1784159 original size:36 final size:37
Alignment explanation
Indices: 1784092--1784162 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
1784082 TTATAAAAAT
*
1784092 TAATATAAAATAATTTAAAATTTTAATTTATTTTAAA
1 TAATATAAAATAATTTAAAATTTTAAATTATTTTAAA
*
1784129 TAATAT-AATTAATATT-AAATTTTAAATTATTTTA
1 TAATATAAAATAAT-TTAAAATTTTAAATTATTTTA
1784163 TATTAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 23 0.74
37 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TAATATAAAATAATTTAAAATTTTAAATTATTTTAAA
Found at i:1784161 original size:46 final size:48
Alignment explanation
Indices: 1784060--1784172 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 48
1784050 AAATAATAAA
* *
1784060 AAATTATTTT-ATTTATATTAAATTATAAAAATTAATATAAAATAATTT
1 AAATTATTTTAATTTATTTTAAATAATAAAAATTAATATAAAAT-ATTT
* *
1784108 AAA--ATTTTAATTTATTTTAAATAAT-ATAATTAATATTAAAT-TTT
1 AAATTATTTTAATTTATTTTAAATAATAAAAATTAATATAAAATATTT
*
1784152 AAATTATTTTATATTAATTTT
1 AAATTATTTTA-ATTTATTTT
1784173 TTAATTTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
44 6 0.11
46 25 0.45
47 22 0.39
48 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (48 bp):
AAATTATTTTAATTTATTTTAAATAATAAAAATTAATATAAAATATTT
Found at i:1784634 original size:10 final size:10
Alignment explanation
Indices: 1784590--1784641 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
1784580 TTTTTTTTAA
1784590 TAATTAAAAT
1 TAATTAAAAT
*
1784600 T-ATTAAATT
1 TAATTAAAAT
*
1784609 TAATTACTAA-
1 TAATTA-AAAT
*
1784619 TCATTAAAAT
1 TAATTAAAAT
1784629 TAATTAAAAT
1 TAATTAAAAT
1784639 TAA
1 TAA
1784642 AATTTTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 10 0.30
10 22 0.67
11 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATTAAAAT
Found at i:1784972 original size:15 final size:17
Alignment explanation
Indices: 1784941--1784972 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1784931 TTTAAAATTT
1784941 AAATATATTATTATAAA
1 AAATATATTATTATAAA
1784958 AAATA-ATTA-TATAAA
1 AAATATATTATTATAAA
1784973 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATATTATTATAAA
Found at i:1787147 original size:34 final size:32
Alignment explanation
Indices: 1787109--1787177 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
1787099 ATTTAACTCG
1787109 TATTTAAA-ATATTATATATTTATATAAATTTTAA
1 TATTTAAATA-ATTA-ATA-TTATATAAATTTTAA
* *
1787143 TATTTTAATAATTAATATTATATATATTTTAA
1 TATTTAAATAATTAATATTATATAAATTTTAA
1787175 TAT
1 TAT
1787178 ATTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 3 0.09
34 11 0.34
35 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTTAAATAATTAATATTATATAAATTTTAA
Found at i:1787179 original size:10 final size:9
Alignment explanation
Indices: 1787120--1787211 Score: 63
Period size: 8 Copynumber: 10.8 Consensus size: 9
1787110 ATTTAAAATA
1787120 TTATATATT
1 TTATATATT
*
1787129 TATATAAATT
1 T-TATATATT
1787139 TTA-ATATT
1 TTATATATT
*
1787147 TTA-ATA-A
1 TTATATATT
1787154 TTA-ATATT
1 TTATATATT
*
1787162 ATATATATT
1 TTATATATT
1787171 TTA-ATATAT
1 TTATATAT-T
1787180 TTATATA-T
1 TTATATATT
*
1787188 TTA-ATTTT
1 TTATATATT
* *
1787196 TTATTTATA
1 TTATATATT
1787205 TTATATA
1 TTATATA
1787212 ATCATTTTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
7 8 0.12
8 24 0.37
9 22 0.34
10 11 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATATATT
Found at i:1787192 original size:34 final size:32
Alignment explanation
Indices: 1787119--1787192 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
1787109 TATTTAAAAT
1787119 ATTATATATTTATATAAATTTTAATATTTTAATA
1 ATTA-ATA-TTATATAAATTTTAATATTTTAATA
*
1787153 ATTAATATTATATATATTTTAATATATTTATATA
1 ATTAATATTATATAAATTTTAATAT-TTTA-ATA
*
1787187 TTTAAT
1 ATTAAT
1787193 TTTTTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 17 0.47
33 7 0.19
34 12 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTAATATTATATAAATTTTAATATTTTAATA
Found at i:1787546 original size:2 final size:2
Alignment explanation
Indices: 1787539--1787565 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1787529 ACATATGCAT
1787539 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 T
1787566 TTCATTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1789540 original size:15 final size:15
Alignment explanation
Indices: 1789505--1789534 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1789495 AATATTAAAA
1789505 AATATTTTTTATATT
1 AATATTTTTTATATT
1789520 AATATTTTTTATATT
1 AATATTTTTTATATT
1789535 TTTATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:1790275 original size:18 final size:17
Alignment explanation
Indices: 1790227--1790277 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1790217 TTTATAAAGT
1790227 AATT-ATATATATTTTTA
1 AATTAATATA-ATTTTTA
* *
1790244 ATTTAATTAAAATTTTTAA
1 AATTAA-TATAATTTTT-A
1790263 AATTAATATAATTTT
1 AATTAATATAATTTT
1790278 AATACGACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.11
