Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 87 of 186
Found at i:28219611 original size:52 final size:54
Alignment explanation
Indices: 28219517--28219687 Score: 202
Period size: 52 Copynumber: 3.1 Consensus size: 54
28219507 ACATACATGT
* * * *
28219517 ATATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATTAGGCCCAAGTCATATTC
1 ATATGGCCCATTAGG-CC-A-CACATTCATATGGCCCATTAGGCCCAAATCACATTC
* * *
28219574 GTATGGCCCATTAGG-C-CGCATTCATATGGCCCATTAGGCCGAAATCACATTC
1 ATATGGCCCATTAGGCCACACATTCATATGGCCCATTAGGCCCAAATCACATTC
28219626 ATATGGCCCATTAGGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCATTAGG-CC--A-CACATTCATATGGCCCATTAGGCCCAAATCACATTC
28219684 ATAT
1 ATAT
28219688 TCATGCTTTC
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
52 46 0.46
54 1 0.01
55 1 0.01
57 13 0.13
58 38 0.38
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (54 bp):
ATATGGCCCATTAGGCCACACATTCATATGGCCCATTAGGCCCAAATCACATTC
Found at i:28219636 original size:81 final size:80
Alignment explanation
Indices: 28219517--28219671 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 80
28219507 ACATACATGT
* * * * *
28219517 ATATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATTAGGCCCAAGTCATATTCGTATGGCC
1 ATATGGCCCACTAGGCCAAATCACATTCATATGGCCCATTAGGCCCAAATCACATTCATATGGCC
28219582 CATTAGGCCGCATTC
66 CATTAGGCCGCATTC
*
28219597 ATATGGCCCATTAGGCCGAAATCACATTCATATGGCCCATTAGGCCCAAATCACATTCATATGGC
1 ATATGGCCCACTAGGCC-AAATCACATTCATATGGCCCATTAGGCCCAAATCACATTCATATGGC
28219662 CCATTAGGCC
65 CCATTAGGCC
28219672 CAAATCACAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 16 0.24
81 52 0.76
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (80 bp):
ATATGGCCCACTAGGCCAAATCACATTCATATGGCCCATTAGGCCCAAATCACATTCATATGGCC
CATTAGGCCGCATTC
Found at i:28227815 original size:23 final size:23
Alignment explanation
Indices: 28227788--28227831 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28227778 TAAACTTATT
*
28227788 CACTTTAATTTTAAATTAATATA
1 CACTTTAATATTAAATTAATATA
28227811 CACTTTAATATTAAATTAATA
1 CACTTTAATATTAAATTAATA
28227832 AAATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
CACTTTAATATTAAATTAATATA
Found at i:28230040 original size:46 final size:46
Alignment explanation
Indices: 28229928--28230048 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 46
28229918 TGTGTGTGCT
* *
28229928 AGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAAATGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CACATTAAGAAATGCC
* *
28229975 AGTGCAAGACATGGCTGGGACATGCAT-AG-ACATTAAGACGAGA-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCACATTAAGA--A-ATGCC
*
28230021 AGTGTAAGACATGTTTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
28230049 GACTACGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
44 8 0.13
46 30 0.48
47 25 0.40
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCACATTAAGAAATGCC
Found at i:28230136 original size:49 final size:49
Alignment explanation
Indices: 28230014--28230242 Score: 158
Period size: 48 Copynumber: 4.8 Consensus size: 49
28230004 ACATTAAGAC
* *
28230014 GAGAGCCAGTGTAAGA-CATGTTTGGGACAT-GCATCGACTACGAGA-TGT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-ACG-GATTGT
* * * *
28230062 --G-TC-AGTATAAGACCATGTCTAGGACATGGCATCGGCACGGATTGT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATTGT
* * * * * * *
28230107 GAGAGCTAGTGTAAGACAATGTTTGGGACATGGCGTCGCCTC-AATTTT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATTGT
* * **
28230155 GATAG-TCAGTGTAAGACCATGTCTGGGACATGGCATTGAC-TTGA-TG-
1 GAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATTGT
* * *
28230201 GATGAGTTAGTGTAAGGCCATGTCTGGGACATGGAATCGACA
1 GA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACA
28230243 TTATACCCTA
Statistics
Matches: 141, Mismatches: 28, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
44 10 0.07
45 19 0.13
46 10 0.07
47 35 0.25
48 39 0.28
49 28 0.20
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (49 bp):
GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATTGT
Found at i:28236846 original size:47 final size:47
Alignment explanation
Indices: 28236686--28236856 Score: 159
Period size: 49 Copynumber: 3.5 Consensus size: 47
28236676 TGTGTTAGTA
* * *
28236686 TAAGACCATGTCTAGGACATGACATCGGAAC-GGATATGTGA-GAGCTAGTG
1 TAAGACCATGTCTAGGACATGGCATC-G-ACTCG--ATG-GATGAGCCAGTG
* * * * * *
28236736 TAAGACCATGTCTGGGAGATGGCGTCGACCTCGATTTTGAT-AGTCAATG
1 TAAGACCATGTCTAGGACATGGCATCGA-CTCGA--TGGATGAGCCAGTG
*
28236785 TAAGACCATGTCTAGGACATGGCATCGACTTGATGGATGAGCCAGTG
1 TAAGACCATGTCTAGGACATGGCATCGACTCGATGGATGAGCCAGTG
28236832 TAAGACCATGTCTAGGACATGGCAT
1 TAAGACCATGTCTAGGACATGGCAT
28236857 TGGCATTATA
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
46 4 0.04
47 31 0.31
48 6 0.06
49 34 0.34
50 24 0.24
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
TAAGACCATGTCTAGGACATGGCATCGACTCGATGGATGAGCCAGTG
Found at i:28239728 original size:46 final size:46
Alignment explanation
Indices: 28239678--28239850 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
28239668 TGGTTGAGCA
*
28239678 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
28239724 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
28239769 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28239817 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA
28239851 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28239834 original size:93 final size:93
Alignment explanation
Indices: 28239675--28239845 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
28239665 GGATGGTTGA
* *
28239675 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
28239740 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
28239768 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
28239833 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28239846 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28250936 original size:26 final size:26
Alignment explanation
Indices: 28250695--28250936 Score: 223
Period size: 26 Copynumber: 9.3 Consensus size: 26
28250685 TGTTACATGT
* * * *
28250695 TAAATAATCACTGACTCAAAGCCTAC
1 TAAATAAACACCGGCTCAAAGCCTGC
*
28250721 TAAATAATCACCGGCTCAAAGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTGC
* * ** *
28250747 TAGATCAACATTGGCTCAAGGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTGC
* * *
28250773 TAAATACACACCGGCTCAAGGCCTAC
1 TAAATAAACACCGGCTCAAAGCCTGC
* *
28250799 TAAATACACACCGGCTCAAGGCCTGC
1 TAAATAAACACCGGCTCAAAGCCTGC
* * *
28250825 TAAATAATCATCGGCTCAAAGCCTTC
1 TAAATAAACACCGGCTCAAAGCCTGC
* *
28250851 TAAATAAACACCAGCTCAAAGCATGC
1 TAAATAAACACCGGCTCAAAGCCTGC
* ** * * *
28250877 TAAATAAAAACTAGCTCAAAACTTGT
1 TAAATAAACACCGGCTCAAAGCCTGC
* **
28250903 TAAATAAACACCGACTCAAAGCCTAT
1 TAAATAAACACCGGCTCAAAGCCTGC
28250929 TAAATAAA
1 TAAATAAA
28250937 GTACATTACG
Statistics
Matches: 178, Mismatches: 38, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 178 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.21
Consensus pattern (26 bp):
TAAATAAACACCGGCTCAAAGCCTGC
Found at i:28252341 original size:21 final size:20
Alignment explanation
Indices: 28252293--28252341 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
28252283 TAGTTGTTTC
*
28252293 TTCTTCATCTTTTTCGGGTT
1 TTCTTTATCTTTTTCGGGTT
*
28252313 TTAGTTTATCATTTTTCGGGTT
1 TT-CTTTATC-TTTTTCGGGTT
28252335 TTCTTTA
1 TTCTTTA
28252342 GTTCCTTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 13 0.54
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.61
Consensus pattern (20 bp):
TTCTTTATCTTTTTCGGGTT
Found at i:28255745 original size:29 final size:29
Alignment explanation
Indices: 28255690--28255745 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
28255680 CATTTAGAGT
** *
28255690 TATAAAAATTATTAAATTTTAATAAATAA
1 TATAAAAATTATTAAAAATTAAAAAATAA
28255719 TATAAAAA-TATTAAAAATTAGAAAAAT
1 TATAAAAATTATTAAAAATTA-AAAAAT
28255746 TGTTTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TATAAAAATTATTAAAAATTAAAAAATAA
Found at i:28256057 original size:30 final size:28
Alignment explanation
Indices: 28255988--28256131 Score: 98
Period size: 29 Copynumber: 5.0 Consensus size: 28
28255978 TCTTTACATT
* * *
28255988 TTTTATAATTTTCT-TATGACTTTATAAAA
1 TTTTATAATTTTTTCTAT-A-TTTTTATAA
* *
28256017 TTTGATAATTTTTTTCTATATTTCTATATA
1 TTTTATAA-TTTTTTCTATATTTTTATA-A
28256047 TTTTATAATTTTTT-TATGATTTTTATAAAA
1 TTTTATAATTTTTTCTAT-ATTTTTAT--AA
* *
28256077 TTTTAT-ATTTTTTATAT-TTTTTACAA
1 TTTTATAATTTTTTCTATATTTTTATAA
* * *
28256103 TTTTTATAATTTTTTTTCTAATTTTATAA
1 -TTTTATAATTTTTTCTATATTTTTATAA
28256132 AATCTATATA
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.02
27 6 0.06
28 18 0.19
29 40 0.43
30 24 0.26
31 4 0.04
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATAATTTTTTCTATATTTTTATAA
Found at i:28256059 original size:9 final size:9
Alignment explanation
Indices: 28256047--28256116 Score: 68
Period size: 9 Copynumber: 7.4 Consensus size: 9
28256037 TTTCTATATA
28256047 TTTTATAATTT
1 TTTTATAA--T
*
28256058 TTTTATGAT
1 TTTTATAAT
*
28256067 TTTTATAAAA
1 TTTTAT-AAT
*
28256077 TTTTATATT
1 TTTTATAAT
*
28256086 TTTTATATT
1 TTTTATAAT
*
28256095 TTTTACAAT
1 TTTTATAAT
28256104 TTTTATAAT
1 TTTTATAAT
28256113 TTTT
1 TTTT
28256117 TTTCTAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
9 36 0.72
10 7 0.14
11 7 0.14
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:28256068 original size:19 final size:19
Alignment explanation
Indices: 28256041--28256118 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
28256031 TCTATATTTC
28256041 TATATATTTTATAATTTTTT
