Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 76 of 325
Found at i:21240839 original size:22 final size:22
Alignment explanation
Indices: 21240811--21240857 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
21240801 TTGTCTTCAT
21240811 TCTATACAAACGTTGCTCTATC
1 TCTATACAAACGTTGCTCTATC
21240833 TCTATACAAACGTTGCTCTATC
1 TCTATACAAACGTTGCTCTATC
21240855 TCT
1 TCT
21240858 TGAGTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTATACAAACGTTGCTCTATC
Found at i:21243389 original size:21 final size:21
Alignment explanation
Indices: 21243363--21243405 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
21243353 TTAGCTTGTG
21243363 AACTTAGTTGTTGGATTCTTT
1 AACTTAGTTGTTGGATTCTTT
*
21243384 AACTTAGTTGTTGGATTGTTT
1 AACTTAGTTGTTGGATTCTTT
21243405 A
1 A
21243406 GTTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.51
Consensus pattern (21 bp):
AACTTAGTTGTTGGATTCTTT
Found at i:21246997 original size:19 final size:19
Alignment explanation
Indices: 21246973--21247021 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
21246963 TTTTTGTTTT
21246973 ATTATTTTATTACCTTAAC
1 ATTATTTTATTACCTTAAC
21246992 ATTATTTTATTACCTTAAC
1 ATTATTTTATTACCTTAAC
21247011 ATTA-TTTATTA
1 ATTATTTTATTA
21247022 ATAAATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTTTATTACCTTAAC
Found at i:21264591 original size:49 final size:49
Alignment explanation
Indices: 21264534--21264627 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
21264524 GTTACTAAAC
21264534 TTACCTTAATCCATTAAAGCATAAAAAATATGTCATACATTTTGGGAAG
1 TTACCTTAATCCATTAAAGCATAAAAAATATGTCATACATTTTGGGAAG
* *
21264583 TTACCTTAATCCATTAAAGCATAAAGAATATTTCATACATTTTGG
1 TTACCTTAATCCATTAAAGCATAAAAAATATGTCATACATTTTGG
21264628 CATTCAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (49 bp):
TTACCTTAATCCATTAAAGCATAAAAAATATGTCATACATTTTGGGAAG
Found at i:21267495 original size:20 final size:21
Alignment explanation
Indices: 21267466--21267504 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21267456 CCTAAATCCA
*
21267466 CTAGT-TTTTCCTTTCCTTTG
1 CTAGTATTTCCCTTTCCTTTG
21267486 CTAGTATTTCCCTTTCCTT
1 CTAGTATTTCCCTTTCCTT
21267505 CTTCAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (21 bp):
CTAGTATTTCCCTTTCCTTTG
Found at i:21268078 original size:12 final size:12
Alignment explanation
Indices: 21268058--21268090 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21268048 TAATTGTTTA
21268058 TATGTTAAAAACT
1 TATGTTAAAAA-T
21268071 TA-GTTAAAAAT
1 TATGTTAAAAAT
21268082 TATGTTAAA
1 TATGTTAAA
21268091 TAAAAGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 14 0.74
13 2 0.11
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (12 bp):
TATGTTAAAAAT
Found at i:21269843 original size:18 final size:18
Alignment explanation
Indices: 21269809--21269843 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21269799 AAAAATATGT
*
21269809 ATATTAAAACATAAAAGA
1 ATATTAAAACACAAAAGA
*
21269827 ATATTAAAACACCAAAG
1 ATATTAAAACACAAAAG
21269844 TCATCTTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (18 bp):
ATATTAAAACACAAAAGA
Found at i:21272266 original size:46 final size:46
Alignment explanation
Indices: 21272143--21272271 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
21272133 TGTAACCCGC
* ** * *
21272143 CCATAAGTGAACTCGGACTCAACTCAATGAGCCCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
21272189 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
21272235 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
21272272 TGCCCAAACA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:21274689 original size:28 final size:28
Alignment explanation
Indices: 21274656--21274738 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
21274646 GATAACAAGA
*
21274656 AAACCGAATAAAGAAATCCAAGATAGAG
1 AAACCGAATAAAGAAATCCAAGATAAAG
21274684 AAACCGAATAAAGAAATCC-AGAATAAAG
1 AAACCGAATAAAGAAATCCAAG-ATAAAG
* * *
21274712 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACC-GAATAAAGAAATCCAAGATA
21274739 CGATACTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.04
28 25 0.53
29 3 0.06
30 15 0.32
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.11
Consensus pattern (28 bp):
AAACCGAATAAAGAAATCCAAGATAAAG
Found at i:21274709 original size:15 final size:15
Alignment explanation
Indices: 21274652--21274729 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
21274642 CAAAGATAAC
*
21274652 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
21274666 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
21274681 GAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
21274694 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
21274709 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
21274724 AAGAAA
1 AAGAAA
21274730 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 8 0.15
14 14 0.26
15 31 0.58
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:21274738 original size:15 final size:15
Alignment explanation
Indices: 21274663--21274738 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
21274653 AGAAAACCGA
21274663 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
21274678 ATAGAGAAA-CCGA-
1 ATAAAGAAATCCAAG
21274691 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
21274705 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
21274721 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
21274736 ATA
1 ATA
21274739 CGATACTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
13 9 0.18
14 5 0.10
15 34 0.69
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:21277752 original size:93 final size:93
Alignment explanation
Indices: 21277645--21277818 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 93
21277635 GCCCATAAGT
* * *
21277645 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
21277710 CGAGCTCGGATGCCCAGTTACATCTCTC
66 CGAGCTCGGATGCCCAGTTACATCTCTC
*
21277738 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
21277803 CGAGTTCGGATGCCCA
66 CGAGCTCGGATGCCCA
21277819 AACATCCTAG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCCAGTTACATCTCTC
Found at i:21277812 original size:46 final size:46
Alignment explanation
Indices: 21277637--21277812 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
21277627 TGTAACCTGC
* * *
21277637 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
21277683 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCCCAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCA--T
* *** *
21277729 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
21277776 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
21277813 TGCCCAAACA
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
44 4 0.04
46 69 0.63
47 32 0.29
49 5 0.05
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:21277831 original size:46 final size:46
Alignment explanation
Indices: 21277688--21277831 Score: 152
Period size: 46 Copynumber: 3.1 Consensus size: 46
21277678 CGCATCCATA
*
21277688 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
21277737 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
21277781 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
21277827 AGTGA
1 AGTGA
21277832 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
44 8 0.10
46 33 0.43
47 31 0.40
49 5 0.06
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:21283753 original size:28 final size:27
Alignment explanation
Indices: 21283709--21283835 Score: 123
Period size: 28 Copynumber: 4.6 Consensus size: 27
21283699 AAAAATTTTC
*
21283709 TCGCACACTTAGTGCTCAATAACCGATT
1 TCGCACACTTAGTGCTCAA-AACCAATT
* *
21283737 TCGTACACTTAGTGCTCGAAAATCCAAAT
1 TCGCACACTTAGTGCTC-AAAA-CCAATT
* * * *
21283766 T-ACACACTTAATGCTTAAAACCAACT
1 TCGCACACTTAGTGCTCAAAACCAATT
* *
21283792 T-GCACACTTAGTGCTCAATGACCGATT
1 TCGCACACTTAGTGCTCAA-AACCAATT
21283819 TCGCACACTTAGTGCTC
1 TCGCACACTTAGTGCTC
21283836 GGTATCAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
26 20 0.25
27 10 0.12
28 44 0.54
29 7 0.09
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
TCGCACACTTAGTGCTCAAAACCAATT
Found at i:21283789 original size:26 final size:28
Alignment explanation
Indices: 21283741--21283807 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 28
21283731 CCGATTTCGT
21283741 ACACTTAGTGCTCGAAAATCCAAATTAC
1 ACACTTAGTGCTCGAAAATCCAAATTAC
* * * *
21283769 ACACTTAATGCT-TAAAA-CCAACTTGC
1 ACACTTAGTGCTCGAAAATCCAAATTAC
21283795 ACACTTAGTGCTC
1 ACACTTAGTGCTC
21283808 AATGACCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 18 0.55
27 4 0.12
28 11 0.33
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.27
Consensus pattern (28 bp):
ACACTTAGTGCTCGAAAATCCAAATTAC
Found at i:21287910 original size:15 final size:16
Alignment explanation
Indices: 21287890--21287921 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21287880 AACTGCATAT
21287890 TTTAAAAAA-TAATAA
1 TTTAAAAAAGTAATAA
21287905 TTTAAAAAAGTAATAA
1 TTTAAAAAAGTAATAA
21287921 T
1 T
