Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 88 of 332
Found at i:28112690 original size:27 final size:26
Alignment explanation
Indices: 28112652--28112703 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
28112642 CTCGCTGCAA
*
28112652 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
28112679 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACTTCGCCACAATATCTG
28112704 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:28112741 original size:67 final size:67
Alignment explanation
Indices: 28112633--28112786 Score: 299
Period size: 67 Copynumber: 2.3 Consensus size: 67
28112623 AAGGAAGCGT
28112633 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
28112698 TA
66 TA
28112700 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
28112765 TA
66 TA
*
28112767 TCTAGCAGCCTCGCTGCAAT
1 TCTGGCAGCCTCGCTGCAAT
28112787 TTTTGTGGTG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 86 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:28112757 original size:27 final size:26
Alignment explanation
Indices: 28112719--28112769 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
28112709 CTCGCTGCAA
*
28112719 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
28112746 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACTTCGCCACAATATCT
28112770 AGCAGCCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:28112898 original size:6 final size:6
Alignment explanation
Indices: 28112889--28113084 Score: 159
Period size: 6 Copynumber: 31.8 Consensus size: 6
28112879 TTGCATTCAC
* * *
28112889 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTA ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* *
28112939 ATTCTG ATTCTG GTTCTG ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * *
28112988 ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG ATTCTG GTTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
28113037 ATTCT- ATCACCTG ATTTTG ATTTTG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
28113085 AGTTATGATA
Statistics
Matches: 153, Mismatches: 22, Indels: 30
0.75 0.11 0.15
Matches are distributed among these distances:
5 10 0.07
6 123 0.80
7 12 0.08
8 8 0.05
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28112920 original size:25 final size:25
Alignment explanation
Indices: 28112889--28113030 Score: 189
Period size: 25 Copynumber: 5.7 Consensus size: 25
28112879 TTGCATTCAC
28112889 ATTCTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* * *
28112914 ATACTGATTCTAATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
*
28112939 ATTCTGATTCTGGTTCTGATT--CTG
1 ATTCTGATTCTGATTCTG-TTACCTG
*
28112963 GTTCTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* *
28112988 ATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
*
28113013 ATTCTGATTCTGGTTCTG
1 ATTCTGATTCTGATTCTG
28113031 ATTTTGATTC
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.02
24 18 0.18
25 78 0.78
26 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTG
Found at i:28112958 original size:37 final size:37
Alignment explanation
Indices: 28112911--28113079 Score: 173
Period size: 37 Copynumber: 4.6 Consensus size: 37
28112901 ATTCTGTTAC
* *
28112911 CTGATACTGATTCTAATTCTGTTACCTAATTCTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
* * *
28112948 CTGGTTCTGATTCTGGTTCTGATT--CTGATTCTG-TT
1 CTGATTCTGATTCTGATTCTG-TTACCTAATTCTGATT
*
28112983 ACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATT
1 --CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
* * * * * *
28113022 CTGGTTCTGATTTTGATTCTATCACCTGATTTTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
*
28113059 TTGATTCTGATTCTGATTCTG
1 CTGATTCTGATTCTGATTCTG
28113080 ATTCTAGTTA
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
35 2 0.02
36 10 0.09
37 82 0.77
38 10 0.09
39 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTTACCTAATTCTGATT
Found at i:28113004 original size:74 final size:74
Alignment explanation
Indices: 28112890--28113033 Score: 279
Period size: 74 Copynumber: 1.9 Consensus size: 74
28112880 TGCATTCACA
28112890 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTGGTTC
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTGGTTC
28112955 TGATTCTGG
66 TGATTCTGG
*
28112964 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTGGTTC
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTGGTTC
28113029 TGATT
66 TGATT
28113034 TTGATTCTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (74 bp):
TTCTGATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTGGTTC
TGATTCTGG
Found at i:28113069 original size:74 final size:73
Alignment explanation
Indices: 28112889--28113079 Score: 251
Period size: 74 Copynumber: 2.6 Consensus size: 73
28112879 TTGCATTCAC
* *
28112889 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACCTAATTCTGATTCTGGTT
1 ATTCTGATCCTGATTCTGTTA-CTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTGGTT
28112954 CTGATTCTG
65 CTGATTCTG
* *
28112963 GTTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTGGTT
1 ATTCTGATCCTGATTCTGTTA-CTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTGGTT
*
28113028 CTGATTTTG
65 CTGATTCTG
* * *
28113037 ATTCT-ATCACCTGATTTTGATT-TTGATTCTGATTCTGATTCTG
1 ATTCTGAT--CCTGATTCTG-TTACTGATACTGATTCTGATTCTG
28113080 ATTCTAGTTA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
73 2 0.02
74 94 0.89
75 8 0.08
76 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (73 bp):
ATTCTGATCCTGATTCTGTTACTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTGGTTC
TGATTCTG
Found at i:28113093 original size:18 final size:18
Alignment explanation
Indices: 28112889--28113082 Score: 96
Period size: 19 Copynumber: 10.5 Consensus size: 18
28112879 TTGCATTCAC
*
28112889 ATTCTGATTCTGATTCTG
1 ATTCTGATTATGATTCTG
*
28112907 -TTACCTGA-TACTGATTCTA
1 ATT--CTGATTA-TGATTCTG
*
28112926 ATTCTG-TTACCTAATTCTG
1 ATTCTGATTA--TGATTCTG
* *
28112945 ATTCTGGTTCTGATTCTG
1 ATTCTGATTATGATTCTG
* *
28112963 GTTCTGATTCTGATTCTG
1 ATTCTGATTATGATTCTG
28112981 -TTACCTGA-TACTGATTCTG
1 ATT--CTGATTA-TGATTCTG
*
28113000 ATTCTG-TTACCTAATTCTG
1 ATTCTGATTA--TGATTCTG
* * *
28113019 ATTCTGGTTCTGATTTTG
1 ATTCTGATTATGATTCTG
* *
28113037 ATTCT-ATCACCTGATTTTG
1 ATTCTGATTA--TGATTCTG
* *
28113056 ATTTTGATTCTGATTCTG
1 ATTCTGATTATGATTCTG
28113074 ATTCTGATT
1 ATTCTGATT
28113083 CTAGTTATGA
Statistics
Matches: 138, Mismatches: 21, Indels: 34
0.72 0.11 0.18
Matches are distributed among these distances:
17 5 0.04
18 61 0.44
19 62 0.45
20 10 0.07
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (18 bp):
ATTCTGATTATGATTCTG
Found at i:28114930 original size:46 final size:46
Alignment explanation
Indices: 28114867--28115032 Score: 133
Period size: 46 Copynumber: 3.6 Consensus size: 46
28114857 TCCAAACTTT
* * *
28114867 TTGAGTTGAGTCGGAGTTCACTTATGGATGCGAACGCCTGAGCTCG
1 TTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCTGAGCTCG
* * * ** * *
28114913 TTGAGTTAAGTCTGAGTTC-GTGA--GATATAACTAGGCATCTGAACTCG
1 TTGAGTTAAGTCCGAGTTCACTTATGGATGCAA--ACGC--CTGAGCTCG
* * *
28114960 TTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAGCTCG
1 TTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCTGAGCTCG
*
28115006 TTGAGTTGAA-TCCAAGTTCACTTATGG
1 TTGAGTT-AAGTCCGAGTTCACTTATGG
28115033 GTGGGTTACA
Statistics
Matches: 91, Mismatches: 21, Indels: 16
0.71 0.16 0.12
Matches are distributed among these distances:
43 4 0.04
45 5 0.05
46 47 0.52
47 26 0.29
48 4 0.04
50 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (46 bp):
TTGAGTTAAGTCCGAGTTCACTTATGGATGCAAACGCCTGAGCTCG
Found at i:28114978 original size:93 final size:93
Alignment explanation
Indices: 28114816--28115012 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 93
28114806 GAGTTACGAA
* * * ** *
28114816 CTCGATGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCAAACTTTTTGAGTTGAGTCGG
1 CTCGTTGAGTTAAGTCCGAGTTCGTGAGATATAACTAGGCATCCAAACTCGTTGAGTTGAGTCCG
* * *
28114881 AGTTCACTTATGGATGCGAACGCCTGAG
66 AGTTCACTTATGGATGCAAACACCCGAG
* **
28114909 CTCGTTGAGTTAAGTCTGAGTTCGTGAGATATAACTAGGCATCTGAACTCGTTGAGTTGAGTCCG
1 CTCGTTGAGTTAAGTCCGAGTTCGTGAGATATAACTAGGCATCCAAACTCGTTGAGTTGAGTCCG
28114974 AGTTCACTTATGGATGCAAACACCCGAG
66 AGTTCACTTATGGATGCAAACACCCGAG
28115002 CTCGTTGAGTT
1 CTCGTTGAGTT
28115013 GAATCCAAGT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (93 bp):
CTCGTTGAGTTAAGTCCGAGTTCGTGAGATATAACTAGGCATCCAAACTCGTTGAGTTGAGTCCG
AGTTCACTTATGGATGCAAACACCCGAG
Found at i:28121048 original size:93 final size:93
Alignment explanation
Indices: 28120909--28121107 Score: 258
Period size: 93 Copynumber: 2.2 Consensus size: 93
28120899 TTCCGAACTC
* *
28120909 GTTGAGT-TGAGTTCGAGAGATGTAACTAGGCATCCAAACTCGTTGAGTTGAGTCCGAGTTTACT
1 GTTGAGTCTGAGTTAGAGAGATGTAACTAGGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACT
* *
28120973 TATAGATATGAACGCCTGAGCTCATTGA
66 TATAGATATGAACACCCGAGCTCATTGA
* * *
28121001 GTTGAGTCTGAGTTAGTGAGATGTAACTAGGCA-GCAGAACTCGTTGAGTTGAGTTCGAGTTCAC
1 GTTGAGTCTGAGTTAGAGAGATGTAACTAGGCATCCA-AACTCGTTGAGTTGAGTCCGAGTTCAC
* * *
28121065 TTATGGATGTGAACACCCGAGCTCGTTGA
65 TTATAGATATGAACACCCGAGCTCATTGA
* * *
28121094 CTTAAGTCCGAGTT
1 GTTGAGTCTGAGTT
28121108 CACTTATGGG
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
92 9 0.10
93 83 0.90
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (93 bp):
GTTGAGTCTGAGTTAGAGAGATGTAACTAGGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACT
TATAGATATGAACACCCGAGCTCATTGA
Found at i:28123139 original size:50 final size:50
Alignment explanation
Indices: 28123037--28123321 Score: 457
Period size: 50 Copynumber: 5.7 Consensus size: 50
28123027 TCTCATATTG
* **
28123037 ATGCCATGTCCCAGACATGGTCTTAAATGAAAT-A-ATATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
* * * *
28123085 ATGCCATATCCCAGATATGGTCTTACATGGAATCACATATATCAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
*
28123135 ATGCCATGTCCCAGACATGGTGTTACATGGGATCACATATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
28123185 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
* *
28123235 ATGCCATGTCCCAGACATGGTCTTACATGGGATTACATATATTGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
*
28123285 ATTCCATGTCCCAGACATGGTCTTACATGGGATCACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
28123322 CATAACCCTA
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
48 29 0.13
49 1 0.00
50 190 0.86
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATATCGATGCCA
Found at i:28131298 original size:6 final size:6
Alignment explanation
Indices: 28131287--28131417 Score: 128
Period size: 6 Copynumber: 21.7 Consensus size: 6
28131277 AACCAAAATG
*
28131287 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * *
28131335 AGTAA-C AAAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
*
28131384 AGAATC AGTAA-C TGAATC AGAATC AGAATC AGAA
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAA
28131418 CTACGTGACA
Statistics
