Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 139 of 190
Found at i:40926943 original size:70 final size:70
Alignment explanation
Indices: 40926753--40927389 Score: 863
Period size: 70 Copynumber: 9.1 Consensus size: 70
40926743 ATGTTCATGT
* *
40926753 AATTTTTATGCTTAAATGCTG-TCCAATTTGTTGTATTTATGCTGCCAAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
40926817 CTGTCC
65 CTGTCC
* * * * * * *
40926823 AATTTTGATG-TAAAATGCTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGCACATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
40926887 TGTCA
66 TGTCC
*
40926892 AATTTTTATGCTAAAATGTTG-TCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
*
40926956 TTGTCC
65 CTGTCC
* * * * * * *
40926962 AATTTTGATG-TAAAATGCTGCTCAATTTGGTATATATATGCTGCTCAAATTGTTGCACATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
40927026 TGTCA
66 TGTCC
* *
40927031 AATTTTTATGCTAAAATGCTG-TCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATATG
1 AATTTTTATGCTAAAATGCTGCT-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
*
40927095 CTGTCA
65 CTGTCC
* * *
40927101 AATTTTTATGCTAAAATGCTGCCCAATTTGTTGTATTTATGCTGCCTAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
40927166 TGTCC
66 TGTCC
* *
40927171 AATTTTTATGCTTAAATGATGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
40927236 TGTCT
66 TGTCC
* * * *
40927241 AATTTTGATG-TAAAAATGCTGCTCAATTTGGTATATATATAGGCTGCCCAAATTGTTGTATATA
1 AATTTTTATGCT-AAAATGCTGCTCAATTT-GT-TGTATTTATGCTGCCCAAATTGTTGTATATA
40927305 TGCTGTCC
63 TGCTGTCC
* *
40927313 AATTTTTATGCTAAAATGCTGCTCAATTTGATGTATATATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
40927378 TGTCC
66 TGTCC
40927383 AATTTTT
1 AATTTTT
40927390 GGTGTGAAAA
Statistics
Matches: 499, Mismatches: 57, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
69 118 0.24
70 316 0.63
71 3 0.01
72 61 0.12
73 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (70 bp):
AATTTTTATGCTAAAATGCTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
TGTCC
Found at i:40927003 original size:139 final size:139
Alignment explanation
Indices: 40926753--40927419 Score: 991
Period size: 139 Copynumber: 4.8 Consensus size: 139
40926743 ATGTTCATGT
* *
40926753 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCAAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
40926818 TGTCCAATTTTGATGTAAAATGCTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGCACAT
66 TGTCCAATTTTGATGTAAAATGCTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGCACAT
40926883 ATGCTGTCA
131 ATGCTGTCA
* *
40926892 AATTTTTATGCTAAAATGTTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGT
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
40926957 TGTCCAATTTTGATGTAAAATGCTGCTCAATTTGGTATATATATGCTG-CTCAAATTGTTGCACA
66 TGTCCAATTTTGATGTAAAATGCTGCTCAATTTGGTATATATATGCTGCCT-AAATTGTTGCACA
40927021 TATGCTGTCA
130 TATGCTGTCA
* *
40927031 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
* * * * * * *
40927096 TGTCAAATTTTTATGCTAAAATGCTGCCCAATTTGTTGTATTTATGCTGCCTAAATTGTTGCATA
66 TGTCCAATTTTGATG-TAAAATGCTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGCACA
*
40927161 TATGCTGTCC
130 TATGCTGTCA
* *
40927171 AATTTTTATGCTTAAATGATG-CTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGTC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
* * *
40927235 CTGTCTAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATAGGCTGCCCAAATTGTTGT
65 CTGTCCAATTTTGATGT-AAAATGCTGCTCAATTTGGTATATATAT--GCTGCCTAAATTGTTGC
* *
40927300 ATATATGCTGTCC
127 ACATATGCTGTCA
* *
40927313 AATTTTTATGCTAAAATGCTG-CTCAATTTGATGTATATATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGTC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
* *
40927377 CTGTCCAATTTTTGGTGTGAAAATGCTG-TCTAGTTTGGTATAT
65 CTGTCCAA-TTTTGATGT-AAAATGCTGCTC-AATTTGGTATAT
40927420 GAACGCTGTC
Statistics
Matches: 483, Mismatches: 36, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
138 2 0.00
139 208 0.43
140 146 0.30
141 2 0.00
142 97 0.20
143 28 0.06
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (139 bp):
AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
TGTCCAATTTTGATGTAAAATGCTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGCACAT
ATGCTGTCA
Found at i:40927212 original size:47 final size:48
Alignment explanation
Indices: 40926753--40927387 Score: 309
Period size: 47 Copynumber: 13.6 Consensus size: 48
40926743 ATGTTCATGT
* * *
40926753 AATTTTTATGCT-TAAATGCTG-TCCAATTTGTTGTATTTATGCTGCCA
1 AATTTGTATGCTATAAATGCTGCT-CAATTTGTTGTATATATGCTGCCC
* * * * *
40926800 AAATTGT-TG-TATATATGCTG-TCCAATTTTGATGTA-AAATGCTGCTC
1 AATTTGTATGCTATAAATGCTGCT-CAA-TTTGTTGTATATATGCTGCCC
* * * * * *
40926846 AATTTGGTA---TATATATGCTGC-CTAAATTGTTGCACATATGCTGTCA
1 AATTT-GTATGCTATAAATGCTGCTC-AATTTGTTGTATATATGCTGCCC
* * *
40926892 AATTTTTATGCTA-AAATGTTG-TCCAATTTGTTGTATTTATGCTGCCC
1 AATTTGTATGCTATAAATGCTGCT-CAATTTGTTGTATATATGCTGCCC
* * * * * *
40926939 AAATTGT-TG-TATATATGTTG-TCCAATTTTGATGTA-AAATGCTGCTC
1 AATTTGTATGCTATAAATGCTGCT-CAA-TTTGTTGTATATATGCTGCCC
* * * * * *
40926985 AATTTGGTA---TATATATGCTGCTCAAATTGTTGCACATATGCTGTCA
1 AATTT-GTATGCTATAAATGCTGCTCAATTTGTTGTATATATGCTGCCC
* *
40927031 AATTTTTATGCTA-AAATGCTG-TCCAATTTGTTGTATTTATGCTGCCC
1 AATTTGTATGCTATAAATGCTGCT-CAATTTGTTGTATATATGCTGCCC
* * * * *
40927078 AAATTG-GTGC-ATATATGCTG-TCAAATTTTTATGCTA-AAATGCTGCCC
1 AATTTGTATGCTATAAATGCTGCTC-AATTTGT-TG-TATATATGCTGCCC
** * * *
40927125 AATTTGT-TG-TATTTATGCTGC-CTAAATTGTTGCATATATGCTGTCC
1 AATTTGTATGCTATAAATGCTGCTC-AATTTGTTGTATATATGCTGCCC
* * *
40927171 AATTTTTATGCT-TAAATGATGCTCAATTTGTTGTATTTATGCTGCCC
1 AATTTGTATGCTATAAATGCTGCTCAATTTGTTGTATATATGCTGCCC
* * * * * *
40927218 AAATTGT-TG-TATATATGCTG-TCTAATTTTGATGTAAAAATGCTGCTC
1 AATTTGTATGCTATAAATGCTGCTC-AA-TTTGTTGTATATATGCTGCCC
* * * * * *
40927265 AATTTGGTAT-ATATATAGGCTGCCCAAATTGTTGTATATATGCTGTCC
1 AATTT-GTATGCTATAAATGCTGCTCAATTTGTTGTATATATGCTGCCC
* *
40927313 AATTTTTATGCTA-AAATGCTGCTCAATTTGATGTATATATGCTGCCC
1 AATTTGTATGCTATAAATGCTGCTCAATTTGTTGTATATATGCTGCCC
* *
40927360 AAATTGT-TG-TATATATGCTG-TCCAATTT
1 AATTTGTATGCTATAAATGCTGCT-CAATTT
40927388 TTGGTGTGAA
Statistics
Matches: 444, Mismatches: 101, Indels: 87
0.70 0.16 0.14
Matches are distributed among these distances:
45 29 0.07
46 163 0.37
47 205 0.46
48 33 0.07
49 13 0.03
50 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (48 bp):
AATTTGTATGCTATAAATGCTGCTCAATTTGTTGTATATATGCTGCCC
Found at i:40927287 original size:25 final size:25
Alignment explanation
Indices: 40927258--40927305 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40927248 ATGTAAAAAT
* *
40927258 GCTGCTCAATTTGGTATATATATAG
1 GCTGCCCAAATTGGTATATATATAG
* *
40927283 GCTGCCCAAATTGTTGTATATAT
1 GCTGCCCAAATTGGTATATATAT
40927306 GCTGTCCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (25 bp):
GCTGCCCAAATTGGTATATATATAG
Found at i:40928591 original size:20 final size:18
Alignment explanation
Indices: 40928535--40928593 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
40928525 TTAATTTAAA
* * *
40928535 TTTAATATGCATAATTAA
1 TTTAATATACACAATTAT
*
40928553 ATTAATATACACAATTAT
1 TTTAATATACACAATTAT
*
40928571 TTTAATATTCAC-ATTAT
1 TTTAATATACACAATTAT
40928588 TATTAA
1 T-TTAA
40928594 ATTAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 6 0.18
18 28 0.82
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAATATACACAATTAT
Found at i:40928593 original size:18 final size:19
Alignment explanation
Indices: 40928553--40928593 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
40928543 GCATAATTAA
40928553 ATTAATATACACAATTATT
1 ATTAATATACACAATTATT
*
40928572 -TTAATATTCAC-ATTATT
1 ATTAATATACACAATTATT
40928589 ATTAA
1 ATTAA
40928594 ATTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATATACACAATTATT
Found at i:40929919 original size:35 final size:36
Alignment explanation
Indices: 40929862--40929929 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
40929852 TTATGCTGCC
*
40929862 TATTGTCCTTTTTATGTCTTTTATTTGTTTTTTCTT
1 TATTGTCCTTTGTATGTCTTTTATTTGTTTTTTCTT
* * *
40929898 TATT-TCCTTTGTCTGTTTTTTATTTTTTTTTT
1 TATTGTCCTTTGTATGTCTTTTATTTGTTTTTT
40929930 GTCCTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.75
Consensus pattern (36 bp):
TATTGTCCTTTGTATGTCTTTTATTTGTTTTTTCTT
Found at i:40929924 original size:30 final size:28
Alignment explanation
Indices: 40929889--40929960 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
40929879 CTTTTATTTG
*
40929889 TTTTTTCTTTATTTCCTTTGTCTGTTTT
1 TTTTTTTTTTATTTCCTTTGTCTGTTTT
*
40929917 TTATTTTTTTT-TTGTCCTTTTTCTGTTTT
1 TT-TTTTTTTTATT-TCCTTTGTCTGTTTT
*
40929946 TTTATTTGTTTATTT
1 TTT-TTTTTTTATTT
40929961 GTTTATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.14
29 30 0.81
30 2 0.05
ACGTcount: A:0.06, C:0.10, G:0.07, T:0.78
Consensus pattern (28 bp):
TTTTTTTTTTATTTCCTTTGTCTGTTTT
Found at i:40930911 original size:25 final size:25
Alignment explanation
Indices: 40930870--40930926 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
40930860 ACAATCCATG
** * *
40930870 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
40930895 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
40930920 TATATCA
1 TAAATCA
40930927 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:40931220 original size:23 final size:22
Alignment explanation
Indices: 40931167--40931255 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 22
40931157 CCATGATCGA
40931167 TAAGCTCATTCTGAGCTGATAAACGG
1 TAAGCTCA-TC-GAGCTG--AAACGG
*
40931193 TAAGCTCTATCGAGCTGAAATGG
1 TAAGCTC-ATCGAGCTGAAACGG
*
40931216 TAAGCTCCATAGAGCTGAAACGG
1 TAAGCT-CATCGAGCTGAAACGG
40931239 TAAGCTCATACGAGCTG
1 TAAGCTCAT-CGAGCTG
40931256 TGGTGAGTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
22 3 0.05
23 36 0.64
24 1 0.02
25 6 0.11
26 9 0.16
