Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 158 of 345
Found at i:43749852 original size:27 final size:27
Alignment explanation
Indices: 43749822--43750025 Score: 291
Period size: 27 Copynumber: 7.6 Consensus size: 27
43749812 TGATTTTTGA
* *
43749822 AATTACCGAAATACCCTTGTAGAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
43749849 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43749876 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43749903 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
43749930 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43749957 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
43749984 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43750011 AATTACCGAGATACC
1 AATTACCGAAATACC
43750026 TTATGGGGTA
Statistics
Matches: 159, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 159 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:43749853 original size:54 final size:54
Alignment explanation
Indices: 43749795--43750015 Score: 284
Period size: 54 Copynumber: 4.1 Consensus size: 54
43749785 TGGTTTGTAA
*** * * * *
43749795 AATTATCAAAATACCCCTG-ATTTTTGAAATTACCGAAATACCCTTGTAGAGTAG
1 AATTATCAAAATACCCCTGTAGGGTAG-AATTATCGAAATACCCCTGTAGGGTAG
**
43749849 AATTATCGGAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAG
1 AATTATCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAG
* *
43749903 AATTACCAAAATACCCCTGTAGGGTAGAATTATCGCAATACCCCTGTAGGGTAG
1 AATTATCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAG
* * *
43749957 AATTATCGAAATACCCCTGTAGGGTAGAATTA-CTAAAATACCCCTGTAGGGTGG
1 AATTATCAAAATACCCCTGTAGGGTAGAATTATC-GAAATACCCCTGTAGGGTAG
43750011 AATTA
1 AATTA
43750016 CCGAGATACC
Statistics
Matches: 147, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 143 0.97
55 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (54 bp):
AATTATCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAG
Found at i:43749853 original size:81 final size:82
Alignment explanation
Indices: 43749740--43750025 Score: 305
Period size: 81 Copynumber: 3.5 Consensus size: 82
43749730 TTTGTTTACA
* * * ** *
43749740 AAATTACCAAAATACCCTTGATCA-A-TAAAATTACCAAAATACCCCTGGT-TTGTAAAATTATC
1 AAATTACCAAAATACCCTTG-T-AGAGTAGAATTATCGAAATACCCCT-GTAGGGTAGAATTATC
* *** *
43749802 AAAATACCCCTG-ATTTTTG
63 GAAATACCCCTGTAGGGTAG
* *
43749821 AAATTACCGAAATACCCTTGTAGAGTAGAATTATCGGAATACCCCTGTAGGGTAGAATTATCGAA
1 AAATTACCAAAATACCCTTGTAGAGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTATCGAA
43749886 ATACCCCTGTAGGGTAG
66 ATACCCCTGTAGGGTAG
* * *
43749903 -AATTACCAAAATACCCCTGTAGGGTAGAATTATCGCAATACCCCTGTAGGGTAGAATTATCGAA
1 AAATTACCAAAATACCCTTGTAGAGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTATCGAA
43749967 ATACCCCTGTAGGGTAG
66 ATACCCCTGTAGGGTAG
* * * * * *
43749984 -AATTACTAAAATACCCCTGTAGGGTGGAATTACCGAGATACC
1 AAATTACCAAAATACCCTTGTAGAGTAGAATTATCGAAATACC
43750026 TTATGGGGTA
Statistics
Matches: 179, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
79 1 0.01
80 4 0.02
81 171 0.96
82 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (82 bp):
AAATTACCAAAATACCCTTGTAGAGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTATCGAA
ATACCCCTGTAGGGTAG
Found at i:43750707 original size:25 final size:27
Alignment explanation
Indices: 43750675--43750768 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
43750665 AATGGCTTTG
* *
43750675 TGCCACATAT-TCTGTT-AAGTGGCTT
1 TGCCACATATATCTGTTCTAGTGGCTA
*
43750700 TGCCACAT-TATCTGTTTCTGGTGGCTA
1 TGCCACATATATCTG-TTCTAGTGGCTA
* *
43750727 TGCCACAAATATCTGTTCTAGTGGCTC
1 TGCCACATATATCTGTTCTAGTGGCTA
43750754 TGCCACA-ATATCTGT
1 TGCCACATATATCTGT
43750769 ATCTGGTGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 12 0.20
26 10 0.17
27 30 0.51
28 6 0.10
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (27 bp):
TGCCACATATATCTGTTCTAGTGGCTA
Found at i:43750723 original size:27 final size:27
Alignment explanation
Indices: 43750693--43750794 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
43750683 ATTCTGTTAA
* *
43750693 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
*
43750720 GTGGCTATGCCACAAATATCTG-TTCTA
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* *
43750747 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * * *
43750774 GTGACTCTGTCATAATATCTG
1 GTGGCTATGCCACAATATCTG
43750795 ATAACTGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 8 0.12
27 49 0.77
28 7 0.11
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:43750750 original size:54 final size:52
Alignment explanation
Indices: 43750675--43750776 Score: 141
Period size: 54 Copynumber: 1.9 Consensus size: 52
43750665 AATGGCTTTG
* * * *
43750675 TGCCACATATTCTGTTAAGTGGCTTTGCCACATTATCTGTTTCTGGTGGCTA
1 TGCCACAAATTCTGTTAAGTGGCTCTGCCACAATATCTGTATCTGGTGGCTA
*
43750727 TGCCACAAATATCTGTTCTAGTGGCTCTGCCACAATATCTGTATCTGGTG
1 TGCCACAAAT-TCTGTT-AAGTGGCTCTGCCACAATATCTGTATCTGGTG
43750777 ACTCTGTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 9 0.21
53 6 0.14
54 28 0.65
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (52 bp):
TGCCACAAATTCTGTTAAGTGGCTCTGCCACAATATCTGTATCTGGTGGCTA
Found at i:43750963 original size:19 final size:19
Alignment explanation
Indices: 43750941--43750998 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
43750931 TTCTGTTTTT
43750941 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
43750960 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
43750972 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
43750991 TGATTCTG
1 TGATTCTG
43750999 ATTTTGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:43750968 original size:6 final size:6
Alignment explanation
Indices: 43750953--43751008 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
43750943 ATTCTGTTAC
* * *
43750953 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
*
43751002 TTGATT C
1 CTGATT C
43751009 CAATCCTAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
5 2 0.05
6 34 0.85
7 3 0.08
8 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:43750974 original size:31 final size:31
Alignment explanation
Indices: 43750938--43751008 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
43750928 ACATTCTGTT
43750938 TTTTGATTCTGTTACCTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
43750969 TTTTGATTCTGTTACCTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
43751000 TTTTGATTC
1 TTTTGATTC
43751009 CAATCCTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTTGATTCTGTTACCTGATACTGATTCTGA
Found at i:43752471 original size:37 final size:37
Alignment explanation
Indices: 43752412--43752557 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
43752402 AGCTCAGACG
* *
43752412 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
43752449 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
43752486 TAATCACCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43752523 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
43752558 ATATATTTCC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:43752858 original size:47 final size:47
Alignment explanation
Indices: 43752766--43752864 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 47
43752756 ATATATATTT
* * ** *
43752766 CACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGACCATTCGGCCTTACCACATATATACACATTCACATTCAC
* * * * *
43752813 CACATTGGCCATTTGGCCTTATCTCATATATACACATTCACATTCAT
1 CACATTGACCATTCGGCCTTACCACATATATACACATTCACATTCAC
43752860 CACAT
1 CACAT
43752865 AAAATCCTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
CACATTGACCATTCGGCCTTACCACATATATACACATTCACATTCAC
Found at i:43759169 original size:22 final size:22
Alignment explanation
Indices: 43759093--43759170 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
43759083 CTGAAACACC
*
43759093 ATTTGTGGACAAGCCACCACTG
1 ATTTGTGGACAAGCCACCACTA
* * * *
43759115 ATTTGTAGATAAACTACCACTGATAA
1 ATTTGTGGACAAGCCACCAC---T-A
43759141 CACTTTGTGGACAAGCCACCACTA
1 -A-TTTGTGGACAAGCCACCACTA
43759165 ATTTGT
1 ATTTGT
43759171 AGATAAACTG
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
22 21 0.51
23 1 0.02
24 1 0.02
25 2 0.05
27 1 0.02
28 15 0.37
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (22 bp):
ATTTGTGGACAAGCCACCACTA
Found at i:43762533 original size:49 final size:49
Alignment explanation
Indices: 43762454--43762565 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 49
43762444 TAAAAAAAGG
* * * *
43762454 GGAA-ACATGGCCATGTGGAACGCCCTAGACCGTTTGACTTTCAAAATT
1 GGAACACATGGCCATGTGGAACGCCCAAGACCATTTGACATTAAAAATT
** *
43762502 GGAACACATGGCTGTGTGGAATGCCCAAGACCATTTGACATTAAAAATT
1 GGAACACATGGCCATGTGGAACGCCCAAGACCATTTGACATTAAAAATT
*
43762551 GGGACACA--GCCATGT
1 GGAACACATGGCCATGT
43762566 CCTTGCTCGT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.09
48 4 0.08
49 44 0.83
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (49 bp):
GGAACACATGGCCATGTGGAACGCCCAAGACCATTTGACATTAAAAATT
Found at i:43764743 original size:19 final size:19
Alignment explanation
Indices: 43764719--43764758 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43764709 CTGTGCATTC
43764719 TTCTTTCTCTTT-TCTTTCT
1 TTCTTT-TCTTTATCTTTCT
*
43764738 TTCTTTTCTTTATTTTTCT
1 TTCTTTTCTTTATCTTTCT
43764757 TT
1 TT
43764759 TAATTTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTTCTTTATCTTTCT
Found at i:43769078 original size:26 final size:26
Alignment explanation
Indices: 43769048--43769122 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
43769038 TTTCACTTGC
43769048 TTTTCTCTCTTCCATTTCCTTTCTTA
1 TTTTCTCTCTTCCATTTCCTTTCTTA
* * *
43769074 TTTTC-C-CAT---TTTACTTGC---