Matches: 104, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
5 8 0.08
6 87 0.84
7 7 0.07
8 2 0.02
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:28131302 original size:30 final size:29
Alignment explanation
Indices: 28131266--28131417 Score: 146
Period size: 30 Copynumber: 5.0 Consensus size: 29
28131256 AAGAAACATT
* *
28131266 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGGAA-CAGAATCAGAATCAGA
* *
28131296 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAAT-TGGAACAGAATCAGAATCAGA
* *
28131326 ATCA-ATATTAGTAACAAAATCAGAATCAGA
1 ATCAGA-ATT-GGAACAGAATCAGAATCAGA
*
28131356 ATCAGAATTAGGTGACAGAATCAGAATCAGA
1 ATCAGAATT-GG-AACAGAATCAGAATCAGA
*
28131387 ATCAGTAACT-GAATCAGAATCAGAATCAGA
1 ATCAG-AATTGGAA-CAGAATCAGAATCAGA
28131417 A
1 A
28131418 CTACGTGACA
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
29 2 0.02
30 74 0.71
31 25 0.24
32 3 0.03
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (29 bp):
ATCAGAATTGGAACAGAATCAGAATCAGA
Found at i:28131380 original size:25 final size:25
Alignment explanation
Indices: 28131346--28131443 Score: 106
Period size: 25 Copynumber: 3.7 Consensus size: 25
28131336 GTAACAAAAT
*
28131346 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATTAAGTGA
*
28131371 CAGAATCAGAATCAGAATCAGTAACTGAA
1 CAGAATCAGAATCAGAAT---TAAGTG-A
* *
28131400 TCAGAATCAGAATCAGAACTACGTGA
1 -CAGAATCAGAATCAGAATTAAGTGA
*
28131426 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
28131444 GTGAATGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
25 34 0.56
26 1 0.02
27 4 0.07
28 4 0.07
29 1 0.02
30 17 0.28
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATTAAGTGA
Found at i:28131402 original size:55 final size:55
Alignment explanation
Indices: 28131280--28131443 Score: 195
Period size: 55 Copynumber: 2.9 Consensus size: 55
28131270 GAATTGGAAC
* * *
28131280 CAAAATGAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAA
1 CAAAATCAGAATCAGAATCAGAATTAGTGACAGAATCAGAATCAGAATC---A--AGTAA
28131340 CAAAATCAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATC-AGTAA
1 CAAAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGAATCAAGTAA
** * *
28131395 CTGAATCAGAATCAGAATCAGAACTACGTGACAGAATCAAAATCAGAAT
1 CAAAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGAAT
28131444 GTGAATGCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
55 49 0.52
60 24 0.25
61 22 0.23
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (55 bp):
CAAAATCAGAATCAGAATCAGAATTAGTGACAGAATCAGAATCAGAATCAAGTAA
Found at i:28132024 original size:27 final size:26
Alignment explanation
Indices: 28131945--28132027 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
28131935 TTGATCGGTC
* * *
28131945 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
28131971 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
28131998 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
28132025 AAC
1 AAC
28132028 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:28132256 original size:27 final size:27
Alignment explanation
Indices: 28132226--28132413 Score: 234
Period size: 27 Copynumber: 7.0 Consensus size: 27
28132216 GGGGCAAAAT
* * *
28132226 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28132253 GGTAATTCTACCCTAC-AGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28132279 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
28132306 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28132333 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28132360 AGTAATTCTACCCTATAAGGGGTATTTC
1 GGTAATTCTACCCTACAA-GGGTATTTC
* *
28132388 GGAAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
28132414 TAGTAATTTC
Statistics
Matches: 138, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.17
27 92 0.67
28 23 0.17
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28132409 original size:82 final size:80
Alignment explanation
Indices: 28132228--28132421 Score: 264
Period size: 82 Copynumber: 2.4 Consensus size: 80
28132218 GGCAAAATGG
* * * * * * *
28132228 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGTATTTCAGTATTTCTACCCT
1 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTAAAGGGTATTTCAGTAATTCTACCCT
28132293 ACAAGGGTATTTCGA
66 ACAAGGGTATTTCGA
*
28132308 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTA-AAGGGTATTTCAGTAATTCTACCC
*
28132373 TATAAGGGGTATTTCGGA
65 TACAA-GGGTATTTC-GA
*
28132391 -AATTCTACCCTACAGGGGTATTTTAGTAATT
1 TAATTCTACCCTACAGGGGTATTTTGGTAATT
28132422 TCACAATCAA
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 34 0.34
81 26 0.26
82 39 0.39
83 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (80 bp):
TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTAAAGGGTATTTCAGTAATTCTACCCT
ACAAGGGTATTTCGA
Found at i:28132456 original size:27 final size:27
Alignment explanation
Indices: 28132426--28132780 Score: 412
Period size: 27 Copynumber: 13.2 Consensus size: 27
28132416 GTAATTTCAC
*
28132426 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28132453 AATCGAGGGCAAAACGATAATT-TGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28132479 AA-CTGAGGGT-AAACTAGTAATTCTATA
1 AATC-GAGGGTAAAAC-GGTAATTCTGTA
* * * **
28132506 AATCAAGGGTAAAATGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
28132533 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** *
28132560 AATCGAGGGTAAAATAGTGATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28132587 AATTGAGGGTAAAACTGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
***
28132614 AATCGAGGGTAAAATATTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
28132641 AATTGAGGGTAAAACGGTAATTCAATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28132668 AATAGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28132695 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* *
28132722 AATCGAAGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28132749 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
28132776 AATCG
1 AATCG
28132781 GGAGTACTTT
Statistics
Matches: 278, Mismatches: 43, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
25 5 0.02
26 16 0.06
27 252 0.91
28 5 0.02
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:28132555 original size:54 final size:54
Alignment explanation
Indices: 28132416--28132811 Score: 315
Period size: 54 Copynumber: 7.4 Consensus size: 54
28132406 GGGTATTTTA
* * * * *
28132416 GTAATTTCAC-AATCAAGGGTAAAACGGTAATTCTGTAAATCGAGGGCAAAACG
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
* * * *
28132469 ATAATTTGTA-AACT-GAGGGT-AAACTAGTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTT-TACAAATCGAGGGTAAAAC-GGTAATTCTGTAAATCAAGGGTAAAATG
* *
28132522 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
* * ** * * * *
28132576 GTGATTCTGTAAATTGAGGGTAAAACTGTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
* * ** * ** **
28132630 TTAATTCTGTAAATTGAGGGTAAAACGGTAATTCAATAAAT-AGAGGGTAAAACA
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCA-AGGGTAAAATG
* *
28132684 GTAATTCTGTA-AACT-GAGGGTAAAATGGTAATTCTGTAAATCGAA-GGTAAAATG
1 GTAATT-T-TACAAATCGAGGGTAAAACGGTAATTCTGTAAATC-AAGGGTAAAATG
* ** * * ***
28132738 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATC-GGGAGTACTTTG
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGG-GTAAAATG
*
28132792 GTAATTTTACAAGTCGAGGG
1 GTAATTTTACAAATCGAGGG
28132812 CATTTCAGTA
Statistics
Matches: 280, Mismatches: 48, Indels: 29
0.78 0.13 0.08
Matches are distributed among these distances:
52 7 0.03
53 47 0.17
54 216 0.77
55 8 0.03
56 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (54 bp):
GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
Found at i:28134812 original size:30 final size:30
Alignment explanation
Indices: 28134776--28134901 Score: 139
Period size: 30 Copynumber: 4.2 Consensus size: 30
28134766 AAGAAACATT
*
28134776 ATCAGAATT-GGAACCAAAATGAGAATCAGA
1 ATCAGAATTAGGAA-CAAAATCAGAATCAGA
* * *
28134806 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGGAACAAAATCAGAATCAGA
*
28134836 ATCA-ATATTAGTAACAAAATCAGAATCAGA
1 ATCAGA-ATTAGGAACAAAATCAGAATCAGA
* * *
28134866 ATCAGAATTAGGTGACAGAATTAGAATCAGA
1 ATCAGAATTAGG-AACAAAATCAGAATCAGA
28134897 ATCAG
1 ATCAG
28134902 TAACTGAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.01
30 57 0.70
31 24 0.29
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.20
Consensus pattern (30 bp):
ATCAGAATTAGGAACAAAATCAGAATCAGA
Found at i:28134912 original size:55 final size:55
Alignment explanation
Indices: 28134790--28134953 Score: 186
Period size: 55 Copynumber: 2.9 Consensus size: 55
28134780 GAATTGGAAC
* * *
28134790 CAAAATGAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAA
1 CAAAATCAGAATCAGAATCAGAATTAGTGACAGAATCAGAATCAGAATC---A--AGTAA
*
28134850 CAAAATCAGAATCAGAATCAGAATTAGGTGACAGAATTAGAATCAGAATC-AGTAA
1 CAAAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGAATCAAGTAA
** * *
28134905 CTGAATCAGAATCAGAATTAGAATTACGTGACAGAATCAAAATCAGAAT
1 CAAAATCAGAATCAGAATCAGAATTA-GTGACAGAATCAGAATCAGAAT
28134954 GTGAATGCAA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
55 48 0.52
60 24 0.26
61 21 0.23
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21
Consensus pattern (55 bp):
CAAAATCAGAATCAGAATCAGAATTAGTGACAGAATCAGAATCAGAATCAAGTAA
Found at i:28134930 original size:6 final size:6
Alignment explanation
Indices: 28134797--28134928 Score: 112
Period size: 6 Copynumber: 21.8 Consensus size: 6
28134787 AACCAAAATG
*
28134797 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * * *
28134845 AGTAA-C AAAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATT AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* *
28134894 AGAATC AGTAA-C TGAATC AGAATC AGAATT AGAAT
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT
28134929 TACGTGACAG
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
5 8 0.08
6 85 0.83
7 7 0.07
8 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:28135108 original size:27 final size:26
Alignment explanation
Indices: 28135071--28135136 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
28135061 AGCATGGCTG
*
28135071 CCAGAACAGATATCGTGACAAAGTCA
1 CCAGAACAGATATCGTGACAAAGCCA
* *
28135097 CCAGATACAGATATTGTGGCAAAGCCA
1 CCAGA-ACAGATATCGTGACAAAGCCA
28135124 CCAGAATCAGATA
1 CCAGAA-CAGATA
28135137 ATGTGGGAAA
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:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAAAGCCA
Found at i:28135141 original size:27 final size:27
Alignment explanation
Indices: 28135071--28135152 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
28135061 AGCATGGCTG
* *
28135071 CCAGAA-CAGAT-ATCGTGACAAAGTCA
1 CCAGAATCAGATAAT-GTGGCAAAGCCA
*
28135097 CCAG-ATACAGATATTGTGGCAAAGCCA
1 CCAGAAT-CAGATAATGTGGCAAAGCCA
* *
28135124 CCAGAATCAGATAATGTGGGAAACCCA
1 CCAGAATCAGATAATGTGGCAAAGCCA
28135151 CC
1 CC
28135153 TAACAGAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 38 0.83
28 3 0.07
