Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 74 of 206
Found at i:20873472 original size:2 final size:2
Alignment explanation
Indices: 20873465--20873491 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20873455 AGAATCTTAA
20873465 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20873492 GATTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20878646 original size:67 final size:67
Alignment explanation
Indices: 20878532--20878788 Score: 324
Period size: 67 Copynumber: 3.8 Consensus size: 67
20878522 AAGGTATAGG
* *
20878532 GTGTAAGACCATAGCTCAACTATGGCAACGA-ATG-GA-TTCTGTTGGGACAGTAAACATGGGGT
1 GTGTAAGACCATAGCTCAACTATGACAAC-ATA-GAGAGTTC-GTAGGGACAGTAAACATGGGGT
20878594 ATGTT
63 ATGTT
*
20878599 GTGTAAGACCATAGCTCATCTATGACAACATAGAGAGTTCGTAGGGACAGTAAACATGGGGTATG
1 GTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCGTAGGGACAGTAAACATGGGGTATG
20878664 TT
66 TT
** * * * *
20878666 GTGTAAGACCATAGCTCGGCTATGACAGCATAGAGAGTTTGCTA-GGACAGTAAACACGAGGTAT
1 GTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCG-TAGGGACAGTAAACATGGGGTAT
20878730 GTT
65 GTT
* * * * *
20878733 GTGTAAGACCATAGGTCAACTATGGCAACATAGAGAGTCCGTTGGGATAGTAAACA
1 GTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCGTAGGGACAGTAAACA
20878789 CGGGAAGTCT
Statistics
Matches: 167, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
66 3 0.02
67 159 0.95
68 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (67 bp):
GTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCGTAGGGACAGTAAACATGGGGTATG
TT
Found at i:20880764 original size:27 final size:26
Alignment explanation
Indices: 20880719--20880791 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
20880709 TAGTTCGCCA
* * * * *
20880719 AGACACTAAACATGGGGTAATCTATTG
1 AGACATTAAACACGAGGTAATCT-GTC
*
20880746 AGACATTAAACACGAGGTAGTCTGTC
1 AGACATTAAACACGAGGTAATCTGTC
*
20880772 AGGACATTAAACACAAGGTA
1 A-GACATTAAACACGAGGTA
20880792 GCCCGTCAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (26 bp):
AGACATTAAACACGAGGTAATCTGTC
Found at i:20880792 original size:27 final size:27
Alignment explanation
Indices: 20880747--20880803 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
20880737 AATCTATTGA
* * *
20880747 GACATTAAACACGAGGTAGTCTGTCAG
1 GACATTAAACACAAGGTAGCCCGTCAG
20880774 GACATTAAACACAAGGTAGCCCGTCAG
1 GACATTAAACACAAGGTAGCCCGTCAG
20880801 GAC
1 GAC
20880804 GTTATGTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
GACATTAAACACAAGGTAGCCCGTCAG
Found at i:20887028 original size:20 final size:20
Alignment explanation
Indices: 20887003--20887052 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
20886993 TATCAGTCCT
* *
20887003 ATGAATAGTGGGGTCAAGTC
1 ATGAATAGTGGAGTCAAATC
*
20887023 ATGAATAGTAGAGTCAAATC
1 ATGAATAGTGGAGTCAAATC
20887043 ATGAATAGTG
1 ATGAATAGTG
20887053 ATAACATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (20 bp):
ATGAATAGTGGAGTCAAATC
Found at i:20892903 original size:70 final size:69
Alignment explanation
Indices: 20892778--20893341 Score: 422
Period size: 70 Copynumber: 8.1 Consensus size: 69
20892768 GATCTCCCCA
* * * * * *
20892778 AAAATAGTTAGTGAGAGCTCAAGCTCCCAGCTATAGCTTTAAGACTCGCAGGTTCAATACCGCAG
1 AAAACAGTTAGCGAGAGCTCAAGCT-CCAACTGTAGCTTTAAGGCTCGCAGGTTCAATATCGCAG
20892843 CCTCT
65 CCTCT
* * * * * *
20892848 GAAACAGGTAGCGAGAGCTCAAGCTCTCAACTGTAGTTTTAAAGCTCCCAGGTTCAAT-TACACA
1 AAAACAGTTAGCGAGAGCTCAAGCTC-CAACTGTAGCTTTAAGGCTCGCAGGTTCAATAT-CGCA
20892912 GCCTCT
64 GCCTCT
* * * * * * *
20892918 AAAGCAGTTAGCAAGAGCTCAAGCTCCCATTGT-GATCTTAAGGCTCGTAAGTTCAATATCGCAG
1 AAAACAGTTAGCGAGAGCTCAAGCTCCAACTGTAGCT-TTAAGGCTCGCAGGTTCAATATCGCAG
*
20892982 CCTTT
65 CCTCT
* * * * * *
20892987 AAAACAATTAGCGAGAGCCCAAGCTCTTAATTGTAGCTTTAAGGCTCGTAGGTTCAATA-CTGTA
1 AAAACAGTTAGCGAGAGCTCAAGCTC-CAACTGTAGCTTTAAGGCTCGCAGGTTCAATATC-GCA
*
20893051 GCCTCC
64 GCCTCT
* ** * * * * * ** *
20893057 AAAATAGTTAATGATAGC-CTAAGCTCCCAGT-TATGATCGTAAGGCTCATAGGTTTAATATCGC
1 AAAACAGTTAGCGAGAGCTC-AAGCTCCAACTGTA-GCT-TTAAGGCTCGCAGGTTCAATATCGC
*
20893120 AGCCTCC
63 AGCCTCT
* * * * * * ***
20893127 AAAACAGTTAGTGCGAGCCCAAGCTCCCAACTATAGCTTTAAAGCTCACAGGTTCAATATTATAG
1 AAAACAGTTAGCGAGAGCTCAAGCT-CCAACTGTAGCTTTAAGGCTCGCAGGTTCAATATCGCAG
20893192 CCTCT
65 CCTCT
* * * * * *
20893197 AAAACAATTAGCGATAGCCCAAGCTCCTAACTGTA-ATCTTAAGGCTCACAGGTTCAATATCGTA
1 AAAACAGTTAGCGAGAGCTCAAGCTCC-AACTGTAGCT-TTAAGGCTCGCAGGTTCAATATCGCA
20893261 GCCTCT
64 GCCTCT
* * * * * *
20893267 AAAATAGTTAGTGTGAGCTGAAGCTCCAACTGTAGCTTTAAGGCTCGCAGGTTCAACA-CTGCAA
1 AAAACAGTTAGCGAGAGCTCAAGCTCCAACTGTAGCTTTAAGGCTCGCAGGTTCAATATC-GCAG
20893331 CCTCT
65 CCTCT
20893336 AAAACA
1 AAAACA
20893342 ATTGAAGCTT
Statistics
Matches: 390, Mismatches: 86, Indels: 37
0.76 0.17 0.07
Matches are distributed among these distances:
68 5 0.01
69 99 0.25
70 274 0.70
71 10 0.03
72 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (69 bp):
AAAACAGTTAGCGAGAGCTCAAGCTCCAACTGTAGCTTTAAGGCTCGCAGGTTCAATATCGCAGC
CTCT
Found at i:20893152 original size:140 final size:138
Alignment explanation
Indices: 20892827--20893344 Score: 489
Period size: 140 Copynumber: 3.7 Consensus size: 138
20892817 TAAGACTCGC
* * * * * * *
20892827 AGGTTCAATACCGCAGCCTCTGAAACAGGTAGCGAGAGCTCAAGCTCTCAACTGTAGTTTTAAAG
1 AGGTTCAATATCGCAGCCTCTAAAACAGTTAGTGAGAGCCCAAGCTC-CAACTGTAGCTTTAAGG
* ** * * * * * * *
20892892 CTCCCAGGTTCAATTAC-ACAGCCTCTAAAGCAGTTAGCAAGAGCTCAAGCTCCCATTGTGATCT
65 CTCGCAGGTTCAA-TACTGTAGCCTCCAAAACAATTAACGATAGCCCAAGCTCCCATTGTGATCT
*
20892956 TAAGGCTCGT
129 TAAGGCTCAT
* * * * * *
20892966 AAGTTCAATATCGCAGCCTTTAAAACAATTAGCGAGAGCCCAAGCTCTTAATTGTAGCTTTAAGG
1 AGGTTCAATATCGCAGCCTCTAAAACAGTTAGTGAGAGCCCAAGCTC-CAACTGTAGCTTTAAGG
* * * * * * *
20893031 CTCGTAGGTTCAATACTGTAGCCTCCAAAATAGTTAATGATAGCCTAAGCTCCCAGTTATGATCG
65 CTCGCAGGTTCAATACTGTAGCCTCCAAAACAATTAACGATAGCCCAAGCTCCCA-TTGTGATCT
20893096 TAAGGCTCAT
129 TAAGGCTCAT
* * * * *
20893106 AGGTTTAATATCGCAGCCTCCAAAACAGTTAGTGCGAGCCCAAGCTCCCAACTATAGCTTTAAAG
1 AGGTTCAATATCGCAGCCTCTAAAACAGTTAGTGAGAGCCCAAGCT-CCAACTGTAGCTTTAAGG
* * * * * * * *
20893171 CTCACAGGTTCAATATTATAGCCTCTAAAACAATTAGCGATAGCCCAAGCTCCTAACTGTAATCT
65 CTCGCAGGTTCAATACTGTAGCCTCCAAAACAATTAACGATAGCCCAAGCTCC-CATTGTGATCT
*
20893236 TAAGGCTCAC
129 TAAGGCTCAT
* * * **
20893246 AGGTTCAATATCGTAGCCTCTAAAATAGTTAGTGTGAGCTGAAGCTCCAACTGTAGCTTTAAGGC
1 AGGTTCAATATCGCAGCCTCTAAAACAGTTAGTGAGAGCCCAAGCTCCAACTGTAGCTTTAAGGC
* * * *
20893311 TCGCAGGTTCAACACTGCAACCTCTAAAACAATT
66 TCGCAGGTTCAATACTGTAGCCTCCAAAACAATT
20893345 GAAGCTTGTG
Statistics
Matches: 306, Mismatches: 69, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
138 3 0.01
139 137 0.45
140 164 0.54
141 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (138 bp):
AGGTTCAATATCGCAGCCTCTAAAACAGTTAGTGAGAGCCCAAGCTCCAACTGTAGCTTTAAGGC
TCGCAGGTTCAATACTGTAGCCTCCAAAACAATTAACGATAGCCCAAGCTCCCATTGTGATCTTA
AGGCTCAT
Found at i:20896504 original size:20 final size:20
Alignment explanation
Indices: 20896474--20896524 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
20896464 ATGTCAGTCC
*
20896474 TATGAATAGTGGGGTC-AAT
1 TATGAATAGTGGAGTCAAAT
*
20896493 TCATGAACAGTGGAGTCAAAT
1 T-ATGAATAGTGGAGTCAAAT
20896514 TATGAATAGTG
1 TATGAATAGTG
20896525 ATAACATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.81
21 4 0.15
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (20 bp):
TATGAATAGTGGAGTCAAAT
Found at i:20902735 original size:9 final size:9
Alignment explanation
Indices: 20902721--20902766 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
20902711 TATAGTTTGA
20902721 TATTCGAAT
1 TATTCGAAT
20902730 TATTCGAAT
1 TATTCGAAT
20902739 TATTCGAAT
1 TATTCGAAT
*
20902748 TATTCGAGT
1 TATTCGAAT
20902757 TATTCGAAT
1 TATTCGAAT
20902766 T
1 T
20902767 CGAAGACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20902837 original size:9 final size:9
Alignment explanation
Indices: 20902820--20902850 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20902810 TCGAGTTGAT
20902820 TCGAATAAC
1 TCGAATAAC
*
20902829 TCGATTAAC
1 TCGAATAAC
20902838 TCGAATAAC
1 TCGAATAAC
20902847 TCGA
1 TCGA
20902851 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:20903213 original size:24 final size:23
Alignment explanation
Indices: 20903143--20903216 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 23
20903133 TAAAAAAGTT
*
20903143 ATTTTAACATTTAAATATTTTGAAAA
1 ATTTTAA-A-TTAAATATTTT-TAAA
* *
20903169 TATTTTTAATT-AATATATTTAAA
1 -ATTTTAAATTAAATATTTTTAAA
20903192 ATTTTAAATTAAATTATTTTTAAA
1 ATTTTAAATTAAA-TATTTTTAAA
20903216 A
1 A
20903217 ATTTGCATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.22
23 5 0.12
24 17 0.43
25 2 0.05
26 1 0.03
27 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
ATTTTAAATTAAATATTTTTAAA
Found at i:20904269 original size:23 final size:24
Alignment explanation
Indices: 20904226--20904271 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
20904216 TAAAGATGAT
20904226 TATATATAAAATTTTAATAAATAAA
1 TATATATAAAA-TTTAATAAATAAA
*
20904251 TATATATAAAA-TTATTAAATA
1 TATATATAAAATTTAATAAATA
20904272 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TATATATAAAATTTAATAAATAAA
Found at i:20909639 original size:29 final size:29
Alignment explanation
Indices: 20909604--20909699 Score: 147
Period size: 29 Copynumber: 3.3 Consensus size: 29
20909594 TGTGATATGC
20909604 GAACCCTAGGAACATGCGAGCCTATGTGT
1 GAACCCTAGGAACATGCGAGCCTATGTGT
20909633 GAACCCTAGGAACATGCGAGCCTATGTGT
1 GAACCCTAGGAACATGCGAGCCTATGTGT
* * * *
20909662 GAACCCTAGTAACATGCTAGCATATGTGA
1 GAACCCTAGGAACATGCGAGCCTATGTGT
*
20909691 AAACCCTAG
1 GAACCCTAG
20909700 AAACTTGCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (29 bp):
GAACCCTAGGAACATGCGAGCCTATGTGT
Found at i:20922920 original size:33 final size:32
Alignment explanation