27 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (22 bp):
TAAGCTCATCGAGCTGAAACGG
Found at i:40932778 original size:20 final size:19
Alignment explanation
Indices: 40932755--40932796 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
40932745 TTTGTGTTTT
40932755 TTTTTTTAAATTTGAAGGTA
1 TTTTTTT-AATTTGAAGGTA
40932775 TTTTTTTAATTTGAAGGTA
1 TTTTTTTAATTTGAAGGTA
40932794 TTT
1 TTT
40932797 AATGTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (19 bp):
TTTTTTTAATTTGAAGGTA
Found at i:40938850 original size:213 final size:213
Alignment explanation
Indices: 40938483--40938877 Score: 754
Period size: 213 Copynumber: 1.9 Consensus size: 213
40938473 ATCTATTTAG
40938483 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
1 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
* *
40938548 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTGATAACCCCAGCCCATTC
66 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTCATAACCCCAACCCATTC
40938613 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAGTAAAGCAAGAACTAAGAAAT
131 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAGTAAAGCAAGAACTAAGAAAT
40938678 AGATCTACTAATTCTTTC
196 AGATCTACTAATTCTTTC
* *
40938696 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCGCTGTTTCGGTATGGAATAAAC
1 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
40938761 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTCATAACCCCAACCCATTC
66 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTCATAACCCCAACCCATTC
40938826 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAGTAAAGCA
131 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAGTAAAGCA
40938878 GGATCTTTAA
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
213 178 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (213 bp):
ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTCATAACCCCAACCCATTC
CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAGTAAAGCAAGAACTAAGAAAT
AGATCTACTAATTCTTTC
Found at i:40947639 original size:2 final size:2
Alignment explanation
Indices: 40947632--40947658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40947622 GGTAACAATT
40947632 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40947659 CTTTATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40954687 original size:23 final size:22
Alignment explanation
Indices: 40954640--40954690 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
40954630 GGAGAGGTAG
40954640 AAAAAGCTTACTTTAATGGACAGA
1 AAAAAGCTTACTTTAA--GACAGA
40954664 AAAAAGCTTACTTTGAA-ACAAGA
1 AAAAAGCTTACTTT-AAGAC-AGA
40954687 AAAA
1 AAAA
40954691 TAAAAGGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 14 0.56
25 2 0.08
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (22 bp):
AAAAAGCTTACTTTAAGACAGA
Found at i:40955500 original size:22 final size:22
Alignment explanation
Indices: 40955472--40955514 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40955462 TTTATTGTTC
40955472 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
40955494 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
40955515 TAGCGTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:40959517 original size:19 final size:20
Alignment explanation
Indices: 40959487--40959524 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40959477 TCAAAACGAA
40959487 AAAAGAAAAATAATTTCTAT
1 AAAAGAAAAATAATTTCTAT
*
40959507 AAAAG-AAAATACTTTCTA
1 AAAAGAAAAATAATTTCTA
40959525 CAAGGCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAGAAAAATAATTTCTAT
Found at i:40960866 original size:20 final size:21
Alignment explanation
Indices: 40960825--40960866 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
40960815 ATATAATAAA
40960825 TAAATATATATTTTTTAATTT
1 TAAATATATATTTTTTAATTT
* *
40960846 TAAA-ATATTTTTTTTATTTT
1 TAAATATATATTTTTTAATTT
40960866 T
1 T
40960867 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TAAATATATATTTTTTAATTT
Found at i:40960885 original size:26 final size:26
Alignment explanation
Indices: 40960822--40960886 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
40960812 AATATATAAT
* *
40960822 AAATAAATATATATTTTTTAATTTTA
1 AAATAAATTTTTATTTTTTAATTTTA
** *
40960848 AAATATTTTTTTTATTTTTTATTTTTA
1 AAATA-AATTTTTATTTTTTAATTTTA
40960875 AAATAAATTTTT
1 AAATAAATTTTT
40960887 GGTGTTTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
AAATAAATTTTTATTTTTTAATTTTA
Found at i:40960885 original size:27 final size:27
Alignment explanation
Indices: 40960833--40960886 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
40960823 AATAAATATA
**
40960833 TATTTTTTAATTTTAAAATATTTTTTT
1 TATTTTTTAATTTTAAAATAAATTTTT
*
40960860 TATTTTTTATTTTTAAAATAAATTTTT
1 TATTTTTTAATTTTAAAATAAATTTTT
40960887 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TATTTTTTAATTTTAAAATAAATTTTT
Found at i:40969139 original size:12 final size:12
Alignment explanation
Indices: 40969122--40969147 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40969112 CAAGATAACC
40969122 AAAAGATGTACA
1 AAAAGATGTACA
40969134 AAAAGATGTACA
1 AAAAGATGTACA
40969146 AA
1 AA
40969148 CAACTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAAGATGTACA
Found at i:40970361 original size:33 final size:33
Alignment explanation
Indices: 40970319--40970388 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
40970309 TTTTGTTGTA
40970319 AATGAGTAGTTGTCGTAGTGGTTAAGTGGTGTC
1 AATGAGTAGTTGTCGTAGTGGTTAAGTGGTGTC
*
40970352 AATGAGTAGTTGTCGTAGTGGTTGAGTGGTGTC
1 AATGAGTAGTTGTCGTAGTGGTTAAGTGGTGTC
40970385 AATG
1 AATG
40970389 TAGGTAAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.21, C:0.06, G:0.37, T:0.36
Consensus pattern (33 bp):
AATGAGTAGTTGTCGTAGTGGTTAAGTGGTGTC
Found at i:40977516 original size:24 final size:25
Alignment explanation
Indices: 40977489--40977541 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
40977479 AAAATCTTCT
*
40977489 CCTTCA-A-AATTTTCACAATTTTC
1 CCTTCACATAATTTGCACAATTTTC
40977512 ACCTTCACATAATTTGCACAATTTTC
1 -CCTTCACATAATTTGCACAATTTTC
40977538 CCTT
1 CCTT
40977542 TCATATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.23
25 5 0.19
26 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (25 bp):
CCTTCACATAATTTGCACAATTTTC
Found at i:40982507 original size:59 final size:59
Alignment explanation
Indices: 40982440--40982628 Score: 213
Period size: 59 Copynumber: 3.2 Consensus size: 59
40982430 AGTGGGGGGA
40982440 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
* * ** * * * * * *
40982499 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
1 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
*
40982560 ATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
40982619 ATTATATATT
1 ATTATATATT
40982629 ATGATTTTAG
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
58 7 0.07
59 42 0.42
60 14 0.14
61 31 0.31
62 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (59 bp):
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
Found at i:40982564 original size:61 final size:61
Alignment explanation
Indices: 40982499--40982687 Score: 217
Period size: 61 Copynumber: 3.1 Consensus size: 61
40982489 ATTTTATAGT
40982499 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * * ** * * * * * *
40982560 ATTATATATTTTTAATAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
40982619 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
40982680 ATTATATA
1 ATTATATA
40982688 NNNNNNNNNN
Statistics
Matches: 98, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 7 0.07
59 31 0.32
60 14 0.14
61 39 0.40
62 7 0.07
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:40982573 original size:120 final size:120
Alignment explanation
Indices: 40982439--40982687 Score: 489
Period size: 120 Copynumber: 2.1 Consensus size: 120
40982429 AAGTGGGGGG
*
40982439 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
40982504 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
40982559 AATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
40982624 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
40982679 AATTATATA
1 AATTATATA
40982688 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
AATTATATATTTTTAATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
Found at i:40982659 original size:59 final size:59
Alignment explanation
Indices: 40982476--40982659 Score: 203
Period size: 59 Copynumber: 3.1 Consensus size: 59
40982466 TAATAATAAT
40982476 TATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
1 TATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
* * * * * ** * * * *
40982535 TA-TTTAATATTAAGAATTTTATTA-AATTATATATTTTTAATAAATTATATTTA-ATAATAA
1 TATTTTAA-ATT-A-TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
40982595 TTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
1 -TATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
40982655 TATTT
1 TATTT
40982660 AATATTAAGA
Statistics
Matches: 95, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 7 0.07
59 36 0.38
60 14 0.15
61 31 0.33
62 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (59 bp):
TATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA
Found at i:40982686 original size:59 final size:59
Alignment explanation
Indices: 40982503--40982686 Score: 200
Period size: 56 Copynumber: 3.1 Consensus size: 59
40982493 TATAGTATTA
40982503 TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
* * * * * *
40982562 TATA-TAT--TTTTAATAAATT-ATATTTAATAATAATT-ATTTTAAATTATATTTTA-TAGTAT
1 TATATTATGATTTTAGTAAATTCATA--TAAGAATATTTAATATT-AA-GA-ATTTTATTA--AA
40982621 T
59 T
40982622 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 -TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
40982682 TATAT
1 TATAT
40982687 ANNNNNNNNN
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
