Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 63 of 433
Found at i:18093983 original size:80 final size:80
Alignment explanation
Indices: 18093849--18093998 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 80
18093839 ATAACCACGT
* * *
18093849 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAACGCCTTCGGGGCTTAGCC
18093914 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** ** *
18093929 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCATTAACGTCTTCGGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAACGCCTTCGGGGCTTAGC
18093993 CCGGAT
65 CCGGAT
18093999 ATCATTCAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.02
80 58 0.98
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAACGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:18098906 original size:11 final size:10
Alignment explanation
Indices: 18098879--18098969 Score: 51
Period size: 10 Copynumber: 8.3 Consensus size: 10
18098869 AATTATAAAC
18098879 ATATAATAAT
1 ATATAATAAT
18098889 ATGATAAGTACTAT
1 AT-ATAA-TA--AT
*
18098903 ATAAAATAAT
1 ATATAATAAT
* *
18098913 ATATATTTAT
1 ATATAATAAT
18098923 A-ATAA-AAT
1 ATATAATAAT
18098931 ATAGGTAACATAAT
1 ATA--T-A-ATAAT
18098945 ATATAATAAT
1 ATATAATAAT
18098955 ATAATAAATAAT
1 AT-AT-AATAAT
18098967 ATA
1 ATA
18098970 CAAAGAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
8 3 0.05
9 4 0.06
10 19 0.30
11 9 0.14
12 14 0.22
13 4 0.06
14 10 0.16
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (10 bp):
ATATAATAAT
Found at i:18101309 original size:220 final size:220
Alignment explanation
Indices: 18100741--18101294 Score: 864
Period size: 220 Copynumber: 2.5 Consensus size: 220
18100731 ATGCTGATAT
* ** * * * *
18100741 TTCGATCTGCTCTCCGTCGAACACAGAGACGCCAAAT-TTTCTTCTTCGATTTGTT-TCCTGACA
1 TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTAT-TTCTTTGATTTATTCT-CTGACA
* *
18100804 ATACAGAGATGCCAAGTCATCTTAGAT-TCGCTTCAGCGTAAACACCTGAAAGCCAAATCTGCTA
64 ATACAGAGATGCCAAATCATCTTAGATCT-GCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTA
* * *
18100868 CGTCTTCGGTCTGCTCCTTGTAAACACAAAGATGCCAAATCATCTTGGATCTGCTTCGATGCAAA
128 TGTCTTCGATCTGCTCCTTGTAAACACAAAGATGCCAAATCATCTTGGATCTCCTTCGATGCAAA
18100933 AACATTCGAAGGTTAGATCTGCTATGTC
193 AACATTCGAAGGTTAGATCTGCTATGTC
*
18100961 TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTCTTTGATTTATTCTCTGACAAC
1 TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTCTTTGATTTATTCTCTGACAAT
* *
18101026 ATAGAGATGCCAAATTATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGT
66 ACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGT
* * * * **
18101091 CTTTGATTTGCTCCTTGTAAACACAAGGATGCTAAATCATCTTGGATCTCCTTCGATGTGAAAAC
131 CTTCGATCTGCTCCTTGTAAACACAAAGATGCCAAATCATCTTGGATCTCCTTCGATGCAAAAAC
18101156 ATTCGAAGGTTAGATCTGCTATGTC
196 ATTCGAAGGTTAGATCTGCTATGTC
18101181 TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTCTTTGATTTATTCTCTGACAAT
1 TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTCTTTGATTTATTCTCTGACAAT
18101246 ACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGT-AAAG
66 ACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
18101295 GTCAGATTTG
Statistics
Matches: 307, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
219 4 0.01
220 299 0.97
221 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (220 bp):
TTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTCTTTGATTTATTCTCTGACAAT
ACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGT
CTTCGATCTGCTCCTTGTAAACACAAAGATGCCAAATCATCTTGGATCTCCTTCGATGCAAAAAC
ATTCGAAGGTTAGATCTGCTATGTC
Found at i:18107637 original size:40 final size:40
Alignment explanation
Indices: 18107555--18107767 Score: 290
Period size: 40 Copynumber: 5.4 Consensus size: 40
18107545 AAGCCAAGTA
* * *
18107555 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
18107593 CCTTCGGGACATAGCCCGGATATAGTAATTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
18107633 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
18107673 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
18107713 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
18107753 CCTTCGGGACTTAGC
1 CCTTCGGGACTTAGC
18107768 TCGGTTATCA
Statistics
Matches: 158, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 129 0.82
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:18113272 original size:49 final size:49
Alignment explanation
Indices: 18113082--18113275 Score: 194
Period size: 50 Copynumber: 3.9 Consensus size: 49
18113072 TCTATTGTGA
* * *
18113082 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTG-T
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTA-CC--AGACTGTT
* * * ** *
18113133 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGA-TGGTGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACT-GT-T
* * **
18113183 GGTCACGTGTGTAGTACTAAGTGAAGGCTACTACATGTACCAGACTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGTT
* *
18113232 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
18113276 TAGCTTCGGC
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 38 0.32
50 41 0.35
51 35 0.30
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGTT
Found at i:18119737 original size:21 final size:21
Alignment explanation
Indices: 18119713--18119758 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
18119703 TAATAAAAAT
18119713 TATAAACGAAATAT-ATAA-TAA
1 TATAAAC--AATATGATAAGTAA
18119734 TATAAACAATATGATAAGTAA
1 TATAAACAATATGATAAGTAA
18119755 TATA
1 TATA
18119759 TAAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 14 0.61
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (21 bp):
TATAAACAATATGATAAGTAA
Found at i:18119783 original size:44 final size:43
Alignment explanation
Indices: 18119722--18119834 Score: 99
Period size: 43 Copynumber: 2.6 Consensus size: 43
18119712 TTATAAACGA
* * *
18119722 AATATATAATAAT-ATAAACAATAT-GATAA-GTAATATATAAAAT
1 AATATATATTTATAATAAA-AATATAGATAACATAATATAT--AAT
*
18119765 AATATATATTTATAAT-AAAATATAGGTAACATAATATATAAT
1 AATATATATTTATAATAAAAATATAGATAACATAATATATAAT
*
18119807 AATATATAATAATATAATAAATAATATA
1 AATATAT-AT-TTATAATAAA-AATATA
18119835 CAAAGAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
42 15 0.26
43 19 0.33
44 16 0.28
45 2 0.03
46 6 0.10
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (43 bp):
AATATATATTTATAATAAAAATATAGATAACATAATATATAAT
Found at i:18123658 original size:42 final size:42
Alignment explanation
Indices: 18123545--18123670 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 42
18123535 GAAAAGCTCG
* * * *
18123545 TACAATGCCAACGTCCCAAAAGTGGTCTTACATGTAATCAAA
1 TACAATGTCAACGTCCCAAACGTGGTCTTACACGAAATCAAA
** * *
18123587 TATTGATGTC-ACTGTCCCAGACAGT-GTCTTATACGAAATCAAA
1 TA-CAATGTCAAC-GTCCCAAAC-GTGGTCTTACACGAAATCAAA
*
18123630 TACAATGTCAACGTCCCAAACGTGGTCTTACTCGTAAATCA
1 TACAATGTCAACGTCCCAAACGTGGTCTTACACG-AAATCA
18123671 TAAGTCGATG
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
41 2 0.03
42 25 0.38
43 36 0.55
44 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (42 bp):
TACAATGTCAACGTCCCAAACGTGGTCTTACACGAAATCAAA
Found at i:18129745 original size:28 final size:29
Alignment explanation
Indices: 18129713--18129811 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 29
18129703 ATAATAAGCC
*
18129713 CGCACACTTAGTGCTTA-ATAGA-CGAACT
1 CGCACACTTAGTGCTTATATA-ATCAAACT
*
18129741 CGCACACGTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
* ** *
18129769 CGCACACTTAGTGC-TATACAATTTGAACC
1 CGCACACTTAGTGCTTATATAA-TCAAACT
18129798 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18129812 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 3 0.05
28 40 0.66
29 18 0.30
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCTTATATAATCAAACT
Found at i:18134341 original size:48 final size:48
Alignment explanation
Indices: 18134286--18134395 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
18134276 TATCTAGGAT
*
18134286 ATGGCATTGGCATCGTTATGCGATCCCCTGTAAGACAATGTCTGGGAC
1 ATGGCATTGGCATCGTTATGCGATCCCATGTAAGACAATGTCTGGGAC
* * * * *
18134334 ATGGCATTGGTATTGTTATGTGATCTCATGTAAGACCATGTCTGGGAC
1 ATGGCATTGGCATCGTTATGCGATCCCATGTAAGACAATGTCTGGGAC
*
18134382 ATGCCATTGGCATC
1 ATGGCATTGGCATC
18134396 AATATGAGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (48 bp):
ATGGCATTGGCATCGTTATGCGATCCCATGTAAGACAATGTCTGGGAC
Found at i:18136780 original size:8 final size:8
Alignment explanation
Indices: 18136767--18136825 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
18136757 GTTGCCATTC
*
18136767 TTTCAGCT
1 TTTCAGCA
18136775 TTTCAGCA
1 TTTCAGCA
*
18136783 TTTCAACA
1 TTTCAGCA
*
18136791 TTTCAACA
1 TTTCAGCA
**
18136799 TTTTGGCA
1 TTTCAGCA
*
18136807 TTTCGGCA
1 TTTCAGCA
*
18136815 TTTCAGGA
1 TTTCAGCA
18136823 TTT
1 TTT
18136826 GCTGATCTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (8 bp):
TTTCAGCA
Found at i:18141675 original size:18 final size:18
Alignment explanation
