Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 43 of 320
Found at i:12139713 original size:16 final size:17
Alignment explanation
Indices: 12139687--12139721 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12139677 TATAATTGGG
*
12139687 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
12139704 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
12139720 TT
1 TT
12139722 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:12142352 original size:107 final size:104
Alignment explanation
Indices: 12142210--12142449 Score: 347
Period size: 107 Copynumber: 2.3 Consensus size: 104
12142200 CTATTGTCAA
* * *
12142210 TACTATATTAACTTTATTTAACTTATTTAACAGACACATACAAAAGATAACTTATATAATAAACC
1 TACTATATTGACTTTATTTAATTTATTTAACAGACACATACAAAAGACAACTTATATAATAAACC
* *
12142275 CGAACAA-GAACAAAAAATAATGGGGGACAAATGCTATGCCAG
66 C-AAAAACGAAC-AAAAA-AAGGGGGGA-AAATGCTATGCCAG
* * *
12142317 TACTGTATTGACTTTATTTAATTTGTTTAATAGACACATACAAAAGACAACTTATATAATAAACC
1 TACTATATTGACTTTATTTAATTTATTTAACAGACACATACAAAAGACAACTTATATAATAAACC
* *
12142382 CAAAAACTAACAAAAAAAGGGGGGAAAATGCTATGTCAG
66 CAAAAACGAACAAAAAAAGGGGGGAAAATGCTATGCCAG
12142421 TACTATATTGACTTTATTTAATTTATTTA
1 TACTATATTGACTTTATTTAATTTATTTA
12142450 CTTTTATATT
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
104 40 0.33
105 8 0.07
106 9 0.08
107 63 0.52
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (104 bp):
TACTATATTGACTTTATTTAATTTATTTAACAGACACATACAAAAGACAACTTATATAATAAACC
CAAAAACGAACAAAAAAAGGGGGGAAAATGCTATGCCAG
Found at i:12146886 original size:20 final size:18
Alignment explanation
Indices: 12146853--12146900 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
12146843 TAACTTTACA
*
12146853 TATAAAAAAATTAAATAAAG
1 TATAATAAAATT-AA-AAAG
* *
12146873 TATAATAAACTTAAAAAT
1 TATAATAAAATTAAAAAG
12146891 TATAATAAAA
1 TATAATAAAA
12146901 ACTCAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 12 0.50
19 2 0.08
20 10 0.42
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TATAATAAAATTAAAAAG
Found at i:12151601 original size:16 final size:16
Alignment explanation
Indices: 12151580--12151621 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
12151570 ATTGCGTTGA
*
12151580 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
12151596 GAAAATTAATTAATT-
1 GAAAATTAATTAATTG
12151611 --AAATTAATTAA
1 GAAAATTAATTAA
12151622 ATAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
16 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:12151616 original size:13 final size:13
Alignment explanation
Indices: 12151598--12151627 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12151588 TTTAATTGGA
*
12151598 AAATTAATTAATT
1 AAATTAATTAAAT
12151611 AAATTAATTAAAT
1 AAATTAATTAAAT
12151624 AAAT
1 AAAT
12151628 AATATTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAATTAAAT
Found at i:12162742 original size:15 final size:16
Alignment explanation
Indices: 12162722--12162751 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12162712 ATGGCCAAAT
12162722 CACATTA-AAACATAG
1 CACATTACAAACATAG
12162737 CACATTACAAACATA
1 CACATTACAAACATA
12162752 CACCAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.20
Consensus pattern (16 bp):
CACATTACAAACATAG
Found at i:12174654 original size:25 final size:26
Alignment explanation
Indices: 12174620--12174680 Score: 106
Period size: 25 Copynumber: 2.4 Consensus size: 26
12174610 ACAAATCAGG
12174620 GTATCACAGAGATTTTCATAACAAT-
1 GTATCACAGAGATTTTCATAACAATC
12174645 GTATCACAGAGATTTTCATAACAATC
1 GTATCACAGAGATTTTCATAACAATC
*
12174671 GTATAACAGA
1 GTATCACAGA
12174681 ACAAAGGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.74
26 9 0.26
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (26 bp):
GTATCACAGAGATTTTCATAACAATC
Found at i:12183672 original size:16 final size:15
Alignment explanation
Indices: 12183650--12183688 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
12183640 AGCTACCATG
12183650 AAAAGAAAAATAGAA
1 AAAAGAAAAATAGAA
*
12183665 AGAAAGAAAAAATAGGA
1 A-AAAG-AAAAATAGAA
12183682 AAAAGAA
1 AAAAGAA
12183689 TAATCCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAATAGAA
Found at i:12183675 original size:17 final size:16
Alignment explanation
Indices: 12183650--12183688 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12183640 AGCTACCATG
12183650 AAAAG-AAAAATAGAA
1 AAAAGAAAAAATAGAA
*
12183665 AGAAAGAAAAAATAGGA
1 A-AAAGAAAAAATAGAA
12183682 AAAAGAA
1 AAAAGAA
12183689 TAATCCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 10 0.48
17 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAATAGAA
Found at i:12187141 original size:42 final size:42
Alignment explanation
Indices: 12187080--12187189 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
12187070 GTGTTTCAAG
* * *
12187080 TCAGTGAGTTACACAGCCTGGCACACCGCCGTGTGTGGTAAC
1 TCAGTGAGTTACACGGCCTGGCACACCGCCGTGTGTAGCAAC
* * **
12187122 TTAGTGAGCTACACGGCCTGGCACATGGCCGTGTGTAGCAAC
1 TCAGTGAGTTACACGGCCTGGCACACCGCCGTGTGTAGCAAC
* * *
12187164 TCAATGAGTTACATGGCCTAGCACAC
1 TCAGTGAGTTACACGGCCTGGCACAC
12187190 GGTCTGGCAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (42 bp):
TCAGTGAGTTACACGGCCTGGCACACCGCCGTGTGTAGCAAC
Found at i:12197965 original size:131 final size:131
Alignment explanation
Indices: 12197731--12197969 Score: 309
Period size: 131 Copynumber: 1.8 Consensus size: 131
12197721 TATCGATTAC
* * * * ** **
12197731 TTTAATATCATGAACACCTTTATTTGAGTTAACTGATTTAAGATCGCTACTCCACATAGTTTGCT
1 TTTAAGATCATGAACACCTTTATTTGAGTTAACTGATTTAAGATCACTACTCCAAACAACTCACT
* **
12197796 GATTTAAGCTCGCAGTTAATATCATTAAAGTTCACTGATTTAAGATCGCAACCTAAGTTCATTTG
66 GATTTAAGATCGCAACTAATATCATTAAAGTTCACTGATTTAAGATCGCAACCTAAGTTCATTTG
12197861 A
131 A
* ** *
12197862 TTTAAGATCATGAACA-ATCTTATTTGAGTTAGTTGATTTAAGATCACTACTCCAAACAACTCAT
1 TTTAAGATCATGAACACCT-TTATTTGAGTTAACTGATTTAAGATCACTACTCCAAACAACTCAC
* *
12197926 TGATTTAAGATCGCAACTGATATCATTAAGGTTCACTGATTTAA
65 TGATTTAAGATCGCAACTAATATCATTAAAGTTCACTGATTTAA
12197970 TATCACAGTT
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
130 1 0.01
131 89 0.99
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (131 bp):
TTTAAGATCATGAACACCTTTATTTGAGTTAACTGATTTAAGATCACTACTCCAAACAACTCACT
GATTTAAGATCGCAACTAATATCATTAAAGTTCACTGATTTAAGATCGCAACCTAAGTTCATTTG
A
Found at i:12197983 original size:36 final size:36
Alignment explanation
Indices: 12197943--12198012 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
12197933 AGATCGCAAC
*
12197943 TGATATCATTAAGGTTCACTGATTTAATATCACAGT
1 TGATATCATTAAGGTTCACTGATTTAAAATCACAGT
**
12197979 TGATATCATTAAGGTTCGTTGATTTAAAATCACA
1 TGATATCATTAAGGTTCACTGATTTAAAATCACA
12198013 ACCTAACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (36 bp):
TGATATCATTAAGGTTCACTGATTTAAAATCACAGT
Found at i:12198035 original size:167 final size:167
Alignment explanation
Indices: 12197794--12198143 Score: 454
Period size: 167 Copynumber: 2.1 Consensus size: 167
12197784 ACATAGTTTG
* * * * * *
12197794 CTGATTTAAGCTCGCAGTTAATATCATTAAAGTTCACTGATTTAAGATCGCAACCTAAGTTCATT
1 CTGATTTAAGATCACAGTTAATATCATTAAAGTTCACTGATTTAAAATCACAACCTAACTTCATC
* * *
12197859 TGATTTAAGATCATGAACAATCTTATTTGAGTTAGTTGATTTAAG-ATC-ACTACTCCAAACAAC
66 AGATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTT-AGTATCGA-TACTCCAAACAAC
12197922 TCATTGATTTAAGATCGCAACTGATATCATTAAGGTTCA
129 TCATTGATTTAAGATCGCAACTGATATCATTAAGGTTCA
* * * **
12197961 CTGATTTAATATCACAGTTGATATCATTAAGGTTCGTTGATTTAAAATCACAACCTAACTTCATA
1 CTGATTTAAGATCACAGTTAATATCATTAAAGTTCACTGATTTAAAATCACAACCTAACTTCAT-
*
12198026 CAG-TTTAAGATCACGAACAATTTTATTTGAGTTAATTGATTTAGTATCGATACTCCAAACAACT
65 CAGATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTTAGTATCGATACTCCAAACAACT
* * * * * *
12198090 CGTTGATTTAATATTGCAGCTGATATCATTAAGTTTTA
130 CATTGATTTAAGATCGCAACTGATATCATTAAGGTTCA
*
12198128 TTGATTTAAGATCACA
1 CTGATTTAAGATCACA
12198144 ATCTAAGTTC
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
166 2 0.01
167 153 0.97
168 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (167 bp):
CTGATTTAAGATCACAGTTAATATCATTAAAGTTCACTGATTTAAAATCACAACCTAACTTCATC
AGATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTTAGTATCGATACTCCAAACAACTC
ATTGATTTAAGATCGCAACTGATATCATTAAGGTTCA
Found at i:12198132 original size:131 final size:131
Alignment explanation
Indices: 12197962--12198307 Score: 381
Period size: 131 Copynumber: 2.6 Consensus size: 131
12197952 TAAGGTTCAC