1 TATAT-TTTTATAATTTTTT
**
28256061 TATGATTTTTATAA-AATTT
1 TAT-ATTTTTATAATTTTTT
28256080 TATATTTTT-T-ATATTTTT
1 TATATTTTTATAAT-TTTTT
*
28256098 TACAATTTTTATAATTTTTT
1 TA-TATTTTTATAATTTTTT
28256118 T
1 T
28256119 TCTAATTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.02
17 1 0.02
18 11 0.23
19 12 0.26
20 18 0.38
21 4 0.09
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (19 bp):
TATATTTTTATAATTTTTT
Found at i:28256068 original size:29 final size:28
Alignment explanation
Indices: 28255988--28256143 Score: 129
Period size: 30 Copynumber: 5.3 Consensus size: 28
28255978 TCTTTACATT
* *
28255988 TTTTATAATTTTCTTATGACTTTATAAAA
1 TTTTATAATTTTTTTAT-ATTTTATAAAA
* *
28256017 TTTGATAATTTTTTTCTATATTTCTAT-ATA
1 TTTTATAA-TTTTTT-TATATTT-TATAAAA
28256047 TTTTATAATTTTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTTAT-A-TTTTATAAAA
* *
28256077 TTTTAT-A-TTTTTTATATTTTTTACAAT
1 TTTTATAATTTTTTTATATTTTATA-AAA
*
28256104 TTTTATAATTTTTTTTCTAATTTTATAAAA
1 TTTTATAA-TTTTTTTAT-ATTTTATAAAA
*
28256134 TCTATATAAT
1 T-TTTATAAT
28256144 GAATCACAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
26 6 0.06
27 9 0.09
28 12 0.12
29 18 0.17
30 39 0.38
31 19 0.18
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTATAATTTTTTTATATTTTATAAAA
Found at i:28256097 original size:37 final size:40
Alignment explanation
Indices: 28256036--28256111 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 40
28256026 TTTTTTCTAT
**
28256036 ATTTCTATATATTTTATAATTTTTTTATGATTTTTATAAA
1 ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAAA
*
28256076 ATTT-TATATTTTTTAT-A-TTTTTTACAATTTTTATAA
1 ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAA
28256112 TTTTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 17 0.52
38 1 0.03
39 11 0.33
40 4 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
ATTTCTATATATTTTATAATTTTTTTACAATTTTTATAAA
Found at i:28256118 original size:20 final size:19
Alignment explanation
Indices: 28255946--28256117 Score: 73
Period size: 19 Copynumber: 8.9 Consensus size: 19
28255936 TTAGTACGAT
*
28255946 AATTTTTATACTTTTTTAC
1 AATTTTTATAATTTTTTAC
*
28255965 GAA-TTTTATATTTTCTTTAC
1 -AATTTTTATAATTT-TTTAC
* *
28255985 ATTTTTTATAATTTTCTTAT
1 AATTTTTATAATTTT-TTAC
* * ** * *
28256005 GA-CTTTATAAAATTTGAT
1 AATTTTTATAATTTTTTAC
* * *
28256023 AATTTTTTTCTATATTTCTA-
1 AATTTTTAT-AAT-TTTTTAC
* *
28256043 TATATTTTATAATTTTTTTAT
1 AAT-TTTTATAA-TTTTTTAC
* ** *
28256064 GATTTTTATAAAATTTTAT
1 AATTTTTATAATTTTTTAC
*
28256083 ATTTTTTAT-ATTTTTTAC
1 AATTTTTATAATTTTTTAC
28256101 AATTTTTATAATTTTTT
1 AATTTTTATAATTTTTT
28256118 TTCTAATTTT
Statistics
Matches: 111, Mismatches: 31, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
18 18 0.16
19 45 0.41
20 37 0.33
21 11 0.10
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTTTTATAATTTTTTAC
Found at i:28271782 original size:47 final size:47
Alignment explanation
Indices: 28271718--28271828 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
28271708 GACATTAAGT
*
28271718 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTATTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * * *
28271765 TGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
28271812 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
28271829 CTTATCCCGG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 50 0.93
48 4 0.07
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:28273848 original size:33 final size:33
Alignment explanation
Indices: 28273806--28273872 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28273796 AATATTAGGG
28273806 ACTAAATTGAATAAATGAAGAACATGTCATGAA
1 ACTAAATTGAATAAATGAAGAACATGTCATGAA
28273839 ACTAAATTGAATAAATGAAGAACATGTCATGAA
1 ACTAAATTGAATAAATGAAGAACATGTCATGAA
28273872 A
1 A
28273873 TTATGCTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (33 bp):
ACTAAATTGAATAAATGAAGAACATGTCATGAA
Found at i:28275005 original size:41 final size:40
Alignment explanation
Indices: 28274930--28275014 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
28274920 TAAAAACATA
*
28274930 AAAACAAATATTAAAACAATAAACAAATAAAAAATGATACT
1 AAAACAAATATTAAAACAATAAACAAATAAAAAAT-ATAAT
* * * **
28274971 AAAACAATTCTTAAAACAATACACAAATTGAAAATATAAT
1 AAAACAAATATTAAAACAATAAACAAATAAAAAATATAAT
28275011 AAAA
1 AAAA
28275015 AGTTGTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.21
Consensus pattern (40 bp):
AAAACAAATATTAAAACAATAAACAAATAAAAAATATAAT
Found at i:28281334 original size:13 final size:13
Alignment explanation
Indices: 28281306--28281344 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
28281296 ACATTAATGA
28281306 ATTTAAATAT--T
1 ATTTAAATATAAT
28281317 ATTTAAATATAAT
1 ATTTAAATATAAT
28281330 ATTTAAATAATAAT
1 ATTTAAAT-ATAAT
28281344 A
1 A
28281345 ATACAACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
13 9 0.36
14 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAAATATAAT
Found at i:28285533 original size:22 final size:22
Alignment explanation
Indices: 28285485--28285534 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
28285475 TCTTGTGTAT
*
28285485 TATTGTAGGAATATTCTGTAAA
1 TATTTTAGGAATATTCTGTAAA
* *
28285507 TATTTTAGGAATATTTTGTAGA
1 TATTTTAGGAATATTCTGTAAA
28285529 TATTTT
1 TATTTT
28285535 CTTTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (22 bp):
TATTTTAGGAATATTCTGTAAA
Found at i:28289294 original size:22 final size:22
Alignment explanation
Indices: 28289266--28289310 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28289256 AAGGGGAGTG
28289266 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
28289288 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
28289310 T
1 T
28289311 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:28295358 original size:6 final size:6
Alignment explanation
Indices: 28295347--28295377 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28295337 ATTTGATTAG
28295347 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
28295378 AATGTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:28310381 original size:15 final size:15
Alignment explanation
Indices: 28310349--28310377 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28310339 TTATTTTGTG
28310349 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
28310364 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
28310378 ATTTTCATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:28310913 original size:15 final size:15
Alignment explanation
Indices: 28310893--28310923 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28310883 AATTATGAAA
28310893 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
28310908 GATATGTTTTGTATT
1 GATATGTTTTGGATT
28310923 G
1 G
28310924 GAATTTTTGA
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:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:28312418 original size:297 final size:297
Alignment explanation
Indices: 28311884--28312477 Score: 1170
Period size: 297 Copynumber: 2.0 Consensus size: 297
28311874 CAAGTTTACC
28311884 AATTTCTAAGTCCATGGAAAAAATAGGACATGGATGGAATTTTTGAAAGTTTAATAAGGAAGGGC
1 AATTTCTAAGTCCATGGAAAAAATAGGACATGGATGGAATTTTTGAAAGTTTAATAAGGAAGGGC
28311949 ATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGGAAAATAACACAAAATTTCAAGGGTTCT
66 ATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGGAAAATAACACAAAATTTCAAGGGTTCT
28312014 CCATAGCTCGGGTTTGTTTCAAGCTTTCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAA
131 CCATAGCTCGGGTTTGTTTCAAGCTTTCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAA
28312079 TGTTCTTTACGTTTTTGGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAG
196 TGTTCTTTACGTTTTTGGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAG
28312144 GGTTCATATTTGGAAAAATACCCATAGGTAAAAAGTG
261 GGTTCATATTTGGAAAAATACCCATAGGTAAAAAGTG
* *
28312181 AATTTCTAAGTTCATGGACAAAATAGGACATGGATGGAATTTTTGAAAGTTTAATAAGGAAGGGC
1 AATTTCTAAGTCCATGGAAAAAATAGGACATGGATGGAATTTTTGAAAGTTTAATAAGGAAGGGC
28312246 ATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGGAAAATAACACAAAATTTCAAGGGTTCT
66 ATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGGAAAATAACACAAAATTTCAAGGGTTCT
28312311 CCATAGCTCGGGTTTGTTTCAAGCTTTCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAA
131 CCATAGCTCGGGTTTGTTTCAAGCTTTCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAA
28312376 TGTTCTTTACGTTTTTGGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAG
196 TGTTCTTTACGTTTTTGGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAG
28312441 GGTTCATATTTGGAAAAATACCCATAGGTAAAAAGTG
261 GGTTCATATTTGGAAAAATACCCATAGGTAAAAAGTG
28312478 TTTATTTTGA
Statistics
Matches: 295, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
297 295 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (297 bp):
AATTTCTAAGTCCATGGAAAAAATAGGACATGGATGGAATTTTTGAAAGTTTAATAAGGAAGGGC
ATTTTGGTCATTTGGATATTAAATGAAATAAAAAGGGGAAAATAACACAAAATTTCAAGGGTTCT
CCATAGCTCGGGTTTGTTTCAAGCTTTCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAA
TGTTCTTTACGTTTTTGGAGTCTCGGTAGCTCGATAAAGCTTATGCTAGCAATAATTTAAGTTAG
GGTTCATATTTGGAAAAATACCCATAGGTAAAAAGTG
Found at i:28314569 original size:40 final size:40
Alignment explanation
Indices: 28314521--28314806 Score: 531
Period size: 40 Copynumber: 7.2 Consensus size: 40
28314511 GGACTAAGAT
28314521 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
28314561 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
28314601 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
28314641 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
28314681 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
28314721 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
