Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 157 of 199
Found at i:46949106 original size:28 final size:27
Alignment explanation
Indices: 46948949--46949105 Score: 115
Period size: 28 Copynumber: 6.1 Consensus size: 27
46948939 TTACATAACT
*
46948949 TATTAATATATATTTTAAAATAT-ATATA
1 TATT-ATATAT-TTTTAAAATTTAATATA
*
46948977 TATATATATATCTTTAAAATTT-A-ATA
1 TAT-TATATATTTTTAAAATTTAATATA
*
46949003 T-GTATATA-TTTTAAAATTTAAT-T-
1 TATTATATATTTTTAAAATTTAATATA
* *
46949026 TA-TATATGTTTTGAAAATTTAATATA
1 TATTATATATTTTTAAAATTTAATATA
* * *
46949052 TATGCATATACTTTCAAAATTTAAT-T-
1 TAT-TATATATTTTTAAAATTTAATATA
46949078 TA-TAT-T-TTTTTAAAATTTAATATA
1 TATTATATATTTTTAAAATTTAATATA
46949102 TATT
1 TATT
46949106 TTTAATATAA
Statistics
Matches: 104, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
22 13 0.12
23 18 0.17
24 25 0.24
25 2 0.02
26 8 0.08
27 11 0.11
28 26 0.25
29 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
TATTATATATTTTTAAAATTTAATATA
Found at i:46949122 original size:75 final size:74
Alignment explanation
Indices: 46948954--46949108 Score: 189
Period size: 74 Copynumber: 2.1 Consensus size: 74
46948944 TAACTTATTA
* * *
46948954 ATATATATTTT-AAAATAT-ATATATATATATATATCTTTAAAATTTAATATGTATATATTTTAA
1 ATATATGTTTTGAAAATTTAATATATATACATATATCTTTAAAATTTAATATGTATATATTTTAA
46949017 AATTTAATTT
66 AATTTAA-TT
* *
46949027 ATATATGTTTTGAAAATTTAATATATATGCATATA-CTTTCAAAATTTAAT-T-TATATTTTTTT
1 ATATATGTTTTGAAAATTTAATATATATACATATATCTTT-AAAATTTAATATGTATA-TATTTT
46949089 AAAATTTAA-T
64 AAAATTTAATT
46949099 ATATAT-TTTT
1 ATATATGTTTT
46949109 AATATAAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
71 4 0.05
72 7 0.10
73 14 0.19
74 25 0.34
75 23 0.32
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (74 bp):
ATATATGTTTTGAAAATTTAATATATATACATATATCTTTAAAATTTAATATGTATATATTTTAA
AATTTAATT
Found at i:46949210 original size:26 final size:28
Alignment explanation
Indices: 46949181--46949233 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
46949171 ATTTTTAATA
46949181 TATATA-TT-GAAAATTTAATATATATG
1 TATATACTTCGAAAATTTAATATATATG
*
46949207 TATATACTTCTAAAATTTAATATATAT
1 TATATACTTCGAAAATTTAATATATAT
46949234 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 16 0.67
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (28 bp):
TATATACTTCGAAAATTTAATATATATG
Found at i:46949253 original size:20 final size:20
Alignment explanation
Indices: 46949207--46949259 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
46949197 AATATATATG
* *
46949207 TATATACTTCTAAAATTTAA
1 TATATATTTTTAAAATTTAA
46949227 TATATATTTTTAAAATTTAA
1 TATATATTTTTAAAATTTAA
*
46949247 TTTATATTTTTAA
1 TATATATTTTTAA
46949260 TATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTTTTAAAATTTAA
Found at i:46949267 original size:12 final size:12
Alignment explanation
Indices: 46949242--46949289 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
46949232 ATTTTTAAAA
*
46949242 TTTAATTTATATT
1 TTTAATATA-ATT
46949255 TTTAATATAATT
1 TTTAATATAATT
46949267 TTTAATATAATT
1 TTTAATATAATT
46949279 TTTAATATAAT
1 TTTAATATAAT
46949290 ACGTACACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 26 0.76
13 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAATATAATT
Found at i:46949284 original size:24 final size:25
Alignment explanation
Indices: 46949222--46949289 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 25
46949212 ACTTCTAAAA
46949222 TTTAATATATATTTTT-A-A-AA--
1 TTTAATATATATTTTTAATATAATT
*
46949242 TTTAATTTATATTTTTAATATAATT
1 TTTAATATATATTTTTAATATAATT
46949267 TTTAATATA-ATTTTTAATATAAT
1 TTTAATATATATTTTTAATATAAT
46949290 ACGTACACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 15 0.37
21 1 0.02
22 1 0.02
23 2 0.05
24 14 0.34
25 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTAATATATATTTTTAATATAATT
Found at i:46949342 original size:25 final size:25
Alignment explanation
Indices: 46949323--46949591 Score: 189
Period size: 25 Copynumber: 10.5 Consensus size: 25
46949313 TATAATATTG
46949323 AACTCACATAATTTTCATAATACAT
1 AACTCACATAATTTTCATAATACAT
* * *
46949348 AACTTACTTAATTTTCATAATAAAT
1 AACTCACATAATTTTCATAATACAT
* * *
46949373 AACTTACATAACTTACATAATACAT
1 AACTCACATAATTTTCATAATACAT
* * * *
46949398 AACTTACATAATATACA-ACTTACAT
1 AACTCACATAATTTTCATA-ATACAT
* ** *** *
46949423 AATTTTCATAATACACAACTTACATAAAATT
1 AACTCACATAATTTTC-A--TA-AT-ACA-T
46949454 GAACTCACATAATTTTCATAATACAT
1 -AACTCACATAATTTTCATAATACAT
* * *
46949480 AACTTACTTAATTTTCATAATAAAT
1 AACTCACATAATTTTCATAATACAT
* * *
46949505 AACTTACATAACTTACATAATACAT
1 AACTCACATAATTTTCATAATACAT
* * * * *
46949530 AACTTACATAACTTACATAATATAC
1 AACTCACATAATTTTCATAATACAT
*
46949555 AACTTACATAATTTTCATAATACAT
1 AACTCACATAATTTTCATAATACAT
*
46949580 AACTTACATAAT
1 AACTCACATAAT
46949592 GTTGAACTTA
Statistics
Matches: 201, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.00
25 175 0.87
26 2 0.01
27 2 0.01
28 2 0.01
29 5 0.02
30 2 0.01
31 2 0.01
32 10 0.05
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.36
Consensus pattern (25 bp):
AACTCACATAATTTTCATAATACAT
Found at i:46949346 original size:41 final size:41
Alignment explanation
Indices: 46949301--46949491 Score: 193
Period size: 41 Copynumber: 4.4 Consensus size: 41
46949291 CGTACACAAC
*
46949301 ATACATAACTTATATAATATTGAACTCACATAATTTTCATA
1 ATACATAACTTACATAATATTGAACTCACATAATTTTCATA
* * * * *
46949342 ATACATAACTTACTTAATTTTCATAATAAATAACTTACATAACTTACATA
1 ATACATAACTTACATAA---T-AT--T---GAACTCACATAATTTTCATA
** *
46949392 ATACATAACTTACATAATATACAACTTACATAATTTTCATA
1 ATACATAACTTACATAATATTGAACTCACATAATTTTCATA
* *
46949433 ATACACAACTTACATAAAATTGAACTCACATAATTTTCATA
1 ATACATAACTTACATAATATTGAACTCACATAATTTTCATA
*
46949474 ATACATAACTTACTTAAT
1 ATACATAACTTACATAAT
46949492 TTTCATAATA
Statistics
Matches: 122, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
41 83 0.68
44 1 0.01
45 2 0.02
46 2 0.02
47 2 0.02
50 32 0.26
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (41 bp):
ATACATAACTTACATAATATTGAACTCACATAATTTTCATA
Found at i:46949375 original size:66 final size:66
Alignment explanation
Indices: 46949305--46949632 Score: 347
Period size: 66 Copynumber: 4.8 Consensus size: 66
46949295 CACAACATAC
* *
46949305 ATAACTTATATAATATTGAACTCACATAATTTTCATAATACATAACTTACTTAATTTTCATAATA
1 ATAACTTACATAATATTGAACTCACATAATTTTCATAATACATAACTTACATAATTTTCATAATA
46949370 A
66 A
* * * * *
46949371 ATAACTTACATAACTTACAT-AA-T-ACATAACTTACATAATATACAACTTACATAATTTTCATA
1 ATAACTTACATAA--TA-TTGAACTCACATAATTTTCATAATACATAACTTACATAATTTTCATA
*
46949433 ATAC
63 ATAA
* * *
46949437 ACAACTTACATAAAATTGAACTCACATAATTTTCATAATACATAACTTACTTAATTTTCATAATA
1 ATAACTTACATAATATTGAACTCACATAATTTTCATAATACATAACTTACATAATTTTCATAATA
46949502 A
66 A
* * * * * *
46949503 ATAACTTACATAACTTACATAATACATAACTTACATAACTTACATAATATACAACTTACATAATT
1 ATAACTTACATAA--T--AT--T---GAACTCACATAATTTTCATAATACATAACTTACATAATT
*
46949568 TTCATAATAC
57 TTCATAATAA
* *
46949578 ATAACTTACATAATGTTGAACTTACATAATTTTCATAATACATAACTTACATAAT
1 ATAACTTACATAATATTGAACTCACATAATTTTCATAATACATAACTTACATAAT
46949633 GTTGAACTCG
Statistics
Matches: 214, Mismatches: 33, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
63 1 0.00
64 3 0.01
65 1 0.00
66 143 0.67
67 1 0.00
68 4 0.02
69 2 0.01
70 2 0.01
71 1 0.00
72 1 0.00
73 1 0.00
75 54 0.25
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.37
Consensus pattern (66 bp):
ATAACTTACATAATATTGAACTCACATAATTTTCATAATACATAACTTACATAATTTTCATAATA
A
Found at i:46949665 original size:25 final size:25
Alignment explanation
Indices: 46949637--46949697 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
46949627 CATAATGTTG
* * *
46949637 AACTCGCATAATTTTCATAATACAT
1 AACTCACATAACTTTCATAATAAAT
* *
46949662 AACTTACTTAACTTTCATAATAAAT
1 AACTCACATAACTTTCATAATAAAT
*
46949687 AACTTACATAA
1 AACTCACATAA
46949698 TACATAACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (25 bp):
AACTCACATAACTTTCATAATAAAT
Found at i:46949715 original size:41 final size:41
Alignment explanation
Indices: 46949363--46949721 Score: 247
Period size: 41 Copynumber: 8.7 Consensus size: 41
46949353 ACTTAATTTT
* *
46949363 CATAATAAATAACTTACATAACTTACATAATACATAACTTA
1 CATAATACATAACTTACATAACTTTCATAATACATAACTTA
* * * *
46949404 CATAATATACAACTTACATAATTTTCATAATACACAACTTA
1 CATAATACATAACTTACATAACTTTCATAATACATAACTTA
* *
46949445 CATAA-A-ATTGAACTCACATAATTTTCATAATACATAACTTA
1 CATAATACA-T-AACTTACATAACTTTCATAATACATAACTTA
* * * *
46949486 CTTAATTTTCATAA--TAAATAACTTACATAACTTACATAA--TA
1 CATAA--TACATAACTTACATAACTTTCATAA--TACATAACTTA
* * * *
46949527 CATAACTTACATAACTTACATAA-TATACA-ACTTACATAATTTT
1 CATAA--TACATAACTTACATAACT-TTCATA-ATACATAACTTA
* * * *
46949570 CATAATACATAACTTACATAA-TGTTGA-ACTTACATAATTTT
1 CATAATACATAACTTACATAACT-TTCATA-ATACATAACTTA
* * * * *
46949611 CATAATACATAACTTACATAA-TGTTGA-ACTCGCATAATTTT
1 CATAATACATAACTTACATAACT-TTCATAAT-ACATAACTTA
* *
46949652 CATAATACATAACTTACTTAACTTTCATAATAAATAACTTA
1 CATAATACATAACTTACATAACTTTCATAATACATAACTTA
* *
46949693 CATAATACATAACTTAAATAACTTACATA
1 CATAATACATAACTTACATAACTTTCATA
46949722 GCTTAATTAT
Statistics
Matches: 266, Mismatches: 35, Indels: 34
0.79 0.10 0.10
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 231 0.87
42 5 0.02
43 25 0.09
44 1 0.00
45 1 0.00
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.36
Consensus pattern (41 bp):
CATAATACATAACTTACATAACTTTCATAATACATAACTTA
Found at i:46955221 original size:39 final size:39
Alignment explanation
Indices: 46955166--46955244 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
46955156 AAACGGAGGC
*
46955166 AGCATCGAGAGAAGCTGAGGTT-AAAAAAAGATATGAAGA
1 AGCAGCGAGAGAAGCTGAGGTTCAAAAAAAG-TATGAAGA
**
46955205 AGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGA
1 AGCAGCGAGAGAAGCTGAGGTTCAAAAAAAGTATGAAGA
46955244 A
1 A
46955245 CTCCAGCTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.46, C:0.10, G:0.30, T:0.14
Consensus pattern (39 bp):
AGCAGCGAGAGAAGCTGAGGTTCAAAAAAAGTATGAAGA
Found at i:46955746 original size:43 final size:42
Alignment explanation
Indices: 46955620--46955863 Score: 215
Period size: 43 Copynumber: 5.9 Consensus size: 42
46955610 GCGTTATTTA
* *
46955620 AAAAAACGCCACTAAA-GTCAGGGTCTTTAGCGGCGTTTG-A
