Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 2 of 31
Found at i:734161 original size:2 final size:2
Alignment explanation
Indices: 734154--734193 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
734144 ACCCTCCAAA
*
734154 CT CT CT CT CT CT CT CT CT CT CT C- CT -T CT -T CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
734193 C
1 C
734194 AATCCTAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:750597 original size:6 final size:6
Alignment explanation
Indices: 750586--750611 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
750576 AAATAGGAAG
750586 GTTCAT GTTCAT GTTCAT GTTCAT GT
1 GTTCAT GTTCAT GTTCAT GTTCAT GT
750612 GCCTGGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (6 bp):
GTTCAT
Found at i:755200 original size:17 final size:18
Alignment explanation
Indices: 755173--755212 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
755163 TAGAAACAGG
*
755173 CTAGAGCTCAATGTTATT
1 CTAGAGCTCAATGTTAAT
755191 CTAG-GCTCAATGTTAAT
1 CTAGAGCTCAATGTTAAT
755208 CTAGA
1 CTAGA
755213 TAATATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (18 bp):
CTAGAGCTCAATGTTAAT
Found at i:768239 original size:8 final size:8
Alignment explanation
Indices: 768222--768251 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
768212 GATTTCTCTC
*
768222 AGAGACGG
1 AGAGAGGG
768230 AGAGAGGG
1 AGAGAGGG
768238 AGAGAGGG
1 AGAGAGGG
768246 AGAGAG
1 AGAGAG
768252 AGAAAAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.03, G:0.57, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:768772 original size:3 final size:3
Alignment explanation
Indices: 768764--768801 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
768754 CAACTAACCC
768764 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
768802 GCTGCCTCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:771715 original size:23 final size:23
Alignment explanation
Indices: 771689--771744 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
771679 AAAAATATAT
*
771689 TATATATTATAAATATTTTAAAA
1 TATATATTATAAATATGTTAAAA
* * *
771712 TATATCTCAAAAATATGTTAAAA
1 TATATATTATAAATATGTTAAAA
771735 -ATATATTATA
1 TATATATTATA
771745 TAGAAATATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
TATATATTATAAATATGTTAAAA
Found at i:771726 original size:13 final size:11
Alignment explanation
Indices: 771690--771742 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
771680 AAAATATATT
*
771690 ATATATTATAA
1 ATATATTAAAA
*
771701 ATAT-TTTAAA
1 ATATATTAAAA
771711 ATATATCTCAAAA
1 ATATAT-T-AAAA
*
771724 ATATGTTAAAA
1 ATATATTAAAA
771735 ATATATTA
1 ATATATTA
771743 TATAGAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 8 0.24
11 16 0.47
12 2 0.06
13 8 0.24
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:783473 original size:2 final size:2
Alignment explanation
Indices: 783466--783499 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
783456 TGCATTTATT
783466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
783500 ATTTCCACAA
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):
TA
Found at i:793787 original size:45 final size:44
Alignment explanation
Indices: 793724--793852 Score: 188
Period size: 45 Copynumber: 2.9 Consensus size: 44
793714 ACAACAACAT
* *
793724 TTTTTTTACATAG-CATGTAACAACCTAATCATGACGTGTCAAGTA
1 TTTTTGTACAT-GTCATGTAACAACTTAA-CATGACGTGTCAAGTA
*
793769 TTTTTGTACATGTCATGTAACAACTTAACCATGACGTGTCACGTA
1 TTTTTGTACATGTCATGTAACAACTTAA-CATGACGTGTCAAGTA
793814 TTTTTGTACATGTCATGTAACAACTTAACTATGACGTGT
1 TTTTTGTACATGTCATGTAACAACTTAAC-ATGACGTGT
793853 AACAACCTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
44 2 0.03
45 76 0.97
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (44 bp):
TTTTTGTACATGTCATGTAACAACTTAACATGACGTGTCAAGTA
Found at i:793855 original size:21 final size:21
Alignment explanation
Indices: 793829--793873 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
793819 GTACATGTCA
* *
793829 TGTAACAACTTAACTATGACG
1 TGTAACAACCTAACCATGACG
*
793850 TGTAACAACCTAACCATGATG
1 TGTAACAACCTAACCATGACG
793871 TGT
1 TGT
793874 CACATGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
TGTAACAACCTAACCATGACG
Found at i:793867 original size:66 final size:66
Alignment explanation
Indices: 793784--793984 Score: 269
Period size: 66 Copynumber: 3.0 Consensus size: 66
793774 GTACATGTCA
* * * * *
793784 TGTAACAACTTAACCATGACGTGTCACGTATTTTTGTACATGTCATGTAACAACTTAACTATGAC
1 TGTAACAACTTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATGAC
793849 G
66 G
* * * **
793850 TGTAACAACCTAACCATGATGTGTCACATGTTTTTGTACATGGCGTGTAACAGTTTAACCAT-AG
1 TGTAACAACTTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATGA-
*
793914 CA
65 CG
* *
793916 TGTAACAACTTAACCATGGCGTGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCATGAC
1 TGTAACAACTTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATGAC
793981 G
66 G
793982 TGT
1 TGT
793985 TACATGTTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
65 1 0.01
66 113 0.98
67 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (66 bp):
TGTAACAACTTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTAACAACTTAACCATGAC
G
Found at i:794057 original size:45 final size:45
Alignment explanation
Indices: 793916--794057 Score: 194
Period size: 45 Copynumber: 3.2 Consensus size: 45
793906 AACCATAGCA
* * *
793916 TGTAACAACTTAACCATGGCGTGTCACATGTTTTTGTACATGACG
1 TGTAACAACCTAACCATGGCGTGTAACATGTTTTTGTACATGGCG
* *
793961 TGTAACAACCTAACCATGACGTGTTACATGTTTTTGTACATGGCG
1 TGTAACAACCTAACCATGGCGTGTAACATGTTTTTGTACATGGCG
* * * *
794006 TGTAACAACCTAACTATGGTGTGTAACATGTTTTTGTATATGGTG
1 TGTAACAACCTAACCATGGCGTGTAACATGTTTTTGTACATGGCG
*
794051 TATAACA
1 TGTAACA
794058 TTATAACGTG
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (45 bp):
TGTAACAACCTAACCATGGCGTGTAACATGTTTTTGTACATGGCG
Found at i:809432 original size:2 final size:2
Alignment explanation
Indices: 809425--809457 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
809415 TGATCCATGT
809425 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 T
809458 GGATTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:820735 original size:17 final size:17
Alignment explanation
Indices: 820702--820736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
820692 ACACTTTTAT
*
820702 TTATATAAAATTATAAA
1 TTATATAAAAATATAAA
*
820719 TTATATAAAAATCTAAA
1 TTATATAAAAATATAAA
820736 T
1 T
820737 CAATTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATATAAAAATATAAA
Found at i:822288 original size:23 final size:23
Alignment explanation
Indices: 822241--822317 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
822231 CTTACTAACA
* * *
822241 AGTCACACACTGCC-TACCAATT
1 AGTCACGCAGTGCCATATCAATT
822263 AGTCACGCAGTGCCATATCAATT
1 AGTCACGCAGTGCCATATCAATT
822286 AGTCACGCAGTGCCATATCAATT
1 AGTCACGCAGTGCCATATCAATT
822309 AGTCACGCA
1 AGTCACGCA
822318 ATACCTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 12 0.24
23 39 0.76
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (23 bp):
AGTCACGCAGTGCCATATCAATT
Found at i:822404 original size:21 final size:21
Alignment explanation
Indices: 822353--822405 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
822343 CTTAAAAACT
* *
822353 AATCATACAATGTCCAAAGTC
1 AATCATGCAATATCCAAAGTC
* * * *
822374 AGTTACGCAATATCTAAAGTC
1 AATCATGCAATATCCAAAGTC
822395 AATCATGCAAT
1 AATCATGCAAT
822406 GCTTAAAAAT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (21 bp):
AATCATGCAATATCCAAAGTC
Found at i:822608 original size:61 final size:59
Alignment explanation
Indices: 822536--822659 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
822526 TTATTTGACA
* * * *
822536 AAAAATACTCAAAATG-TTCAAAGGTTTTTTTTCATATATAAAAAATTACTACAAAATGCTT
1 AAAAATACTCAAAACGCTT-AAAAG-TTTTTTT-ATATATAAAAAACTACTACAAAATGCTC
* *
822597 AAAAATGCTCAAAACGCTTAAAAGTTTTTTTATATATAAAAAACTACTCCAAAATGCTC
1 AAAAATACTCAAAACGCTTAAAAGTTTTTTTATATATAAAAAACTACTACAAAATGCTC
822656 AAAA
1 AAAA
822660 TGATTAAACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 29 0.52
60 7 0.12
61 18 0.32
62 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (59 bp):
AAAAATACTCAAAACGCTTAAAAGTTTTTTTATATATAAAAAACTACTACAAAATGCTC
Found at i:837807 original size:25 final size:26
Alignment explanation
Indices: 837773--837822 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
837763 TCCAACTTCT
*
837773 AATAAAATATTAATA-TTAAATTATA
1 AATAAAATATGAATATTTAAATTATA
837798 AATAAAATATGAATATTTAAATTAT
1 AATAAAATATGAATATTTAAATTAT
837823 CAATTATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAATATGAATATTTAAATTATA
Found at i:837854 original size:27 final size:27
Alignment explanation