1 TTTTCTCTCTTCCATTTCCTTTCTTA
43769092 TTTTCTCTCTTCCATTTCCTTTCTTA
1 TTTTCTCTCTTCCATTTCCTTTCTTA
43769118 TTTTC
1 TTTTC
43769123 CCATTCCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 2 0.06
21 7 0.20
23 7 0.20
24 2 0.06
25 1 0.03
26 10 0.29
ACGTcount: A:0.08, C:0.29, G:0.01, T:0.61
Consensus pattern (26 bp):
TTTTCTCTCTTCCATTTCCTTTCTTA
Found at i:43769084 original size:20 final size:20
Alignment explanation
Indices: 43769059--43769133 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
43769049 TTTCTCTCTT
43769059 CCATTTCCTTTCTTATTTTC
1 CCATTTCCTTTCTTATTTTC
* *
43769079 CCATTTTACTTGCTT-TTCTCTC
1 CCA-TTTCCTTTCTTATT-T-TC
43769101 TTCCATTTCCTTTCTTATTTTC
1 --CCATTTCCTTTCTTATTTTC
*
43769123 CCATTCCCTTT
1 CCATTTCCTTT
43769134 GCTGATTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 15 0.34
21 10 0.23
22 4 0.09
23 10 0.23
24 5 0.11
ACGTcount: A:0.09, C:0.32, G:0.01, T:0.57
Consensus pattern (20 bp):
CCATTTCCTTTCTTATTTTC
Found at i:43769091 original size:44 final size:44
Alignment explanation
Indices: 43769042--43769127 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
43769032 TCTCTCTTTC
43769042 ACTTGCTTTTCTCTCTTCCATTTCCTTTCTTATTTTCCCATTTT
1 ACTTGCTTTTCTCTCTTCCATTTCCTTTCTTATTTTCCCATTTT
43769086 ACTTGCTTTTCTCTCTTCCATTTCCTTTCTTATTTTCCCATT
1 ACTTGCTTTTCTCTCTTCCATTTCCTTTCTTATTTTCCCATT
43769128 CCCTTTGCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.09, C:0.30, G:0.02, T:0.58
Consensus pattern (44 bp):
ACTTGCTTTTCTCTCTTCCATTTCCTTTCTTATTTTCCCATTTT
Found at i:43771895 original size:19 final size:19
Alignment explanation
Indices: 43771871--43771910 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43771861 GATTTGGCTG
43771871 AACCCTTATAGGGTGTTCT
1 AACCCTTATAGGGTGTTCT
43771890 AACCCTTATAGGGTGTTCT
1 AACCCTTATAGGGTGTTCT
43771909 AA
1 AA
43771911 GGCTGGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (19 bp):
AACCCTTATAGGGTGTTCT
Found at i:43776866 original size:50 final size:49
Alignment explanation
Indices: 43776810--43776946 Score: 211
Period size: 50 Copynumber: 2.8 Consensus size: 49
43776800 GTATGAGATC
43776810 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGTGAT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGTGAT
*
43776859 CTCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGTGAAT
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGTG-AT
* * * *
43776910 CCATGTAAGACCATATCTGGGATACGACATTGGCATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
43776947 TTACTATGTG
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.01
50 76 0.95
51 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGTGAT
Found at i:43778690 original size:40 final size:40
Alignment explanation
Indices: 43778607--43778903 Score: 379
Period size: 40 Copynumber: 7.5 Consensus size: 40
43778597 AAGCCAAGTA
* * * * * *
43778607 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
43778646 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
43778686 CCTTCGGGACTTAGCCCGGA-ACTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
43778726 CCTTCGGGACTTAGCCCGGATATGGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
43778766 CCTTCGGGACTTAGCTCGGATATGGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
43778806 CCTTTGGGACTTAGCCCGGATATGGTAACTCGCACATATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
43778846 CCTTCGGG-CTTAGCCCGGA-ATTAGCCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
43778885 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
43778904 TTATCAATCC
Statistics
Matches: 231, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.00
39 45 0.19
40 184 0.80
41 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:43791052 original size:22 final size:23
Alignment explanation
Indices: 43791027--43791080 Score: 101
Period size: 22 Copynumber: 2.4 Consensus size: 23
43791017 GTAATTATAG
43791027 AAAATTAAAGTGGCTAACAT-AA
1 AAAATTAAAGTGGCTAACATAAA
43791049 AAAATTAAAGTGGCTAACATAAA
1 AAAATTAAAGTGGCTAACATAAA
43791072 AAAATTAAA
1 AAAATTAAA
43791081 AGTTGGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.22
Consensus pattern (23 bp):
AAAATTAAAGTGGCTAACATAAA
Found at i:43793724 original size:25 final size:21
Alignment explanation
Indices: 43793698--43793739 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43793688 AAAGATAAAG
43793698 AAAGAAAAACAAAGTTTTAGT
1 AAAGAAAAACAAAGTTTTAGT
43793719 AAAGAAAAACAAAGTTTTAGT
1 AAAGAAAAACAAAGTTTTAGT
43793740 TGTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGAAAAACAAAGTTTTAGT
Found at i:43796476 original size:27 final size:27
Alignment explanation
Indices: 43796391--43796478 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
43796381 ACCCCAATTT
* * **
43796391 GTAAAATTACCGAAATACCCCTG-ATTT
1 GTAAAATTATCGAAATACCCTTGTA-AG
*
43796418 GTAAAATTATCGAAATACCCTTAT-AG
1 GTAAAATTATCGAAATACCCTTGTAAG
*
43796444 CATAAAATTATCGAAATACCCTTGTAAG
1 -GTAAAATTATCGAAATACCCTTGTAAG
43796472 GTAAAAT
1 GTAAAAT
43796479 GACTATTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
27 48 0.96
28 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCTTGTAAG
Found at i:43798275 original size:23 final size:23
Alignment explanation
Indices: 43798249--43798296 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
43798239 AGGTAAGTTC
43798249 ATACATTATGAATCTATTCGTTT
1 ATACATTATGAATCTATTCGTTT
43798272 ATACATTATGAATCTATTCGTTT
1 ATACATTATGAATCTATTCGTTT
43798295 AT
1 AT
43798297 GTTTGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (23 bp):
ATACATTATGAATCTATTCGTTT
Found at i:43798590 original size:46 final size:46
Alignment explanation
Indices: 43798489--43798591 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
43798479 TATGCTGCAG
* *
43798489 ACTCGAGAATAGAGGATTAGGTTCCAAGCTCTTGCATATGTTGTGG
1 ACTCGAGAATAGAGGATTAGGTTCCAAGCTCCTGCATATGTTGTGA
* * * * *
43798535 ACTCAAGAATATG-GGATTAGGTTCCGAGTTCCTGTATATGTTTTGA
1 ACTCGAGAATA-GAGGATTAGGTTCCAAGCTCCTGCATATGTTGTGA
*
43798581 ACTTGAGAATA
1 ACTCGAGAATA
43798592 CATGAATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 46 0.98
47 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (46 bp):
ACTCGAGAATAGAGGATTAGGTTCCAAGCTCCTGCATATGTTGTGA
Found at i:43803924 original size:45 final size:45
Alignment explanation
Indices: 43803837--43803927 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
43803827 GCCTAGGTCT
* *
43803837 CAAGCTCCTGCATATGTTGCAAACTCGAGAATATAGAATAGGTTC
1 CAAGCTCCTACATATGTTGCAAACTCGAGAATACAGAATAGGTTC
* *
43803882 CAAGCTCCTACATATGTTGCAGACTCGAG-ATACAGGATTAGGTTC
1 CAAGCTCCTACATATGTTGCAAACTCGAGAATACA-GAATAGGTTC
43803927 C
1 C
43803928 GGGATCTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (45 bp):
CAAGCTCCTACATATGTTGCAAACTCGAGAATACAGAATAGGTTC
Found at i:43806457 original size:48 final size:48
Alignment explanation
Indices: 43806371--43806693 Score: 380
Period size: 48 Copynumber: 6.7 Consensus size: 48
43806361 TAAAGTACCA
* * *
43806371 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATCCACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCA--CACATATCAACGCCG
* * * * * * *
43806419 ATGCTATGTCCCAAACACGGTCTTACACCGGCATACATATCAACACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
* * *
43806467 ATGCCATGTCCCAGACATAGTCTTACACTGGCACACATATCGATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
* * *
43806515 ATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAACGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
* * *
43806563 ATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAACGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
* * * *
43806611 ATGCCATGTCCCAGACAGGGTCTTACACGGGCACACATATCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
* * *
43806659 ATGCCATGTCCCAAACATGGTCTTTCACAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACA
43806694 TTTAGCACAG
Statistics
Matches: 238, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
48 236 0.99
50 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCG
Found at i:43810494 original size:26 final size:26
Alignment explanation
Indices: 43810465--43810530 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
43810455 CCTGTTATAT
* *
43810465 GGCTCTTCGTGAGCTTTCTGATTAAA
1 GGCTCTTCGTGAGCTTCCTAATTAAA
* *
43810491 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCGTGAGCTTCCTAATTAAA
*
43810517 GGCTCTCCG-GAGCT
1 GGCTCTTCGTGAGCT
43810531 ACCTGATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCTAATTAAA
Found at i:43810602 original size:25 final size:25
Alignment explanation
Indices: 43810449--43810654 Score: 88
Period size: 25 Copynumber: 8.3 Consensus size: 25
43810439 TAGCTCTTAT
*
43810449 GAGCGTCCTG-TTATATGGCTCTTCG
1 GAGCTTCCTGATTA-ATGGCTCTTCG
* * *
43810474 TGAGCTTTCTGATTAAAGGCTCTTTG
1 -GAGCTTCCTGATTAATGGCTCTTCG
* *
43810500 TGAGCTTCCTAATTAATGGCTCTCCG
1 -GAGCTTCCTGATTAATGGCTCTTCG
*
43810526 GAGCTACCTGA-T-ATGGCTCGCTT--
1 GAGCTTCCTGATTAATGGCT--CTTCG
* * * * **
43810549 AAACTT-CTCGATAAATGGCTATTTA
1 GAGCTTCCT-GATTAATGGCTCTTCG
*
43810574 GAGCTTCCTGATTAATGGCTCGTCG
1 GAGCTTCCTGATTAATGGCTCTTCG
* * * * *
43810599 GAGCTACCCG-TTATTGGCTC-ACAT
1 GAGCTTCCTGATTAATGGCTCTTC-G
* **
43810623 GAGCTTCTTGATT-ATGGCTCTTAT
1 GAGCTTCCTGATTAATGGCTCTTCG
43810647 GAGCTTCC
1 GAGCTTCC
43810655 CATTATACAG
Statistics
Matches: 132, Mismatches: 36, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
22 2 0.02
23 14 0.11
24 31 0.23
25 42 0.32
26 40 0.30
27 3 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTTCG
Found at i:43810640 original size:73 final size:73
Alignment explanation
Indices: 43810487--43810654 Score: 173
Period size: 73 Copynumber: 2.3 Consensus size: 73
