Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 61 of 362
Found at i:18601919 original size:47 final size:47
Alignment explanation
Indices: 18601854--18601955 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 47
18601844 CTATTTGGCC
* *
18601854 TTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCA-TACTCTGATAGCA
1 TTTGTGGCATATTCTGTATGTTGCCTTTGTGG-AGTACTCTAATAGCA
* ** *
18601901 TTTGTGGCATATTTTGTATGTTTTCTTTGTGGAGTACTCTAATAGCC
1 TTTGTGGCATATTCTGTATGTTGCCTTTGTGGAGTACTCTAATAGCA
18601948 TTTGTGGC
1 TTTGTGGC
18601956 GTATCTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 1 0.02
47 47 0.98
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.46
Consensus pattern (47 bp):
TTTGTGGCATATTCTGTATGTTGCCTTTGTGGAGTACTCTAATAGCA
Found at i:18601971 original size:21 final size:21
Alignment explanation
Indices: 18601925--18601981 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
18601915 TGTATGTTTT
*
18601925 CTTTGTGGAGTACTCTAATAGC
1 CTTTGTGGCGTA-TCTAATAGC
*
18601947 CTTTGTGGCGTATCTATTTAGC
1 CTTTGTGGCGTATCTA-ATAGC
*
18601969 TTTTGTGGCGTAT
1 CTTTGTGGCGTAT
18601982 TCTGATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (21 bp):
CTTTGTGGCGTATCTAATAGC
Found at i:18605656 original size:18 final size:17
Alignment explanation
Indices: 18605630--18605663 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18605620 GAAAAATGGG
*
18605630 TTAAGTTTCGATTGAATA
1 TTAAATTTCGA-TGAATA
18605648 TTAAATTTCGATGAAT
1 TTAAATTTCGATGAAT
18605664 GTATATGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TTAAATTTCGATGAATA
Found at i:18608597 original size:77 final size:77
Alignment explanation
Indices: 18608470--18608624 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
18608460 CGGATGCGGT
*
18608470 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
1 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTAACAGCTCTAAA
18608535 GCCGAGCAATCC
66 GCCGAGCAATCC
18608547 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTAACAGCTCTAAA
1 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTAACAGCTCTAAA
18608612 GCCGAGCAATCC
66 GCCGAGCAATCC
18608624 T
1 T
18608625 ATTGGGAGAG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (77 bp):
TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTAACAGCTCTAAA
GCCGAGCAATCC
Found at i:18619598 original size:46 final size:48
Alignment explanation
Indices: 18619548--18619670 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 48
18619538 TGTGCACTAG
18619548 TGTAAGATATGTTTGGGACATGCATCGGCCAC-A-AT-TTGAGAGCCAA
1 TGTAAGATATGTTTGGGACATGCATCGGCCACGAGATATTGA-AGCCAA
* * * * * *
18619594 TGTAAGATATGTCTGGGACATGCTTTGGCCTCGAGATATTTAAGCCAG
1 TGTAAGATATGTTTGGGACATGCATCGGCCACGAGATATTGAAGCCAA
*
18619642 TGTAAGACATGTTTGGGACATGCATCGGC
1 TGTAAGATATGTTTGGGACATGCATCGGC
18619671 ATTGAGACGA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 28 0.44
47 1 0.02
48 32 0.50
49 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGATATGTTTGGGACATGCATCGGCCACGAGATATTGAAGCCAA
Found at i:18619719 original size:94 final size:94
Alignment explanation
Indices: 18619546--18619726 Score: 229
Period size: 94 Copynumber: 1.9 Consensus size: 94
18619536 TTTGTGCACT
* *** *
18619546 AGTGTAAGATATGTTTGGGACATGCATCGGCCACAATTTGAGAGCCAATGTAAGATATGTCTGGG
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCACAAGACGAGAGCCAATGTAAGACATGTCTGGG
* **
18619611 ACATGCTTTGGCCTCGAGATATTTAAGCC
66 ACATGCATCAGCCTCGAGATATTTAAGCC
** * *
18619640 AGTGTAAGACATGTTTGGGACATGCATCGG-CATTGAGACGAGAGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCA-CAAGACGAGAGCCAATGTAAGACATGTCTGG
*
18619704 GACATGCATCAGCCTCGCGATAT
65 GACATGCATCAGCCTCGAGATAT
18619727 ACAAGCTAGT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
93 2 0.03
94 71 0.97
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (94 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCCACAAGACGAGAGCCAATGTAAGACATGTCTGGG
ACATGCATCAGCCTCGAGATATTTAAGCC
Found at i:18619753 original size:94 final size:94
Alignment explanation
Indices: 18619585--18619757 Score: 220
Period size: 94 Copynumber: 1.8 Consensus size: 94
18619575 GCCACAATTT
* * ** ** *
18619585 GAGAGCCAATGTAAGATATGTCTGGGACATGCTTTGGCCTCGAGATATTTAAGCCAGTGTAAGAC
1 GAGAGCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAGCCAGTATAAGAC
*
18619650 ATGTTTGGGACATGCATCGGCATTGAGAC
66 ATGTCTGGGACATGCATCGGCATTGAGAC
* * * * *
18619679 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATATACAAGCTAGTATACGAC
1 GAGAGCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAGCCAGTATAAGAC
*
18619744 CTGTCTGGGACATG
66 ATGTCTGGGACATG
18619758 GCGTCAGCTT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 65 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (94 bp):
GAGAGCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAGCCAGTATAAGAC
ATGTCTGGGACATGCATCGGCATTGAGAC
Found at i:18619884 original size:49 final size:49
Alignment explanation
Indices: 18619682--18619886 Score: 133
Period size: 49 Copynumber: 4.3 Consensus size: 49
18619672 TTGAGACGAG
* *
18619682 AGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATAT-ACA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGA-A
* * * * **
18619730 AGCTAGTATACGACCTGTCTGGGACATGGCGTCAG-CT---TGT-TGCCT
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATG-AA
* * * * * * * *
18619775 ATC-AGTGTCAGAACTATCTCGGACATGGCATC-GACAC-CGATAGATGAG
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAG-C-CTCGCTATATGAA
* * *
18619823 AGCCAGTATAAGACCTGTCTGGGACATGGCATTAGCCTCGCTATATGAA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGAA
18619872 AGCTAGTGTAAGACC
1 AGCTAGTGTAAGACC
18619887 ATGTTGTTCG
Statistics
Matches: 112, Mismatches: 32, Indels: 25
0.66 0.19 0.15
Matches are distributed among these distances:
43 1 0.01
44 23 0.21
45 3 0.03
46 1 0.01
48 30 0.27
49 53 0.47
50 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (49 bp):
AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGAA
Found at i:18626862 original size:49 final size:49
Alignment explanation
Indices: 18626759--18626868 Score: 143
Period size: 49 Copynumber: 2.2 Consensus size: 49
18626749 TGTTGTGTGT
* * *
18626759 CAGTGTAAGACCTGCCTAGGACATGGCATCGACACTGATAGATGAGAGC
1 CAGTGTAAGACCTGCCTAGAACATGGCATCGACACTCATAGATGAAAGC
*
18626808 CAGTGTAAGACCTGCCTAGAACATGGCATC-AGC-CTCACTATATGAAAGC
1 CAGTGTAAGACCTGCCTAGAACATGGCATCGA-CACTCA-TAGATGAAAGC
*
18626857 TAGTGTAAGACC
1 CAGTGTAAGACC
18626869 ATGTCTGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 4 0.07
49 50 0.93
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.20
Consensus pattern (49 bp):
CAGTGTAAGACCTGCCTAGAACATGGCATCGACACTCATAGATGAAAGC
Found at i:18640780 original size:27 final size:27
Alignment explanation
Indices: 18640742--18640796 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
18640732 AGCTCTGAAC
18640742 TTTTCAGCCCTGTGTTTACGGATCTTA
1 TTTTCAGCCCTGTGTTTACGGATCTTA
18640769 TTTTCAGCCCTGTGTTTACGGATCTTA
1 TTTTCAGCCCTGTGTTTACGGATCTTA
18640796 T
1 T
18640797 CTACTGGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTTCAGCCCTGTGTTTACGGATCTTA
Found at i:18643103 original size:53 final size:54
Alignment explanation
Indices: 18643039--18643245 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 54
18643029 TCCTATTTTA
* *
18643039 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
18643092 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * * * * *
18643146 TAGTTTATCAATGCCAGGTCTTGACATGTTATTACATGATTTCCTTACCTTTTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
18643201 AACTTGCCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
18643246 AAACCCTAAT
Statistics
Matches: 117, Mismatches: 35, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
53 47 0.40
54 34 0.29
55 36 0.31
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:18647716 original size:32 final size:32
Alignment explanation
Indices: 18647677--18647743 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
18647667 TATGACATTT
*
18647677 ATACAATTCACAACATAACATTTAATTCAAGC
1 ATACAATTCAAAACATAACATTTAATTCAAGC
**
18647709 ATACAATTCAAAATGTAACATTTAATTCAAGC
1 ATACAATTCAAAACATAACATTTAATTCAAGC
18647741 ATA
1 ATA
18647744 TAAACATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (32 bp):
ATACAATTCAAAACATAACATTTAATTCAAGC
Found at i:18650105 original size:31 final size:31
Alignment explanation
Indices: 18650070--18650152 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
18650060 CTTCCTGCAT
* *
18650070 TAAAATCCAACCAAATACAAAAAATATAGTA
1 TAAAATCCAACCAAAAACAAAAAATATAGCA
* * * *
18650101 TAAAATGCAGCCAAAAACAACAAATTTAGCA
1 TAAAATCCAACCAAAAACAAAAAATATAGCA
*
18650132 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
18650153 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAAAAAATATAGCA
Found at i:18650397 original size:21 final size:20
Alignment explanation
Indices: 18650373--18650420 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
18650363 TTTTGCTCTG
18650373 CTCTGCTGCCATCGCT-GCTGC
1 CTCTGCT-CCATCGCTCG-TGC
*
18650394 CTCTGCCTCCCTCGCTCGTGC
1 CTCTG-CTCCATCGCTCGTGC
18650415 CTCTGC
1 CTCTGC
18650421 CTCTCTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.02, C:0.48, G:0.21, T:0.29
Consensus pattern (20 bp):
CTCTGCTCCATCGCTCGTGC
Found at i:18650421 original size:21 final size:21
Alignment explanation
Indices: 18650417--18650469 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18650407 GCTCGTGCCT
* *
18650417 CTGCCTCTCTCACTGATGCCG