Indices: 837815--837880 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
837805 TATGAATATT
* **
837815 TAAATTATCAATTATTAGTATTTAAAA
1 TAAATTATAAATTATTACCATTTAAAA
*
837842 TAAATTATAAATTATTACCATTTACAA
1 TAAATTATAAATTATTACCATTTAAAA
837869 TAAA--ATAAATTA
1 TAAATTATAAATTA
837881 AAAATAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 8 0.23
27 27 0.77
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAATTATAAATTATTACCATTTAAAA
Found at i:837977 original size:27 final size:27
Alignment explanation
Indices: 837928--838046 Score: 82
Period size: 27 Copynumber: 4.1 Consensus size: 27
837918 AAATATTAAT
* *
837928 AATAAAATTATCAATTATAAATATTTTA
1 AATAAAA-TAACAATTATTAATATTTTA
*
837956 AATAAAATAACAATTATTAATATTTAAA
1 AATAAAATAACAATTATTAATATTT-TA
* *
837984 AACAAAATAAAAAATTAATCATAATAGTATTTA
1 AATAAAAT-AACAATT-AT--TAATA-T-TTTA
838017 ACAT-AAATAA-AA-TATTAATATTTTCA
1 A-ATAAAATAACAATTATTAATATTTT-A
838043 AATA
1 AATA
838047 TTAATGATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
25 5 0.07
26 3 0.04
27 21 0.28
28 15 0.20
29 8 0.11
30 3 0.04
31 2 0.03
32 7 0.09
33 7 0.09
34 3 0.04
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (27 bp):
AATAAAATAACAATTATTAATATTTTA
Found at i:838084 original size:15 final size:14
Alignment explanation
Indices: 838045--838126 Score: 59
Period size: 15 Copynumber: 6.0 Consensus size: 14
838035 TATTTTCAAA
838045 TATTAATGATTAAAT
1 TATTAAT-ATTAAAT
838060 TA-T-ATA-TAAAT
1 TATTAATATTAAAT
838071 TATTAATATTTAAAT
1 TATTAATA-TTAAAT
*
838086 TATTTATTATTAATAT
1 TA-TTAATATTAA-AT
838102 T-TT-A-ATTAAAT
1 TATTAATATTAAAT
* *
838113 TATAAAAATTAAAT
1 TATTAATATTAAAT
838127 AAAAATAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
11 10 0.18
12 8 0.15
13 6 0.11
14 10 0.18
15 13 0.24
16 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:840834 original size:12 final size:12
Alignment explanation
Indices: 840819--840934 Score: 56
Period size: 12 Copynumber: 9.4 Consensus size: 12
840809 TGGTGGGAAT
840819 GGTGGAGGAGGA
1 GGTGGAGGAGGA
* *
840831 GGTGGGGGTGGAGGC
1 GGT---GGAGGAGGA
* * *
840846 GGTGGCGGTGGT
1 GGTGGAGGAGGA
* * *
840858 GGTGGCGGTGGT
1 GGTGGAGGAGGA
* *
840870 GGTGGCGGTGGA
1 GGTGGAGGAGGA
*
840882 GGAGGAGGAGGA
1 GGTGGAGGAGGA
*
840894 GGAGGAGGAGGA
1 GGTGGAGGAGGA
*
840906 GGTGGAGGTTGG-
1 GGTGGAGG-AGGA
840918 GGTTGG-GGAGGA
1 GG-TGGAGGAGGA
840930 GGTGG
1 GGTGG
840935 CAACCCTGGT
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
11 5 0.06
12 66 0.77
13 5 0.06
15 10 0.12
ACGTcount: A:0.14, C:0.03, G:0.68, T:0.15
Consensus pattern (12 bp):
GGTGGAGGAGGA
Found at i:840834 original size:32 final size:31
Alignment explanation
Indices: 840776--840844 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
840766 TCATGGATGG
840776 GGTGGAGGAAATGGAGGGGAGGAGGTGGGGA
1 GGTGGAGGAAATGGAGGGGAGGAGGTGGGGA
* * *
840807 GGTGGTGGGAATGGTGGAGGAGGAGGT-GGG-
1 GGTGGAGGAAATGGAGG-GGAGGAGGTGGGGA
840837 GGTGGAGG
1 GGTGGAGG
840845 CGGTGGCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.21
31 17 0.52
32 9 0.27
ACGTcount: A:0.20, C:0.00, G:0.67, T:0.13
Consensus pattern (31 bp):
GGTGGAGGAAATGGAGGGGAGGAGGTGGGGA
Found at i:840885 original size:3 final size:3
Alignment explanation
Indices: 840879--840913 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
840869 TGGTGGCGGT
*
840879 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGT GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
840914 TTGGGGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.69, T:0.03
Consensus pattern (3 bp):
GGA
Found at i:840914 original size:6 final size:6
Alignment explanation
Indices: 840819--840914 Score: 66
Period size: 6 Copynumber: 15.5 Consensus size: 6
840809 TGGTGGGAAT
* * * * * *
840819 GGTGGA GGAGGA GGTGGG GGTGGA GGCGGTGGC GGTGGT GGTGGC GGTGGT
1 GGTGGA GGTGGA GGTGGA GGTGGA ---GGTGGA GGTGGA GGTGGA GGTGGA
* * * * *
840870 GGTGGC GGTGGA GGAGGA GGAGGA GGAGGA GGAGGA GGTGGA GGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGT
840915 TGGGGTTGGG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
6 70 0.93
9 5 0.07
ACGTcount: A:0.15, C:0.04, G:0.68, T:0.14
Consensus pattern (6 bp):
GGTGGA
Found at i:844295 original size:35 final size:37
Alignment explanation
Indices: 844253--844337 Score: 129
Period size: 35 Copynumber: 2.3 Consensus size: 37
844243 TGCTTGTTAC
844253 TTATTTGATGTGAAATTTCATA-AATTTTTTT-TTAT
1 TTATTTGATGTGAAATTTCATACAATTTTTTTATTAT
* *
844288 TTATTTGATGTGAAATTTTATACTATTTTTTTATTAT
1 TTATTTGATGTGAAATTTCATACAATTTTTTTATTAT
844325 TTATGTTGATGTG
1 TTAT-TTGATGTG
844338 GCATTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 21 0.47
36 8 0.18
37 8 0.18
38 8 0.18
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (37 bp):
TTATTTGATGTGAAATTTCATACAATTTTTTTATTAT
Found at i:847636 original size:18 final size:20
Alignment explanation
Indices: 847613--847649 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
847603 TGTTCACCAC
847613 TTTTCT-TTTTCTT-TTTTT
1 TTTTCTATTTTCTTATTTTT
847631 TTTTCTATTTTCTTATTTT
1 TTTTCTATTTTCTTATTTT
847650 GTTTATTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTCTATTTTCTTATTTTT
Found at i:854313 original size:38 final size:39
Alignment explanation
Indices: 854257--854336 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 39
854247 CATGTGTATA
854257 TATATGTAATCATTGGTTGATTGTCTGAATAAATTAGTT
1 TATATGTAATCATTGGTTGATTGTCTGAATAAATTAGTT
854296 TATA-GTAATCATTGGTTGATTGTCTGAATAAATTAGTT
1 TATATGTAATCATTGGTTGATTGTCTGAATAAATTAGTT
854334 TAT
1 TAT
854337 CTGTTAAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 37 0.90
39 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.46
Consensus pattern (39 bp):
TATATGTAATCATTGGTTGATTGTCTGAATAAATTAGTT
Found at i:858529 original size:45 final size:45
Alignment explanation
Indices: 858459--858544 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
858449 TTGAGAAACA
* *
858459 CTTTTGTACACCTTTTAGTTATGTAATTTCACCTGCTGCAATCCC
1 CTTTTGTACACCTTTCAGTTATGTAATTCCACCTGCTGCAATCCC
* * * *
858504 CTTTTGTACTCGTTTCAGTTTTGTAATTCCATCTGCTGCAA
1 CTTTTGTACACCTTTCAGTTATGTAATTCCACCTGCTGCAA
858545 ACTATTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (45 bp):
CTTTTGTACACCTTTCAGTTATGTAATTCCACCTGCTGCAATCCC
Found at i:859020 original size:6 final size:6
Alignment explanation
Indices: 859009--859034 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
858999 AGTACATCTT
859009 ATTTTG ATTTTG ATTTTG ATTTTG AT
1 ATTTTG ATTTTG ATTTTG ATTTTG AT
859035 CATGTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:874662 original size:12 final size:12
Alignment explanation
Indices: 874618--874658 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
874608 AATATTAAAT
874618 TATATTATATTA
1 TATATTATATTA
874630 TATATTATA-TA
1 TATATTATATTA
*
874641 T-TATTTTTATTA
1 TATA-TTATATTA
874653 TATATT
1 TATATT
874659 TTATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
12 14 0.56
13 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATTATATTA
Found at i:881587 original size:33 final size:33
Alignment explanation
Indices: 881537--881630 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
881527 AATGACTTAA
*
881537 TTTAGTTTT-ACTAGAATCTATTCTTTGTTTAG
1 TTTAGTTTTCACTAGAATCTATACTTTGTTTAG
881569 TTTAGTTTTCACTAGAATCTATACTTTGTTTAG
1 TTTAGTTTTCACTAGAATCTATACTTTGTTTAG
* *
881602 TTTAGTTTTCACTAAAACCTATACTTTGT
1 TTTAGTTTTCACTAGAATCTATACTTTGT
881631 CAATGGATCT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 49 0.84
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (33 bp):
TTTAGTTTTCACTAGAATCTATACTTTGTTTAG
Found at i:891184 original size:13 final size:13
Alignment explanation
Indices: 891168--891192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
891158 TTTAGAACAA
891168 AATAAAACTGATG
1 AATAAAACTGATG
891181 AATAAAACTGAT
1 AATAAAACTGAT
891193 AAAACAGTTT
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:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
AATAAAACTGATG
Found at i:898291 original size:14 final size:15
Alignment explanation
Indices: 898257--898286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
898247 TTAATTAGAT
898257 AAAAAA-TTTAAATA
1 AAAAAATTTTAAATA
898271 AAAAAATTTTAAATA
1 AAAAAATTTTAAATA
898286 A
1 A
898287 TAAATATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAATTTTAAATA
Found at i:900054 original size:6 final size:6
Alignment explanation
Indices: 900043--900074 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
900033 CATCTTAGCA
*
900043 GGGGGT GGGGGT GGGGAT GGGGGT GGGGGT GG
1 GGGGGT GGGGGT GGGGGT GGGGGT GGGGGT GG
900075 CACGGAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.81, T:0.16
