Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold111
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: 1194829
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.25
Warning! 272571 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:472125 original size:21 final size:21
Alignment explanation
Indices: 472072--472129 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
472062 AATTTTTATA
* *
472072 TAATTTTGATAACTTTTGACG
1 TAATTTTGACAACCTTTGACG
*
472093 TAATTTTAACAACCTTTGACG
1 TAATTTTGACAACCTTTGACG
472114 TAATTTTGACAACCTT
1 TAATTTTGACAACCTT
472130 GACATAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (21 bp):
TAATTTTGACAACCTTTGACG
Found at i:472140 original size:20 final size:21
Alignment explanation
Indices: 472071--472140 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
472061 TAATTTTTAT
* * *
472071 ATAATTTTGATAACTTTTGAC
1 ATAATTTTAACAACCTTTGAC
*
472092 GTAATTTTAACAACCTTTGAC
1 ATAATTTTAACAACCTTTGAC
* *
472113 GTAATTTTGACAACC-TTGAC
1 ATAATTTTAACAACCTTTGAC
*
472133 ATAGTTTT
1 ATAATTTT
472141 CATTACTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 11 0.26
21 31 0.74
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (21 bp):
ATAATTTTAACAACCTTTGAC
Found at i:472249 original size:32 final size:31
Alignment explanation
Indices: 472207--472301 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 31
472197 CATAATTTCG
* *
472207 ATAATATTTAATTAATATTGATAACTTTTTAA
1 ATAATTTTTAATTAATTTTGATAACTTTTT-A
* * *
472239 ATAATTTTTAAATATTTTTGGA-AACTTTTTG
1 ATAATTTTTAATTAATTTT-GATAACTTTTTA
* *
472270 ATATATTTTAAATATTATTTTGATAACTTTTT
1 ATA-ATTTTTAAT-TAATTTTGATAACTTTTT
472302 GGAAAACTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
31 3 0.06
32 32 0.64
33 15 0.30
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
ATAATTTTTAATTAATTTTGATAACTTTTTA
Found at i:472298 original size:33 final size:34
Alignment explanation
Indices: 472224--472302 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 34
472214 TTAATTAATA
472224 TTGATAACTTTTT-AAATAATTTTTAAATATTTT
1 TTGATAACTTTTTGAAATAATTTTTAAATATTTT
* *
472257 TGGA-AACTTTTTGATAT-A-TTTTAAATATTATT
1 TTGATAACTTTTTGAAATAATTTTTAAATATT-TT
472289 TTGATAACTTTTTG
1 TTGATAACTTTTTG
472303 GAAAACTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 11 0.28
32 14 0.35
33 15 0.38
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (34 bp):
TTGATAACTTTTTGAAATAATTTTTAAATATTTT
Found at i:473093 original size:16 final size:17
Alignment explanation
Indices: 473072--473109 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
473062 TTTTTATATA
473072 TTAATA-AAA-ATATTAT
1 TTAATATAAATATATT-T
473088 TTAATATAAATATATTT
1 TTAATATAAATATATTT
473105 TTAAT
1 TTAAT
473110 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATAAATATATTT
Found at i:473604 original size:22 final size:22
Alignment explanation
Indices: 473579--473620 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
473569 CACAATTATT
*
473579 TTAAAA-AATAACATTTAATAAA
1 TTAAAATAAAAAC-TTTAATAAA
473601 TTAAAATAAAAACTTTAATA
1 TTAAAATAAAAACTTTAATA
473621 TTTATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAAATAAAAACTTTAATAAA
Found at i:473743 original size:2 final size:2
Alignment explanation
Indices: 473731--473770 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
473721 GATATTCTCT
473731 TA TA T- 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 TA TA TA T
473771 GTTTTTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:474250 original size:4 final size:4
Alignment explanation
Indices: 474241--474273 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
474231 AACCTGCAAG
474241 AATT AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT A
474274 TATACTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:474799 original size:18 final size:18
Alignment explanation
Indices: 474747--474802 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
474737 ATTACTATTA
474747 TTAT-TTTATTTT-ATAAT
1 TTATATTTATTTTAAT-AT
*
474764 TT-TAATTT-TTTTATTAT
1 TTAT-ATTTATTTTAATAT
474781 TTATATTTATTTTAATAT
1 TTATATTTATTTTAATAT
474799 TTAT
1 TTAT
474803 TAAATTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
18 17 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTATTTTAATAT
Found at i:474800 original size:12 final size:13
Alignment explanation
Indices: 474773--474829 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
474763 TTTTAATTTT
*
474773 TTTATTATTTATA
1 TTTATTATTAATA
474786 TTTATT-TTAATA
1 TTTATTATTAATA
474798 TTTATTA--AAT-
1 TTTATTATTAATA
*
474808 TTAATTATAATAATA
1 TTTATTAT--TAATA
474823 TTTATTA
1 TTTATTA
474830 AATTTATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
12 11 0.31
13 6 0.17
14 3 0.09
15 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:474809 original size:27 final size:26
Alignment explanation
Indices: 474779--474857 Score: 97
Period size: 25 Copynumber: 3.0 Consensus size: 26
474769 TTTTTTTATT
*
474779 ATTTATATTTATTTTAATATTTATTAA
1 ATTTATA-TTATATTAATATTTATTAA
*
474806 ATTTA-ATTATAATAATATTTATTAA
1 ATTTATATTATATTAATATTTATTAA
* *
474831 ATTTATACTTATATTAAAATATATTAA
1 ATTTATA-TTATATTAATATTTATTAA
474858 CGATCCTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
25 22 0.49
26 2 0.04
27 21 0.47
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTATATTATATTAATATTTATTAA
Found at i:486444 original size:32 final size:34
Alignment explanation
Indices: 486401--486492 Score: 118
Period size: 36 Copynumber: 2.7 Consensus size: 34
486391 CAACACTATC
486401 TTTC-AAGGCTAAGATAGAAAC-CTCCCCATC-T
1 TTTCAAAGGCTAAGATAGAAACTCTCCCCATCTT
** *
486432 TTTCATGGGCTAAGATAGAACCTCTCTCCCCATCTT
1 TTTCAAAGGCTAAGATAGAA--ACTCTCCCCATCTT
486468 TTTCAAAGGCTAAGATAGAAACTCT
1 TTTCAAAGGCTAAGATAGAAACTCT
486493 TAATTACTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 4 0.08
32 13 0.26
34 5 0.10
35 9 0.18
36 19 0.38
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAAACTCTCCCCATCTT
Found at i:486927 original size:21 final size:21
Alignment explanation
Indices: 486901--486958 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
486891 CCGTTGGGCT
*
486901 CAATGTATCGATACAATTCAC
1 CAATGTATTGATACAATTCAC
* *
486922 CAATGTATTAATACAATTCAT
1 CAATGTATTGATACAATTCAC
486943 C-ATGTATTGATACAAT
1 CAATGTATTGATACAAT
486959 GTATCAATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (21 bp):
CAATGTATTGATACAATTCAC
Found at i:486964 original size:20 final size:20
Alignment explanation
Indices: 486911--486958 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
486901 CAATGTATCG
*
486911 ATACAATTCACCAATGTATTA
1 ATACAATTCATC-ATGTATTA
*
486932 ATACAATTCATCATGTATTG
1 ATACAATTCATCATGTATTA
486952 ATACAAT
1 ATACAAT
486959 GTATCAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (20 bp):
ATACAATTCATCATGTATTA
Found at i:487047 original size:13 final size:13
Alignment explanation
Indices: 487029--487053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487019 TACTAAGAAC
487029 ATGTATCGATACA
1 ATGTATCGATACA
487042 ATGTATCGATAC
1 ATGTATCGATAC
487054 TTAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:487052 original size:32 final size:33
Alignment explanation
Indices: 487011--487074 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
487001 TATTTCAAGG
487011 TGTATCGATACTAAG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
* *
487043 TGTATCGATACTTAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
487075 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:487195 original size:20 final size:21
Alignment explanation
Indices: 487170--487210 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
487160 GATACTGGGA
487170 ATTATTTTTA-CTTGAAAAAT
1 ATTATTTTTAGCTTGAAAAAT
487190 ATTATTTTTATGCTTGAAAAA
1 ATTATTTTTA-GCTTGAAAAA
487211 CATCTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAT
Found at i:488748 original size:45 final size:49
Alignment explanation
Indices: 488682--488868 Score: 193
Period size: 52 Copynumber: 3.8 Consensus size: 49
488672 TATGACACTG
** *
488682 CTTAAAGATAAGAAAGGTGCCAATGTGCTGATTCGAGGCCA-G-C-A-A
1 CTTAAAGATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAGGACTAGA
*
488727 CTTAAAGATAAGAAAAATGCCAACGTGCTGATTCAAGGCCAGTGACATTAGA
1 CTTAAAGATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAG-GAC--TAGA
* *
488779 CTTAAAAATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAAGCGACATTGA
1 CTTAAAGATAAGAAAAATGCCAATGTGCTGATTCAAGGCC-AG-GAC-TAGA
* * * *
488831 GCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAG
1 -CTTAAAGATAAGAAAAATGCCAATGTGCTGATTCAAG
488869 ACTAGCGACA
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
45 37 0.31
47 1 0.01
48 1 0.01
51 1 0.01
52 42 0.35
53 39 0.32
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (49 bp):
CTTAAAGATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAGGACTAGA
Found at i:488807 original size:52 final size:52
Alignment explanation
Indices: 488726--489414 Score: 440
Period size: 52 Copynumber: 13.2 Consensus size: 52
488716 GAGGCCAGCA
* * * * *
488726 ACTTAAAGATAAGAAAAATGCCAACGTGCTGATTCAAGGCCAGTGACATTAG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
*
488778 ACTTAAAAATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAAGCGACATT-G
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCC-AGCGACATTGG
* * * * * *
488830 AGCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAG
1 A-CTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * * * * * *
488883 ACTTAGAAA-GAGAAGAATACCAATATTCTAATACAAGGCCAACGACATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * *
488934 GCTTAAAAATGAGAAGAATTCCATTGTGCTGATTCAAGGCTAGCAGCCAGCGACATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTC-A----AG--GCCAGCGACATTGG
* * * * * * *
488993 GCTTAAAAATGATAAGAATGCTAATGTGCTGATTCAAGGCTAGCGACACTAG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * * *
489045 ACTTAGAAA-GAGAAAAATGCTAATGTACTGATACAAGGCCAACGACATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * *
489096 GCTTAAAAATGGGAAAAATG-CAATATGCTGATTCAAGGCCAGTGACATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
** * * * * * *
489147 ACTTAAAAAT-AGTAAATGTGCTAATATGCTGATTCAAGGCTAGCTATATCGG
1 ACTTAAAAATGAG-AAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * ** * *
489199 A-TTTAAGATGA-TAAGGTGCCAATGTGCTGATTCAAGGCCAGTGGCATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * ** * * * *
489249 GCTTAAAGATGATAAAGGTTCCAATGTGCTTATTCATGGCCAGCAACATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
** * * * ** * * * * ***
489301 GTTTAAAGAA-AATAGAGGTGCTAATATGCTGATTCAAGTCCAGCGATATCAA
1 ACTTAAA-AATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
* * * * * * * *
489353 ACTTAAAGATGACAAAGATTCCAATGTGCTGATTCAAAGCTAGCAATATTGG
1 ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
489405 ACTTAGAAAA
1 ACTTA-AAAA
489415 AGATCATTGA
Statistics
Matches: 499, Mismatches: 118, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
50 30 0.06
51 136 0.27
52 234 0.47
53 50 0.10
54 2 0.00
57 2 0.00
58 1 0.00
59 44 0.09
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (52 bp):
ACTTAAAAATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
Found at i:488964 original size:103 final size:105
Alignment explanation
Indices: 488727--488977 Score: 308
Period size: 105 Copynumber: 2.4 Consensus size: 105
488717 AGGCCAGCAA
* * * * * * *
488727 CTTAAAGATAAGAAAAATGCCAACGTGCTGATTCAAGGCCAGTGACATTAGACTTAAAAATAAGA
1 CTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGCGACACTAGACTTAAAAATAAGA
* * * *
488792 AAAATGCCAATGTGCTGATTCAAGGCCAAGCGACATTGAG
66 AAAATACCAATATGCTAATACAAGGCCAAGCGACATTGAG
* * * *
488832 CTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAGACTTAGAAA-GAGA
1 CTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGCGACACTAGACTTAAAAATAAGA
* * *
488896 AGAATACCAATATTCTAATACAAGGCCAA-CGACATTGGG
66 AAAATACCAATATGCTAATACAAGGCCAAGCGACATTGAG
* *
488935 CTTAAAAATGAGAAGAATTCCATTGTGCTGATTCAAGGCTAGC
1 CTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGC
488978 AGCCAGCGAC
Statistics
Matches: 124, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
103 48 0.39
104 26 0.21
105 50 0.40
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (105 bp):
CTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGCGACACTAGACTTAAAAATAAGA
AAAATACCAATATGCTAATACAAGGCCAAGCGACATTGAG
Found at i:489021 original size:59 final size:59
Alignment explanation
Indices: 488920--489036 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
488910 CTAATACAAG
* *
488920 GCCAACGACATTGGGCTTAAAAATGAGAAGAATTCCATTGTGCTGATTCAAGGCTAGCA
1 GCCAACGACATTGGGCTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGCA
* * *
488979 GCCAGCGACATTGGGCTTAAAAATGATAAGAATGCTAATGTGCTGATTCAAGGCTAGC
1 GCCAACGACATTGGGCTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGC
489037 GACACTAGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (59 bp):
GCCAACGACATTGGGCTTAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCTAGCA
Found at i:489027 original size:162 final size:155
Alignment explanation
Indices: 488760--489190 Score: 501
Period size: 162 Copynumber: 2.7 Consensus size: 155
488750 CGTGCTGATT
** * * * *
488760 CAAGGCCAGTGACATTAGACTTAAAAATAAGAAAAATGCCAATGTGCTGATTCAAGGCCAAGCGA
1 CAAGGCCAACGACATTGGGCTTAAAAATGAG-AAAATTCCAATGTGCTGATTCAAGGCCAAGCGA
488825 CATTGAGCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAGACTTAGA
65 CATTGAGCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAGACTTAGA
* *
488890 AAGAGAAGAATACCAATATTCTAATA
130 AAGAGAAAAATACCAATATACTAATA
*
488916 CAAGGCCAACGACATTGGGCTTAAAAATGAGAAGAATTCCATTGTGCTGATTCAAGGCTAGCAGC
1 CAAGGCCAACGACATTGGGCTTAAAAATGAGAA-AATTCCAATGTGCTGATTCAAGGC---CA--
* * * * *
488981 CAGCGACATTGGGCTTAAAAATGATAAGAATGCTAATGTGCTGATTCAAGGCTAGCGACACTAGA
60 -AGCGACATTGAGCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAGA
* * * *
489046 CTTAGAAAGAGAAAAATGCTAATGTACTGATA
124 CTTAGAAAGAGAAAAATACCAATATACTAATA
* * * * *
489078 CAAGGCCAACGACATTGGGCTTAAAAATGGGAAAAATGCAATATGCTGATTCAAGGCC-AGTGAC
1 CAAGGCCAACGACATTGGGCTTAAAAATGAGAAAATTCCAATGTGCTGATTCAAGGCCAAGCGAC
* * *
489142 ATTG-GACTTAAAAAT-AGTAA-ATGTGCTAATATGCTGATTCAAGGCTAGC
66 ATTGAG-CTTAAAAATGAG-AAGA-ATGCCAATATGCTGATTCAAGACTAGC
489191 TATATCGGAT
Statistics
Matches: 238, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
153 3 0.01
154 45 0.19
155 2 0.01
156 48 0.20
158 1 0.00
159 2 0.01
161 20 0.08
162 117 0.49
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (155 bp):
CAAGGCCAACGACATTGGGCTTAAAAATGAGAAAATTCCAATGTGCTGATTCAAGGCCAAGCGAC
ATTGAGCTTAAAAATGAGAAGAATGCCAATATGCTGATTCAAGACTAGCGACACTAGACTTAGAA
AGAGAAAAATACCAATATACTAATA
Found at i:489067 original size:51 final size:51
Alignment explanation
Indices: 488979--489186 Score: 220
Period size: 51 Copynumber: 4.0 Consensus size: 51
488969 AAGGCTAGCA
* * * *
488979 GCCAGCGACATTGGGCTTAAAAATGATAAGAATGCTAATGTGCTGATTCAAG
1 GCCAGCGACATTGGACTTAAAAA-GAGAAAAATGCTAATATGCTGATTCAAG
* * * * * * *
489031 GCTAGCGACACTAGACTTAGAAAGAGAAAAATGCTAATGTACTGATACAAG
1 GCCAGCGACATTGGACTTAAAAAGAGAAAAATGCTAATATGCTGATTCAAG
* * *
489082 GCCAACGACATTGGGCTTAAAAATGGGAAAAATGC-AATATGCTGATTCAAG
1 GCCAGCGACATTGGACTTAAAAA-GAGAAAAATGCTAATATGCTGATTCAAG
* * **
489133 GCCAGTGACATTGGACTTAAAAATAGTAAATGTGCTAATATGCTGATTCAAG
1 GCCAGCGACATTGGACTTAAAAAGAG-AAAAATGCTAATATGCTGATTCAAG
489185 GC
1 GC
489187 TAGCTATATC
Statistics
Matches: 127, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 1 0.01
51 80 0.63
52 46 0.36
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (51 bp):
GCCAGCGACATTGGACTTAAAAAGAGAAAAATGCTAATATGCTGATTCAAG
Found at i:489306 original size:102 final size:104
Alignment explanation
Indices: 489116--489398 Score: 284
Period size: 102 Copynumber: 2.7 Consensus size: 104
489106 GGGAAAAATG
* * * * *
489116 CAATATGCTGATTCAAGGCCAGTGACATTGGACTTAAAAAT-AGTAAATGTGCTAATATGCTGAT
1 CAATATGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGA-TAAAGGTTCCAATGTGCTGAT
* * * **
489180 TCAAGGCTAGCTATATCGGATTT-AAGATGATA-AGGTGC
65 TCAAGGCCAGCAACATCGGATTTAAAGAAAATAGAGGTGC
* * * *
489218 CAATGTGCTGATTCAAGGCCAGTGGCATTGGGCTTAAAGATGATAAAGGTTCCAATGTGCTTATT