1 CTGCCTCCCTCGCTGATGCCG
* * *
18650438 CTACCTCCCTCGCTGCTGTCG
1 CTGCCTCCCTCGCTGATGCCG
18650459 CTGCCTCCCTC
1 CTGCCTCCCTC
18650470 TCTACTGCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.49, G:0.17, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGATGCCG
Found at i:18650920 original size:13 final size:14
Alignment explanation
Indices: 18650895--18650923 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18650885 TGATGAATTG
18650895 AATTAAACAATTAT
1 AATTAAACAATTAT
18650909 AATTAAAC-ATTAT
1 AATTAAACAATTAT
18650922 AA
1 AA
18650924 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:18651112 original size:17 final size:19
Alignment explanation
Indices: 18651076--18651112 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18651066 ACAATATTGC
18651076 AGTAAAAATATTATTTAAT
1 AGTAAAAATATTATTTAAT
18651095 AGTAAAAAT-TTA-TTAAT
1 AGTAAAAATATTATTTAAT
18651112 A
1 A
18651113 TTTGAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AGTAAAAATATTATTTAAT
Found at i:18656111 original size:9 final size:9
Alignment explanation
Indices: 18656097--18656331 Score: 194
Period size: 9 Copynumber: 26.7 Consensus size: 9
18656087 TATTTAAGTA
18656097 TTATGTAAG
1 TTATGTAAG
18656106 TTATGTAAG
1 TTATGTAAG
*
18656115 TTATGATATG
1 TTATG-TAAG
* * *
18656125 ATATAT-AT
1 TTATGTAAG
18656133 TTATGTAAG
1 TTATGTAAG
* *
18656142 TTATAT-AT
1 TTATGTAAG
*
18656150 TTATCTAAG
1 TTATGTAAG
*
18656159 TTATATAAG
1 TTATGTAAG
18656168 TTATGTAAG
1 TTATGTAAG
18656177 TTATGTAAG
1 TTATGTAAG
* *
18656186 TTATAT-AT
1 TTATGTAAG
*
18656194 TTATCTAAG
1 TTATGTAAG
*
18656203 TTATATAAG
1 TTATGTAAG
*
18656212 TTATCTAAG
1 TTATGTAAG
18656221 TTATGTAAG
1 TTATGTAAG
* *
18656230 TTATAT-AT
1 TTATGTAAG
*
18656238 TTATCTAAG
1 TTATGTAAG
18656247 TTATGTAAG
1 TTATGTAAG
* *
18656256 TTATAT-AT
1 TTATGTAAG
*
18656264 TTATCTAAG
1 TTATGTAAG
*
18656273 TTATATAAG
1 TTATGTAAG
* *
18656282 TTATAT-AT
1 TTATGTAAG
*
18656290 TTATCTAAG
1 TTATGTAAG
*
18656299 TTATATAAG
1 TTATGTAAG
18656308 TTATGTAAG
1 TTATGTAAG
*
18656317 TTTTGTAAG
1 TTATGTAAG
18656326 TTATGT
1 TTATGT
18656332 TAAATATTTA
Statistics
Matches: 181, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
8 34 0.19
9 141 0.78
10 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:18656162 original size:26 final size:27
Alignment explanation
Indices: 18656097--18656329 Score: 217
Period size: 26 Copynumber: 8.8 Consensus size: 27
18656087 TATTTAAGTA
* * *
18656097 TTATGTAAGTTATGTAAGTTATGATATG
1 TTATATAAGTTATCTAAGTTAT-ATAAG
* * * *
18656125 ATATAT-ATTTATGTAAGTTATAT-AT
1 TTATATAAGTTATCTAAGTTATATAAG
* * *
18656150 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
* * * *
18656177 TTATGTAAGTTATAT-ATTTATCTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
18656203 TTATATAAGTTATCTAAGTTATGTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
* *
18656230 TTATAT-ATTTATCTAAGTTATGTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
18656256 TTATAT-ATTTATCTAAGTTATATAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
18656282 TTATAT-ATTTATCTAAGTTATATAAG
1 TTATATAAGTTATCTAAGTTATATAAG
* * *
18656308 TTATGTAAGTTTTGTAAGTTAT
1 TTATATAAGTTATCTAAGTTAT
18656330 GTTAAATATT
Statistics
Matches: 177, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
25 4 0.02
26 113 0.64
27 56 0.32
28 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (27 bp):
TTATATAAGTTATCTAAGTTATATAAG
Found at i:18656181 original size:44 final size:44
Alignment explanation
Indices: 18656133--18656329 Score: 277
Period size: 44 Copynumber: 4.3 Consensus size: 44
18656123 TGATATATAT
*
18656133 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
18656177 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
*
18656221 TTATGTAAGTTATATATTTATCTAAGTTATGTAAGTTATATATTTATCTAAG
1 TTATGTAAGTTATATATTTATCTAAG---T-T-A--TATA-AGTTATCTAAG
* *
18656273 TTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
*
18656317 TTTTGTAAGTTAT
1 TTATGTAAGTTAT
18656330 GTTAAATATT
Statistics
Matches: 138, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
44 89 0.64
45 4 0.03
47 2 0.01
48 2 0.01
49 2 0.01
51 4 0.03
52 35 0.25
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (44 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
Found at i:18656461 original size:15 final size:15
Alignment explanation
Indices: 18656441--18656496 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
18656431 GTAAGTTGTG
18656441 AATTAAATAATATTT
1 AATTAAATAATATTT
18656456 AATTAAATAATATTT
1 AATTAAATAATATTT
18656471 -A-TAAA-AATTATTTT
1 AATTAAATAA-TA-TTT
18656485 AATTAAATAATA
1 AATTAAATAATA
18656497 CTAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:18656504 original size:28 final size:29
Alignment explanation
Indices: 18656453--18656525 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 29
18656443 TTAAATAATA
* *
18656453 TTTAATTAAATAATATTTATAAAAATTAT
1 TTTAATTAAATAATATCTAAAAAAATTAT
18656482 TTTAATTAAATAATA-CTAAAAAAATTAT
1 TTTAATTAAATAATATCTAAAAAAATTAT
*
18656510 TTTAATTCAATAATAT
1 TTTAATTAAATAATAT
18656526 ACATGTCGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 25 0.62
29 15 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTAATTAAATAATATCTAAAAAAATTAT
Found at i:18658423 original size:26 final size:26
Alignment explanation
Indices: 18658387--18658496 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
18658377 TGATACAAAT
18658387 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
18658413 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
18658439 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
18658465 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
18658491 TGATAA
1 TGATAA
18658497 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:18660218 original size:27 final size:26
Alignment explanation
Indices: 18660114--18660228 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
18660104 TGGAGGAAGC
* *
18660114 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
18660141 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
18660168 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* * * *
18660195 GTATCTGGTGACTTTGTCATATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
18660222 GTTCTGG
1 GTTCTGG
18660229 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 56 0.73
28 15 0.19
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:18660221 original size:54 final size:54
Alignment explanation
Indices: 18660114--18660228 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
18660104 TGGAGGAAGC
*
18660114 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * * *
18660168 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTTTGTCATAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
18660222 GTTCTGG
1 GTTCTGG
18660229 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 37 0.70
55 16 0.30
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:18662061 original size:103 final size:104
Alignment explanation
Indices: 18661944--18662153 Score: 239
Period size: 103 Copynumber: 2.0 Consensus size: 104
18661934 TAGGGCCAGA
* * * *
18661944 TTTATAATTTAGGGTATAATG-GTTTAAGGATTTA-GTTTTTAGAGTTTAGAGTTTTAGGGTTTA
1 TTTATAATTTAGGGTATAAGGAGTTTAAGGATTTAGGATATT-G-CTTTAGAG-TTTAGGGTTTA
*
18662007 AAAGATTT-A-TAGGTCATGGGTTATGATTTAGGGGTTAGGC
63 AAAGATTTGATTAGATCATGGGTTATGATTTAGGGGTTAGGC
* * *
18662047 TTTATATTTTAGGGTTTAAGGCAGTTTAAGGTTTTAGGATATTGCTTTAGAGTTTAGGGTTTAAA
1 TTTATAATTTAGGGTATAAGG-AGTTTAAGGATTTAGGATATTGCTTTAGAGTTTAGGGTTTAAA
* *
18662112 TGGTTTGGAGTTTAGATCATGGGTTATGATTTAGGGGTTAGG
65 AGATTT-GA--TTAGATCATGGGTTATGATTTAGGGGTTAGG
18662154 TGATCATGGG
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
103 35 0.39
104 7 0.08
105 14 0.16
106 4 0.04
108 29 0.33
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (104 bp):
TTTATAATTTAGGGTATAAGGAGTTTAAGGATTTAGGATATTGCTTTAGAGTTTAGGGTTTAAAA
GATTTGATTAGATCATGGGTTATGATTTAGGGGTTAGGC
Found at i:18662151 original size:14 final size:14
Alignment explanation
Indices: 18662132--18662180 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
18662122 TTTAGATCAT
18662132 GGGTTATGATTTAG
1 GGGTTATGATTTAG
* *
18662146 GGGTTAGGTGA-TCAT
1 GGGTTA--TGATTTAG
18662161 GGGTTATGATTTAG
1 GGGTTATGATTTAG
18662175 GGGTTA
1 GGGTTA
18662181 GGCTTCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (14 bp):
GGGTTATGATTTAG
Found at i:18662158 original size:29 final size:29
Alignment explanation
Indices: 18662126--18662182 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
18662116 TTGGAGTTTA
18662126 GATCATGGGTTATGATTTAGGGGTTAGGT
1 GATCATGGGTTATGATTTAGGGGTTAGGT
18662155 GATCATGGGTTATGATTTAGGGGTTAGG
1 GATCATGGGTTATGATTTAGGGGTTAGG
18662183 CTTCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.04, G:0.39, T:0.37
Consensus pattern (29 bp):
GATCATGGGTTATGATTTAGGGGTTAGGT
Found at i:18662904 original size:41 final size:41
Alignment explanation
Indices: 18662792--18662905 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
18662782 TGCGATGTTT
* * * * * *
18662792 AACGCCACTATTTCTCAATTTTTTGCGGCATTTTGGATGAA
1 AACGCCACTATTGCTCAGTTTTTAGCGGCGTTATGGATAAA
18662833 AACGCCACTATTGCTCAGTTTTTAGCGGCGTTATGGATAAA
1 AACGCCACTATTGCTCAGTTTTTAGCGGCGTTATGGATAAA
*
18662874 AACGCCACTATTGCTCAGTTTTTAGGGGCGTT
1 AACGCCACTATTGCTCAGTTTTTAGCGGCGTT
18662906 TTGTTTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (41 bp):
AACGCCACTATTGCTCAGTTTTTAGCGGCGTTATGGATAAA