1 AAAAAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
** *
46955660 AAGAAAAGCGCCATTAAAGGTCAGGGTCTTTAGCGGTGTTTGTT
1 AA-AAAA-CGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
46955704 AAAAAACCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
1 AAAAAA-CGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
* * *
46955747 GAAAAA----GC-----GTCAGGGCCTTTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
* * * * *
46955780 CCACAATCGCTGCTAAAAGGTCATGGTCTTT-GCAGGCGTTTGTT
1 -AAAAAACGCCGCT-AAAGGTCAGGGTCTTTAGC-GGCGTTTGTT
*
46955824 ACAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1 A-AAAAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTT
46955864 TTGGCAAAGT
Statistics
Matches: 166, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
33 23 0.14
34 3 0.02
38 4 0.02
40 2 0.01
41 4 0.02
42 9 0.05
43 89 0.54
44 32 0.19
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTT
Found at i:46955820 original size:44 final size:43
Alignment explanation
Indices: 46955763--46955927 Score: 147
Period size: 44 Copynumber: 3.8 Consensus size: 43
46955753 GCGTCAGGGC
* * * *
46955763 CTTTAGCGGCGTTTTTTCCACAATCGCTGCTAAAAGGTCATGGT
1 CTTTAGCGGCGTTTTTTACAAAAACGCCGCT-AAAGGTCATGGT
*
46955807 CTTT-GCAGGCGTTTGTTACAAAAACGCCGCTAAAGGTCATGGT
1 CTTTAGC-GGCGTTTTTTACAAAAACGCCGCTAAAGGTCATGGT
** ** * **
46955850 CTTTAGCGGCGTTTTTGGC-AAAGTGCCGCTATAGGTCATGAC
1 CTTTAGCGGCGTTTTTTACAAAAACGCCGCTAAAGGTCATGGT
* *
46955892 CTTTAGCGGCGTTTATTT-CTAAAAATGTCGCTAAAG
1 CTTTAGCGGCGTTT-TTTAC-AAAAACGCCGCTAAAG
46955928 TTAGCGACGC
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 33 0.33
43 29 0.29
44 37 0.37
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTTACAAAAACGCCGCTAAAGGTCATGGT
Found at i:46955820 original size:77 final size:75
Alignment explanation
Indices: 46955675--46955823 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 75
46955665 AAGCGCCATT
* *
46955675 AAAGGTCAGGGTCTTTAGCGGTGTTTGTTAAAAAACCGCCGCTAAAGGTCAGGGTCTTTAGCGGC
1 AAAGGTCAGGGCCTTTAGCGGCGTTTGTTAAAAAACCGCCGCTAAAGGTCAGGGTCTTTAGCGGC
46955740 GTTTGTTGAA
66 GTTTGTTGAA
* ** * * * *
46955750 AAAGCGTCAGGGCCTTTAGCGGCGTTTTTTCCACAATCGCTGCTAAAAGGTCATGGTCTTT-GCA
1 AAAG-GTCAGGGCCTTTAGCGGCGTTTGTTAAAAAACCGCCGCT-AAAGGTCAGGGTCTTTAGC-
46955814 GGCGTTTGTT
63 GGCGTTTGTT
46955824 ACAAAAACGC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 4 0.06
76 33 0.53
77 25 0.40
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (75 bp):
AAAGGTCAGGGCCTTTAGCGGCGTTTGTTAAAAAACCGCCGCTAAAGGTCAGGGTCTTTAGCGGC
GTTTGTTGAA
Found at i:46955879 original size:42 final size:40
Alignment explanation
Indices: 46955763--46955905 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 40
46955753 GCGTCAGGGC
* *
46955763 CTTTAGCGGCGTTTTTTCCACAATCGCTGCTAAAAGGTCATGGT
1 CTTTAGCGGCG-TTTTTACA-AAT-GCCGCT-AAAGGTCATGGT
*
46955807 CTTT-GCAGGCGTTTGTTACAAAAACGCCGCTAAAGGTCATGGT
1 CTTTAGC-GGCGTTT-TTAC--AAATGCCGCTAAAGGTCATGGT
* * **
46955850 CTTTAGCGGCGTTTTTGGCAAAGTGCCGCTATAGGTCATGAC
1 CTTTAGCGGCGTTTTT-ACAAA-TGCCGCTAAAGGTCATGGT
46955892 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
46955906 ATTTCTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
41 3 0.04
42 31 0.37
43 29 0.35
44 18 0.21
45 2 0.02
46 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTACAAATGCCGCTAAAGGTCATGGT
Found at i:46958364 original size:56 final size:56
Alignment explanation
Indices: 46958278--46958390 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
46958268 ATATCTTACC
46958278 TATGAATAAATAAATAAAAGGACGGGGAGGTTGAAGGCTTATAACAAATGAGAACT
1 TATGAATAAATAAATAAAAGGACGGGGAGGTTGAAGGCTTATAACAAATGAGAACT
46958334 TATGAATAAATAAATAAAAGGACGGGGAGGTTGAAGGCTTATAACAAATGAGAACT
1 TATGAATAAATAAATAAAAGGACGGGGAGGTTGAAGGCTTATAACAAATGAGAACT
46958390 T
1 T
46958391 GTTGAGAACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (56 bp):
TATGAATAAATAAATAAAAGGACGGGGAGGTTGAAGGCTTATAACAAATGAGAACT
Found at i:46959644 original size:19 final size:20
Alignment explanation
Indices: 46959612--46959649 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
46959602 TAAAGCTTAA
*
46959612 TTTAAATATATAAACTATAT
1 TTTAAACATATAAACTATAT
*
46959632 TTTAAACAT-TAAAGTATA
1 TTTAAACATATAAACTATA
46959650 ATCATTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTAAACATATAAACTATAT
Found at i:46963864 original size:3 final size:3
Alignment explanation
Indices: 46963847--46963882 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
46963837 TTTAGGGTTT
*
46963847 AAG AAG AGG AA- AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
46963883 GGAGGAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46963887 original size:3 final size:3
Alignment explanation
Indices: 46963881--46963925 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
46963871 AGAAGAAGAA
46963881 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
46963926 AAGAAGAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:46964451 original size:3 final size:3
Alignment explanation
Indices: 46964443--46964485 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
46964433 GGAAAGAGTC
46964443 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
46964486 GCAAAGACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46964566 original size:3 final size:3
Alignment explanation
Indices: 46964560--46964589 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
46964550 TTTTATAGTC
46964560 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
46964590 CCTTTGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:46964703 original size:20 final size:20
Alignment explanation
Indices: 46964680--46964722 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
46964670 CCACGTGACA
46964680 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
*
46964700 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
46964720 AGT
1 AGT
46964723 CCCGTTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:46966206 original size:46 final size:46
Alignment explanation
Indices: 46966103--46966302 Score: 325
Period size: 46 Copynumber: 4.4 Consensus size: 46
46966093 TACGTATGAT
* * *
46966103 CACTAATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
46966146 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
46966192 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
46966238 CGCTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
46966284 CACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACT
46966303 AATCAGAAGT
Statistics
Matches: 145, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 9 0.06
44 5 0.03
45 20 0.14
46 111 0.77
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:46986198 original size:3 final size:3
Alignment explanation
Indices: 46986190--46986251 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
46986180 TGAATCAATG
46986190 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46986238 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
46986252 TGTACAGCTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:46987333 original size:16 final size:16
Alignment explanation
Indices: 46987312--46987346 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
46987302 ACCTGTGATC
46987312 CAAGTCAATGTAGGAA
1 CAAGTCAATGTAGGAA
*
46987328 CAAGTCAATGTATGAA
1 CAAGTCAATGTAGGAA
46987344 CAA
1 CAA
46987347 TAGAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (16 bp):
CAAGTCAATGTAGGAA
Found at i:46991027 original size:46 final size:46
Alignment explanation
Indices: 46990934--46991119 Score: 142
Period size: 46 Copynumber: 4.1 Consensus size: 46
46990924 GTAAGATTTA
* * * * *
46990934 ATTCTGTTATTTGAATTAATTATGTCTGATCTGCATATTCGTATTG
1 ATTCTGTTATTCGAAATAATAATGTCTGATCTGCATATCCATATTG
* * *
46990980 ATTCTATTATTCGAAATAATAATGTCTGATCTGTATATCCATTTTG
1 ATTCTGTTATTCGAAATAATAATGTCTGATCTGCATATCCATATTG
* * * * * * **
46991026 ATTCCGTTATTCAAAATAATTACGTCCGATCTATC-TATCTGTATTG
1 ATTCTGTTATTCGAAATAATAATGTCTGATCT-GCATATCCATATTG
* * * * * * *
46991072 ATTTTGTCATTCGAAATCATTATGTCCGATCTACATAT-CGTATTG
1 ATTCTGTTATTCGAAATAATAATGTCTGATCTGCATATCCATATTG
46991117 ATT
1 ATT
46991120 TTATTACTGG
Statistics
Matches: 111, Mismatches: 27, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
45 10 0.09
46 101 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (46 bp):
ATTCTGTTATTCGAAATAATAATGTCTGATCTGCATATCCATATTG
Found at i:46992736 original size:24 final size:24
Alignment explanation
Indices: 46992704--46992751 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
46992694 CAGATAGATT
46992704 TTTGATCAATATGAAAACATATTG
1 TTTGATCAATATGAAAACATATTG
46992728 TTTGATCAATATGAAAACATATTG
1 TTTGATCAATATGAAAACATATTG
46992752 ACCCAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
TTTGATCAATATGAAAACATATTG
Found at i:46997853 original size:34 final size:34
Alignment explanation
Indices: 46997805--46997872 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
46997795 TTGTCTCCAA
*
46997805 ACTCTCCTTCTAGCAACTTTAAGCTCTATTAGCT
1 ACTCTCATTCTAGCAACTTTAAGCTCTATTAGCT
* **
46997839 ACTCTCATTTTAGCAGTTTTAAGCTCTATTAGCT
1 ACTCTCATTCTAGCAACTTTAAGCTCTATTAGCT
46997873 TTATCTTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (34 bp):
ACTCTCATTCTAGCAACTTTAAGCTCTATTAGCT
Found at i:46999072 original size:17 final size:17
Alignment explanation
Indices: 46999052--46999084 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46999042 TATATTTTTA
46999052 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
46999069 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
46999085 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:46999542 original size:21 final size:21
Alignment explanation
Indices: 46999517--46999573 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
46999507 CCTTTGTTTC
46999517 TAATCTCATTGCTACAAT-AT
1 TAATCTCATTGCTACAATAAT
**
46999537 TCAATCTCATCACTACAATAAT
1 T-AATCTCATTGCTACAATAAT
*
46999559 TAATTTCATTGCTAC
1 TAATCTCATTGCTAC
46999574 CGCTGTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.87
22 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (21 bp):
TAATCTCATTGCTACAATAAT
Found at i:47000109 original size:16 final size:15
Alignment explanation
Indices: 47000088--47000146 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