Indices: 20922878--20923093 Score: 168
Period size: 33 Copynumber: 6.6 Consensus size: 32
20922868 AATATAGAGG
20922878 GGTTGCTAAGTGCTGATTCCCCTATTCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCAT-GGT
* * *
20922911 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CA--T----GGT
20922954 GGTTGCTAAGTGCTGATTCCCC----CGA-GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTC-ATGGT
20922981 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCA-TGGT
20923014 GGTTGCTAAGTGCTGATTCCCC----CGA-GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTC-ATGGT
20923041 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCA-TGGT
*
20923074 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
20923094 ACCGCATCTG
Statistics
Matches: 150, Mismatches: 7, Indels: 52
0.72 0.03 0.25
Matches are distributed among these distances:
27 44 0.29
28 4 0.03
29 1 0.01
30 3 0.02
31 2 0.01
32 4 0.03
33 60 0.40
34 2 0.01
35 3 0.02
37 2 0.01
38 1 0.01
40 1 0.01
42 2 0.01
43 21 0.14
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCTATTCATGGT
Found at i:20922989 original size:27 final size:27
Alignment explanation
Indices: 20922952--20923062 Score: 152
Period size: 27 Copynumber: 3.9 Consensus size: 27
20922942 AATGTGAAAG
20922952 GGGGTTGCTAAGTGCTGATTCCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCCGA
20922979 GGGGTTGCTAAGTGCTGATTCCCCTATTC-A
1 GGGGTTGCTAAGTGCTGATTCCCC----CGA
20923009 TTGGTGGTTGCTAAGTGCTGATTCCCCCGA
1 --GG-GGTTGCTAAGTGCTGATTCCCCCGA
20923039 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
20923063 TATTCATTGG
Statistics
Matches: 76, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
27 46 0.61
28 2 0.03
29 1 0.01
30 2 0.03
31 1 0.01
32 2 0.03
33 22 0.29
ACGTcount: A:0.14, C:0.24, G:0.31, T:0.31
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCGA
Found at i:20923047 original size:60 final size:60
Alignment explanation
Indices: 20922954--20923093 Score: 271
Period size: 60 Copynumber: 2.3 Consensus size: 60
20922944 TGTGAAAGGG
20922954 GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
20923014 GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
*
20923074 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
20923094 ACCGCATCTG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (60 bp):
GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
Found at i:20923173 original size:162 final size:163
Alignment explanation
Indices: 20922874--20923184 Score: 516
Period size: 162 Copynumber: 1.9 Consensus size: 163
20922864 ATTGAATATA
* *
20922874 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATT
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGCATC
* * *
20922939 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCT
66 TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCG
20923004 ATTCATTGGTGGTTGCTAAGTGCTGATTCCCCC
131 ATTCATTGGTGGTTGCTAAGTGCTGATTCCCCC
* * *
20923037 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGCATC
1 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGCATC
** *
20923102 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTCCTCG
66 TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCG
20923166 ATTCATTGGTGGTTGCTAA
131 ATTCATTGGTGGTTGCTAA
20923185 CTGCGGAATC
Statistics
Matches: 137, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
162 69 0.50
163 68 0.50
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (163 bp):
GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGCATC
TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCG
ATTCATTGGTGGTTGCTAAGTGCTGATTCCCCC
Found at i:20923197 original size:102 final size:102
Alignment explanation
Indices: 20923014--20923199 Score: 291
Period size: 102 Copynumber: 1.8 Consensus size: 102
20923004 ATTCATTGGT
* *
20923014 GGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTG
* ** *
20923079 CTAAGTGTTGATTCCACCGCATCTGAAATGTGAAGGG
66 CTAACTGCGGAATCCACCGCATCTGAAATGTGAAGGG
** *
20923116 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTCCTCGATTCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTG
20923181 CTAACTGCGGAATCCACCG
66 CTAACTGCGGAATCCACCG
20923200 ATAACGGTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 75 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (102 bp):
GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTG
CTAACTGCGGAATCCACCGCATCTGAAATGTGAAGGG
Found at i:20933554 original size:20 final size:20
Alignment explanation
Indices: 20933527--20933575 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
20933517 CCTTTGCATA
20933527 GCTCTGTTCAGCACTGCTCT
1 GCTCTGTTCAGCACTGCTCT
* * **
20933547 GTTCTGTTTAGTTCTGCTCT
1 GCTCTGTTCAGCACTGCTCT
20933567 GCTCTGTTC
1 GCTCTGTTC
20933576 TGTTATGTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.06, C:0.29, G:0.20, T:0.45
Consensus pattern (20 bp):
GCTCTGTTCAGCACTGCTCT
Found at i:20933568 original size:25 final size:25
Alignment explanation
Indices: 20933531--20933592 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
20933521 TGCATAGCTC
* *
20933531 TGTTCAGCACTGCTCTGTTCTGTT-
1 TGTTCTGCTCTGCTCTGTTCTGTTA
20933555 TAGTTCTGCTCTGCTCTGTTCTGTTA
1 T-GTTCTGCTCTGCTCTGTTCTGTTA
20933581 TGTTCTGCTCTG
1 TGTTCTGCTCTG
20933593 TCCTATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.06, C:0.24, G:0.21, T:0.48
Consensus pattern (25 bp):
TGTTCTGCTCTGCTCTGTTCTGTTA
Found at i:20933601 original size:25 final size:25
Alignment explanation
Indices: 20933540--20933601 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
20933530 CTGTTCAGCA
*
20933540 CTGCTCTGTTCTGTTTAGTTCTGCT
1 CTGCTCTATTCTGTTTAGTTCTGCT
*
20933565 CTGCTCTGTTCTG-TTATGTTCTGCT
1 CTGCTCTATTCTGTTTA-GTTCTGCT
20933590 CTG-TCCTATTCT
1 CTGCT-CTATTCT
20933602 ATTTGTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.05, C:0.26, G:0.18, T:0.52
Consensus pattern (25 bp):
CTGCTCTATTCTGTTTAGTTCTGCT
Found at i:20946266 original size:23 final size:23
Alignment explanation
Indices: 20946240--20946285 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20946230 GCGTAACTGC
20946240 TGTATAGTAATAGGGTGCCCGAA
1 TGTATAGTAATAGGGTGCCCGAA
* *
20946263 TGTATAGTTATAGGGTGCGCGAA
1 TGTATAGTAATAGGGTGCCCGAA
20946286 GCCCACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (23 bp):
TGTATAGTAATAGGGTGCCCGAA
Found at i:20948548 original size:23 final size:23
Alignment explanation
Indices: 20948517--20948562 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20948507 GGAGGTGGGC
20948517 TTCGCGCACCCTATAACTATACA
1 TTCGCGCACCCTATAACTATACA
* *
20948540 TTCGGGCACCCTATTACTATACA
1 TTCGCGCACCCTATAACTATACA
20948563 GCAGTTACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (23 bp):
TTCGCGCACCCTATAACTATACA
Found at i:20960349 original size:45 final size:45
Alignment explanation
Indices: 20960285--20960376 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
20960275 TTCAAGATTG
*
20960285 TGAGTTTCCAGTAGACCTTATGGCTCTTCCGTTCCACGAGTTTGA
1 TGAGTTTCCAGCAGACCTTATGGCTCTTCCGTTCCACGAGTTTGA
20960330 TGAGTTTCCAGCAGACCTTATGGCTCTTCCGTTCCACGAGTTTGA
1 TGAGTTTCCAGCAGACCTTATGGCTCTTCCGTTCCACGAGTTTGA
20960375 TG
1 TG
20960377 TAATTTTGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (45 bp):
TGAGTTTCCAGCAGACCTTATGGCTCTTCCGTTCCACGAGTTTGA
Found at i:20963372 original size:19 final size:19
Alignment explanation
Indices: 20963345--20963391 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
20963335 TAAAGAATTG
*
20963345 AGAGAAGGCATCATAATAC
1 AGAGGAGGCATCATAATAC
*
20963364 AGAGGAGGCATCATAATAT
1 AGAGGAGGCATCATAATAC
20963383 AGAGGAGGC
1 AGAGGAGGC
20963392 TACCTGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.15
Consensus pattern (19 bp):
AGAGGAGGCATCATAATAC
Found at i:20963605 original size:15 final size:15
Alignment explanation
Indices: 20963585--20963618 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
20963575 AGAAATTTTG
20963585 AGTAATAAATTAGGA
1 AGTAATAAATTAGGA
20963600 AGTAATAAATTAGGA
1 AGTAATAAATTAGGA
20963615 AGTA
1 AGTA
20963619 CTTAGACCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (15 bp):
AGTAATAAATTAGGA
Found at i:20969584 original size:12 final size:12
Alignment explanation
Indices: 20969550--20969625 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
20969540 ATTATTAAAC
20969550 ATAATTTAATAA
1 ATAATTTAATAA
**
20969562 A-AATAAAAATAA
1 ATAAT-TTAATAA
20969574 ATAATTTAATAA
1 ATAATTTAATAA
*
20969586 CAT-TTTTAATATA
1 -ATAATTTAATA-A
20969599 AT-ATTTAAT-A
1 ATAATTTAATAA
20969609 ATAATTTTAATATA
1 ATAA-TTTAATA-A
20969623 ATA
1 ATA
20969626 TTATTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
10 3 0.06
11 4 0.08
12 33 0.66
13 6 0.12
14 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATTTAATAA
Found at i:20969596 original size:24 final size:25
Alignment explanation
Indices: 20969550--20969625 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 25
20969540 ATTATTAAAC
* ***
20969550 ATAATTTAATAAAAATAAAAATA-A
1 ATAATTTAATAACAATTTTAATATA
*
20969574 ATAATTTAATAACATTTTTAATATA
1 ATAATTTAATAACAATTTTAATATA
*
20969599 AT-ATTTAATAATAATTTTAATATA
1 ATAATTTAATAACAATTTTAATATA
20969623 ATA
1 ATA
20969626 TTATTATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 40 0.93
25 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATTTAATAACAATTTTAATATA
Found at i:20979195 original size:2 final size:2
Alignment explanation
Indices: 20979188--20979213 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20979178 GAATAGGTGG
20979188 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
20979214 GTTAAGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20987164 original size:41 final size:41
Alignment explanation
Indices: 20987107--20987274 Score: 273
Period size: 41 Copynumber: 4.1 Consensus size: 41
20987097 GTTTGGAATT