Found at i:18665320 original size:13 final size:12
Alignment explanation
Indices: 18665302--18665345 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
18665292 AATATATATT
18665302 AACCCAAGTACCC
1 AACCCAA-TACCC
18665315 AACCCAAT--CC
1 AACCCAATACCC
18665325 AACCCAATTACCC
1 AACCCAA-TACCC
18665338 AACCCAAT
1 AACCCAAT
18665346 CATAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.32
11 1 0.04
12 2 0.07
13 16 0.57
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.11
Consensus pattern (12 bp):
AACCCAATACCC
Found at i:18665336 original size:23 final size:23
Alignment explanation
Indices: 18665302--18665346 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18665292 AATATATATT
18665302 AACCCAAGTACCCAACCCAATCC
1 AACCCAAGTACCCAACCCAATCC
*
18665325 AACCCAATTACCCAACCCAATC
1 AACCCAAGTACCCAACCCAATC
18665347 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.47, G:0.02, T:0.11
Consensus pattern (23 bp):
AACCCAAGTACCCAACCCAATCC
Found at i:18665381 original size:6 final size:6
Alignment explanation
Indices: 18665370--18665410 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
18665360 ATAATTTAAT
18665370 AAATAA AAATAA AAATATA AAACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATA-A AAA-TAA AAATAA AAATAA AAA
18665411 ACATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.70
7 8 0.24
8 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:18665398 original size:20 final size:20
Alignment explanation
Indices: 18665373--18665412 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18665363 ATTTAATAAA
*
18665373 TAAAAATAAAAATATAAAAC
1 TAAAAATAAAAATAAAAAAC
18665393 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
18665413 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:18665444 original size:9 final size:9
Alignment explanation
Indices: 18665430--18665506 Score: 104
Period size: 9 Copynumber: 8.6 Consensus size: 9
18665420 TTTATACAAA
18665430 TAATTCGGT
1 TAATTCGGT
18665439 TAATTCGGT
1 TAATTCGGT
18665448 TAATTCAGG-
1 TAATTC-GGT
18665457 TAATTCAGG-
1 TAATTC-GGT
18665466 TAATTCGGT
1 TAATTCGGT
* *
18665475 TAATTTGAT
1 TAATTCGGT
18665484 TAATTCGGT
1 TAATTCGGT
18665493 TAATTCGGT
1 TAATTCGGT
18665502 TAATT
1 TAATT
18665507 TTACACTTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
8 2 0.03
9 58 0.94
10 2 0.03
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:18665618 original size:29 final size:29
Alignment explanation
Indices: 18665579--18665658 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
18665569 CGAATTAGCC
*
18665579 GAAAAATTTTCGGTTCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
*
18665608 GAAAAAATTTCGATTCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
18665637 GAAAAAATTTCGGTTCGGTTAA
1 GAAAAAATTTCGGTTCGGTTAA
18665659 CGGTTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (29 bp):
GAAAAAATTTCGGTTCGGTTAATTTTTTT
Found at i:18676275 original size:18 final size:18
Alignment explanation
Indices: 18676237--18676277 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
18676227 ATAAGACTAA
* *
18676237 GGAAGCTACTTAGGTGTC
1 GGAAGCTACTTAGGAGCC
18676255 GGAAGCTACTTAGGAGCC
1 GGAAGCTACTTAGGAGCC
18676273 GGAAG
1 GGAAG
18676278 ATATCATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.17, G:0.37, T:0.20
Consensus pattern (18 bp):
GGAAGCTACTTAGGAGCC
Found at i:18680250 original size:28 final size:28
Alignment explanation
Indices: 18680218--18680274 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18680208 TATTCCAAAG
18680218 TAAGCTTCAATAACACATTATTTACATA
1 TAAGCTTCAATAACACATTATTTACATA
18680246 TAAGCTTCAATAACACATTATTTACATA
1 TAAGCTTCAATAACACATTATTTACATA
18680274 T
1 T
18680275 GTACTTACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (28 bp):
TAAGCTTCAATAACACATTATTTACATA
Found at i:18681486 original size:48 final size:48
Alignment explanation
Indices: 18681431--18681714 Score: 230
Period size: 48 Copynumber: 5.9 Consensus size: 48
18681421 GGTGAATTGC
* * *
18681431 CGATGCCATGTTCCAAACATGGTCTTACACT-GTCTCACATGTCGAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAG-CTCACATATCAAGGT
* * * * * *
18681479 CGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCGTCTCAATGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGT
* * * * *
18681527 CGTTGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGT
* * * * * **
18681575 CGATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCACATCATTG-
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGT
* * * * * *** *
18681622 CTGATGCCATGTTCCAAACATGGTCTTACAATGGCTCTCCTATTGTGGC
1 C-GATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGT
* * * *
18681671 CGACGCCATGTCCCAAACACGGTCTTACACTAACGCACATATCA
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
18681715 CTCAAATGTC
Statistics
Matches: 193, Mismatches: 40, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 190 0.98
49 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGT
Found at i:18681673 original size:96 final size:96
Alignment explanation
Indices: 18681426--18681699 Score: 284
Period size: 96 Copynumber: 2.9 Consensus size: 96
18681416 AATAGGGTGA
* * * * * *
18681426 ATTGCCGATGCCATGTTCCAAACATGGTCTTACACTGTCTCACATGTCGAGGTCGATGCCATGTC
1 ATTGCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATAGTGGCCGATGCCATGTC
* * *
18681491 CCAGATATGGTCTTACACTAGCTCTCGTCTC
66 CCAGACATGGTCTTACAATAGCTCTCGACTC
* * * * * * *
18681522 AATG-TCGTTGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAAT-GCCGATGCCATG
1 ATTGCT-GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAT-AGTGGCCGATGCCATG
*
18681585 TCCCAGACATGGTCTTACAATGGCTCTC-ACATC
64 TCCCAGACATGGTCTTACAATAGCTCTCGAC-TC
* * * * *
18681618 ATTGCTGATGCCATGTTCCAAACATGGTCTTACAATGGCTCTCCTATTGTGGCCGACGCCATGTC
1 ATTGCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATAGTGGCCGATGCCATGTC
* *
18681683 CCAAACACGGTCTTACA
66 CCAGACATGGTCTTACA
18681700 CTAACGCACA
Statistics
Matches: 142, Mismatches: 31, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
95 2 0.01
96 139 0.98
97 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (96 bp):
ATTGCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATAGTGGCCGATGCCATGTC
CCAGACATGGTCTTACAATAGCTCTCGACTC
Found at i:18687235 original size:25 final size:25
Alignment explanation
Indices: 18687206--18687253 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
18687196 GGCTCCCTGC
18687206 TTCCTAATTCTGTCAACTAGAGGAT
1 TTCCTAATTCTGTCAACTAGAGGAT
18687231 TTCCTAATTCTGTCAACTAGAGG
1 TTCCTAATTCTGTCAACTAGAGG
18687254 TTCCTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (25 bp):
TTCCTAATTCTGTCAACTAGAGGAT
Found at i:18689878 original size:48 final size:48
Alignment explanation
Indices: 18689823--18690191 Score: 404
Period size: 48 Copynumber: 7.7 Consensus size: 48
18689813 GGGTGAATTA
* * * * * * * *
18689823 CCGATGCCATGTTCCAAACTTGGTCTTACACTAGCACACATGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
* * *
18689871 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCAATA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
* *
18689919 CCGATGCCATGT-CCAGACATGGTCTTACACTGGCTCTCATA--ATGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA-AT-G
* * *
18689966 CCGATGCTATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
* * * *
18690014 CCGATGCCATGTCCCAGACATGGTCTTACACGAGCGCACATATTAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
* * * *
18690062 TCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAACATTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
* * * *
18690110 CCGATGCCATATTCCAAACATGGTCTTACACTAGCTCTCATATC-GTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT-G
* * *
18690158 CTGACGCCATGTCCCAGACATGGTCTTATACTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG
18690192 TGCACATATC
Statistics
Matches: 271, Mismatches: 44, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.00
46 1 0.00
47 38 0.14
48 229 0.85
49 1 0.00
50 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG
Found at i:18690143 original size:144 final size:142
Alignment explanation
Indices: 18689823--18690202 Score: 474
Period size: 144 Copynumber: 2.6 Consensus size: 142
18689813 GGGTGAATTA
* * *
18689823 CCGATGCCATGTTCCAAACTTGGTCTTACACTAGCACACATGTCGAGGCCGATGCCATGTCCCAG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCACACATATC-ATGCCGATGCCATGTCCCAG
* * *
18689888 ACATGGTCTTACACTAGC-TATCATCTCAATACCGATGCCATGTCCAGACATGGTCTTACACTGG
65 ACATGGTCTTACACTAGCGCA-CATATCAATACCGATGCCATGTCCAGACATGGTCTTACACTAG
* **
18689952 CTCTCATAATGTGG
129 CTCTCACAACATGG
* * * *
18689966 CCGATGCTATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCAG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCACACATATC-ATGCCGATGCCATGTCCCAG
* * **
18690031 ACATGGTCTTACACGAGCGCACATATTAATGTCGATGCCATGTCCCAGACATGGTCTTACACTAG
65 ACATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGT-CCAGACATGGTCTTACACTAG
*
18690096 CTCTCACAACATTG
129 CTCTCACAACATGG
* * * * * *
18690110 CCGATGCCATATTCCAAACATGGTCTTACACTAGCTCTCATATCGTGGCTGACGCCATGTCCCAG
1 CCGATGCCATGTTCCAAACATGGTCTTACACTAGCACACATATCAT-GCCGATGCCATGTCCCAG
* *
18690175 ACATGGTCTTATACTAGTGCACATATCA
65 ACATGGTCTTACACTAGCGCACATATCA
18690203 CCCAAATGTT
Statistics
Matches: 202, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
143 93 0.46
144 109 0.54
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (142 bp):
CCGATGCCATGTTCCAAACATGGTCTTACACTAGCACACATATCATGCCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGTCCAGACATGGTCTTACACTAGCT