18 15 0.56
19 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTAATATAATTTTTA
Found at i:1791123 original size:19 final size:19
Alignment explanation
Indices: 1791091--1791136 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1791081 AATTTATATT
1791091 AATTTTA-A-AATAATAAA
1 AATTTTATATAATAATAAA
1791108 AATTTTATATAATAATAAA
1 AATTTTATATAATAATAAA
*
1791127 AATTATATAT
1 AATTTTATAT
1791137 TCGTTAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 18 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTTATATAATAATAAA
Found at i:1791487 original size:20 final size:21
Alignment explanation
Indices: 1791455--1791496 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1791445 TTTTTTCGGG
1791455 TTTTTTTTGTTATAA-TTATA
1 TTTTTTTTGTTATAATTTATA
1791475 TTTTTATTT-TTATAATTTATA
1 TTTTT-TTTGTTATAATTTATA
1791496 T
1 T
1791497 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTTTGTTATAATTTATA
Found at i:1791541 original size:17 final size:18
Alignment explanation
Indices: 1791501--1791542 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1791491 TTATATAAAA
1791501 TTTAATAAATTAATAATT
1 TTTAATAAATTAATAATT
*
1791519 TATAATAAATGT-A-AATT
1 TTTAATAAAT-TAATAATT
1791536 TTTAATA
1 TTTAATA
1791543 GTTTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 10 0.48
19 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAATAAATTAATAATT
Found at i:1791564 original size:27 final size:27
Alignment explanation
Indices: 1791481--1791565 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
1791471 TATATTTTTA
*
1791481 TTTTT-ATAATTTATATAAAATTTAAT
1 TTTTTAATAATTTATATAAATTTTAAT
*** * *
1791507 AAATTAATAATTTATAATAAA-TGTAAA
1 TTTTTAATAATTTAT-ATAAATTTTAAT
* *
1791534 TTTTTAATAGTTTATATAAATTTTTAT
1 TTTTTAATAATTTATATAAATTTTAAT
1791561 TTTTT
1 TTTTT
1791566 TTAATATTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 7 0.16
27 32 0.73
28 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTAATAATTTATATAAATTTTAAT
Found at i:1792120 original size:41 final size:41
Alignment explanation
Indices: 1792049--1792126 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
1792039 TTAAATAATT
*
1792049 AAAATATATTTATTTAATTTTAATTATAAATATTAATATTA
1 AAAATATATTTATTTAATTTTAATTATAAATAATAATATTA
* *
1792090 AAAATATTTTTAATTT-ATTATT-ATTTTAAATAATAAT
1 AAAATATATTT-ATTTAATT-TTAATTATAAATAATAAT
1792127 TTATATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 26 0.81
42 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
AAAATATATTTATTTAATTTTAATTATAAATAATAATATTA
Found at i:1793083 original size:50 final size:50
Alignment explanation
Indices: 1793024--1793282 Score: 430
Period size: 50 Copynumber: 5.2 Consensus size: 50
1793014 TATATTTAGA
*
1793024 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1793074 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1793124 GTCAACAATTATGGCCACCTCCCTCTATTGTTAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
**
1793174 GTCAACAATTATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1793224 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
1793274 GTCAACAAT
1 GTCAACAAT
1793283 GATAACAACT
Statistics
Matches: 197, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 196 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1797739 original size:50 final size:50
Alignment explanation
Indices: 1797679--1797937 Score: 412
Period size: 50 Copynumber: 5.2 Consensus size: 50
1797669 TATATTTAGA
* *
1797679 GTCAATAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1797729 GTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1797779 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGATTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1797829 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1797879 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
1797929 GTCAACAAT
1 GTCAACAAT
1797938 GACAACAATT
Statistics
Matches: 194, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 193 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1799391 original size:21 final size:20
Alignment explanation
Indices: 1799352--1799394 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1799342 TAAATTATAC
*
1799352 ATATTTTTTATATTATAATT
1 ATATTTTTTAAATTATAATT
*
1799372 ATATTTATTTAAATTTTAATT
1 ATATTT-TTTAAATTATAATT
1799393 AT
1 AT
1799395 TAATAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTTAAATTATAATT
Found at i:1799419 original size:32 final size:30
Alignment explanation
Indices: 1799362--1799422 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
1799352 ATATTTTTTA
*
1799362 TATTATAATTATATTTATTTAAATTTTAAT
1 TATTATAATTATATTTATATAAATTTTAAT
1799392 TATTAATAATTTATATTT-TATATAATTTTAA
1 TATT-ATAA-TTATATTTATATA-AATTTTAA
1799423 AAATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 7 0.26