47000078 ATTTTAAAAC
47000088 AAATTAAAAATTTTAA
1 AAATTAAAAATTTT-A
*
47000104 AAATT-ATAATTGTTA
1 AAATTAAAAATT-TTA
47000119 AAA-TAAAAACTCTTTA
1 AAATTAAAAA-T-TTTA
47000135 AAATTCAAAAAT
1 AAATT-AAAAAT
47000147 AAAAATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 14 0.40
17 3 0.09
18 5 0.14
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
AAATTAAAAATTTTA
Found at i:47000159 original size:25 final size:24
Alignment explanation
Indices: 47000118--47000171 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
47000108 TATAATTGTT
* *
47000118 AAAATAAAAACTCTTTAAAATTCA
1 AAAATAAAAACTCTTTAAAAATAA
* *
47000142 AAAATAAAAATTATTTTAAAAATAA
1 AAAATAAAAACT-CTTTAAAAATAA
47000167 AAAAT
1 AAAAT
47000172 TTCCAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATAAAAACTCTTTAAAAATAA
Found at i:47004598 original size:91 final size:91
Alignment explanation
Indices: 47004443--47004609 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 91
47004433 TTTAATGGTG
* ** * * * *
47004443 GCATGTTAGAGGGATGATAAGAAAATGGCGATGGTGAAGGAGTCGAGAGGGATGAAGAAAAATGG
1 GCATGTGAGAGGGACAATAAGAAAATGGCGATGGTGAAGGAGCCAAAAAGGATGAAGAAAAATGG
47004508 TGAAAAAGCCCCCTTGTTTAGTAGTT
66 TGAAAAAGCCCCCTTGTTTAGTAGTT
* * *
47004534 GCATGTGAGAGGGACAATAAGAAAATGGTGGTGGTGAGGGAGCCAAAAAGGATGAAGAAAAATGG
1 GCATGTGAGAGGGACAATAAGAAAATGGCGATGGTGAAGGAGCCAAAAAGGATGAAGAAAAATGG
47004599 TGAAAAAGCCC
66 TGAAAAAGCCC
47004610 TCCCTTTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 66 1.00
ACGTcount: A:0.38, C:0.09, G:0.35, T:0.18
Consensus pattern (91 bp):
GCATGTGAGAGGGACAATAAGAAAATGGCGATGGTGAAGGAGCCAAAAAGGATGAAGAAAAATGG
TGAAAAAGCCCCCTTGTTTAGTAGTT
Found at i:47006659 original size:17 final size:16
Alignment explanation
Indices: 47006637--47006672 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
47006627 TTTTCAACGT
*
47006637 AAATTAAATTAAATTCA
1 AAATTAAAATAAATT-A
47006654 AAATTAAAATAAATTA
1 AAATTAAAATAAATTA
47006670 AAA
1 AAA
47006673 CAAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAATAAATTA
Found at i:47011245 original size:86 final size:87
Alignment explanation
Indices: 47011099--47011275 Score: 338
Period size: 86 Copynumber: 2.0 Consensus size: 87
47011089 ACAGAGTGAC
47011099 TGTTAGTGTAATTTACCCTAAAAAAATAATTTTAATATTAGGCTCCGCTTGTTTGCATGTAAAAT
1 TGTTAGTGTAATTTACCCTAAAAAAATAATTTTAATATTAGGCTCCGCTTGTTTGCATGTAAAAT
47011164 ATTTTAATTATTTTATTATGTT
66 ATTTTAATTATTTTATTATGTT
*
47011186 TGTTAGTGTAATTTACCCT-AAAAAATAATTTTAATATTAGGCTTCGCTTGTTTGCATGTAAAAT
1 TGTTAGTGTAATTTACCCTAAAAAAATAATTTTAATATTAGGCTCCGCTTGTTTGCATGTAAAAT
47011250 ATTTTAATTATTTTATTATGTT
66 ATTTTAATTATTTTATTATGTT
47011272 TGTT
1 TGTT
47011276 TGGTGGAAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 70 0.79
87 19 0.21
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (87 bp):
TGTTAGTGTAATTTACCCTAAAAAAATAATTTTAATATTAGGCTCCGCTTGTTTGCATGTAAAAT
ATTTTAATTATTTTATTATGTT
Found at i:47014472 original size:30 final size:26
Alignment explanation
Indices: 47014419--47014472 Score: 63
Period size: 30 Copynumber: 1.9 Consensus size: 26
47014409 TATAAATGCA
*
47014419 TAAAATAATAATGTTATTTTAAGTTT
1 TAAAATAATAATGTTATTGTAAGTTT
47014445 TAAAATAAGTAATTTGTATATTGTAAGT
1 TAAAATAA-TAA--TGT-TATTGTAAGT
47014473 GTTGAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
29 3 0.13
30 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (26 bp):
TAAAATAATAATGTTATTGTAAGTTT
Found at i:47016209 original size:2 final size:2
Alignment explanation
Indices: 47016202--47016281 Score: 58
Period size: 2 Copynumber: 41.0 Consensus size: 2
47016192 AGGTGTATTG
** * * *
47016202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GG AT AT GT AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
47016244 AT -T AT AG AA AT AT AT AT A- AA AT AT A- AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
47016282 TACAAGATAT
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
1 3 0.05
2 56 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:47016637 original size:14 final size:15
Alignment explanation
Indices: 47016618--47016646 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47016608 GCATAAAAGG
47016618 ACATAAT-AAATAAT
1 ACATAATAAAATAAT
47016632 ACATAATAAAATAAT
1 ACATAATAAAATAAT
47016647 TATATACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
ACATAATAAAATAAT
Found at i:47017992 original size:13 final size:14
Alignment explanation
Indices: 47017974--47018006 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
47017964 ATAATTATAA
*
47017974 TTATTTTTAA-ATT
1 TTATTTTCAACATT
47017987 TTATTTTCAACATT
1 TTATTTTCAACATT
47018001 TTATTT
1 TTATTT
47018007 ATTTTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTCAACATT
Found at i:47018404 original size:15 final size:17
Alignment explanation
Indices: 47018364--47018409 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
47018354 TTTATGTTAA
*
47018364 ATATATTTAATAATTTT
1 ATATAATTAATAATTTT
*
47018381 ATGTAATTAA-AATTTT
1 ATATAATTAATAATTTT
47018397 A-ATAATTAATAAT
1 ATATAATTAATAAT
47018410 ATATTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATAATTAATAATTTT
Found at i:47020367 original size:40 final size:40
Alignment explanation
Indices: 47020315--47020398 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
47020305 GCTCCTGTAG
47020315 TTTATTCCGATTTTCTAGTTTTTGCTCGTTTTTCACTCCT
1 TTTATTCCGATTTTCTAGTTTTTGCTCGTTTTTCACTCCT
*
47020355 TTTATTCTGATTTTCTAGTTTTTGCTCGTTTTTCACTCCT
1 TTTATTCCGATTTTCTAGTTTTTGCTCGTTTTTCACTCCT
47020395 TTTA
1 TTTA
47020399 CTCCCAAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.11, C:0.20, G:0.10, T:0.60
Consensus pattern (40 bp):
TTTATTCCGATTTTCTAGTTTTTGCTCGTTTTTCACTCCT
Found at i:47030322 original size:38 final size:38
Alignment explanation
Indices: 47030275--47030347 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
47030265 CAAGATTGGT
*
47030275 ACATTTTGTTCATATGGGAACCA-TTTGTTGATAAGGGA
1 ACATCTTGTTCATATGGGAA-CATTTTGTTGATAAGGGA
* *
47030313 ACATCTTGTTTATATTGGAACATTTTGTTGATAAG
1 ACATCTTGTTCATATGGGAACATTTTGTTGATAAG
47030348 ATGCATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (38 bp):
ACATCTTGTTCATATGGGAACATTTTGTTGATAAGGGA
Found at i:47030340 original size:19 final size:19
Alignment explanation
Indices: 47030275--47030341 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
47030265 CAAGATTGGT
47030275 ACATTTTGTTCATATGGGA
1 ACATTTTGTTCATATGGGA
* *
47030294 ACCA-TTTGTTGATAAGGGA
1 A-CATTTTGTTCATATGGGA
* * *
47030313 ACATCTTGTTTATATTGGA
1 ACATTTTGTTCATATGGGA
47030332 ACATTTTGTT
1 ACATTTTGTT
47030342 GATAAGATGC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.05
19 35 0.90
20 2 0.05
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.43
Consensus pattern (19 bp):
ACATTTTGTTCATATGGGA
Found at i:47031349 original size:95 final size:95
Alignment explanation
Indices: 47031233--47031425 Score: 230
Period size: 97 Copynumber: 2.0 Consensus size: 95
47031223 TTATTGTATA
* * **
47031233 ATAATGCAATTAATCATATTTTGATTCATATTGCTTCATTC-AACTTCACAAGAAAAAATACTGT
1 ATAATGCAATTAATCA-ATTTTGACTCATATTCCTTCATTCAAACTTCACAAGAAAAAATACTAC
47031297 TAATATCAAATAA-AAAAGTATTATTAAATAT
65 TAATATCAAATAATAAAA-TATTATTAAATAT
* * * * *
47031328 ATAATGCAATTAAGTGC-ATTTTTACTCTTGTTCCTTCATTCAAAACTTCACAAGAAAAGATATT
1 ATAATGCAATTAA-T-CAATTTTGACTCATATTCCTTCATTC-AAACTTCACAAGAAAAAATACT
47031392 ACTAATATCAAATAATTAAAATATTATTAAATAT
63 ACTAATATCAAATAA-TAAAATATTATTAAATAT
47031426 CAAATAATAA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
95 32 0.39
96 1 0.01
97 33 0.40
98 13 0.16
99 4 0.05
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (95 bp):
ATAATGCAATTAATCAATTTTGACTCATATTCCTTCATTCAAACTTCACAAGAAAAAATACTACT
AATATCAAATAATAAAATATTATTAAATAT
Found at i:47031436 original size:25 final size:25
Alignment explanation
Indices: 47031387--47031439 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
47031377 ACAAGAAAAG
47031387 ATATTACTAATATCAAATAATTAAA
1 ATATTACTAATATCAAATAATTAAA
*
47031412 ATATTATTAAATATCAAATAA-TAAA
1 ATATTACT-AATATCAAATAATTAAA
47031437 ATA
1 ATA
47031440 ATAAAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATTACTAATATCAAATAATTAAA
Found at i:47032072 original size:20 final size:20
Alignment explanation
Indices: 47032047--47032086 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
47032037 CGAGTTAAGA
47032047 CTTAGTCGGCTTTAAATGTT
1 CTTAGTCGGCTTTAAATGTT
47032067 CTTAGTCGGCTTTAAATGTT
1 CTTAGTCGGCTTTAAATGTT
47032087 ACTTGAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
CTTAGTCGGCTTTAAATGTT
Found at i:47032654 original size:38 final size:39
Alignment explanation
Indices: 47032607--47032680 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
47032597 TTCTTTTCTG
*
47032607 CCCTCTGTTTATTTTC-TTTTCTTTTCTACCGATTTGCT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
* * *
47032645 CCCTTTGTTTCTTCTCATTTTCTTTTCTGCCGATTT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTT
47032681 TCGATTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 13 0.42
39 18 0.58
ACGTcount: A:0.07, C:0.27, G:0.08, T:0.58
Consensus pattern (39 bp):
CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
Found at i:47035775 original size:16 final size:16
Alignment explanation
Indices: 47035754--47035784 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
47035744 CTAACGCCCC
47035754 CTCTAATCCAATACAT
1 CTCTAATCCAATACAT
47035770 CTCTAATCCAATACA
1 CTCTAATCCAATACA
47035785 GCGAACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
CTCTAATCCAATACAT
Found at i:47036247 original size:16 final size:17
Alignment explanation
Indices: 47036226--47036257 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47036216 CAATTTTATA
47036226 ATTATTAATT-TAAAAT
1 ATTATTAATTATAAAAT
47036242 ATTATTAATTATAAAA
1 ATTATTAATTATAAAA
47036258 AAAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTATTAATTATAAAAT
Found at i:47036678 original size:28 final size:29
Alignment explanation
Indices: 47036640--47036695 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
47036630 CATGCATATT
*
47036640 AAACTTTTTTTA-TTTATCATTT-AAACTA
1 AAACTATTTTTAGTTT-TCATTTGAAACTA
47036668 AAACTATTTTTAGTTTTCATTTGAAACT
1 AAACTATTTTTAGTTTTCATTTGAAACT
