Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 163 of 276
Found at i:53211995 original size:28 final size:28
Alignment explanation
Indices: 53211963--53212060 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
53211953 TTGTGAAAAA
*
53211963 GGCACTTAGTGTGCGAATTATTGGGGAT
1 GGCACTTAGTGTGCGAATTATTGGAGAT
* ** *
53211991 GGCACTTAGTGTGCGAAATATCCAGAAAT
1 GGCACTTAGTGTGCGAATTAT-TGGAGAT
* * *
53212020 AG-ACTTAGTGTGCAAATTATTGAAGAT
1 GGCACTTAGTGTGCGAATTATTGGAGAT
53212047 GGCACTTAGTGTGC
1 GGCACTTAGTGTGC
53212061 AAGACATCCA
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 4 0.07
28 47 0.85
29 4 0.07
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.30
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAATTATTGGAGAT
Found at i:53212070 original size:56 final size:56
Alignment explanation
Indices: 53211966--53212125 Score: 164
Period size: 56 Copynumber: 2.9 Consensus size: 56
53211956 TGAAAAAGGC
* ** *
53211966 ACTTAGTGTGCGAATTATTGGGGATGGCACTTAGTGTGCGAAATATCCAGAAATAG-
1 ACTTAGTGTGCAAATTATTGAAGATGGCACTTAGTGTGCGAAACATCCAG-AATAGT
* *
53212022 ACTTAGTGTGCAAATTATTGAAGATGGCACTTAGTGTGC-AAGACATCCAGGATGGT
1 ACTTAGTGTGCAAATTATTGAAGATGGCACTTAGTGTGCGAA-ACATCCAGAATAGT
* * ** * *
53212078 ACTTAGTGTGCGAGA-CATCCAGGATGGCACTTAGTGTGCGATACATCC
1 ACTTAGTGTGC-AAATTATTGAAGATGGCACTTAGTGTGCGAAACATCC
53212126 GTGAAGGCAC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
55 5 0.06
56 80 0.91
57 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (56 bp):
ACTTAGTGTGCAAATTATTGAAGATGGCACTTAGTGTGCGAAACATCCAGAATAGT
Found at i:53212075 original size:28 final size:27
Alignment explanation
Indices: 53211987--53212149 Score: 132
Period size: 28 Copynumber: 5.8 Consensus size: 27
53211977 GAATTATTGG
*
53211987 GGATGGCACTTAGTGTGCGAAATATCCA
1 GGATGGCACTTAGTGTGC-AAACATCCA
* * * **
53212015 GAAATAG-ACTTAGTGTGCAAATTATTGA
1 G-GATGGCACTTAGTGTGCAAA-CATCCA
*
53212043 AGATGGCACTTAGTGTGCAAGACATCCA
1 GGATGGCACTTAGTGTGCAA-ACATCCA
* *
53212071 GGATGGTACTTAGTGTGCGAGACATCCA
1 GGATGGCACTTAGTGTGC-AAACATCCA
*
53212099 GGATGGCACTTAGTGTGCGATACATCC-
1 GGATGGCACTTAGTGTGC-AAACATCCA
* *
53212126 GTGAAGGCACTGAGTGTGCGAAAC
1 G-GATGGCACTTAGTGTGC-AAAC
53212150 TTTGAGAACA
Statistics
Matches: 111, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
27 7 0.06
28 99 0.89
29 5 0.05
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (27 bp):
GGATGGCACTTAGTGTGCAAACATCCA
Found at i:53221993 original size:50 final size:50
Alignment explanation
Indices: 53221883--53222162 Score: 245
Period size: 50 Copynumber: 5.7 Consensus size: 50
53221873 AGGGTAAGGT
* ** * * * *
53221883 GCCGACGCCATGTCCTGGACATGGTCTTACACT-G-GCTCACACATCAAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAG
* * * *
53221931 GTCGATGCCATGTCCCAGACATGGTCTTACA-TTGACTTTCGTATATCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATATATCAAG
* * * *
53221981 GCTGATGCCATGTCCTAGACATGGTCTTACGCTAGCTCTCATCTATC-AG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAG
* * *
53222030 TGCCGATGCCATGTCCCAAACATGGTCTTACACT-G---ACACATATCAA-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAG
* * * * *
53222076 GCCAATGACATGTCCCAGAGATGGTCTTACACTAGCTCTCATATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAG
* * *
53222126 GCCAATGCCATGTCCTAGGCATGGTCTTACACTAGCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
53222163 TTAATATCTC
Statistics
Matches: 184, Mismatches: 37, Indels: 20
0.76 0.15 0.08
Matches are distributed among these distances:
45 29 0.16
46 7 0.04
47 2 0.01
48 28 0.15
49 10 0.05
50 106 0.58
51 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAG
Found at i:53222117 original size:95 final size:97
Alignment explanation
Indices: 53221891--53222158 Score: 276
Period size: 95 Copynumber: 2.8 Consensus size: 97
53221881 GTGCCGACGC
** * * * *
53221891 CATGTCCTGGACATGGTCTTACACTGGCTCACA-C-ATCAAAGTCGATGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCATCTATC-AGGCCGATGCCATGTCCCAGACATG
* * ** *
53221954 GTCTTACATTGACTTTCGTATATCAAGGCTGATGC
65 GTCTTACACTGAC-TACG-ATATCAAGGCCAATGA
* * *
53221989 CATGTCCTAGACATGGTCTTACGCTAGCTCTCATCTATCAGTGCCGATGCCATGTCCCAAACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCATCTATCAG-GCCGATGCCATGTCCCAGACATG
53222054 GTCTTACACTGAC-AC-ATATCAA-GCCAATGA
65 GTCTTACACTGACTACGATATCAAGGCCAATGA
* * * * * *
53222084 CATGTCCCAGAGATGGTCTTACACTAGCTCTCATATCTCGAGGCCAATGCCATGTCCTAGGCATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCATCTATC-AGGCCGATGCCATGTCCCAGACATG
53222149 GTCTTACACT
65 GTCTTACACT
53222159 AGCTTTAATA
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
95 68 0.47
96 9 0.06
98 30 0.21
99 2 0.01
100 36 0.25
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (97 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTCATCTATCAGGCCGATGCCATGTCCCAGACATGG
TCTTACACTGACTACGATATCAAGGCCAATGA
Found at i:53222149 original size:145 final size:148
Alignment explanation
Indices: 53221881--53222162 Score: 356
Period size: 145 Copynumber: 1.9 Consensus size: 148
53221871 ATAGGGTAAG
*** * * * *
53221881 GTGCCGACGCCATGTCCTGGACATGGTCTTACACTGGCTCACACATCAAAGTCGATGCCATGTCC
1 GTGCCGACGCCATGTCCCAAACATGGTCTTACACTGGCACACACATCAAAGCCAATGACATGTCC
* * * **
53221946 CAGACATGGTCTTACATTGACTTTCGTATATCAAGGCTGATGCCATGTCCTAGACATGGTCTTAC
66 CAGACATGGTCTTACATAGACTCTCATATATCAAGGCCAATGCCATGTCCTAGACATGGTCTTAC
*
53222011 GCTAGCTCTCATCTATCA
131 ACTAGCTCTCATCTATCA
* *
53222029 GTGCCGATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATATC-AAGCCAATGACATGTCC
1 GTGCCGACGCCATGTCCCAAACATGGTCTTACACTGGCACACACATCAAAGCCAATGACATGTCC
* * * *
53222091 CAGAGATGGTCTTACACTAG-CTCTCATATCTCGAGGCCAATGCCATGTCCTAGGCATGGTCTTA
66 CAGACATGGTCTTACA-TAGACTCTCATATATCAAGGCCAATGCCATGTCCTAGACATGGTCTTA
53222155 CACTAGCT
130 CACTAGCT
53222163 TTAATATCTC
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
145 73 0.64
146 9 0.08
147 1 0.01
148 31 0.27
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (148 bp):
GTGCCGACGCCATGTCCCAAACATGGTCTTACACTGGCACACACATCAAAGCCAATGACATGTCC
CAGACATGGTCTTACATAGACTCTCATATATCAAGGCCAATGCCATGTCCTAGACATGGTCTTAC
ACTAGCTCTCATCTATCA
Found at i:53225085 original size:27 final size:26
Alignment explanation
Indices: 53225054--53225112 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
53225044 CACTATCTAA
*
53225054 TTCTGGTGGCTCTGCCACAATATCTG
1 TTCTGGTGACTCTGCCACAATATCTG
* *
53225080 TATCTGGTGACTCTGTCACGATATCTG
1 T-TCTGGTGACTCTGCCACAATATCTG
53225107 TTCTGG
1 TTCTGG
53225113 CAGCCATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (26 bp):
TTCTGGTGACTCTGCCACAATATCTG
Found at i:53225264 original size:6 final size:6
Alignment explanation
Indices: 53225255--53225389 Score: 132
Period size: 6 Copynumber: 22.3 Consensus size: 6
53225245 CTGTCACGTA
*
53225255 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACCG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * *
53225303 ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG
* * **
53225352 ATTCTG ATTCTG ATTCTC ATTCTG GTTCCA ATTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT
53225390 CATGTTTCTT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
5 5 0.05
6 93 0.89
7 5 0.05
8 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:53225325 original size:61 final size:61
Alignment explanation
Indices: 53225230--53225368 Score: 217
Period size: 61 Copynumber: 2.3 Consensus size: 61
53225220 TTGCATTCAC
* * **
53225230 ATTCTAATTCTGATTCTGTCACGTAATTCTGATTCTGATTCTGATTCTGATT-CTGTTACCG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTG-TTACTAATACCG
*
53225291 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACCG
53225352 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
53225369 CATTCTGGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 2 0.03
61 70 0.97
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (61 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACCG
Found at i:53226402 original size:43 final size:42
Alignment explanation
Indices: 53226258--53226412 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 42
53226248 ATCGAGATGG
* *
53226258 GATTACATGTAAGACCATGTCTGGGACATTGGTATTGTATTAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTAATGTA-TAT
* * *
53226301 GATTATGTGTAAGACCAAGTCTGGGACATTGG-CATCGTTATAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTAAT-G-TATAT
* * *
53226344 GTTTTCGTGTAAGACCACGTCTGGGACATTGGTAATGATATAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTAATG-TATAT
* * *
53226387 GATAACATGCT-AGACCATATCTGGGA
1 GATTACGTG-TAAGACCATGTCTGGGA
53226413 TATGGCATTG
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 85 0.93
44 5 0.05
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGTAATGTATAT
Found at i:53226961 original size:16 final size:16
Alignment explanation
Indices: 53226940--53226971 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53226930 ATGATAATGA
53226940 TGTATAGAATATGGTC
1 TGTATAGAATATGGTC
53226956 TGTATAGAATATGGTC
1 TGTATAGAATATGGTC
53226972 ATTTTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
TGTATAGAATATGGTC
Found at i:53232260 original size:16 final size:16
Alignment explanation
Indices: 53232235--53232267 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53232225 GTTCGGGGCA
53232235 TAAAAAA-TTTAATTT
1 TAAAAAATTTTAATTT
53232250 TAAAAACATTTTAATTT
1 TAAAAA-ATTTTAATTT
53232267 T
1 T
53232268 CTCACATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 1 0.06
17 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAAAATTTTAATTT
Found at i:53235856 original size:49 final size:49
Alignment explanation
Indices: 53235787--53236186 Score: 625
Period size: 49 Copynumber: 8.3 Consensus size: 49
53235777 GTGAACATGC
* *
53235787 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
* *
53235836 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
* * *
53235883 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
* *
53235932 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
53235981 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
53236030 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
53236079 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--T
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
* * * *
53236126 ATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATATGTGATAAG-GCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
53236175 A-A-ATGTGATAAG
1 ATATATGTGATAAG
53236187 TCCCGAAGGG
Statistics
Matches: 336, Mismatches: 9, Indels: 13
0.94 0.03 0.04
Matches are distributed among these distances:
46 2 0.01
47 92 0.27
48 3 0.01
49 239 0.71
