Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 171 of 325
Found at i:53858202 original size:12 final size:12
Alignment explanation
Indices: 53858185--53858209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53858175 CCAACTCAAA
53858185 ATTTTTTTTTTG
1 ATTTTTTTTTTG
53858197 ATTTTTTTTTTG
1 ATTTTTTTTTTG
53858209 A
1 A
53858210 CTTCCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTTTG
Found at i:53859860 original size:30 final size:30
Alignment explanation
Indices: 53859826--53859922 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
53859816 AAAACTAAAA
53859826 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53859856 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
53859886 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
53859915 ATGAGCTA
1 -TGAGCTA
53859923 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53862018 original size:6 final size:6
Alignment explanation
Indices: 53862007--53862039 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
53861997 GCTTCGTACC
53862007 CACTCT CACTCT CACTCT CACTCT CACTCT CAC
1 CACTCT CACTCT CACTCT CACTCT CACTCT CAC
53862040 ATGTGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CACTCT
Found at i:53864852 original size:6 final size:6
Alignment explanation
Indices: 53864843--53864905 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
53864833 AATTTCACAT
* * *
53864843 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GCGAGA GCGAGA ATGAGA
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA
53864891 GTGAGA GTGAGA GTG
1 GTGAGA GTGAGA GTG
53864906 GGTACGAAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.03, G:0.49, T:0.14
Consensus pattern (6 bp):
GTGAGA
Found at i:53866481 original size:14 final size:14
Alignment explanation
Indices: 53866462--53866506 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53866452 AACTCATCTT
*
53866462 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
53866476 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
53866489 AATTTAATTTAATG
1 AGTTTAATTTAATG
53866503 AGTT
1 AGTT
53866507 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53869282 original size:15 final size:13
Alignment explanation
Indices: 53869244--53869285 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
53869234 AACCTCTTTT
*
53869244 AAAAGAAAACGAG
1 AAAAGAAAAAGAG
53869257 AAAAGAAAAAGATG
1 AAAAGAAAAAGA-G
53869271 AAAAGCAAAAAGAG
1 AAAAG-AAAAAGAG
53869285 A
1 A
53869286 TCAAAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 8 0.31
15 7 0.27
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:53879668 original size:14 final size:14
Alignment explanation
Indices: 53879635--53879677 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
53879625 ACTTTTTCCA
53879635 CTCTTTTTCTTTT-
1 CTCTTTTTCTTTTG
53879648 CATTCTTTTTCTTTTG
1 C--TCTTTTTCTTTTG
53879664 CTCTTTTTCTTTTG
1 CTCTTTTTCTTTTG
53879678 ATCTCTCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.04
14 13 0.48
15 12 0.44
16 1 0.04
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.72
Consensus pattern (14 bp):
CTCTTTTTCTTTTG
Found at i:53888806 original size:11 final size:11
Alignment explanation
Indices: 53888790--53888884 Score: 74
Period size: 10 Copynumber: 8.9 Consensus size: 11
53888780 ACAATGTTCA
53888790 AATTTTTTTTC
1 AATTTTTTTTC
*
53888801 AATTTTTTTTTTG
1 AA--TTTTTTTTC
*
53888814 AA-TTTTTTTG
1 AATTTTTTTTC
*
53888824 AAATTTTTTTC
1 AATTTTTTTTC
53888835 AA-TTTTTTTC
1 AATTTTTTTTC
53888845 -A-TTTTTTTC
1 AATTTTTTTTC
** *
53888854 GTTTTTTTTTA
1 AATTTTTTTTC
53888865 AATTTTTTTT-
1 AATTTTTTTTC
*
53888875 GATTTTTTTT
1 AATTTTTTTT
53888885 AAAACTTACT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
9 9 0.12
10 27 0.38
11 26 0.36
13 10 0.14
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:53888843 original size:13 final size:13
Alignment explanation
Indices: 53888792--53888822 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
53888782 AATGTTCAAA
53888792 TTTTTTTTCAATT
1 TTTTTTTTCAATT
*
53888805 TTTTTTTTGAATT
1 TTTTTTTTCAATT
53888818 TTTTT
1 TTTTT
53888823 GAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:53888858 original size:9 final size:9
Alignment explanation
Indices: 53888826--53888861 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
53888816 TTTTTTTGAA
53888826 ATTTTTTTC
1 ATTTTTTTC
53888835 AATTTTTTTC
1 -ATTTTTTTC
53888845 ATTTTTTTC
1 ATTTTTTTC
*
53888854 GTTTTTTT
1 ATTTTTTT
53888862 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:53888862 original size:19 final size:19
Alignment explanation
Indices: 53888806--53888853 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
53888796 TTTTCAATTT
* *
53888806 TTTTTTTGAATTTTTTTGAAA
1 TTTTTTTCAATTTTTTT--CA
53888827 TTTTTTTCAATTTTTTTCA
1 TTTTTTTCAATTTTTTTCA
53888846 TTTTTTTC
1 TTTTTTTC
53888854 GTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
21 16 0.64
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTTTTCAATTTTTTTCA
Found at i:53892769 original size:10 final size:10
Alignment explanation
Indices: 53892745--53892778 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
53892735 TAAGCGCGAT
53892745 TGAGCTCAAA
1 TGAGCTCAAA
* *
53892755 CGAGCTGAAA
1 TGAGCTCAAA
53892765 TGAGCTCAAA
1 TGAGCTCAAA
53892775 TGAG
1 TGAG
53892779 TGAATTGAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:53892787 original size:19 final size:20
Alignment explanation
Indices: 53892743--53892787 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
53892733 AGTAAGCGCG
53892743 ATTGAGCTCAAACGAGCTGA
1 ATTGAGCTCAAACGAGCTGA
* *
53892763 AATGAGCTCAAATGAG-TGA
1 ATTGAGCTCAAACGAGCTGA
53892782 ATTGAG
1 ATTGAG
53892788 TTGGACGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (20 bp):
ATTGAGCTCAAACGAGCTGA
Found at i:53896022 original size:47 final size:46
Alignment explanation
Indices: 53895907--53896320 Score: 320
Period size: 47 Copynumber: 8.8 Consensus size: 46
53895897 TTGGATTTCT
* * **
53895907 TGAGTGCCAGTGTAAGACATGTCTGGGACATACATCGGCCACA-TTA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CATAGAGA
* *
53895953 TGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATAGAGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGAGA
* **
53896001 TGAGTGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCATA-TTA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CATAGAGA
* * **
53896047 TGAGTGCTAGTATAAGACCATGTCTGGGACATGGCATCGGTGTAGAGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGAGA
* * * *
53896095 TGAGTGCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGATGA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGA-GA
* * *
53896142 TGA-TAGCTAGTGTAAGACGTGTCTGGGACACGCATCGGC-TA-AGA
1 TGAGT-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGAGA
* * * * * * *
53896186 -GTTGTGCTAGTGTAAGACGTGTCTAGGACATGCATCAGCATGTATATA
1 TG-AGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--TAGAGA
* * * * *
53896234 TGAGAGCTAGTATAAGACCATGTCTGGGACATGGCATCGGCTTCGATGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGA-GA
* *
53896283 TG-CTAGCCAGTGTAGGACCATGTCTGGGACATGGCATC
1 TGAGT-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
53896321 AAAAACTTAT
Statistics
Matches: 297, Mismatches: 51, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
43 1 0.00
44 33 0.11
45 2 0.01
46 49 0.16
47 99 0.33
48 60 0.20
49 46 0.15
50 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (46 bp):
TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGAGA
Found at i:53896068 original size:94 final size:93
Alignment explanation
Indices: 53895907--53896321 Score: 459
Period size: 94 Copynumber: 4.4 Consensus size: 93
53895897 TTGGATTTCT
* * * *
53895907 TGAGTGCCAGTGTAAGACATGTCTGGGACATACATCGGCCACATTATGAGTGCCAGTATAAGACC
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTGCTAGTATAAGACC
*
53895972 ATGTCTGGGACATGGCATTGGCATAGAGA
66 ATGTCTGGGACATGGCATCGGC-TAGAGA
* *
53896001 TGAGTGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCATATTATGAGTGCTAGTATAAGACC
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTGCTAGTATAAGACC
*
53896066 ATGTCTGGGACATGGCATCGGTGTAGAGA
66 ATGTCTGGGACATGGCATCGG-CTAGAGA
* * *
53896095 TGAGTGCCAATGTAAGACATGTCTGGGACATGCATCAGCC-TCGATGATGA-TAGCTAGTGTAAG
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ATTATGAGT-GCTAGTATAAG
* *
53896158 A-CGTGTCTGGGACA-CGCATCGGCTA-AGA
63 ACCATGTCTGGGACATGGCATCGGCTAGAGA
* * * * *
53896186 -GTTGTGCTAGTGTAAGACGTGTCTAGGACATGCATCAG-CATGTATATATGAGAGCTAGTATAA
1 TG-AGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCA--TAT-TATGAGTGCTAGTATAA
*
53896249 GACCATGTCTGGGACATGGCATCGGCTTCGATGA
62 GACCATGTCTGGGACATGGCATCGGC-TAGA-GA
* *
53896283 TG-CTAGCCAGTGTAGGACCATGTCTGGGACATGGCATCA
1 TGAGT-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCA
53896322 AAAACTTATC
Statistics
Matches: 272, Mismatches: 30, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
90 2 0.01
91 36 0.13
92 17 0.06
93 21 0.08
94 145 0.53
95 18 0.07
96 2 0.01
97 12 0.04
98 13 0.05
99 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (93 bp):
TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTGCTAGTATAAGACC
ATGTCTGGGACATGGCATCGGCTAGAGA
Found at i:53896178 original size:141 final size:141
Alignment explanation
Indices: 53895952--53896313 Score: 396
Period size: 141 Copynumber: 2.6 Consensus size: 141
53895942 CGGCCACATT
* *
53895952 ATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATAGA-GATGAGT-GCCAGTGTA
1 ATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATCGATGATGA-TAGCCAGTGTA
* * ** *
53896015 AGACATGTTTGGGACATGCATCGGCCATATTA-TGAGTGCTAGTATAAGACCATGTCTGGGACAT
65 AGACATGTCTGGGACACGCATCGG-C-TAAGAGT-AGTGCTAGTATAAGA-CATGTCTAGGACAT
*
53896079 GGCATC-G-GTGTAGAG
126 -GCATCAGCATGTAGAG
* * * * *
53896094 ATGAGTGCCAATGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGATGATGATAGCTAGTGTAA
1 ATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATCGATGATGATAGCCAGTGTAA
* * * *
53896157 GACGTGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTGTAAGACGTGTCTAGGACATGCATC
66 GACATGTCTGGGACACGCATCGGCTAAGAGTAGTGCTAGTATAAGACATGTCTAGGACATGCATC
* *
53896222 AGCATGTATAT
131 AGCATGTAGAG
* * * * *
53896233 ATGAGAGCTAGTATAAGACCATGTCTGGGACATGGCATCGGCTTCGATGATGCTAGCCAGTGTAG
1 ATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATCGATGATGATAGCCAGTGTAA
53896298 GACCATGTCTGGGACA
66 GA-CATGTCTGGGACA
53896314 TGGCATCAAA
Statistics
Matches: 183, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
137 5 0.03
138 13 0.07
139 35 0.19
140 26 0.14
141 76 0.42
142 28 0.15
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (141 bp):
ATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATCGATGATGATAGCCAGTGTAA
GACATGTCTGGGACACGCATCGGCTAAGAGTAGTGCTAGTATAAGACATGTCTAGGACATGCATC
AGCATGTAGAG
Found at i:53897210 original size:54 final size:55
Alignment explanation
Indices: 53897085--53897217 Score: 178
Period size: 54 Copynumber: 2.4 Consensus size: 55
53897075 TAAAATTTTT
* *
53897085 AGTCAGTGTTGTACACGGGTAGGCCACACGGGCGTGTGCCATGGCCGTGTCTTAA
1 AGTCAGTGTTGTACACGGGTAAGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
* * * * *
53897140 AGTCAGTATCGTACACGGG-AAGTCACACAGGCGTGTGCCATGGCCGTGTGTTGA
1 AGTCAGTGTTGTACACGGGTAAGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
*
53897194 AGTCAGTGTTGCACACGGGCTAAG
1 AGTCAGTGTTGTACACGGG-TAAG
53897218 GGCATGGGCG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
54 46 0.70
55 17 0.26
56 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (55 bp):
AGTCAGTGTTGTACACGGGTAAGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
Found at i:53898320 original size:18 final size:19
Alignment explanation
Indices: 53898284--53898355 Score: 80
Period size: 18 Copynumber: 3.9 Consensus size: 19
53898274 TTTCTCGCAC
53898284 TCTTTCTTTTCTTTCTTCAA
1 TCTTTCTTTTCTTT-TTCAA
*
53898304 TCTTT-TTTGCTTTTTCAA
1 TCTTTCTTTTCTTTTTCAA
53898322 T-TTTCTTTTCTTTTTC-A
1 TCTTTCTTTTCTTTTTCAA
*
53898339 -CATTCTTTTTCTTTTTC
1 TCTTTC-TTTTCTTTTTC
53898356 TTTCTCTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.15
18 27 0.59
19 7 0.15
20 5 0.11
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.69
Consensus pattern (19 bp):
TCTTTCTTTTCTTTTTCAA
Found at i:53898356 original size:12 final size:11
Alignment explanation
Indices: 53898322--53898369 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
53898312 GCTTTTTCAA
53898322 TTTTCTTTTCT
1 TTTTCTTTTCT
**
53898333 TTTTCACATTCT
1 TTTTC-TTTTCT
53898345 TTTTCTTTTTCT
1 TTTTC-TTTTCT
*
53898357 TTCTCTTTTCT
1 TTTTCTTTTCT
53898368 TT
1 TT
53898370 CAAGCTCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 13 0.43
12 17 0.57
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:53899044 original size:36 final size:36
Alignment explanation
Indices: 53898997--53899084 Score: 158
Period size: 36 Copynumber: 2.4 Consensus size: 36
53898987 AAAGAAAATT
*
53898997 CACTCACTTGGCTTTTGTTCACTTGAATAGACTCAC
1 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
53899033 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
1 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
*
53899069 CACTCTCTTGCCTTTT
1 CACTCTCTTGGCTTTT
53899085 CCGCTCAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.40
Consensus pattern (36 bp):
CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
Found at i:53900542 original size:16 final size:17
Alignment explanation
Indices: 53900517--53900564 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
53900507 ATAAGCACAA
53900517 TTAAACAAG-TAAATGT
1 TTAAACAAGTTAAATGT
*
53900533 TTAAATAAGTTAAATGGT
1 TTAAACAAGTTAAAT-GT
*
53900551 TGTAAACAATTTAA
1 T-TAAACAAGTTAA
53900565 TTAAGCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 3 0.12
19 10 0.38
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAACAAGTTAAATGT
Found at i:53900695 original size:50 final size:50
Alignment explanation
Indices: 53900591--53900740 Score: 250
Period size: 49 Copynumber: 3.0 Consensus size: 50
53900581 TAATTGCCAA
* *
53900591 AATTAGTTAAGCAACTAAAGAAAATTAAAAA-AACTTAATTAATTAAACT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
53900640 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
* *
53900690 AATTATTTAAGAAACTAAAGACAATT-AAAACAACTTAATTAATTAAGCT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
53900739 AA
1 AA
53900741 AATAACTAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
49 53 0.55
50 43 0.45
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (50 bp):
AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
Found at i:53902382 original size:20 final size:20
Alignment explanation
Indices: 53902357--53902411 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53902347 TATGGTTCAA
*
53902357 CTCATTCAAGCTCAAGTTAG
1 CTCATTCAAGCTCAAGTCAG
**
53902377 CTCATTCGTGCTCAAGTCAG
1 CTCATTCAAGCTCAAGTCAG
53902397 CTCATTCAAGCTCAA
1 CTCATTCAAGCTCAA
53902412 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (20 bp):
CTCATTCAAGCTCAAGTCAG
Found at i:53905244 original size:17 final size:15
Alignment explanation
Indices: 53905224--53905262 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
53905214 GCGAGCGAGA
53905224 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
53905241 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
53905256 AAGATGA
1 AA-ATGA
53905263 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:53906770 original size:20 final size:20
Alignment explanation
Indices: 53906745--53906799 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53906735 TGTGGTTCAA
*
53906745 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53906765 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53906785 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53906800 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53910174 original size:43 final size:43
Alignment explanation
Indices: 53910063--53910176 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
53910053 ACCGAGATGT
* * * *
53910063 GATTACATGTAAGACCATGCCTAGGACATTGGCATTGTAATGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAATGC
*
53910106 GATTACGTGTAAGACCATGTATGGGACATTGGCATCAT-TAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCAT--TGTAATGC
53910149 GATTACGTGTAAGACCCA-GTCTGGGACA
1 GATTACGTGTAAGA-CCATGTCTGGGACA
53910177 GTGACATCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 54 0.87
44 7 0.11
45 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAATGC
Found at i:53911032 original size:15 final size:15
Alignment explanation
Indices: 53911012--53911059 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53911002 TCAAAGATGG
53911012 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53911027 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
53911041 GTTTATGGATATAAA
1 GTTTATGGATATGAA
53911056 GTTT
1 GTTT
53911060 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53911046 original size:14 final size:14
Alignment explanation
Indices: 53911006--53911049 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53910996 AAGGATTCAA
53911006 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53911020 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53911035 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53911049 A
1 A
53911050 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53911075 original size:29 final size:29
Alignment explanation
Indices: 53911006--53911065 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53910996 AAGGATTCAA
*
53911006 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
53911035 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
53911064 AG
1 AG
53911066 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:53914479 original size:12 final size:12
Alignment explanation
Indices: 53914446--53914479 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53914436 TGTTTTTTTT
*
53914446 CTTTTTCAACGA
1 CTTTTTCAATGA
53914458 CTTTTTCAATGA
1 CTTTTTCAATGA
*
53914470 CTTTCTCAAT
1 CTTTTTCAAT
53914480 CTCTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:53915677 original size:15 final size:15
Alignment explanation
Indices: 53915657--53915704 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53915647 TCAAAGATGG
53915657 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53915672 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
53915687 -TTTATGGATATAAA
1 GTTTATGGATATGAA
53915701 GTTT
1 GTTT
53915705 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53915684 original size:29 final size:29
Alignment explanation
Indices: 53915651--53915710 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
53915641 AAGGATTCAA
* *
53915651 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
53915680 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
53915709 AG
1 AG
53915711 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:53927603 original size:22 final size:21
Alignment explanation
Indices: 53927572--53927612 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53927562 GTGATAGCCA
*
53927572 CTTTTATTTGGGTTTAATCTTT
1 CTTTTATTT-GATTTAATCTTT
*
53927594 CTTTTCTTTGATTTAATCT
1 CTTTTATTTGATTTAATCT
53927613 GAAAACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.15, C:0.12, G:0.10, T:0.63
Consensus pattern (21 bp):
CTTTTATTTGATTTAATCTTT
Found at i:53929439 original size:49 final size:49
Alignment explanation
Indices: 53929367--53929560 Score: 212
Period size: 49 Copynumber: 3.9 Consensus size: 49
53929357 GCCGAAGCTA
*
53929367 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
* * *
53929416 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACAG
** * * * * *
53929466 TCTAATACACGTAGTAGCCCGCACTTAGTACTACACACGTGATC-ACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