Indices: 18141654--18141688 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18141644 CTGGCACTCT
*
18141654 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
*
18141672 ATAATAGTCAATTATTC
1 ATAACAGTCAATTATTC
18141689 CGTAGTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:18142197 original size:3 final size:3
Alignment explanation
Indices: 18142189--18142239 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
18142179 ATTCAATACC
18142189 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
18142237 ATA
1 ATA
18142240 CTTACCATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18142908 original size:16 final size:15
Alignment explanation
Indices: 18142886--18142924 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
18142876 CTTTCTCTCC
18142886 TTCTTTCTCCCCTGT
1 TTCTTTCTCCCCTGT
* *
18142901 TTCGTTTCTTCTCTGT
1 TTC-TTTCTCCCCTGT
18142917 TTCTTTCT
1 TTCTTTCT
18142925 ATTCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (15 bp):
TTCTTTCTCCCCTGT
Found at i:18142964 original size:2 final size:2
Alignment explanation
Indices: 18142957--18142993 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18142947 TTTCTTTTGT
18142957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18142994 TAATAATAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18144217 original size:48 final size:49
Alignment explanation
Indices: 18144161--18144258 Score: 171
Period size: 48 Copynumber: 2.0 Consensus size: 49
18144151 CCCAAAAAAA
*
18144161 AAGAGCAAAAGATAATCGTTCAGAGAATCCCTAAAACTAC-ACACTCTT
1 AAGAGCAAAAGATAATCGTTCAGAGAACCCCTAAAACTACAACACTCTT
*
18144209 AAGAGCAAAAGATAATCGTTCAGAGAACCCCTAAAACTTCAACACTCTT
1 AAGAGCAAAAGATAATCGTTCAGAGAACCCCTAAAACTACAACACTCTT
18144258 A
1 A
18144259 CAGCACTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 38 0.81
49 9 0.19
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.20
Consensus pattern (49 bp):
AAGAGCAAAAGATAATCGTTCAGAGAACCCCTAAAACTACAACACTCTT
Found at i:18150032 original size:33 final size:33
Alignment explanation
Indices: 18149989--18150091 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 33
18149979 TTTTGCTACT
* **
18149989 ATTTTCTTATTATATTTTTACTATTTTGTTATC
1 ATTTTATTATTATATTACTACTATTTTGTTATC
* ** * *
18150022 CTTTTATTATTAGGTTACTACTTTTTTGTTATT
1 ATTTTATTATTATATTACTACTATTTTGTTATC
* * * *
18150055 ATTTTATTATTATGTTACTATTATTTTTTTATT
1 ATTTTATTATTATATTACTACTATTTTGTTATC
18150088 ATTT
1 ATTT
18150092 GAATATTGTA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (33 bp):
ATTTTATTATTATATTACTACTATTTTGTTATC
Found at i:18150064 original size:11 final size:11
Alignment explanation
Indices: 18149988--18150091 Score: 68
Period size: 11 Copynumber: 9.5 Consensus size: 11
18149978 GTTTTGCTAC
*
18149988 TATTTTCTTAT
1 TATTTTATTAT
*
18149999 TATATTT-TTAC
1 TAT-TTTATTAT
*
18150010 TATTTTGTTAT
1 TATTTTATTAT
**
18150021 CCTTTTATTAT
1 TATTTTATTAT
** *
18150032 TAGGTTACTACT
1 TATTTTATTA-T
*
18150044 T-TTTTGTTAT
1 TATTTTATTAT
18150054 TATTTTATTAT
1 TATTTTATTAT
* *
18150065 TATGTTACTAT
1 TATTTTATTAT
*
18150076 TATTTTTTTAT
1 TATTTTATTAT
18150087 TATTT
1 TATTT
18150092 GAATATTGTA
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
10 5 0.07
11 59 0.86
12 5 0.07
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:18150098 original size:22 final size:22
Alignment explanation
Indices: 18150051--18150098 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18150041 ACTTTTTTGT
*
18150051 TATTATTTTATTATTATGTTAC
1 TATTATTTTATTATTATGTTAA
*
18150073 TATTATTTTTTTATTAT-TTGAA
1 TATTATTTTATTATTATGTT-AA
18150095 TATT
1 TATT
18150099 GTATAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATGTTAA
Found at i:18161302 original size:18 final size:19
Alignment explanation
Indices: 18161281--18161322 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
18161271 TTTTTTAGAG
18161281 TTTTACAATTT-TTA-ATAA
1 TTTTACAATTTGTTACA-AA
*
18161299 TTTTATAATTTGTTACAAA
1 TTTTACAATTTGTTACAAA
18161318 TTTTA
1 TTTTA
18161323 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 10 0.48
20 1 0.05
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTACAATTTGTTACAAA
Found at i:18161302 original size:28 final size:28
Alignment explanation
Indices: 18161259--18161334 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
18161249 AATCTTGAAA
*
18161259 AAATTTT-ATAATTTTTTTAGAGTT-TTAC
1 AAATTTTAATAA-TTTTATA-AGTTGTTAC
* *
18161287 AATTTTTAATAATTTTATAATTTGTTAC
1 AAATTTTAATAATTTTATAAGTTGTTAC
18161315 AAATTTTAATAATTTTATAA
1 AAATTTTAATAATTTTATAA
18161335 TTATTTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.07
28 35 0.83
29 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (28 bp):
AAATTTTAATAATTTTATAAGTTGTTAC
Found at i:18161321 original size:19 final size:17
Alignment explanation
Indices: 18161258--18161330 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 17
18161248 TAATCTTGAA
18161258 AAAATTTTATAATTTTTTT
1 AAAATTTTATAA--TTTTT
* * *
18161277 AGAGTTTTACAATTTTT
1 AAAATTTTATAATTTTT
18161294 AATAATTTTATAATTTGTT
1 AA-AATTTTATAATTT-TT
18161313 ACAAATTTTAATAATTTT
1 A-AAATTTT-ATAATTTT
18161331 ATAATTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.14
18 11 0.25
19 19 0.43
20 8 0.18
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (17 bp):
AAAATTTTATAATTTTT
Found at i:18161335 original size:28 final size:28
Alignment explanation
Indices: 18161283--18161336 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
18161273 TTTTAGAGTT
*
18161283 TTACAATTTTTAATAATTTTATAATTTG
1 TTACAAATTTTAATAATTTTATAATTTG
18161311 TTACAAATTTTAATAATTTTATAATT
1 TTACAAATTTTAATAATTTTATAATT
18161337 ATTTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
TTACAAATTTTAATAATTTTATAATTTG
Found at i:18164659 original size:40 final size:40
Alignment explanation
Indices: 18164576--18164796 Score: 243
Period size: 40 Copynumber: 5.5 Consensus size: 40
18164566 ACCCAAGTAT
** * *
18164576 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
18164614 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
18164654 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
18164694 CTTCGGGTTTTGGCCTGGATATAGTAACTCA-CACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACT-AGCACAAATGC
* * *
18164734 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
*
18164775 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
18164797 CATTCGAATA
Statistics
Matches: 151, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 15 0.10
40 95 0.63
41 29 0.19
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:18172324 original size:40 final size:40
Alignment explanation
Indices: 18172241--18172461 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
18172231 ACCCAAGTAT
** * *
18172241 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
18172279 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
18172319 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
18172359 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
18172399 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
*
18172440 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
18172462 CATTCGAATA
Statistics
Matches: 153, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 15 0.10
40 97 0.63
41 29 0.19
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:18175899 original size:42 final size:42
Alignment explanation
Indices: 18175840--18175924 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
18175830 CTTGTGAGTA
18175840 GACCGTGTGACTCACACAACCAAGTGACATCCCATGTCTTAG
1 GACCGTGTGACTCACACAACCAAGTGACATCCCATGTCTTAG
* *
18175882 GACCGTGTGGCTCACACAACCAAGTGACATCCCATGTTTTAG
1 GACCGTGTGACTCACACAACCAAGTGACATCCCATGTCTTAG
18175924 G
1 G
18175925 CTGTGTAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (42 bp):
GACCGTGTGACTCACACAACCAAGTGACATCCCATGTCTTAG
Found at i:18187077 original size:2 final size:2
Alignment explanation
Indices: 18187070--18187095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18187060 GCTCTTGCAC
18187070 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18187096 GTTTGCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18188025 original size:80 final size:79
Alignment explanation
Indices: 18187808--18188040 Score: 267
Period size: 80 Copynumber: 2.9 Consensus size: 79
18187798 TCGAATGATG
* *
18187808 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAACCGGACTAAGATCCGAAGGCATT
*
18187872 TGTGCGAGTTACTAAA
64 TGTACGAGTTACTAAA
* * * *
18187888 TCCAGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTA-AATCCGGACAAAGATCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA-CCGGACTAAGATCCGAAGGCAT
18187951 TTGTACGAGTTACTAAA
63 TTGTACGAGTTACTAAA
* * * *
18187968 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAACCGGGCTATG-TCCCGAAGGTATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAACCGGACTAAGAT-CCGAAGGCATT
*
18188032 TGAACGAGT
64 TGTACGAGT
18188041 AGCTATATTC
Statistics
Matches: 129, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