28314761 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
28314800 CCGAAGG
1 CCGAAGG
28314807 TACTTGGGTT
Statistics
Matches: 243, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
39 15 0.06
40 226 0.93
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:28328308 original size:27 final size:27
Alignment explanation
Indices: 28328275--28328398 Score: 194
Period size: 27 Copynumber: 4.6 Consensus size: 27
28328265 TAAATTGTGC
28328275 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
28328302 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
28328329 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
28328357 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
28328384 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28328399 GACTTAATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 65 0.71
28 26 0.29
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:28328362 original size:55 final size:54
Alignment explanation
Indices: 28328275--28328398 Score: 194
Period size: 55 Copynumber: 2.3 Consensus size: 54
28328265 TAAATTGTGC
*
28328275 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
* * *
28328329 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
*
28328384 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28328399 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
54 16 0.25
55 48 0.75
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
Found at i:28330849 original size:45 final size:45
Alignment explanation
Indices: 28330794--28330891 Score: 189
Period size: 45 Copynumber: 2.2 Consensus size: 45
28330784 TTGTTGAATG
28330794 AAAT-AGATATAAATAATAGTTTATTTCCTTTGATCATTGAATAT
1 AAATGAGATATAAATAATAGTTTATTTCCTTTGATCATTGAATAT
28330838 AAATGAGATATAAATAATAGTTTATTTCCTTTGATCATTGAATAT
1 AAATGAGATATAAATAATAGTTTATTTCCTTTGATCATTGAATAT
28330883 AAATGAGAT
1 AAATGAGAT
28330892 GTTAAGCATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.08
45 49 0.92
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (45 bp):
AAATGAGATATAAATAATAGTTTATTTCCTTTGATCATTGAATAT
Found at i:28335737 original size:25 final size:25
Alignment explanation
Indices: 28335635--28335742 Score: 141
Period size: 25 Copynumber: 4.4 Consensus size: 25
28335625 CTGGAGGCCT
28335635 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTAATAAACTGGGGCAAA
*
28335659 AGCCCTTTTAACAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
28335684 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
** *
28335709 AGCCCTTTTCGGTAAACTGGGGC-AT
1 AGCCCTTTT-AATAAACTGGGGCAAA
28335734 AGCCCTTTT
1 AGCCCTTTT
28335743 TGCACTTCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.09
24 13 0.17
25 45 0.59
26 11 0.14
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:28335812 original size:9 final size:9
Alignment explanation
Indices: 28335798--28335854 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
28335788 ACATCATGTG
28335798 CATATCATA
1 CATATCATA
*
28335807 CATATCATGTG
1 CATATCA--TA
28335818 CATATCATA
1 CATATCATA
28335827 CATATCATGA
1 CATATCAT-A
28335837 GCATATCATA
1 -CATATCATA
28335847 CATATCAT
1 CATATCAT
28335855 GTGCATATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 24 0.57
10 2 0.05
11 16 0.38
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (9 bp):
CATATCATA
Found at i:28335813 original size:20 final size:20
Alignment explanation
Indices: 28335790--28335866 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
28335780 TTATGAATAC
28335790 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
28335810 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28335830 ATCATGAGCATATCATACAT
1 ATCATGTGCATATCATACAT
28335850 ATCATGTGCATATCATA
1 ATCATGTGCATATCATA
28335867 TCAAAACCCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28335820 original size:40 final size:40
Alignment explanation
Indices: 28335776--28335860 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
28335766 CCCAACCCAA
*
28335776 TGCATTATGAATAC-ATCATGTGCATATCATACATATCATG
1 TGCATTAT-AATACAATCATGAGCATATCATACATATCATG
*
28335816 TGCA-TATCATACATATCATGAGCATATCATACATATCATG
1 TGCATTATAATACA-ATCATGAGCATATCATACATATCATG
28335856 TGCAT
1 TGCAT
28335861 ATCATATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 4 0.10
39 3 0.08
40 33 0.82
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (40 bp):
TGCATTATAATACAATCATGAGCATATCATACATATCATG
Found at i:28335821 original size:11 final size:11
Alignment explanation
Indices: 28335790--28335865 Score: 74
Period size: 11 Copynumber: 7.5 Consensus size: 11
28335780 TTATGAATAC
28335790 ATCATGTGCAT
1 ATCATGTGCAT
*
28335801 ATCA--TACAT
1 ATCATGTGCAT
28335810 ATCATGTGCAT
1 ATCATGTGCAT
*
28335821 ATCA--TACAT
1 ATCATGTGCAT
*
28335830 ATCATGAGCAT
1 ATCATGTGCAT
*
28335841 ATCA--TACAT
1 ATCATGTGCAT
28335850 ATCATGTGCAT
1 ATCATGTGCAT
28335861 ATCAT
1 ATCAT
28335866 ATCAAAACCC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 23 0.45
11 28 0.55
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:28336578 original size:304 final size:303
Alignment explanation
Indices: 28335999--28336606 Score: 907
Period size: 304 Copynumber: 2.0 Consensus size: 303
28335989 ATTTTCCATG
*
28335999 TTCATTATCAGTTACTAACAATTCATGTGCTTAAACAGCGATTCTGGCCCATTTTTAGCGAAACC
1 TTCATTATCAGTTACTAACAATTCATGTGCTTAAACAGCGATTCTGGCCCATTTTCAGCGAAACC
* * * * *
28336064 GAATTATTGGGCTAAAAACCCCTAATGGGCCCTATATAGTCGAATTAGTCATCTAGGCCCATTTA
66 GAATTATTGGGCCAAAAACCCCTAATAGGCCCTACATAGCCGAATTAGTCATCTAGGCCCATTCA
* * * * * *
28336129 GCCTATATTCCTCAACAGTAATAGCAGTCTTAACGCACAAATTAGCAGAATTCCTTTTTCTCCCA
131 GCCTATATTCCTCAACAGTAATACCAGTCTTAACGCACAAATTACCAGAATTCCATTTCCTACAA
28336194 AATTTACCCAAATGGGCCCAGAAGCCCATTTGGCCCGATTTCAGCCCCTCGAGGCCCAACTTACC
196 AATTTACCCAAATGGGCCCAGAAGCCCATTTGGCCCGATTTCAGCCCCTCGAGGCCCAACTTACC
*
28336259 GTGATGCCAAAAGTCGTGCTCTTACCTTTTCCAATGTTTCTGA
261 GTGATGCCAAAAGTCGTGCTCTTACCCTTTCCAATGTTTCTGA
* * *
28336302 TTCATTATCAGTTACTAACAATTCATGTGTTTTAAACAGCGATTCTGGCCCATTTTCAGGGAAAT
1 TTCATTATCAGTTACTAACAATTCATGTG-CTTAAACAGCGATTCTGGCCCATTTTCAGCGAAAC
* * *
28336367 CGAGTTATTGGGCCAAAAACCCCTAATAGGCCCTACATAGCCGATTTAGTCATCTAGGCCCGTTC
65 CGAATTATTGGGCCAAAAACCCCTAATAGGCCCTACATAGCCGAATTAGTCATCTAGGCCCATTC
** * * * * *
28336432 AGCCTATATTCCAT-AATGGTATTACCAGTCTTATCGCGCAATTTAACCAG-ATTTCATTTCCTA
130 AGCCTATATTCC-TCAACAGTAATACCAGTCTTAACGCACAAATT-ACCAGAATTCCATTTCCTA
* *
28336495 CAAAATTTTCCCAAATGGGCCC-GTAAGCTCATTTGGCCCGATTTCAGCCCCTCGAGGCCCAACT
193 CAAAATTTACCCAAATGGGCCCAG-AAGCCCATTTGGCCCGATTTCAGCCCCTCGAGGCCCAACT
28336559 TACCGTGATGCCAAAAGTCGTGCTCTTACCCTTTCCAATGTTTCTGA
257 TACCGTGATGCCAAAAGTCGTGCTCTTACCCTTTCCAATGTTTCTGA
28336606 T
1 T
28336607 CGTCAACTTA
Statistics
Matches: 273, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
303 30 0.11
304 238 0.87
305 5 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (303 bp):
TTCATTATCAGTTACTAACAATTCATGTGCTTAAACAGCGATTCTGGCCCATTTTCAGCGAAACC
GAATTATTGGGCCAAAAACCCCTAATAGGCCCTACATAGCCGAATTAGTCATCTAGGCCCATTCA
GCCTATATTCCTCAACAGTAATACCAGTCTTAACGCACAAATTACCAGAATTCCATTTCCTACAA
AATTTACCCAAATGGGCCCAGAAGCCCATTTGGCCCGATTTCAGCCCCTCGAGGCCCAACTTACC
GTGATGCCAAAAGTCGTGCTCTTACCCTTTCCAATGTTTCTGA
Found at i:28340174 original size:15 final size:15
Alignment explanation
Indices: 28340154--28340183 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28340144 ATTATGAAAT
28340154 ATATGTTTTGGATTG
1 ATATGTTTTGGATTG
*
28340169 ATATGTTTTGTATTG
1 ATATGTTTTGGATTG
28340184 GAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTG
Found at i:28340850 original size:45 final size:42
Alignment explanation
Indices: 28340801--28340898 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 42
28340791 ATCTAAGACG
* *
28340801 TTGGCATCGATATATGTGGTTACGTGTAAGACCATTTCTGGGACA
1 TTGGCATCGATAT-T-TGATT-CGTGTAAGACCATGTCTGGGACA
*
28340846 TTGGCATCG-TATTTGATTCGTGTAAGACCCTGTCTGGGACA
1 TTGGCATCGATATTTGATTCGTGTAAGACCATGTCTGGGACA
* *
28340887 GTGGCACCGATA
1 TTGGCATCGATA
28340899 CGAGATAGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 28 0.60
42 6 0.13
43 1 0.02
44 3 0.06
45 9 0.19
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
TTGGCATCGATATTTGATTCGTGTAAGACCATGTCTGGGACA
Found at i:28345394 original size:94 final size:91
Alignment explanation
Indices: 28345237--28345445 Score: 217
Period size: 94 Copynumber: 2.3 Consensus size: 91
28345227 GTGCTGACGC
*
28345237 CATGTCCCAGACATGGTCTTACAC-TGACACATTTCACAGCCGATGCATGTCCCAAACATGTCTT
1 CATGTCCCAGACAT-GTCTTACACTTGACACATCTCACAGCCGATGCATGTCCCAAACATGTCTT
* * **
28345301 ACACTGGCT-TACGTCCCGAGGCCAATG
65 ACAATGGCTCT-CATAACGAGGCCAATG
* * * * *
28345328 CATGTCCCAGACATGTCTTACACTTGCACTCGTCTCA-ATGCTGATGCCATGTCCTAGACATGGT
1 CATGTCCCAGACATGTCTTACACTTG-ACACATCTCACA-GCCGATG-CATGTCCCAAACAT-GT
* * *
28345392 CTTACAATGGCTCTCATAACGTGGGCGATG
62 CTTACAATGGCTCTCATAACGAGGCCAATG
*
28345422 CATGTACCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
28345446 AGCCCACAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
90 9 0.09
91 17 0.17
92 13 0.13
93 12 0.12
94 46 0.47
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (91 bp):
CATGTCCCAGACATGTCTTACACTTGACACATCTCACAGCCGATGCATGTCCCAAACATGTCTTA
CAATGGCTCTCATAACGAGGCCAATG
Found at i:28356447 original size:111 final size:110
Alignment explanation
Indices: 28356264--28356469 Score: 313
Period size: 111 Copynumber: 1.9 Consensus size: 110
28356254 CAGACAGGGT
* * * * *
28356264 CTTACTCGTACACATATATCGGATTCATATATCAATGCCAACATATTAAAGTGGTCTTACTCGCA
1 CTTACTCGCACACATATATCAGAGTCAAATATCAATGCCAACATATTAAAGTGGACTTACTCGCA
28356329 CAAATATATCAGAGTCACATATCGATGCCAACGTATTAACGTGGA