55 3 0.03
56 15 0.15
57 11 0.11
58 6 0.06
59 15 0.15
60 4 0.04
61 10 0.10
62 6 0.06
63 11 0.11
64 15 0.15
65 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (59 bp):
TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
Found at i:40982979 original size:44 final size:45
Alignment explanation
Indices: 40982916--40983009 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
40982906 GTTATTACAC
*
40982916 TTCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTA
1 TTCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTA
* *
40982960 TTCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTA
1 TTCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTA
40983005 TTCCA
1 TTCCA
40983010 ATATAGTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.53
45 20 0.44
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (45 bp):
TTCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTA
Found at i:40983624 original size:6 final size:6
Alignment explanation
Indices: 40983613--40983658 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
40983603 TGCCCTTACC
40983613 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAA
1 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAA
40983659 GGTCTCTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:40983759 original size:2 final size:2
Alignment explanation
Indices: 40983752--40983783 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40983742 CCTTCGCCAA
40983752 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40983784 ACTTATTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40985148 original size:3 final size:3
Alignment explanation
Indices: 40985140--40985172 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40985130 AATTTTGGTT
40985140 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40985173 AAAGAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40996910 original size:14 final size:14
Alignment explanation
Indices: 40996891--40996919 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40996881 AGAGTAGCAT
40996891 ACTTTTTTTTGGAC
1 ACTTTTTTTTGGAC
40996905 ACTTTTTTTTGGAC
1 ACTTTTTTTTGGAC
40996919 A
1 A
40996920 ATGTGCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (14 bp):
ACTTTTTTTTGGAC
Found at i:41001033 original size:45 final size:45
Alignment explanation
Indices: 41000974--41001126 Score: 243
Period size: 45 Copynumber: 3.4 Consensus size: 45
41000964 CACCAGTATA
* * *
41000974 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
41001020 CTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
41001065 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
41001110 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
41001127 GTCGGCACAT
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 94 0.95
46 5 0.05
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:41001150 original size:38 final size:39
Alignment explanation
Indices: 41000978--41001153 Score: 149
Period size: 45 Copynumber: 4.2 Consensus size: 39
41000968 AGTATACAGT
* * *
41000978 AATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
*
41001017 AACCTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AA----T--CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
41001062 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 A------ATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
41001107 AATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCC-G
41001146 -ATCAGTAA
1 AATCAGTAA
41001154 GCCGGCAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
38 15 0.13
39 28 0.24
43 1 0.01
45 72 0.62
51 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
Found at i:41003379 original size:90 final size:90
Alignment explanation
Indices: 41003087--41003363 Score: 367
Period size: 90 Copynumber: 3.1 Consensus size: 90
41003077 GATTAATAAT
* * * * * * * *
41003087 CTGCAACTCTGGTGATTCATCCA-CAACTTATCTAGAAACTTTAATCTGCAAATATGTTGTGCAT
1 CTGCAACACTGGTGGTTCATCCACCCACAT-TCTGGAAACTCTCATATGCAAATATGTTGTGCAT
*
41003151 TCACAACCATCTGACAACGTATTAAC
65 TCACAACCATCTGACAGCGTATTAAC
* * * * *
41003177 TTGCAACACTGGTGGTTCATCCACCCATATTCTGGTAACTCTTATATGCAAATATGTTGTGTATT
1 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTCTCATATGCAAATATGTTGTGCATT
*
41003242 CAGAACCATCTGACAGCGTATTAAC
66 CACAACCATCTGACAGCGTATTAAC
41003267 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTCTCATATGCAAATATGTTGTGCATT
1 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTCTCATATGCAAATATGTTGTGCATT
** *
41003332 CACAACCATCTGGTAGCATATTAAC
66 CACAACCATCTGACAGCGTATTAAC
*
41003357 CTACAAC
1 CTGCAAC
41003364 TTTTGCCGTT
Statistics
Matches: 162, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
90 159 0.98
91 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (90 bp):
CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTCTCATATGCAAATATGTTGTGCATT
CACAACCATCTGACAGCGTATTAAC
Found at i:41013268 original size:43 final size:43
Alignment explanation
Indices: 41013220--41013440 Score: 343
Period size: 43 Copynumber: 5.1 Consensus size: 43
41013210 CGGCGTTTAT
*
41013220 GCTAAAGAACATGATCTTTAACGGCGCTTTACCCACAAACGCC
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
41013263 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
* * *
41013306 GCTAAAGAACATGATCTTTAGCGGCGCTTTACTCATAAACGCT
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
* * *
41013349 GCTAAAGAACATGATCTGTAGCAGCGCTTTACCCACAAACGTC
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
* * * *
41013392 GCTAAAGAACATGACCTTTAGCGACGCTTTACGCGCAAACGCC
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
41013435 GCTAAA
1 GCTAAA
41013441 AGTACGTTCT
Statistics
Matches: 161, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 161 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (43 bp):
GCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCC
Found at i:41018170 original size:16 final size:16
Alignment explanation
Indices: 41018149--41018195 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
41018139 AATTCCTAAA
41018149 CCCTAACCACTAAATC-
1 CCCTAACC-CTAAATCT
41018165 CCCTAACCCATAAATCT
1 CCCTAACCC-TAAATCT
41018182 CCCTAACCTCTAAA
1 CCCTAACC-CTAAA
41018196 GCATAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 12 0.43
18 1 0.04
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (16 bp):
CCCTAACCCTAAATCT
Found at i:41018711 original size:114 final size:114
Alignment explanation
Indices: 41018451--41019132 Score: 870
Period size: 114 Copynumber: 5.9 Consensus size: 114
41018441 CAAATTATTT
* * *
41018451 TAAATCCCTGAGCATTAGCGGCGCTT-TTGTAAAAACGCCGCTAAATCCCCGAAATCTCAAAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAA
* * *
41018515 CGGCGCCGTTGAGTTTAGTTTTTTTTTACGGCGCTTTCCCAAAAACGCCGC
65 CGGCGCCGTTGGGCTTAG-TTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
*
41018566 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAC
* * *
41018631 GGCGTCGTTGTGTTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
41018680 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCT-AAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAA-AAAA
41018744 CGGCGCCGTTGGGCTTAGTTTTTTTTTGCGGCGC-TTCCCAAAAACGCCGC
65 CGGCGCCGTTGGGCTTAG-TTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
41018794 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAC
** * *
41018859 TACGTCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACACCGC
66 GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * ** * *
41018908 TAAAGCCCTGAGCATTAGCGGTGCTTTCTTAAAAACATCGCTAAATCCACGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAC
* * *
41018973 GGCGCCATTGGGCTTAG-TTTTTTTGCGGC-ATTTCAGCAAAAACGCCGC
66 GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTC-CCAAAAACGCCGC
* * * *
41019021 TAAATCCCTGAGCATTAGCGGAGCGTTAGCGGCGTTTTTTAGAAAGCGCCGCTAAATCACCGAAA
1 TAAAGCCCTGAGCATTAGCGGCGC-TT--C--C-----TTA-AAAACGCCGCTAAATCCCCGAAA
* * * * * *
41019086 GCTCAGAAAACGGTGTCGTTTGGCTTAGGTTTTTTTGTGGCGCTTTC
55 GCTCAAAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTC
41019133 TTAAAAGCAC
Statistics
Matches: 505, Mismatches: 43, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
112 4 0.01
113 62 0.12
114 286 0.57
115 91 0.18
116 1 0.00
118 1 0.00
123 3 0.01
124 42 0.08
125 11 0.02
126 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAC
GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:41019809 original size:50 final size:50
Alignment explanation
Indices: 41019753--41019982 Score: 280
Period size: 50 Copynumber: 4.5 Consensus size: 50
41019743 GGTCTTACAT
** *
41019753 GACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAATGCTATGTCCCA
1 GACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGCCATGTCCCA
** *
41019803 GACATGGTCTTACATGGGACCTCTCATCGCGGTGCCAACGCCATGTCCCA
1 GACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGCCATGTCCCA
* * * * *
41019853 TACATGGTCTTACACGAGACCTCTCATCTTGTTGCCAAAGCCATGTCCCA
1 GACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGCCATGTCCCA
* *
41019903 GACATGGTTTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCA
1 GACATGGTCTTACATGGGACCTCTC---ATCT---TGGTGCCAATGCCATGTCCCA
*
41019959 GACATGGTCTTACATGGGATCTCT
1 GACATGGTCTTACATGGGACCTCT
41019983 TTACCTAAAT
Statistics
Matches: 153, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 108 0.71
53 4 0.03
56 41 0.27
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
GACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGCCATGTCCCA
Found at i:41023623 original size:44 final size:44
Alignment explanation
Indices: 41023575--41023705 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 44
41023565 CTTCGATCTG
*
41023575 CTCCACTACTGCTTAGGGAGGTAAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
* * * * * * * *