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAAAGCCA
Found at i:28135534 original size:27 final size:26
Alignment explanation
Indices: 28135455--28135537 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
28135445 TTGATCGGTC
* * * *
28135455 AACAAATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
*
28135481 ATAAAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
28135508 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
28135535 AAC
1 AAC
28135538 GCTTCCTCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.15
27 41 0.85
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:28135873 original size:81 final size:82
Alignment explanation
Indices: 28135738--28135931 Score: 257
Period size: 81 Copynumber: 2.4 Consensus size: 82
28135728 GGAAAAATGG
* * * * * * *
28135738 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
*
28135803 TACAAGGGTA-TTTCGA
66 TACAAGGGTATTTTAGA
* *
28135819 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
* *
28135884 TATAGGGGTATTTTAGA
66 TACAAGGGTATTTTAGA
*
28135901 -AATTCTACCCTACAGGGGTATTTTAGTAATT
1 TAATTCTACCCTACAGGGGTATTTTGGTAATT
28135932 TCACAATCAA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 94 0.95
82 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (82 bp):
TAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
TACAAGGGTATTTTAGA
Found at i:28135924 original size:27 final size:27
Alignment explanation
Indices: 28135737--28135931 Score: 221
Period size: 27 Copynumber: 7.2 Consensus size: 27
28135727 GGGAAAAATG
* * * * **
28135737 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTTA
*
28135764 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTTA
* * *
28135791 GTATTTCTACCCTACAAGGGTA-TTTC
1 GTAATTCTACCCTACAGGGGTATTTTA
*
28135817 GATAATTCTACCCTACAGGGGTATTTTG
1 G-TAATTCTACCCTACAGGGGTATTTTA
* * * *
28135845 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTTA
*
28135872 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTA
*
28135899 GAAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTA
28135926 GTAATT
1 GTAATT
28135932 TCACAATCAA
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 3 0.02
27 136 0.95
28 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTTA
Found at i:28135966 original size:27 final size:27
Alignment explanation
Indices: 28135936--28136316 Score: 452
Period size: 27 Copynumber: 14.2 Consensus size: 27
28135926 GTAATTTCAC
* *
28135936 AATCAAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28135963 AATCGAGGGTAAAACGATAATT-TGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * **
28135989 AA-CTGAGGGTAAACCAGTAATTCTACA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
28136016 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
28136043 AATCGAGGGTAAAATGGTGATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28136070 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28136097 AA-CTGAGGGTAAAACTGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** *
28136124 AATCGAGGGTAAAATAGTACTTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28136151 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
28136178 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
28136205 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
28136232 AATCGAGGGTAAAACGGTAATT-TTTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
28136258 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* *
28136285 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
28136312 AATCG
1 AATCG
28136317 GGAGTACTTT
Statistics
Matches: 305, Mismatches: 37, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.01
26 47 0.15
27 251 0.82
28 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:28136073 original size:54 final size:53
Alignment explanation
Indices: 28135941--28136313 Score: 505
Period size: 54 Copynumber: 6.9 Consensus size: 53
28135931 TTCACAATCA
* *
28135941 AGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGATAATTTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTGTAAACTG
* * ** * *
28135994 AGGGTAAACCAGTAATTCTACAAATCAAGGGTAAAACGGTAATTT-TACAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTGTA-AACT-G
* * *
28136048 AGGGTAAAATGGTGATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-TGTAAACTG
* ** *
28136102 AGGGTAAAACTGTAATTCTGTAAATCGAGGGTAAAATAGTACTTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-TGTAAACTG
* *
28136156 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-TGTAAACTG
* *
28136210 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTGTAAACTG
*
28136263 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTGTAAA
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAA-TTTGTAAA
28136314 TCGGGAGTAC
Statistics
Matches: 284, Mismatches: 31, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
52 2 0.01
53 89 0.31
54 187 0.66
55 4 0.01
56 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (53 bp):
AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTGTAAACTG
Found at i:28138749 original size:27 final size:27
Alignment explanation
Indices: 28138708--28138890 Score: 204
Period size: 27 Copynumber: 6.8 Consensus size: 27
28138698 CCTTTATCGA
* * *
28138708 TAAAATAATTATTTTGCCTTTATGGGG
1 TAAAATGACTATTTTGCCCTTATGGGG
* * *
28138735 TAAAATGACTGTTTTACCCTTGTGGGG
1 TAAAATGACTATTTTGCCCTTATGGGG
* *
28138762 TAAAATGACTATTTTGCCTTTATGGTG
1 TAAAATGACTATTTTGCCCTTATGGGG
* * *
28138789 TAAAATAATTATTTTGCCCTTATAGGG
1 TAAAATGACTATTTTGCCCTTATGGGG
*
28138816 TAAAATGACTATTTTGCCCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGGGG
** * *
28138843 TAAAATGGTTGTTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGGGG
* *
28138870 TAAAATGATTGTTTTGCCCTT
1 TAAAATGACTATTTTGCCCTT
28138891 TTATTGTAAG
Statistics
Matches: 131, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 131 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGGGG
Found at i:28138792 original size:54 final size:54
Alignment explanation
Indices: 28138708--28138920 Score: 216
Period size: 54 Copynumber: 3.9 Consensus size: 54
28138698 CCTTTATCGA
* * * *
28138708 TAAAATAATTATTTTGCCTTTATGGGGTAAAATGACTGTTTTACCCTTGTGGGG
1 TAAAATGACTATTTTGCCTTTATGGTGTAAAATGACTGTTTTACCCTTATGGGG
* * * * *
28138762 TAAAATGACTATTTTGCCTTTATGGTGTAAAATAATTATTTTGCCCTTATAGGG
1 TAAAATGACTATTTTGCCTTTATGGTGTAAAATGACTGTTTTACCCTTATGGGG
* ** * *
28138816 TAAAATGACTATTTTGCCCTTATGAG-GTAAAATGGTTGTTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCTTTATG-GTGTAAAATGACTGTTTTACCCTTATGGGG
* * * *
28138870 TAAAATGATTGTTTTGCCCTTTTAT--TGTAAGATGACTGTTTTACCCCTATG
1 TAAAATGACTATTTTG-CC-TTTATGGTGTAAAATGACTGTTTTACCCTTATG
28138921 TGATGTATGT
Statistics
Matches: 132, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
54 125 0.95
55 3 0.02
56 4 0.03
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (54 bp):
TAAAATGACTATTTTGCCTTTATGGTGTAAAATGACTGTTTTACCCTTATGGGG
Found at i:28138802 original size:81 final size:80
Alignment explanation
Indices: 28138708--28138920 Score: 241
Period size: 81 Copynumber: 2.6 Consensus size: 80
28138698 CCTTTATCGA
* *
28138708 TAAAATAATTATTTTGCCTTTATGGGGTAAAATGACTGTTTTACCCTTGTGGGGTAAAATGACTA
1 TAAAATAATTATTTTGCCTTTAT-GGGTAAAATGACTGTTTTACCCTTATGAGGTAAAATGACTA
*
28138773 TTTTGCCTTTATG-GTG
65 TTTTGCCCTTATGTG-G
* * * ** *
28138789 TAAAATAATTATTTTGCCCTTATAGGGTAAAATGACTATTTTGCCCTTATGAGGTAAAATGGTTG
1 TAAAATAATTATTTTGCCTTTAT-GGGTAAAATGACTGTTTTACCCTTATGAGGTAAAATGACTA
28138854 TTTTGCCCTTATGTGG
65 TTTTGCCCTTATGTGG
* * * * *
28138870 TAAAATGATTGTTTTGCCCTTTTAT-TGTAAGATGACTGTTTTACCCCTATG
1 TAAAATAATTATTTTG-CC-TTTATGGGTAAAATGACTGTTTTACCCTTATG
28138921 TGATGTATGT
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
81 104 0.94
82 3 0.03
83 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (80 bp):
TAAAATAATTATTTTGCCTTTATGGGTAAAATGACTGTTTTACCCTTATGAGGTAAAATGACTAT
TTTGCCCTTATGTGG
Found at i:28138899 original size:27 final size:27
Alignment explanation
Indices: 28138733--28138911 Score: 139
Period size: 27 Copynumber: 6.6 Consensus size: 27
28138723 GCCTTTATGG
* * **
28138733 GGTAAAATGACTGTTTTACCCTTGTGG
1 GGTAAAATGACTGTTTTGCCCTTTTAT
*
28138760 GGTAAAATGACTATTTTG-CC-TTTAT
1 GGTAAAATGACTGTTTTGCCCTTTTAT
* * * * *
28138785 GGTGTAAAATAATTATTTTGCCCTTATAG
1 -G-GTAAAATGACTGTTTTGCCCTTTTAT
* *
28138814 GGTAAAATGACTATTTTGCCCTTATGA-
1 GGTAAAATGACTGTTTTGCCCTT-TTAT
** * *
28138841 GGTAAAATGGTTGTTTTGCCCTTATGT
1 GGTAAAATGACTGTTTTGCCCTTTTAT
*
28138868 GGTAAAATGATTGTTTTGCCCTTTTAT
1 GGTAAAATGACTGTTTTGCCCTTTTAT
* *
28138895 TGTAAGATGACTGTTTT
1 GGTAAAATGACTGTTTT
28138912 ACCCCTATGT
Statistics
Matches: 121, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
25 2 0.02
26 3 0.02
27 109 0.90
28 4 0.03
29 3 0.02
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (27 bp):
GGTAAAATGACTGTTTTGCCCTTTTAT
Found at i:28141312 original size:47 final size:47
Alignment explanation
Indices: 28141253--28141381 Score: 206
Period size: 47 Copynumber: 2.8 Consensus size: 47
28141243 GTGTGAATAA
* *
28141253 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTCAGAGATGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGATAAGT
* * *
28141300 TACCTTGATTTGGCTACGGGACATGGTATAGGTACTCTGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGATAAGT
28141347 TACCTTGATTTGGCTAC-GGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
28141382 TATCAATTGA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 17 0.22
47 59 0.78
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGATAAGT
Found at i:28141399 original size:46 final size:47
Alignment explanation
Indices: 28141255--28141400 Score: 130
Period size: 47 Copynumber: 3.1 Consensus size: 47
28141245 GTGAATAATA
* *
28141255 CCTTGATTTGGCTACGGGCCATGGTATAGGTA--T-TCAGAGATGAGTT
1 CCTTGATTTGGCTACGGGCCATGGTATAGGTACTTATCA-AGTTGA-AT
*
28141301 ACCTTGATTTGGCTACGGGACATGGTATAGGTACTCTGGGAT-AAGTT--A-
1 -CCTTGATTTGGCTACGGGCCATGGTATAGGTACT-T---ATCAAGTTGAAT
28141349 CCTTGATTTGGCTAC-GGCCATGGTATAGGTACTTATCAA-TTGAAAT
1 CCTTGATTTGGCTACGGGCCATGGTATAGGTACTTATCAAGTTG-AAT
28141395 CCTTGA
1 CCTTGA
28141401 GTATTTGATT
Statistics
Matches: 83, Mismatches: 4, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
42 4 0.05
43 2 0.02
45 2 0.02
46 23 0.28
47 46 0.55
50 1 0.01
52 3 0.04
53 1 0.01
54 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (47 bp):
CCTTGATTTGGCTACGGGCCATGGTATAGGTACTTATCAAGTTGAAT
Found at i:28141431 original size:23 final size:23
Alignment explanation
Indices: 28141401--28141448 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
28141391 AAATCCTTGA
*
28141401 GTATTTGATTTTTATTCTGAATG
1 GTATTTGATTTTTATTCCGAATG
28141424 GTATTTGATTTTTATTCCGAATG
1 GTATTTGATTTTTATTCCGAATG
28141447 GT
1 GT
28141449 TCAATGGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.54
Consensus pattern (23 bp):
GTATTTGATTTTTATTCCGAATG
Found at i:28143643 original size:45 final size:44
Alignment explanation