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (49 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
Found at i:53235866 original size:96 final size:96
Alignment explanation
Indices: 53235766--53236186 Score: 616
Period size: 96 Copynumber: 4.4 Consensus size: 96
53235756 TTAGGTTTCT
* * * *
53235766 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* *
53235830 GTGTATATATATGTGATAAGGCCTAATGGCCG
65 GTGTATATATATGTGATAAGGCCGAATGGCCA
* * *
53235862 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
53235927 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TGTATATATATGTGATAAGGCCGAATGGCCA
53235958 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
53236023 AGTGTATATATATGTGATAAGGCCGAATGGCCA
64 AGTGTATATATATGTGATAAGGCCGAATGGCCA
53236056 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
53236121 AGTG--TATATATGTGA-CAGAGCCGAGTGGCCA
64 AGTGTATATATATGTGATAAG-GCCGAATGGCCA
* * *
53236152 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53236187 TCCCGAAGGG
Statistics
Matches: 308, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
94 14 0.05
95 3 0.01
96 151 0.49
98 140 0.45
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
TGTATATATATGTGATAAGGCCGAATGGCCA
Found at i:53239588 original size:19 final size:19
Alignment explanation
Indices: 53239564--53239602 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
53239554 TTTTGTATCA
53239564 ACACAAGATTGAAGAGACT
1 ACACAAGATTGAAGAGACT
53239583 ACACAAGATTGAAGAGACT
1 ACACAAGATTGAAGAGACT
53239602 A
1 A
53239603 TGTGAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (19 bp):
ACACAAGATTGAAGAGACT
Found at i:53241006 original size:43 final size:43
Alignment explanation
Indices: 53240910--53241011 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
53240900 TCGAGATGGG
* *
53240910 ATTA-CATGTAAGACCATGTCTGGGACATTGGCATTGTATTGT
1 ATTATCATGTAAGACCATGTCAGGGACATTGGCATCGTATTGT
*
53240952 GATTAT-GTGTAAGACCATGTCAGGGACATTGGCATCGTTATATGT
1 -ATTATCATGTAAGACCATGTCAGGGACATTGGCATCG-TAT-TGT
53240997 -TT-TCATGTAAGACCA
1 ATTATCATGTAAGACCA
53241012 CATCTAGGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
42 1 0.02
43 44 0.86
44 3 0.06
45 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
ATTATCATGTAAGACCATGTCAGGGACATTGGCATCGTATTGT
Found at i:53242417 original size:60 final size:59
Alignment explanation
Indices: 53242301--53242441 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 59
53242291 CCCAACTGTG
* *
53242301 CTGATATGGGCAAGGCCCAATATATCTCGACTTGTATAGGGCTACGGCCCAGATTAATA
1 CTGATATGGGCTAGGCCCAGTATATCTCGACTTGTATAGGGCTACGGCCCAGATTAATA
*
53242360 CTGATATGGGCTAGGCCCAGTATA-CTCTGA-TACTGTA-AGGGGCTATGGCCCAGATTAATA
1 CTGATATGGGCTAGGCCCAGTATATCTC-GACT--TGTATA-GGGCTACGGCCCAGATTAATA
*
53242420 TTGATATGGGCTAAGGCCCAGT
1 CTGATATGGGCT-AGGCCCAGT
53242442 TAACACTGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
58 4 0.05
59 25 0.34
60 35 0.48
61 9 0.12
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (59 bp):
CTGATATGGGCTAGGCCCAGTATATCTCGACTTGTATAGGGCTACGGCCCAGATTAATA
Found at i:53242439 original size:28 final size:28
Alignment explanation
Indices: 53242339--53242451 Score: 97
Period size: 28 Copynumber: 3.9 Consensus size: 28
53242329 GACTTGTATA
*
53242339 GGGCTACGGCCCAGATTAATACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
* *
53242367 GGGCT-AGGCCCAGTATACTCTGATACTG-TAAG
1 GGGCTAAGGCCCAG---A-T-TAATACTGAT-AT
* *
53242399 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
*
53242427 GGGCTAAGGCCCAG-TTAACACTGAT
1 GGGCTAAGGCCCAGATTAATACTGAT
53242452 TTCTGAATAG
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
27 16 0.24
28 25 0.37
29 2 0.03
30 2 0.03
31 2 0.03
32 13 0.19
33 7 0.10
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAATACTGATAT
Found at i:53251727 original size:28 final size:28
Alignment explanation
Indices: 53251664--53252629 Score: 1835
Period size: 28 Copynumber: 34.5 Consensus size: 28
53251654 ATATTAAGTC
* * *
53251664 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAATT
* *
53251691 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAATT
*
53251719 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAATT
53251747 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251775 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251803 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251831 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251859 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251887 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251915 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251943 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251971 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53251999 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252027 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252055 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252083 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252111 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252139 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252167 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252195 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252223 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252251 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252279 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252307 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252335 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252363 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252391 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252419 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252447 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252475 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252503 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
53252531 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAATT
**
53252559 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAATT
**
53252587 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAATT
53252615 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53252630 GTACAATTTA
Statistics
Matches: 933, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
27 22 0.02
28 911 0.98
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAATT
Found at i:53254033 original size:92 final size:93
Alignment explanation
Indices: 53253916--53254101 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 93
53253906 ATTTTTTTTT
53253916 CTTTCTTCTTTAGATTCGGCTAGCAAGAACATGAATGATGATCCCC-TTTTTTTTTTCCTTTCAT
1 CTTTCTTCTTTAGATTCGGCTAGCAAGAACATGAATGATGATCCCCTTTTTTTTTTTCCTTTCAT
53253980 CATTCTTTTTTTTCCATTTCTTTATTAC
66 CATTCTTTTTTTTCCATTTCTTTATTAC
53254008 CTTTCTTCTTTAGATTCGGCTAGCAAGAACATGAATGATGATCCCCTTTTTTTTTTTTCCTTTCA
1 CTTTCTTCTTTAGATTCGGCTAGCAAGAACATGAATGATGATCCCC-TTTTTTTTTTTCCTTTCA
53254073 TCATTCTTTTTTTTCCATTTCTTTATTAC
65 TCATTCTTTTTTTTCCATTTCTTTATTAC
53254102 TAACTTTTTA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
92 46 0.50
94 46 0.50
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.52
Consensus pattern (93 bp):
CTTTCTTCTTTAGATTCGGCTAGCAAGAACATGAATGATGATCCCCTTTTTTTTTTTCCTTTCAT
CATTCTTTTTTTTCCATTTCTTTATTAC
Found at i:53260642 original size:68 final size:68
Alignment explanation
Indices: 53260562--53260698 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
53260552 GCAAGCTCAT
*
53260562 TCATTACCAAATCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGG
1 TCATTACCAAATCACGTACCTTCAGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGG
53260627 ACA
66 ACA
53260630 TCATTACCAAATCACGTACCTTCAGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGG
1 TCATTACCAAATCACGTACCTTCAGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGG
53260695 ACA
66 ACA
53260698 T
1 T
53260699 AGCCCGGTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (68 bp):
TCATTACCAAATCACGTACCTTCAGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGG
ACA
Found at i:53260775 original size:40 final size:40
Alignment explanation
Indices: 53260720--53260915 Score: 209
Period size: 40 Copynumber: 4.9 Consensus size: 40
53260710 AGTAACTCAC
*
53260720 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 ATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
*
53260760 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 ATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
* * * *
53260800 GTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT-
1 ATAACTCGCACAAATGCCTTCGGGACTTAACCCGG-ATTTA
* * ** *
53260840 GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATA
1 ATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTA
* * * *
53260880 TTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 ATAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGA
53260916 CAGCATTCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
39 5 0.04
40 116 0.85
41 15 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
ATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
Found at i:53260924 original size:41 final size:41
Alignment explanation
Indices: 53260847--53260924 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53260837 TTTGTATCTC
* * *
53260847 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53260888 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53260925 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:53262012 original size:54 final size:54
Alignment explanation
Indices: 53261954--53262059 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
53261944 GTGAGAAAAG
*
53261954 GATGAACAAAGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAATGGGGGGGAA
1 GATGAACAAAGATCTTCTCCTCTCTTTTATTTAGCTCACGGCAATGGGGGGGAA
53262008 GATGAACAAAGATCTTCTCCTCTCTTTTATTTAGCTCACGGCAATGGGGGGG
1 GATGAACAAAGATCTTCTCCTCTCTTTTATTTAGCTCACGGCAATGGGGGGG
53262060 GGAAGAATCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (54 bp):
GATGAACAAAGATCTTCTCCTCTCTTTTATTTAGCTCACGGCAATGGGGGGGAA
Found at i:53283214 original size:87 final size:85
Alignment explanation
Indices: 53283099--53283757 Score: 626
Period size: 87 Copynumber: 7.6 Consensus size: 85
53283089 TATTCTGATA
* * * *
53283099 TTTTT-ATTTCTGTTTCAAAAATCGACTCATATAGCGAGAGATGAGTTGAGCCTCAGGGCACACT
1 TTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACT
* *
53283163 GAGGTATGCTT-AGTTTGTGT
66 GAGGTAT-TTTCAGTTTCTGT
*
53283183 TTTTTAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGATTTGAGCCTCAGGGCACA
1 TTTTTAATTTATGTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACA
* *
53283248 CTGAGGTATGTTCAGTTTGTGT
64 CTGAGGTATTTTCAGTTTCTGT
* * ** *