41023619 CTCCACTGCTG-TTCAGGGAGACAAG-GCTG-AGGTCTTCGATCTG
1 CTCCACTACTGCTT-AGGGAGATAAGATCTGTA-ATTTTCAACCTA
*
41023662 CTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
41023706 ATTCACTGCT
Statistics
Matches: 64, Mismatches: 18, Indels: 10
0.70 0.20 0.11
Matches are distributed among these distances:
42 1 0.02
43 31 0.48
44 31 0.48
45 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
Found at i:41023658 original size:87 final size:87
Alignment explanation
Indices: 41023563--41023721 Score: 282
Period size: 87 Copynumber: 1.8 Consensus size: 87
41023553 TAGGATTAGA
* * *
41023563 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGGTAAGATCTGTAATTTTCAACCTACTCCACTGC
1 GTCTTCGATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAATCCACTGC
41023628 TGTTCAGGGAGACAAGGCTGAG
66 TGTTCAGGGAGACAAGGCTGAG
*
41023650 GTCTTCGATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAATTCACTGC
1 GTCTTCGATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAATCCACTGC
41023715 TGTTCAG
66 TGTTCAG
41023722 AGAGCTAGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
GTCTTCGATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAATCCACTGC
TGTTCAGGGAGACAAGGCTGAG
Found at i:41023680 original size:43 final size:44
Alignment explanation
Indices: 41023562--41023693 Score: 117
Period size: 44 Copynumber: 3.0 Consensus size: 44
41023552 ATAGGATTAG
** *
41023562 AGTCTTCGATCTGCTCCACTACTGCTTAGGGAGGTAAGATCTGT
1 AGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGAGCTGT
* * * * * *
41023606 AATTTTCAACCTACTCCACTGCTG-TTCAGGGAGACAAG-GCTG-
1 AGTCTTCGATCTGCTCCACTACTGCTT-AGGGAGACAAGAGCTGT
* * *
41023648 AGGTCTTCGATCTGCTCCAATACTGCTTAGGGAGATAAGATCTGT
1 A-GTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGAGCTGT
41023693 A
1 A
41023694 ATTTTCAACC
Statistics
Matches: 65, Mismatches: 18, Indels: 9
0.71 0.20 0.10
Matches are distributed among these distances:
42 1 0.02
43 31 0.48
44 32 0.49
45 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (44 bp):
AGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGAGCTGT
Found at i:41023766 original size:44 final size:44
Alignment explanation
Indices: 41023739--41024043 Score: 448
Period size: 44 Copynumber: 6.9 Consensus size: 44
41023729 GGACATGCAA
* * ** * *
41023739 TCTTCCACCTATTCCATTGCTGGTCAGAGAGTTAGGACTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
*
41023783 TCTTCCACTTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
* *
41023827 CCTTCCACCTATTCCACTGCTGGTCAGAGAACTAGGGCTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
* * *
41023871 TCTTCCACCTATTCCAACTGCTGGTCAGGGAACTAAGACTTACAT
1 TCTTCCACCTATTCC-ACTGCTGGTCAGGGAACTAGGGCTTACAG
* *
41023916 TCTTCCACCTATTCCACTGCTGGTTAGGGAGCTAGGGCTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
* *
41023960 TCTTCCACTTATTCCACTGCTGGTCAGGGAACTAGGGCTTACTG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
*
41024004 TCTTCCACCTATTTCACTGCTGGTCAGGGAACTAGGGCTT
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTT
41024044 GTGATTTCAC
Statistics
Matches: 234, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
44 194 0.83
45 40 0.17
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAG
Found at i:41025407 original size:47 final size:46
Alignment explanation
Indices: 41025339--41025428 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 46
41025329 TCATTTTTCA
* * *
41025339 TTTTTTGGACTCAAAGTGCCCTTTGAGGGTTTTCACTTTGATCTTT
1 TTTTTTGAACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATCTTT
*
41025385 TTTTTTCGAACTCAAAGCGCCCTTTGTGGGTTTTCACCTTGATC
1 TTTTTT-GAACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATC
41025429 CCTTCTCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 6 0.15
47 33 0.85
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (46 bp):
TTTTTTGAACTCAAAGCGCCCTTTGAGGGTTTTCACCTTGATCTTT
Found at i:41030922 original size:6 final size:6
Alignment explanation
Indices: 41030907--41030963 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
41030897 ATTGAAATTC
* * **
41030907 AAAA-A AAAATA AAAATA AAAATA AAACACTA CAAATA GAAATA AAAGGA
1 AAAATA AAAATA AAAATA AAAATA AAA-A-TA AAAATA AAAATA AAAATA
41030956 AAAATA AA
1 AAAATA AA
41030964 GGTGAACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
5 4 0.10
6 32 0.76
7 2 0.05
8 4 0.10
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:41031225 original size:22 final size:22
Alignment explanation
Indices: 41031195--41031247 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
41031185 CAGAGTGAGC
*
41031195 GGATCTGGGACCGGATCGGGTT
1 GGATTTGGGACCGGATCGGGTT
41031217 GGATTTGGGACCGGATCGGGTT
1 GGATTTGGGACCGGATCGGGTT
41031239 GGATCTTGG
1 GGAT-TTGG
41031248 TTCAATGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.13, C:0.15, G:0.45, T:0.26
Consensus pattern (22 bp):
GGATTTGGGACCGGATCGGGTT
Found at i:41031565 original size:20 final size:19
Alignment explanation
Indices: 41031536--41031573 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41031526 GTTTTGCAAA
41031536 GAAGAAAGAAAAAAGAGAAC
1 GAAGAAAGAAAAAA-AGAAC
*
41031556 GAAGAGAGAAAAAAAGAA
1 GAAGAAAGAAAAAAAGAA
41031574 AATCGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (19 bp):
GAAGAAAGAAAAAAAGAAC
Found at i:41042641 original size:83 final size:84
Alignment explanation
Indices: 41042543--41042904 Score: 292
Period size: 83 Copynumber: 4.3 Consensus size: 84
41042533 TCTTCTATTT
41042543 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCT-CTCTGCAACCTCAGAAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCCTCTGCAACCTCAGAAAGAT
*
41042607 AAGATCTAGATGTTAATCC
66 AAGATCTGGATGTTAATCC
* * *** * * * **
41042626 GCTCCACTACAACTTCAGGGAGATAGGATTAACTTCTTCTG-TCTGCTCCCCTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATA--A--GACTGGATGTGATCTGCTCCTCTGCAACCTCAGAA
** *
41042690 AGATAAGA-CTGGATG-CGATCT
62 AGATAAGATCTGGATGTTAATCC
* * ** * * * * **
41042711 GCT-CTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAG
1 GCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATG-TGATCTGCTCCTCTGCAACCTCAGAAAG
* **
41042775 ATAGGAT-T-GAT-TTCTTCTGTC
64 ATAAGATCTGGATGTTAATC---C
* ** *
41042796 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCT-CTCTACAACCTCAGAAAGA
1 -GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCCTCTGCAACCTCAGAAAGA
41042860 TAAGATCTGGATGTTAATCC
65 TAAGATCTGGATGTTAATCC
41042880 GCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
41042905 GGATTGATTT
Statistics
Matches: 212, Mismatches: 49, Indels: 36
0.71 0.16 0.12
Matches are distributed among these distances:
80 1 0.00
81 3 0.01
82 7 0.03
83 78 0.37
84 36 0.17
85 14 0.07
86 23 0.11
87 50 0.24
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCCTCTGCAACCTCAGAAAGAT
AAGATCTGGATGTTAATCC
Found at i:41042646 original size:127 final size:127
Alignment explanation
Indices: 41042412--41043081 Score: 1178
Period size: 127 Copynumber: 5.3 Consensus size: 127
41042402 GCTATTTTTA
*
41042412 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
*
41042477 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * *
41042539 ATTTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
* * * *
41042604 GATAAGATCTAGATGTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAACTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
*
41042666 GTCTGCTCCCCTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
41042731 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * *
41042793 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTCTACAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
41042858 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * *
41042920 GTCTGCTCCACTGCAACTTCAGGAAGATAAGACTGGATACGATCTGCTCTCTGTAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
*
41042985 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTT
66 GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
*
41043047 GTCTGCTCCACTACAACTTCAGGGAGATAAGACTG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
41043082 TTTCACCGAT
Statistics
Matches: 515, Mismatches: 28, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 515 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (127 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
GATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
Found at i:41044254 original size:1 final size:1
Alignment explanation
Indices: 41044250--41044397 Score: 71
Period size: 1 Copynumber: 148.0 Consensus size: 1
41044240 TCATTTTTCC
* * * * * * * * * * * *
41044250 TTTTTTTTCTTTTCTTTTCTTTCTTTCTTTTTTTCTTTTTCTTTTCTTTCTTTCTTCTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
41044315 TTTTCTTCTTTTTTTCTTTTCTTTTCTTTTTTTCTTCTTTTTTTTCTTTTCTTTTCTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
41044380 TTTTCTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
41044398 AAGAAAAGTA
Statistics
Matches: 97, Mismatches: 50, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 97 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (1 bp):
T
Found at i:41044262 original size:8 final size:8
Alignment explanation
Indices: 41044251--41044397 Score: 122
Period size: 8 Copynumber: 17.6 Consensus size: 8
41044241 CATTTTTCCT
41044251 TTTTTTTC
1 TTTTTTTC
41044259 TTTTCTTTTC
1 -TTT-TTTTC
*
41044269 TTTCTTTC
1 TTTTTTTC
41044277 TTTTTTTC
1 TTTTTTTC
41044285 TTTTTCTTTTC
1 --TTT-TTTTC
*
41044296 TTTCTTTC
1 TTTTTTTC
*
41044304 TTCTTTTC
1 TTTTTTTC
41044312 TTTTTTTC
1 TTTTTTTC
41044320 TTCTTTTT-
1 TT-TTTTTC
*
41044328 TTCTTTTC
1 TTTTTTTC
41044336 TTTTCTTT-
1 TTTT-TTTC
*
41044344 TTTTCTTC
1 TTTTTTTC
41044352 TTTTTTTTC
1 -TTTTTTTC
41044361 TTTTCTTT-
1 TTTT-TTTC
*
41044369 TCTTTTTC
1 TTTTTTTC
41044377 TTTTTTTC
1 TTTTTTTC
41044385 TTTTCTTT-
1 TTTT-TTTC
41044393 TTTTT
1 TTTTT
41044398 AAGAAAAGTA
Statistics