79 3 0.02
80 116 0.90
81 10 0.08
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAACCGGACTAAGATCCGAAGGCATTTG
TACGAGTTACTAAA
Found at i:18188027 original size:40 final size:40
Alignment explanation
Indices: 18187808--18188005 Score: 249
Period size: 40 Copynumber: 5.0 Consensus size: 40
18187798 TCGAATGATG
* * * *
18187808 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
18187848 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* *
18187888 TCCAGACTAAGATCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* *
18187928 TCCGGACAAAGATCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
** *
18187968 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGCTACTA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
18188006 TAACCGGGCT
Statistics
Matches: 140, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 131 0.94
41 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18188033 original size:40 final size:40
Alignment explanation
Indices: 18187808--18188039 Score: 197
Period size: 40 Copynumber: 5.8 Consensus size: 40
18187798 TCGAATGATG
* * *
18187808 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGCT-ACTAAA
* * *
18187848 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGCTACTAAA
* * ** *
18187888 TCCAGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGCTACTAAA
* * *
18187928 TCCGGACAAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGCTACTAAA
* *
18187968 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGCTACTA-AA
* * *
18188009 -CCGGGCTATGTCCCGAAGGTATTTGAACGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAG
18188040 TAGCTATATT
Statistics
Matches: 168, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 156 0.93
41 11 0.07
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGCTACTAAA
Found at i:18189820 original size:2 final size:2
Alignment explanation
Indices: 18189813--18189848 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18189803 GGGATGTTAC
18189813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18189849 TAACATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18189933 original size:14 final size:15
Alignment explanation
Indices: 18189914--18189943 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18189904 AATGGCTAGA
18189914 TTACAAG-CATCCAT
1 TTACAAGCCATCCAT
18189928 TTACAAGCCATCCAT
1 TTACAAGCCATCCAT
18189943 T
1 T
18189944 GGCTAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (15 bp):
TTACAAGCCATCCAT
Found at i:18191925 original size:40 final size:40
Alignment explanation
Indices: 18191880--18192047 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
18191870 CGGAATATAA
18191880 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
18191920 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
18191960 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
18192000 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
18192040 CCGGATAT
1 CCGGATAT
18192048 CATTCAATTT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 103 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:18192030 original size:80 final size:80
Alignment explanation
Indices: 18191896--18192045 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
18191886 ATAACCACGT
* *
18191896 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
18191961 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
18191976 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
18192039 CCCGGAT
64 CCCGGAT
18192046 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:18196799 original size:40 final size:40
Alignment explanation
Indices: 18196727--18196932 Score: 186
Period size: 40 Copynumber: 5.2 Consensus size: 40
18196717 CAATTGAATG
* * * *
18196727 ATATCCGGGCTAAG-CCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAATT
* * * *
18196766 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAATT
* **
18196806 ACAT-CGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAATT
* * * **
18196845 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAATT
* * **
18196885 CTATCCGGGCTAAGACCCGAAGGC-ATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAATT
18196925 ATATCCGG
1 ATATCCGG
18196933 TTGTATTCCG
Statistics
Matches: 139, Mismatches: 23, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
38 3 0.02
39 44 0.32
40 90 0.65
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAATT
Found at i:18196863 original size:79 final size:80
Alignment explanation
Indices: 18196728--18196932 Score: 238
Period size: 79 Copynumber: 2.6 Consensus size: 80
18196718 AATTGAATGA
* ** * * *
18196728 TATCCGGGCTAAG-CCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
18196792 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
18196805 TA-CATCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 TATC--CGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
18196869 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
18196886 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
18196933 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
76 1 0.01
77 2 0.02
78 9 0.08
79 50 0.47
80 41 0.38
81 3 0.03
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:18204817 original size:40 final size:40
Alignment explanation
Indices: 18204758--18204965 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
18204748 CAATTGAATG
* * * *
18204758 ATATCCGGGCTAAGCCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * *
18204798 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * * **
18204838 ACATCTGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
18204878 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
18204918 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
18204958 ATATCCGG
1 ATATCCGG
18204966 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
39 2 0.01
40 136 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:18204898 original size:80 final size:80
Alignment explanation
Indices: 18204759--18204965 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 80
18204749 AATTGAATGA
* * ** * * *
18204759 TATCCGGGCTAAGCCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCCA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CA
*
18204824 -TTGTGCTAGT-G-AC
65 TTTGTGCAAGTCGTAC
* * * *
18204837 TACATCTGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
*
18204902 ATTTGTGCAAGTCGTTC
64 ATTTGTGCAAGTCGTAC
* *
18204919 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
18204966 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
78 1 0.01
79 2 0.02
80 101 0.94
81 1 0.01
82 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCAAGTCGTAC
Found at i:18215327 original size:8 final size:8
Alignment explanation
Indices: 18215314--18215358 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
18215304 AATTTGTTCT
18215314 TAAAAAAA
1 TAAAAAAA
18215322 T-AAAAAA
1 TAAAAAAA
* *
18215329 TTAAAAAT
1 TAAAAAAA
18215337 TAAAAAAA
1 TAAAAAAA
18215345 T-AAAAAA
1 TAAAAAAA
18215352 TAAAAAA
1 TAAAAAA
18215359 CATGTATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:18215328 original size:7 final size:7
Alignment explanation
Indices: 18215316--18215358 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
18215306 TTTGTTCTTA
18215316 AAAAAAT
1 AAAAAAT
18215323 AAAAAATT
1 AAAAAA-T
*
18215331 AAAAATT
1 AAAAAAT
18215338 AAAAAAAT
1 -AAAAAAT
18215346 AAAAAAT
1 AAAAAAT
18215353 AAAAAA
1 AAAAAA
18215359 CATGTATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 20 0.62
8 12 0.38
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:18215339 original size:23 final size:23
Alignment explanation
Indices: 18215313--18215358 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18215303 TAATTTGTTC
*
18215313 TTAAAAAAATAAAAAATTAAAAA
1 TTAAAAAAATAAAAAATAAAAAA
18215336 TTAAAAAAATAAAAAATAAAAAA
1 TTAAAAAAATAAAAAATAAAAAA
18215359 CATGTATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (23 bp):
TTAAAAAAATAAAAAATAAAAAA
Found at i:18215340 original size:15 final size:15
Alignment explanation
Indices: 18215316--18215358 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
18215306 TTTGTTCTTA
*
18215316 AAAAAATAAAAAATT
1 AAAAAATAAAAAAAT
*
18215331 AAAAATTAAAAAAAT
1 AAAAAATAAAAAAAT
18215346 AAAAAATAAAAAA
1 AAAAAATAAAAAA
18215359 CATGTATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:18219573 original size:34 final size:34
Alignment explanation
Indices: 18219525--18219592 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
18219515 AAACTACGTG
*
18219525 ACCGGTACTAATACTGAGATGG-GCTAAGGCCCAA
1 ACCGGTACTAATACTGA-AAGGTGCTAAGGCCCAA
* *
18219559 ACCGTTACTAATACTGAAAGGTGCTTAGGCCCAA
1 ACCGGTACTAATACTGAAAGGTGCTAAGGCCCAA
18219593 GACTGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (34 bp):
ACCGGTACTAATACTGAAAGGTGCTAAGGCCCAA
Found at i:18220375 original size:25 final size:26
Alignment explanation
Indices: 18220316--18220377 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