43810477 GCTTTCTGAT
* * * *
43810487 TAAA-GGCTCTTTGTGAGCTTCCTAATTAATGGCTCTCCGGAGCTACCTGATATGGCTCGCTTAA
1 TAAATGGCTC-TTATGAGCTTCCTAATTAATGGCTCTCCGGAGCTACCCGATATGGCTCACATAA
43810551 ACTTCTCGA
65 ACTTCTCGA
* * *
43810560 TAAATGGCTATT-TAGAGCTTCCTGATTAATGGCTCGT-CGGAGCTACCCGTTATTGGCTCACAT
1 TAAATGGCTCTTAT-GAGCTTCCTAATTAATGGCTC-TCCGGAGCTACCCGATA-TGGCTCACAT
* * *
43810623 GAGCTTCTTGA
63 AAACTTCTCGA
*
43810634 T-TATGGCTCTTATGAGCTTCC
1 TAAATGGCTCTTATGAGCTTCC
43810655 CATTATACAG
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
72 1 0.01
73 55 0.70
74 23 0.29
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (73 bp):
TAAATGGCTCTTATGAGCTTCCTAATTAATGGCTCTCCGGAGCTACCCGATATGGCTCACATAAA
CTTCTCGA
Found at i:43810701 original size:25 final size:24
Alignment explanation
Indices: 43810644--43810709 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
43810634 TTATGGCTCT
43810644 TATGAGCTTCCCATTATACAGCCCGA
1 TATGAGCTTCCCA-T-TACAGCCCGA
*
43810670 -ATAAGCTTCCCATTACATGCCTC-A
1 TATGAGCTTCCCATTACA-GCC-CGA
*
43810694 TATGAGCTTCTCATTA
1 TATGAGCTTCCCATTA
43810710 TATGGCTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 25 0.74
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (24 bp):
TATGAGCTTCCCATTACAGCCCGA
Found at i:43813589 original size:47 final size:47
Alignment explanation
Indices: 43813536--43813728 Score: 264
Period size: 47 Copynumber: 4.1 Consensus size: 47
43813526 TTAGGATTTT
* * *
43813536 ATGTGATGAATGTGAACGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43813583 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
43813630 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
43813677 ATGTGGTGAATATGAGATATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGA-ACATGCATATATGTGATAAGGCCGAATGGCCA
43813723 ATGTGA
1 ATGTGA
43813729 AATATATATA
Statistics
Matches: 131, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
46 25 0.19
47 102 0.78
48 4 0.03
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:43813636 original size:22 final size:22
Alignment explanation
Indices: 43813565--43813636 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
43813555 GTATATATGA
43813565 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
43813587 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
43813612 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
43813634 GAT
1 GAT
43813637 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:43813685 original size:25 final size:25
Alignment explanation
Indices: 43813610--43813685 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
43813600 ATGCATATAT
43813610 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
43813635 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
43813657 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
43813682 GTGA
1 GTGA
43813686 ATATGAGATA
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:43813753 original size:50 final size:50
Alignment explanation
Indices: 43813686--43813783 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
43813676 AATGTGGTGA
43813686 ATATGAGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATAT
** *
43813736 ATATGAGATATTTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
43813784 GTAGGCGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATATAT
Found at i:43814078 original size:37 final size:37
Alignment explanation
Indices: 43813935--43814077 Score: 232
Period size: 37 Copynumber: 3.9 Consensus size: 37
43813925 AAATATATTT
*
43813935 CGGGTAAAACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
43813972 CGGGTAAGACCCGATGACTACGTGTGGAGAGTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
43814009 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
* * *
43814046 CGGGTAAGACCCGATAACTTCGTGTGGTGATT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATT
43814078 TCGTCTGAGC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
Found at i:43831803 original size:6 final size:6
Alignment explanation
Indices: 43831794--43831819 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43831784 CCATTTGCAT
43831794 TTGGGA TTGGGA TTGGGA TTGGGA TT
1 TTGGGA TTGGGA TTGGGA TTGGGA TT
43831820 TTTTTCCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTGGGA
Found at i:43834821 original size:40 final size:40
Alignment explanation
Indices: 43834696--43834847 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
43834686 TCGAATGATG
* * *
43834696 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAG-TGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACCAAA
* * *
43834736 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAA
* **
43834776 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCA-AA
* * *
43834817 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
43834848 TCGCTATATC
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 80 0.87
41 11 0.12
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCAAA
Found at i:43842068 original size:40 final size:40
Alignment explanation
Indices: 43841985--43842137 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
43841975 TCGAATGATG
* *
43841985 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
43842025 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
43842065 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
43842106 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
43842138 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:43849014 original size:10 final size:10
Alignment explanation
Indices: 43848993--43849025 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
43848983 ACATTAGTAT
43848993 TACTCAGATGG
1 TACTC-GATGG
43849004 TACTCGATGG
1 TACTCGATGG
43849014 TACTCGATGG
1 TACTCGATGG
43849024 TA
1 TA
43849026 TAGTCATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (10 bp):
TACTCGATGG
Found at i:43850584 original size:17 final size:17
Alignment explanation
Indices: 43850562--43850595 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43850552 TTGGAATCAT
43850562 TTATAAATCTTATTTAC
1 TTATAAATCTTATTTAC
43850579 TTATAAATCTTATTTAC
1 TTATAAATCTTATTTAC
43850596 ATGCACAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAAATCTTATTTAC
Found at i:43852638 original size:9 final size:9
Alignment explanation
Indices: 43852624--43852656 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
43852614 AAAGTCCATA
43852624 ATAAAATCC
1 ATAAAATCC
43852633 ATAAAAAT-C
1 AT-AAAATCC
43852642 ATAAAATCC
1 ATAAAATCC
43852651 ATAAAA
1 ATAAAA
43852657 GTCCCAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 12 0.55
10 5 0.23
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAATCC
Found at i:43862214 original size:30 final size:31
Alignment explanation
Indices: 43862138--43862220 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
43862128 TCAGTCTCGA
43862138 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
43862168 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
43862199 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
43862221 ACTGTAAGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 18 0.35
31 34 0.65
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:43862460 original size:24 final size:25
Alignment explanation
Indices: 43862433--43862484 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
43862423 GCCTAGCCTC
43862433 TTTTAAT-AACTGGGGAAAAGCCCT
1 TTTTAATAAACTGGGGAAAAGCCCT
* *
43862457 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGAAAAGCCCT
43862482 TTT
1 TTT
43862485 CGGTAAACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGAAAAGCCCT
Found at i:43862499 original size:25 final size:25
Alignment explanation
Indices: 43862440--43862509 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
43862430 CTCTTTTAAT
* *
43862440 AACTGGGGAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
43862465 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
43862490 AACTGAGGCATAA-CCCTTTT
1 AACTGGGGCA-AAGCCCTTTT
43862510 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 38 0.95
26 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:43863467 original size:27 final size:26
Alignment explanation
Indices: 43863437--43863544 Score: 92
Period size: 27 Copynumber: 3.9 Consensus size: 26
43863427 GTAAATCTAC
43863437 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTC-GTAATTTTGT
* *
43863464 AAACCAATGGTATTTC-TATATTTTTT
1 AAACCAAGGGTATTTCGTA-ATTTTGT
*
43863490 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTC-GTAATTTTGT
* * *
43863520 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTA-TTTCGTAATTTT
43863545 ACAAATTGAG
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.03
26 6 0.09
27 31 0.46
28 9 0.13
29 11 0.16
30 6 0.09
31 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.43
Consensus pattern (26 bp):
AAACCAAGGGTATTTCGTAATTTTGT
Found at i:43863550 original size:27 final size:27
Alignment explanation
Indices: 43863486--43863623 Score: 138
Period size: 27 Copynumber: 5.1 Consensus size: 27
43863476 TTTCTATATT
* *
43863486 TTTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTTACAAA-TCAGGGGTATTT-TGGTAA
**
43863514 TTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
* *
43863541 TTTTACAAAT-TGAGGGTATTTCGGTAA
1 TTTTACAAATCAG-GGGTATTTTGGTAA
* * *
43863568 TTTCACAAACCAGTGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
43863595 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
43863622 TT
1 TT
43863624 CTACCCTATA
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.03
27 81 0.88
28 8 0.09
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