Matches: 114, Mismatches: 12, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
7 10 0.09
8 61 0.54
9 30 0.26
10 8 0.07
11 5 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:41044264 original size:5 final size:5
Alignment explanation
Indices: 41044244--41044397 Score: 143
Period size: 5 Copynumber: 31.8 Consensus size: 5
41044234 GGCCTCTCAT
41044244 TTTTCC TTTT- TTTTC TTTTC TTTTC -TTTC -TTTC -TTT- TTTTC TTTTTC
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC
*
41044291 TTTTC -TTTC TTTCTTC TTTTC -TTT- TTTTC TTCTTT TTTTC TTTTC
1 TTTTC TTTTC -TT-TTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
*
41044336 TTTTC TTTTT TTCTTC TTTT- TTTTC TTTTC TTTTC TTTT- TCTTT- TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC
41044385 TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTT
41044398 AAGAAAAGTA
Statistics
Matches: 130, Mismatches: 4, Indels: 30
0.79 0.02 0.18
Matches are distributed among these distances:
4 40 0.31
5 67 0.52
6 20 0.15
7 3 0.02
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:41044282 original size:35 final size:35
Alignment explanation
Indices: 41044243--41044388 Score: 149
Period size: 36 Copynumber: 4.1 Consensus size: 35
41044233 TGGCCTCTCA
41044243 TTTTTCCTTTTTTTTCTTTTCTTTTCTTTCTTTCT
1 TTTTTCCTTTTTTTTCTTTTCTTTTCTTTCTTTCT
*
41044278 TTTTTTCTTTTTCTTT-TCTTTC-TTTC-TTCTTTTCTT
1 TTTTTCCTTTTT-TTTCT-TTTCTTTTCTTTC-TTTC-T
* *
41044314 TTTTTCTTCTTTTTTTCTTTTCTTTTCTTTTTTTCT
1 TTTTTCCT-TTTTTTTCTTTTCTTTTCTTTCTTTCT
*
41044350 TCTTTT--TTTTCTTTTCTTTTCTTTTTCTTTTTTTCT
1 T-TTTTCCTTTT-TTTTCTTTTC-TTTTCTTTCTTTCT
41044386 TTT
1 TTT
41044389 CTTTTTTTTA
Statistics
Matches: 96, Mismatches: 4, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
34 6 0.06
35 33 0.34
36 38 0.40
37 17 0.18
38 2 0.02
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (35 bp):
TTTTTCCTTTTTTTTCTTTTCTTTTCTTTCTTTCT
Found at i:41044332 original size:54 final size:51
Alignment explanation
Indices: 41044250--41044397 Score: 185
Period size: 54 Copynumber: 2.8 Consensus size: 51
41044240 TCATTTTTCC
* *
41044250 TTTT-TTTTCTTTTCTTTTCTTTCTTTCTTTTTTTCTTTTTCTT-TTCTTTCT
1 TTTTCTTTTCTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTT-TTCTTCTTT-T
41044301 TTCTTCTTTTCTTTTTTTCTTCTTTTTTTCTTTTCTTTTCTTTTTTTCTTCTTTT
1 TT-TTCTTTTCTTTTTTT-TTCTTTTTTTC-TTT-TTTTCTTTTTTTCTTCTTTT
*
41044356 TTTTCTTTTCTTTTCTTTTTCTTTTTTTCTTTTCTT-TTTTTT
1 TTTTCTTTTCTTTT-TTTTTCTTTTTTTCTTTTTTTCTTTTTT
41044398 AAGAAAAGTA
Statistics
Matches: 87, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
51 8 0.09
52 5 0.06
53 14 0.16
54 33 0.38
55 11 0.13
56 16 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (51 bp):
TTTTCTTTTCTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTCTTTT
Found at i:41044394 original size:19 final size:19
Alignment explanation
Indices: 41044250--41044394 Score: 164
Period size: 19 Copynumber: 7.8 Consensus size: 19
41044240 TCATTTTTCC
41044250 TTTT-TTTTC-TTTTCTTT
1 TTTTCTTTTCTTTTTCTTT
41044267 TCTTTC-TTTCTTTTT-TTCT
1 T-TTTCTTTTCTTTTTCTT-T
*
41044286 TTTTCTTTTCTTTCTTTCTTC
1 TTTTCTTTTC-TT-TTTCTTT
41044307 TTTTCTTTT-TTTCTTCTTT
1 TTTTCTTTTCTTT-TTCTTT
41044326 TTTTCTTTTC-TTTTCTTT
1 TTTTCTTTTCTTTTTCTTT
41044344 TTTTC--TTCTTTTT-TTT
1 TTTTCTTTTCTTTTTCTTT
41044360 CTTTTCTTTTCTTTTTCTTT
1 -TTTTCTTTTCTTTTTCTTT
41044380 TTTTCTTTTCTTTTT
1 TTTTCTTTTCTTTTT
41044395 TTTAAGAAAA
Statistics
Matches: 111, Mismatches: 2, Indels: 28
0.79 0.01 0.20
Matches are distributed among these distances:
16 6 0.05
17 10 0.09
18 25 0.23
19 51 0.46
20 5 0.05
21 12 0.11
22 2 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTCTTT
Found at i:41044394 original size:35 final size:35
Alignment explanation
Indices: 41044243--41044394 Score: 176
Period size: 35 Copynumber: 4.5 Consensus size: 35
41044233 TGGCCTCTCA
* *
41044243 TTTTTCCTTT-TTTTTCTTTTCTTTTCTTTC--TT
1 TTTTTCTTTTCTTTTTCTTTTCTTTTCTTTTTCTT
*
41044275 TCTTT-TTTTCTTTTTCTTTTC-TTTCTTTCTTCTT
1 TTTTTCTTTTCTTTTTCTTTTCTTTTCTTT-TTCTT
41044309 TTCTTT-TTTTCTTCTTT-TTTTCTTTTC-TTTTCTT
1 TT-TTTCTTTTCTT-TTTCTTTTCTTTTCTTTTTCTT
*
41044343 TTTTTCTTCTTTTTTTTCTTTTCTTTTCTTTTTCTT
1 TTTTTCTT-TTCTTTTTCTTTTCTTTTCTTTTTCTT
41044379 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
41044395 TTTAAGAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
31 10 0.10
32 15 0.15
33 3 0.03
34 15 0.15
35 38 0.37
36 22 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (35 bp):
TTTTTCTTTTCTTTTTCTTTTCTTTTCTTTTTCTT
Found at i:41047803 original size:28 final size:28
Alignment explanation
Indices: 41047745--41047803 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
41047735 AATGATGTAG
* *
41047745 AAAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAAGAATAAAAGAATAATGACTCAA
* *
41047773 AAAAAAGAATAAAAGAATACTGGCTCAA
1 AAAAAAGAATAAAAGAATAATGACTCAA
41047801 AAA
1 AAA
41047804 TGCATACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.15
Consensus pattern (28 bp):
AAAAAAGAATAAAAGAATAATGACTCAA
Found at i:41055029 original size:13 final size:14
Alignment explanation
Indices: 41055006--41055035 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41054996 ATAAATATTA
41055006 TTTATTAAATTAAT
1 TTTATTAAATTAAT
41055020 TTTATT-AATTAAT
1 TTTATTAAATTAAT
41055033 TTT
1 TTT
41055036 CCAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTAAATTAAT
Found at i:41075801 original size:17 final size:17
Alignment explanation
Indices: 41075781--41075815 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41075771 TTAATTTATA
41075781 TATTTTTAAATATTTTT
1 TATTTTTAAATATTTTT
**
41075798 TATTTTTATTTATTTTT
1 TATTTTTAAATATTTTT
41075815 T
1 T
41075816 CACGTGGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTTTTAAATATTTTT
Found at i:41081174 original size:33 final size:32
Alignment explanation
Indices: 41081103--41081175 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
41081093 GTGTATATAT
* * * *
41081103 GTAAGACCATAGCTAGGCTATGGCATTCTGAT
1 GTAAGACCATAACTAGGCTATGGCACTATGAA
*
41081135 GATAAGACCATAACTAGGTTATGGCACTATGAAA
1 G-TAAGACCATAACTAGGCTATGGCACTATG-AA
41081169 GTAAGAC
1 GTAAGAC
41081176 TATGGCAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.03
33 31 0.91
34 2 0.06
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (32 bp):
GTAAGACCATAACTAGGCTATGGCACTATGAA
Found at i:41083654 original size:21 final size:21
Alignment explanation
Indices: 41083624--41083684 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
41083614 TTGGGTGGAC
*
41083624 CAGCTCTTACAAGCTTTTGTT
1 CAGCTTTTACAAGCTTTTGTT
* * *
41083645 CAGCTTTTACGAGCTTCTATT
1 CAGCTTTTACAAGCTTTTGTT
*
41083666 TAGC-TTT-CAAGCTTTTGTT
1 CAGCTTTTACAAGCTTTTGTT
41083685 GACGATGACT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 9 0.28
20 3 0.09
21 20 0.62
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (21 bp):
CAGCTTTTACAAGCTTTTGTT
Found at i:41087849 original size:33 final size:33
Alignment explanation
Indices: 41087812--41087884 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
41087802 TTACATTTGA
41087812 GAGATTAGCGGAACTATATATATCTGAGATTGT
1 GAGATTAGCGGAACTATATATATCTGAGATTGT
*
41087845 GAGATTAGCGGAACTATATATATCTTAGATTGT
1 GAGATTAGCGGAACTATATATATCTGAGATTGT
41087878 GAGATTA
1 GAGATTA
41087885 CACGGAGTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (33 bp):
GAGATTAGCGGAACTATATATATCTGAGATTGT
Found at i:41090801 original size:4 final size:4
Alignment explanation
Indices: 41090792--41091213 Score: 835
Period size: 4 Copynumber: 105.2 Consensus size: 4
41090782 AGTATGAGTG
41090792 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41090840 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41090888 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41090936 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41090984 ATGT ATGT ATGT ATGT ATGT ATGT ATGTT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG-T ATGT ATGT ATGT ATGT ATGT
41091033 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41091081 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41091129 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41091177 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
41091214 ACCTAAGTCA
Statistics
Matches: 417, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
4 413 0.99
5 4 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:41095202 original size:18 final size:18
Alignment explanation
Indices: 41095179--41095215 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41095169 TAATAAAGTG
41095179 TGTATAA-TAAAATTAAAA
1 TGTATAAGT-AAATTAAAA
41095197 TGTATAAGTAAATTAAAA
1 TGTATAAGTAAATTAAAA
41095215 T
1 T
41095216 AAAACTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
TGTATAAGTAAATTAAAA
Found at i:41095602 original size:157 final size:156
Alignment explanation
Indices: 41095297--41095602 Score: 348
Period size: 157 Copynumber: 1.9 Consensus size: 156
41095287 CATTTTTTTG
* *
41095297 TTTTTTATTAATTAAAAAATTAAAGTGCCCTCGAATAATATAACTTATTTTAAATACGAAAGATC
1 TTTTTTA-TAATTAAAAAACTAAAGTACCCTCGAATAATATAACTTATTTTAAATACGAAAGATC
* ** *
41095362 ATTTTATAATTTCCTAACTGAATTGGTGCCTAGTTGACTCACGACACCAACTCAGTCAGAAATTT
65 ATTTTATAATTTCCTAACCGAATTAATGCCTAGTTGACTCACGACACCAACTCAGTCAGAAATTC
*
41095427 TATTAATAGTATAGATATATACTATTA
130 TATTAATAGTAAAGATATATACTATTA
* *
41095454 TTTTTTA-AATTAAAAAGACTAAAGTACCCTTGAATAATATAACTTATTTTAAATATGAAA-AGT
1 TTTTTTATAATTAAAAA-ACTAAAGTACCCTCGAATAATATAACTTATTTTAAATACGAAAGA-T
* * * * * * * ** * *
41095517 TATTTTTGTTATTTTCTAACCGAGTTAATGTCTGGTTGACTCGTGACACCAACTCATTCATG-GA
64 CA-TTTTATAATTTCCTAACCGAATTAATGCCTAGTTGACTCACGACACCAACTCAGTCA-GAAA
* *
41095581 TTCTATTAATGGTAAATATATA
127 TTCTATTAATAGTAAAGATATA
41095603 CAACTAATGG
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
155 10 0.08
156 41 0.33
