Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 50 of 66
Found at i:18155346 original size:48 final size:48
Alignment explanation
Indices: 18155288--18155566 Score: 166
Period size: 48 Copynumber: 5.5 Consensus size: 48
18155278 ACGCAACGCT
*
18155288 AACAAATATTCAGTCACGTGATGCCTATAAAAAACTCACGCAATGTTC
1 AACAAATATTCAGTCACGTAATGCCTATAAAAAACTCACGCAATGTTC
* * ** * *
18155336 AACAAATATTCAGTCAGGTAATATTCAGTCACGTAT-TAACTCTCACGCAACGCTC
1 AACAAATATTCAGTCACGT-A-A-T--G-C-C-TATAAAAAACTCACGCAATGTTC
* * * *
18155391 AACATATGTTTAGTCACGTAATGCCTATAAAGAACTCACGCAATGTTC
1 AACAAATATTCAGTCACGTAATGCCTATAAAAAACTCACGCAATGTTC
* * * ** ***
18155439 AACTAATATTCAGTCAGGTAATATTCAGTCAC-ATATTAACTCTCACGCAACACTC
1 AACAAATATTCAGTCACGT-A-A-T--G-C-CTATA-AAAAACTCACGCAATGTTC
* * * *
18155494 AACATATATTCAGTCATGTAATGCCTATAAAGAACTCACGCAATGCTC
1 AACAAATATTCAGTCACGTAATGCCTATAAAAAACTCACGCAATGTTC
* * *
18155542 AACAAATATTTAGGCACCTAATGCC
1 AACAAATATTCAGTCACGTAATGCC
18155567 AAATAAACAG
Statistics
Matches: 170, Mismatches: 43, Indels: 36
0.68 0.17 0.14
Matches are distributed among these distances:
47 3 0.02
48 80 0.47
49 6 0.04
50 4 0.02
51 2 0.01
52 2 0.01
53 4 0.02
54 7 0.04
55 59 0.35
56 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (48 bp):
AACAAATATTCAGTCACGTAATGCCTATAAAAAACTCACGCAATGTTC
Found at i:18155451 original size:103 final size:103
Alignment explanation
Indices: 18155205--18155551 Score: 480
Period size: 103 Copynumber: 3.4 Consensus size: 103
18155195 AAAGTCACAC
* * * * * * * *
18155205 AATGCCTACAAATAAGTCATGCCATGCTCAACAAATATTCAGTCACGTAATATTAAGTCACGTAA
1 AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGGTAATATTCAGTCACGTAT
*** * *
18155270 CGCCTGTCACGCAACGCT-AACAAATATTCAGTCACGT
66 TAACTCTCACGCAACGCTCAACATATATTCAGTCACGT
* * *
18155307 GATGCCTATAAAAAACTCACGCAATGTTCAACAAATATTCAGTCAGGTAATATTCAGTCACGTAT
1 AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGGTAATATTCAGTCACGTAT
* *
18155372 TAACTCTCACGCAACGCTCAACATATGTTTAGTCACGT
66 TAACTCTCACGCAACGCTCAACATATATTCAGTCACGT
* * *
18155410 AATGCCTATAAAGAACTCACGCAATGTTCAACTAATATTCAGTCAGGTAATATTCAGTCACATAT
1 AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGGTAATATTCAGTCACGTAT
* *
18155475 TAACTCTCACGCAACACTCAACATATATTCAGTCATGT
66 TAACTCTCACGCAACGCTCAACATATATTCAGTCACGT
18155513 AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATT
1 AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATT
18155552 TAGGCACCTA
Statistics
Matches: 217, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
102 69 0.32
103 148 0.68
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
AATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCAGGTAATATTCAGTCACGTAT
TAACTCTCACGCAACGCTCAACATATATTCAGTCACGT
Found at i:18160568 original size:24 final size:23
Alignment explanation
Indices: 18160535--18160585 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
18160525 TCATTAAATG
18160535 TTAAAACCTT-TGAAATATTTAGTT
1 TTAAAACCTTATG-AATA-TTAGTT
*
18160559 TTAAATCCTTAATGAATATTAGTT
1 TTAAAACCTT-ATGAATATTAGTT
18160583 TTA
1 TTA
18160586 CCTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 18 0.75
25 4 0.17
26 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (23 bp):
TTAAAACCTTATGAATATTAGTT
Found at i:18161660 original size:89 final size:88
Alignment explanation
Indices: 18161503--18161729 Score: 219
Period size: 89 Copynumber: 2.6 Consensus size: 88
18161493 CAATGAGTTT
* *
18161503 TTGTTAAAGTTGGGGAGGATGTCGCAGTCCCAACGGGGAACCATGTGAATCCAGGATACTAACAA
1 TTGTTGAAGTTGGGGAGGATGTCGCAGTCCCAACGGGGAACCATGTGAATCCAGGATAATAACAA
* *
18161568 TGTGCTATTGA-AATTA-GTGCGTCC
66 TGTGCT-TTGAGAATAATGGGC-T-C
* * ** ** * *
18161592 TTGTTGAAGTTGGGGAGGATGTCGCAGTTCTAGTGGGGAACCATGTGAAATTGAGG-TAATAGCG
1 TTGTTGAAGTTGGGGAGGATGTCGCAGTCCCAACGGGGAACCATGTG-AATCCAGGATAATAACA
18161656 ATGTGCTTTGAGAATAATGGGCTC
65 ATGTGCTTTGAGAATAATGGGCTC
* * * * **
18161680 TTGTTGAAG-TGGGTGAAGATGTCGCGGTACCAACAGAAAACCATGTGAAT
1 TTGTTGAAGTTGGG-GAGGATGTCGCAGTCCCAACGGGGAACCATGTGAAT
18161730 TCGTCGTATG
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
87 7 0.06
88 38 0.34
89 59 0.52
90 9 0.08
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (88 bp):
TTGTTGAAGTTGGGGAGGATGTCGCAGTCCCAACGGGGAACCATGTGAATCCAGGATAATAACAA
TGTGCTTTGAGAATAATGGGCTC
Found at i:18162912 original size:20 final size:20
Alignment explanation
Indices: 18162887--18162925 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18162877 AGAGAGAAAA
*
18162887 AATTATTTATTTATTTAATT
1 AATTATTAATTTATTTAATT
*
18162907 AATTATTAATTTTTTTAAT
1 AATTATTAATTTATTTAAT
18162926 ATTTATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTATTAATTTATTTAATT
Found at i:18166916 original size:42 final size:42
Alignment explanation
Indices: 18166870--18166955 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
18166860 TAGGATCTTT
* *
18166870 TTCTTTTTCATCTTATTTGACTTTTTCTTGTTTGTGATAATC
1 TTCTTTTTCATCTTACTTGACTTCTTCTTGTTTGTGATAATC
18166912 TTCTTTTTCATCTTACTTGACTTCTTCTTGTTTGTGATAATC
1 TTCTTTTTCATCTTACTTGACTTCTTCTTGTTTGTGATAATC
18166954 TT
1 TT
18166956 TTGCTATTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (42 bp):
TTCTTTTTCATCTTACTTGACTTCTTCTTGTTTGTGATAATC
Found at i:18168949 original size:43 final size:43
Alignment explanation
Indices: 18168888--18168993 Score: 194
Period size: 43 Copynumber: 2.4 Consensus size: 43
18168878 ACTTGAAGGT
*
18168888 CAGCTTTAAGAATTTTCAACAAATAAAATTCCCTATCCTGGTG
1 CAGCTTTAAGAATTTTCAACAAATAAAATTCCCTATCCTGGTA
18168931 CAGCTTTAAGAATTTTCAACAAATAAAATTCCCTATCCTGGTA
1 CAGCTTTAAGAATTTTCAACAAATAAAATTCCCTATCCTGGTA
18168974 CAGCTTTAAGAATATTTCAA
1 CAGCTTTAAGAAT-TTTCAA
18168994 AATTTGATAT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
43 55 0.90
44 6 0.10
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (43 bp):
CAGCTTTAAGAATTTTCAACAAATAAAATTCCCTATCCTGGTA
Found at i:18179214 original size:19 final size:19
Alignment explanation
Indices: 18179187--18179224 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18179177 ACATTTGACT
18179187 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
18179206 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
18179225 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:18186841 original size:31 final size:29
Alignment explanation
Indices: 18186779--18186847 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
18186769 GAATATAGCG
*
18186779 TGTAACAACAATATTTTTTCAATATCACA
1 TGTAACAACAATATTTTTTCAACATCACA
**
18186808 TGTAACAACAATATTTTTTTACAACATGGCA
1 TGTAACAACAATA-TTTTTT-CAACATCACA
18186839 TGTAACAAC
1 TGTAACAAC
18186848 CTTTTTTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 13 0.37
30 6 0.17
31 16 0.46
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAACATCACA
Found at i:18186878 original size:26 final size:27
Alignment explanation
Indices: 18186821--18186871 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
18186811 AACAACAATA
18186821 TTTTTTTACAACATGGCATGTAACAAC
1 TTTTTTTACAACATGGCATGTAACAAC
* * *
18186848 CTTTTTTA-ACCATGGCGTGTAACA
1 TTTTTTTACAACATGGCATGTAACA
18186872 TGTTTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTTTTTACAACATGGCATGTAACAAC
Found at i:18186967 original size:45 final size:45
Alignment explanation
Indices: 18186918--18187006 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
18186908 TTTTTTGAGG
* * * * *
18186918 TGTAACAACCTAACTATAGCGTGTCACATGTTTTTGTATATGGCA
1 TGTAACAACCTAACCATAGCATGTAACATGTTTTTATACATGGCA
18186963 TGTAACAACCTAACCATAGCATGTAACATGTTTTTATACATGGC
1 TGTAACAACCTAACCATAGCATGTAACATGTTTTTATACATGGC
18187007 GTGTCACATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (45 bp):
TGTAACAACCTAACCATAGCATGTAACATGTTTTTATACATGGCA
Found at i:18187038 original size:69 final size:68
Alignment explanation
Indices: 18186936--18187155 Score: 206
Period size: 69 Copynumber: 3.1 Consensus size: 68
18186926 CCTAACTATA
* * * * *
18186936 GCGTGTCACATGTTTTTGTATATGGCATGTAACAACCTAACCATAGCATGTAACATGTTTTTATA
1 GCGTGTCACATGTTTTTGTACATGACGTATAACAACCTAACCAT-GCATGTAACATGTTTTTGTA
18187001 CATG
65 CATG
* * * *
18187005 GCGTGTCACATGTTTTTGTACATAACGTATAACAACCTAACCATGACGTGTAATATGTTTTTGCA
1 GCGTGTCACATGTTTTTGTACATGACGTATAACAACCTAACCATG-CATGTAACATGTTTTTGTA
18187070 CATG
65 CATG
* * * * * *
18187074 GCGTATAACAACAATATTTTTTTTCAACATGACGTATAACAACCTGATCATGGCATGTCACATGT
1 GCGTGT--C-AC-AT-GTTTTTGT--ACATGACGTATAACAACCTAACCAT-GCATGTAACATGT
18187139 TTTTGTACATG
58 TTTTGTACATG
*
18187150 TCGTGT
1 GCGTGT
18187156 AACAACTTAA
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
68 1 0.01
69 63 0.52
71 1 0.01
72 2 0.02
73 2 0.02
74 6 0.05
76 45 0.37
77 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (68 bp):
GCGTGTCACATGTTTTTGTACATGACGTATAACAACCTAACCATGCATGTAACATGTTTTTGTAC
ATG
Found at i:18187104 original size:31 final size:30
Alignment explanation
Indices: 18187056--18187116 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
18187046 CATGACGTGT
*
18187056 AATATGTTTTTGCACATGGCGTATAACAAC
1 AATATGTTTTTGCACATGACGTATAACAAC
* *
18187086 AATATTTTTTTTCAACATGACGTATAACAAC
1 AATATGTTTTTGC-ACATGACGTATAACAAC
18187117 CTGATCATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (30 bp):
AATATGTTTTTGCACATGACGTATAACAAC
Found at i:18187149 original size:24 final size:24
Alignment explanation
Indices: 18187122--18187218 Score: 58
Period size: 24 Copynumber: 4.2 Consensus size: 24
18187112 ACAACCTGAT
*
18187122 CATGGCATGTCACATGTTTTTGTA
1 CATGGCATGTAACATGTTTTTGTA
* * ** *
18187146 CATGTCGTGTAACA---ACTT-AA
1 CATGGCATGTAACATGTTTTTGTA
* *
18187166 CCATGGCATGTAACATATTTTTATA
1 C-ATGGCATGTAACATGTTTTTGTA
* * *
18187191 CATGACGTGTCACATGTTTTTGTA
1 CATGGCATGTAACATGTTTTTGTA
18187215 CATG
1 CATG
18187219 ACGTGTAGCA
Statistics
Matches: 52, Mismatches: 16, Indels: 10
0.67 0.21 0.13
Matches are distributed among these distances:
20 2 0.04
21 13 0.25
24 35 0.67
25 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
CATGGCATGTAACATGTTTTTGTA
Found at i:18187159 original size:45 final size:45
Alignment explanation
Indices: 18187100--18187200 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