47036696 TTTATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.52
Consensus pattern (29 bp):
AAACTATTTTTAGTTTTCATTTGAAACTA
Found at i:47036745 original size:25 final size:25
Alignment explanation
Indices: 47036697--47036745 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
47036687 TTTGAAACTT
* **
47036697 TTATAAATATATTTATATTCTAAAA
1 TTATAAATATATATATATGATAAAA
*
47036722 TTATATATATATATATATGATAAA
1 TTATAAATATATATATATGATAAA
47036746 CTAGTGTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TTATAAATATATATATATGATAAAA
Found at i:47042605 original size:63 final size:64
Alignment explanation
Indices: 47042520--47042642 Score: 205
Period size: 63 Copynumber: 1.9 Consensus size: 64
47042510 GATCATGTTC
47042520 TTTAGCGGCGTTTTTCCTTAAGCGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTTTTATTTT
1 TTTAGCGGCGTTTTTCCTTAAGCGCCACTAAAGAACATGTTCTTTAGCGGCGCTTTTTTATTTT
* *
47042583 TTTAGCGGCGTTTTT-TTCTAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGCTTTTTTA
1 TTTAGCGGCGTTTTTCCT-TAAGCGCCACTAAAGAACATGTTCTTTAGCGGCGCTTTTTTA
47042643 CAAAAACGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 1 0.02
63 48 0.86
64 7 0.12
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.42
Consensus pattern (64 bp):
TTTAGCGGCGTTTTTCCTTAAGCGCCACTAAAGAACATGTTCTTTAGCGGCGCTTTTTTATTTT
Found at i:47047365 original size:114 final size:113
Alignment explanation
Indices: 47047153--47047681 Score: 508
Period size: 115 Copynumber: 4.6 Consensus size: 113
47047143 AAAGCAAGAT
* * * * * * * * *
47047153 CTTTTACGGTGTTTTAACAAAAACGCCACTAAAAA-CATAAAAAACAGTAACGTTTTTATTAAAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAATCCTACAGAACGGCAGCGTTTTTATTAAAA
* *
47047217 CAAAATAACATTTTGCGGCGTTTTCAACGTAGCGCCGCTAAAGGCTGAC
66 CAAAATCACATTTTGCGGCGTTTT-AACATAGCGCCGCTAAAGGCTGAC
* * * * * *
47047266 CTTTTTCGGCGTTTTACAAAAAACGCCACTAACAAATCCTATAGCATGGCAGCG-TTTTAATAAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAA-AAATCCTACAGAACGGCAGCGTTTTTATTAAA
**
47047330 ACAGGATCACATTTTGCGGCGTTTTAA-ATCTAGCGCCGCTAAAGGCTGAC
65 ACAAAATCACATTTTGCGGCGTTTTAACA--TAGCGCCGCTAAAGGCTGAC
* * * * * *
47047380 CTTTTGCGGCATTTTAGCAAAAACGCCAGTAAAAATTCCCACAAAACGGCAAG-GTTTTTATTGA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAA-TCCTACAGAACGGC-AGCGTTTTTATTAA
* * *
47047444 AACAAAATCACATTTTGCGGCGTTTTTAACATAGCGCCTCTAAAGGATGAT
64 AACAAAATCACATTTTGCGGCG-TTTTAACATAGCGCCGCTAAAGGCTGAC
* * * *
47047495 CTTTTGCGGCGTTTTACCAAAAATGCCAGTAAGAAATCCTACAGAACGGCAACGTTTTTATTGAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAA-AAATCCTACAGAACGGCAGCGTTTTTATTAAA
* * * * * ** *
47047560 ACAAAATCACATTTTGCAGCGTTTTCAGCTTAGCGCCGCGAAAGACCAAA
65 ACAAAATCACATTTTGCGGCGTTTT-AACATAGCGCCGCTAAAGGCTGAC
* * * * * * * *
47047610 CTTTTACGGCGTTTTACCCAAAATGCCACTAATATATCCTATAGAACGCCACCGTTTTTATTGAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAA-AAATCCTACAGAACGGCAGCGTTTTTATTAAA
47047675 ACAAAAT
65 ACAAAAT
47047682 TCCTTTAAAT
Statistics
Matches: 346, Mismatches: 58, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
113 33 0.10
114 96 0.28
115 207 0.60
116 9 0.03
117 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (113 bp):
CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAATCCTACAGAACGGCAGCGTTTTTATTAAAA
CAAAATCACATTTTGCGGCGTTTTAACATAGCGCCGCTAAAGGCTGAC
Found at i:47048164 original size:8 final size:7
Alignment explanation
Indices: 47048125--47048271 Score: 88
Period size: 7 Copynumber: 21.1 Consensus size: 7
47048115 ACTAATCAAT
47048125 CTAAACC
1 CTAAACC
47048132 CTAAACAC
1 CTAAAC-C
* *
47048140 ATAACCC
1 CTAAACC
47048147 CTAAATCC
1 CTAAA-CC
47048155 CTTAAACC
1 C-TAAACC
47048163 CTAAACC
1 CTAAACC
* *
47048170 CAAAATC
1 CTAAACC
*
47048177 ATAAACC
1 CTAAACC
47048184 CTAAACC
1 CTAAACC
*
47048191 C---AGC
1 CTAAACC
*
47048195 CTAGACC
1 CTAAACC
47048202 CTAAACC
1 CTAAACC
*
47048209 C-CAACC
1 CTAAACC
*
47048215 TGTAAACC
1 -CTAAACC
*
47048223 TTAAACC
1 CTAAACC
47048230 CT-AACC
1 CTAAACC
47048236 CTAAACC
1 CTAAACC
*
47048243 CTAAACT
1 CTAAACC
*
47048250 GTAAACC
1 CTAAACC
* * *
47048257 ATAATCA
1 CTAAACC
47048264 CTAAACC
1 CTAAACC
47048271 C
1 C
47048272 ATAATTCGCA
Statistics
Matches: 104, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
4 3 0.03
6 10 0.10
7 72 0.69
8 15 0.14
9 4 0.04
ACGTcount: A:0.42, C:0.38, G:0.03, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:47048350 original size:7 final size:7
Alignment explanation
Indices: 47048338--47048380 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
47048328 CATGCATAAT
47048338 CCCTAAA
1 CCCTAAA
47048345 CCCTAAA
1 CCCTAAA
* * *
47048352 TCTTATA
1 CCCTAAA
47048359 CCCTAAA
1 CCCTAAA
*
47048366 CCATAAA
1 CCCTAAA
47048373 CCCTAAA
1 CCCTAAA
47048380 C
1 C
47048381 TATAATGATA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:47048363 original size:14 final size:14
Alignment explanation
Indices: 47048341--47048385 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
47048331 GCATAATCCC
* *
47048341 TAAACCCTAAATCT
1 TAAACCCTAAACCA
*
47048355 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
47048369 TAAACCCTAAACTA
1 TAAACCCTAAACCA
47048383 TAA
1 TAA
47048386 TGATATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:47048843 original size:73 final size:72
Alignment explanation
Indices: 47048706--47048847 Score: 178
Period size: 73 Copynumber: 2.0 Consensus size: 72
47048696 ATCCCCAATC
* *** *
47048706 AAAGACTCAAAAACTAAGAAAACGATGTCATTGGGCTTAGGTTTTTTGCGGCGCTTCTCCAAAAA
1 AAAGACTCAAAAACTAAGAAAACGACGTCATTGGGCTTAGGTTTTTTGCGGAAATTCTCAAAAAA
47048771 CGCCACA
66 CGCCACA
* * * *
47048778 AAAGCCTCGAAAACTAAGAAAAACGACGT-AGTTGGGCTTAGGTTTTTTGCGGAAATTTTTAAAA
1 AAAGACTCAAAAACTAAG-AAAACGACGTCA-TTGGGCTTAGGTTTTTTGCGGAAATTCTCAAAA
47048842 AACGCC
64 AACGCC
47048848 GCTAAAACCC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 17 0.29
73 42 0.71
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (72 bp):
AAAGACTCAAAAACTAAGAAAACGACGTCATTGGGCTTAGGTTTTTTGCGGAAATTCTCAAAAAA
CGCCACA
Found at i:47048900 original size:114 final size:113
Alignment explanation
Indices: 47048754--47049072 Score: 516
Period size: 113 Copynumber: 2.8 Consensus size: 113
47048744 AGGTTTTTTG
* *
47048754 CGGCGC-TTCTCCAAAAACGCCACAAAAGCCTCGAAAACTAAGAAAAACGACGTAGTTGGGCTTA
1 CGGCGCTTTC-CCAAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAACGACGTCGTTGGGCTTA
* ***
47048818 GGTTTTTTGCGGAAATTTTTAAAAAACGCCGCTAAAACCCTGAGAATTAC
64 GGTCTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTAC
*
47048868 CGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGCTGGGCTTAGG
1 CGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTGGGCTTAGG
* * *
47048933 TCTTTTGCGGCGCTTTTTACAAAACGCTGCTAAAACCCTGAGAATTAG
66 TCTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTAC
47048981 CGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTGGGCTTAGG
1 CGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTGGGCTTAGG
47049046 TCTTTTGCGGCGCTTTTT-AAAAACGCC
66 TCTTTTGCGGCGCTTTTTAAAAAACGCC
47049073 ACCAAAGCCT
Statistics
Matches: 191, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
112 7 0.04
113 144 0.75
114 37 0.19
115 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (113 bp):
CGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTGGGCTTAGG
TCTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTAC
Found at i:47049073 original size:71 final size:73
Alignment explanation
Indices: 47048993--47049145 Score: 265
Period size: 72 Copynumber: 2.1 Consensus size: 73
47048983 GCGCTTTCCC
*
47048993 AAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAACGACGTCGTTGGGCTTAGGTCTTTTGCGGC
1 AAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTGGACTTAGGTCTTTTGCGGC
47049057 GCTTTTT-
66 GCTTTTTA
* *
47049064 AAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTGGACTTAGGTTTTTTGTGGC
1 AAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTGGACTTAGGTCTTTTGCGGC
47049129 GCTTTTTA
66 GCTTTTTA
47049137 AAAAACGCC
1 AAAAACGCC
47049146 GCTAATGCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
71 30 0.39
72 38 0.49
73 9 0.12
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (73 bp):
AAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTGGACTTAGGTCTTTTGCGGC
GCTTTTTA
Found at i:47049185 original size:39 final size:40
Alignment explanation
Indices: 47049142--47049256 Score: 106
Period size: 39 Copynumber: 2.9 Consensus size: 40
47049132 TTTTAAAAAA
*
47049142 CGCCGCTAATGCTCATTTTTAGCGGCGTTTTTGTAT-AAG
1 CGCCGCTAATGCTAATTTTTAGCGGCGTTTTTGTATAAAG
* * * * ** * * *
47049181 CGCCGGTAATACTGATCTTTAGATGCGTTTTTTTTTAAAT
1 CGCCGCTAATGCTAATTTTTAGCGGCGTTTTTGTATAAAG
*
47049221 CGCCGCTACTGCTTAATTTTTAGCGGCGTTTGTTGT
1 CGCCGCTAATGC-TAATTTTTAGCGGCGTTT-TTGT
47049257 CCAATCGCCT
Statistics
Matches: 56, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
39 28 0.50
40 11 0.20
41 14 0.25
42 3 0.05
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (40 bp):
CGCCGCTAATGCTAATTTTTAGCGGCGTTTTTGTATAAAG
Found at i:47051555 original size:2 final size:2
Alignment explanation
Indices: 47051544--47051573 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47051534 ATTTATGATG
47051544 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47051574 CACATTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47054343 original size:23 final size:20
Alignment explanation
Indices: 47054288--47054328 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
47054278 TTTTTAAAAA
*
47054288 ATAAAGTAA-TTATAAATAAT
1 ATAAA-TAATTTAAAAATAAT
47054308 ATAAATAATTTAAAAATAAT
1 ATAAATAATTTAAAAATAAT
47054328 A
1 A
47054329 ATAATTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAATAATTTAAAAATAAT
Found at i:47056681 original size:17 final size:18
Alignment explanation
Indices: 47056652--47057051 Score: 222
Period size: 18 Copynumber: 22.1 Consensus size: 18
47056642 ACACAATAAT
47056652 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
47056670 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
47056687 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
47056707 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
47056725 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
47056743 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