* * * *
12197962 TGATTTAATATCACAGTTGATATCATTAAGGTTCGTTGATTTAAAATCACAACCTAACTTCATAC
1 TGATTTAATATCGCAGCTGATATCATTAAGATTCGTTGATTTAAGATCACAACCTAACTTCAT-C
*
12198027 AG-TTTAAGATCACGAACAATTTTATTTGAGTTAATTGATTT-AGTATCGATACTCCAAACAACT
65 AGATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTTAAG-ATCGATACTCCAAACAACT
12198090 CGT
129 CGT
* * ** * * **
12198093 TGATTTAATATTGCAGCTGATATCATTAAGTTTTATTGATTTAAGATCACAATCTAAGTTCATTT
1 TGATTTAATATCGCAGCTGATATCATTAAGATTCGTTGATTTAAGATCACAACCTAACTTCATCA
* * * * * * *
12198158 GATTTAAGATCATGAACAATCTTATTTGAGTTAGTTGATTTAAGATTGCTACTCCAGACAGCTCT
66 GATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTTAAGATCGATACTCCAAACAACTCG
12198223 T
131 T
* * * * * * * **
12198224 TGATTTAAGATCGGAGCTAATATCATTAAGATTCGCTGATCTAAGATCACAACCTAAGTTTATTT
1 TGATTTAATATCGCAGCTGATATCATTAAGATTCGTTGATTTAAGATCACAACCTAACTTCATCA
* *
12198289 GATTTAATATCATGAACAA
66 GATTTAAGATCACGAACAA
12198308 GCTCATCTAT
Statistics
Matches: 182, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
130 1 0.01
131 179 0.98
132 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (131 bp):
TGATTTAATATCGCAGCTGATATCATTAAGATTCGTTGATTTAAGATCACAACCTAACTTCATCA
GATTTAAGATCACGAACAATCTTATTTGAGTTAATTGATTTAAGATCGATACTCCAAACAACTCG
T
Found at i:12200677 original size:20 final size:21
Alignment explanation
Indices: 12200652--12200693 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
12200642 AATATGCTGT
*
12200652 AAAATGAAAG-TTTTTGATAG
1 AAAATGAAAGATTATTGATAG
12200672 AAAATGAAAGATTATTGATAG
1 AAAATGAAAGATTATTGATAG
12200693 A
1 A
12200694 TAAACCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (21 bp):
AAAATGAAAGATTATTGATAG
Found at i:12201414 original size:33 final size:33
Alignment explanation
Indices: 12201377--12201490 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
12201367 TACCCAAATG
* *
12201377 GTACAACTTGAAAAGGTTATGTATACTTTGTGT
1 GTACCACTTGAAAAGGTTAAGTATACTTTGTGT
* * *
12201410 GTA-CATTTGGAAAGGTTAGGTATACTTTGTGT
1 GTACCACTTGAAAAGGTTAAGTATACTTTGTGT
* **
12201442 ATACCA-TATGAAAA-GAAAAGTTATACTTTGTGT
1 GTACCACT-TGAAAAGGTTAAG-TATACTTTGTGT
*
12201475 GTACCACTTGGAAAGG
1 GTACCACTTGAAAAGG
12201491 AATGTACACC
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
32 31 0.48
33 32 0.49
34 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (33 bp):
GTACCACTTGAAAAGGTTAAGTATACTTTGTGT
Found at i:12201425 original size:32 final size:33
Alignment explanation
Indices: 12201388--12201490 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 33
12201378 TACAACTTGA
*
12201388 AAAGGTTATGTATACTTTGTGTGTA-CATTTGG
1 AAAGGTTAAGTATACTTTGTGTGTACCATTTGG
* * *
12201420 AAAGGTTAGGTATACTTTGTGTATACCATAT-G
1 AAAGGTTAAGTATACTTTGTGTGTACCATTTGG
* ** *
12201452 AAAAGAAAAGTTATACTTTGTGTGTACCACTTGG
1 AAAGGTTAAG-TATACTTTGTGTGTACCATTTGG
12201486 AAAGG
1 AAAGG
12201491 AATGTACACC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 30 0.53
33 22 0.39
34 5 0.09
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (33 bp):
AAAGGTTAAGTATACTTTGTGTGTACCATTTGG
Found at i:12212400 original size:3 final size:3
Alignment explanation
Indices: 12212392--12212439 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12212382 ATTAACCCAG
12212392 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12212440 TGAAAATTTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12212765 original size:19 final size:20
Alignment explanation
Indices: 12212741--12212815 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 20
12212731 ATCACTAAAT
12212741 TAATTTTAAAAAAGAATTA-
1 TAATTTTAAAAAAGAATTAC
* *
12212760 TAA-TTTAATTAAA-AATTAT
1 TAATTTTAA-AAAAGAATTAC
* **
12212779 TAA-TTTAAATAATTA-TAC
1 TAATTTTAAAAAAGAATTAC
*
12212797 TAATTTTAAAATAGAATTA
1 TAATTTTAAAAAAGAATTA
12212816 TTATTTAGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
18 17 0.40
19 23 0.55
20 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (20 bp):
TAATTTTAAAAAAGAATTAC
Found at i:12215013 original size:17 final size:19
Alignment explanation
Indices: 12214988--12215024 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12214978 AAACAATTAA
12214988 TTAATATT-GGAAATAAAT
1 TTAATATTGGGAAATAAAT
12215006 TTAA-ATTGGGAAATAAAT
1 TTAATATTGGGAAATAAAT
12215024 T
1 T
12215025 CGGATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAATATTGGGAAATAAAT
Found at i:12217147 original size:24 final size:24
Alignment explanation
Indices: 12217098--12217173 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
12217088 TATATAACGA
* * *
12217098 GAAGTTC-ATAAGAGCCATAATTGG
1 GAAGTTCAAAAAGAACCAT-ATCGG
* * *
12217122 GAAGTTCACAAAGAACCTTGTCGG
1 GAAGTTCAAAAAGAACCATATCGG
*
12217146 GAAGTTCAAAAAGATCCATATCGG
1 GAAGTTCAAAAAGAACCATATCGG
12217170 GAAG
1 GAAG
12217174 CTCTGGATGG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 34 0.83
25 7 0.17
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (24 bp):
GAAGTTCAAAAAGAACCATATCGG
Found at i:12224895 original size:17 final size:17
Alignment explanation
Indices: 12224875--12224912 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
12224865 AATTGTCAGG
12224875 AGTTATCACACTATCAC
1 AGTTATCACACTATCAC
12224892 AGTTATCACACTATCAC
1 AGTTATCACACTATCAC
12224909 AGTT
1 AGTT
12224913 CGTATATCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (17 bp):
AGTTATCACACTATCAC
Found at i:12234950 original size:23 final size:24
Alignment explanation
Indices: 12234900--12234952 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12234890 CTTGTAACGA
* *
12234900 GAAGCTCACACAGAGCCATTTCAG
1 GAAGCTCACAAAGAGCCATATCAG
*
12234924 GAAGCTCATAAAGAGCC-TATCAG
1 GAAGCTCACAAAGAGCCATATCAG
12234947 GAAGCT
1 GAAGCT
12234953 TATCTGAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.17
Consensus pattern (24 bp):
GAAGCTCACAAAGAGCCATATCAG
Found at i:12239245 original size:27 final size:27
Alignment explanation
Indices: 12239207--12239452 Score: 339
Period size: 27 Copynumber: 9.1 Consensus size: 27
12239197 GGTCATTATT
* * *
12239207 TGACCGTGATGCCCCTGTAGAGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* *
12239234 TGACTGTAATGCCCCTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
*
12239261 TGACCGTAATACCCCTATAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
12239288 TGACCGTAATACCCCTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * *
12239315 TGACCGTAATACCCTTATAAGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* *
12239342 TGACCGTAACACCCTTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
*
12239369 TGAACGTAATACCCCTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* *
12239396 TGACTGTAATGCCCCTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * *
12239423 TGACTGTAATACCCTTGTATGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
12239450 TGA
1 TGA
12239453 TAATTATGCC
Statistics
Matches: 197, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 197 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
TGACCGTAATACCCCTGTAGGGTAAAA
Found at i:12252151 original size:4 final size:4
Alignment explanation
Indices: 12252142--12252175 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
12252132 TTGCTTGTAC
*
12252142 ATAA ATAA ATAA ATAAA ATGA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A
12252176 GGCTCAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:12252867 original size:12 final size:12
Alignment explanation
Indices: 12252852--12252877 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12252842 AAAAAAAATC
12252852 TTATTTTATTAT
1 TTATTTTATTAT
12252864 TTATTTTATTAT
1 TTATTTTATTAT
12252876 TT
1 TT
12252878 TAATTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:12255620 original size:20 final size:21
Alignment explanation
Indices: 12255577--12255620 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
12255567 ACAGTTCACG
12255577 TATATTTCTAAAAATTAATACA
1 TATATTTCTAAAAA-TAATACA
* *
12255599 TATATTTTTAAAAA-AATTCA
1 TATATTTCTAAAAATAATACA
12255619 TA
1 TA
12255621 AAAACTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATTTCTAAAAATAATACA
Found at i:12256164 original size:18 final size:18
Alignment explanation
Indices: 12256143--12256202 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
12256133 AATCATTTAC
12256143 ATTTTAATATTATTTTCA
1 ATTTTAATATTATTTTCA
*
12256161 ATTTTATAAATT-TTTT-A
1 ATTTTA-ATATTATTTTCA
* *
12256178 ATTCTTAATAATAATTTTCT
1 ATT-TTAAT-ATTATTTTCA
12256198 ATTTT