18220306 TGAAGCTATG
* *
18220316 ATATTCTGAAACTACTATAGGTAGTA
1 ATATACTGAAAATACTATAGGTAGTA
* *
18220342 AAATA-TGAAAATACTATAGTTAGT-
1 ATATACTGAAAATACTATAGGTAGTA
18220366 ATATACTGAAAA
1 ATATACTGAAAA
18220378 CTGTAGTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (26 bp):
ATATACTGAAAATACTATAGGTAGTA
Found at i:18223940 original size:45 final size:45
Alignment explanation
Indices: 18223876--18224005 Score: 183
Period size: 45 Copynumber: 2.9 Consensus size: 45
18223866 GTTGTACAGT
* **
18223876 ATTATTCGGGCCTTGGAGCCTAGCAGGCTATAATGCTGGTGAGAC
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
18223921 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGAT
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
18223966 ATTTTTCGGGCC-TCGAGCCTAGCAGGC-AAAATGCCAGTGA
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
18224006 ATAAATTCGG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 12 0.15
44 14 0.18
45 52 0.67
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (45 bp):
ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
Found at i:18227653 original size:18 final size:18
Alignment explanation
Indices: 18227613--18227659 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
18227603 AATCTAGGCG
*
18227613 TGTGGG-CCACACGAGCG
1 TGTGGGTCCACACGAGCA
* *
18227630 TATGGGTCCACGCGAGCA
1 TGTGGGTCCACACGAGCA
*
18227648 TGTGGGTTCACA
1 TGTGGGTCCACA
18227660 TGGGTAGGCC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.19, C:0.26, G:0.36, T:0.19
Consensus pattern (18 bp):
TGTGGGTCCACACGAGCA
Found at i:18233275 original size:38 final size:38
Alignment explanation
Indices: 18233230--18233307 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
18233220 ACTAATAATG
18233230 TCAATATAAATTGTGACAATTGATAATTTTATTGTCAT
1 TCAATATAAATTGTGACAATTGATAATTTTATTGTCAT
18233268 TCAATATAAATTGTGACAATTGATAATTTTATTGTCAT
1 TCAATATAAATTGTGACAATTGATAATTTTATTGTCAT
18233306 TC
1 TC
18233308 TTTTTACTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (38 bp):
TCAATATAAATTGTGACAATTGATAATTTTATTGTCAT
Found at i:18237337 original size:3 final size:3
Alignment explanation
Indices: 18237323--18237359 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
18237313 TTTTTATCTT
*
18237323 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18237360 AAAAGAAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18237854 original size:37 final size:39
Alignment explanation
Indices: 18237783--18237857 Score: 102
Period size: 38 Copynumber: 1.9 Consensus size: 39
18237773 AAAATATATA
18237783 TTAAAAATAATATTTTAAATAATTTTAATGATTTTTAATT
1 TTAAAAATAATATTTTAAATAATTTTAA-GATTTTTAATT
*
18237823 TTAAAAAT-AT-TTTTATATAATTTTTAA-ATTTTTAA
1 TTAAAAATAATATTTTAAATAA-TTTTAAGATTTTTAA
18237858 AAAATTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 8 0.24
38 9 0.27
39 8 0.24
40 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TTAAAAATAATATTTTAAATAATTTTAAGATTTTTAATT
Found at i:18237890 original size:15 final size:15
Alignment explanation
Indices: 18237870--18237899 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18237860 AATTAATTAA
18237870 ATATTGATATGTCGT
1 ATATTGATATGTCGT
18237885 ATATTGATATGTCGT
1 ATATTGATATGTCGT
18237900 CTATGTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
ATATTGATATGTCGT
Found at i:18238152 original size:2 final size:2
Alignment explanation
Indices: 18238140--18238181 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
18238130 ACCGTCCAAG
* *
18238140 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18238182 AACTATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18244044 original size:3 final size:3
Alignment explanation
Indices: 18244038--18244063 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18244028 TCTTCTTCTT
18244038 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
18244064 TCTTTGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:18244261 original size:30 final size:30
Alignment explanation
Indices: 18244221--18244288 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
18244211 ATTGTTAATC
* * *
18244221 AGTGACTGTTTTGTCACTTTTTATAACGTT-
1 AGTGATTGTTTTGTCA-TTTTTAAAAAGTTG
*
18244251 AGTGATTGTTTTGTTATTTTTAAAAAGTTG
1 AGTGATTGTTTTGTCATTTTTAAAAAGTTG
18244281 AGTGATTG
1 AGTGATTG
18244289 AAATAAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.50
Consensus pattern (30 bp):
AGTGATTGTTTTGTCATTTTTAAAAAGTTG
Found at i:18244612 original size:13 final size:15
Alignment explanation
Indices: 18244594--18244626 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18244584 ATATTAAATA
18244594 TTTTATAT-T-CTTT
1 TTTTATATATACTTT
18244607 TTTTATATATACTTT
1 TTTTATATATACTTT
18244622 TTTTA
1 TTTTA
18244627 AAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 1 0.06
15 9 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATATACTTT
Found at i:18258063 original size:29 final size:28
Alignment explanation
Indices: 18258031--18258133 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 28
18258021 GGGACGAGAT
* *
18258031 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
18258060 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
** * *
18258089 TGGCACTGTGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
18258118 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
18258134 TTATTGAGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.05
29 56 0.93
30 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:18260798 original size:59 final size:59
Alignment explanation
Indices: 18260706--18260829 Score: 248
Period size: 59 Copynumber: 2.1 Consensus size: 59
18260696 ATATTATGTA
18260706 TTCATTAATTCGTTATTATTATAAAATGGTCTTATACCACATCGTTTGCTAATTTCCAC
1 TTCATTAATTCGTTATTATTATAAAATGGTCTTATACCACATCGTTTGCTAATTTCCAC
18260765 TTCATTAATTCGTTATTATTATAAAATGGTCTTATACCACATCGTTTGCTAATTTCCAC
1 TTCATTAATTCGTTATTATTATAAAATGGTCTTATACCACATCGTTTGCTAATTTCCAC
18260824 TTCATT
1 TTCATT
18260830 TTGTACATGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (59 bp):
TTCATTAATTCGTTATTATTATAAAATGGTCTTATACCACATCGTTTGCTAATTTCCAC
Found at i:18261361 original size:131 final size:132
Alignment explanation
Indices: 18261142--18261407 Score: 338
Period size: 131 Copynumber: 2.0 Consensus size: 132
18261132 ATTATTCATT
** * *
18261142 TAAAAACCCTTTAAAACCAAGGTGATGTTCGATATTTGGCAATTCGCGGAGTCGTGCCCTATCGT
1 TAAAAACCCTTTAAAACCAAGGAAATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTATCGT
* * * * * * *
18261207 GTTGGGTTGCAACTTCTCGTTTGCTCCAAATAATCGAATGTCCTTTTAGAATTTCACTCATGTTT
66 GCTGGGTTGCAACTTCTCATTTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTTT
18261272 TC
131 TC
* * * *
18261274 TAAAAACTCTTTGAAACGAAGGAAATGTTCGATGTTTGGCAATTCG-AGAATCGTGCCCTATCGT
1 TAAAAACCCTTTAAAACCAAGGAAATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTATCGT
* * * *
18261338 GCTGGGTTGCAATTTC-CTATTTGCTCAAAACAATTGAATATCCCTTCGGAATTTCACTCGTGTT
66 GCTGGGTTGCAACTTCTC-ATTTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTT
18261402 TTC
130 TTC
18261405 TAA
1 TAA
18261408 GGCGAGGCAA
Statistics
Matches: 114, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
130 1 0.01
131 73 0.64
132 40 0.35
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (132 bp):
TAAAAACCCTTTAAAACCAAGGAAATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTATCGT
GCTGGGTTGCAACTTCTCATTTGCTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATGTTT
TC
Found at i:18266086 original size:22 final size:22
Alignment explanation
Indices: 18266017--18266086 Score: 59
Period size: 27 Copynumber: 2.9 Consensus size: 22
18266007 AAATTTTCCA
*
18266017 ATAAAGTTATAAAAATTAATTTT
1 ATAAA-TTATAAATATTAATTTT
*
18266040 AAAAATTATAAAAGAATATTTAATTTT
1 ATAAATTAT---A-AATA-TTAATTTT
*
18266067 TTAAATTATAAATATTAATT
1 ATAAATTATAAATATTAATT
18266087 AAATTACTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
22 10 0.26
23 8 0.21
24 1 0.03
25 1 0.03
26 3 0.08
27 15 0.39
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
ATAAATTATAAATATTAATTTT
Found at i:18267012 original size:20 final size:18
Alignment explanation
Indices: 18266957--18267014 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 18
18266947 CAGCAACAGT
*
18266957 AAAAAAAAAACACTGAAAAC
1 AAAAAAAAAA-A-TAAAAAC
*
18266977 AAAAAAAAAAGTTAAAAAC
1 AAAAAAAAAA-ATAAAAAC
18266996 GAAAAAAAAATAATAAAAA
1 -AAAAAAAAA-AATAAAAA
18267015 AGGGTCATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.19
20 25 0.78
21 1 0.03
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (18 bp):
AAAAAAAAAAATAAAAAC
Found at i:18267013 original size:19 final size:19
Alignment explanation
Indices: 18266957--18267013 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
18266947 CAGCAACAGT
* *
18266957 AAAAAAAAAACACTGAAAAC
1 AAAAAAAAAATAAT-AAAAC
*
18266977 AAAAAAAAAAGTTA-AAAAC
1 AAAAAAAAAA-TAATAAAAC
*
18266996 GAAAAAAAAATAATAAAA
1 AAAAAAAAAATAATAAAA
18267014 AAGGGTCATG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.07