47056758 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
47056776 AA-TTTCGAAAACATG-A
1 AATTTTTGAAAACACGAA
* * *
47056792 ATTTTTTAAAAACATG--
1 AATTTTTGAAAACACGAA
*
47056808 AATTTTTAAAAAAAACACGAGA
1 AATTTTT---GAAAACACGA-A
*
47056830 ATTTTTTGAAAACACGAAA
1 AATTTTTGAAAACACG-AA
47056849 ACATGAAAATTTTGAAAACACGAGA
1 A-AT-----TTTTGAAAACACGA-A
*
47056874 ATTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
47056892 AATTTTTG-AAACATGAGA
1 AATTTTTGAAAACACGA-A
* *
47056910 ATTTTTTG---ACACTAA
1 AATTTTTGAAAACACGAA
*
47056925 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
47056943 AA-TTTAGAAAACATG--
1 AATTTTTGAAAACACGAA
** *
47056958 AATTTTTTTAAATACGAA
1 AATTTTTGAAAACACGAA
** *
47056976 TTTTTTTAAAAACACGAGA
1 AATTTTTGAAAACACGA-A
47056995 AATTTTTTGAAAACACGAA
1 AA-TTTTTGAAAACACGAA
47057014 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
* *
47057032 ATTTTTTGAGAACACGAA
1 AATTTTTGAAAACACGAA
47057050 AA
1 AA
47057052 CACGAAAAAA
Statistics
Matches: 295, Mismatches: 54, Indels: 66
0.71 0.13 0.16
Matches are distributed among these distances:
15 16 0.05
16 25 0.08
17 63 0.21
18 88 0.30
19 61 0.21
20 19 0.06
22 6 0.02
24 2 0.01
25 15 0.05
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:47056694 original size:19 final size:18
Alignment explanation
Indices: 47056636--47057051 Score: 165
Period size: 17 Copynumber: 22.8 Consensus size: 18
47056626 ACACGAGAAC
47056636 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
47056656 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
47056674 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
47056692 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
47056711 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
47056729 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
47056747 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
47056762 TTTGAAAACACGAAAA--T
1 TTTG-AAACACGAAAATTT
* *
47056779 TTCGAAA-AC-ATGAATTT
1 TTTGAAACACGA-AAATTT
* *
47056796 TTT-AAAAAC-ATGAATTT
1 TTTGAAACACGA-AAATTT
** *
47056813 TTAAAAAAAACACGAGAATTT
1 TT---TGAAACACGAAAATTT
*
47056834 TTTGAAAACACGAAAACATGAAAAT
1 TTTG-AAACACG-AAA-AT----TT
*
47056859 TTTGAAAACACGAGAATTT
1 TTTG-AAACACGAAAATTT
47056878 TTTGAAAACACGAAAA-TT
1 TTTG-AAACACGAAAATTT
* *
47056896 TTTGAAACATGAGAATTT
1 TTTGAAACACGAAAATTT
* *
47056914 TTTG--ACACTAAAA-AT
1 TTTGAAACACGAAAATTT
47056929 TTTGAAAACACGAAAA--T
1 TTTG-AAACACGAAAATTT
* *
47056946 TTAGAAA-AC-ATGAATTT
1 TTTGAAACACGA-AAATTT
* * *
47056963 TTTTAAATACG-AATTTT
1 TTTGAAACACGAAAATTT
*
47056980 TTTAAAAACACGAGAAATTT
1 TTT-GAAACACGA-AAATTT
47057000 TTTGAAAACACGAAAA-TT
1 TTTG-AAACACGAAAATTT
*
47057018 TTTGAAACACGAGAATTT
1 TTTGAAACACGAAAATTT
47057036 TTTGAGAACACGAAAA
1 TTTGA-AACACGAAAA
47057052 CACGAAAAAA
Statistics
Matches: 311, Mismatches: 46, Indels: 79
0.71 0.11 0.18
Matches are distributed among these distances:
14 2 0.01
15 18 0.06
16 22 0.07
17 72 0.23
18 72 0.23
19 61 0.20
20 22 0.07
21 22 0.07
22 3 0.01
23 2 0.01
24 2 0.01
25 13 0.04
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:47056813 original size:16 final size:17
Alignment explanation
Indices: 47056783--47056819 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
47056773 GAAAATTTCG
47056783 AAAACATGAATTTTTTA
1 AAAACATGAATTTTTTA
47056800 AAAACATGAA-TTTTTA
1 AAAACATGAATTTTTTA
47056816 AAAA
1 AAAA
47056820 AAACACGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AAAACATGAATTTTTTA
Found at i:47056859 original size:27 final size:25
Alignment explanation
Indices: 47056819--47056871 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
47056809 ATTTTTAAAA
*
47056819 AAAACACGAGAATTTTTTGAAAACACG
1 AAAACACGA-AA-ATTTTGAAAACACG
*
47056846 AAAACATGAAAATTTTGAAAACACG
1 AAAACACGAAAATTTTGAAAACACG
47056871 A
1 A
47056872 GAATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (25 bp):
AAAACACGAAAATTTTGAAAACACG
Found at i:47056881 original size:167 final size:166
Alignment explanation
Indices: 47056691--47057015 Score: 512
Period size: 167 Copynumber: 2.0 Consensus size: 166
47056681 CACGAAAATT
* *
47056691 TTTTGAAAACACGGAATTTTTTTGAAAACAAGGAAATTTTCGATACATGAGAATTTTTTGACACG
1 TTTTGAAAACACGGAATTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACACG
*
47056756 AAAAATTTTGAAAACACGAAAATTTCGAAAACATGAA-TTTTTTAAAAACATGAATTTTTAAAAA
66 AAAAATTTTGAAAACACGAAAATTTAGAAAACATGAATTTTTTTAAAAAC--GAATTTTT-AAAA
47056820 AAACACGAG-AATTTTTTGAAAACACGAAAACATGAAAA
128 AAACACGAGAAATTTTTTGAAAACACGAAAACATGAAAA
* *
47056858 TTTTGAAAACACGAGAA-TTTTTTGAAAACACGAAAATTTTTGAAACATGAGAATTTTTTGACAC
1 TTTTGAAAACACG-GAATTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACAC
* * **
47056922 TAAAAATTTTGAAAACACGAAAATTTAGAAAACATGAATTTTTTTAAATACGAATTTTTTTAAAA
65 GAAAAATTTTGAAAACACGAAAATTTAGAAAACATGAATTTTTTTAAAAACGAATTTTTAAAAAA
47056987 ACACGAGAAATTTTTTGAAAACACGAAAA
130 ACACGAGAAATTTTTTGAAAACACGAAAA
47057016 TTTTTGAAAC
Statistics
Matches: 146, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 11 0.08
166 29 0.20
167 92 0.63
168 14 0.10
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (166 bp):
TTTTGAAAACACGGAATTTTTTTGAAAACAAGAAAATTTTCGAAACATGAGAATTTTTTGACACG
AAAAATTTTGAAAACACGAAAATTTAGAAAACATGAATTTTTTTAAAAACGAATTTTTAAAAAAA
CACGAGAAATTTTTTGAAAACACGAAAACATGAAAA
Found at i:47057085 original size:167 final size:162
Alignment explanation
Indices: 47056660--47057051 Score: 486
Period size: 167 Copynumber: 2.4 Consensus size: 162
47056650 ATAATTTTTG
*
47056660 AAAACACGA-AGA-TTTTTG-AAACACG-AAA-ATTTTTTGAAAACACG-GAATTTTTTTGAAAA
1 AAAACACGAGA-ATTTTTTGAAAACACGAAAACATATTTTGAAAACACGAGAA-TTTTTTGAAAA
* * * * *
47056719 CAAG-GAAATTTTCGATACATGAGAATTTTTTGACACGAAAAATTTTGAAAACACGAAAATTTCG
64 CACGAAAAATTTT-GAAACACGAGAATTTTTTGACACGAAAAATTTTGAAAACACGAAAATTTAG
47056783 AAAACATGAATTTTTTAAAAACATGAATTTTTAAAA
128 AAAACATGAATTTTTTAAAAACA-GAATTTTTAAAA
47056819 AAAACACGAGAATTTTTTGAAAACACGAAAACATGAAAATTTTGAAAACACGAGAATTTTTTGAA
1 AAAACACGAGAATTTTTTGAAAACACGAAAACAT----ATTTTGAAAACACGAGAATTTTTTGAA
* * *
47056884 AACACGAAAATTTTTGAAACATGAGAATTTTTTGACACTAAAAATTTTGAAAACACGAAAATTTA
62 AACACGAAAAATTTTGAAACACGAGAATTTTTTGACACGAAAAATTTTGAAAACACGAAAATTTA
* **
47056949 GAAAACATGAATTTTTTTAAATAC-GAATTTTT-TTA
127 GAAAACATGAA-TTTTTTAAAAACAGAATTTTTAAAA
*
47056984 AAAACACGAGAAATTTTTTGAAAACACG-AAA-AT-TTTTG-AAACACGAGAATTTTTTGAGAAC
1 AAAACACGAG-AATTTTTTGAAAACACGAAAACATATTTTGAAAACACGAGAATTTTTTGAAAAC
47057045 ACGAAAA
65 ACGAAAA
47057052 CACGAAAAAA
Statistics
Matches: 209, Mismatches: 11, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
158 29 0.14
159 15 0.07
160 7 0.03
161 7 0.03
162 3 0.01
163 2 0.01
164 2 0.01
165 14 0.07
166 25 0.12
167 85 0.41
168 20 0.10
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (162 bp):
AAAACACGAGAATTTTTTGAAAACACGAAAACATATTTTGAAAACACGAGAATTTTTTGAAAACA
CGAAAAATTTTGAAACACGAGAATTTTTTGACACGAAAAATTTTGAAAACACGAAAATTTAGAAA
ACATGAATTTTTTAAAAACAGAATTTTTAAAA
Found at i:47057135 original size:17 final size:16
Alignment explanation
Indices: 47057064--47057134 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
47057054 CGAAAAAAAA
47057064 TTTT-AAACACGGGAAT
1 TTTTGAAACAC-GGAAT
*
47057080 TTTTGAAAACACGAAATT
1 TTTTG-AAACACGGAA-T
* **
47057098 TTTTTATTCACGAGAAT
1 TTTTGAAACACG-GAAT
47057115 TTTTGAAACACGGAAT
1 TTTTGAAACACGGAAT
47057131 TTTT
1 TTTT
47057135 TTTAAAGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.28
17 18 0.42
18 13 0.30
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (16 bp):
TTTTGAAACACGGAAT
Found at i:47057138 original size:35 final size:35
Alignment explanation
Indices: 47057071--47057136 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
47057061 AAATTTTAAA
*
47057071 CACGGGAATTTTTGAAAACACGAAATTTTTTTATT
1 CACGAGAATTTTTGAAAACACGAAATTTTTTTATT
*
47057106 CACGAGAATTTTTG-AAACACGGAATTTTTTT
1 CACGAGAATTTTTGAAAACACGAAATTTTTTT
47057137 TAAAGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (35 bp):
CACGAGAATTTTTGAAAACACGAAATTTTTTTATT
Found at i:47057213 original size:17 final size:16
Alignment explanation
Indices: 47057191--47057239 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
47057181 TATTATTATT
47057191 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGA-AA
*
47057208 ATTTTGAAGACATGAAA
1 ATTTTGAA-ACACGAAA
47057225 ATTTTCGAAACACGA
1 ATTTT-GAAACACGA
47057240 TTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (16 bp):
ATTTTGAAACACGAAA
Found at i:47058079 original size:7 final size:7
Alignment explanation
Indices: 47058067--47058146 Score: 56
Period size: 7 Copynumber: 11.0 Consensus size: 7
47058057 AAAAAAATTA
47058067 TTTTCTT
1 TTTTCTT
47058074 TTTTCTT
1 TTTTCTT
47058081 TTTT-TT
1 TTTTCTT
47058087 TTCTTCTT
1 TT-TTCTT
*
47058095 TCTTC-T
1 TTTTCTT
**
47058101 TCCTCTT
1 TTTTCTT
47058108 TTCTTCTT
1 TT-TTCTT
47058116 TCTTTCTT
1 T-TTTCTT
*
47058124 CTTTCTT
1 TTTTCTT
*
47058131 CTTCTTCCT
1 -TT-TTCTT
47058140 TTTTCTT
1 TTTTCTT
47058147 CTTCCTTCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
6 9 0.16
7 28 0.48
8 16 0.28
9 5 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTT
Found at i:47058088 original size:11 final size:12
Alignment explanation
Indices: 47058067--47058136 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 12
47058057 AAAAAAATTA
47058067 TTTTCTTTTTTC
1 TTTTCTTTTTTC
47058079 TTTT-TTTTTTC
1 TTTTCTTTTTTC
*
47058090 TTCTTTCTTCTTCCTC
1 -T-TTTCTT-TT-TTC
*
47058106 TTTTCTTCTTTC
1 TTTTCTTTTTTC
*
47058118 -TTTCTTCTTTC
1 TTTTCTTTTTTC
47058129 TTCTTCTT
1 TT-TTCTT
47058137 CCTTTTTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
11 18 0.38
12 8 0.17
13 9 0.19
14 8 0.17
15 3 0.06
16 2 0.04
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:47058093 original size:3 final size:3
Alignment explanation
Indices: 47058087--47058160 Score: 69
Period size: 3 Copynumber: 23.0 Consensus size: 3
47058077 TCTTTTTTTT
*
47058087 TTC TTC TTTC TTC TTC CTC TT- TTC TTC TTTC TTTC TTC TTTC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC -TTC TTC TTC
*
47058135 TTCC TTT TTC TTC TTCC TTC TTC TTC
1 TT-C TTC TTC TTC TT-C TTC TTC TTC
47058161 AAAGTTTAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 2 0.03
3 40 0.66
4 19 0.31