53283270 TTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAAGCGAGTTGAGCCTCAGGATACGC
1 TTTTTAATTTATGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAC
* *
53283335 TGAGGTATTTTCAATTTCTAT
65 TGAGGTATTTTCAGTTTCTGT
* *
53283356 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCGC
1 TTTTTAA-TT-TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---GC
**
53283420 ATGCTGAGGTATTTTCAGTTTCTGT
61 ACACTGAGGTATTTTCAGTTTCTGT
* * *
53283445 TTTTCAAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTT-TAATTTATG-TT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
*
53283510 ACTGAGGTATTTTCAATTTCTGT
63 ACTGAGGTATTTTCAGTTTCTGT
*
53283533 TTTTTAATTTATATATTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCAC
1 TTTTTAA-TT-TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CAC
* **
53283597 ATGTTGAGGTATTTTCAAAATT-TG-
63 A--CTGAGGTATTTTC-AGTTTCTGT
* * * *
53283621 CTTTT-A---A-GTTTCAAAAAAACTAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCAC
1 TTTTTAATTTATGTTTC-AAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC
* * *
53283680 GTGCTGAGCTATTTTCAATTTCTG-
63 --ACTGAGGTATTTTCAGTTTCTGT
* * * **
53283704 TTTTTAATGTTTAT-TTTTAAAGATTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TTTTTAA--TTTATGTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
53283758 TCAAGGTCAC
Statistics
Matches: 488, Mismatches: 53, Indels: 64
0.81 0.09 0.11
Matches are distributed among these distances:
81 4 0.01
82 11 0.02
83 52 0.11
84 6 0.01
85 10 0.02
86 71 0.15
87 162 0.33
88 72 0.15
89 52 0.11
90 46 0.09
91 2 0.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (85 bp):
TTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACT
GAGGTATTTTCAGTTTCTGT
Found at i:53283361 original size:14 final size:14
Alignment explanation
Indices: 53283342--53283376 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53283332 CGCTGAGGTA
*
53283342 TTTTCAATTTCTAT
1 TTTTCAATTTATAT
53283356 TTTTCAATTTATAT
1 TTTTCAATTTATAT
53283370 TTTTCAA
1 TTTTCAA
53283377 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:53283458 original size:15 final size:15
Alignment explanation
Indices: 53283438--53283467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53283428 GTATTTTCAG
*
53283438 TTTCTGTTTTTCAAA
1 TTTCTGTTTGTCAAA
53283453 TTTCTGTTTGTCAAA
1 TTTCTGTTTGTCAAA
53283468 AATCAACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (15 bp):
TTTCTGTTTGTCAAA
Found at i:53283517 original size:177 final size:172
Alignment explanation
Indices: 53283099--53283757 Score: 718
Period size: 177 Copynumber: 3.8 Consensus size: 172
53283089 TATTCTGATA
* * * *
53283099 TTTTT-ATTTCTGTTTC-AAAAATCGACTCATATAGCGAGAGATGAGTTGAGCCTCAGGGCACAC
1 TTTTTAATTTCTGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAC
* * * * ***
53283162 TGAGGTATGCTT-AGTTTGTGTTTTTTAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAG
66 TGAGGTAT-TTTCAATTTCTGTTTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAG
* ** *
53283226 GTGATTTGAGCCTCAGG--GCACACTGAGGTATGTTCAGTTTGTG
130 GTGAGTTGAGCCTC-GGTCGCATGCTGAGGTATTTTCAGTTT-TG
* * * * *
53283269 TTTTTTAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAAGCGAGTTGAGCCTCAGGATACG
1 -TTTTTAATTTCTGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA
* *
53283334 CTGAGGTATTTTCAATTTCTATTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAG
65 CTGAGGTATTTTCAATTTCTGTTTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAG
53283399 GTGAGTTGAGCCTCGGCTCGCATGCTGAGGTATTTTCAGTTTCTG
130 GTGAGTTGAGCCTCGG-TCGCATGCTGAGGTATTTTCAGTTT-TG
53283444 TTTTTCAAATTTCTGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTT--AATTTCTG-TT-TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
*
53283508 ACACTGAGGTATTTTCAATTTCTGTTTTTTAATTTATATATTTCAAAAATCAACTCATATTGCGA
62 ACACTGAGGTATTTTCAATTTCTGTTTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGA
* * **
53283573 GAGGTGAGTTGAGCCTCGGGTCACATGTTGAGGTATTTTCAAAATTTG
127 GAGGTGAGTTGAGCCTC-GGTCGCATGCTGAGGTATTTTC-AGTTTTG
* * * *
53283621 CTTTTAA-----GTTTCAAAAAAACTAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCAC
1 TTTTTAATTTCTGTTTCAAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
* * * *
53283680 GTGCTGAGCTATTTTCAATTTCTG-TTTTTAATGTT-TATTTTT-AAAGATTCAATTCATATTGC
64 --ACTGAGGTATTTTCAATTTCTGTTTTTTAAT-TTATATTTTTCAAA-AATCAACTCATATTGC
**
53283742 GAGAAATGAGTTGAGC
125 GAGAGGTGAGTTGAGC
53283758 TCAAGGTCAC
Statistics
Matches: 423, Mismatches: 46, Indels: 38
0.83 0.09 0.07
Matches are distributed among these distances:
168 2 0.00
169 10 0.02
170 37 0.09
171 47 0.11
172 36 0.09
173 104 0.25
174 5 0.01
175 24 0.06
176 7 0.02
177 144 0.34
178 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (172 bp):
TTTTTAATTTCTGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAC
TGAGGTATTTTCAATTTCTGTTTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGG
TGAGTTGAGCCTCGGTCGCATGCTGAGGTATTTTCAGTTTTG
Found at i:53284733 original size:23 final size:23
Alignment explanation
Indices: 53284703--53284757 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
53284693 ATTTTAATAC
*
53284703 TATATTATATATATAT-TTTTTCA
1 TATATTATATACATATGTTTTT-A
*
53284726 TATATTATATACATGTGTTTTTA
1 TATATTATATACATATGTTTTTA
53284749 -ATATTATAT
1 TATATTATAT
53284758 TTTATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
23 15 0.52
24 5 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATTATATACATATGTTTTTA
Found at i:53287535 original size:15 final size:15
Alignment explanation
Indices: 53287483--53287536 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
53287473 TAAAGATAAC
*
53287483 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
53287497 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
53287512 GAA-AAACCCAGAATA
1 -AAGAAACCCAGAATA
53287527 AAGAAACCCA
1 AAGAAACCCA
53287537 AGATACGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.61, C:0.19, G:0.13, T:0.07
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:53288770 original size:17 final size:17
Alignment explanation
Indices: 53288744--53288777 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53288734 TAAAAAATAT
53288744 CATTAACATTC-ATCAA
1 CATTAACATTCAATCAA
53288760 CATTCAACATTCAATCAA
1 CATT-AACATTCAATCAA
53288778 GGCAATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (17 bp):
CATTAACATTCAATCAA
Found at i:53290598 original size:49 final size:50
Alignment explanation
Indices: 53290542--53290685 Score: 175
Period size: 49 Copynumber: 2.9 Consensus size: 50
53290532 GCCGAAGCTA
53290542 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGT
* * * * **
53290591 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTACAGTT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-T
* * *
53290641 TTTGGGTACGCATAATAGCCCGCACTTAGTACTACACATGCGACC
1 TCT-GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
53290686 TCACAATAGC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
48 4 0.05
49 38 0.49
50 2 0.03
51 33 0.43
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (50 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGT
Found at i:53291005 original size:16 final size:16
Alignment explanation
Indices: 53290981--53291012 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53290971 TTAAGAATTT
53290981 ATATATCATATATCAC
1 ATATATCATATATCAC
*
53290997 ATATTTCATATATCAC
1 ATATATCATATATCAC
53291013 TTGTCATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATCATATATCAC
Found at i:53295477 original size:55 final size:54
Alignment explanation
Indices: 53295376--53295481 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 54
53295366 AATCATCTGG
53295376 AAATGCTTTGAGAAAATATTTTTTTAAATTTCACCTATAAATTAATTATTTTGA
1 AAATGCTTTGAGAAAATATTTTTTTAAATTTCACCTATAAATTAATTATTTTGA
53295430 AAATGCTTTGAGAAAATATTTTTTTAAAATTTCACCTATAAATTAATTATTT
1 AAATGCTTTGAGAAAATATTTTTTT-AAATTTCACCTATAAATTAATTATTT
53295482 CAAAAAATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 25 0.49
55 26 0.51
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (54 bp):
AAATGCTTTGAGAAAATATTTTTTTAAATTTCACCTATAAATTAATTATTTTGA
Found at i:53299909 original size:2 final size:2
Alignment explanation
Indices: 53299902--53299930 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53299892 GTAACATAGG
53299902 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
53299931 TTAAGGCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53300239 original size:19 final size:19
Alignment explanation
Indices: 53300215--53300254 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53300205 AAGTATGCCA
53300215 TATTTTTCATTTTGATCTT
1 TATTTTTCATTTTGATCTT
53300234 TATTTTTCATTTTGATCTT
1 TATTTTTCATTTTGATCTT
53300253 TA
1 TA
53300255 AAGTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTTTTCATTTTGATCTT
Found at i:53300558 original size:14 final size:14
Alignment explanation
Indices: 53300534--53300567 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53300524 ATAATTCAAT
53300534 AAATT-GGAATTTA
1 AAATTAGGAATTTA
*
53300547 AATTTAGGAATTTA
1 AAATTAGGAATTTA
53300561 AAATTAG
1 AAATTAG
53300568 TAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (14 bp):
AAATTAGGAATTTA
Found at i:53301100 original size:26 final size:27
Alignment explanation
Indices: 53301071--53301121 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53301061 AGTAAATCTG
*
53301071 ATTTATAA-AATTTTAAAAATATTAAT
1 ATTTATAATAATTTTAAAAAAATTAAT
*
53301097 ATTTATAATTATTTTAAAAAAATTA
1 ATTTATAATAATTTTAAAAAAATTA
53301122 GTAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTATAATAATTTTAAAAAAATTAAT
Found at i:53301208 original size:19 final size:19
Alignment explanation
Indices: 53301164--53301208 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53301154 ACTTTTCCTA
53301164 ATTTTTTATAATTTTAAAT
1 ATTTTTTATAATTTTAAAT
53301183 -TTGTTTTA-AATTCTTAAAT
1 ATT-TTTTATAATT-TTAAAT
53301202 ATTTTTT
1 ATTTTTT
53301209 TTTGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.26
19 15 0.65
20 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTATAATTTTAAAT
Found at i:53304805 original size:23 final size:23
Alignment explanation
Indices: 53304779--53304876 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
53304769 ATAAGTGCCA
53304779 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53304802 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
53304825 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53304847 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53304870 CACTGAT
1 CACTGAT
53304877 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53304844 original size:45 final size:45
Alignment explanation