1 CAATATGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGATAAAGGTTCCAATGTGCTGATT
* * *
489283 CATGGCCAGCAACATTGGGTTTAAAGAAAATAGAGGTGC
66 CAAGGCCAGCAACATCGGATTTAAAGAAAATAGAGGTGC
* * * * *** * *
489322 TAATATGCTGATTCAAGTCCAGCGATATCAAACTTAAAGATGACAAAGATTCCAATGTGCTGATT
1 CAATATGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGATAAAGGTTCCAATGTGCTGATT
* *
489387 CAAAGCTAGCAA
66 CAAGGCCAGCAA
489399 TATTGGACTT
Statistics
Matches: 145, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
102 70 0.48
103 8 0.06
104 67 0.46
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (104 bp):
CAATATGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGATAAAGGTTCCAATGTGCTGATT
CAAGGCCAGCAACATCGGATTTAAAGAAAATAGAGGTGC
Found at i:489609 original size:32 final size:31
Alignment explanation
Indices: 489508--489932 Score: 369
Period size: 31 Copynumber: 13.6 Consensus size: 31
489498 TTGAGAGAGC
* *
489508 TGCCACCAACTTGTGTGGACTTT-GAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
* *
489538 TGCCACCTACTTCTGTGGGCTTTAAAAGGG-
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
* *
489568 TGCCACTAACTTGTGTAGGCTTTAAAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GGT
* * **
489600 TGCCACTAACTTGTGTGGGATTTTGCAA-GGT
1 TGCCACCAACTTGTGTGGG-CTTTAAAAGGGT
*
489631 TGCCATCGAA-TTGTGTGGGCTTT-AAAGAGGT
1 TGCCA-CCAACTTGTGTGGGCTTTAAAAG-GGT
** * ** *
489662 CACCACCGACTTGTGTGGGCTTTTGAAGGGC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
*** * **
489693 TGCCATTGACTTGTGTAGGCTTTTGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
* *
489724 TGCCACCGACTTGTATGGG-TGTTAGAAAGAGGT
1 TGCCACCAACTTGTGTGGGCT-TTA-AAAG-GGT
* * *
489757 TGCCACCGACTTATGTAGGCTTTAAAGAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAA-AGGGT
* *
489789 TGTCA-CAGACTTGTGTGGGCTTTAGAAGGGGT
1 TGCCACCA-ACTTGTGTGGGCTTTA-AAAGGGT
*
489821 TACCACCAACTTGTGTGGGCTTTAAAGAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAA-AGGGT
489853 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
* ** *
489884 TGTCACTGACTTGTGTGGGCTTTAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
* *
489915 TGCCATCGACTTGTGTGG
1 TGCCACCAACTTGTGTGG
489933 ATTTTTAAAA
Statistics
Matches: 325, Mismatches: 52, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.01
30 50 0.15
31 137 0.42
32 102 0.31
33 33 0.10
34 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGGT
Found at i:489777 original size:64 final size:64
Alignment explanation
Indices: 489476--489932 Score: 409
Period size: 62 Copynumber: 7.3 Consensus size: 64
489466 GAGAAGAAGA
* * * * * * * *
489476 TGCCACCGACTTATGTAGGCTTTTGAGAGAGCTGCCACCAACTTGTGT-GGACTTT-GA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGG-CTTTAAAGAGGGT
* * **
489538 TGCCACCTACTTCTGTGGGCTTTA-AAAGGG-TGCCACTAACTTGTGTAGGCTTTAAA-AGAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAG-GGT
** * * * * * *
489600 TGCCACTAACTTGTGTGGGATTTTGCAA-GGTTGCCATCGAATTGTGTGGGCTTTAAAGA-GGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGGT
** * * ** **
489662 CACCACCGACTTGTGTGGGCTTTTG-AAGGGCTGCCATTGACTTGTGTAGGCTTTTGA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGGT
* *
489724 TGCCACCGACTTGTATGGG-TGTTAGAAAGAGGTTGCCACCGACTTATGTAGGCTTTAAAGAGGG
1 TGCCACCGACTTGTGTGGGCT-TTAGAAAG-GGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGG
489788 T
64 T
* * * * * *
489789 TGTCACAGACTTGTGTGGGCTTTAGAAGGGGTTACCACCAACTTGTGTGGGCTTTAAAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGGT
* * * * *
489853 TGCCACCAACTTGTGTGGGCTTTA-AAAGGGTTGTCACTGACTTGTGTGGGCTTTAGA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGGT
*
489915 TGCCATCGACTTGTGTGG
1 TGCCACCGACTTGTGTGG
489933 ATTTTTAAAA
Statistics
Matches: 323, Mismatches: 59, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
60 19 0.06
61 13 0.04
62 133 0.41
63 53 0.16
64 76 0.24
65 28 0.09
66 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (64 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCACCGACTTGTGTAGGCTTTAAAGAGGGT
Found at i:489990 original size:27 final size:28
Alignment explanation
Indices: 489968--490575 Score: 238
Period size: 29 Copynumber: 20.6 Consensus size: 28
489958 TGTGGATTTT
*
489968 AAAGGGTGCCACGGGGTTATGGACTTAA
1 AAAGGGTGCCACGGAGTTATGGACTTAA
*
489996 AAAGGGTGCCACGGAGTTGTGGACTTAAAAAGAA
1 AAAGGGTGCCACGGAGTTATGGACTT------AA
* *
490030 AAAGGGTGCCACAGAGTTATAGACTTAAAA
1 AAAGGGTGCCACGGAGTTATGGACTT--AA
* * * *
490060 AAAAGG-GCCATGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTATGGACTTAA
* * *
490087 AAAGAGATGCAACGGAGTTGTGGACTTTGAAGA
1 AAAG-GGTGCCACGGAGTTATGGAC-TT--A-A
* * * *
490120 AAAAGGTGCCACAGAGTTGTGGACTT-C
1 AAAGGGTGCCACGGAGTTATGGACTTAA
* *
490147 AAAGGGTGCCACGAAGTTGTGGACTTAA
1 AAAGGGTGCCACGGAGTTATGGACTTAA
* * *
490175 AAA-GGTGTCATGGAGTTGTGGACTTTAA
1 AAAGGGTGCCACGGAGTTATGGAC-TTAA
** * *
490203 AAAGGGTGCCATAGAGTTGTAGACTT-A
1 AAAGGGTGCCACGGAGTTATGGACTTAA
* ** *
490230 AAAGGTTGCCACAAAGTTGTGGACTT-A
1 AAAGGGTGCCACGGAGTTATGGACTTAA
* ** *
490257 AAAGGATGCCATAGAGATATGGACTTTAAA
1 AAAGGGTGCCACGGAGTTATGGAC-TT-AA
** ** * *
490287 GGAAAAAGTGCCATAGATTTGTGGACTTTGAA
1 --AAAGGGTGCCACGGAGTTATGGAC-TT-AA
* * *
490319 GTAAAAGGTGCCATGGAGTTGTGGACTTTAA
1 --AAAGGGTGCCACGGAGTTATGGAC-TTAA
* * *
490350 AAAAGGTGCCACGGAGTTTTGGACTTAT
1 AAAGGGTGCCACGGAGTTATGGACTTAA
490378 AAA-GGTGCCACGGAGTTATGGACTTAAAAAGAA
1 AAAGGGTGCCACGGAGTTATGGACTT------AA
* * *
490411 AAAGGGTGTCACAGAGTTGTGGACTTTAAA
1 AAAGGGTGCCACGGAGTTATGGAC-TT-AA
* * * **
490441 AAAAGATGCCACTGAGTCGTGGACTTTAA
1 AAAGGGTGCCACGGAGTTATGGAC-TTAA
* ** ** *
490470 GAAGGGTGCCACTAAGTCGTGGACTTTGA
1 AAAGGGTGCCACGGAGTTATGGAC-TTAA
* * * * *
490499 GAAGAGATGCCACTGAGTCAAGGACTTTAA
1 AAAG-GGTGCCACGGAGTTATGGAC-TTAA
* * ** *
490529 AAAGAGTGTCATTGAGTTATGGATTTTAA
1 AAAGGGTGCCACGGAGTTATGGA-CTTAA
490558 AAAGGGTGCCACGGAGTT
1 AAAGGGTGCCACGGAGTT
490576 GTGAACTTTT
Statistics
Matches: 462, Mismatches: 88, Indels: 59
0.76 0.14 0.10
Matches are distributed among these distances:
27 108 0.23
28 45 0.10
29 130 0.28
30 58 0.13
31 4 0.01
32 65 0.14
33 8 0.02
34 42 0.09
35 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (28 bp):
AAAGGGTGCCACGGAGTTATGGACTTAA
Found at i:490083 original size:29 final size:29
Alignment explanation
Indices: 489972--490495 Score: 302
Period size: 27 Copynumber: 17.8 Consensus size: 29
489962 GATTTTAAAG
* * *
489972 GGTGCCACGGGGTTATGGACTT-AAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
490000 GGTGCCACGGAGTTGTGGACTTAAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGACTT---AA-AAAAA
* * *
490033 GGGTGCCACAGAGTTATAGACTTAAAAAAAA
1 -GGTGCCACGGAGTTGTGGACTT-AAAAAAA
* * *
490064 GG-GCCATGGAGTTGTGGACTTTAAAAGA
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
* *
490092 GATGCAACGGAGTTGTGGACTTTGAAGAAAAA
1 GGTGCCACGGAGTTGTGGAC-TT-AA-AAAAA
* * *
490124 GGTGCCACAGAGTTGTGGACTT--CAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
*
490151 GGTGCCACGAAGTTGTGGACTT--AAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
* * * *
490178 GGTGTCATGGAGTTGTGGACTTTAAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
** *
490207 GGTGCCATAGAGTTGTAGACTT---AAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
**
490233 GGTTGCCACAAAGTTGTGGACTT---AAAA
1 GG-TGCCACGGAGTTGTGGACTTAAAAAAA
** * *
490260 GGATGCCATAGAGATATGGACTTTAAAGGAAAA
1 GG-TGCCACGGAGTTGTGGAC-TTAAA--AAAA
* ** * *
490293 AGTGCCATAGATTTGTGGACTTTGAAGTAAAA
1 GGTGCCACGGAGTTGTGGAC-TT-AA-AAAAA
* *
490325 GGTGCCATGGAGTTGTGGACTTTAAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
* *
490354 GGTGCCACGGAGTTTTGGACTT--ATAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
*
490381 GGTGCCACGGAGTTATGGACTTAAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGACTT---AA-AAAAA
* *
490414 GGGTGTCACAGAGTTGTGGACTTTAAAAAAA
1 -GGTGCCACGGAGTTGTGGAC-TTAAAAAAA
* * * * * *
490445 GATGCCACTGAGTCGTGGACTTTAAGAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAAAA
** *
490474 GGTGCCACTAAGTCGTGGACTT
1 GGTGCCACGGAGTTGTGGACTT
490496 TGAGAAGAGA
Statistics
Matches: 398, Mismatches: 69, Indels: 57
0.76 0.13 0.11
Matches are distributed among these distances:
26 5 0.01
27 107 0.27
28 28 0.07
29 103 0.26
30 21 0.05
31 15 0.04
32 66 0.17
33 15 0.04
34 36 0.09
35 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (29 bp):
GGTGCCACGGAGTTGTGGACTTAAAAAAA
Found at i:490282 original size:54 final size:53
Alignment explanation
Indices: 490120--490406 Score: 200
Period size: 56 Copynumber: 5.1 Consensus size: 53
490110 ACTTTGAAGA
* *
490120 AAAAGGTGCCACAGAGTTGTGGACTTCAAAGGGTGCCA-CGAAGTTGTGGACTT
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATAG-AGTTGTGGACTT
* ** *
490173 AAAAAGGTGTCATGGAGTTGTGGACTTTAAAAAGGGTGCCATAGAGTTGTAGACTT
1 -AAAAGGTGCCACAGAGTTGTGGAC-TT-AAAAGGGTGCCATAGAGTTGTGGACTT
* * * *
490229 AAAAGGTTGCCACAAAGTTGTGGACTTAAAAGGATGCCATAGAGATATGGACTTT
1 AAAAGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCATAGAGTTGTGGAC-TT
* * * * *
490284 AAAGGAAAAAGTGCCATAGATTTGTGGACTTTGAAGTAAAAGGTGCCATGGAGTTGTGGACTTT
1 -----AAAAGGTGCCACAGAGTTGTGGAC-TT--A--AAAGGGTGCCATAGAGTTGTGGAC-TT
* * ** *
490348 AAAAAAGGTGCCACGGAGTTTTGGACTTATAAA-GGTGCCACGGAGTTATGGACTT
1 --AAAAGGTGCCACAGAGTTGTGGACTTA-AAAGGGTGCCATAGAGTTGTGGACTT
490403 AAAA
1 AAAA
490407 AGAAAAAGGG
Statistics
Matches: 186, Mismatches: 32, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
53 4 0.02
54 42 0.23
55 14 0.08
56 54 0.29
57 5 0.03
58 1 0.01
59 15 0.08
60 9 0.05
61 19 0.10
62 1 0.01
64 22 0.12
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (53 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATAGAGTTGTGGACTT
Found at i:490348 original size:64 final size:61
Alignment explanation
Indices: 490029--490469 Score: 180
Period size: 56 Copynumber: 7.5 Consensus size: 61
490019 CTTAAAAAGA
** * * ** *
490029 AAAAGGGTGCCACAGAGTTATAGAC-TTAAA-AAAAAGGGCCATGGAGTTGTGGACTTTAA-
1 AAAA-GGTGCCATGGAGTTATGGACTTTAAAGAAAAAGTGCCACAGATTTGTGGACTTTAAT
* * * * * * * *
490088 AAGAGATGCAACGGAGTTGTGGACTTTGAAGAAAAAGGTGCCACAGAGTTGTGGAC-TT--C
1 AAAAGGTGCCATGGAGTTATGGACTTTAAAGAAAAA-GTGCCACAGATTTGTGGACTTTAAT
* * * * * * ** *
490147 AAAGGGTGCCACGAAGTTGTGGAC-TT--A-AAAAGGTGTCATGGAGTTGTGGACTTTAA-
1 AAAAGGTGCCATGGAGTTATGGACTTTAAAGAAAAAGTGCCACAGATTTGTGGACTTTAAT
* * * * * * *
490203 AAAGGGTGCCATAGAGTTGTAGAC-TT----AAAAGGTTGCCACAAAGTTGTGGAC--T--T
1 AAAAGGTGCCATGGAGTTATGGACTTTAAAGAAAAAG-TGCCACAGATTTGTGGACTTTAAT
* * *
490256 AAAAGGATGCCATAGAGATATGGACTTTAAAGGAAAAAGTGCCATAGATTTGTGGACTTTGAAGT
1 AAAAGG-TGCCATGGAGTTATGGACTTTAAA-GAAAAAGTGCCACAGATTTGTGGACTTT-AA-T
* * *
490321 AAAAGGTGCCATGGAGTTGTGGACTTT-AA-AAAAGGTGCCACGGAGTTT-TGGAC-TT-AT
1 AAAAGGTGCCATGGAGTTATGGACTTTAAAGAAAAAGTGCCACAGA-TTTGTGGACTTTAAT
* * * * *
490378 -AAAGGTGCCACGGAGTTATGGACTTAAAAAGAAAAAGGGTGTCACAGAGTTGTGGACTTTAAA
1 AAAAGGTGCCATGGAGTTATGGACTT-TAAAGAAAAA--GTGCCACAGATTTGTGGACTTTAAT
* **
490441 AAAAGATGCCACT-GAGTCGTGGACTTTAA
1 AAAAGGTGCCA-TGGAGTTATGGACTTTAA
490470 GAAGGGTGCC
Statistics
Matches: 295, Mismatches: 54, Indels: 62
0.72 0.13 0.15
Matches are distributed among these distances:
53 5 0.02
54 32 0.11
55 14 0.05
56 60 0.20
57 1 0.00
58 20 0.07
59 45 0.15
60 16 0.05
61 47 0.16
62 5 0.02
63 5 0.02
64 38 0.13
65 7 0.02
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (61 bp):
AAAAGGTGCCATGGAGTTATGGACTTTAAAGAAAAAGTGCCACAGATTTGTGGACTTTAAT
Found at i:490398 original size:120 final size:114
Alignment explanation
Indices: 489947--490616 Score: 439
Period size: 120 Copynumber: 5.7 Consensus size: 114
489937 TTAAAAGAGA
* * * * * *
489947 TGCCAT-GAAGTTGTGGA-TTT-TAAAGGGTGCCACGGGGTTATGGAC-TTAAAAAGGGTGCCAC
1 TGCCATAG-AGTTGTGGACTTTAAAAAAGGTGCCATGGAGTTGTGGACTTTAAAAAAGGTGCCAC
* *
490008 GGAGTTGTGGACTTAAAAAGAAAAAGGGTGCCACAGAGTTATAGACTTAAAAAAAAG
65 AGAGTTGTGGACTT------AAAAA-GGTGCCACAGAGTTATGGACTTAAAAAAAAG
* * * * * *
490065 GGCCATGGAGTTGTGGACTTTAAAAGAGATGCAACGGAGTTGTGGACTTTGAAGAAAAAGGTGCC
1 TGCCATAGAGTTGTGGACTTTAAAAAAGGTGCCATGGAGTTGTGGACTTT--A-AAAAAGGTGCC
* * * *
490130 ACAGAGTTGTGGACTTCAAAGGGTGCCAC-GAAGTTGTGGACTT--AAAAAGG
63 ACAGAGTTGTGGACTTAAAAAGGTGCCACAG-AGTTATGGACTTAAAAAAAAG
* * * * *
490180 TGTCATGGAGTTGTGGACTTTAAAAAGGGTGCCATAGAGTTGTAGAC-TT--AAAAGGTTGCCAC
1 TGCCATAGAGTTGTGGACTTTAAAAAAGGTGCCATGGAGTTGTGGACTTTAAAAAAGG-TGCCAC
* * *
490242 AAAGTTGTGGACTT-AAAAGGATGCCATAGAGATATGGACTTTAAAGGAAAAAG
65 AGAGTTGTGGACTTAAAAAGG-TGCCACAGAGTTATGGAC-TTAAA--AAAAAG
*
490295 TGCCATAGATTTGTGGACTTTGAAGTAAAAGGTGCCATGGAGTTGTGGACTTTAAAAAAGGTGCC
1 TGCCATAGAGTTGTGGACTTT-AA--AAAAGGTGCCATGGAGTTGTGGACTTTAAAAAAGGTGCC
* * * *
490360 ACGGAGTTTTGGACTTATAAAGGTGCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
63 ACAGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTATGGACTT--AAA-AAAAA--G
* * * * * *
490417 TGTCACAGAGTTGTGGACTTTAAAAAAAGATGCCACT-GAGTCGTGGACTTTAAGAAGGGTGCCA
1 TGCCATAGAGTTGTGGACTTT-AAAAAAGGTGCCA-TGGAGTTGTGGACTTTAAAAAAGGTGCCA
* * * * * * * *
490481 CTA-AGTCGTGGACTTTGAGAAGAGATGCCACTGAGTCAAGGACTTTAAAAAGAG
64 C-AGAGTTGTGGAC-TT-A-AAAAGGTGCCACAGAGTTATGGACTTAAAAAAAAG
* * * * * * *
490535 TGTCATTGAGTTATGGATTTTAAAAAGGGTGCCACGGAGTTGTGAACTTTTGAAAAAAGAGATGC
1 TGCCATAGAGTTGTGGACTTTAAAAAAGGTGCCATGGAGTTGTGGAC-TTT-AAAAAAG-G-TGC
* * *
490600 CACTGAATTGTAGACTT
62 CACAGAGTTGTGGACTT
490617 TGAAGGAAAA
Statistics
Matches: 437, Mismatches: 77, Indels: 74
0.74 0.13 0.13
Matches are distributed among these distances:
109 11 0.03
110 32 0.07
111 3 0.01
113 1 0.00
114 2 0.00
115 67 0.15
116 3 0.01
117 38 0.09
118 59 0.14
119 13 0.03
120 106 0.24
121 34 0.08
122 22 0.05
123 21 0.05
124 25 0.06
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (114 bp):
TGCCATAGAGTTGTGGACTTTAAAAAAGGTGCCATGGAGTTGTGGACTTTAAAAAAGGTGCCACA
GAGTTGTGGACTTAAAAAGGTGCCACAGAGTTATGGACTTAAAAAAAAG
Found at i:490493 original size:59 final size:59
Alignment explanation
Indices: 490412--490528 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
490402 TAAAAAGAAA
* * **
490412 AAGGGTGTCACAGAGTTGTGGACTTTAAAAAAAGATGCCACTGAGTCGTGGACTTTAAG
1 AAGGGTGCCACAGAGTCGTGGACTTTAAAAAAAGATGCCACTGAGTCAAGGACTTTAAG
* * *
490471 AAGGGTGCCACTA-AGTCGTGGACTTTGAGAAGAGATGCCACTGAGTCAAGGACTTTAA
1 AAGGGTGCCAC-AGAGTCGTGGACTTTAAAAAAAGATGCCACTGAGTCAAGGACTTTAA
490529 AAAGAGTGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 49 0.98
60 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (59 bp):
AAGGGTGCCACAGAGTCGTGGACTTTAAAAAAAGATGCCACTGAGTCAAGGACTTTAAG
Found at i:490557 original size:88 final size:91
Alignment explanation
Indices: 490431--490605 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 91
490421 ACAGAGTTGT
* * * *
490431 GGACTTTAAAAAAAGATGCCACTGAGTCGTGGACTTTAAGAAGGGTGCCACTAAGTCGTGGAC-T
1 GGACTTTAAAAAAAGATGCCACTGAGTCATGGACTTTAAAAAGGGTGCCACGAAGTCGTGAACTT
*
490495 TTG-AGAAGAGATGCCACTGAGTCAA
66 TTGAAAAAGAGATGCCACTGAGTCAA
* * * * * * *
490520 GGACTTTAAAAAGAG-TGTCATTGAGTTATGGATTTTAAAAAGGGTGCCACGGAGTTGTGAACTT
1 GGACTTTAAAAAAAGATGCCACTGAGTCATGGACTTTAAAAAGGGTGCCACGAAGTCGTGAACTT
490584 TTGAAAAAAGAGATGCCACTGA
66 TTG-AAAAAGAGATGCCACTGA
490606 ATTGTAGACT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
88 37 0.52
89 18 0.25
91 16 0.23
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (91 bp):
GGACTTTAAAAAAAGATGCCACTGAGTCATGGACTTTAAAAAGGGTGCCACGAAGTCGTGAACTT
TTGAAAAAGAGATGCCACTGAGTCAA
Found at i:494058 original size:155 final size:155
Alignment explanation
Indices: 493653--494178 Score: 599
Period size: 157 Copynumber: 3.4 Consensus size: 155
493643 GTTTTGTAGG
*** * * * *
493653 AAAATTACTGAAAATGCTTATAAGGGATACCTTTGATGTAAAAGTAC-CTAATACTCCTAAAGGA
1 AAAATTAC-GAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTC-GATACCCCTAAAGGA
* * * *
493717 CTTAAAAGGGATAATAGATGAGATGAACCTATCATAAATATCTACCTTCAGTATAAAAG-CGAAC
64 CTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGTAG-AC
* *
493781 TCGGTGATAACTTAGGACACTAATTCTAA
128 TCGGTGATAACTTAGGACTC-AGTTCTAA
*
493810 AAAATTAC-AGAAATGCCCTCT-AGGAGATACCTTCGACGTAAAAGTACTCGATACCTCTAAAGG
1 AAAATTACGA-AAATGCCC-CTAAGG-GATACCTTCGACGTAAAAGTACTCGATACCCCTAAAGG
* * * *
493873 ACTTAAAAATGATAATAGATGAAATAAACCTATCCTAAATATCTACCTTCAACATAAAAGTAGAC
63 ACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGTAGAC
* * *
493938 CCGGTGATAACTTAGGACTCGGTTCTGA