1 ATTTT
12256203 CTATAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
17 5 0.15
18 15 0.45
19 10 0.30
20 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAATATTATTTTCA
Found at i:12256202 original size:37 final size:37
Alignment explanation
Indices: 12256138--12256229 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
12256128 TTTAAAATCA
*
12256138 TTTACATTTTAATATTATTTTCAATTTTATA-AATTT
1 TTTACATTTTAATATAATTTTCAATTTTATATAATTT
* *
12256174 TTTA-ATTCTTAATAATAATTTTCTATTTTCTATAATTT
1 TTTACATT-TTAAT-ATAATTTTCAATTTTATATAATTT
12256212 TTGTAC-TTTT-ATATAATT
1 TT-TACATTTTAATATAATT
12256230 ATTTAATGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
35 3 0.06
36 15 0.31
37 17 0.35
38 9 0.19
39 4 0.08
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.61
Consensus pattern (37 bp):
TTTACATTTTAATATAATTTTCAATTTTATATAATTT
Found at i:12256331 original size:19 final size:18
Alignment explanation
Indices: 12256138--12256336 Score: 70
Period size: 19 Copynumber: 10.3 Consensus size: 18
12256128 TTTAAAATCA
* *
12256138 TTTACATTTTAATATTATT
1 TTTATATTTT-ATATAATT
*
12256157 TTCA-ATTTTATA-AATT
1 TTTATATTTTATATAATT
12256173 TTT-TAATTCTTA-ATAATAAT
1 TTTAT-ATT-TTATATAAT--T
* *
12256193 TTTCTATTTTCTATAATT
1 TTTATATTTTATATAATT
*
12256211 TTTGTACTTTTATATAATT
1 TTTATA-TTTTATATAATT
12256230 ATTTAATGATTTTAT-TAATT
1 -TTT-AT-ATTTTATATAATT
* *
12256250 TTTAAATATTTTCTATACCGTT
1 TTT--ATATTTTATATA--ATT
*
12256272 TTCTATAATTTT-TAAAATATT
1 TT-TAT-ATTTTAT-ATA-ATT
*
12256293 TTTATTATCTTT-TATTATT
1 TTTA-TAT-TTTATATAATT
12256312 TTGTATATTTTATATAATT
1 TT-TATATTTTATATAATT
*
12256331 TCTATA
1 TTTATA
12256337 AACACCATTT
Statistics
Matches: 141, Mismatches: 16, Indels: 47
0.69 0.08 0.23
Matches are distributed among these distances:
16 5 0.04
17 7 0.05
18 24 0.17
19 40 0.28
20 32 0.23
21 20 0.14
22 12 0.09
23 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTATATTTTATATAATT
Found at i:12263318 original size:33 final size:33
Alignment explanation
Indices: 12263276--12263342 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12263266 AAAAAGTATA
12263276 ATTATAAGCAAGTATATACCAATCGAGCATAAC
1 ATTATAAGCAAGTATATACCAATCGAGCATAAC
12263309 ATTATAAGCAAGTATATACCAATCGAGCATAAC
1 ATTATAAGCAAGTATATACCAATCGAGCATAAC
12263342 A
1 A
12263343 GATATAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (33 bp):
ATTATAAGCAAGTATATACCAATCGAGCATAAC
Found at i:12270010 original size:17 final size:18
Alignment explanation
Indices: 12269990--12270027 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12269980 TTAAAAAACC
12269990 TAAAATA-ATATAAAAAT
1 TAAAATATATATAAAAAT
*
12270007 TAAAATATTATTTAAAAAT
1 TAAAATA-TATATAAAAAT
12270026 TA
1 TA
12270028 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATATATAAAAAT
Found at i:12270157 original size:26 final size:25
Alignment explanation
Indices: 12270128--12270177 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
12270118 ATAATCTTTT
*
12270128 AAATA-ATATTATACTTTTATAAATTC
1 AAATACATA-TATAATTTTA-AAATTC
12270154 AAATACATATATAATTTTAAAATT
1 AAATACATATATAATTTTAAAATT
12270178 TTACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 14 0.64
27 3 0.14
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATACATATATAATTTTAAAATTC
Found at i:12279177 original size:25 final size:25
Alignment explanation
Indices: 12279149--12279205 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
12279139 CCGTTATTTA
* *
12279149 GCTCTTATGAGCATCCTGTTATATG
1 GCTCTTATAAGCATCCTGATATATG
* * * *
12279174 GCTCTCATAAGCTTTCTGATATTTG
1 GCTCTTATAAGCATCCTGATATATG
12279199 GCTCTTA
1 GCTCTTA
12279206 CAAGTTTCCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (25 bp):
GCTCTTATAAGCATCCTGATATATG
Found at i:12282151 original size:43 final size:43
Alignment explanation
Indices: 12282080--12282181 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
12282070 GTGTTGATAT
* * * *
12282080 TATTGTGATATATTATATTTTAGAAATTTGATTCTTAAT-AGGA
1 TATTATGAGATATTATATCTTAGAAATTTGATTCCTAATGA-GA
* *
12282123 TATTATGAGATATTATCTCTTAGTAATTTGATTCCTAATGAGA
1 TATTATGAGATATTATATCTTAGAAATTTGATTCCTAATGAGA
12282166 TATTAT-AGAATATTAT
1 TATTATGAG-ATATTAT
12282182 TATAAGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 48 0.94
44 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (43 bp):
TATTATGAGATATTATATCTTAGAAATTTGATTCCTAATGAGA
Found at i:12282673 original size:6 final size:6
Alignment explanation
Indices: 12282664--12282706 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
12282654 TATTTCGTAG
* * *
12282664 TTTTAA TTTTAA TTTTAA CTTTAA CTTTAG TCTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T-TTTAA TTTTAA
12282707 AATCCCCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (6 bp):
TTTTAA
Found at i:12287750 original size:39 final size:40
Alignment explanation
Indices: 12287655--12287917 Score: 301
Period size: 40 Copynumber: 6.7 Consensus size: 40
12287645 TTGAATGATG
*
12287655 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
12287693 ATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
12287734 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
12287773 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
12287812 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
12287852 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
12287891 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
12287918 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 15, Indels: 17
0.86 0.06 0.07
Matches are distributed among these distances:
39 90 0.45
40 99 0.50
41 10 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:12287849 original size:79 final size:80
Alignment explanation
Indices: 12287655--12287917 Score: 322
Period size: 79 Copynumber: 3.3 Consensus size: 80
12287645 TTGAATGATG
* * * *
12287655 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCCGGGCTAAGACCCGAAGGCAT
* * *
12287717 TTGTACGAGATACTAAT
64 TTGTGCGAGTTACTAAA
* *
12287734 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAG-CCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGACCCGAAGGCATTT
12287797 GTGCGAGTTACTAAA
66 GTGCGAGTTACTAAA
* * * *
12287812 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGACCCGAAGGCATTT
*
12287877 GTGCGAATTACTATAA
66 GTGCGAGTTACTA-AA
*
12287893 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
12287918 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
78 43 0.27
79 59 0.37
80 57 0.35
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:12287935 original size:80 final size:77
Alignment explanation
Indices: 12287656--12287950 Score: 262
Period size: 79 Copynumber: 3.7 Consensus size: 77
12287646 TGAATGATGT
* * **
12287656 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTA-ATCCGGGTTAAG-TCCCGAAGGCATT
* *
12287718 TGTACGAGA-TACTAATT
62 TGTGCGA-ATTACTAA-A
* * *
12287735 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAG-CCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACTAA-TCCGGGTTAAGTCCCGAAGGCATTTG
*
12287798 TGCGAGTTACTAAA
64 TGCGAATTACTAAA
* *
12287812 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACT-AATCCGGGTTAAGTCCCGAAGGCATTT
12287877 GTGCGAATTACTATAA
63 GTGCGAATTACTA-AA
* ** * *
12287893 CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTA-ATCCGGGTTAAGTCCCGAAGG
12287951 TACGTGATTT
Statistics
Matches: 183, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
78 42 0.23
79 73 0.40
80 66 0.36
81 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTAATCCGGGTTAAGTCCCGAAGGCATTTGTG
CGAATTACTAAA
Found at i:12289487 original size:15 final size:16
Alignment explanation
Indices: 12289461--12289495 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12289451 TTGGAGTAAT
12289461 TCCTTACTCCCTATTC
1 TCCTTACTCCCTATTC
*
12289477 TCCTT-CTCCCTTTTC
1 TCCTTACTCCCTATTC
12289492 TCCT
1 TCCT
12289496 CTTCTAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.06, C:0.46, G:0.00, T:0.49
Consensus pattern (16 bp):
TCCTTACTCCCTATTC
Found at i:12316720 original size:26 final size:26
Alignment explanation
Indices: 12316670--12316719 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
12316660 GGTTTCTTGG
12316670 TTTTTTTTTTTGGGGTTAGGTTTTTC
1 TTTTTTTTTTTGGGGTTAGGTTTTTC
12316696 TTTTTTTTTTT-GGGTTAGGTTTTT
1 TTTTTTTTTTTGGGGTTAGGTTTTT
12316720 TTTGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.72
Consensus pattern (26 bp):