Consensus pattern (6 bp):
GGGGGT
Found at i:900802 original size:16 final size:16
Alignment explanation
Indices: 900763--900809 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
900753 TTTGCATGTC
*
900763 TATATGTATATGTATA
1 TATATGTATATATATA
* *
900779 TGTGTGTATATATATA
1 TATATGTATATATATA
*
900795 TATATGTAAATATAT
1 TATATGTATATATAT
900810 GTATGATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (16 bp):
TATATGTATATATATA
Found at i:905856 original size:16 final size:16
Alignment explanation
Indices: 905837--905867 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
905827 TTCAAAATAG
905837 ATATTAATTAAAATTA
1 ATATTAATTAAAATTA
905853 ATATTAATTAAAATT
1 ATATTAATTAAAATT
905868 TTCAATAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTAATTAAAATTA
Found at i:914106 original size:32 final size:32
Alignment explanation
Indices: 914070--914130 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
914060 AACATCACCA
914070 AAGTTCCACTAA-CATTCAAAGTTTAAAACCTT
1 AAGTTCCA-TAAGCATTCAAAGTTTAAAACCTT
*
914102 AAGTTCCATAAGTATTCAAAGTTTAAAAC
1 AAGTTCCATAAGCATTCAAAGTTTAAAAC
914131 GTGGTATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (32 bp):
AAGTTCCATAAGCATTCAAAGTTTAAAACCTT
Found at i:917981 original size:29 final size:30
Alignment explanation
Indices: 917948--918020 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
917938 ATATTTATCA
* *
917948 ATATTGTATTATACACGATAAAT-TATATT
1 ATATTATATTATACACGATAAATATAAATT
**
917977 ATATTATATTATACGTGATAAATATAAATT
1 ATATTATATTATACACGATAAATATAAATT
918007 ATAATTATATTATA
1 AT-ATTATATTATA
918021 TAAAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 20 0.53
30 7 0.18
31 11 0.29
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (30 bp):
ATATTATATTATACACGATAAATATAAATT
Found at i:918636 original size:29 final size:30
Alignment explanation
Indices: 918603--918672 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
918593 ATATTTATCA
* *
918603 ATATTGTATTATACGTGATAAAT-TATATT
1 ATATTATATTATACGTGATAAATATAAATT
*
918632 ATATTATATTATATGTGATAAATATAAATT
1 ATATTATATTATACGTGATAAATATAAATT
918662 ATAATTATATT
1 AT-ATTATATT
918673 TTATGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 21 0.58
30 7 0.19
31 8 0.22
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (30 bp):
ATATTATATTATACGTGATAAATATAAATT
Found at i:918904 original size:655 final size:655
Alignment explanation
Indices: 917624--919554 Score: 2510
Period size: 655 Copynumber: 3.0 Consensus size: 655
917614 AGCCTTCCAG
* *
917624 AAACTTCGAGACTCTAGGGTTTCATCGGACGGTAATCCCGACGGCTCGATGGTCCCTGAGCTCTG
1 AAACTTCGAGACTCTAGGGTTTCATCTGATGGTAATCCCGACGGCTCGATGGTCCCTGAGCTCTG
* * *
917689 CGGCACATCGGGTCCGGAAATCTGCAGTGGCGACGGTGGTGTTGTGACTAAGCACACTTTCTGAG
66 CGGCATATCGGGTCCGAAAATCTGCAGTGGCGGCGGTGGTGTTGTGACTAAGCACACTTTCTGAG
*
917754 TCGCGACAGTTCTGGCGCCGCCTTCATCGTCGCTGCTGGTTACCTCTACGAA-CTTGAGAGGCCG
131 TCGCGACAGTTCTGGCGCCGCCTTCATCGTCGCTGCTAGTTACCTCTAC-AACCTTGAGAGGCCG
* ** * * *
917818 CTCTTTTTCTGTCTTCGGTGGCATTCCTTTAATTTTTATCTCCTGAAATCGGAAATTAAGATTCC
195 CTCTTTTTCTATCTTCGGCAGCATTCCTTTAATTTTTATCTCCTGAGATCGAAAATTAAGATT-T
* * *
917883 CGACAGAGCGTTTTATTTTTTCGAAGATAAAAAGTTTTAATTGCGAAGATATAAAATATTTATCA
259 CGATAGAGCGCTTTATTTTTTCGAAGATAAAAATTTTTAATTGCGAAGATATAAAATATTTATCA
** *
917948 ATATTGTATTATACACGATAAATTATATTATATTATATTATACGTGATAAATATAAATTATAATT
324 ATATTGTATTATACGTGATAAATTATATTATATTATATTATATGTGATAAATATAAATTATAATT
918013 ATATTATATAAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGATA
389 ATATTATATAAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGATA
* *
918078 ATAATAAAAAATAATAATAATATTGTATTTGTGGATACCCAATTTGAGTTTTACAAAATAATTAC
454 ATAATAAAAAATAATAACAACATTGTATTTGTGGATACCCAATTTGAGTTTTACAAAATAATTAC
* * * *
918143 ATTAGGCTGTTCTAAGGGTTCCCTAATATGTTCCAAGCGAAGAGTATTCAAAGTGTAAAAATGCT
519 ATTAGGATGTTCTAAGCGTTCCCTAAGATGTTCCAAGCGAAGAGTATTCAAAGTGTAAAAACGCT
* * * * *
918208 TAGGGTGTTCTAAATATAAAAATATTCAAGTGTTTCAAGTACATAAGCACTCAAAAGGCGTTCCA
584 TAGGGTGTTCTAAATACAAAAATACTCAAGTGTTCCAAGTACAGAAGCACCCAAAAGGCGTTCCA
918273 AGTAT-A
649 AGTATAA
* * * * * * * * *
918279 AAACTTTTGAGATTCTAAGGTTTCATCTGATGGTAATTCTGGCGGCTTGATGGTTCCTTAGCGT-
1 AAAC-TTCGAGACTCTAGGGTTTCATCTGATGGTAATCCCGACGGCTCGATGGTCCCTGAGC-TC
* * *
918343 TGCGGCATATCGGGTCTGAAAATCTGCAGTGGCGGCGGTGGCGTTGTGACTAAGCACACTTTTTG
64 TGCGGCATATCGGGTCCGAAAATCTGCAGTGGCGGCGGTGGTGTTGTGACTAAGCACACTTTCTG
* * *
918408 AGTCGCGACAGTTTTGGCGCCACCTTCATCGTCGCTGCTAGTTACCTCTACAACCTTGAGAGGTC
129 AGTCGCGACAGTTCTGGCGCCGCCTTCATCGTCGCTGCTAGTTACCTCTACAACCTTGAGAGGCC
* **
918473 GCTCTTTTTCTATCTTCGACAATATTCCTTTAATTTTTATCTCCTGAGATCGAAAATTAAGATTT
194 GCTCTTTTTCTATCTTCGGCAGCATTCCTTTAATTTTTATCTCCTGAGATCGAAAATTAAGATTT
* * * *
918538 CGATAAAGCGCTTTATTTTTTCAAAGATAAAAATTTTTAATTGCTAATATATAAAATATTTATCA
259 CGATAGAGCGCTTTATTTTTTCGAAGATAAAAATTTTTAATTGCGAAGATATAAAATATTTATCA
918603 ATATTGTATTATACGTGATAAATTATATTATATTATATTATATGTGATAAATATAAATTATAATT
324 ATATTGTATTATACGTGATAAATTATATTATATTATATTATATGTGATAAATATAAATTATAATT
* *
918668 ATATTTTATGAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGATA
389 ATATTATATAAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGATA
* * *
918733 ATAGTAAAAAATAATAACAACATTGTATTTGTGGATACCCAATTTTAGTTTTACAAAATAATTGC
454 ATAATAAAAAATAATAACAACATTGTATTTGTGGATACCCAATTTGAGTTTTACAAAATAATTAC
* * *
918798 ATTAGGATGTTCTAAGCGTTCCCTGAGATGTTCTAAGCGAAGAGTATTTAAAGTGTAAAAACGCT
519 ATTAGGATGTTCTAAGCGTTCCCTAAGATGTTCCAAGCGAAGAGTATTCAAAGTGTAAAAACGCT
* * * *
918863 TAGGGTGTTTTAAATACAGAAATGCTCAGGTGTTCCAAGTACAGAAGCACCCAAAAGGCGTTCCA
584 TAGGGTGTTCTAAATACAAAAATACTCAAGTGTTCCAAGTACAGAAGCACCCAAAAGGCGTTCCA
918928 AGTATAA
649 AGTATAA
918935 AAACTTCGAGACTCTAGGGTTTCAT-TGGAT--T--TCCCGACGGCTCGATGGTCCCTGAGCTCT
1 AAACTTCGAGACTCTAGGGTTTCATCT-GATGGTAATCCCGACGGCTCGATGGTCCCTGAGCTCT
* * * * * *
918995 GCAGCATATCGAGTCCGAAAATTTGTAGTGGCGGCAGTGGTGTTGTGACTAAGCACACTTTCTAA
65 GCGGCATATCGGGTCCGAAAATCTGCAGTGGCGGCGGTGGTGTTGTGACTAAGCACACTTTCTGA
* *
919060 GTCGCGACAGTTCTGGCACCGCCTTCATCGTCGCTGCTAGTTACCTCTACAACCTTGAGAGGCCA
130 GTCGCGACAGTTCTGGCGCCGCCTTCATCGTCGCTGCTAGTTACCTCTACAACCTTGAGAGGCCG
* * * * *
919125 CTCTTTTTCTACCTTCGGCAGCATT-CTTTAATTTTTATCCCCCGAGATTGAAAATTAAG-GTTC
195 CTCTTTTTCTATCTTCGGCAGCATTCCTTTAATTTTTATCTCCTGAGATCGAAAATTAAGATTTC
919188 TGATAGAGCGCTTTATTGTTTT-GAAGATAAAAATTTTTAATTGCGAAGATATAAAATATTTATC
260 -GATAGAGCGCTTTATT-TTTTCGAAGATAAAAATTTTTAATTGCGAAGATATAAAATATTTATC
919252 AATATTGTATTATACGTGATAAA-TATA--A-A-T-TA-TA-AT-T-AT--AT-T--A-TAT-A-
323 AATATTGTATTATACGTGATAAATTATATTATATTATATTATATGTGATAAATATAAATTATAAT
* *
919299 -A-A--A-AT----AT-TT-AAAAATATAATAATTTACTATACGTGATAAATTGTATGGTATGAT
388 TATATTATATAAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGAT
* * * * *
919353 AATAGTAA-AAAATAAT-A-A-CAATATCGTATTTGTAGATACCTAATTTTAGTTTTACAAAATA
453 -A-A-TAATAAAA-AATAATAACAACATTGTATTTGTGGATACCCAATTTGAGTTTTACAAAATA
* * * * * * * * * * *
919414 ATTGCATCAGAATGTTCCAAGCGTTCCTTGAGGTGTTCCAAGCCAGGAGTATTCAAAGTGCAGAA
514 ATTACATTAGGATGTTCTAAGCGTTCCCTAAGATGTTCCAAGCGAAGAGTATTCAAAGTGTAAAA
** * * * * * * * * *
919479 GTGCCTAGGGTGTTCCAAATACAGAAATACTCAGGTGTTCCAAGCACAGAAACACCCAGAGGGTG
579 ACGCTTAGGGTGTTCTAAATACAAAAATACTCAAGTGTTCCAAGTACAGAAGCACCCAAAAGGCG
919544 TTCCAAGTATA
644 TTCCAAGTATA
919555 GAAGCGTCCA
Statistics
Matches: 1136, Mismatches: 128, Indels: 58
0.86 0.10 0.04
Matches are distributed among these distances:
621 201 0.18
622 4 0.00
623 8 0.01
624 5 0.00
627 2 0.00
630 1 0.00
631 1 0.00
633 1 0.00
634 3 0.00
635 1 0.00
637 1 0.00
638 2 0.00
640 2 0.00
641 1 0.00
642 2 0.00
643 2 0.00
644 2 0.00
645 1 0.00
646 1 0.00
647 1 0.00
649 7 0.01
650 109 0.10
651 162 0.14
653 1 0.00
654 1 0.00
655 389 0.34
656 224 0.20
657 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (655 bp):
AAACTTCGAGACTCTAGGGTTTCATCTGATGGTAATCCCGACGGCTCGATGGTCCCTGAGCTCTG
CGGCATATCGGGTCCGAAAATCTGCAGTGGCGGCGGTGGTGTTGTGACTAAGCACACTTTCTGAG
TCGCGACAGTTCTGGCGCCGCCTTCATCGTCGCTGCTAGTTACCTCTACAACCTTGAGAGGCCGC
TCTTTTTCTATCTTCGGCAGCATTCCTTTAATTTTTATCTCCTGAGATCGAAAATTAAGATTTCG
ATAGAGCGCTTTATTTTTTCGAAGATAAAAATTTTTAATTGCGAAGATATAAAATATTTATCAAT
ATTGTATTATACGTGATAAATTATATTATATTATATTATATGTGATAAATATAAATTATAATTAT
ATTATATAAAAATATTAAAAAATATAATAACTTACTATACATGATAAATTGTATGGTATGATAAT
AATAAAAAATAATAACAACATTGTATTTGTGGATACCCAATTTGAGTTTTACAAAATAATTACAT
TAGGATGTTCTAAGCGTTCCCTAAGATGTTCCAAGCGAAGAGTATTCAAAGTGTAAAAACGCTTA
GGGTGTTCTAAATACAAAAATACTCAAGTGTTCCAAGTACAGAAGCACCCAAAAGGCGTTCCAAG
TATAA
Found at i:919583 original size:26 final size:27
Alignment explanation
Indices: 919511--919585 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 27
919501 AGAAATACTC
*
919511 AGGTGTTCCAAGCACAGAAACACCCAG