32 16 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTATAATTATATTTATATAAATTTTAAT
Found at i:1799468 original size:14 final size:15
Alignment explanation
Indices: 1799434--1799472 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
1799424 AATATTTATA
1799434 TATTTA-AATTATTT
1 TATTTATAATTATTT
1799448 T-TTTATAA-TATTT
1 TATTTATAATTATTT
1799461 TATTTAT-ATTAT
1 TATTTATAATTAT
1799473 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATAATTATTT
Found at i:1799469 original size:11 final size:11
Alignment explanation
Indices: 1799403--1799485 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 11
1799393 ATTAATAATT
1799403 TATATTTTATA
1 TATATTTTATA
*
1799414 TA-ATTTTAAA
1 TATATTTTATA
*
1799424 AATA-TTTATA
1 TATATTTTATA
**
1799434 TAT-TTAAAT-
1 TATATTTTATA
*
1799443 TAT-TTTTTTA
1 TATATTTTATA
*
1799453 TAATATTTTATT
1 T-ATATTTTATA
1799465 TATATTATATATA
1 TATATT-T-TATA
1799478 TATATTTT
1 TATATTTT
1799486 TTGGTGTGTA
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
9 6 0.11
10 19 0.36
11 11 0.21
12 8 0.15
13 9 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTTATA
Found at i:1807455 original size:3 final size:3
Alignment explanation
Indices: 1807447--1807486 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1807437 TATTATAGAT
1807447 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1807487 GGAAAAACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1808383 original size:28 final size:28
Alignment explanation
Indices: 1808343--1808398 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1808333 TGGCCAGTTT
1808343 ACATTAATAAAATAACATTCTTTATTAA
1 ACATTAATAAAATAACATTCTTTATTAA
1808371 ACATTAATAAAATAACATTCTTTATTAA
1 ACATTAATAAAATAACATTCTTTATTAA
1808399 TCCTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (28 bp):
ACATTAATAAAATAACATTCTTTATTAA
Found at i:1811961 original size:2 final size:2
Alignment explanation
Indices: 1811954--1811983 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1811944 CTAGCCATCA
1811954 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
1811984 CACTTTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1813397 original size:11 final size:11
Alignment explanation
Indices: 1813364--1813402 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1813354 TTAAAATATT
1813364 TATATTTAATA
1 TATATTTAATA
*
1813375 TTATATTCAATA
1 -TATATTTAATA
*
1813387 CATATTTAATA
1 TATATTTAATA
1813398 TATAT
1 TATAT
1813403 ATATGTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
TATATTTAATA
Found at i:1813581 original size:19 final size:19
Alignment explanation
Indices: 1813559--1813623 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 19
1813549 TAATATTAAA
1813559 AAATTAATATAATATATTT
1 AAATTAATATAATATATTT
*
1813578 AAATTTAAATAAAATTATATTT
1 AAA-TT-AATATAA-TATATTT
*
1813600 ATTATATAA-ATAATA-ATTT
1 A-AAT-TAATATAATATATTT
1813619 AAATT
1 AAATT
1813624 GAATTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 1 0.03
18 2 0.05
19 8 0.22
20 4 0.11
21 9 0.24
22 11 0.30
23 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATATAATATATTT
Found at i:1818688 original size:16 final size:16
Alignment explanation
Indices: 1818669--1818735 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
1818659 TTATATTATT
1818669 AAATATTTAAA-AATAA
1 AAAT-TTTAAATAATAA
**
1818685 AAATTTTAAAT--TTT
1 AAATTTTAAATAATAA
1818699 AAATTTTAAATAATAA
1 AAATTTTAAATAATAA
* *
1818715 AAATATAAAATAATAA
1 AAATTTTAAATAATAA
1818731 AAATT
1 AAATT
1818736 ACGATATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 12 0.29
15 6 0.15
16 23 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTTTAAATAATAA
Found at i:1818695 original size:7 final size:7
Alignment explanation
Indices: 1818685--1818709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1818675 TTAAAAATAA
1818685 AAATTTT
1 AAATTTT
1818692 AAATTTT
1 AAATTTT
1818699 AAATTTT
1 AAATTTT
1818706 AAAT
1 AAAT
1818710 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:1818714 original size:30 final size:31
Alignment explanation
Indices: 1818658--1818718 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1818648 AGTGATTATA
*
1818658 TTTATATTATTAAATATTTAAAAATAAAAAT
1 TTTAAATTATTAAATATTTAAAAATAAAAAT
1818689 TTTAAATT-TTAAAT-TTTAAATAATAAAAAT
1 TTTAAATTATTAAATATTTAAA-AATAAAAAT
1818719 ATAAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.21
30 15 0.54
31 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAAATTATTAAATATTTAAAAATAAAAAT
Found at i:1819431 original size:29 final size:30
Alignment explanation
Indices: 1819396--1819508 Score: 108
Period size: 30 Copynumber: 3.8 Consensus size: 30
1819386 AGATTAATTT
* *
1819396 ATGTTAACATTTATTTAGATATAAATTAAA
1 ATGTTAAAATTTATTTAGATACAAATTAAA
* *
1819426 AT-TTAAAAGTTTAGTTGGATACAAATT-AA
1 ATGTTAAAA-TTTATTTAGATACAAATTAAA
1819455 ATGTTAAAATTTATTTTAG-TACAAATTAAA