21287922 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTTAAAAAAGTAATAA
Found at i:21287912 original size:16 final size:16
Alignment explanation
Indices: 21287888--21287921 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21287878 TGAACTGCAT
*
21287888 ATTTTAAAAAATAATA
1 ATTTAAAAAAATAATA
*
21287904 ATTTAAAAAAGTAATA
1 ATTTAAAAAAATAATA
21287920 AT
1 AT
21287922 AATAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTAAAAAAATAATA
Found at i:21291193 original size:7 final size:7
Alignment explanation
Indices: 21291181--21291208 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21291171 TTTCAAAATA
21291181 ATGAGAT
1 ATGAGAT
21291188 ATGAGAT
1 ATGAGAT
21291195 ATGAGAT
1 ATGAGAT
21291202 ATGAGAT
1 ATGAGAT
21291209 CAATTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
ATGAGAT
Found at i:21295803 original size:13 final size:13
Alignment explanation
Indices: 21295785--21295809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21295775 CGATAATGCT
21295785 GCTTTGCTCCTTC
1 GCTTTGCTCCTTC
21295798 GCTTTGCTCCTT
1 GCTTTGCTCCTT
21295810 TGCTGATGGC
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:0.00, C:0.36, G:0.16, T:0.48
Consensus pattern (13 bp):
GCTTTGCTCCTTC
Found at i:21298016 original size:79 final size:79
Alignment explanation
Indices: 21297885--21298043 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
21297875 CATTGCAAGA
21297885 ATGAAGTAATGAATGAAAACTGAACACCAGGTAGGGTTGTAAAGAAAGTGAGGTAAGTCATTAAG
1 ATGAAGTAATGAATGAAAACTGAACACCAGGTAGGGTTGTAAAGAAAGTGAGGTAAGTCATTAAG
21297950 ACTGCTTAAATACC
66 ACTGCTTAAATACC
*
21297964 ATGAAGTAATGAATGAAAACTGAACACCAGGTAGGGTTGTAAAGAAAGTGAGGTGAGTCATTAAG
1 ATGAAGTAATGAATGAAAACTGAACACCAGGTAGGGTTGTAAAGAAAGTGAGGTAAGTCATTAAG
21298029 ACTGCTTAAATACC
66 ACTGCTTAAATACC
21298043 A
1 A
21298044 AGTCTTTCCT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (79 bp):
ATGAAGTAATGAATGAAAACTGAACACCAGGTAGGGTTGTAAAGAAAGTGAGGTAAGTCATTAAG
ACTGCTTAAATACC
Found at i:21301168 original size:50 final size:50
Alignment explanation
Indices: 21301050--21301342 Score: 282
Period size: 50 Copynumber: 5.8 Consensus size: 50
21301040 TTGTGAGAAT
* * * * ***
21301050 ACATGTGTAGTACTATGTGCATGCTATTATGTGTTTAAGATGGTTGTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG-T-TAGGTC
*
21301102 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTC
* * * * *** * *
21301152 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAACCTTCGATC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATGGTTAGGTC
* * * **
21301203 ACATGTGTAATACTAAGTGCAGGCTATTACATGTATTAGATGGTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTC
* * * *
21301253 ACATGTGTAGTACTAAATGCAGGCTACTACGTGTACCATATTGTT-GATC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTC
* * * *
21301302 GCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGAT
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
21301343 AGCTTCAGTT
Statistics
Matches: 193, Mismatches: 47, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
49 38 0.20
50 83 0.43
51 37 0.19
52 35 0.18
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTC
Found at i:21301227 original size:101 final size:99
Alignment explanation
Indices: 21301100--21301342 Score: 299
Period size: 101 Copynumber: 2.4 Consensus size: 99
21301090 TGGTTGTAGG
* *
21301100 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
* *
21301165 TAAGTGCAGGCTACTATGCGTACCCGAAACCT-TCGA
66 TAAATGCAGGCTACTACGCGTA-CC-AAA-CTGTCGA
* * * **
21301201 TCACATGTGTAATACTAAGTGCAGGCTATTACATGTATTAGATGGTTAGGTCACATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
* * * *
21301266 TAAATGCAGGCTACTACGTGTACCATATTGTTGA
66 TAAATGCAGGCTACTACGCGTACCAAACTGTCGA
* * * *
21301300 TCGCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGAT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
21301343 AGCTTCAGTT
Statistics
Matches: 119, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
98 1 0.01
99 39 0.33
100 2 0.02
101 77 0.65
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
TAAATGCAGGCTACTACGCGTACCAAACTGTCGA
Found at i:21301373 original size:150 final size:153
Alignment explanation
Indices: 21301063--21301376 Score: 404
Period size: 150 Copynumber: 2.1 Consensus size: 153
21301053 TGTGTAGTAC
* ** * *
21301063 TATGTGCATGCTATTATGTGTTTAAGATGGTTGTAGGTCACGTGTGTAGTACTAAGTGCAGGCTA
1 TATGTGCAGGCTATTACATGTTTAAGATGGTTGTAGGTCACATGTGTAGTACTAAATGCAGGCTA
* * *
21301128 CTACGTGTACCAGATGGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAA
66 CTACGTGTACCAGATGGTTAGATCGCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGAA
* * *
21301193 ACCTTCGATCACATGTGTAATAC
131 ACCTTCGATCACAAGGGTAATAA
*
21301216 TAAGTGCAGGCTATTACATGTATT-AGATGG-T-TAGGTCACATGTGTAGTACTAAATGCAGGCT
1 TATGTGCAGGCTATTACATGT-TTAAGATGGTTGTAGGTCACATGTGTAGTACTAAATGCAGGCT
* *
21301278 ACTACGTGTACCATATTGTT-GATCGCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGA
65 ACTACGTGTACCAGATGGTTAGATCGCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGA
* * * **
21301342 TAGCTTC-AGTTACAAGGGTGGTAA
130 AACCTTCGA-TCACAAGGGTAATAA
21301366 TATGTGCAGGC
1 TATGTGCAGGC
21301377 AACCGTGTAT
Statistics
Matches: 139, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
149 1 0.01
150 65 0.47
151 47 0.34
152 1 0.01
153 23 0.17
154 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (153 bp):
TATGTGCAGGCTATTACATGTTTAAGATGGTTGTAGGTCACATGTGTAGTACTAAATGCAGGCTA
CTACGTGTACCAGATGGTTAGATCGCATGTGTAGTACTAAGTGCAGCCTACTATGCGTACCAGAA
ACCTTCGATCACAAGGGTAATAA
Found at i:21303297 original size:552 final size:552
Alignment explanation
Indices: 21302254--21303357 Score: 2118
Period size: 552 Copynumber: 2.0 Consensus size: 552
21302244 AATTTCTTTA
*
21302254 GTGTTGACAGGTTAGCTCGGGGTTGGAGCTCATCGGAAGCAACCTCACACTATCAAGCGACCTCC
1 GTGTTGACAGGTTAGCTCAGGGTTGGAGCTCATCGGAAGCAACCTCACACTATCAAGCGACCTCC
*
21302319 TTTAGAGTATTGATGAATCTTAATGTCTTCAAGTGAGTGGCATGTATGGGGACTTAGTTTTATGA
66 TTTAGAGTATTAATGAATCTTAATGTCTTCAAGTGAGTGGCATGTATGGGGACTTAGTTTTATGA
21302384 TAGATGTTGTTATGATTAGCCATATGTATTGGCTTATATTGATTTACTATATATAGCCATGAGAT
131 TAGATGTTGTTATGATTAGCCATATGTATTGGCTTATATTGATTTACTATATATAGCCATGAGAT
21302449 GTGGCTTGTAAGCCTAATTATCCATGATAAGTTCTAATGCTTGTGATGCGATGATGTGTTTATGC
196 GTGGCTTGTAAGCCTAATTATCCATGATAAGTTCTAATGCTTGTGATGCGATGATGTGTTTATGC
21302514 TTGTGGGATATGTATGGTTGGTATTATGACATATATGCATGATGGGTGCTTCTTGACCGATCGAA
261 TTGTGGGATATGTATGGTTGGTATTATGACATATATGCATGATGGGTGCTTCTTGACCGATCGAA
* *
21302579 ATGGTCATAGCCATGTGTTAAATGTATAATATGGGAATAAGTTGATAATGTTTGAACATAAATAC
326 ATGGTCATAGCCATGTGGTAAATGTATAATATAGGAATAAGTTGATAATGTTTGAACATAAATAC
*
21302644 TTGATGTTGATTGAAGCTACTTGATAAATTGATGGTTATGGAAGTTTGGTAAAAGTGGTCATCAA
391 TTGATGTTGATTGAAGCTACTTGATAAATTGATGGTTATAGAAGTTTGGTAAAAGTGGTCATCAA
21302709 ATGATAAGGTCAATGAATATAGAATTGTTGTGTCTAGATTTGATATTATATGAGTACATGTAATA
456 ATGATAAGGTCAATGAATATAGAATTGTTGTGTCTAGATTTGATATTATATGAGTACATGTAATA
21302774 AGTGAATGATAGCATGTTAAACTTAAGAATAT
521 AGTGAATGATAGCATGTTAAACTTAAGAATAT
*
21302806 GTGTTGACAGGTTAGCTCAGGGTTGGAGCTCATCGGAAGCAACCTCACACTATCAAGCTACCTCC
1 GTGTTGACAGGTTAGCTCAGGGTTGGAGCTCATCGGAAGCAACCTCACACTATCAAGCGACCTCC
21302871 TTTAGAGTATTAATGAATCTTAATGTCTTCAAGTGAGTGGCATGTATGGGGACTTAGTTTTATGA
66 TTTAGAGTATTAATGAATCTTAATGTCTTCAAGTGAGTGGCATGTATGGGGACTTAGTTTTATGA
*
21302936 TAGATGTTGTTATGATTAGCCATATGTATTGGCTTATATTGATTTACTGTATATAGCCATGAGAT
131 TAGATGTTGTTATGATTAGCCATATGTATTGGCTTATATTGATTTACTATATATAGCCATGAGAT
*
21303001 GTGGCTTGTAAGCTTAATTATCCATGATAAGTTCTAATGCTTGTGATGCGATGATGTGTTTATGC
196 GTGGCTTGTAAGCCTAATTATCCATGATAAGTTCTAATGCTTGTGATGCGATGATGTGTTTATGC
21303066 TTGTGGGATATGTATGGTTGGTATTATGACATATATGCATGATGGGTGCTTCTTGACCGATCGAA
261 TTGTGGGATATGTATGGTTGGTATTATGACATATATGCATGATGGGTGCTTCTTGACCGATCGAA
*
21303131 ATGGTCATAGCCATGTGGTAAATGTATAATATAGGAATAAGTTGATAATTTTTGAACATAAATAC
326 ATGGTCATAGCCATGTGGTAAATGTATAATATAGGAATAAGTTGATAATGTTTGAACATAAATAC
21303196 TTGATGTTGATTGAAGCTACTTGATAAATTGATGGTTATAGAAGTTTGGTAAAAGTGGTCATCAA
391 TTGATGTTGATTGAAGCTACTTGATAAATTGATGGTTATAGAAGTTTGGTAAAAGTGGTCATCAA
21303261 ATGATAAGGTCAATGAATATAGAATTGTTGTGTCTAGATTTGATATTATATGAGTACATGTAATA
456 ATGATAAGGTCAATGAATATAGAATTGTTGTGTCTAGATTTGATATTATATGAGTACATGTAATA
*
21303326 AGTGAATGATAGCATGTTAAAGTTAAGAATAT
521 AGTGAATGATAGCATGTTAAACTTAAGAATAT
21303358 ACCTTAGTGA
Statistics
Matches: 542, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
552 542 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (552 bp):
GTGTTGACAGGTTAGCTCAGGGTTGGAGCTCATCGGAAGCAACCTCACACTATCAAGCGACCTCC
TTTAGAGTATTAATGAATCTTAATGTCTTCAAGTGAGTGGCATGTATGGGGACTTAGTTTTATGA
TAGATGTTGTTATGATTAGCCATATGTATTGGCTTATATTGATTTACTATATATAGCCATGAGAT
GTGGCTTGTAAGCCTAATTATCCATGATAAGTTCTAATGCTTGTGATGCGATGATGTGTTTATGC
TTGTGGGATATGTATGGTTGGTATTATGACATATATGCATGATGGGTGCTTCTTGACCGATCGAA
ATGGTCATAGCCATGTGGTAAATGTATAATATAGGAATAAGTTGATAATGTTTGAACATAAATAC
TTGATGTTGATTGAAGCTACTTGATAAATTGATGGTTATAGAAGTTTGGTAAAAGTGGTCATCAA