128 TCGGTGATAACTTAGGACTCAGTTCTAA
* * *
493966 AAAATTACGAAAATGCTCCT-AGGAAATACCTTCGATGTAAAAGTACTCGATACCCCTAAAGGAC
1 AAAATTACGAAAATGCCCCTAAGG-GATACCTTCGACGTAAAAGTACTCGATACCCCTAAAGGAC
** *
494030 TTAAAAAGGATAATAGATGAGATGAACCTATCCT-AA-A--TACCTTGGGCATAAAAGTGGACTC
65 TTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGTAGACTC
* * * *
494091 AGTGACAACCTAGGACTCAG-TCTCA
130 GGTGATAACTTAGGACTCAGTTCTAA
* *
494116 AAAATTACAAAAATACCCCTAAGGGATACCTTCGACGTAAAAGTACTCGATA--CCTAAAGGACT
1 AAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAGGACT
494179 GGATAATGCT
Statistics
Matches: 319, Mismatches: 43, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
148 11 0.03
150 47 0.15
151 38 0.12
153 1 0.00
154 2 0.01
155 75 0.24
156 29 0.09
157 114 0.36
158 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (155 bp):
AAAATTACGAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAGGACT
TAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGTAGACTCG
GTGATAACTTAGGACTCAGTTCTAA
Found at i:495710 original size:14 final size:15
Alignment explanation
Indices: 495680--495720 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
495670 TGTTGGGAAT
*
495680 TTTCTTTTTT-TTCC
1 TTTCTTTTTTCATCC
495694 TTTCTTTTTTCAT-C
1 TTTCTTTTTTCATCC
*
495708 TTTTTTTTTTCAT
1 TTTCTTTTTTCAT
495721 TTTTGTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTTCATCC
Found at i:496544 original size:20 final size:20
Alignment explanation
Indices: 496519--496594 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
496509 CAAAACCCAG
*
496519 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAAA
* * ****
496539 AATGTATCGATATATTTTCT
1 AATGTATCGATACAATGAAA
* *
496559 TATGTATCGATACATTGAAA
1 AATGTATCGATACAATGAAA
496579 AATGTATCGATACAAT
1 AATGTATCGATACAAT
496595 ATCCTTCCAG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:496674 original size:20 final size:20
Alignment explanation
Indices: 496640--496693 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
496630 CATTTCAAGC
*
496640 ATGTATTGATACATT-CACTT
1 ATGTATCGATACATTGCA-TT
*
496660 ATGTATCGATGCATTGCATT
1 ATGTATCGATACATTGCATT
*
496680 ATTGTATCAATACA
1 A-TGTATCGATACA
496694 AATTGTTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGCATT
Found at i:499995 original size:32 final size:33
Alignment explanation
Indices: 499934--499997 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
499924 AGACTCAGAA
*
499934 GTATCGATACATATTGCTTTGTATCAATACACT
1 GTATCGATACATATTGCTTGGTATCAATACACT
499967 GTATCGATACATGA-T-CTTGGTATCAATACAC
1 GTATCGATACAT-ATTGCTTGGTATCAATACAC
499998 AATGAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (33 bp):
GTATCGATACATATTGCTTGGTATCAATACACT
Found at i:501650 original size:9 final size:9
Alignment explanation
Indices: 501636--501666 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
501626 TCAACCATCA
501636 AAGATGATG
1 AAGATGATG
501645 AAGATGATG
1 AAGATGATG
*
501654 ATGATGATG
1 AAGATGATG
501663 AAGA
1 AAGA
501667 AGTTGACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (9 bp):
AAGATGATG
Found at i:502132 original size:15 final size:16
Alignment explanation
Indices: 502092--502133 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
502082 TAATAAATCA
502092 AAAATTGTTGAAAATG
1 AAAATTGTTGAAAATG
*
502108 -AAATTCTTGAAAA-G
1 AAAATTGTTGAAAATG
*
502122 AAAATAGTTGAA
1 AAAATTGTTGAA
502134 CTAGAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (16 bp):
AAAATTGTTGAAAATG
Found at i:506022 original size:13 final size:13
Alignment explanation
Indices: 506004--506040 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
505994 AAGGATCTTA
506004 GTATCGATACATT
1 GTATCGATACATT
*
506017 GTATCGAGACATT
1 GTATCGATACATT
506030 GTATCGATACA
1 GTATCGATACA
506041 AGGGCACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:508614 original size:19 final size:18
Alignment explanation
Indices: 508589--508644 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
508579 ATCAATACAC
**
508589 TGTATCGATACATGATCT
1 TGTATCGATACATGAAAT
508607 TGGTATCGATACATAGCAAAT
1 T-GTATCGATACAT-G-AAAT
508628 TGTATCGATACATGAAA
1 TGTATCGATACATGAAA
508645 CTGGAAGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 13 0.39
20 13 0.39
21 3 0.09
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (18 bp):
TGTATCGATACATGAAAT
Found at i:509910 original size:59 final size:59
Alignment explanation
Indices: 509704--509959 Score: 193
Period size: 58 Copynumber: 4.4 Consensus size: 59
509694 TTAGATCGTA
* ** * * * * *
509704 AAAAATGACCTAAATGACATCAA-ACTACATGAATTTTGCATGAATG-TCCTTAGACCATCG
1 AAAAATAACCTAAATGACCCCAACA-TACATGAAATTTGAATAAAAGTTCCTT-GATCAT-G
* * * * * *
509764 -AAAATAACCTAAATGA-TCCAACATACATGGAATTTAAATAAAA-TACCTAGATTATG
1 AAAAATAACCTAAATGACCCCAACATACATGAAATTTGAATAAAAGTTCCTTGATCATG
* ** * *
509820 AAAAAAAACCTAAATGACCTTAACATACATGAAATTTGTATAAAAGTTCCTTGATCGTG
1 AAAAATAACCTAAATGACCCCAACATACATGAAATTTGAATAAAAGTTCCTTGATCATG
* * * *
509879 AAAAATGACCTAAATGACCCCAACATGCATGAAA-TTGGATAAAAG-TCTTTAGATCATG
1 AAAAATAACCTAAATGACCCCAACATACATGAAATTTGAATAAAAGTTCCTT-GATCATG
* **
509937 GAAAATAACCTAAAAAACCCCAA
1 AAAAATAACCTAAATGACCCCAA
509960 AAATATATAA
Statistics
Matches: 154, Mismatches: 36, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
56 1 0.01
57 23 0.15
58 76 0.49
59 54 0.35
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.25
Consensus pattern (59 bp):
AAAAATAACCTAAATGACCCCAACATACATGAAATTTGAATAAAAGTTCCTTGATCATG
Found at i:510733 original size:20 final size:20
Alignment explanation
Indices: 510708--510745 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
510698 AATATAATTG
510708 GTGAATATATCGATACATAA
1 GTGAATATATCGATACATAA
*
510728 GTGAATGTATCGATACAT
1 GTGAATATATCGATACAT
510746 GTCTCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
GTGAATATATCGATACATAA
Found at i:514661 original size:166 final size:163
Alignment explanation
Indices: 514432--515024 Score: 660
Period size: 166 Copynumber: 3.6 Consensus size: 163
514422 AATTTTTTTG
* * * *
514432 TTTTT-AAAAATGGAGTTTTCTACTCTGTAAGTG-TTTCGGAGGGATTTTTCTTGGTTTTTAATT
1 TTTTTGAAAAATAGAGTTTTCTACTCCGTAAATGTTTTAGG-GGGATTTTTCTTGGTTTTTAATT
* * *
514495 TTTAAAATTCATCAAATATTATTATTTAATTTATACTAAATCTGTTTTAAAAAATTAATTCATTT
65 TTTAAAATTCATCAAATATTATTATTTAATTCATAC-AAATCTGTTTTCAAAAATTAATTTATTT
* *
514560 TCATAAGTTTTTCATTTTTTCCTTGAAATTCTCCTA
129 TCATGAGTTTTTCATTTTTTCTTTGAAATTCT-CTA
* ** * *
514596 TTTTTGAAAAACAGAGTTTTCTGGTCCATAAATGTTTTCGAGGGGATTTTTCTTGGTTTTTAATT
1 TTTTTGAAAAATAGAGTTTTCTACTCCGTAAATGTTTTAG-GGGGATTTTTCTTGGTTTTTAATT
* * * *
514661 TTTAAAATTCATCAAATATTATCATTTAATTCATAAAAAATCTTTTTTCAAAAATTCATTTATTT
65 TTTAAAATTCATCAAATATTATTATTTAATTCAT-ACAAATCTGTTTTCAAAAATTAATTTATTT
* *
514726 TCATGAGTTTTTCATTTTTTATTTGAAATT-TCTT
129 TCATGAGTTTTTCATTTTTTCTTTGAAATTCTCTA
* * *
514760 TGTTTCTGAAAAATAGATTTTTCTACTCCGTAAATGTTTTTTGGAGGAATTTTTCTTGGTTTTTA
1 T-TTT-TGAAAAATAGAGTTTTCTACTCCGTAAATG-TTTTAGG-GGGATTTTTCTTGGTTTTTA
**
514825 ATTTTTTAAAATTCATCAAATATTATTATTTAATTCATAGCAAAT-TAG-TTTCAAAAATTTGTT
62 A-TTTTTAAAATTCATCAAATATTATTATTTAATTCATA-CAAATCT-GTTTTCAAAAATTAATT
* * * * *
514888 TATTTTCATGACTTTTTTA-CTTTTCTTTAAAATCCTTCTA
124 TATTTTCATGAGTTTTTCATTTTTTCTTTGAAATTC-TCTA
* * * * * *
514928 TTTTCGAAAAATGGAGTTTTCTACTCCGTAAATATTTTAGGGGGATTTTTCCTTAG-TTTAAAAT
1 TTTTTGAAAAATAGAGTTTTCTACTCCGTAAATGTTTTAGGGGGATTTTT-CTTGGTTTTTAATT
* * *
514992 TTTAAAATTCATCTAATATTGTTATTAAATTCA
65 TTTAAAATTCATCAAATATTATTATTTAATTCA
515025 AATTAAATTA
Statistics
Matches: 366, Mismatches: 49, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
163 31 0.08
164 21 0.06
165 35 0.10
166 174 0.48
167 62 0.17
168 43 0.12
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (163 bp):
TTTTTGAAAAATAGAGTTTTCTACTCCGTAAATGTTTTAGGGGGATTTTTCTTGGTTTTTAATTT
TTAAAATTCATCAAATATTATTATTTAATTCATACAAATCTGTTTTCAAAAATTAATTTATTTTC
ATGAGTTTTTCATTTTTTCTTTGAAATTCTCTA
Found at i:515413 original size:24 final size:25
Alignment explanation
Indices: 515398--515443 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
515388 AATTAGAGAG
515398 AAAAGAGAGAAGAAAA-AAGAAAGA
1 AAAAGAGAGAAGAAAATAAGAAAGA
*
515422 AAAATAGAGAAGAAAAT-AGAAA
1 AAAAGAGAGAAGAAAATAAGAAA
515444 ACTAGCTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (25 bp):
AAAAGAGAGAAGAAAATAAGAAAGA
Found at i:515417 original size:14 final size:12
Alignment explanation
Indices: 515392--515437 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
515382 AGGAAAAATT
*
515392 AGAG-AGAAAAG
1 AGAGAAGAAAAA
515403 AGAGAAGAAAAA
1 AGAGAAGAAAAA
515415 AGA-AAGAAAAA
1 AGAGAAGAAAAA
515426 TAGAGAAGAAAA
1 -AGAGAAGAAAA
515438 TAGAAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 12 0.39
12 12 0.39
13 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (12 bp):
AGAGAAGAAAAA
Found at i:515438 original size:12 final size:12
Alignment explanation
Indices: 515386--515441 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
515376 GTTGGTAGGA
515386 AAAATTAGAG-AG
1 AAAA-TAGAGAAG
*
515398 AAAAGAGAGAAG
1 AAAATAGAGAAG
*
515410 AAAAAAGA-AAG
1 AAAATAGAGAAG
515421 AAAAATAGAGAAG
1 -AAAATAGAGAAG
515434 AAAATAGA
1 AAAATAGA
515442 AAACTAGCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.18
12 28 0.74
13 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (12 bp):
AAAATAGAGAAG
Found at i:516190 original size:20 final size:20
Alignment explanation
Indices: 516145--516200 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
516135 GCTAAGAGAA
*
516145 TGTATCGATACATGCTTGTAAT
1 TGTATCGATACAT--TTCTAAT
*
516167 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTAAT
*
516187 TGTATCCATACATT
1 TGTATCGATACATT
516201 ATGGGTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 18 0.58
22 13 0.42
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTCTAAT
Found at i:520225 original size:79 final size:79
Alignment explanation
Indices: 520068--520286 Score: 246
Period size: 79 Copynumber: 2.8 Consensus size: 79
520058 TGAGAAATTT
* * * *
520068 AATATTTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGAGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
** *
520132 CGGTTGTGAAAAATC
65 CAATTATGAAAAATC
* * * *
520147 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTAGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
520211 CAATTAT-AAGAAATC
65 CAATTATGAA-AAATC
* * * **
520226 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTAT
1 AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTAT
520287 GCCCGATGAA
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
78 5 0.04
79 111 0.95
80 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCC
AATTATGAAAAATC
Found at i:520374 original size:52 final size:50
Alignment explanation
Indices: 520304--520526 Score: 225
Period size: 52 Copynumber: 4.3 Consensus size: 50
520294 GAAATAACGA
*
520304 GGTTGGAGTATCCTCGATTGTGACAAATTGGTGTTTTTGGAAATAAAATCA-G
1 GGTTGGAGTATCCCCGATTGTGA-AAATTGGTG-TTTTGGAAATAAAA-CAGG
* *
520356 AGTTGGAGTATCCCCGATTAAAG-GAAAATTGGTGTTTTGAAAATAAAACCAGG
1 GGTTGGAGTATCCCCGATT---GTGAAAATTGGTGTTTTGGAAATAAAA-CAGG
* *
520409 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACTAGG
1 GGTTGGAGTATCCCCGATTGT-GAAAATTGGTGTTTTGGAAATAAAAC-AGG
* *** * * * *
520461 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAATTGGTGTTTTGGAAATAAAACAGG
520512 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
520527 TCGGAGGTAA
Statistics
Matches: 147, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
50 1 0.01
51 20 0.14
52 95 0.65
53 28 0.19
54 2 0.01
55 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAATTGGTGTTTTGGAAATAAAACAGG
Found at i:520638 original size:52 final size:50
Alignment explanation
Indices: 520566--520701 Score: 139
Period size: 52 Copynumber: 2.6 Consensus size: 50
520556 ATGAAATAAT
* * *
520566 GAGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATC
1 GAGGTCGGAGTATCC-CGATTATGAAAAATTGATG-TTTTGAAAATAAAATC
* * *
520618 G-GAGTCGGAGTATTCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATC
1 GAG-GTCGGAGTA-TCCCGATT-ATGAAAAATTGATGTTTTGAAAATAAAATC
* *
520670 GAGGTTGGAGTATCCCTGATTATGAACAATTG
1 GAGGTCGGAGTATCCC-GATTATGAAAAATTG
520702 GGAAACTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
51 13 0.19
52 42 0.61
53 14 0.20
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.32
Consensus pattern (50 bp):
GAGGTCGGAGTATCCCGATTATGAAAAATTGATGTTTTGAAAATAAAATC
Found at i:523085 original size:21 final size:21
Alignment explanation
Indices: 523059--523099 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
523049 ACAAAGATCG
523059 ATGTATCGATACATTTCCTTA
1 ATGTATCGATACATTTCCTTA
523080 ATGTATCGATACATTTCCTT
1 ATGTATCGATACATTTCCTT
523100 GGCAGTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATTTCCTTA
Found at i:523134 original size:13 final size:13
Alignment explanation
Indices: 523116--523167 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
523106 AACTTCATAG
523116 CGATACATTGTAT
1 CGATACATTGTAT
523129 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
523148 CGATACATTGTAT
1 CGATACATTGTAT
523161 CGATACA
1 CGATACA
523168 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:523148 original size:19 final size:18
Alignment explanation
Indices: 523124--523186 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
523114 AGCGATACAT
523124 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
523143 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
523156 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
523175 TGTATCGATACA
1 TGTATCGATACA
523187 TTTTCTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:523154 original size:32 final size:32
Alignment explanation
Indices: 523116--523188 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
523106 AACTTCATAG
523116 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
523148 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
523180 CGATACATT
1 CGATACATT
523189 TTCTGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:523215 original size:19 final size:19
Alignment explanation
Indices: 523155--523216 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
523145 TATCGATACA
523155 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
523174 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
523195 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
523214 TTG
1 TTG
523217 AAATTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:523317 original size:9 final size:8
Alignment explanation
Indices: 523292--523316 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
523282 GGATAAAAAG
523292 TGATTTTT
1 TGATTTTT
523300 TGATTTTT
1 TGATTTTT
523308 TGATTTTT
1 TGATTTTT
523316 T
1 T
523317 TTTGCCTTCC
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:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TGATTTTT
Found at i:525053 original size:50 final size:51
Alignment explanation
Indices: 524950--525070 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
524940 CCTTGAAAAC
* * * *
524950 AATGGGGGTAGAGTATCCCTGATGGTGAAAAATCAATATTTTTGAAATAAA
1 AATGGGGTTAGAGTATCCCCGATGGTGAAAAATCAACATTTTGGAAATAAA
* **
525001 AATGGGGTTGGAGTATCCCCGATGGTGAAAAATTGACATTTTGGAAAT-AA
1 AATGGGGTTAGAGTATCCCCGATGGTGAAAAATCAACATTTTGGAAATAAA
525051 AATGGGGTTAGAGTATCCCC
1 AATGGGGTTAGAGTATCCCC
525071 TCAAAAACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
50 21 0.34
51 41 0.66
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (51 bp):
AATGGGGTTAGAGTATCCCCGATGGTGAAAAATCAACATTTTGGAAATAAA
Found at i:525117 original size:29 final size:30
Alignment explanation
Indices: 525079--525140 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
525069 CCTCAAAAAC
525079 AATGCGGTTGGAGTATCCC-AGATGGT-GAA
1 AATGCGGTTGGAGTATCCCTA-ATGGTGGAA
*
525108 AATGGGGTTGGAGTATCCCTAATGGTGGAA
1 AATGCGGTTGGAGTATCCCTAATGGTGGAA
525138 AAT
1 AAT
525141 TAGTGCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (30 bp):
AATGCGGTTGGAGTATCCCTAATGGTGGAA
Found at i:525354 original size:79 final size:79
Alignment explanation
Indices: 525229--525450 Score: 270
Period size: 79 Copynumber: 2.8 Consensus size: 79
525219 AAATAATAAA
* * *
525229 GTTAGAGTATCCTCGATAGTGGAAAATCGGTGTTTTAGAAACAAAATCAGGGTTGGAGTATCCCT