TTTTTTTTTTTGGGGTTAGGTTTTTC
Found at i:12321687 original size:15 final size:15
Alignment explanation
Indices: 12321667--12321732 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
12321657 GATTGTAAAC
12321667 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
12321682 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
12321701 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
12321716 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
12321729 ATTT
1 ATTT
12321733 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:12321782 original size:16 final size:16
Alignment explanation
Indices: 12321751--12321787 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12321741 ATGTGAATAA
12321751 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
12321767 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
12321783 TATTA
1 TATTA
12321788 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:12321839 original size:22 final size:22
Alignment explanation
Indices: 12321799--12321854 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12321789 AATAAAATTG
*
12321799 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
12321819 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
12321841 TATTAATAATTTAT
1 AAATAATAAATTAT
12321855 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:12327858 original size:46 final size:46
Alignment explanation
Indices: 12327791--12328053 Score: 245
Period size: 46 Copynumber: 5.7 Consensus size: 46
12327781 TGTAACCCGC
* *
12327791 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCATTTACAT
** * *
12327837 CCATAAGTGAACTCAAACTCAACTCAACAAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-G-C-ATTTACAT
* * * *
12327887 CTC-TCA---AACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCATTTACAT
*
12327930 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-G-C-ATTTACAT
* * * *
12327980 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCATTTACAT
12328023 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
12328054 TTCGGATGCC
Statistics
Matches: 174, Mismatches: 25, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.01
43 17 0.10
44 2 0.01
46 82 0.47
47 50 0.29
48 1 0.01
49 2 0.01
50 16 0.09
51 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCATTTACAT
Found at i:12327904 original size:93 final size:93
Alignment explanation
Indices: 12327800--12328063 Score: 438
Period size: 93 Copynumber: 2.8 Consensus size: 93
12327790 CCCATAAGTG
* * * ** **
12327800 AACTCGGACTCAACTCAACGAGCTCGAGCGTTTGCATCCATAAGTGAACTCAAACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
*
12327865 AAGCTCGGATGCCTAGTTACATCTCTCA
66 GAGCTCGGATGCCTAGTTACATCTCTCA
12327893 AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
*
12327958 GAGCTCGGATGCCTAGTTACATCTCTCG
66 GAGCTCGGATGCCTAGTTACATCTCTCA
12327986 AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
*
12328051 GAGTTCGGATGCC
66 GAGCTCGGATGCC
12328064 CAAATATCCT
Statistics
Matches: 161, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 161 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTCA
Found at i:12327910 original size:47 final size:47
Alignment explanation
Indices: 12327853--12328007 Score: 178
Period size: 47 Copynumber: 3.3 Consensus size: 47
12327843 GTGAACTCAA
*
12327853 ACTCAACTCAACAAGCTCGGATGCCTAGTTACATCTCTCAAACTCGG
1 ACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCAAACTCGG
* * *
12327900 ACTCAACTCAACGAGTTC-GA--AC-A-TTCACATC-CATAAGTGAACTCGG
1 ACTCAACTCAACGAGCTCGGATGCCTAGTT-ACATCTC-TCA---AACTCGG
*
12327946 ACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGG
1 ACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCAAACTCGG
12327993 ACTCAACTCAACGAG
1 ACTCAACTCAACGAG
12328008 TTCGAACATT
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
42 3 0.03
43 8 0.09
44 1 0.01
46 26 0.29
47 40 0.45
49 1 0.01
50 7 0.08
51 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (47 bp):
ACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCAAACTCGG
Found at i:12329690 original size:53 final size:53
Alignment explanation
Indices: 12329602--12329705 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 53
12329592 CCACGACACT
* * * *
12329602 AAAGAAGGCCATACTATGTAAGATCATAACTGGTGGGTTATGGTATCATATGG
1 AAAGAAGACCATACTATGTAAGACCATAACCGGTGGGTTATGGCATCATATGG
* * * *
12329655 AAAGAAGACCATATTGTGTAAGACCCTAACCGGTGGGTTCTGGCATCATAT
1 AAAGAAGACCATACTATGTAAGACCATAACCGGTGGGTTATGGCATCATAT
12329706 AAGGAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (53 bp):
AAAGAAGACCATACTATGTAAGACCATAACCGGTGGGTTATGGCATCATATGG
Found at i:12329923 original size:61 final size:61
Alignment explanation
Indices: 12329826--12329957 Score: 192
Period size: 61 Copynumber: 2.2 Consensus size: 61
12329816 CCAAGAGAAT
* ** *
12329826 GAAAGCCGTTGTGGTGAGTACTGAATGTAAAGGATAGCCTTTATGGCACAACTTTGGACAG
1 GAAAGCCTTTGTGGTGAGTACCAAATGTAAAGGATAGCCTTTATGGCACAACTTTGGACAA
* * * *
12329887 GAAAGCCTTTGTGGTGAGTACCAAATTTAAATGATAGCCTTTGTGGCACAACTTTGGATAA
1 GAAAGCCTTTGTGGTGAGTACCAAATGTAAAGGATAGCCTTTATGGCACAACTTTGGACAA
12329948 GAAAGCCTTT
1 GAAAGCCTTT
12329958 ATGGCACAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (61 bp):
GAAAGCCTTTGTGGTGAGTACCAAATGTAAAGGATAGCCTTTATGGCACAACTTTGGACAA
Found at i:12329990 original size:28 final size:29
Alignment explanation
Indices: 12329922--12329990 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
12329912 TTTAAATGAT
12329922 AGCCTTTGTGGCACAACTTTGGATAAGAA
1 AGCCTTTGTGGCACAACTTTGGATAAGAA
*
12329951 AGCCTTTATGGCACAACTTTGGAT-AGAA
1 AGCCTTTGTGGCACAACTTTGGATAAGAA
12329979 AGCCTTTGTGGC
1 AGCCTTTGTGGC
12329991 TAGTACTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (29 bp):
AGCCTTTGTGGCACAACTTTGGATAAGAA
Found at i:12330017 original size:89 final size:90
Alignment explanation
Indices: 12329861--12330048 Score: 238
Period size: 89 Copynumber: 2.1 Consensus size: 90
12329851 TGTAAAGGAT
* ** * *
12329861 AGCCTTTATGGCACAACTTTGGACAGGAAAGCCTTTGTGGTGAGTACCAAATTTAAATGATAGCC
1 AGCCTTTATGGCACAACTTTGGACAGGAAAGCCTTTGTGGTGAGTACCAAATGTAAAAAACAACC
* *
12329926 TTTGTGGCACAACTT-TGGATAAGAA
66 TTTGTGGCACAA-TTCTAGACAAGAA
* **
12329951 AGCCTTTATGGCACAACTTTGGATA-GAAAGCCTTTGTGGCT-AGTACTGAATGTAAAAAACAAC
1 AGCCTTTATGGCACAACTTTGGACAGGAAAGCCTTTGTGG-TGAGTACCAAATGTAAAAAACAAC
*
12330014 CTTTGTGGCACAATTCTAGACAGGAA
65 CTTTGTGGCACAATTCTAGACAAGAA
12330040 AGCCTTTAT
1 AGCCTTTAT
12330049 AGCGAGTACT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 2 0.02
89 58 0.68
90 25 0.29
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (90 bp):
AGCCTTTATGGCACAACTTTGGACAGGAAAGCCTTTGTGGTGAGTACCAAATGTAAAAAACAACC
TTTGTGGCACAATTCTAGACAAGAA
Found at i:12330025 original size:60 final size:61
Alignment explanation
Indices: 12329953--12330067 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
12329943 GATAAGAAAG
* * * * *
12329953 CCTTTATGGCACAACTT-TGGATA-GAAAGCCTTTGTGGCTAGTACTGAATGTAAAAAACAA
1 CCTTTATGGCACAA-TTCTAGACAGGAAAGCCTTTATAGCGAGTACTGAATGTAAAAAACAA
*
12330013 CCTTTGTGGCACAATTCTAGACAGGAAAGCCTTTATAGCGAGTACTGAATGTAAA
1 CCTTTATGGCACAATTCTAGACAGGAAAGCCTTTATAGCGAGTACTGAATGTAAA
12330068 GGAAAGTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.04
60 17 0.36
61 28 0.60
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (61 bp):
CCTTTATGGCACAATTCTAGACAGGAAAGCCTTTATAGCGAGTACTGAATGTAAAAAACAA
Found at i:12330776 original size:8 final size:8
Alignment explanation
Indices: 12330753--12330787 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
12330743 AAGATTTTTT
12330753 TTATATTTA
1 TTATA-TTA
*
12330762 GTATATTA
1 TTATATTA
12330770 TTATATTA
1 TTATATTA
12330778 TTATATTA
1 TTATATTA
12330786 TT
1 TT
12330788 TTATAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTATATTA
Found at i:12330778 original size:5 final size:5
Alignment explanation
Indices: 12330753--12330850 Score: 74
Period size: 5 Copynumber: 19.2 Consensus size: 5
12330743 AAGATTTTTT
* * * * * *
12330753 TTATA TT-TA GTATA TTAT- TATATTA TTATA TTATT TTATA ATAAA GATATT
1 TTATA TTATA TTATA TTATA T-TA-TA TTATA TTATA TTATA TTATA -TTATA
* *
12330804 TTATG TTTTA ATTATA TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
12330851 AAACTAAAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
4 4 0.05
5 59 0.80
6 10 0.14
7 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:12342932 original size:26 final size:26