1 ATGTTAAAATTTA-TTTAGATACAAATTAAA
* * *
1819485 GTTTTAAACTTTATTT-GAATACAA
1 ATGTTAAAATTTATTTAG-ATACAA
1819509 TAAAAGTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 24 0.35
30 43 0.63
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (30 bp):
ATGTTAAAATTTATTTAGATACAAATTAAA
Found at i:1819507 original size:59 final size:59
Alignment explanation
Indices: 1819396--1819508 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1819386 AGATTAATTT
* * * *
1819396 ATGTTAACATTTATTTAGATATAAATTAAAATTTAAAAGTTTAGTTGGATACAAATTAA
1 ATGTTAAAATTTATTTAGATACAAATTAAAATTTAAAACTTTAGTTGAATACAAATTAA
* * *
1819455 ATGTTAAAATTTATTTTAG-TACAAATTAAAGTTTTAAACTTTATTTGAATACAA
1 ATGTTAAAATTTA-TTTAGATACAAATTAAAATTTAAAACTTTAGTTGAATACAA
1819509 TAAAAGTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 41 0.89
60 5 0.11
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (59 bp):
ATGTTAAAATTTATTTAGATACAAATTAAAATTTAAAACTTTAGTTGAATACAAATTAA
Found at i:1826671 original size:2 final size:2
Alignment explanation
Indices: 1826664--1826698 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1826654 ATATAACAAA
1826664 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
1826699 AAACAAGGGT
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:1829670 original size:3 final size:3
Alignment explanation
Indices: 1829662--1829690 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1829652 TTGGGTTTAT
1829662 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1829691 TTGCTTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1830006 original size:19 final size:19
Alignment explanation
Indices: 1829954--1830010 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 19
1829944 AAAATTTAAT
1829954 TTTTTATTAAATAATATATAA
1 TTTTTATT--ATAATATATAA
1829975 TTTTTATT-T-ATATATAA
1 TTTTTATTATAATATATAA
1829992 -TTTTATTTATAATATATAA
1 TTTTTA-TTATAATATATAA
1830011 ATATCAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.15
17 10 0.30
18 2 0.06
19 8 0.24
21 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTATTATAATATATAA
Found at i:1830442 original size:70 final size:70
Alignment explanation
Indices: 1830352--1830491 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 70
1830342 TGATATTTAA
* * * *
1830352 GTTAATTTTTATTATATGCTTATAATTCAAATTCAAATTAGATAATAATATCTGATGGAAAGACT
1 GTTAATTTTTATTACATGCTTATAATTCAAATCCAAATTAGATAACAATATCTGATCGAAAGACT
1830417 CTAAT
66 CTAAT
* *
1830422 GTTAGTTTTTATTACCTGCTTATAATTCAAATCCAAATTAGATAACAATATCTGATCGAAAGACT
1 GTTAATTTTTATTACATGCTTATAATTCAAATCCAAATTAGATAACAATATCTGATCGAAAGACT
1830487 CTAAT
66 CTAAT
1830492 TCTAAAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (70 bp):
GTTAATTTTTATTACATGCTTATAATTCAAATCCAAATTAGATAACAATATCTGATCGAAAGACT
CTAAT
Found at i:1830833 original size:2 final size:2
Alignment explanation
Indices: 1830828--1830854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1830818 TGTGTGTGTC
1830828 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 T
1830855 CATTGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1840474 original size:23 final size:23
Alignment explanation
Indices: 1840432--1840475 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1840422 ATATTTTATA
1840432 AAATTATAAAATATTAATATATT
1 AAATTATAAAATATTAATATATT
1840455 AAATATATCAAAAT-TT-ATATA
1 AAAT-TAT-AAAATATTAATATA
1840476 AATATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 5 0.26
25 5 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTATAAAATATTAATATATT
Found at i:1844017 original size:3 final size:3
Alignment explanation
Indices: 1844009--1844036 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1843999 ATTTTTATTT
1844009 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1844037 ATCTCCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1844420 original size:18 final size:16
Alignment explanation
Indices: 1844383--1844434 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
1844373 TATATTTATA
*
1844383 TTATATTTGAATATTT
1 TTATATTTAAATATTT
1844399 TTATATTATAAATATGTT
1 TTATATT-TAAATAT-TT
*
1844417 TTATATATTATATATTT
1 TTATAT-TTAAATATTT
1844434 T
1 T
1844435 ATAAAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
18 14 0.45
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TTATATTTAAATATTT
Found at i:1845322 original size:22 final size:21
Alignment explanation
Indices: 1845267--1845322 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
1845257 ATTCTTGTTA
**
1845267 ATTA-TAAATTTTAATTTAAT
1 ATTATTAAATTTTAATAAAAT
*
1845287 TTTATTTAAA-TTTAATAAAAAT
1 ATTA-TTAAATTTTAAT-AAAAT
1845309 ATTATTAAATTTTA
1 ATTATTAAATTTTA
1845323 TTAATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTAAATTTTAATAAAAT
Found at i:1845701 original size:15 final size:15
Alignment explanation
Indices: 1845681--1845754 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