20987107 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
20987148 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
20987189 GGTGATCTGAATCAGGCTGTAAGCCTAGTAGGCTAAATGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * * *
20987230 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGTC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
20987271 GGTG
1 GGTG
20987275 TCTAAATATG
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
Found at i:20990346 original size:18 final size:19
Alignment explanation
Indices: 20990323--20990372 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
20990313 TAAGGAACTT
20990323 TGGTATCGATAAAAA-ATA
1 TGGTATCGATAAAAACATA
20990341 TGGTATCGATAAAAATCATA
1 TGGTATCGATAAAAA-CATA
20990361 TGGATATCGATA
1 TGG-TATCGATA
20990373 CTTTTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.52
20 6 0.21
21 8 0.28
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (19 bp):
TGGTATCGATAAAAACATA
Found at i:20993860 original size:7 final size:7
Alignment explanation
Indices: 20993850--20993880 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
20993840 TTTATATTAT
20993850 ATATATG
1 ATATATG
20993857 ATATATG
1 ATATATG
20993864 ATATATG
1 ATATATG
20993871 ATATATG
1 ATATATG
20993878 ATA
1 ATA
20993881 ACATAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (7 bp):
ATATATG
Found at i:20997545 original size:3 final size:3
Alignment explanation
Indices: 20997537--20997631 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
20997527 TTCGGTGGAA
20997537 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20997585 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
20997632 ACGCCATTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21008239 original size:27 final size:27
Alignment explanation
Indices: 21008209--21008269 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
21008199 ATTTTTAAAG
* *
21008209 AAAAATAGAAACTTTTGAAACAATA-TA
1 AAAAATAGAAAATTTT-AAACAAAATTA
* *
21008236 AAAAATATAAAATTTTAAATAAAATTA
1 AAAAATAGAAAATTTTAAACAAAATTA
21008263 AAAAATA
1 AAAAATA
21008270 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATAGAAAATTTTAAACAAAATTA
Found at i:21027122 original size:27 final size:27
Alignment explanation
Indices: 21027076--21027198 Score: 120
Period size: 27 Copynumber: 4.6 Consensus size: 27
21027066 GTACGTTATC
* * * * *
21027076 AAGGCATTCTTTTTAGAGTTTTCCATG
1 AAGGCATTCCTTTCAGAGTCTACCACG
* * * *
21027103 AAGGCATTCCTTTCAAAGTTTTCCATG
1 AAGGCATTCCTTTCAGAGTCTACCACG
* *
21027130 AATGCATTCCATTCAGAGTCTACCACG
1 AAGGCATTCCTTTCAGAGTCTACCACG
* *
21027157 AAGGCATTCCCTTCAGAGTCTACCACA
1 AAGGCATTCCTTTCAGAGTCTACCACG
*
21027184 AAGGCATTTCTTTCA
1 AAGGCATTCCTTTCA
21027199 TATATTTCCA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (27 bp):
AAGGCATTCCTTTCAGAGTCTACCACG
Found at i:21028975 original size:16 final size:16
Alignment explanation
Indices: 21028951--21028987 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
21028941 TGGTTCACTA
* *
21028951 TAATAGAATAGGGTTG
1 TAATTGAATAGAGTTG
21028967 TAATTGAATAGAGTTG
1 TAATTGAATAGAGTTG
21028983 TAATT
1 TAATT
21028988 AGTAATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (16 bp):
TAATTGAATAGAGTTG
Found at i:21029193 original size:26 final size:25
Alignment explanation
Indices: 21029144--21029199 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
21029134 ATTGTTATTA
* ** *
21029144 AATTTTAATAAAATTATTATTAAAT
1 AATTTTAATAAAAATAAAAATAAAT
21029169 ATATTTTAATAAAAATAAAAATAAAT
1 A-ATTTTAATAAAAATAAAAATAAAT
21029195 AATTT
1 AATTT
21029200 AATCATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTTTAATAAAAATAAAAATAAAT
Found at i:21029240 original size:61 final size:58
Alignment explanation
Indices: 21029145--21029282 Score: 181
Period size: 61 Copynumber: 2.3 Consensus size: 58
21029135 TTGTTATTAA
* *
21029145 ATTTTAATAAAATTATTATTAAATATATTTTAATAAAAATAAAAATAAATAATTTAAT-CAT
1 ATTTTAATATAATTATTATTAAATACATTTTAAT-AAAAT---AATAAATAATTTAATACAT
*
21029206 ATTTTAATATAATTATTATTAAATACATTTTAATAAAATAATATATAATTTAATAGCAT
1 ATTTTAATATAATTATTATTAAATACATTTTAATAAAATAATAAATAATTTAATA-CAT
*
21029265 -TCTTAATATAATTATTAT
1 ATTTTAATATAATTATTAT
21029283 ATGAATTAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
57 14 0.20
58 17 0.24
59 3 0.04
60 5 0.07
61 32 0.45
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATACATTTTAATAAAATAATAAATAATTTAATACAT
Found at i:21029318 original size:23 final size:21
Alignment explanation
Indices: 21029287--21029329 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21029277 TATTATATGA
21029287 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
21029310 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
21029330 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:21030003 original size:266 final size:266
Alignment explanation
Indices: 21029528--21030066 Score: 1024
Period size: 266 Copynumber: 2.0 Consensus size: 266
21029518 TATGTCATAA
* *
21029528 TCCATATGTTAAATTTTAAAATATCAAAAAGTTATAACATTGTAATGGTATTTTGTCATGTCATT
1 TCCATATGTTAAATTTTAAAATATCAAAAAGTTATAACATTGTAATGGCATTCTGTCATGTCATT
21029593 ATACCATCCAAATATTACAAACACAAAAAGTTACCAAAATATCACCAACACAACCATGATTTTTA
66 ATACCATCCAAATATTACAAACACAAAAAGTTACCAAAATATCACCAACACAACCATGATTTTTA
21029658 ATGGTCAGTAAGAAATCTTCTGACCCATTCCAATCGCATAAAAGAAGGTAAACTAAAGAAAATGA
131 ATGGTCAGTAAGAAATCTTCTGACCCATTCCAATCGCATAAAAGAAGGTAAACTAAAGAAAATGA
*
21029723 GCATTTGCGTTGGATGGTTTGGAATTCTGCTTAACACGTGATAGCGCTCATCCTCAATTAAATCT
196 GCATTTGCGTTGGATGGTTTGGAATTCTGCTTAACACGTGATAGAGCTCATCCTCAATTAAATCT
21029788 TCTACT
261 TCTACT
21029794 TCCATATGTTAAATTTTAAAATATCAAAAAGTTATAACATTGTAATGGCATTCTGTCATGTCATT
1 TCCATATGTTAAATTTTAAAATATCAAAAAGTTATAACATTGTAATGGCATTCTGTCATGTCATT
21029859 ATACCATCCAAATATTACAAACACAAAAAGTTACCAAAATATCACCAACACAACCATGATTTTTA
66 ATACCATCCAAATATTACAAACACAAAAAGTTACCAAAATATCACCAACACAACCATGATTTTTA
21029924 ATGGTCAGTAAGAAATCTTCTGACCCATTCCAATCGCATAAAAGAAGGTAAACTAAAGAAAATGA
131 ATGGTCAGTAAGAAATCTTCTGACCCATTCCAATCGCATAAAAGAAGGTAAACTAAAGAAAATGA
* *
21029989 GCATTTGTGTTGGATGGTTTGGAATTCTGCTTAACACGTGATAGAGCTCATCCTCAGTTAAATCT
196 GCATTTGCGTTGGATGGTTTGGAATTCTGCTTAACACGTGATAGAGCTCATCCTCAATTAAATCT
21030054 TCTACT
261 TCTACT
21030060 TCACATA
1 TC-CATA
21030067 AGGTTTAATA
Statistics
Matches: 267, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
266 263 0.99
267 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (266 bp):
TCCATATGTTAAATTTTAAAATATCAAAAAGTTATAACATTGTAATGGCATTCTGTCATGTCATT
ATACCATCCAAATATTACAAACACAAAAAGTTACCAAAATATCACCAACACAACCATGATTTTTA
ATGGTCAGTAAGAAATCTTCTGACCCATTCCAATCGCATAAAAGAAGGTAAACTAAAGAAAATGA
GCATTTGCGTTGGATGGTTTGGAATTCTGCTTAACACGTGATAGAGCTCATCCTCAATTAAATCT
TCTACT
Found at i:21032711 original size:21 final size:21
Alignment explanation
Indices: 21032687--21032755 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
21032677 TATGAATGCC
21032687 ACACACGTCTGTGTGGAGGCT
1 ACACACGTCTGTGTGGAGGCT
* * *
21032708 ACACATGTCTGTGTGTAGGCC
1 ACACACGTCTGTGTGGAGGCT
* * *
21032729 ACACACGCCCGTGTAGAGGCT
1 ACACACGTCTGTGTGGAGGCT
21032750 ACACAC
1 ACACAC
21032756 ACCCATGTGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.29, G:0.28, T:0.20
Consensus pattern (21 bp):
ACACACGTCTGTGTGGAGGCT
Found at i:21032768 original size:21 final size:21
Alignment explanation
Indices: 21032719--21032768 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
21032709 CACATGTCTG
* * *
21032719 TGTGTAGGCCACACACGCCCG
1 TGTGGAGGCCACACACACCCA
* *
21032740 TGTAGAGGCTACACACACCCA
1 TGTGGAGGCCACACACACCCA
21032761 TGTGGAGG
1 TGTGGAGG
21032769 GGAGACACGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
TGTGGAGGCCACACACACCCA
Found at i:21032986 original size:65 final size:65
Alignment explanation
Indices: 21032903--21033037 Score: 270
Period size: 65 Copynumber: 2.1 Consensus size: 65
21032893 CAGGCCGTGT
21032903 GGCACTAAAAATATCAAAAACCCTAAATTCCCAACGGCACATGGTCGTGTGTACCGCCCGTGTGC
1 GGCACTAAAAATATCAAAAACCCTAAATTCCCAACGGCACATGGTCGTGTGTACCGCCCGTGTGC
21032968 GGCACTAAAAATATCAAAAACCCTAAATTCCCAACGGCACATGGTCGTGTGTACCGCCCGTGTGC
1 GGCACTAAAAATATCAAAAACCCTAAATTCCCAACGGCACATGGTCGTGTGTACCGCCCGTGTGC
21033033 GGCAC
1 GGCAC
21033038 ACACCCGTGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (65 bp):
GGCACTAAAAATATCAAAAACCCTAAATTCCCAACGGCACATGGTCGTGTGTACCGCCCGTGTGC
Found at i:21033794 original size:20 final size:20
Alignment explanation
Indices: 21033769--21033808 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21033759 TACCAATCAC
21033769 ATAACTTCTAACCCTAAAAT
1 ATAACTTCTAACCCTAAAAT
21033789 ATAACTTCTAACCCTAAAAT
1 ATAACTTCTAACCCTAAAAT
21033809 TTGAGGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAACTTCTAACCCTAAAAT
Found at i:21036382 original size:25 final size:25
Alignment explanation
Indices: 21036341--21036389 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21036331 TCGTTTTGTA
*
21036341 TTATATATTTTTATATTTTTATAAT
1 TTATATATTTTTATATTTCTATAAT
21036366 TTATATATATTTT-TATTTCTATAA
1 TTATATAT-TTTTATATTTCTATAA
21036390 ATTGAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATATTTTTATATTTCTATAAT
Found at i:21039442 original size:11 final size:11
Alignment explanation
Indices: 21039426--21039450 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21039416 GGGCCTGCAA
21039426 AATAGACTTGT
1 AATAGACTTGT
21039437 AATAGACTTGT
1 AATAGACTTGT
21039448 AAT
1 AAT
21039451 GGCATAGCCA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATAGACTTGT
Found at i:21042921 original size:26 final size:27
Alignment explanation
Indices: 21042892--21042948 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 27
21042882 TAAAAAAATA
21042892 TGTGCTAAATATCTTCCCTTAACAAATG
1 TGTGCTAAATATCTTCCCTTAACAAA-G
*
21042920 TGTGCTAAATATCTTCCCTTAACTAAG