Alignment explanation
Indices: 12342903--12342960 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
12342893 CCCGTTATAT
*
12342903 GGCTCTTCATAAGCTTCTTGATTAAA
1 GGCTCTTCATAAGCTTCCTGATTAAA
** * *
12342929 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCATAAGCTTCCTGATTAAA
12342955 GGCTCT
1 GGCTCT
12342961 CTGGAGCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (26 bp):
GGCTCTTCATAAGCTTCCTGATTAAA
Found at i:12343041 original size:24 final size:24
Alignment explanation
Indices: 12342974--12343041 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
12342964 GAGCTTTCTA
*
12342974 ATAATGGCTCGTTTGAA-CTTCCCG
1 ATAATGGCTC-TTCGAAGCTTCCCG
* *
12342998 ATATATGGCT-ATCTGGAGCTTCCCG
1 ATA-ATGGCTCTTC-GAAGCTTCCCG
*
12343023 TTAATGGCTCTTCGAAGCT
1 ATAATGGCTCTTCGAAGCT
12343042 ACCTATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 17 0.50
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (24 bp):
ATAATGGCTCTTCGAAGCTTCCCG
Found at i:12347069 original size:5 final size:5
Alignment explanation
Indices: 12347059--12347089 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
12347049 TTAAGTATAT
12347059 TATTA TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
12347090 TATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:12347095 original size:15 final size:16
Alignment explanation
Indices: 12347056--12347096 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
12347046 TAATTAAGTA
12347056 TATTATTATATTATAT
1 TATTATTATATTATAT
12347072 TA-TATTATATTATAT
1 TATTATTATATTATAT
12347087 TATTA-TATAT
1 TATTATTATAT
12347097 AAAAGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTATATTATAT
Found at i:12348276 original size:45 final size:45
Alignment explanation
Indices: 12348171--12348269 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
12348161 CGACTACTGT
* * *
12348171 TACTGTTACCATTACTGTTACCGATTCGACACTTTGTGTGTTGAA
1 TACTGTTACAATTACTATTACAGATTCGACACTTTGTGTGTTGAA
*
12348216 TATTGTTACAATTACTATTACAGATTC-AGCACTTTGTGTGTTGAA
1 TACTGTTACAATTACTATTACAGATTCGA-CACTTTGTGTGTTGAA
12348261 TACTGTTAC
1 TACTGTTAC
12348270 TGTTACTGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (45 bp):
TACTGTTACAATTACTATTACAGATTCGACACTTTGTGTGTTGAA
Found at i:12348292 original size:18 final size:18
Alignment explanation
Indices: 12348261--12348295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12348251 GTGTGTTGAA
* *
12348261 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
12348279 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
12348296 ATTACTGATT
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:12349276 original size:4 final size:4
Alignment explanation
Indices: 12349269--12349301 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
12349259 AAAAAATATA
12349269 AAAT AAAT -AAT AAAT -AAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
12349302 AATTGGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12349280 original size:7 final size:7
Alignment explanation
Indices: 12349270--12349304 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
12349260 AAAAATATAA
12349270 AATAAAT
1 AATAAAT
12349277 AATAAAT
1 AATAAAT
12349284 AATAAAT
1 AATAAAT
12349291 AAATAAAT
1 -AATAAAT
12349299 AA-AAAT
1 AATAAAT
12349305 TGGAGTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 4 0.15
7 16 0.59
8 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:12353186 original size:26 final size:26
Alignment explanation
Indices: 12353157--12353214 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
12353147 CCCGTTATAT
*
12353157 GGCTCTTCGTGAACTTCCTTATTAAA
1 GGCTCTTCGTGAACTTCCTAATTAAA
* * *
12353183 GGCTCTTTGTGAGCTTCCTAATTAAC
1 GGCTCTTCGTGAACTTCCTAATTAAA
12353209 GGCTCT
1 GGCTCT
12353215 CCAGAGCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (26 bp):
GGCTCTTCGTGAACTTCCTAATTAAA
Found at i:12353284 original size:24 final size:24
Alignment explanation
Indices: 12353257--12353303 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12353247 TTCCGATATG
*
12353257 TGGCTATTCGGAGCTTCCTGTTAA
1 TGGCTATTCGGAGCTACCTGTTAA
*
12353281 TGGCTCTTCGGAGCTACCTGTTA
1 TGGCTATTCGGAGCTACCTGTTA
12353304 TTGACTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (24 bp):
TGGCTATTCGGAGCTACCTGTTAA
Found at i:12353930 original size:52 final size:52
Alignment explanation
Indices: 12353862--12353962 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
12353852 ACTTGGTCGA
*
12353862 AGTCACATCACACTATCCTTTAGACTTTTCGGTATATAAAGCAAACTAAATG
1 AGTCACATCACACTATCCCTTAGACTTTTCGGTATATAAAGCAAACTAAATG
12353914 AGTCACATCACACTATCCCTTAGACTTTTCGGTATATAAAGCAAACTAA
1 AGTCACATCACACTATCCCTTAGACTTTTCGGTATATAAAGCAAACTAA
12353963 CTTTTGGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (52 bp):
AGTCACATCACACTATCCCTTAGACTTTTCGGTATATAAAGCAAACTAAATG
Found at i:12354378 original size:29 final size:29
Alignment explanation
Indices: 12354333--12354388 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12354323 ATGCCCTCAG
* * *
12354333 CCCGTGTGCAACCCTGACTTTAACCTTAT
1 CCCGTGTACAACACTGACTTAAACCTTAT
12354362 CCCGTGTACAACACTGACTTAAACCTT
1 CCCGTGTACAACACTGACTTAAACCTT
12354389 TAGGTGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.34, G:0.12, T:0.29
Consensus pattern (29 bp):
CCCGTGTACAACACTGACTTAAACCTTAT
Found at i:12359314 original size:31 final size:29
Alignment explanation
Indices: 12359266--12359348 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 29
12359256 ATATCAAAAT
* *
12359266 TATACATGATC-TATGATTTAATGTATAATTG
1 TATACATGAACAT-TGATTTAATG--CAATTG
* *
12359297 TATACATGAACATTGATTTTATGCAATTT
1 TATACATGAACATTGATTTAATGCAATTG
12359326 TATACATGAA-ATTTTGATTTAAT
1 TATACATGAACA--TTGATTTAAT
12359349 CTACTTATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.02
29 14 0.32
30 9 0.20
31 19 0.43
32 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (29 bp):
TATACATGAACATTGATTTAATGCAATTG
Found at i:12360277 original size:21 final size:21
Alignment explanation
Indices: 12360212--12360277 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
12360202 AGCTGTTGCT
12360212 ACCATTATCAATATGGTATCG
1 ACCATTATCAATATGGTATCG
* ** *
12360233 ACCACTAT-GTTAT-GTACTCA
1 ACCATTATCAATATGGTA-TCG
12360253 ACCATTATCAATATGGTATCG
1 ACCATTATCAATATGGTATCG
12360274 ACCA
1 ACCA
12360278 CTATGTTACG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
21 16 0.47
22 3 0.09
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (21 bp):
ACCATTATCAATATGGTATCG
Found at i:12361568 original size:28 final size:28
Alignment explanation
Indices: 12361528--12361585 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12361518 ATGTATTGAC
12361528 ATAGTTCGCATGTCAATACAGCTCACAG
1 ATAGTTCGCATGTCAATACAGCTCACAG
*
12361556 ATAGTTCGCATGTCAATACAGCTCATAG
1 ATAGTTCGCATGTCAATACAGCTCACAG
12361584 AT
1 AT
12361586 TTACACAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (28 bp):
ATAGTTCGCATGTCAATACAGCTCACAG
Found at i:12361658 original size:26 final size:26
Alignment explanation
Indices: 12361606--12361658 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12361596 TGCATATTAT
*
12361606 TACTTTATAGGCTAGCTCACACTTAGA
1 TACTTTATAGGC-AGCTCACACATAGA
*
12361633 TACTTTATAGAG-AGCTCGCACATAGA
1 TACTTTATAG-GCAGCTCACACATAGA
12361659 CACCATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 12 0.52
27 10 0.43
28 1 0.04
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (26 bp):
TACTTTATAGGCAGCTCACACATAGA
Found at i:12361843 original size:17 final size:17
Alignment explanation
Indices: 12361823--12361885 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
12361813 ACATAAATCG
*
12361823 CATATAAACATAGCTCA
1 CATATAAACACAGCTCA
* * *
12361840 CATATAGAGACAGCTCG
1 CATATAAACACAGCTCA
* * *
12361857 CATATAAACGCAACTCG
1 CATATAAACACAGCTCA
12361874 CATATAAACACA
1 CATATAAACACA
12361886 CACACACACA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (17 bp):
CATATAAACACAGCTCA
Found at i:12361888 original size:2 final size:2
Alignment explanation
Indices: 12361881--12361909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12361871 TCGCATATAA
12361881 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12361910 TATATATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12365182 original size:15 final size:16
Alignment explanation
Indices: 12365162--12365191 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12365152 GAAAATTGCC