66 CAAATATATCAGAGTCACATATCGATGCCAACGTATTAACGTGGA
* ** *
28356374 CTTACTCGCACATATATATCAGAGTCAAATATGGATGCCAACGTATTAAACGTGGACTTACTCGC
1 CTTACTCGCACACATATATCAGAGTCAAATATCAATGCCAACATATTAAA-GTGGACTTACTCGC
*
28356439 ACATATATATCAGAGTCACATATCGATGCCA
65 ACAAATATATCAGAGTCACATATCGATGCCA
28356470 CATATACTTC
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
110 42 0.49
111 43 0.51
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (110 bp):
CTTACTCGCACACATATATCAGAGTCAAATATCAATGCCAACATATTAAAGTGGACTTACTCGCA
CAAATATATCAGAGTCACATATCGATGCCAACGTATTAACGTGGA
Found at i:28356451 original size:56 final size:56
Alignment explanation
Indices: 28356264--28356469 Score: 299
Period size: 55 Copynumber: 3.7 Consensus size: 56
28356254 CAGACAGGGT
* * * * * * * *
28356264 CTTACTCGTACACATATATCGGATTCATATATCAATGCCAACATATTAAA-GTGGT
1 CTTACTCGCACATATATATCAGAGTCACATATCGATGCCAACGTATTAAACGTGGA
*
28356319 CTTACTCGCACAAATATATCAGAGTCACATATCGATGCCAACGTATT-AACGTGGA
1 CTTACTCGCACATATATATCAGAGTCACATATCGATGCCAACGTATTAAACGTGGA
* *
28356374 CTTACTCGCACATATATATCAGAGTCAAATATGGATGCCAACGTATTAAACGTGGA
1 CTTACTCGCACATATATATCAGAGTCACATATCGATGCCAACGTATTAAACGTGGA
28356430 CTTACTCGCACATATATATCAGAGTCACATATCGATGCCA
1 CTTACTCGCACATATATATCAGAGTCACATATCGATGCCA
28356470 CATATACTTC
Statistics
Matches: 136, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 2 0.01
55 88 0.65
56 46 0.34
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (56 bp):
CTTACTCGCACATATATATCAGAGTCACATATCGATGCCAACGTATTAAACGTGGA
Found at i:28358095 original size:29 final size:29
Alignment explanation
Indices: 28358043--28358110 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
28358033 ATGATCAACC
** * **
28358043 ATCCCTTTTCATAGTTGATGGTCGTCACT
1 ATCCCTTTTCATAGTCAATAGTCGAAACT
28358072 ATCCCTTTTCATAGTCAATAGTCGAAACT
1 ATCCCTTTTCATAGTCAATAGTCGAAACT
*
28358101 ATCCTTTTTC
1 ATCCCTTTTC
28358111 TTTAATCGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (29 bp):
ATCCCTTTTCATAGTCAATAGTCGAAACT
Found at i:28364814 original size:55 final size:53
Alignment explanation
Indices: 28364689--28364877 Score: 245
Period size: 55 Copynumber: 3.5 Consensus size: 53
28364679 AACTTACCAT
* * *
28364689 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* *
28364742 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
28364797 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
*
28364851 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
28364878 ATATCCTTAT
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
52 2 0.02
53 35 0.29
54 35 0.29
55 45 0.38
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:28365012 original size:47 final size:46
Alignment explanation
Indices: 28364848--28365072 Score: 177
Period size: 47 Copynumber: 4.8 Consensus size: 46
28364838 TAGAACTTAT
* * * * * * *
28364848 CAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATC-TTAC
1 CAATGCCATGTCTTGACGTGGTCTTACATGGTATCCTTGTCAATGC
*** * *
28364893 CAAATGCCATGTTCCAAACATGGTCTTACATGGTATCCTTGTCTTAGTGC
1 C-AATGCCATG-TCTTGACGTGGTCTTACATGGTATCCTTGTC--AATGC
** *
28364943 CAATGCCACATCTTGATGTGGTCTTACATGG-AGTCCTTAGTCAATGC
1 CAATGCCATGTCTTGACGTGGTCTTACATGGTA-TCCTT-GTCAATGC
* * * ** *
28364990 CGATGCCATGTCTTGACGTGGTCTTACACGGGATCCTTG-CCTTAC
1 CAATGCCATGTCTTGACGTGGTCTTACATGGTATCCTTGTCAATGC
*
28365035 CAATGCCATGTCTTGACATGGTCTTACATGGTATCCTT
1 CAATGCCATGTCTTGACGTGGTCTTACATGGTATCCTT
28365073 AACCGTCAAT
Statistics
Matches: 143, Mismatches: 29, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
45 38 0.27
46 10 0.07
47 60 0.42
48 22 0.15
49 10 0.07
50 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (46 bp):
CAATGCCATGTCTTGACGTGGTCTTACATGGTATCCTTGTCAATGC
Found at i:28365126 original size:44 final size:44
Alignment explanation
Indices: 28365077--28365161 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
28365067 ATCCTTAACC
* *
28365077 GTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGAATTTTCT
1 GTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGAATTTTCT
* *
28365121 GTCAATTCTTCCTTAATTGCCATGGTACAACCATGGAATTT
1 GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGAATTT
28365162 GAGATATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (44 bp):
GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGAATTTTCT
Found at i:28365744 original size:30 final size:30
Alignment explanation
Indices: 28365699--28365759 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28365689 TCCCTAACTC
* *
28365699 AAACTTTTTCAAAATTACAATTTTGCCCCT
1 AAACCTTTGCAAAATTACAATTTTGCCCCT
**
28365729 AAACCTTTGCAAAATTATGATTTTGCCCCT
1 AAACCTTTGCAAAATTACAATTTTGCCCCT
28365759 A
1 A
28365760 GGCTTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACCTTTGCAAAATTACAATTTTGCCCCT
Found at i:28369956 original size:40 final size:40
Alignment explanation
Indices: 28369858--28370028 Score: 254
Period size: 40 Copynumber: 4.2 Consensus size: 40
28369848 CGGATGATAA
* *
28369858 CCGGGCTAAGTCCTGAAGGCATTTGTGTGAGTTACTATGAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
* * *
28369899 AATCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TATCTATAT
1 --CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
28369941 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28369981 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28370021 CCGGGCTA
1 CCGGGCTA
28370029 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
40 82 0.69
41 2 0.02
42 4 0.03
43 30 0.25
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28380127 original size:43 final size:43
Alignment explanation
Indices: 28380066--28380270 Score: 305
Period size: 43 Copynumber: 4.9 Consensus size: 43
28380056 GAATATTCGG
*
28380066 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* ** *
28380109 ATGATAACCGGGCCAAGTCTTGAAGGCATTTGTGTGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28380152 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28380195 AT-AT--CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
28380235 AT-AT--CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
28380271 AGCTATATCC
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 70 0.46
42 2 0.01
43 81 0.53
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:28380214 original size:40 final size:40
Alignment explanation
Indices: 28380073--28380296 Score: 290
Period size: 40 Copynumber: 5.5 Consensus size: 40
28380063 CGGATGATAA
*
28380073 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATGAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
* ** *
28380114 AACCGGGCCAAGTCTTGAAGGCATTTGTGTGAGTTACTATGAT
1 --CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
28380157 AACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 --CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28380199 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28380239 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
28380279 CC-GACTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28380297 TACTTGGTTT
Statistics
Matches: 169, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 16 0.09
40 77 0.46
42 2 0.01
43 74 0.44
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28380279 original size:80 final size:82
Alignment explanation
Indices: 28380066--28380296 Score: 299
Period size: 86 Copynumber: 2.8 Consensus size: 82
28380056 GAATATTCGG
* * **
28380066 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATGATAACCGGGCCAAGTCTTG
1 ATGAT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT--CCGGGCTAAGTCCCG
*
28380131 AAGGCATTTGTGTGAGTTACT
62 AAGGCATTTGTGCGAGTTACT
28380152 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAG
1 ATGAT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAG
28380217 GCATTTGTGCGAGTTACT
65 GCATTTGTGCGAGTTACT
* * * *
28380235 AT-AT-CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATATCC-GACTAAATCCCGAAG
1 ATGATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAG
28380296 G
65 G
28380297 TACTTGGTTT
Statistics
Matches: 135, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
79 16 0.12
80 37 0.27
82 2 0.01
83 34 0.25
85 2 0.01
86 44 0.33
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (82 bp):
ATGATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGG
CATTTGTGCGAGTTACT
Found at i:28381690 original size:6 final size:6
Alignment explanation
Indices: 28381681--28381811 Score: 81
Period size: 6 Copynumber: 21.3 Consensus size: 6
28381671 TTGCATTCAC
* * *
28381681 ATTCTT ATTCTG ATTCT- ATTACGTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT-C-TG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * *
28381731 ATTTTG ATTCTG ATTTTG ATTTTG ATTCTG CCA-CCTG ATTCTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG --ATTCTG ATTCTG ATTCTG
* *
28381780 ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
28381812 AATGTTTCTT
Statistics
Matches: 97, Mismatches: 17, Indels: 22
0.71 0.12 0.16
Matches are distributed among these distances:
5 7 0.07
6 77 0.79
7 8 0.08
8 5 0.05
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:28381721 original size:25 final size:25
Alignment explanation
Indices: 28381687--28381745 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
28381677 TCACATTCTT
* *
28381687 ATTCTGATTCTATTACGTGATACTG
1 ATTCTGATTCTATTACCTAATACTG
* **
28381712 ATTCTGATTCTGTTACCTAATTTTG
1 ATTCTGATTCTATTACCTAATACTG
28381737 ATTCTGATT
1 ATTCTGATT
28381746 TTGATTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (25 bp):
ATTCTGATTCTATTACCTAATACTG
Found at i:28381751 original size:37 final size:37
Alignment explanation