ATGATAAGGTCAATGAATATAGAATTGTTGTGTCTAGATTTGATATTATATGAGTACATGTAATA
AGTGAATGATAGCATGTTAAACTTAAGAATAT
Found at i:21306017 original size:49 final size:49
Alignment explanation
Indices: 21305952--21306074 Score: 158
Period size: 49 Copynumber: 2.5 Consensus size: 49
21305942 GTCAATGTCG
* *
21305952 TGTCCCAGACAGGTCTTACACTGACTTTCATTTATCGAG-GCCGATGCCA
1 TGTCCCAGACAAGTCTTACACTGACTCTCATTTATC-AGTGCCGATGCCA
* * * *
21306001 TGTCCCAAACAAGTCTTACACTGGCTCTCATTTATCAGTGTCGATGTCA
1 TGTCCCAGACAAGTCTTACACTGACTCTCATTTATCAGTGCCGATGCCA
* *
21306050 TGTCCCGGACAATTCTTACACTGAC
1 TGTCCCAGACAAGTCTTACACTGAC
21306075 ACACAACAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 2 0.03
49 61 0.97
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (49 bp):
TGTCCCAGACAAGTCTTACACTGACTCTCATTTATCAGTGCCGATGCCA
Found at i:21310274 original size:9 final size:9
Alignment explanation
Indices: 21310260--21310285 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21310250 GCTTCTGGAA
21310260 TTCAATTTT
1 TTCAATTTT
21310269 TTCAATTTT
1 TTCAATTTT
21310278 TTCAATTT
1 TTCAATTT
21310286 AGTCCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (9 bp):
TTCAATTTT
Found at i:21314372 original size:33 final size:33
Alignment explanation
Indices: 21314335--21314400 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
21314325 CCTTGTCCAC
21314335 TCCTAATTTGATGTTGGTTCCCCATATAGTACA
1 TCCTAATTTGATGTTGGTTCCCCATATAGTACA
21314368 TCCTAATTTGATGTTGGTTCCCCATATAGTACA
1 TCCTAATTTGATGTTGGTTCCCCATATAGTACA
21314401 CTGACTCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (33 bp):
TCCTAATTTGATGTTGGTTCCCCATATAGTACA
Found at i:21319105 original size:25 final size:25
Alignment explanation
Indices: 21319077--21319124 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21319067 TCATGTAGTC
21319077 CACACG-GTCTACATGATTTCACATG
1 CACACGAG-CTACATGATTTCACATG
* *
21319102 CACACGAGCTGCATTATTTCACA
1 CACACGAGCTACATGATTTCACA
21319125 CTGCCGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (25 bp):
CACACGAGCTACATGATTTCACATG
Found at i:21320763 original size:11 final size:12
Alignment explanation
Indices: 21320736--21320764 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21320726 CTTCCCCTAG
21320736 ATGCAAATACAA
1 ATGCAAATACAA
21320748 ATGCAAATAC-A
1 ATGCAAATACAA
21320759 ATGCAA
1 ATGCAA
21320765 TCAATCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.17
Consensus pattern (12 bp):
ATGCAAATACAA
Found at i:21320778 original size:15 final size:15
Alignment explanation
Indices: 21320758--21320786 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21320748 ATGCAAATAC
21320758 AATGCAATCAATCAT
1 AATGCAATCAATCAT
21320773 AATGCAATCAATCA
1 AATGCAATCAATCA
21320787 ATATCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATGCAATCAATCAT
Found at i:21321250 original size:29 final size:29
Alignment explanation
Indices: 21321132--21321272 Score: 126
Period size: 29 Copynumber: 4.9 Consensus size: 29
21321122 TAATTTTTGT
*
21321132 GAAAAATAGTGGCAAAATTGTACAATCTT-
1 GAAAAATAGTGGCAAAATTGTAAAAT-TTA
*
21321161 -AAAAATAGTGGCAAAATTGTAAAATATA
1 GAAAAATAGTGGCAAAATTGTAAAATTTA
* * *** * *
21321189 AAAAAAAAGTGGTTGAATTG-AAAACTCTG
1 GAAAAATAGTGGCAAAATTGTAAAA-TTTA
* *
21321218 GAAAACTAGTGGCAAAACTGTAAAATTTA
1 GAAAAATAGTGGCAAAATTGTAAAATTTA
* *
21321247 GAAAAATAGTGGCATAATTGAAAAAT
1 GAAAAATAGTGGCAAAATTGTAAAAT
21321273 AGTGGCAAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.01
28 28 0.32
29 54 0.62
30 4 0.05
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (29 bp):
GAAAAATAGTGGCAAAATTGTAAAATTTA
Found at i:21321266 original size:58 final size:56
Alignment explanation
Indices: 21321132--21321270 Score: 154
Period size: 58 Copynumber: 2.4 Consensus size: 56
21321122 TAATTTTTGT
* * * *
21321132 GAAAAATAGTGGCAAAATTGTACAATCTTAAAAATAGTGGCAAAATTGTAAAATATA
1 GAAAAATAGTGGCATAATTG-AAAATCTGAAAAATAGTGGCAAAACTGTAAAATATA
* * * * *
21321189 AAAAAAAAGTGG-TTGAATTGAAAACTCTGGAAAACTAGTGGCAAAACTGTAAAATTTA
1 GAAAAATAGTGGCAT-AATTGAAAA-TCT-GAAAAATAGTGGCAAAACTGTAAAATATA
21321247 GAAAAATAGTGGCATAATTGAAAA
1 GAAAAATAGTGGCATAATTGAAAA
21321271 ATAGTGGCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
56 3 0.05
57 18 0.27
58 44 0.67
59 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.24
Consensus pattern (56 bp):
GAAAAATAGTGGCATAATTGAAAATCTGAAAAATAGTGGCAAAACTGTAAAATATA
Found at i:21326513 original size:20 final size:18
Alignment explanation
Indices: 21326490--21326539 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
21326480 TTCCTGTATG
21326490 AGTATTGATATTTCTATAAA
1 AGTATTGATATTT-T-TAAA
*
21326510 AGTATCGATATTTTTAAA
1 AGTATTGATATTTTTAAA
21326528 ATGGTATTGATA
1 A--GTATTGATA
21326540 CCAATTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 20 0.77
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (18 bp):
AGTATTGATATTTTTAAA
Found at i:21332674 original size:20 final size:20
Alignment explanation
Indices: 21332620--21332689 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
21332610 GACTTGTTTG
*
21332620 AAAATCATTTTGA-TGT-CTT
1 AAAATCATTTTGACT-TAATT
* * *
21332639 AAAATGAATTTAACTTAATT
1 AAAATCATTTTGACTTAATT
* **
21332659 GAAATCATTTTGACTTGGTT
1 AAAATCATTTTGACTTAATT
21332679 AAAATCATTTT
1 AAAATCATTTT
21332690 CACTCGATTT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
19 11 0.29
20 27 0.71
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (20 bp):
AAAATCATTTTGACTTAATT
Found at i:21334848 original size:13 final size:13
Alignment explanation
Indices: 21334830--21334857 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21334820 GTAATGGTTT
21334830 AGACATTAATTAG
1 AGACATTAATTAG
21334843 AGACATTAATTAG
1 AGACATTAATTAG
21334856 AG
1 AG
21334858 GAATAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (13 bp):
AGACATTAATTAG
Found at i:21337353 original size:49 final size:49
Alignment explanation
Indices: 21337258--21337477 Score: 161
Period size: 49 Copynumber: 4.6 Consensus size: 49
21337248 GTTAAGATGC
* * *
21337258 TGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAGGCCGATGCCA
1 TGTCCCAGACA-GGTCTTACACTAGCTCTCATATAGTCAGGCCGATGCCA
* * *
21337308 TGTCCTAGACAGGTCTTACACTAGCTCTCATCTA-TCAGTGTCGATGCCA
1 TGTCCCAGACAGGTCTTACACTAGCTCTCATATAGTCAG-GCCGATGCCA
* * * * * * * *
21337357 TGTCCCAGACAAGTCTTACACT-G-ACACACA-A--CAAGCTGACGTCA
1 TGTCCCAGACAGGTCTTACACTAGCTCTCATATAGTCAGGCCGATGCCA
* * * *
21337401 TGTCCCAGACAAGTCTTACACTAGCTTGTC-TAT-CTCGAGGCCAATG-CA
1 TGTCCCAGACAGGTCTTACACTAGC-TCTCATATAGTC-AGGCCGATGCCA
* *
21337449 TGTCCCAGACATGTCTTACATTAGCTCTC
1 TGTCCCAGACAGGTCTTACACTAGCTCTC
21337478 GTCTCAACGC
Statistics
Matches: 134, Mismatches: 28, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
44 28 0.21
45 3 0.02
46 2 0.01
47 7 0.05
48 30 0.22
49 54 0.40
50 10 0.07
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTAGCTCTCATATAGTCAGGCCGATGCCA
Found at i:21337507 original size:46 final size:48
Alignment explanation
Indices: 21337399--21337519 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 48
21337389 AAGCTGACGT
* * * *
21337399 CATGTCCCAGACAAGTCTTACACTAGCTTGTCTATCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTCTCTATCTCAACGCCAATG
* * *
21337447 CATGTCCCAGACATGTCTTACATTAGC-TCTC-GTCTCAACGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTCTCTATCTCAACGCCAATG
* *
21337493 CATGTCCTAGACATGTCTTATACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
21337520 ACACATATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
46 35 0.56
47 3 0.05
48 25 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCTCTATCTCAACGCCAATG
Found at i:21340214 original size:31 final size:31
Alignment explanation
Indices: 21340179--21340241 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
21340169 AATAATGTTT
21340179 CACATGACATTGATAACATAGGTTATCTTTA
1 CACATGACATTGATAACATAGGTTATCTTTA
21340210 CACATGACATTGATAACATAGGTTATCTTTA
1 CACATGACATTGATAACATAGGTTATCTTTA
21340241 C
1 C
21340242 CCTTTAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (31 bp):
CACATGACATTGATAACATAGGTTATCTTTA
Found at i:21341326 original size:13 final size:13
Alignment explanation
Indices: 21341308--21341344 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21341298 CTCTGCCAAT
21341308 AATAATTTTTTAA
1 AATAATTTTTTAA
*
21341321 AATAATTTTATAA
1 AATAATTTTTTAA
21341334 ATATAATTTTT
1 A-ATAATTTTT
21341345 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATAATTTTTTAA
Found at i:21341480 original size:3 final size:3
Alignment explanation
Indices: 21341472--21341519 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
21341462 AATCGGATAT
21341472 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21341520 ATTCTATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21342648 original size:20 final size:21
Alignment explanation
Indices: 21342618--21342659 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
21342608 AAAATTCAAA
*
21342618 AAAATTATAAAAACTATTTTT
1 AAAATTATAAAAAATATTTTT