12365162 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
12365177 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
12365192 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:12370312 original size:21 final size:21
Alignment explanation
Indices: 12370286--12370327 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12370276 AAGATATGAA
12370286 ACACCGCTACACATAAATCCC
1 ACACCGCTACACATAAATCCC
12370307 ACACCGCTACACATAAATCCC
1 ACACCGCTACACATAAATCCC
12370328 CCACTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.43, G:0.05, T:0.14
Consensus pattern (21 bp):
ACACCGCTACACATAAATCCC
Found at i:12375008 original size:13 final size:13
Alignment explanation
Indices: 12374992--12375039 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
12374982 TATATTATAA
*
12374992 AAATATAAAAACT
1 AAATATAAAAATT
*
12375005 AAATCATATCAAATT
1 AAAT-ATA-AAAATT
12375020 AAAATATAAAAATT
1 -AAATATAAAAATT
12375034 AAATAT
1 AAATAT
12375040 TATAGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 7 0.24
16 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAAAATT
Found at i:12379566 original size:94 final size:94
Alignment explanation
Indices: 12379468--12379641 Score: 231
Period size: 94 Copynumber: 1.9 Consensus size: 94
12379458 CATCGAGGCC
* * * * * * * *
12379468 GATGCATGTCCCAGACATGTCTTATACTGGCACTTACCTCTACGCCGATGCCATGTCCCAGACGT
1 GATGCATGTCCCAAACACGTCTTAGACTAGCACTCACCTCAACGCCGATGCCATGCCCCAGACAT
12379533 GGTCTTATACGGGCTATCATGATGCGGCT
66 GGTCTTATACGGGCTATCATGATGCGGCT
* * * *
12379562 GATGCATGTCCCAAACACGTCTTAGACTAGCCCTCGCCTCAATGTCGATGCCATGCCCCAGACAT
1 GATGCATGTCCCAAACACGTCTTAGACTAGCACTCACCTCAACGCCGATGCCATGCCCCAGACAT
*
12379627 GGTCTTATACTGGCT
66 GGTCTTATACGGGCT
12379642 CTCACATAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
94 67 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (94 bp):
GATGCATGTCCCAAACACGTCTTAGACTAGCACTCACCTCAACGCCGATGCCATGCCCCAGACAT
GGTCTTATACGGGCTATCATGATGCGGCT
Found at i:12392161 original size:46 final size:44
Alignment explanation
Indices: 12392069--12392189 Score: 172
Period size: 46 Copynumber: 2.7 Consensus size: 44
12392059 GTGTTGAAAC
*
12392069 CATGTCCTAGACATGGTCTTACACTGACACATCTCGTAGCCGATG
1 CATGTCCTAGACAT-GTCTTACACTGGCACATCTCGTAGCCGATG
*
12392114 CATGTCCTAGACATGTCTTACACTGGCTTACATCTCG-AGGTCGATG
1 CATGTCCTAGACATGTCTTACACTGGC--ACATCTCGTA-GCCGATG
*
12392160 CATGTCCCAGACATGTCTTACACTGGCACA
1 CATGTCCTAGACATGTCTTACACTGGCACA
12392190 CAAATAACCC
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
44 15 0.21
45 15 0.21
46 40 0.57
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (44 bp):
CATGTCCTAGACATGTCTTACACTGGCACATCTCGTAGCCGATG
Found at i:12403149 original size:19 final size:19
Alignment explanation
Indices: 12403125--12403164 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12403115 ATTAATTTTG
12403125 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
12403144 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
12403163 AT
1 AT
12403165 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:12406269 original size:94 final size:94
Alignment explanation
Indices: 12406147--12406318 Score: 249
Period size: 94 Copynumber: 1.8 Consensus size: 94
12406137 CCACAGTATA
* *
12406147 AGAGCCAGTGTAAGACATGTCTGAGACATGCATCGGCC-C-CGAGATATTTAAGCCAGTGTAAGA
1 AGAGCCAGTGTAAGACATGTCTGAGACATGCATCAGCCTCACGAGATA--CAAGCCAGTGTAAGA
*
12406210 CATGTCTGGGACATGCATCAACATTGAAGCG
64 CATGCCTGGGACATGCATCAACATTGAAGCG
* * * *
12406241 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCACGAGATACAAGCTAGTGTAAGACC
1 AGAGCCAGTGTAAGACATGTCTGAGACATGCATCAGCCTCACGAGATACAAGCCAGTGTAAGACA
12406306 TGCCTGGGACATG
66 TGCCTGGGACATG
12406319 GCGTCAGCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 61 0.88
95 1 0.01
96 7 0.10
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (94 bp):
AGAGCCAGTGTAAGACATGTCTGAGACATGCATCAGCCTCACGAGATACAAGCCAGTGTAAGACA
TGCCTGGGACATGCATCAACATTGAAGCG
Found at i:12406314 original size:48 final size:47
Alignment explanation
Indices: 12406104--12406318 Score: 199
Period size: 46 Copynumber: 4.6 Consensus size: 47
12406094 TCATTTGTGT
* * *
12406104 GCTAGTGTAAGACATGTCTAGAACATGCATCAGCCAC-AGTATA-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCCCGAG-ATACAGA
* * * *
12406150 GCCAGTGTAAGACATGTCTGAGACATGCATCGGCCCCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCCCGAGATA--CAGA
* * *** *
12406198 GCCAGTGTAAGACATGTCTGGGACATGCATCAACATTGA-A-GCGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCCCGAGATAC-AGA
12406244 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCACGAGATACA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCC-C-CGAGATACAGA
* *
12406292 GCTAGTGTAAGACCTGCCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
12406319 GCGTCAGCTT
Statistics
Matches: 137, Mismatches: 22, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
45 1 0.01
46 67 0.49
47 3 0.02
48 62 0.45
49 3 0.02
50 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCCCGAGATACAGA
Found at i:12413732 original size:48 final size:46
Alignment explanation
Indices: 12413612--12413733 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 46
12413602 TTTGTGTACT
* *
12413612 AGTGTAAGACATGTTTGGGACATGCATCAACCACAGTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCC
** * * *
12413658 AGCATAAGACACGTCTGGGACATGCATCAACCCCAAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAACCAC-AG-TA-TGAGAGCC
*
12413706 AGTGTAAGACATGTCTAGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
12413734 GGCATTAAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 29 0.47
47 2 0.03
48 29 0.47
49 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCC
Found at i:12414315 original size:25 final size:25
Alignment explanation
Indices: 12414286--12414335 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12414276 GGATCATCAA
*
12414286 ACGTCGGAGGCATCGATCACACTAT
1 ACGTCAGAGGCATCGATCACACTAT
12414311 ACGTCAGAGGCATCGATCACACTAT
1 ACGTCAGAGGCATCGATCACACTAT
12414336 CATCCGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (25 bp):
ACGTCAGAGGCATCGATCACACTAT
Found at i:12419167 original size:32 final size:32
Alignment explanation
Indices: 12419118--12419180 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
12419108 TATATGTTTA
12419118 TGAAAATATGATATTCTGATTC-GAAATATGTC
1 TGAAAATATGATATTCTG-TTCAGAAATATGTC
* *
12419150 TGAAAATATGGCT-TTCTGTTCAGATATATGT
1 TGAAAATAT-GATATTCTGTTCAGAAATATGT
12419181 TTATGGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 22 0.81
33 2 0.07
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (32 bp):
TGAAAATATGATATTCTGTTCAGAAATATGTC
Found at i:12420142 original size:11 final size:11
Alignment explanation
Indices: 12420126--12420150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12420116 TTATTTGTAT
12420126 ATAAAAATTAA
1 ATAAAAATTAA
12420137 ATAAAAATTAA
1 ATAAAAATTAA
12420148 ATA
1 ATA
12420151 TGATATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAAATTAA
Found at i:12421631 original size:23 final size:24
Alignment explanation
Indices: 12421603--12421648 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12421593 TAATTTCTAC
12421603 ATTTTAATTTGATAAT-ATATTAT
1 ATTTTAATTTGATAATCATATTAT
* *
12421626 ATTTTATTTTTATAATCATATTA
1 ATTTTAATTTGATAATCATATTA
12421649 GTTAGTGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTTTAATTTGATAATCATATTAT
Found at i:12425372 original size:59 final size:59
Alignment explanation
Indices: 12425280--12425397 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
12425270 GTTTTGCAGA
*
12425280 TTAATGCTTAGTATGTTCAAATGGAATTTACAACACTTACCTTGCTCATAGGTAAGCAT
1 TTAATGCTTAGTATGTTCAAATGAAATTTACAACACTTACCTTGCTCATAGGTAAGCAT
* *
12425339 TTAATGCTTTGTATGTTCAAATGAAATTTACAACACTTACCTTGCTCATAGGTGAGCAT
1 TTAATGCTTAGTATGTTCAAATGAAATTTACAACACTTACCTTGCTCATAGGTAAGCAT
12425398 GTTACTACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (59 bp):
TTAATGCTTAGTATGTTCAAATGAAATTTACAACACTTACCTTGCTCATAGGTAAGCAT
Found at i:12435633 original size:22 final size:22
Alignment explanation
Indices: 12435608--12435655 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12435598 TAATTAAATT
*
12435608 AAGTTAAAATAATAATAA-TAGA
1 AAGTTAAAA-AATAAAAATTAGA
*
12435630 AAGTTAAAACATAAAAATTAGA
1 AAGTTAAAAAATAAAAATTAGA
12435652 AAGT
1 AAGT
12435656 CATCATCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.25
Consensus pattern (22 bp):