18187090 TTTTTTTTCA
* * * * * *
18187100 ACATGACGTATAACAACCTGATCATGGCATGTCACATGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGGCATGTAACATATTTTTAT
* *
18187145 ACATGTCGTGTAACAACTTAACCATGGCATGTAACATATTTTTAT
1 ACATGACGTGTAACAACCTAACCATGGCATGTAACATATTTTTAT
18187190 ACATGACGTGT
1 ACATGACGTGT
18187201 CACATGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (45 bp):
ACATGACGTGTAACAACCTAACCATGGCATGTAACATATTTTTAT
Found at i:18187177 original size:190 final size:190
Alignment explanation
Indices: 18186854--18187497 Score: 794
Period size: 190 Copynumber: 3.4 Consensus size: 190
18186844 CAACCTTTTT
* * ** * * * *** *
18186854 TAACCATGGCGTGTAACATGTTTTTATATATGGTGTGTAACAACAGTATTTTTTTT--TTTTGAG
1 TAACCATGACGTGTAAAATGTTTTTGCACATGGCGTGTAACAACAATATTTTTTTTCAACATGAC
* * *
18186917 GTGTAACAACCTAACTATAGCGTGTCACATGTTTTTGTATATGGCATGTAACAACCTAACCATAG
66 GTGTAACAACCTAACTATAGCATGTCACATGTTTTTGTACATGGCATGTAACAACTTAACCATAG
* *
18186982 CATGTAACATGTTTTTATACATGGCGTGTCACATGTTTTTGTACATAACGTATAACAACC
131 CATGTAACATATTTTTATACATGGCGTGTCACATGTTTTTGTACATGACGTATAACAACC
* *
18187042 TAACCATGACGTGTAATATGTTTTTGCACATGGCGTATAACAACAATATTTTTTTTCAACATGAC
1 TAACCATGACGTGTAAAATGTTTTTGCACATGGCGTGTAACAACAATATTTTTTTTCAACATGAC
* * * * * *
18187107 GTATAACAACCTGA-TCATGGCATGTCACATGTTTTTGTACATGTCGTGTAACAACTTAACCATG
66 GTGTAACAACCTAACT-ATAGCATGTCACATGTTTTTGTACATGGCATGTAACAACTTAACCATA
* * *
18187171 GCATGTAACATATTTTTATACATGACGTGTCACATGTTTTTGTACATGACGTGTAGCAACC
130 GCATGTAACATATTTTTATACATGGCGTGTCACATGTTTTTGTACATGACGTATAACAACC
* * * ** * *
18187232 TAACCATGACGTGTAAAATGTTGTCGTACATGGCACGTAACAACAATATTTGTTTTCAACATGGC
1 TAACCATGACGTGTAAAATGTTTTTGCACATGGCGTGTAACAACAATATTTTTTTTCAACATGAC
** *
18187297 GTGTAACAACCTAACTATAGTGTGTCACATGTTTTTATACATGGCATGTAACAACTTAACCA-AG
66 GTGTAACAACCTAACTATAGCATGTCACATGTTTTTGTACATGGCATGTAACAACTTAACCATAG
* * * * *
18187361 CGTGTAACATATTTTTCTACATAGCGTGTCACATGTTTTTGCACATGACGTATAACAACT
131 CATGTAACATATTTTTATACATGGCGTGTCACATGTTTTTGTACATGACGTATAACAACC
* ** * ** *
18187421 TAACTATGGTGTGTAACATGTTTTTGCACATTACGTGTAACAATAATATTTTTTTT-AACATGAC
1 TAACCATGACGTGTAAAATGTTTTTGCACATGGCGTGTAACAACAATATTTTTTTTCAACATGAC
*
18187485 ATGTAACAACCTA
66 GTGTAACAACCTA
18187498 CCATGACGTA
Statistics
Matches: 385, Mismatches: 67, Indels: 8
0.84 0.15 0.02
Matches are distributed among these distances:
188 67 0.17
189 97 0.25
190 220 0.57
191 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (190 bp):
TAACCATGACGTGTAAAATGTTTTTGCACATGGCGTGTAACAACAATATTTTTTTTCAACATGAC
GTGTAACAACCTAACTATAGCATGTCACATGTTTTTGTACATGGCATGTAACAACTTAACCATAG
CATGTAACATATTTTTATACATGGCGTGTCACATGTTTTTGTACATGACGTATAACAACC
Found at i:18187219 original size:24 final size:24
Alignment explanation
Indices: 18187178--18187224 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18187168 ATGGCATGTA
18187178 ACATATTTTTATACATGACGTGTC
1 ACATATTTTTATACATGACGTGTC
* *
18187202 ACATGTTTTTGTACATGACGTGT
1 ACATATTTTTATACATGACGTGT
18187225 AGCAACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (24 bp):
ACATATTTTTATACATGACGTGTC
Found at i:18187262 original size:69 final size:69
Alignment explanation
Indices: 18187129--18187263 Score: 180
Period size: 69 Copynumber: 2.0 Consensus size: 69
18187119 GATCATGGCA
* * * * * *
18187129 TGTCACATGTTTTTGTACATGTCGTGTAACAACTTAACCATGGCATGTAACATATTTTTATACAT
1 TGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATGTAAAATATTGTCATACAT
18187194 GACG
66 GACG
* * * *
18187198 TGTCACATGTTTTTGTACATGACGTGTAGCAACCTAACCATGACGTGTAAAATGTTGTCGTACAT
1 TGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATGTAAAATATTGTCATACAT
18187263 G
66 G
18187264 GCACGTAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (69 bp):
TGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGACATGTAAAATATTGTCATACAT
GACG
Found at i:18187347 original size:45 final size:44
Alignment explanation
Indices: 18187282--18187382 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
18187272 CAACAATATT
* * * * *
18187282 TGTTTTCA-ACATGGCGTGTAACAACCTAACTATAGTGTGTCACA
1 TGTTTTTATACATGGCATGTAACAACCTAACCA-AGCGTGTAACA
*
18187326 TGTTTTTATACATGGCATGTAACAACTTAACCAAGCGTGTAACA
1 TGTTTTTATACATGGCATGTAACAACCTAACCAAGCGTGTAACA
* *
18187370 TATTTTTCTACAT
1 TGTTTTTATACAT
18187383 AGCGTGTCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 27 0.56
45 21 0.44
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (44 bp):
TGTTTTTATACATGGCATGTAACAACCTAACCAAGCGTGTAACA
Found at i:18187507 original size:95 final size:97
Alignment explanation
Indices: 18187404--18187605 Score: 327
Period size: 95 Copynumber: 2.1 Consensus size: 97
18187394 TGTTTTTGCA
* * *
18187404 CATGACGTATAACAACTTAACTATGGTGTGTAACATGTTTTTGCACATTACGTGTAACAATAATA
1 CATGACGTATAACAACTTAACTATGGTGTGTAACATATTTTTGCACATGACGTGTAACAACAATA
18187469 TTTTTTTT-AACATGACATGTAACAACCT-AC
66 TTTTTTTTCAACATGACATGTAACAACCTAAC
* *
18187499 CATGACGTATAACAACTTAATTATGGTGTGTAACATATTTTTGTACATGACGTGTAACAACAATA
1 CATGACGTATAACAACTTAACTATGGTGTGTAACATATTTTTGCACATGACGTGTAACAACAATA
* *
18187564 TTTTTTTTCAACATGACGTGTAACAACTTAAC
66 TTTTTTTTCAACATGACATGTAACAACCTAAC
18187596 CATGACGTAT
1 CATGACGTAT
18187606 CACATATTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
95 68 0.69
96 18 0.18
97 12 0.12
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (97 bp):
CATGACGTATAACAACTTAACTATGGTGTGTAACATATTTTTGCACATGACGTGTAACAACAATA
TTTTTTTTCAACATGACATGTAACAACCTAAC
Found at i:18187667 original size:45 final size:45
Alignment explanation
Indices: 18187581--18187668 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
18187571 TCAACATGAC
* * * *
18187581 GTGTAACAACTTAACCATGACGTATCACATATTTTTGTACATGTA
1 GTGTAACAACCTAACCATGACGTATAACATAGTTTTATACATGTA
* * *
18187626 GTGTAACAACCTAACCATGGCGTGTAACATGGTTTTATACATG
1 GTGTAACAACCTAACCATGACGTATAACATAGTTTTATACATG
18187669 GTGTGTCACA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (45 bp):
GTGTAACAACCTAACCATGACGTATAACATAGTTTTATACATGTA
Found at i:18187674 original size:24 final size:24
Alignment explanation
Indices: 18187641--18187699 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
18187631 ACAACCTAAC
*
18187641 CATGGCGTGTAACATGGTTTTATA
1 CATGGAGTGTAACATGGTTTTATA
* * * *
18187665 CATGGTGTGTCACATGTTTTTGTA
1 CATGGAGTGTAACATGGTTTTATA
18187689 CATGGAGTGTA
1 CATGGAGTGTA
18187700 GCAACCTAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (24 bp):
CATGGAGTGTAACATGGTTTTATA
Found at i:18187689 original size:69 final size:68
Alignment explanation
Indices: 18187605--18188032 Score: 258
Period size: 69 Copynumber: 6.0 Consensus size: 68
18187595 CCATGACGTA
*
18187605 TCACATATTTTTGTACATGTAGTGTAACAACCTAACCATGGCGTGTAACATGGTTTTATACATGG
1 TCACATGTTTTTGTACATGTAGTGTAACAACCTAACCATGGCGTGTAACAT-GTTTTATACATGG
18187670 TGTG
65 TGTG
* * * * *
18187674 TCACATGTTTTTGTACATGGAGTGTAGCAACCTAACCATGGAGTATAACATGTTTTGTACATGGC
1 TCACATGTTTTTGTACATGTAGTGTAACAACCTAACCATGGCGTGTAACATGTTTTATACAT-G-
18187739 GTGTG
64 GTGTG
* * * * * * * *
18187744 ACAACAATATTTGTTTTCAACAT-AACGTGCAACAACTTAACCATGGTGTGTAACATATTTCTAT
1 TC-AC-ATGTTT-TTGT--ACATGTA-GTGTAACAACCTAACCATGGCGTGTAACATGTTT-TAT
*
18187808 ACATGGTGTA
59 ACATGGTGTG
* * * * * ***
18187818 TAATATGTTTTTGTACATG-ATGTGTAACAACAATATTTTTTTTCAACATGGTGTGTAACA-ACC
1 TCACATGTTTTTGTACATGTA-GTGTAACAAC-CTA---------ACCATGGCGTGTAACATGTT
* *
18187881 TAAT-CATAGTGTG
55 TTATACATGGTGTG
*
18187894 TCACATGTTTTTGTACATGTCA-TGCAACAACCTAACCATAGG-GTGTAACATGTTTTTATACAT
1 TCACATGTTTTTGTACATGT-AGTGTAACAACCTAACCAT-GGCGTGTAACATG-TTTTATACAT
*
18187957 GGCGTG
63 GGTGTG
** * * * * *
18187963 TCTTATGTTTTTATACATAGCA-TGTAGCAACCTAACCATAGCGTGTAACATGTTTTCGTACATG
1 TCACATGTTTTTGTACAT-GTAGTGTAACAACCTAACCATGGCGTGTAACATGTTTT-ATACATG
*
18188027 GCGTG
64 GTGTG
18188032 T
1 T
18188033 AATAACAATA
Statistics
Matches: 279, Mismatches: 51, Indels: 58
0.72 0.13 0.15
Matches are distributed among these distances:
66 12 0.04
67 2 0.01
68 18 0.06
69 121 0.43
70 9 0.03
71 5 0.02
72 10 0.04
73 4 0.01
74 5 0.02
75 35 0.13
76 38 0.14
77 2 0.01
78 3 0.01
79 15 0.05
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (68 bp):
TCACATGTTTTTGTACATGTAGTGTAACAACCTAACCATGGCGTGTAACATGTTTTATACATGGT
GTG
Found at i:18187812 original size:24 final size:24
Alignment explanation
Indices: 18187785--18187846 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
18187775 ACAACTTAAC
18187785 CATGGTGTGTAACATATTTCTATA
1 CATGGTGTGTAACATATTTCTATA
* * * * *
18187809 CATGGTGTATAATATGTTTTTGTA
1 CATGGTGTGTAACATATTTCTATA
*
18187833 CATGATGTGTAACA
1 CATGGTGTGTAACA
18187847 ACAATATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (24 bp):
CATGGTGTGTAACATATTTCTATA
Found at i:18187856 original size:289 final size:284
Alignment explanation
Indices: 18187268--18188056 Score: 942
Period size: 289 Copynumber: 2.8 Consensus size: 284
18187258 TACATGGCAC
* *
18187268 GTAACAACAATATTTGTTTTCAACATGGCGTGTAACAACCTAACTATAGTGTGTCACATGTTTTT
1 GTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCTAACCATAGTGTGTCACATGTTTTT
* * * * * * *
18187333 ATACATGGCATGTAACAACTTAACCA-AGCGTGTAACATATTTTTCTACATAGCGTGTCACATGT
66 GTACAT-GTATGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGGCGTGTCACATGT
* * * * * * * **
18187397 TTTTGCACAT-GACGTATAACAACTTAACTATGGTGTGTAACATGTTTTTGCACATTACGTGTAA
130 TTTTGTACATGGA-GTGTAGCAACCTAACCATGGAGTGTAACATG-TTTTGTACATGGCGTGTAA
* * * * *
18187461 CAATAATATTT-TTTTTAACATGACATGTAACAACCTACCATGACGTATAACAACTTAATTATGG
193 CAACAATATTTGTTTTCAACATAACATGCAACAACCTACCATGACGTATAACAACTTAATCATGG
*
18187525 TGTGTAACATATTTTTGTACATGACGT
258 TGTATAACATATTTTTGTACATGACGT
* * * * *
18187552 GTAACAACAATATTTTTTTTCAACATGACGTGTAACAACTTAACCAT-GACGTATCACATATTTT
1 GTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCTAACCATAG-TGTGTCACATGTTTT
* *
18187616 TGTACATGTAGTGTAACAACCTAACCATGGCGTGTAACATGGTTTTATACATGGTGTGTCACATG
65 TGTACATGTA-TGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGGCGTGTCACATG
* *
18187681 TTTTTGTACATGGAGTGTAGCAACCTAACCATGGAGTATAACATGTTTTGTACATGGCGTGTGAC
129 TTTTTGTACATGGAGTGTAGCAACCTAACCATGGAGTGTAACATGTTTTGTACATGGCGTGTAAC
* * ** * * *