21342639 AAAATT-TAAAAAATATTTTT
1 AAAATTATAAAAAATATTTTT
21342659 A
1 A
21342660 TAAGTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTATAAAAAATATTTTT
Found at i:21343675 original size:270 final size:272
Alignment explanation
Indices: 21343185--21343728 Score: 932
Period size: 270 Copynumber: 2.0 Consensus size: 272
21343175 TACCAGGGAA
* *
21343185 GTAGTTGTTTGAGGTATATCATCGTTTATACAAACGATAGAACAGTTCAAAGACATAACATTTAC
1 GTAGTTGTTTGAGGTATATCATCGTTTATACAAACGACAGAACAGTTCAAAGACATAACATCTAC
*
21343250 TAGTAAGCTAGTAAAGTAAATATATTTTCACAAAGGGATGGTTCAAGGGTGGATGCTTAACTATT
66 TAGTAAGCTAGTAAAGTAAATATATTTTCACAAAGGGAAGGTTCAAGGGTGGATGCTTAACTATT
* *
21343315 CTATATAACTATCGATCATAGATTCTATCACCACATCGAGTTAATGTTTTTCCGTTAAAACTATC
131 CTATACAACTATCGATCATAGATTCTATCACCACATCAAGTTAATGTTTTTCCGTTAAAACTATC
* *
21343380 AATTTTCATTCCTGCGAGAGATTGTTGGAAAAATTGTAATTTTTGGAAACTTTAAGGCATATTCT
196 AATTTTCATTCATGAGAGAGATTGTTGGAAAAATTGTAATTTTTGGAAACTTTAAGGCATATTCT
21343445 CGATTGGTAAAG
261 CGATTGGTAAAG
* *
21343457 GTAGTTGTTTGAGGTATATCATCGTTTATACAAACGACATAACAG-TCAAAGACATCACATCTAC
1 GTAGTTGTTTGAGGTATATCATCGTTTATACAAACGACAGAACAGTTCAAAGACATAACATCTAC
* *
21343521 TAGTTAGCTAGTAAAGTAAATATTTTTTCAC-AAGGGAAGGTTCAAGGGTGGATGCTTAACTATT
66 TAGTAAGCTAGTAAAGTAAATATATTTTCACAAAGGGAAGGTTCAAGGGTGGATGCTTAACTATT
* *
21343585 CTATACAACTATCGATCATAGATTTTATCACCACATCAAGTTAATGTTTTTTCGTTAAAACTATC
131 CTATACAACTATCGATCATAGATTCTATCACCACATCAAGTTAATGTTTTTCCGTTAAAACTATC
*
21343650 AATTTTCATTCATGTAG-GGGATTGTTGGAAAAATTGTAATTTTTGGAAACTTTAAGGCATATTC
196 AATTTTCATTCATG-AGAGAGATTGTTGGAAAAATTGTAATTTTTGGAAACTTTAAGGCATATTC
21343714 TCGATTGGTAAAG
260 TCGATTGGTAAAG
21343727 GT
1 GT
21343729 GGAGAGTTGA
Statistics
Matches: 257, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
270 167 0.65
271 47 0.18
272 43 0.17
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (272 bp):
GTAGTTGTTTGAGGTATATCATCGTTTATACAAACGACAGAACAGTTCAAAGACATAACATCTAC
TAGTAAGCTAGTAAAGTAAATATATTTTCACAAAGGGAAGGTTCAAGGGTGGATGCTTAACTATT
CTATACAACTATCGATCATAGATTCTATCACCACATCAAGTTAATGTTTTTCCGTTAAAACTATC
AATTTTCATTCATGAGAGAGATTGTTGGAAAAATTGTAATTTTTGGAAACTTTAAGGCATATTCT
CGATTGGTAAAG
Found at i:21345461 original size:41 final size:41
Alignment explanation
Indices: 21345404--21345482 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
21345394 TGGAGGTTTG
21345404 GTCCTTGAGAATGGAGTACATCTTAAGGTCAGTTGTTTTTT
1 GTCCTTGAGAATGGAGTACATCTTAAGGTCAGTTGTTTTTT
21345445 GTCCTTGAGAATGGAGTACATCTTAAGGTCAGTTGTTT
1 GTCCTTGAGAATGGAGTACATCTTAAGGTCAGTTGTTT
21345483 CCCGTTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (41 bp):
GTCCTTGAGAATGGAGTACATCTTAAGGTCAGTTGTTTTTT
Found at i:21354012 original size:138 final size:138
Alignment explanation
Indices: 21353815--21354091 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
21353805 TAGTACATGA
21353815 TGGTGTAAAGATAAATTGTGGTACCCAATGGCTTGGAGCTGGATAATTTCTATGACATCTTATAT
1 TGGTGTAAAGATAAATTGTGGTACCCAATGGCTTGGAGCTGGATAATTTCTATGACATCTTATAT
21353880 AGATTTGTTTTTCTTTTAAATGATGCATATTAAGCTTACGCCACTTTATGATATCATTTTCTTGA
66 AGATTTGTTTTTCTTTTAAATGATGCATATTAAGCTTACGCCACTTTATGATATCATTTTCTTGA
21353945 ATCTGTTT
131 ATCTGTTT
21353953 TGGTGTAAAGATAAATTGTGGTACCCAATGGCTTGGAGCTGGATAATTTCTATGACATCTTATAT
1 TGGTGTAAAGATAAATTGTGGTACCCAATGGCTTGGAGCTGGATAATTTCTATGACATCTTATAT
21354018 AGATTTGTTTTTCTTTTAAATGATGCATATTAAGCTTACGCCACTTTATGATATCATTTTCTTGA
66 AGATTTGTTTTTCTTTTAAATGATGCATATTAAGCTTACGCCACTTTATGATATCATTTTCTTGA
21354083 ATCTGTTT
131 ATCTGTTT
21354091 T
1 T
21354092 TGTTATTTTA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (138 bp):
TGGTGTAAAGATAAATTGTGGTACCCAATGGCTTGGAGCTGGATAATTTCTATGACATCTTATAT
AGATTTGTTTTTCTTTTAAATGATGCATATTAAGCTTACGCCACTTTATGATATCATTTTCTTGA
ATCTGTTT
Found at i:21356376 original size:17 final size:18
Alignment explanation
Indices: 21356343--21356376 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21356333 TTTATGAAAT
21356343 TATAGGTTGTCCGGTTAC
1 TATAGGTTGTCCGGTTAC
*
21356361 TATATGTTGT-CGGTTA
1 TATAGGTTGTCCGGTTA
21356377 GTTTAGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (18 bp):
TATAGGTTGTCCGGTTAC
Found at i:21357599 original size:6 final size:6
Alignment explanation
Indices: 21357590--21357617 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21357580 AGAAAAAAAA
21357590 ACAGTG ACAGTG ACAGTG ACAGTG ACAG
1 ACAGTG ACAGTG ACAGTG ACAGTG ACAG
21357618 GAATAACCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.32, T:0.14
Consensus pattern (6 bp):
ACAGTG
Found at i:21358091 original size:26 final size:24
Alignment explanation
Indices: 21358052--21358110 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
21358042 TTATTTCATT
* * *
21358052 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
21358076 TAAATTAAATATATTTAAAAACATAA
1 -AAA-TAAATATATTTAAAAACATAA
21358102 AAATAAATA
1 AAATAAATA
21358111 GTAAAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.20
25 6 0.20
26 18 0.60
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:21358126 original size:22 final size:21
Alignment explanation
Indices: 21358098--21358140 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21358088 ATTTAAAAAC
*
21358098 ATAAAAATAAATAGTAAAACAA
1 ATAAAAAT-AATACTAAAACAA
21358120 ATAAAAATAATACTAAAACAA
1 ATAAAAATAATACTAAAACAA
21358141 TTCTTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (21 bp):
ATAAAAATAATACTAAAACAA
Found at i:21358216 original size:15 final size:16
Alignment explanation
Indices: 21358186--21358218 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21358176 AAATAGTTAT
21358186 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
21358203 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
21358218 A
1 A
21358219 AAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:21358427 original size:2 final size:2
Alignment explanation
Indices: 21358420--21358445 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21358410 TGATCAGCTC
21358420 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
21358446 GGAGTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21361503 original size:25 final size:25
Alignment explanation
Indices: 21361460--21361520 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
21361450 AATATTAAAT
*
21361460 TATAATAAAATTATAATTTAAAAGAA
1 TATAAT-AAGTTATAATTTAAAAGAA
* *
21361486 TATAATAAGTTATAATTTAGAAGAT
1 TATAATAAGTTATAATTTAAAAGAA
21361511 TATAATAAGT
1 TATAATAAGT
21361521 ACTATATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (25 bp):
TATAATAAGTTATAATTTAAAAGAA
Found at i:21370354 original size:27 final size:27
Alignment explanation
Indices: 21370316--21370369 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21370306 GAAAGAAAAG
21370316 TATCTTTGTTTGGGTATTTCATTCTAA
1 TATCTTTGTTTGGGTATTTCATTCTAA
21370343 TATCTTTGTTTGGGTATTTCATTCTAA
1 TATCTTTGTTTGGGTATTTCATTCTAA
21370370 CTTCTAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.56
Consensus pattern (27 bp):
TATCTTTGTTTGGGTATTTCATTCTAA
Found at i:21373175 original size:24 final size:22
Alignment explanation
Indices: 21373116--21373159 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21373106 CCCTTTTTAA
*
21373116 AAACCCTAAACCTAAAAATATT
1 AAACCCTAAATCTAAAAATATT
21373138 AAACCCTAAATCTAAAAATATT
1 AAACCCTAAATCTAAAAATATT
21373160 TAAAATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCCTAAATCTAAAAATATT
Found at i:21374118 original size:36 final size:36
Alignment explanation
Indices: 21374071--21374143 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
21374061 CTGACTATGC
21374071 TCCCAGACTACTTTTCCCCCTTTGTTTCCCTTGCTT
1 TCCCAGACTACTTTTCCCCCTTTGTTTCCCTTGCTT
21374107 TCCCAGACTACTTTTCCCCCTTTGTTTCCCTTGCTT
1 TCCCAGACTACTTTTCCCCCTTTGTTTCCCTTGCTT
21374143 T
1 T
21374144 TGTGTTGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.45
Consensus pattern (36 bp):
TCCCAGACTACTTTTCCCCCTTTGTTTCCCTTGCTT
Found at i:21377156 original size:25 final size:25
Alignment explanation
Indices: 21377128--21377189 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
21377118 TTTTCAAAAT
*
21377128 AAAATTATAATTTAAAATAT-TTATA
1 AAAATTATAATTTAAAAT-TGTTAAA
* * *
21377153 AAAATTCTAAATTTTATATTGTTAAA
1 AAAATTAT-AATTTAAAATTGTTAAA
21377179 AAAATTATAAT
1 AAAATTATAAT
21377190 AATTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATTATAATTTAAAATTGTTAAA
Found at i:21378050 original size:137 final size:137
Alignment explanation
Indices: 21377792--21378067 Score: 471
Period size: 137 Copynumber: 2.0 Consensus size: 137
21377782 ATTACTCAAA
* * *
21377792 TTTTAAAAAATTTCAATGTTTTGAGTAATTTTATGTATTATAAATTACTAAATTTTTCAAAACAT
1 TTTTAAAAAATTTCAATGTTTTGAGTAAATTTATGCATTATAAATTACTAAATTTTTCAAAAAAT
* *
21377857 TTCTCATGTTTTAAATATTGATTTCATTGTTGACTAAATCTTAGCTCAGCCAGTATAAACATTAT
66 TTCTCATGTTTTAAATAGTGATTTCATTGTTGACTAAATCTTAACTCAGCCAGTATAAACATTAT
21377922 TGCTAGT
131 TGCTAGT
*
21377929 TTTTTAAAAATTTCAATGTTTTGAGTAAATTTATGCATTATAAATTACTAAATTTTTCAAAAAAT