CTCACAACATGG
Found at i:18702911 original size:19 final size:20
Alignment explanation
Indices: 18702884--18702922 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18702874 AAATCGAGTT
*
18702884 TAGTCT-AAAATCCCATAAA
1 TAGTCTAAAAATCCAATAAA
*
18702903 TAGTTTAAAAATCCAATAAA
1 TAGTCTAAAAATCCAATAAA
18702923 GTCCATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
TAGTCTAAAAATCCAATAAA
Found at i:18706613 original size:16 final size:16
Alignment explanation
Indices: 18706558--18706614 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
18706548 AAAGACCAGA
18706558 TATTATTAAATTTAAAT
1 TATT-TTAAATTTAAAT
* * *
18706575 AATTTTGAATTTAATTT
1 TATTTTAAATTTAA-AT
* *
18706592 TTTTTTAAATTTAAGT
1 TATTTTAAATTTAAAT
18706608 TATTTTA
1 TATTTTA
18706615 GATTCAAGTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
TATTTTAAATTTAAAT
Found at i:18706939 original size:22 final size:23
Alignment explanation
Indices: 18706890--18706939 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 23
18706880 TATCTTACAA
18706890 GCTATAATGATTTACTATATTAT
1 GCTATAATGATTTACTATATTAT
18706913 G---TAAT-ATTATACTATA-TAT
1 GCTATAATGATT-TACTATATTAT
18706932 GCTATAAT
1 GCTATAAT
18706940 CTATCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
22 4 0.17
23 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (23 bp):
GCTATAATGATTTACTATATTAT
Found at i:18707531 original size:14 final size:13
Alignment explanation
Indices: 18707507--18707545 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
18707497 AATTTATTTT
18707507 TAATATATTAATA
1 TAATATATTAATA
*
18707520 TAAATATTTTAA-A
1 T-AATATATTAATA
18707533 TAATATATTAATA
1 TAATATATTAATA
18707546 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.41
13 4 0.18
14 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATTAATA
Found at i:18707534 original size:23 final size:22
Alignment explanation
Indices: 18707473--18707534 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 22
18707463 CATTCATTAT
18707473 TAAATATTTATAAAT-TCTAATA
1 TAAATATTT-TAAATATCTAATA
18707495 TAAATTTATTTTTAATATAT-TAATA
1 TAAA--TA-TTTTAA-ATATCTAATA
18707520 TAAATATTTTAAATA
1 TAAATATTTTAAATA
18707535 ATATATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
21 3 0.09
22 10 0.29
23 2 0.06
24 5 0.14
25 14 0.40
26 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATATTTTAAATATCTAATA
Found at i:18707542 original size:26 final size:26
Alignment explanation
Indices: 18707507--18707559 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
18707497 AATTTATTTT
18707507 TAATATATTAAT-ATAAATATTTTAAA
1 TAATATATTAATAAT-AATATTTTAAA
*
18707533 TAATATATTAATAATATTATTTTAAA
1 TAATATATTAATAATAATATTTTAAA
18707559 T
1 T
18707560 TTAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATATATTAATAATAATATTTTAAA
Found at i:18707660 original size:25 final size:23
Alignment explanation
Indices: 18707628--18707687 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
18707618 ACTAAAAATA
*
18707628 TATTATATTAATTATATTAATAATT
1 TATTATATTAATTAAATT--TAATT
18707653 TATTATATT-ATTAAATTTAATT
1 TATTATATTAATTAAATTTAATT
*
18707675 AATTA-ATTAATTA
1 TATTATATTAATTA
18707688 CGTATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 3 0.09
22 13 0.41
24 7 0.22
25 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATATTAATTAAATTTAATT
Found at i:18707678 original size:4 final size:4
Alignment explanation
Indices: 18707629--18707687 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
18707619 CTAAAAATAT
*
18707629 ATTA TATTA ATTA TATTA A-TA ATTT ATTA TATT- ATTAA ATTTA ATTA
1 ATTA -ATTA ATTA -ATTA ATTA ATTA ATTA -ATTA ATT-A A-TTA ATTA
18707676 ATTA ATTA ATTA
1 ATTA ATTA ATTA
18707688 CGTATAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
3 6 0.13
4 24 0.52
5 14 0.30
6 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
ATTA
Found at i:18707682 original size:30 final size:30
Alignment explanation
Indices: 18707626--18707687 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
18707616 TCACTAAAAA
* *
18707626 TATATTATATTAATTATATTAATAATTTAT
1 TATATTATATAAATTATATTAATAATTAAT
18707656 TATATTAT-TAAATT-TAATTAATTAATTAAT
1 TATATTATATAAATTAT-ATTAA-TAATTAAT
18707686 TA
1 TA
18707688 CGTATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 10 0.36
30 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATATTATATAAATTATATTAATAATTAAT
Found at i:18714778 original size:93 final size:93
Alignment explanation
Indices: 18714666--18714837 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
18714656 CGCCCATAAG
* *
18714666 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
18714731 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
18714759 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
18714824 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
18714838 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:18714834 original size:46 final size:46
Alignment explanation
Indices: 18714659--18714834 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
18714649 TGTAACCCGC
* * *
18714659 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
18714705 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
18714755 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
18714798 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
18714835 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:18719648 original size:63 final size:63
Alignment explanation
Indices: 18719529--18719650 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
18719519 TGGTAGGCCA
* * * * * *
18719529 TGTAACTTACTGTTTTAGAATTAGAGACACATGGGCTAGAGATACGGGTGCATGCCTAGATCG
1 TGTAACTCACTATTTTAGAATTAGAGACACACGGGCCAGAGACACGGGCGCATGCCTAGATCG
* * **
18719592 TGTAACTCACTATTTTGGAATTAGAGACACACGGGCCAGAGACATGGGCGTGTGCCTAG
1 TGTAACTCACTATTTTAGAATTAGAGACACACGGGCCAGAGACACGGGCGCATGCCTAG
18719651 GCCATGTGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (63 bp):
TGTAACTCACTATTTTAGAATTAGAGACACACGGGCCAGAGACACGGGCGCATGCCTAGATCG
Found at i:18722908 original size:13 final size:14
Alignment explanation
Indices: 18722882--18722909 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18722872 CTGCAAAAAG
18722882 TTAGGGGGATTTTT
1 TTAGGGGGATTTTT
18722896 TTAGGGGGATTTTT
1 TTAGGGGGATTTTT
18722910 CGTATGGATA
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:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (14 bp):
TTAGGGGGATTTTT
Found at i:18733931 original size:20 final size:19
Alignment explanation
Indices: 18733910--18733958 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
18733900 TTTAAAAATA
*
18733910 TATAAAT-TTTAGAATTTC
1 TATAAATATTTTGAATTTC
18733928 TATAAATATTTTGAATTT-
1 TATAAATATTTTGAATTTC
*
18733946 TAAAAATTATTTT
1 TATAAA-TATTTT
18733959 CAAATTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTGAATTTC
Found at i:18733952 original size:18 final size:21
Alignment explanation
Indices: 18733915--18733975 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
18733905 AAATATATAA
*
18733915 ATTTTAGAATTTCTATAAA-T
1 ATTTTAGAATTTCTAAAAATT
18733935 ATTTT-GAATTT-TAAAAATT
1 ATTTTAGAATTTCTAAAAATT
* *
18733954 ATTTTCA-AATTTTTGAAAATT
1 ATTTT-AGAATTTCTAAAAATT
18733975 A
1 A
18733976 CTTTGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 5 0.14
19 12 0.34
20 10 0.29
21 8 0.23
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTTAGAATTTCTAAAAATT
Found at i:18734394 original size:8 final size:8
Alignment explanation
Indices: 18734381--18734415 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
18734371 GACGTTCTCC
18734381 TTTTTCTT
1 TTTTTCTT
18734389 TTTTTCTT
1 TTTTTCTT
*
18734397 TTTTGCTT
1 TTTTTCTT
*
18734405 TTGTTCTT
1 TTTTTCTT
18734413 TTT
1 TTT
18734416 GGCTTCTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:18734405 original size:16 final size:16
Alignment explanation
Indices: 18734381--18734420 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
18734371 GACGTTCTCC
*
18734381 TTTTT-CTTTTTTTCT
1 TTTTTGCTTTTGTTCT
18734396 TTTTTGCTTTTGTTCT
1 TTTTTGCTTTTGTTCT
*
18734412 TTTTGGCTT
1 TTTTTGCTT
18734421 CTTCTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTTTGTTCT
Found at i:18736602 original size:19 final size:18
Alignment explanation
Indices: 18736568--18736603 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18736558 TCTCTAGATG
18736568 TTTTCCTTTTTTCTTTTC
1 TTTTCCTTTTTTCTTTTC
*
18736586 TTTTGCTTTTGTTCTTTT
1 TTTTCCTTTT-TTCTTTT
18736604 TGGCTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (18 bp):
TTTTCCTTTTTTCTTTTC
Found at i:18737186 original size:21 final size:21
Alignment explanation
Indices: 18737160--18737200 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18737150 GATCCTTCAC
*
18737160 GGGCGTGTGTTATGGACACAT
1 GGGCGTATGTTATGGACACAT
*
18737181 GGGCGTATGTTATGGTCACA
1 GGGCGTATGTTATGGACACA
18737201 CAGCCGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.37, T:0.29
Consensus pattern (21 bp):
GGGCGTATGTTATGGACACAT
Found at i:18737303 original size:21 final size:21
Alignment explanation
Indices: 18737279--18737331 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
18737269 AGGGATCCTT
18737279 CACGAGCGTGTGTTATGGTCA
1 CACGAGCGTGTGTTATGGTCA
* *
18737300 CACGGGCGTATGTTATGGTCA
1 CACGAGCGTGTGTTATGGTCA
18737321 CAC-AGCCGTGT
1 CACGAG-CGTGT
18737332 CTAGGGGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (21 bp):
CACGAGCGTGTGTTATGGTCA
Found at i:18737340 original size:122 final size:122