TTTTACAAATCAGGGGTATTTTGGTAA
Found at i:43863642 original size:54 final size:54
Alignment explanation
Indices: 43863499--43863623 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
43863489 TAGAAAGTCA
* *** * *
43863499 AGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAATAG
*
43863553 AGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACTAG
1 AGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAA-TAG
*
43863608 -GGGTATTTTGGTAATT
1 AGGGTATTTCGGTAATT
43863624 CTACCCTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 60 0.97
55 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (54 bp):
AGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAATAG
Found at i:43863663 original size:27 final size:26
Alignment explanation
Indices: 43863521--43863663 Score: 110
Period size: 27 Copynumber: 5.3 Consensus size: 26
43863511 TAATTTTGTA
*
43863521 AATCAGGGGTATTTTGGTAATTTTAC
1 AATCAGGGGTATTTTGGTAATTTCAC
* *
43863547 AAAT-TGAGGGTATTTCGGTAATTTCAC
1 -AATCAG-GGGTATTTTGGTAATTTCAC
* * *
43863574 AAACCAGTGGTATTTTGGTAATTTTAC
1 -AATCAGGGGTATTTTGGTAATTTCAC
* *
43863601 AAACTAGGGGTATTTTGGTAATTCTACCC
1 AATC-AGGGGTATTTTGGTAATT-T-CAC
* **
43863630 TAT-AGGGGTATTTAAGTAATTTCAC
1 AATCAGGGGTATTTTGGTAATTTCAC
43863655 AATCGAGGG
1 AATC-AGGG
43863664 TAAAATGGTA
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 78 0.86
28 2 0.02
29 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (26 bp):
AATCAGGGGTATTTTGGTAATTTCAC
Found at i:43863685 original size:27 final size:27
Alignment explanation
Indices: 43863655--43863746 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
43863645 GTAATTTCAC
** *
43863655 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
43863682 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
43863709 AATCAAGGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
43863736 AATCGAGGGTA
1 AATCGAGGGTA
43863747 CTTTGGTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:43869527 original size:73 final size:74
Alignment explanation
Indices: 43869347--43869510 Score: 249
Period size: 73 Copynumber: 2.2 Consensus size: 74
43869337 TGTGCTACAT
* * * *
43869347 GGCCTAGAACACGGGCGTGTGTGTTGGCCGTGTGAAACCTACACCTAATTTTGAAAGAATTTAAT
1 GGCCTAGCACACGGGCGTGTGTCTTGGCAGTGTGAAACCTACACCTAATTTCGAAAGAATTTAAT
43869412 TAACCACAC
66 TAACCACAC
* * * *
43869421 GGCCTAGCACATGAGCGTGTGTCTTGGCAGTGTGAAACCTAGA-CTAATTTCGAAATAATTTAAT
1 GGCCTAGCACACGGGCGTGTGTCTTGGCAGTGTGAAACCTACACCTAATTTCGAAAGAATTTAAT
43869485 TAACCACAC
66 TAACCACAC
43869494 GGCCTAGCACACGGGCG
1 GGCCTAGCACACGGGCG
43869511 CGTGACATGG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 43 0.54
74 37 0.46
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (74 bp):
GGCCTAGCACACGGGCGTGTGTCTTGGCAGTGTGAAACCTACACCTAATTTCGAAAGAATTTAAT
TAACCACAC
Found at i:43876168 original size:46 final size:46
Alignment explanation
Indices: 43876025--43876242 Score: 260
Period size: 46 Copynumber: 4.7 Consensus size: 46
43876015 ATGTGTGTGT
* **
43876025 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGAGA
* * * ** *
43876071 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGATGAGA
* *
43876119 GCTAGTGTAAGACATGCCTGGGACATGCATCAGCCTCAAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-AGA
*
43876165 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-AGA
* *
43876211 GCCAGCGTAAGACATGTCTGGGACATGCATCG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCG
43876243 ACACGGATAT
Statistics
Matches: 147, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
46 96 0.65
47 28 0.19
48 23 0.16
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGAGA
Found at i:43876172 original size:94 final size:92
Alignment explanation
Indices: 43876025--43876241 Score: 276
Period size: 94 Copynumber: 2.3 Consensus size: 92
43876015 ATGTGTGTGT
* **
43876025 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAGTGTAAGA-CATGTC
*
43876090 TGGGACATGGCATCGACATTGAGACG-AGA
65 TGGGACAT-GCATCGACATCGAGACGTA-A
* * *
43876119 GCTAGTGTAAGACATGCCTGGGACATGCATCAGCCTCAAGATGTA-AGCTAGTGTAAGACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATG-AGAGCCAGTGTAAGACATGTC
* * *
43876183 TGGGACATGCATCGGCCTCGAGATGTAA
65 TGGGACATGCATCGACATCGAGACGTAA
* *
43876211 GCCAGCGTAAGACATGTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
43876242 GACACGGATA
Statistics
Matches: 108, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
92 42 0.39
93 15 0.14
94 50 0.46
95 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCGACATCGAGACGTAA
Found at i:43878288 original size:28 final size:27
Alignment explanation
Indices: 43878225--43878294 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
43878215 ATAGTGAGTC
*
43878225 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
43878252 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
43878280 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43878295 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43882337 original size:10 final size:10
Alignment explanation
Indices: 43882322--43882348 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
43882312 TGCAGTAATG
43882322 CAATCCATCC
1 CAATCCATCC
43882332 CAATCCATCC
1 CAATCCATCC
43882342 CAATCCA
1 CAATCCA
43882349 GCCAACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (10 bp):
CAATCCATCC
Found at i:43882444 original size:23 final size:24
Alignment explanation
Indices: 43882424--43882478 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
43882414 CACCAATATT
*
43882424 GCAGCATAGCTGCCAGAAATAATAAC
1 GCAGCAAAGCTGCCAGAAAT-AT-AC
*
43882450 GCAGTAAAGCTGCCAGAAATATAC
1 GCAGCAAAGCTGCCAGAAATATAC
*
43882474 ACAGC
1 GCAGC
43882479 TTACAGCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.15
Consensus pattern (24 bp):
GCAGCAAAGCTGCCAGAAATATAC
Found at i:43882519 original size:32 final size:32
Alignment explanation
Indices: 43882483--43882645 Score: 222
Period size: 32 Copynumber: 5.2 Consensus size: 32
43882473 CACAGCTTAC
* *
43882483 AGCCATCAGTAGCGGTAATATGATCGGCAGAA
1 AGCCATCAGTAGCTGTAATATGATCGGCACAA
* * * *
43882515 AGCCAACAGTAACTATAATATGATCGGTACAA
1 AGCCATCAGTAGCTGTAATATGATCGGCACAA
43882547 AGCCATCAGTAGCTGTAATATGATCGGCACAA
1 AGCCATCAGTAGCTGTAATATGATCGGCACAA
43882579 AGCCATCAGTA-CTGTAATATGATCGGCACAA
1 AGCCATCAGTAGCTGTAATATGATCGGCACAA
* * * *
43882610 AGCCATCAGTA-CTGTAACATAATCGTCACCA
1 AGCCATCAGTAGCTGTAATATGATCGGCACAA
43882641 AGCCA
1 AGCCA
43882646 CTGGTAAATA
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
31 52 0.44
32 65 0.56
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (32 bp):
AGCCATCAGTAGCTGTAATATGATCGGCACAA
Found at i:43883102 original size:27 final size:27
Alignment explanation
Indices: 43883072--43883160 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
43883062 CAAAACAATC
*
43883072 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
43883099 ATTTTACACTACAAGGGTATTTCTGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
* ***
43883126 ATTTTACA-AATTGGGGCTATTTCGGTA
1 ATTTTACACTACAAGGG-TATTTCGGTA
43883153 ATTTTACA
1 ATTTTACA
43883161 AACTGGGGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 4 0.07
27 50 0.93
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:43883161 original size:27 final size:26
Alignment explanation
Indices: 43883086--43883196 Score: 114
Period size: 27 Copynumber: 4.2 Consensus size: 26
43883076 TACCCTACAA
* **
43883086 GGGTATTTCGGTAATTTTACACTACAA
1 GGGTATTTCGGTAATTTTACA-AACTG
* *
43883113 GGGTATTTCTGTAATTTTACAAATTG
1 GGGTATTTCGGTAATTTTACAAACTG
43883139 GGGCTATTTCGGTAATTTTACAAACTGG
1 GGG-TATTTCGGTAATTTTACAAACT-G
* * * *
43883167 GGGTATTTTGATAATCTTACAAACCG
1 GGGTATTTCGGTAATTTTACAAACTG
43883193 GGGT
1 GGGT
43883197 CTTAACGACC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
26 9 0.13
27 58 0.82
28 4 0.06
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
GGGTATTTCGGTAATTTTACAAACTG
Found at i:43885372 original size:7 final size:7
Alignment explanation
Indices: 43885337--43885401 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
43885327 AACTTTTAAC
43885337 CCCTAAA
1 CCCTAAA
43885344 CCCATAAA
1 CCC-TAAA
** *
43885352 CTATAGA
1 CCCTAAA
43885359 CCCTAAA
1 CCCTAAA
*
43885366 TCCTAAA
1 CCCTAAA
43885373 CCCTAAA
1 CCCTAAA
**
43885380 CTTTAAA
1 CCCTAAA
43885387 CCCTAAA
1 CCCTAAA
*
43885394 TCCTAAA
1 CCCTAAA
43885401 C
1 C
43885402 TCTTAAACTA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
7 38 0.88
8 5 0.12
ACGTcount: A:0.43, C:0.34, G:0.02, T:0.22
Consensus pattern (7 bp):
CCCTAAA
Found at i:43885386 original size:21 final size:22
Alignment explanation
Indices: 43885362--43885430 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
43885352 CTATAGACCC
*
43885362 TAAATCCTAAACCCTAAACT-T
1 TAAACCCTAAACCCTAAACTCT
*
43885383 TAAACCCTAAATCCTAAACTCT
1 TAAACCCTAAACCCTAAACTCT
** * *
43885405 TAAACTATAAACCTTAAAATCT
1 TAAACCCTAAACCCTAAACTCT
43885427 TAAA
1 TAAA
43885431 AATAAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 18 0.45
22 22 0.55
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAACCCTAAACCCTAAACTCT
Found at i:43885389 original size:28 final size:28
Alignment explanation
Indices: 43885338--43885422 Score: 116
Period size: 29 Copynumber: 3.0 Consensus size: 28
43885328 ACTTTTAACC
*
43885338 CCTAAACCCATAAACTATAGACCCTAAAT
1 CCTAAACCC-TAAACTATAAACCCTAAAT
*
43885367 CCTAAACCCTAAACTTTAAACCCTAAAT
1 CCTAAACCCTAAACTATAAACCCTAAAT
* *
43885395 CCTAAACTCTTAAACTATAAACCTTAAA
1 CCTAAAC-CCTAAACTATAAACCCTAAA
43885423 ATCTTAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 24 0.48
29 26 0.52
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (28 bp):