Indices: 28143577--28143661 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
28143567 ATGCGACCTA
* *
28143577 AACTCATGAGTTATGGAATGAGTTTATGATATATGCGACATCTG
1 AACTCATGAGTTATGGAATGAGTTCATGATACATGCGACATCTG
* * *
28143621 AACTCATTGAGTTGTGGTATGAGTTCATGATACATGTGACA
1 AACTCA-TGAGTTATGGAATGAGTTCATGATACATGCGACA
28143662 CATGTTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 6 0.17
45 29 0.83
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (44 bp):
AACTCATGAGTTATGGAATGAGTTCATGATACATGCGACATCTG
Found at i:28147750 original size:96 final size:96
Alignment explanation
Indices: 28147584--28147804 Score: 252
Period size: 96 Copynumber: 2.3 Consensus size: 96
28147574 ATGAGTTTTC
** * *
28147584 GTGTAAGACCATGTCTGGGACATGGCATTGGCATCCGAGATATGTGCTTGTGTAAGACCATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCAT-CGAGATATGTGCTAGTGTAAGACAATGTCT
*
28147649 GGGACATAGCATCAG-CGATAATATGT-ATGCCA
65 AGGACATAGCAT-AGACGATAATATGTGAT-CCA
* *
28147681 GTGTAAGACTATGTCTGGGACATGGCATCAGCGAT-GATATATGTGCTAGTGTAAGACAATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGC-ATCGAGATATGTGCTAGTGTAAGACAATGTCT
* * * *
28147745 AGGACATGGCATTGACGATGATATGTGGATTCA
65 AGGACATAGCATAGACGATAATATGT-GATCCA
* *
28147778 -TGTAAGACGATGTCGGGGACATGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCAT
28147805 TGGTACTTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 71 0.66
97 31 0.29
98 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (96 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAGCATCGAGATATGTGCTAGTGTAAGACAATGTCTA
GGACATAGCATAGACGATAATATGTGATCCA
Found at i:28147805 original size:48 final size:49
Alignment explanation
Indices: 28147584--28147806 Score: 208
Period size: 48 Copynumber: 4.6 Consensus size: 49
28147574 ATGAGTTTTC
* * *
28147584 GTGTAAGACCATGTCTGGGACATGGCATTG-GC-ATCCGAGATATGTGCTT
1 GTGTAAGACAATGTCTGGGACATGGCATTGAGCGAT--GATATATGTGCTA
* * * * * * *
28147633 GTGTAAGACCATGTCTGGGACATAGCA-TCAGCGATAATATGTATGCCA
1 GTGTAAGACAATGTCTGGGACATGGCATTGAGCGATGATATATGTGCTA
* *
28147681 GTGTAAGACTATGTCTGGGACATGGCA-TCAGCGATGATATATGTGCTA
1 GTGTAAGACAATGTCTGGGACATGGCATTGAGCGATGATATATGTGCTA
* * *
28147729 GTGTAAGACAATGTCTAGGACATGGCATTGA-CGATGATATGTG-GATTCA
1 GTGTAAGACAATGTCTGGGACATGGCATTGAGCGATGATATATGTG-CT-A
* *
28147778 -TGTAAGACGATGTCGGGGACATGGCATTG
1 GTGTAAGACAATGTCTGGGACATGGCATTG
28147807 GTACTTTATT
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.01
48 113 0.77
49 31 0.21
50 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (49 bp):
GTGTAAGACAATGTCTGGGACATGGCATTGAGCGATGATATATGTGCTA
Found at i:28154589 original size:49 final size:47
Alignment explanation
Indices: 28154527--28154641 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 47
28154517 GTGTCAAACA
* *
28154527 ATGTCTGGAACATGGCATCAGC-ATCCGAGATATG-TGCCTGTGTAAGACC
1 ATGTCTGGGACATGGCATCAGCGAT---A-ATATGATGCCAGTGTAAGACC
* *
28154576 ATGTCTGGGACATGGCATCGGCGATAATATGTATGCCAGTTTAAGACC
1 ATGTCTGGGACATGGCATCAGCGATAATATG-ATGCCAGTGTAAGACC
28154624 ATGTCTGGGACATGGCAT
1 ATGTCTGGGACATGGCAT
28154642 TGGCGATGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
46 5 0.08
47 1 0.02
48 31 0.53
49 20 0.34
50 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTCTGGGACATGGCATCAGCGATAATATGATGCCAGTGTAAGACC
Found at i:28156067 original size:54 final size:54
Alignment explanation
Indices: 28156002--28156135 Score: 214
Period size: 54 Copynumber: 2.5 Consensus size: 54
28155992 GTCACTATAA
*
28156002 GGGATTTAGCCTGGACTGGTAATCTCAACATTACCTTATGAGTTTACGATAAGG
1 GGGATTTAGCCTGGACTGGTAATCTCAACATTACCTTATGAGTTTAAGATAAGG
** * *
28156056 GGGATTTAGCCTGGACTACTAATCTCAGCATTACCTTATGAGTTTAAGATACGG
1 GGGATTTAGCCTGGACTGGTAATCTCAACATTACCTTATGAGTTTAAGATAAGG
*
28156110 GGGATTTAGCCTGGATTGGTAATCTC
1 GGGATTTAGCCTGGACTGGTAATCTC
28156136 GCCGTAGAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (54 bp):
GGGATTTAGCCTGGACTGGTAATCTCAACATTACCTTATGAGTTTAAGATAAGG
Found at i:28159961 original size:40 final size:37
Alignment explanation
Indices: 28159843--28159969 Score: 146
Period size: 38 Copynumber: 3.3 Consensus size: 37
28159833 GCAGGCTATA
* **
28159843 TGCTGGAATTATATCTGGTTAAATCTGGCAGGCTTCG
1 TGCTGGTATTATATCTGGTTAAATCCCGCAGGCTTCG
* * *
28159880 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTATTATAT-CTGGTTAAATCCCGCAGGCTTCG
*
28159918 TGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGCTTCG
1 TGCTGGTATTATATCTG-G-TTAAA-TCCCGCAGGCTTCG
*
28159958 TGCTGGTGTTAT
1 TGCTGGTATTAT
28159970 GTTCGGGTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
37 15 0.20
38 33 0.44
39 5 0.07
40 22 0.29
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (37 bp):
TGCTGGTATTATATCTGGTTAAATCCCGCAGGCTTCG
Found at i:28169446 original size:18 final size:18
Alignment explanation
Indices: 28169402--28169438 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28169392 AAGGAGATAG
28169402 AGTGAAAAAAGTAAACAA
1 AGTGAAAAAAGTAAACAA
28169420 AGTGAAAAAAGTAAACAA
1 AGTGAAAAAAGTAAACAA
28169438 A
1 A
28169439 CGTAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (18 bp):
AGTGAAAAAAGTAAACAA
Found at i:28169447 original size:17 final size:17
Alignment explanation
Indices: 28169406--28169446 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 17
28169396 AGATAGAGTG
28169406 AAAAAAGTAAACAAAGT
1 AAAAAAGTAAACAAAGT
28169423 GAAAAAAGTAAACAAACGT
1 -AAAAAAGTAAACAAA-GT
28169442 AAAAA
1 AAAAA
28169447 GAAGGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAAAAGTAAACAAAGT
Found at i:28178489 original size:54 final size:53
Alignment explanation
Indices: 28178425--28178621 Score: 202
Period size: 54 Copynumber: 3.7 Consensus size: 53
28178415 TTGGTAAGAT
* * *
28178425 AAGGATATCATGTAAGACCATGCCATGGCATGGCATTGATAAGTTCTATAAGG
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGG
* *
28178478 CAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGG
1 -AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGG
* * *
28178533 AA--AATGTCCCATGTAAGACCATGCCAAGGCATGGCTTTGGTGAGTTC-ATAAGG
1 AAGGAA-AT--CATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGG
* * * * *
28178586 AAAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 -AAGGAAATCATGTAAGACCATGCCAAGGCATGGCA
28178622 ATGGTAAATT
Statistics
Matches: 119, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
52 2 0.02
53 30 0.25
54 45 0.38
55 41 0.34
56 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGG
Found at i:28178554 original size:55 final size:52
Alignment explanation
Indices: 28178433--28178621 Score: 193
Period size: 55 Copynumber: 3.5 Consensus size: 52
28178423 ATAAGGATAT
* * * *
28178433 CATGTAAGACCATGCCATGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAAT-
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGG-AA--AAGTC
*
28178487 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGAAAATGTCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGAAAA-GT-C
* * * *
28178542 CATGTAAGACCATGCCAAGGCATGGCTTTGGTGAGTTC-ATAAGGAAAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGAAAAG-T-C
* *
28178595 CACGTAAGACCATGTCAAGACATGGCA
1 CATGTAAGACCATGCCAAGACATGGCA
28178622 ATGGTAAATT
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
52 3 0.03
53 35 0.30
54 36 0.31
55 41 0.36
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (52 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGAAAAGTC
Found at i:28185039 original size:54 final size:54
Alignment explanation
Indices: 28184975--28185169 Score: 205
Period size: 54 Copynumber: 3.6 Consensus size: 54
28184965 TGGCATTTGG
* * *
28184975 TAAGATAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
1 TAAGGTAAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTA
* * ** * *
28185029 TAAGGTAAGGAAATCATGTAAGACCATGTTAAGACATGGCGTTGATGAGTTACTA
1 TAAGGTAAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTA
* * * * *
28185084 TAAGGAAAAGG-TCCCATATAAGACCATGCCAAGGCATGGCATTGGTGATTTC-A
1 TAAGG-TAAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTA
* * *
28185137 TAAGGCAAGGATACCACGTAAGACCATGTCAAG
1 TAAGGTAAGGATACCATGTAAGACCATGCCAAG
28185170 ATATGGCAAT
Statistics
Matches: 115, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
52 4 0.03
53 24 0.21
54 45 0.39
55 38 0.33
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (54 bp):
TAAGGTAAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTA
Found at i:28185122 original size:55 final size:54
Alignment explanation
Indices: 28184993--28185169 Score: 160
Period size: 55 Copynumber: 3.3 Consensus size: 54
28184983 GGATATCATG
* * *
28184993 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAAGGAAATCATG
1 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCATA
** * * * **
28185047 TAAGACCATGTTAAGACATGGCGTTGATGAGTTACTATAAGGAAAAGG-TCCCATA
1 TAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGG-AAAGGAAACCATA
* * * * * **
28185102 TAAGACCATGCCAAGGCATGGCATTGGTGATTTC-ATAAGGCAAGGATACCACG
1 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCATA
*
28185155 TAAGACCATGTCAAG
1 TAAGACCATGCCAAG
28185170 ATATGGCAAT
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
52 4 0.04
53 24 0.24
54 29 0.29
55 38 0.38
56 4 0.04
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (54 bp):
TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCATA
Found at i:28187151 original size:24 final size:24
Alignment explanation
Indices: 28187124--28187173 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28187114 AGGACTAGAG
28187124 TATGTCAATTAGAAATCATTATCC
1 TATGTCAATTAGAAATCATTATCC
*
28187148 TATGTCACTTAGAAATCATTATCC
1 TATGTCAATTAGAAATCATTATCC
28187172 TA
1 TA
28187174 ACTGTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (24 bp):
TATGTCAATTAGAAATCATTATCC
Found at i:28191323 original size:40 final size:40
Alignment explanation
Indices: 28191268--28191534 Score: 376
Period size: 40 Copynumber: 6.6 Consensus size: 40
28191258 TATTCGAATG
* * * *
28191268 ATATCCGGGTTAAGTCCCGAGGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
28191308 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
28191348 ATATCCGGGCTAAGTCGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAA---GTCCCGAAGGCATTTGTGCTATTGATT
*
28191391 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
* *
28191431 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
* * * *
28191471 ATATCCGGGCTAAGACCCGAAGGCATCTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGATT
*
28191511 ATATCC-GGCTAAATCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCA
28191535 CTTGAGTTTG
Statistics
Matches: 209, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
39 16 0.08
40 150 0.72
41 3 0.01
43 40 0.19
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
Found at i:28191551 original size:123 final size:121
Alignment explanation
Indices: 28191268--28191534 Score: 369
Period size: 123 Copynumber: 2.2 Consensus size: 121
28191258 TATTCGAATG
* * * * *
