Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 168 of 284
Found at i:56412340 original size:42 final size:42
Alignment explanation
Indices: 56412281--56412360 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
56412271 TTGGTATCAG
* *
56412281 AGCTATACATGGCATATTTATGAACTGCTATAGTGTGAGTCT
1 AGCTATACATGCCATATTTATGAACTGCGATAGTGTGAGTCT
*
56412323 AGCTATACATGCCATATTTATGAACTGGGATAGTGTGA
1 AGCTATACATGCCATATTTATGAACTGCGATAGTGTGA
56412361 TGAATCATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (42 bp):
AGCTATACATGCCATATTTATGAACTGCGATAGTGTGAGTCT
Found at i:56417734 original size:29 final size:30
Alignment explanation
Indices: 56417687--56417744 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
56417677 CAATTTTCGA
*
56417687 GCCTAGGGGCAAAATGGTCATTTTGCCAAG
1 GCCTAGGGGCAAAATGGTCATTTTACCAAG
56417717 GCCTAGGGG-AAAATGGTCATTTTACCAA
1 GCCTAGGGGCAAAATGGTCATTTTACCAA
56417745 AGATGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (30 bp):
GCCTAGGGGCAAAATGGTCATTTTACCAAG
Found at i:56418119 original size:46 final size:46
Alignment explanation
Indices: 56418069--56418288 Score: 175
Period size: 46 Copynumber: 4.7 Consensus size: 46
56418059 ACTTATGTAT
* *
56418069 GCTAGTGTAAGACATTTCTGGGACATGCATCGGCCACATTATGGAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAA
* * *
56418115 GCTAGTGTAAGACCATGTCTGCGACATCACATCGG-CAC-TGA-GACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATGATG--GA-A
* * ** *
56418163 GCTAGTGTAAGACTTGTTTGGGACATGCATCGGCCTTGA-GATGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-ACATGATGGAA
* *
56418209 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGGA-A
*
56418255 G-TCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCG
56418289 ACTTGAGATA
Statistics
Matches: 138, Mismatches: 22, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
45 2 0.01
46 66 0.48
47 43 0.31
48 26 0.19
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAA
Found at i:56418294 original size:93 final size:94
Alignment explanation
Indices: 56418068--56418339 Score: 265
Period size: 94 Copynumber: 2.9 Consensus size: 94
56418058 CACTTATGTA
* * ** *
56418068 TGCTAGTGTAAGACATTTCTGGGACATGCATCGGCCACATT---ATGGAAGCTAGTGTAAGACCA
1 TGCTAGTGTAAGACATGTCTAGGACATGCATCGG--AC-TTGAGATATAAGCCAGTGTAAGACCA
* *
56418130 TGTCTGCGACATCACATCGGCACTGAGACGAG
63 TGTCTGGGACATCGCATCGGCACTGAGACGAG
* * * * *
56418162 TGCTAGTGTAAGACTTGTTTGGGACATGCATCGGCCTTGAGATGTAAGCCAGTGTAAGA-CATGT
1 TGCTAGTGTAAGACATGTCTAGGACATGCATCGGACTTGAGATATAAGCCAGTGTAAGACCATGT
*
56418226 CTGGGACAT-GCATCGGCTAC-GAGATGA-
66 CTGGGACATCGCATCGGC-ACTGAGACGAG
*
56418253 TAG-TCAGTGTAAGACCATGTCTAGGACATGGCATC-GACTTGAGATATGAGCCAGTGTAAGACC
1 T-GCT-AGTGTAAGA-CATGTCTAGGACAT-GCATCGGACTTGAGATATAAGCCAGTGTAAGACC
* *
56418316 ATGTCTAGGACATGGCATCGGCAC
62 ATGTCTGGGACATCGCATCGGCAC
56418340 CTTACCCATA
Statistics
Matches: 152, Mismatches: 16, Indels: 20
0.81 0.09 0.11
Matches are distributed among these distances:
91 4 0.03
92 24 0.16
93 49 0.32
94 67 0.44
95 8 0.05
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (94 bp):
TGCTAGTGTAAGACATGTCTAGGACATGCATCGGACTTGAGATATAAGCCAGTGTAAGACCATGT
CTGGGACATCGCATCGGCACTGAGACGAG
Found at i:56418297 original size:47 final size:46
Alignment explanation
Indices: 56418166--56418335 Score: 184
Period size: 47 Copynumber: 3.6 Consensus size: 46
56418156 GACGAGTGCT
* * * *
56418166 AGTGTAAGACTTGTTTGGGACATGCATCGGCCTTGAGATG-TAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATC-GACTTGAGATGATAAGCC
* * * *
56418212 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAT-AGTC
1 AGTGTAAGACATGTCTAGGACATGCATCGACT-TGAGATGATAAGCC
*
56418258 AGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGAT-ATGAGCC
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCGACTTGAGATGATAAGCC
56418305 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCG
56418336 GCACCTTACC
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.03
46 46 0.42
47 53 0.48
48 8 0.07
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACTTGAGATGATAAGCC
Found at i:56418327 original size:140 final size:141
Alignment explanation
Indices: 56418063--56418337 Score: 314
Period size: 140 Copynumber: 2.0 Consensus size: 141
56418053 TGGGTCACTT
* * * *
56418063 ATGTATGCTAGTGTAAGACATTTCTGGGACATGCATCGGCCACATTATGGAAGCTAGTGTAAGAC
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAAGCTAGTGTAAGAC
* * * * *
56418128 CATGTCTGCGACATCACATCGGCACTGAGACGAGTGCTAGTGTAAGACTTGTTTGGGACAT-GCA
66 CATGTCTGCGACATCACATCGGCACTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
56418192 TCGGCCTTGAG
131 TCGGCCTTGAG
*
56418203 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GATAG-TCAGTGTAA
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGGA-AGCT-AGTGTAA
** *
56418265 GACCATGTCTAG-GACATGGCATC-G-ACTTGAGA-TATGAGCCAGTGTAAGACCATGTCTAGGA
63 GACCATGTCT-GCGACATCACATCGGCAC-TGAGACGA-GAGCCAGTGTAAGA-CATGTCTAGGA
56418326 CATGGCATCGGC
124 CATGGCATCGGC
56418338 ACCTTACCCA
Statistics
Matches: 114, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
138 3 0.03
139 21 0.18
140 80 0.70
141 10 0.09
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (141 bp):
ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAAGCTAGTGTAAGAC
CATGTCTGCGACATCACATCGGCACTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
TCGGCCTTGAG
Found at i:56423694 original size:46 final size:46
Alignment explanation
Indices: 56423550--56423766 Score: 213
Period size: 46 Copynumber: 4.6 Consensus size: 46
56423540 TGTGTGTGCT
** * *
56423550 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGGAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGTAAGCC
** * ** *
56423596 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGTGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CAAGATGTAAGCC
*
56423644 AGTGTAAGACATGTCTGGGACATGCATCGGCCCCAAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGTAAGCC
* * * * *
56423690 AGTGTAAGATATGTCCGGGACATGCATCGGCTACGAGATG-ATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGTA-AGCC
*
56423736 AGTGTAAGACCATGTCTGAGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
56423767 ACTTGAGATA
Statistics
Matches: 140, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.50
47 42 0.30
48 27 0.19
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGTAAGCC
Found at i:56423765 original size:94 final size:94
Alignment explanation
Indices: 56423543--56423814 Score: 279
Period size: 94 Copynumber: 2.9 Consensus size: 94
56423533 GGTCACTTGT
** *
56423543 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGGAAGCTAGTGTAAGACCA
1 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGGAAGCCAGTGTAAGACCA
* *
56423608 TGTCTGGGACATGGCATCGGCATTGAGAC
66 TGTCCGGGACATGGCATCGGCATCGAGAC
* * *
56423637 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCAAGATGTAAGCCAGTGTAAGA-TA
1 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGGAAGCCAGTGTAAGACCA
*
56423701 TGTCCGGGACAT-GCATCGGC-TACGAGAT
66 TGTCCGGGACATGGCATCGGCAT-CGAGAC
* * *** * *
56423729 GATAGT-C-AGTGTAAGACCATGTCTGAGACATGGCATC-GACTTGAGATACG-AGCCAGTCTAA
1 G-T-GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAAGAT-GGAAGCCAGTGTAA
* *
56423790 GACCATGTCTGGGATATGGCATCGG
61 GACCATGTCCGGGACATGGCATCGG
56423815 TACCTTACCC
Statistics
Matches: 150, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
91 1 0.01
92 22 0.15
93 45 0.30
94 75 0.50
95 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (94 bp):
GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGGAAGCCAGTGTAAGACCA
TGTCCGGGACATGGCATCGGCATCGAGAC
Found at i:56423775 original size:47 final size:46