18187746 AACAATATTTGTTTTCAACATAACGTGCAACAACTTAACCATGGTGTGTAACATATTTCTATACA
194 AACAATATTTGTTTTCAACATAACATGCAACAACCT-ACCATGACGTATAACA-ACTT-AAT-CA
* * *
18187811 TGGTGTATAATATGTTTTTGTACATGATGT
255 TGGTGTATAACATATTTTTGTACATGACGT
* *
18187841 GTAACAACAATATTTTTTTTCAACATGGTGTGTAACAACCTAATCATAGTGTGTCACATGTTTTT
1 GTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCTAACCATAGTGTGTCACATGTTTTT
* **
18187906 GTACATGTCATGCAACAACCTAACCATAGG-GTGTAACATGTTTTTATACATGGCGTGTCTTATG
66 GTACATGT-ATGTAACAACCTAACCAT-GGCGTGTAACATGTTTTTATACATGGCGTGTCACATG
* * * *
18187970 TTTTTATACATAGCA-TGTAGCAACCTAACCATAGCGTGTAACATGTTTTCGTACATGGCGTGTA
129 TTTTTGTACAT-GGAGTGTAGCAACCTAACCATGGAGTGTAACATGTTTT-GTACATGGCGTGTA
*
18188034 ATAACAATATTTGTTTTCAACAT
192 ACAACAATATTTGTTTTCAACAT
18188057 GGCGTATAAC
Statistics
Matches: 429, Mismatches: 62, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
283 3 0.01
284 101 0.24
285 86 0.20
286 15 0.03
287 3 0.01
288 2 0.00
289 178 0.41
290 41 0.10
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (284 bp):
GTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCTAACCATAGTGTGTCACATGTTTTT
GTACATGTATGTAACAACCTAACCATGGCGTGTAACATGTTTTTATACATGGCGTGTCACATGTT
TTTGTACATGGAGTGTAGCAACCTAACCATGGAGTGTAACATGTTTTGTACATGGCGTGTAACAA
CAATATTTGTTTTCAACATAACATGCAACAACCTACCATGACGTATAACAACTTAATCATGGTGT
ATAACATATTTTTGTACATGACGT
Found at i:18187912 original size:100 final size:99
Alignment explanation
Indices: 18187710--18187899 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 99
18187700 GCAACCTAAC
* *
18187710 CATGGAGTATAACATGTTTTGTACATGGCGTGTGACAACAATATTTGTTTTCAACATAACGTGCA
1 CATGGAGTATAACATGTTTTGTACATGACGTGTAACAACAATATTTGTTTTCAACATAACGTGCA
* *
18187775 ACAACTTAACCATGGTGTGTAACATATTTCTATA
66 ACAACCTAACCATAGTGTGTAACATATTTCTATA
* * * * *** *
18187809 CATGGTGTATAATATGTTTTTGTACATGATGTGTAACAACAATATTTTTTTTCAACATGGTGTGT
1 CATGGAGTATAACATG-TTTTGTACATGACGTGTAACAACAATATTTGTTTTCAACATAACGTGC
* *
18187874 AACAACCTAATCATAGTGTGTCACAT
65 AACAACCTAACCATAGTGTGTAACAT
18187900 GTTTTTGTAC
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
99 14 0.18
100 62 0.82
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (99 bp):
CATGGAGTATAACATGTTTTGTACATGACGTGTAACAACAATATTTGTTTTCAACATAACGTGCA
ACAACCTAACCATAGTGTGTAACATATTTCTATA
Found at i:18196927 original size:23 final size:23
Alignment explanation
Indices: 18196896--18196951 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
18196886 GCAAGGTTTA
* *
18196896 GAATTTGTGAAACGCCATGGTAG
1 GAATATGTGAAACGCCATGATAG
* * * *
18196919 GAATGTGTGACACGGCATGATGG
1 GAATATGTGAAACGCCATGATAG
18196942 GAATATGTGA
1 GAATATGTGA
18196952 CACGTCATAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (23 bp):
GAATATGTGAAACGCCATGATAG
Found at i:18196952 original size:23 final size:23
Alignment explanation
Indices: 18196918--18196977 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
18196908 CGCCATGGTA
*
18196918 GGAATGTGTGACACGGCAT-GATG
1 GGAATATGTGACACGGCATAG-TG
*
18196941 GGAATATGTGACACGTCATAGTG
1 GGAATATGTGACACGGCATAGTG
*
18196964 AGAATATGTGACAC
1 GGAATATGTGACAC
18196978 AAATGTGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (23 bp):
GGAATATGTGACACGGCATAGTG
Found at i:18197033 original size:23 final size:22
Alignment explanation
Indices: 18197007--18197104 Score: 74
Period size: 23 Copynumber: 4.3 Consensus size: 22
18196997 TTAGAGTTTA
*
18197007 TGACACACCATGGAAGGAAAATG
1 TGACACA-CATGGAAGGAATATG
* *
18197030 TGACACTGCAGGGTAA-GAATATG
1 TGACAC-ACATGG-AAGGAATATG
*
18197053 TGACACGACTTGGAAGGAATATG
1 TGACAC-ACATGGAAGGAATATG
* *
18197076 TGAGACGACATGG-TGAGAATATG
1 TGACAC-ACATGGAAG-GAATATG
18197099 TGACAC
1 TGACAC
18197105 GCTAGTGTGA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 3 0.05
23 55 0.92
24 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (22 bp):
TGACACACATGGAAGGAATATG
Found at i:18197068 original size:46 final size:46
Alignment explanation
Indices: 18197017--18197105 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
18197007 TGACACACCA
18197017 TGGAAGGAAAATGTGACACTG-CAGGGTAAGAATATGTGACACGACT
1 TGGAAGGAAAATGTGACAC-GACAGGGTAAGAATATGTGACACGACT
* * * *
18197063 TGGAAGGAATATGTGAGACGACATGGTGAGAATATGTGACACG
1 TGGAAGGAAAATGTGACACGACAGGGTAAGAATATGTGACACG
18197106 CTAGTGTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.20
Consensus pattern (46 bp):
TGGAAGGAAAATGTGACACGACAGGGTAAGAATATGTGACACGACT
Found at i:18197114 original size:23 final size:22
Alignment explanation
Indices: 18197069--18197308 Score: 102
Period size: 23 Copynumber: 10.6 Consensus size: 22
18197059 GACTTGGAAG
* *
18197069 GAATATGTGAGACGACATGGTGA
1 GAATATGTGACACG-TATGGTGA
18197092 GAATATGTGACACGCTA-GTGTGA
1 GAATATGTGACACG-TATG-GTGA
* *
18197115 G-A-ATGTGACATGTTATGGTGT
1 GAATATGTGACACG-TATGGTGA
18197136 GAATATGTGACACGTCATGGTGA
1 GAATATGTGACACGT-ATGGTGA
*
18197159 GAATATGTGAAACTGCTTAT-G-G-
1 GAATATGTGACAC-G--TATGGTGA
* * * * *
18197181 GCATATATGACACGACAAGGTTTA
1 GAATATGTGACACG-TATGG-TGA
* * * *
18197205 GAGTTTATGACACACTA-GTGTGA
1 GAATATGTGACAC-GTATG-GTGA
* *
18197228 G-A-ATGTGACACGCCATGGTGT
1 GAATATGTGACACG-TATGGTGA
*
18197249 GAACATGTGACACGTCATGGTGA
1 GAATATGTGACACGT-ATGGTGA
* *
18197272 GAATATGTGTCACGTCATGGTAA
1 GAATATGTGACACGT-ATGGTGA
*
18197295 GCATATGTGACACG
1 GAATATGTGACACG
18197309 GCTGTGACAT
Statistics
Matches: 163, Mismatches: 35, Indels: 38
0.69 0.15 0.16
Matches are distributed among these distances:
20 1 0.01
21 29 0.18
22 17 0.10
23 99 0.61
24 14 0.09
25 2 0.01
26 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.27
Consensus pattern (22 bp):
GAATATGTGACACGTATGGTGA
Found at i:18197384 original size:23 final size:23
Alignment explanation
Indices: 18197355--18197421 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
18197345 CATACAAAGT
*
18197355 ATCTGTGACATGGCAT-GTCGA-A
1 ATCTGTGACACGGCATGGT-GAGA
*
18197377 ATCATGTGAGACGGCATGGTGAGA
1 ATC-TGTGACACGGCATGGTGAGA
*
18197401 ATCTGTGACACGTCATGGTGA
1 ATCTGTGACACGGCATGGTGA
18197422 ACATATATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 3 0.08
23 29 0.76
24 6 0.16
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (23 bp):
ATCTGTGACACGGCATGGTGAGA
Found at i:18198233 original size:31 final size:31
Alignment explanation
Indices: 18198191--18198266 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
18198181 CAGCATTGGA
* *
18198191 GTGTAATAACATTTGACTTGGTATGCTTAGC
1 GTGTAACAACATTTGACTTGGTATGCATAGC
18198222 GTGTAACAACATTTGACTTGGTATGCATAGC
1 GTGTAACAACATTTGACTTGGTATGCATAGC
18198253 GTGTAACAACATTT
1 GTGTAACAACATTT
18198267 ATTTCTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (31 bp):
GTGTAACAACATTTGACTTGGTATGCATAGC
Found at i:18202852 original size:2 final size:2
Alignment explanation
Indices: 18202845--18202881 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18202835 AATAATGAAA
18202845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18202882 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18203047 original size:2 final size:2
Alignment explanation
Indices: 18203040--18203078 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18203030 NNNNNNNNTA
18203040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18203079 GTGTCTACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18204141 original size:13 final size:13
Alignment explanation
Indices: 18204123--18204154 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18204113 ATGTGCACGT
*
18204123 GATGCAATTGTGA
1 GATGCAATTATGA
18204136 GATGCAATTATGA
1 GATGCAATTATGA
18204149 GATGCA
1 GATGCA
18204155 TGACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (13 bp):
GATGCAATTATGA
Found at i:18205081 original size:5 final size:5
Alignment explanation
Indices: 18205065--18205107 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
18205055 TGTTAGGTCG
18205065 TATTT T-TTT TATTT TATTT TATTT TATATT TA-TT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT
18205108 ATTGACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.34
5 19 0.54
6 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:18205591 original size:19 final size:17
Alignment explanation
Indices: 18205556--18205594 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
18205546 TCTCTACTCC
18205556 TCTTTCTTTTTCTTTCT
1 TCTTTCTTTTTCTTTCT
18205573 TCTTATCTTTTTCTCTTCT
1 TCTT-TCTTTTTCT-TTCT
18205592 TCT
1 TCT
18205595 CCGATCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTCTTTTTCTTTCT
Found at i:18205906 original size:7 final size:8
Alignment explanation
Indices: 18205891--18205917 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
18205881 CTATTGTATA
18205891 TATTTTTT
1 TATTTTTT
18205899 TATTTTTT
1 TATTTTTT
18205907 TATTTTTT
1 TATTTTTT
18205915 TAT
1 TAT
18205918 GGTTATTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:18206290 original size:24 final size:26
Alignment explanation
Indices: 18206263--18206315 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
18206253 TAAAAAAAAA
18206263 TTTATTT-ATCA-TTTTTTTAGTTTT
1 TTTATTTCATCATTTTTTTTAGTTTT
* *
18206287 TTTATTTCATTATTTTTTTTATTTTT
1 TTTATTTCATCATTTTTTTTAGTTTT
18206313 TTT
1 TTT
18206316 CTTGAAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 3 0.12
26 15 0.60
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTATTTCATCATTTTTTTTAGTTTT
Found at i:18206315 original size:9 final size:9
Alignment explanation
Indices: 18206274--18206315 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
18206264 TTATTTATCA
*
18206274 TTTTTTTAG
1 TTTTTTTAT
18206283 TTTTTTTA-
1 TTTTTTTAT
**
18206291 TTTCATTAT
1 TTTTTTTAT
18206300 TTTTTTTAT
1 TTTTTTTAT
18206309 TTTTTTT
1 TTTTTTT
18206316 CTTGAAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:18208202 original size:76 final size:76
Alignment explanation
Indices: 18208110--18208325 Score: 270
Period size: 76 Copynumber: 2.8 Consensus size: 76
18208100 GTGTCACCAA
* * * *
18208110 AATACTGCAATGACTTAGCGTGTCACCATAAGATGTCAACAACATCTAACAATTAAAGCGTGACG
1 AATACTGCAACGACTTAGCATGTCACCATAAGATGTCAACAACATCTAACAATTGAAGCGTGACA
18208175 TATCACCCCAT
66 TATCACCCCAT
* * * * * *