1 GTTAGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATC-GGGTTGGAGTATCCCT
** *
525294 -TCTTAAATAA-TGG
65 CTCAGAAATAACAGG
* * * *
525307 TGTTGGAGTATCCTCGATGGTGTAAAATCGATGTTTTAGAAATAAAATTGGGGTTGGAGTAT-CC
1 -GTTAGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAA-TCGGGTTGGAGTATCCC
525371 TCTCAGAAATAACAGG
64 TCTCAGAAATAACAGG
* * *
525387 GTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTCAGAAATAAAATCGAGGTTGGAGTATCCC
1 GTTAGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCG-GGTTGGAGTATCCC
525451 CGATGGTGGA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
78 5 0.04
79 112 0.92
80 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (79 bp):
GTTAGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCGGGTTGGAGTATCCCTC
TCAGAAATAACAGG
Found at i:525451 original size:51 final size:51
Alignment explanation
Indices: 525386--525483 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
525376 GAAATAACAG
525386 GGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTCAGAAATAAAATCGA
1 GGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTCAGAAATAAAATCGA
* * *
525437 GGTTGGAGTATCCCCGATGGTGGAAAATTGGTGTTTTAGAAATAAAA
1 GGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTCAGAAATAAAA
525484 ACATCAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.29
Consensus pattern (51 bp):
GGTTAGAGTATCCCCGATGGTGAAAAATTGGTGTTTCAGAAATAAAATCGA
Found at i:527018 original size:13 final size:13
Alignment explanation
Indices: 527000--527024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
526990 ATAACGCACA
527000 GTATCGATACATT
1 GTATCGATACATT
527013 GTATCGATACAT
1 GTATCGATACAT
527025 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:527021 original size:33 final size:33
Alignment explanation
Indices: 526979--527042 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
526969 CACCTTCAAA
*
526979 TGTATCGATACATAACGCACA-GTATCGATACAT
1 TGTATCGATACATAAC-CAAATGTATCGATACAT
*
527012 TGTATCGATACATGACCAAATGTATCGATAC
1 TGTATCGATACATAACCAAATGTATCGATAC
527043 TAGTTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACATAACCAAATGTATCGATACAT
Found at i:527134 original size:19 final size:19
Alignment explanation
Indices: 527106--527155 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
527096 CTTAACTGTT
*
527106 TGTATTGATACACACAAGA
1 TGTATCGATACACACAAGA
*
527125 TGTATCGATACACATAAGA
1 TGTATCGATACACACAAGA
527144 TGTATCGATACA
1 TGTATCGATACA
527156 ATGTATCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACACAAGA
Found at i:527161 original size:13 final size:13
Alignment explanation
Indices: 527143--527168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
527133 TACACATAAG
527143 ATGTATCGATACA
1 ATGTATCGATACA
527156 ATGTATCGATACA
1 ATGTATCGATACA
527169 TCCCAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:533315 original size:13 final size:13
Alignment explanation
Indices: 533297--533321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
533287 AAAACTCAGA
533297 TGTATCGATACAG
1 TGTATCGATACAG
533310 TGTATCGATACA
1 TGTATCGATACA
533322 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:535889 original size:13 final size:13
Alignment explanation
Indices: 535871--535897 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
535861 ACACACAAGA
535871 TGTATCGATACAT
1 TGTATCGATACAT
535884 TGTATCGATACAT
1 TGTATCGATACAT
535897 T
1 T
535898 AGCTTGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:537912 original size:22 final size:20
Alignment explanation
Indices: 537859--537914 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
537849 CAAAACCCAG
537859 AATGTATCGATACAATGATA
1 AATGTATCGATACAATGATA
* *
537879 AATGTATTGATACAATTATA
1 AATGTATCGATACAATGATA
537899 AGTATGTATCGATACA
1 A--ATGTATCGATACA
537915 TTTACTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACAATGATA
Found at i:538933 original size:154 final size:154
Alignment explanation
Indices: 538565--538993 Score: 490
Period size: 154 Copynumber: 2.8 Consensus size: 154
538555 AGGAGTATGG
* * ** *
538565 GTACTTCT-TCGTCAAAGGTATCCCTTAAGGGTATATTTGTAATTTCTCTAGAACCAAGTCCTAG
1 GTACTTCTAT-GTCAAAGGTATCCCTTAAGGGCATCTTCATAATTT-TCTAGAACCAACTCCTAG
** * *
538629 GTTGTCATTGAGTTTAG-TTTTATGCTGAAAATGAGTATTTAGGATAGGTTCATCCCTTTTTAAA
64 GTTGTCA-TGAGTTT-GCTTTTATGCTGAAGGTGAGTATTTAGGATAAGTTCAT-CCGTTTTAAA
**
538693 ATCCTTTTTTAGTCATTTAAGGGTATCAA
126 ATCCTTTTGAAGTCATTTAAGGGTATCAA
* ** * * *
538722 GTACTTTTACATCAAAGGCATCCCCT-AGGAGCATCTTCATAATTTTCTAGAACCAACTCCTATG
1 GTACTTCTATGTCAAAGGTATCCCTTAAGG-GCATCTTCATAATTTTCTAGAACCAACTCCTAGG
** * *
538786 TTGTCATCGAGCCTGCTTTTATGCCGAAGGTGAGTATTTAAGATAAGTTCATCCGTTTTAAAATC
65 TTGTCAT-GAGTTTGCTTTTATGCTGAAGGTGAGTATTTAGGATAAGTTCATCCGTTTTAAAATC
* *
538851 CTTTTGAAGTTC-TTT-TGGGTATCGA
129 CTTTTGAAG-TCATTTAAGGGTATCAA
*
538876 GTACTTCTATGTCGAAGGTATCCCTTAAGGGCATCTTCATAATTTTCTAGAACCAACTCCTAGGT
1 GTACTTCTATGTCAAAGGTATCCCTTAAGGGCATCTTCATAATTTTCTAGAACCAACTCCTAGGT
* * * *
538941 TGTCATTAGGTTTGCTTTTATGTTGAAGGAGGGTATTTAGGATAAGTTCATCC
66 TGTCATGA-GTTTGCTTTTATGCTGAAGGTGAGTATTTAGGATAAGTTCATCC
538994 CTTCTATAAT
Statistics
Matches: 227, Mismatches: 38, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
153 1 0.00
154 105 0.46
155 27 0.12
156 63 0.28
157 31 0.14
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (154 bp):
GTACTTCTATGTCAAAGGTATCCCTTAAGGGCATCTTCATAATTTTCTAGAACCAACTCCTAGGT
TGTCATGAGTTTGCTTTTATGCTGAAGGTGAGTATTTAGGATAAGTTCATCCGTTTTAAAATCCT
TTTGAAGTCATTTAAGGGTATCAA
Found at i:543461 original size:159 final size:158
Alignment explanation
Indices: 543139--543540 Score: 418
Period size: 159 Copynumber: 2.5 Consensus size: 158
543129 TCATTGATAT
* * * * **
543139 TTTTATTTCTAAAATA-TCAATTTTCCACCATCGAGGATACTCCAACTCCATTA-TTTCCGAAGG
1 TTTTATTCCTAAAACACT-AATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCC-AAAA
* * ** * * *
543202 GATACTCCAACTCTAGCTTTATT-TCTAATACA-CTAATTTTTCACTATCGGGGATACTCCAACC
64 GACACTCCAACACTAATTTTATTCT-TAAAACATC-GATTTTTCACTATCGAGGATACTCCAACC
* * * *
543265 TCATTATTTCTGAGGGGATCCTCCAACCTCGG
127 CCATTATTCCTGAGGGGATACTCCAACCTCAG
* * * * * *
543297 TTTTATTCTTAAAACACTGATTTTTCACCATCGAGGATACTCTAATCCCGTTATTTTCGAAAAGA
1 TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCCAAAAGA
* * * *
543362 CACTCTAACACTAATTTTATTCTTAAAACATCGATTTTTCCACTATTGAGGATACTCTAACCCCG
66 CACTCCAACACTAATTTTATTCTTAAAACATCGATTTTT-CACTATCGAGGATACTCCAACCCCA
543427 TTATTCCTGAGGGGATACTCCAACC-CTAG
130 TTATTCCTGAGGGGATACTCCAACCTC-AG
* * *
543456 TTTTATTCCTAAAACACTAATTTTCCACCATTGAGGATACTCCAACCCCGTTGTTTTCCAGAAGA
1 TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCCAAAAGA
* * *
543521 TACTCCAACCCTATTTTTAT
66 CACTCCAACACTAATTTTAT
543541 CTCCAAAATA
Statistics
Matches: 198, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
158 75 0.38
159 123 0.62
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (158 bp):
TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCCAAAAGA
CACTCCAACACTAATTTTATTCTTAAAACATCGATTTTTCACTATCGAGGATACTCCAACCCCAT
TATTCCTGAGGGGATACTCCAACCTCAG
Found at i:543506 original size:79 final size:79
Alignment explanation
Indices: 543139--543548 Score: 339
Period size: 79 Copynumber: 5.2 Consensus size: 79
543129 TCATTGATAT
* * * *
543139 TTTTATTTCTAAAATA-TCAATTTTCCACCATCGAGGATACTCCAACTCCATTATTTCC-GAAGG
1 TTTTATTCCTAAAACACT-AATTTTCCACCATCGAGGATACTCCAACCCCGTTA-TTCCTGAAGG
*
543202 GATACTCCAACTCTAG
64 GATACTCCAACCCTAG
* * * * * * * * * *
543218 CTTTATTTCTAATACACTAATTTTTCACTATCGGGGATACTCCAACCTCATTATTTCTGAGGGGA
1 TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTCCTGAAGGGA
* *
543283 TCCTCCAA-CCTCGG
66 TACTCCAACCCT-AG
* * * * * * **
543297 TTTTATTCTTAAAACACTGATTTTTCACCATCGAGGATACTCTAATCCCGTTATT-TTCGAAAAG
1 TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTCCT-GAAGGG
* * * *
543361 ACACTCTAACACTAA
65 ATACTCCAACCCTAG
* * * * * * *
543376 TTTTATTCTTAAAACATCGATTTTTCCACTATTGAGGATACTCTAACCCCGTTATTCCTGAGGGG
1 TTTTATTCCTAAAACA-CTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTCCTGAAGGG
543441 ATACTCCAACCCTAG
65 ATACTCCAACCCTAG
* * *
543456 TTTTATTCCTAAAACACTAATTTTCCACCATTGAGGATACTCCAACCCCGTTGTTTTCCAGAA--
1 TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCG-T-TATTCCTGAAGG
*
543519 GATACTCCAACCCTAT
64 GATACTCCAACCCTAG
543535 TTTTATCTCC-AAAA
1 TTTTAT-TCCTAAAA
543549 TATTAAAATT
Statistics
Matches: 263, Mismatches: 58, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
78 6 0.02
79 181 0.69
80 68 0.26
81 8 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.35
Consensus pattern (79 bp):
TTTTATTCCTAAAACACTAATTTTCCACCATCGAGGATACTCCAACCCCGTTATTCCTGAAGGGA
TACTCCAACCCTAG
Found at i:553493 original size:52 final size:52
Alignment explanation
Indices: 553415--553543 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
553405 CAAAATATGA
*
553415 AAATTTCCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
553467 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
553519 AAATTTGCCTGCTTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
553544 AAGATTAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:553553 original size:52 final size:52
Alignment explanation
Indices: 553415--553564 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
553405 CAAAATATGA
* * * *
553415 AAATTTCCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATTGATACATCTGGGC
*
553467 AAATTTGCCTGCATGTATCGATAC-ATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATTAT-TAGTGTATTGATACATCTGGGC
* **
553519 AAATTTGCCTGCTTGTATCGATACAAAGATTAGTGTATTGATACAT
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATTGATACAT
553565 TGTATCGATA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATTGATACATCTGGGC
Found at i:553656 original size:13 final size:13
Alignment explanation
Indices: 553638--553694 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
553628 ACAAAACTTA
553638 TGTATCGATACAT
1 TGTATCGATACAT
553651 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
553669 ATGTATCGATACAT
1 -TGTATCGATACAT
*
553683 TGTATTGATACA
1 TGTATCGATACA
553695 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:553662 original size:32 final size:32
Alignment explanation
Indices: 553617--553714 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
553607 AGTAGCTTAT
* *
553617 ATTGTATCAATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
553649 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
553681 ATTGTATTGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
553714 A
1 A
553715 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.76
33 15 0.24
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:553675 original size:19 final size:19
Alignment explanation
Indices: 553619--553715 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
553609 TAGCTTATAT
* *
553619 TGTATCAATACAAAACTTA
1 TGTATCGATACAACACTTA
553638 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
553651 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
553670 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
553683 TGTATTGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
553703 TGTATCGATACAA
1 TGTATCGATACAA
553716 ATCGTTGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 25
0.68 0.04 0.28
Matches are distributed among these distances:
13 17 0.28
14 2 0.03
16 11 0.18
18 1 0.02
19 18 0.30
20 12 0.20
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:554750 original size:49 final size:48
Alignment explanation
Indices: 554580--555241 Score: 717
Period size: 49 Copynumber: 13.9 Consensus size: 48
554570 AAAGATGAGA
* * * *
554580 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A--G
* *
554633 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* *
554677 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
*
554724 AAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 AA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* *
554769 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
554816 ATGAAGGTGCCAATATGATGATTCAAGGCCAGCGATATTGGACTT----
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* *
554861 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G
* *
554911 ACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* *
554960 ATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G
* *
555012 ACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
*
555061 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---G
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
555107 --GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
*
555153 AAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 AA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
* * *
555198 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAGTGGACTTA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
555242 GAAGGGTTGC
Statistics
Matches: 528, Mismatches: 50, Indels: 71
0.81 0.08 0.11
Matches are distributed among these distances:
43 194 0.37
44 2 0.00
46 2 0.00
48 1 0.00
49 200 0.38
50 4 0.01
51 5 0.01
52 114 0.22
53 6 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (48 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
Found at i:554766 original size:92 final size:92
Alignment explanation
Indices: 554581--555246 Score: 771
Period size: 92 Copynumber: 7.1 Consensus size: 92
554571 AAGATGAGAA
* *
554581 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
*
554646 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
*
554677 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
554742 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
** *
554769 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
554834 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
554861 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGACAAAGGCGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--A-AAAGGTGCCAATA
554926 TGCTGATTCAAGGCCAGCGATATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
* *
554956 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCG
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--A-AAAGGTG
555021 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
57 CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T
* * * * *
555063 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---G---GAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
* *
555122 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
555149 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCCA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCA
* * * *
555208 ATGTGCTGATTCAAGGCCAGCTACAGTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
555241 AGAAGG
1 A-AAGG
555247 GTTGCCACCG
Statistics
Matches: 528, Mismatches: 20, Indels: 53
0.88 0.03 0.09
Matches are distributed among these distances:
86 1 0.00
87 6 0.01
91 2 0.00
92 297 0.56
95 81 0.15
96 5 0.01
98 1 0.00
99 1 0.00
101 131 0.25
102 1 0.00
103 1 0.00
107 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:555241 original size:337 final size:330
Alignment explanation
Indices: 554590--555241 Score: 1040
Period size: 337 Copynumber: 2.0 Consensus size: 330
554580 AAAAGGATGT
* *
554590 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATT
* * * * *
554655 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
65 CAAGGCCAGCGACATTGGACTTAAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
554720 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGC
130 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGC
*
554785 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGATGATTCAAGGCCAGCG
195 TGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGATGATTCAAGGCCAGCG
*
554850 ATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGACAA
260 ATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAGTGGACTTAAAGATGACAA
554915 AGGCGC
325 AGGCGC
* * *
554921 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G-AAGGTGCCAATGTGCTGATTC
1 CAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
*
554984 AAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
66 AAGGCCAGCGACATTGGAC-T-----T---AAAGGCGCCAATATGCTGATTCAAGGCCAGCGACA