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:47058093 original size:21 final size:21
Alignment explanation
Indices: 47058069--47058146 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
47058059 AAAAATTATT
47058069 TTCTTTTTTCTTTTTTTTTTC
1 TTCTTTTTTCTTTTTTTTTTC
* ** *
47058090 TTCTTTCTTCTTCCTCTTTTC
1 TTCTTTTTTCTTTTTTTTTTC
*
47058111 TTCTTTCTTTCTTCTTTCTTCTTC
1 TTCTTT-TTTCTT-TTT-TTTTTC
*
47058135 TTCCTTTTTCTT
1 TTCTTTTTTCTT
47058147 CTTCCTTCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 23 0.52
22 5 0.11
23 7 0.16
24 9 0.20
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCTTTTTTCTTTTTTTTTTC
Found at i:47058110 original size:32 final size:32
Alignment explanation
Indices: 47058074--47058159 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
47058064 TTATTTTCTT
* *
47058074 TTTTCTTTTTTTTTTCTTCTTTCTTCTTCCTC
1 TTTTCTTCTTTCTTTCTTCTTTCTTCTTCCTC
*
47058106 TTTTCTTCTTTCTTTCTTCTTTCTTCTTCTTCC
1 TTTTCTTCTTTCTTTCTTCTTTCTTCTTCCT-C
*
47058139 TTTTTCTTC-TTCCTTCTTCTT
1 -TTTTCTTCTTTCTTTCTTCTT
47058160 CAAAGTTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
32 28 0.58
33 12 0.25
34 8 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTTCTTCTTTCTTTCTTCTTTCTTCTTCCTC
Found at i:47058155 original size:10 final size:10
Alignment explanation
Indices: 47058087--47058160 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
47058077 TCTTTTTTTT
*
47058087 TTCTTCTTTC
1 TTCTTCCTTC
47058097 TTCTTCC-TC
1 TTCTTCCTTC
47058106 TT-TT-CTTC
1 TTCTTCCTTC
*
47058114 TTTCTTTCTTC
1 -TTCTTCCTTC
47058125 TTTCTT-CTTC
1 -TTCTTCCTTC
*
47058135 TTCCTT-TTTC
1 TT-CTTCCTTC
47058145 TTCTTCCTTC
1 TTCTTCCTTC
47058155 TTCTTC
1 TTCTTC
47058161 AAAGTTTAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
9 11 0.20
10 29 0.53
11 10 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCCTTC
Found at i:47058156 original size:7 final size:7
Alignment explanation
Indices: 47058089--47058157 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
47058079 TTTTTTTTTT
*
47058089 CTTCTTT
1 CTTCTTC
47058096 CTTCTTC
1 CTTCTTC
*
47058103 C-TCTTTT
1 CTTC-TTC
47058110 CTTCTTTC
1 CTTC-TTC
*
47058118 TTTCTTC
1 CTTCTTC
*
47058125 TTTCTT-
1 CTTCTTC
47058131 CTTCTTC
1 CTTCTTC
*
47058138 CTT-TTT
1 CTTCTTC
47058144 CTTCTTC
1 CTTCTTC
47058151 CTTCTTC
1 CTTCTTC
47058158 TTCAAAGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
6 12 0.24
7 31 0.61
8 8 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (7 bp):
CTTCTTC
Found at i:47058512 original size:30 final size:30
Alignment explanation
Indices: 47058476--47058613 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
47058466 AAATACAGCA
* * *
47058476 AAAGTTTTGGTGTCGAAACATAATTTAGAG
1 AAAGTTTAGGGGTCGAAATATAATTTAGAG
* *
47058506 AAAGTTTAGGGGTC-AAAAAGTAATTTTGAG
1 AAAGTTTAGGGGTCGAAATA-TAATTTAGAG
* * *
47058536 AAATTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTCGAAATATAATTTAGAG
* * *
47058565 AAAGTTTAGGGGTTGAAATGTAATTTCGAG
1 AAAGTTTAGGGGTCGAAATATAATTTAGAG
** *
47058595 AAAGTACAGGGGTCAAAAT
1 AAAGTTTAGGGGTCGAAAT
47058614 GAAAATTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
29 29 0.33
30 57 0.64
31 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
AAAGTTTAGGGGTCGAAATATAATTTAGAG
Found at i:47058573 original size:59 final size:60
Alignment explanation
Indices: 47058496--47058614 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 60
47058486 TGTCGAAACA
* * **
47058496 TAATTTAGAGAAAGTTTAGGGGTCAAAAAGTAATTTTGAGAAATTTTAGGGGTCAAAATG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAAAGTAATTTCGAGAAAGTACAGGGGTCAAAATG
** *
47058556 TAATTTAGA-AAAGTTTAGGGGTTGAAATGTAATTTCGAGAAAGTACAGGGGTCAAAATG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAAAGTAATTTCGAGAAAGTACAGGGGTCAAAATG
47058615 AAAATTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
59 43 0.83
60 9 0.17
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.30
Consensus pattern (60 bp):
TAATTTAGAGAAAGTTTAGGGGTCAAAAAGTAATTTCGAGAAAGTACAGGGGTCAAAATG
Found at i:47058614 original size:30 final size:30
Alignment explanation
Indices: 47058496--47058614 Score: 159
Period size: 30 Copynumber: 4.0 Consensus size: 30
47058486 TGTCGAAACA
*
47058496 TAATTTAGAGAAAGTTTAGGGGTCAAAAAG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAATG
* *
47058526 TAATTTTGAGAAATTTTAGGGGTCAAAATG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAATG
**
47058556 TAATTTAGA-AAAGTTTAGGGGTTGAAATG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAATG
* **
47058585 TAATTTCGAGAAAGTACAGGGGTCAAAATG
1 TAATTTAGAGAAAGTTTAGGGGTCAAAATG
47058615 AAAATTTTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
29 25 0.33
30 51 0.67
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.30
Consensus pattern (30 bp):
TAATTTAGAGAAAGTTTAGGGGTCAAAATG
Found at i:47059084 original size:77 final size:74
Alignment explanation
Indices: 47058806--47059264 Score: 555
Period size: 80 Copynumber: 5.9 Consensus size: 74
47058796 AGCTCGGCGT
* * * *
47058806 GTGACCCAAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTG-AAAAACATG-AATTGAAA
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAACA-GAAATT-TAA
47058869 AAATACCTCAGC
63 AAATACCTCAGC
* *
47058881 GTGACGCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAACAGAAA-T---TT
47058946 AAAAAAAATACCTCAGC
61 ---AAAAATACCTCAGC
47058963 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAGCAGAAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTGAAAAAA-CAGAAATTTAA
47059028 AAATACCTCAGC
63 AAATACCTCAGC
* * *
47059040 GTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAACAGAAA-TT
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTG----AAAAAACAGAAATTT
47059104 AAAAATACCTCAGC
61 AAAAATACCTCAGC
*
47059118 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTCAAAAAACAGAAATTAAATTA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAACAGAAA-T---TT-
47059183 AAAAAATACCTCAGC
61 -AAAAATACCTCAGC
*
47059198 GTGACCCGAGACTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTTAAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAA-CAGAAATTTAAA
47059263 AA
64 AA
47059265 ATATTTCTTG
Statistics
Matches: 341, Mismatches: 17, Indels: 51
0.83 0.04 0.12
Matches are distributed among these distances:
73 12 0.04
74 11 0.03
75 30 0.09
76 20 0.06
77 56 0.16
78 56 0.16
79 6 0.02
80 61 0.18
81 12 0.04
82 57 0.17
83 14 0.04
84 6 0.02
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (74 bp):
GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAACAGAAATTTAAAAA
TACCTCAGC
Found at i:47059106 original size:78 final size:78
Alignment explanation
Indices: 47058806--47059249 Score: 530
Period size: 78 Copynumber: 5.7 Consensus size: 78
47058796 AGCTCGGCGT
* * *
47058806 GTGACCCAAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTG-----AAAAACATG-AATT
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAAAAAACA-GAAATT
47058865 GAAAAAATACCTCAGC
64 -AAAAAATACCTCAGC
* * **
47058881 GTGACGCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAACAGAAA-TTAAAT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAA-A-AAACAGAAAT
47058945 TAAAAAAAATACCTCAGC
63 T--AAAAAATACCTCAGC
*** * *
47058963 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT-TTGAAAAAAGCAGAAATTTA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAAAACAGAAATTAA
47059027 AAAATACCTCAGC
66 AAAATACCTCAGC
* * *
47059040 GTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAACAGAAATT-
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAAAAAACAGAAATTA
47059104 AAAAATACCTCAGC
65 AAAAATACCTCAGC
* **
47059118 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTCAAAAAACAGAAA-TTAAATT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAA-A-AAACAGAAATT
47059182 AAAAAAATACCTCAGC
64 -AAAAAATACCTCAGC
*
47059198 GTGACCCGAGACTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAA
47059250 GCAGAAATTT
Statistics
Matches: 319, Mismatches: 32, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
74 11 0.03
75 29 0.09
77 61 0.19
78 63 0.20
79 23 0.07
80 56 0.18
81 21 0.07
82 55 0.17
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (78 bp):
GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAAAACAGAAATTAA
AAAATACCTCAGC
Found at i:47059213 original size:80 final size:80
Alignment explanation
Indices: 47058806--47059258 Score: 580
Period size: 77 Copynumber: 5.8 Consensus size: 80
47058796 AGCTCGGCGT
* * *
47058806 GTGACCCAAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTTG-AAAAACATG-AA-T---
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAACA-GAAATTAAA
*
47058864 TGAAAAAATACCTCAGC
64 TTAAAAAATACCTCAGC
* *
47058881 GTGACGCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATT
47058946 AAAAAAAATACCTCAGC
66 --AAAAAATACCTCAGC
47058963 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAAAGCAGAAA-T---
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAAA-CAGAAATTAAA
47059024 TT-AAAAATACCTCAGC
64 TTAAAAAATACCTCAGC
* * * **
47059040 GTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAA-A-AAACAGAAA
1 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAACAGAAA-TTAAA
47059102 TT-AAAAATACCTCAGC
64 TTAAAAAATACCTCAGC
*
47059118 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTCAAAAAACAGAAATTAAATT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATT
47059182 AAAAAAATACCTCAGC
66 -AAAAAATACCTCAGC
*
47059198 GTGACCCGAGACTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATT
1 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-CAGAAATT
47059259 TAAAAAATAT
Statistics
Matches: 335, Mismatches: 20, Indels: 39
0.85 0.05 0.10
Matches are distributed among these distances:
73 3 0.01
74 12 0.04
75 30 0.09
76 21 0.06
77 62 0.19
78 58 0.17
79 3 0.01
80 55 0.16
81 11 0.03
82 60 0.18
83 14 0.04
84 6 0.02
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (80 bp):
GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATT
AAAAAATACCTCAGC
Found at i:47060129 original size:1 final size:1
Alignment explanation
Indices: 47060123--47060213 Score: 65
Period size: 1 Copynumber: 91.0 Consensus size: 1
47060113 TTCATCTTGA
* * * * * * * * ** *
47060123 TTTTTTTCTTTTTCTTTTCTTTGTTTTTTCTTTTTTCTTTTTTTGTTTTTTTGTTCCTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