1845671 AAATTTTTAT
*
1845681 TTTTTAGTTATATAA
1 TTTTTAATTATATAA
1845696 TTTTTAATTATATAA
1 TTTTTAATTATATAA
*
1845711 -----AATTACATAA
1 TTTTTAATTATATAA
*
1845721 CTTTTAATTATATAAA
1 TTTTTAATTATAT-AA
1845737 TTATTTTAA-TATATAA
1 -T-TTTTAATTATATAA
1845753 TT
1 TT
1845755 AGGAAACCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
10 9 0.19
14 1 0.02
15 22 0.47
16 4 0.09
17 5 0.11
18 6 0.13
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (15 bp):
TTTTTAATTATATAA
Found at i:1851781 original size:33 final size:33
Alignment explanation
Indices: 1851744--1851834 Score: 87
Period size: 33 Copynumber: 2.7 Consensus size: 33
1851734 TTGATAATAA
*
1851744 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
* * *
1851777 ATATAATATTAAT-TATTACAT-TATTAAATTTT
1 ATATAATATAAATATA-TAAATATATTAAAATTT
*
1851809 ATATAAATATAACATATTTTAAATAT
1 ATAT-AATATAA-ATA-TATAAATAT
1851835 CACGATAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
32 15 0.33
33 22 0.49
34 2 0.04
35 4 0.09
36 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:1872769 original size:12 final size:12
Alignment explanation
Indices: 1872754--1872786 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1872744 GCAAATGCAT
1872754 CAGCAACAGCCA
1 CAGCAACAGCCA
*
1872766 CAGCCACAGCCA
1 CAGCAACAGCCA
1872778 CAGCAACAG
1 CAGCAACAG
1872787 TTTGCTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.42, G:0.18, T:0.00
Consensus pattern (12 bp):
CAGCAACAGCCA
Found at i:1873411 original size:51 final size:51
Alignment explanation
Indices: 1873356--1873457 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
1873346 AGATGGCTCC
1873356 CCGTTCTGATAATACTTCTCAAGGTCAGGTCTCTGCAGTGCCTTCTGGTCA
1 CCGTTCTGATAATACTTCTCAAGGTCAGGTCTCTGCAGTGCCTTCTGGTCA
* *
1873407 CCGTTCTGATAATAGTTCTCAAGGTCAGGTTTCTGCAGTGCCTTCTGGTCA
1 CCGTTCTGATAATACTTCTCAAGGTCAGGTCTCTGCAGTGCCTTCTGGTCA
1873458 TACACTATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (51 bp):
CCGTTCTGATAATACTTCTCAAGGTCAGGTCTCTGCAGTGCCTTCTGGTCA
Found at i:1880038 original size:30 final size:30
Alignment explanation
Indices: 1880002--1880061 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1879992 CACAGGTTAC
1880002 ATCATCTGCCAACAGCACCAAATTAAGATG
1 ATCATCTGCCAACAGCACCAAATTAAGATG
1880032 ATCATCTGCCAACAGCACCAAATTAAGATG
1 ATCATCTGCCAACAGCACCAAATTAAGATG
1880062 TAAAAGCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (30 bp):
ATCATCTGCCAACAGCACCAAATTAAGATG
Found at i:1885163 original size:18 final size:18
Alignment explanation
Indices: 1885121--1885168 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1885111 AATATATATT
* *
1885121 AATATTAATATATTTTTTA
1 AATATTTAT-TATATTTTA
1885140 AA-ATTTATTATATTTTA
1 AATATTTATTATATTTTA
*
1885157 AATATTTTTTAT
1 AATATTTATTAT
1885169 TTATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATATTTATTATATTTTA
Found at i:1885167 original size:21 final size:22
Alignment explanation
Indices: 1885143--1885186 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1885133 TTTTTTAAAA
* *
1885143 TTTA-TTATATTTTAAATATTT
1 TTTATTTATATATAAAATATTT
1885164 TTTATTTATATATAAAATATTT
1 TTTATTTATATATAAAATATTT
1885186 T
1 T
1885187 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTATATATAAAATATTT
Found at i:1885187 original size:16 final size:16
Alignment explanation
Indices: 1885168--1885198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1885158 ATATTTTTTA
*
1885168 TTTATATATAAAATAT
1 TTTAAATATAAAATAT
1885184 TTTAAATATAAAATA
1 TTTAAATATAAAATA
1885199 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATATAAAATAT
Found at i:1885347 original size:32 final size:29
Alignment explanation
Indices: 1885301--1885383 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 29
1885291 AAGATTAAAA
*
1885301 TTTTTAATAATTATTAAATTTATGAATAAT
1 TTTTTAATAATTATTAAATTTATAAAT-AT
*
1885331 TATATTTAATATTTATTAAATTTATAAATAT
1 T-T-TTTAATAATTATTAAATTTATAAATAT
*
1885362 TTTTTAAAAATTATTAAATTTA
1 TTTTTAATAATTATTAAATTTA
1885384 CAATCAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.38
30 2 0.04
31 4 0.09
32 23 0.49
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTTTAATAATTATTAAATTTATAAATAT
Found at i:1885382 original size:19 final size:19
Alignment explanation
Indices: 1885298--1885383 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
1885288 AATAAGATTA
*
1885298 AAATTT-TTAATAATTATT
1 AAATTTATTAAAAATTATT
* *
1885316 AAATTTATGAATAATTATATTT
1 AAATTTATTAA-AAAT-TA-TT
* *
1885338 AATATTTATT-AAATTTATA
1 AA-ATTTATTAAAAATTATT
*
1885357 AATATTTTTTAAAAATTATT
1 AA-ATTTATTAAAAATTATT
1885377 AAATTTA
1 AAATTTA
1885384 CAATCAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 6 0.11
19 17 0.32
20 13 0.25
21 6 0.11
22 5 0.09
23 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
AAATTTATTAAAAATTATT
Found at i:1888026 original size:13 final size:13