1 TTTTAAAAAATTTCAATGTTTTGAGTAAATTTATGCATTATAAATTACTAAATTTTTCAAAAAAT
* * *
21377994 TTCTCATGTTTTAAATAGTGATTTCATTGTTGACTCAATCTTAACTTAGCCGGTATAAACATTAT
66 TTCTCATGTTTTAAATAGTGATTTCATTGTTGACTAAATCTTAACTCAGCCAGTATAAACATTAT
21378059 TGCTAGT
131 TGCTAGT
21378066 TT
1 TT
21378068 AACATTTTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
137 130 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (137 bp):
TTTTAAAAAATTTCAATGTTTTGAGTAAATTTATGCATTATAAATTACTAAATTTTTCAAAAAAT
TTCTCATGTTTTAAATAGTGATTTCATTGTTGACTAAATCTTAACTCAGCCAGTATAAACATTAT
TGCTAGT
Found at i:21384997 original size:43 final size:41
Alignment explanation
Indices: 21384895--21385000 Score: 149
Period size: 41 Copynumber: 2.5 Consensus size: 41
21384885 GATTAACGAG
* *
21384895 ATGTGACTATGTGTAAGACCATGTCGGGACATTGGCATCAT
1 ATGTGATTACGTGTAAGACCATGTCGGGACATTGGCATCAT
*
21384936 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTACGTGTAAGACCATGTC-GGGACATTGGCATC-AT
* *
21384979 ATTTGATTTCGTGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
21385001 AGCTGGGCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 23 0.40
42 14 0.24
43 21 0.36
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
ATGTGATTACGTGTAAGACCATGTCGGGACATTGGCATCAT
Found at i:21385007 original size:43 final size:41
Alignment explanation
Indices: 21384895--21385043 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 41
21384885 GATTAACGAG
* *
21384895 ATGTGACTATGTGTAAGACCATG-TCGGGACATTGGCATCAT
1 ATGTGATTACGTGTAAGACCATGCT-GGGACATTGGCATCAT
*
21384936 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTACGTGTAAGACCATG-CTGGGACATTGGCATC-AT
* * *
21384979 ATTTGATTTCGTGTAAGACCATAGCTGGG-CTATCGGCATCGAT
1 ATGTGATTACGTGTAAGACCAT-GCTGGGAC-ATTGGCATC-AT
* * * *
21385022 ATATGATAACATGTAATACCAT
1 ATGTGATTACGTGTAAGACCAT
21385044 ATCTGAGATA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
41 21 0.23
42 15 0.16
43 54 0.59
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (41 bp):
ATGTGATTACGTGTAAGACCATGCTGGGACATTGGCATCAT
Found at i:21389584 original size:26 final size:26
Alignment explanation
Indices: 21389547--21389604 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
21389537 CGACCTCGTC
*
21389547 CTTGC-AAGGTTTACACAAGTTCACT
1 CTTGCAAAGGTTTACACAAGCTCACT
21389572 CTTGCAAAGGTTTACACAAGCTCACT
1 CTTGCAAAGGTTTACACAAGCTCACT
21389598 CTTGCAA
1 CTTGCAA
21389605 CCTTACCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (26 bp):
CTTGCAAAGGTTTACACAAGCTCACT
Found at i:21393442 original size:46 final size:46
Alignment explanation
Indices: 21393374--21393550 Score: 171
Period size: 47 Copynumber: 3.8 Consensus size: 46
21393364 ATAATCTCAC
* * *
21393374 CCATAAT-AACTTGGAACGCAACTCAACGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTC-CAT
*
21393419 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTTCCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCCAT
* ** * * *
21393465 CCATAGGTGAACTCAAAATGCAACTCAACGAGTTCGGATGCCTCATAAT
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTC--CAT
* * * *
21393514 TC-TCATGAACTCGGACCACAACTCAACGAGTTCGGAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAT
21393551 CTCAATTTCC
Statistics
Matches: 108, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
45 7 0.06
46 35 0.32
47 62 0.57
48 1 0.01
49 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCCAT
Found at i:21404907 original size:14 final size:15
Alignment explanation
Indices: 21404883--21404911 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21404873 ATCCCACTCC
21404883 AATTACAGATACAGA
1 AATTACAGATACAGA
21404898 AATT-CAGATACAGA
1 AATTACAGATACAGA
21404912 TATAACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (15 bp):
AATTACAGATACAGA
Found at i:21409320 original size:17 final size:17
Alignment explanation
Indices: 21409283--21409320 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
21409273 GACACACAAT
*
21409283 TTAAAAAAATAAAAATT
1 TTAAAAAAATAAAAATA
*
21409300 TTAAAAAAATAAAAGTA
1 TTAAAAAAATAAAAATA
21409317 TTAA
1 TTAA
21409321 CTATTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATAAAAATA
Found at i:21411328 original size:5 final size:5
Alignment explanation
Indices: 21411318--21411374 Score: 114
Period size: 5 Copynumber: 11.4 Consensus size: 5
21411308 TTGTTTAATA
21411318 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
21411368 ATTAT AT
1 ATTAT AT
21411375 ATAAAAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:21412215 original size:40 final size:40
Alignment explanation
Indices: 21412153--21412233 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
21412143 AATTATGGGA
* ** *
21412153 TACTGAATATTGTTTTGAATACTGAATTGAACTGTGAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
* *
21412193 TACTGAATAATGTTACGTATACTGCATTGAACTGTAAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
21412233 T
1 T
21412234 TCTAATGAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (40 bp):
TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
Found at i:21412496 original size:45 final size:45
Alignment explanation
Indices: 21412446--21412541 Score: 149
Period size: 45 Copynumber: 2.1 Consensus size: 45
21412436 TGACTACTGT
*
21412446 TACTGTTACCATTACTGTTATC-GATTCGACACTTTGTGTGTCGAA
1 TACTGTTACCATTACTGTTA-CAGATTCAACACTTTGTGTGTCGAA
* *
21412491 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACCATTACTGTTACAGATTCAACACTTTGTGTGTCGAA
21412536 TACTGT
1 TACTGT
21412542 GACTGTTACT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (45 bp):
TACTGTTACCATTACTGTTACAGATTCAACACTTTGTGTGTCGAA
Found at i:21412550 original size:45 final size:45
Alignment explanation
Indices: 21412446--21412552 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
21412436 TGACTACTGT
* * *
21412446 TACTGTTACCATTACTGTTATCGATTCGACACTTTGTGTGTCGAA
1 TACTGTGACCGTTACTGTTATCGATTCAACACTTTGTGTGTCGAA
* *
21412491 TACTGTTACCGTTACTGTTA-CAGATTCAACACTTTGTGTGTTGAA
1 TACTGTGACCGTTACTGTTATC-GATTCAACACTTTGTGTGTCGAA
*
21412536 TACTGTGACTGTTACTG
1 TACTGTGACCGTTACTG
21412553 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.02
45 55 0.98
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTGACCGTTACTGTTATCGATTCAACACTTTGTGTGTCGAA
Found at i:21421685 original size:40 final size:40
Alignment explanation
Indices: 21421623--21421703 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
21421613 AATTATGGGA
* ** *
21421623 TACTGAATATTGTTTTGAATACTGAATTGAACTGTGAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
* *
21421663 TACTGAATAATGTTACGTATACTGCATTGAACTGTAAAAT
1 TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
21421703 T
1 T
21421704 TCTAATGAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (40 bp):
TACTGAATAATGTTACGAATACTGAATTGAACTGTAAAAT
Found at i:21421967 original size:45 final size:45
Alignment explanation
Indices: 21421916--21422020 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
21421906 CGACTCCTGT
* *
21421916 CTGTTACCGTTACTGTTACCGATT-TGACACTTTGTGTGTCGAATA
1 CTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAATA
* *
21421961 CTGTTACCGTTACTATTACAGATTCAGCACTTTGTGTGTTGAATA
1 CTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATA
*
21422006 CTGTTACTGTTACTG
1 CTGTTACCGTTACTG
21422021 CTACTGCTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (45 bp):
CTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATA
Found at i:21422035 original size:18 final size:18
Alignment explanation
Indices: 21422004--21422038 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21421994 GTGTGTTGAA
* *
21422004 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
21422022 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
21422039 ATTGCTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:21426606 original size:23 final size:24
Alignment explanation
Indices: 21426576--21426623 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
21426566 GTTCACATGG
21426576 GTTTGCATGGGGTTCG-TAGGGGT
1 GTTTGCATGGGGTTCGATAGGGGT
21426599 GTTTGCATGGGGTTCGAATAGGGGT
1 GTTTGCATGGGGTTCG-ATAGGGGT
21426624 TCATAGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 16 0.70
25 7 0.30
ACGTcount: A:0.12, C:0.08, G:0.46, T:0.33
Consensus pattern (24 bp):
GTTTGCATGGGGTTCGATAGGGGT
Found at i:21426635 original size:11 final size:12
Alignment explanation
Indices: 21426619--21426684 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
21426609 GGTTCGAATA
*
21426619 GGGGTTCATA-G
1 GGGGTTCACATG
21426630 GGGGTTCACATG
1 GGGGTTCACATG
**
21426642 GGGGTTCGTATG
1 GGGGTTCACATG
* *
21426654 GGAGGCTCGCA-G
1 GG-GGTTCACATG
*
21426666 GGGGTTCACAAG
1 GGGGTTCACATG
21426678 GGGGTTC
1 GGGGTTC
21426685 GCAAAGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
11 15 0.33
12 24 0.53
13 6 0.13
ACGTcount: A:0.15, C:0.15, G:0.47, T:0.23
Consensus pattern (12 bp):
GGGGTTCACATG
Found at i:21426686 original size:23 final size:23
Alignment explanation
Indices: 21426607--21426687 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