* *
53929514 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
53929561 TCACAATAGA
Statistics
Matches: 120, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 39 0.32
50 39 0.32
51 39 0.32
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (49 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
Found at i:53929496 original size:50 final size:49
Alignment explanation
Indices: 53929378--53929560 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 49
53929368 CTGGTACGCA
* **
53929378 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTAATACACG
*
53929427 TAGTAGCCTGCACTTAGTACTACACATGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAACAGTCTAATACACG
* * * *** * *
53929477 TAGTAGCCCGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAG---TCTAATACACG
*
53929528 TAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
53929561 TCACAATAGA
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 30 0.27
50 39 0.35
51 39 0.35
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTAATACACG
Found at i:53929551 original size:101 final size:99
Alignment explanation
Indices: 53929378--53929564 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 99
53929368 CTGGTACGCA
* * * *
53929378 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCCGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
53929443 GTACTACACATGTGACCTCACCATCTAATACACG
66 GTACTACACATGCGACCTCACCATCTAATACACG
* * *
53929477 TAGTAGCCCGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCCGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
53929541 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACATGCGACCTCAC
53929565 AATAGATCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 4 0.05
99 29 0.38
101 44 0.57
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGTAGCCCGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACATGCGACCTCACCATCTAATACACG
Found at i:53935610 original size:14 final size:14
Alignment explanation
Indices: 53935573--53935616 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
53935563 ATTCTCTTCC
53935573 TTGCTATTTTTGTT
1 TTGCTATTTTTGTT
53935587 TT-C-ATCTTTTGTT
1 TTGCTAT-TTTTGTT
*
53935600 TTGCTATTTTTCTT
1 TTGCTATTTTTGTT
53935614 TTG
1 TTG
53935617 GTAGCCGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.70
Consensus pattern (14 bp):
TTGCTATTTTTGTT
Found at i:53936371 original size:6 final size:6
Alignment explanation
Indices: 53936356--53936390 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
53936346 TTGTGTAAAA
*
53936356 ATATAT ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
53936391 TAAATTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:53947426 original size:17 final size:17
Alignment explanation
Indices: 53947404--53947437 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53947394 TGAACTTAAC
53947404 AATTAAGTA-ATGAACCT
1 AATTAAG-ACATGAACCT
53947421 AATTAAGACATGAACCT
1 AATTAAGACATGAACCT
53947438 TCTAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (17 bp):
AATTAAGACATGAACCT
Found at i:53947905 original size:13 final size:13
Alignment explanation
Indices: 53947887--53947911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53947877 TAACCTACAA
53947887 AATTAAATAACAT
1 AATTAAATAACAT
53947900 AATTAAATAACA
1 AATTAAATAACA
53947912 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:53948169 original size:10 final size:10
Alignment explanation
Indices: 53948136--53948184 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
53948126 AAAAAGGAAT
*
53948136 GAGCTGAAAC
1 GAGCTCAAAC
53948146 GAGCT-AAATTC
1 GAGCTCAAA--C
53948157 GAGCTCAAAC
1 GAGCTCAAAC
*
53948167 GAGCTAAAAC
1 GAGCTCAAAC
53948177 GAGCTCAA
1 GAGCTCAA
53948185 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:53948191 original size:20 final size:21
Alignment explanation
Indices: 53948136--53948184 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
53948126 AAAAAGGAAT
* *
53948136 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
53948157 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
53948177 GAGCTCAA
1 GAGCTCAA
53948185 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:53954945 original size:6 final size:6
Alignment explanation
Indices: 53954936--53954989 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
53954926 AATTAAAATG
* *
53954936 AGAATC AGAATC AGAATC AGAATC AGTATC AGGTAA-C AGAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
53954985 AGAAT
1 AGAAT
53954990 GTGAATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 2 0.05
6 35 0.85
7 3 0.07
8 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:53955684 original size:27 final size:27
Alignment explanation
Indices: 53955494--53955676 Score: 219
Period size: 27 Copynumber: 6.8 Consensus size: 27
53955484 AACACCCTAG
53955494 GGGTAAAAC-GATAATTCTT-TAAATCGA
1 GGGTAAAACAG-TAATT-TTGTAAATCGA
*
53955521 GGGTAAAACAGTAATTTTGTAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
53955548 AGGTAAAACAGTAATTTTGTAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
53955575 GGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * *
53955602 GGGTAAAAC-GATAATTCTATAAATTGA
1 GGGTAAAACAG-TAATTTTGTAAATCGA
* * *
53955629 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
53955656 GGGTAAAACAGTAATTTTGTA
1 GGGTAAAACAGTAATTTTGTA
53955677 CATTGAGGAT
Statistics
Matches: 138, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
26 3 0.02
27 134 0.97
28 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (27 bp):
GGGTAAAACAGTAATTTTGTAAATCGA
Found at i:53955749 original size:26 final size:27
Alignment explanation
Indices: 53955693--53955752 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
53955683 GGATATTTGG
*
53955693 GTAATTTTATAAACCGGGGGTACTTTG
1 GTAATTTTATAAACCGGGGGTACTTTA
* *
53955720 GTAATTTTA-CAACTGGGGGTA-TTTCA
1 GTAATTTTATAAACCGGGGGTACTTT-A
53955746 GTAATTT
1 GTAATTT
53955753 GGTAAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.10
26 17 0.59
27 9 0.31
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (27 bp):
GTAATTTTATAAACCGGGGGTACTTTA
Found at i:53957685 original size:6 final size:6
Alignment explanation
Indices: 53957676--53957726 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
53957666 AATTAAAATG
* * *
53957676 AGAATC AGAATC AGAATC AG-GTGAC AGAATT AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
53957725 AG
1 AG
53957727 GTAACAGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 1 0.03
6 32 0.86
7 3 0.08
8 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:53957713 original size:31 final size:31
Alignment explanation
Indices: 53957676--53957734 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
53957666 AATTAAAATG
*
53957676 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
53957707 AGAATCAGAATCAGTATCAGGTAACAGA
1 AGAATCAGAATCAGAATCAGGTAACAGA
53957735 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:53957748 original size:31 final size:31
Alignment explanation
Indices: 53957678--53957748 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
53957668 TTAAAATGAG
* *
53957678 AATCAGAATCAGAATCAGGTGACAGAATTAG
1 AATCAGAATCAGAATCAGGTAACAGAATTAA
*
53957709 AATCAGAATCAGTATCAGGTAACAG-ATTCAA
1 AATCAGAATCAGAATCAGGTAACAGAATT-AA
*
53957740 AATTAGAAT
1 AATCAGAAT
53957749 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATTAA
Found at i:53958017 original size:27 final size:26
Alignment explanation
Indices: 53957969--53958020 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53957959 GCGAGGCTGC
*
53957969 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
53957995 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
53958021 TTGCAGCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:53958287 original size:27 final size:27
Alignment explanation
Indices: 53958257--53958447 Score: 240
Period size: 27 Copynumber: 7.1 Consensus size: 27
53958247 AACACCCTAG
* *
53958257 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
53958284 GGGTAAAACAGTAATTTTGTAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
53958311 GGGTAAAATAATAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
53958338 GGGTAAAACAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
53958365 GGGTAAAAC-GATAATTCTGTAAATCGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* * *
53958392 GGGTAAAACAATAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
53958419 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
53958446 GG
1 GG
53958448 ATATTTGGGT
Statistics
Matches: 140, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 139 0.99
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:53958444 original size:81 final size:81
Alignment explanation
Indices: 53958257--53958447 Score: 267
Period size: 81 Copynumber: 2.4 Consensus size: 81
53958247 AACACCCTAG
* * * *
53958257 GGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTGTAAATTGAGGGTAAAATAA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAA
* *
53958322 TAATTTTGTAAATCGA
66 TAATTCTATAAATCGA
* * *
53958338 GGGTAAAACAGTAATTCTATCAATCGAGGGTAAAAC-GATAATTCTGTAAATCGAGGGTAAAACA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG-TAATTCTGTAAATCGAGGGTAAAACA
*
53958402 ATAATTCTATAAATTGA
65 ATAATTCTATAAATCGA
*
53958419 GGGTAAAACGGTAATTTTGTAAATCGAGG
1 GGGTAAAACGGTAATTCTGTAAATCGAGG
53958448 ATATTTGGGT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
80 1 0.01
81 94 0.99
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (81 bp):
GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAA
TAATTCTATAAATCGA
Found at i:53958469 original size:54 final size:54
Alignment explanation
Indices: 53958257--53958447 Score: 274
Period size: 54 Copynumber: 3.5 Consensus size: 54
53958247 AACACCCTAG
* * * *
53958257 GGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTGTAAATTGA
1 GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATTGA
** * * *
53958311 GGGTAAAATAATAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATCAATCGA
1 GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATTGA
*
53958365 GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAAATTGA
1 GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATTGA
* *
53958419 GGGTAAAACGGTAATTTTGTAAATCGAGG
1 GGGTAAAACGATAATTCTGTAAATCGAGG
53958448 ATATTTGGGT
Statistics
Matches: 120, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (54 bp):
GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATTGA
Found at i:53958485 original size:27 final size:27
Alignment explanation
Indices: 53958428--53958494 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
53958418 AGGGTAAAAC
*
53958428 GGTAATTTTGTAAATCGAGGATATTTG
1 GGTAATTTTATAAATCGAGGATATTTG
*
53958455 GGTAATTTTATAAATC-AGGGGTACTTT-
1 GGTAATTTTATAAATCGA-GGATA-TTTG
53958482 GGTAATTTTATAA
1 GGTAATTTTATAA
53958495 TTGGGGGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.89
28 3 0.08
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.42
Consensus pattern (27 bp):
GGTAATTTTATAAATCGAGGATATTTG
Found at i:53958512 original size:26 final size:27
Alignment explanation
Indices: 53958456--53958515 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
53958446 GGATATTTGG
*
53958456 GTAATTTTATAAATCAGGGGTACTTTG
1 GTAATTTTATAAATCAGGGGTACTTTA
**
53958483 GTAATTTTAT-AATTGGGGGTA-TTTCA
1 GTAATTTTATAAATCAGGGGTACTTT-A
53958509 GTAATTT
1 GTAATTT
53958516 GGTAAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.10
26 16 0.55
27 10 0.34
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (27 bp):
GTAATTTTATAAATCAGGGGTACTTTA
Found at i:53963461 original size:31 final size:32
Alignment explanation
Indices: 53963371--53963488 Score: 157
Period size: 32 Copynumber: 3.7 Consensus size: 32
53963361 TCATATGGCT
* *
53963371 TTGATATTGAAATGGGCTAGGCCCAACTGATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
* *
53963403 TTGAGTCTGATATGGGCTAGGCCCAACTGATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
*
53963435 TTGATTTTGATATGGGCTA-GCCCAACTAATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
* * *
53963466 GTGATTTTGAGATTGGCTAGGCC
1 TTGATTTTGATATGGGCTAGGCC
53963489 TAATTGAGAC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
31 27 0.36
32 48 0.64
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (32 bp):
TTGATTTTGATATGGGCTAGGCCCAACTGATA
Found at i:53965916 original size:36 final size:36
Alignment explanation
Indices: 53965869--53965942 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
53965859 TTAATAAAGA
*
53965869 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGCTT
1 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
53965905 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
1 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
53965941 TC
1 TC
53965943 TTCTTTCTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (36 bp):
TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
Found at i:53966928 original size:18 final size:19
Alignment explanation
Indices: 53966901--53966942 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
53966891 GTAGTTATAA
*
53966901 CCAAAGT-AAATTAAAATC
1 CCAAAGTAAAAATAAAATC
*
53966919 CCAAATTAAAAATAAAAT-
1 CCAAAGTAAAAATAAAATC
53966937 CCAAAG
1 CCAAAG
53966943 AGGCCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.19
Consensus pattern (19 bp):
CCAAAGTAAAAATAAAATC
Found at i:53967720 original size:18 final size:17
Alignment explanation
Indices: 53967694--53967727 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53967684 CATAATGCAG
53967694 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
53967712 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
53967728 TAGCCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:53974152 original size:68 final size:68
Alignment explanation
Indices: 53974073--53974231 Score: 182
Period size: 67 Copynumber: 2.4 Consensus size: 68
53974063 GAGTGCACAT
* * * *
53974073 CATGTGTACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TG
1 CATGTGGACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAG
*
53974136 TACAC
64 GACAC
* * *
53974141 CATGTGGACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGG
1 CATGTGGACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGG
53974204 ACAC
65 ACAC
*
53974208 CATGTAGACAAGAGAGCTACGAGA
1 CATGTGGACAAGAGAGCTACGAGA
53974232 TAAACTGGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
64 24 0.31
65 3 0.04
66 3 0.04
67 26 0.34
68 21 0.27
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (68 bp):
CATGTGGACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGA
CAC
Found at i:53983986 original size:27 final size:27
Alignment explanation
Indices: 53983948--53984045 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
53983938 CGTACCTGAA
* *
53983948 CCCTTATCTGATAAAATAATAATTTTG
1 CCCTTATGTGATAAAATAACAATTTTG
* *
53983975 CCCTCATGTGATAAAATGACAATTTTG
1 CCCTTATGTGATAAAATAACAATTTTG
* * * *
53984002 CCCTTACGTAATAAAATAACGATTTTT
1 CCCTTATGTGATAAAATAACAATTTTG
53984029 CCCTTATGTGATAAAAT
1 CCCTTATGTGATAAAAT
53984046 GACCGAAATA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (27 bp):
CCCTTATGTGATAAAATAACAATTTTG
Found at i:53984074 original size:27 final size:27
Alignment explanation
Indices: 53984043--53984109 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
53984033 TATGTGATAA
*
53984043 AATGACCGAAATA-CCTTCATAGGGTA-
1 AATGACCGAAATACCCTT-ATAAGGTAG
* *
53984069 ACATGATCAAAATACCCTTATAAGGTAG
1 A-ATGACCGAAATACCCTTATAAGGTAG
*
53984097 AATGACTGAAATA
1 AATGACCGAAATA
53984110 TCTCTGTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.03
27 26 0.81
28 5 0.16
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (27 bp):
AATGACCGAAATACCCTTATAAGGTAG
Found at i:53984122 original size:27 final size:27
Alignment explanation
Indices: 53984078--53984159 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
53984068 AACATGATCA
* * *
53984078 AAATACCCTTATAAGGTAGAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
* * *
53984105 AAATATCTCTGTAGGGTAAAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
*
53984132 TAATACCCCTGTAAGGTAAAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
53984159 A
1 A
53984160 TTTGCCCGAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (27 bp):
AAATACCCCTGTAAGGTAAAATGACTG
Found at i:53987587 original size:18 final size:18
Alignment explanation
Indices: 53987560--53987610 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
53987550 TGTTTGCATT
53987560 CTGCACTGATTACTGTTA
1 CTGCACTGATTACTGTTA
* *
53987578 CTGCATTGATCA-TGGTTA
1 CTGCACTGATTACT-GTTA
*
53987596 CTGTACTGATTACTG
1 CTGCACTGATTACTG
53987611 CCATTGCTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (18 bp):
CTGCACTGATTACTGTTA
Found at i:53998420 original size:21 final size:20
Alignment explanation
Indices: 53998396--53998434 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53998386 AAATTATGAC
*
53998396 TTATAATTATATTTTTAAAAT
1 TTATAATGA-ATTTTTAAAAT
*
53998417 TTATGATGAATTTTTAAA
1 TTATAATGAATTTTTAAA
53998435 GTCAGAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATAATGAATTTTTAAAAT
Found at i:53999913 original size:30 final size:30
Alignment explanation
Indices: 53999879--53999938 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53999869 ATTTAATACG
53999879 AACTTTGGAAAAATTACA-TTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTT-CCCCTA
* * *
53999909 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTTCCCCTA
53999939 GTGTAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTTCCCCTA
Found at i:54001279 original size:46 final size:46
Alignment explanation
Indices: 54001229--54001357 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
54001219 TGATTGAGCA
*
54001229 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
54001275 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
54001321 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54001358 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:54008787 original size:46 final size:45
Alignment explanation
Indices: 54008738--54008909 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
54008728 GATTGAGCAT
54008738 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54008783 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAG
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
*
54008827 CATCGAACTCGTTGAGTT-AGTCCGAGTTCACTTATGGATGCGAACG
1 C--CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54008873 CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54008910 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 6 0.06
44 13 0.12
45 32 0.30
46 48 0.45
47 4 0.04
48 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54008893 original size:90 final size:92
Alignment explanation
Indices: 54008733--54008902 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 92
54008723 AGGATGATTG
*
54008733 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
54008798 TTGAGTCCGAGTTCGTGAGATGTAACT
66 TTGAGTCCGAGTTCGTGAGATGTAACT
*
54008825 AGCAT-CGAACTCGTTGAGTT-AGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGA
1 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
54008887 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
54008903 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
89 2 0.03
90 53 0.71
91 15 0.20
92 5 0.07
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (92 bp):
AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACT
Found at i:54020779 original size:31 final size:31
Alignment explanation
Indices: 54020738--54020801 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
54020728 CCTTTTCATA
*
54020738 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