28191268 ATATCCGGGTTAAGTCCCGAGGGCATTTATGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCAAGTGATTATATCCGGGCTAAGTCCCGAAGGCA
* * * * *
28191333 TTTGTGCTATTGATTATATCCGGGCTAAGTCGTCCCGAAGGCATTTGTGCTATTGATT
66 TTTGTGCTATTGACTATATCCGGGCTAA--CGACCCGAAGGCATCTGTGCGATTGACT
* * *
28191391 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCT
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCAAGTGATTATATCCGGGCTAAGTCCCGAAGGCA
28191456 TTTGTGCTATTGACTATATCCGGGCTAA-GACCCGAAGGCATCTGTGCGAGTTG-CT
66 TTTGTGCTATTGACTATATCCGGGCTAACGACCCGAAGGCATCTGTGCGA-TTGACT
28191511 ATATCC-GGCTAAATCCCGAAGGCA
1 ATATCCGGGCTAAATCCCGAAGGCA
28191535 CTTGAGTTTG
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
119 17 0.13
120 25 0.19
121 3 0.02
123 88 0.66
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (121 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCAAGTGATTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCTATTGACTATATCCGGGCTAACGACCCGAAGGCATCTGTGCGATTGACT
Found at i:28205498 original size:60 final size:59
Alignment explanation
Indices: 28205371--28205509 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
28205361 ATTAGAGTTA
* * *
28205371 ACTGGGCCTTAGCCCATATCAATATTAATTTGGGCCATAGCCCCTTACAGTATCAGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTAT
* * *
28205432 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACA-AGTC-GAGATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TAT
* *
28205492 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
28205510 TAACACAGCT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 50 0.75
61 13 0.19
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTAT
Found at i:28212025 original size:90 final size:90
Alignment explanation
Indices: 28211837--28212047 Score: 217
Period size: 90 Copynumber: 2.3 Consensus size: 90
28211827 AATAGGGTGA
* *
28211837 CAAAGCCATGTCCCAAACATGGTCTTACATGGGACCACACATCGATGCCATATTCCAAATATGGT
1 CAAAGCCATGTCCCAAACATGGTCTTACACGAGACCACACATCGATGCCATATTCCAAATATGGT
** * * * * **
28211902 CTTATATGAAGTCCCTAATTAGTGT
66 CTTATACAAAATCACTAATCAATAC
* * * * * *
28211927 CGACGCCATGTCCCAGACATGGTCTT-CTACGAGACCTCATATCGATGCCATCTTCCAAATATGG
1 CAAAGCCATGTCCCAAACATGGTCTTAC-ACGAGACCACACATCGATGCCATATTCCAAATATGG
* *
28211991 TGTTATACAAAATCACTTATCAATAC
65 TCTTATACAAAATCACTAATCAATAC
* * *
28212017 CAAAGCCATATCCCTAATATGGTCTTACACG
1 CAAAGCCATGTCCCAAACATGGTCTTACACG
28212048 GGATCGCGTA
Statistics
Matches: 95, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
89 1 0.01
90 93 0.98
91 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (90 bp):
CAAAGCCATGTCCCAAACATGGTCTTACACGAGACCACACATCGATGCCATATTCCAAATATGGT
CTTATACAAAATCACTAATCAATAC
Found at i:28216744 original size:27 final size:27
Alignment explanation
Indices: 28216714--28216792 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
28216704 ATAAATCACA
*
28216714 TAGGGGCAAAATAATTATTTTATCATG
1 TAGGGGCAAAATAATCATTTTATCATG
* *
28216741 TAGGGGCAAAATAGTCATATTATCATG
1 TAGGGGCAAAATAATCATTTTATCATG
*
28216768 TAGGGGCAAAACAATCATTTTATCA
1 TAGGGGCAAAATAATCATTTTATCA
28216793 AATAGGGGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (27 bp):
TAGGGGCAAAATAATCATTTTATCATG
Found at i:28216798 original size:27 final size:27
Alignment explanation
Indices: 28216708--28216800 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
28216698 ACAGTCATAA
* *
28216708 ATCACATAGGGGCAAAATAATTATTTT
1 ATCATATAGGGGCAAAATAATCATTTT
* * *
28216735 ATCATGTAGGGGCAAAATAGTCATATT
1 ATCATATAGGGGCAAAATAATCATTTT
* *
28216762 ATCATGTAGGGGCAAAACAATCATTTT
1 ATCATATAGGGGCAAAATAATCATTTT
*
28216789 ATCAAATAGGGG
1 ATCATATAGGGG
28216801 TCTAGGTACA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (27 bp):
ATCATATAGGGGCAAAATAATCATTTT
Found at i:28218329 original size:13 final size:13
Alignment explanation
Indices: 28218313--28218337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28218303 TTAAATCTGT
28218313 TAATTAGTTTAAA
1 TAATTAGTTTAAA
28218326 TAATTAGTTTAA
1 TAATTAGTTTAA
28218338 TAAACAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:28223681 original size:7 final size:6
Alignment explanation
Indices: 28223640--28223711 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
28223630 TGAATCCTCC
* * * *
28223640 TATTTT T-TATT TAGTTT TATTTT TATTTT TCTTTT GATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
* *
28223687 CA-TTT TAATTT TATTATTT TATTTT
1 TATTTT TATTTT TA-T-TTT TATTTT
28223712 GAAATACATA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
5 8 0.16
6 37 0.73
7 1 0.02
8 5 0.10
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:28226636 original size:13 final size:13
Alignment explanation
Indices: 28226620--28226644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28226610 TTAAATCCGT
28226620 TAATTAGTTTAAA
1 TAATTAGTTTAAA
28226633 TAATTAGTTTAA
1 TAATTAGTTTAA
28226645 TAAACTAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:28234469 original size:53 final size:53
Alignment explanation
Indices: 28234398--28234518 Score: 215
Period size: 53 Copynumber: 2.3 Consensus size: 53
28234388 TGAAAGAAGG
28234398 AAAAGAAAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAGA
1 AAAAG-AAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAGA
28234452 AAAAGAAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAGA
1 AAAAGAAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAGA
* *
28234505 AAAGGAAGGAAAAA
1 AAAAGAAGAAAAAA
28234519 GAACTTTGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
53 60 0.92
54 5 0.08
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (53 bp):
AAAAGAAGAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAAAGA
Found at i:28235018 original size:40 final size:40
Alignment explanation
Indices: 28234954--28235171 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
28234944 TGGATGATAA
* * *
28234954 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
28234994 CCGGGCTAAGTCCCAAAGGAATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28235034 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28235074 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * * * *
28235114 CCGAGCTATGTCCTGAAGGTATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
28235154 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28235172 TACTTGGCTT
Statistics
Matches: 157, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 15 0.10
40 142 0.90
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28238869 original size:107 final size:107
Alignment explanation
Indices: 28238683--28238889 Score: 326
Period size: 107 Copynumber: 1.9 Consensus size: 107
28238673 GCATTCATTC
*
28238683 ATATCATAGACCTCATAAGAATCATAAAATAATTATTTCTATCTCAGATTTGTGGTCTCAAAACC
1 ATATCATAGACCTCATAAGAATCATAAAATAATTATTTCTATCTCAAATTTGTGGTCTCAAAACC
*
28238748 ACTGTTCCGACTAGGCCCT-AATTCAGGATGTTACATGCATAA
66 ACTGTTCCAACTAGGCCCTGAATT-AGGATGTTACATGCATAA
* * * *
28238790 ATATCCTAGACTTTATAATAATCATAAAATAATTATTTCTATCTCAAATTTGTGGTCTCAAAACC
1 ATATCATAGACCTCATAAGAATCATAAAATAATTATTTCTATCTCAAATTTGTGGTCTCAAAACC
* *
28238855 ACTGTTCCAACTAGGCCTTGAATTGGGATGTTACA
66 ACTGTTCCAACTAGGCCCTGAATTAGGATGTTACA
28238890 ATTCTCCCCC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 87 0.96
108 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (107 bp):
ATATCATAGACCTCATAAGAATCATAAAATAATTATTTCTATCTCAAATTTGTGGTCTCAAAACC
ACTGTTCCAACTAGGCCCTGAATTAGGATGTTACATGCATAA
Found at i:28244656 original size:93 final size:93
Alignment explanation
Indices: 28244500--28244703 Score: 259
Period size: 93 Copynumber: 2.2 Consensus size: 93
28244490 TTGAGTTCCG
* * * * ** * *
28244500 AACTCGTTGAGTTAAGTCCGAGTT-CGTGAGATGTAACTAGGCATCCGTGCTCGTTGAGTTGAGT
1 AACTCATTGAGTTGAGTCTGA-TTGCGCGAGATGTAACTAGGCATCCGAACTCGTTCACTTGAGT
*
28244564 CCGAGTTCACTTATGGATGCGAATG-CCC
65 CCGAGTTCACTTATGGATGCAAATGTCCC
* *
28244592 GAACTCATTTAGTTGAGTCTGATTGCGCGAGATGTAACTAGGCATCTGAACTCGTTCACTTGAGT
1 -AACTCATTGAGTTGAGTCTGATTGCGCGAGATGTAACTAGGCATCCGAACTCGTTCACTTGAGT
*
28244657 CTGAGTTCACTTATGGATGCAAATGTCCC
65 CCGAGTTCACTTATGGATGCAAATGTCCC
*
28244686 AACTCGTTGAGTTGAGTC
1 AACTCATTGAGTTGAGTC
28244704 CGAGTTCACT
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
92 2 0.02
93 90 0.95
94 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (93 bp):
AACTCATTGAGTTGAGTCTGATTGCGCGAGATGTAACTAGGCATCCGAACTCGTTCACTTGAGTC
CGAGTTCACTTATGGATGCAAATGTCCC
Found at i:28244701 original size:46 final size:46
Alignment explanation
Indices: 28244549--28244764 Score: 208
Period size: 46 Copynumber: 4.7 Consensus size: 46
28244539 GGCATCCGTG
*
28244549 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAA
* * * * * * * *
28244595 CTCATTTAGTTGAGTCTGA-TTGCGC-GA--GATGTAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCCGAGTT-CACTTATGGATGCAA--ATGC--CCGAA
* * *
28244642 CTCGTTCACTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCC-AA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG-CCCGAA
* *
28244688 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAA
*
28244734 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28244765 GCGGGTTACA
Statistics
Matches: 136, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
43 5 0.04
45 9 0.07
46 87 0.64
47 23 0.17
48 5 0.04
49 1 0.01
50 6 0.04
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAA
Found at i:28247764 original size:15 final size:15
Alignment explanation
Indices: 28247744--28247799 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
28247734 GTATCTTAGG
28247744 TTTCTTTATTCTAGA
1 TTTCTTTATTCTAGA
* *
28247759 TTTCTTTATTCTGGG
1 TTTCTTTATTCTAGA
*
28247774 TTTCTCTA-TCTTAGA
1 TTTCTTTATTC-TAGA
28247789 TTTCTTTATTC
1 TTTCTTTATTC
28247800 GGGTTTCTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 2 0.06
15 29 0.88
16 2 0.06
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTAGA
Found at i:28247778 original size:30 final size:29
Alignment explanation
Indices: 28247742--28247808 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
28247732 TCGTATCTTA
28247742 GGTTTCTTTAT-TCTAGATTTCTTTATTCTG
1 GGTTTCTTTATCT-TAGATTTCTTTATTC-G
*
28247772 GGTTTCTCTATCTTAGATTTCTTTATTCG
1 GGTTTCTTTATCTTAGATTTCTTTATTCG
28247801 GGTTTCTT
1 GGTTTCTT
28247809 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 8 0.24
30 25 0.74
31 1 0.03
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (29 bp):
GGTTTCTTTATCTTAGATTTCTTTATTCG
Found at i:28250320 original size:47 final size:47
Alignment explanation
Indices: 28250246--28250366 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
28250236 GGTTGACTTT
*
28250246 CGAAATCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
28250293 C-AAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
*
28250340 CGAACTCGTTGAGTTGAGTCTGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
28250367 ACTTATGGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
46 2 0.03
47 66 0.94
48 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