1 TGTGCTAAATATCTTCCCTTAACAAAG
21042947 TG
1 TG
21042949 GCAATCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (27 bp):
TGTGCTAAATATCTTCCCTTAACAAAG
Found at i:21042927 original size:28 final size:28
Alignment explanation
Indices: 21042887--21042942 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
21042877 TATGCTAAAA
21042887 AAATATGTGCTAAATATCTTCCCTTAAC
1 AAATATGTGCTAAATATCTTCCCTTAAC
*
21042915 AAATGTGTGCTAAATATCTTCCCTTAAC
1 AAATATGTGCTAAATATCTTCCCTTAAC
21042943 TAAGTGGCAA
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:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (28 bp):
AAATATGTGCTAAATATCTTCCCTTAAC
Found at i:21049121 original size:26 final size:25
Alignment explanation
Indices: 21049073--21049122 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
21049063 TAAAGACTTT
* *
21049073 CTAGATAGCTCACCACTAGGGCTTC
1 CTAGATAACTCACCACTAAGGCTTC
*
21049098 CTAGATAACTTCACCATTAAGGCTT
1 CTAGATAAC-TCACCACTAAGGCTT
21049123 TCCAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (25 bp):
CTAGATAACTCACCACTAAGGCTTC
Found at i:21050408 original size:18 final size:18
Alignment explanation
Indices: 21050385--21050421 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
21050375 TGCTCATGGA
21050385 AACCGAGCGTTCTATACT
1 AACCGAGCGTTCTATACT
21050403 AACCGAGCGTTCTATACT
1 AACCGAGCGTTCTATACT
21050421 A
1 A
21050422 TGGCAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (18 bp):
AACCGAGCGTTCTATACT
Found at i:21053697 original size:21 final size:22
Alignment explanation
Indices: 21053655--21053707 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
21053645 GGTTGAAACC
*
21053655 AAAAATGAATCGTGTGTTTGAAT
1 AAAAATGAATC-TGTATTTGAAT
21053678 AAAAATGAAT-TGTATTTGAAT
1 AAAAATGAATCTGTATTTGAAT
*
21053699 AGAAATGAA
1 AAAAATGAA
21053708 AGGAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.64
23 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (22 bp):
AAAAATGAATCTGTATTTGAAT
Found at i:21054012 original size:26 final size:26
Alignment explanation
Indices: 21053973--21054038 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
21053963 TATTTTCTCG
21053973 AAATTTTACTAAGGGCAAAATCATCA
1 AAATTTTACTAAGGGCAAAATCATCA
* *
21053999 AAATTTTA-TCAAGGGTAAAATCGTCA
1 AAATTTTACT-AAGGGCAAAATCATCA
* *
21054025 AACTTTTGCTAAGG
1 AAATTTTACTAAGG
21054039 ATAAAATAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 32 0.94
27 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (26 bp):
AAATTTTACTAAGGGCAAAATCATCA
Found at i:21056246 original size:36 final size:36
Alignment explanation
Indices: 21056199--21056272 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
21056189 CACTGAAAAC
21056199 AAACTGAATGGAAACAACTGTAAGAAAAGTAAAAGG
1 AAACTGAATGGAAACAACTGTAAGAAAAGTAAAAGG
21056235 AAACTGAATGGAAACAACTGTAAGAAAAGTAAAAGG
1 AAACTGAATGGAAACAACTGTAAGAAAAGTAAAAGG
21056271 AA
1 AA
21056273 CTTGATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.14
Consensus pattern (36 bp):
AAACTGAATGGAAACAACTGTAAGAAAAGTAAAAGG
Found at i:21067737 original size:38 final size:38
Alignment explanation
Indices: 21067686--21067776 Score: 110
Period size: 38 Copynumber: 2.4 Consensus size: 38
21067676 AAAAACAGTT
* *
21067686 GACATGTTTAACATGTATTCAGTTCAACAGTAGCAATA
1 GACATGCTTAACATGTATTCAGTTCAACAGTAACAATA
** * *
21067724 GACATGCTTAACATGTATTTGGTTTAACAGTAACAGTA
1 GACATGCTTAACATGTATTCAGTTCAACAGTAACAATA
* *
21067762 GGCATGCTAAACATG
1 GACATGCTTAACATG
21067777 CAATCAGTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (38 bp):
GACATGCTTAACATGTATTCAGTTCAACAGTAACAATA
Found at i:21068666 original size:18 final size:20
Alignment explanation
Indices: 21068624--21068666 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
21068614 AAAATATGAT
21068624 GCAAATAAGAGAAAAGAAAA
1 GCAAATAAGAGAAAAGAAAA
*
21068644 G-AAAT-AGAGAGAAG-AAA
1 GCAAATAAGAGAAAAGAAAA
21068661 GCAAAT
1 GCAAAT
21068667 TTCTAATAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 4 0.19
20 1 0.05
ACGTcount: A:0.65, C:0.05, G:0.23, T:0.07
Consensus pattern (20 bp):
GCAAATAAGAGAAAAGAAAA
Found at i:21086487 original size:23 final size:22
Alignment explanation
Indices: 21086445--21086491 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
21086435 AATATGTTAA
21086445 AAATATTTTTATGTATTATTTG
1 AAATATTTTTATGTATTATTTG
*
21086467 AAATTTTTTTAT-TATAATATTTG
1 AAATATTTTTATGTAT--TATTTG
21086490 AA
1 AA
21086492 TTGATAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.50
23 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
AAATATTTTTATGTATTATTTG
Found at i:21103828 original size:17 final size:17
Alignment explanation
Indices: 21103791--21103828 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
21103781 ATTTAACCAT
*
21103791 TTTTATTTTTATTATAT
1 TTTTATTTTTATTATAA
21103808 TTTTATTTTTAGTT-TAA
1 TTTTATTTTTA-TTATAA
21103825 TTTT
1 TTTT
21103829 TGTTTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTATTATAA
Found at i:21112718 original size:19 final size:19
Alignment explanation
Indices: 21112682--21112719 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21112672 TTTGGTATAG
*
21112682 GGACTAAATCGTAAAAACT
1 GGACTAAATCGAAAAAACT
21112701 GGACTAAATC-AAATAAACT
1 GGACTAAATCGAAA-AAACT
21112720 TCAAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (19 bp):
GGACTAAATCGAAAAAACT
Found at i:21123683 original size:23 final size:23
Alignment explanation
Indices: 21123652--21123695 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21123642 GCTTGAGAGA
21123652 AATACTTTT-TCTCGAAAAAAAAG
1 AATACTTTTATCTC-AAAAAAAAG
*
21123675 AATATTTTTATCTCAAAAAAA
1 AATACTTTTATCTCAAAAAAA
21123696 GTGTGTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (23 bp):
AATACTTTTATCTCAAAAAAAAG
Found at i:21125680 original size:4 final size:4
Alignment explanation
Indices: 21125671--21125748 Score: 156
Period size: 4 Copynumber: 19.5 Consensus size: 4
21125661 ATCTATATTA
21125671 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
21125719 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
21125749 CAGTGTCAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 74 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:21126027 original size:2 final size:2
Alignment explanation
Indices: 21126020--21126068 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
21126010 TTAGTAAAAC
21126020 TA TA TA TA 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 TA TA TA TA
21126062 TA TA TA T
1 TA TA TA T
21126069 TGCTATAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21133202 original size:26 final size:24
Alignment explanation
Indices: 21133145--21133221 Score: 61
Period size: 26 Copynumber: 3.1 Consensus size: 24
21133135 AATTTTCTAA
*
21133145 TTATTATTTAAAATTTAAA-TTAATT
1 TTATTA-TT-AAATTTAAATTTACTT
*
21133170 CTAATTACTTGAAATTTAAATTTACTT
1 -TTATTA-TT-AAATTTAAATTTACTT
*
21133197 TTATTATTACA-TTAAATTT-CTT
1 TTATTATTAAATTTAAATTTACTT
21133219 TTA
1 TTA
21133222 AATTATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.14
23 8 0.18
24 2 0.05
25 2 0.05
26 21 0.48
27 5 0.11
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (24 bp):
TTATTATTAAATTTAAATTTACTT
Found at i:21135393 original size:50 final size:50
Alignment explanation
Indices: 21135205--21135399 Score: 246
Period size: 50 Copynumber: 3.9 Consensus size: 50
21135195 CATTGAGATT
* * * *
21135205 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTCGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAG
* *
21135255 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAG
** * * *
21135305 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAG
** * * *
21135355 ATGAGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21135400 GTACAAGAAA
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 128 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAG
Found at i:21135433 original size:49 final size:50
Alignment explanation
Indices: 21135216--21135438 Score: 164
Period size: 50 Copynumber: 4.5 Consensus size: 50
21135206 TGAGAGGTCC
* * * * * * ** *
21135216 CATGTAAGACCATGTTTGGGACATGGCGTCGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCT
* * * * * * ** *
21135266 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCT
** * *
21135316 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCT
* * * *
21135366 CATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AACATC-
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC-TCT
*
21135414 CGATGTAAGACTATGTCTGGGACAT
1 C-ATGTAAGACCATGTCTGGGACAT
21135439 AGCTTTGGCA
Statistics
Matches: 148, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
48 4 0.03
49 27 0.18
50 117 0.79
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCT
Found at i:21140814 original size:18 final size:18
Alignment explanation
Indices: 21140791--21140826 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21140781 AATATTTATG
21140791 GTAGAAGTTCTTGAATAA
1 GTAGAAGTTCTTGAATAA
*
21140809 GTAGAATTTCTTGAATAA
1 GTAGAAGTTCTTGAATAA
21140827 ATGATCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (18 bp):
GTAGAAGTTCTTGAATAA
Found at i:21153227 original size:23 final size:23
Alignment explanation
Indices: 21153177--21153275 Score: 94
Period size: 23 Copynumber: 4.3 Consensus size: 23
21153167 CTTAAGGGCG
* * *
21153177 TTAC-GAATACGCCACACAGGCA
1 TTACAGAATATGCCACAAAGGCT
* * *
21153199 TCACAGAATATTCCACAAAGACT
1 TTACAGAATATGCCACAAAGGCT
**
21153222 TTACAGAATATGCCACGTAGGCT
1 TTACAGAATATGCCACAAAGGCT
21153245 TTATC-GAATATGCCACAAAGGCT
1 TTA-CAGAATATGCCACAAAGGCT
*
21153268 TTATAGAA
1 TTACAGAA
21153276 AATTACGTGT
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
22 3 0.05
23 56 0.93
24 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (23 bp):
TTACAGAATATGCCACAAAGGCT