**
555049 TTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTG
122 TTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
*
555113 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCA
186 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGATGATTCA
555178 AGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAGTGGACTTA
251 AGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAGTGGACTTA
555242 GAAGGGTTGC
Statistics
Matches: 295, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
328 37 0.13
329 1 0.00
330 1 0.00
331 37 0.13
334 1 0.00
337 217 0.74
338 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (330 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
AAGGCCAGCGACATTGGACTTAAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
AAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCT
GATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGATGATTCAAGGCCAGCGA
TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAGTGGACTTAAAGATGACAAA
GGCGC
Found at i:555283 original size:32 final size:33
Alignment explanation
Indices: 555241--555377 Score: 217
Period size: 32 Copynumber: 4.2 Consensus size: 33
555231 CAGTGGACTT
555241 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
555274 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
555306 AGAAGGGTTACCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
**
555338 AGAAGGGCGGCCACCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
555370 AAAAGGGT
1 AGAAGGGT
555378 GAAAGGTGCC
Statistics
Matches: 96, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
32 67 0.70
33 29 0.30
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:555320 original size:65 final size:64
Alignment explanation
Indices: 555241--555377 Score: 213
Period size: 65 Copynumber: 2.1 Consensus size: 64
555231 CAGTGGACTT
* **
555241 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTACCACCGACTTGTGTGGGCTTT-GAGAAGGGCGGCCACCGACTTGTGTGGGCTTTA
555305 GAGAAGGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGCGGCCACCGACTTGTGTGGGCTTTA
1 -AGAAGGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGCGGCCACCGACTTGTGTGGGCTTTA
*
555370 AAAAGGGT
1 AGAAGGGT
555378 GAAAGGTGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 12 0.18
65 55 0.82
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (64 bp):
AGAAGGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGCGGCCACCGACTTGTGTGGGCTTTA
Found at i:555851 original size:100 final size:99
Alignment explanation
Indices: 555379--557717 Score: 1297
Period size: 100 Copynumber: 23.7 Consensus size: 99
555369 AAAAAGGGTG
* * *
555379 AAAGGTGCCACGA-AGTTGTGGAC-TTAAAAGGAACAATGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* * *
555442 AAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
66 AGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * *
555476 AAAGAGTGCCACG-GAGTTGTGGGC-TT-AAACG-----GGTGCCACGGAGTTATGGACTTAGAA
1 AAAG-GTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* ** *
555533 GGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGGGAA
65 --AAGAAGA-TGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* * *
555573 AAAGAGTGCCAC-AGAGTTGTGGGCTTTGAAAA-G---AAGGTGCCATGGAGTTGT-GGATTTAG
1 AAAG-GTGCCACGAGAGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-G
* * *
555632 AAGGAAAAAGAGTGCCACGGAGTTTTGGGCTTTAAAAAGGAA
63 AA--AAGAAGA-TGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * * * * * *
555674 AAAGATGCCAC-AGAGTTGTGGGCTCT-AAA--AAGAAGGTGCCACAGAGTCGTGGACTTTGAAA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* *
555735 GGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
66 AGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
555769 CAAGGTGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
*
555833 AAAGAAGATGCCACGGAGTTGTGGACTTAGAAGGAA
64 AAAGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * *
555869 AAAGAGTGCCACG-GAGTTGTGGGC-TT-AAACG-----GGTGCCACGGAGTTATGGACTTAGAA
1 AAAG-GTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* ** *
555926 GGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGTGAA
65 --AAGAAGA-TGCCACGGAGTTGTGGAC-TTAAAAG-GAA
* * *
555966 AAAGAGTGCCAC-AAAGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGGAGTTGT-GGATTTAG
1 AAAG-GTGCCACGAGAGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-G
* *
556025 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
63 AA--AAGAAGA-TGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * * * * *
556067 AAAGATGCCAC-AGAGTTGTGGGCTCTGAAAA-G---AAGGTGCCACAGAGTCGTGGACTTTGAA
1 AAAGGTGCCACGAGAGTTGTGGACT-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* * **
556127 AGGAAGGTGCCACGGAGTCATGGACTTAAAAGGAA
65 AAGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
*
556162 CAAGGTGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
* ** * *
556226 AAAGAAGGTGCCATAGAGTCGTGGACTTAGAAGGAA
64 AAAGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * *
556262 AAAGAGTACCACG-GAGTTGTGGGC-TT-AAACG-----GGTGCCACGGAGTTGTGGACTTAGAA
1 AAAG-GTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* * *
556319 GGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAACG--
65 --AAGAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
556354 ---GGTGCCACG-GAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCAAGAAGTTATGGGCTTT-AA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
* * **
556413 AAGGGAAAAAGAGTGCCACGGTGTTGTGGGCTTTGAA--AA
65 AA--G---AAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
556452 GAAGGTGCCACG-GAGTTGTGGA-TTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
* * **
556515 AAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAA--AA
65 AA-G---AAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * * * * * **
556552 GATGGTGCCA-TAGAGTCGCGGACTTTGAAAGG---AAGGTGCCACGGAGTCGTGGACTTAAAAG
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA-
* * *
556613 GAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAA
65 -AAGAAGATGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* * * * *
556651 AAATAGTGCCACG-GAGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGGAGTCGTGGACTTAGA
1 AAA-GGTGCCACGAGAGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
* * *
556711 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAACG--
64 A--AAGAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * *
556747 ---GGTGCCAC-AAAGTTGTGGAC-TTAGAAGGAAAAAAAGTGCCACGAAGTTGTAGGCTTT-AA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* * *
556806 AAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAA--AA
65 AA--G---AAGA-TGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
556845 GAAGGTGCCACG-GAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
* * **
556908 AAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAA--AA
65 AA-G---AAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * * * * **
556945 GAAGGTGCCAC-AGAGTCGCGGACTTTGAGAGG---AAGGTGCCACGGAGTCGTGGACTTAAAAG
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA-
* * *
557006 GAACAAGGTGCCATGG-GTTTGTGGACTTTAAAAAGGAA
65 -AAGAAGATGCCACGGAG-TTGTGGAC-TT-AAAAGGAA
* * * * **
557044 AAAGAGTGCCAC-AAAGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGGAGTCGTGGACTTAAA
1 AAAG-GTGCCACGAGAGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
* * *
557104 AGGAACAAGGTGCCAC-GATGTTGTGGACTTTAAAAGGGAG
64 A--AAGAAGATGCCACGGA-GTTGTGGAC-TTAAAA-GGAA
* * * **
557144 AAAGAGTGCCACG-GAGTTGTGGGCTTTGAAAA-G---AAGGTGCCACGAAGTTGTGGACTTAAA
1 AAAG-GTGCCACGAGAGTTGTGGACTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
* *
557204 AGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAGGAA
64 A--AAGAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGAA
* * *
557244 CAAGGTGCCACG-GGGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
*
557308 AAAGAATG-TGCCACGGAGTCGTGGACTTAAAAGGAA
64 AAAGAA-GATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * *
557344 CAAGGTGCCACG-GAGTTGTGGACTTTAAAAGGGAAAAAGAGTGACTCAGAGTTATGGGCTTTGA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
* *
557408 AAAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
64 AAAGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * * *
557444 AAAGAGTGCCACGA-AGTTGTGAACTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTT-AA
1 AAAG-GTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
* *
557507 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAA-GAA
65 AA--G---AAGA-TGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * * *
557549 AAAGGTGCCAC-AGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTAAAA
1 AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* * *
557613 AGAAAAAGGTGCCCCGGAGTTGTGGGCTTTAAAAAGG-A
66 AG---AAGATGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * * *
557651 AAAGGTGTCACG-GAGTTATGGGA-TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAG
1 AAAGGTGCCACGAGAGTTGT-GGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
557714 AAGA
65 AAGA
557718 GATTGAAGAA
Statistics
Matches: 1846, Mismatches: 250, Indels: 290
0.77 0.10 0.12
Matches are distributed among these distances:
88 19 0.01
89 4 0.00
90 3 0.00
91 3 0.00
92 86 0.05
93 2 0.00
94 31 0.02
95 169 0.09
96 29 0.02
97 185 0.10
98 56 0.03
99 72 0.04
100 609 0.33
101 359 0.19
102 103 0.06
103 18 0.01
104 82 0.04
105 13 0.01
106 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (99 bp):
AAAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
AGAAGATGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:555989 original size:393 final size:395
Alignment explanation
Indices: 555380--557712 Score: 2412
Period size: 393 Copynumber: 5.9 Consensus size: 395
555370 AAAAGGGTGA
* *
555380 AAGGTGCCACGA-AGTTGTGGAC-TTAAAAGGAACAA-TGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
555442 AAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAA
66 AGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
** *
555505 CGGGTGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGG
131 CGGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAA-C
* * *
555570 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCATGGAGTTGT-GGATTTAGAA
195 GAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGAAGTTGTGGGATTTAAAA
* * * *
555634 GGAAAAAGAGTGCCACGGAGTTTTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTC
259 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG-AAAAGGTGCCACGGAGTTGTGGGCTT
* * * *
555699 TAAA-AAGAAG-GTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTA
323 TAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTA
555762 AAAGGAAC
388 AAAGGAAC
*
555770 AAGGTGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
555834 AAGAAGATGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AA
65 AAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
**
555897 ACGGGTGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAG
130 ACGGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAA-
* * * *
555962 TGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGT-GGATTTAGA
194 CGAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGAAGTTGTGGGATTTAAA
* *
556026 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCT
258 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG-AAAAGGTGCCACGGAGTTGTGGGCT
* * * * * * **
556091 CTGAA-AAGAAG-GTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTT
322 TTAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTT
556154 AAAAGGAAC
387 AAAAGGAAC
*
556163 AAGGTGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
** * *
556227 AAGAAGGTGCCATAGAGTCGTGGACTTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGC-TT-AA
65 AAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
* **
556290 ACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAC
130 ACGGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAC
* * * * * * *
556353 G-----GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCAAGAAGTTATGGGCTTTAA
195 GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGAAGTTGTGGGATTTAA
* * *
556413 AAGGGAAAAAGAGTGCCACGGTGTTGTGGGCTTTGAAAA-G--AAGGTGCCACGGAGTTGT-GGA
257 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTGTGGGC
* * *
556474 TTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTG
321 TTTA-AA-GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-GAAAGG---AAGGTGCCACGGAGTTG
* ** *
556539 TGGGCTTTGAA--AAG
380 TGGACTTAAAAGGAAC
* * * * * * * *
556553 ATGGTGCCA-TAGAGTCGCGGACTTTGAAAGG---AAG-GTGCCACGGAGTCGTGGACTTAAAAG
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-
* * * *
556613 GAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTT
65 -AAGAAGGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* **
556678 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
127 GAAACG--GGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTT
* * * * * * *
556742 -AAACG-----GGTGCCACAAAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGAAGTTGTAGGC
190 AAAACGAAAAAGGTGCCACAGAGTTGTGGGCTTTG-A--AAAGAAGGTGCCACGAAGTTGTGGGA
*
556801 TTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAA-G--AAGGTGCCACGGAGTTG
252 TTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTG
* * * *
556863 TGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAG
316 TGGGCTTTA-AA-GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-GAAAGG---AAGGTGCCACGG
* ** *
556927 AGTTGTGGGCTTTGAA--AAG
375 AGTTGTGGACTTAAAAGGAAC
* * * * * * *
556946 AAGGTGCCAC-AGAGTCGCGGACTTTGAGAGG---AAG-GTGCCACGGAGTCGTGGACTTAAAAG
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-
* * * **
557006 GAACAAGGTGCCATGG-GTTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTT
65 -AAGAAGGTGCCACGGAG-TTGTGGAC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * * * *
557070 TGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAG-GTGCCACGATGTTGTGGACTT
126 TGAAACG--GGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTT
* * *
557134 TAAAAGGGAGAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGAAGTTGT-GGA
189 TAAAA-CGAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGAAGTTGTGGGA
* * * * *
557198 CTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTT-GAAAGGAACAAGGTGCCACGGGGTCG
252 TTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA-AAGGTGCCACGGAGTTG
* * *
557262 TGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAATGTGCCACGGAGT
316 TGGGCTTT-AAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGT
*
557327 CGTGGACTTAAAAGGAAC
378 TGTGGACTTAAAAGGAAC
* * * * *
557345 AAGGTGCCACG-GAGTTGTGGACTTTAAAAGGGAAAAAGAGTGACTCAGAGTTATGGGCTTTGAA
1 AAGGTGCCACGAGAGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* **
557409 AAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGAAGTTGTGAACTTTGAA
65 AAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG--
* * * *
557474 AGGAACAAGGTGCCACGGGGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCT
128 A--AAC-GGGTGCCACGGAGTCGTGGAC-TTAGAA-GGAAAAAGAGTGCCACAAAGTTGTGGGCT
* * *
557539 TTGAAAA-GAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTATG
188 TT-AAAACGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGAAGTTGTG
* * * *
557603 GGCTTTAAAAAGAAAAAG-GTGCCCCGGAGTTGTGGGCTTTAAAAAGGAAAAGGTGTCACGGAGT
249 GGATTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGT
* *
557667 TATGGGATTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGA
314 TGTGGGCTTT--AAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
557713 GAAGAGATTG
Statistics
Matches: 1711, Mismatches: 159, Indels: 131
0.86 0.08 0.07
Matches are distributed among these distances:
384 25 0.01
385 40 0.02
386 8 0.00
387 37 0.02
388 33 0.02
389 69 0.04
390 47 0.03
391 13 0.01
392 46 0.03
393 909 0.53
394 14 0.01
395 4 0.00
396 31 0.02
397 29 0.02
398 20 0.01
399 46 0.03
400 44 0.03
401 53 0.03
402 22 0.01
403 23 0.01
404 51 0.03
405 37 0.02
406 25 0.01
407 59 0.03
408 26 0.02
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (395 bp):
AAGGTGCCACGAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
CGGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAACG
AAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGAAGTTGTGGGATTTAAAAGG
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAA
AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTAAAA
GGAAC
Found at i:556308 original size:27 final size:27
Alignment explanation
Indices: 556270--556376 Score: 124
Period size: 27 Copynumber: 3.7 Consensus size: 27
556260 AAAAAGAGTA
*
556270 CCACGGAGTTGTGGGCTTAAACGGGTG
1 CCACGGAGTTGTGGACTTAAACGGGTG
*
556297 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTG
1 CCACGGAGTTGTGGACTTA-AACG-----G-GTG
*
556331 CCACGGAGTTGTGGGCTTAAACGGGTG
1 CCACGGAGTTGTGGACTTAAACGGGTG
556358 CCACGGAGTTGTGGACTTA
1 CCACGGAGTTGTGGACTTA
556377 GAAGGAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
27 39 0.57
28 4 0.06
33 4 0.06
34 21 0.31
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.21
Consensus pattern (27 bp):
CCACGGAGTTGTGGACTTAAACGGGTG
Found at i:556328 original size:454 final size:453
Alignment explanation
Indices: 555382--556910 Score: 1806
Period size: 454 Copynumber: 3.4 Consensus size: 453
555372 AAGGGTGAAA
* * * **
555382 GGTGCCACGAAGTTGTGGACTTAAAAGGAACAA-TGTGCCACGGAGTTGTGGGCTTTAAAAAAAA
1 GGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT---AAACG
**
555446 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAA-CG-
62 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGCGA
* * * * ** * *
555507 ----G-GTGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAA
127 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGGAGTTGT-GGATTTAGA
* * * ** *
555567 AGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAA-G---AAGGTGCCATGGAGTTGT-GGA
188 A-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGC
* * ** * * * * *
555627 TTTAGAAGGAAAAAGAGTGCCACGGAGTTTTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTG
252 TTT-GAA--AAGAAG-GTGCCACAGAGTCGTGGACTTT-GAAAGG---AAGGTGCCACGGAGTCG
* * * *
555692 TGGGCTCT-AAA--AAGAAGGTGCCAC-AGAGTCGTGGACTTTGAAA-GG---AAG-GTGCCACG
309 TGGACT-TAAAAGGAACAAGGTGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACG
* ** * * * *
555748 GAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGC
372 GAGTTGTGGGCTTTGAA--AAGAAGGTGCCAAGA-GTCGTGGAC-TTAGAA-GGAAAAAGAGTGC
*
555813 CACGGAGTTGTGGGCTTTGAAAAG
432 CACGGAGTTGTGGGC-TT-AAACG
* *
555837 AAGATGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGG
1 --GGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGG
* *
555902 TGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGTGAAA
64 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGCGAAA
**
555967 AAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAA
129 AAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAA
*
556032 AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCTGAAA
194 AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAA
*
556097 AGAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTTAAAAGGAA
259 AGAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
556162 CAAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
324 CAAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
*
556227 AAGAAGGTGCCATAGAGTCGTGGACTTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGCTTAAAC
389 AAGAAGGTGCCA-AGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAC
556292 G
453 G
*
556293 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
1 GGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
* *
556358 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCA-AGAAGTTATGGGCTTTAAAAGGGAAAA
66 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACA-AAGTTGTGGGCTTTAAAAGCGAAAA
*
556422 AGAGTGCCACGGTGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAA
130 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAA
556487 AGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAA
195 AGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAA
* * *
556552 GATGGTGCCATAGAGTCGCGGACTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAAC
260 GAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAAC
* *
556617 AAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTTGAAA
325 AAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
*
556682 AGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
390 AGAAGGTGCCA-AGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
* * * * *
556747 GGTGCCACAAAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGAAGTTGTAGGCTTTAAAAGGGA
1 GGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAA-CG-
* * * ** * *
556812 AAAAGAGTGCCACGAAGTTGTGGGCTTTA-AA--AAGAAG-GTGCCACGGAGTTGTGGAC-TTAG
62 ----G-GTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
*
556872 AAG-GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
121 AAGCGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
556911 GAAAAAGATG
Statistics
Matches: 951, Mismatches: 84, Indels: 73
0.86 0.08 0.07
Matches are distributed among these distances:
453 1 0.00
454 539 0.57
455 25 0.03
456 10 0.01
457 61 0.06
458 123 0.13
459 38 0.04
460 51 0.05
461 15 0.02
462 42 0.04
463 43 0.05
464 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (453 bp):
GGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGCGAAAAA
GAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAAA
GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAAG
AAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACA
AGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
GAAGGTGCCAAGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
Found at i:557079 original size:847 final size:848
Alignment explanation
Indices: 555380--557607 Score: 3357
Period size: 847 Copynumber: 2.6 Consensus size: 848
555370 AAAAGGGTGA
* *
555380 AAGGTGCCAC-GAAGTTGTGGACTTAAAAGGAACAATGTGCCACGGAGTTGTGGGCTTTAAAAAA
1 AAGGTGCCACAG-AGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT--AAAA
*
555444 AAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGG
63 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGG
*
555509 TGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACA-AAGTTGTGGGCTTTAAAAGGGAA
128 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCA-AGAAGTTGTGGGCTTTAAAAGGGAA
* *
555573 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCATGGAGTTGTGGATTTAGAAGGAA
192 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAA
* * *
555638 AAAGAGTGCCACGGAGTTTTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCTAAA
257 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAA
555703 AAGAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
322 AAGAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
*
555768 ACAAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
387 ACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
*
555833 AAAGAAGATGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
452 AAAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
** * * *
555898 CGGGTGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGT
517 CGGGTGCCACAAAGTTATGGACTTAGAAGGAAAAAAAGTGCCACAAAGTTGTAGGCTTTAAAAGG
* *
555963 GAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAG
582 GAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTTGTGGACTTAGAAG
556028 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCT
647 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCT
*
556093 GAAAAGAAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTTAAAA
712 GAAAAGAAGGTGCCACAGAGTCGCGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTTAAAA
* **
556158 GGAACAAGGTGCCACGAGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
777 GGAACAAGGTGCCACGAGGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTT
556223 TGAAAAG
842 TGAAAAG
* * * * *
556230 AAGGTGCCATAGAGTCGTGGACTTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGC-TT-AAACG
1 AAGGTGCCACAGAGTCGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
556293 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
65 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
*
556358 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCAAGAAGTTATGGGCTTTAAAAGGGAAAAA
130 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCAAGAAGTTGTGGGCTTTAAAAGGGAAAAA
*
556423 GAGTGCCACGGTGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAAA
195 GAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAAA
556488 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAAG
260 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAAG
* * * *
556553 ATGGTGCCATAGAGTCGCGGACTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACA
325 AAGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAACA
*
556618 AGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTTGAAAA
390 AGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
*
556683 GAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGG
455 GAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGG
* *
556748 GTGCCACAAAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGAAGTTGTAGGCTTTAAAAGGGAA
520 GTGCCACAAAGTTATGGACTTAGAAGGAAAAAAAGTGCCACAAAGTTGTAGGCTTTAAAAGGGAA
*
556813 AAAGAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
585 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
556878 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAA
650 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCTGAA
* *
556943 AAGAAGGTGCCACAGAGTCGCGGACTTTGAGAGGAAGGTGCCACGGAGTCGTGGACTTAAAAGGA
715 AAGAAGGTGCCACAGAGTCGCGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTTAAAAGGA
*
557008 ACAAGGTGCCATG-GGTTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTG
780 ACAAGGTGCCACGAGG-TTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTG
557072 AAAAG
844 AAAAG
* *
557077 AAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCAC-GATGTTGTGGACTTTAAAAGG
1 AAGGTGCCACAGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGA-GTTGTGGGCTTTAAAA--
* * * * *
557141 GAGAAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGAAGTTGTGGACTTAA
63 -AG---G-GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-A
* * * * ** * *
557203 AAGGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAGGAACAAG-GTGCCACGGGGTCGTGGAC
122 AACG-----G-GTGCCACGGAGTTGTGGACTTAG-AAGGAAAAAGAGTGCCAAGAAGTTGTGGGC
* *
557267 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAATGTGCCACGGAGTCGTGG
180 TTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGG
* * * * * * *
557332 ACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGACTCAGAGT
245 ATTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGA-TGCCACAGAGT
* * * * *
557396 TATGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGACTTAG-AAGGAAAAAGAGTGCCACGAAG
309 TGTGGGCTTTGAAAAGAAGGTGCCACAGAGTCGTGGACTTTGAAAGG---AAG-GTGCCACGGAG
* * *
557460 TTGTGAACTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCA
370 TTGTGGAC-TTAAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCA
* * * * *
557525 CAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAG-GT
434 CGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGT
*
557589 GCCACGGAGTTATGGGCTT
495 GCCACGGAGTTGTGGGCTT
557608 TAAAAAGAAA
Statistics
Matches: 1253, Mismatches: 93, Indels: 48
0.90 0.07 0.03
Matches are distributed among these distances:
845 2 0.00
846 17 0.01
847 782 0.62
848 3 0.00
850 31 0.02
851 20 0.02
852 19 0.02
853 9 0.01
854 1 0.00
855 23 0.02
858 39 0.03
859 154 0.12
860 9 0.01
861 3 0.00
862 16 0.01
863 74 0.06
866 39 0.03
867 12 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (848 bp):
AAGGTGCCACAGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGG
GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGC
CACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCAAGAAGTTGTGGGCTTTAAAAGGGAAAAAG
AGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGATTTAGAAGGAAAAAG
AGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTTGAAAAGA
AGGTGCCACAGAGTCGTGGACTTTGAAAGGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAA
GGTGCCACGGGGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
AAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGG
TGCCACAAAGTTATGGACTTAGAAGGAAAAAAAGTGCCACAAAGTTGTAGGCTTTAAAAGGGAAA
AAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAA
AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTCTGAAA
AGAAGGTGCCACAGAGTCGCGGACTTTGAAAGGAAGGTGCCACGGAGTCATGGACTTAAAAGGAA
CAAGGTGCCACGAGGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAA
AAG
Found at i:559035 original size:14 final size:15
Alignment explanation
Indices: 559005--559043 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
558995 CCTTTGCACC
559005 TTTTT-TGTTTTGTT
1 TTTTTGTGTTTTGTT
559019 TTTTTGTGTTTTG-T
1 TTTTTGTGTTTTGTT
559033 TTTTTGTGTTT
1 TTTTTGTGTTT
559044 ACTTTTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (15 bp):
TTTTTGTGTTTTGTT
Found at i:559071 original size:13 final size:14
Alignment explanation
Indices: 559053--559085 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
559043 TACTTTTGAC
559053 TTTTTCA-TCATTT
1 TTTTTCATTCATTT
559066 TTTTTCATTTCATTT
1 TTTTTCA-TTCATTT
559081 TTTTT
1 TTTTT
559086 AAGGGAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCATTCATTT
Found at i:566033 original size:52 final size:52
Alignment explanation
Indices: 565953--566083 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
565943 CCCAAAATAT
*
565953 GAAAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTAG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAG
* * * * *
566005 GCAAATTTGCCTGCATGTATCAATACATTTTATAGTGTATTGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAG
566057 GAAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
566084 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAG
Found at i:566094 original size:52 final size:51
Alignment explanation
Indices: 565953--566103 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 51
565943 CCCAAAATAT
*
565953 GAAAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTAG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAG
* * * * *
566005 GCAAATTTGCCTGCATGTATCAATACATTTTATAGTGTATTGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAG
*
566057 GAAAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
566104 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (51 bp):
GAAAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAG
Found at i:566110 original size:13 final size:13
Alignment explanation
Indices: 566092--566116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566082 CAAAGATCAG
566092 TGTATCGATACAA
1 TGTATCGATACAA
566105 TGTATCGATACA
1 TGTATCGATACA
566117 TTTGGATAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566183 original size:19 final size:18
Alignment explanation
Indices: 566159--566221 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
566149 TAGCTTATAT
566159 TGTATCAATACAAAACTTA
1 TGTATCAATAC-AAACTTA
*
566178 TGTATCGATAC--A--T-
1 TGTATCAATACAAACTTA
566191 TGTATCAATACAACACTTA
1 TGTATCAATACAA-ACTTA
*
566210 TGTATCGATACA
1 TGTATCAATACA
566222 TTGTATGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.60
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (18 bp):
TGTATCAATACAAACTTA
Found at i:566197 original size:32 final size:32
Alignment explanation
Indices: 566157--566254 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 32
566147 AGTAGCTTAT
*
566157 ATTGTATCAATACAAAACTTATGTATCGATAC
1 ATTGTATCAATACAACACTTATGTATCGATAC
566189 ATTGTATCAATACAACACTTATGTATCGATAC
1 ATTGTATCAATACAACACTTATGTATCGATAC
** *
566221 ATTGTATGGATACAACACTTTATGTATTGATAC
1 ATTGTATCAATACAACAC-TTATGTATCGATAC
566254 A
1 A
566255 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 47 0.77
33 14 0.23
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTGTATCAATACAACACTTATGTATCGATAC
Found at i:572744 original size:60 final size:59
Alignment explanation
Indices: 572497--573239 Score: 520
Period size: 61 Copynumber: 12.4 Consensus size: 59
572487 AACCTTTTAT
* * * * *
572497 CCTTTTAGTCCTCAAAAAGCAGAACATCTTTTCCTCTTAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACA--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
572558 CCTTTCAGTCCTCAAAGAGTAGGACGCATTTTCCTTTTAAAGCCCACACAGGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGA--CATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *** *