157 71 0.58
158 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (156 bp):
TTTTTTATAATTAAAAAACTAAAGTACCCTCGAATAATATAACTTATTTTAAATACGAAAGATCA
TTTTATAATTTCCTAACCGAATTAATGCCTAGTTGACTCACGACACCAACTCAGTCAGAAATTCT
ATTAATAGTAAAGATATATACTATTA
Found at i:41109738 original size:19 final size:20
Alignment explanation
Indices: 41109702--41109745 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
41109692 CAGTAAAATA
41109702 TTTTCTGGAAAATAATTTAC
1 TTTTCTGGAAAATAATTTAC
*
41109722 TTTTCTGG-AAATGATTTAC
1 TTTTCTGGAAAATAATTTAC
41109741 TTTTC
1 TTTTC
41109746 GGTGTTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
TTTTCTGGAAAATAATTTAC
Found at i:41115642 original size:25 final size:25
Alignment explanation
Indices: 41115613--41115688 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 25
41115603 GTTCATATTA
41115613 TATTTTAATTTTTTTTTAAAATAAT
1 TATTTTAATTTTTTTTTAAAATAAT
* * *
41115638 TATTTT-ATTATATTTTAATATTAAT
1 TATTTTAATTTTTTTTTAA-AATAAT
* *
41115663 AATTTTATTATTTATTTATTAAAATA
1 TATTTTA--ATTT-TTTTTTAAAATA
41115689 TTTTATATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
24 10 0.26
25 16 0.42
28 6 0.16
29 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTTAATTTTTTTTTAAAATAAT
Found at i:41115776 original size:16 final size:16
Alignment explanation
Indices: 41115755--41115793 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
41115745 TTTATTGTGT
*
41115755 TATAAATTACATAATA
1 TATAAATAACATAATA
*
41115771 TATAAAAAACATAATA
1 TATAAATAACATAATA
41115787 TA-AAATA
1 TATAAATA
41115794 TTATAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (16 bp):
TATAAATAACATAATA
Found at i:41117414 original size:22 final size:22
Alignment explanation
Indices: 41117391--41117432 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41117381 AAATCAATTA
41117391 AAAG-GATATAAGT-AAATAAAT
1 AAAGCGATATAA-TAAAATAAAT
41117412 AAAGCGATATAATAAAATAAA
1 AAAGCGATATAATAAAATAAA
41117433 CGTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAGCGATATAATAAAATAAAT
Found at i:41117524 original size:14 final size:14
Alignment explanation
Indices: 41117495--41117545 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
41117485 CTAATTAATT
41117495 TAATAATATAGT-AA
1 TAATAATA-AGTAAA
41117509 TAATAATAAGTAAA
1 TAATAATAAGTAAA
*
41117523 TAAATAA-AAGGAGAA
1 T-AATAATAAGTA-AA
41117538 TAATAATA
1 TAATAATA
41117546 CTGGTAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 20 0.62
15 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (14 bp):
TAATAATAAGTAAA
Found at i:41118168 original size:20 final size:21
Alignment explanation
Indices: 41118143--41118182 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41118133 CTTTTATATA
41118143 TATATATATATATC-ATATGT
1 TATATATATATATCTATATGT
*
41118163 TATATATATTTATCTATATG
1 TATATATATATATCTATATG
41118183 CAGTTCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TATATATATATATCTATATGT
Found at i:41119049 original size:243 final size:243
Alignment explanation
Indices: 41118621--41119107 Score: 974
Period size: 243 Copynumber: 2.0 Consensus size: 243
41118611 TTAGGTTTTG
41118621 GGCCTGTTAGGCCTTTAGGTTTTTTTTTATTTTGGGCTACACGGGCCACATATAATTTTGGGCTT
1 GGCCTGTTAGGCCTTTAGGTTTTTTTTTATTTTGGGCTACACGGGCCACATATAATTTTGGGCTT
41118686 GATAGACTATTTGTAATGGACATTTGGACTGTTTGCTGGGCTCTGGCAAATTGGGCCTACTACAG
66 GATAGACTATTTGTAATGGACATTTGGACTGTTTGCTGGGCTCTGGCAAATTGGGCCTACTACAG
41118751 CTGCCCCTCTTTGCTCGTTGTCGTGTAACGAGACTGGAGCAAAGACTTTTAAGAAGAACCAATTT
131 CTGCCCCTCTTTGCTCGTTGTCGTGTAACGAGACTGGAGCAAAGACTTTTAAGAAGAACCAATTT
41118816 TGCCCGGTCTCACCGAATCTTGACTTTGGTGCTCATCTTTTTCATATA
196 TGCCCGGTCTCACCGAATCTTGACTTTGGTGCTCATCTTTTTCATATA
41118864 GGCCTGTTAGGCCTTTAGGTTTTTTTTTATTTTGGGCTACACGGGCCACATATAATTTTGGGCTT
1 GGCCTGTTAGGCCTTTAGGTTTTTTTTTATTTTGGGCTACACGGGCCACATATAATTTTGGGCTT
41118929 GATAGACTATTTGTAATGGACATTTGGACTGTTTGCTGGGCTCTGGCAAATTGGGCCTACTACAG
66 GATAGACTATTTGTAATGGACATTTGGACTGTTTGCTGGGCTCTGGCAAATTGGGCCTACTACAG
41118994 CTGCCCCTCTTTGCTCGTTGTCGTGTAACGAGACTGGAGCAAAGACTTTTAAGAAGAACCAATTT
131 CTGCCCCTCTTTGCTCGTTGTCGTGTAACGAGACTGGAGCAAAGACTTTTAAGAAGAACCAATTT
41119059 TGCCCGGTCTCACCGAATCTTGACTTTGGTGCTCATCTTTTTCATATA
196 TGCCCGGTCTCACCGAATCTTGACTTTGGTGCTCATCTTTTTCATATA
41119107 G
1 G
41119108 CCTCGTTCTT
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
243 244 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (243 bp):
GGCCTGTTAGGCCTTTAGGTTTTTTTTTATTTTGGGCTACACGGGCCACATATAATTTTGGGCTT
GATAGACTATTTGTAATGGACATTTGGACTGTTTGCTGGGCTCTGGCAAATTGGGCCTACTACAG
CTGCCCCTCTTTGCTCGTTGTCGTGTAACGAGACTGGAGCAAAGACTTTTAAGAAGAACCAATTT
TGCCCGGTCTCACCGAATCTTGACTTTGGTGCTCATCTTTTTCATATA
Found at i:41119455 original size:143 final size:143
Alignment explanation
Indices: 41119128--41119714 Score: 861
Period size: 143 Copynumber: 4.1 Consensus size: 143
41119118 ACCTACTGTC
** *
41119128 ACTTTAGGGAGATAAAACCGGTGGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATCCA
1 ACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCA
* * *
41119193 CCATAATTTGTAGCTTTAATCTCTTCCATTGCAACG-CAAGGAAATAAGATTCGCTGTCTTCAGT
66 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGT
**
41119257 CTGCTCCGCCGCA
131 CTGCTCCGCTACA
* * *
41119270 ACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCG
1 ACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCA
* * *
41119335 CCATAATTTGTAGCTTTAATCTGTTCCATTACAACGCCATGGAAATAAGATTCGTTGTCTTCAGT
66 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGT
41119400 CTGCTCCGCTACA
131 CTGCTCCGCTACA
* * *
41119413 ACTTCAGGGAGATAAGGCCGGTGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTA
1 ACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCA
* * * * *
41119478 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGCTTCGATGTCTTTAGT
66 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGT
* *
41119543 CTACTCCGCTGCA
131 CTGCTCCGCTACA
* * * * **
41119556 ACTTTAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCATTGCAACTTCAGGAAGAAAAGATCTG
1 ACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCA
* *
41119621 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAAGGCGAAGGAAATAAGATTCGTTGTCTTCAGT
66 CCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGT
41119686 CTGCTCCGCTACA
131 CTGCTCCGCTACA
* *
41119699 ACTTCAGGGAAATAAG
1 ACTTTAGGGAGATAAG
41119715 ATTGTCATTT
Statistics
Matches: 399, Mismatches: 45, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
142 93 0.23
143 306 0.77
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (143 bp):
ACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCA
CCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGT
CTGCTCCGCTACA
Found at i:41128447 original size:46 final size:45
Alignment explanation
Indices: 41128380--41128642 Score: 310
Period size: 46 Copynumber: 6.2 Consensus size: 45
41128370 TTTGAGTACT
*
41128380 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
41128426 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
41128462 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
41128508 TCTGATCAAGTGAAAAAGTGAT-A-----AGC---GCTATACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
41128544 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
41128590 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
41128635 TCTGATCA
1 TCTGATCA
41128643 GGGACAAGTG
Statistics
Matches: 188, Mismatches: 9, Indels: 41
0.79 0.04 0.17
Matches are distributed among these distances:
36 60 0.32
37 3 0.02
40 5 0.03
42 4 0.02
43 1 0.01
45 24 0.13
46 91 0.48
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:41128457 original size:36 final size:36
Alignment explanation
Indices: 41128416--41128570 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
41128406 GGTAGCATTA
41128416 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
41128452 GCTACACTTATCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
41128497 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGC
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
41128534 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
41128570 G
1 G
41128571 GTAGCCTTAG
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 64 0.63
37 1 0.01
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.30
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:41128483 original size:82 final size:82
Alignment explanation
Indices: 41128380--41128616 Score: 411
Period size: 82 Copynumber: 2.9 Consensus size: 82
41128370 TTTGAGTACT
41128380 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
41128445 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
41128462 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
41128527 GATAAGCGCTATACTTA
66 GATAAGTGCTACACTTA
* * *
41128544 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
41128609 GATAAGTG
66 GATAAGTG
41128617 GTAGCCTAGC
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 146 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:41128642 original size:45 final size:46
Alignment explanation
Indices: 41128534--41128655 Score: 205
Period size: 46 Copynumber: 2.7 Consensus size: 46
41128524 AGTGATAAGC
*
41128534 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
41128580 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
41128625 GCTACACTTATCTGATC-AGGGAC-AAGTGATA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATA
41128656 TGTGATCATA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
43 8 0.11
44 5 0.07
45 19 0.26
46 42 0.57
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:41129558 original size:22 final size:21
Alignment explanation
Indices: 41129529--41129571 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
41129519 AAATCAATTA
41129529 AAAGGATATAAGT-AAATAAAT
1 AAAGGATATAA-TAAAATAAAT
41129550 AAAGCGATATAATAAAATAAAT