CCTAAACCCTAAACTATAAACCCTAAAT
Found at i:43885420 original size:14 final size:14
Alignment explanation
Indices: 43885340--43885422 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 14
43885330 TTTTAACCCC
43885340 TAAACCCATAAACTA
1 TAAACCC-TAAACTA
* *
43885355 TAGACCCTAAA-TCC
1 TAAACCCTAAACT-A
*
43885369 TAAACCCTAAACTT
1 TAAACCCTAAACTA
*
43885383 TAAACCCTAAA-TCC
1 TAAACCCTAAACT-A
*
43885397 TAAACTCTTAAACTA
1 TAAAC-CCTAAACTA
*
43885412 TAAACCTTAAA
1 TAAACCCTAAA
43885423 ATCTTAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.04
14 36 0.64
15 17 0.30
16 1 0.02
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:43886059 original size:115 final size:116
Alignment explanation
Indices: 43885750--43886136 Score: 399
Period size: 116 Copynumber: 3.4 Consensus size: 116
43885740 AAGCTTTGTT
* * * *
43885750 TTTAGTGGCATTTTCACAAAAAACGCCGCAAATATGTTTTAAAAGTGTGCAAAACGCTGTCATTT
1 TTTAGTGGCGTTTTCATAAAAAACGCCGCAAAAATGTTTTAAGAGTGTGCAAAACGCTGTCATTT
* * * * *
43885815 TT-TTTAACTACTAGTGGCGTTTTTAACAAAAACGCCGCAAACAGATAG-C
66 TTGTCTGACTATTAGTGGTGTTTTTAACAAAAACGCCGCAAAAAGATAGCC
* * * * * * * * * *
43885864 TTTTGTGGCGTTTTCACAAAAAAAAAGTCGCAAATATGTTTTAAGCGTATGGAAATCGGTGTCAT
1 TTTAGTGGCGTTTT--CATAAAAAACGCCGCAAAAATGTTTTAAGAGTGTGCAAAACGCTGTCAT
*
43885929 TTTTGTCTGACTATTAGTGGTGTTTTTAAC-CAAACGCCGCAAAAAGA-AGCC
64 TTTTGTCTGACTATTAGTGGTGTTTTTAACAAAAACGCCGCAAAAAGATAGCC
* * * *
43885980 TTTAGTGGCGTTTTCTTATAAAACGCCGCGAAAAATATTTTAAGAGTGTGCAAAACGCTGTCGTT
1 TTTAGTGGCGTTTTCATAAAAAACGCCGC-AAAAATGTTTTAAGAGTGTGCAAAACGCTGTCATT
* * * * *
43886045 TTTGTCTGCCTATTAGTGGTGTTTTT-ACTAAAACGCCACAAAAGGATATCC
65 TTTGTCTGACTATTAGTGGTGTTTTTAACAAAAACGCCGCAAAAAGATAGCC
* ** *
43886096 TTTAGTAGCGTTTTC-TCTTAAAACCCCGCAAAAATGTTTTA
1 TTTAGTGGCGTTTTCAT-AAAAAACGCCGCAAAAATGTTTTA
43886137 CGACTATTCA
Statistics
Matches: 225, Mismatches: 40, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
114 24 0.11
115 80 0.36
116 100 0.44
117 21 0.09
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (116 bp):
TTTAGTGGCGTTTTCATAAAAAACGCCGCAAAAATGTTTTAAGAGTGTGCAAAACGCTGTCATTT
TTGTCTGACTATTAGTGGTGTTTTTAACAAAAACGCCGCAAAAAGATAGCC
Found at i:43886149 original size:115 final size:115
Alignment explanation
Indices: 43885923--43886186 Score: 302
Period size: 115 Copynumber: 2.3 Consensus size: 115
43885913 TGGAAATCGG
* * * *
43885923 TGTCATTTTTGTCTGACTATTAGTGGTGTTTTTAACCAAACGCCGCAAAAAGAAGCCTTTAGTGG
1 TGTCGTTTTTGTCTGACTATTAGTGGTGTTTTTAACAAAACGCCACAAAAAGAAGCCTTTAGTAG
* * * *
43885988 CGTTTTCTTATAAAACGCCGCGAAAAATATTTTAAGAGTGTGCAAAACGC
66 CGTTTTCTTATAAAACCCCGCGAAAAATATTTTAAGACTATGCAAAACAC
* * *
43886038 TGTCGTTTTTGTCTGCCTATTAGTGGTGTTTTT-ACTAAAACGCCACAAAAGGATATCCTTTAGT
1 TGTCGTTTTTGTCTGACTATTAGTGGTGTTTTTAAC-AAAACGCCACAAAAAGA-AGCCTTTAGT
* * * *
43886102 AGCGTTTTCTCT-TAAAACCCCGC-AAAAATGTTTTACGACTATTCAAAACAT
64 AGCGTTTTCT-TATAAAACCCCGCGAAAAATATTTTAAGACTATGCAAAACAC
* * * *
43886153 TGTCGTTTTTATCT-ACTTTTAGTAGTTTTTTTAA
1 TGTCGTTTTTGTCTGACTATTAGTGGTGTTTTTAA
43886187 AACGCCGCAA
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
114 16 0.13
115 80 0.64
116 28 0.22
117 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (115 bp):
TGTCGTTTTTGTCTGACTATTAGTGGTGTTTTTAACAAAACGCCACAAAAAGAAGCCTTTAGTAG
CGTTTTCTTATAAAACCCCGCGAAAAATATTTTAAGACTATGCAAAACAC
Found at i:43886423 original size:70 final size:71
Alignment explanation
Indices: 43886340--43886475 Score: 197
Period size: 70 Copynumber: 1.9 Consensus size: 71
43886330 ATCAGATTAC
* *
43886340 CCCGATTTCATTCCACT-AATTTCCCAATTTC-TTCTCT-AGTTTTCCTTAACTGCGTCTTCCCC
1 CCCGATTTCATTCC-CTCAATTTCCCAATTTCTTTCTCTCA-TTTTCCCTAACTGCATCTTCCCC
43886402 AAGTTAAA
64 AAGTTAAA
*
43886410 CCCGATTTCATTCCCTCAATTTCCCAATTTCTTTTCTCTCATTTTCCCTAACTGCATCTTTCCCA
1 CCCGATTTCATTCCCTCAATTTCCCAATTTC-TTTCTCTCATTTTCCCTAACTGCATCTTCCCCA
43886475 A
65 A
43886476 ATTATTTTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
69 2 0.03
70 28 0.47
72 28 0.47
73 1 0.02
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.41
Consensus pattern (71 bp):
CCCGATTTCATTCCCTCAATTTCCCAATTTCTTTCTCTCATTTTCCCTAACTGCATCTTCCCCAA
GTTAAA
Found at i:43886569 original size:19 final size:19
Alignment explanation
Indices: 43886545--43886589 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
43886535 GAAATCCCTT
* *
43886545 TTCTCTCTGCCGCATCCTC
1 TTCTCTCTGCCACAGCCTC
*
43886564 TTCTCTCTGTCACAGCCTC
1 TTCTCTCTGCCACAGCCTC
43886583 TTCTCTC
1 TTCTCTC
43886590 CGTTGCTGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.44, G:0.09, T:0.40
Consensus pattern (19 bp):
TTCTCTCTGCCACAGCCTC
Found at i:43887640 original size:42 final size:42
Alignment explanation
Indices: 43887593--43887675 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
43887583 TTCTCAAAAC
*
43887593 ATACTATTTAGTTACTAAGTTTAGTTTCAGTCTCCAATTAAT
1 ATACTATTTAGTTACTAAGTTTAGTTTCAATCTCCAATTAAT
43887635 ATACTATTTAGTTACTAAGTTTAGTTTCAATCTCCAATTAA
1 ATACTATTTAGTTACTAAGTTTAGTTTCAATCTCCAATTAA
43887676 GCAAGCTGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (42 bp):
ATACTATTTAGTTACTAAGTTTAGTTTCAATCTCCAATTAAT
Found at i:43889466 original size:9 final size:9
Alignment explanation
Indices: 43889454--43889626 Score: 64
Period size: 9 Copynumber: 19.9 Consensus size: 9
43889444 TATATGATAT
43889454 CATAAATTA
1 CATAAATTA
*
43889463 CATAACTTA
1 CATAAATTA
43889472 CA-AAACTTA
1 CATAAA-TTA
43889481 CAT-AA-TA
1 CATAAATTA
43889488 CATAAA-TA
1 CATAAATTA
* **
43889496 TATATTTTA
1 CATAAATTA
*
43889505 TCATAACTTA
1 -CATAAATTA
43889515 CAT-AA-TA
1 CATAAATTA
43889522 CATAAA-TA
1 CATAAATTA
* *
43889530 TATATCATATA
1 CATA-AAT-TA
*
43889541 -ATAACTTA
1 CATAAATTA
*
43889549 CATAACTTA
1 CATAAATTA
43889558 CAT-AA-TA
1 CATAAATTA
43889565 CATAAA-TA
1 CATAAATTA
* *
43889573 TATATCA-TA
1 CATA-AATTA
*
43889582 TCATAACTTA
1 -CATAAATTA
*
43889592 CATAACTTA
1 CATAAATTA
*
43889601 CATAACTTA
1 CATAAATTA
**
43889610 CATACCTTA
1 CATAAATTA
43889619 CATAAATT
1 CATAAATT
43889627 TATATCATAT
Statistics
Matches: 128, Mismatches: 22, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
7 15 0.12
8 27 0.21
9 70 0.55
10 14 0.11
11 2 0.02
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAAATTA
Found at i:43889470 original size:43 final size:43
Alignment explanation
Indices: 43889414--43889605 Score: 246
Period size: 43 Copynumber: 4.5 Consensus size: 43
43889404 TAACTTACAC
* * *
43889414 AACTTACAAAACTTACACAATACATAAATATATATGATATCAT
1 AACTTACATAACTTACATAATACATAAATATATATCATATCAT
* * * *
43889457 AAATTACATAACTTACAAAACTTACAT-AATACATA-AATAT-AT
1 AACTTACATAACTTACATAA--TACATAAATATATATCATATCAT
** *
43889499 ATTTTATCATAACTTACATAATACATAAATATATATCATATAAT
1 AACTTA-CATAACTTACATAATACATAAATATATATCATATCAT
43889543 AACTTACATAACTTACATAATACATAAATATATATCATATCAT
1 AACTTACATAACTTACATAATACATAAATATATATCATATCAT
43889586 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
43889606 CTTACATACC
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.04
42 13 0.10
43 94 0.72
44 13 0.10
45 5 0.04
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.34
Consensus pattern (43 bp):
AACTTACATAACTTACATAATACATAAATATATATCATATCAT
Found at i:43889492 original size:34 final size:34
Alignment explanation
Indices: 43889454--43889664 Score: 129
Period size: 34 Copynumber: 5.8 Consensus size: 34
43889444 TATATGATAT
43889454 CATAAATTACATAACTTACAAAACTTACATAATA
1 CATAAATTACATAACTTACAAAACTTACATAATA
* ** *
43889488 CATAAA-TATATATTTTATCATAACTTACATAATA
1 CATAAATTACATAACTTA-CAAAACTTACATAATA
*
43889522 CATAAATATATATCATATAATAACTTACATAACTTACATAATA
1 CAT-AA-AT-TA-C-----ATAACTTACAAAACTTACATAATA
* * * *
43889565 CATAAA-TATATATCATATCATAACTTACATAACTTA
1 CATAAATTACATAACTTA-CAAAACTTACATAA--TA
* * * * *
43889601 CATAACTTACATACCTTACATAAATTTATATCATA
1 CATAAATTACATAACTTACA-AAACTTACATAATA
* *
43889636 TCATAACTTACAAAACTTACAAAACTTAC
1 -CATAAATTACATAACTTACAAAACTTAC
43889665 TTAACTTACG
Statistics
Matches: 138, Mismatches: 22, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
33 14 0.10
34 38 0.28
35 10 0.07
36 28 0.20
37 16 0.12
38 2 0.01
39 2 0.01
41 1 0.01
42 2 0.01
43 19 0.14
44 6 0.04
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (34 bp):
CATAAATTACATAACTTACAAAACTTACATAATA
Found at i:43889517 original size:52 final size:52
Alignment explanation
Indices: 43889395--43889519 Score: 196
Period size: 52 Copynumber: 2.4 Consensus size: 52
43889385 AATTAAATAC
* *
43889395 ATGAAATCATAACTTACACAACTTACAAAACTTACACAATACATAAATATAT
1 ATGATATCATAACTTACATAACTTACAAAACTTACACAATACATAAATATAT
* *
43889447 ATGATATCATAAATTACATAACTTACAAAACTTACATAATACATAAATATAT
1 ATGATATCATAACTTACATAACTTACAAAACTTACACAATACATAAATATAT
**
43889499 ATTTTATCATAACTTACATAA
1 ATGATATCATAACTTACATAA
43889520 TACATAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (52 bp):
ATGATATCATAACTTACATAACTTACAAAACTTACACAATACATAAATATAT
Found at i:43889638 original size:54 final size:53
Alignment explanation
Indices: 43889541--43889673 Score: 196
Period size: 54 Copynumber: 2.5 Consensus size: 53
43889531 ATATCATATA
*
43889541 ATAACTTACATAACTTACATA-ATACATAAATATATATCATATCATAACTTAC
1 ATAACTTACATAACTTACATACTTACATAAATATATATCATATCATAACTTAC
*
43889593 ATAACTTACATAACTTACATACCTTACATAAATTTATATCATATCATAACTTAC
1 ATAACTTACATAACTTACATA-CTTACATAAATATATATCATATCATAACTTAC
* * *
43889647 AAAACTTACAAAACTTACTTAACTTAC
1 ATAACTTACATAACTTACAT-ACTTAC
43889674 GTAATACATA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
52 21 0.29
54 51 0.70
55 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (53 bp):
ATAACTTACATAACTTACATACTTACATAAATATATATCATATCATAACTTAC
Found at i:43889673 original size:9 final size:9