572619 CTTTTCAATCCTTAAAGAGTAGGATGCCTTTTCCTTTTAAAG--CTCATTGGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGA--CATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
572678 CTTTTCAGTCCTCAAAGAGTAGGACATTTTACTTTTTAAAGCCCACACAGGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACATTTT-CCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
572738 CCTTTCAGTTCTTAAAGAGTAGGACATTTTCCTTTTTAAAGCTCATACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACATTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
572798 CCTTTTAGTCCTAAAAAAGCAGGATGCCTTCTT-CTTTCAAAGCCTACACAAGTTGGTAGG-A
1 CCTTTCAGTCCTCAAAGAGCAGGA--CATT-TTCCTTTTAAAGCCCACACAAGTTGGT-GGCA
* * * * * * *** **
572859 CCTTTCAGCCCTGAAAAAGTC-GGATGCCTTCTCCTTTCAAAGCTTGCACAAGTTGGTTACA
1 CCTTTCAGTCCTCAAAGAG-CAGGA--CATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
572920 CCTTTCAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTAGCA
1 CCTTTCAGTCCTCAAAGAGCAGGA--CATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * * * *
572981 CCTTCCAATCCTCAAGGAACAAGACACTTTCATTTCAAAGCCCATACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
573040 CC-TTCTAGTCCTCAAATAGGAAGGACACTTTCCTTTCAAAGCTCACACAAGTTGGGGGTA
1 CCTTTC-AGTCCTCAAAGA-GCAGGACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * *
573100 CC-CCCTAGTCC-CTAAAGAGGAGAACATTTTCCTTTCAAAGCCCACACAAGTTGGT-GAA
1 CCTTTC-AGTCCTC-AAAGAGCAGGACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
573158 TTCTTTTAGTCCTCGAAGAGCAAGACA-CTT-CTTTTAAAGCCCACACAAGCTGGTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
573216 -CTTTCTAGTCCTCAAAGAGCAGGA
1 CCTTTC-AGTCCTCAAAGAGCAGGA
573240 TGCTCTCTAT
Statistics
Matches: 550, Mismatches: 110, Indels: 48
0.78 0.16 0.07
Matches are distributed among these distances:
56 4 0.01
57 43 0.08
58 17 0.03
59 123 0.22
60 132 0.24
61 220 0.40
62 7 0.01
63 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (59 bp):
CCTTTCAGTCCTCAAAGAGCAGGACATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:574058 original size:51 final size:51
Alignment explanation
Indices: 573925--574060 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
573915 ATTTACTATT
* *
573925 TGTATCGATACATTTTTCATTGTATTGATACATTCTGGATTTTAACTTAGA
1 TGTATCGATACATTTTTCATTGTATTGATATATTATGGATTTTAACTTAGA
* * * **
573976 TGTAGCGACACATTTTTCATTGCATCAATATATTATGGGA-TTTAACTTAGA
1 TGTATCGATACATTTTTCATTGTATTGATATATTAT-GGATTTTAACTTAGA
* * *
574027 TGTATCGATGCATTTCTCAATGTATTGATATATT
1 TGTATCGATACATTTTTCATTGTATTGATATATT
574061 CAAGCATTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
51 66 0.96
52 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (51 bp):
TGTATCGATACATTTTTCATTGTATTGATATATTATGGATTTTAACTTAGA
Found at i:576574 original size:79 final size:78
Alignment explanation
Indices: 576412--576719 Score: 216
Period size: 79 Copynumber: 3.9 Consensus size: 78
576402 AAATATCGAG
* * * * * * * **
576412 TTTTCATCATCGAGGATACTCCAACCCTGCTGTTTCTAAAGGGATACTCCAACTCCAGCTTTATT
1 TTTTCACCATCGAGGATACTCCAACCCTGTTATTT-TCAAGGGATACACAAACCCCAATTTTATT
* ** **
576477 TCTAGTACACTGGA-
65 CCTAAAACAC-CAAT
* * **
576491 TTTTCACCATCGAGGATACTCCAACCTTGTTATTTTCAAGAGGATACTC-TGCCTCCAATTTTAT
1 TTTTCACCATCGAGGATACTCCAACCCTGTTATTTTCAAG-GGATACACAAACC-CCAATTTTAT
**
576555 TTTTAAAACACCAAT
64 TCCTAAAACACCAAT
* * * * *
576570 TTTTCACCATC-AGGGATACTCTAACCCTATTATTTCTGATGGGATACACAAACCCCAGTTTTAT
1 TTTTCACCATCGA-GGATACTCCAACCCTGTTATTT-TCAAGGGATACACAAACCCCAATTTTAT
576634 TCCTAAAACACCAAT
64 TCCTAAAACACCAAT
* * * *
576649 TTTCCACTATCG-GGAATACTCCAACCCTGTTGTTTTCAAGGGGATATC-C-AACCCCATTTTTA
1 TTTTCACCATCGAGG-ATACTCCAACCCTGTTATTTTCAA-GGGATA-CACAAACCCCAATTTTA
576711 TCTCC-AAAA
63 T-TCCTAAAA
576720 TATTAAATTT
Statistics
Matches: 184, Mismatches: 34, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
78 28 0.15
79 150 0.82
80 6 0.03
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (78 bp):
TTTTCACCATCGAGGATACTCCAACCCTGTTATTTTCAAGGGATACACAAACCCCAATTTTATTC
CTAAAACACCAAT
Found at i:579448 original size:10 final size:11
Alignment explanation
Indices: 579424--579452 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
579414 GCCGTTACAA
579424 GCTTGTTTAGT
1 GCTTGTTTAGT
579435 GCTTGTTT-GT
1 GCTTGTTTAGT
579445 GCTTGTTT
1 GCTTGTTT
579453 TAATGCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.03, C:0.10, G:0.28, T:0.59
Consensus pattern (11 bp):
GCTTGTTTAGT
Found at i:579579 original size:13 final size:13
Alignment explanation
Indices: 579563--579593 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
579553 ACAATTCATC
579563 ATGTATCGATACA
1 ATGTATCGATACA
579576 ATGTATCGATACA
1 ATGTATCGATACA
*
579589 TTGTA
1 ATGTA
579594 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:579584 original size:33 final size:33
Alignment explanation
Indices: 579541--579609 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
579531 CCGTTACAAG
*
579541 CAATGCATCGATACAATT-CATCATGTATCGATA
1 CAATGCATCGATAC-ATTGCACCATGTATCGATA
* *
579574 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGCATCGATACATTGCACCATGTATCGATA
579607 CAA
1 CAA
579610 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATGCATCGATACATTGCACCATGTATCGATA
Found at i:579682 original size:19 final size:19
Alignment explanation
Indices: 579638--579693 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
579628 CTGCCAACCT
**
579638 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
579658 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
579677 CATGTATCCATACAATG
1 CATGTATCGATACAATG
579694 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:582555 original size:87 final size:84
Alignment explanation
Indices: 582340--582658 Score: 236
Period size: 88 Copynumber: 3.7 Consensus size: 84
582330 TATATTAGGA
* * * * ** **
582340 TTAGACTG-CATTAGTATTTCCATCTTTTCATATGCATTTGTC-ATTCTATTGATAATTGCATTT
1 TTAGA-TGACATTGGTATTTGCATCATTT-ATATGCATTTGCCTATT-TATTGATGCTTATATTT
* *
582403 GCATTGTCTCACCTACATTTGCAT
63 GCATTGT-T-ACATGCATTTGCAT
* * ** *
582427 ATTAGATGACATTGGTATTTGCATCATTGCAGATGTGTTTGCCTATTTGTTGATGCTTGCATATG
1 -TTAGATGACATTGGTATTTGCATCATT-TATATGCATTTGCCTATTTATTGATGCTT--ATAT-
582492 TAT-CATT-TTACATGCATTTGCAT
61 T-TGCATTGTTACATGCATTTGCAT
* * * *
582515 TTAGATAACATTGGCATTTGCATCATTTAATATGCATTTGCC-ACTTTACTGATGCCTATATTTG
1 TTAGATGACATTGGTATTTGCATCATTT-ATATGCATTTGCCTA-TTTATTGATGCTTATATTTG
*
582579 CATTGTTTCATGCATATTAGCATT
64 CATTGTTACATGCAT-TT-GCA-T
* *
582603 TTACATGACATTGGTATGTGCATCATGTTATATGCATTTGCCCT-TTTATTGATGCT
1 TTAGATGACATTGGTATTTGCATCAT-TTATATGCATTTG-CCTATTTATTGATGCT
582659 CGCAATTGCG
Statistics
Matches: 183, Mismatches: 31, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
83 1 0.01
84 5 0.03
85 13 0.07
86 3 0.02
87 50 0.27
88 94 0.51
89 8 0.04
90 3 0.02
91 5 0.03
92 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (84 bp):
TTAGATGACATTGGTATTTGCATCATTTATATGCATTTGCCTATTTATTGATGCTTATATTTGCA
TTGTTACATGCATTTGCAT
Found at i:583718 original size:75 final size:76
Alignment explanation
Indices: 583575--583722 Score: 172
Period size: 75 Copynumber: 2.0 Consensus size: 76
583565 TTTTTTTCAG
* * * ** * * * * * *
583575 CTTTTGATGAAAATTTTAGAAACCACATATTTCCCATTGTGATCATCTTCTTCGGCCTCTTGTTA
1 CTTTTAATGAAAATTATAGAAACCACATATTCCCCATCATGATCATATTCGTCAGCATCTTATCA
583640 GTTTGTTTTGA
66 GTTTGTTTTGA
* *
583651 CTTTTAATGGAAATTATAG-AACCACATATTCCCCATCATGATTATATTCGTCAGCATCTTATCA
1 CTTTTAATGAAAATTATAGAAACCACATATTCCCCATCATGATCATATTCGTCAGCATCTTATCA
583715 GTTTGTTT
66 GTTTGTTT
583723 CAAATATTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
75 43 0.73
76 16 0.27
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (76 bp):
CTTTTAATGAAAATTATAGAAACCACATATTCCCCATCATGATCATATTCGTCAGCATCTTATCA
GTTTGTTTTGA
Found at i:584733 original size:22 final size:22
Alignment explanation
Indices: 584707--584751 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
584697 GTCCTTAGAA
584707 ATCTTAAATGATGGATTACTAC
1 ATCTTAAATGATGGATTACTAC
584729 ATCTTAAATGATGGATTACTAC
1 ATCTTAAATGATGGATTACTAC
584751 A
1 A
584752 GCCTTACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
ATCTTAAATGATGGATTACTAC
Found at i:584976 original size:44 final size:44
Alignment explanation
Indices: 584913--586104 Score: 387
Period size: 44 Copynumber: 27.3 Consensus size: 44
584903 CTTTGGTCTG
*
584913 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGATGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * ** * * *
584957 ACGGTTACCACCCTAGTTAAATCTGCTTCTTTCCTG-TTTAACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATT-CTGATTTGACGT
* * * * *** * **
585001 GTGGTTACCACCCTAGTCAAATATGCCTCTTTCCTG-TTTGACAC
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATT-CTGATTTGACGT
** *
585045 ATGGTTACCACCCTGGTTAAACATTTTTCATT-TCGATCTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCT-GATTTGACGT
* * * * *
585089 ATAGTTACCACTCTGGTTAGATTTTTTTCATTCTAATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * **
585133 ATGTTTACCACCCTAGTCAAATCAGCCCTTTTC--T-TG-TTTGACGT
1 ATGGTTACCACCCTGGTTAAAT----TTTTTTCATTCTGATTTGACGT
* * * * * * * * *
585177 ATGGCTACCACCCTAGTCAAATGCTTCTT-ATTTTGGTCTGACAT
1 ATGGTTACCACCCTGGTTAAAT-TTTTTTCATTCTGATTTGACGT
* *
585221 ATGGTTACCACCCTGGTTAGATTTTTTTCATTTTGATTTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * *** * * *
585265 ACGGTTACTACCCTGGTCAAATTTGCCTCTTTTCT-ATTTAATGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTC-ATTCTGATTTGACGT
* ** * * *
585309 ATGGTTACCACCCTAGTTAAATGCTTCTCATT-TCAGTCTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGA-TTTGACGT
* *
585353 ATGGTTACCACCCTGGTTAGATTCTTTTCATTCTGATTTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * * * * *** * *
585397 ACGATTACCA-CTTCAGTCAAATCTGCCTCTTTCCT-ATTTGACAT
1 ATGGTTACCACCCT-GGTTAAATTTTTTTCATT-CTGATTTGACGT
* * * * *
585441 AT-G-----ACCCTGGTCAAACTCTTCTT-ATTTTGGTTTGACGT
1 ATGGTTACCACCCTGGTTAAA-TTTTTTTCATTCTGATTTGACGT
* * * * *
585479 ATGTTTACCACCCTAGTTAGATTTTATTCATTCAGATTTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
** * *
585523 ATGGTTACCACCCCAGTTAAATCTATCTTT--TTCTG-TTTGACAT
1 ATGGTTACCACCCTGGTTAAAT-T-TTTTTCATTCTGATTTGACGT
* ** * * * * * * * *
585566 ATGGTTACCACCCAGGCCAAACTCTTTTAATTTTGGTCTAACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * *
585610 ATGGTTACCACCCTGGTCAGATTTTTTTCATTTTGATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * * *** * *
585654 ACGATTACCACCTTGGTCAAATTTGCCTCCTACCT-ATTTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCAT-TCTGATTTGACGT
** * * * * * * *
585698 ATGCCTACTAACCTGGTCAAACTCTTTTCATT-TCGGTTTGACTT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCT-GATTTGACGT
* ** * * * * *
585742 TTATTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGATGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
** ** *** *
585786 ACAGTTACCACCCTGGTTAAACCTACCTCATTTCT-ATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCA-TTCTGATTTGACGT
* * * ** * * *
585830 GTGGTTACCA--C-GATCAAATTTGCCTCCTTTCT-ATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTT-TTTTCATTCTGATTTGACGT
* * * * * *
585871 ATGGTTACCACCCAGGTAAAACTCTTTTCATT-TCGATATGATGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCT-GATTTGACGT
* * * * *
585915 ATGATTACCACCCTGGTCAAATTCTTTTCATTCTTATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * *** *
585959 ATGGTTACCACCCTAGTCAAATTTACCTCATTCCT-ATTTGACAT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATT-CTGATTTGACGT
* * * * * * * * *
586003 ATGGTTACCACTCTAGTTAAACTCTTCTCGTTTTGGTCTGACGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
* * * * * * *
586047 ATGGTTATCACCCTGGTCAAATTTATCTCTTTCTTG-TTTAATGT
1 ATGGTTACCACCCTGGTTAAATTTTTTTCATTC-TGATTTGACGT
586091 ATGGTTACCACCCT
1 ATGGTTACCACCCT
586105 AGTCAAACTC
Statistics
Matches: 838, Mismatches: 261, Indels: 98
0.70 0.22 0.08
Matches are distributed among these distances:
37 1 0.00
38 18 0.02
39 7 0.01
41 35 0.04
42 9 0.01
43 51 0.06
44 684 0.82
45 24 0.03
46 4 0.00
48 5 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (44 bp):
ATGGTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGACGT
Found at i:585141 original size:132 final size:132
Alignment explanation
Indices: 585005--586251 Score: 734
Period size: 132 Copynumber: 9.5 Consensus size: 132
584995 TAACATGTGG
* * *
585005 TTACCACCCTAGTCAAATATGCCTCTTTCCTGTTTGACACATGGTTACCACCCTGGTTAAACAT-
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAAC-TC
* * * * *
585069 TTTTCATTTCGATCTGACGTATAGTTACCACTCTGGTTAGATTTTTTTCATTCTAATTTGACATA
65 TTTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTA
* *
585134 TGT
130 CGA
* * * * *
585137 TTACCACCCTAGTCAAATCA-GCC-CTTTTCTTGTTTGACGTATGGCTACCACCCTAGTCAAA-T
1 TTACCACCCTAGTCAAAT-ATGCCTC-TTTCCTATTTGACATATGGTTACCACCCTGGTCAAACT
* * *
585199 GCTTCTT-ATTTTGGTCTGACATATGGTTACCACCCTGGTTAGATTTTTTTCATTTTGATTTGAC
64 -CTT-TTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGAC
*
585263 GTACGG
127 GTACGA
* * * * * ** * *
585269 TTACTACCCTGGTCAAATTTGCCTCTTTTCTATTTAATGTATGGTTACCACCCTAGTTAAA-TGC
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACT-C
* * *
585333 TTCTCATTTCAGTCTGACGTATGGTTACCACCCTGGTTAGATTCTTTTCATTCTGATTTGACGTA
65 TTTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTA
585398 CGA
130 CGA
* *
585401 TTACCA-CTTCAGTCAAATCTGCCTCTTTCCTATTTGACATAT-G-----ACCCTGGTCAAACTC
1 TTACCACCCT-AGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTC
* * * * * *
585459 TTCTT-ATTTTGGTTTGACGTATGTTTACCACCCTAGTTAGATTTTATTCATTCAGATTTGACGT
65 TT-TTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGT
* *
585523 ATGG
129 ACGA
* * * ** * * * *
585527 TTACCACCCCAGTTAAATCTATCT-TTTTCTGTTTGACATATGGTTACCACCCAGGCCAAACTCT
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCT
* * * * * * *
585591 TTTAATTTTGGTCTAACATATGGTTACCACCCTGGTCAGATTTTTTTCATTTTGATTTGACATAC
66 TTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTAC
585656 GA
131 GA
* * * * * * ** * *
585658 TTACCACCTTGGTCAAATTTGCCTCCTACCTATTTGACGTATGCCTACTAACCTGGTCAAACTCT
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCT
* * * ** * * * *
585723 TTTCATTTCGGTTTGACTTTTATTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGATGTAC
66 TTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTAC
585788 -A
131 GA
* * ** * * *
585789 GTTACCACCCTGGTTAAACCTACCTCATTT-CTATTTGACATGTGGTTACCA--C-GATCAAA-T
1 -TTACCACCCTAGTCAAATATGCCTC-TTTCCTATTTGACATATGGTTACCACCCTGGTCAAACT
* * ** * * * * * * * *
585849 -TTGCCTCCTTTCTATTTGACATATGGTTACCACCCAGGTAAAACTCTTTTCATT-TCGATATGA
64 CTT--TTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCT-GATTTGA
* *
585912 TGTATGA
126 CGTACGA
* * * * *
585919 TTACCACCCTGGTCAAAT-T-CTTTTCATTCTTATTTGACATATGGTTACCACCCTAGTCAAA-T
1 TTACCACCCTAGTCAAATATGC--CTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACT
* * ** * * * * * * * * * * * *
585981 -TTACCTCATTCCTATTTGACATATGGTTACCACTCTAGTTAAACTCTTCTCGTTTTGGTCTGAC
64 CTT--TTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGAC
* *
586045 GTATGG
127 GTACGA
* * * ** * * * ** *
586051 TTATCACCCTGGTCAAATTTATCTCTTTCTTGTTTAATGTATGGTTACCACCCTAGTCAAACTCT
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCT
* * * * * * * * ** *
586116 TCTCATTTTGGTCTGACATATGGTTACTACCCTAGTCAGATTCTTCTT-ATTCCGATTTGTTGCA
66 TTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATT-TTTTTCATTCTGATTTGACGTA
* *
586180 TGG
130 CGA
* * * * * * * * * * *
586183 TTACCA-CATGGTCAAATCTACCTCCTTCTTGTTTGACGTATGCTTATCACTCTGGTCAAACTCT
1 TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCT
586247 TTTCA
66 TTTCA
586252 AGTTAGTTTG
Statistics
Matches: 881, Mismatches: 196, Indels: 77
0.76 0.17 0.07
Matches are distributed among these distances:
125 15 0.02
126 84 0.10
127 6 0.01
128 5 0.01
129 90 0.10
130 5 0.01
131 142 0.16
132 522 0.59
133 10 0.01
134 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (132 bp):
TTACCACCCTAGTCAAATATGCCTCTTTCCTATTTGACATATGGTTACCACCCTGGTCAAACTCT
TTTCATTTCGGTCTGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATTTGACGTAC
GA
Found at i:585188 original size:176 final size:176
Alignment explanation
Indices: 584916--585288 Score: 437
Period size: 176 Copynumber: 2.1 Consensus size: 176
584906 TGGTCTGATG
* ** * *