18208186 AATACTGCAACCACTTAGCATGTTACCATAAAATGTCAACGACATCTACCAATTGAAGCGTGGCA
1 AATACTGCAACGACTTAGCATGTCACCATAAGATGTCAACAACATCTAACAATTGAAGCGTGACA
* *
18208251 TGTCACCCTAT
66 TATCACCCCAT
* * * * * *
18208262 AATACTGCAACGACTAAGCATGTCACTACAAGATGTCAACAGCATCTATCAATTGGAGCGTGAC
1 AATACTGCAACGACTTAGCATGTCACCATAAGATGTCAACAACATCTAACAATTGAAGCGTGAC
18208326 TTGTGACAAT
Statistics
Matches: 117, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 117 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (76 bp):
AATACTGCAACGACTTAGCATGTCACCATAAGATGTCAACAACATCTAACAATTGAAGCGTGACA
TATCACCCCAT
Found at i:18210483 original size:63 final size:63
Alignment explanation
Indices: 18210380--18210534 Score: 193
Period size: 63 Copynumber: 2.5 Consensus size: 63
18210370 ACATCATAGT
* ** * *** *
18210380 CGGCATGTGCACTTCCCACTCCGCACATGCACAATTGTAATTTTCACAACATTATCATTCAAC
1 CGGCATGTGCACTACCCACTCCATACATGTATGGTTGTAATTGTCACAACATTATCATTCAAC
* * *
18210443 CGGTATGTGCACTGCCCACTCCATACATGTATGGTTGTAATTGTCACAACATTGTCATTCAAC
1 CGGCATGTGCACTACCCACTCCATACATGTATGGTTGTAATTGTCACAACATTATCATTCAAC
* *
18210506 CGGCGTGTGCACTACCCACTCCGTACATG
1 CGGCATGTGCACTACCCACTCCATACATG
18210535 CACGGTTACA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (63 bp):
CGGCATGTGCACTACCCACTCCATACATGTATGGTTGTAATTGTCACAACATTATCATTCAAC
Found at i:18213503 original size:23 final size:25
Alignment explanation
Indices: 18213477--18213539 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
18213467 ACAGTCATGT
18213477 TGTTACACGTCATGTTC-A-AAAAA
1 TGTTACACGTCATGTTCAATAAAAA
** *
18213500 TGTTACACACCATGCTCAATAAAAA
1 TGTTACACGTCATGTTCAATAAAAA
18213525 TGTTACACGTCATGT
1 TGTTACACGTCATGT
18213540 ACTAACACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 14 0.44
24 1 0.03
25 17 0.53
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (25 bp):
TGTTACACGTCATGTTCAATAAAAA
Found at i:18213573 original size:24 final size:24
Alignment explanation
Indices: 18213546--18213596 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
18213536 ATGTACTAAC
18213546 ACATGTTAGTTCAATATATTTTTT
1 ACATGTTAGTTCAATATATTTTTT
18213570 ACATGTTAGTTCAATATATTTTTT
1 ACATGTTAGTTCAATATATTTTTT
18213594 ACA
1 ACA
18213597 CATCATGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (24 bp):
ACATGTTAGTTCAATATATTTTTT
Found at i:18216924 original size:22 final size:23
Alignment explanation
Indices: 18216899--18216951 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
18216889 TACATAAGCA
*
18216899 TTATTATA-ATTTATAATAAACT
1 TTATTATAGATTAATAATAAACT
*
18216921 TTATTTATATGATTAATAATTAACT
1 TTA-TTATA-GATTAATAATAAACT
18216946 TTATTA
1 TTATTA
18216952 GTTATCACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 5 0.19
24 3 0.12
25 15 0.58
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTATAGATTAATAATAAACT
Found at i:18217058 original size:2 final size:2
Alignment explanation
Indices: 18217051--18217104 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
18217041 TCATTAATTT
* *
18217051 TA TA TA TA -A TA AA GTA TA T- TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
18217092 TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA
18217105 AGTATTACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
1 3 0.07
2 38 0.90
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18217089 original size:21 final size:21
Alignment explanation
Indices: 18217049--18217109 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
18217039 TGTCATTAAT
*
18217049 TTTATATATA-ATAAAGTATA
1 TTTATATATATATATAGTATA
18217069 TTATATATATATATATA-TATA
1 TT-TATATATATATATAGTATA
*
18217090 TTTA-ATTTATATATAAGTAT
1 TTTATATATATATAT-AGTAT
18217110 TACTAAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 9 0.26
20 5 0.14
21 17 0.49
22 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TTTATATATATATATAGTATA
Found at i:18218179 original size:3 final size:3
Alignment explanation
Indices: 18218171--18218228 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
18218161 TAAAGNTTAT
18218171 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
18218219 ATA ATA ATA A
1 ATA ATA ATA A
18218229 CCCAATTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18236296 original size:24 final size:23
Alignment explanation
Indices: 18236264--18236330 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
18236254 ACGCACGAGC
18236264 CTCTTTCTACTTGTTTTTTTCTTT
1 CTCTTTCTACTT-TTTTTTTCTTT
***
18236288 CTCTTTCTACCTCACTTTTTCTTT
1 CTCTTTCTA-CTTTTTTTTTCTTT
*
18236312 C-CTTT-TTCTTTTTTTTTCT
1 CTCTTTCTACTTTTTTTTTCT
18236331 ATGCCCTCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
21 9 0.26
22 1 0.03
23 4 0.11
24 19 0.54
25 2 0.06
ACGTcount: A:0.04, C:0.25, G:0.01, T:0.69
Consensus pattern (23 bp):
CTCTTTCTACTTTTTTTTTCTTT
Found at i:18236722 original size:21 final size:22
Alignment explanation
Indices: 18236688--18236733 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
18236678 ATTATCTTAT
*
18236688 ATTATAATTATTTATTAA-AAA
1 ATTATAATTATTTAATAATAAA
* *
18236709 ATTATTATTTTTTAATAATAAA
1 ATTATAATTATTTAATAATAAA
18236731 ATT
1 ATT
18236734 TTCACACAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATAATTATTTAATAATAAA
Found at i:18236869 original size:28 final size:27
Alignment explanation
Indices: 18236825--18236912 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
18236815 TAATGCGTAG
*
18236825 GTGATGTT-CCAAATATGTAACGTACAA
1 GTGACGTTCCCAAATATGTAACG-ACAA
*
18236852 GTGACGTTCCCAAATATGTATC-ACATA
1 GTGACGTTCCCAAATATGTAACGACA-A
** *
18236879 GGTGACGTTCCCAAATGCGTAACGCACGA
1 -GTGACGTTCCCAAATATGTAACG-ACAA
18236908 GTGAC
1 GTGAC
18236913 ATGCAACATA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 3 0.06
27 8 0.16
28 36 0.72
29 1 0.02
30 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (27 bp):
GTGACGTTCCCAAATATGTAACGACAA
Found at i:18237658 original size:3 final size:3
Alignment explanation
Indices: 18237650--18237680 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18237640 TAAAGTATAT
18237650 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18237681 ATTTTTTATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18245081 original size:26 final size:26
Alignment explanation
Indices: 18245052--18245101 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18245042 TACAAGATAC
* *
18245052 GCTTGTTTAGTCTTCGCAATATTCTA
1 GCTTGCTTAGTCTCCGCAATATTCTA
*
18245078 GCTTGCTTAGTCTCCGCATTATTC
1 GCTTGCTTAGTCTCCGCAATATTC
18245102 AGAACCATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (26 bp):
GCTTGCTTAGTCTCCGCAATATTCTA
Found at i:18245399 original size:79 final size:72
Alignment explanation
Indices: 18245216--18245441 Score: 236
Period size: 74 Copynumber: 3.0 Consensus size: 72
18245206 GAGTTAGATT
* * * *
18245216 ATTACAAGATAGACTTGCTTAGTATCCACAATATTCAGTATCATTACGAGATAGATAAGCTTTGC
1 ATTACAAGATAGGCCTGCTTAATATCCACAATATT-AGTATCATTACGAGATAGATAGGC-TTGC
*
18245281 TCAGTCTCA
64 TTAGTCTCA
* **
18245290 ATTACAAGATAGGCTTGCTTAGCATCCACAATACTTAGTATCATTACGAGATAGATAGGCTTGCT
1 ATTACAAGATAGGCCTGCTTAATATCCACAATA-TTAGTATCATTACGAGATAGATAGGCTTGCT
18245355 TAGTCTCGATTA
65 TAGTCTC----A
* * * * *
18245367 TCATTACGAGATAGGCCTGTTTAATATCCACAATATTTAGTATCATTAATGAGACAGATCGGCTT
1 --ATTACAAGATAGGCCTGCTTAATATCCACAATA-TTAGTATCATT-ACGAGATAGATAGGCTT
18245432 GCTTAGTCTC
62 GCTTAGTCTC
18245442 CCCAATATTC
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
73 11 0.08
74 54 0.41
75 2 0.02
77 1 0.01
79 39 0.30
80 24 0.18
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (72 bp):
ATTACAAGATAGGCCTGCTTAATATCCACAATATTAGTATCATTACGAGATAGATAGGCTTGCTT
AGTCTCA
Found at i:18245505 original size:57 final size:57
Alignment explanation
Indices: 18245427--18245566 Score: 172
Period size: 57 Copynumber: 2.5 Consensus size: 57
18245417 GAGACAGATC
* * * *
18245427 GGCTTGCTTAGTCTCCCCAATATTCAACATCATTACAAGATAGATCATTCCAAAATA
1 GGCTTGCTTAGTATCCGCAATATTCAACATCAGTACAAGATAGATCATTACAAAATA
* * * *
18245484 GGCTTGCTTAGTTTCCGCAATATTTAGCATCAGTACAAGATAGATCATTACAAGATA
1 GGCTTGCTTAGTATCCGCAATATTCAACATCAGTACAAGATAGATCATTACAAAATA
** **
18245541 AACTTGCTTAGTATATGCAATATTCA
1 GGCTTGCTTAGTATCCGCAATATTCA
18245567 GTATCTTTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 70 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (57 bp):
GGCTTGCTTAGTATCCGCAATATTCAACATCAGTACAAGATAGATCATTACAAAATA
Found at i:18245582 original size:57 final size:57
Alignment explanation
Indices: 18245429--18245582 Score: 164
Period size: 57 Copynumber: 2.7 Consensus size: 57
18245419 GACAGATCGG
* * * * * **
18245429 CTTGCTTAGTCTCCCCAATATTCAACATCATTACAAGATAGATCATTCCAAAATAGG
1 CTTGCTTAGTATACGCAATATTCAGCATCATTACAAGATAGATCATTACAAAATAAA
* * * * *
18245486 CTTGCTTAGTTTCCGCAATATTTAGCATCAGTACAAGATAGATCATTACAAGATAAA
1 CTTGCTTAGTATACGCAATATTCAGCATCATTACAAGATAGATCATTACAAAATAAA
* * * *
18245543 CTTGCTTAGTATATGCAATATTCAGTATCTTTACGAGATA
1 CTTGCTTAGTATACGCAATATTCAGCATCATTACAAGATA
18245583 AGCTTGCTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 80 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (57 bp):
CTTGCTTAGTATACGCAATATTCAGCATCATTACAAGATAGATCATTACAAAATAAA
Found at i:18245938 original size:22 final size:21
Alignment explanation
Indices: 18245913--18245960 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
18245903 GTTTGAATGA
*
18245913 TTTATCTTATAATTTAGATATT
1 TTTATATT-TAATTTAGATATT
*
18245935 TTTAATATTTATTTTAGATATT
1 TTT-ATATTTAATTTAGATATT
18245957 TTTA
1 TTTA
18245961 AGTAAAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATATTTAATTTAGATATT
Found at i:18251877 original size:3 final size:3
Alignment explanation
Indices: 18251869--18251893 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18251859 GGCGTGAACC
18251869 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
18251894 TACGTATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18255804 original size:27 final size:28
Alignment explanation
Indices: 18255732--18255797 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
18255722 CTTAAAAATG
*
18255732 TTAATAATAAATTATAAATTATTGATAT
1 TTAATAATAAATTATAAATTATTAATAT