47060188 TTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
47060214 CAAGCATAAT
Statistics
Matches: 66, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.08, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:47060143 original size:23 final size:23
Alignment explanation
Indices: 47060117--47060214 Score: 76
Period size: 23 Copynumber: 4.1 Consensus size: 23
47060107 CGGGTTTTCA
47060117 TCTTGATTTTTTTC-TTTTTCTTT
1 TCTTG-TTTTTTTCTTTTTTCTTT
47060140 TCTT-TGTTTTTTCTTTTTTCTTT
1 TCTTGT-TTTTTTCTTTTTTCTTT
* *
47060163 TTTTGTTTTTTTGTTCCTTTTTGTTTTT
1 TCTTG--TTTTT-TT-CTTTTT-TCTTT
* *
47060191 TTTTGTTTTTTTGTTTTTT-TTT
1 TCTTGTTTTTTTCTTTTTTCTTT
47060213 TC
1 TC
47060215 AAGCATAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
21 1 0.02
22 11 0.17
23 17 0.27
24 5 0.08
25 6 0.10
26 8 0.13
27 6 0.10
28 9 0.14
ACGTcount: A:0.01, C:0.09, G:0.07, T:0.83
Consensus pattern (23 bp):
TCTTGTTTTTTTCTTTTTTCTTT
Found at i:47060149 original size:22 final size:22
Alignment explanation
Indices: 47060124--47060173 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
47060114 TCATCTTGAT
47060124 TTTTTTC-TTTTTCTTTTCTTTG
1 TTTTTTCTTTTTTCTTTT-TTTG
47060146 TTTTTTCTTTTTTCTTTTTTTG
1 TTTTTTCTTTTTTCTTTTTTTG
47060168 TTTTTT
1 TTTTTT
47060174 TGTTCCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (22 bp):
TTTTTTCTTTTTTCTTTTTTTG
Found at i:47060160 original size:18 final size:17
Alignment explanation
Indices: 47060131--47060213 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 17
47060121 GATTTTTTTC
*
47060131 TTTTTCTTTTCTTTGTT
1 TTTTTTTTTTCTTTGTT
*
47060148 TTTTCTTTTTTCTTTTTT
1 TTTT-TTTTTTCTTTGTT
47060166 TGTTTTTTTGTTCCTTTTTGTT
1 T-TTTTTTT-TT-C--TTTGTT
*
47060188 TTTTTTTGTTTTTTTGTT
1 TTTTTTT-TTTCTTTGTT
47060206 TTTTTTTT
1 TTTTTTTT
47060214 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
17 5 0.09
18 29 0.53
19 5 0.09
20 1 0.02
21 8 0.15
22 7 0.13
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTCTTTGTT
Found at i:47065702 original size:21 final size:22
Alignment explanation
Indices: 47065676--47065716 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47065666 TTATTTTCAC
47065676 TAAAACACAAA-CTAAAAAACG
1 TAAAACACAAAGCTAAAAAACG
**
47065697 TAAAACTTAAAGCTAAAAAA
1 TAAAACACAAAGCTAAAAAA
47065717 AAATAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.15
Consensus pattern (22 bp):
TAAAACACAAAGCTAAAAAACG
Found at i:47066343 original size:17 final size:18
Alignment explanation
Indices: 47066314--47066442 Score: 106
Period size: 18 Copynumber: 7.3 Consensus size: 18
47066304 ACACAATAAT
47066314 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
47066332 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
47066349 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
47066369 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
47066387 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
47066405 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
*
47066420 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
47066438 AATTT
1 AATTT
47066443 CGAAAACATG
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
15 7 0.08
16 5 0.06
17 15 0.17
18 38 0.44
19 18 0.21
20 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:47066356 original size:19 final size:18
Alignment explanation
Indices: 47066298--47066442 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 18
47066288 ACACGAGAAC
47066298 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
47066318 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
47066336 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
47066354 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
47066373 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
47066391 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
47066409 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
47066424 TTTGAAAACACGAAAATTT
1 TTTG-AAACACGAAAATTT
47066443 CGAAAACATG
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.05
16 7 0.07
17 17 0.17
18 31 0.31
19 27 0.27
20 4 0.04
21 7 0.07
22 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:47066361 original size:36 final size:38
Alignment explanation
Indices: 47066298--47066383 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
47066288 ACACGAGAAC
47066298 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACAATAAT-ATTTTTGAAAACACGGAAGATT
**
47066336 TTTGAAACACGAA-AAT-TTTTTGAAAACACGGAATTTT
1 TTTGAAACAC-AATAATATTTTTGAAAACACGGAAGATT
47066373 TTTGAAA-ACAA
1 TTTGAAACACAA
47066384 GGAAATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 12 0.27
38 13 0.30
39 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAACACAATAATATTTTTGAAAACACGGAAGATT
Found at i:47066447 original size:17 final size:18
Alignment explanation
Indices: 47066413--47066450 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
47066403 GAATTTTTTG
*
47066413 ACACGAAAAATTTTGAAA
1 ACACGAAAAATTTCGAAA
47066431 ACACG-AAAATTTCGAAA
1 ACACGAAAAATTTCGAAA
47066448 ACA
1 ACA
47066451 TGAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (18 bp):
ACACGAAAAATTTCGAAA
Found at i:47066468 original size:18 final size:19
Alignment explanation
Indices: 47066445--47066485 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
47066435 GAAAATTTCG
47066445 AAAACATGAA-TTTTTTTT
1 AAAACATGAATTTTTTTTT
47066463 AAAACATGAATTTTTTTTT
1 AAAACATGAATTTTTTTTT
47066482 AAAA
1 AAAA
47066486 AAAAACACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
AAAACATGAATTTTTTTTT
Found at i:47066517 original size:27 final size:25
Alignment explanation
Indices: 47066487--47066539 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
47066477 TTTTTAAAAA
*
47066487 AAAACACGAGAATTTTTTGAAAACACG
1 AAAACACGA-AA-ATTTTGAAAACACG
*
47066514 AAAACATGAAAATTTTGAAAACACG
1 AAAACACGAAAATTTTGAAAACACG
47066539 A
1 A
47066540 GAATTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (25 bp):
AAAACACGAAAATTTTGAAAACACG
Found at i:47066566 original size:10 final size:10
Alignment explanation
Indices: 47066543--47066592 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
47066533 AACACGAGAA
47066543 TTCTTTCTTTC
1 TTCTTTC-TTC
47066554 TTCTTTCTTC
1 TTCTTTCTTC
47066564 TTC-TTC--C
1 TTCTTTCTTC
47066571 TT-TTTCTTC
1 TTCTTTCTTC
*
47066580 TTCCTTCTTC
1 TTCTTTCTTC
47066590 TTC
1 TTC
47066593 AAAGTTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
7 6 0.18
9 6 0.18
10 15 0.44
11 7 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:47066569 original size:13 final size:13
Alignment explanation
Indices: 47066543--47066592 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
47066533 AACACGAGAA
47066543 TTCTTTC-T-TTC
1 TTCTTTCTTCTTC
47066554 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
47066567 TTCCTTT-TTCTTC
1 TT-CTTTCTTCTTC
*
47066580 TTCCTTCTTCTTC
1 TTCTTTCTTCTTC
47066593 AAAGTTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 7 0.21
12 4 0.12
13 19 0.56
14 4 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:47066999 original size:59 final size:60
Alignment explanation
Indices: 47066887--47067031 Score: 193
Period size: 59 Copynumber: 2.4 Consensus size: 60
47066877 AAATACAGTA
* * *
47066887 AAAGTTTTGGGGCCAAAACGTAATTTAGAGAAAGTTTAGGGGTCAAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATGTAATTTTAAG
** *
47066947 AAAGTTTAGGGGTCAAAATGTAATTTAGA-AAAGTTTAGGGGTTGAAATGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATGTAATTTTAAG
** * *
47067006 AAAGTACAAGGGTCAAAATGCAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
47067032 TTTTAATTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 49 0.65
60 26 0.35
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (60 bp):
AAAGTTTAGGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATGTAATTTTAAG
Found at i:47067032 original size:30 final size:30
Alignment explanation
Indices: 47066887--47067032 Score: 177
Period size: 30 Copynumber: 4.9 Consensus size: 30
47066877 AAATACAGTA
* * * *
47066887 AAAGTTTTGGGGCCAAAACGTAATTTAGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
47066917 AAAGTTTAGGGGTCAAAATGTAATTTTAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
*
47066947 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
**
47066976 AAAGTTTAGGGGTTGAAATGTAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGAG
** * *
47067006 AAAGTACAAGGGTCAAAATGCAATTTT
1 AAAGTTTAGGGGTCAAAATGTAATTTT
47067033 TTTAATTTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
29 26 0.26
30 73 0.74
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGAG
Found at i:47067144 original size:22 final size:22
Alignment explanation
Indices: 47067110--47067161 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
47067100 TCGTTAGGTA
*
47067110 TCAATATCGCGATACCCAAACT
1 TCAATATCACGATACCCAAACT
* *
47067132 TCGATATCACGATACCCAATCT
1 TCAATATCACGATACCCAAACT
47067154 TCAATATC
1 TCAATATC
47067162 GCAATTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.27
Consensus pattern (22 bp):
TCAATATCACGATACCCAAACT
Found at i:47070055 original size:43 final size:43
Alignment explanation
Indices: 47069907--47070063 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
47069897 TGTGATTAAG
* * *
47069907 TGTAAGACCACATCTAGGAC-GTTTGCATCGAT-TTGTGATTTACA
1 TGTAAGACCACGTCTGGGACAG-TGGCATCGATATT-TGATTT-CA
* ** * *
47069951 TGTAAGACCATGTCTGGGACA-TCGGCATCG-TATACGAGTTCG
1 TGTAAGACCACGTCTGGGACAGT-GGCATCGATATTTGATTTCA
*
47069993 TGTAAGACC-CTGTCAGGGACAGTGGCATCGATATTTGATTTCA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGATATTTGATTTCA
*
47070036 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACAGTGGCAT
47070064 TGTATGAGCT
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
42 26 0.29
43 39 0.43
44 25 0.28
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATTTCA
Found at i:47073435 original size:11 final size:12
Alignment explanation
Indices: 47073404--47073437 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
47073394 GTTTACGAGG
47073404 ATATTATATATT
1 ATATTATATATT
47073416 ATATATATATATT
1 ATAT-TATATATT
47073429 A-ATTATATA
1 ATATTATATA
47073438 GTAACATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 6 0.29