Indices: 28381709--28381790 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
28381699 TTACGTGATA
** * *
28381709 CTGATTCTGATTCTGTTACCTAATTTTGATTCTGATT
1 CTGATTCTGATTCTGCCACCTAATTCTGATTCTAATT
* * *
28381746 TTGATTTTGATTCTGCCACCTGATTCTGATTCTAATT
1 CTGATTCTGATTCTGCCACCTAATTCTGATTCTAATT
28381783 CTGATTCT
1 CTGATTCT
28381791 CATTTTGATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.50
Consensus pattern (37 bp):
CTGATTCTGATTCTGCCACCTAATTCTGATTCTAATT
Found at i:28389136 original size:49 final size:49
Alignment explanation
Indices: 28389072--28389296 Score: 263
Period size: 49 Copynumber: 4.5 Consensus size: 49
28389062 CTGGTACACA
* *
28389072 TAGTAGTCTGCACTTAGTGCTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACATG
* * ** * *
28389121 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACATG
* * * * * **
28389171 TAGTAGCTTGCACTTAGTACTACACA-CCTGATCAAAGTTATCGGGTATACA
1 TAGTAGCCTGCACTTAGTACTACACATGC-GA-CCAA-TTATCCGGTACATG
*
28389222 TAGTAGCCTGCACTTCGTACTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACATG
28389271 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28389297 CGTGACCTCA
Statistics
Matches: 143, Mismatches: 28, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
49 64 0.45
50 44 0.31
51 34 0.24
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACATG
Found at i:28389560 original size:27 final size:27
Alignment explanation
Indices: 28389530--28389583 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28389520 AGGTACAACC
* *
28389530 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
*
28389557 CATGTAACAATAATTTACCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
28389584 TCACATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:28395255 original size:14 final size:12
Alignment explanation
Indices: 28395223--28395252 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
28395213 GTTTGAGCTC
28395223 TATAGTTTTATGA
1 TATA-TTTTATGA
28395236 TATATTTTATGA
1 TATATTTTATGA
28395248 TATAT
1 TATAT
28395253 ATTAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
TATATTTTATGA
Found at i:28395710 original size:25 final size:28
Alignment explanation
Indices: 28395658--28395711 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
28395648 TTATCGCTCT
* *
28395658 TATGTGTTGAATGATCGATTTTGCATAA
1 TATGTGTTGAATGATCGATTATGAATAA
28395686 TATG-GTTGAAT-AT-GATTATGAATAA
1 TATGTGTTGAATGATCGATTATGAATAA
28395711 T
1 T
28395712 GCATGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 7 0.29
28 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (28 bp):
TATGTGTTGAATGATCGATTATGAATAA
Found at i:28398738 original size:17 final size:19
Alignment explanation
Indices: 28398709--28398746 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28398699 TTAGCATTCT
28398709 TACCAAGAGTTCAT-CTCA
1 TACCAAGAGTTCATACTCA
28398727 TACCAA-AGTTCATACTCA
1 TACCAAGAGTTCATACTCA
28398745 TA
1 TA
28398747 GGTTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (19 bp):
TACCAAGAGTTCATACTCA
Found at i:28402238 original size:40 final size:40
Alignment explanation
Indices: 28402138--28402402 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
28402128 GCTCCTCGTT
* * * *
28402138 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
28402178 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28402217 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28402257 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28402297 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
28402337 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28402378 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28402403 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28402362 original size:80 final size:80
Alignment explanation
Indices: 28402105--28402402 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
28402095 AAATCACGTA
* ** * * *
28402105 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28402167 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
28402183 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
28402246 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
28402263 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28402327 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
28402343 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
28402403 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:28402411 original size:41 final size:41
Alignment explanation
Indices: 28402334--28402411 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28402324 TTTGTATCTC
* * *
28402334 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28402375 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28402412 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28404600 original size:34 final size:33
Alignment explanation
Indices: 28404552--28404641 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
28404542 GTTTCAGTTA
*
28404552 AGGCCTTAG-CCATTTCAGAATCAGAAACAGTG
1 AGGCCTAAGCCCATTTCAGAATCAGAAACAGTG
* * * *
28404584 TAGGCCTGAGCCCATTTCAATAAT-AGTATCAGTG
1 -AGGCCTAAGCCCATTTC-AGAATCAGAAACAGTG
* *
28404618 GGGCCTAAGCCCATTACAGAATCA
1 AGGCCTAAGCCCATTTCAGAATCA
28404642 ATACAGTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
32 4 0.09
33 23 0.50
34 15 0.33
35 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (33 bp):
AGGCCTAAGCCCATTTCAGAATCAGAAACAGTG
Found at i:28407043 original size:29 final size:28
Alignment explanation
Indices: 28407006--28407061 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
28406996 TGCGAGTTAT
*
28407006 ACTGATTTGGCTTCGGGCCATGCATATCG
1 ACTGATTTGGCTTCGAGCCATG-ATATCG
*
28407035 ACTGGTTTGGCTTCGAGCCATGATATC
1 ACTGATTTGGCTTCGAGCCATGATATC
28407062 AGTATTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (28 bp):
ACTGATTTGGCTTCGAGCCATGATATCG
Found at i:28409134 original size:30 final size:31
Alignment explanation
Indices: 28409098--28409158 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28409088 TTCCCGAGCC
*
28409098 TAGGGGC-AAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAAATGTAATTATGCAAAAGTT
* *
28409128 TAGGGGCAAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAAATGTAATTATGCAAAAGTT
28409159 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (31 bp):
TAGGGGCAAAAAATGTAATTATGCAAAAGTT
Found at i:28412988 original size:24 final size:24
Alignment explanation
Indices: 28412961--28413031 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
28412951 CTAGATTTCC
**
28412961 TCCCTTATCTGCTCCTAAA-CCGTA
1 TCCCTTATCAACTCCTAAATCC-TA
28412985 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28413009 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
28413032 CTCCTGACAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.25, C:0.38, G:0.03, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:28425650 original size:46 final size:46
Alignment explanation
Indices: 28425600--28425772 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 46
28425590 TGGTTGAGCA
28425600 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
28425646 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
28425691 CATCCGAACTCGATAAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
28425739 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
28425773 AGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 55 0.53
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28425756 original size:93 final size:93
Alignment explanation
Indices: 28425597--28425767 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
28425587 GGATGGTTGA
* * * *
28425597 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGATAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
28425662 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
28425690 GCATCCGAACTCGATAAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGATAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG
28425754 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
28425768 ACTTAAGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGATAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28426064 original size:40 final size:39
Alignment explanation
Indices: 28425992--28426099 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 39
28425982 CTTTTAGTGG
* * *
28425992 CTTTAGCGGCGCTTCTTAAAAACGCCGCTATAGGTACAC
1 CTTTAGCGGCGTTTTTTAAAAGCGCCGCTATAGGTACAC
28426031 CTTTAGCGGCGTTTTTTAAGAAGCGCCGCTATAGGTACAC
1 CTTTAGCGGCGTTTTTTAA-AAGCGCCGCTATAGGTACAC
* *
28426071 CTATAGCGGCGTTTTTCAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTT-TAAAAGCGCCGC
28426100 AAAAGAGTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 17 0.27
40 43 0.69
41 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (39 bp):
CTTTAGCGGCGTTTTTTAAAAGCGCCGCTATAGGTACAC
Found at i:28426242 original size:40 final size:41
Alignment explanation
Indices: 28426159--28426255 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 41
28426149 TTAGCGGTGC
* * *
28426159 TTTTTAAAAA-CACCACTATAGGTACACCTTTAGCGGCATT
1 TTTTTAAAAAGCACCGCTATAGGTACACCTATAGCGGCAGT
*
28426199 TTTTTAAAAAGCACCGCTATAGGTACACCTATAGTGGC-GT
1 TTTTTAAAAAGCACCGCTATAGGTACACCTATAGCGGCAGT
* *
28426239 TTTTCAAAAAGCGCCGC
1 TTTTTAAAAAGCACCGC
28426256 AAAAGAGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 26 0.52
41 24 0.48
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (41 bp):
TTTTTAAAAAGCACCGCTATAGGTACACCTATAGCGGCAGT
Found at i:28426297 original size:156 final size:155
Alignment explanation
Indices: 28425879--28426339 Score: 789
Period size: 156 Copynumber: 3.0 Consensus size: 155
28425869 AGAACGAGCA