21426597 GTGTTTGCAT
* * *
21426607 GGGGTTCGAATAGGGGTTCATAG
1 GGGGTTCGCATGGGGGTTCAAAG
* * *
21426630 GGGGTTCACATGGGGGTTCGTATG
1 GGGGTTCGCATGGGGGTTC-AAAG
*
21426654 GGAGGCTCGCA-GGGGGTTCACAAG
1 GG-GGTTCGCATGGGGGTTCA-AAG
21426678 GGGGTTCGCA
1 GGGGTTCGCA
21426688 AAGGGTTTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
23 23 0.52
24 15 0.34
25 6 0.14
ACGTcount: A:0.17, C:0.15, G:0.46, T:0.22
Consensus pattern (23 bp):
GGGGTTCGCATGGGGGTTCAAAG
Found at i:21428264 original size:151 final size:152
Alignment explanation
Indices: 21428077--21428381 Score: 594
Period size: 152 Copynumber: 2.0 Consensus size: 152
21428067 ATTAGAAGAG
21428077 GAGGAATTGAACCTGAGATTGAAAAATAAAATTATTATTATTTAACCATTTAACCAATAAAGCTA
1 GAGGAATTGAACCTGAGATTGAAAAATAAAATTATTATTATTTAACCATTTAACCAATAAAGCTA
21428142 ATATATT-AAAATAATAAGAATCTTAAAACAACATGAAATAAAAAATACAAATACGAGTGAGAGA
66 ATATATTAAAAATAATAAGAATCTTAAAACAACATGAAATAAAAAATACAAATACGAGTGAGAGA
21428206 AGAATTGAACCCAAGACTCAAT
131 AGAATTGAACCCAAGACTCAAT
21428228 GAGGAATTGAACCTGAGATTGAAAAATAAAATTATTATTATTTAACCATTTAACCAATAAAGCTA
1 GAGGAATTGAACCTGAGATTGAAAAATAAAATTATTATTATTTAACCATTTAACCAATAAAGCTA
*
21428293 ATATATTAAAAATAATAAGAATCTTAAAATAACATGAAATAAAAAATACAAATACGAGTGAGAGA
66 ATATATTAAAAATAATAAGAATCTTAAAACAACATGAAATAAAAAATACAAATACGAGTGAGAGA
21428358 AGAATTGAACCCAAGACTCAAT
131 AGAATTGAACCCAAGACTCAAT
21428380 GA
1 GA
21428382 CATAATTACT
Statistics
Matches: 152, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 72 0.47
152 80 0.53
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (152 bp):
GAGGAATTGAACCTGAGATTGAAAAATAAAATTATTATTATTTAACCATTTAACCAATAAAGCTA
ATATATTAAAAATAATAAGAATCTTAAAACAACATGAAATAAAAAATACAAATACGAGTGAGAGA
AGAATTGAACCCAAGACTCAAT
Found at i:21433236 original size:12 final size:13
Alignment explanation
Indices: 21433219--21433260 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
21433209 AGTATACTCA
21433219 TTTTTACATTTT-
1 TTTTTACATTTTC
*
21433231 TTTTTAAATTTTC
1 TTTTTACATTTTC
21433244 TTTTTAC-TTTTAC
1 TTTTTACATTTT-C
21433257 TTTT
1 TTTT
21433261 ACTTAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTACATTTTC
Found at i:21434588 original size:20 final size:22
Alignment explanation
Indices: 21434563--21434605 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21434553 TCAATGCCTC
*
21434563 AAAAAGA-GT-ATTTGAGGAAG
1 AAAAAGATGTCATTCGAGGAAG
21434583 AAAAAGATGTCATTCGAGGAAG
1 AAAAAGATGTCATTCGAGGAAG
21434605 A
1 A
21434606 GGTTGGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.49, C:0.05, G:0.28, T:0.19
Consensus pattern (22 bp):
AAAAAGATGTCATTCGAGGAAG
Found at i:21436056 original size:46 final size:46
Alignment explanation
Indices: 21436003--21436178 Score: 228
Period size: 46 Copynumber: 3.8 Consensus size: 46
21435993 TATTTGGGCA
21436003 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
*** * * * *
21436049 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCG
* *
21436096 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
21436142 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21436179 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
46 73 0.66
47 37 0.34
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:21436158 original size:93 final size:93
Alignment explanation
Indices: 21435999--21436170 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
21435989 GGGATATTTG
* *
21435999 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
21436064 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
21436092 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
21436157 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
21436171 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:21443517 original size:3 final size:3
Alignment explanation
Indices: 21443509--21443546 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
21443499 ACGAATCATT
*
21443509 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
21443547 GTAGAAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:21449497 original size:57 final size:60
Alignment explanation
Indices: 21449427--21449567 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 60
21449417 ATCGTATTAC
* * * *
21449427 AGGATTACTAGTCCAGGCTAAATCCATTA-TGTAA-CGTATG-TTCAAAAGAACTTA-ATT
1 AGGATTACCAGTCCAGGCTAAATCCATAATTGTAATCATATGCTT-AAAAGAAATTATATT
* * *
21449484 AGGATTACCAGTCCAGGCTAAA-CCCTAATTGTAATCATATGCTTGAGAGAAATTATATT
1 AGGATTACCAGTCCAGGCTAAATCCATAATTGTAATCATATGCTTAAAAGAAATTATATT
*
21449543 AGGATTACCCGTCCAGGCTAAATCC
1 AGGATTACCAGTCCAGGCTAAATCC
21449568 TTTCTATAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 26 0.37
58 13 0.18
59 26 0.37
60 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (60 bp):
AGGATTACCAGTCCAGGCTAAATCCATAATTGTAATCATATGCTTAAAAGAAATTATATT
Found at i:21452737 original size:20 final size:20
Alignment explanation
Indices: 21452692--21452740 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
21452682 GGCATCATAG
21452692 ATGCATAACAGGGGCACCAAA
1 ATGCA-AACAGGGGCACCAAA
*
21452713 GTGCAAACAGGGGCA-CAAA
1 ATGCAAACAGGGGCACCAAA
21452732 TATGCAAAC
1 -ATGCAAAC
21452741 GAAGGCACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (20 bp):
ATGCAAACAGGGGCACCAAA
Found at i:21461294 original size:17 final size:17
Alignment explanation
Indices: 21461272--21461304 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21461262 CTTTGGTGTC
21461272 TTTTTACTTCAACTAAA
1 TTTTTACTTCAACTAAA
21461289 TTTTTACTTCAACTAA
1 TTTTTACTTCAACTAA
21461305 TCTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTACTTCAACTAAA
Found at i:21464345 original size:108 final size:110
Alignment explanation
Indices: 21464187--21464407 Score: 360
Period size: 108 Copynumber: 2.0 Consensus size: 110
21464177 TCGTAATATG
*
21464187 GCAATTTTGATAAAGGGAAAAAATATATAAATTTAGTAAACATTACATTAAAAAAATATAAATAT
1 GCAATTTTGATAAAGGG-AAAAATATATAAATTTA-TAAACATTAAATTAAAAAAATATAAATA-
21464252 TTTTTC-AAAAAATAAAAAAATAAAATGGGTAGACTT-AAATGGGTTT
63 TTTTTCAAAAAAATAAAAAAATAAAATGGGTAGACTTAAAATGGGTTT
21464298 GCAATTTTGATAAAAGGG-AAAATATATAAATTT-TAAACATTAAATTAAAAAAATATAAATATT
1 GCAATTTTGAT-AAAGGGAAAAATATATAAATTTATAAACATTAAATTAAAAAAATATAAATATT
*
21464361 TTTCAAAAAAATGAAAAAATAAAATGGGTAGACTTAAAATGGGTTT
65 TTTCAAAAAAATAAAAAAATAAAATGGGTAGACTTAAAATGGGTTT
21464407 G
1 G
21464408 GGCTAAACAT
Statistics
Matches: 105, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
107 6 0.06
108 56 0.53
109 11 0.10
110 15 0.14
111 11 0.10
112 6 0.06
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (110 bp):
GCAATTTTGATAAAGGGAAAAATATATAAATTTATAAACATTAAATTAAAAAAATATAAATATTT
TTCAAAAAAATAAAAAAATAAAATGGGTAGACTTAAAATGGGTTT
Found at i:21464925 original size:19 final size:19
Alignment explanation
Indices: 21464901--21464997 Score: 53
Period size: 19 Copynumber: 5.3 Consensus size: 19
21464891 CTAGAATGTT
21464901 TTTTTTGAAATTTTTATAA
1 TTTTTTGAAATTTTTATAA
**
21464920 TTTTTT-AAA--AATATAA
1 TTTTTTGAAATTTTTATAA
* *
21464936 -ATTTTGAAATTTTCATAAA
1 TTTTTTGAAATTTTTAT-AA
* * *
21464955 TATTTTG-AATTTTAAAAA
1 TTTTTTGAAATTTTTATAA
*
21464973 TTATTTTG-AATATTTTGTAA
1 TT-TTTTGAAAT-TTTTATAA
21464993 TTTTT
1 TTTTT
21464998 ATTAAGAGAG
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
15 4 0.07
16 8 0.14
18 8 0.14
19 26 0.44
20 13 0.22
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTTGAAATTTTTATAA
Found at i:21469062 original size:15 final size:14
Alignment explanation
Indices: 21469041--21469078 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
21469031 TTATTATTAG
21469041 TTTTATTTTTATAT
1 TTTTATTTTTATAT
*
21469055 TTTGTATTTGTATAT
1 TTT-TATTTTTATAT
21469070 TTTTATTTT
1 TTTTATTTT
21469079 AAGGTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTATAT
Found at i:21470621 original size:2 final size:2
Alignment explanation
Indices: 21470614--21470650 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21470604 TTCTTTTTGG
21470614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21470651 GGTTTAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21478780 original size:27 final size:27
Alignment explanation
Indices: 21478732--21478833 Score: 120
Period size: 27 Copynumber: 3.8 Consensus size: 27
21478722 GCGAGGCTGC
* *
21478732 CAGATATTGTGACGA-AGTCACCAGATA
1 CAGATATTGTGGC-ATAGCCACCAGATA
21478759 CAGATATTGTGGCATAGCCACCAGA-A
1 CAGATATTGTGGCATAGCCACCAGATA
* *
21478785 TAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCATAGCCACCAGATA
21478812 CAGATAATTGTGGCATAGCCAC
1 CAGAT-ATTGTGGCATAGCCAC
21478834 AAGGAAACTT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.12
27 55 0.85
28 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (27 bp):
CAGATATTGTGGCATAGCCACCAGATA
Found at i:21479004 original size:28 final size:26
Alignment explanation
Indices: 21478942--21479015 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 26
21478932 AAATTAACCC
** * *
21478942 TAGGGGTATAACGGTAATTTTGCACC
1 TAGGGGTATAATAGTAATTTTCCACA