18255760 TT--TGAATAAATTATAAATTATTAATAT
1 TTAAT-AATAAATTATAAATTATTAATAT
18255787 TTAATAATAAA
1 TTAATAATAAA
18255798 ATAAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 1 0.03
27 24 0.71
28 8 0.24
29 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TTAATAATAAATTATAAATTATTAATAT
Found at i:18260398 original size:37 final size:37
Alignment explanation
Indices: 18260345--18260419 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
18260335 GCTTCCTAGA
18260345 TTTCTTCTTCTAAGAAAGGTCTTTCTAGCAGCCTCAT
1 TTTCTTCTTCTAAGAAAGGTCTTTCTAGCAGCCTCAT
*
18260382 TTTCTTCTTCTGAGAAAGGTCTTTCTAGCAGCCTCAT
1 TTTCTTCTTCTAAGAAAGGTCTTTCTAGCAGCCTCAT
18260419 T
1 T
18260420 GATTCCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTCTTCTTCTAAGAAAGGTCTTTCTAGCAGCCTCAT
Found at i:18271520 original size:221 final size:221
Alignment explanation
Indices: 18271130--18271568 Score: 745
Period size: 221 Copynumber: 2.0 Consensus size: 221
18271120 AATGGTGGAA
* * *
18271130 TTTGTCACTGTTTGGAAATTGATAGAATTTCACCTTTTATCCACATTATATGTTTTCTTTATCTT
1 TTTGTCACTGTTTGGAAATTGATAGAATTTCACCTTGTATCCACATCATATGTTTTCTTAATCTT
*
18271195 TTTCTAGGTCTTATTCTGAGCTCCAATTTGCTTTTTAAATTAATCAAGATTTCAGAGTAAGACCA
66 TTTCTAGGTCTTATTCTGAGCTCCAATTTGCTTTTTAAATTAATCAAGATATCAGAGTAAGACCA
*
18271260 CATATGATAATGGTCTTCTAAAGTAGTTGAAAAAGATAACAGAAAGATCATCTAAACCATTTTTC
131 CATATGATAATGGTCTTCTAAAGTAGTTGAAAAAGATAACAGAAAGACCATCTAAACCATTTTTC
18271325 TGATAT-TGTAAGGCATTGAATGCAAT
196 TGAT-TGTGTAAGGCATTGAATGCAAT
* * *
18271351 TTTGTCGCTGTTTGGAAATTGATAGACTTTCACCTTGTATCCACGTCATATGTTTTCTTAATCTT
1 TTTGTCACTGTTTGGAAATTGATAGAATTTCACCTTGTATCCACATCATATGTTTTCTTAATCTT
* *
18271416 TTTCTAGGTCTTATTCTGAGTTCCAATTTGCTTTTTAAATTAATCAAGATATCAGAGTACGACCA
66 TTTCTAGGTCTTATTCTGAGCTCCAATTTGCTTTTTAAATTAATCAAGATATCAGAGTAAGACCA
* *
18271481 CATATGATAATGGTCTTCTAAAGTTGTTGAAAAAGATAACAGAAAGACCATCTACACCATTTTTC
131 CATATGATAATGGTCTTCTAAAGTAGTTGAAAAAGATAACAGAAAGACCATCTAAACCATTTTTC
*
18271546 TGATTGTGTACGGCATTGAATGC
196 TGATTGTGTAAGGCATTGAATGC
18271569 TTCAAGGCTT
Statistics
Matches: 204, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
220 1 0.00
221 203 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (221 bp):
TTTGTCACTGTTTGGAAATTGATAGAATTTCACCTTGTATCCACATCATATGTTTTCTTAATCTT
TTTCTAGGTCTTATTCTGAGCTCCAATTTGCTTTTTAAATTAATCAAGATATCAGAGTAAGACCA
CATATGATAATGGTCTTCTAAAGTAGTTGAAAAAGATAACAGAAAGACCATCTAAACCATTTTTC
TGATTGTGTAAGGCATTGAATGCAAT
Found at i:18272199 original size:177 final size:177
Alignment explanation
Indices: 18271896--18272420 Score: 852
Period size: 172 Copynumber: 3.0 Consensus size: 177
18271886 CAGATGGCAC
18271896 AACATTGTTTGTC--TAGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
1 AACATTGTTTGTCTATAGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
18271959 ATATATATATATA--TAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
66 ATATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
*
18272022 AGAGCAGTGAACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
131 AGAGCAGTGGACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
* * * *
18272069 AACGTTGTTTGTCTATACATCATTTTGTAGAGCCACTGAAGTTTAAAGTGATAGTGGTAATGTTG
1 AACATTGTTTGTCTATAGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
* *
18272134 ATATATATATATATTTATCTAGGCTTCTATTCACACATTATCATCGAAGGTAAAGGGGACCATTA
66 ATATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
* * * * *
18272199 AGAGCAGTGGACTGGCAAGGCTCGAAATGATGGATTAACTACTCAAA
131 AGAGCAGTGGACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
*
18272246 AA-ATTGTTTGTCTATGGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
1 AACATTGTTTGTCTATAGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
*
18272310 ---T-TATATATATTTAGCTAGGCTTCTATTCACACATTATAATTGAAGGTAAAGGGGACCATTA
66 ATATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
*
18272371 AGAGCAGTGGACTGGCATGGCTTGAAATGATGGGTCAATTACTGAAA
131 AGAGCAGTGGACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
18272418 AAC
1 AAC
18272421 CTAAGCTTTG
Statistics
Matches: 321, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
172 100 0.31
173 13 0.04
175 60 0.19
176 57 0.18
177 91 0.28
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (177 bp):
AACATTGTTTGTCTATAGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
ATATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
AGAGCAGTGGACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
Found at i:18272375 original size:172 final size:174
Alignment explanation
Indices: 18271896--18272420 Score: 824
Period size: 177 Copynumber: 3.0 Consensus size: 174
18271886 CAGATGGCAC
18271896 AACATTGTTTGTCTA-GATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTGA
1 AACATTGTTTGTCTATGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTGA
*
18271960 TATATATATATATAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTAAGA
66 TATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTAAGA
* * * *
18272025 GCAGTGAACTGGCAAGGCTTGAAATGATGGGTCAATTACTGAAA
131 GCAGTGGACTGGCAAGGCTTGAAATGATGGATCAACTACTCAAA
* * * *
18272069 AACGTTGTTTGTCTATACATCATTTTGTAGAGCCACTGAAGTTTAAAGTGATAGTGGTAATGTTG
1 AACATTGTTTGTCTAT-GATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
* *
18272134 ATATATATATATATTTATCTAGGCTTCTATTCACACATTATCATCGAAGGTAAAGGGGACCATTA
65 --ATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTA
* *
18272199 AGAGCAGTGGACTGGCAAGGCTCGAAATGATGGATTAACTACTCAAA
128 AGAGCAGTGGACTGGCAAGGCTTGAAATGATGGATCAACTACTCAAA
18272246 AA-ATTGTTTGTCTATGGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
1 AACATTGTTTGTCTAT-GATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTG
*
18272310 -T-TATATATATTTAGCTAGGCTTCTATTCACACATTATAATTGAAGGTAAAGGGGACCATTAAG
65 ATATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTAAG
* * * *
18272373 AGCAGTGGACTGGCATGGCTTGAAATGATGGGTCAATTACTGAAA
130 AGCAGTGGACTGGCAAGGCTTGAAATGATGGATCAACTACTCAAA
18272418 AAC
1 AAC
18272421 CTAAGCTTTG
Statistics
Matches: 320, Mismatches: 27, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
172 100 0.31
173 15 0.05
175 45 0.14
176 57 0.18
177 103 0.32
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (174 bp):
AACATTGTTTGTCTATGATCATTTTGTAGAGTCACTGAAGTTTAAAGTGATAGTGGTGATGTTGA
TATATATATATTTAGCTAGGCTTCTATTCACACATTATCATTGAAGGTAAAGGGGACCATTAAGA
GCAGTGGACTGGCAAGGCTTGAAATGATGGATCAACTACTCAAA
Found at i:18278567 original size:53 final size:54
Alignment explanation
Indices: 18278508--18278616 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
18278498 ATAATAAAAC
*
18278508 AAGTGAATATA-AAGAGAATGGG-TAACAATTAACAAAAACTGATAAACAAATAA
1 AAGTGAATATAGAA-AGAAGGGGTTAACAATTAACAAAAACTGATAAACAAATAA
* *
18278561 AAGTGAATATAGAAAGAAGGGGTTAATAATTAACAAAAACTGGTAAACAAATAA
1 AAGTGAATATAGAAAGAAGGGGTTAACAATTAACAAAAACTGATAAACAAATAA
18278615 AA
1 AA
18278617 ATAATAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
53 18 0.35
54 33 0.65
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (54 bp):
AAGTGAATATAGAAAGAAGGGGTTAACAATTAACAAAAACTGATAAACAAATAA
Found at i:18278680 original size:119 final size:118
Alignment explanation
Indices: 18278461--18278681 Score: 388
Period size: 119 Copynumber: 1.9 Consensus size: 118
18278451 ATTAAAGGCT
18278461 GGGGTAACAATTAACAAAAACTGATAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAA
1 GGGGTAACAATTAACAAAAACTGATAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAA
*
18278526 TGGGTAACAATTAACAAAAACTGATAAACAAATAAAAGTGAATATAGAAAGAA
66 GGGGTAACAATTAACAAAAACTGATAAACAAATAAAAGTGAATATAGAAAGAA
* * *
18278579 GGGGTTAATAATTAACAAAAACTGGTAAACAAATAAAAATAATAAAATAAGTGAATATAAAGAGA
1 GGGG-TAACAATTAACAAAAACTGATAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGA
*
18278644 AGGGGTAACAATTAACAAAAACTGATAAATAAATAAAA
65 AGGGGTAACAATTAACAAAAACTGATAAACAAATAAAA
18278682 ATAAATAAGC
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
118 4 0.04
119 93 0.96
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (118 bp):
GGGGTAACAATTAACAAAAACTGATAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAA
GGGGTAACAATTAACAAAAACTGATAAACAAATAAAAGTGAATATAGAAAGAA
Found at i:18278725 original size:71 final size:70
Alignment explanation
Indices: 18278549--18278760 Score: 274
Period size: 71 Copynumber: 3.1 Consensus size: 70
18278539 ACAAAAACTG
* * * *
18278549 ATAAACAAATAAAAGTGAATATAGAAAGAAGGGGTTAATAATTAACAAAAACTGGTAAACAAATA
1 ATAAGCAAATAAAAGTGAATATAGAAAGAA-GGGATAACAATTAACAAAAACTGATAAACAAATA
18278614 AAAATA
65 AAAATA
* *
18278620 AT-A--AAAT--AAGTGAATATA-AAGAGAAGGGGTAACAATTAACAAAAACTGATAAATAAATA
1 ATAAGCAAATAAAAGTGAATATAGAA-AGAAGGGATAACAATTAACAAAAACTGATAAACAAATA
18278679 AAAATAA
65 AAAAT-A
* * *
18278686 ATAAGCAAATAAAAGTGAATATAGAAAGAAAGGATAACAATTAATAAAAATTGATAAACAAATAA
1 ATAAGCAAATAAAAGTGAATATAGAAAGAAGGGATAACAATTAACAAAAACTGATAAACAAATAA
18278751 AAATA
66 AAATA
18278756 ATAAG
1 ATAAG
18278761 GTAAGTGAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
65 37 0.30
66 18 0.15
67 1 0.01
68 4 0.03
69 4 0.03
70 7 0.06
71 51 0.41
72 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.20
Consensus pattern (70 bp):
ATAAGCAAATAAAAGTGAATATAGAAAGAAGGGATAACAATTAACAAAAACTGATAAACAAATAA
AAATA
Found at i:18278743 original size:119 final size:118
Alignment explanation
Indices: 18278469--18278706 Score: 345
Period size: 119 Copynumber: 2.0 Consensus size: 118
18278459 CTGGGGTAAC
* *
18278469 AATTAACAAAAACTGATAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAATGGGTAAC
1 AATTAACAAAAAC-GGTAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAAGGGGTAAC
* * ** *
18278534 AATTAACAAAAACTGATAAACAAATAAAAGTGAATATAGAAAGAAGGGGTTAAT
65 AATTAACAAAAACTGATAAACAAATAAAAATAAATATAGAAAGAAGAAGTGAAT
*
18278588 AATTAACAAAAACTGGTAAACAAATAAAAATAATAAAATAAGTGAATATAAAGAGAAGGGGTAAC
1 AATTAACAAAAAC-GGTAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAAGGGGTAAC
* *
18278653 AATTAACAAAAACTGATAAATAAATAAAAATAAATA-AGCAAATAA-AAGTGAAT
65 AATTAACAAAAACTGATAAACAAATAAAAATAAATATAG-AAAGAAGAAGTGAAT
18278706 A
1 A
18278707 TAGAAAGAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
118 8 0.07
119 100 0.93
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (118 bp):