Alignment explanation
Indices: 1888005--1888039 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1887995 TTTGAATATC
*
1888005 AAAATTTAGATAA
1 AAAAATTAGATAA
1888018 AAAAATTAGATAA
1 AAAAATTAGATAA
1888031 AATAAATTA
1 AA-AAATTA
1888040 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
AAAAATTAGATAA
Found at i:1888042 original size:18 final size:18
Alignment explanation
Indices: 1888021--1888059 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1888011 TAGATAAAAA
*
1888021 AATTAGATAAAATAAATT
1 AATTAAATAAAATAAATT
* *
1888039 AATTAAATTAATTAAATT
1 AATTAAATAAAATAAATT
1888057 AAT
1 AAT
1888060 AATTTATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAAATAAAATAAATT
Found at i:1888047 original size:9 final size:9
Alignment explanation
Indices: 1888033--1888059 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1888023 TTAGATAAAA
1888033 TAAATTAAT
1 TAAATTAAT
1888042 TAAATTAAT
1 TAAATTAAT
1888051 TAAATTAAT
1 TAAATTAAT
1888060 AATTTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAATTAAT
Found at i:1888244 original size:20 final size:20
Alignment explanation
Indices: 1888221--1888262 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1888211 AAACCAAATA
*
1888221 TATATTTATTAATTATTAAT
1 TATATTTAATAATTATTAAT
* *
1888241 TATATTTAATATTTATTTAT
1 TATATTTAATAATTATTAAT
1888261 TA
1 TA
1888263 AACTTATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTTAATAATTATTAAT
Found at i:1893757 original size:14 final size:14
Alignment explanation
Indices: 1893738--1893766 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1893728 ATTATTGTTG
1893738 GTGTGGGTGTGGGT
1 GTGTGGGTGTGGGT
1893752 GTGTGGGTGTGGGT
1 GTGTGGGTGTGGGT
1893766 G
1 G
1893767 GCGGTTGAAT
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:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (14 bp):
GTGTGGGTGTGGGT
Found at i:1893922 original size:3 final size:3
Alignment explanation
Indices: 1893914--1893943 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1893904 ATCACCAGTT
1893914 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1893944 TATATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1894027 original size:20 final size:20
Alignment explanation
Indices: 1893999--1894037 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1893989 AAATATAATT
*
1893999 TTTAAAATTTTTTATTATAA
1 TTTAAAATTTTATATTATAA
*
1894019 TTTATAATTTTATATTATA
1 TTTAAAATTTTATATTATA
1894038 TTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAAATTTTATATTATAA
Found at i:1895321 original size:21 final size:21
Alignment explanation
Indices: 1895297--1895345 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1895287 TAGAAGTTCG
*
1895297 AAAAGTATTGCATGTATGAAC
1 AAAAGTATTGCATGCATGAAC
1895318 AAAAGTATTGCATGCATGAAC
1 AAAAGTATTGCATGCATGAAC
1895339 AAAAGTA
1 AAAAGTA
1895346 GGGAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.24
Consensus pattern (21 bp):
AAAAGTATTGCATGCATGAAC
Found at i:1904673 original size:37 final size:37
Alignment explanation
Indices: 1904626--1904696 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1904616 GACAACTAAA
1904626 CAAGCAAGTAATAGATGCC-AACAAGCAAATACAAAAG
1 CAAGCAAGTAATAGATGCCGAA-AAGCAAATACAAAAG
1904663 CAAGCAAGTAATAGATGCCGAAAAGCAAATACAA
1 CAAGCAAGTAATAGATGCCGAAAAGCAAATACAA
1904697 CCATTTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.54, C:0.18, G:0.17, T:0.11
Consensus pattern (37 bp):
CAAGCAAGTAATAGATGCCGAAAAGCAAATACAAAAG
Found at i:1907873 original size:26 final size:24
Alignment explanation
Indices: 1907837--1907886 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1907827 TTGTTTAATT
* *
1907837 TTAAAATTTTAAATATTAAATAAA
1 TTAAAATTTTAAAAAATAAATAAA
1907861 TTAAATATATTTAAAAAATAAATAAA
1 TTAAA-AT-TTTAAAAAATAAATAAA
1907887 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAATTTTAAAAAATAAATAAA
Found at i:1907891 original size:19 final size:22
Alignment explanation
Indices: 1907854--1907896 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
1907844 TTTAAATATT
1907854 AAATAAATTAAATATATTTAAA
1 AAATAAATTAAATATATTTAAA
1907876 AAATAAA-TAAA-A-ATTTAAA
1 AAATAAATTAAATATATTTAAA
1907895 AA
1 AA
1907897 TTTAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 4 0.19
22 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAAATTAAATATATTTAAA
Found at i:1907910 original size:20 final size:18
Alignment explanation
Indices: 1907858--1907913 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 18
1907848 AATATTAAAT
1907858 AAATTAAATAT-ATTTAA
1 AAATTAAATATAATTTAA
* *
1907875 AAAATAAATAAAAATTTAA
1 AAATTAAAT-ATAATTTAA
1907894 AAATTTAAATATGAATTTAA
1 AAA-TTAAATAT-AATTTAA
1907914 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 8 0.26
18 1 0.03
19 10 0.32
20 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATTAAATATAATTTAA
Found at i:1907933 original size:39 final size:37