Indices: 53304786--53304874 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
53304776 CCACACTGAT
* *
53304786 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
53304831 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
53304875 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:53315532 original size:43 final size:43
Alignment explanation
Indices: 53315468--53315608 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 43
53315458 TTCATGAGAT
* * *
53315468 ATGTG-GCATCCGAGCTTGTTGAAAGGTCCGAGTTCATCATGG
1 ATGTGAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGG
53315510 ATGTGAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGG
1 ATGTGAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGG
* *
53315553 ATGTGATTCATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCGTTATGG
1 ATGTG----A-G---CATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGG
53315604 ATGTG
1 ATGTG
53315609 TTACATATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
42 5 0.06
43 39 0.46
47 1 0.01
48 1 0.01
51 39 0.46
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
ATGTGAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGG
Found at i:53317298 original size:40 final size:40
Alignment explanation
Indices: 53317267--53317557 Score: 449
Period size: 40 Copynumber: 7.3 Consensus size: 40
53317257 GGACTAAGAT
53317267 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
53317307 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
*
53317347 CCGAAGTCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
53317387 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
*
53317427 CCGAAGGCATTTATGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
53317467 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* *
53317507 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
53317547 CCGAAGGCATT
1 CCGAAGGCATT
53317558 GTATGAGTTA
Statistics
Matches: 226, Mismatches: 24, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
39 1 0.00
40 225 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:53317351 original size:80 final size:80
Alignment explanation
Indices: 53317267--53317554 Score: 524
Period size: 80 Copynumber: 3.6 Consensus size: 80
53317257 GGACTAAGAT
53317267 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
53317332 ATTCCGGGTTAAGTC
66 ATTCCGGGTTAAGTC
*
53317347 CCGAAGTCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
53317412 ATTCCGGGTTAAGTC
66 ATTCCGGGTTAAGTC
*
53317427 CCGAAGGCATTTATGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
53317492 ATTCCGGGTTAAGTC
66 ATTCCGGGTTAAGTC
* *
53317507 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGGC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTCCCGAAGGC
53317555 ATTGTATGAG
Statistics
Matches: 201, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
79 2 0.01
80 199 0.99
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (80 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTA
ATTCCGGGTTAAGTC
Found at i:53322682 original size:54 final size:48
Alignment explanation
Indices: 53322610--53322781 Score: 182
Period size: 48 Copynumber: 3.5 Consensus size: 48
53322600 TTGGTTGCCT
* * *
53322610 TGTCCCAGACATGATCTTACACTTCCACTTGCACACTTATCATCACTGATGACA
1 TGTCCCAGACATGGTCTTACACTGCCA--T--ACA--TATCAACACTGATGACA
* * *
53322664 TGTCCCAGACATGGTCTTACACTGGCATACATATCAACGCTGATGCCA
1 TGTCCCAGACATGGTCTTACACTGCCATACATATCAACACTGATGACA
* * * * *
53322712 TGTCCCAGACATGGTCTTACACTGGCATACACATCAACGCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGCCATACATATCAACACTGATGACA
*
53322760 TGTCCTAGACATGGTCTTACAC
1 TGTCCCAGACATGGTCTTACAC
53322782 GGGATCTCAC
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
48 81 0.74
50 3 0.03
52 1 0.01
54 24 0.22
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (48 bp):
TGTCCCAGACATGGTCTTACACTGCCATACATATCAACACTGATGACA
Found at i:53322707 original size:48 final size:48
Alignment explanation
Indices: 53322655--53322781 Score: 218
Period size: 48 Copynumber: 2.6 Consensus size: 48
53322645 CTTATCATCA
* *
53322655 CTGATGACATGTCCCAGACATGGTCTTACACTGGCATACATATCAACG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCATACACATCAACG
53322703 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCATACACATCAACG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCATACACATCAACG
* *
53322751 CCGATGCCATGTCCTAGACATGGTCTTACAC
1 CTGATGCCATGTCCCAGACATGGTCTTACAC
53322782 GGGATCTCAC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (48 bp):
CTGATGCCATGTCCCAGACATGGTCTTACACTGGCATACACATCAACG
Found at i:53324660 original size:32 final size:32
Alignment explanation
Indices: 53324611--53324685 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
53324601 GCCAATCAAT
53324611 CTGTGTAA--TTTTTCTTGACACAGTTTAGGC
1 CTGTGTAATTTTTTTCTTGACACAGTTTAGGC
53324641 CTGTGTAATTTTTTTCTTGACACAGTTTAGGC
1 CTGTGTAATTTTTTTCTTGACACAGTTTAGGC
53324673 CTGTGTAATTTTT
1 CTGTGTAATTTTT
53324686 ATTACAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 8 0.19
32 35 0.81
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (32 bp):
CTGTGTAATTTTTTTCTTGACACAGTTTAGGC
Found at i:53327007 original size:247 final size:250
Alignment explanation
Indices: 53326563--53327062 Score: 882
Period size: 247 Copynumber: 2.0 Consensus size: 250
53326553 TGTGTCGCCA
* * *
53326563 ATGTGTCAGGCAGCACCAGTGGGAATTAAAAGGAAAACAGGTGAAATAGGAAAATAAAGATGAAA
1 ATGTGTCAGGCAACACCAGTGGGAATTAAAAGGAAAACAGGTGAAATACGAAAAGAAAGATGAAA
*
53326628 AGAAAGAGTTGTAATAGAAAAAAAAACCAAAAAAAATAAAAGGGAAAGTCCATGACCAATGCTTG
66 AGAAAGAGTTGTAATAGAAAAAAAAACC--AAAAAATAAAAGGGAAAGCCCATGACCAATGCTTG
*
53326693 CTTCATAAGTGGTTCTTTTCTTCTTAACTTGTCAATGTCACCATCAGTAGATGAAAAATATTTTC
129 CTTCATAAGTGGTTCTTGTCTTCTTAACTTGTCAATGTCACCATCAGTAGATGAAAAATATTTTC
*
53326758 AAAAAAATAATCTTAAATAAGATTAAAGTAGGAAAGAAAGAGATATGAGAGAAAGAT
194 AAAAAAATAATCTTAAATAAGATAAAAGTAGGAAAGAAAGAGATATGAGAGAAAGAT
53326815 ATGTGTCAGGCAACACCAGTGGGAATTAAAAGGAAAACAGGTGAAATACGAAAAGAAAGATGAAA
1 ATGTGTCAGGCAACACCAGTGGGAATTAAAAGGAAAACAGGTGAAATACGAAAAGAAAGATGAAA
53326880 AGAAAGAGTTGTAATAG-AAAAAAAACC-AAAAA-AAAAGGGAAAGCCCATGACCAATGCTTGCT
66 AGAAAGAGTTGTAATAGAAAAAAAAACCAAAAAATAAAAGGGAAAGCCCATGACCAATGCTTGCT
*
53326942 TCATAAGTGGTTCTTGTCTTCTTAATTTGTCAATGTCACCATCAGTAGATGAAAAAT-TATTTCA
131 TCATAAGTGGTTCTTGTCTTCTTAACTTGTCAATGTCACCATCAGTAGATGAAAAATAT-TTTCA
53327006 AAAAAATAATCTTAAATAAGATAAAAGTAGGAAAGAAAGAGATATGAGAGAAAGAT
195 AAAAAATAATCTTAAATAAGATAAAAGTAGGAAAGAAAGAGATATGAGAGAAAGAT
53327062 A
1 A
53327063 GAGAGACAGG
Statistics
Matches: 240, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
246 1 0.00
247 145 0.60
248 5 0.02
251 10 0.04
252 79 0.33
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (250 bp):
ATGTGTCAGGCAACACCAGTGGGAATTAAAAGGAAAACAGGTGAAATACGAAAAGAAAGATGAAA
AGAAAGAGTTGTAATAGAAAAAAAAACCAAAAAATAAAAGGGAAAGCCCATGACCAATGCTTGCT
TCATAAGTGGTTCTTGTCTTCTTAACTTGTCAATGTCACCATCAGTAGATGAAAAATATTTTCAA
AAAAATAATCTTAAATAAGATAAAAGTAGGAAAGAAAGAGATATGAGAGAAAGAT
Found at i:53327067 original size:21 final size:19
Alignment explanation
Indices: 53327036--53327081 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
53327026 ATAAAAGTAG
* *
53327036 GAAAGAAAGAGATATGAGA
1 GAAAGAAAGAGACAGGAGA
53327055 GAAAGATAGAGAGACAGGAGA
1 GAAAGA-A-AGAGACAGGAGA
53327076 GAAAGA
1 GAAAGA
53327082 GATATAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.57, C:0.02, G:0.35, T:0.07
Consensus pattern (19 bp):
GAAAGAAAGAGACAGGAGA
Found at i:53327080 original size:36 final size:37
Alignment explanation
Indices: 53327034--53327117 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
53327024 AGATAAAAGT
* * *
53327034 AGGAAAGAAAGAGATATGAGAGAAAGATAGAGAGAC-
1 AGGAGAGAAAGAGATATAAGAGAAAGATAGAAAGACG
*
53327070 AGGAGAGAAAGAGATATAAGAGAAATATAGAAAGACG
1 AGGAGAGAAAGAGATATAAGAGAAAGATAGAAAGACG
*
53327107 AGGAGGGAAAG
1 AGGAGAGAAAG
53327118 GAAAGAGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 32 0.76
37 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.35, T:0.08
Consensus pattern (37 bp):
AGGAGAGAAAGAGATATAAGAGAAAGATAGAAAGACG
Found at i:53327282 original size:23 final size:23
Alignment explanation
Indices: 53327253--53327299 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
53327243 ATTTAATATT
*
53327253 TTCATATTTT-TTATTCTATTTTC
1 TTCATATTTTATT-CTCTATTTTC
53327276 TTCATATTTTATTCTCTATTTTC
1 TTCATATTTTATTCTCTATTTTC
53327299 T
1 T
53327300 ATATACTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (23 bp):
TTCATATTTTATTCTCTATTTTC
Found at i:53327303 original size:21 final size:21
Alignment explanation
Indices: 53327249--53327303 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
53327239 GAGAATTTAA
*
53327249 TATTTTC-ATATTTTTTATTC
1 TATTTTCTATATTTTTTACTC
53327269 TATTTTCTTCATATTTTATT-CTC
1 TATTTTC-T-ATATTTT-TTACTC
53327292 TATTTTCTATAT
1 TATTTTCTATAT
53327304 ACTCTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
22 1 0.03
23 16 0.53
24 2 0.07
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTCTATATTTTTTACTC
Found at i:53347269 original size:37 final size:37
Alignment explanation
Indices: 53347214--53347293 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
53347204 ACTATCGTCC
* *
53347214 TCTTGCCCTTCCTCTATGTATCGTAGGCTTTGCCTTA
1 TCTTTCCCTTCCTCTATGTATCGTAGGCTTCGCCTTA
*
53347251 TCTTTCCCTTTCTCTATGTATCGTAGGCTTCGCCTTA
1 TCTTTCCCTTCCTCTATGTATCGTAGGCTTCGCCTTA
*
53347288 TTTTTC
1 TCTTTC
53347294 TTCGATTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.10, C:0.29, G:0.14, T:0.47
Consensus pattern (37 bp):
TCTTTCCCTTCCTCTATGTATCGTAGGCTTCGCCTTA
Found at i:53355820 original size:29 final size:28
Alignment explanation
Indices: 53355784--53355861 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
53355774 TCATGAGATT
53355784 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
53355814 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
53355841 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
53355862 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:53356079 original size:174 final size:174
Alignment explanation
Indices: 53355814--53356141 Score: 575
Period size: 174 Copynumber: 1.9 Consensus size: 174
53355804 AAATTGTACA
*
53355814 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* **
53355879 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGC
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
53355944 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATACATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATACATG
* * *
53355988 GCACTAAGTGTGTGAGTTTAAAGTGCATTGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