AATTAACAAAAACGGTAAACAAATAAAAATAATAAAACAAGTGAATATAAAGAGAAGGGGTAACA
ATTAACAAAAACTGATAAACAAATAAAAATAAATATAGAAAGAAGAAGTGAAT
Found at i:18279152 original size:29 final size:29
Alignment explanation
Indices: 18279096--18279152 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
18279086 CGTGTATGTG
* *
18279096 TTGTATGCGTGTGCATGTATGTATGCATT
1 TTGTATGCGTGTGCATGCATGTACGCATT
* * *
18279125 TTGTGTGCGTGTGCATGCGTGTGCGCAT
1 TTGTATGCGTGTGCATGCATGTACGCAT
18279153 ATGTGTGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.12, C:0.14, G:0.33, T:0.40
Consensus pattern (29 bp):
TTGTATGCGTGTGCATGCATGTACGCATT
Found at i:18279292 original size:4 final size:4
Alignment explanation
Indices: 18279283--18279335 Score: 88
Period size: 4 Copynumber: 13.2 Consensus size: 4
18279273 GTTGTATCTA
* *
18279283 TATG TATG TATA TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
18279331 TATG T
1 TATG T
18279336 GTGTGAGCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:18279584 original size:76 final size:76
Alignment explanation
Indices: 18279501--18279652 Score: 223
Period size: 76 Copynumber: 2.0 Consensus size: 76
18279491 TTGTGTATGC
* * * *
18279501 CAATCCGATATCAATCTTTGGTTTTACCTTGGTGTGCATTGCGTGTGTATGTGTGCACGCACGCA
1 CAATCCGAGATCAATCATTGGTTTCACCTTGGTGTGCATTGCATGTGTATGTGTGCACGCACGCA
18279566 TGTGTGAGTGT
66 TGTGTGAGTGT
* ** * *
18279577 CAATCCGAGATCAATCATTGGTTTCGCCTTGGTGTGTGTTGCATGTGTGTGTGTGCACGCGCGCA
1 CAATCCGAGATCAATCATTGGTTTCACCTTGGTGTGCATTGCATGTGTATGTGTGCACGCACGCA
18279642 TGTGTGAGTGT
66 TGTGTGAGTGT
18279653 GTGTATTGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (76 bp):
CAATCCGAGATCAATCATTGGTTTCACCTTGGTGTGCATTGCATGTGTATGTGTGCACGCACGCA
TGTGTGAGTGT
Found at i:18282072 original size:3 final size:3
Alignment explanation
Indices: 18282064--18282088 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18282054 ACTTCATATG
18282064 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
18282089 ATATATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:18284752 original size:21 final size:21
Alignment explanation
Indices: 18284726--18284800 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
18284716 AATCACTATG
18284726 TGATTGATTTTAGGCATTACA
1 TGATTGATTTTAGGCATTACA
* * *
18284747 TGATTGGTTTTAGGTATTACG
1 TGATTGATTTTAGGCATTACA
* *
18284768 TGACTAGTTTTTAGGCATTACA
1 TGA-TTGATTTTAGGCATTACA
*
18284790 TGACTGATTTT
1 TGATTGATTTT
18284801 TAAGTAATGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 26 0.60
22 17 0.40
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (21 bp):
TGATTGATTTTAGGCATTACA
Found at i:18284782 original size:22 final size:22
Alignment explanation
Indices: 18284733--18284802 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
18284723 ATGTGATTGA
* *
18284733 TTTTAGGCATTACATGATTG-G
1 TTTTAGGCATTACATGACTGAT
* *
18284754 TTTTAGGTATTACGTGACT-AGT
1 TTTTAGGCATTACATGACTGA-T
18284776 TTTTAGGCATTACATGACTGAT
1 TTTTAGGCATTACATGACTGAT
18284798 TTTTA
1 TTTTA
18284803 AGTAATGCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 16 0.40
22 23 0.57
23 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (22 bp):
TTTTAGGCATTACATGACTGAT
Found at i:18284848 original size:23 final size:23
Alignment explanation
Indices: 18284815--18284902 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
18284805 TAATGCCTAT
* *
18284815 GTCACACAATGCCTTATTAACTA
1 GTCACATAATGCCTTATCAACTA
*
18284838 GTCACATAATGTCTTATCAACTA
1 GTCACATAATGCCTTATCAACTA
**
18284861 GTCATGTAATGCC-TATCAACTA
1 GTCACATAATGCCTTATCAACTA
** *
18284883 GTCACGCAATACCTTATCAA
1 GTCACATAATGCCTTATCAA
18284903 AAACTAGTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 19 0.35
23 36 0.65
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (23 bp):
GTCACATAATGCCTTATCAACTA
Found at i:18284909 original size:26 final size:26
Alignment explanation
Indices: 18284878--18284947 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
18284868 AATGCCTATC
18284878 AACTAGTCACGCAATACCTTATCAAA
1 AACTAGTCACGCAATACCTTATCAAA
* * *
18284904 AACTAGTCACGCAATGCTTTATTAAA
1 AACTAGTCACGCAATACCTTATCAAA
18284930 AACTAGTCACGCAATACC
1 AACTAGTCACGCAATACC
18284948 CAAAGTCAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (26 bp):
AACTAGTCACGCAATACCTTATCAAA
Found at i:18284960 original size:21 final size:21
Alignment explanation
Indices: 18284934--18285008 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
18284924 ATTAAAAACT
* *
18284934 AGTCACGCAATACCCAAAGTC
1 AGTCACGTAATACCCAAAATC
* *
18284955 AGTCACGTAATATCTAAAATC
1 AGTCACGTAATACCCAAAATC
* *
18284976 AGTCACGTAATACCTAAAAAC
1 AGTCACGTAATACCCAAAATC
*
18284997 TAGTCACATAAT
1 -AGTCACGTAAT
18285009 TTTCAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 36 0.78
22 10 0.22
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (21 bp):
AGTCACGTAATACCCAAAATC
Found at i:18288615 original size:2 final size:2
Alignment explanation
Indices: 18288597--18288658 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
18288587 ATAGATGTTT
* * * * * * * *
18288597 TA TA CA TA TA AA TA TA TA TA CA TA TA TA TA CA CA CA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18288639 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
18288659 AGTAGACGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (2 bp):
TA
Found at i:18289037 original size:12 final size:13
Alignment explanation
Indices: 18289022--18289051 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18289012 TAAAAAAATT
18289022 AAATAAA-ATTAA
1 AAATAAATATTAA
18289034 AAATAAATATTAA
1 AAATAAATATTAA
18289047 AAATA
1 AAATA
18289052 TTTTTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAATATTAA
Found at i:18290187 original size:3 final size:3
Alignment explanation
Indices: 18290179--18290215 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
18290169 TCTTCCACCC
18290179 CAA CAA CAA CAA CAA C-A CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
18290216 TTATGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:18290201 original size:17 final size:17
Alignment explanation
Indices: 18290179--18290212 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18290169 TCTTCCACCC
18290179 CAACAACAACAACAACA
1 CAACAACAACAACAACA
18290196 CAACAACAACAACAACA
1 CAACAACAACAACAACA
18290213 ACATTATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (17 bp):
CAACAACAACAACAACA
Found at i:18309662 original size:23 final size:23
Alignment explanation
Indices: 18309633--18309678 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18309623 TTATAAGGAG
18309633 TTTTATGCATGAAACAAGAAGAT
1 TTTTATGCATGAAACAAGAAGAT
18309656 TTTTATGCATGAAACAAGAAGAT
1 TTTTATGCATGAAACAAGAAGAT
18309679 ACACATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (23 bp):
TTTTATGCATGAAACAAGAAGAT
Found at i:18310148 original size:22 final size:22
Alignment explanation
Indices: 18310123--18310164 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18310113 TTATAAAGAG
18310123 TTTTATGCATAAAACAAGAAAT
1 TTTTATGCATAAAACAAGAAAT
*
18310145 TTTTATGCATGAAACAAGAA
1 TTTTATGCATAAAACAAGAA
18310165 GATGCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (22 bp):
TTTTATGCATAAAACAAGAAAT
Found at i:18310849 original size:23 final size:23
Alignment explanation
Indices: 18310777--18310850 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
18310767 AACATATTTT
**
18310777 TATTACAATTAAATAATATTTTG
1 TATTACAATTAAATAATATTTAA
* * * *
18310800 TATTAGAATCTAATTAA-ATCTAT
1 TATTACAAT-TAAATAATATTTAA
*
18310823 TATTATAATTAAATAATATTTAA
1 TATTACAATTAAATAATATTTAA
18310846 TATTA
1 TATTA
18310851 AAAGATAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 6 0.15
23 28 0.70
24 6 0.15
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (23 bp):
TATTACAATTAAATAATATTTAA
Found at i:18310954 original size:28 final size:27
Alignment explanation
Indices: 18310923--18310994 Score: 72
Period size: 32 Copynumber: 2.4 Consensus size: 27
18310913 ATCATATTCA
**
18310923 AATAATAATATTAAATAATATATTTTAT
1 AATAATAATATTAAATAATAT-TAATAT
18310951 AATAATTATTATAGTTAAATAATATTAATAT
1 AATAA-TA--ATA-TTAAATAATATTAATAT
18310982 AATAAATAATATT
1 AAT-AATAATATT
18310995 TACATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 7 0.19
29 5 0.14
31 12 0.32
32 13 0.35
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AATAATAATATTAAATAATATTAATAT
Found at i:18311958 original size:40 final size:40
Alignment explanation
Indices: 18311914--18312015 Score: 152
Period size: 40 Copynumber: 2.5 Consensus size: 40
18311904 CGTGGCGAGA
18311914 TTGAAAACCCCACTAAGGTGAATCACCAATCTTGGT-AAGG
1 TTGAAAACCCCACTAAGGTGAATCACCAATCTT-GTCAAGG
** * *
18311954 TTGAAAACTTCACTAAAGTGAATCACTAATCTTGTCAAGG
1 TTGAAAACCCCACTAAGGTGAATCACCAATCTTGTCAAGG
18311994 TTGAAAACCCCACTAAGGTGAA
1 TTGAAAACCCCACTAAGGTGAA
18312016 AAATAGCTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.04
40 52 0.96
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (40 bp):
TTGAAAACCCCACTAAGGTGAATCACCAATCTTGTCAAGG
Found at i:18314466 original size:253 final size:252
Alignment explanation
Indices: 18314016--18314508 Score: 968
Period size: 253 Copynumber: 2.0 Consensus size: 252
18314006 ATTAACTCTC
18314016 AACTCTTAATATGAATAATAACTAAACTTAAGGGTCCTATTTATAGTATTATACGCCCACATCCT
1 AACTCTTAATATGAATAATAACTAAACTTAAGGGTCCTATTTATAGTATTATACGCCCACATCCT
18314081 AATAAAACTATACTTCTAGTTGTCTAATACAATTAGAATAATTAACAAGAGATTTAAATAAAATA
66 AATAAAACTATACTTCTAGTTGTCTAATACAATTAGAATAATTAACAAGAGATTTAAATAAAATA
18314146 GGTGTTCTATTCCTAAATAGAACATGACTATCCTAATCAAATACTAATCTTAAAAGTATTAAAAT
131 GGTGTTCTATTCCTAAATAGAACATGACTATCCTAATCAAATACTAATCTTAAAAGTATTAAAAT
*
18314211 AAAAATAAGAAAAGAATCCTACTCTAAATAAAATAAAAAAAATAATTAAATAAAATA
196 AAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAATTAAATAAAATA
18314268 AANCTCTTAATATGAATAATAACTAAACTTAAGGGTCCTATTTATAGTATTATACGCCCACATCC
1 AA-CTCTTAATATGAATAATAACTAAACTTAAGGGTCCTATTTATAGTATTATACGCCCACATCC
18314333 TAATAAAACTATACTTCTAGTTGTCTAATACAATTAGAATAATTAACAAGAGATTTAAATAAAAT
65 TAATAAAACTATACTTCTAGTTGTCTAATACAATTAGAATAATTAACAAGAGATTTAAATAAAAT