21478968 TAGGGGTATAATAGTAATTTTCCATACA
1 TAGGGGTATAATAGTAATTTTCC--ACA
*
21478996 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAATAGTAATTT
21479016 AGATGCTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 20 0.49
28 21 0.51
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.36
Consensus pattern (26 bp):
TAGGGGTATAATAGTAATTTTCCACA
Found at i:21480489 original size:26 final size:26
Alignment explanation
Indices: 21480458--21480565 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
21480448 TGAAATGCCC
*
21480458 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
21480484 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21480510 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
21480536 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
21480562 ATCA
1 ATCA
21480566 ATTTGTACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:21486067 original size:37 final size:37
Alignment explanation
Indices: 21486017--21486107 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
21486007 TTATTACGAA
21486017 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
21486054 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
21486091 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
21486108 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:21486205 original size:48 final size:48
Alignment explanation
Indices: 21486147--21486250 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
21486137 TGTTACAACA
21486147 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
*
21486195 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
21486243 TTCACATT
1 TTCACATT
21486251 CATCACATCG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
Found at i:21486299 original size:49 final size:49
Alignment explanation
Indices: 21486242--21486432 Score: 346
Period size: 49 Copynumber: 3.9 Consensus size: 49
21486232 CACACATATA
21486242 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
21486291 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
21486340 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
* *
21486389 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
21486433 CATCTCATAC
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 138 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (49 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
Found at i:21501307 original size:69 final size:69
Alignment explanation
Indices: 21501192--21501353 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 69
21501182 CATAAAAATG
* * * * * **
21501192 TGCAAGACCATGGTTGGACTATGGTAATGTTTATGTAAGACTATAGCGAGGCTATTGTAGTTTTT
1 TGCAAGACCATGGTTGGACCATGGAAATGTTTAAGTAAGACCATAGCGAGACTACGGTAGTTTTT
21501257 CAGA
66 CAGA
21501261 TGCAAGACCATGGTTGGACCATGGAAATGTTTAAGTAAGACCATAGCGAGACTACGGTAGTTTTT
1 TGCAAGACCATGGTTGGACCATGGAAATGTTTAAGTAAGACCATAGCGAGACTACGGTAGTTTTT
21501326 CAGA
66 CAGA
* *
21501330 CGTAAGACCATGGTTGGACCATGG
1 TGCAAGACCATGGTTGGACCATGG
21501354 CAGTGTATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 84 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (69 bp):
TGCAAGACCATGGTTGGACCATGGAAATGTTTAAGTAAGACCATAGCGAGACTACGGTAGTTTTT
CAGA
Found at i:21504466 original size:27 final size:26
Alignment explanation
Indices: 21504422--21504475 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
21504412 TATTTAGTTT
21504422 TGATTTTGTTTTAGTTT-ATTTTATTA
1 TGATTTTGTTTTAGTTTAATTTT-TTA
21504448 TGATTTTGATTTCTA-TTTAATTTTTTA
1 TGATTTTG-TTT-TAGTTTAATTTTTTA
21504475 T
1 T
21504476 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.32
27 10 0.40
28 7 0.28
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (26 bp):
TGATTTTGTTTTAGTTTAATTTTTTA
Found at i:21505896 original size:21 final size:21
Alignment explanation
Indices: 21505870--21505916 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
21505860 AAAAATATCC
*
21505870 AACATTATATTCCATTATAGT
1 AACATTATATTCCATTATAAT
* *
21505891 AACATTATATTTCATTTTAAT
1 AACATTATATTCCATTATAAT
21505912 AACAT
1 AACAT
21505917 CACTAGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (21 bp):
AACATTATATTCCATTATAAT
Found at i:21513858 original size:40 final size:40
Alignment explanation
Indices: 21513813--21513979 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
21513803 CGGAATATAA
21513813 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
21513853 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
21513893 CCGGACATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
21513933 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
21513972 CCGGATAT
1 CCGGATAT
21513980 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:21515244 original size:63 final size:60
Alignment explanation
Indices: 21515172--21515297 Score: 150
Period size: 63 Copynumber: 2.0 Consensus size: 60
21515162 CCTCCCCCTT
21515172 TTTCCTTAGTA-ATTTCGGCCAAGAAGAT-GAGAAAGGATGAACAAAATTTTTTTT-TTTCTTTT
1 TTTCCTTAGTACA-TTCGGCCAAGAAGATGGAG-AAGGATGAAC---ATTTTTTTTCTTT-TTTT
21515234 C
60 C
***
21515235 TTTCCTTAGTACATTCGGCCAAGCCTATGGAGAAGGATGAACATTTTTTTTCTTTTTTTC
1 TTTCCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACATTTTTTTTCTTTTTTTC
21515295 TTT
1 TTT
21515298 TTCATATTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
60 17 0.30
61 3 0.05
63 33 0.58
64 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (60 bp):
TTTCCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACATTTTTTTTCTTTTTTTC
Found at i:21525468 original size:5 final size:5
Alignment explanation
Indices: 21525439--21525489 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
21525429 AAAATAATTT
21525439 TAAAA TATAAA TAAAGA TAAAAA TAAAA T-AAA T-AAA TAAAA TAAAAA
1 TAAAA TA-AAA TAAA-A T-AAAA TAAAA TAAAA TAAAA TAAAA T-AAAA
21525486 TAAA
1 TAAA
21525490 TAATAGGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 8 0.20
5 16 0.39
6 14 0.34
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:21525477 original size:13 final size:13
Alignment explanation
Indices: 21525445--21525483 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
21525435 ATTTTAAAAT
21525445 ATAAATAAAGAT-A
1 ATAAATAAA-ATAA
21525458 A-AAATAAAATAA
1 ATAAATAAAATAA
21525470 ATAAATAAAATAA
1 ATAAATAAAATAA
21525483 A
1 A
21525484 AATAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 9 0.38
13 13 0.54
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:21525479 original size:19 final size:20
Alignment explanation
Indices: 21525439--21525492 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
21525429 AAAATAATTT
21525439 TAAAATATAAATAAAGATAAAA
1 TAAAA-ATAAAT-AAGATAAAA
21525461 -ATAAAATAAATAA-ATAAAA
1 TA-AAAATAAATAAGATAAAA
21525480 TAAAAATAAATAA
1 TAAAAATAAATAA
21525493 TAGGTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.57
20 3 0.10
21 7 0.23
22 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAAAATAAATAAGATAAAA
Found at i:21530325 original size:21 final size:21
Alignment explanation
Indices: 21530280--21530346 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
21530270 ACGGGCTGTT
***
21530280 CACACGGGCGTGTGCCCCCTC
1 CACACGGGCGTGTGAGGCCTC
* * *
21530301 CACACCGGCGTGTGGGGCCTT
1 CACACGGGCGTGTGAGGCCTC
21530322 CACACGGGCGTGTGAGGCCTC
1 CACACGGGCGTGTGAGGCCTC
21530343 CACA
1 CACA
21530347 TGAGCATGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.13, C:0.39, G:0.33, T:0.15
Consensus pattern (21 bp):
CACACGGGCGTGTGAGGCCTC
Found at i:21530693 original size:14 final size:14
Alignment explanation
Indices: 21530671--21530709 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
21530661 TGAGTTGGGG
* *
21530671 CATCCGCATACATA
1 CATCTGCATACACA
21530685 CATCTGCATACACA
1 CATCTGCATACACA
21530699 CATCTGCATAC
1 CATCTGCATAC
21530710 GAAGTGTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.36, G:0.08, T:0.23
Consensus pattern (14 bp):
CATCTGCATACACA
Found at i:21532241 original size:40 final size:40
Alignment explanation
Indices: 21532172--21532248 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
21532162 ACAGTACCAC
*
21532172 TTGGTGTGTAGGGCCGGATGGGCCAATTTTATCCCCATAA
1 TTGGTGTATAGGGCCGGATGGGCCAATTTTATCCCCATAA
* * * * *
21532212 TTGGTGTATAGGGCTGGGTGGGTCGATTTTATTCCCA
1 TTGGTGTATAGGGCCGGATGGGCCAATTTTATCCCCA
21532249 CATGGTGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (40 bp):
TTGGTGTATAGGGCCGGATGGGCCAATTTTATCCCCATAA
Found at i:21532255 original size:38 final size:38
Alignment explanation
Indices: 21532168--21532256 Score: 88
Period size: 40 Copynumber: 2.3 Consensus size: 38
21532158 AATTACAGTA
* *
21532168 CCACTTGGTGTGTAGGGCCGGATGGGCCAATTTTATCC
1 CCACATGGTGTATAGGGCCGGATGGGCCAATTTTATCC
* * * * * *
21532206 CCATAATTGGTGTATAGGGCTGGGTGGGTCGATTTTATTC
1 CCA-CA-TGGTGTATAGGGCCGGATGGGCCAATTTTATCC
21532246 CCACATGGTGT
1 CCACATGGTGT
21532257 GTTGGGTTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
38 9 0.22
39 1 0.03
40 30 0.75
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (38 bp):