53356053 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
*
53356118 TTTTGGACAGCTGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
53356142 ACCTTGAGTT
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 145 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATACATG
Found at i:53358546 original size:27 final size:27
Alignment explanation
Indices: 53358511--53358565 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53358501 AGACAATAGC
53358511 GGCCAATTCCAAATCATGTGTAGGATA
1 GGCCAATTCCAAATCATGTGTAGGATA
53358538 GGCCAATTCCAAATCATGTGTAGGATA
1 GGCCAATTCCAAATCATGTGTAGGATA
53358565 G
1 G
53358566 TTCTTCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (27 bp):
GGCCAATTCCAAATCATGTGTAGGATA
Found at i:53375735 original size:24 final size:24
Alignment explanation
Indices: 53375691--53375736 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
53375681 AAAAGTTATT
* *
53375691 TAAAAAGATAAATAAAGATAAAAG
1 TAAAAAAATAAATAAAAATAAAAG
53375715 TAAAAAAAT-AATAAATAATAAA
1 TAAAAAAATAAATAAA-AATAAA
53375737 TAAAAGTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
TAAAAAAATAAATAAAAATAAAAG
Found at i:53386958 original size:21 final size:20
Alignment explanation
Indices: 53386934--53387009 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
53386924 CATCATGAAC
53386934 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTC-ATGAGT
* * **
53386955 TCAGATGTCACATATATCATGAAC
1 TCAGA--CCACA-A-CTCATGAGT
53386979 TCAGACCACAACTCGATGAGT
1 TCAGACCACAACTC-ATGAGT
*
53387000 TCAGATCACA
1 TCAGACCACA
53387010 TAGTTCCTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 2 0.05
21 19 0.46
22 4 0.10
23 4 0.10
24 10 0.24
25 2 0.05
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.22
Consensus pattern (20 bp):
TCAGACCACAACTCATGAGT
Found at i:53386974 original size:45 final size:45
Alignment explanation
Indices: 53386919--53387005 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
53386909 AACATGTGTT
53386919 ACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGTC
1 ACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGTC
* *
53386964 ACATATATCATGAACTCAGACCACAACTCGATGAGTTCAGAT
1 ACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGAT
53387006 CACATAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (45 bp):
ACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGTC
Found at i:53388596 original size:40 final size:40
Alignment explanation
Indices: 53388552--53388751 Score: 273
Period size: 40 Copynumber: 5.0 Consensus size: 40
53388542 GGATTTAACT
* *
53388552 GGATATAGCT-ACTCGCTCGAATGCCTTCGGGACTTAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
**
53388592 GGATATAGTAGTTCGCACAAATGCCTTCGGGACTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
*
53388632 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCT
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
53388672 GGA-ATTAGTAACTCGCA-ACAATGCCTTCGGGACTTAGCCC
1 GGATA-TAGTAACTCGCACA-AATGCCTTCGGGACTTAGCCC
* *
53388712 GGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
53388752 AGTTATCATC
Statistics
Matches: 146, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 142 0.97
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:53403364 original size:52 final size:52
Alignment explanation
Indices: 53403303--53403406 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
53403293 AATTTTGAAA
53403303 TTATAACTATTTTATGAATCCAAACTAGTTAGATTCCCTACACTGTATCGAT
1 TTATAACTATTTTATGAATCCAAACTAGTTAGATTCCCTACACTGTATCGAT
*
53403355 TTATAACTATTTTATGAATCCAAACTAGTTAGATTCCTTACACTGTATCGAT
1 TTATAACTATTTTATGAATCCAAACTAGTTAGATTCCCTACACTGTATCGAT
53403407 ACAAACTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (52 bp):
TTATAACTATTTTATGAATCCAAACTAGTTAGATTCCCTACACTGTATCGAT
Found at i:53404832 original size:28 final size:28
Alignment explanation
Indices: 53404790--53404902 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 28
53404780 TACTTGTATC
* *
53404790 TGGCCCATTAAGCCC-AATCATATTCAT
1 TGGCCCATTAGGCCCAAATCACATTCAT
*
53404817 GTGGCCCATTAGGCCCAAATCACCTGTACA-
1 -TGGCCCATTAGGCCCAAATCACAT-T-CAT
*
53404847 TGGCCCATTAGGCCCAAATCACATTTAT
1 TGGCCCATTAGGCCCAAATCACATTCAT
* *
53404875 ATGGCCCGTTAGGCCC-AGTCACATTCAT
1 -TGGCCCATTAGGCCCAAATCACATTCAT
53404903 ATTTATGCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 25 0.35
29 43 0.60
30 1 0.01
31 2 0.03
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCACATTCAT
Found at i:53405136 original size:16 final size:16
Alignment explanation
Indices: 53405115--53405148 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53405105 GTAGCCAAAC
53405115 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
53405131 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
53405147 TT
1 TT
53405149 CGGCATTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:53405139 original size:23 final size:23
Alignment explanation
Indices: 53405115--53405164 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
53405105 GTAGCCAAAC
*
53405115 TTTCGACTTTTCGGCATTTCGACT
1 TTTCGAC-ATTCGGCATTTCGACT
* *
53405139 TTTCGGCATTCGGCATTTCGAAT
1 TTTCGACATTCGGCATTTCGACT
53405162 TTT
1 TTT
53405165 GCCAATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (23 bp):
TTTCGACATTCGGCATTTCGACT
Found at i:53405172 original size:23 final size:23
Alignment explanation
Indices: 53405124--53405168 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53405114 CTTTCGACTT
* *
53405124 TTCGGCATTTCGACTTTTCGGCA
1 TTCGGCATTTCGAATTTTCGCCA
53405147 TTCGGCATTTCGAATTTT-GCCA
1 TTCGGCATTTCGAATTTTCGCCA
53405169 ATTCATAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (23 bp):
TTCGGCATTTCGAATTTTCGCCA
Found at i:53412420 original size:57 final size:57
Alignment explanation
Indices: 53412351--53412464 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
53412341 ACCGCTTAAG
*
53412351 TACCAAGCTCTCCCTAGATCCAATCCTAGACATGCCTATACCCGTTGCCACACCTTA
1 TACCAAGCTCTCCCGAGATCCAATCCTAGACATGCCTATACCCGTTGCCACACCTTA
53412408 TACCAAGCTCTCCCGAGATCCAATCCTAGACATGCCTATACCCGTTGCCACACCTTA
1 TACCAAGCTCTCCCGAGATCCAATCCTAGACATGCCTATACCCGTTGCCACACCTTA
53412465 ACCCTATAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.39, G:0.11, T:0.24
Consensus pattern (57 bp):
TACCAAGCTCTCCCGAGATCCAATCCTAGACATGCCTATACCCGTTGCCACACCTTA
Found at i:53412633 original size:29 final size:29
Alignment explanation
Indices: 53412601--53412675 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
53412591 TCATATTCAT
* *
53412601 ATGGCCCATTAGGCGCAAATCACCTGTAC
1 ATGGCCCATTAGGCCCAAATCACATGTAC
* * * *
53412630 ATGGCCCACTAGGCCCAAGTCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACATGTAC
*
53412659 ATGGCCCGTTAGGCCCA
1 ATGGCCCATTAGGCCCA
53412676 GCGACATTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.21
Consensus pattern (29 bp):
ATGGCCCATTAGGCCCAAATCACATGTAC
Found at i:53412937 original size:65 final size:65
Alignment explanation
Indices: 53412856--53413690 Score: 1661
Period size: 65 Copynumber: 12.8 Consensus size: 65
53412846 TGGTCTCCCC
*
53412856 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGGTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53412921 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53412986 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413051 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413116 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413181 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413246 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413311 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413376 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413441 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413506 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413571 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
53413636 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCG
1 CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCG
53413691 GCATTTCAGC
Statistics
Matches: 769, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 769 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (65 bp):
CTTATGAGTGTTCACGCACTCGCAAGACTACCGTAGCTAAACTTTCGGCTTTTCGCTACGGTAGT
Found at i:53433299 original size:14 final size:14
Alignment explanation
Indices: 53433277--53433313 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53433267 TCAAAGGTTG
*
53433277 TTTGATTGATGATT
1 TTTGCTTGATGATT
53433291 TTTGCTTGATGATT
1 TTTGCTTGATGATT
53433305 TTTGCTTGA
1 TTTGCTTGA
53433314 AAGTGCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (14 bp):
TTTGCTTGATGATT
Found at i:53449132 original size:18 final size:18
Alignment explanation
Indices: 53449109--53449153 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
53449099 ACAAATGAAT
*
53449109 ATGTTTTATAATACTAGG
1 ATGTTTTATAATACTAGA
53449127 ATGTTTTATAATACTAGA
1 ATGTTTTATAATACTAGA
53449145 ATGTTTTAT
1 ATGTTTTAT
53449154 CAAATATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (18 bp):
ATGTTTTATAATACTAGA
Found at i:53455573 original size:10 final size:10
Alignment explanation
Indices: 53455555--53455593 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
53455545 AATGTAAGGT
*
53455555 ATAATATATA
1 ATAAAATATA
53455565 ATAAAATATAA
1 ATAAAATAT-A
53455576 ATAAAATATA
1 ATAAAATATA
*
53455586 ATGAAATA
1 ATAAAATA
53455594 AAAATACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
ATAAAATATA
Found at i:53455579 original size:21 final size:21
Alignment explanation
Indices: 53455555--53455599 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53455545 AATGTAAGGT
* *
53455555 ATAATATATAATAAAATATAA
1 ATAAAATATAATAAAATAAAA
*
53455576 ATAAAATATAATGAAATAAAA
1 ATAAAATATAATAAAATAAAA
53455597 ATA
1 ATA
53455600 CTATCATATA
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:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAAAATATAATAAAATAAAA
Found at i:53455580 original size:11 final size:11
Alignment explanation
Indices: 53455557--53455599 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
53455547 TGTAAGGTAT
53455557 AATATATAATAA
1 AATATA-AATAA
53455569 AATATAAATAA
1 AATATAAATAA
*
53455580 AATAT-AATGA
1 AATATAAATAA
*
53455590 AATAAAAATA
1 AATATAAATA
53455600 CTATCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.30
11 13 0.48
12 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AATATAAATAA
Found at i:53455748 original size:34 final size:36
Alignment explanation
Indices: 53455683--53455754 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 36
53455673 ATTTATAAAA
**
53455683 AATAAAAATAAAATATAATTTATAAGTAAAAT-ATAT
1 AATAAAAAT-AAATATAATGGATAAGTAAAATAATAT
53455719 AATAAAAAT-AATATAATGGATAA-TAAAAATAATAT