18314398 AGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATCAAATACTAATCTTAAAAGTATTAAAA
130 AGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATCAAATACTAATCTTAAAAGTATTAAAA
18314463 TAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAA
195 TAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAA
18314509 ATCCTAAATA
Statistics
Matches: 239, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
252 2 0.01
253 237 0.99
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.30
Consensus pattern (252 bp):
AACTCTTAATATGAATAATAACTAAACTTAAGGGTCCTATTTATAGTATTATACGCCCACATCCT
AATAAAACTATACTTCTAGTTGTCTAATACAATTAGAATAATTAACAAGAGATTTAAATAAAATA
GGTGTTCTATTCCTAAATAGAACATGACTATCCTAATCAAATACTAATCTTAAAAGTATTAAAAT
AAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAATTAAATAAAATA
Found at i:18315793 original size:40 final size:41
Alignment explanation
Indices: 18315741--18315873 Score: 130
Period size: 41 Copynumber: 3.2 Consensus size: 41
18315731 TACTACTTAT
* *
18315741 AATACTTTTTCTTTTCTAGAAGTGTTCC-AATATAACTCAC
1 AATACTTCTTCTTTTCTAGAAGTGTTCCAAATACAACTCAC
*
18315781 AATACTTCTTCTTATCCT-GAAGGTGTTCCAAATACAACT-AGC
1 AATACTTCTTCTT-TTCTAGAA-GTGTTCCAAATACAACTCA-C
** * * *
18315823 AACGCATCTTCTTCTCTTAG-AGTGTTCCAAATACAACTCGC
1 AATACTTCTTCTTTTC-TAGAAGTGTTCCAAATACAACTCAC
18315864 AATACTTCTT
1 AATACTTCTT
18315874 ATTTCCATGT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
40 15 0.20
41 37 0.50
42 21 0.28
43 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (41 bp):
AATACTTCTTCTTTTCTAGAAGTGTTCCAAATACAACTCAC
Found at i:18316567 original size:105 final size:104
Alignment explanation
Indices: 18316452--18316977 Score: 437
Period size: 105 Copynumber: 5.1 Consensus size: 104
18316442 AAGCTTGTGA
* * *
18316452 TTGAAATATAAGTGATGAATTACATGGTCAAAGAATAAGTGATGAAGCTT-T-CTATCATGTGCA
1 TTGAAATATAAGTGATGAATTATATGGTCAAAGAATAAGCGATAAAGCTTGTACTA-CA--TGCA
* *
18316515 GCAATAACATT-CTAGCAAAAGTAAGAGCGATAAAGTTTACAG
63 ACAATAACATTAC-AGCAAAAGTAAGAGCGATAAAGCTTACAG
*
18316557 TTGAAATATAAGTGATGAATTATATGGTCAAAGAATGAGCGATAAAGCTTGTGACTACATGCAAC
1 TTGAAATATAAGTGATGAATTATATGGTCAAAGAATAAGCGATAAAGCTTGT-ACTACATGCAAC
* *
18316622 AATAACATTACAGCCAAAGTAAGAGCGATAAAGCTTGCAG
65 AATAACATTACAGCAAAAGTAAGAGCGATAAAGCTTACAG
* * *
18316662 TTGAAATATGAGTGATGAATTATATGATCAAAGAATGAA-CGATAGAA-CTTGTGACCA-AGTGC
1 TTGAAATATAAGTGATGAATTATATGGTCAAAGAAT-AAGCGATA-AAGCTTGT-ACTACA-TGC
* ** *
18316724 AAAAATAACATT--A-C--AACCAA-A--GNTAAAGCTTACAG
62 AACAATAACATTACAGCAAAAGTAAGAGCGATAAAGCTTACAG
** * * * *
18316759 TTGATGT-TAAAGTGATGAA-T-TATGGTTAAAGAATGAGCAATAAAGCTTGTGACCA-AGTGCA
1 TTGAAATAT-AAGTGATGAATTATATGGTCAAAGAATAAGCGATAAAGCTTGT-ACTACA-TGCA
* * * *
18316820 ACAATAATATTACAGCCAAAGTAAGAGCGATAAGGCTTGCAG
63 ACAATAACATTACAGCAAAAGTAAGAGCGATAAAGCTTACAG
* * * *
18316862 TTGAAAAATGAGTGATGAATTATATGATCAAAGAATGAA-CGATAGAA-CTTGTGACCA-AGTGC
1 TTGAAATATAAGTGATGAATTATATGGTCAAAGAAT-AAGCGATA-AAGCTTGT-ACTACA-TGC
* * * * * *
18316924 AAAAATAACATTACAACCAAAGTAAAAGTGATAAAGCTTGCAG
62 AACAATAACATTACAGCAAAAGTAAGAGCGATAAAGCTTACAG
*
18316967 CTGAAATATAA
1 TTGAAATATAA
18316978 CTTATTTATT
Statistics
Matches: 350, Mismatches: 48, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
94 3 0.01
95 41 0.12
96 2 0.01
97 27 0.08
98 1 0.00
99 1 0.00
100 8 0.02
101 1 0.00
102 1 0.00
103 25 0.07
104 3 0.01
105 224 0.64
106 8 0.02
107 2 0.01
108 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (104 bp):
TTGAAATATAAGTGATGAATTATATGGTCAAAGAATAAGCGATAAAGCTTGTACTACATGCAACA
ATAACATTACAGCAAAAGTAAGAGCGATAAAGCTTACAG
Found at i:18316843 original size:200 final size:201
Alignment explanation
Indices: 18316566--18316949 Score: 675
Period size: 200 Copynumber: 1.9 Consensus size: 201
18316556 GTTGAAATAT
* *
18316566 AAGTGATGAATTATATGGTCAAAGAATGAGCGATAAAGCTTGTGACTACATGCAACAATAACATT
1 AAGTGATGAATTATATGGTCAAAGAATGAGCAATAAAGCTTGTGACCACATGCAACAATAACATT
*
18316631 ACAGCCAAAGTAAGAGCGATAAAGCTTGCAGTTGAAATATGAGTGATGAATTATATGATCAAAGA
66 ACAGCCAAAGTAAGAGCGATAAAGCTTGCAGTTGAAAAATGAGTGATGAATTATATGATCAAAGA
18316696 ATGAACGATAGAACTTGTGACCAAGTGCAAAAATAACATTACAACCAAAGNTAAAGCTTACAGTT
131 ATGAACGATAGAACTTGTGACCAAGTGCAAAAATAACATTACAACCAAAG-TAAAGCTTACAGTT
18316761 GATGTTA
195 GATGTTA
* *
18316768 AAGTGATGAA-T-TATGGTTAAAGAATGAGCAATAAAGCTTGTGACCA-AGTGCAACAATAATAT
1 AAGTGATGAATTATATGGTCAAAGAATGAGCAATAAAGCTTGTGACCACA-TGCAACAATAACAT
*
18316830 TACAGCCAAAGTAAGAGCGATAAGGCTTGCAGTTGAAAAATGAGTGATGAATTATATGATCAAAG
65 TACAGCCAAAGTAAGAGCGATAAAGCTTGCAGTTGAAAAATGAGTGATGAATTATATGATCAAAG
18316895 AATGAACGATAGAACTTGTGACCAAGTGCAAAAATAACATTACAACCAAAGTAAA
130 AATGAACGATAGAACTTGTGACCAAGTGCAAAAATAACATTACAACCAAAGTAAA
18316950 AGTGATAAAG
Statistics
Matches: 175, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
199 5 0.03
200 159 0.91
201 1 0.01
202 10 0.06
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (201 bp):
AAGTGATGAATTATATGGTCAAAGAATGAGCAATAAAGCTTGTGACCACATGCAACAATAACATT
ACAGCCAAAGTAAGAGCGATAAAGCTTGCAGTTGAAAAATGAGTGATGAATTATATGATCAAAGA
ATGAACGATAGAACTTGTGACCAAGTGCAAAAATAACATTACAACCAAAGTAAAGCTTACAGTTG
ATGTTA
Found at i:18323567 original size:15 final size:15
Alignment explanation
Indices: 18323547--18323583 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18323537 ATTTCACTTA
18323547 AAATTTTAAAA-ATT
1 AAATTTTAAAATATT
18323561 AATATTTTAAAATATT
1 AA-ATTTTAAAATATT
18323577 AAATTTT
1 AAATTTT
18323584 TATTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTTAAAATATT
Found at i:18323616 original size:22 final size:22
Alignment explanation
Indices: 18323577--18323626 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
18323567 TTAAAATATT
* *
18323577 AAAT-TTTTATTTATAATTT-A
1 AAATATTTTAATTAAAATTTGA
18323597 AATATATTTTAATTAAAATTTGA
1 AA-ATATTTTAATTAAAATTTGA
18323620 AAATATT
1 AAATATT
18323627 AATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 18 0.72
23 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATATTTTAATTAAAATTTGA
Found at i:18323688 original size:21 final size:21
Alignment explanation
Indices: 18323635--18323688 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
18323625 TTAATAATTT
*
18323635 TTAAATTTT-AATTTAAAGTA
1 TTAATTTTTAAATTTAAAGTA
*
18323655 TTAATTTTATAAATTT-AAGTG
1 TTAATTTT-TAAATTTAAAGTA
18323676 TGTAATTTTTAAA
1 T-TAATTTTTAAA
18323689 AATAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 10 0.34
22 12 0.41
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TTAATTTTTAAATTTAAAGTA
Found at i:18330136 original size:43 final size:43
Alignment explanation
Indices: 18330046--18330222 Score: 214
Period size: 43 Copynumber: 4.1 Consensus size: 43
18330036 TTGTTTGATA
* * * * *
18330046 ATGATGACCC-AGCTATGTGCGATGTGA-GAATGCACATGAGCTG
1 ATGATGACCCGA-CTATGTGCGA-GTAAGGAGTGCGCATAAGCCG
* * * *
18330089 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGTATAAGCCA
1 ATGATGACCCGACTATGTGCGAGTAAGGAGTGCGCATAAGCCG
18330132 ATGATGACCCGACTATGTGCGAGTAAGGAGTGCGCATAAGCCG
1 ATGATGACCCGACTATGTGCGAGTAAGGAGTGCGCATAAGCCG
* **
18330175 ATGATGACCCGATTATGTGTAAGTAAGGAGTGCGCATAAGCCG
1 ATGATGACCCGACTATGTGCGAGTAAGGAGTGCGCATAAGCCG
18330218 ATGAT
1 ATGAT
18330223 TATGACTCGG
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 2 0.02
43 114 0.98
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (43 bp):
ATGATGACCCGACTATGTGCGAGTAAGGAGTGCGCATAAGCCG
Found at i:18332267 original size:21 final size:22
Alignment explanation
Indices: 18332242--18332282 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18332232 CCTAGGTGGA
*
18332242 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18332263 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18332283 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18332283 original size:20 final size:21
Alignment explanation
Indices: 18332242--18332286 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18332232 CCTAGGTGGA
*
18332242 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
18332263 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
18332283 AAAA
1 AAAA
18332287 AAGGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:18332287 original size:21 final size:20
Alignment explanation
Indices: 18332240--18332287 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
18332230 ACCCTAGGTG
*
18332240 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
18332260 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
18332282 GAAAAA
1 GAAAAA
18332288 AGGTAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:18338538 original size:4 final size:4
Alignment explanation
Indices: 18338529--18338553 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18338519 TGGTTTGCAA
18338529 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
18338554 GTCCCTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:18338710 original size:16 final size:15
Alignment explanation
Indices: 18338684--18338718 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
18338674 AGTATAAAAG
*
18338684 AATAGTAAATAATTA
1 AATAGTAAATAAATA
18338699 AATAGATAAATAAATA
1 AATAG-TAAATAAATA
18338715 AATA
1 AATA
18338719 CTAGTTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AATAGTAAATAAATA
Found at i:18339469 original size:29 final size:29
Alignment explanation
Indices: 18339422--18339479 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
18339412 AATTATTTTG
** *
18339422 ATTTTTAATGGGAAGTGAGATAAATAGTT
1 ATTTTTAATGAAAAATGAGATAAATAGTT
18339451 ATTTTTAATGAAAAATGAGATAAATAGTT
1 ATTTTTAATGAAAAATGAGATAAATAGTT
18339480 GAGAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (29 bp):
ATTTTTAATGAAAAATGAGATAAATAGTT
Found at i:18342919 original size:3 final size:3
Alignment explanation
Indices: 18342911--18342938 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18342901 TCTAGTATTC
18342911 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18342939 AGCAATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18351699 original size:2 final size:2
Alignment explanation
Indices: 18351692--18351750 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
18351682 ATCTTCATTT