19 18 0.60
20 10 0.33
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (19 bp):
AAAAAAAAAATAATAAAAC
Found at i:18267255 original size:15 final size:15
Alignment explanation
Indices: 18267226--18267289 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
18267216 ATTTTTTGCT
18267226 AAAATAATATA--AA
1 AAAATAATATACGAA
*
18267239 AAAATAAAATACGAA
1 AAAATAATATACGAA
***
18267254 AATAAT-ATATTTTAA
1 AA-AATAATATACGAA
18267269 AAAATAATATACGAA
1 AAAATAATATACGAA
18267284 AAAATA
1 AAAATA
18267290 CGAATAAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
13 10 0.26
14 3 0.08
15 23 0.59
16 3 0.08
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAATAATATACGAA
Found at i:18267284 original size:147 final size:145
Alignment explanation
Indices: 18267110--18267565 Score: 711
Period size: 147 Copynumber: 3.1 Consensus size: 145
18267100 AGCACTATAA
*
18267110 AATATATTTTAAAAAATAAGATACGAAAAAATACGAAGAAAGTGTCAAAATCAAGGTTATTTATT
1 AATATATTTTAAAAAATAAGATACGAAAAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATT
* *
18267175 AAATTAATATAAAAAAAACATTTACATAATACATTTGAAATATTTTTTGCTAAAATAATATAAAA
66 AAATTAATAT-AAAAAAACA-TTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAG
18267240 AAATAAAATACGAAAAT
129 AAATAAAATACGAAAAT
* * *
18267257 AATATATTTTAAAAAATAATATACGAAAAAATACGAATAAAGT-ACTAAAATCAGGGTTATTTAT
1 AATATATTTTAAAAAATAAGATACGAAAAAATACGAAGAAAGTGTC-AAAATCAGGGTTATTTAT
* * * * * * * *
18267321 GAAA-AAATATAAAAATAC-TTAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAGA
65 TAAATTAATATAAAAAAACATTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAGA
18267384 AATAAAATACGAAAAT
130 AATAAAATACGAAAAT
18267400 AATATATTTTAAAAAATAAGATACGAAAAAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTAT
1 AATATATTTTAAAAAATAAGATACG-AAAAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTAT
18267465 TAAATTAATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAG
65 TAAATTAATATAAAAAAACA-TTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAG
18267530 AAATAAAATACGAAAAT
129 AAATAAAATACGAAAAT
*
18267547 AATATATTTTAAAATATAA
1 AATATATTTTAAAAAATAA
18267566 TATTTTGACA
Statistics
Matches: 277, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
143 78 0.28
144 38 0.14
145 20 0.07
146 6 0.02
147 135 0.49
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (145 bp):
AATATATTTTAAAAAATAAGATACGAAAAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATT
AAATTAATATAAAAAAACATTACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAGAA
ATAAAATACGAAAAT
Found at i:18267732 original size:145 final size:144
Alignment explanation
Indices: 18267567--18268049 Score: 744
Period size: 145 Copynumber: 3.4 Consensus size: 144
18267557 AAAATATAAT
18267567 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTTTTTT
1 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTTTTTT
* * * * *
18267632 ATTTCTTCATATTATTTTAGTACATAATATTTTAAATGTATTATTTAAGTATTTTTTATATT-TT
66 ATTTCTT-ATATTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAGTATTTTTTATATTATT
18267696 TCAATAAATAACCCTG
130 T-AATAAATAACCCTG
*
18267712 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTT
1 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTTTTTT
* *
18267777 ATTTCTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTGTTTTTTATATTAAT
66 ATTTC-TTATATTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAGTATTTTTTATATT-AT
18267842 TTAATAAATAACCCTG
129 TTAATAAATAACCCTG
*
18267858 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTA-TTTTTAAAATATATTATTTTCG-TATTT
1 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTTTTTT
*
18267921 -TTT-TTATATTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAATATTTTTTATATTAATT
66 ATTTCTTATATTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAGTATTTTTTATATT-ATT
**
18267984 TAATAAATAACTTTG
130 TAATAAATAACCCTG
* * *
18267999 ATTTTGACA-TTTTTTTGTATTTTTTTCATATCTTATTTTTTAAAATATATT
1 ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATT
18268050 TTACAGTGCT
Statistics
Matches: 316, Mismatches: 18, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
140 23 0.07
141 94 0.30
143 3 0.01
144 3 0.01
145 138 0.44
146 52 0.16
147 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (144 bp):
ATTTTGACACTTTCTTCGTATTTTTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTTTTTT
ATTTCTTATATTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAGTATTTTTTATATTATTT
AATAAATAACCCTG
Found at i:18267948 original size:40 final size:39
Alignment explanation
Indices: 18267872--18267948 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
18267862 TGACACTTTC
* * *
18267872 TTCGTATTTTTTTCGTATCTTATTTTTAAAATATATTATT
1 TTCGTATTTTTTTC-TATATTATTTTCAAAAAATATTATT
18267912 TTCGTATTTTTTT-TATATTATTTTAGCAAAAAATATT
1 TTCGTATTTTTTTCTATATTATTTT--CAAAAAATATT
18267949 TCAAATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 10 0.31
40 22 0.69
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (39 bp):
TTCGTATTTTTTTCTATATTATTTTCAAAAAATATTATT
Found at i:18268181 original size:19 final size:18
Alignment explanation
Indices: 18268157--18268199 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18268147 ATTATTATTA
*
18268157 TTTTTTCGTTGTCAGCT-T
1 TTTTTTTGTTGTCAG-TGT
*
18268175 TTTTTTTGTTTTCAGTGT
1 TTTTTTTGTTGTCAGTGT
18268193 TTTTTTT
1 TTTTTTT
18268200 TTACTGTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.05, C:0.09, G:0.14, T:0.72
Consensus pattern (18 bp):
TTTTTTTGTTGTCAGTGT
Found at i:18269925 original size:22 final size:24
Alignment explanation
Indices: 18269900--18269958 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
18269890 TAATTGAATG
18269900 ATTTAAATAAAAT-TTTTA-AATA
1 ATTTAAATAAAATATTTTATAATA
*
18269922 ATTT-AAT-AATTATTTTATAATA
1 ATTTAAATAAAATATTTTATAATA
*
18269944 TTTTAAAATAAAATA
1 ATTT-AAATAAAATA
18269959 ATTAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 11 0.38
24 3 0.10
25 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTAAATAAAATATTTTATAATA
Found at i:18272183 original size:15 final size:15
Alignment explanation
Indices: 18272163--18272208 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
18272153 AAAAGTCAAC
18272163 TTCTACTTTAAAGAG
1 TTCTACTTTAAAGAG
*
18272178 TTCTACTTAAAAAGAG
1 TTCTACTT-TAAAGAG
*
18272194 -TCAACTTTAAAGAG
1 TTCTACTTTAAAGAG
18272208 T
1 T
18272209 ATTTGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
TTCTACTTTAAAGAG
Found at i:18274337 original size:49 final size:49
Alignment explanation
Indices: 18274199--18274359 Score: 168
Period size: 48 Copynumber: 3.3 Consensus size: 49
18274189 GTGGTATGTG
* * * *
18274199 AGCTAGTGTAAGACATGTGTGGGACAT-GCATTGGCCTCGAGATAT-ACA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGA-A
* * * * * *
18274247 AGATAGTGTACGACCTGTCT-AGACATGGCATCGACAC-CGATAGATGAG
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTCGATATATGAA
18274295 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAA
* *
18274344 AGCCAATGTAAGACCT
1 AGCTAGTGTAAGACCT
18274360 ATTTGGGGCA
Statistics
Matches: 90, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
47 5 0.06
48 47 0.52
49 38 0.42
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (49 bp):
AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAA
Found at i:18277800 original size:16 final size:16
Alignment explanation
Indices: 18277779--18277813 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
18277769 TACTCCCTAT
18277779 AGACCTTGAGATTGAA
1 AGACCTTGAGATTGAA
18277795 AGACCTTGAGATTGAA
1 AGACCTTGAGATTGAA
18277811 AGA
1 AGA
18277814 ACTTTTCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (16 bp):
AGACCTTGAGATTGAA
Found at i:18292358 original size:39 final size:39
Alignment explanation
Indices: 18292304--18292383 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
18292294 CTTGGAGTTA
*
18292304 GAGCACAAAGCTTACTGGGCTCTTCAACAATTCAACTTG
1 GAGCACAAAGCTTACTGGGCTCTTCAACAACTCAACTTG
18292343 GAGCACAAAGCTTACTGGGCTCTTCAACAACTCAACTTG
1 GAGCACAAAGCTTACTGGGCTCTTCAACAACTCAACTTG
18292382 GA
1 GA
18292384 TCTTAAGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (39 bp):
GAGCACAAAGCTTACTGGGCTCTTCAACAACTCAACTTG
Found at i:18293907 original size:25 final size:26
Alignment explanation
Indices: 18293861--18293909 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
18293851 TTTTTCTCCT
* **
18293861 AAATTTTAATTTTATTTTATTATTCA
1 AAATTTCAATTTTATTGAATTATTCA
18293887 AAATTTCAA-TTTATTGAATTATT
1 AAATTTCAATTTTATTGAATTATT
18293910 AATAGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (26 bp):
AAATTTCAATTTTATTGAATTATTCA
Found at i:18295374 original size:2 final size:2
Alignment explanation
Indices: 18295367--18295392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18295357 AAGTGTGACA
18295367 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18295393 CTAGGATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18296809 original size:10 final size:10
Alignment explanation