Alignment explanation
Indices: 1907845--1907934 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 37
1907835 TTTTAAAATT
1907845 TTAAATATTAAATAAATTAAATATATTTAAAAAATAAA
1 TTAAA-ATTAAATAAATTAAATATATTTAAAAAATAAA
* * **
1907883 TAAAAATTTAAA-AATTTAAATATGAATTTAATTAATAAAA
1 TTAAAA-TTAAATAAATTAAATAT--ATTTAAAAAAT-AAA
1907923 TTAAAATTAAAT
1 TTAAAATTAAAT
1907935 GATCTTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
37 11 0.26
38 9 0.21
39 14 0.33
40 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (37 bp):
TTAAAATTAAATAAATTAAATATATTTAAAAAATAAA
Found at i:1908057 original size:23 final size:23
Alignment explanation
Indices: 1908006--1908051 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1907996 AGTTGAATAA
*
1908006 AAATATATAATTTATTTTTAATT
1 AAATATATAATTTATTTATAATT
1908029 AAATAT-TAATTTATTTGATAATT
1 AAATATATAATTTATTT-ATAATT
1908052 TTATATACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AAATATATAATTTATTTATAATT
Found at i:1919230 original size:2 final size:2
Alignment explanation
Indices: 1919223--1919252 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1919213 GAGTAAAAAC
1919223 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
1919253 TAATAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1920648 original size:16 final size:18
Alignment explanation
Indices: 1920627--1920664 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1920617 TTATAATTAA
1920627 ATAT-AAATT-AATAATG
1 ATATAAAATTAAATAATG
*
1920643 ATATAAAATTAAATAATT
1 ATATAAAATTAAATAATG
1920661 ATAT
1 ATAT
1920665 CTTGTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATAAAATTAAATAATG
Found at i:1989940 original size:75 final size:75
Alignment explanation
Indices: 1989803--1989955 Score: 263
Period size: 75 Copynumber: 2.0 Consensus size: 75
1989793 CCGACTTAGC
1989803 TAACTACACTGCTTCTTCTTCTTCTTCTCTTACAATGTTTCAAATCGGTATTCATTGCTTGATTA
1 TAACTACACTG--TCTTCTTCTTCTTCTCTTACAATGTTTCAAATCGGTATTCATTGCTTGATTA
1989868 TACATTTTATTT
64 TACATTTTATTT
*
1989880 TAACTACACTG-CTTCTTCTTCTTCTCTTACAATGTTTTCAAATCGGTATTCATTGCTTGATTCT
1 TAACTACACTGTCTTCTTCTTCTTCTCTTACAATG-TTTCAAATCGGTATTCATTGCTTGATTAT
1989944 ACATTTTATTT
65 ACATTTTATTT
1989955 T
1 T
1989956 TTCAAATTTC
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
74 23 0.31
75 40 0.54
77 11 0.15
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.50
Consensus pattern (75 bp):
TAACTACACTGTCTTCTTCTTCTTCTCTTACAATGTTTCAAATCGGTATTCATTGCTTGATTATA
CATTTTATTT
Found at i:1990659 original size:73 final size:73
Alignment explanation
Indices: 1990520--1990664 Score: 258
Period size: 71 Copynumber: 2.0 Consensus size: 73
1990510 TTTCTCTAGA
* *
1990520 GTATCTGTATTCAACATATATTTTGGACGTGAGGGATGAAAGTATCAACCTTCAAATATTTTAAA
1 GTATCTATATTCAACATATATTTTGGACGTGAGGGATGAAAGTATCAACCTTCAAATATTTAAAA
1990585 AAAAGCTT
66 AAAAGCTT
1990593 GTATCTATATTCAACATATA-TTTGGACGTGA-GGATGAAAGTATCAACCTTCAAATATTTAAAA
1 GTATCTATATTCAACATATATTTTGGACGTGAGGGATGAAAGTATCAACCTTCAAATATTTAAAA
1990656 AAAAGCTT
66 AAAAGCTT
1990664 G
1 G
1990665 AAAAATATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 40 0.57
72 11 0.16
73 19 0.27
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (73 bp):
GTATCTATATTCAACATATATTTTGGACGTGAGGGATGAAAGTATCAACCTTCAAATATTTAAAA
AAAAGCTT
Found at i:1993037 original size:89 final size:89
Alignment explanation
Indices: 1992881--1993058 Score: 311
Period size: 89 Copynumber: 2.0 Consensus size: 89
1992871 AATCCTAAGC
* *
1992881 TTGGTAAACTTGGTAGCCATATGGTGTGCATATTTCCTTAATGCCATTACTATTTTCTCTCTGAA
1 TTGGTAAACTTGGTAGCCATATGGTGTGCATATTTACTTAATGCCATTACTATTTTCTCTCTCAA
*
1992946 AGCCTTAGCTTCTTCGTACTTTTT
66 AGCCTTAGCTTCTTCGAACTTTTT
* *
1992970 TTGGTAAAGTTGGTAGCCATATGGTTTGCATATTTACTTAATGCCATTACTATTTTCTCTCTCAA
1 TTGGTAAACTTGGTAGCCATATGGTGTGCATATTTACTTAATGCCATTACTATTTTCTCTCTCAA
1993035 AGCCTTAGCTTCTTCGAACTTTTT
66 AGCCTTAGCTTCTTCGAACTTTTT
1993059 CTGTGATCAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (89 bp):
TTGGTAAACTTGGTAGCCATATGGTGTGCATATTTACTTAATGCCATTACTATTTTCTCTCTCAA
AGCCTTAGCTTCTTCGAACTTTTT
Found at i:1996722 original size:11 final size:11
Alignment explanation
Indices: 1996706--1996749 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1996696 TAATAATTTA
1996706 TATATTTATAT
1 TATATTTATAT
1996717 TATATTT-TAT
1 TATATTTATAT
*
1996727 TATTTTTATAT
1 TATATTTATAT
* *
1996738 CATAATTATAT
1 TATATTTATAT
1996749 T
1 T
1996750 TTAAATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1996749 original size:19 final size:19
Alignment explanation
Indices: 1996698--1996751 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1996688 TGACCTAATA
* *
1996698 ATAATTTATATATTTATATT
1 ATAA-TTATATTTTTATATC
*
1996718 ATATTTTATTATTTTTATATC
1 ATA-ATTA-TATTTTTATATC
1996739 ATAATTATATTTT
1 ATAATTATATTTT