1 AAAG-GATATAATAAAATAAAT
41129572 GTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAGGATATAATAAAATAAAT
Found at i:41130892 original size:16 final size:17
Alignment explanation
Indices: 41130873--41130905 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41130863 AAACTCACAA
41130873 AACAAAATTCT-TTTAT
1 AACAAAATTCTCTTTAT
41130889 AACAAAATTCTCTTTAT
1 AACAAAATTCTCTTTAT
41130906 TATTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
AACAAAATTCTCTTTAT
Found at i:41132642 original size:23 final size:20
Alignment explanation
Indices: 41132614--41132666 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
41132604 TAAATATAAA
*
41132614 TTATTTTATACTAAATTAATT
1 TTATTTTATAATAAATT-ATT
41132635 TAATATTTTATAATAAATTATT
1 T--TATTTTATAATAAATTATT
41132657 TTATTTTATA
1 TTATTTTATA
41132667 TTTTTTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 4 0.14
23 15 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTTATAATAAATTATT
Found at i:41135153 original size:14 final size:15
Alignment explanation
Indices: 41135120--41135157 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
41135110 ATTTTAAGGT
41135120 TTAGGGATTATGGAA
1 TTAGGGATTATGGAA
41135135 TTAGGGATTATGG-A
1 TTAGGGATTATGGAA
41135149 TTAGGGATT
1 TTAGGGATT
41135158 CTGATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (15 bp):
TTAGGGATTATGGAA
Found at i:41135340 original size:13 final size:14
Alignment explanation
Indices: 41135290--41135344 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
41135280 TATTAAATAA
41135290 GGTTTAGGGGTTAAG
1 GGTTTAGGGGTT-AG
41135305 GG-TTAGGGGTTAG
1 GGTTTAGGGGTTAG
*
41135318 GAATTT--GGGTTAG
1 G-GTTTAGGGGTTAG
*
41135331 GGTTTAGGGTTTAG
1 GGTTTAGGGGTTAG
41135345 ATTAATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.09
13 11 0.33
14 15 0.45
15 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.36
Consensus pattern (14 bp):
GGTTTAGGGGTTAG
Found at i:41136421 original size:3 final size:3
Alignment explanation
Indices: 41136413--41136472 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
41136403 TTATTTTTTG
41136413 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41136461 TAT TAT TAT TAT
1 TAT TAT TAT TAT
41136473 ACTCTTATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41136578 original size:2 final size:2
Alignment explanation
Indices: 41136571--41136602 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41136561 TCATATCTTT
*
41136571 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41136603 CCCATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41137683 original size:14 final size:14
Alignment explanation
Indices: 41137653--41137712 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
41137643 TAAATAAGGT
*
41137653 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
41137667 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
**
41137681 TTAGATGTTA-GATG
1 TTAGGGGTTAGGA-G
* *
41137695 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
41137709 TTAG
1 TTAG
41137713 TGATTTAGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
13 1 0.03
14 35 0.92
15 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:41137697 original size:21 final size:21
Alignment explanation
Indices: 41137653--41137712 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
41137643 TAAATAAGGT
*
41137653 TTAGGGGTTAG-TAGTTAGGGG
1 TTAGGGGTTAGAT-GTTAGAGG
*
41137674 TTAGGGGTTAGATGTTAGATG
1 TTAGGGGTTAGATGTTAGAGG
*
41137695 TTAGAGGTTAAGA-GTTAG
1 TTAGGGGTT-AGATGTTAG
41137713 TGATTTAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (21 bp):
TTAGGGGTTAGATGTTAGAGG
Found at i:41137903 original size:14 final size:14
Alignment explanation
Indices: 41137856--41137904 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
41137846 ATGTTTTATA
41137856 ATTTAGGGTTTAAG
1 ATTTAGGGTTTAAG
** *
41137870 AGATAGGGGTTAAGG
1 ATTTAGGGTTTAA-G
*
41137885 GTTTAGGGTTTAAG
1 ATTTAGGGTTTAAG
41137899 ATTTAG
1 ATTTAG
41137905 ATTAATTGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (14 bp):
ATTTAGGGTTTAAG
Found at i:41139698 original size:9 final size:9
Alignment explanation
Indices: 41139684--41139714 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41139674 GTTAAACGAA
41139684 TCGAGTTAT
1 TCGAGTTAT
*
41139693 TCGAGTTAA
1 TCGAGTTAT
41139702 TCGAGTTAT
1 TCGAGTTAT
41139711 TCGA
1 TCGA
41139715 ATCAACTCAA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:41139787 original size:9 final size:9
Alignment explanation
Indices: 41139768--41139804 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
41139758 TGATTTTTCG
41139768 AATTCGAAT
1 AATTCGAAT
41139777 AACTT-GAAT
1 AA-TTCGAAT
41139786 AATTCGAAT
1 AATTCGAAT
41139795 AATTCGAAT
1 AATTCGAAT
41139804 A
1 A
41139805 TCAAACTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41143735 original size:42 final size:42
Alignment explanation
Indices: 41143649--41143736 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
41143639 TAATTTTTTT
* * * *
41143649 TAAAGGTTATGTTTTTAGTGGCATTTTTGCGAGAAGCACTGC
1 TAAAGGTTATGTTTTTAGTGGCATTTGTGAGAAAAGCACCGC
* * *
41143691 TAAAGGTT-TGTTCTTTAGTGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTTATGTT-TTTAGTGGCATTTGTGAGAAAAGCACCGC
41143733 TAAA
1 TAAA
41143737 AGTCATGATC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.36
Consensus pattern (42 bp):
TAAAGGTTATGTTTTTAGTGGCATTTGTGAGAAAAGCACCGC
Found at i:41145054 original size:37 final size:37
Alignment explanation
Indices: 41144999--41145072 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
41144989 AGTTCGGAAG
*
41144999 AAAAGTTATTTTTAAATTATTTCATGGTCTGTATTAT
1 AAAAATTATTTTTAAATTATTTCATGGTCTGTATTAT
41145036 AAAAATTATTTTTAAATTATTTCATGGTCTGTATTAT
1 AAAAATTATTTTTAAATTATTTCATGGTCTGTATTAT
41145073 GATTGAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.51
Consensus pattern (37 bp):
AAAAATTATTTTTAAATTATTTCATGGTCTGTATTAT
Found at i:41146240 original size:24 final size:24
Alignment explanation
Indices: 41146213--41146270 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
41146203 CGAAAGAGTG
* *
41146213 TCCCGTTATTAGCTCTCATGTGCA
1 TCCCGTTATTAGCTCTCACGAGCA
* * *
41146237 TCCCGATATTTGGCTCTCACGAGCT
1 TCCCGTTA-TTAGCTCTCACGAGCA
41146262 TCCCGTTAT
1 TCCCGTTAT
41146271 ATGGTTCTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTCACGAGCA
Found at i:41152834 original size:2 final size:2
Alignment explanation
Indices: 41152822--41152861 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
41152812 NNNNNNNNNG
41152822 TA TA CTA 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 T
41152862 TCATATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41153309 original size:16 final size:14
Alignment explanation
Indices: 41153272--41153310 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
41153262 ATAGACTCAT
41153272 TAATAATTTAAACA
1 TAATAATTTAAACA
*
41153286 TAAAAATTTAAAACCA
1 TAATAATTT-AAA-CA
41153302 TAATAATTT
1 TAATAATTT
41153311 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATTTAAACA
Found at i:41154619 original size:3 final size:3
Alignment explanation
Indices: 41154611--41154645 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41154601 CTTCTTAATC
41154611 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41154646 CTTTTATCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41156978 original size:31 final size:31
Alignment explanation
Indices: 41156943--41157004 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41156933 GGATGCAATG
41156943 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
1 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
41156974 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
1 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
41157005 GTTTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (31 bp):
ATTGCTTATAAATCCTTTCATAAGCTTTTCT
Found at i:41161332 original size:6 final size:6
Alignment explanation
Indices: 41161319--41161351 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
41161309 GAGAAAGAGA
41161319 AAGA-G AAGATG AAGATG AAGATG AAGATG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGA
41161352 AAGGCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (6 bp):
AAGATG
Found at i:41162549 original size:10 final size:9
Alignment explanation
Indices: 41162525--41162560 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
41162515 TTTATTATAT
41162525 AATTTTTAG
1 AATTTTTAG
41162534 AATTTTTAG
1 AATTTTTAG
41162543 AATTTTTATG
1 AATTTTTA-G
41162553 AATTTTTA
1 AATTTTTA
41162561 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
AATTTTTAG
Found at i:41162555 original size:19 final size:18
Alignment explanation
Indices: 41162525--41162560 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
41162515 TTTATTATAT
41162525 AATTTTTAGAATTTTTAG
1 AATTTTTAGAATTTTTAG
41162543 AATTTTTATGAATTTTTA
1 AATTTTTA-GAATTTTTA
41162561 ATTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
AATTTTTAGAATTTTTAG
Found at i:41162662 original size:20 final size:20
Alignment explanation
Indices: 41162633--41162670 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41162623 TTTTTAGACA
41162633 TTTTTAAGATTCTTTTTTATG
1 TTTTTAAGATT-TTTTTTATG
41162654 TTTTT-AGATTTTTTTTA
1 TTTTTAAGATTTTTTTTA
41162671 ATAATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTTAAGATTTTTTTTATG
Found at i:41162678 original size:21 final size:21
Alignment explanation
Indices: 41162632--41162679 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
41162622 ATTTTTAGAC
41162632 ATTTTTAAGATTCTTTTTTAT
1 ATTTTTAAGATTCTTTTTTAT
*
41162653 GTTTTT-AGATT-TTTTTTAAT
1 ATTTTTAAGATTCTTTTTT-AT
41162673 AATTTTT
1 -ATTTTT
41162680 CCAGAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 10 0.43
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