Alignment explanation
Indices: 18737118--18737366 Score: 437
Period size: 122 Copynumber: 2.0 Consensus size: 122
18737108 ATTTGGTGCT
* * *
18737118 ACACGGCCGTGTGGCTAATTTGGAGATTTAGGGATCCTTCACGGGCGTGTGTTATGGACACATGG
1 ACACGACCGTGTGGCTAATTTGGAGATTTAGGGATCCTTCACGAGCGTGTGTTATGGACACACGG
18737183 GCGTATGTTATGGTCACACAGCCGTGTCTGAGGGGCACACAGACATGTGAGACCTTC
66 GCGTATGTTATGGTCACACAGCCGTGTCTGAGGGGCACACAGACATGTGAGACCTTC
*
18737240 ACACGACCGTGTGGCTAATTTGGAGATTTAGGGATCCTTCACGAGCGTGTGTTATGGTCACACGG
1 ACACGACCGTGTGGCTAATTTGGAGATTTAGGGATCCTTCACGAGCGTGTGTTATGGACACACGG
*
18737305 GCGTATGTTATGGTCACACAGCCGTGTCT-AGGGGGCACACAGACGTGTGAGACCTTC
66 GCGTATGTTATGGTCACACAGCCGTGTCTGA-GGGGCACACAGACATGTGAGACCTTC
18737362 ACACG
1 ACACG
18737367 GCCATGTCTA
Statistics
Matches: 121, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
121 1 0.01
122 120 0.99
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (122 bp):
ACACGACCGTGTGGCTAATTTGGAGATTTAGGGATCCTTCACGAGCGTGTGTTATGGACACACGG
GCGTATGTTATGGTCACACAGCCGTGTCTGAGGGGCACACAGACATGTGAGACCTTC
Found at i:18744549 original size:30 final size:30
Alignment explanation
Indices: 18744514--18744587 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
18744504 GAAAAAATGA
*
18744514 GTAAATTAGCCCCTATACATTTTGAAACAT
1 GTAAATTAGCCCCTATACATTTCGAAACAT
* *
18744544 GTAAATTATCCCTTATACATTTCGAAACAT
1 GTAAATTAGCCCCTATACATTTCGAAACAT
*
18744574 GCAAATTAGCCCCT
1 GTAAATTAGCCCCT
18744588 CGTTAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (30 bp):
GTAAATTAGCCCCTATACATTTCGAAACAT
Found at i:18749159 original size:14 final size:14
Alignment explanation
Indices: 18749136--18749165 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18749126 ATTTAATAAA
18749136 TAAAAATAAAAATC
1 TAAAAATAAAAATC
*
18749150 TAAAAGTAAAAATC
1 TAAAAATAAAAATC
18749164 TA
1 TA
18749166 CTAAAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAAATAAAAATC
Found at i:18750052 original size:2 final size:2
Alignment explanation
Indices: 18750039--18750069 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18750029 CATAAAACTA
*
18750039 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18750070 AAAGAGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18750497 original size:12 final size:11
Alignment explanation
Indices: 18750468--18750501 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
18750458 TTGTACCAAT
18750468 ATTTTATTTAA
1 ATTTTATTTAA
*
18750479 TTTTTATTATAA
1 ATTTTATT-TAA
18750491 ATTTTATTTAA
1 ATTTTATTTAA
18750502 CAAGTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATTTAA
Found at i:18750588 original size:19 final size:21
Alignment explanation
Indices: 18750549--18750594 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
18750539 ATGAAAATTG
18750549 TTTAATATTATAAATATGTAT
1 TTTAATATTATAAATATGTAT
18750570 TTTAATATTAT-AA-ATGTAT
1 TTTAATATTATAAATATGTAT
18750589 TTTAAT
1 TTTAAT
18750595 TAATTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.48
20 2 0.08
21 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAATATTATAAATATGTAT
Found at i:18750604 original size:23 final size:22
Alignment explanation
Indices: 18750549--18750606 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 22
18750539 ATGAAAATTG
18750549 TTTAATATTATA-AATATGTAT
1 TTTAATATTATATAATATGTAT
18750570 TTTAATA-T-TATAA-ATGTAT
1 TTTAATATTATATAATATGTAT
18750589 TTTAATTAATTATATAAT
1 TTTAA-T-ATTATATAAT
18750607 TTTTTCTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 8 0.26
22 1 0.03
23 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTAATATTATATAATATGTAT
Found at i:18753046 original size:17 final size:17
Alignment explanation
Indices: 18753026--18753160 Score: 56
Period size: 17 Copynumber: 7.5 Consensus size: 17
18753016 ATTTCAAGAC
18753026 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
18753043 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
* * *
18753062 CT-TGTAATGTTTTAAA
1 TTATGTAATATTTTTAA
* **
18753078 TTATGTAGTGATTCATAGA
1 TTATGTAAT-ATTTTTA-A
18753097 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ***
18753115 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
*
18753134 CTTATGTAATGTTTTTAA
1 -TTATGTAATATTTTTAA
18753152 TTATGTAAT
1 TTATGTAAT
18753161 GATTCAATTC
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
16 2 0.02
17 34 0.41
18 18 0.22
19 12 0.15
20 16 0.20
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.48
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:18753080 original size:35 final size:37
Alignment explanation
Indices: 18753021--18753167 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
18753011 TGTTAATTTC
18753021 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
* *
18753058 AAGAC-T-TGTAATGTTTTAAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
*
18753093 TAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
* *
18753130 AAGACTTATGTAATGTTTTTAATTATGTAATGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
18753167 A
1 A
18753168 TTCGGGTATT
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
35 31 0.31
36 2 0.02
37 67 0.67
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:18753102 original size:72 final size:73
Alignment explanation
Indices: 18753018--18753167 Score: 259
Period size: 72 Copynumber: 2.1 Consensus size: 73
18753008 ATGTGTTAAT
18753018 TTCAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGAC-T-TGTAATGTTTTAAATTA
1 TTCAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATGTAATGTTTTAAATTA
*
18753081 TGTAGTGA
66 TGTAATGA
*
18753089 TTCATAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATGTAATGTTTTTAATT
1 TTCA-AGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATGTAATGTTTTAAATT
18753154 ATGTAATGA
65 ATGTAATGA
18753163 TTCAA
1 TTCAA
18753168 TTCGGGTATT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
71 4 0.05
72 41 0.55
73 2 0.03
74 27 0.36
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (73 bp):
TTCAAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATGTAATGTTTTAAATTA
TGTAATGA
Found at i:18753103 original size:20 final size:20
Alignment explanation
Indices: 18753078--18753141 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
18753068 ATGTTTTAAA
18753078 TTATGTAGTGATTCATAGAC
1 TTATGTAGTGATTCATAGAC
* **
18753098 TTATGTAAT-ATTTTTA-A-
1 TTATGTAGTGATTCATAGAC
*
18753115 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCATAGAC
18753135 TTATGTA
1 TTATGTA
18753142 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (20 bp):
TTATGTAGTGATTCATAGAC
Found at i:18753161 original size:17 final size:17
Alignment explanation
Indices: 18753064--18753161 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
18753054 TTCAAAGACT
*
18753064 TGTAATGTTTTAAATTA
1 TGTAATGTTTTTAATTA
* **
18753081 TGTAGTGATTCATAGACTTA
1 TGTAATG-TTTTTA-A-TTA
*
18753101 TGTAATATTTTTAATTA
1 TGTAATGTTTTTAATTA
* ***
18753118 TGTAGTGATTCAAAGACTTA
1 TGTAATG-TTTTTA-A-TTA
18753138 TGTAATGTTTTTAATTA
1 TGTAATGTTTTTAATTA
18753155 TGTAATG
1 TGTAATG
18753162 ATTCAATTCG
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 24 0.41
18 8 0.14
19 9 0.16
20 17 0.29
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (17 bp):
TGTAATGTTTTTAATTA
Found at i:18753189 original size:9 final size:9
Alignment explanation
Indices: 18753166--18753240 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
18753156 GTAATGATTC
*
18753166 AATTCGGGT
1 AATTCGGTT
18753175 -ATTCGGTT
1 AATTCGGTT
18753183 AATTCGGTT
1 AATTCGGTT
*
18753192 AATCCGGTT
1 AATTCGGTT
18753201 AATTCGGTT
1 AATTCGGTT
18753210 AATTCGGTT
1 AATTCGGTT
* *
18753219 AACTCGTTT
1 AATTCGGTT
18753228 AATTCGGTT
1 AATTCGGTT
18753237 AATT
1 AATT
18753241 TTTAATCACA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
8 7 0.12
9 51 0.88
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:18754914 original size:21 final size:21
Alignment explanation
Indices: 18754890--18754930 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18754880 GACTGAATTT
*
18754890 GAGACCTCCAATTTTGACCAA
1 GAGACCCCCAATTTTGACCAA
18754911 GAGACCCCCAATTTTGACCA
1 GAGACCCCCAATTTTGACCA
18754931 TACTCAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.22
Consensus pattern (21 bp):
GAGACCCCCAATTTTGACCAA
Found at i:18756621 original size:16 final size:16
Alignment explanation
Indices: 18756600--18756632 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18756590 TTTTATCAAC
18756600 AATTTGAA-ATTTTGAA
1 AATTTGAAGA-TTTGAA
18756616 AATTTGAAGATTTGAA
1 AATTTGAAGATTTGAA
18756632 A
1 A
18756633 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
AATTTGAAGATTTGAA
Found at i:18757863 original size:14 final size:14
Alignment explanation
Indices: 18757844--18757872 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18757834 TCTTGAGGAA
18757844 GAAAATAGTAGTAG
1 GAAAATAGTAGTAG
18757858 GAAAATAGTAGTAG
1 GAAAATAGTAGTAG
18757872 G
1 G
18757873 GGTGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (14 bp):
GAAAATAGTAGTAG
Found at i:18762512 original size:16 final size:16
Alignment explanation
Indices: 18762491--18762533 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
18762481 GTAGATCGGT
18762491 AAAAGCCGAAATGCCA
1 AAAAGCCGAAATGCCA
*
18762507 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCA
*
18762523 AAAAGCTGAAA
1 AAAAGCCGAAA
18762534 GTTTGACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:18762533 original size:8 final size:8
Alignment explanation