13 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTATATATT
Found at i:47074215 original size:5 final size:5
Alignment explanation
Indices: 47074166--47074253 Score: 92
Period size: 5 Copynumber: 17.4 Consensus size: 5
47074156 TTATGTTATG
* * *
47074166 TATAT TAT-T T-TAT TATAT AATATAA TATAA TATAA TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
47074216 T-TAT TATAT TATAT TATAT TATAT TATTAT ATATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA-TAT -TATAT TA
47074254 AATAAAGTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
3 1 0.01
4 8 0.11
5 53 0.72
6 6 0.08
7 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:47075748 original size:2 final size:2
Alignment explanation
Indices: 47075741--47075775 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47075731 TAGTATGTAA
47075741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47075776 AATTTAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47077028 original size:20 final size:19
Alignment explanation
Indices: 47076997--47077047 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
47076987 TTAATTGAGG
*
47076997 TGAATGTGATATGGAATTA
1 TGAATATGATATGGAATTA
* *
47077016 TGAAATATGATATTGAATTG
1 TG-AATATGATATGGAATTA
*
47077036 TGTATATGATAT
1 TGAATATGATAT
47077048 TATGGATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (19 bp):
TGAATATGATATGGAATTA
Found at i:47077155 original size:35 final size:34
Alignment explanation
Indices: 47077095--47077275 Score: 175
Period size: 34 Copynumber: 5.3 Consensus size: 34
47077085 CGGCTAGTGT
*
47077095 TGGGCACAACCATCGTCAGTTATCTGACTAGCGC
1 TGGGCGCAACCATCGTCAGTTATCTGACTAGCGC
* * *
47077129 TAGGCGCAA-CTTCTGTCAGTTTATCTGACTAGCGT
1 TGGGCGCAACCATC-GTCAG-TTATCTGACTAGCGC
** * * * *
47077164 TGGGTACAATCATCGTCTGTTATCCGATTAGCGC
1 TGGGCGCAACCATCGTCAGTTATCTGACTAGCGC
** * *
47077198 TGGGCGCAACTTTCGTCAATTTATCTGACTAGTGC
1 TGGGCGCAACCATCGTC-AGTTATCTGACTAGCGC
* *
47077233 TGGGCACAACCATCGTCGGTTATCTGACTAGCGC
1 TGGGCGCAACCATCGTCAGTTATCTGACTAGCGC
*
47077267 TAGGCGCAA
1 TGGGCGCAA
47077276 AACATTGTCA
Statistics
Matches: 113, Mismatches: 30, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
33 3 0.03
34 57 0.50
35 50 0.44
36 3 0.03
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (34 bp):
TGGGCGCAACCATCGTCAGTTATCTGACTAGCGC
Found at i:47077204 original size:69 final size:69
Alignment explanation
Indices: 47077088--47077310 Score: 274
Period size: 69 Copynumber: 3.2 Consensus size: 69
47077078 ATTCGTTCGG
*
47077088 CTAGTGTTGGGCACAACCATCGTCAGTTATCTGACTAGCGCTAGGCGCAAC-TTCTGTCAGTTTA
1 CTAGTGTTGGGCACAACCATCGTCAGTTATCTGACTAGCGCTAGGCGCAACTTTC-GTCAATTTA
47077152 TCTGA
65 TCTGA
* * * * * * *
47077157 CTAGCGTTGGGTACAATCATCGTCTGTTATCCGATTAGCGCTGGGCGCAACTTTCGTCAATTTAT
1 CTAGTGTTGGGCACAACCATCGTCAGTTATCTGACTAGCGCTAGGCGCAACTTTCGTCAATTTAT
47077222 CTGA
66 CTGA
* * *
47077226 CTAGTGCTGGGCACAACCATCGTCGGTTATCTGACTAGCGCTAGGCGCAAAACATT-GTCAACTT
1 CTAGTGTTGGGCACAACCATCGTCAGTTATCTGACTAGCGCTAGGCGC--AACTTTCGTCAA-TT
47077290 GT-TC-GA
63 -TATCTGA
47077296 CTAGTGTTGGGCACA
1 CTAGTGTTGGGCACA
47077311 CAAATGATCT
Statistics
Matches: 131, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
69 97 0.74
70 24 0.18
71 9 0.07
72 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (69 bp):
CTAGTGTTGGGCACAACCATCGTCAGTTATCTGACTAGCGCTAGGCGCAACTTTCGTCAATTTAT
CTGA
Found at i:47079130 original size:17 final size:18
Alignment explanation
Indices: 47079108--47079141 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47079098 AATCCATACA
47079108 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
47079125 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
47079142 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:47081458 original size:21 final size:21
Alignment explanation
Indices: 47081408--47081460 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
47081398 GATTAGGCAT
*
47081408 TTAAGATGGTTGTTTTGAGAATG
1 TTAA-ATGG-TGTTTTGAGAAGG
*
47081431 TTTAATGGTGTTTTGA-ATAGG
1 TTAAATGGTGTTTTGAGA-AGG
47081452 TTAAATGGT
1 TTAAATGGT
47081461 TGATGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 4 0.15
23 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
TTAAATGGTGTTTTGAGAAGG
Found at i:47086957 original size:20 final size:20
Alignment explanation
Indices: 47086932--47086973 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
47086922 ATATTTCATT
47086932 AAAATAT-TCATAAAAATAAA
1 AAAATATATCA-AAAAATAAA
*
47086952 AAAATATATTAAAAAATAAA
1 AAAATATATCAAAAAATAAA
47086972 AA
1 AA
47086974 TTAGTGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATATATCAAAAAATAAA
Found at i:47089603 original size:29 final size:27
Alignment explanation
Indices: 47089570--47089648 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 27
47089560 AGAAATCTCA
* *
47089570 AATTTTATATGAATTTTGGTTTAATGTAT
1 AATTTTATATAAATTTTGATTT--TGTAT
47089599 AATTTTACATATAAATTTTGATTTTGTAT
1 AATTTT--ATATAAATTTTGATTTTGTAT
* *
47089628 AATTTTAT-GAAATTTAGATTT
1 AATTTTATATAAATTTTGATTT
47089649 GATTCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.25
27 2 0.05
29 17 0.39
31 14 0.32
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (27 bp):
AATTTTATATAAATTTTGATTTTGTAT
Found at i:47089618 original size:31 final size:29
Alignment explanation
Indices: 47089576--47089634 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
47089566 CTCAAATTTT
* *
47089576 ATATGAATTTTGGTTTAATGTATAATTTTAC
1 ATATAAATTTTGATTT--TGTATAATTTTAC
47089607 ATATAAATTTTGATTTTGTATAATTTTA
1 ATATAAATTTTGATTTTGTATAATTTTA
47089635 TGAAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
31 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (29 bp):
ATATAAATTTTGATTTTGTATAATTTTAC
Found at i:47091075 original size:20 final size:20
Alignment explanation
Indices: 47091039--47091087 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
47091029 TTAGTGTTAT
47091039 TTTATATTTATTGTTATAAA
1 TTTATATTTATTGTTATAAA
*
47091059 TTTA-ATTTATCTTTTATAGAA
1 TTTATATTTAT-TGTTATA-AA
*
47091080 TGTATATT
1 TTTATATT
47091088 CATATAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 5 0.21
22 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (20 bp):
TTTATATTTATTGTTATAAA
Found at i:47097172 original size:43 final size:43
Alignment explanation
Indices: 47097102--47097184 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
47097092 ATATTCTAGA
* * *
47097102 AAGGAAAGAAATCATCTAAAGTGAAATCGCAATAGAGAAACCT
1 AAGGAAAGAAATCATCTAAAATAAAATCACAATAGAGAAACCT
*
47097145 AAGGAAAGAAATCAAT-TAAAATAAAATCACAATCGAGAAA
1 AAGGAAAGAAATC-ATCTAAAATAAAATCACAATAGAGAAA
47097185 TCTACTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16
Consensus pattern (43 bp):
AAGGAAAGAAATCATCTAAAATAAAATCACAATAGAGAAACCT
Found at i:47097493 original size:32 final size:32
Alignment explanation
Indices: 47097455--47097519 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
47097445 TCAATTGTCT
47097455 TCCCCTTATCTAGATTTTGGAATGACCTGTTG
1 TCCCCTTATCTAGATTTTGGAATGACCTGTTG
47097487 TCCCCTTATCTAGATTTTGGAATGACCTGTTG
1 TCCCCTTATCTAGATTTTGGAATGACCTGTTG
47097519 T
1 T
47097520 GGTTGGCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (32 bp):
TCCCCTTATCTAGATTTTGGAATGACCTGTTG
Found at i:47102974 original size:78 final size:79
Alignment explanation
Indices: 47102809--47102976 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 79
47102799 GGCTCTCATG
* * * * * * *
47102809 ACTTTTTGCACAAGGTTTAAAGTTGGTAGGTTGCCAATGAGGTACATTGGTGCTCCTTTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGATACATTGGTGCACCTCTTGTTTC
*
47102874 TCAGAAGCAATTTC
66 TCAGAAGCAATCTC
47102888 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGATAC-TTGGTGCACCTCTTGTTTC
1 ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGATACATTGGTGCACCTCTTGTTTC
** **
47102952 TTGGAAGCTGTCTC
66 TCAGAAGCAATCTC
47102966 ACTTCTTGCAC
1 ACTTCTTGCAC
47102977 GTCTCACTTC
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 37 0.48
79 40 0.52
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (79 bp):
ACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGATACATTGGTGCACCTCTTGTTTC
TCAGAAGCAATCTC
Found at i:47102982 original size:16 final size:16
Alignment explanation
Indices: 47102961--47102992 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
47102951 CTTGGAAGCT
47102961 GTCTCACTTCTTGCAC
1 GTCTCACTTCTTGCAC
47102977 GTCTCACTTCTTGCAC
1 GTCTCACTTCTTGCAC
47102993 AAGGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (16 bp):
GTCTCACTTCTTGCAC
Found at i:47103060 original size:95 final size:94
Alignment explanation
Indices: 47102886--47103060 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 94
47102876 AGAAGCAATT
*
47102886 TCACTTCTTGCACAAGGTTTAAAGTTGGTAAGCTACCAATGAGATACTTGGTGCACCTCTTGTTT
1 TCACTTCTTGCACAAGGTTTAAAGTCGGTAAGCTACCAATGAGATACTTGGTGCACCTCTTGTTT
*
47102951 CTTGGAAGCTGTCTCACTTCTTGCACGTC
66 CTCGGAAGCTGTCTCACTTCTTGCACGTC
* *** * * **
47102980 TCACTTCTTGCACAAGGTTTAAAGTCGGTAGGCTGTTAGTGAGGTACTTTGGTGTTCCTCTTGTT
1 TCACTTCTTGCACAAGGTTTAAAGTCGGTAAGCTACCAATGAGATAC-TTGGTGCACCTCTTGTT
47103045 TCTCGGAAGCTGTCTC
65 TCTCGGAAGCTGTCTC
47103061 GATCTAACTG
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
94 40 0.57
95 30 0.43
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (94 bp):
TCACTTCTTGCACAAGGTTTAAAGTCGGTAAGCTACCAATGAGATACTTGGTGCACCTCTTGTTT
CTCGGAAGCTGTCTCACTTCTTGCACGTC
Found at i:47103382 original size:76 final size:76
Alignment explanation
Indices: 47103256--47103404 Score: 246
Period size: 76 Copynumber: 2.0 Consensus size: 76
47103246 TTCATATCAT
47103256 AAACCAAACAAAATCAATCATATGGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAGA
1 AAACCAAACAAAATCAATCATATGGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAGA
*
47103321 AACAAGTCGGG
66 AAAAAGTCGGG
* * *
47103332 AAACCAAA-AACAATCAATCATGTGGTCCCTTATATGAACTCTCGAGGCCCAAAATACACATTAG
1 AAACCAAACAA-AATCAATCATATGGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAG
47103396 AAAAAAGTC
65 AAAAAAGTC
47103405 AAGACTAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 2 0.03
76 66 0.97
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (76 bp):
AAACCAAACAAAATCAATCATATGGTCCCTTATATGAACCCTCAAGGCCCAAAATACACATTAGA
AAAAAGTCGGG
Done.