Found at i:21154692 original size:17 final size:17
Alignment explanation
Indices: 21154670--21154706 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21154660 TTAGTTGATA
21154670 CTCGCTTATCTCTCAAC
1 CTCGCTTATCTCTCAAC
*
21154687 CTCGCTTATCTCTCGAC
1 CTCGCTTATCTCTCAAC
21154704 CTC
1 CTC
21154707 ATTTAGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.43, G:0.08, T:0.35
Consensus pattern (17 bp):
CTCGCTTATCTCTCAAC
Found at i:21157844 original size:29 final size:29
Alignment explanation
Indices: 21157812--21157880 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
21157802 AAAAAGTTTG
*
21157812 GTTCGGTTAATTTTTTTGAAA-AAATTTCA
1 GTTCGATTAATTTTTTT-AAATAAATTTCA
21157841 GTTCGATTAATTTTTTTAAATAAATTTC-
1 GTTCGATTAATTTTTTTAAATAAATTTCA
21157869 GTTTCGATTAAT
1 G-TTCGATTAAT
21157881 AGTTAAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 4 0.11
29 33 0.89
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (29 bp):
GTTCGATTAATTTTTTTAAATAAATTTCA
Found at i:21163143 original size:35 final size:35
Alignment explanation
Indices: 21163104--21163200 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 35
21163094 ATTTATTGAT
* * *
21163104 ATTATGTTTCGCATATTGAGCATGCTATTATTCTG
1 ATTATGATTCGCATATTAAGCATGCCATTATTCTG
* *
21163139 ATTATGATTCGCATGTTAAGCATGCCATTATTTTG
1 ATTATGATTCGCATATTAAGCATGCCATTATTCTG
* * * *
21163174 ATTTTGATTCGTATGTTAAACATGCCA
1 ATTATGATTCGCATATTAAGCATGCCA
21163201 CTGTGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (35 bp):
ATTATGATTCGCATATTAAGCATGCCATTATTCTG
Found at i:21164628 original size:16 final size:15
Alignment explanation
Indices: 21164588--21164639 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 15
21164578 AATATAGATT
*
21164588 ACTATAGATTGTG-A
1 ACTATAGATTCTGAA
* *
21164602 ACTCTAAATTCTGAAA
1 ACTATAGATTCTG-AA
21164618 ACTATAGATTCTGAA
1 ACTATAGATTCTGAA
21164633 ACTATAG
1 ACTATAG
21164640 TGACGAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 12 0.39
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
ACTATAGATTCTGAA
Found at i:21170837 original size:16 final size:16
Alignment explanation
Indices: 21170805--21170837 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21170795 TAATTCTGAT
21170805 TCACATGATAAACATG
1 TCACATGATAAACATG
21170821 TCACTATGATAAA-ATG
1 TCAC-ATGATAAACATG
21170837 T
1 T
21170838 AATAAGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (16 bp):
TCACATGATAAACATG
Found at i:21172837 original size:68 final size:68
Alignment explanation
Indices: 21172728--21172856 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 68
21172718 ATCATATTTG
* *
21172728 GGCATGCCACTAATATCCCAATAGTTCTAAATTCCATCTACTTGGGCATTAAGGCTGAGTTCCTT
1 GGCATGCCACCAATATCCCAATAGTTCTAAATTCCATCTACTTGGACATTAAGGCTGAGTTCCTT
21172793 AAT
66 AAT
* * *
21172796 GGCATGCCACCAATATCTCAGTAGTTCTAAATTTCATCTACTTGGACATTAAGGCTGAGTT
1 GGCATGCCACCAATATCCCAATAGTTCTAAATTCCATCTACTTGGACATTAAGGCTGAGTT
21172857 TTATACATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (68 bp):
GGCATGCCACCAATATCCCAATAGTTCTAAATTCCATCTACTTGGACATTAAGGCTGAGTTCCTT
AAT
Found at i:21182034 original size:26 final size:26
Alignment explanation
Indices: 21182005--21182066 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
21181995 ATAGTTACCC
21182005 ATTTTTTAGATT-TAT-TTTTATTTAAT
1 ATTTTTTA-ATTATATATTTTA-TTAAT
**
21182031 ATTTAGTAATTATATATTTTATTAAT
1 ATTTTTTAATTATATATTTTATTAAT
21182057 A-TTTTTAATT
1 ATTTTTTAATT
21182067 TTATGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 10 0.33
26 15 0.50
27 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (26 bp):
ATTTTTTAATTATATATTTTATTAAT
Found at i:21184073 original size:29 final size:26
Alignment explanation
Indices: 21184029--21184082 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 26
21184019 CAATTTCCAC
21184029 ATTTTTTTTTCATTTTTATT-TTGAAT
1 ATTTTTTTTTCATTTTT-TTGTTGAAT
21184055 ATTTATTTTTTCAGCTTTTTTTGTTGAA
1 ATTT-TTTTTTCA--TTTTTTTGTTGAA
21184083 AGGCGACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.17
27 8 0.33
28 2 0.08
29 10 0.42
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.69
Consensus pattern (26 bp):
ATTTTTTTTTCATTTTTTTGTTGAAT
Found at i:21189099 original size:76 final size:78
Alignment explanation
Indices: 21188894--21189101 Score: 219
Period size: 76 Copynumber: 2.6 Consensus size: 78
21188884 GTTTAGTTAT
* *
21188894 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TGGTTAGTTAT
21188959 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* *** * * **
21188977 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATT-GTTAGTTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
21189039 TTTAGT-AAAACCC
65 ATTAGTAAAAACCC
21189052 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTT-AGTAAAAAACTATTATTATT
21189102 ATTATTGTGT
Statistics
Matches: 104, Mismatches: 17, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
75 25 0.24
76 39 0.38
77 1 0.01
78 1 0.01
79 5 0.05
80 2 0.02
82 18 0.17
83 13 0.12
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:21193563 original size:156 final size:154
Alignment explanation
Indices: 21192828--21193739 Score: 1299
Period size: 155 Copynumber: 5.9 Consensus size: 154
21192818 ACTTCAAAAC
* * *
21192828 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTT
1 AAATTTA-AAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
* *
21192892 -TAAAAAATATACTATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
65 CAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
21192956 TATTAATTTAGTGTGTTTTTTAAAT
130 TATTAATTTAGTGTGTTTTTTAAAT
*
21192981 AAATTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTC
1 AAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTC
* ** *
21193046 AATAAAAATATATTATTTTCTAATTTTATTATTCGACATTATTTTAGTACATTATGTTTTAAATG
66 AA-AAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
21193111 TATTAATTTA--GTG-TTTTTAAAT
130 TATTAATTTAGTGTGTTTTTTAAAT
* * * *
21193133 AAATTTTAAAAAAACCCTTATTTCGGCCCTTAGTTCGTATTTTTTCCCCGGATTTTATTACTTT-
1 AAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTC
* * *
21193197 TAAAAAATATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATAT
66 AAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGT
21193262 ATTAATTTAGTGTGTTTTTTAAAT
131 ATTAATTTAGTGTGTTTTTTAAAT
*
21193286 AAATTTCAAAAAACAACCCTTATCTT-GGCCCTTTATTCGTATTTTTTTCCCGAATTTTATTACT
1 AAATTT-AAAAAA-AACCCTTAT-TTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTAC-
* * * *
21193350 TTTTAAAAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTAAA
62 TTTCAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
21193415 ATGTATTAATTTAGTGTGTTTTTTAAAT
127 ATGTATTAATTTAGTGTGTTTTTTAAAT
21193443 AAATTTCAAAAAATAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGAATTTTATTACTT
1 AAATTT-AAAAAA-AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTT
* *
21193507 TCAATAAAAATATATTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
64 TCAA-AAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
21193572 TGTATTAATTTAGTGTGTTTTTTAAAT
128 TGTATTAATTTAGTGTGTTTTTTAAAT
* * * * ** * *
21193599 AAATTTAGTAAAAAAA-CTTTATTTCAGCCCTTTGTTCATATTTTTTTACCGAAGCCTCATT-GT
1 AAATTTA--AAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAA-TTTTATTACT
* * *
21193662 TTC-AAAAAATATATTATTTTCGT-ATTTTATTATTTTACGTTATTTTAGTACATTATGTTTTAA
63 TTCAAAAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
*
21193725 ATGCATTAATTTAGT
127 ATGTATTAATTTAGT
21193740 AAAAAAAACC
Statistics
Matches: 689, Mismatches: 52, Indels: 35
0.89 0.07 0.05
Matches are distributed among these distances:
150 66 0.10
151 1 0.00
152 101 0.15
153 47 0.07
154 75 0.11
155 138 0.20
156 133 0.19
157 128 0.19
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (154 bp):
AAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTC
AAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGT
ATTAATTTAGTGTGTTTTTTAAAT
Found at i:21193694 original size:16 final size:18
Alignment explanation
Indices: 21193673--21193708 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
21193663 TCAAAAAATA
21193673 TATTATTTT-CG-TATTT
1 TATTATTTTACGTTATTT
21193689 TATTATTTTACGTTATTT
1 TATTATTTTACGTTATTT
21193707 TA
1 TA
21193709 GTACATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (18 bp):
TATTATTTTACGTTATTT
Found at i:21194033 original size:26 final size:27
Alignment explanation
Indices: 21193982--21194035 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
21193972 AGTTTTTTCG
* * *
21193982 TGCTAAATAAATTTCATAAAATATATA
1 TGCTAAATAAATATAATAAAACATATA
21194009 TGCTAAATAAA-ATAATAAAACATATA
1 TGCTAAATAAATATAATAAAACATATA
21194035 T
1 T
21194036 AATGTACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (27 bp):
TGCTAAATAAATATAATAAAACATATA
Found at i:21194139 original size:20 final size:20
Alignment explanation
Indices: 21194124--21194168 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
21194114 CCTCTTCTTC
21194124 TTCTTCTCCTTTTCTTTCCT
1 TTCTTCTCCTTTTCTTTCCT
* *
21194144 TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTCCTTTTCTTTCCT
21194164 TTCTT
1 TTCTT
21194169 TTTCTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTCTCCTTTTCTTTCCT
Found at i:21194175 original size:20 final size:20
Alignment explanation
Indices: 21194091--21194176 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 20
21194081 TACCTTATTT
*
21194091 TTTTCTTTCTTTTTCCTTCC
1 TTTTCTTTCTTTTTCTTTCC
* ** *
21194111 CTCCCTCTTCTTCTTCTTCTCC
1 TTTTCT-TTCTTTTTCTT-TCC
21194133 TTTTCTTTCCTTTCTTCTCCTTTCC
1 TTTTCTTT-C-TT-TT-T-CTTTCC
21194158 TTTTCTTTCTTTTTCTTTC
1 TTTTCTTTCTTTTTCTTTC
21194177 TTCTCCTTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
20 8 0.16
21 12 0.24
22 9 0.18
23 4 0.08
24 2 0.04
25 12 0.24
26 3 0.06