*
28425879 TTAGTGGCGTTTTTTAAAAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTC-AAAAGCGCC
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTCAAAAAGCGCC
* *
28425943 GCAAAGGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGCGCTTCT
66 GCAAAAGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGCGCTTTT
*
28426008 TAAAAACGCCGCTATAGGTACACCT
131 TAAAAACACCGCTATAGGTACACCT
*
28426033 TTAGCGGCGTTTTTTAAGAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTCAAAAAGCGCC
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTCAAAAAGCGCC
*
28426098 GCAAAAGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGTGCTTTT
66 GCAAAAGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGCGCTTTT
*
28426163 TAAAAACACCACTATAGGTACACCT
131 TAAAAACACCGCTATAGGTACACCT
* * *
28426188 TTAGCGGCATTTTTTTAAAAAGCACCGCTATAGGTACACCTATAGTGGCGTTTTTCAAAAAGCGC
1 TTAGCGGC-GTTTTTTAAAAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTCAAAAAGCGC
* * *
28426253 CGCAAAAGAGTTTTACAAAACGACATCGTTTTATATTGACCTTTTAGTGGCTTTAGCGGCGCTTT
65 CGCAAAAGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGCGCTTT
28426318 TTAAAAACACCGCTATAGGTAC
130 TTAAAAACACCGCTATAGGTAC
28426340 TGTAACACCC
Statistics
Matches: 289, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
154 53 0.18
155 102 0.35
156 134 0.46
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (155 bp):
TTAGCGGCGTTTTTTAAAAAGCGCCGCTATAGGTACACCTATAGCGGCGTTTTTCAAAAAGCGCC
GCAAAAGAGTTTTACAAAACAACGTCGTTTTGTATTGACCTTTTAGTGGCTTTAGCGGCGCTTTT
TAAAAACACCGCTATAGGTACACCT
Found at i:28426938 original size:6 final size:6
Alignment explanation
Indices: 28426927--28427081 Score: 142
Period size: 6 Copynumber: 25.5 Consensus size: 6
28426917 AACCAAAATG
* *
28426927 AGAATC AGAATC AGAATC AGTAAT- AGAATC AAAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
28426975 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* *
28427024 AGAATC AGTAA-C AGAATC AGAATC AGAATC AGAATT ACGTGA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
28427073 AGAATC AGA
1 AGAATC AGA
28427082 CTGTGAATGC
Statistics
Matches: 123, Mismatches: 12, Indels: 28
0.75 0.07 0.17
Matches are distributed among these distances:
5 10 0.08
6 100 0.81
7 10 0.08
8 3 0.02
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:28427038 original size:55 final size:55
Alignment explanation
Indices: 28426927--28427081 Score: 219
Period size: 55 Copynumber: 2.8 Consensus size: 55
28426917 AACCAAAATG
* * *
28426927 AGAATCAGAATCAGAATCAGTAA-TAG-AATCAAAATCAGAATCA-ATATTAGTAAC
1 AGAATCAGAATCAGAATCAG-AATTAGTGA-CAGAATCAGAATCAGATATCAGTAAC
28426981 AGAATCAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGA-ATCAGTAAC
1 AGAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGATATCAGTAAC
28427036 AGAATCAGAATCAGAATCAGAATTACGTGACAGAATCAGAATCAGA
1 AGAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGA
28427082 CTGTGAATGC
Statistics
Matches: 93, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
53 2 0.02
54 22 0.24
55 67 0.72
56 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (55 bp):
AGAATCAGAATCAGAATCAGAATTAGTGACAGAATCAGAATCAGATATCAGTAAC
Found at i:28427238 original size:27 final size:26
Alignment explanation
Indices: 28427201--28427266 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
28427191 AGCATGGCTG
*
28427201 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
28427227 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
28427254 CCAGAATCAGATA
1 CCAGAA-CAGATA
28427267 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:28427271 original size:27 final size:27
Alignment explanation
Indices: 28427201--28427274 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
28427191 AGCATGGCTG
* *
28427201 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
28427227 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
28427254 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
28427275 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:28427281 original size:27 final size:27
Alignment explanation
Indices: 28427225--28427282 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28427215 GTGACAGAGT
* * *
28427225 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
28427252 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
28427279 CACC
1 CACC
28427283 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:28427487 original size:22 final size:22
Alignment explanation
Indices: 28427439--28427497 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
28427429 GTAAATACGT
*
28427439 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
28427461 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
28427483 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
28427498 TAATAACGGG
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:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:28427664 original size:27 final size:26
Alignment explanation
Indices: 28427585--28427667 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
28427575 TCGATCGGTC
* * *
28427585 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
28427611 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
28427638 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
28427665 AAC
1 AAC
28427668 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:28427896 original size:27 final size:27
Alignment explanation
Indices: 28427866--28428061 Score: 207
Period size: 27 Copynumber: 7.3 Consensus size: 27
28427856 GGGGCAAAAT
* * *
28427866 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28427893 GGTAATTCTACCCTAC-AGAAGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
*
28427920 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
28427947 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28427974 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
28428001 AGTAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28428028 AGAAATTCTACCCTAC-AGAGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
*
28428055 AGTAATT
1 GGTAATT
28428062 TCACAATCAA
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.02
27 139 0.97
28 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28428102 original size:27 final size:27
Alignment explanation
Indices: 28428066--28428663 Score: 758
Period size: 27 Copynumber: 22.1 Consensus size: 27
28428056 GTAATTTCAC
*
28428066 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
28428093 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
28428120 AA-CTGAGGGTAAACCAGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* * * *
28428147 AATCAAGGGTAAAACAGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
28428174 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
** *
28428201 AATCGAGGGTAAAACAATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
28428228 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
** *
28428255 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * * *
28428282 AA-CTAAGGATAAAACAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* * *
28428309 AATCGAGGGTAAAACAGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
28428336 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
28428363 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
28428390 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
28428417 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTATA
28428444 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
28428471 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
28428498 AA-CTGAGGGTAAAATGATAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
28428525 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
28428552 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
28428579 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
28428606 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
28428633 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
28428660 AATC
1 AATC
28428664 AGGAGTACTT
Statistics
Matches: 497, Mismatches: 62, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.01
27 485 0.98
28 6 0.01
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:28430155 original size:11 final size:11
Alignment explanation
Indices: 28430139--28430181 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
28430129 TTAGGGATCA
28430139 TGGTTTAAGGG
1 TGGTTTAAGGG
28430150 TGGTTTAAGGG
1 TGGTTTAAGGG
28430161 TGGTTTAAGGG
1 TGGTTTAAGGG
*
28430172 TAGTTTAAGG
1 TGGTTTAAGG
28430182 TTGGGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (11 bp):
TGGTTTAAGGG
Found at i:28430233 original size:36 final size:35
Alignment explanation
Indices: 28430176--28430250 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
28430166 TAAGGGTAGT
* *
28430176 TTAA-GGTTGGGGTTTAAGGTTTAGG-TGTTAGGGG
1 TTAAGGGTTGGGGTTCAAGGTTTAGGAT-TTAGGGC
*
28430210 TTAAGGGTTAGGGGTTCATGGTTTAGGATTTAGGGC
1 TTAAGGGTT-GGGGTTCAAGGTTTAGGATTTAGGGC
28430246 TTAAG
1 TTAAG
28430251 ATTTAAGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.11
35 4 0.11
36 26 0.74
37 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.40, T:0.37
Consensus pattern (35 bp):
TTAAGGGTTGGGGTTCAAGGTTTAGGATTTAGGGC
Found at i:28431049 original size:9 final size:8
Alignment explanation
Indices: 28431031--28431096 Score: 50
Period size: 7 Copynumber: 8.2 Consensus size: 8
28431021 TTAATATGAT
28431031 AATTTAAA
1 AATTTAAA
28431039 AATTATAAA
1 AATT-TAAA
*
28431048 AATGCTCAAAA
1 AAT--T-TAAA
*
28431059 AAATTAAA
1 AATTTAAA
28431067 AA-TTAAA
1 AATTTAAA
28431074 AA-TTAAA
1 AATTTAAA
28431081 AA-TTAAA
1 AATTTAAA
28431088 AA-TTAAA