1 AGGTGTTCCAAGCACAGAAGCACCCAG
* * **
919538 AGGGTGTTCCAAGTATAGAAGCGTCCA-
1 A-GGTGTTCCAAGCACAGAAGCACCCAG
*
919565 AGGTGTTCCAAGCGCAGAAGC
1 AGGTGTTCCAAGCACAGAAGC
919586 TTCTAGTGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 17 0.44
27 2 0.05
28 20 0.51
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (27 bp):
AGGTGTTCCAAGCACAGAAGCACCCAG
Found at i:919681 original size:52 final size:52
Alignment explanation
Indices: 919619--919795 Score: 162
Period size: 52 Copynumber: 3.4 Consensus size: 52
919609 AAGCGCCTAG
* *
919619 GGGTGTTCCAAGTACAAAAGCGCCCAAGGTGTTTCAAGTACAAAAGTGTCCA
1 GGGTGTTCCAAGTACAAAAGCGCCCAAGGTGTTTCAAGTATAGAAGTGTCCA
* * * * *
919671 GGGTGTTCCAAGTACAGAAA-CACCAAAAGTGTTTCAAGTGTAGAAGTGCCCA
1 GGGTGTTCCAAGTACA-AAAGCGCCCAAGGTGTTTCAAGTATAGAAGTGTCCA
** * * * * * *
919723 GTGACGTTCCAAGTGCAGAAGTGCTCAGGGTG-TTCAAAGTATAGAAGTGT-TA
1 G-GGTGTTCCAAGTACAAAAGCGCCCAAGGTGTTTC-AAGTATAGAAGTGTCCA
*
919775 GGGTGTTCCAAGTACAGAAGC
1 GGGTGTTCCAAGTACAAAAGC
919796 ACTAGGGGCA
Statistics
Matches: 97, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
51 16 0.16
52 49 0.51
53 32 0.33
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (52 bp):
GGGTGTTCCAAGTACAAAAGCGCCCAAGGTGTTTCAAGTATAGAAGTGTCCA
Found at i:919768 original size:26 final size:25
Alignment explanation
Indices: 919728--919794 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
919718 GCCCAGTGAC
* *
919728 GTTCCAAGTGCAGAAGTGCTCAGGGT
1 GTTCAAAGTACAGAAGTG-TCAGGGT
* *
919754 GTTCAAAGTATAGAAGTGTTAGGGT
1 GTTCAAAGTACAGAAGTGTCAGGGT
*
919779 GTTCCAAGTACAGAAG
1 GTTCAAAGTACAGAAG
919795 CACTAGGGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.25
Consensus pattern (25 bp):
GTTCAAAGTACAGAAGTGTCAGGGT
Found at i:919787 original size:25 final size:26
Alignment explanation
Indices: 919469--919846 Score: 137
Period size: 26 Copynumber: 14.4 Consensus size: 26
919459 GGAGTATTCA
*
919469 AAGTGCAGAAGTGC-CTAGGGTGTTCC
1 AAGTACAGAAGTGCTC-AGGGTGTTCC
* * *
919495 AAATACAGAAATACTCA-GGTGTTCC
1 AAGTACAGAAGTGCTCAGGGTGTTCC
* *** *
919520 AAGCACAGAAACACCCAGAGGGTGTTCC
1 AAGTACAGAAGTGCTC--AGGGTGTTCC
* * *
919548 AAGTATAGAAGCG-TCCAAGGTGTTCC
1 AAGTACAGAAGTGCT-CAGGGTGTTCC
** * * *
919574 AAGCGCAGAAGCTTCT-AGTGGCGTTAC
1 AAGTACAGAAG-TGCTCAG-GGTGTTCC
* * * *
919601 AAATGCTGAAGCGC-CTAGGGGTGTTCC
1 AAGTACAGAAGTGCTC-A-GGGTGTTCC
* * * * *
919628 AAGTACAAAAGCGCCCAAGGTGTTTC
1 AAGTACAGAAGTGCTCAGGGTGTTCC
*
919654 AAGTACAAAAGTG-TCCAGGGTGTTCC
1 AAGTACAGAAGTGCT-CAGGGTGTTCC
*** ** *
919680 AAGTACAGAAACAC-CAAAAGTGTTTC
1 AAGTACAGAAGTGCTC-AGGGTGTTCC
** * **
919706 AAGTGTAGAAGTGCCCAGTGACGTTCC
1 AAGTACAGAAGTGCTCAG-GGTGTTCC
* *
919733 AAGTGCAGAAGTGCTCAGGGTGTTCA
1 AAGTACAGAAGTGCTCAGGGTGTTCC
* *
919759 AAGTATAGAAGTG-TTAGGGTGTTCC
1 AAGTACAGAAGTGCTCAGGGTGTTCC
**
919784 AAGTACAGAAGCACT-AGGG-GCATTCC
1 AAGTACAGAAGTGCTCAGGGTG--TTCC
* * * *
919810 AAGTGCAGAAGCGCTGAGAGTGTTCC
1 AAGTACAGAAGTGCTCAGGGTGTTCC
919836 AAGTACAGAAG
1 AAGTACAGAAG
919847 CCCCCAAAAG
Statistics
Matches: 258, Mismatches: 72, Indels: 44
0.69 0.19 0.12
Matches are distributed among these distances:
24 1 0.00
25 45 0.17
26 132 0.51
27 58 0.22
28 22 0.09
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (26 bp):
AAGTACAGAAGTGCTCAGGGTGTTCC
Found at i:919899 original size:28 final size:28
Alignment explanation
Indices: 919826--919900 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 28
919816 AGAAGCGCTG
* * *
919826 AGAGTGTTCCAAGTACAGAAGCCCCCAA
1 AGAGTGTTCCAAGCATAGAAGCACCCAA
* **
919854 A-AGTGTTCCGAGGTTAGAAGCACCCAA
1 AGAGTGTTCCAAGCATAGAAGCACCCAA
*
919881 AGAGTGTTACAAGCATAGAA
1 AGAGTGTTCCAAGCATAGAA
919901 ACACTCAGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (28 bp):
AGAGTGTTCCAAGCATAGAAGCACCCAA
Found at i:924822 original size:28 final size:28
Alignment explanation
Indices: 924791--924845 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
924781 AAAATTATTT
*
924791 ATAAAGTGTTAATTCAGAAAAA-AAAATC
1 ATAAAGTGTTAATT-AAAAAAATAAAATC
*
924819 ATAAGGTGTTAATTAAAAAAATAAAAT
1 ATAAAGTGTTAATTAAAAAAATAAAAT
924846 TCTATATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (28 bp):
ATAAAGTGTTAATTAAAAAAATAAAATC
Found at i:936934 original size:7 final size:7
Alignment explanation
Indices: 936907--936944 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
936897 TTGCTCATTT
936907 CTGCTG-
1 CTGCTGC
936913 CTGCTG-
1 CTGCTGC
*
936919 CTGCCGC
1 CTGCTGC
936926 CTGCTGC
1 CTGCTGC
936933 CTGCTGC
1 CTGCTGC
936940 CTGCT
1 CTGCT
936945 TTTCGTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.00, C:0.42, G:0.29, T:0.29
Consensus pattern (7 bp):
CTGCTGC
Found at i:949899 original size:20 final size:20
Alignment explanation
Indices: 949874--949914 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
949864 TATTATCAAC
949874 TCAAACAAAAAGAAAATATT
1 TCAAACAAAAAGAAAATATT
949894 TCAAACAAAAAGAAAATATT
1 TCAAACAAAAAGAAAATATT
949914 T
1 T
949915 GAATATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (20 bp):
TCAAACAAAAAGAAAATATT
Found at i:954816 original size:4 final size:4
Alignment explanation
Indices: 954807--954835 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
954797 ATTTAAATTA
954807 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
954836 TATGTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:978696 original size:2 final size:2
Alignment explanation
Indices: 978689--978713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
978679 TAGACACTTC
978689 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 T
978714 GAGAGAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:991657 original size:27 final size:29
Alignment explanation
Indices: 991595--991657 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
991585 AAAAAAGATA
*
991595 ATTAAA-AATAAAATAATATATAAATTAT
1 ATTAAATAATAAAATAATATATAAATAAT
* *
991623 TTTAAAATAATAAAA-AATATA-ATATAAT
1 ATT-AAATAATAAAATAATATATAAATAAT
991651 ATTAAAT
1 ATTAAAT
991658 TTTGTTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 4 0.14
28 9 0.31
29 9 0.31
30 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTAAATAATAAAATAATATATAAATAAT
Found at i:994145 original size:32 final size:35
Alignment explanation
Indices: 994089--994157 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 35
994079 TTAATTAATA
*
994089 AATTAAATATTTAAATGTTATTATTTAT-ATTTTT
1 AATTAAATATTAAAATGTTATTATTTATAATTTTT
* *
994123 AATTAAAT-TTAAAAT-TTTTTATTTTTAATTTTT
1 AATTAAATATTAAAATGTTATTATTTATAATTTTT
994156 AA
1 AA
994158 AAAAATTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.29
33 14 0.45
34 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
AATTAAATATTAAAATGTTATTATTTATAATTTTT
Found at i:1005947 original size:20 final size:20
Alignment explanation
Indices: 1005922--1005960 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1005912 TTTAGATATG
1005922 TTATTTAAAAAAATTTTAAA
1 TTATTTAAAAAAATTTTAAA
**
1005942 TTATTTTTAAAAATTTTAA
1 TTATTTAAAAAAATTTTAA
1005961 TTTTTTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTAAAAAAATTTTAAA
Found at i:1005962 original size:19 final size:19
Alignment explanation
Indices: 1005930--1005966 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1005920 TGTTATTTAA
1005930 AAAAATTTTAAATTATTTTT
1 AAAAATTTTAAATT-TTTTT
1005950 AAAAATTTT-AATTTTTT
1 AAAAATTTTAAATTTTTT
1005967 ATTGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAAAATTTTAAATTTTTTT
Found at i:1010302 original size:6 final size:6
Alignment explanation
Indices: 1010288--1010318 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1010278 CATCCATCAA
*
1010288 CCAATC CCAACC CCAACC CCAACC CCAACC C
1 CCAACC CCAACC CCAACC CCAACC CCAACC C
1010319 GGACGCCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (6 bp):
CCAACC
Found at i:1031499 original size:2 final size:2
Alignment explanation
Indices: 1031492--1031519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1031482 CATAAGATTG
1031492 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
1031520 CAGTTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1035589 original size:18 final size:19
Alignment explanation
Indices: 1035566--1035610 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1035556 GAGATTTTTA
1035566 AAATTTATATAAAAATT-T
1 AAATTTATATAAAAATTAT
1035584 AAATTT-T-TAAAAATTAT
1 AAATTTATATAAAAATTAT
1035601 ATAATTTATA
1 A-AATTTATA
1035611 CTTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
18 11 0.48
19 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTATATAAAAATTAT
Found at i:1040919 original size:31 final size:30
Alignment explanation
Indices: 1040858--1040922 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1040848 ATAGAACAAA