Alignment explanation
Indices: 43889640--43889664 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
43889630 ATCATATCAT
43889640 AACTTACAA
1 AACTTACAA
43889649 AACTTACAA
1 AACTTACAA
43889658 AACTTAC
1 AACTTAC
43889665 TTAACTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (9 bp):
AACTTACAA
Found at i:43895951 original size:49 final size:49
Alignment explanation
Indices: 43895891--43896203 Score: 554
Period size: 49 Copynumber: 6.4 Consensus size: 49
43895881 TACATATATG
* * * * *
43895891 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGGATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
43895940 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
43895989 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
43896038 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
43896087 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
43896136 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
43896185 TGTGATAAGGCCTAATGGC
1 TGTGATAAGGCCTAATGGC
43896204 TAATGTAAAA
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 255 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.29
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:43896354 original size:37 final size:37
Alignment explanation
Indices: 43896304--43896388 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
43896294 GGAATATGTT
*
43896304 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
43896341 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
43896378 CCGGGTAAGAC
1 CCGGGTAAGAC
43896389 TTCTTTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:43898856 original size:96 final size:96
Alignment explanation
Indices: 43898738--43898931 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 96
43898728 TCGCTTCTTT
** * * *
43898738 TTGCTCCTCTTAGCCCTTTTGGCTTCGGCTTTACCTTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTCTTAGCCCCCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGATTCTTGGGCTCCGT
* * * *
43898803 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
66 ATCTGCTCCATCATTCCCATCGATAACAGAC
* *
43898834 TTGCTCCTCTTTGCCCCCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGATTCTTGGGCTCCGT
1 TTGCTCCTCTTAGCCCCCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGATTCTTGGGCTCCGT
* *
43898899 ATCTGCTCGATCATTTCCATCGATAACAGAC
66 ATCTGCTCCATCATTCCCATCGATAACAGAC
43898930 TT
1 TT
43898932 CCTAGGACAC
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.13, C:0.33, G:0.18, T:0.36
Consensus pattern (96 bp):
TTGCTCCTCTTAGCCCCCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGATTCTTGGGCTCCGT
ATCTGCTCCATCATTCCCATCGATAACAGAC
Found at i:43902128 original size:14 final size:14
Alignment explanation
Indices: 43902104--43902138 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
43902094 TTAAATATTT
43902104 ATAAT-GTTTAATC
1 ATAATGGTTTAATC
*
43902117 ATAATGGTTTAATT
1 ATAATGGTTTAATC
43902131 ATAATGGT
1 ATAATGGT
43902139 ATATTCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (14 bp):
ATAATGGTTTAATC
Found at i:43907142 original size:15 final size:15
Alignment explanation
Indices: 43907122--43907152 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43907112 ACAAACATTC
43907122 ATATTCCTCCCTTAA
1 ATATTCCTCCCTTAA
*
43907137 ATATTCCTCTCTTAA
1 ATATTCCTCCCTTAA
43907152 A
1 A
43907153 CATCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTCCTCCCTTAA
Found at i:43908833 original size:57 final size:57
Alignment explanation
Indices: 43908767--43908959 Score: 255
Period size: 57 Copynumber: 3.4 Consensus size: 57
43908757 ACACTTAGTG
*
43908767 TTTAGCCTGGACTAGTAATCCTAATTGAGCTTTTTTGAGCGTACGTC-CAATTATGGA
1 TTTAGCCTGGACTAGTAATCCTAATTGAGCTTTTTTGAGCGTACGTCAC-ATAATGGA
* * * *
43908824 TTTAGCCTGGACTGGTAATCCTAATTGAGCTTTTATGCGCGTACATCACATAATGGA
1 TTTAGCCTGGACTAGTAATCCTAATTGAGCTTTTTTGAGCGTACGTCACATAATGGA
* * * * *
43908881 TTTAGCCTGAAGTAGTAATCCTAATTGAGCTCTTTTGAGCATACGTTACATAATGGA
1 TTTAGCCTGGACTAGTAATCCTAATTGAGCTTTTTTGAGCGTACGTCACATAATGGA
*
43908938 TTTAGCTTGGACT-GATAATCCT
1 TTTAGCCTGGACTAG-TAATCCT
43908960 GTAATACGAT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
56 1 0.01
57 115 0.98
58 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (57 bp):
TTTAGCCTGGACTAGTAATCCTAATTGAGCTTTTTTGAGCGTACGTCACATAATGGA
Found at i:43910068 original size:13 final size:14
Alignment explanation
Indices: 43910045--43910079 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
43910035 TTTAGTTAAC
43910045 CACATGGCCTAGCA
1 CACATGGCCTAGCA
43910059 CACA-GGCCTAGCA
1 CACATGGCCTAGCA
*
43910072 TACATGGC
1 CACATGGC
43910080 TGCAGCACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (14 bp):
CACATGGCCTAGCA
Found at i:43914282 original size:8 final size:8
Alignment explanation
Indices: 43914269--43914300 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
43914259 CTAGATCGGC
43914269 AAAAGCCG
1 AAAAGCCG
43914277 AAAAGCCG
1 AAAAGCCG
*
43914285 AAATGCCG
1 AAAAGCCG
43914293 AAAAGCCG
1 AAAAGCCG
43914301 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:43914587 original size:28 final size:28
Alignment explanation
Indices: 43914547--43914611 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
43914537 ATGTACTAGA
*
43914547 ATACCCCTATGTATACAAAATTACCATT
1 ATACCCCTATGTATACAAAATGACCATT
* *
43914575 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATACAAAATGACCATT
43914603 ATACCCCTA
1 ATACCCCTA
43914612 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATACAAAATGACCATT
Found at i:43914758 original size:28 final size:27
Alignment explanation
Indices: 43914717--43914806 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
43914707 AGGAAGCATC
43914717 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
43914745 CTGGTGGCCCTGCCACATATATCTATT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
43914772 TTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
43914801 CTGGTG
1 CTGGTG
43914807 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 21 0.41
28 24 0.47
29 6 0.12
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:43914776 original size:27 final size:28
Alignment explanation
Indices: 43914717--43914806 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
43914707 AGGAAGCATC
*
43914717 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTATT
* *
43914745 CTGGTGGCCCTGCCACATA-TATCTATT
1 CTGGTGGCACTGCCACAAATTATCTATT
* * *
43914772 TTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTAT-T
43914801 CTGGTG
1 CTGGTG
43914807 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 23 0.45
28 22 0.43
29 6 0.12
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.33
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTATT
Found at i:43918367 original size:33 final size:33
Alignment explanation
Indices: 43918295--43918367 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
43918285 ATTGGGACAA
* *
43918295 TAAACACAGAATAGAAATAGATCATTAGGATAG
1 TAAACATAGAATAGAAATAGATCACTAGGATAG
*
43918328 TAAACATAGAATAGAAATA-ATCCACTGGGATAG
1 TAAACATAGAATAGAAATAGAT-CACTAGGATAG
43918361 TAAACAT
1 TAAACAT
43918368 CTGATTGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (33 bp):
TAAACATAGAATAGAAATAGATCACTAGGATAG
Found at i:43921241 original size:47 final size:47
Alignment explanation
Indices: 43921178--43921519 Score: 567
Period size: 47 Copynumber: 7.3 Consensus size: 47
43921168 CCCTTCGGGA
* *
43921178 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43921225 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43921272 CTTATCTCATATATACACTTTCACATTCATCACGTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43921319 CCTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
43921366 CCTATCACATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43921413 CCTATCACATATATATACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43921460 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43921507 CTTATCACATATA
1 CTTATCACATATA
43921520 CATATCTTGT
Statistics
Matches: 279, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 279 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43921469 original size:22 final size:22
Alignment explanation
Indices: 43921441--43921516 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
43921431 TTTCACATTC
43921441 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
43921463 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
43921487 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43921510 ATCACAT
1 ATCACAT
43921517 ATACATATCT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43925630 original size:40 final size:40
Alignment explanation
Indices: 43925568--43925748 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
43925558 CATTTGAATG
*
43925568 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* *
43925608 ATATCCGGGTTAAGACCTGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
43925648 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
43925688 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
43925728 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
43925749 AAACTTGGGT
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.10
40 112 0.90
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:43933953 original size:28 final size:28
Alignment explanation
Indices: 43933882--43933980 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
43933872 ATAATAAGCC
*
43933882 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCGAACT
* *
43933910 CACACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCGAACT
* * *
43933938 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA-TCGAACT