Indices: 18296794--18296836 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
18296784 AATTATTAAC
18296794 TAATTAATTT
1 TAATTAATTT
18296804 TAATTAATTTT
1 TAATTAA-TTT
18296815 ATAATTAATTT
1 -TAATTAATTT
*
18296826 TTATTAATTT
1 TAATTAATTT
18296836 T
1 T
18296837 GGTTATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 17 0.57
11 6 0.20
12 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TAATTAATTT
Found at i:18296842 original size:26 final size:22
Alignment explanation
Indices: 18296794--18296836 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18296784 AATTATTAAC
18296794 TAATTAATTTTAATTAATTTTA
1 TAATTAATTTTAATTAATTTTA
*
18296816 TAATTAATTTTTATTAATTTT
1 TAATTAATTTTAATTAATTTT
18296837 GGTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTAATTTTAATTAATTTTA
Found at i:18309325 original size:40 final size:40
Alignment explanation
Indices: 18309259--18309409 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
18309249 AAATTGAATG
* *
18309259 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
18309298 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
18309338 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
18309378 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
18309410 ACGTGGTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 16 0.18
40 72 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:18309423 original size:40 final size:40
Alignment explanation
Indices: 18309296--18309425 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
18309286 ATGCTGGAAA
* * *
18309296 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
18309336 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
18309376 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
18309416 TTATATCCGG
1 TTATATCCGG
18309426 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:18309424 original size:80 final size:79
Alignment explanation
Indices: 18309259--18309425 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
18309249 AAATTGAATG
*
18309259 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
18309324 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * * *
18309338 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
18309401 CATTTGTGC-ACGTGGTT
63 CAATTGTGCTA-GTGGCT
18309418 ATATCCGG
1 ATATCCGG
18309426 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.24
80 57 0.76
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:18317380 original size:40 final size:40
Alignment explanation
Indices: 18317255--18317404 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
18317245 AATTGAATGA
* * * * *
18317255 TATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGACATTC
* * *
18317295 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCT-G-GACATTC
18317336 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GACATTC
*
18317375 TATCCGGGCTAAGA-CCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
18317405 ACGTGGTTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
38 3 0.03
39 17 0.19
40 68 0.75
41 2 0.02
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGACATTC
Found at i:18317389 original size:80 final size:79
Alignment explanation
Indices: 18317256--18317404 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 79
18317246 ATTGAATGAT
* *
18317256 ATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGA-CCGAAGGCAAT
18317321 TGTGCTAGTGGCTAC
65 TGTGCTAGTGGCTAC
* * * * *
18317336 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCGAAGGCAA
18317399 TTGTGC
64 TTGTGC
18317405 ACGTGGTTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
79 19 0.32
80 41 0.68
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (79 bp):
ATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCGAAGGCAATT
GTGCTAGTGGCTAC
Found at i:18317418 original size:39 final size:40
Alignment explanation
Indices: 18317292--18317420 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
18317282 ATGCTGGAAA
* * *
18317292 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
18317332 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
18317372 TTCTATCCGGGCTAAGA-CCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
18317411 TTATATCCGG
1 TTATATCCGG
18317421 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
38 1 0.01
39 25 0.35
40 45 0.63
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:18325216 original size:40 final size:40
Alignment explanation
Indices: 18325171--18325337 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
18325161 CGGAATATAA
18325171 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
18325211 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
18325251 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
18325291 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
18325330 CCGGATAT
1 CCGGATAT
18325338 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:18326179 original size:17 final size:19
Alignment explanation
Indices: 18326156--18326201 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
18326146 AAGAAGCATG
18326156 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
18326174 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
18326192 AATCATGCTC
1 AATCATGCTC
18326202 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:18331799 original size:13 final size:13
Alignment explanation
Indices: 18331781--18331806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18331771 ATGAGAAAGA
18331781 TGGACATGATTTT
1 TGGACATGATTTT
18331794 TGGACATGATTTT
1 TGGACATGATTTT
18331807 GACTTGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TGGACATGATTTT
Found at i:18337789 original size:2 final size:2
Alignment explanation
Indices: 18337782--18337808 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18337772 AGGCATCATC
18337782 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 A
18337809 CTTAACCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18342808 original size:43 final size:43
Alignment explanation
Indices: 18342740--18342914 Score: 201
Period size: 43 Copynumber: 4.1 Consensus size: 43
18342730 ATAGCTCGTA
* * * * *
18342740 CAATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCATATAT
* * *
18342782 CAATGCCAATGTCCTAGACATGGTCTTACACGAAATCATATAA
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCATATAT
*
18342825 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCATA-AT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCATATAT
* * * * *
18342867 ACAATGCCAATGTCCTAGACATGGCCTTACATGTAATCAAATCT
1 -CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCATATAT
18342911 CAAT
1 CAAT
18342915 AATCCTAATG
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 8 0.07
43 103 0.92
44 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCATATAT
Found at i:18343045 original size:18 final size:18
Alignment explanation
Indices: 18343022--18343072 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
18343012 GTTCAACATT
18343022 TAGCAATTCAATGACAAA
1 TAGCAATTCAATGACAAA
*
18343040 TAGCAACTCAATGACAAA
1 TAGCAATTCAATGACAAA
18343058 TAGCAATTCAATGAC
1 TAGCAATTCAATGAC
18343073 GAATGAACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.22
Consensus pattern (18 bp):
TAGCAATTCAATGACAAA
Found at i:18344998 original size:20 final size:19
Alignment explanation
Indices: 18344959--18345010 Score: 86
Period size: 20 Copynumber: 2.7 Consensus size: 19
18344949 ATAGGATACG
*
18344959 TGTAAGACCATGTCTTACA
1 TGTAAGACCATGTATTACA
18344978 TGTAAGACCATGTGATTACA
1 TGTAAGACCATGT-ATTACA
18344998 TGTAAGACCATGT
1 TGTAAGACCATGT
18345011 CTGGGACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (19 bp):
TGTAAGACCATGTATTACA
Found at i:18345048 original size:43 final size:42
Alignment explanation
Indices: 18344991--18345137 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 42
18344981 AAGACCATGT
*
18344991 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATT-A
*
18345034 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTAATCA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T-ATTA
*** * * *
18345078 -ATTTTGTGTAAGACCCTATCTGGGACAGTGGCATCG-ATATA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TA
18345119 TGATTACATGTAAGACCAT
1 -GATTACATGTAAGACCAT
18345138 CTCTAGGATA
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.02
41 1 0.01
43 79 0.92
44 2 0.02
45 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTA
Found at i:18346935 original size:46 final size:47
Alignment explanation
Indices: 18346878--18347051 Score: 137
Period size: 46 Copynumber: 3.7 Consensus size: 47
18346868 GTTATTGTGG
* * *
18346878 GCTAGTGTAAGACGTGTCTGGGACATGCATCGGCCATATA-ATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATAGAGACGAGA
* * * *
18346924 GCCT-GTGTAAGACCATGTCTGTGACATGCCATC--ACATCGAGACGAGT
1 G-CTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCATAGAGACGAGA
* *
18346971 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-TACGAGATGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATA-GAGACGAGA