584916 GTTACCACCCTGGTTAAATTTTTTTCATTCTGATTTGATGTACGGTTACCACCCTAGTTAAATCT
1 GTTACCACCCTGGTTAAATTTTTTTCATTCTAATTTGACATACGGTTACCACCCTAGTCAAATCA
* * * *
584981 GCTTCTTTCCTGTTTAACATGTGGTTACCACCCTAGTCAAATATGCCTCTT-TCCT-GTTTGACA
66 GCCTCTTTCCTGTTTAACATATGGCTACCACCCTAGTC-AA-ATGCCTCTTATCCTGGTCTGACA
585044 CATGGTTACCACCCTGGTTAAACATTTTTCATTTCGATCTGACGTATA
129 CATGGTTACCACCCTGGTTAAACATTTTTCATTTCGATCTGACGTATA
* * * *
585092 GTTACCACTCTGGTTAGATTTTTTTCATTCTAATTTGACATATGTTTACCACCCTAGTCAAATCA
1 GTTACCACCCTGGTTAAATTTTTTTCATTCTAATTTGACATACGGTTACCACCCTAGTCAAATCA
* * * * ** *
585157 GCC-CTTTTCTTGTTTGACGTATGGCTACCACCCTAGTCAAATGCTTCTTATTTTGGTCTGACAT
66 GCCTC-TTTCCTGTTTAACATATGGCTACCACCCTAGTCAAATGCCTCTTATCCTGGTCTGACAC
* ** * * **
585221 ATGGTTACCACCCTGGTTAGATTTTTTTCATTTTGATTTGACGTACG
130 ATGGTTACCACCCTGGTTAAACATTTTTCATTTCGATCTGACGTATA
* *
585268 GTTACTACCCTGGTCAAATTT
1 GTTACCACCCTGGTTAAATTT
585289 GCCTCTTTTC
Statistics
Matches: 163, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
174 8 0.05
175 5 0.03
176 150 0.92
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (176 bp):
GTTACCACCCTGGTTAAATTTTTTTCATTCTAATTTGACATACGGTTACCACCCTAGTCAAATCA
GCCTCTTTCCTGTTTAACATATGGCTACCACCCTAGTCAAATGCCTCTTATCCTGGTCTGACACA
TGGTTACCACCCTGGTTAAACATTTTTCATTTCGATCTGACGTATA
Found at i:585925 original size:173 final size:173
Alignment explanation
Indices: 585670--586013 Score: 431
Period size: 173 Copynumber: 2.0 Consensus size: 173
585660 ACCACCTTGG
* * * * *
585670 TCAAATTTGCCTCCTACCTATTTGACGTATGCCTACTAACCTGGTCAAACTCTTTTCATTTCGGT
1 TCAAATTTGCCTCCTACCTATTTGACATATGCCTACCAACCAGGTAAAACTCTTTTCATTTCGAT
* * * **
585735 TTGACTTTTATTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGATGTACAGTTACCACCCT
66 ATGACTTTGATTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACATACAGTTACCACCCT
* * * *
585800 GGTTAAACCTACCTCATTTCTATTTGACATGTGGTTACCACGA
131 AGTCAAACCTACCTCATTCCTATTTGACATATGGTTACCACGA
** ** *
585843 TCAAATTTGCCTCCTTTCTATTTGACATATGGTTACCACCCAGGTAAAACTCTTTTCATTTCGAT
1 TCAAATTTGCCTCCTACCTATTTGACATATGCCTACCAACCAGGTAAAACTCTTTTCATTTCGAT
* * **
585908 ATGA-TGTATGA-TTACCACCCTGGTCAAATTCTTTTCATTCTTATTTGACATATGGTTACCACC
66 ATGACT-T-TGATTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACATACAGTTACCACC
**
585971 CTAGTCAAATTTACCTCATTCCTATTTGACATATGGTTACCAC
129 CTAGTCAAACCTACCTCATTCCTATTTGACATATGGTTACCAC
586014 TCTAGTTAAA
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
172 1 0.01
173 141 0.98
174 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (173 bp):
TCAAATTTGCCTCCTACCTATTTGACATATGCCTACCAACCAGGTAAAACTCTTTTCATTTCGAT
ATGACTTTGATTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACATACAGTTACCACCCT
AGTCAAACCTACCTCATTCCTATTTGACATATGGTTACCACGA
Found at i:586183 original size:88 final size:88
Alignment explanation
Indices: 585904--586189 Score: 285
Period size: 88 Copynumber: 3.2 Consensus size: 88
585894 CTTTTCATTT
* * * * * * * *
585904 CGATATGATGTATGATTACCACCCTGGTCAAATTCTTTTCATTCTT-ATTTGACATATGGTTACC
1 CGATTTGATGTATGGTTACCACCCTAGTCAAACTCTTCTCATT-TTGGTCTGACATATGGTTACT
* *
585968 ACCCTAGTCAAATTTACCTCATTC
65 ACCCTAGTCAAATTTATCTTATTC
* ** * * * *
585992 CTATTTGACATATGGTTACCACTCTAGTTAAACTCTTCTCGTTTTGGTCTGACGTATGGTTA-TC
1 CGATTTGATGTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTGGTCTGACATATGGTTACT-
*
586056 ACCCTGGTCAAATTTATCTCT-TTC
65 ACCCTAGTCAAATTTATCT-TATTC
* *
586080 TTG-TTTAATGTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTGGTCTGACATATGGTTACT
1 -CGATTTGATGTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTGGTCTGACATATGGTTACT
*
586144 ACCCTAGTCAGATTCT-TCTTATTC
65 ACCCTAGTCAAATT-TATCTTATTC
* *
586168 CGATTTGTTGCATGGTTACCAC
1 CGATTTGATGTATGGTTACCAC
586190 ATGGTCAAAT
Statistics
Matches: 157, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
87 4 0.03
88 151 0.96
89 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (88 bp):
CGATTTGATGTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTGGTCTGACATATGGTTACTA
CCCTAGTCAAATTTATCTTATTC
Found at i:586299 original size:131 final size:131
Alignment explanation
Indices: 586060--586299 Score: 275
Period size: 131 Copynumber: 1.8 Consensus size: 131
586050 GTTATCACCC
* * * * * **
586060 TGGTCAAATTTATCTCTTTCTTGTTTAATGTATGGTTACCACCCTAGTCAAACTCTTCTCATTTT
1 TGGTCAAATCTACCTCCTTCTTGTTTAACGTATGCTTACCACCCTAGTCAAACTCTTCTCAAGTT
* * * * *
586125 GGTCTGACATATGGTTACTACCCTAGTCAGATTCTTCTTATTCCGATTTGTTGCATGGTTACCAC
66 AGTCTGACATATGGATACCACCCTAGTCAGATCCTTCTCATTCCGATTTGTTGCATGGTTACCAC
586190 A
131 A
* * * * *
586191 TGGTCAAATCTACCTCCTTCTTGTTTGACGTATGCTTATCACTCTGGTCAAACTCTTTTCAAGTT
1 TGGTCAAATCTACCTCCTTCTTGTTTAACGTATGCTTACCACCCTAGTCAAACTCTTCTCAAGTT
* ** *
586256 AGTTTGATGTATGGATACCATCCTAGTCAGACTCCTT-TCATTCC
66 AGTCTGACATATGGATACCACCCTAGTCAGA-TCCTTCTCATTCC
586300 TGCTTGACAT
Statistics
Matches: 87, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
131 83 0.95
132 4 0.05
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (131 bp):
TGGTCAAATCTACCTCCTTCTTGTTTAACGTATGCTTACCACCCTAGTCAAACTCTTCTCAAGTT
AGTCTGACATATGGATACCACCCTAGTCAGATCCTTCTCATTCCGATTTGTTGCATGGTTACCAC
A
Found at i:586385 original size:44 final size:44
Alignment explanation
Indices: 586293--586385 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
586283 CAGACTCCTT
* * * * * * *
586293 TCATTCCTGCTTGACATGTGGTTACCACCCTGGTCAAGCTTTTT
1 TCATTCCTGCTTAACATATGATTACCACCCAGGTCAAACATTTA
* *
586337 TCATTCCTGTTTAACATATGATTACCACTCAGGTCAAACATTTA
1 TCATTCCTGCTTAACATATGATTACCACCCAGGTCAAACATTTA
586381 TCATT
1 TCATT
586386 TTCGTCTAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (44 bp):
TCATTCCTGCTTAACATATGATTACCACCCAGGTCAAACATTTA
Found at i:586968 original size:84 final size:84
Alignment explanation
Indices: 586609--586973 Score: 347
Period size: 84 Copynumber: 4.4 Consensus size: 84
586599 AGCTCAATTC
* * *
586609 CTAGTAAACTCTTTTACCTTTTGTTGACTTATCGATTCAGCCTTGGTCAACCTTTTATCCCTTGC
1 CTAGTAAACTCTTTTACCCTTTGTTGACTTATCGGTTCAGCCTTAGTCAACCTTTTATCCCTTGC
* *
586674 TTACCTAT-GAGTTTAGTCC
66 TTACCTATCG-GCTTAGTCT
* * * * *
586693 CTGGTAAACTCCTTAACCCTTTGTTGACTTATCGGTTCAGCCTTAGTTAACCATTTATCCCTTGC
1 CTAGTAAACTCTTTTACCCTTTGTTGACTTATCGGTTCAGCCTTAGTCAACCTTTTATCCCTTGC
* * * **
586758 TTACTTATTGGCTGAGTAG
66 TTACCTATCGGCTTAGTCT
* * * * * ** * **
586777 CTAGTGAACTCCTTTATCCTTTGTTGACTTATCGGTTTAGCCCTAGTCAATTTTTTAT-CTTTTT
1 CTAGTAAACTCTTTTACCCTTTGTTGACTTATCGGTTCAGCCTTAGTCAACCTTTTATCCCTTGC
* * * *
586841 TTACTTGTCGGCTCAATCT
66 TTACCTATCGGCTTAGTCT
* * * * *
586860 CTAGTAAACTCTTTTACCCGTTGTTGACTTATCGGTTTAGCCTTGGTCAACCTTTCATCCCTTGT
1 CTAGTAAACTCTTTTACCCTTTGTTGACTTATCGGTTCAGCCTTAGTCAACCTTTTATCCCTTGC
*
586925 TTACCTGTCGGCTTAGTCT
66 TTACCTATCGGCTTAGTCT
* * * * *
586944 CAAGTAAATTTTTTTATCCTTTGTTAACTT
1 CTAGTAAACTCTTTTACCCTTTGTTGACTT
586974 GTCAATTTTA
Statistics
Matches: 227, Mismatches: 52, Indels: 4
0.80 0.18 0.01
Matches are distributed among these distances:
83 65 0.29
84 161 0.71
85 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (84 bp):
CTAGTAAACTCTTTTACCCTTTGTTGACTTATCGGTTCAGCCTTAGTCAACCTTTTATCCCTTGC
TTACCTATCGGCTTAGTCT
Found at i:588155 original size:166 final size:164
Alignment explanation
Indices: 587845--588718 Score: 884
Period size: 166 Copynumber: 5.3 Consensus size: 164
587835 TTTTAATTCC
* * * * * *
587845 AAAATTCCTTAAATATTATAATTTAA-TCACCATTAAATCAGTTTTAAAAAATTTCTTTTATTTT
1 AAAATTCATCAAATATTATTATTTAATTCA-TATTAAATCAGTTTTCAAAAA-TTCATTTATTTT
** * * *
587909 -ATGAGTCATTGATTTTTT-TTAGAATTTTATTTATTTTCAAAAAACAGAGTTTTCTACTCCGTA
64 CATGAGTTTTTCATTTTTTCTT-GAATTCT-CTTATTTTCAAAAAACAGAGTTTTCTACTCCGTA
* * *
587972 AATATTTTCGAGGGGATTTTTTTTGGTTTTTAATTATT
127 AATATTTTCGGGGGGATTTTTCTTGGTTTTTAATTTTT
* * * *
588010 AAAGTTCATCAAATATTATCATTCAATTTATATTAAATCAGTTTTCAAAAATTCATTTATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTTATTTTCA
* * *
588075 TGAGTTTTTCATTTTTTCCTTGAATTGCTCTTATTTTCAAAAAACAGAGTTTTTTGCTCCGTCAA
66 TGAGTTTTTCATTTTTT-CTTGAATT-CTCTTATTTTCAAAAAACAGAGTTTTCTACTCCGTAAA
588140 TATTTTCGGGGGGATTTTTCTTGGTTTTTAATTTTT
129 TATTTTCGGGGGGATTTTTCTTGGTTTTTAATTTTT
* * * *
588176 AAAATTCATCAAATATTATTATTTAATTCATAATATATTAGCTTTCAAAAATTC----A--TTC-
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTTATTTTCA
* * * *
588234 --A-TTTTTCATTTTTTCCTTGAAATT-TCTTTGTTTTCAAAAAATAGAGCTTTCTACTCTGTAA
66 TGAGTTTTTCATTTTTT-CTTG-AATTCTC-TTATTTTCAAAAAACAGAGTTTTCTACTCCGTAA
* * *
588295 ATATTTTCGGGAGGATTTTTTTTGGTTTCTAATTTTT
128 ATATTTTCGGGGGGATTTTTCTTGGTTTTTAATTTTT
** * * * *
588332 AAAATTTTTCAAATATTATCATTTAATTCATACTAAATCAATTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTTATTTTCA
* * ** * *
588397 TTCA--TTTTCTATTTTTTCTTGAAATTCTCCTATTTTTGAAAAATAGAGTTTTCTGCTCCGTAA
66 -TGAGTTTTTC-ATTTTTTCTTG-AATTCTCTTATTTTCAAAAAACAGAGTTTTCTACTCCGTAA
* * *
588460 ATGTTTTCAAGGGGAATTTTTCTTGGTTTTTAATTTTT
128 ATATTTTC-GGGGGGATTTTTCTTGGTTTTTAATTTTT
* * *
588498 AAAATTCATCAAATATTATTATTTAATTTATATTAAAT-TGATTTCAAAAAATTCATTTATTTTC
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTC-AAAAATTCATTTATTTTC
* * * *
588562 ATGAGTTTTGCATTTTTTTATTTGAAATCCTTTTATTTTCAAAAAATCA-AGTTTTCTACTCCGT
65 ATGAGTTTTTCA-TTTTTT-CTTG-AATTCTCTTATTTTCAAAAAA-CAGAGTTTTCTACTCCGT
* **
588626 AAATGTTTTCGGGGGGATTTTTCCTTGGTTTAAAATTTTT
126 AAATATTTTCGGGGGGATTTTT-CTTGGTTTTTAATTTTT
* * * * * *
588666 AAAATTCATCTAATATTGTTATTAAATTCACATTGAATCAGTTTTGAAAAATT
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATT
588719 TTAATTATTT
Statistics
Matches: 590, Mismatches: 91, Indels: 53
0.80 0.12 0.07
Matches are distributed among these distances:
155 2 0.00
156 125 0.21
157 5 0.01
160 4 0.01
162 4 0.01
164 11 0.02
165 109 0.18
166 204 0.35
167 23 0.04
168 98 0.17
169 5 0.01
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (164 bp):
AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTTATTTTCA
TGAGTTTTTCATTTTTTCTTGAATTCTCTTATTTTCAAAAAACAGAGTTTTCTACTCCGTAAATA
TTTTCGGGGGGATTTTTCTTGGTTTTTAATTTTT
Found at i:588384 original size:322 final size:322
Alignment explanation
Indices: 587942--588718 Score: 895
Period size: 322 Copynumber: 2.4 Consensus size: 322
587932 ATTTTATTTA
* *
587942 TTTTCAAAAAACAGAGTTTTCTACTCCGTAAATATTTTCGAGGGGATTTTTTTTGGTTTTTAATT
1 TTTTCAAAAAACAGAGCTTTCTACTCCGTAAATATTTTCGAGGGGATTTTTTTTGGTTTCTAATT
* * * * *
588007 ATTAAAGTTCATCAAATATTATCATTCAATTTATATTAAATCAGTTTTCAAAAATTCATTTATTT
66 ATTAAAATTCATCAAATATTATCATTCAATTCATACTAAATCAATTTTCAAAAATTCATTCATTT
* * *
588072 TCA-TGAGTTTT-TCATTTTTTCCTTG-AATTGCTCTTATTTTCAAAAAACAGAGTTTTTTGCTC
131 TCATTCA-TTTTCT-ATTTTTT-CTTGAAATT-CTCCTATTTTCAAAAAACAGAGTTTTCTGCTC
* * *
588134 CGTCAATATTTTC-GGGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTAT
192 CGTAAATATTTTCAAGGGGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTAT
* *
588198 TTAATTCATAATATATTAGCTTTC-AAAAATTCATTCATTTTTCATTTTTTCCTTGAAATTTCTT
257 TTAATTCATAATAAATT-GATTTCAAAAAATTCATTCATTTTTCATTTTTTCCTTGAAATTTCTT
588262 TG
321 TG
* *
588264 TTTTCAAAAAATAGAGCTTTCTACTCTGTAAATATTTTCG-GGAGGATTTTTTTTGGTTTCTAAT
1 TTTTCAAAAAACAGAGCTTTCTACTCCGTAAATATTTTCGAGG-GGATTTTTTTTGGTTTCTAAT
* ** *
588328 TTTTAAAATTTTTCAAATATTATCATTTAATTCATACTAAATCAATTTTCAAAAATTCATTCATT
65 TATTAAAATTCATCAAATATTATCATTCAATTCATACTAAATCAATTTTCAAAAATTCATTCATT
** *
588393 TTCATTCATTTTCTATTTTTTCTTGAAATTCTCCTATTTTTGAAAAATAGAGTTTTCTGCTCCGT
130 TTCATTCATTTTCTATTTTTTCTTGAAATTCTCCTATTTTCAAAAAACAGAGTTTTCTGCTCCGT
*
588458 AAATGTTTTCAAGGGGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTA
195 AAATATTTTCAAGGGGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTA
* * **
588523 ATTTATATTAAATTGATTTCAAAAAATTCATTTATTTTCATGAGTTTTGCATTTTTTTATTTGAA
260 ATTCATAATAAATTGATTTCAAAAAATTC----A--TTCAT---TTTT-CA-TTTTTTCCTTGAA
* *
588588 A-TCCTTTTA
314 ATTTC-TTTG
* * * * **
588597 TTTTCAAAAAATCA-AGTTTTCTACTCCGTAAATGTTTTCGGGGGGATTTTTCCTTGGTTTAAAA
1 TTTTCAAAAAA-CAGAGCTTTCTACTCCGTAAATATTTTCGAGGGGATTTTT-TTTGGTTTCTAA
* * * * * * * * * *
588661 TTTTTAAAATTCATCTAATATTGTTATTAAATTCACATTGAATCAGTTTTGAAAAATT
64 TTATTAAAATTCATCAAATATTATCATTCAATTCATACTAAATCAATTTTCAAAAATT
588719 TTAATTATTT
Statistics
Matches: 385, Mismatches: 49, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
321 49 0.13
322 203 0.53
323 3 0.01
326 1 0.00
328 5 0.01
331 4 0.01
332 4 0.01
333 57 0.15
334 59 0.15
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (322 bp):
TTTTCAAAAAACAGAGCTTTCTACTCCGTAAATATTTTCGAGGGGATTTTTTTTGGTTTCTAATT
ATTAAAATTCATCAAATATTATCATTCAATTCATACTAAATCAATTTTCAAAAATTCATTCATTT
TCATTCATTTTCTATTTTTTCTTGAAATTCTCCTATTTTCAAAAAACAGAGTTTTCTGCTCCGTA
AATATTTTCAAGGGGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAA
TTCATAATAAATTGATTTCAAAAAATTCATTCATTTTTCATTTTTTCCTTGAAATTTCTTTG
Found at i:590372 original size:186 final size:184
Alignment explanation
Indices: 589920--590373 Score: 454
Period size: 186 Copynumber: 2.5 Consensus size: 184
589910 TTTAAAAGTC
* * **
589920 TTTAAAACTTTTTGTATCTTTTCAG-GTCTCCATTAAGGTACGAAATGATATTTTTGAAA-AGGA
1 TTTAAAACTTTTTCTATCTTTTCAGAGTCTCCATTAAGGTACGAAATGATATTTTTAAAATAAAA
* * * *
589983 AAT-AT-AT---TAAAATTAAATAAACAATGCATAAATATTATTTTATTGAATAAAAATTATTAT
66 AATAATAATAAATAAAATTAAATAAAAAATGAAAAAATATTATTTTA-T-AATAAAAATTAATAT
* * ** * *
590043 ACCTATTTTTCAGAATTTTTAATATTCCTATGGGCATCCGTAAGAGTATAAGAATT
129 ACCTATTTTTCAAAACTTCCAATATTCCTATGGGCATCCGTAAGAGTACAAAAATT
* * *
590099 TTCAAAAC-TTTTCATATC-TTTCTA-AGTCTCCTTTAAGGTACGAAATGATATTTTCGAAAATA
1 TTTAAAACTTTTTC-TATCTTTTC-AGAGTCTCCATTAAGGTACGAAATGATATTTT-TAAAATA
* *
590161 AACCAAAGTAA-AATTAAAT-AAATTAAATAAAAAATGAAAAAATATTCTTTTA-AATAAAATTT
63 AA--AAA-TAATAA-TAAATAAAATTAAATAAAAAATGAAAAAATATTATTTTATAATAAAAATT
* * *
590223 AATAT-CCTAATTTTTCAAAAACTTCCAATATTCCTATGGGCATTCGTAGGGGTACAAAAATT
124 AATATACCT-ATTTTTC-AAAACTTCCAATATTCCTATGGGCATCCGTAAGAGTACAAAAATT
*
590285 TTTAAAACTTTTTCTATCTTTTCAGAAT-TCCATTAAGGTAC-AGAATGATATTTTTAAAATAAT
1 TTTAAAACTTTTTCTATCTTTTCAGAGTCTCCATTAAGGTACGA-AATGATATTTTTAAAATAA-
590348 AATAATAATAATAAAATAAAATTAAA
64 AA-AATAATAAT-AAATAAAATTAAA
590374 CGTGGCAATA
Statistics
Matches: 224, Mismatches: 26, Indels: 43
0.76 0.09 0.15
Matches are distributed among these distances:
178 8 0.04
179 40 0.18
180 3 0.01
181 1 0.00
183 3 0.01
184 9 0.04
185 38 0.17
186 81 0.36
187 11 0.05
188 29 0.13
189 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (184 bp):
TTTAAAACTTTTTCTATCTTTTCAGAGTCTCCATTAAGGTACGAAATGATATTTTTAAAATAAAA
AATAATAATAAATAAAATTAAATAAAAAATGAAAAAATATTATTTTATAATAAAAATTAATATAC
CTATTTTTCAAAACTTCCAATATTCCTATGGGCATCCGTAAGAGTACAAAAATT
Found at i:591196 original size:21 final size:21
Alignment explanation
Indices: 591170--591224 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
591160 GTTACAAGCA
591170 ATGTATCGATACAACTT-AATC
1 ATGTATCGATACAA-TTGAATC
**
591191 ATGTATCGATAC-ATTGTCTC
1 ATGTATCGATACAATTGAATC
591211 ATGTATCGATACAA
1 ATGTATCGATACAA
591225 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 13 0.43
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGAATC
Found at i:591311 original size:13 final size:13
Alignment explanation
Indices: 591293--591319 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
591283 TACAATGAGC
591293 ATGTATCAATACA
1 ATGTATCAATACA
591306 ATGTATCAATACA
1 ATGTATCAATACA
591319 A
1 A
591320 AGCAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:598334 original size:3 final size:3
Alignment explanation
Indices: 598326--598350 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
598316 TCCGAGTCAC
598326 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
598351 TTCCTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:600681 original size:13 final size:13
Alignment explanation
Indices: 600663--600688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600653 CAATTTTTTG
600663 TGTATCGATACAT
1 TGTATCGATACAT
600676 TGTATCGATACAT
1 TGTATCGATACAT
600689 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:603254 original size:13 final size:13
Alignment explanation
Indices: 603236--603274 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
603226 ATAATCCTCC
*
603236 TGTATCGATACAG
1 TGTATCGATACAA
603249 TGTATCGATACAA
1 TGTATCGATACAA
603262 TGTATCGATACAA
1 TGTATCGATACAA
603275 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.