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTCTTTCTTTTTCTTTCC
Found at i:21194180 original size:13 final size:13
Alignment explanation
Indices: 21194142--21194198 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
21194132 CTTTTCTTTC
21194142 CTTTCTTCTCCTTT
1 CTTTCTTCTCC-TT
**
21194156 CCTTTTCTTTCTTTTT
1 -C-TTTC-TTCTCCTT
21194172 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
21194185 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
21194198 C
1 C
21194199 AGTCGAATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 20 0.56
14 4 0.11
15 2 0.06
16 6 0.17
17 4 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTCTTCTCCTT
Found at i:21194193 original size:20 final size:20
Alignment explanation
Indices: 21194116--21194190 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
21194106 CTTCCCTCCC
*
21194116 TCTTCTTCTTC-TTCTCCTTT
1 TCTTCTCCTTCTTTCTCC-TT
21194136 TCTT-TCCTT-TCTTCTCCTT
1 TCTTCTCCTTCT-TTCTCCTT
* * *
21194155 TCCTTTTCTTTCTTT-TTCTT
1 T-CTTCTCCTTCTTTCTCCTT
21194175 TCTTCTCCTTCTTTCT
1 TCTTCTCCTTCTTTCT
21194191 TCTCCTTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 18 0.41
20 19 0.43
21 6 0.14
22 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTCTCCTTCTTTCTCCTT
Found at i:21197092 original size:14 final size:14
Alignment explanation
Indices: 21197073--21197100 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21197063 TATCAAGAAT
21197073 GATGTTTGGATGGA
1 GATGTTTGGATGGA
21197087 GATGTTTGGATGGA
1 GATGTTTGGATGGA
21197101 TTCCTAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (14 bp):
GATGTTTGGATGGA
Found at i:21198735 original size:22 final size:22
Alignment explanation
Indices: 21198710--21198754 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
21198700 AATGTTAATT
21198710 ATGTG-TTGAATGATTTTTTTGG
1 ATGTGCTT-AATGATTTTTTTGG
*
21198732 ATGTGCCTTTATGATTTTTTTGG
1 ATGTG-CTTAATGATTTTTTTGG
21198755 GTAAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 13 0.65
24 2 0.10
ACGTcount: A:0.16, C:0.04, G:0.24, T:0.56
Consensus pattern (22 bp):
ATGTGCTTAATGATTTTTTTGG
Found at i:21201038 original size:10 final size:11
Alignment explanation
Indices: 21201015--21201049 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21201005 ATTTAAAACG
21201015 AAATAAAAGAA
1 AAATAAAAGAA
21201026 AAATAAAAGAA
1 AAATAAAAGAA
*
21201037 AATAAAAAAGAA
1 AA-ATAAAAGAA
21201049 A
1 A
21201050 TATATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAATAAAAGAA
Found at i:21203112 original size:30 final size:28
Alignment explanation
Indices: 21203040--21203116 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
21203030 GCGCGCGTCA
* *
21203040 CGATTTAGTCCCTTTTGTTTTTTTTATTT
1 CGATTTAGT-CCTTTTTTTTTTTTTACTT
* *
21203069 CGATTTCGCCCTTTATTTTTTCTTTTACTT
1 CGATTTAGTCCTTT-TTTTTT-TTTTACTT
*
21203099 CTATTTAGTCCTTTTTTT
1 CGATTTAGTCCTTTTTTT
21203117 AACACTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.13
29 16 0.41
30 18 0.46
ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64
Consensus pattern (28 bp):
CGATTTAGTCCTTTTTTTTTTTTTACTT
Found at i:21203180 original size:3 final size:3
Alignment explanation
Indices: 21203166--21203285 Score: 143
Period size: 3 Copynumber: 40.0 Consensus size: 3
21203156 CATCTTTTAA
*
21203166 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
21203214 TAT TAT TAT TAT TAT TAT TAT TAT CAT CT-T TAC CAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * *
21203259 TAC TAA TGT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
21203286 ATTTCTATTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
2 1 0.01
3 98 0.99
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:21203426 original size:16 final size:17
Alignment explanation
Indices: 21203389--21203430 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
21203379 TTATTTAATA
21203389 TATATAT-TAAATACTT
1 TATATATGTAAATACTT
* *
21203405 TTTATATGTACATA-TT
1 TATATATGTAAATACTT
21203421 TATATATGTA
1 TATATATGTA
21203431 TATCTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (17 bp):
TATATATGTAAATACTT
Found at i:21203683 original size:15 final size:15
Alignment explanation
Indices: 21203663--21203693 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21203653 TATTATTCGT
*
21203663 TTTTTGCTCATATTA
1 TTTTTGCTCACATTA
21203678 TTTTTGCTCACATTA
1 TTTTTGCTCACATTA
21203693 T
1 T
21203694 CATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTTGCTCACATTA
Found at i:21203696 original size:23 final size:20
Alignment explanation
Indices: 21203670--21203722 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 20
21203660 CGTTTTTTGC
21203670 TCATATTATTTTTGCTCACATTA
1 TCATATTATTTTT--TC-CATTA
21203693 TCATATTTATTTTTTCCATTA
1 TCATA-TTATTTTTTCCATTA
21203714 TGCATATTA
1 T-CATATTA
21203723 ACACCACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.32
22 6 0.21
23 5 0.18
24 8 0.29
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (20 bp):
TCATATTATTTTTTCCATTA
Found at i:21204030 original size:112 final size:111
Alignment explanation
Indices: 21203743--21204181 Score: 607
Period size: 112 Copynumber: 4.0 Consensus size: 111
21203733 TCAAAAAAAG
* * * * * *
21203743 AAAATTTTTCTAAATGAGGCAATATTTAGCATTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
21203808 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT-
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* * *
21203853 AAAAATTTTTAAAACAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGC
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAGAAAACATGCCCTAAGGTGC
* *
21203918 TGGGTGTCAATTTTTCTCATTCAACCAAATGGCTAAATATCATTTTA
65 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
*
21203965 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGC
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAGAAAACATGCCCTAAGGTGC
*
21204030 TGGGTGTCGATTTTTCTTATTCAACCAAATGGCTAAATATCCTTTTA
65 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* * * *
21204077 AAAAATTTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTTGAG-GAACGTACCCTAAGGTGC
1 AAAAA-TTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGC
* * * * *
21204141 TGGGTTTCGA--TTTCTCGTTTAACCAAATTGCCAAATATCCT
65 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
21204182 CTCGAATTTC
Statistics
Matches: 297, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
109 26 0.09
110 26 0.09
111 95 0.32
112 122 0.41
113 28 0.09
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (111 bp):
AAAAATTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
Found at i:21204136 original size:223 final size:220
Alignment explanation
Indices: 21203743--21204179 Score: 617
Period size: 223 Copynumber: 2.0 Consensus size: 220
21203733 TCAAAAAAAG
* * * *
21203743 AAAATTTTTCTAAATGAGGCAATATTTAGCATTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAAATAAGGCAATATTTAGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
21203808 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTTAAAACAAGGC
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTTAAAACAAGGC
* *
21203873 AATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCTCAT
131 AATGTTTTGCATTTGGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCAA--TTTCTCAT
*
21203938 TCAACCAAATGGCTAAATATCATTTTA
194 TCAACCAAATGGCCAAATATCATTTTA
* * *
21203965 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGC
1 AAAAATTTTCAAAATAAGGCAATATTTAGCATTT-GGAAATTCGAGAAAACATGCCCTAAGGTGC
* *
21204030 TGGGTGTCGATTTTTCTTATTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTTCAAAATAA
65 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTT-AAAACAA
* * * * * *
21204095 GGCAATGTTTTGCATTT-GGAAATTTGAG-GAACGTACCCTAAGGTGCTGGGTTTCGATTTCTCG
128 GGCAATGTTTTGCATTTGGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCAATTTCTCA
* *
21204158 TTTAACCAAATTGCCAAATATC
193 TTCAACCAAATGGCCAAATATC
21204180 CTCTCGAATT
Statistics
Matches: 190, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
221 25 0.13
222 28 0.15
223 95 0.50
224 20 0.11
225 22 0.12
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (220 bp):
AAAAATTTTCAAAATAAGGCAATATTTAGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTTAAAACAAGGC
AATGTTTTGCATTTGGGAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCAATTTCTCATTC
AACCAAATGGCCAAATATCATTTTA
Found at i:21207616 original size:17 final size:16
Alignment explanation
Indices: 21207590--21207624 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
21207580 GACTCGAAAG
21207590 AAAAATAAAAAAATCA
1 AAAAATAAAAAAATCA
21207606 AAAAATGAAAAAAATCA
1 AAAAAT-AAAAAAATCA
21207623 AA
1 AA
21207625 GTCAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAATAAAAAAATCA
Found at i:21207646 original size:6 final size:6
Alignment explanation
Indices: 21207637--21207676 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
21207627 CAAAAATAGG
*
21207637 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAG AGAAAA AG
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA AG
21207677 GAGAGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 21 0.70
7 6 0.20
8 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:21207650 original size:10 final size:10
Alignment explanation
Indices: 21207637--21207674 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
21207627 CAAAAATAGG
21207637 AGAAAAAGAA
1 AGAAAAAGAA
21207647 AGAAGAAA-AA
1 AGAA-AAAGAA
21207657 AGAAAAAGAA
1 AGAAAAAGAA
21207667 AGAGAAAA
1 AGA-AAAA
21207675 AGGAGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.12
10 15 0.60
11 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:21207662 original size:20 final size:19
Alignment explanation
Indices: 21207637--21207675 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
21207627 CAAAAATAGG