Indices: 18762491--18762533 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
18762481 GTAGATCGGT
18762491 AAAAGCCG
1 AAAAGCCG
* *
18762499 AAATGCCA
1 AAAAGCCG
18762507 AAAAGCCG
1 AAAAGCCG
*
18762515 AAATGCCG
1 AAAAGCCG
*
18762523 AAAAGCTG
1 AAAAGCCG
18762531 AAA
1 AAA
18762534 GTTTGACTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:18762827 original size:28 final size:28
Alignment explanation
Indices: 18762746--18762835 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 28
18762736 TGAGCATGAC
*
18762746 TATAAATGTGAATCGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
*
18762775 TATAAATGTGGTTTGGGCCTAGTGGGCCA
1 TATAAATGT-GATTGGGCCTAGTGGGCCA
*
18762804 TATAAATGTGATTGGGCCTAGTGGGTCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
18762832 TATA
1 TATA
18762836 CAGGTATGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
28 21 0.38
29 32 0.58
30 2 0.04
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:18764676 original size:39 final size:39
Alignment explanation
Indices: 18764622--18764702 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
18764612 AGTCTTTTAA
* *
18764622 AAATGCTATGTGATTATATGAGTATTGTGATATATGCTT
1 AAATGCTATGCGATTATATGAGTAATGTGATATATGCTT
* *
18764661 AAATGTTATGCGATTATATGTGTAATGTGATATATGCTT
1 AAATGCTATGCGATTATATGAGTAATGTGATATATGCTT
18764700 AAA
1 AAA
18764703 AGTGAATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (39 bp):
AAATGCTATGCGATTATATGAGTAATGTGATATATGCTT
Found at i:18779119 original size:37 final size:37
Alignment explanation
Indices: 18779069--18779142 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
18779059 AAGTACAAAT
18779069 TTACCATATATGAATATATAATTTCATTGTTTAGATA
1 TTACCATATATGAATATATAATTTCATTGTTTAGATA
18779106 TTACCATATATGAATATATAATTTCATTGTTTAGATA
1 TTACCATATATGAATATATAATTTCATTGTTTAGATA
18779143 AGGACTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (37 bp):
TTACCATATATGAATATATAATTTCATTGTTTAGATA
Found at i:18780069 original size:10 final size:10
Alignment explanation
Indices: 18780039--18780077 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
18780029 TTAATTTTAA
18780039 AAAAAATATTT
1 AAAAAAT-TTT
18780050 AACAATAATTTT
1 AA-AA-AATTTT
18780062 AAAAAATTTT
1 AAAAAATTTT
18780072 AAAAAA
1 AAAAAA
18780078 ATCTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 12 0.46
11 4 0.15
12 7 0.27
13 3 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:18780076 original size:11 final size:11
Alignment explanation
Indices: 18780031--18780086 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
18780021 ATATCATTTT
18780031 AATTTTAAAAAA
1 AATTTT-AAAAA
*
18780043 AATATTTAACAAT
1 AAT-TTTAA-AAA
18780056 AATTTT-AAAA
1 AATTTTAAAAA
18780066 AATTTTAAAAA
1 AATTTTAAAAA
*
18780077 AATCTTAAAA
1 AATTTTAAAA
18780087 TATTATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.21
11 14 0.37
12 8 0.21
13 8 0.21
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTTTAAAAA
Found at i:18780084 original size:21 final size:21
Alignment explanation
Indices: 18780039--18780095 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
18780029 TTAATTTTAA
* *
18780039 AAAAAATATTTAACAATAATTTT
1 AAAAAAT-TTTAA-AAAAATCTT
18780062 AAAAAATTTTAAAAAAATCTT
1 AAAAAATTTTAAAAAAATCTT
* *
18780083 AAAATATTATAAA
1 AAAAAATTTTAAA
18780096 TTATTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 5 0.17
23 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATTTTAAAAAAATCTT
Found at i:18780115 original size:19 final size:18
Alignment explanation
Indices: 18780081--18780118 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
18780071 TAAAAAAATC
*
18780081 TTAAAATATTATAAATTA
1 TTAAAATATTAAAAATTA
18780099 TTAAAACTATTAAAAATTA
1 TTAAAA-TATTAAAAATTA
18780118 T
1 T
18780119 GTTAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAATATTAAAAATTA
Found at i:18785604 original size:27 final size:27
Alignment explanation
Indices: 18785574--18785849 Score: 270
Period size: 27 Copynumber: 10.3 Consensus size: 27
18785564 GGGCATAATC
* *
18785574 GTCATTTTACTATACATGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* * * *
18785601 GTCATTTTACCATATAGGGGCATCACA
1 GTCATTTTACCATACAGGGGTATTACG
*
18785628 GTCATTTTACCATTCAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* * * *
18785655 ATCATTTTA-GACTACAGGGGCATTAGG
1 GTCATTTTACCA-TACAGGGGTATTACG
* * *
18785682 GTCATTTTACCCTACAGGGGCA-TAGG
1 GTCATTTTACCATACAGGGGTATTACG
* *
18785708 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
18785735 GTCATTTTACCCTACGGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
18785762 GTTATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
18785789 ATCATTTTATCC-TACAGGGGTATTACA
1 GTCATTTTA-CCATACAGGGGTATTACG
* * * * *
18785816 GTTATTTTACCCTATAAGGGTATTACA
1 GTCATTTTACCATACAGGGGTATTACG
18785843 GTCATTT
1 GTCATTT
18785850 ATTACGGTCA
Statistics
Matches: 212, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 29 0.14
27 181 0.85
28 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:18785632 original size:54 final size:54
Alignment explanation
Indices: 18785574--18785849 Score: 304
Period size: 54 Copynumber: 5.1 Consensus size: 54
18785564 GGGCATAATC
** * * * *
18785574 GTCATTTTACTATACATGGGTATTACGGTCATTTTACCATATAGGGGCATCACA
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
* * * ** **
18785628 GTCATTTTACCATTCAGGGGTATTACGATCATTTTAGACTACAGGGGCATTAGG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
* * *
18785682 GTCATTTTACCCTACAGGGGCA-TAGGGTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
* * *
18785735 GTCATTTTACCCTACGGGGGTATTACGGTTATTTTACCCTACAGGGGTATTAC-
1 GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
* * * * * *
18785788 GATCATTTTATCCTACAGGGGTATTACAGTTATTTTACCCTATAAGGGTATTACA
1 G-TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
18785843 GTCATTT
1 GTCATTT
18785850 ATTACGGTCA
Statistics
Matches: 190, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 47 0.25
54 142 0.75
55 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (54 bp):
GTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACA
Found at i:18785879 original size:27 final size:27
Alignment explanation
Indices: 18785849--18786048 Score: 310
Period size: 27 Copynumber: 7.4 Consensus size: 27
18785839 TACAGTCATT
18785849 TATTACGGTCATTTTACCCTATAGGGG
1 TATTACGGTCATTTTACCCTATAGGGG
* *
18785876 TATTACGGCCATTTTACCCTACAGGGG
1 TATTACGGTCATTTTACCCTATAGGGG
* *
18785903 TATTACGGTCATTTTACCCTACAGAGG
1 TATTACGGTCATTTTACCCTATAGGGG
*
18785930 AATTACGGTCATTTTACCCTATAGGGG
1 TATTACGGTCATTTTACCCTATAGGGG
* *
18785957 TATTACGATCATTTTACCCTATAGAGG
1 TATTACGGTCATTTTACCCTATAGGGG
* *
18785984 CATTACGGTCATTCTACCCTATAGGGG
1 TATTACGGTCATTTTACCCTATAGGGG
*
18786011 TATTACGGTCATATTACCCTATAGGGG
1 TATTACGGTCATTTTACCCTATAGGGG
18786038 TATTACGGTCA
1 TATTACGGTCA
18786049 AATAAATACC
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 156 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
TATTACGGTCATTTTACCCTATAGGGG
Found at i:18785889 original size:40 final size:40
Alignment explanation
Indices: 18785809--18785889 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
18785799 CCTACAGGGG
* *
18785809 TATTACAGTTATTTTACCCTATAAGGGTATTACAGTCATT
1 TATTACAGTCATTTTACCCTATAAGGGTATTACAGCCATT
* * *
18785849 TATTACGGTCATTTTACCCTATAGGGGTATTACGGCCATT
1 TATTACAGTCATTTTACCCTATAAGGGTATTACAGCCATT
18785889 T
1 T
18785890 TACCCTACAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (40 bp):
TATTACAGTCATTTTACCCTATAAGGGTATTACAGCCATT
Found at i:18785890 original size:67 final size:67
Alignment explanation
Indices: 18785782--18785916 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
18785772 CCTACAGGGG
* ** *
18785782 TATTACGATCATTTTATCCTACAGGGGTATTACAGTTATTTTACCCTATAAGGGTATTACAGTCA
1 TATTACGATCATTTTACCCTACAGGGGTATTACAGCCATTTTACCCTACAAGGGTATTACAGTCA
18785847 TT
66 TT
* * * * *
18785849 TATTACGGTCATTTTACCCTATAGGGGTATTACGGCCATTTTACCCTACAGGGGTATTACGGTCA
1 TATTACGATCATTTTACCCTACAGGGGTATTACAGCCATTTTACCCTACAAGGGTATTACAGTCA
18785914 TT
66 TT
18785916 T
1 T
18785917 TACCCTACAG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (67 bp):
TATTACGATCATTTTACCCTACAGGGGTATTACAGCCATTTTACCCTACAAGGGTATTACAGTCA
TT
Found at i:18785944 original size:121 final size:121
Alignment explanation
Indices: 18785729--18785970 Score: 369
Period size: 121 Copynumber: 2.0 Consensus size: 121
18785719 CTACAGGGGC
* **
18785729 ATTACGGTCATTTTACCCTACGGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATCAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGCCATTTTACCCTACAGGGGTATTACGATCAT
* * * *
18785794 TTTATCCTACAGGGGTATTACAGTTATTTTACCCTATAAGGGTATTAC-AGTCATTT
66 TTTACCCTACAGAGGAATTACAGTCATTTTACCCTATAAGGGTATTACGA-TCATTT
* *
18785850 ATTACGGTCATTTTACCCTATAGGGGTATTACGGCCATTTTACCCTACAGGGGTATTACGGTCAT
1 ATTACGGTCATTTTACCCTACAGGGGTATTACGGCCATTTTACCCTACAGGGGTATTACGATCAT
* *
18785915 TTTACCCTACAGAGGAATTACGGTCATTTTACCCTATAGGGGTATTACGATCATTT
66 TTTACCCTACAGAGGAATTACAGTCATTTTACCCTATAAGGGTATTACGATCATTT
18785971 TACCCTATAG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 108 0.99
122 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (121 bp):
ATTACGGTCATTTTACCCTACAGGGGTATTACGGCCATTTTACCCTACAGGGGTATTACGATCAT
TTTACCCTACAGAGGAATTACAGTCATTTTACCCTATAAGGGTATTACGATCATTT
Found at i:18789678 original size:28 final size:28
Alignment explanation
Indices: 18789646--18789700 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
18789636 TAGTATAGTC
* *
18789646 TAGGCCTTAGCCCTATACAGTAACAGTG