*
1040858 CCTAATCAAATAATAAAAATAAAAAAAAAT
1 CCTAATCAAATAATAAAAAGAAAAAAAAAT
**
1040888 CCTAATCTAAATAA-AATAAAGAAAATGAAAT
1 CCTAATC-AAATAATAA-AAAGAAAAAAAAAT
1040919 CCTA
1 CCTA
1040923 GACTAACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.63, C:0.12, G:0.03, T:0.22
Consensus pattern (30 bp):
CCTAATCAAATAATAAAAAGAAAAAAAAAT
Found at i:1042432 original size:25 final size:25
Alignment explanation
Indices: 1042402--1042461 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
1042392 GTATTAGAAC
1042402 TTTAATTTTAATAAAAATTAAATAT
1 TTTAATTTTAATAAAAATTAAATAT
1042427 TTTAATTTTAATAAAAATTAAATAT
1 TTTAATTTTAATAAAAATTAAATAT
1042452 TTTAATTTTA
1 TTTAATTTTA
1042462 TTAACTATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAATTTTAATAAAAATTAAATAT
Found at i:1043103 original size:17 final size:17
Alignment explanation
Indices: 1043081--1043148 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1043071 CAAAAAAAGT
1043081 AAATATATTTATATTTA
1 AAATATATTTATATTTA
* * *
1043098 AAATATATATATACTAA
1 AAATATATTTATATTTA
*
1043115 AAATAT-TTTAATATATA
1 AAATATATTT-ATATTTA
* *
1043132 TAATAGTAATTATATTT
1 AAATA-TATTTATATTT
1043149 TTTATAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
16 2 0.05
17 28 0.74
18 6 0.16
19 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
AAATATATTTATATTTA
Found at i:1043146 original size:26 final size:27
Alignment explanation
Indices: 1043089--1043149 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1043079 GTAAATATAT
1043089 TTATA-TTTAAAATATATATATACTAA
1 TTATATTTTAAAATATATATATACTAA
** * *
1043115 AAATATTTTAATATATATA-ATAGTAA
1 TTATATTTTAAAATATATATATACTAA
1043141 TTATATTTT
1 TTATATTTT
1043150 TTATAAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TTATATTTTAAAATATATATATACTAA
Found at i:1058968 original size:15 final size:14
Alignment explanation
Indices: 1058948--1058998 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1058938 TAGATACAAC
1058948 ATGATTACAGATAAT
1 ATGATTACA-ATAAT
*
1058963 ATGATTATAAATAAT
1 ATGATTA-CAATAAT
*
1058978 GTGATTACAAGTAAT
1 ATGATTACAA-TAAT
1058993 ATGATT
1 ATGATT
1058999 GTAAGTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 27 0.90
16 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (14 bp):
ATGATTACAATAAT
Found at i:1058983 original size:30 final size:31
Alignment explanation
Indices: 1058949--1059019 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
1058939 AGATACAACA
1058949 TGATTACAGA-TAATATGATTATAAATAATG
1 TGATTACAGAGTAATATGATTATAAATAATG
* *
1058979 TGATTACA-AGTAATATGATTGTAAGTAATG
1 TGATTACAGAGTAATATGATTATAAATAATG
*
1059009 TAATTACAGAG
1 TGATTACAGAG
1059020 AAAATAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.92
31 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (31 bp):
TGATTACAGAGTAATATGATTATAAATAATG
Found at i:1059004 original size:15 final size:15
Alignment explanation
Indices: 1058959--1059007 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1058949 TGATTACAGA
*
1058959 TAATATGATTATAAA
1 TAATATGATTATAAG
* *
1058974 TAATGTGATTACAAG
1 TAATATGATTATAAG
*
1058989 TAATATGATTGTAAG
1 TAATATGATTATAAG
1059004 TAAT
1 TAAT
1059008 GTAATTACAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (15 bp):
TAATATGATTATAAG
Found at i:1059171 original size:19 final size:20
Alignment explanation
Indices: 1059116--1059168 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1059106 CTTTAATAAG
1059116 AATAT-AATGTTAATTATTAA
1 AATATAAAT-TTAATTATTAA
**
1059136 AAT-TATCTTTAATTATTAA
1 AATATAAATTTAATTATTAA
1059155 AATATAAATTTAAT
1 AATATAAATTTAAT
1059169 ATTTATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATATAAATTTAATTATTAA
Found at i:1059226 original size:11 final size:12
Alignment explanation
Indices: 1059198--1059230 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1059188 AATTTTTATA
1059198 TAATATCATTTT
1 TAATATCATTTT
1059210 TAAATAT-ATTTT
1 T-AATATCATTTT
1059222 TAATATCAT
1 TAATATCAT
1059231 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATCATTTT
Found at i:1059265 original size:20 final size:20
Alignment explanation
Indices: 1059240--1059431 Score: 80
Period size: 20 Copynumber: 9.4 Consensus size: 20
1059230 TATATTTTAT
1059240 TTTTATTTATTATTATAATA
1 TTTTATTTATTATTATAATA
*
1059260 TTTTATATT-TTATTTTTAATATA
1 TTTTAT-TTATTA-TTAT-A-ATA
1059283 TTTGTATTTA-TATTATTAAT-
1 TTT-TATTTATTATTA-TAATA
* * *
1059303 TTTTATATAATATTATATTA
1 TTTTATTTATTATTATAATA
*
1059323 TATATATTT-TTAATGTCATAA-A
1 T-TTTATTTATT-AT-T-ATAATA
* *
1059345 TTTATTTTTATT-TTTTAATA
1 TTT-TATTTATTATTATAATA
* **
1059365 TATTTTTTTATT-TTATTTTA
1 T-TTTATTTATTATTATAATA
*
1059385 TTTTAATTTATT-TTACTTATA
1 TTTT-ATTTATTATTA-TAATA
*
1059406 TTATATTTA-TATTAT-ATA
1 TTTTATTTATTATTATAATA
1059424 TTTTATTT
1 TTTTATTT
1059432 TAATATTTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
18 10 0.07
19 16 0.12
20 53 0.40
21 25 0.19
22 11 0.08
23 16 0.12
24 3 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTATTTATTATTATAATA
Found at i:1059265 original size:26 final size:26
Alignment explanation
Indices: 1059243--1059383 Score: 92
Period size: 27 Copynumber: 5.2 Consensus size: 26
1059233 ATTTTATTTT
*
1059243 TATTTATTATTATAATATTTTATATTT
1 TATTT-TTAATATAATATTTTATATTT
* *
1059270 TATTTTTAATATATTTGTATTTATATTAT
1 TATTTTTAATATA-ATAT-TTTATATT-T
* *
1059299 TAATTTTT-ATATAATATTATATTATATA
1 T-ATTTTTAATATAATATTTTA-TAT-TT
* * *
1059327 TATTTTTAATGTCATAAATTTAT-TTT
1 TATTTTTAATATAAT-ATTTTATATTT
*
1059353 TATTTTTTAATAT-AT-TTTTTTATTT
1 TA-TTTTTAATATAATATTTTATATTT
1059378 TATTTT
1 TATTTT
1059384 ATTTTAATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
24 8 0.09
25 5 0.06
26 12 0.13
27 26 0.29
28 20 0.22
29 12 0.13
30 6 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TATTTTTAATATAATATTTTATATTT
Found at i:1059329 original size:34 final size:32
Alignment explanation
Indices: 1059205--1059332 Score: 104
Period size: 33 Copynumber: 4.0 Consensus size: 32
1059195 ATATAATATC
* *
1059205 ATTTTTAAAT-ATATTTTTAATATCATATATTTT
1 ATTTTTATATAATA-TTATAATAT-ATATATTTT
* * *
1059238 ATTTTTATTTATTATTATAATATTTTATATTTT
1 ATTTTTATATAATATTATAATA-TATATATTTT
* *
1059271 ATTTTTA-AT-ATATT-T-GTATTTATATTATT
1 ATTTTTATATAATATTATAATATATATATT-TT
*
1059300 AATTTTTATATAATATTATATTATATATATTTT
1 -ATTTTTATATAATATTATAATATATATATTTT
1059333 TAATGTCATA
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
28 8 0.10
29 4 0.05
30 8 0.10
31 6 0.08
32 6 0.08
33 33 0.43
34 12 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
ATTTTTATATAATATTATAATATATATATTTT
Found at i:1059370 original size:10 final size:10
Alignment explanation
Indices: 1059343--1059435 Score: 61
Period size: 10 Copynumber: 9.3 Consensus size: 10
1059333 TAATGTCATA
1059343 AATTTATTTT
1 AATTTATTTT
*
1059353 TA-TT-TTTT
1 AATTTATTTT
*
1059361 AATATATTTT
1 AATTTATTTT
1059371 --TTTATTTT
1 AATTTATTTT
*
1059379 ATTTTATTTT
1 AATTTATTTT
1059389 AATTTATTTT
1 AATTTATTTT
* *
1059399 -ACTTATATT
1 AATTTATTTT
1059408 ATATTTATATTAT
1 A-ATTTAT-TT-T
1059421 ATATTTTATTTT
1 A-A-TTTATTTT
1059433 AAT
1 AAT
1059436 ATTTTTATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
8 12 0.18
9 10 0.15
10 23 0.35
11 6 0.09
12 3 0.05
13 6 0.09
14 5 0.08
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (10 bp):
AATTTATTTT
Found at i:1059380 original size:5 final size:5
Alignment explanation
Indices: 1059370--1059447 Score: 68
Period size: 5 Copynumber: 15.0 Consensus size: 5
1059360 TAATATATTT
* * *
1059370 TTTTA TTTTA TTTTA TTTTA ATTTA TTTTA CTTATA TTATA TTTATA TTATATA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTT-TA TT-T-TA
* *
1059424 TTTTA TTTTA ATAT- TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
1059448 ATTATAACAT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
4 2 0.03
5 44 0.72
6 9 0.15
7 6 0.10
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:1059437 original size:20 final size:20
Alignment explanation
Indices: 1059219--1059461 Score: 62
Period size: 20 Copynumber: 12.7 Consensus size: 20
1059209 TTAAATATAT
*
1059219 TTTTAATATCATATATTTTA
1 TTTTAATATTATATATTTTA
1059239 TTTT--TA-T-T-TA--TTA
1 TTTTAATATTATATATTTTA
* *
1059252 TTATAATATTTTATATTTTA
1 TTTTAATATTATATATTTTA
1059272 TTTT--TA--ATATATTTGTA
1 TTTTAATATTATATATTT-TA
*
1059289 TTTATATTATTA-AT-TTTTA
1 TTT-TAATATTATATATTTTA
* *
1059308 -TATAATATTATATTATATATA
1 TTTTAATATTATA-TAT-TTTA
* * *
1059329 TTTTTAATGTCATA-AATTTA
1 -TTTTAATATTATATATTTTA
* * * *
1059349 TTTTTATTTTTTAATATATT-
1 TTTTAATATTAT-ATATTTTA
1059369 TTTT--TATT-T-TATTTTA
1 TTTTAATATTATATATTTTA
* *
1059385 TTTTAATTTATTTTACTTATATTA
1 TTTTAA--TATTATA--TATTTTA