21207637 AGAAAAAGAAAGAAGAAAAA
1 AGAAAAAGAAAG-AGAAAAA
21207657 AGAAAAAGAAAGAGAAAAA
1 AGAAAAAGAAAGAGAAAAA
21207676 GGAGAGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAGAGAAAAA
Found at i:21208664 original size:20 final size:20
Alignment explanation
Indices: 21208632--21208673 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
21208622 AAAAAAAACA
21208632 AAAAAAATGAAGA-AAGGAAG
1 AAAAAAATGAAGAGAA-GAAG
21208652 AAAAAAA-GAAAGAGAAGAAG
1 AAAAAAATG-AAGAGAAGAAG
21208672 AA
1 AA
21208674 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.05
20 17 0.85
21 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAAAAATGAAGAGAAGAAG
Found at i:21208871 original size:44 final size:43
Alignment explanation
Indices: 21208776--21208889 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 43
21208766 AAAAAGGGTG
* * *
21208776 GCTCAAATTTTGGAACAAAATGGGGC-CCGAAGTGATCAGAGC
1 GCTCAAATTTTGGATCAAATTGGGGCATCGAAGTGATCAGAGC
* * **
21208818 GACTTAAATTTTGGATCAAATTGGGGCATGGTGGTGATCAGAGC
1 G-CTCAAATTTTGGATCAAATTGGGGCATCGAAGTGATCAGAGC
* *
21208862 AGCTCAAATTTT-GATCAGATCGGGGCAT
1 -GCTCAAATTTTGGATCAAATTGGGGCAT
21208890 ATGATGATCT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
42 1 0.02
43 36 0.61
44 21 0.36
45 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (43 bp):
GCTCAAATTTTGGATCAAATTGGGGCATCGAAGTGATCAGAGC
Found at i:21208878 original size:43 final size:44
Alignment explanation
Indices: 21208807--21208889 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
21208797 GGGGCCCGAA
* *
21208807 GTGATCAGAGCGACTTAAATTTTGGATCAAATTGGGGCATGGTG
1 GTGATCAGAGCGACTCAAATTTTGGATCAAATCGGGGCATGGTG
*
21208851 GTGATCAGAGC-AGCTCAAATTTT-GATCAGATCGGGGCAT
1 GTGATCAGAGCGA-CTCAAATTTTGGATCAAATCGGGGCAT
21208890 ATGATGATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 15 0.43
44 20 0.57
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (44 bp):
GTGATCAGAGCGACTCAAATTTTGGATCAAATCGGGGCATGGTG
Found at i:21210055 original size:46 final size:46
Alignment explanation
Indices: 21209992--21210396 Score: 643
Period size: 46 Copynumber: 8.8 Consensus size: 46
21209982 AACAGATCAA
*
21209992 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGGCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
* *
21210038 CGAAGATAGCAGATCTTGTCTTCTTGTATTTGGCAGCAGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
*
21210084 CGAAGATAGCAGATCTTGTCTTCTTGTATTTGGCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
* *
21210130 CGAAGATGGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
**
21210176 CGAAGAT-GCCAGATCTTGTCTTCCTGTATTTGGCAGTAGAGGAGAT
1 CGAAGATAG-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
*
21210222 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
* *
21210268 CAAAGATAGCAGATCCTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
* * *
21210314 CGAAGATAGCAGATCTTGTCTTCCTGTATTTAGCAGCAGAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
* *
21210360 CGAAGATAGCAGATCTTGTCTCCCTGTA-CTGGCAGCG
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
21210397 AAACAGATCG
Statistics
Matches: 336, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
45 7 0.02
46 328 0.98
47 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
Found at i:21211963 original size:3 final size:3
Alignment explanation
Indices: 21211949--21212047 Score: 101
Period size: 3 Copynumber: 33.0 Consensus size: 3
21211939 CATCTTTTAA
*
21211949 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
21211997 TAT CAT CT-T TAC CAT TAT TAT TAA TAC TAA TGT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
21212042 CAT TAT
1 TAT TAT
21212048 ATTTCTATTT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
2 1 0.01
3 77 0.99
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:21212188 original size:16 final size:17
Alignment explanation
Indices: 21212151--21212192 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
21212141 TTATTTTATA
21212151 TATATAT-TAAATACTT
1 TATATATGTAAATACTT
* *
21212167 TTTATATGTACATA-TT
1 TATATATGTAAATACTT
21212183 TATATATGTA
1 TATATATGTA
21212193 TATCTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (17 bp):
TATATATGTAAATACTT
Found at i:21212454 original size:23 final size:22
Alignment explanation
Indices: 21212428--21212480 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
21212418 CATTTTTTGC
21212428 TCATATTAT-TTTTGTTCACATTA
1 TCATATTATATTTT-TTC-CATTA
21212451 TCATATT-TATTTTTTCCATTA
1 TCATATTATATTTTTTCCATTA
21212472 TGCATATTA
1 T-CATATTA
21212481 ACACCACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.22
22 10 0.37
23 11 0.41
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (22 bp):
TCATATTATATTTTTTCCATTA
Found at i:21212472 original size:21 final size:24
Alignment explanation
Indices: 21212428--21212479 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
21212418 CATTTTTTGC
21212428 TCATA-TTATTTTTGTTCACATTA
1 TCATATTTATTTTTGTTCACATTA
21212451 TCATATTTA-TTTT-TTC-CATTA
1 TCATATTTATTTTTGTTCACATTA
21212472 TGCATATT
1 T-CATATT
21212480 AACACCACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.22
22 9 0.33
23 9 0.33
24 3 0.11
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (24 bp):
TCATATTTATTTTTGTTCACATTA
Found at i:21212779 original size:111 final size:112
Alignment explanation
Indices: 21212500--21212825 Score: 403
Period size: 111 Copynumber: 3.0 Consensus size: 112
21212490 TTCAAAAAAG
* * * * *
21212500 AAATTTTTTCTAAATGAGGCAATATTTAGCATTTGGAAATTCAAGAAAACGTGCCCTAAGGTGCT
1 AAATTTTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
21212565 GGGTGT-GATTTTTCTCGTTCAACCGAATGGCTTAATATCCTTTTAA
66 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
* * * *
21212611 AAA-ATTTT-AAAATAAGACAATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTAC
1 AAATTTTTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGC
*
21212674 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAA
65 TGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
* * * * **
21212722 AAATTTTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAGCGTATCCTAAGGTGCT
1 AAATTTTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
21212786 GGGTTTCGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCT
21212826 CTCAAATTTC
Statistics
Matches: 184, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
109 46 0.25
110 38 0.21
111 64 0.35
112 14 0.08
113 22 0.12
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (112 bp):
AAATTTTTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
Found at i:21216132 original size:23 final size:23
Alignment explanation
Indices: 21216102--21216153 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
21216092 AAGTCAGCCT
*
21216102 TAACTCAAGTGAGTATTCTTTTA
1 TAACTCAAGTGAGGATTCTTTTA
*
21216125 TAACTCAATTGAGGATTCTTTTA
1 TAACTCAAGTGAGGATTCTTTTA
*
21216148 AAACTC
1 TAACTC
21216154 CTCCAAGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (23 bp):
TAACTCAAGTGAGGATTCTTTTA
Found at i:21225062 original size:57 final size:57
Alignment explanation
Indices: 21224970--21225084 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
21224960 TTAAATTGGT
**
21224970 GGGAACCTCTAAGAACGTCATGTAAATATGGACGATAGTAACATTTCTCAATAGAGG
1 GGGAACCTCTAAGAACGTCATGTAAATATAAACGATAGTAACATTTCTCAATAGAGG
21225027 GGGAACCTCTAAGAACGTCATGTAAATATAAACGATAGTAACATTTCTCAATAGAGG
1 GGGAACCTCTAAGAACGTCATGTAAATATAAACGATAGTAACATTTCTCAATAGAGG
21225084 G
1 G
21225085 CCGTGTCCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (57 bp):
GGGAACCTCTAAGAACGTCATGTAAATATAAACGATAGTAACATTTCTCAATAGAGG
Found at i:21232473 original size:38 final size:38
Alignment explanation
Indices: 21232425--21232514 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
21232415 CGACCGTCAG
21232425 TTTGTCCATCGAACACCCAATGCCCTTCCGCACGTAGT
1 TTTGTCCATCGAACACCCAATGCCCTTCCGCACGTAGT
21232463 TTTGTCCATCGAACACCCAATGCCCTTCCGCACGTAGT
1 TTTGTCCATCGAACACCCAATGCCCTTCCGCACGTAGT
*
21232501 TTTGTCCATTGAAC
1 TTTGTCCATCGAAC
21232515 GCCCCTAGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (38 bp):
TTTGTCCATCGAACACCCAATGCCCTTCCGCACGTAGT
Found at i:21234225 original size:13 final size:14
Alignment explanation
Indices: 21234194--21234226 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21234184 TTAAAATCAT
*
21234194 ATAAAAGGATATAA
1 ATAAAACGATATAA
21234208 ATAAAACGATAT-A
1 ATAAAACGATATAA
21234221 ATAAAA
1 ATAAAA
21234227 TAAATGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (14 bp):
ATAAAACGATATAA
Found at i:21236049 original size:51 final size:45
Alignment explanation
Indices: 21235921--21236367 Score: 153
Period size: 45 Copynumber: 9.7 Consensus size: 45
21235911 TTATGGCTTC
*
21235921 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTAT
1 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
* * * * *
21235966 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTTAAACTTT
1 AATCTGTTCCACTGCAACTTCAGGGAAATAAGA--T-TCGC--T-AACTAT
* **
21236017 AATCTGTTCCACTGCAACCTT-AGGGAAATAAGATTAGCGT--CTCC
1 AATCTGTTCCACTGCAA-CTTCAGGGAAATAAGATTCGC-TAACTAT
* * * * * ** * *
21236061 AATTTGCTCCACTGCAACTTTAGGGAGATAAGGTT-TATAGCTTT
1 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
* ** * * * **
21236105 AATCTGCTCTC-CTGCAACTTCAAAGAGATAAGATTTGCTATCTCC
1 AATCTGTTC-CACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
* ** * * * **
21236150 GATCTACTCCACTGTAACTTTAGGGAGATAAGATT-TATAACT-T
1 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
* * * * * *
21236193 CAATCTGCTCCACCGTAACTTCA-GAAAGATAAGATTTG-TAATTTAT
1 -AATCTGTTCCACTGCAACTTCAGGGAA-ATAAGATTCGCTAA-CTAT
* * * * *
21236239 AGCTTTATTCTGTTCTATTGCAACTTTAGGGAAATAAGATTCACTATCT-T
1 A-----A-TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
* * * *
21236289 CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCT-T