1 TAGGCCTAAGCCCAATACAGTAACAGTG
* *
18789674 TAGGCCTAAGCCCAATGCAGTATCAGT
1 TAGGCCTAAGCCCAATACAGTAACAGT
18789701 TCAGTGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (28 bp):
TAGGCCTAAGCCCAATACAGTAACAGTG
Found at i:18790132 original size:27 final size:27
Alignment explanation
Indices: 18790102--18790457 Score: 478
Period size: 27 Copynumber: 13.1 Consensus size: 27
18790092 AAAGGTATTC
*
18790102 CGGTTATTTTACCCTACAGGGGCATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
* * *
18790129 CGGTCATTTCACCCTTCAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
* * * *
18790156 CAGTCATTGTACCCTATAGGGACATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
*
18790183 GGGTCATTTTTACCCTACAGGGGCATTA
1 CGGTCA-TTTTACCCTACAGGGGCATTA
* * * *
18790211 CAGTCATTTTACCCTACAAGGGTATGA
1 CGGTCATTTTACCCTACAGGGGCATTA
* *
18790238 CGGTCATTTTACACTACAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
* *
18790265 CGGTCATTTTACCCTATAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
** *
18790292 CAATCATTTTACCCTACAGGGGCGTTA
1 CGGTCATTTTACCCTACAGGGGCATTA
* *
18790319 CGGTCATTTTACCCTACAGAGACATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
18790346 CGGTCATTTTACCCTACAGGGGCATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
18790373 CGGTCATTTTACCCTACAGGGGCATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
* *
18790400 CGGTTATTTTACCCTACAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
*
18790427 CGGTCATTTTACCCTACAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGCATTA
18790454 CGGT
1 CGGT
18790458 TAAATAAAGA
Statistics
Matches: 286, Mismatches: 42, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
27 264 0.92
28 22 0.08
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (27 bp):
CGGTCATTTTACCCTACAGGGGCATTA
Found at i:18799319 original size:14 final size:15
Alignment explanation
Indices: 18799293--18799321 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18799283 TTGCAAGTAT
18799293 CTACATAACTTGCTC
1 CTACATAACTTGCTC
18799308 CTACAT-ACTTGCTC
1 CTACATAACTTGCTC
18799322 TAGAAGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (15 bp):
CTACATAACTTGCTC
Found at i:18800856 original size:25 final size:24
Alignment explanation
Indices: 18800823--18800875 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
18800813 ATTAAAGGAG
* * *
18800823 AAATTAAATCAATTTGATTAAAAT
1 AAATCAAATCAATTGGAATAAAAT
*
18800847 CAAATCAAATTAATTGGAATAAAAT
1 -AAATCAAATCAATTGGAATAAAAT
18800872 AAAT
1 AAAT
18800876 TAGGATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATCAAATCAATTGGAATAAAAT
Found at i:18801358 original size:9 final size:9
Alignment explanation
Indices: 18801344--18801390 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
18801334 AAACAAATTC
18801344 AAAAATATT
1 AAAAATATT
*
18801353 AAAAATAAAT
1 AAAAAT-ATT
*
18801363 ATAAATTATT
1 A-AAAATATT
18801373 AAAAATATT
1 AAAAATATT
18801382 AAAAA-ATT
1 AAAAATATT
18801390 A
1 A
18801391 TGTTAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 4 0.12
9 18 0.56
10 6 0.19
11 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATATT
Found at i:18801388 original size:20 final size:20
Alignment explanation
Indices: 18801344--18801414 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
18801334 AAACAAATTC
18801344 AAAAA-TATTAAAAATA--A
1 AAAAATTATTAAAAATATTA
18801361 ATATAAATTATTAAAAATATTA
1 A-A-AAATTATTAAAAATATTA
18801383 AAAAATTATGTTAAAATATATTTA
1 AAAAATTA--TTAAAA-ATA-TTA
18801407 AAAAATTA
1 AAAAATTA
18801415 ATATATAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 3 0.07
20 17 0.38
21 1 0.02
22 8 0.18
23 3 0.07
24 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAAATTATTAAAAATATTA
Found at i:18801403 original size:23 final size:23
Alignment explanation
Indices: 18801371--18801465 Score: 77
Period size: 24 Copynumber: 3.9 Consensus size: 23
18801361 ATATAAATTA
18801371 TTAAAAATA-TTAAAAAATTATG
1 TTAAAAATATTTAAAAAATTATG
*
18801393 TTAAAATATATTTAAAAAATTAATA
1 TTAAAA-ATATTTAAAAAATT-ATG
*
18801418 TATAAAACAAAATTCT-AAAAATATATG
1 T-T-AAA-AATATT-TAAAAAAT-TATG
* *
18801445 TAAAAAATCTTTAAAAAATTA
1 TTAAAAATATTTAAAAAATTA
18801466 CAAAAAAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
22 6 0.10
23 6 0.10
24 20 0.34
25 6 0.10
26 1 0.02
27 16 0.28
28 3 0.05
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (23 bp):
TTAAAAATATTTAAAAAATTATG
Found at i:18809994 original size:23 final size:23
Alignment explanation
Indices: 18809968--18810030 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
18809958 CGTATACTGT
18809968 TATTAGCAGCTCTACTGCGTTAC
1 TATTAGCAGCTCTACTGCGTTAC
*
18809991 TATTAGCAGCTCTGCTGCGTTAC
1 TATTAGCAGCTCTACTGCGTTAC
* *
18810014 TGTTAGCAGCTTTACTG
1 TATTAGCAGCTCTACTG
18810031 TGATATTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.37
Consensus pattern (23 bp):
TATTAGCAGCTCTACTGCGTTAC
Found at i:18811950 original size:48 final size:48
Alignment explanation
Indices: 18811885--18812111 Score: 225
Period size: 48 Copynumber: 4.8 Consensus size: 48
18811875 GTTATGTGTA
* * *
18811885 ATCCCATGTAAGACCATGTTTGGAACATGGGATTGGCATCGATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
* *
18811933 ATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATCGATATTTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
* * * *
18811981 ATCCCATATAAGACCATATCTGGGATATGGCATTGGCATCGATATGAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
*** * * * *
18812029 A-CATTGTGTAAGACCATAG-CTGGG-C-T---ATCGGCTTCGATCTATG
1 ATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGTG
* *
18812072 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
18812112 TTACTATGGG
Statistics
Matches: 142, Mismatches: 28, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
43 29 0.20
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 109 0.77
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
Found at i:18813991 original size:84 final size:84
Alignment explanation
Indices: 18813843--18814066 Score: 430
Period size: 84 Copynumber: 2.7 Consensus size: 84
18813833 TAATTGAAAT
*
18813843 ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTATGTGGAAATT
1 ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTATGTGAAAATT
18813908 TGGTTATTATTGAGTCCAC
66 TGGTTATTATTGAGTCCAC
*
18813927 ATATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTATGTGAAAATT
1 ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTATGTGAAAATT
18813992 TGGTTATTATTGAGTCCAC
66 TGGTTATTATTGAGTCCAC
18814011 ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTAT
1 ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTAT
18814067 ATGGAAAGTA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 137 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (84 bp):
ACATGGGTATGATTTGTATATGTTATATGAATTCATGATGTGGAAAGTATATGTATGTGAAAATT
TGGTTATTATTGAGTCCAC
Found at i:18817020 original size:90 final size:90
Alignment explanation
Indices: 18816898--18817146 Score: 295
Period size: 90 Copynumber: 2.8 Consensus size: 90
18816888 AATATGCTAG
* ** *
18816898 CAGAAGGTTGTGAATGCACAAAATATTCGTAGATAAGAGCTACCAAAAAATAGGTGGATGAACCA
1 CAGATGGTTGTGAATGCACAACGTATTTGTAGATAAGAGCTACCAAAAAATAGGTGGATGAACCA
*
18816963 CCAATGTTGTAGGTTAATACACTGC
66 CCAATGTTGCAGGTTAATACACTGC
* * *
18816988 CAGATGGTTGAGAATGCACAACGTATTTGTAGATAAGAGCTGCCAAAAAATGGGTGGATGAACCA
1 CAGATGGTTGTGAATGCACAACGTATTTGTAGATAAGAGCTACCAAAAAATAGGTGGATGAACCA
* * * *
18817053 TCAGTGTTGCAGTTTAATACGCTGC
66 CCAATGTTGCAGGTTAATACACTGC
* * * * ** *
18817078 CAGATGGTTGTGAATGAACAACGCATTT-TCATATAAGAGCTA-CAAGAAAGTTTGTGGATTAAC
1 CAGATGGTTGTGAATGCACAACGTATTTGT-AGATAAGAGCTACCAA-AAAATAGGTGGATGAAC
18817141 CACCAA
64 CACCAA
18817147 AGCTGCAGAT
Statistics
Matches: 134, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
89 4 0.03
90 130 0.97
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (90 bp):
CAGATGGTTGTGAATGCACAACGTATTTGTAGATAAGAGCTACCAAAAAATAGGTGGATGAACCA
CCAATGTTGCAGGTTAATACACTGC
Found at i:18826556 original size:19 final size:19
Alignment explanation
Indices: 18826532--18826573 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18826522 GAGAGCAGGG
*
18826532 GAAAGAAAGAAGGAAGGAA
1 GAAAGAAAGAAAGAAGGAA
18826551 GAAAGAAAGAAAGAAGGAA
1 GAAAGAAAGAAAGAAGGAA
18826570 -AAAG
1 GAAAG
18826574 GGAAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAAGAAGGAA
Found at i:18827802 original size:170 final size:172
Alignment explanation
Indices: 18827513--18827858 Score: 579
Period size: 170 Copynumber: 2.0 Consensus size: 172
18827503 CAGGGATATC
*
18827513 CCGACTGTGTGTCAATGAGACACTATATGTGTCGACTACTGCGACTGCTCCGGATTCGTTCCGAA
1 CCGACTGTGTGTCAATGAGACACTATATGTGTCGACTACTGCGACTGCTCCGGATTCATTCCGAA
* * * *
18827578 GAGGTACTCTGTACCTGACTGTTACTGTTACTATTCCGGATTTGTTCTGATGAGGTACTTTGTGT
66 GAGATACTCCGTACCTGACTGTTACTGTTACTATTCCAGATTTGTTCCGATGAGGTACTTTGTGT
18827643 A-AC-GCTACTGTTATTGTTACTGTTACCCTTACGGTGTATT
131 AGACTGCTACTGTTATTGTTACTGTTACCCTTACGGTGTATT
*
18827683 CCGACTGTGTGTCGATGAGACACTATATGTGTCGACTACTGCGACTGCTCCGGATTCATTCCGAA
1 CCGACTGTGTGTCAATGAGACACTATATGTGTCGACTACTGCGACTGCTCCGGATTCATTCCGAA
18827748 GAGATACTCCGTACCTGACTGTTACTGTTACTATTCCAGATTTGTTCCGATGAGGTACTTTGTGT
66 GAGATACTCCGTACCTGACTGTTACTGTTACTATTCCAGATTTGTTCCGATGAGGTACTTTGTGT
*
18827813 AGCGGTACTGTTACTGTTATTGTTACTGTTACCCTTACGGTGTATT
131 A---G-ACTGCTACTGTTATTGTTACTGTTACCCTTACGGTGTATT
18827859 TCGGCTTAGG
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
170 125 0.77