* *
18347017 G-TCAGTGTAAGACCATATCTGGGATATGGCATCGG
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
18347052 TACCCTACCC
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
45 6 0.06
46 46 0.45
47 40 0.39
48 11 0.11
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATAGAGACGAGA
Found at i:18352900 original size:49 final size:49
Alignment explanation
Indices: 18352843--18352941 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
18352833 ATGTATGATG
18352843 TTTAGAAACTAAATTGGAATGGACAAATTGCATATTATGCTGCATTTTT
1 TTTAGAAACTAAATTGGAATGGACAAATTGCATATTATGCTGCATTTTT
* *
18352892 TTTAGAAACTAAATTGGAATGGACCAATTGCATATTATGCTGTATTTTT
1 TTTAGAAACTAAATTGGAATGGACAAATTGCATATTATGCTGCATTTTT
18352941 T
1 T
18352942 AGGTCTGGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.40
Consensus pattern (49 bp):
TTTAGAAACTAAATTGGAATGGACAAATTGCATATTATGCTGCATTTTT
Found at i:18357295 original size:31 final size:30
Alignment explanation
Indices: 18357255--18357369 Score: 124
Period size: 31 Copynumber: 3.8 Consensus size: 30
18357245 CTTAACAACC
*
18357255 TAGTGACTTAAATAAAAACTTTTGAATAGTT
1 TAGTGACTTAAATGAAAACTTTT-AATAGTT
* *
18357286 TAGTAACTTAAATGAAAACTTTTAAGTAGCT
1 TAGTGACTTAAATGAAAACTTTTAA-TAGTT
* * *
18357317 CAGTGACTTAAATGAAAATTTTTAAACAGTT
1 TAGTGACTTAAATGAAAACTTTT-AATAGTT
* *
18357348 TAGTGA-TTAAATTATAACTTTT
1 TAGTGACTTAAATGAAAACTTTT
18357370 TTAATTAAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 15 0.21
31 53 0.76
32 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (30 bp):
TAGTGACTTAAATGAAAACTTTTAATAGTT
Found at i:18363416 original size:20 final size:20
Alignment explanation
Indices: 18363378--18363416 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18363368 CATTTCTCTA
*
18363378 ACCATAAACATGCATAATAT
1 ACCATAAACATGCAAAATAT
18363398 ACCATTAAACAT-CAAAATA
1 ACCA-TAAACATGCAAAATA
18363417 CACAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (20 bp):
ACCATAAACATGCAAAATAT
Found at i:18366179 original size:26 final size:26
Alignment explanation
Indices: 18366150--18366205 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
18366140 CCCGATATAT
*
18366150 GGCTCTTAATGAGCTTTCTGATTAAA
1 GGCTCTTAATGAGCTTCCTGATTAAA
** *
18366176 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTAATGAGCTTCCTGATTAAA
18366202 GGCT
1 GGCT
18366206 ATCCAGTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (26 bp):
GGCTCTTAATGAGCTTCCTGATTAAA
Found at i:18367028 original size:17 final size:17
Alignment explanation
Indices: 18367006--18367055 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
18366996 TGAGTAGTAA
18367006 AAATGTGTTTTAATGAG
1 AAATGTGTTTTAATGAG
*
18367023 AAATGTGTTTTAGTGA-
1 AAATGTGTTTTAATGAG
*
18367039 AAATGTATTTTAATGAG
1 AAATGTGTTTTAATGAG
18367056 TAGTTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (17 bp):
AAATGTGTTTTAATGAG
Found at i:18367044 original size:16 final size:16
Alignment explanation
Indices: 18367000--18367050 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
18366990 TAAAAATGAG
*
18367000 TAGTAAAAATGTGTTT
1 TAGTGAAAATGTGTTT
*
18367016 TAATGAGAAATGTGTTT
1 TAGTGA-AAATGTGTTT
*
18367033 TAGTGAAAATGTATTT
1 TAGTGAAAATGTGTTT
18367049 TA
1 TA
18367051 ATGAGTAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
TAGTGAAAATGTGTTT
Found at i:18367669 original size:45 final size:45
Alignment explanation
Indices: 18367613--18367698 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
18367603 TATGAAAGCT
*
18367613 GAACTCATTGAGTTGTGGTCTGAGTTCATGATATATATGACGTCC
1 GAACCCATTGAGTTGTGGTCTGAGTTCATGATATATATGACGTCC
* *
18367658 GAACCCATTGAGTTGTGGTCTGAGTTCGTGATATATGTGAC
1 GAACCCATTGAGTTGTGGTCTGAGTTCATGATATATATGAC
18367699 AAATGTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (45 bp):
GAACCCATTGAGTTGTGGTCTGAGTTCATGATATATATGACGTCC
Found at i:18370615 original size:40 final size:40
Alignment explanation
Indices: 18370566--18370806 Score: 348
Period size: 40 Copynumber: 6.1 Consensus size: 40
18370556 ATGATAATTT
*
18370566 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
*
18370606 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
*
18370646 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
*
18370685 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
* *
18370725 CGGGCTAAGTCCCGAAGACATTTGTGCGAACT-ACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTATATC
* *
18370765 C-GGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
18370804 CGG
1 CGG
18370807 TTAAAGCCGA
Statistics
Matches: 188, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
38 2 0.01
39 69 0.37
40 115 0.61
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
Found at i:18370727 original size:79 final size:80
Alignment explanation
Indices: 18370566--18370806 Score: 355
Period size: 79 Copynumber: 3.0 Consensus size: 80
18370556 ATGATAATTT
* *
18370566 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTG
*
18370630 TGCTAGTGACTA-ATTC
65 TGCGAGTGACTATA-TC
18370646 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
*
18370710 GCGAGTTACTATATC
66 GCGAGTGACTATATC
* ** *
18370725 CGGGCTAAGTCCCGAAGACATTTGTGCGAACTACTATATCC-GGCTAAGTCCCGAAGGCATTTGA
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
*
18370789 GCGAGTGGCTATATC
66 GCGAGTGACTATATC
18370804 CGG
1 CGG
18370807 TTAAAGCCGA
Statistics
Matches: 148, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
79 108 0.73
80 40 0.27
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTGACTATATC
Found at i:18370802 original size:119 final size:119
Alignment explanation
Indices: 18370566--18370806 Score: 346
Period size: 119 Copynumber: 2.0 Consensus size: 119
18370556 ATGATAATTT
* *
18370566 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGACATTTGT
* * * *
18370631 GCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATATATC
66 GCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGATATATC
*
18370685 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGACATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAGTCCCGAAGACATTTG
*
18370749 TGCGAACT-ACT-ATATCC-GGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATC
65 TGC-AACTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-GATATATC
18370804 CGG
1 CGG
18370807 TTAAAGCCGA
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
118 32 0.29
119 76 0.69
120 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGACATTTGT
GCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGATATATC
Found at i:18372994 original size:4 final size:4
Alignment explanation
Indices: 18372985--18373018 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
18372975 AGAACGGGGG
18372985 AGAA AGAA AGGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A
18373019 AGGGAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:18373619 original size:22 final size:22
Alignment explanation
Indices: 18373559--18373619 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
18373549 ATTGAATTGA
18373559 GAAAGTGAATTATAATTGATACT
1 GAAAGTGAATTA-AATTGATACT
* *
18373582 GAAA-TAAGATAGAAATT-ATACT
1 GAAAGTGA-AT-TAAATTGATACT
18373604 GAAAAGTGAATTAAAT
1 G-AAAGTGAATTAAAT
18373620 ACCCTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
22 12 0.40
23 15 0.50
24 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (22 bp):
GAAAGTGAATTAAATTGATACT
Found at i:18373733 original size:6 final size:6
Alignment explanation
Indices: 18373722--18373772 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
18373712 ATGTGCCGAC
* * *
18373722 TACTGT TACTGT TACTGT TACTAT TACTGT TATTGT TATTGT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT
18373770 TAC
1 TAC
18373773 CGATTCGGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.53
Consensus pattern (6 bp):
TACTGT
Found at i:18373810 original size:45 final size:45
Alignment explanation
Indices: 18373755--18373862 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
18373745 TTACTGTTAT
* *
18373755 TGTTATTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATAC
1 TGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAATAC
* * *
18373800 TGTTACTGTTACCGTTATCGATTCAGCACTTTGTGTGTTGAATAC
1 TGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAATAC
*
18373845 TGTTACTGTTACTATTAC
1 TGTTACTGTTACTGTTAC
18373863 TGTTCCGGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (45 bp):
TGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAATAC
Found at i:18374088 original size:18 final size:18
Alignment explanation
Indices: 18374047--18374081 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18374037 GATTATTTCT
18374047 GAATAATTGACTGTTACC
1 GAATAATTGACTGTTACC
18374065 GAATAATTGACTGTTAC
1 GAATAATTGACTGTTAC
18374082 TGGATAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
GAATAATTGACTGTTACC
Found at i:18374148 original size:18 final size:18
Alignment explanation
Indices: 18374127--18374186 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