43933967 CGCACACTTAGTGC
1 CGCACACTTAGTGC
43933981 CAATCTCATG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 42 0.69
29 19 0.31
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCGAACT
Found at i:43934441 original size:2 final size:2
Alignment explanation
Indices: 43934434--43934461 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43934424 CATACTTATG
43934434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43934462 CACTTCCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43938422 original size:46 final size:45
Alignment explanation
Indices: 43938326--43938542 Score: 169
Period size: 46 Copynumber: 4.8 Consensus size: 45
43938316 GCCCATCTGT
* * * *
43938326 GTCGATGTCGTGTCCCAGACA-GGTTTTACACTGACACATGTCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATCAA
* *
43938370 GCCGATGCCATGTCCCAAACATGGTCTTACACT-ATCCACATATCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGA--CACATATCAA
43938416 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCATCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGAC-A-CAT-ATCAA
* * * * * * **
43938464 GGCCGATG-CGTGTCCTAGACA-CGTCTTACACTAGCACTCGTCCCAA
1 -GTCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATATCAA
43938510 -TACCGATG-CATGTCCCAGACAT-GTCTTACACTG
1 GT--CGATGCCATGTCCCAGACATGGTCTTACACTG
43938543 GCTTTCACTA
Statistics
Matches: 141, Mismatches: 19, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
44 18 0.13
45 12 0.09
46 70 0.50
47 16 0.11
48 17 0.12
49 8 0.06
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (45 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGACACATATCAA
Found at i:43939707 original size:13 final size:13
Alignment explanation
Indices: 43939689--43939721 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43939679 TTCGTGTGTC
43939689 ACACACGGCCTAG
1 ACACACGGCCTAG
*
43939702 ACACACAGCCTAG
1 ACACACGGCCTAG
43939715 ACACACG
1 ACACACG
43939722 CCCGTGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.39, G:0.18, T:0.06
Consensus pattern (13 bp):
ACACACGGCCTAG
Found at i:43941971 original size:40 final size:40
Alignment explanation
Indices: 43941910--43942090 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
43941900 TATTCGGATG
* * *
43941910 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43941950 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43941990 ATATCCGGGCTAAATCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43942030 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
43942070 ATATCC-GGCTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
43942091 ATACTTGGGT
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 14 0.11
40 110 0.87
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:43943148 original size:37 final size:37
Alignment explanation
Indices: 43943095--43943193 Score: 180
Period size: 37 Copynumber: 2.7 Consensus size: 37
43943085 CGAATAGTCC
*
43943095 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
43943132 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
43943169 CCACACGTAGTCATCGGGTCTTACC
1 CCACACGTAGTCATCGGGTCTTACC
43943194 GGAAATATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:43943396 original size:48 final size:48
Alignment explanation
Indices: 43943338--43943489 Score: 232
Period size: 48 Copynumber: 3.2 Consensus size: 48
43943328 ATATACACAC
* * *
43943338 ATCTCCTACATATTTCACATTAGCCATCCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
43943386 ATCTCATACATATTTCACATTAGCCATTCGGATTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* **
43943434 ATCTCATAAATATTTCATGTTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
43943482 ATCTCATA
1 ATCTCATA
43943490 TATACCACAT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:43943500 original size:24 final size:24
Alignment explanation
Indices: 43943468--43943513 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
43943458 CATTCGGCTT
43943468 TACCACATATACATATCTCATATA
1 TACCACATATACATATCTCATATA
*
43943492 TACCACATATATATATCTCATA
1 TACCACATATACATATCTCATA
43943514 CATATTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (24 bp):
TACCACATATACATATCTCATATA
Found at i:43943519 original size:72 final size:72
Alignment explanation
Indices: 43943420--43943561 Score: 257
Period size: 72 Copynumber: 2.0 Consensus size: 72
43943410 CATTCGGATT
*
43943420 TACCACATATATATATCTCATAAATATTTCATGTTAGCCATTCGGCTTTACCACATATACATATC
1 TACCACATATATATATCTCATAAATATTTCATATTAGCCATTCGGCTTTACCACATATACATATC
43943485 TCATATA
66 TCATATA
* *
43943492 TACCACATATATATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCATATATACATATC
1 TACCACATATATATATCTCATAAATATTTCATATTAGCCATTCGGCTTTACCACATATACATATC
43943557 TCATA
66 TCATA
43943562 CATATTTCAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (72 bp):
TACCACATATATATATCTCATAAATATTTCATATTAGCCATTCGGCTTTACCACATATACATATC
TCATATA
Found at i:43943550 original size:48 final size:48
Alignment explanation
Indices: 43943492--43943605 Score: 201
Period size: 48 Copynumber: 2.4 Consensus size: 48
43943482 ATCTCATATA
*
43943492 TACCACATATATATATCTCATACATATTTCATATTAGCCATTCGGCTT
1 TACCACATATATATATCTCATACATATTTCACATTAGCCATTCGGCTT
* *
43943540 TACCATATATACATATCTCATACATATTTCACATTAGCCATTCGGCTT
1 TACCACATATATATATCTCATACATATTTCACATTAGCCATTCGGCTT
43943588 TACCACATATATATATCT
1 TACCACATATATATATCT
43943606 ATTTATCTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (48 bp):
TACCACATATATATATCTCATACATATTTCACATTAGCCATTCGGCTT
Found at i:43943585 original size:120 final size:120
Alignment explanation
Indices: 43943372--43943605 Score: 378
Period size: 120 Copynumber: 1.9 Consensus size: 120
43943362 CATCCGGCTT
*
43943372 TACCAAATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCACATATATATATC
1 TACCAAATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCACATATACATATC
**
43943437 TCATAAATATTTCATGTTAGCCATTCGGCTTTACCACATATACATATCTCATATA
66 TCATAAATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATA
* * * * *
43943492 TACCACATATATATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCATATATACATATC
1 TACCAAATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCACATATACATATC
* *
43943557 TCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATATATCT
66 TCATAAATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
43943606 ATTTATCTTG
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 104 1.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.38
Consensus pattern (120 bp):
TACCAAATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCACATATACATATC
TCATAAATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATA
Found at i:43946175 original size:22 final size:22
Alignment explanation
Indices: 43946135--43946176 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43946125 GAATGTGCAT
*
43946135 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
43946157 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
43946177 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:43962378 original size:2 final size:2
Alignment explanation
Indices: 43962371--43962419 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
43962361 TTGAGTTTGG
43962371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43962413 AT AT AT A
1 AT AT AT A
43962420 AAACATGTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43965428 original size:12 final size:12
Alignment explanation
Indices: 43965400--43965430 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43965390 CAGGTTGTTG
*
43965400 CACGACCTAGCA
1 CACGGCCTAGCA
43965412 CACGGCCTAGCA
1 CACGGCCTAGCA
43965424 CACGGCC
1 CACGGCC
43965431 GTGTGAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.45, G:0.23, T:0.06
Consensus pattern (12 bp):
CACGGCCTAGCA
Found at i:43970598 original size:14 final size:17
Alignment explanation
Indices: 43970571--43970609 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
43970561 TGAATTTAAG
43970571 AAGAA-ATATGTTGG-T
1 AAGAAGATATGTTGGAT
43970586 -AGAAGATAT-TTGGAT
1 AAGAAGATATGTTGGAT
43970601 AAGAAGATA
1 AAGAAGATA
43970610 AGAGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (17 bp):
AAGAAGATATGTTGGAT
Found at i:43974198 original size:19 final size:19
Alignment explanation
Indices: 43974171--43974219 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
43974161 GGAAATTGAA
*
43974171 GAGAAAGTTTGGATTATTC
1 GAGATAGTTTGGATTATTC
*
43974190 GAGATAGTTCGGATTATTC
1 GAGATAGTTTGGATTATTC
43974209 GAGATAGTTTG
1 GAGATAGTTTG
43974220 AAAGCTGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (19 bp):
GAGATAGTTTGGATTATTC
Found at i:43974326 original size:18 final size:18
Alignment explanation
Indices: 43974303--43974345 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
43974293 GTGTGTTCTT
43974303 GAAAGTTTCCCCATGGAA
1 GAAAGTTTCCCCATGGAA
43974321 GAAAGTTTCCCCATGGAA
1 GAAAGTTTCCCCATGGAA
43974339 GAAAGTT
1 GAAAGTT
43974346 CTATGGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (18 bp):
GAAAGTTTCCCCATGGAA
Found at i:43974725 original size:14 final size:15
Alignment explanation
Indices: 43974696--43974728 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
43974686 ATCCGTATTT
43974696 ATTTTCAGGTACGAA
1 ATTTTCAGGTACGAA
*
43974711 ATTTTGAGG-ACGAA
1 ATTTTCAGGTACGAA
43974725 ATTT
1 ATTT
43974729 CCTAAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (15 bp):
ATTTTCAGGTACGAA
Found at i:43979809 original size:66 final size:68
Alignment explanation
Indices: 43979733--43979919 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
43979723 TAGTACCACT
*
43979733 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