** *
54020769 TTTCAAATTTCATATTATTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
54020800 TT
1 TT
54020802 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:54022163 original size:46 final size:46
Alignment explanation
Indices: 54021976--54022153 Score: 284
Period size: 46 Copynumber: 3.9 Consensus size: 46
54021966 CACAATATAT
* * * * *
54021976 ATATACATCTCATACATATCTCACATTAGCCATTCGCCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
54022022 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
* *
54022068 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGACTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
54022114 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTT
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTT
54022154 CGCCACATAT
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.35
Consensus pattern (46 bp):
ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
Found at i:54022208 original size:47 final size:45
Alignment explanation
Indices: 54022157--54022511 Score: 467
Period size: 47 Copynumber: 7.5 Consensus size: 45
54022147 TCGGCTTCGC
* * **
54022157 CACATATATACACTTCCACGTTCATCACATTGGCCATTCTACCTTAT
1 CACATATATGCA-TT-CACATTCATCACATTGGCCATTCGGCCTTAT
*
54022204 CACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCA--TTCACATTCATCACATTGGCCATTCGGCCTTAT
54022251 CACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCA--TTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
54022298 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
54022345 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
*
54022392 CACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
*
54022439 CACGTATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCAT-T-CACATTCATCACATTGGCCATTCGGCCTTAT
54022486 CACATATATGCATGTTCACATTCATC
1 CACATATATGCA--TTCACATTCATC
54022512 TCATAAAATC
Statistics
Matches: 291, Mismatches: 11, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
45 1 0.00
46 2 0.01
47 283 0.97
48 4 0.01
49 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (45 bp):
CACATATATGCATTCACATTCATCACATTGGCCATTCGGCCTTAT
Found at i:54022255 original size:94 final size:94
Alignment explanation
Indices: 54022157--54022511 Score: 550
Period size: 94 Copynumber: 3.8 Consensus size: 94
54022147 TCGGCTTCGC
* * ** * * *
54022157 CACATATATACACT-TCCACGTTCATCACATTGGCCATTCTACCTTATCACATATATACATGTTC
1 CACATATATGCA-TGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTC
54022221 ACATTCATCACATTGGCCATTCGGCCTTAT
65 ACATTCATCACATTGGCCATTCGGCCTTAT
*
54022251 CACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
*
54022316 CATTGATCACATTGGCCATTCGGCCTTAT
66 CATTCATCACATTGGCCATTCGGCCTTAT
* * * *
54022345 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
54022410 CATTCATCACATTGGCCATTCGGCCTTAT
66 CATTCATCACATTGGCCATTCGGCCTTAT
* * *
54022439 CACGTATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
54022504 CATTCATC
66 CATTCATC
54022512 TCATAAAATC
Statistics
Matches: 240, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
93 1 0.00
94 239 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (94 bp):
CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
CATTCATCACATTGGCCATTCGGCCTTAT
Found at i:54022328 original size:141 final size:141
Alignment explanation
Indices: 54022171--54022511 Score: 556
Period size: 141 Copynumber: 2.4 Consensus size: 141
54022161 TATATACACT
* ** *
54022171 TCCACGTTCATCACATTGGCCATTCTACCTTATCACATATATACATGTTCACATTCATCACATTG
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
54022236 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
54022301 ACATATGCAAG
131 ACATATGCAAG
* * * * *
54022312 TTCACATTGATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCACATTGATCACATTG
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
54022377 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
** *
54022442 GTATATGCATG
131 ACATATGCAAG
54022453 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATC
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATC
54022512 TCATAAAATC
Statistics
Matches: 181, Mismatches: 19, Indels: 0
0.90 0.09 0.00
Matches are distributed among these distances:
141 181 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (141 bp):
TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
ACATATGCAAG
Found at i:54025451 original size:24 final size:24
Alignment explanation
Indices: 54025415--54025518 Score: 149
Period size: 23 Copynumber: 4.4 Consensus size: 24
54025405 CTGGAGGCCT
*
54025415 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
54025440 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
54025464 AGCCC-TTTAATAACTAGGGCACA
1 AGCCCTTTTAATAACTGGGGCATA
54025487 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
54025510 AGCCATTTT
1 AGCCCTTTT
54025519 TCACTTCCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 41 0.57
24 27 0.38
25 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:54025596 original size:20 final size:20
Alignment explanation
Indices: 54025568--54025608 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54025558 TTATGATTAC
54025568 ATCACGTGCATATCATACAT
1 ATCACGTGCATATCATACAT
*
54025588 ATCATGTGCATATCATACAT
1 ATCACGTGCATATCATACAT
54025608 A
1 A
54025609 CCTTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (20 bp):
ATCACGTGCATATCATACAT
Found at i:54027958 original size:40 final size:42
Alignment explanation
Indices: 54027873--54028041 Score: 234
Period size: 42 Copynumber: 4.1 Consensus size: 42
54027863 CTCGATATAT
* * * *
54027873 TATATATCCAGGTTAAATCCTGCAGGCATCGTGTTGGTAATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
54027915 TATATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGT-A-A
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * *
54027955 TATATATCCGGGTTAAATCCCGTAGGCTTTGTGTTGGTAATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* *
54027997 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTACTA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
54028039 TAT
1 TAT
54028042 CCGGGCTTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 37 0.32
41 2 0.02
42 75 0.66
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:54027989 original size:82 final size:81
Alignment explanation
Indices: 54027873--54028067 Score: 275
Period size: 82 Copynumber: 2.4 Consensus size: 81
54027863 CTCGATATAT
* * * * *
54027873 TATATATCCAGGTTAAATCCTGCAGGCATCGTGTTGGTAATATATATATCCGGGTTAAATCCCGT
1 TATATATCCGGGTTAAATCCCGCAGGCTTTGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
*
54027938 AGGCTTCGTGCTGGTAA
66 AGGCTTAGTGCTGGT-A
*
54027955 TATATATCCGGGTTAAATCCCGTAGGCTTTGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
1 TATATATCCGGGTTAAATCCCGCAGGCTTTGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
54028020 AGGCTTAGTGCTGGTA
66 AGGCTTAGTGCTGGTA
* *
54028036 -CTATATCCGGGCTTAAAGTTCCGCAGGCTTTG
1 TATATATCCGGG-TTAAA-TCCCGCAGGCTTTG
54028068 AGCTAGTGAC
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 10 0.10
81 6 0.06
82 85 0.84
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (81 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTTGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
AGGCTTAGTGCTGGTA
Found at i:54028060 original size:40 final size:39
Alignment explanation
Indices: 54027873--54028065 Score: 190
Period size: 42 Copynumber: 4.7 Consensus size: 39
54027863 CTCGATATAT
* * * * *
54027873 TATATATCCAGGTTAAATCCTGCAGGCATCGTGTTGGTAATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG---TA
* *
54027915 TATATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGT-A
* * *
54027955 TATATATCCGGGTTAAATCCCGTAGGCTTTGTGTTGGTAATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG---TA
54027997 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTA
1 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTA
* *
54028036 -CTATATCCGGGCTTAAAGTTCCGCAGGCTT
1 TATATATCCGGG-TTAAA-TCCCGCAGGCTT
54028066 TGAGCTAGTG
Statistics
Matches: 133, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
38 10 0.08
39 8 0.06
40 47 0.35
42 67 0.50
43 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (39 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTA
Found at i:54032724 original size:49 final size:49
Alignment explanation
Indices: 54032639--54032756 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
54032629 TGCGTGTCAT
*
54032639 TGTAAGACCTTTCTGGGACATGGCATCAACACCGATAGAT-AAGAGCCAA
1 TGTAAGACCTCTCTGGGACATGGCATCAACACCGATAGATGAA-AGCCAA
* * * * * *
54032688 TGTAAGATCTCTCTGGGACATGGGATCAGC-CTCGATATATGAAAGTCAG
1 TGTAAGACCTCTCTGGGACATGGCATCAACAC-CGATAGATGAAAGCCAA
*
54032737 TGTAAGACCTGTCTGGGACA
1 TGTAAGACCTCTCTGGGACA
54032757 CAGCATCGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 55 0.95
50 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (49 bp):
TGTAAGACCTCTCTGGGACATGGCATCAACACCGATAGATGAAAGCCAA
Found at i:54041044 original size:81 final size:81
Alignment explanation
Indices: 54040947--54041102 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
54040937 ATTACCAAAG
54040947 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCATTTTACCCTCAATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCATTTTACCCTCAATT
54041012 TAAAAAATTACCATTT
66 TAAAAAATTACCATTT
** * * ** **
54041028 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCATTTTACCCTCAATT
*
54041093 TACAAAATTA
66 TAAAAAATTA
54041103 TTAAAATACC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCATTTTACCCTCAATT
TAAAAAATTACCATTT
Found at i:54041095 original size:27 final size:27
Alignment explanation
Indices: 54040947--54041102 Score: 195
Period size: 27 Copynumber: 5.8 Consensus size: 27
54040937 ATTACCAAAG
*
54040947 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
54040974 TACCCTCGACTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
54041001 TACCCTCAATTTAAAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* **
54041028 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* **
54041055 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
54041082 TACCCTTGATTTACAAAATTA
1 TACCCTCGATTTACAGAATTA
54041103 TTAAAATACC
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:54041113 original size:81 final size:81
Alignment explanation
Indices: 54040934--54041132 Score: 227
Period size: 81 Copynumber: 2.5 Consensus size: 81
54040924 CTTAAATTGT
*
54040934 AAAATTACCAAAGTACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCAT
1 AAAATTACCAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCAT
54040999 TTTACCCTCAATTTAA
66 TTTACCCTCAATTTAA
*** ** * * **
54041015 AAAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGT
1 AAAATTACCAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCAT
** *
54041080 TTTACCCTTGATTTAC
66 TTTACCCTCAATTTAA
** * * * *
54041096 AAAATTATTAAAATACCCTTGGTTTACAAAATTACCA
1 AAAATTACCAAAATACCCTCGATTTATAGAATTACCA
54041133 AAATACCCTC
Statistics
Matches: 95, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCAT
TTTACCCTCAATTTAA
Found at i:54041167 original size:81 final size:80
Alignment explanation
Indices: 54041082--54041384 Score: 272
Period size: 81 Copynumber: 3.7 Consensus size: 80
54041072 ATTACTGTTT
* * *
54041082 TACCCTTGATTTACAAAATTATTAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCAAT
1 TACCC-TGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCT-AAT
*
54041146 CAGTAAAATTACCAAAA
64 TAGTAAAATTACCAAAA
* * * * ** * *
54041163 TACCCTGGTCTATAAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTT
1 TACCCTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAATTA
54041228 GTAAAATTACCAAAA
66 GTAAAATTACCAAAA
* * * * * * **
54041243 TACCACTGGTTTGTGAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATT
1 TACC-CTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAA-T
*
54041308 TA-TAAAATTACAAAAA
64 TAGTAAAATTACCAAAA
* * **
54041324 TACCCTTGACTGTCTA-AAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCC
1 TACCC-TGA-T-T-TATAAAATTACTA-AAATACCCTTAGTTTACAAAATTACCAAAATACCC
54041385 TTGGTTTGTA
Statistics
Matches: 179, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
80 63 0.35
81 77 0.43
82 4 0.02
83 34 0.19
84 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (80 bp):
TACCCTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAATTA
GTAAAATTACCAAAA
Found at i:54041388 original size:27 final size:27
Alignment explanation
Indices: 54041082--54041414 Score: 235
Period size: 27 Copynumber: 12.3 Consensus size: 27
54041072 ATTACTGTTT
* * **
54041082 TACCCTTGATTTACAAAATTATTAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*
54041109 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*** *
54041136 TACCC-TCAATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTA-TAAAATTACCAAAA
* * *
54041163 TACCC-TGGTCTATAAAATTGCTAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* * *
54041189 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* * *
54041216 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* *
54041243 TACCAC-TGGTTTGTGAAATTACCAAAA
1 TACC-CTTGGTTTATAAAATTACCAAAA
*** *
54041270 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* ** *
54041297 TACCCCTAATTTATAAAATTACAAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* *
54041324 TACCCTTGACTGTCTA-AAAATTA-TAGAAA
1 TACCCTTG---GTTTATAAAATTACCA-AAA
* * **
54041353 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* * *
54041380 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*
54041407 CACCCTTG
1 TACCCTTG
54041415 TAGGATGAAA
Statistics
Matches: 250, Mismatches: 46, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
26 25 0.10
27 202 0.81
28 3 0.01
29 17 0.07
30 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TACCCTTGGTTTATAAAATTACCAAAA
Found at i:54041475 original size:27 final size:27
Alignment explanation
Indices: 54041432--54041505 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
54041422 AAATGACCAA
*
54041432 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
* **
54041459 AA-AGCCTCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
*
54041486 AATACCCCTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
54041506 TGATGAATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
26 3 0.08
27 33 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:54042395 original size:52 final size:51
Alignment explanation
Indices: 54042317--54042452 Score: 197
Period size: 52 Copynumber: 2.7 Consensus size: 51
54042307 GAGGAAGTGC
* * * *
54042317 AAAAGTGCTTATACCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAATTTACCA
54042369 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCA
54042420 AAAAGGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
54042453 GGGCCTCCAG
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 8 0.10
51 23 0.29
52 34 0.43
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCA
Found at i:54042416 original size:25 final size:26
Alignment explanation
Indices: 54042317--54042452 Score: 163
Period size: 26 Copynumber: 5.3 Consensus size: 26
54042307 GAGGAAGTGC
* *
54042317 AAAAGTGCTTATACCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
54042343 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
54042369 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* ***
54042395 AAAAGGGCTT-TGCCCCAATTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTG
54042420 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
54042443 AAAAGAGGCT
1 AAAAG-GGCT
54042453 GGGCCTCCAG
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 28 0.29
26 56 0.58
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:54042735 original size:31 final size:31
Alignment explanation
Indices: 54042700--54042809 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
54042690 CGTTTACAGT
*
54042700 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
54042731 AAAGGCTTCGGCCCAGTGCTATAATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
54042762 AAAGACTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
54042793 AAAGGCTTCGGACCAGT
1 AAAGGCTTCGGCCCAGT
54042810 AACCGTTAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:54052647 original size:24 final size:25
Alignment explanation
Indices: 54052620--54052682 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
54052610 TCAACCGTAT
* * *
54052620 TCGCACACATAGTGCTA-ATTACAC
1 TCGCACACATAGTGCCATAGTAAAC
54052644 TCGCACACATAGTGCCATAGTAAAC
1 TCGCACACATAGTGCCATAGTAAAC
54052669 -CGCACACATAGTGC
1 TCGCACACATAGTGC
54052683 ATTGGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (25 bp):
TCGCACACATAGTGCCATAGTAAAC
Found at i:54067936 original size:55 final size:53
Alignment explanation
Indices: 54067801--54068009 Score: 208
Period size: 55 Copynumber: 3.9 Consensus size: 53
54067791 ATCCTTTTGA
* * *
54067801 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCTTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * *
54067854 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* *** *
54067908 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCATA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* *
54067961 AAACCTTACCAATTGCCATGCCTTTG-CATGGTCTTACATGGTATCCTTG
1 -AA-CTTACCAA-TGCCATGTC-TTGACATGGTCTTACATGGGATCCTTG
54068010 AACTCAAATG
Statistics
Matches: 128, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
52 2 0.02
53 45 0.35
54 8 0.06
55 68 0.53
56 5 0.04
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:54067945 original size:108 final size:110
Alignment explanation
Indices: 54067801--54068001 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
54067791 ATCCTTTTGA
* * **
54067801 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCTTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCATA-GAAACCTCACCAA
54067864 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
* * *
54067909 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCATAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCATAGAAACCTCACCAAT
*
54067974 TGCCATGCCTTTGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
54068002 TATCCTTGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.57
109 7 0.09
110 27 0.33
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCATAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
Found at i:54075215 original size:27 final size:27
Alignment explanation
Indices: 54074844--54075331 Score: 563
Period size: 27 Copynumber: 18.1 Consensus size: 27
54074834 CCAAAGTACT
54074844 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
*
54074871 CTCGATTTACAGAATTATCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
** * * *
54074898 CTCGATTTTTAAAATTATCATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
54074925 CTCGATTTACAGAATTACCGTTTT-CC
1 CTCGATTTACAGAATTACCGTTTTACC
*
54074951 CTC-AGTTTACAGAATTACCATTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
* *
54074978 CTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
**
54075005 CTC-AGTTTACAGAATTACTATTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
54075032 CTAC-ATTTACAGAATTACCGTTTTACC
1 CT-CGATTTACAGAATTACCGTTTTACC
* ** * ***
54075059 CTCAATTTGTAAAATTATTATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
54075086 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
*
54075113 CTC-AGTTTACAGAATTACCATTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
*
54075140 CTCGATTTACAGAATTATCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* *
54075167 CTCAATTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
**
54075194 CTCGATTTACAGAATTATTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
** * *
54075221 CTCGATTTGTAAAATTATCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* * * *