1059409 TATTT-ATATTATATATTTTA
1 T-TTTAATATTATATATTTTA
*
1059429 TTTTAATATT-TTTATTTTAA
1 TTTTAATATTATATATTTT-A
* *
1059449 TTATAACATTATA
1 TTTTAATATTATA
1059462 AAATATTTTT
Statistics
Matches: 162, Mismatches: 27, Indels: 67
0.63 0.11 0.26
Matches are distributed among these distances:
13 6 0.04
15 9 0.06
16 13 0.08
17 14 0.09
18 12 0.07
19 21 0.13
20 49 0.30
21 11 0.07
22 7 0.04
23 9 0.06
24 8 0.05
25 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTAATATTATATATTTTA
Found at i:1059437 original size:26 final size:26
Alignment explanation
Indices: 1059224--1059444 Score: 80
Period size: 26 Copynumber: 8.2 Consensus size: 26
1059214 TATATTTTTA
*
1059224 ATATCATATATTTTATTTT--TATTT
1 ATATTATATATTTTATTTTAATATTT
* *
1059248 ATTATTATAATATTTTATATTTTATTTTT
1 A-TATTAT-ATATTTTAT-TTTAATATTT
* * *
1059277 AATATATTTGTATTTATATTATTAATTTTT
1 -ATAT-TATATATTT-TATT-TTAATATTT
* *
1059307 ATA-TA-ATATTATATTATATATATTT
1 ATATTATATATTTTATTTTA-ATATTT
* * *
1059332 TTAATGTCATA-AATTTATTTTTAT-TTT
1 AT-AT-T-ATATATTTTATTTTAATATTT
* * *
1059359 TTAATATATTTTTTTATTTT-AT-TTT
1 ATATTATA-TATTTTATTTTAATATTT
* * *
1059384 ATTTTAATTTATTTTACTTATATTATATTT
1 ATATT-ATATATTTTA-TT-T-TAATATTT
1059414 ATATTATATATTTTATTTTAATATTT
1 ATATTATATATTTTATTTTAATATTT
*
1059440 TTATT
1 ATATT
1059445 TTAATTATAA
Statistics
Matches: 147, Mismatches: 27, Indels: 44
0.67 0.12 0.20
Matches are distributed among these distances:
24 6 0.04
25 29 0.20
26 38 0.26
27 11 0.07
28 6 0.04
29 35 0.24
30 22 0.15
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
ATATTATATATTTTATTTTAATATTT
Found at i:1059445 original size:14 final size:14
Alignment explanation
Indices: 1059347--1059449 Score: 66
Period size: 14 Copynumber: 7.1 Consensus size: 14
1059337 GTCATAAATT
1059347 TATTTTTATTTTTTAA
1 TATTTTTA--TTTTAA
* *
1059363 TATATTT-TTTTAT
1 TATTTTTATTTTAA
*
1059376 TTTATTTTATTTTAA
1 TAT-TTTTATTTTAA
* * *
1059391 TTTATTTTACTTATAT
1 TAT-TTTTA-TTTTAA
* *
1059407 TATATTTATATT-A
1 TATTTTTATTTTAA
1059420 TATATTTTATTTTAA
1 TAT-TTTTATTTTAA
1059435 TATTTTTATTTTAA
1 TATTTTTATTTTAA
1059449 T
1 T
1059450 TATAACATTA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
13 10 0.15
14 24 0.35
15 22 0.32
16 12 0.18
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:1079308 original size:27 final size:27
Alignment explanation
Indices: 1079266--1079331 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
1079256 CAGGACAGGT
**
1079266 CTCAGGCTTCCCATCATCTTTCTTCGG
1 CTCAGGCTTCTTATCATCTTTCTTCGG
*
1079293 GTCAGGCTTCTTATCATCTTTCTTCGG
1 CTCAGGCTTCTTATCATCTTTCTTCGG
1079320 CTCAGGCTTCTT
1 CTCAGGCTTCTT
1079332 CTCTTTGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.11, C:0.32, G:0.17, T:0.41
Consensus pattern (27 bp):
CTCAGGCTTCTTATCATCTTTCTTCGG
Found at i:1086722 original size:36 final size:36
Alignment explanation
Indices: 1086682--1086766 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
1086672 ATTCAAGGTT
* *
1086682 AAACTATTTCTTTGATCT-TCTAGTTGTATCAGGGTA
1 AAACTATTTCCTTGATCTCT-TAGATGTATCAGGGTA
*
1086718 AAACTATTTCCTTGATCTCTTAGATGTTTCAGGGTA
1 AAACTATTTCCTTGATCTCTTAGATGTATCAGGGTA
*
1086754 AAAGTA-TTCCTTG
1 AAACTATTTCCTTG
1086767 TATTGTATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 7 0.16
36 36 0.82
37 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (36 bp):
AAACTATTTCCTTGATCTCTTAGATGTATCAGGGTA
Found at i:1087283 original size:20 final size:21
Alignment explanation
Indices: 1087258--1087297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1087248 TATCAATTCA
1087258 TGAG-AAACCATAAAT-TTTTT
1 TGAGAAAACCA-AAATCTTTTT
1087278 TGAGAAAACCAAAATCTTTT
1 TGAGAAAACCAAAATCTTTT
1087298 CGTAGACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (21 bp):
TGAGAAAACCAAAATCTTTTT
Found at i:1087288 original size:21 final size:19
Alignment explanation
Indices: 1087258--1087297 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1087248 TATCAATTCA
*
1087258 TGAGAAACCATAAATTTTTT
1 TGAGAAACCA-AAATCTTTT
1087278 TGAGAAAACCAAAATCTTTT
1 TGAG-AAACCAAAATCTTTT
1087298 CGTAGACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TGAGAAACCAAAATCTTTT
Found at i:1089166 original size:26 final size:25
Alignment explanation
Indices: 1089137--1089197 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 25
1089127 AAAAAATATA
1089137 TTTATTAAATAATAAAAAATT-TATTT
1 TTTATTAAAT-ATAAAAAATTAT-TTT
1089163 TTTA--AAATATAAAAAATTATTTT
1 TTTATTAAATATAAAAAATTATTTT
1089186 TTTATT-AATATA
1 TTTATTAAATATA
1089198 CACAAAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 17 0.53
24 11 0.34
26 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTATTAAATATAAAAAATTATTTT
Found at i:1089186 original size:23 final size:25
Alignment explanation
Indices: 1089127--1089189 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
1089117 TTGTCAATTC
*
1089127 AAAAAA-TATATTTATT-AAATAAT
1 AAAAAATTATATTTTTTAAAATAAT
1089150 AAAAAATT-TATTTTTTAAAAT-AT
1 AAAAAATTATATTTTTTAAAATAAT
1089173 AAAAAATTAT-TTTTTTA
1 AAAAAATTATATTTTTTA
1089190 TTAATATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 30 0.83
24 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAAATTATATTTTTTAAAATAAT
Found at i:1089561 original size:116 final size:115
Alignment explanation
Indices: 1089382--1089682 Score: 458
Period size: 116 Copynumber: 2.6 Consensus size: 115
1089372 TTATTTTAAA
* * * * * *
1089382 ATTTTATAATTTTACTCTTATTTTGTAAAACATTTTATAATTTCATTCCTTCAAATATTAAATTT
1 ATTTTAAAATTTTACTTTTATTTT-TAAAAAAATTTATAATTTCACTCCTCCAAATATTAAATTT
* *
1089447 TTTATGTATACCTCTCAAAGTTTTAAAATTTTATGATTTCATCTTTATTTT
65 TTTATGTATACCTCTCAAAGTTTTAAAAATTTATAATTTCATCTTTATTTT
* * *
1089498 GTTTTAAAATTTTACTTTTATTTTTCAAAAAAATTTATAATTTCAGTCCTCCAATTATTAAATTT
1 ATTTTAAAATTTTACTTTTATTTTT-AAAAAAATTTATAATTTCACTCCTCCAAATATTAAATTT
* *
1089563 TTTATTTTTACCTCTCAAAGTTTTAAAAATTTATAATTTCATCTTTATTTT
65 TTTATGTATACCTCTCAAAGTTTTAAAAATTTATAATTTCATCTTTATTTT
*
1089614 ATTTTAAAATTTTACTTTTATTTTTTAAAAAATTTATAATTTCACTCCTCCAAATATTAAATTTT
1 ATTTTAAAATTTTACTTTTATTTTTAAAAAAATTTATAATTTCACTCCTCCAAATATTAAATTTT
1089679 TTAT
66 TTAT
1089683 TTTCATCCGT
Statistics
Matches: 168, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
115 42 0.25
116 126 0.75
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (115 bp):
ATTTTAAAATTTTACTTTTATTTTTAAAAAAATTTATAATTTCACTCCTCCAAATATTAAATTTT
TTATGTATACCTCTCAAAGTTTTAAAAATTTATAATTTCATCTTTATTTT
Found at i:1102082 original size:15 final size:17
Alignment explanation
Indices: 1102043--1102083 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1102033 TATTATTTTC
1102043 AAATATTGAATTCTATA
1 AAATATTGAATTCTATA
*
1102060 AGAATATTTAATT-TAT-
1 A-AATATTGAATTCTATA
1102076 AAATATTG
1 AAATATTG
1102084 TTTTCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 1 0.05
17 4 0.19
18 10 0.48
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (17 bp):
AAATATTGAATTCTATA
Found at i:1103014 original size:24 final size:25
Alignment explanation
Indices: 1102986--1103032 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1102976 CCAGCTATAA
* *
1102986 AATTTAA-TATTAGTATTTTATTTG
1 AATTTAATTAATAATATTTTATTTG
1103010 AATTTAATTAATAATATTTTATT
1 AATTTAATTAATAATATTTTATT
1103033 AAAATCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
AATTTAATTAATAATATTTTATTTG
Found at i:1105269 original size:37 final size:38
Alignment explanation
Indices: 1105228--1105304 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1105218 AATCTACCAG
*
1105228 GACTTGAAATACT-TTATCTACTTTTTCTAAAATATTT
1 GACTTGAAATACTCTTATCTACTTTTTCTAAAACATTT
* *
1105265 GACTTGAAATACTCTTATCTATTTTTTCTGAAACATTT
1 GACTTGAAATACTCTTATCTACTTTTTCTAAAACATTT
1105303 GA
1 GA
1105305 TGTGACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 13 0.36
38 23 0.64
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (38 bp):
GACTTGAAATACTCTTATCTACTTTTTCTAAAACATTT
Found at i:1108976 original size:45 final size:45
Alignment explanation
Indices: 1108827--1108969 Score: 196
Period size: 45 Copynumber: 3.2 Consensus size: 45
1108817 CACGTCATGA
* * *
1108827 TGTTACACACCATGTACAGAAACGTGTTACATGTCATGGTTAAAT
1 TGTTACACACCATGTACAAAAACGTGTTACACGTCATGGTTAGAT
* * * *
1108872 TATTACACACCATGTACAAAAACGTGTGACACGTTATGGTTAGGT
1 TGTTACACACCATGTACAAAAACGTGTTACACGTCATGGTTAGAT
* * *
1108917 TGTTACACGCCATGTACAAAAACATGTTACACGCCATGGTTAGAT
1 TGTTACACACCATGTACAAAAACGTGTTACACGTCATGGTTAGAT
1108962 TGTTACAC
1 TGTTACAC
1108970 GTCATGTTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
TGTTACACACCATGTACAAAAACGTGTTACACGTCATGGTTAGAT
Found at i:1109093 original size:29 final size:29
Alignment explanation