AAGTTAAAAAATAAAAATTAGA
Found at i:12439768 original size:15 final size:15
Alignment explanation
Indices: 12439744--12439773 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12439734 ACTAATGTAT
12439744 TTTTGAGGTTTCGGC
1 TTTTGAGGTTTCGGC
*
12439759 TTTTGTGGTTTCGGC
1 TTTTGAGGTTTCGGC
12439774 ACAAGTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTTGAGGTTTCGGC
Found at i:12440427 original size:20 final size:20
Alignment explanation
Indices: 12440404--12440441 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12440394 CACATCCAAA
* *
12440404 TACAAAATTTTTAAAATCTT
1 TACAAAATATTGAAAATCTT
12440424 TACAAAATATTGAAAATC
1 TACAAAATATTGAAAATC
12440442 GCGAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (20 bp):
TACAAAATATTGAAAATCTT
Found at i:12446691 original size:6 final size:6
Alignment explanation
Indices: 12446680--12446722 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
12446670 AAAGCAACAT
* *
12446680 AATAAA AATAAA AGTAAAA AATAGA AATAAAA AATAAA AATAA
1 AATAAA AATAAA AAT-AAA AATAAA AAT-AAA AATAAA AATAA
12446723 CATAAGTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:12446720 original size:13 final size:13
Alignment explanation
Indices: 12446683--12446722 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
12446673 GCAACATAAT
*
12446683 AAAAATAAAAGTA
1 AAAAATAAAAATA
*
12446696 AAAAATAGAAATA
1 AAAAATAAAAATA
12446709 AAAAATAAAAATA
1 AAAAATAAAAATA
12446722 A
1 A
12446723 CATAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:12448282 original size:3 final size:3
Alignment explanation
Indices: 12448258--12448302 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
12448248 AATCACTAAT
* *
12448258 TAA TAA TGAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12448303 ACTAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12454841 original size:22 final size:23
Alignment explanation
Indices: 12454798--12454847 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
12454788 AAATAAAAGA
*
12454798 AAAATTAGTAATTGAAATAAAAAC
1 AAAATTAG-AATTGAAACAAAAAC
* *
12454822 AAAATTA-AATTGCAACAAAAAT
1 AAAATTAGAATTGAAACAAAAAC
12454844 AAAA
1 AAAA
12454848 ATGGCTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.70
24 7 0.30
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAATTAGAATTGAAACAAAAAC
Found at i:12456617 original size:17 final size:18
Alignment explanation
Indices: 12456597--12456630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12456587 AAGTGAATTG
12456597 AAATTG-AGAAATTAAAT
1 AAATTGTAGAAATTAAAT
12456614 AAATTGTAGAAATTAAA
1 AAATTGTAGAAATTAAA
12456631 AAGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (18 bp):
AAATTGTAGAAATTAAAT
Found at i:12457343 original size:10 final size:10
Alignment explanation
Indices: 12457324--12457373 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
12457314 TGAAATTCTA
12457324 AAAGATAAAT
1 AAAGATAAAT
12457334 ACAA-ATAAAT
1 A-AAGATAAAT
12457344 AAAGATAAAT
1 AAAGATAAAT
12457354 AAAGATAAAT
1 AAAGATAAAT
12457364 GAAA-ATAAAT
1 -AAAGATAAAT
12457374 CCTAGAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:12463710 original size:26 final size:26
Alignment explanation
Indices: 12463681--12463761 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
12463671 GTGAGAACAC
12463681 ATGTGTAGTATTATGTGCAGGCTACT
1 ATGTGTAGTATTATGTGCAGGCTACT
* * *
12463707 ATGTGT-TTATGATGGTTGTAGG-TCAC-
1 ATGTGTAGTATTAT-G-TGCAGGCT-ACT
* *
12463733 ATGTGTAGTACTAAGTGCAGGCTACT
1 ATGTGTAGTATTATGTGCAGGCTACT
12463759 ATG
1 ATG
12463762 CGTACCCGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
25 12 0.29
26 19 0.46
27 10 0.24
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.37
Consensus pattern (26 bp):
ATGTGTAGTATTATGTGCAGGCTACT
Found at i:12463868 original size:101 final size:103
Alignment explanation
Indices: 12463682--12463868 Score: 229
Period size: 101 Copynumber: 1.8 Consensus size: 103
12463672 TGAGAACACA
* * * * *
12463682 TGTGTAGTATTATGTGCAGGCTACTATGTGTTTATGATGGTTGTAGGTCACATGTGTAGTACTAA
1 TGTGTAGTACTAAGTGCAGACTACTATGTGTTCATGATGGTTGTAGGTCACATGTGTAGCACTAA
*
12463747 GTGCAGGCTACTATGCGTACCCGACAACTTTGATCACG
66 CTGCAGGCTACTATGCGTACCCGACAACTTTGATCACG
**
12463785 TGTGTAGTACTAAGTGCAGACTACTACT-TGTATCA-GATGG-T-TAGGTCATGTGTGTAGCACT
1 TGTGTAGTACTAAGTGCAGACTACTA-TGTGT-TCATGATGGTTGTAGGTCACATGTGTAGCACT
* * *
12463846 AACTGTAGGTTACTATGTGTACC
64 AACTGCAGGCTACTATGCGTACC
12463869 TGATTGTTGG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
101 36 0.51
102 1 0.01
103 31 0.44
104 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (103 bp):
TGTGTAGTACTAAGTGCAGACTACTATGTGTTCATGATGGTTGTAGGTCACATGTGTAGCACTAA
CTGCAGGCTACTATGCGTACCCGACAACTTTGATCACG
Found at i:12464140 original size:16 final size:15
Alignment explanation
Indices: 12464119--12464148 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12464109 GAAAGGAGTA
12464119 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
12464135 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
12464149 TAAAATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:12467264 original size:3 final size:3
Alignment explanation
Indices: 12467256--12467280 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12467246 AAGCAAGATG
12467256 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12467281 ACTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12467893 original size:18 final size:18
Alignment explanation
Indices: 12467858--12467893 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12467848 TCACCTAAGT
*
12467858 AAAAACTAAGAATGAAAA
1 AAAAACTAAGAATCAAAA
*
12467876 AAAAACTAAGAGTCAAAA
1 AAAAACTAAGAATCAAAA
12467894 CCCTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.08, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAACTAAGAATCAAAA
Found at i:12468097 original size:21 final size:19
Alignment explanation
Indices: 12468057--12468099 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
12468047 TTTTTAGTTG
**
12468057 CATAGGAGGTATGTTGCGA
1 CATAGGAGGTATGTCCCGA
12468076 CATAGGAGGGCTATGTCCCGA
1 CATAGGA-GG-TATGTCCCGA
12468097 CAT
1 CAT
12468100 TGAGGGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (19 bp):
CATAGGAGGTATGTCCCGA
Found at i:12472735 original size:26 final size:26
Alignment explanation
Indices: 12472706--12472756 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
12472696 CCAACCTACC
12472706 AATATCGTAGCAAAGCTACCAGTAAT
1 AATATCGTAGCAAAGCTACCAGTAAT
*
12472732 AATATCGTAGCAAAGCTGCCAGTAA
1 AATATCGTAGCAAAGCTACCAGTAA
12472757 CAGTAATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (26 bp):
AATATCGTAGCAAAGCTACCAGTAAT
Found at i:12472769 original size:26 final size:26
Alignment explanation
Indices: 12472705--12472781 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
12472695 ACCAACCTAC
* *
12472705 CAATATCGTAGCAAAGCTACCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* *
12472731 TAATATCGTAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* *
12472757 CAGTAAT-GCAGCAGAGCTGCCAGTA
1 CAAT-ATCGCAGCAAAGCTGCCAGTA
12472782 TCAGAATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 42 0.95
27 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGTAA
Found at i:12482036 original size:28 final size:28
Alignment explanation
Indices: 12482004--12482059 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
12481994 ACTACAACAC
*
12482004 CCTATTCAAACTCTTTTCAGACTCTCAT
1 CCTATTCAAACTCTATTCAGACTCTCAT
12482032 CCTATTCAAACTCTATTCAGACTCTCAT
1 CCTATTCAAACTCTATTCAGACTCTCAT
12482060 GACCAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.32, G:0.04, T:0.38
Consensus pattern (28 bp):
CCTATTCAAACTCTATTCAGACTCTCAT
Found at i:12482368 original size:58 final size:58
Alignment explanation
Indices: 12482278--12482397 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 58
12482268 TTAAGAACAA
* *
12482278 CACTAAAAATTTTGCAAAAGCCATGACTTGAACCAGGCTTCTCAAACACTCCCAAACC
1 CACTAAAAATTTTGCAAAAGCCAAGACTTGAACCAGGATTCTCAAACACTCCCAAACC
12482336 CACTAAAAATTTTGCAAAAGCCAAGACTTGAACCAGGATTCTCAAACACTCCCAAACC
1 CACTAAAAATTTTGCAAAAGCCAAGACTTGAACCAGGATTCTCAAACACTCCCAAACC
12482394 CACT
1 CACT
12482398 CAAATCACCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (58 bp):
CACTAAAAATTTTGCAAAAGCCAAGACTTGAACCAGGATTCTCAAACACTCCCAAACC
Found at i:12483413 original size:21 final size:21
Alignment explanation
Indices: 12483387--12483436 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