1 AATTTAAA
28431095 AA
1 AA
28431097 ACTAAAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
7 28 0.55
8 9 0.18
9 8 0.16
11 6 0.12
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (8 bp):
AATTTAAA
Found at i:28431103 original size:21 final size:21
Alignment explanation
Indices: 28431057--28431104 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
28431047 AAATGCTCAA
*
28431057 AAAAATTAAAAATTAAAAATT
1 AAAAATTAAAAATTAAAAACT
28431078 AAAAATTAAAAATTAAAAAACT
1 AAAAATTAAAAATT-AAAAACT
28431100 AAAAA
1 AAAAA
28431105 ACTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATTAAAAATTAAAAACT
Found at i:28431112 original size:7 final size:7
Alignment explanation
Indices: 28431057--28431096 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
28431047 AAATGCTCAA
28431057 AAAAATT
1 AAAAATT
28431064 AAAAATT
1 AAAAATT
28431071 AAAAATT
1 AAAAATT
28431078 AAAAATT
1 AAAAATT
28431085 AAAAATT
1 AAAAATT
28431092 AAAAA
1 AAAAA
28431097 ACTAAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:28431239 original size:17 final size:18
Alignment explanation
Indices: 28431217--28431255 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28431207 ATTTGAAAGA
*
28431217 AAAAAT-AAAAAAATATT
1 AAAAATGAAAAAAAAATT
28431234 AAAAATGAAAAAAAAATT
1 AAAAATGAAAAAAAAATT
28431252 AAAA
1 AAAA
28431256 TTAAGCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAATGAAAAAAAAATT
Found at i:28431301 original size:23 final size:24
Alignment explanation
Indices: 28431275--28431321 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28431265 AGTGGCGTTT
*
28431275 TTAAG-AAAAAATGCCACAAAAAA
1 TTAAGCAAAAAACGCCACAAAAAA
* *
28431298 TTAAGCTAAAAACGCCGCAAAAAA
1 TTAAGCAAAAAACGCCACAAAAAA
28431322 CTAAACTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (24 bp):
TTAAGCAAAAAACGCCACAAAAAA
Found at i:28433361 original size:43 final size:42
Alignment explanation
Indices: 28433308--28433392 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 42
28433298 TTTTTGTTGT
*
28433308 CGTGTGGTACTTAGAAAACATTTTGTTGTGTCTAGGAAAATG
1 CGTGTGGTACTTAGAAAACATTTTGTTGTGTCCAGGAAAATG
28433350 CGTGTAGGTACTTAGAAAACATTTTGTTGTGTCCAGGAAAATG
1 CGTGT-GGTACTTAGAAAACATTTTGTTGTGTCCAGGAAAATG
28433393 GTGAAAATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (42 bp):
CGTGTGGTACTTAGAAAACATTTTGTTGTGTCCAGGAAAATG
Found at i:28435659 original size:23 final size:23
Alignment explanation
Indices: 28435632--28435880 Score: 247
Period size: 23 Copynumber: 10.9 Consensus size: 23
28435622 TGGATGCTGT
*
28435632 TGTTTAAATGCTGCAAATTGAAG
1 TGTTTAAATGCTGTAAATTGAAG
*
28435655 TGTTTAAATGCTGTAAATTGCAG
1 TGTTTAAATGCTGTAAATTGAAG
* *
28435678 TGTTTAAATGTTGTAAATTGCAG
1 TGTTTAAATGCTGTAAATTGAAG
*
28435701 TGTTTAAATGTTGTAAATTGAAG
1 TGTTTAAATGCTGTAAATTGAAG
* * *
28435724 TGTTTAAGTACTGCAAATTGAAG
1 TGTTTAAATGCTGTAAATTGAAG
** *
28435747 TGTTTAGTTGCTGGAAATTG-AG
1 TGTTTAAATGCTGTAAATTGAAG
* * *
28435769 ATGTTTTATTGTTGT-AATTG-AG
1 -TGTTTAAATGCTGTAAATTGAAG
* * *
28435791 TTGTATAAATGTTGTTAATTG-AG
1 -TGTTTAAATGCTGTAAATTGAAG
*
28435814 ATG-TTAAAGTGCTGCAAATTGAAG
1 -TGTTTAAA-TGCTGTAAATTGAAG
28435838 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGCTGTAAATTGAAG
* *
28435861 TGCTTAAATGTTGTAAATTG
1 TGTTTAAATGCTGTAAATTG
28435881 GCATCTGTTT
Statistics
Matches: 193, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
22 24 0.12
23 162 0.84
24 7 0.04
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (23 bp):
TGTTTAAATGCTGTAAATTGAAG
Found at i:28436142 original size:19 final size:19
Alignment explanation
Indices: 28436119--28436165 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28436109 ATTTAATCTA
*
28436119 ATTTTTATTATTTA-TTTT
1 ATTTTTATTATATATTTTT
* *
28436137 AGTTTTGATTCTATATTTTT
1 A-TTTTTATTATATATTTTT
28436157 ATTTTTATT
1 ATTTTTATT
28436166 TTAATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:28436489 original size:43 final size:43
Alignment explanation
Indices: 28436428--28436614 Score: 234
Period size: 43 Copynumber: 4.3 Consensus size: 43
28436418 TTAAAATTTT
* ** ***
28436428 ATGACCTTTAGCGGCGTTTGTGGGATTAGTAACGCTAAAGGTC
1 ATGACCATTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
28436471 ATGACCATTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
1 ATGACCATTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
*
28436514 ATGA-CATTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTC
1 ATGACCA-TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
** * *
28436557 ATGACTTTTAGCGGCGTTTGTGTGAAAAGTGCCGCTAAAGGTC
1 ATGACCATTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
*
28436600 ATCA-CATTTAGCGGC
1 ATGACCA-TTAGCGGC
28436615 ATTTTTTTAA
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.02
43 124 0.98
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (43 bp):
ATGACCATTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
Found at i:28436538 original size:86 final size:86
Alignment explanation
Indices: 28436428--28436614 Score: 275
Period size: 86 Copynumber: 2.2 Consensus size: 86
28436418 TTAAAATTTT
* ** *
28436428 ATGACCTTTAGCGGCGTTTGTGGGATTAGTAACGCTAAAGGTCATGACCATTAGCGGCGTTTGTG
1 ATGACATTTAGCGGCGTTTGTGGGAAAAGCAACGCTAAAGGTCATGACCATTAGCGGCGTTTGTG
28436493 GGAAAAGCGCCGCTAAAGGTC
66 GGAAAAGCGCCGCTAAAGGTC
** **
28436514 ATGACATTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGACTTTTAGCGGCGTTTGTG
1 ATGACATTTAGCGGCGTTTGTGGGAAAAGCAACGCTAAAGGTCATGACCATTAGCGGCGTTTGTG
* *
28436579 TGAAAAGTGCCGCTAAAGGTC
66 GGAAAAGCGCCGCTAAAGGTC
*
28436600 ATCACATTTAGCGGC
1 ATGACATTTAGCGGC
28436615 ATTTTTTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (86 bp):
ATGACATTTAGCGGCGTTTGTGGGAAAAGCAACGCTAAAGGTCATGACCATTAGCGGCGTTTGTG
GGAAAAGCGCCGCTAAAGGTC
Found at i:28439500 original size:23 final size:24
Alignment explanation
Indices: 28439474--28439532 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
28439464 CCCTTATCTG
*
28439474 CTCCTAAATCGTATC-CGTATCAA
1 CTCCTAAATCCTATCGCGTATCAA
*
28439497 CTCCTAAATCCTATCGCTTATCAA
1 CTCCTAAATCCTATCGCGTATCAA
28439521 CTCCTAAATCCT
1 CTCCTAAATCCT
28439533 CTCCTGACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (24 bp):
CTCCTAAATCCTATCGCGTATCAA
Found at i:28449778 original size:27 final size:27
Alignment explanation
Indices: 28449748--28449925 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28449738 ATATTGAGTC
* * * *
28449748 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28449775 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28449802 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28449830 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28449857 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28449884 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28449911 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28449926 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28449887 original size:82 final size:81
Alignment explanation
Indices: 28449769--28449924 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28449759 TGCTATATAA
* *
28449769 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28449834 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28449851 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28449915 CACTTAGTGC
65 CACTTAGTGC
28449925 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28456417 original size:29 final size:29
Alignment explanation
Indices: 28456335--28456418 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
28456325 TATACTAAAT
* * * *
28456335 GATGGTTGTAACCATCTCTTTTTAAATTC
1 GATGGTCGTAACCATCCCTTTTCATATTC
*
28456364 GATGGTCGTTACCATCCCTTTTCATATTC
1 GATGGTCGTAACCATCCCTTTTCATATTC
*
28456393 GATGGTCGGAACCATCCCTTTTCATA
1 GATGGTCGTAACCATCCCTTTTCATA
28456419 GTCAATAGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (29 bp):
GATGGTCGTAACCATCCCTTTTCATATTC
Found at i:28456429 original size:29 final size:29
Alignment explanation
Indices: 28456374--28456429 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
28456364 GATGGTCGTT
* * *
28456374 ACCATCCCTTTTCATATTCGATGGTCGGA
1 ACCATCCCTTTTCATAGTCAATAGTCGGA
28456403 ACCATCCCTTTTCATAGTCAATAGTCG
1 ACCATCCCTTTTCATAGTCAATAGTCG
28456430 AAATTGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (29 bp):
ACCATCCCTTTTCATAGTCAATAGTCGGA
Found at i:28462253 original size:12 final size:13
Alignment explanation
Indices: 28462225--28462257 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28462215 TTATTTCTTT
28462225 TTCTCCATCTACC
1 TTCTCCATCTACC
*
28462238 TTCTCC-TCTTCC
1 TTCTCCATCTACC
28462250 TTCTCCAT
1 TTCTCCAT
28462258 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:28463114 original size:28 final size:28
Alignment explanation
Indices: 28463082--28463146 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28463072 ATTTACTAGA
*
28463082 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
28463110 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28463138 ATACCCCTA
1 ATACCCCTA
28463147 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:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28463310 original size:27 final size:28
Alignment explanation
Indices: 28463252--28463341 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28463242 AGGAAGCGTC
*
28463252 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
28463280 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
28463307 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
28463336 CTGGTG
1 CTGGTG
28463342 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:28463352 original size:29 final size:28
Alignment explanation