Found at i:28253888 original size:90 final size:90
Alignment explanation
Indices: 28253734--28253899 Score: 206
Period size: 90 Copynumber: 1.8 Consensus size: 90
28253724 ACATCGATGT
* * * * * ** *
28253734 CATATTCTAAATATGGTCTTATACGAAGTCTCGAATTAGTGCCGACGCCATGTCTCAAACATGGT
1 CATATTCCAAATATGGTCTTATACGAAATCACGAATTAATGCCGAAGCCAAATCCCAAACATGGT
*
28253799 CTTATACGGGACCTCATATCAATGC
66 CTTACACGGGACCTCATATCAATGC
** ** *
28253824 CATATTCCAAATATGGTCTTATACGAAATCACTTATTAATGCCGAAGCCAAATCCCTGATATGGT
1 CATATTCCAAATATGGTCTTATACGAAATCACGAATTAATGCCGAAGCCAAATCCCAAACATGGT
28253889 CTTACACGGGA
66 CTTACACGGGA
28253900 TCGTGTATCG
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 62 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (90 bp):
CATATTCCAAATATGGTCTTATACGAAATCACGAATTAATGCCGAAGCCAAATCCCAAACATGGT
CTTACACGGGACCTCATATCAATGC
Found at i:28257116 original size:16 final size:16
Alignment explanation
Indices: 28257082--28257118 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28257072 TTTTAATATG
*
28257082 ATATAAATTATATAAT
1 ATATAAATTATAAAAT
28257098 ATATAAATTA-AAAAT
1 ATATAAATTATAAAAT
28257113 -TATAAA
1 ATATAAA
28257119 AACCCAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 4 0.20
16 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATTATAAAAT
Found at i:28259467 original size:29 final size:29
Alignment explanation
Indices: 28259435--28259535 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 29
28259425 TACGCGTAGG
* *
28259435 GGTTCCTTGATTTTCTTTTCTATTAAAGT
1 GGTTCCTTGATTTTCTTTTCTGTTGAAGT
* *
28259464 GGTTCCTTGATTTACTTTTTTGTTGAAGT
1 GGTTCCTTGATTTTCTTTTCTGTTGAAGT
* *
28259493 GGTTCATTGATTTCCTTTTCTGTTGAAGT
1 GGTTCCTTGATTTTCTTTTCTGTTGAAGT
28259522 GGTTCCTTGATTTT
1 GGTTCCTTGATTTT
28259536 TGCTTATCGT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.13, G:0.19, T:0.54
Consensus pattern (29 bp):
GGTTCCTTGATTTTCTTTTCTGTTGAAGT
Found at i:28259861 original size:31 final size:31
Alignment explanation
Indices: 28259821--28259977 Score: 124
Period size: 31 Copynumber: 5.2 Consensus size: 31
28259811 TTCGAGCTCT
*
28259821 ATGTAGGTGAGCTGTTATAGCTGTGAGCTTC
1 ATGTAGGTGAGCTGTTATAGCTATGAGCTTC
* * * * * * *
28259852 ATGTTGGTGAGCTATGATAGTTGTAAGCTCC
1 ATGTAGGTGAGCTGTTATAGCTATGAGCTTC
* * *
28259883 ATGTAAGCGAG--G-AATA-CATATGAGCTTC
1 ATGTAGGTGAGCTGTTATAGC-TATGAGCTTC
* *
28259911 ATGGAGGTGAGCTGTTATAGCTACGAGCTTC
1 ATGTAGGTGAGCTGTTATAGCTATGAGCTTC
* * * *
28259942 ATGTTGGTGAACTGTTATAGCTACGAGCTCC
1 ATGTAGGTGAGCTGTTATAGCTATGAGCTTC
28259973 ATGTA
1 ATGTA
28259978 AGAGAGCAAT
Statistics
Matches: 96, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
28 18 0.19
30 1 0.01
31 76 0.79
32 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (31 bp):
ATGTAGGTGAGCTGTTATAGCTATGAGCTTC
Found at i:28259901 original size:90 final size:90
Alignment explanation
Indices: 28259787--28260012 Score: 258
Period size: 90 Copynumber: 2.5 Consensus size: 90
28259777 GTGAGGTATG
* * **
28259787 AGCTCCATGTAGGCAAGCAATACATTCGAGCTCTATGTAGGTGAGCTGTTATAGCTGTGAGCTTC
1 AGCTCCATGTAAGCGAGCAATACATTCGAGCTCTATGTAGGTGAGCTGTTATAGCTACGAGCTTC
* * **
28259852 ATGTTGGTGAGCTATGATAGTTGTA
66 ATGTTGGTGAACTATGATAGCTACA
* *
28259877 AGCTCCATGTAAGCGAGGAATACATAT-GAGCT-TCATGGAGGTGAGCTGTTATAGCTACGAGCT
1 AGCTCCATGTAAGCGAGCAATACAT-TCGAGCTCT-ATGTAGGTGAGCTGTTATAGCTACGAGCT
* * *
28259940 TCATGTTGGTGAACTGTTATAGCTACG
64 TCATGTTGGTGAACTATGATAGCTACA
* * * * *
28259967 AGCTCCATGTAAGAGAGCAATGCATGCGAGCTCCATGTAGGCGAGC
1 AGCTCCATGTAAGCGAGCAATACATTCGAGCTCTATGTAGGTGAGC
28260013 AATGCATGCG
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
89 1 0.01
90 110 0.98
91 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (90 bp):
AGCTCCATGTAAGCGAGCAATACATTCGAGCTCTATGTAGGTGAGCTGTTATAGCTACGAGCTTC
ATGTTGGTGAACTATGATAGCTACA
Found at i:28260012 original size:15 final size:15
Alignment explanation
Indices: 28259992--28260046 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
28259982 AGCAATGCAT
28259992 GCGAGCTCCATGTAG
1 GCGAGCTCCATGTAG
* * *
28260007 GCGAG--CAATGCAT
1 GCGAGCTCCATGTAG
* *
28260020 GCGAACTCTATGTAG
1 GCGAGCTCCATGTAG
28260035 GCGAGCTCCATG
1 GCGAGCTCCATG
28260047 CTTGCGAGCT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
13 9 0.31
15 20 0.69
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (15 bp):
GCGAGCTCCATGTAG
Found at i:28260034 original size:28 final size:28
Alignment explanation
Indices: 28259969--28260040 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
28259959 TAGCTACGAG
* * *
28259969 CTCCATGTAAGAGAGCAATGCATGCGAG
1 CTCCATGTAGGCGAGCAATGCATGCGAA
28259997 CTCCATGTAGGCGAGCAATGCATGCGAA
1 CTCCATGTAGGCGAGCAATGCATGCGAA
*
28260025 CTCTATGTAGGCGAGC
1 CTCCATGTAGGCGAGC
28260041 TCCATGCTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (28 bp):
CTCCATGTAGGCGAGCAATGCATGCGAA
Found at i:28266830 original size:14 final size:14
Alignment explanation
Indices: 28266813--28266840 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28266803 TTAGTACATA
28266813 ATAGAATAAAATTT
1 ATAGAATAAAATTT
28266827 ATAGAATAAAATTT
1 ATAGAATAAAATTT
28266841 GATTTAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
ATAGAATAAAATTT
Found at i:28269577 original size:21 final size:22
Alignment explanation
Indices: 28269551--28269592 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28269541 ATAACCATGG
28269551 ATTTAAT-GATTGAGTATTCAA
1 ATTTAATCGATTGAGTATTCAA
* *
28269572 ATTTAATCGATTTATTATTCA
1 ATTTAATCGATTGAGTATTCA
28269593 TCAATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTAATCGATTGAGTATTCAA
Found at i:28290427 original size:25 final size:25
Alignment explanation
Indices: 28290393--28290442 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28290383 GCCAGTGTAA
28290393 GACCATGTTTGGGACATGGCATCGG
1 GACCATGTTTGGGACATGGCATCGG
28290418 GACCATGTTTGGGACATGGCATCGG
1 GACCATGTTTGGGACATGGCATCGG
28290443 CCTCGACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (25 bp):
GACCATGTTTGGGACATGGCATCGG
Found at i:28290465 original size:73 final size:73
Alignment explanation
Indices: 28290345--28290488 Score: 191
Period size: 73 Copynumber: 2.0 Consensus size: 73
28290335 GCTAGTGTAA
* * * * *
28290345 GACCATGTCTAGGACATGTCATCGGCCAGAATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT
1 GACCATGTCTAGGACATGGCATCGGCCAGAACATGAGAGCCAATGTAAAACCATGTTTGGAACAT
28290410 GGCATCGG
66 GGCATCGG
* * * *
28290418 GACCATGTTTGGGACATGGCATCGGCCTCG-ACATGTGAGCCAATGTAAAACCATGTTTGGAACA
1 GACCATGTCTAGGACATGGCATCGGCC-AGAACATGAGAGCCAATGTAAAACCATGTTTGGAACA
28290482 TGGCATC
65 TGGCATC
28290489 AGCAATTCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 60 0.98
74 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (73 bp):
GACCATGTCTAGGACATGGCATCGGCCAGAACATGAGAGCCAATGTAAAACCATGTTTGGAACAT
GGCATCGG
Found at i:28291065 original size:13 final size:13
Alignment explanation
Indices: 28291047--28291071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28291037 GATAGATGTG
28291047 ATACTCATTTTGC
1 ATACTCATTTTGC
28291060 ATACTCATTTTG
1 ATACTCATTTTG
28291072 TATAGGCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (13 bp):
ATACTCATTTTGC
Found at i:28301495 original size:48 final size:48
Alignment explanation
Indices: 28301420--28301697 Score: 185
Period size: 48 Copynumber: 5.8 Consensus size: 48
28301410 TGATATGTGT
* * * * * *
28301420 GCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCCACG-ATTTTAGA
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAACGTA-ATGAGA
* * *
28301468 GCCT-GTGTAAGACCATGTTTGGAACATGGCATTGACAATGTAATGAGA
1 G-CTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAACGTAATGAGA
* ** * * *
28301516 GCTAGTGTAAGACCATGTTTGGTACATGGCATCGGCATTG-ATGTGTGT
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAACGTA-ATGAGA
* * * ** *
28301564 GCTAGCGTAAGACCATGTCTAGG-ACATGGCATCGGTATTG-AGACGAGA
1 GCTAGTGTAAGACCATGT-TTGGAACATGGCATCGGCAACGTA-ATGAGA
* * * *
28301612 GCTACTGTAAGACCATGTCT-GAGACATGGCATCGGC--CTTGACATGTGA
1 GCTAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCAACGT-A-ATGAGA
* *
28301660 GCTAGTGTAAGATCATGTTTGGGACATGGCATCGGCAA
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAA
28301698 TTCATCCTCT
Statistics
Matches: 180, Mismatches: 38, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
46 1 0.01
47 3 0.02
48 169 0.94
49 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAACGTAATGAGA
Found at i:28301591 original size:96 final size:95
Alignment explanation
Indices: 28301474--28301698 Score: 247
Period size: 96 Copynumber: 2.3 Consensus size: 95
28301464 TAGAGCCTGT
* * * * *
28301474 GTAAGACCATGTTTGGAACATGGCATTGACAATGTA-ATGAGAGCTAGTGTAAGACCATGTTTG-
1 GTAAGACCATGTTAGG-ACATGGCATCGACAATG-AGACGAGAGCTACTGTAAGACCATGTCTGA
** *
28301537 GTACATGGCATCGGCATTGATGTGTGTGCTAGC
64 G-ACATGGCATCGGCATTGACATGTGAGCTAGC
** *
28301570 GTAAGACCATGTCTAGGACATGGCATCGGTATTGAGACGAGAGCTACTGTAAGACCATGTCTGAG
1 GTAAGACCATGT-TAGGACATGGCATCGACAATGAGACGAGAGCTACTGTAAGACCATGTCTGAG
* *
28301635 ACATGGCATCGGCCTTGACATGTGAGCTAGT
65 ACATGGCATCGGCATTGACATGTGAGCTAGC
* * *
28301666 GTAAGATCATGTTTGGGACATGGCATCGGCAAT
1 GTAAGACCATG-TTAGGACATGGCATCGACAAT
28301699 TCATCCTCTT
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
95 1 0.01
96 102 0.94
97 5 0.05
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (95 bp):
GTAAGACCATGTTAGGACATGGCATCGACAATGAGACGAGAGCTACTGTAAGACCATGTCTGAGA
CATGGCATCGGCATTGACATGTGAGCTAGC
Found at i:28308425 original size:64 final size:64
Alignment explanation
Indices: 28308344--28308527 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28308334 AGACATTATG
* * *
28308344 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28308408 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCCTGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28308473 AA
63 AA
* * *
28308475 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
28308528 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 25 0.26
66 21 0.22
67 30 0.31
68 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28314034 original size:18 final size:19
Alignment explanation
Indices: 28314011--28314051 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
28314001 CGAGGATTTC
28314011 AAAAATGTAAAGAACA-TA
1 AAAAATGTAAAGAACATTA
28314029 AAAAATGTAAAGAACATTA
1 AAAAATGTAAAGAACATTA
28314048 AAAA
1 AAAA
28314052 GTGCTGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (19 bp):
AAAAATGTAAAGAACATTA
Found at i:28319611 original size:27 final size:27
Alignment explanation
Indices: 28319576--28319644 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
28319566 CCTATAGAAC
*
28319576 TCAAATTTTGCACCTATTGGAATTTAG
1 TCAAATTTTGCACCTATTGCAATTTAG
28319603 TCAAATTTTGCACCTATTGCAATTTAG
1 TCAAATTTTGCACCTATTGCAATTTAG
*
28319630 TCAAATTTTACACCT
1 TCAAATTTTGCACCT
28319645 TTAGTCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (27 bp):
TCAAATTTTGCACCTATTGCAATTTAG