12483377 AAAGGAACCG
12483387 AAGTGCAAAATAGAAACACCA
1 AAGTGCAAAATAGAAACACCA
*** **
12483408 AAGTGCCTTATAGAGGCACCA
1 AAGTGCAAAATAGAAACACCA
12483429 AAGTGCAA
1 AAGTGCAA
12483437 TCCCGTACAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (21 bp):
AAGTGCAAAATAGAAACACCA
Found at i:12486114 original size:29 final size:27
Alignment explanation
Indices: 12486039--12486120 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
12486029 GCGAGGCTGC
* *
12486039 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGGCGAAGCCACCAGATA
* *
12486066 CAGATATTGTGGCTAGGCCACCAGA-A
1 CAGATATTGTGGCGAAGCCACCAGATA
12486092 CAGATATATATGTGGCGAAGCCACCAGAT
1 CAG--ATAT-TGTGGCGAAGCCACCAGAT
12486121 TGCAATGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 21 0.47
28 4 0.09
29 16 0.36
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCGAAGCCACCAGATA
Found at i:12511898 original size:6 final size:6
Alignment explanation
Indices: 12511887--12511978 Score: 89
Period size: 6 Copynumber: 15.3 Consensus size: 6
12511877 AATTCTCCTA
* *
12511887 TTTTAT TTTTAT TTTTA- -TTTAT TCTTAT TTTTAT TTTTAT TCTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * * *
12511933 TTTATTT ATTTTAT TCTTAT TTTTCT TTTGAT TTTTAT TTTCAT TT
1 TTT-TAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
12511979 CAAATTTCTT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.06
6 58 0.84
7 4 0.06
8 3 0.04
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:12511955 original size:38 final size:38
Alignment explanation
Indices: 12511885--12511978 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 38
12511875 TGAATTCTCC
*
12511885 TATTTTATTTTTATTTTTATTTATTCTTATTTTTATTTT
1 TATTTTA-TTTTATTTATATTTATTCTTATTTTTATTTT
*
12511924 TATTCTTATTTTATTTAT-TTTATTCTTATTTTTCTTTT
1 TATT-TTATTTTATTTATATTTATTCTTATTTTTATTTT
*
12511962 GATTTTTATTTTCATTT
1 TA-TTTTATTTT-ATTT
12511979 CAAATTTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
38 27 0.55
39 19 0.39
40 3 0.06
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (38 bp):
TATTTTATTTTATTTATATTTATTCTTATTTTTATTTT
Found at i:12519044 original size:31 final size:31
Alignment explanation
Indices: 12519009--12519081 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
12518999 ATATTGGGCC
*
12519009 GAAGCCTTTACATTATTCATGTCACTAGGCA
1 GAAGCCTTTACATTATTCATATCACTAGGCA
* * *
12519040 GAAGCCTTTTCATTATTCATATCACTGGGCC
1 GAAGCCTTTACATTATTCATATCACTAGGCA
12519071 GAAGCCTTTAC
1 GAAGCCTTTAC
12519082 TGTAAATGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (31 bp):
GAAGCCTTTACATTATTCATATCACTAGGCA
Found at i:12519314 original size:25 final size:25
Alignment explanation
Indices: 12519286--12519370 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
12519276 CTGGAGGCCT
12519286 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCC-CTTTTAATAAACTGGGGCAAA
*
12519311 AGCCCTTTTTGATAAACTGGGGCAAA
1 AGCCC-TTTTAATAAACTGGGGCAAA
** *
12519337 AGCCCTTTTCGGTAAACTAGGGC-AA
1 AGCCCTTTT-AATAAACTGGGGCAAA
12519362 AGCCCTTTT
1 AGCCCTTTT
12519371 CGGTAACTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
24 1 0.02
25 25 0.46
26 28 0.52
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:12519371 original size:25 final size:26
Alignment explanation
Indices: 12519299--12519394 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
12519289 CTCTTTTAAT
* *
12519299 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
12519325 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
12519351 AACTAGGGC-AAAGCCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
* *
12519375 AACTGGAGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
12519395 GCACTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 17 0.27
25 15 0.23
26 32 0.50
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:12519535 original size:25 final size:25
Alignment explanation
Indices: 12519507--12519554 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12519497 ATAATTAAAC
* **
12519507 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
12519532 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
12519555 CTTATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:12538418 original size:22 final size:21
Alignment explanation
Indices: 12538374--12538418 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
12538364 AGGTGATGAC
*
12538374 TTTATTTGTTTTATCTTATAT
1 TTTATTTGTTTTATATTATAT
12538395 TTTATCTTGTTTTATTATTA-AT
1 TTTAT-TTGTTTTA-TATTATAT
12538417 TT
1 TT
12538419 AATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTATTTGTTTTATATTATAT
Found at i:12551193 original size:13 final size:13
Alignment explanation
Indices: 12551175--12551201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12551165 AAAGTAATCG
12551175 CACACGGGTGTGT
1 CACACGGGTGTGT
12551188 CACACGGGTGTGT
1 CACACGGGTGTGT
12551201 C
1 C
12551202 CGTACCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (13 bp):
CACACGGGTGTGT
Found at i:12574863 original size:93 final size:93
Alignment explanation
Indices: 12574702--12574887 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
12574692 ATGATACGTG
* * *
12574702 ATATTCGTAATAGGTTTTAAATATTTATAATGAATCGTTCTTGAAACTAACAATTATCACGATGA
1 ATATTCGTAACAGGTTTTAAATATTTATAATGAATCATTCTTGAAACTAACAATTATCACGATAA
12574767 AGGCAAGTGTACCTATCAAACAATAGTA
66 AGGCAAGTGTACCTATCAAACAATAGTA
* *
12574795 ATATTCGTGACAGGTTTTAAATATTTATAATGAATCATTCTTGAAACTAACTATTATCACGATAA
1 ATATTCGTAACAGGTTTTAAATATTTATAATGAATCATTCTTGAAACTAACAATTATCACGATAA
* *
12574860 AGGCAAGTGTACCTATCGAACAGTAGTA
66 AGGCAAGTGTACCTATCAAACAATAGTA
12574888 TAACTTTAGC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (93 bp):
ATATTCGTAACAGGTTTTAAATATTTATAATGAATCATTCTTGAAACTAACAATTATCACGATAA
AGGCAAGTGTACCTATCAAACAATAGTA
Found at i:12575834 original size:13 final size:13
Alignment explanation
Indices: 12575816--12575849 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
12575806 CTCGATAGGG
12575816 ACACACCCGTATA
1 ACACACCCGTATA
*
12575829 ACACACCCGTATG
1 ACACACCCGTATA
12575842 ACACACCC
1 ACACACCC
12575850 ATGTGCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.44, G:0.09, T:0.12
Consensus pattern (13 bp):
ACACACCCGTATA
Found at i:12578969 original size:27 final size:27
Alignment explanation
Indices: 12578939--12578996 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
12578929 GTGAATAAAA
12578939 TGTAAGATGATATATTCGAATGATGCT
1 TGTAAGATGATATATTCGAATGATGCT
*
12578966 TGTAGGATGATATATTCGAATGATGCT
1 TGTAAGATGATATATTCGAATGATGCT
12578993 TGTA
1 TGTA
12578997 CCTAATTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (27 bp):
TGTAAGATGATATATTCGAATGATGCT
Found at i:12579118 original size:45 final size:45
Alignment explanation
Indices: 12579051--12579270 Score: 268
Period size: 45 Copynumber: 5.0 Consensus size: 45
12579041 TATCGTACAG
* *
12579051 TACTATTCGAGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * **
12579096 TATTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCTAGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
12579141 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * * *
12579186 TACTATTCGGGCCTTCGAGCCTAGCAAGCTATAATGTCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * **
12579231 TGA-TA-TCGAG-CTTCGAGCCTAGCAGGAGA-AATGCCGGTGA
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
12579271 ATAAATTCGG
Statistics
Matches: 153, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
42 10 0.07
43 16 0.10
44 4 0.03
45 122 0.80
46 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:12584740 original size:63 final size:64
Alignment explanation
Indices: 12584586--12584755 Score: 175
Period size: 63 Copynumber: 2.7 Consensus size: 64
12584576 CTCGTGTGTC
* * **
12584586 TTACATGGCCTA-ACACACGGTCATGTCCTCCGCCCATGTGATCATTATTTTGTAATCAGAGAG
1 TTACATGTCCTAGACACACGCTCATGTCCTTGGCCCATGTGATCATTATTTTGTAATCAGAGAG
* * * * * * *
12584649 TTACATGGT-CTGGACATACGCCCGTGTCCTTGGCCCATGTGATC-TTATTTTGTTATTAGTGAG
1 TTACAT-GTCCTAGACACACGCTCATGTCCTTGGCCCATGTGATCATTATTTTGTAATCAGAGAG
** * *
12584712 TTACATGTCCTAGACACACATTCATGTCCTTGACCCGTGTGATC
1 TTACATGTCCTAGACACACGCTCATGTCCTTGGCCCATGTGATC
12584756 CTACACTAAC
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
62 2 0.02
63 57 0.67
64 26 0.31
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (64 bp):
TTACATGTCCTAGACACACGCTCATGTCCTTGGCCCATGTGATCATTATTTTGTAATCAGAGAG
Done.