1 -AATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTAACTAT
* * *
21236334 CAGTCCGTTCCACTGCAACTTCAGGGAGATAAGA
1 -AATCTGTTCCACTGCAACTTCAGGGAAATAAGA
21236368 CTTGTGGCTT
Statistics
Matches: 305, Mismatches: 69, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 93 0.30
45 129 0.42
46 3 0.01
47 2 0.01
48 6 0.02
49 1 0.00
50 3 0.01
51 54 0.18
52 8 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (45 bp):
AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAACTAT
Found at i:21236104 original size:95 final size:96
Alignment explanation
Indices: 21235784--21236106 Score: 255
Period size: 96 Copynumber: 3.5 Consensus size: 96
21235774 ACGAGAGATT
* * * * *
21235784 TAGTCTGCTCCACTGCAACTTTAGGGCGATAAGAC-T-T-G---T-AACTTCAACCTGCTCCACT
1 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAAACTTTAATCTGTTCCACT
* * * *
21235842 ACAACTTCAGGGAGATAAGGTTTGCTAT---
66 GCAACTTCAGGGAAATAAGATTAGCTATCCA
* * * * * * ** *
21235870 GA-TCTGCTCTACTGCAACTTCAGAGAGATTAGA-TATCTA-ATTTATGGCTTCAATCTGTTCCA
1 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TATAGCTTTA-AACTTTAATCTGTTCCA
* *
21235932 CTGCAACTTCAGGGAAATAAGATTCGCTATCTA
64 CTGCAACTTCAGGGAAATAAGATTAGCTATCCA
* *
21235965 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTTAAACTTTAATCTGTTCCACT
1 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAAACTTTAATCTGTTCCACT
*
21236030 GCAACCTT-AGGGAAATAAGATTAGCGTCTCCA
66 GCAA-CTTCAGGGAAATAAGATTAGC-TATCCA
* * **
21236062 -A-TTTGCTCCACTGCAACTTTAGGGAGATAAGGTTTATAGCTTTAA
1 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAA
21236107 TCTGCTCTCC
Statistics
Matches: 187, Mismatches: 33, Indels: 25
0.76 0.13 0.10
Matches are distributed among these distances:
85 26 0.14
86 2 0.01
87 1 0.01
90 1 0.01
92 39 0.21
95 39 0.21
96 67 0.36
97 12 0.06
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (96 bp):
TAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAAACTTTAATCTGTTCCACT
GCAACTTCAGGGAAATAAGATTAGCTATCCA
Found at i:21236176 original size:89 final size:89
Alignment explanation
Indices: 21236067--21236400 Score: 244
Period size: 89 Copynumber: 3.7 Consensus size: 89
21236057 CTCCAATTTG
* * * *
21236067 CTCCACTGCAACTTTAGGGAGATAAGGTTTATAGCTTTAATCTGCTCTC-CTGCAACTTCA-AAG
1 CTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTCAATCTGCTC-CACCGCAACTTCAGAA-
21236130 AGATAAGATTTGCTATCTCCGATCTA
64 AGATAAGATTTGCTATCTCCGATCTA
* *
21236156 CTCCACTGTAACTTTAGGGAGATAAGATTTATAACTTCAATCTGCTCCACCGTAACTTCAGAAAG
1 CTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTCAATCTGCTCCACCGCAACTTCAGAAAG
* ** *
21236221 ATAAGATTTG-TAATTTATAGCTTTATTCTG
66 ATAAGATTTGCT-A--TCT--C-CGA-TCTA
* * * * * * * * **
21236251 TTCTATTGCAACTTTAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTTAGGGAGATAAGATTTA-TAACTTCAATCTGCTCCACCGCAACTTCAGAAA
* * **
21236316 GATAAGACTTGCTATCTTC-AGTCCG
65 GATAAGATTTGCTATCTCCGA-TCTA
* * * * ** * **
21236341 TTCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTTAATCTGCTCCACTACAACTTCA
1 CTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTCAATCTGCTCCACCGCAACTTCA
21236401 AGGAGATAAA
Statistics
Matches: 194, Mismatches: 40, Indels: 22
0.76 0.16 0.09
Matches are distributed among these distances:
88 2 0.01
89 89 0.46
90 30 0.15
91 2 0.01
93 1 0.01
94 3 0.02
95 28 0.14
96 38 0.20
97 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (89 bp):
CTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTCAATCTGCTCCACCGCAACTTCAGAAAG
ATAAGATTTGCTATCTCCGATCTA
Found at i:21236406 original size:44 final size:45
Alignment explanation
Indices: 21235787--21236409 Score: 326
Period size: 44 Copynumber: 13.6 Consensus size: 45
21235777 AGAGATTTAG
* * *
21235787 TCTGCTCCACTGCAACTTTAGGGCGATAAGACTTG-TAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* * ** *
21235831 CCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTA---T-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* * * *
21235872 TCTGCTCTACTGCAACTTCAGAGAGATTAGATATCTAAT-TTATGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGA-TA-AGA-CT--TGCTA--GCTTCAA
* * * *
21235923 TCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTAT-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTAGCT-TCAA
* *
21235968 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTTAAACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAC-T-T-GC--T-AGCTTCAA
* * *
21236019 TCTGTTCCACTGCAACCTT-AGGGAAATAAGA-TTAGC--GTCTCCAA
1 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGACTT-GCTAG-CTTCAA
* * * ** *
21236063 TTTGCTCCACTGCAACTTTAGGGAGATAAG-GTTTATAGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
** * * * *
21236107 TCTGCTCTC-CTGCAACTTCAAAGAGATAAGATTTGCTATCTCCGA
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* * * ** *
21236152 TCTACTCCACTGTAACTTTAGGGAGATAAGA-TTTATAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* * ** * * * *
21236196 TCTGCTCCACCGTAACTTCAGAAAGATAAGATTTGTAATTTATAGCTTTAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG------CTAGCTTCAA
* * * * * * * *
21236247 TCTGTTCTATTGCAACTTTAGGGAAATAAGA-TTCACTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTAGCTTCAA
* *
21236292 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* * * *
21236337 TCCGTTCCACTGCAACTTCAGGGAGATAAGACTTG-TGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
* *
21236381 TCTGCTCCACTACAACTTCAAGGAGATAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA
21236410 AGTTTACAGC
Statistics
Matches: 437, Mismatches: 102, Indels: 80
0.71 0.16 0.13
Matches are distributed among these distances:
41 23 0.05
42 3 0.01
43 4 0.01
44 152 0.35
45 147 0.34
46 4 0.01
47 4 0.01
48 6 0.01
49 3 0.01
50 7 0.02
51 81 0.19
52 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAGCTTCAA
Found at i:21243844 original size:12 final size:12
Alignment explanation
Indices: 21243829--21243858 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
21243819 ATTGAGTTCC
21243829 AAATTTCTTGGA
1 AAATTTCTTGGA
21243841 AAATTTCTTGGA
1 AAATTTCTTGGA
21243853 AAATTT
1 AAATTT
21243859 ATTTTTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (12 bp):
AAATTTCTTGGA
Found at i:21245789 original size:45 final size:45
Alignment explanation
Indices: 21245714--21245820 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
21245704 TACACGGTGG
* * * *
21245714 ATCAGCACACATC-ACCACCCTTATAGTCAATAGTACTCGATGAA
1 ATCAGCACATAGCAACCACCCTTATACTCAATAGTACCCGATGAA
* * * *
21245758 ATCAGCACATAGCAACCACCTTTGTACTCAATGGTACCCGGTGAA
1 ATCAGCACATAGCAACCACCCTTATACTCAATAGTACCCGATGAA
*
21245803 ATCAACACATAGCAACCA
1 ATCAGCACATAGCAACCA
21245821 TCTATATAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 11 0.21
45 42 0.79
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCCTTATACTCAATAGTACCCGATGAA
Found at i:21245838 original size:45 final size:45
Alignment explanation
Indices: 21245727--21245917 Score: 136
Period size: 45 Copynumber: 4.2 Consensus size: 45
21245717 AGCACACATC
* * * * *
21245727 ACCACCCT-TATAGTCAATAGTACTCGATGAAATCAGCACATAGCA
1 ACCA-CCTATATACTCAATGGTACCCGGTGAAATCAACACATAGCA
* *
21245772 ACCACCTTTGTACTCAATGGTACCCGGTGAAATCAACACATAGCA
1 ACCACCTATATACTCAATGGTACCCGGTGAAATCAACACATAGCA
* * * * *
21245817 ACCATCTATATAAC-CATTGGTATCTGGTGAAATCAGA-ACATAACA
1 ACCACCTATAT-ACTCAATGGTACCCGGTGAAATCA-ACACATAGCA
* ** * ** * * *
21245862 ACCACCTTTATTTTCATTAATATCGGGTGGAATCAACACATAGCA
1 ACCACCTATATACTCAATGGTACCCGGTGAAATCAACACATAGCA
*
21245907 TCCACCTATAT
1 ACCACCTATAT
21245918 TTCCAACGAT
Statistics
Matches: 117, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
44 4 0.03
45 110 0.94
46 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (45 bp):
ACCACCTATATACTCAATGGTACCCGGTGAAATCAACACATAGCA
Found at i:21245919 original size:45 final size:45
Alignment explanation
Indices: 21245797--21245922 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 45
21245787 AATGGTACCC
* ** ** *
21245797 GGTGAAATCAACACATAGCAACCATCTATATAACCATTGGTATCT
1 GGTGAAATCAACACATAGCAACCACCTATATTTCCATTAATATCG
* * *
21245842 GGTGAAATCAGA-ACATAACAACCACCTTTATTTTCATTAATATCG
1 GGTGAAATCA-ACACATAGCAACCACCTATATTTCCATTAATATCG
* *
21245887 GGTGGAATCAACACATAGCATCCACCTATATTTCCA
1 GGTGAAATCAACACATAGCAACCACCTATATTTCCA
21245923 ACGATATCCG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 1 0.02
45 63 0.97
46 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (45 bp):
GGTGAAATCAACACATAGCAACCACCTATATTTCCATTAATATCG
Found at i:21260125 original size:13 final size:14
Alignment explanation
Indices: 21260094--21260126 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21260084 TTAAAATCAT
*
21260094 ATAAAAGGATATAA
1 ATAAAACGATATAA
21260108 ATAAAACGATAT-A
1 ATAAAACGATATAA
21260121 ATAAAA
1 ATAAAA
21260127 TAAACGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (14 bp):
ATAAAACGATATAA
Found at i:21262021 original size:17 final size:17
Alignment explanation
Indices: 21261999--21262054 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
21261989 TCAAACGTCC
*
21261999 AAAAAACATTTCCTAGT
1 AAAAAACATTTCCTAAT
*
21262016 AAAAAACATTTCGTAAT
1 AAAAAACATTTCCTAAT
21262033 AAAAAACATTTCCTAAT
1 AAAAAACATTTCCTAAT
21262050 CAAAA
1 -AAAA
21262055 CTCTATGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
17 31 0.89
18 4 0.11
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.27
Consensus pattern (17 bp):
AAAAAACATTTCCTAAT
Found at i:21264024 original size:18 final size:18
Alignment explanation
Indices: 21264001--21264035 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21263991 ATACATACTT
21264001 ATTAAATTAATCAATCTC
1 ATTAAATTAATCAATCTC
21264019 ATTAAATTAATCAATCT
1 ATTAAATTAATCAATCT
21264036 ATTGAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATCAATCTC
Done.