Alignment explanation
Indices: 56423550--56423814 Score: 215
Period size: 47 Copynumber: 5.7 Consensus size: 46
56423540 TGTGTGTGCT
* * * *
56423550 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGGAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTC-GA-GAT-GTAGCC
* *
56423596 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGTGT-GCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGA--TGTAGCC
* *
56423644 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCCAAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGAGATGT-AGCC
* * *
56423690 AGTGTAAGA-TATGTCCGGGACAT-GCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGAGATG-TAGCC
* * *
56423736 AGTGTAAGACCATGTCTGAGACATGGCATCGACTTGAGATACG-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGAT--GTAGCC
* *
56423783 AGTCTAAGACCATGTCTGGGATATGGCATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
56423815 TACCTTACCC
Statistics
Matches: 181, Mismatches: 23, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 67 0.37
47 77 0.43
48 29 0.16
49 3 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGTAGCC
Found at i:56423802 original size:140 final size:141
Alignment explanation
Indices: 56423550--56423814 Score: 342
Period size: 140 Copynumber: 1.9 Consensus size: 141
56423540 TGTGTGTGCT
* * *
56423550 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGGAAGCTAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCCGGGACATGCATCGGCCACATGATGGAAGCTAGTGTAAGACCATGTCTGA
* ** * * *
56423615 GACATGGCATCGGCATTGAGACGTGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCCCA
66 GACATGGCATCGACATTGAGACACGAGCCAGTCTAAGACATGTCTGGGACATGGCATCGGCCCCA
56423679 AGATGTAAGCC
131 AGATGTAAGCC
* *
56423690 AGTGTAAGATATGTCCGGGACATGCATCGGCTACGA-GAT-GATAG-TCAGTGTAAGACCATGTC
1 AGTGTAAGACATGTCCGGGACATGCATCGGCCAC-ATGATGGA-AGCT-AGTGTAAGACCATGTC
* *
56423752 TGAGACATGGCATCGAC-TTGAGATACGAGCCAGTCTAAGACCATGTCTGGGATATGGCATCGG
63 TGAGACATGGCATCGACATTGAGACACGAGCCAGTCTAAGA-CATGTCTGGGACATGGCATCGG
56423815 TACCTTACCC
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
139 20 0.19
140 79 0.74
141 8 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTCCGGGACATGCATCGGCCACATGATGGAAGCTAGTGTAAGACCATGTCTGA
GACATGGCATCGACATTGAGACACGAGCCAGTCTAAGACATGTCTGGGACATGGCATCGGCCCCA
AGATGTAAGCC
Found at i:56428188 original size:39 final size:39
Alignment explanation
Indices: 56428144--56428263 Score: 204
Period size: 39 Copynumber: 3.1 Consensus size: 39
56428134 ATGCAAGACA
56428144 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
56428183 CTGGAAATGTATCCGGGCCAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
56428222 CTGGAAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
56428261 CTG
1 CTG
56428264 ATAATATAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:56432681 original size:47 final size:43
Alignment explanation
Indices: 56432571--56432697 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 43
56432561 TTATTTGTGT
*
56432571 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGCGAGA
* **
56432617 GCCAGCATAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT--G-CGAGA
56432665 GCTAGTGTAAGACATGTCT-GGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC
56432698 TACAAGATGT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
45 12 0.17
46 15 0.22
47 22 0.32
48 20 0.29
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (43 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGCGAGA
Found at i:56432736 original size:91 final size:93
Alignment explanation
Indices: 56432571--56432740 Score: 238
Period size: 91 Copynumber: 1.8 Consensus size: 93
56432561 TTATTTGTGT
*
56432571 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTGAGAGCCAGCATAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATAGT-AGAGCCAGCATAAGACCATGTC