Indices: 28463262--28463352 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
28463252 CTGGTGGCTA
* * *
28463262 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
28463290 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28463317 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
28463346 TGTCACA
1 TGCCACA
28463353 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:28463360 original size:55 final size:56
Alignment explanation
Indices: 28463252--28463366 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
28463242 AGGAAGCGTC
* * *
28463252 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
28463307 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28463363 CTGG
1 CTGG
28463367 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28469871 original size:12 final size:13
Alignment explanation
Indices: 28469843--28469875 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28469833 TTATTTCTTT
28469843 TTCTCCATCTACC
1 TTCTCCATCTACC
*
28469856 TTCTCC-TCTTCC
1 TTCTCCATCTACC
28469868 TTCTCCAT
1 TTCTCCAT
28469876 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:28477998 original size:28 final size:28
Alignment explanation
Indices: 28477966--28478022 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28477956 TCTTATGTGT
28477966 AGAAATAAGGAAGGTGAGAGAATGAGAC
1 AGAAATAAGGAAGGTGAGAGAATGAGAC
28477994 AGAAATAAGGAAGGTGAGAGAATGAGAC
1 AGAAATAAGGAAGGTGAGAGAATGAGAC
28478022 A
1 A
28478023 TAAGGTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.35, T:0.11
Consensus pattern (28 bp):
AGAAATAAGGAAGGTGAGAGAATGAGAC
Found at i:28479090 original size:15 final size:15
Alignment explanation
Indices: 28479066--28479101 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
28479056 AGACACACCT
*
28479066 TTTTCCTTTGTATAA
1 TTTTCTTTTGTATAA
28479081 TTTTCTTTTGTATAA
1 TTTTCTTTTGTATAA
28479096 TTTTCT
1 TTTTCT
28479102 CTTTAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTCTTTTGTATAA
Found at i:28485317 original size:40 final size:39
Alignment explanation
Indices: 28485182--28485323 Score: 149
Period size: 40 Copynumber: 3.6 Consensus size: 39
28485172 AATTATTGTG
**
28485182 TGAATGCACATACGCGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTC-GTACCCC
* ** ** * *
28485222 TGAATGTACATATGTAACCATGTTTGTACTTCGATACCAC
1 TGAATGCACATACATGCCCCTGTTTGTACTTCG-TACCCC
*
28485262 TAAATGCACATACATGCCCCTGTTTGTACTTCAGTACCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTC-GTACCCC
* *
28485302 TGAATGCATATACATGCTCCTG
1 TGAATGCACATACATGCCCCTG
28485324 ATTTTATTAT
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 80 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (39 bp):
TGAATGCACATACATGCCCCTGTTTGTACTTCGTACCCC
Found at i:28488954 original size:21 final size:21
Alignment explanation
Indices: 28488930--28488970 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28488920 CAAACATGCC
*
28488930 AACAAAAGCTCATAAGAGCTT
1 AACAAAAGCTCAAAAGAGCTT
* *
28488951 AACAGAAGCTTAAAAGAGCT
1 AACAAAAGCTCAAAAGAGCT
28488971 GATCCACCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (21 bp):
AACAAAAGCTCAAAAGAGCTT
Found at i:28493109 original size:27 final size:27
Alignment explanation
Indices: 28493079--28493256 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28493069 ATATTGAGTC
* * * *
28493079 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28493106 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28493133 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28493161 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28493188 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28493215 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28493242 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28493257 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28493218 original size:82 final size:81
Alignment explanation
Indices: 28493100--28493255 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28493090 TGCTATATAA
* *
28493100 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28493165 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28493182 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28493246 CACTTAGTGC
65 CACTTAGTGC
28493256 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28501728 original size:27 final size:27
Alignment explanation
Indices: 28501698--28501875 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28501688 ATATTGAGTC
* * * *
28501698 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28501725 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28501752 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28501780 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28501807 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28501834 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28501861 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28501876 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28501837 original size:82 final size:81
Alignment explanation
Indices: 28501719--28501874 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28501709 TGCTATATAA
* *
28501719 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28501784 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28501801 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28501865 CACTTAGTGC
65 CACTTAGTGC
28501875 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28507505 original size:12 final size:11
Alignment explanation
Indices: 28507473--28507506 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28507463 GACCCGCCCG
28507473 TGTTAATTTTTA
1 TGTT-ATTTTTA
*
28507485 TATTATTTTTA
1 TGTTATTTTTA
28507496 TGTTATTTTTA
1 TGTTATTTTTA
28507507 AATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
TGTTATTTTTA
Found at i:28507683 original size:30 final size:31
Alignment explanation
Indices: 28507628--28507691 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
28507618 ACTTAACAAG
*
28507628 CAAATGCCTCTAAAATAATTAAAAAAATTAA
1 CAAACGCCTCTAAAATAATTAAAAAAATTAA
* *
28507659 CAAACGCCTTTAAAATAA-TAAAAAATTTAA
1 CAAACGCCTCTAAAATAATTAAAAAAATTAA
28507689 CAA
1 CAA
28507692 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (31 bp):
CAAACGCCTCTAAAATAATTAAAAAAATTAA
Found at i:28524012 original size:19 final size:20
Alignment explanation
Indices: 28523976--28524014 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28523966 AATGGCCCAA
28523976 GGCCCATTAGTCGACCCAAGT
1 GGCCCATTAG-CGACCCAAGT
*
28523997 GGCCCATTA-CGGCCCAAG
1 GGCCCATTAGCGACCCAAG
28524015 CCCCTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
GGCCCATTAGCGACCCAAGT
Found at i:28529512 original size:6 final size:6
Alignment explanation
Indices: 28529501--28529541 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
28529491 TATAGATACG
* *
28529501 GTTTTA GTTTTA TTTTTA GTTTTA GTTTTA GTTCTA GTTTT
1 GTTTTA GTTTTA GTTTTA GTTTTA GTTTTA GTTTTA GTTTT
28529542 TTTTTCTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (6 bp):
GTTTTA
Found at i:28536241 original size:35 final size:35
Alignment explanation
Indices: 28536195--28536267 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
28536185 GCTTCTTGCA
28536195 AAATTTTCCAAATAA-TTTCATTTTTTTGGGTACAC
1 AAATTTTCCAAATAAGTTT-ATTTTTTTGGGTACAC
28536230 AAATTTTCCAAATAAGTTTATTTTTTTGGGTACAC
1 AAATTTTCCAAATAAGTTTATTTTTTTGGGTACAC
28536265 AAA
1 AAA
28536268 CCCTATATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 34 0.92
36 3 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (35 bp):
AAATTTTCCAAATAAGTTTATTTTTTTGGGTACAC
Found at i:28537800 original size:68 final size:66
Alignment explanation
Indices: 28537728--28537899 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
28537718 CATCATGTGT
* * * *
28537728 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
28537791 TGTAG
62 TGTAG
** * *
28537796 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
28537861 AG
65 AG
* * * *
28537863 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
28537900 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:28537833 original size:64 final size:64
Alignment explanation
Indices: 28537752--28537935 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
28537742 AGACATTATG
* * *
28537752 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
28537816 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28537881 AA
63 AA
* * *
28537883 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
28537936 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28544601 original size:93 final size:93
Alignment explanation
Indices: 28544489--28544660 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28544479 GCCCATAAGT
*
28544489 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28544554 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
28544582 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28544647 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
28544661 CAAATATCCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28544656 original size:46 final size:46
Alignment explanation
Indices: 28544481--28544656 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
28544471 TGTAACCCGC
*
28544481 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28544527 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
28544573 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28544620 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
28544657 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 70 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Done.