1996752 AAATATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 6 0.21
20 9 0.32
21 13 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATAATTATATTTTTATATC
Found at i:2002987 original size:31 final size:30
Alignment explanation
Indices: 2002952--2003009 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2002942 ATATTAATTT
*
2002952 TTTAAATTAAAATTAAAATTTATAAATTAAA
1 TTTAAATTAAAA-TAAAATTTAAAAATTAAA
*
2002983 TTTAAATTATAATAAAATTTAAAAATT
1 TTTAAATTAAAATAAAATTTAAAAATT
2003010 TTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAATTAAAATAAAATTTAAAAATTAAA
Found at i:2003012 original size:26 final size:29
Alignment explanation
Indices: 2002951--2003021 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 29
2002941 TATATTAATT
*
2002951 TTTTAAATTAAAATTAAAATTTATAAATTAA
1 TTTTAAATTATAA-TAAAATTTATAAA-TAA
*
2002982 ATTTAAATTATAATAAAA-TT-TAAA-AA
1 TTTTAAATTATAATAAAATTTATAAATAA
2003008 TTTTAAATTATAAT
1 TTTTAAATTATAAT
2003022 TGAATCTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.41
28 4 0.11
29 2 0.05
30 5 0.14
31 11 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTAAATTATAATAAAATTTATAAATAA
Found at i:2003301 original size:21 final size:22
Alignment explanation
Indices: 2003255--2003305 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2003245 TATAATATAT
2003255 TTATATA-TTATTTATTTTTACC
1 TTATATATTTATTTATTTTTA-C
2003277 TTATATATTTATATT-TTTTTA-
1 TTATATATTTAT-TTATTTTTAC
2003298 TTATATAT
1 TTATATAT
2003306 CACGTACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.30
22 7 0.26
23 10 0.37
24 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATATATTTATTTATTTTTAC
Found at i:2003683 original size:17 final size:17
Alignment explanation
Indices: 2003661--2003693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2003651 ATAATTTTTA
2003661 TTATAA-TTAAAGTAATT
1 TTATAAGTTAAA-TAATT
2003678 TTATAAGTTAAATAAT
1 TTATAAGTTAAATAAT
2003694 AAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTATAAGTTAAATAATT
Found at i:2003733 original size:23 final size:26
Alignment explanation
Indices: 2003688--2003747 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 26
2003678 TTATAAGTTA
*
2003688 AATAATAAAAATTTAATACTAAATTT
1 AATAATAAAAATTTAATAATAAATTT
*
2003714 AATAA-AAAAA-TT-ATAATAAATAT
1 AATAATAAAAATTTAATAATAAATTT
*
2003737 AA-AATTAAAAT
1 AATAATAAAAAT
2003748 ACATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 15 0.52
24 2 0.07
25 5 0.17
26 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAATAAAAATTTAATAATAAATTT
Found at i:2003742 original size:17 final size:17
Alignment explanation
Indices: 2003720--2003753 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2003710 ATTTAATAAA
*
2003720 AAAATTATAATAAATAT
1 AAAATTAAAATAAATAT
*
2003737 AAAATTAAAATACATAT
1 AAAATTAAAATAAATAT
2003754 TTTAATATCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTAAAATAAATAT
Found at i:2016476 original size:8 final size:8
Alignment explanation
Indices: 2016463--2016487 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2016453 GATATTTTAA
2016463 TAATAATT
1 TAATAATT
2016471 TAATAATT
1 TAATAATT
2016479 TAATAATT
1 TAATAATT
2016487 T
1 T
2016488 TTTGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAATAATT
Found at i:2016513 original size:16 final size:16
Alignment explanation
Indices: 2016494--2016524 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2016484 ATTTTTTGAA
*
2016494 TTAATTTAAATTTAAT
1 TTAACTTAAATTTAAT
2016510 TTAACTTAAATTTAA
1 TTAACTTAAATTTAA
2016525 ATAAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAACTTAAATTTAAT
Found at i:2016894 original size:6 final size:6
Alignment explanation
Indices: 2016883--2016909 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2016873 ACCAAACCAA
2016883 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
2016910 TAAATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:2016966 original size:2 final size:2
Alignment explanation
Indices: 2016959--2017010 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2016949 ACCCAAAGAC
2016959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2017001 TA TA TA TA TA
1 TA TA TA TA TA
2017011 ATTCTTAGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2017573 original size:2 final size:2
Alignment explanation
Indices: 2017566--2017601 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2017556 ATTTGCACAT
2017566 TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2017602 TTGTATACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2017590 original size:19 final size:18
Alignment explanation
Indices: 2017566--2017601 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2017556 ATTTGCACAT
2017566 TATATATAATATATATATA
1 TATATATAATATA-ATATA
*
2017585 TATATATATTATAATAT
1 TATATATAATATAATAT
2017602 TTGTATACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATATAATATAATATA
Done.