18374117 GGTTATTATT
*
18374127 GAATAATTGACTGTTACC
1 GAATAACTGACTGTTACC
*
18374145 GAATAACTGATTGTTACC
1 GAATAACTGACTGTTACC
* *
18374163 GAATAACTGACTATTACT
1 GAATAACTGACTGTTACC
18374181 GAATAA
1 GAATAA
18374187 ATAATTGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:18374149 original size:36 final size:36
Alignment explanation
Indices: 18374109--18374186 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
18374099 GATCAATACT
* ** * *
18374109 GAATAACTGGTTATTATTGAATAATTGACTGTTACC
1 GAATAACTGATTATTACCGAATAACTGACTATTACC
* *
18374145 GAATAACTGATTGTTACCGAATAACTGACTATTACT
1 GAATAACTGATTATTACCGAATAACTGACTATTACC
18374181 GAATAA
1 GAATAA
18374187 ATAATTGTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (36 bp):
GAATAACTGATTATTACCGAATAACTGACTATTACC
Found at i:18374194 original size:36 final size:36
Alignment explanation
Indices: 18374127--18374195 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
18374117 GGTTATTATT
* * * *
18374127 GAATAATTGACTGTTACCGAATAACTGATTGTTACC
1 GAATAACTGACTATTACCGAATAAATAATTGTTACC
*
18374163 GAATAACTGACTATTACTGAATAAATAATTGTT
1 GAATAACTGACTATTACCGAATAAATAATTGTT
18374196 CTGATTGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (36 bp):
GAATAACTGACTATTACCGAATAAATAATTGTTACC
Found at i:18381240 original size:45 final size:45
Alignment explanation
Indices: 18381171--18381256 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
18381161 TATGAAATCT
*
18381171 GAACTCATTGAGTTATGGCTTGAGTTCATGATATATGTGACGTTC
1 GAACTCATTGAGTTATGGCTTGAGTTCATGATATAGGTGACGTTC
* *
18381216 GAACTCATTGAGTTGTGG-TCTGAGTTCGTGATATAGGTGAC
1 GAACTCATTGAGTTATGGCT-TGAGTTCATGATATAGGTGAC
18381257 ACATGATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (45 bp):
GAACTCATTGAGTTATGGCTTGAGTTCATGATATAGGTGACGTTC
Found at i:18382710 original size:20 final size:20
Alignment explanation
Indices: 18382685--18382732 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
18382675 CAGGCGAAGG
18382685 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
*
18382705 ACACGGGAGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
18382725 ACACGGGC
1 ACACGGGC
18382733 TTGTGTGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:18383126 original size:25 final size:24
Alignment explanation
Indices: 18383098--18383164 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 24
18383088 TTTCCATTAC
18383098 ATGGCTCACATGAGCTTCCTGTTAT
1 ATGGCTCACATGAGCTTCCTGTT-T
* *
18383123 ATGGCTCGAGAGAGAGCTTCCTGTTT
1 ATGGCTC-ACA-TGAGCTTCCTGTTT
*
18383149 ATGTTCTCACATGAGC
1 ATG-GCTCACATGAGC
18383165 ATTCTATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 11 0.32
26 8 0.24
27 15 0.44
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (24 bp):
ATGGCTCACATGAGCTTCCTGTTT
Found at i:18386804 original size:40 final size:40
Alignment explanation
Indices: 18386767--18386952 Score: 236
Period size: 40 Copynumber: 4.7 Consensus size: 40
18386757 GCTACTCGTT
*
18386767 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
18386807 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
18386847 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
18386887 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
18386928 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18386953 CATCATTCGA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.89
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:18394894 original size:39 final size:38
Alignment explanation
Indices: 18394791--18394931 Score: 167
Period size: 39 Copynumber: 3.6 Consensus size: 38
18394781 GCTACTCGTT
* *
18394791 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGATT-TAGTAACTCGCA
*
18394830 CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGATTTAGTAACTCGCA
* * * *
18394869 CAAATGCCTTCGGATCTTAGTCCGATATAGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGATTTAGTAAC-TCGCA
18394909 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTC-GGACTTAGCCCG
18394932 GACATCATTC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.03
39 63 0.71
40 23 0.26
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:18401387 original size:25 final size:24
Alignment explanation
Indices: 18401336--18401384 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
18401326 TTATTAAGCG
18401336 ATTCCTCATACAAAAACAAGTTGA
1 ATTCCTCATACAAAAACAAGTTGA
18401360 ATTCCTCATACAAAAACAAGTTGA
1 ATTCCTCATACAAAAACAAGTTGA
18401384 A
1 A
18401385 ATTTTGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (24 bp):
ATTCCTCATACAAAAACAAGTTGA
Found at i:18406009 original size:6 final size:6
Alignment explanation
Indices: 18405998--18406033 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
18405988 ATGAAAATAA
18405998 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
18406034 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:18406674 original size:12 final size:12
Alignment explanation
Indices: 18406621--18406681 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
18406611 AAACCAAATT
18406621 TTTTAAAAGTAC
1 TTTTAAAAGTAC
* * *
18406633 TTCTCAAAAATATT
1 TT-TTAAAAGTA-C
* * *
18406647 TTTTACAATTAT
1 TTTTAAAAGTAC
18406659 TTTTAAAAGTAC
1 TTTTAAAAGTAC
18406671 TTTTAAAAGTA
1 TTTTAAAAGTA
18406682 TTGCTAAACT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
12 23 0.61
13 13 0.34
14 2 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (12 bp):
TTTTAAAAGTAC
Found at i:18410598 original size:3 final size:3
Alignment explanation
Indices: 18410592--18410645 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
18410582 ACCAACATCC
18410592 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18410640 ATT ATT
1 ATT ATT
18410646 GAGATAGTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18413908 original size:20 final size:20
Alignment explanation
Indices: 18413883--18413920 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18413873 CGATAATTTT
18413883 GAAAGCTAACACAACTAGTC
1 GAAAGCTAACACAACTAGTC
18413903 GAAAGCTAACACAACTAG
1 GAAAGCTAACACAACTAG
18413921 GGGTGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAGCTAACACAACTAGTC
Found at i:18414173 original size:69 final size:69
Alignment explanation
Indices: 18413976--18414521 Score: 449
Period size: 69 Copynumber: 8.0 Consensus size: 69
18413966 GATAACAAGC
* * * * * * ** *
18413976 TGAGAGTTTTGCTCTCGCTAACTGTCTTGGA-GTTGAGGTTCTTCACCTGTAAACCTTAATATTA
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
* *
18414040 TAGC
66 CAGT
* ** * * * * * * ** *
18414044 T-AGGAGCTTTGATCTTACTAACTTTTTTGAAAGTTGTAGCTCTTTGCTTTAGAACATTAATATG
1 TGA-GAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATG
18414108 ACAGT
65 ACAGT
* * * * * * * *
18414113 TGAGAGGTTTGCTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTTGCCTACGATCCTTAATATGA
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
*
18414178 TAGT
66 CAGT
* * * * * *
18414182 TAAAAGTTTTGCTCTCACTAACTATTTTGAAGG-T-T-GCTCTTCGCCTGCGAACCTTAATATTA
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
18414244 CAGT
66 CAGT
* * * * * * *
18414248 TGGGAGCTTTGCTCTTGCAAACTGTTTTGGAGGTTGTGGCTCTTCGTCTGCGAATCTTAATATAA
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
*
18414313 CAGC
66 CAGT
* * * * * **
18414317 TGGGAGCTTTGCTCTCACTAAATATTTTGGAGGTTGTGGCTCTTCACTTATGAACCTTAATATGA
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
*
18414382 -AAT
66 CAGT
* ** *
18414385 CTGAGAGCTTTGCTCTCGCTAACTATTTTAGAGGTTGTGGCTCTTTACTTGCGAACCTTAATATG
1 -TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATG
18414450 ACAGT
65 ACAGT
* ** * *
18414455 TGAGAGCTTCGCTCTCGCTAACTATTTTGGAGACTGCGGCTC-TCTGCCTGCGAATCTTAATATG
1 TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTC-GCCTGCGAACCTTAATATG
18414519 ACA
65 ACA
18414522 AAAAAAATGC
Statistics
Matches: 374, Mismatches: 95, Indels: 17
0.77 0.20 0.03
Matches are distributed among these distances:
66 48 0.13
67 2 0.01
68 26 0.07
69 295 0.79
70 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (69 bp):
TGAGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGGCTCTTCGCCTGCGAACCTTAATATGA
CAGT
Found at i:18417889 original size:2 final size:2
Alignment explanation
Indices: 18417884--18417947 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
18417874 TATATATATA
18417884 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18417926 TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
18417948 AATGAAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18421658 original size:16 final size:16
Alignment explanation
Indices: 18421634--18421684 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
18421624 ATAGTAAAAA
18421634 TATAATTTTATT-ATTT
1 TATAATTTT-TTAATTT
*
18421650 TATATTTTTTTAATTT
1 TATAATTTTTTAATTT
*
18421666 TAAAATTTTAATTAATTT
1 TATAATTTT--TTAATTT
18421684 T
1 T
18421685 TTATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 19 0.66
18 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATAATTTTTTAATTT
Done.