Indices: 1109060--1109136 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
1109050 TGTCATCTTA
1109060 AAAAAAATATTATTATTACACACCATATT
1 AAAAAAATATTATTATTACACACCATATT
*
1109089 AAAAAAATATTATTGTTACACACCATATT
1 AAAAAAATATTATTATTACACACCATATT
* *
1109118 -CAAAAATATT-TTACTACAC
1 AAAAAAATATTATTATTACAC
1109137 TTTAATACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.16
28 9 0.20
29 28 0.64
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAAAAATATTATTATTACACACCATATT
Found at i:1109095 original size:81 final size:76
Alignment explanation
Indices: 1108927--1109080 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
1108917 TGTTACACGC
* * * *
1108927 CATGTACAAAAACATGTTACACGCCATGGTTAGATTGTTACACGTCATGTTAAAATAAAATAATG
1 CATGTAAAAAAACATATTACACGCCATGGTTAGATTGTTACACGTCATCTTAAAATAAAATAATA
*
1108992 TTGTTACACTA
66 TTATTACACTA
* *
1109003 CATGTACAAAAACATATTACACGCCATGGTTAAAAAAGATTGTTACATGTCATCTTAAAA-AAAA
1 CATGTAAAAAAACATATTACACGCCATGGTT-----AGATTGTTACACGTCATCTTAAAATAAAA
*
1109067 TATTATTATTACAC
61 TAATATTATTACAC
1109081 ACCATATTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
76 30 0.45
80 15 0.22
81 22 0.33
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (76 bp):
CATGTAAAAAAACATATTACACGCCATGGTTAGATTGTTACACGTCATCTTAAAATAAAATAATA
TTATTACACTA
Found at i:1113821 original size:58 final size:58
Alignment explanation
Indices: 1113742--1113869 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 58
1113732 CAAAGGTAAT
* * * *
1113742 TTGTATTGATTTTTAGCACATGTGAACTATGATTTTAAATTGTTGTTTGTACTTGATC
1 TTGTGTTGATTTTTAGCACATGTGAACTATGATATTAAACTGTTGTTTGTACATGATC
* *** *
1113800 TTGTGTTGATTTTTAGCACATGTGAGCTATGATATTGGGCTGTTGTTTGTACATGATT
1 TTGTGTTGATTTTTAGCACATGTGAACTATGATATTAAACTGTTGTTTGTACATGATC
*
1113858 TTGTGCTGATTT
1 TTGTGTTGATTT
1113870 AATTGTAGTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.49
Consensus pattern (58 bp):
TTGTGTTGATTTTTAGCACATGTGAACTATGATATTAAACTGTTGTTTGTACATGATC
Found at i:1117943 original size:37 final size:38
Alignment explanation
Indices: 1117875--1117951 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1117865 TTTTGTCACA
*
1117875 TCAAATGTTTCAGAAAAAATAGATAAGAGTATTTCAAG
1 TCAAATATTTCAGAAAAAATAGATAAGAGTATTTCAAG
* *
1117913 TCAAATATTTTAGAAAAAGTAGATAA-AGTATTTCAAG
1 TCAAATATTTCAGAAAAAATAGATAAGAGTATTTCAAG
1117950 TC
1 TC
1117952 CTGGTAGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 13 0.36
38 23 0.64
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (38 bp):
TCAAATATTTCAGAAAAAATAGATAAGAGTATTTCAAG
Found at i:1129517 original size:19 final size:19
Alignment explanation
Indices: 1129484--1129540 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1129474 TTTAAAATTT
*
1129484 AAATTATATTTTTAAATAAA
1 AAATTATA-TATTAAATAAA
*
1129504 AAATTATATATT-AATCAAT
1 AAATTATATATTAAAT-AAA
*
1129523 AAATTAAATATTTAAATA
1 AAATTATATA-TTAAATA
1129541 CAATTAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.10
19 14 0.45
20 11 0.35
21 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATATATTAAATAAA
Found at i:1130830 original size:6 final size:6
Alignment explanation
Indices: 1130819--1130845 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1130809 TTCTCTTCTC
1130819 TGAGAT TGAGAT TGAGAT TGAGAT TGA
1 TGAGAT TGAGAT TGAGAT TGAGAT TGA
1130846 TAAAATCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAGAT
Found at i:1134929 original size:14 final size:15
Alignment explanation
Indices: 1134892--1134932 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1134882 AATCTACCAG
1134892 GACTTGAAATACTTT
1 GACTTGAAATACTTT
* *
1134907 GTC-TAAAATA-TTT
1 GACTTGAAATACTTT
1134920 GACTTGAAATACT
1 GACTTGAAATACT
1134933 CTTTATCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 4
0.71 0.14 0.14
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (15 bp):
GACTTGAAATACTTT
Found at i:1152103 original size:18 final size:18
Alignment explanation
Indices: 1152058--1152099 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1152048 GGTTAAATAA
1152058 ATATTT-ATTATATTATT
1 ATATTTAATTATATTATT
*
1152075 ATATTTAATTATATTTTT
1 ATATTTAATTATATTATT
1152093 AT-TTTAA
1 ATATTTAA
1152100 ATTAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTAATTATATTATT
Found at i:1155839 original size:16 final size:18
Alignment explanation
Indices: 1155803--1155849 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1155793 TGATATTTAT
* *
1155803 TTTTAATTTTTTTTCTCA
1 TTTTAACTTTTTTTCTAA
*
1155821 -TTTACCTTTTTTT-TAA
1 TTTTAACTTTTTTTCTAA
1155837 TTTTAACTTTTTT
1 TTTTAACTTTTTT
1155850 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAACTTTTTTTCTAA
Found at i:1162446 original size:39 final size:38
Alignment explanation
Indices: 1162364--1162457 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
1162354 ATTCTCCATA
** *
1162364 TCTTCTCACTTTCTTCTAGTTCACGAGCTTCCTTCTCTT
1 TCTTCTCA-TTTCTTCTAGTTCACGAGCTTCCTTCAATC
* *
1162403 TCTTCTCGATTTCTTCTCGTTCATGAGCTTCCTTCAATC
1 TCTTCTC-ATTTCTTCTAGTTCACGAGCTTCCTTCAATC
*
1162442 TCTTCTCTTTTTCTTC
1 TCTTCTC-ATTTCTTC
1162458 CTGTTCGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 46 0.98
40 1 0.02
ACGTcount: A:0.10, C:0.32, G:0.07, T:0.51
Consensus pattern (38 bp):
TCTTCTCATTTCTTCTAGTTCACGAGCTTCCTTCAATC
Found at i:1176290 original size:19 final size:19
Alignment explanation
Indices: 1176266--1176304 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1176256 CATTAACAAA
*
1176266 ACTAATCCATTAAGTATTT
1 ACTAATCCATTAAATATTT
*
1176285 ACTAATTCATTAAATATTT
1 ACTAATCCATTAAATATTT
1176304 A
1 A
1176305 GTGATATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (19 bp):
ACTAATCCATTAAATATTT
Found at i:1177164 original size:25 final size:25
Alignment explanation
Indices: 1177122--1177170 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1177112 TTTTATTTTA
1177122 AATTAAATAAGTTATATTAATTAAT
1 AATTAAATAAGTTATATTAATTAAT
* * *
1177147 AATTAATTAATTTTTATTAATTAA
1 AATTAAATAAGTTATATTAATTAA
1177171 AATATTACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTAAATAAGTTATATTAATTAAT
Found at i:1177260 original size:13 final size:13
Alignment explanation
Indices: 1177239--1177281 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1177229 AAAAATATCA
1177239 TATGATCATATTAT
1 TATG-TCATATTAT
*
1177253 TATGTCATATTAA
1 TATGTCATATTAT
* *
1177266 CATGTTATATTAT
1 TATGTCATATTAT
1177279 TAT
1 TAT
1177282 CGATTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (13 bp):
TATGTCATATTAT
Found at i:1179752 original size:40 final size:40
Alignment explanation
Indices: 1179708--1179787 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1179698 CTCAAAGGTT
1179708 TTTTGATTTTATTTCTCTTGCTTGGATTGATTAGATGCAG
1 TTTTGATTTTATTTCTCTTGCTTGGATTGATTAGATGCAG
1179748 TTTTGATTTTATTTCTCTTGCTTGGATTGATTAGATGCAG
1 TTTTGATTTTATTTCTCTTGCTTGGATTGATTAGATGCAG
1179788 CATGTTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (40 bp):
TTTTGATTTTATTTCTCTTGCTTGGATTGATTAGATGCAG
Found at i:1196599 original size:22 final size:22
Alignment explanation
Indices: 1196574--1196624 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1196564 TATAAATATT
1196574 ATTTATAT-TATGTTTATATTTA
1 ATTTATATGTAT-TTTATATTTA
1196596 ATTT-TAATGTATTTTATATTTA
1 ATTTAT-ATGTATTTTATATTTA
1196618 A-TTATAT
1 ATTTATAT
1196625 CTAACACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 5 0.19
22 18 0.69
23 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
ATTTATATGTATTTTATATTTA
Found at i:1217229 original size:36 final size:36
Alignment explanation
Indices: 1217137--1217264 Score: 170
Period size: 36 Copynumber: 3.4 Consensus size: 36
1217127 GGAATCAAAG
1217137 CTAAATTAACAGCAAATTGGC-TATATCTAGTTGTAT
1 CTAAATTAACAGCAAATT-GCTTATATCTAGTTGTAT
*
1217173 -TATTTTCTTATTAACAGCAAATTGCTTATATCTAGTTGTAT
1 CTA------AATTAACAGCAAATTGCTTATATCTAGTTGTAT
1217214 CTAAATTAACAGCAAATTGCTTATATCTAGTTGTAT
1 CTAAATTAACAGCAAATTGCTTATATCTAGTTGTAT
1217250 CTAAATTAACAGCAA
1 CTAAATTAACAGCAA
1217265 GCATGCACAC
Statistics
Matches: 82, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
35 2 0.02
36 47 0.57
40 2 0.02
41 29 0.35
42 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (36 bp):
CTAAATTAACAGCAAATTGCTTATATCTAGTTGTAT
Found at i:1224637 original size:41 final size:42
Alignment explanation
Indices: 1224587--1224666 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1224577 ATAAAAACAA
* * *
1224587 CCCAAAATCCGACAAAT-AAAAAAAATCCAGCCAATAAAGAG
1 CCCAAAATCCAACAAATAAAAAAAAATCCAACAAATAAAGAG
1224628 CCCAAAATCCAACAAATAAAAAAAAATCCAACAAATAAA
1 CCCAAAATCCAACAAATAAAAAAAAATCCAACAAATAAA
1224667 ACAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 16 0.46
42 19 0.54
ACGTcount: A:0.61, C:0.24, G:0.05, T:0.10