43979795 CACG
65 CACG
43979799 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
43979864 ATCACG
63 ATCACG
43979870 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
43979920 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:43979844 original size:71 final size:71
Alignment explanation
Indices: 43979756--43979919 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
43979746 CGATTTGTCT
43979756 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
43979821 CTTTCA
66 CTTTCA
43979827 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
43979892 CTTTCA
66 CTTTCA
43979898 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
43979920 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:43979957 original size:71 final size:70
Alignment explanation
Indices: 43979756--43979953 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
43979746 CGATTTGTCT
* * *
43979756 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
43979821 CTTTCA
65 CTTTCA
* * *
43979827 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
43979892 CTTTCA
65 CTTTCA
* *
43979898 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
43979954 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:43998402 original size:49 final size:48
Alignment explanation
Indices: 43998349--43998441 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
43998339 AGAGGGTTTA
* *
43998349 AAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAATTTG
1 AAATAAATAATATAT-AAA-AGTTTAAAATAAATAATGTATATAAATTTG
*
43998398 AAATAAATAATATGTAAAAGTTTAAAATAAATAATGTATATAAA
1 AAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
43998442 AAGAAAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 5 0.12
48 21 0.52
49 14 0.35
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (48 bp):
AAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAATTTG
Found at i:43998425 original size:24 final size:24
Alignment explanation
Indices: 43998344--43998442 Score: 94
Period size: 24 Copynumber: 4.0 Consensus size: 24
43998334 AATAAAGAGG
43998344 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
43998370 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
* *
43998394 -TTTGAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
43998417 GTTTAAAATAAATAATGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
43998443 AGAAAATCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
23 6 0.10
24 27 0.46
25 14 0.24
26 12 0.20
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:44000358 original size:89 final size:87
Alignment explanation
Indices: 44000204--44000619 Score: 378
Period size: 86 Copynumber: 4.7 Consensus size: 87
44000194 GCCTACTCCA
* * *
44000204 CTACTGCTTAGGGAGATAGGGTCTACAATTTCTAGCCTGTTACCTTACTGCTTAAGGGG-TTAAG
1 CTACTGCTTAGGGAGATAAGATCTACAATTTC-AGCCTGTTACCCTACTGCTT-AGGGGTTTAAG
* *
44000268 GCTCGTCGTCTTCGATCTATTTCC
64 GCCCTTCGTCTTCGATCTATTTCC
* * * * *
44000292 CTATTGCTTAGGGTGATGAGATCTACAAATTTTCAGCCTATTACCCTACTGTTTAGGGGTTTAAG
1 CTACTGCTTAGGGAGATAAGATCTAC-AA-TTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
44000357 GCCCTTCGTCTTTGATCTA-CTCC
64 GCCCTTCGTCTTCGATCTATTTCC
** ** * * * * *
44000380 ACTACAACTTCAGGGAGGCAAAATTTGCAATTT-GGTCTGTTACCCTACCT-CTTA-GGGTTTAA
1 -CTACTGCTT-AGGGAGATAAGATCTACAATTTCAGCCTGTTACCCTA-CTGCTTAGGGGTTTAA
* *
44000442 GACCCTTCGTCTTCGATCTGTTTCC
63 GGCCCTTCGTCTTCGATCTATTTCC
* * * * * * * *
44000467 CCACTACTTAGGGGGATAAGGTCTACAA-TTCGGTCTGTTACCCTACTGCTCAGGGGTTTAAGAC
1 CTACTGCTTAGGGAGATAAGATCTACAATTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
*
44000531 CCTTCGTCTTCGATCTGTTTCC
66 CCTTCGTCTTCGATCTATTTCC
* * *
44000553 CTACTGCTTAGGGGGTTAAGATCTGTA-AATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAA
1 CTACTGCTTAGGGAGATAAGATC--TACAAT-TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
44000617 GGC
63 GGC
44000620 TTGTAAATTC
Statistics
Matches: 265, Mismatches: 49, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
84 4 0.02
85 29 0.11
86 84 0.32
87 19 0.07
88 36 0.14
89 79 0.30
90 14 0.05
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
CTACTGCTTAGGGAGATAAGATCTACAATTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
CCTTCGTCTTCGATCTATTTCC
Found at i:44000555 original size:44 final size:44
Alignment explanation
Indices: 44000415--44000705 Score: 190
Period size: 44 Copynumber: 6.7 Consensus size: 44
44000405 TGCAATTTGG
* *
44000415 TCTGTTACCCTACCT-CTTA-GGGTTTAAGACCCTTCGTCTTCGA
1 TCTGTTTCCCTA-CTGCTTAGGGGGTTAAGACCCTTCGTCTTCGA
* * * ** * ** *
44000458 TCTGTTTCCCCACTACTTAGGGGGATAAG-GTCTAC-AATTCGG
1 TCTGTTTCCCTACTGCTTAGGGGGTTAAGACCCTTCGTCTTCGA
* * *
44000500 TCTGTTACCCTACTGCTCAGGGGTTTAAGACCCTTCGTCTTCGA
1 TCTGTTTCCCTACTGCTTAGGGGGTTAAGACCCTTCGTCTTCGA
* **
44000544 TCTGTTTCCCTACTGCTTAGGGGGTTAAGA-TCTGTAAATCTTC-A
1 TCTGTTTCCCTACTGCTTAGGGGGTTAAGACCCT-T-CGTCTTCGA
* * * *
44000588 GCCTGTTACCCTACTGCTTAGGGGGTTAAG--GCTT-GTAAATTC-A
1 -TCTGTTTCCCTACTGCTTAGGGGGTTAAGACCCTTCGT--CTTCGA
* * * *
44000631 GCTTGTTACCCTACTGCTTAGGGGGTTAA-AGCCCATCATCTTCGA
1 TC-TGTTTCCCTACTGCTTAGGGGGTTAAGA-CCCTTCGTCTTCGA
* *
44000676 TCTATTTCCCTACTGCTTAGGGGGTCAAGA
1 TCTGTTTCCCTACTGCTTAGGGGGTTAAGA
44000706 TCTGCGAATT
Statistics
Matches: 190, Mismatches: 42, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.16
43 53 0.28
44 68 0.36
45 37 0.19
46 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (44 bp):
TCTGTTTCCCTACTGCTTAGGGGGTTAAGACCCTTCGTCTTCGA
Found at i:44000594 original size:45 final size:43
Alignment explanation
Indices: 44000545--44000659 Score: 169
Period size: 43 Copynumber: 2.6 Consensus size: 43
44000535 CGTCTTCGAT
* *
44000545 CTGTTTCCCTACTGCTTAGGGGGTTAA-GATCTGTAAATCTTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCT-TGTAAA--TTCAGC
44000590 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTCAGC
*
44000633 TTGTTACCCTACTGCTTAGGGGGTTAA
1 CTGTTACCCTACTGCTTAGGGGGTTAA
44000660 AGCCCATCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
43 32 0.48
45 32 0.48
46 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTCAGC
Found at i:44000645 original size:43 final size:44
Alignment explanation
Indices: 44000545--44000659 Score: 171
Period size: 45 Copynumber: 2.6 Consensus size: 44
44000535 CGTCTTCGAT
*
44000545 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA-CTTCAGC
*
44000590 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAA-TTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAACTTCAGC
*
44000633 TTGTTACCCTACTGCTTAGGGGGTTAA
1 CTGTTACCCTACTGCTTAGGGGGTTAA
44000660 AGCCCATCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
43 32 0.48
44 1 0.02
45 33 0.50
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAACTTCAGC
Found at i:44004040 original size:27 final size:28
Alignment explanation
Indices: 44004010--44004079 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
44004000 ATAATAAGTC
*
44004010 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
44004037 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
44004065 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44004080 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:44007134 original size:39 final size:38
Alignment explanation
Indices: 44007012--44007136 Score: 144
Period size: 40 Copynumber: 3.2 Consensus size: 38
44007002 TTCGAATGAT
*
44007012 ATCCGGGCTAAG-TCCCGAAGGCTTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCTTTGTGC-AAGT-ACTAA
* **
44007052 ATCCGGACTAAGATCCGACGGCATACGTGCAAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGC-TTTGTGCAAG-TACTAA
*
44007092 ATCCGGACTAAGATCCGAAGGCTTTGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCTTTGTGCAAG-TACTAA
44007131 ATCCGG
1 ATCCGG
44007137 GTTGAGTCCC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.26
40 47 0.64
41 7 0.10
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.22
Consensus pattern (38 bp):
ATCCGGACTAAGATCCGAAGGCTTTGTGCAAGTACTAA
Found at i:44007166 original size:79 final size:80
Alignment explanation
Indices: 44007012--44007198 Score: 186
Period size: 79 Copynumber: 2.3 Consensus size: 80
44007002 TTCGAATGAT
* * *
44007012 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGACTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
44007077 CGTGCAAGTTACTAA
66 CGTGCAAGTTACTAA
** *
44007092 ATCCGGACTAAGAT-CCGAAGGCTTTGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGGC
1 ATCCGGACTAAG-TCCCGAAGGCTTTGAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGGC
* * * *
44007153 ATTCGTGCGAGTTATTGTA
63 ATACGTGCAAGTTACT-AA
* *
44007172 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGACTAAGTCCCGAAGGC-TTTGA
44007199 ATGTGTAGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
78 2 0.02
79 53 0.60
80 33 0.37
81 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
ATCCGGACTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCAAGTTACTAA
Found at i:44015164 original size:40 final size:38
Alignment explanation
Indices: 44015046--44015171 Score: 128
Period size: 40 Copynumber: 3.2 Consensus size: 38
44015036 TTCGAATGAT
*
44015046 ATCCGGGCTAAG-TCCCGAAGGCTTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCTTTGTGC-AAGT-ACTAA
* ** *
44015086 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGC-TTTGTGCAAG-TACTAA
*
44015126 ATCCGGACTAAGATCCGAAGGCTTTTGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGC-TTTGTGCAAG-TACTAA
44015166 ATCCGG
1 ATCCGG
44015172 GTTGAGTCCC
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
40 64 0.90
41 7 0.10
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (38 bp):
ATCCGGACTAAGATCCGAAGGCTTTGTGCAAGTACTAA
Done.