1 AATAAAAATAAATATAATGGATAAGT-AAAATAATAT
53455754 A
1 A
53455755 CATTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 1 0.03
34 17 0.53
35 5 0.16
36 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (36 bp):
AATAAAAATAAATATAATGGATAAGTAAAATAATAT
Found at i:53455823 original size:18 final size:19
Alignment explanation
Indices: 53455802--53455838 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53455792 ATATATAAGG
53455802 TATTTA-AAATAA-ATTAAA
1 TATTTATAAA-AAGATTAAA
53455820 TATTTATAAAAAGATTAAA
1 TATTTATAAAAAGATTAAA
53455839 ATTGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATTTATAAAAAGATTAAA
Found at i:53457789 original size:221 final size:218
Alignment explanation
Indices: 53457398--53457851 Score: 667
Period size: 221 Copynumber: 2.1 Consensus size: 218
53457388 ACCATGTTGA
* *
53457398 TATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTTGGATCTACTTCAGCGTAAACAC
1 TATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTTAGATCTACTTCAGCATAAACAC
* * * *
53457463 GTGAAAGCCAAATCAGCTATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCTTCTT
66 GTGAAAGCCAAATCAGCTACATCTTCAATCTGCTACTTATAAACGCAAGGATGCCAAATCATCTT
* * *
53457528 GGATCTACTTCGATGTGAAAACATCCAAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCATT
131 GGATCTACTTCGATGTGAAAACATCCAAAGGTTAGATCTGCTATGTCTCCGATCTACTCTCCATC
*
53457593 GAATATAGAGATGCCAAATTTGT
196 GAATATAGAGATGCCAAATCTGT
* * *
53457616 TATCTTCGATCTGCTCTCTGACAATATAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAA
1 TATCTTCGATCTGCTCTCTGACAATACAGAGACGCC-AA--ATCTTAGATCTACTTCAGCATAAA
* * * *
53457681 CATGTGAAAGCCAAATCTGCTACGTCTTCGATCTGCTACTTATAAACGCAAGGATGCCAAATCAT
63 CACGTGAAAGCCAAATCAGCTACATCTTCAATCTGCTACTTATAAACGCAAGGATGCCAAATCAT
* *
53457746 CTTGGATCTACTTCGATGT-AGAAACATCCGAAGGTTTGATCTGCTATGTCTCCGATCTACTCTC
128 CTTGGATCTACTTCGATGTGA-AAACATCCAAAGGTTAGATCTGCTATGTCTCCGATCTACTCTC
* *
53457810 CATCGGATATGGAGATGCCAAATCTGT
192 CATCGAATATAGAGATGCCAAATCTGT
*
53457837 TATCTTGGATCTGCT
1 TATCTTCGATCTGCT
53457852 TTGATGTGAA
Statistics
Matches: 210, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
218 34 0.16
219 2 0.01
220 1 0.00
221 173 0.82
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (218 bp):
TATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTTAGATCTACTTCAGCATAAACAC
GTGAAAGCCAAATCAGCTACATCTTCAATCTGCTACTTATAAACGCAAGGATGCCAAATCATCTT
GGATCTACTTCGATGTGAAAACATCCAAAGGTTAGATCTGCTATGTCTCCGATCTACTCTCCATC
GAATATAGAGATGCCAAATCTGT
Found at i:53457938 original size:44 final size:44
Alignment explanation
Indices: 53457878--53457968 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
53457868 CAAAGGTCAG
* *
53457878 ATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAA
1 ATCTACTATATTCGATCTACTCTCTGACAATACAGAGATGCCAA
*
53457922 ATCTACTATATTCGATCTGCTCTCTGACAATACAGAGATGCCAA
1 ATCTACTATATTCGATCTACTCTCTGACAATACAGAGATGCCAA
53457966 ATC
1 ATC
53457969 ATCTTAGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (44 bp):
ATCTACTATATTCGATCTACTCTCTGACAATACAGAGATGCCAA
Found at i:53458178 original size:94 final size:91
Alignment explanation
Indices: 53458056--53458254 Score: 247
Period size: 94 Copynumber: 2.2 Consensus size: 91
53458046 ATGCCAAATC
* *
53458056 ATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTAGATCTGCTATGTCACCGATCTGCTCT
1 ATCTTGGATCTACTTCGACGTAGAAACATCCGAAGGTCAGATCTGCTA--TCACCGATCTGCTCT
* * *
53458121 CCGTCGAATATACAGATGCCAAATCTGTT
64 CCGGC-AATACACAGATGCCAAATCTGCT
** **
53458150 ATCTTGGATCTGTTTCGACGT-GAAAACATCCGAAGGTCAGATCTGCTATCTTCGATCTGCTCTC
1 ATCTTGGATCTACTTCGACGTAG-AAACATCCGAAGGTCAGATCTGCTATCACCGATCTGCTCTC
* *
53458214 TGGCAATACAGAGATGCCAAATCTGCT
65 CGGCAATACACAGATGCCAAATCTGCT
*
53458241 ATCTTCGATCTACT
1 ATCTTGGATCTACT
53458255 CTCTGACAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
91 31 0.34
92 16 0.18
93 1 0.01
94 42 0.47
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (91 bp):
ATCTTGGATCTACTTCGACGTAGAAACATCCGAAGGTCAGATCTGCTATCACCGATCTGCTCTCC
GGCAATACACAGATGCCAAATCTGCT
Found at i:53458245 original size:44 final size:44
Alignment explanation
Indices: 53458190--53458280 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
53458180 CGAAGGTCAG
* *
53458190 ATCTGCTATCTTCGATCTGCTCTCTGGCAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAA
53458234 ATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAA
53458278 ATC
1 ATC
53458281 ATCTTTGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAA
Found at i:53458327 original size:312 final size:312
Alignment explanation
Indices: 53457524--53458328 Score: 1254
Period size: 312 Copynumber: 2.6 Consensus size: 312
53457514 TGCCAAATCT
** *
53457524 TCTTGGATCTACTTCGATGTGAAAACATCCAAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTC
1 TCTTGGATCTGTTTCGATGTGAAAACATCCAAAGGTCAGATCTGCTA--TCTTCGATCTGCTCT-
* * * * *
53457589 CATTG-AATATAGAGATGCCAAATTTGTTATCTTCGATCTGCTCTCTGACAATATAGAGATGCCA
63 C-TGGCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCA
* * * *
53457653 AATCATCTTAGATCTGCTTCAGCATAAACATGTGAAAGCCAAATCTGCTACGTCTTCGATCTGCT
127 AATCATCTTAGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCT
*
53457718 ACTTATAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTT
192 ACTTATAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTA
* * **
53457783 GATCTGCTATGTCTCCGATCTACTCTCCATCGGATATGGAGATGCCAAATCTGTTA
257 GATCTGCTATGTCACCGATCTACTCTCCATCGAATATACAGATGCCAAATCTGTTA
*
53457839 TCTTGGATCTGCTTT-GATGTGAAAACATCCAAAGGTCAGATCTGCTATCTTCGATCTACTCTCT
1 TCTTGGATCTG-TTTCGATGTGAAAACATCCAAAGGTCAGATCTGCTATCTTCGATCTGCTCTCT
* * *
53457903 GACAATACAGAGATGCCAAATCTACTATATTCGATCTGCTCTCTGACAATACAGAGATGCCAAAT
65 GGCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAAT
* * * *
53457968 CATCTTAGATTTGCTTCAGTGTAAACACATAAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCT
130 CATCTTAGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTACT
* *
53458033 TATAAATGCAATGATGCCAAATCATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTAGAT
195 TATAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTAGAT
* *
53458098 CTGCTATGTCACCGATCTGCTCTCCGTCGAATATACAGATGCCAAATCTGTTA
260 CTGCTATGTCACCGATCTACTCTCCATCGAATATACAGATGCCAAATCTGTTA
* *
53458151 TCTTGGATCTGTTTCGACGTGAAAACATCCGAAGGTCAGATCTGCTATCTTCGATCTGCTCTCTG
1 TCTTGGATCTGTTTCGATGTGAAAACATCCAAAGGTCAGATCTGCTATCTTCGATCTGCTCTCTG
*
53458216 GCAATACAGAGATGCCAAATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATC
66 GCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATC
*
53458281 ATCTTTGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATG
131 ATCTTAGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATG
53458329 CTTTAGCCTG
Statistics
Matches: 447, Mismatches: 40, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
311 4 0.01
312 386 0.86
313 14 0.03
315 41 0.09
316 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (312 bp):
TCTTGGATCTGTTTCGATGTGAAAACATCCAAAGGTCAGATCTGCTATCTTCGATCTGCTCTCTG
GCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATC
ATCTTAGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTACTT
ATAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGTAGAAACATCCGAAGGTTAGATC
TGCTATGTCACCGATCTACTCTCCATCGAATATACAGATGCCAAATCTGTTA
Found at i:53469420 original size:20 final size:20
Alignment explanation
Indices: 53469354--53469420 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53469344 ATTTTAGTAA
* *
53469354 ACATGGTATGTGTGATATGC
1 ACATGATATGTATGATATGC
* *
53469374 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
53469394 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53469414 ACATGAT
1 ACATGAT
53469421 GTATTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53469549 original size:24 final size:24
Alignment explanation
Indices: 53469470--53469587 Score: 170
Period size: 23 Copynumber: 5.0 Consensus size: 24
53469460 GAGGAATTGC
*
53469470 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53469494 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53469517 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53469540 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53469564 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53469588 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
23 45 0.52
24 31 0.36
25 11 0.13
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53469563 original size:47 final size:46
Alignment explanation
Indices: 53469471--53469566 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 46
53469461 AGGAATTGCA
*
53469471 AAAGGGCTTATGCCCTAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
53469517 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
53469564 AAA
1 AAA
53469567 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 22 0.47
47 25 0.53
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:53469815 original size:31 final size:31
Alignment explanation
Indices: 53469780--53469843 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53469770 CGTTTACAGT
53469780 AAAGGCATCGGCCCAGTAATATGAAATATGA
1 AAAGGCATCGGCCCAGTAATATGAAATATGA
* **
53469811 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCATCGGCCCAGTAATATGAAATATGA
53469842 AA
1 AA
53469844 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCATCGGCCCAGTAATATGAAATATGA
Found at i:53476230 original size:82 final size:82
Alignment explanation
Indices: 53476093--53476252 Score: 284
Period size: 82 Copynumber: 2.0 Consensus size: 82
53476083 TCAAGTCAAA
* *
53476093 TGCATAGATTAAGGAGGGATAAGGGGAGAGATTTTAGCGATTTGATATGAGGATAGAGTTGGCCG
1 TGCATAGATTAAGGAGGGATAAGGGGAGAGATTTCAGCGATTTGATATGAGGATAGAGTTGGCCA
53476158 AATAAGGGAGATTCGAC
66 AATAAGGGAGATTCGAC
*
53476175 TGCATAGATTAAGGAGGGATAAGGGGAGAGATTTCAGCTATTTGATATGAGGATAGAGTTGGCCA
1 TGCATAGATTAAGGAGGGATAAGGGGAGAGATTTCAGCGATTTGATATGAGGATAGAGTTGGCCA
*
53476240 AATAAGTGAGATT
66 AATAAGGGAGATT
53476253 GGAGGGGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.26
Consensus pattern (82 bp):
TGCATAGATTAAGGAGGGATAAGGGGAGAGATTTCAGCGATTTGATATGAGGATAGAGTTGGCCA
AATAAGGGAGATTCGAC
Found at i:53476489 original size:84 final size:84
Alignment explanation
Indices: 53476348--53476514 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
53476338 AGTCTTTTTT
*
53476348 CTCTCTTTTTCTTTTGCAGCCGAATCTACCATCTCTTCTTCCATCTTTTCTTCCTTCTCCTTCTT
1 CTCTCTTTTTCTTTTGCAGCCGAATCTACCATCTCTTCTTCCATCTTTTATTCCTTCTCCTTCTT
53476413 TCAAACCAGCCCACTATTA
66 TCAAACCAGCCCACTATTA
53476432 CTCTCTTTTTCTTTTGCAGCCGAATCTACCATCTCTTCTTCCATCTTTTATTCCTTCTCCTTCTT
1 CTCTCTTTTTCTTTTGCAGCCGAATCTACCATCTCTTCTTCCATCTTTTATTCCTTCTCCTTCTT
*
53476497 TTAAACCAGCCCACTATT