Found at i:28339229 original size:14 final size:14
Alignment explanation
Indices: 28339212--28339239 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28339202 TATTAAAAGG
28339212 AAATAAATAAATAA
1 AAATAAATAAATAA
28339226 AAATAAATAAATAA
1 AAATAAATAAATAA
28339240 TTTCAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:28346224 original size:40 final size:41
Alignment explanation
Indices: 28346169--28346359 Score: 248
Period size: 40 Copynumber: 4.8 Consensus size: 41
28346159 ATTTGAATGA
* *
28346169 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATAT
* *
28346209 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATAT
*
28346249 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATAT
* * *
28346290 -ATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATAT
* * *
28346329 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCT
28346360 TGTGGTAATA
Statistics
Matches: 138, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.25
40 99 0.72
41 5 0.04
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (41 bp):
GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATAT
Found at i:28346371 original size:79 final size:80
Alignment explanation
Indices: 28346172--28346387 Score: 226
Period size: 79 Copynumber: 2.7 Consensus size: 80
28346162 TGAATGAGAT
* * * * *
28346172 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAT-TTGATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTAAT-ATCCGGGCTAAGTACCGAAGGCATTC
* * *
28346236 GTGCTAGTGATTTGAT
65 GTGCGAGTGATATGAC
* *
28346252 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-ATATATCCGGGCTAAG-ACCGAAGGCATTC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTA-ATATCCGGGCTAAGTACCGAAGGCATTC
*
28346315 GTGCGAGTTGCTATG-C
65 GTGCGAG-TGATATGAC
* * * * *
28346331 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTAATATCC-GGCTAAATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTAATATCCGGGCTAAGTACCGAAG
28346388 AAACTTGGGT
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
78 6 0.05
79 58 0.51
80 48 0.42
81 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTAATATCCGGGCTAAGTACCGAAGGCATTCG
TGCGAGTGATATGAC
Found at i:28354592 original size:59 final size:59
Alignment explanation
Indices: 28354516--28354634 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
28354506 TGAATGAGAT
*
28354516 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGG
**
28354575 CCGGGCTAAGTTTCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGG
28354634 C
1 C
28354635 ATTTGTGCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (59 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGG
Found at i:28354632 original size:40 final size:41
Alignment explanation
Indices: 28354588--28354723 Score: 170
Period size: 40 Copynumber: 3.4 Consensus size: 41
28354578 GGCTAAGTTT
*
28354588 CGAAGGCATTTGTGCTAG-TGATTTGATCCGGGCTAAGACC
1 CGAAGGCATTTGTGCTAGTTGATATGATCCGGGCTAAGACC
*
28354628 CGAAGGCATTTGTGCAAGTTGATAT-ATCCGGGCTAAGACC
1 CGAAGGCATTTGTGCTAGTTGATATGATCCGGGCTAAGACC
** * * * *
28354668 CGAAGGCATTCATGCGAGTTGCTATG-CCCGGGTTAAGACC
1 CGAAGGCATTTGTGCTAGTTGATATGATCCGGGCTAAGACC
*
28354708 CGAAGGCAATTGTGCT
1 CGAAGGCATTTGTGCT
28354724 TGTGGTAATA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 77 0.94
41 5 0.06
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (41 bp):
CGAAGGCATTTGTGCTAGTTGATATGATCCGGGCTAAGACC
Found at i:28359299 original size:47 final size:47
Alignment explanation
Indices: 28359221--28359484 Score: 429
Period size: 47 Copynumber: 5.6 Consensus size: 47
28359211 CCCTTCGGGA
* * * * * *
28359221 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28359268 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28359315 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28359362 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28359409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28359456 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
28359485 TATTCAAATA
Statistics
Matches: 203, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
47 184 0.91
49 19 0.09
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28367695 original size:37 final size:37
Alignment explanation
Indices: 28367645--28367723 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
28367635 TTATTACGAA
* *
28367645 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
28367682 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
28367719 GTCTT
1 GTCTT
28367724 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:28367920 original size:47 final size:47
Alignment explanation
Indices: 28367842--28368288 Score: 714
Period size: 47 Copynumber: 9.5 Consensus size: 47
28367832 CTCTTCGGGA
* * * * * * *
28367842 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28367889 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28367936 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28367983 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28368030 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28368077 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28368124 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28368173 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28368220 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28368267 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
28368289 TTGGCTGAAT
Statistics
Matches: 377, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 332 0.88
49 45 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28368201 original size:190 final size:188
Alignment explanation
Indices: 28367842--28368288 Score: 741
Period size: 190 Copynumber: 2.4 Consensus size: 188
28367832 CTCTTCGGGA
** * * * * * * * *
28367842 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28367907 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
28367972 GGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
28368030 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
28368095 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
28368160 TCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 TCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
28368220 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28368285 TTTC
66 TTTC
28368289 TTGGCTGAAT
Statistics
Matches: 240, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
188 89 0.37
190 151 0.63
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:28371934 original size:40 final size:40
Alignment explanation
Indices: 28371882--28372018 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
28371872 ATTACCACAA
* * *
28371882 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGACATAGCAACTC
* * *
28371922 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGACATAGCAACTC
** * * * *
28371962 TTACAAATGTCTTCGGGTCTTAGCCCGGATCAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGA-CATAGCAACTC
28372002 GCACAAATGCCTTCGGG
1 GCACAAATGCCTTCGGG
28372019 ACACAAATGC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 76 0.95
41 4 0.05
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGACATAGCAACTC
Found at i:28372025 original size:17 final size:17
Alignment explanation
Indices: 28372003--28372037 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28371993 AAATCACTAG
28372003 CACAAATGCCTTCGGGA
1 CACAAATGCCTTCGGGA
28372020 CACAAATGCCTTCGGGA
1 CACAAATGCCTTCGGGA
28372037 C
1 C
28372038 TTAGCCCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (17 bp):
CACAAATGCCTTCGGGA
Found at i:28372052 original size:57 final size:57
Alignment explanation
Indices: 28371964--28372077 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
28371954 ATCAACTCTT
* *
28371964 ACAAATGTCTTCGGGTCTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGAC
1 ACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGAC
28372021 ACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGAC
1 ACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGAC
28372078 TTAGCCCGGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (57 bp):
ACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGAC
Found at i:28380302 original size:40 final size:40
Alignment explanation
Indices: 28380249--28380480 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
28380239 TATTACCACA
* * * * * *
28380249 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* * * *
28380289 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* *
28380329 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
28380369 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
28380409 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
28380449 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
28380481 TCATTCAAAT
Statistics
Matches: 180, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 176 0.98
41 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
Found at i:28392411 original size:28 final size:27
Alignment explanation
Indices: 28392379--28392480 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 27
28392369 TCAAGCTTTA
*
28392379 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATTAAT
* *
28392407 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTAT--TA--AT
28392439 ACTGGGCCTAGCCCATATCAGTATTAAT
1 -CTGGGCCTAGCCCATATCAGTATTAAT
28392467 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
28392481 TATACAAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
27 8 0.13
28 27 0.45
30 2 0.03
32 15 0.25
33 8 0.13
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATTAAT
Found at i:28392451 original size:60 final size:59
Alignment explanation
Indices: 28392377--28392517 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 59
28392367 GTTCAAGCTT
28392377 TACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCT-TAC-AGTATC-AGAGTA
1 TACTGGGCC-TAGCCCATATCAATATTAATCTGGGCCATAG-CCCTATACAAG--TCGAGA-TA
* *
28392438 TACTGGGCCTAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATACAAGTCGAGATA
1 TACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATA
* *
28392497 TATTGGGCCTTGCCCATATCA
1 TACTGGGCCTAGCCCATATCA
28392518 GCACAGTTGG
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
59 27 0.37
60 35 0.48
61 11 0.15
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
TACTGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCTATACAAGTCGAGATA
Found at i:28392598 original size:22 final size:21
Alignment explanation
Indices: 28392573--28392613 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28392563 GATAACCCCA
*
28392573 TCCAACCCTGCACTTGCCTGAG
1 TCCAACCCTACACTT-CCTGAG
*
28392595 TCCATCCCTACACTTCCTG
1 TCCAACCCTACACTTCCTG
28392614 TGGGGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.44, G:0.12, T:0.27
Consensus pattern (21 bp):
TCCAACCCTACACTTCCTGAG
Found at i:28392862 original size:26 final size:26
Alignment explanation
Indices: 28392833--28392882 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28392823 TCAAAATTAA