18351692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18351734 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
18351751 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18354286 original size:31 final size:31
Alignment explanation
Indices: 18354217--18354291 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
18354207 CATATAGATA
* **
18354217 AAATTGAACAAAATTGTATAATATAGGGGGT
1 AAATTGAACAAAATTGAATAATATAGGGACT
* *
18354248 AATTTGAACAAAATTGAAGT-GTATAGGGACT
1 AAATTGAACAAAATTGAA-TAATATAGGGACT
*
18354279 AAATTGAATAAAA
1 AAATTGAACAAAA
18354292 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (31 bp):
AAATTGAACAAAATTGAATAATATAGGGACT
Found at i:18355604 original size:18 final size:19
Alignment explanation
Indices: 18355581--18355634 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
18355571 AGGAAATGAA
18355581 AATATATAAATATTATTT-
1 AATATATAAATATTATTTC
*
18355599 AATATATTAATATTATTTC
1 AATATATAAATATTATTTC
*
18355618 ACTATAATAAATATTAT
1 AATAT-ATAAATATTAT
18355635 AAAGCATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 17 0.55
19 4 0.13
20 10 0.32
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATATAAATATTATTTC
Found at i:18358064 original size:13 final size:14
Alignment explanation
Indices: 18358045--18358082 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
18358035 ACAACTTTTT
18358045 TTAAAAAACAAAAA-
1 TTAAAAAA-AAAAAC
18358059 TTAAAAAAAAAAAC
1 TTAAAAAAAAAAAC
18358073 TTAAAAAAAA
1 TTAAAAAAAA
18358083 GGCTCTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (14 bp):
TTAAAAAAAAAAAC
Found at i:18361700 original size:126 final size:126
Alignment explanation
Indices: 18361475--18361989 Score: 906
Period size: 126 Copynumber: 4.1 Consensus size: 126
18361465 TGCAAGAGGG
* *
18361475 TCCTTGAGATGACCCTTGCTAAAGTCTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGGG
1 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
18361540 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
66 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
*
18361601 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTGATGTAGGGCG
1 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
*
18361666 AGGGTTACAAACATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
66 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
18361727 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
1 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
18361792 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
66 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
* * * *
18361853 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGTATAGAATTATCATGTTGATACCAATCTAGGGTG
1 TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
* ** *
18361918 AGGGTTACAACCTTATCAGTCAAGTAGTTCACAACTTGCTCAAAACATTGCTCTAACTTGT
66 AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
*
18361979 TCCCTGA-ATGA
1 TCCTTGAGATGA
18361990 GTTGAAGTCA
Statistics
Matches: 374, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
125 4 0.01
126 370 0.99
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (126 bp):
TCCTTGAGATGACCCTTGCTAAAGTTTGAGGGATAGAATTATCATGTTGATACTAATGTAGGGCG
AGGGTTACAACCATATCAGTCAAGTAGTTCACAACTCACTCAAAACATTGCTCCAACTTGT
Found at i:18365508 original size:2 final size:2
Alignment explanation
Indices: 18365501--18365537 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
18365491 TTCCTCTTCA
18365501 CT CT CT CT CT CT CT CT C- CT C- CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18365538 ATAATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:18365526 original size:16 final size:16
Alignment explanation
Indices: 18365505--18365536 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18365495 TCTTCACTCT
18365505 CTCTCTCTCTCTCCTC
1 CTCTCTCTCTCTCCTC
18365521 CTCTCTCTCTCTCCTC
1 CTCTCTCTCTCTCCTC
18365537 TATAATATAT
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:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (16 bp):
CTCTCTCTCTCTCCTC
Found at i:18368398 original size:2 final size:2
Alignment explanation
Indices: 18368391--18368447 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
18368381 NNNNNNNNNN
18368391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18368433 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
18368448 TTTCAATTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18377737 original size:2 final size:2
Alignment explanation
Indices: 18377730--18377773 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
18377720 GTACTCACAG
*
18377730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18377772 TA
1 TA
18377774 AGTAGTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18384810 original size:24 final size:21
Alignment explanation
Indices: 18384755--18384811 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
18384745 ATACCTTGCT
*
18384755 TGGGTCTTCATCAACAGCTGC
1 TGGGTCTTCATCAAAAGCTGC
* *
18384776 TAGTTCTTCATCAAAAGCTGTTAC
1 TGGGTCTTCATCAAAAGCTG---C
18384800 TGGGTCTTCATC
1 TGGGTCTTCATC
18384812 TAGAGTTGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 17 0.61
24 11 0.39
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (21 bp):
TGGGTCTTCATCAAAAGCTGC
Found at i:18385516 original size:23 final size:24
Alignment explanation
Indices: 18385486--18385553 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
18385476 TTTTTATATC
18385486 CATTTAATATTTCAATAA-TTTTG
1 CATTTAATATTTCAATAACTTTTG
* *
18385509 CATTTAATATTACAACAACTTTTG
1 CATTTAATATTTCAATAACTTTTG
* *
18385533 GATTCAATATTTCAATAACTT
1 CATTTAATATTTCAATAACTT
18385554 CCAACAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 16 0.42
24 22 0.58
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (24 bp):
CATTTAATATTTCAATAACTTTTG
Found at i:18386560 original size:14 final size:14
Alignment explanation
Indices: 18386543--18386570 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18386533 TGGTATTACA
18386543 GTATGTGTATATAT
1 GTATGTGTATATAT
18386557 GTATGTGTATATAT
1 GTATGTGTATATAT
18386571 ATATATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
GTATGTGTATATAT
Found at i:18389772 original size:2 final size:2
Alignment explanation
Indices: 18389765--18389797 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18389755 TGTTTTACTT
18389765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18389798 TTGAAGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18392611 original size:89 final size:90
Alignment explanation
Indices: 18392439--18392620 Score: 287
Period size: 89 Copynumber: 2.0 Consensus size: 90
18392429 TCCAAAATCA
* * *
18392439 TTCCAAATTATGTAAGTAAAACGAAATTAGGTCAGACAATGGTTACCACACTGCCAAATAAAGTA
1 TTCCAAAGTATATAAGTAAAACGAAATTAGGTCAGACAA-GGTCACCACACTGCCAAATAAAGTA
*
18392504 ACAAAAGTGTAAACAACCAGTGGCAG
65 ACAAAAGAGTAAACAACCAGTGGCAG
*
18392530 TTCCAAAGTATATAAGTAAAACGAAATTAGGTCAGAC-A-GTCATCCACGCTGCCAAATAAAGTA
1 TTCCAAAGTATATAAGTAAAACGAAATTAGGTCAGACAAGGTCA-CCACACTGCCAAATAAAGTA
18392593 ACAAAAGAGTAAACAACCAGTGGCAG
65 ACAAAAGAGTAAACAACCAGTGGCAG
18392619 TT
1 TT
18392621 ATTAAATGCT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
88 3 0.04
89 46 0.54
90 1 0.01
91 35 0.41
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (90 bp):
TTCCAAAGTATATAAGTAAAACGAAATTAGGTCAGACAAGGTCACCACACTGCCAAATAAAGTAA
CAAAAGAGTAAACAACCAGTGGCAG
Found at i:18396547 original size:18 final size:18
Alignment explanation
Indices: 18396507--18396548 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
18396497 TGCTGCCGCT
*
18396507 GCCACCGCGACCCCACAC
1 GCCACCGCCACCCCACAC
*
18396525 ACCACCGCCACCCCA-AC
1 GCCACCGCCACCCCACAC
18396542 GGCCACC
1 -GCCACC
18396549 TTGCCCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.24, C:0.62, G:0.14, T:0.00
Consensus pattern (18 bp):
GCCACCGCCACCCCACAC
Found at i:18401723 original size:41 final size:42
Alignment explanation
Indices: 18401649--18401730 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
18401639 AAACAATAAA
18401649 CTTAAGCAATATATCTGTATACAAAACAAGTAAATTACAGAG
1 CTTAAGCAATATATCTGTATACAAAACAAGTAAATTACAGAG
* * *
18401691 CTTAAGCAATGTA-CTGTATATC-GAACATGTAAATTACAGA
1 CTTAAGCAATATATCTGTATA-CAAAACAAGTAAATTACAGA
18401731 TTAAATGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 23 0.64
42 13 0.36
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (42 bp):
CTTAAGCAATATATCTGTATACAAAACAAGTAAATTACAGAG
Found at i:18406547 original size:20 final size:19
Alignment explanation
Indices: 18406522--18406560 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18406512 TTTGTTGGCC
*
18406522 ATTCAATAGCATGAGTAAAT
1 ATTCAA-AGCATAAGTAAAT
*
18406542 ATTCAAAGCCTAAGTAAAT
1 ATTCAAAGCATAAGTAAAT
18406561 GTCGAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (19 bp):
ATTCAAAGCATAAGTAAAT
Found at i:18413875 original size:117 final size:115
Alignment explanation
Indices: 18413737--18413964 Score: 429
Period size: 117 Copynumber: 2.0 Consensus size: 115
18413727 TTCTTTCTCT
18413737 TTCTCCCTCTCTCTCTCTCTCTCTCTCTATCTAACCATTGTTGTCCTTTTAGTGGTATTGATATG
1 TTCTCCCTCTCTCTCTCTCTCTCTCTCTATCTAACCATTGTTGTCCTTTTAGTGGTATTGATATG
18413802 AAGAATAAAATTACTATATATCCATGTTATAACGTCACATCATTATNCTTC
66 AAGAATAAAATTACTATATATCCATGTTATAACGTCACATCATTAT-CTTC
*
18413853 TTCTTCCTCCTCTCTCTCTCTCTCTCTCTATCTAACCATTGTTGTCCTTTTAGTGGTATTGATAT
1 TTCTCCCT-CTCTCTCTCTCTCTCTCTCTATCTAACCATTGTTGTCCTTTTAGTGGTATTGATAT
18413918 GAAGAATAAAATTACTATATATCCATGTTATAACGTCACATCATTAT
65 GAAGAATAAAATTACTATATATCCATGTTATAACGTCACATCATTAT
18413965 TTGACATGTT
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
116 7 0.06
117 103 0.94
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.43
Consensus pattern (115 bp):
TTCTCCCTCTCTCTCTCTCTCTCTCTCTATCTAACCATTGTTGTCCTTTTAGTGGTATTGATATG
AAGAATAAAATTACTATATATCCATGTTATAACGTCACATCATTATCTTC
Found at i:18418195 original size:3 final size:3
Alignment explanation
Indices: 18418187--18418215 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18418177 TATATTAAAT
18418187 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18418216 CTTTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.