66 TCAAACCAGCCCACTATT
53476515 CCCTCCATTC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.45
Consensus pattern (84 bp):
CTCTCTTTTTCTTTTGCAGCCGAATCTACCATCTCTTCTTCCATCTTTTATTCCTTCTCCTTCTT
TCAAACCAGCCCACTATTA
Found at i:53477708 original size:20 final size:20
Alignment explanation
Indices: 53477642--53477708 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53477632 ATTTTAGTAA
* *
53477642 ACATGGTATGTGTGATATGC
1 ACATGATATGTATGATATGC
* *
53477662 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
53477682 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53477702 ACATGAT
1 ACATGAT
53477709 GTATTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53477837 original size:24 final size:24
Alignment explanation
Indices: 53477758--53477875 Score: 170
Period size: 23 Copynumber: 5.0 Consensus size: 24
53477748 GAGGAATTGC
*
53477758 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53477782 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53477805 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53477828 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53477852 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53477876 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
23 45 0.52
24 31 0.36
25 11 0.13
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53477851 original size:47 final size:46
Alignment explanation
Indices: 53477759--53477854 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 46
53477749 AGGAATTGCA
*
53477759 AAAGGGCTTATGCCCTAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
53477805 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
53477852 AAA
1 AAA
53477855 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 22 0.47
47 25 0.53
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:53478103 original size:31 final size:31
Alignment explanation
Indices: 53478068--53478131 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53478058 CGTTTACAGT
53478068 AAAGGCATCGGCCCAGTAATATGAAATATGA
1 AAAGGCATCGGCCCAGTAATATGAAATATGA
* **
53478099 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCATCGGCCCAGTAATATGAAATATGA
53478130 AA
1 AA
53478132 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCATCGGCCCAGTAATATGAAATATGA
Found at i:53486565 original size:40 final size:40
Alignment explanation
Indices: 53486520--53486711 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
53486510 ATAACCACAA
* * *
53486520 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
53486560 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
53486600 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
53486640 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
53486680 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
53486712 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:53489144 original size:20 final size:20
Alignment explanation
Indices: 53489121--53489178 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
53489111 TAAACATGGT
53489121 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
* *
53489141 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAC
*
53489161 GTGTATGATATGC-CATGA
1 ATGTATGATATGCACATGA
53489179 TGTATTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:53489260 original size:23 final size:23
Alignment explanation
Indices: 53489230--53489302 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
53489220 AGGAAGTGCA
53489230 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
53489253 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
53489276 AAAAGGGCTTTTGACCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
53489300 AAA
1 AAA
53489303 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:53489285 original size:24 final size:24
Alignment explanation
Indices: 53489229--53489309 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
53489219 AAGGAAGTGC
53489229 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53489253 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
53489276 AAAAGGGCTTTTGACCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53489300 AAAAGAGGCT
1 AAAAG-GGCT
53489310 AGGCCTCTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
23 23 0.43
24 26 0.49
25 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53489552 original size:31 final size:31
Alignment explanation
Indices: 53489517--53489580 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53489507 CGTTTACAGT
53489517 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
53489548 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53489579 AA
1 AA
53489581 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53490890 original size:53 final size:53
Alignment explanation
Indices: 53490827--53490932 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
53490817 AGCCCACTGG
*
53490827 TGTGACAGCCCTAAAGTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAAC
1 TGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAAC
* * *
53490880 TGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAAC
1 TGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAAC
53490933 CGAGTCATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (53 bp):
TGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAAC
Found at i:53493743 original size:40 final size:40
Alignment explanation
Indices: 53492801--53493729 Score: 1797
Period size: 40 Copynumber: 23.2 Consensus size: 40
53492791 TAAGATCTGA
*
53492801 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGA
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53492841 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53492881 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53492921 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53492961 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493001 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493041 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493081 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493121 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493161 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493201 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493241 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493281 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493321 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493361 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493401 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493441 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493481 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493521 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493561 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
53493601 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
*
53493641 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGA
1 AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
* * *
53493681 AGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGA
1 AGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGG
53493721 AGGCATTTG
1 AGGCATTTG
53493730 AACGAGTAGC
Statistics
Matches: 884, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
40 882 1.00
41 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
AGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGG
Found at i:53496521 original size:79 final size:81
Alignment explanation
Indices: 53496385--53496567 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
53496375 TCGAATGATG
* *
53496385 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
53496449 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
53496464 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
53496526 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
53496544 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53496568 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:53496583 original size:40 final size:40
Alignment explanation
Indices: 53496386--53496569 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
53496376 CGAATGATGT
* * * *
53496386 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
53496426 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
53496466 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
53496504 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
53496545 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
53496570 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:53496591 original size:79 final size:79
Alignment explanation
Indices: 53496438--53496602 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
53496428 GGACTAAGAT
* **
53496438 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
53496503 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
53496517 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
53496580 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
53496596 CCGAAGG
1 CCGAAGG
53496603 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:53500877 original size:40 final size:40
Alignment explanation
Indices: 53500753--53501053 Score: 288
Period size: 40 Copynumber: 7.5 Consensus size: 40
53500743 TATTCGAATG
* *
53500753 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
53500794 ATAACCGGACTAAGATCCAAAGGCATTCGTG-TGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCT-AG-TGACT
* * *
53500834 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * *
53500874 ATATCCAGGCTAAAACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
53500914 ATATCCGGGCTAAAACCTGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * *
53500954 ATATCCGGGCTAAGTCCCGAAGGAATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * * * *
53500994 ACATCCGGGCTAAGACCCGAGGGC-CTTGTGCAAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
53501033 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
53501054 ATTACTTGAG
Statistics
Matches: 217, Mismatches: 38, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
37 1 0.00
38 12 0.06
39 15 0.07
40 161 0.74
41 28 0.13
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:53509035 original size:40 final size:40
Alignment explanation
Indices: 53508941--53509156 Score: 213
Period size: 40 Copynumber: 5.4 Consensus size: 40
53508931 TATTCGAATG
* *
53508941 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GCGACT
* * * * ** *
53508982 ATAACCAGACTAAGATCCGAAGGCATTCGTGGGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-CGACT
* *
53509022 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* *
53509062 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * * *
53509102 ATATCCGGGCTAAG-TCCCAAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
*
53509142 ACATCCGGGCTAAGA
1 ATATCCGGGCTAAGA
53509157 CCCTAGGGCC
Statistics
Matches: 145, Mismatches: 25, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 116 0.80
41 27 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Found at i:53509125 original size:80 final size:80
Alignment explanation
Indices: 53508941--53509201 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
53508931 TATTCGAATG
* * * * *
53508941 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
* *
53509006 ATTCGTGGGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
53509022 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
53509087 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * * * *
53509102 ATATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCTAGGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
53509167 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
53509181 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
53509202 ATTACTTGAG
Statistics
Matches: 149, Mismatches: 29, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
78 13 0.09
79 14 0.09
80 90 0.60
81 32 0.21
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:53511702 original size:17 final size:17
Alignment explanation
Indices: 53511677--53511709 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53511667 GTAAGGTATA
53511677 ATATATAATAAAATATG
1 ATATATAATAAAATATG
*
53511694 ATATGTAATAAAATAT
1 ATATATAATAAAATAT
53511710 AAATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
ATATATAATAAAATATG
Found at i:53511736 original size:28 final size:29
Alignment explanation
Indices: 53511676--53511732 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 29
53511666 TGTAAGGTAT
*
53511676 AATATATAATAAAATATGATATGTAATAA
1 AATATATAATAAAATATGATATGAAATAA
53511705 AATATA-AATAAAATAT-A-ATGAAATAA
1 AATATATAATAAAATATGATATGAAATAA
53511731 AA
1 AA
53511733 AATACTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 1 0.04
28 10 0.37
29 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
AATATATAATAAAATATGATATGAAATAA
Found at i:53511889 original size:41 final size:37
Alignment explanation
Indices: 53511791--53511878 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
53511781 TTTACACAAT
* * *
53511791 TAATGAATAATAATACATAATTTATAAAAAATAGAAA
1 TAATAAATAATAAAATATAATTTATAAAAAATAGAAA
* *
53511828 TAATATATAATAAAATATAATTTATAAGTAAAATATATAA
1 TAATAAATAATAAAATATAATTTATAA--AAAATAGA-AA
53511868 TAA-AAATAATA
1 TAATAAATAATA
53511879 TAATGGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
37 23 0.55
39 14 0.33
40 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (37 bp):
TAATAAATAATAAAATATAATTTATAAAAAATAGAAA
Found at i:53511970 original size:18 final size:19
Alignment explanation
Indices: 53511949--53511985 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53511939 ATATATAAGG
53511949 TATTTA-AAATAA-ATTAAA
1 TATTTATAAA-AAGATTAAA
53511967 TATTTATAAAAAGATTAAA
1 TATTTATAAAAAGATTAAA
53511986 ATTGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATTTATAAAAAGATTAAA
Found at i:53516108 original size:11 final size:11
Alignment explanation
Indices: 53516092--53516139 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 11
53516082 TAATTAGCCA
53516092 TATAAGATCAT
1 TATAAGATCAT
53516103 TATAAGATCAT
1 TATAAGATCAT
53516114 TATAATGTATAGCAT
1 TATAA-G-AT--CAT
53516129 TATAAGATCAT
1 TATAAGATCAT
53516140 ATTTTGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.58
12 1 0.03
13 4 0.12
14 1 0.03
15 8 0.24
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (11 bp):
TATAAGATCAT
Found at i:53534757 original size:8 final size:8
Alignment explanation
Indices: 53534744--53534779 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
53534734 GGCCAATCCT
53534744 GAAATGCC
1 GAAATGCC
*
53534752 GAAATGTC
1 GAAATGCC
53534760 GAAATGCC
1 GAAATGCC
53534768 GAAATGCC
1 GAAATGCC
53534776 GAAA
1 GAAA
53534780 ACCCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (8 bp):
GAAATGCC
Found at i:53535011 original size:28 final size:29
Alignment explanation
Indices: 53534979--53535095 Score: 157
Period size: 29 Copynumber: 4.1 Consensus size: 29
53534969 TGAGCATGAC
* *
53534979 TATAAAAGTGA-TTGGGCCTAGTGGACCA
1 TATAAAAGTGATTTGGGCCTAATGGGCCA
53535007 TATAAAAGTGATTTGGGCCTAATGGGCCA
1 TATAAAAGTGATTTGGGCCTAATGGGCCA
*
53535036 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATAAAAGTGATTTGGGCCTAATGGGCCA
* * **
53535065 TATGAAAGAGA-TTGGGCCTTGTGGGCCA
1 TATAAAAGTGATTTGGGCCTAATGGGCCA
53535093 TAT
1 TAT
53535096 GTAGGTATGT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 29 0.36
29 51 0.64
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (29 bp):
TATAAAAGTGATTTGGGCCTAATGGGCCA
Found at i:53535080 original size:57 final size:57
Alignment explanation
Indices: 53534979--53535095 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
53534969 TGAGCATGAC
* *
53534979 TATAAAAGTGATTGGGCCTAGTGGACCATATAAAAGTGATTTGGGCCTAATGGGCCA
1 TATAAAAGTGATTGGGCCTAATGGACCATATAAAAGAGATTTGGGCCTAATGGGCCA
* * * **
53535036 TATAAATGTGATTTGGGCCTAATGGGCCATATGAAAGAGA-TTGGGCCTTGTGGGCCA
1 TATAAAAGTGA-TTGGGCCTAATGGACCATATAAAAGAGATTTGGGCCTAATGGGCCA
53535093 TAT
1 TAT
53535096 GTAGGTATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 28 0.54
58 24 0.46
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (57 bp):
TATAAAAGTGATTGGGCCTAATGGACCATATAAAAGAGATTTGGGCCTAATGGGCCA
Found at i:53538679 original size:27 final size:26
Alignment explanation
Indices: 53538635--53538686 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53538625 CTCACTGCAA
*
53538635 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
53538662 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
53538687 GTAGCCTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:53538754 original size:26 final size:27
Alignment explanation
Indices: 53538725--53538784 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
53538715 TCACATATAT
*
53538725 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
53538751 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
53538778 ATATCTG
1 ATATCTG
53538785 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:53548265 original size:43 final size:42
Alignment explanation
Indices: 53548149--53548298 Score: 219
Period size: 42 Copynumber: 3.5 Consensus size: 42
53548139 GATAATGCAT
* *
53548149 AGACCATATCTGGGATATGGCATCGATATGAGACTTCATGTA
1 AGACCATATCTAGGATATGGCATCGATATGAGATTTCATGTA
*
53548191 AGACCATATCTAGGATATGGCATCGATATGAGATTTCGTGTA
1 AGACCATATCTAGGATATGGCATCGATATGAGATTTCATGTA
* * * *
53548233 AGACCATAGCTCGGCTATTGGCATCGATATGAGATTACATGTA
1 AGACCATATCTAGGATA-TGGCATCGATATGAGATTTCATGTA
*
53548276 AGACCATATCTGGGATATGGCAT
1 AGACCATATCTAGGATATGGCAT
53548299 TGGTACGATA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 59 0.61
43 37 0.39
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
AGACCATATCTAGGATATGGCATCGATATGAGATTTCATGTA
Found at i:53554895 original size:42 final size:42
Alignment explanation
Indices: 53554843--53554996 Score: 211
Period size: 42 Copynumber: 3.6 Consensus size: 42
53554833 TGAGATAATA
** *
53554843 TGTAAGACCATATCTGGGATATGGCATTGATATGAGACTTTG
1 TGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCG
*
53554885 TGTAAAACCATATCTGGGATATGGCATCAATATGAGACTTCG
1 TGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCG
* * *
53554927 TGTAAGACCATAGCTGGGTTATTGGCATCAATATGAGA-TTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCAATATGAGACTT-CG
*
53554970 TGTAAGACCATATTTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
53554997 TGGTATGGTA
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
42 64 0.65
43 35 0.35
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCG
Found at i:53556720 original size:46 final size:46
Alignment explanation
Indices: 53556653--53556824 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
53556643 AACCCGCCCC
* *
53556653 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
53556699 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
53556747 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
53556792 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
53556825 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 59 0.56
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:53556766 original size:93 final size:93
Alignment explanation
Indices: 53556658--53556828 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
53556648 GCCCCTAAGT
* *
53556658 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53556723 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
53556751 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53556816 CGAGTTCGGATGC
66 CGAGTTCGGATGC
53556829 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53583498 original size:39 final size:40
Alignment explanation
Indices: 53583453--53583624 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
53583443 GCTCCTCGTT
* * *
53583453 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
53583493 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
53583532 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
53583572 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
*
53583612 CAAAAGCCTTCGG
1 CAAATGCCTTCGG
53583625 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:53583637 original size:80 final size:79
Alignment explanation
Indices: 53583453--53583677 Score: 204
Period size: 80 Copynumber: 2.8 Consensus size: 79
53583443 GCTCCTCGTT
* * * * * * *
53583453 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
53583517 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * *
53583532 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
** *
53583597 AATTT-GTATCTCGCA
64 AATTTAACAACTCGCA
** * * * *
53583612 CAAAAGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAAGCCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
53583676 GA
63 GA
53583678 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 67 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAAAGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAACAACTCGCA
Found at i:53583686 original size:41 final size:41
Alignment explanation
Indices: 53583609--53583686 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53583599 TTTGTATCTC
* * *
53583609 GCACAAAAGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53583650 GCAC-AAAGCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAAGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53583687 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.