CCACATGGTGTATAGGGCCGGATGGGCCAATTTTATCC
Found at i:21534172 original size:34 final size:34
Alignment explanation
Indices: 21534131--21534208 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
21534121 GTTCACATAT
* *
21534131 ATATAGGCTCGCATATTCCT-AGGTTTTGCATAAC
1 ATATAGGCTCGCACATTCCTAAGG-TTAGCATAAC
*
21534165 ATATAGGCTCGCACATTCCTAAGGTTAGTATAAC
1 ATATAGGCTCGCACATTCCTAAGGTTAGCATAAC
*
21534199 ATATAAGCTC
1 ATATAGGCTC
21534209 ACATGCTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 36 0.92
35 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (34 bp):
ATATAGGCTCGCACATTCCTAAGGTTAGCATAAC
Found at i:21534342 original size:14 final size:14
Alignment explanation
Indices: 21534323--21534389 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
21534313 TAGGTGTTGT
21534323 CTTGCATATATTGA
1 CTTGCATATATTGA
*
21534337 CTTGCA-ATTATTGG
1 CTTGCATA-TATTGA
* * *
21534351 CTCGCATGTATAGA
1 CTTGCATATATTGA
* *
21534365 CTTGCATGTATTAA
1 CTTGCATATATTGA
*
21534379 CTCGCATATAT
1 CTTGCATATAT
21534390 ACAACAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
13 1 0.02
14 40 0.98
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (14 bp):
CTTGCATATATTGA
Found at i:21534357 original size:28 final size:28
Alignment explanation
Indices: 21534326--21534390 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
21534316 GTGTTGTCTT
* **
21534326 GCATATATTGACTTGCAAT-TATTGGCTC
1 GCATATATAGACTTGC-ATGTATTAACTC
*
21534354 GCATGTATAGACTTGCATGTATTAACTC
1 GCATATATAGACTTGCATGTATTAACTC
21534382 GCATATATA
1 GCATATATA
21534391 CAACAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (28 bp):
GCATATATAGACTTGCATGTATTAACTC
Found at i:21535416 original size:68 final size:66
Alignment explanation
Indices: 21535253--21535417 Score: 206
Period size: 68 Copynumber: 2.4 Consensus size: 66
21535243 TATATCATCT
* * *
21535253 TACAATTACATACAAAAAAGTTATATTACTCTACCACTACACCAAACTACACATACAAAAAGTGA
1 TACAATTACATAC-AAAAAGTTATATTAGTCCACCACTACACC-AACTACACATACAAAAAATGA
21535318 ACC
64 ACC
* * **
21535321 TACAATTACATACAAAAAGTGATATTAGTCCACCATTACATCC-TTTACACATACAAAAAATGAC
1 TACAATTACATACAAAAAGTTATATTAGTCCACCACTACA-CCAACTACACATACAAAAAATG--
21535385 AACC
63 AACC
*
21535389 TACAATTACATGCAAAAAGTTATATTAGT
1 TACAATTACATACAAAAAGTTATATTAGT
21535418 TCTGTAACAC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 16 0.19
67 23 0.27
68 46 0.54
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (66 bp):
TACAATTACATACAAAAAGTTATATTAGTCCACCACTACACCAACTACACATACAAAAAATGAAC
C
Found at i:21540038 original size:22 final size:22
Alignment explanation
Indices: 21539994--21540038 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21539984 TTAAGTATAC
* *
21539994 CTGTAACACCTCTAACCCGTAT
1 CTGTAACACCCCTAACCCATAT
*
21540016 CTGTAACACCCCTAACTCATAT
1 CTGTAACACCCCTAACCCATAT
21540038 C
1 C
21540039 CGACACCGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.38, G:0.07, T:0.27
Consensus pattern (22 bp):
CTGTAACACCCCTAACCCATAT
Found at i:21541594 original size:43 final size:43
Alignment explanation
Indices: 21541529--21541695 Score: 185
Period size: 43 Copynumber: 3.9 Consensus size: 43
21541519 AACTCGTACA
* * * *
21541529 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATTG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * * * * *
21541571 ATGCCACTGTCCCAGATAGGGTCTTACACGAAATCATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* *
21541614 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT-CG
*
21541657 ATGCCAATGTCCCATACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
21541696 CTTGATAACC
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 6 0.06
43 97 0.94
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:21543776 original size:100 final size:100
Alignment explanation
Indices: 21543662--21543849 Score: 322
Period size: 100 Copynumber: 1.9 Consensus size: 100
21543652 GAAGCTATCT
**
21543662 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATTTGGTACACGTAGCAGCC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGCAGCC
21543727 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* * *
21543762 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGCAGCC
*
21543827 TGCACTTTGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
21543850 CCTCACAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGCAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:21543784 original size:51 final size:48
Alignment explanation
Indices: 21543662--21543851 Score: 202
Period size: 49 Copynumber: 3.9 Consensus size: 48
21543652 GAAGCTATCT
* * *
21543662 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATTT-
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT--TTTC
* * * *
21543711 GGTACACGTAGCAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAATTTTC
* * *
21543761 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCC
1 -GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATT-TTC
* * *
21543811 GGTACACGTAGTAGCCTGCACTTTGTACTACACACGTGACC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
21543852 TCACAATAGT
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 76 0.65
50 4 0.03
51 37 0.32
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (48 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTTTC
Found at i:21552195 original size:28 final size:27
Alignment explanation
Indices: 21552137--21552196 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
21552127 CGATCTCAAC
* *
21552137 AAAATATAATTTAAGGAAAAAATAAAT
1 AAAATATAATTTAAAGAAAAAATAAAG
*
21552164 AAAATATAAATTTATAAGAAATAA-AAAG
1 AAAATAT-AATTTA-AAGAAAAAATAAAG
21552192 AAAAT
1 AAAAT
21552197 GAGAGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 14 0.50
29 7 0.25
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATATAATTTAAAGAAAAAATAAAG
Found at i:21553199 original size:3 final size:3
Alignment explanation
Indices: 21553191--21553243 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
21553181 GTTGCTAAGG
21553191 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21553239 TTA TT
1 TTA TT
21553244 TTGGGTTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21561800 original size:18 final size:18
Alignment explanation
Indices: 21561779--21561819 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
21561769 ATATATTAGT
21561779 ATGGTTAAATCACATGAG
1 ATGGTTAAATCACATGAG
21561797 ATGGTTAAATCACATGAG
1 ATGGTTAAATCACATGAG
21561815 ATGGT
1 ATGGT
21561820 AACCTGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (18 bp):
ATGGTTAAATCACATGAG
Found at i:21570507 original size:34 final size:34
Alignment explanation
Indices: 21570456--21570559 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 34
21570446 CTTTTTACAA
* * * *
21570456 ATCAACACAATAGCAATTTATATGCGTATAACAG
1 ATCAATACATTAGCAATTAATATGCTTATAACAG
* * *
21570490 ATCAATACGA-TATCAATTAATATGCTTATAGCAA
1 ATCAATAC-ATTAGCAATTAATATGCTTATAACAG
*
21570524 ATCAGTACATTAGCAATTAATATGCTTATAACAG
1 ATCAATACATTAGCAATTAATATGCTTATAACAG
21570558 AT
1 AT
21570560 TGATATGGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
33 1 0.02
34 56 0.97
35 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (34 bp):
ATCAATACATTAGCAATTAATATGCTTATAACAG
Found at i:21574757 original size:2 final size:2
Alignment explanation
Indices: 21574750--21574783 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21574740 GAGTGTTACA
21574750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21574784 GCGGGGCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21575183 original size:29 final size:29
Alignment explanation
Indices: 21575151--21575237 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
21575141 AAATTGAATC
*
21575151 AAATCAAAATTTCAT-TATAAAATTGCACA
1 AAATCAAACTTT-ATATATAAAATTGCACA
** * *
21575180 AAATTGAACTTTATATATAACATTACACA
1 AAATCAAACTTTATATATAAAATTGCACA
* *
21575209 AAATCAAACTTTATGTATAATATTGCACA
1 AAATCAAACTTTATATATAAAATTGCACA
21575238 TTGAGTGAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.04
29 45 0.96
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATCAAACTTTATATATAAAATTGCACA
Found at i:21582321 original size:20 final size:22
Alignment explanation
Indices: 21582291--21582335 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
21582281 GTTATTTAAT
*
21582291 TATTATTTT-AAAATTAAAAAA
1 TATTATTTTAAAAAATAAAAAA
21582312 TATT-TTTTAAAAAATAAAAAA
1 TATTATTTTAAAAAATAAAAAA
21582333 TAT
1 TAT
21582336 AAATTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTATTTTAAAAAATAAAAAA
Found at i:21582342 original size:21 final size:21
Alignment explanation
Indices: 21582300--21582347 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
21582290 TTATTATTTT
* ***
21582300 AAAATTAAAAAATATTTTTTA
1 AAAAATAAAAAATATAAATTA
21582321 AAAAATAAAAAATATAAATTA
1 AAAAATAAAAAATATAAATTA
21582342 ATAAAA
1 A-AAAA
21582348 AATGTAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATAAAAAATATAAATTA
Done.