54075248 CTCGATTTATAAAATTACTGGTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* ***
54075275 CTCGATTTACAAAATTATTATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* *
54075302 CTCAATTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
54075329 CTC
1 CTC
54075332 AATTGTGAAA
Statistics
Matches: 400, Mismatches: 53, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
25 1 0.00
26 26 0.06
27 369 0.92
28 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
CTCGATTTACAGAATTACCGTTTTACC
Found at i:54075377 original size:26 final size:26
Alignment explanation
Indices: 54075348--54075530 Score: 208
Period size: 27 Copynumber: 7.0 Consensus size: 26
54075338 GAAATTACTA
*
54075348 AAATACCCCTGTAGGGTAGAATTTCG
1 AAATACCCCTGTAGGGTAGAATTACG
*
54075374 AAATACCCCTATAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTAC-G
* * *
54075401 AAATACCCTTATA-GGTAGAATTACC
1 AAATACCCCTGTAGGGTAGAATTACG
54075426 AAATACCCC-GTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTA-CG
* *
54075452 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAATTA-CG
54075479 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTA-CG
* ** * *
54075506 AGATACCTTTGTGGGGTAAAATTAC
1 AAATACCCCTGTAGGGTAGAATTAC
54075531 CATTTTGCTC
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.01
25 18 0.13
26 44 0.32
27 72 0.53
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (26 bp):
AAATACCCCTGTAGGGTAGAATTACG
Found at i:54075467 original size:78 final size:79
Alignment explanation
Indices: 54075348--54075504 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 79
54075338 GAAATTACTA
* * *
54075348 AAATACCCCTGTAGGGTAGAATTTCGAAATACCCCTATAGGGTAGAATTACTGAAATACCCTTAT
1 AAATACCCCTGTAGGGTAGAATTTCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTAT
54075413 A-GGTAGAATTACC
66 AGGGTAGAATTACC
* * *
54075426 AAATACCCC-GTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTG
1 AAATACCCCTGTAGGGTAGAATT-TCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTA
54075490 TAGGGTAGAATTACC
65 TAGGGTAGAATTACC
54075505 GAGATACCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
77 13 0.18
78 46 0.65
79 12 0.17
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (79 bp):
AAATACCCCTGTAGGGTAGAATTTCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTAT
AGGGTAGAATTACC
Found at i:54075768 original size:27 final size:26
Alignment explanation
Indices: 54075730--54075812 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
54075720 CGGAGGAAGC
*
54075730 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
54075757 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
54075783 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
54075810 GTT
1 GTT
54075813 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:54075932 original size:22 final size:22
Alignment explanation
Indices: 54075900--54075958 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
54075890 CCCATTTTTA
*
54075900 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
54075922 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
54075944 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
54075959 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:54076323 original size:6 final size:6
Alignment explanation
Indices: 54076314--54076421 Score: 132
Period size: 6 Copynumber: 17.8 Consensus size: 6
54076304 TTGCATTCAC
*
54076314 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* *
54076362 -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
54076411 ATTCTG ATTCT
1 ATTCTG ATTCT
54076422 CATTTTGGTT
Statistics
Matches: 89, Mismatches: 6, Indels: 14
0.82 0.06 0.13
Matches are distributed among these distances:
5 5 0.06
6 78 0.88
7 5 0.06
8 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:54078463 original size:27 final size:27
Alignment explanation
Indices: 54078431--54078916 Score: 530
Period size: 27 Copynumber: 18.0 Consensus size: 27
54078421 AAAGTACTCC
*
54078431 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078458 CAATTTATAGAATTATCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078485 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078512 CGATTTACAAAATTACCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* * *
54078539 C-AGTTTACATAATTACCATTTTACCCT
1 CGA-TTTATAGAATTACCGTTTTACCCT
* *
54078566 TGATTTATAGAATTACCATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* * **
54078593 C-AGTTTACAAAATTACTATTTTACCCT
1 CGA-TTTATAGAATTACCGTTTTACCCT
54078620 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* * * *
54078647 CAATTTGTAAAATTACTGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* * * *
54078674 TGATTTACAGAATTATCATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078701 C-ATTTACAGAATTACCATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078727 CGATTTATAGAATTATCATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
**
54078754 C-AGTTTATAGAATTATTGTTTTACCCT
1 CGA-TTTATAGAATTACCGTTTTACCCT
* *
54078781 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078808 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* *
54078835 CGATTTATAGAATTACTGGTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* * * *
54078862 CGGTTTACAGAATTATCATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
* **
54078889 CAATTTATAGAATTACTATTTTACCCT
1 CGATTTATAGAATTACCGTTTTACCCT
54078916 C
1 C
54078917 AATTATGAAA
Statistics
Matches: 391, Mismatches: 61, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
26 28 0.07
27 360 0.92
28 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
CGATTTATAGAATTACCGTTTTACCCT
Found at i:54078939 original size:26 final size:27
Alignment explanation
Indices: 54078883--54078941 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
54078873 ATTATCATTT
***
54078883 TACCCTCAATTTATAGAATTACTATTT
1 TACCCTCAATTTATAGAATTACTAAAA
54078910 TACCCTCAA-TTAT-GAAATTACTAAAA
1 TACCCTCAATTTATAG-AATTACTAAAA
54078936 TACCCT
1 TACCCT
54078942 TGTAGGGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.64
27 9 0.32
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (27 bp):
TACCCTCAATTTATAGAATTACTAAAA
Found at i:54078963 original size:27 final size:27
Alignment explanation
Indices: 54078933--54079119 Score: 225
Period size: 27 Copynumber: 7.0 Consensus size: 27
54078923 GAAATTACTA
54078933 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
54078960 AAATACCCCTATAGGGTAGAATTA-CT
1 AAATACCCTTGTAGGGTAGAATTACCG
* *
54078986 ATATTACCCTTATAGGGT-GAATTACCG
1 A-AATACCCTTGTAGGGTAGAATTACCG
** *
54079013 AAATACCCCCGTAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACCG
*
54079040 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* *
54079067 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
54079094 AGATACCTTTGTGGGGTAGAATTACC
1 AAATACCCTTGTAGGGTAGAATTACC
54079120 ATTTTGCCCC
Statistics
Matches: 134, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 20 0.15
27 114 0.85
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (27 bp):
AAATACCCTTGTAGGGTAGAATTACCG
Found at i:54078980 original size:80 final size:80
Alignment explanation
Indices: 54078896--54079060 Score: 206
Period size: 80 Copynumber: 2.1 Consensus size: 80
54078886 CCTCAATTTA
* ** * **
54078896 TAGAATTACTATTTTACCCTCA-ATTATGAAATTACTAAAATACCCTTGTAGGGTAGAATTACCG
1 TAGAATTACTATATTACCCTCATAGGATG-AATTACCAAAATACCCCCGTAGGGTAGAATTACCG
54078960 AAATACCCCTATAGGG
65 AAATACCCCTATAGGG
* * * *
54078976 TAGAATTACTATATTACCCTTATAGGGTGAATTACCGAAATACCCCCGTAGGGTAGAATTATCGA
1 TAGAATTACTATATTACCCTCATAGGATGAATTACCAAAATACCCCCGTAGGGTAGAATTACCGA
* *
54079041 AATACCCTTGTAGGG
66 AATACCCCTATAGGG
54079056 TAGAA
1 TAGAA
54079061 ATACCGAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 69 0.96
81 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (80 bp):
TAGAATTACTATATTACCCTCATAGGATGAATTACCAAAATACCCCCGTAGGGTAGAATTACCGA
AATACCCCTATAGGG
Found at i:54078995 original size:54 final size:54
Alignment explanation
Indices: 54078933--54079119 Score: 270
Period size: 54 Copynumber: 3.5 Consensus size: 54
54078923 GAAATTACTA
* *
54078933 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTA-CT
1 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCG
* * *
54078986 ATATTACCCTTATAGGGT-GAATTACCGAAATACCCCCGTAGGGTAGAATTATCG
1 A-AATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCG
*
54079040 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCG
* * *
54079094 AGATACCTTTGTGGGGTAGAATTACC
1 AAATACCCTTGTAGGGTAGAATTACC
54079120 ATTTTGCCCC
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
53 46 0.39
54 72 0.61
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (54 bp):
AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCG
Found at i:54079356 original size:27 final size:26
Alignment explanation
Indices: 54079318--54079400 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
54079308 CGGAGGAAGC
*
54079318 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
54079345 GTTCTGGTGGCTCTGCTACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
54079371 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
54079398 GTT
1 GTT
54079401 GACCGATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 10 0.20
27 39 0.80
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:54079733 original size:27 final size:27
Alignment explanation
Indices: 54079711--54079777 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
54079701 TAGGTGGGTT
*
54079711 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
54079738 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
54079765 TGTCACGATATCT
1 TGCCACAATATCT
54079778 ATTCTGGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:54079934 original size:6 final size:6
Alignment explanation
Indices: 54079927--54080064 Score: 133
Period size: 6 Copynumber: 22.8 Consensus size: 6
54079917 CGGTCACGTA
*