Consensus pattern (42 bp):
CCCAAAATCCAACAAATAAAAAAAAATCCAACAAATAAAGAG
Found at i:1224682 original size:19 final size:19
Alignment explanation
Indices: 1224590--1224674 Score: 82
Period size: 19 Copynumber: 4.3 Consensus size: 19
1224580 AAAACAACCC
*
1224590 AAAATCCGACAAAT-AAAA
1 AAAATCCAACAAATAAAAA
* * *
1224608 AAAATCCAGCCAATAAAGAGCCC
1 AAAATCCAACAAATAAA-A---A
1224631 AAAATCCAACAAATAAAAA
1 AAAATCCAACAAATAAAAA
*
1224650 AAAATCCAACAAATAAAAC
1 AAAATCCAACAAATAAAAA
1224669 AAAATC
1 AAAATC
1224675 TACAAAATCG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.20
19 26 0.48
20 1 0.02
22 1 0.02
23 15 0.28
ACGTcount: A:0.64, C:0.21, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAATCCAACAAATAAAAA
Found at i:1244337 original size:17 final size:18
Alignment explanation
Indices: 1244315--1244349 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1244305 ATAATTTCTG
*
1244315 TTTTTAT-ATTAAAAATA
1 TTTTTATCATAAAAAATA
1244332 TTTTTATCATAAAAAATA
1 TTTTTATCATAAAAAATA
1244350 ATATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTATCATAAAAAATA
Found at i:1260672 original size:18 final size:19
Alignment explanation
Indices: 1260631--1260690 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
1260621 ATTACAAAAA
*
1260631 AAAAAAAG-ATTTTTT-TC
1 AAAAAAAGTTTTTTTTGTC
*
1260648 AACAAAA-TTTTTTTTGTC
1 AAAAAAAGTTTTTTTTGTC
*
1260666 AAAAAAAGTTTATTTTAGTC
1 AAAAAAAGTTT-TTTTTGTC
1260686 AAAAA
1 AAAAA
1260691 TGTCTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.34
18 8 0.23
19 3 0.09
20 12 0.34
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
AAAAAAAGTTTTTTTTGTC
Found at i:1260686 original size:20 final size:18
Alignment explanation
Indices: 1260646--1260690 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1260636 AAGATTTTTT
* *
1260646 TCAACAAAATTTTTTTTG
1 TCAAAAAAATTTTTTTAG
1260664 TCAAAAAAAGTTTATTTTAG
1 TCAAAAAAA-TTT-TTTTAG
1260684 TCAAAAA
1 TCAAAAA
1260691 TGTCTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 3 0.13
20 12 0.52
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (18 bp):
TCAAAAAAATTTTTTTAG
Found at i:1261077 original size:14 final size:14
Alignment explanation
Indices: 1261058--1261091 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1261048 TAGTTTTGAG
1261058 TTGAATGCTAATTA
1 TTGAATGCTAATTA
1261072 TTGAATGCTAATTA
1 TTGAATGCTAATTA
1261086 TTGAAT
1 TTGAAT
1261092 TTATTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (14 bp):
TTGAATGCTAATTA
Found at i:1263174 original size:60 final size:61
Alignment explanation
Indices: 1263082--1263210 Score: 190
Period size: 60 Copynumber: 2.1 Consensus size: 61
1263072 AAAACATTTA
* * *
1263082 AGCA-TTTTAAGTATTTCAGAGTAGCTTTTGATACATGAAAAAAA-CTTTTGAGCGTTTTG
1 AGCATTTTTAAGTATTTCAGAGTAACTTTTGATACATGAAAAAAACCCTTTGAGCCTTTTG
* * *
1263141 AGCATTTTTAAGTATTTTAGAGTAATTTTTGATATATGAAAAAAACCCTTTGAGCCTTTTG
1 AGCATTTTTAAGTATTTCAGAGTAACTTTTGATACATGAAAAAAACCCTTTGAGCCTTTTG
1263202 AGCATTTTT
1 AGCATTTTT
1263211 TGTCAAGTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
59 4 0.06
60 36 0.58
61 22 0.35
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (61 bp):
AGCATTTTTAAGTATTTCAGAGTAACTTTTGATACATGAAAAAAACCCTTTGAGCCTTTTG
Found at i:1263379 original size:44 final size:44
Alignment explanation
Indices: 1263307--1263393 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
1263297 GTAGTTTTGG
* *
1263307 TAGTTTTTAAGTATTACGTAATTGATTTTTGAACATTGTGTGAT
1 TAGTTTTTAAGTATTACGTAACTAATTTTTGAACATTGTGTGAT
* * *
1263351 TAGTTTTTAGGTATTACGTTACTAATTTTTGAGCATTGTGTGA
1 TAGTTTTTAAGTATTACGTAACTAATTTTTGAACATTGTGTGA
1263394 CTGACTTCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (44 bp):
TAGTTTTTAAGTATTACGTAACTAATTTTTGAACATTGTGTGAT
Found at i:1263563 original size:22 final size:22
Alignment explanation
Indices: 1263535--1263671 Score: 118
Period size: 22 Copynumber: 6.3 Consensus size: 22
1263525 TAAGCATTGT
1263535 TTAAAAATTAATCACGTAATAC
1 TTAAAAATTAATCACGTAATAC
1263557 TTAAAAATTAATCACGTAATAC
1 TTAAAAATTAATCACGTAATAC
* * *
1263579 CT-AAAATCAATCACGTAATGC
1 TTAAAAATTAATCACGTAATAC
* * ** *
1263600 TTAAAAATTAGTTATATAAT-G
1 TTAAAAATTAATCACGTAATAC
*
1263621 TCT-AAAATTAGTCACGTAATAC
1 T-TAAAAATTAATCACGTAATAC
* * * * *
1263643 CTAAAATTTAGTCTCATAATAC
1 TTAAAAATTAATCACGTAATAC
1263665 TTAAAAA
1 TTAAAAA
1263672 CTAGTTTAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 34 0.37
22 57 0.63
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (22 bp):
TTAAAAATTAATCACGTAATAC
Found at i:1263626 original size:43 final size:43
Alignment explanation
Indices: 1263538--1263670 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 43
1263528 GCATTGTTTA
* *
1263538 AAAATTAATCACGTAATACTTAAAAATTAATCACGTAATACCT
1 AAAATTAATCACGTAATACTTAAAAATTAGTCACATAATACCT
* * * * **
1263581 AAAATCAATCACGTAATGCTTAAAAATTAGTTATATAATGTCT
1 AAAATTAATCACGTAATACTTAAAAATTAGTCACATAATACCT
* * * * *
1263624 AAAATTAGTCACGTAATACCTAAAATTTAGTCTCATAATACTT
1 AAAATTAATCACGTAATACTTAAAAATTAGTCACATAATACCT
1263667 AAAA
1 AAAA
1263671 ACTAGTTTAA
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (43 bp):
AAAATTAATCACGTAATACTTAAAAATTAGTCACATAATACCT
Found at i:1270325 original size:17 final size:17
Alignment explanation
Indices: 1270300--1270353 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 17
1270290 TCGATCGACT
*
1270300 AAAAATATT-ATTTACTC
1 AAAATTATTAATTTA-TC
1270317 AAAATTATTAATTTATC
1 AAAATTATTAATTTATC
1270334 -AAA-TATTAATTTAT-
1 AAAATTATTAATTTATC
1270348 AAAATT
1 AAAATT
1270354 TATACTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 14 0.42
16 4 0.12
17 10 0.30
18 5 0.15
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTATTAATTTATC
Found at i:1270341 original size:18 final size:17
Alignment explanation
Indices: 1270300--1270341 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1270290 TCGATCGACT
*
1270300 AAAAATATTATTTACTC
1 AAAATTATTATTTACTC
1270317 AAAATTATTAATTTA-TC
1 AAAATTATT-ATTTACTC
1270334 AAATATTA
1 AAA-ATTA
1270342 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTATTATTTACTC
Found at i:1282531 original size:14 final size:15
Alignment explanation
Indices: 1282512--1282547 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1282502 TGGGGTTGTT
1282512 TTCTTTCCTTTTTC-
1 TTCTTTCCTTTTTCG
*
1282526 TTCTTTCTTTTTTCG
1 TTCTTTCCTTTTTCG
1282541 TTCTTTC
1 TTCTTTC
1282548 ATCTTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (15 bp):
TTCTTTCCTTTTTCG
Found at i:1286473 original size:5 final size:5
Alignment explanation
Indices: 1286465--1286494 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1286455 AATTTTGTAT
1286465 TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC
1 TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC
1286495 ATGCCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.20, T:0.60
Consensus pattern (5 bp):
TTTGC
Found at i:1287082 original size:12 final size:12
Alignment explanation
Indices: 1287065--1287098 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1287055 GATTTCCCTC
1287065 TTTTTCTTTTCT
1 TTTTTCTTTTCT
1287077 TTTTTC-TTTCT
1 TTTTTCTTTTCT
1287088 TTCTTTCTTTT
1 TT-TTTCTTTT
1287099 TACCTGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 10 0.50
13 3 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:1287108 original size:20 final size:20
Alignment explanation
Indices: 1287067--1287108 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1287057 TTTCCCTCTT
* *
1287067 TTTCTTTTCTTTTTTCTTTC
1 TTTCTTTTCTTTTTCCTGTC
1287087 TTTC-TTTCTTTTTACCTGTC
1 TTTCTTTTCTTTTT-CCTGTC
1287107 TT
1 TT
1287109 GTGAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTCTTTTCTTTTTCCTGTC
Found at i:1290998 original size:48 final size:48
Alignment explanation
Indices: 1290939--1291034 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
1290929 CATTTATTTT
* *
1290939 CAATTTGCAATGTTTTATTTACTATACTATTCAATTAACTGATAATGC
1 CAATTTCCAATGTTTTATTTACTACACTATTCAATTAACTGATAATGC
* *
1290987 CAATTTCCAATGTTTTATTTACTACACTATTTAATTAACTTATAATGC
1 CAATTTCCAATGTTTTATTTACTACACTATTCAATTAACTGATAATGC
1291035 ATAGGTTCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (48 bp):
CAATTTCCAATGTTTTATTTACTACACTATTCAATTAACTGATAATGC
Found at i:1301971 original size:12 final size:11
Alignment explanation
Indices: 1301938--1301971 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1301928 AAATTAAAAA
1301938 TTAAAAATATT
1 TTAAAAATATT
1301949 TTAAAATATATAT
1 TTAAAA-ATAT-T
1301962 TTAAAAATAT
1 TTAAAAATAT
1301972 GAGCATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 8 0.38
13 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAAAATATT
Done.