ATTTTTAAGATTCTTTTTTAT
Found at i:41163790 original size:23 final size:24
Alignment explanation
Indices: 41163755--41163804 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
41163745 GAAACAATAT
*
41163755 AAAAAATACACAAAAATAACAACA
1 AAAAAATACACAAAAACAACAACA
* *
41163779 AAAAAATA-ACAATAACAACACCA
1 AAAAAATACACAAAAACAACAACA
41163802 AAA
1 AAA
41163805 CGCTAGGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.08
Consensus pattern (24 bp):
AAAAAATACACAAAAACAACAACA
Found at i:41164699 original size:44 final size:45
Alignment explanation
Indices: 41164613--41164703 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
41164603 TTTGGTTCGC
* * *
41164613 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
41164658 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
41164702 TG
1 TG
41164704 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:41164885 original size:16 final size:16
Alignment explanation
Indices: 41164848--41164902 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
41164838 ATAATCATAT
*
41164848 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
41164864 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
41164879 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
41164897 -TAAAAT
1 TTAAAAT
41164903 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:41164895 original size:18 final size:18
Alignment explanation
Indices: 41164854--41164902 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
41164844 ATATTTAAAC
41164854 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
41164872 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
41164888 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
41164903 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:41171717 original size:19 final size:20
Alignment explanation
Indices: 41171693--41171732 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41171683 GTTTTTGTAT
*
41171693 TTTTAAGTAATATA-ATTTA
1 TTTTAAATAATATATATTTA
*
41171712 TTTTAAATATTATATATTTA
1 TTTTAAATAATATATATTTA
41171732 T
1 T
41171733 ATATAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTAAATAATATATATTTA
Found at i:41174696 original size:3 final size:3
Alignment explanation
Indices: 41174690--41174732 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
41174680 CATTATTACC
** *
41174690 TTA TTA TTA TTA TTA TCG TTA TTA TTA TTA TTA TCA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41174733 GTTTATACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:41174704 original size:9 final size:9
Alignment explanation
Indices: 41174633--41174732 Score: 53
Period size: 9 Copynumber: 10.9 Consensus size: 9
41174623 TAGGTTTTCT
*
41174633 TTATTTTTA
1 TTATTATTA
41174642 TTAATT-TTA
1 TT-ATTATTA
*
41174651 TTAATATTA
1 TTATTATTA
* *
41174660 TTAATACTA
1 TTATTATTA
*
41174669 TTA-TAGTGCA
1 TTATTA-T-TA
*
41174679 TCATTATTA
1 TTATTATTA
41174688 CCTTATTATTA
1 --TTATTATTA
**
41174699 TTATTATCG
1 TTATTATTA
41174708 TTATTATTA
1 TTATTATTA
*
41174717 TTATTATCA
1 TTATTATTA
41174726 -TATTATT
1 TTATTATT
41174733 GTTTATACTT
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
8 10 0.14
9 44 0.62
10 7 0.10
11 10 0.14
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (9 bp):
TTATTATTA
Found at i:41174875 original size:25 final size:23
Alignment explanation
Indices: 41174828--41174873 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41174818 ATACATTTGA
*
41174828 TTTTATAATATATATATGCATAT
1 TTTTATAATATATATATACATAT
* *
41174851 TTTTATAATCTATATATATATAT
1 TTTTATAATATATATATACATAT
41174874 ATATATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAATATATATATACATAT
Found at i:41176396 original size:21 final size:21
Alignment explanation
Indices: 41176366--41176519 Score: 87
Period size: 21 Copynumber: 7.3 Consensus size: 21
41176356 ACAGAAACCT
*
41176366 ATAAGGGTTGAACGGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
* * * *
41176387 GTAAGAGTTGAACGAAAACCC
1 ATAAGAGTTGAACGGAAGCTC
* **
41176408 ATAAG-GGTGAAATAGAAGCTC
1 ATAAGAGTTG-AACGGAAGCTC
* * * *
41176429 AAAAGAGTTGAACGAAAACCC
1 ATAAGAGTTGAACGGAAGCTC
* * *
41176450 ATAAGGGTTAAACAGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
* *
41176471 GA-AAAAGTTGAACGGAAACTC
1 -ATAAGAGTTGAACGGAAGCTC
* * *
41176492 ATAAGGGTTAAACAGAAGCTC
1 ATAAGAGTTGAACGGAAGCTC
*
41176513 ATGAGAG
1 ATAAGAG
41176520 CTAAACAAAA
Statistics
Matches: 91, Mismatches: 38, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
20 4 0.04
21 83 0.91
22 4 0.04
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (21 bp):
ATAAGAGTTGAACGGAAGCTC
Found at i:41176406 original size:42 final size:42
Alignment explanation
Indices: 41176360--41176512 Score: 216
Period size: 42 Copynumber: 3.6 Consensus size: 42
41176350 AGCTAAACAG
* * * *
41176360 AAACCTATAAGGGTTGAACGGAAGCTCGTAAGAGTTGAACGA
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
* * *
41176402 AAACCCATAAGGGTGAAATAGAAGCTCAAAAGAGTTGAACGA
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
* *
41176444 AAACCCATAAGGGTTAAACAGAAGCTCGAAAAAGTTGAACGG
1 AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
*
41176486 AAACTCATAAGGGTTAAACAGAAGCTC
1 AAACCCATAAGGGTTAAACAGAAGCTC
41176513 ATGAGAGCTA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACAGAAGCTCGAAAGAGTTGAACGA
Found at i:41182563 original size:15 final size:16
Alignment explanation
Indices: 41182543--41182578 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
41182533 GGTTATTGGT
41182543 TGGGTTAGGG-TTTTG
1 TGGGTTAGGGCTTTTG
41182558 TGGGTTAGGGCTTTTG
1 TGGGTTAGGGCTTTTG
41182574 -GGGTT
1 TGGGTT
41182579 TATTGGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.06, C:0.03, G:0.47, T:0.44
Consensus pattern (16 bp):
TGGGTTAGGGCTTTTG
Found at i:41188549 original size:3 final size:3
Alignment explanation
Indices: 41188541--41188571 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41188531 CTGCTTTTGA
41188541 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41188572 CCTGCATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41194098 original size:43 final size:41
Alignment explanation
Indices: 41194038--41194193 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 41
41194028 TATGTATTTT
41194038 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TTGTG-ATA
* * *
41194081 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTGATA
*
41194122 TGTGTAAG-CC-CTGTCTGGGACAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TGTGA-TA
* *
41194164 CATGTAAGACCACGTCTGGGACGTTAGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
41194194 TGTATGAGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
39 2 0.02
40 20 0.21
41 12 0.13
42 10 0.11
43 48 0.51
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTGTGATA
Found at i:41194383 original size:16 final size:17
Alignment explanation
Indices: 41194354--41194385 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41194344 TGAATTGATG
41194354 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
41194371 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
41194386 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:41199053 original size:21 final size:22
Alignment explanation
Indices: 41199029--41199131 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 22
41199019 TGAACGAAAA
*
41199029 CTCATAATG-GTTAAATTGAAG
1 CTCATAATGAGTTAAACTGAAG
*
41199050 CTCA-AAAGAGTTAAACTGCAA-
1 CTCATAATGAGTTAAACTG-AAG
* * * *
41199071 CCCAGAA-GGGTTAAACTGAAA
1 CTCATAATGAGTTAAACTGAAG
41199092 CTCAT-ATGAGTT-AACTGAAG
1 CTCATAATGAGTTAAACTGAAG
* *
41199112 CTCATAA-GAGCTAAAATGAA
1 CTCATAATGAGTTAAACTGAA
41199132 AACAAACACG
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 22 0.34
21 39 0.60
22 4 0.06
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (22 bp):
CTCATAATGAGTTAAACTGAAG
Found at i:41206506 original size:59 final size:60
Alignment explanation
Indices: 41206403--41206520 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
41206393 GGCACTCAAA
* * * * *
41206403 CTTTCAGTAGAATCTAGAGATTATATCTCACCGAGGACAGTATCAAACTTATT-AAAGAG
1 CTTTCAATAGAATCTAGAGATTAAATCTCACCAAAGACAATATCAAACTTATTGAAAGAG
* *
41206462 CTTTCAATATAATTTAGAGATTAAA-CTCTACCAAAGACAATATCAAACTTATTGAAAGA
1 CTTTCAATAGAATCTAGAGATTAAATCTC-ACCAAAGACAATATCAAACTTATTGAAAGA
41206521 TGTCGACTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 3 0.06
59 42 0.84
60 5 0.10
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (60 bp):
CTTTCAATAGAATCTAGAGATTAAATCTCACCAAAGACAATATCAAACTTATTGAAAGAG
Found at i:41207256 original size:21 final size:21
Alignment explanation
Indices: 41207230--41207270 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41207220 TTTGACTATG
* *
41207230 CTTTCTTCTTCCTTTTTAATT
1 CTTTCTTCTACCTTTATAATT
41207251 CTTTCTTCTACCTTTATAAT
1 CTTTCTTCTACCTTTATAAT
41207271 GTTTAACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTTCTTCTACCTTTATAATT
Found at i:41214809 original size:14 final size:13
Alignment explanation
Indices: 41214780--41214823 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
41214770 TATTTACAAA
41214780 TTTAAATTTTAGTT
1 TTTAAATTTTA-TT
41214794 TTTAAATTTTTATT
1 TTTAAA-TTTTATT
*
41214808 TTCTAAAATTTATT
1 TT-TAAATTTTATT
41214822 TT
1 TT
41214824 GATAGCCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (13 bp):
TTTAAATTTTATT
Found at i:41215089 original size:10 final size:10
Alignment explanation
Indices: 41215074--41215115 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
41215064 TTATATTCAC
41215074 AATAATTTTT
1 AATAATTTTT
41215084 AATAATTTATT
1 AATAATTT-TT
*
41215095 -ATAATTCTT
1 AATAATTTTT
*
41215104 AACAATTTTT
1 AATAATTTTT
41215114 AA
1 AA
41215116 ATATTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (10 bp):
AATAATTTTT
Done.