54079927 ATTCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * *
54079975 ATTCTG -TCACCTA ATTCTG ATTCTG ATTTTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
*
54080024 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
54080065 CATTTTGGTT
Statistics
Matches: 110, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
5 8 0.07
6 93 0.85
7 7 0.06
8 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:54079969 original size:30 final size:30
Alignment explanation
Indices: 54079930--54080064 Score: 167
Period size: 30 Copynumber: 4.7 Consensus size: 30
54079920 TCACGTAATT
54079930 CTAATTCTGATTCTGATTCTGATTCTG-T-
1 CTAATTCTGATTCTGATTCTGATTCTGTTA
*
54079958 -T-A--CTGATTCTGATTCTGATTCTGTCA
1 CTAATTCTGATTCTGATTCTGATTCTGTTA
*
54079984 CCTAATTCTGATTCTGATTTTGATTCTGTTA
1 -CTAATTCTGATTCTGATTCTGATTCTGTTA
54080015 CTAATAT-TGATTCTGATTCTGATTCTGTTA
1 CTAAT-TCTGATTCTGATTCTGATTCTGTTA
* *
54080045 CTGATTCTGATTTTGATTCT
1 CTAATTCTGATTCTGATTCT
54080065 CATTTTGGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
24 21 0.23
26 1 0.01
27 1 0.01
28 1 0.01
29 2 0.02
30 43 0.47
31 23 0.25
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.50
Consensus pattern (30 bp):
CTAATTCTGATTCTGATTCTGATTCTGTTA
Found at i:54079989 original size:55 final size:55
Alignment explanation
Indices: 54079930--54080035 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
54079920 TCACGTAATT
*
54079930 CTAATTCTGATTCTGATTCTGATTCTGTTACTGAT-TCTGATTCTGATTCTGTCAC
1 CTAATTCTGATTCTGATTCTGATTCTGTTACTAATAT-TGATTCTGATTCTGTCAC
*
54079985 CTAATTCTGATTCTGATTTTGATTCTGTTACTAATATTGATTCTGATTCTG
1 CTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTCTGATTCTG
54080036 ATTCTGTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
55 47 0.98
56 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (55 bp):
CTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTCTGATTCTGTCAC
Found at i:54079998 original size:61 final size:61
Alignment explanation
Indices: 54079902--54080064 Score: 213
Period size: 61 Copynumber: 2.7 Consensus size: 61
54079892 TTGCATTCAC
* * * **
54079902 ATTCTGATTCTGATTCGGTCACGTAATTCTAATTCTGATTCTGATTCTGATT-CTGTTACTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG-TTACTAATACTG
* *
54079963 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTTTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
* * *
54080024 ATTCTGATTCTGATTCTGTTA-CTGATTCTGATTTTGATTCT
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCT
54080065 CATTTTGGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
60 19 0.21
61 71 0.79
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (61 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:54081730 original size:39 final size:39
Alignment explanation
Indices: 54081687--54081885 Score: 283
Period size: 39 Copynumber: 5.1 Consensus size: 39
54081677 ATGCAAGATA
* *
54081687 CTGGAAATGTATCTGGGCTAAAGTCCCACAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
54081726 CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
** *
54081765 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCATG
1 CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
* * *
54081804 CTGGAAATGTATTCGGGCTAAAGT-CCAGTAAGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCA-CAGGCTTCGTG
* * *
54081843 CAGGAAATGTATCCGGGCTAAAGTCCTACAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
54081882 CTGG
1 CTGG
54081886 TAATATAATT
Statistics
Matches: 142, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 2 0.01
39 138 0.97
40 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTG
Found at i:54086121 original size:16 final size:16
Alignment explanation
Indices: 54086102--54086132 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54086092 CTTCTTCACT
54086102 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54086118 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54086133 TTAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:54086122 original size:20 final size:20
Alignment explanation
Indices: 54086099--54086138 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54086089 AAACTTCTTC
*
54086099 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATTAAAT
*
54086119 ACTTACTTACTTAATTAAAT
1 ACTTACTCACTTAATTAAAT
54086139 TTATTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (20 bp):
ACTTACTCACTTAATTAAAT
Found at i:54086579 original size:55 final size:53
Alignment explanation
Indices: 54086347--54086579 Score: 201
Period size: 55 Copynumber: 4.4 Consensus size: 53
54086337 TGACTTGTTG
* * * *
54086347 TGGTCTTACGTGGTATCCTT---TT-GAAACTTACCATTGTCATGTCTTGACA
1 TGGTCTTACATGGTATCCTTGCCTTAGAAACTTACCAATGCCATGCCTTGACA
* * * *
54086396 TGGTCTTACATGATATCCTTTCCTTATG-AACTCACCAATGCCATGCCTTGGCA
1 TGGTCTTACATGGTATCCTTGCCTTA-GAAACTTACCAATGCCATGCCTTGACA
* * * * * *
54086449 TGGTTTTACATGGGA-CCTTTTCCTTATAGTAACTTATCAATGCCATGTCTTGACA
1 TGGTCTTACATGGTATCC-TTGCC-T-TAGAAACTTACCAATGCCATGCCTTGACA
* * *
54086504 -GAGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAATTGCCATGCCTTGGCA
1 TG-GTCTTACATGGTATCCTTGCCTTAGAAA-CTTACCAA-TGCCATGCCTTGACA
54086559 TGGTCTTACATGGTATCCTTG
1 TGGTCTTACATGGTATCCTTG
54086580 AACCCTAATG
Statistics
Matches: 145, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
49 18 0.12
52 4 0.03
53 42 0.29
54 12 0.08
55 66 0.46
56 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (53 bp):
TGGTCTTACATGGTATCCTTGCCTTAGAAACTTACCAATGCCATGCCTTGACA
Found at i:54088958 original size:22 final size:23
Alignment explanation
Indices: 54088930--54088973 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
54088920 TATCCCTACA
*
54088930 TGGAGTGTAG-GGCTGGATGGAG
1 TGGAGTGTAGAGGATGGATGGAG
54088952 TGGAGTGTAGAGGATGGATGGA
1 TGGAGTGTAGAGGATGGATGGA
54088974 TAGGAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.23, C:0.02, G:0.52, T:0.23
Consensus pattern (23 bp):
TGGAGTGTAGAGGATGGATGGAG
Found at i:54092790 original size:21 final size:21
Alignment explanation
Indices: 54092764--54092808 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
54092754 TTTGGGTTGT
54092764 GTGTTGGTGCAAAAAGGTAAG
1 GTGTTGGTGCAAAAAGGTAAG
54092785 GTGTTGGTGCAAAAAGGTAAG
1 GTGTTGGTGCAAAAAGGTAAG
54092806 GTG
1 GTG
54092809 GTGGCTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.40, T:0.24
Consensus pattern (21 bp):
GTGTTGGTGCAAAAAGGTAAG
Found at i:54101172 original size:27 final size:27
Alignment explanation
Indices: 54101121--54101220 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 27
54101111 AGGAAGTGTC
*
54101121 CTGGTGGCTATG-C-CATAATTATCTGAT
1 CTGGTGGCTCTGTCACAT-ATT-TCTGAT
*
54101148 CTGGTGGCTCTGTCACATATTTCTGTT
1 CTGGTGGCTCTGTCACATATTTCTGAT
*
54101175 CTGGTGGCTCT-TCCACGAT-TATCTGTAT
1 CTGGTGGCTCTGT-CAC-ATATTTCTG-AT
*
54101203 CTGGTGACTCTGTCACAT
1 CTGGTGGCTCTGTCACAT
54101221 TATCTGTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 37 0.60
28 20 0.32
29 4 0.06
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTCTGTCACATATTTCTGAT
Found at i:54101222 original size:27 final size:26
Alignment explanation
Indices: 54101138--54101232 Score: 120
Period size: 27 Copynumber: 3.5 Consensus size: 26
54101128 CTATGCCATA
*
54101138 ATTATCTGATCTGGTGGCTCTGTCAC
1 ATTATCTGTTCTGGTGGCTCTGTCAC
*
54101164 ATATTTCTGTTCTGGTGGCTCT-TCCAC
1 AT-TATCTGTTCTGGTGGCTCTGT-CAC
*
54101191 GATTATCTGTATCTGGTGACTCTGTCAC
1 -ATTATCTGT-TCTGGTGGCTCTGTCAC
54101219 ATTATCTGTTCTGG
1 ATTATCTGTTCTGG
54101233 CAGCCATGCT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
26 8 0.13
27 35 0.58
28 16 0.27
29 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (26 bp):
ATTATCTGTTCTGGTGGCTCTGTCAC
Found at i:54104663 original size:43 final size:43
Alignment explanation
Indices: 54104580--54104664 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
54104570 AAGTCGTACA
** *
54104580 ATGCCAATGTCCCAGACGTGGTCTTACATGTAGCCTCATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACACATATCG
*
54104623 ATGCCATTGTCCCAGACAG-GGTCTTAC-TCGTAAACACATATC
1 ATGCCAATGTCCCAGAC-GTGGTCTTACAT-GTAAACACATATC
54104665 AGAATCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 34 0.94
44 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:54112679 original size:27 final size:27
Alignment explanation
Indices: 54112648--54112825 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54112638 TAAATTGTAC
54112648 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54112675 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54112701 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54112729 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54112757 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54112784 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54112811 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54112826 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54112762 original size:82 final size:81
Alignment explanation
Indices: 54112649--54112804 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54112639 AAATTGTACA
* *
54112649 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54112713 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54112730 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54112795 TGCGAGTTGA
65 TGCGAATTGA
54112805 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54112816 original size:82 final size:81
Alignment explanation
Indices: 54112645--54112825 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54112635 GATTAAATTG
* *
54112645 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54112710 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54112726 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54112790 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54112808 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54112826 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.