175 2 0.01
176 36 0.22
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (172 bp):
CCGACTGTGTGTCAATGAGACACTATATGTGTCGACTACTGCGACTGCTCCGGATTCATTCCGAA
GAGATACTCCGTACCTGACTGTTACTGTTACTATTCCAGATTTGTTCCGATGAGGTACTTTGTGT
AGACTGCTACTGTTATTGTTACTGTTACCCTTACGGTGTATT
Found at i:18833051 original size:19 final size:19
Alignment explanation
Indices: 18833027--18833068 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18833017 GAGAGCAGGG
*
18833027 GAAAGAAAGAAGGAAGGAA
1 GAAAGAAAGAAAGAAGGAA
18833046 GAAAGAAAGAAAGAAGGAA
1 GAAAGAAAGAAAGAAGGAA
18833065 -AAAG
1 GAAAG
18833069 GGAAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAAGAAGGAA
Found at i:18839182 original size:19 final size:19
Alignment explanation
Indices: 18839158--18839197 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18839148 ACAGAGAGCA
* *
18839158 GAGGAACGAAAGAAGGAAG
1 GAGGAAAGAAAGAAAGAAG
18839177 GAGGAAAGAAAGAAAGAAG
1 GAGGAAAGAAAGAAAGAAG
18839196 GA
1 GA
18839198 AAAAGGGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (19 bp):
GAGGAAAGAAAGAAAGAAG
Found at i:18840288 original size:6 final size:6
Alignment explanation
Indices: 18840277--18840315 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
18840267 TGTGTAACGC
*
18840277 TACTGT TACTGT TACTGT TACTGT TACTGT TATTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
18840316 CCTTACGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
TACTGT
Found at i:18840321 original size:18 final size:18
Alignment explanation
Indices: 18840282--18840321 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18840272 AACGCTACTG
**
18840282 TTACTGTTACTGTTACTG
1 TTACTGTTACTGTTACCC
*
18840300 TTACTGTTATTGTTACCC
1 TTACTGTTACTGTTACCC
18840318 TTAC
1 TTAC
18840322 GGTGTATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.50
Consensus pattern (18 bp):
TTACTGTTACTGTTACCC
Found at i:18842548 original size:25 final size:24
Alignment explanation
Indices: 18842511--18842557 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
18842501 AAATTTCAAT
* *
18842511 TTTATTTAATTATTTAATTTTTTTA
1 TTTATTGAATTA-TTAATATTTTTA
*
18842536 TTTATTGACTTATTAATATTTT
1 TTTATTGAATTATTAATATTTT
18842558 ATACTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTATTGAATTATTAATATTTTTA
Found at i:18855212 original size:40 final size:40
Alignment explanation
Indices: 18855147--18855371 Score: 303
Period size: 40 Copynumber: 5.7 Consensus size: 40
18855137 GGATATAACC
* * * * *
18855147 ACTCGCAC-AAGGCCGTCGGGTCTTAGCCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* *
18855186 ACTAGCGCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
18855226 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
18855266 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
18855306 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAATC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
18855346 ACTAGCACAAATGTCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
18855372 ACCCCGTTAG
Statistics
Matches: 169, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 6 0.04
40 161 0.95
41 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:18858284 original size:47 final size:47
Alignment explanation
Indices: 18858231--18858354 Score: 169
Period size: 47 Copynumber: 2.6 Consensus size: 47
18858221 GATAAATATT
* *
18858231 TATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCTCAGAGTACC
1 TATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAGAATACC
* * * *
18858278 TATACCATGGCCTC-TACCCAAATTAAGGTAACTCCTCTCTGAATACC
1 TATACCATGGCC-CGTAGCCAAATCAAGGTAACTCATCTCAGAATACC
*
18858325 TCTACCATGGCCCGTAGCCAAATCAAGGTA
1 TATACCATGGCCCGTAGCCAAATCAAGGTA
18858355 TTATTCACAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 1 0.02
47 64 0.97
48 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (47 bp):
TATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAGAATACC
Found at i:18875518 original size:47 final size:47
Alignment explanation
Indices: 18875462--18875593 Score: 203
Period size: 47 Copynumber: 2.8 Consensus size: 47
18875452 TCACAATCCA
*
18875462 TAAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATC-C
1 TAAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTAATCTC
*
18875508 TCGAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTAATCTC
1 T-AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTAATCTC
* * *
18875556 TAAATACGTATACCATGGCCCGTAGCAAAATCAAGGTA
1 TAAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
18875594 TTATTCGCAC
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 75 0.96
48 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (47 bp):
TAAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTAATCTC
Found at i:18880284 original size:47 final size:47
Alignment explanation
Indices: 18880227--18880357 Score: 183
Period size: 47 Copynumber: 2.8 Consensus size: 47
18880217 TCACAACCGA
*
18880227 TAAATACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTTATC-C
1 TAAATACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTC
* * * * *
18880273 TAGAGTACCTATACCATGGTCTGTAGCCAAATCAAGGCAACTCCTCTT
1 TA-AATACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTC
*
18880321 TAAATACCTATACCATGGCCTATAGCCAAATCAAGGT
1 TAAATACCTATACCATGGCCTGTAGCCAAATCAAGGT
18880358 TTTATTTGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
46 2 0.03
47 69 0.95
48 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (47 bp):
TAAATACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCATCTC
Found at i:18891557 original size:51 final size:51
Alignment explanation
Indices: 18891480--18891679 Score: 285
Period size: 51 Copynumber: 3.9 Consensus size: 51
18891470 CGGATACACG
** * *
18891480 GTGGCCTTCATGTAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
* *
18891531 GTGGCCTTCAGATAGTACCACACTTGTGTCCAAAGCTATTATATTCAGAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* *
18891582 GTGGCCTTCACATAGTACTACACTTCTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* * *
18891633 GTGCCCTTCACATAGTACCACACTTATGTCCAAAGCTATTTTATTCA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCA
18891680 TAAGGTTCAA
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 1 0.01
51 134 0.99
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:18891739 original size:28 final size:27
Alignment explanation
Indices: 18891702--18891904 Score: 237
Period size: 28 Copynumber: 7.7 Consensus size: 27
18891692 GAGAAATTTC
18891702 TCACTTAGCACCATGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
*
18891730 TCATTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
18891758 TCACTTAG---ATGACAT-GATCTTATT
1 TCACTTAGCACATGCCATGGA-CTTATT
18891782 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* *
18891810 TCACTTAG---ATGACATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
18891834 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
18891862 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
18891886 TCACTTAGCACAATGCCAT
1 TCACTTAGCAC-ATGCCAT
18891905 ATCCTAGATA
Statistics
Matches: 151, Mismatches: 9, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.01
24 62 0.41
25 3 0.02
27 4 0.03
28 78 0.52
29 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:18891773 original size:24 final size:26
Alignment explanation
Indices: 18891715--18891895 Score: 205
Period size: 24 Copynumber: 7.0 Consensus size: 26
18891705 CTTAGCACCA
*
18891715 TGCCATGGACTTATTTCATTTAGCACAT
1 TGCCATGGACTTATTTCACTTAG--CAT
18891743 TGCCATGGACTTATTTCACTTAG-A-
1 TGCCATGGACTTATTTCACTTAGCAT
*
18891767 TGACAT-GATCTTATTTCACTTAGCACAT
1 TGCCATGGA-CTTATTTCACTTAG--CAT
18891795 TGCCATGGACTTATTTCACTTAG-A-
1 TGCCATGGACTTATTTCACTTAGCAT
* *
18891819 TGACATGGTCTTATTTCACTTAGCACAT
1 TGCCATGGACTTATTTCACTTAG--CAT
18891847 TGCCATGGACTTATTTCACTTAG-A-
1 TGCCATGGACTTATTTCACTTAGCAT
*
18891871 TGCCATGGTCTTATTTCACTTAGCA
1 TGCCATGGACTTATTTCACTTAGCA
18891896 CAATGCCATA
Statistics
Matches: 134, Mismatches: 8, Indels: 25
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.01
24 62 0.46
25 4 0.03
27 2 0.01
28 62 0.46
29 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (26 bp):
TGCCATGGACTTATTTCACTTAGCAT
Found at i:18891780 original size:52 final size:52
Alignment explanation
Indices: 18891718--18891904 Score: 329
Period size: 52 Copynumber: 3.6 Consensus size: 52
18891708 AGCACCATGC
* *
18891718 CATGGACTTATTTCATTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
1 CATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
*
18891770 CATGATCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
1 CATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
*
18891822 CATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGC
1 CATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
*
18891874 CATGGTCTTATTTCACTTAGCACAATGCCAT
1 CATGGTCTTATTTCACTTAGCACATTGCCAT
18891905 ATCCTAGATA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 129 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (52 bp):
CATGGTCTTATTTCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGA
Found at i:18902239 original size:16 final size:17
Alignment explanation
Indices: 18902209--18902241 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18902199 AGTTTTCATA
*
18902209 ACTTATTCCATTGCATG
1 ACTTATTCCACTGCATG
18902226 ACTT-TTCCACTGCATG
1 ACTTATTCCACTGCATG
18902242 TTAATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39
Consensus pattern (17 bp):
ACTTATTCCACTGCATG
Done.