* * *
28392833 CCCTAGGGGTATAATGGTCATTTTGC
1 CCCTAGGGGCAAAATGGTAATTTTGC
28392859 CCCTAGGGGCAAAATGGTAATTTT
1 CCCTAGGGGCAAAATGGTAATTTT
28392883 CATACTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (26 bp):
CCCTAGGGGCAAAATGGTAATTTTGC
Found at i:28393855 original size:43 final size:41
Alignment explanation
Indices: 28393790--28393901 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 41
28393780 TCATATATTG
* * ** *
28393790 ATGCCAACGTCCTAGATGTGGTCTTACATGAA-AACATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACAT-AATAACA-AT-ACA
* *
28393833 ATGCCAATGTCCCTGACATGGTCTTACACATAATCACAATACA
1 ATGCCAATGTCCCAGACATGGTCTT--ACATAATAACAATACA
28393876 ATGCCAATGTCCCAGACATGGTCTTA
1 ATGCCAATGTCCCAGACATGGTCTTA
28393902 TATGTAATCC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.02
43 46 0.79
44 4 0.07
45 7 0.12
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACATGGTCTTACATAATAACAATACA
Found at i:28398174 original size:55 final size:53
Alignment explanation
Indices: 28398111--28398248 Score: 150
Period size: 53 Copynumber: 2.6 Consensus size: 53
28398101 GCAAGAAAAT
* * *
28398111 CATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGCAAAGATCC
1 CATGTAAGACCATGTCAAGACATGGCAATGAT-AACT-CCATAAGGCAAAGATAC
* * * * * * *
28398166 CATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTCCATAAGGCAAGGATAT
1 CATGTAAGACCATGTCAAGACATGGCAATGATAACTCCATAAGGCAAAGATAC
**
28398219 CACATAAGACCATGTCAAGACATGGCAATG
1 CATGTAAGACCATGTCAAGACATGGCAATG
28398249 GTAAGTTTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
53 39 0.57
54 2 0.03
55 28 0.41
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (53 bp):
CATGTAAGACCATGTCAAGACATGGCAATGATAACTCCATAAGGCAAAGATAC
Found at i:28399424 original size:37 final size:37
Alignment explanation
Indices: 28399365--28399473 Score: 175
Period size: 37 Copynumber: 2.9 Consensus size: 37
28399355 AGCTCAGATG
*
28399365 AAATCTCCACACGA-AGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACAC-ATAGTCATCGGGTCTTACCCGGACA
28399402 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* *
28399439 AAATCTCCATACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGA
28399474 ATATATTTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 1 0.01
37 67 0.99
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
Found at i:28399673 original size:48 final size:47
Alignment explanation
Indices: 28399620--28399754 Score: 234
Period size: 48 Copynumber: 2.8 Consensus size: 47
28399610 GCACATCGCC
28399620 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA-ATATCTCA
*
28399668 TACATATTTCACACTAGCCATTCGGCTTTACCACATATGAATGTCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATAT-AATATCTCA
*
28399716 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
28399755 TGCATGTTCA
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
47 1 0.01
48 82 0.98
49 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.34
Consensus pattern (47 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATAATATCTCA
Found at i:28399796 original size:22 final size:22
Alignment explanation
Indices: 28399770--28399845 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28399760 GTTCATATTC
28399770 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
28399792 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
28399816 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28399839 ATCACAT
1 ATCACAT
28399846 ACATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28399803 original size:47 final size:47
Alignment explanation
Indices: 28399724--28399917 Score: 298
Period size: 47 Copynumber: 4.1 Consensus size: 47
28399714 CATACATATT
* * * *
28399724 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
28399771 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
28399818 TCACATTGGCCATTCGGCCTTATCACATACATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* **
28399865 TCACATTGGCCATTCGGCCTTATCTCATATATGCACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
28399912 TCACAT
1 TCACAT
28399918 AAAATCCTAA
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 134 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:28399918 original size:25 final size:25
Alignment explanation
Indices: 28399839--28399918 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
28399829 ATTCGGCCTT
* **
28399839 ATCACATACATGCATGTTCACATTC
1 ATCACATATATGCACATTCACATTC
* * *
28399864 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACATTC-ACATTC
*
28399886 ATCTCATATATGCACATTCACATTC
1 ATCACATATATGCACATTCACATTC
28399911 ATCACATA
1 ATCACATA
28399919 AAATCCTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
22 9 0.23
23 6 0.15
24 5 0.13
25 19 0.49
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (25 bp):
ATCACATATATGCACATTCACATTC
Found at i:28403394 original size:16 final size:16
Alignment explanation
Indices: 28403368--28403400 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28403358 TGAATGTGAG
28403368 AAAATTAAAATGTTTTT
1 AAAATTAAAAT-TTTTT
28403385 AAAATT-AAATTTTTT
1 AAAATTAAAATTTTTT
28403400 A
1 A
28403401 TGCCCCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AAAATTAAAATTTTTT
Found at i:28405683 original size:26 final size:24
Alignment explanation
Indices: 28405646--28405695 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
28405636 TAACTCATAA
28405646 ATTTAACATTCA-CAAATTAGTCCCT
1 ATTTAACATTCATCAAA--AGTCCCT
*
28405671 ATTTCACATTTCATCAAAAGTCCCT
1 ATTTAACA-TTCATCAAAAGTCCCT
28405696 TAACAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 14 0.64
26 4 0.18
27 4 0.18
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTTAACATTCATCAAAAGTCCCT
Found at i:28408685 original size:16 final size:16
Alignment explanation
Indices: 28408664--28408695 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28408654 ATACCAAAAT
28408664 GACCATATTCTATACA
1 GACCATATTCTATACA
28408680 GACCATATTCTATACA
1 GACCATATTCTATACA
28408696 TCATTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
GACCATATTCTATACA
Found at i:28409280 original size:43 final size:43
Alignment explanation
Indices: 28409246--28409377 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
28409236 CTAGCATGTT
* *
28409246 ATCATATATCAATACCAATGTCCCAGACGTGGTCTTACACGAA
1 ATCATATATCAATACCAATGTCCCAGACATGGTCTTACACGTA
* * * * * *
28409289 AACATATAACGATGCCAATGTCCCAGACTTGGTCTTACACATA
1 ATCATATATCAATACCAATGTCCCAGACATGGTCTTACACGTA
*
28409332 ATCATA-ATACAATACCAATGTCCCAGACATGGTCTTACATGTA
1 ATCATATAT-CAATACCAATGTCCCAGACATGGTCTTACACGTA
28409375 ATC
1 ATC
28409378 CCATCTCGAT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 73 0.99
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27
Consensus pattern (43 bp):
ATCATATATCAATACCAATGTCCCAGACATGGTCTTACACGTA
Found at i:28410295 original size:30 final size:30
Alignment explanation
Indices: 28410261--28410423 Score: 185
Period size: 30 Copynumber: 5.6 Consensus size: 30
28410251 AACCAGAATG
28410261 AGAATCAGAATCAGAATCAGTATTAGTAAC
1 AGAATCAGAATCAGAATCAGTATTAGTAAC
** *
28410291 AGAATCAGAATCAGAATCAAAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGTATTA-GTAAC
*
28410322 AGAATCAGAATCA-AA--A-TA--GGTAAC
1 AGAATCAGAATCAGAATCAGTATTAGTAAC
28410346 AGAATCAGAATCAGAATCAGTATTAGTAAC
1 AGAATCAGAATCAGAATCAGTATTAGTAAC
* * * *
28410376 AAAATCAGAATGAGAATCAGAATTACGTGAC
1 AGAATCAGAATCAGAATCAGTATTA-GTAAC
*
28410407 AGAATCAGAATTAGAAT
1 AGAATCAGAATCAGAAT
28410424 GTGAATGCAA
Statistics
Matches: 112, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
24 17 0.15
25 2 0.02
27 2 0.02
28 3 0.03
30 52 0.46
31 36 0.32
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (30 bp):
AGAATCAGAATCAGAATCAGTATTAGTAAC
Found at i:28410351 original size:85 final size:85
Alignment explanation
Indices: 28410261--28410417 Score: 278
Period size: 85 Copynumber: 1.8 Consensus size: 85
28410251 AACCAGAATG
* *
28410261 AGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGAATCAAAATTAGGTGACAGAA
1 AGAATCAGAATCAGAATCAGTATTAGTAACAAAATCAGAATCAGAATCAAAATTACGTGACAGAA
28410326 TCAGAATCAAAATAGGTAAC
66 TCAGAATCAAAATAGGTAAC
* *
28410346 AGAATCAGAATCAGAATCAGTATTAGTAACAAAATCAGAATGAGAATCAGAATTACGTGACAGAA
1 AGAATCAGAATCAGAATCAGTATTAGTAACAAAATCAGAATCAGAATCAAAATTACGTGACAGAA
28410411 TCAGAAT
66 TCAGAAT
28410418 TAGAATGTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTATTAGTAACAAAATCAGAATCAGAATCAAAATTACGTGACAGAA
TCAGAATCAAAATAGGTAAC
Found at i:28410417 original size:6 final size:6
Alignment explanation
Indices: 28410240--28410398 Score: 103
Period size: 6 Copynumber: 26.3 Consensus size: 6
28410230 AAGAAACATG
** * * * *
28410240 ATCAGA ATTGGA ACCAGA ATGAGA ATCAGA ATCAGA ATCAGT ATTAGTA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A
* * * *
28410289 A-CAGA ATCAGA ATCAGA ATCAAA ATTAG- GTGACAGA ATCAGA ATCAAA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* * *
28410337 AT-AGGTA A-CAGA ATCAGA ATCAGA ATCAGT ATTAGTA A-CAAA ATCAGA
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A ATCAGA ATCAGA
*
28410385 ATGAGA ATCAGA AT
1 ATCAGA ATCAGA AT
28410399 TACGTGACAG
Statistics
Matches: 114, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
5 8 0.07
6 98 0.86
7 7 0.06
8 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:28410605 original size:27 final size:27
Alignment explanation
Indices: 28410541--28410612 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
28410531 AGCATGGCTG
* * *
28410541 CCAGAA-TAGATATCGTGACAGAGTCA
1 CCAGAATTAGATATTGTGGCAGAGCCA
*
28410567 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-TAGATATTGTGGCAGAGCCA
*
28410594 CCAGAATTAGATAGTGTGG
1 CCAGAATTAGATATTGTGG
28410613 TAAACCCCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 30 0.81
28 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (27 bp):
CCAGAATTAGATATTGTGGCAGAGCCA
Found at i:28410827 original size:22 final size:22
Alignment explanation
Indices: 28410779--28410837 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
28410769 GTAAATACGT
*
28410779 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
28410801 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
28410823 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
28410838 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:28410993 original size:27 final size:27
Alignment explanation
Indices: 28410925--28411006 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
28410915 TCGATCGGTC
* * *
28410925 AACAGATA-TTGTGACAGAGTCACCAA
1 AACAGATATTTGTGGCAGAGCCACCAG
28410951 ATACAG--ATTTGTGGCAGAGCCACCAG
1 A-ACAGATATTTGTGGCAGAGCCACCAG
*
28410977 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATATTTGTGGCAGAGCCACCAG
28411004 AAC
1 AAC
28411007 GCTTCCTCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 5 0.10
26 17 0.35
27 26 0.54
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (27 bp):
AACAGATATTTGTGGCAGAGCCACCAG
Done.