*
56432636 TGGGACATGGCATCGGCATTGAGACGAGA
65 TAGGACATGGCATCGGCATTGAGACGAGA
* * * **
56432665 GCTAGTGTAAGACATGTCT-GGACATGCATCGGCTACA-AG-ATGTGTCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATAGTA-GAGCCAGCATAAGACCATGTC
56432727 TAGGACATGGCATC
65 TAGGACATGGCATC
56432741 AATTTAATAG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
90 1 0.01
91 30 0.44
92 1 0.01
93 17 0.25
94 19 0.28
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATAGTAGAGCCAGCATAAGACCATGTCT
AGGACATGGCATCGGCATTGAGACGAGA
Found at i:56432927 original size:31 final size:31
Alignment explanation
Indices: 56432889--56432954 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
56432879 AAGTATAACC
56432889 ATGTTGTGAGTGGTATAAGTACCTATTTGAA
1 ATGTTGTGAGTGGTATAAGTACCTATTTGAA
*
56432920 ATGTTGTGAGTGGTATAGGTACCTATTTGAA
1 ATGTTGTGAGTGGTATAAGTACCTATTTGAA
56432951 ATGT
1 ATGT
56432955 ATGAAATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.39
Consensus pattern (31 bp):
ATGTTGTGAGTGGTATAAGTACCTATTTGAA
Found at i:56437135 original size:17 final size:17
Alignment explanation
Indices: 56437115--56437147 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56437105 TTATGATTAC
56437115 TATTATGTTATTATTTT
1 TATTATGTTATTATTTT
56437132 TATTATGTTATTATTT
1 TATTATGTTATTATTT
56437148 GTTTACTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TATTATGTTATTATTTT
Found at i:56437238 original size:18 final size:19
Alignment explanation
Indices: 56437194--56437238 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
56437184 TAGTTTTTTT
* *
56437194 TATTTGTTGTAATTTAGATA
1 TATTT-TTGTAATATAAATA
56437214 TATTTTTGTAATATAAATA
1 TATTTTTGTAATATAAATA
56437233 -ATTTTT
1 TATTTTT
56437239 TGATAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (19 bp):
TATTTTTGTAATATAAATA
Found at i:56444184 original size:22 final size:22
Alignment explanation
Indices: 56444156--56444276 Score: 59
Period size: 22 Copynumber: 5.2 Consensus size: 22
56444146 TTCCACATCC
56444156 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
56444178 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
56444202 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
56444225 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
56444249 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
56444272 ATCAC
1 ATCAC
56444277 GCATATATAT
Statistics
Matches: 69, Mismatches: 18, Indels: 24
0.62 0.16 0.22
Matches are distributed among these distances:
22 25 0.36
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:56444301 original size:49 final size:47
Alignment explanation
Indices: 56444128--56444337 Score: 305
Period size: 47 Copynumber: 4.4 Consensus size: 47
56444118 CCCTTCGGGA
* * *
56444128 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
56444175 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
56444222 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
56444269 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
56444318 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
56444338 GTACATCAAT
Statistics
Matches: 149, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
46 1 0.01
47 106 0.71
49 41 0.28
50 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:56444329 original size:96 final size:94
Alignment explanation
Indices: 56444149--56444331 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 94
56444139 TATACACTTC
56444149 CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGC
1 CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGC
* * *
56444214 CATTCGGCCTTATCTCATATATGCATGTT
66 CACTCGGCCCTATCACATATATGCATGTT
* *
56444243 CACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATACTTTCACATTCATCACATTG
1 CACATCCATCACATTGGCCATTCGGCCTTATCA--CATATATACACTTTCACATTCATCACATTG
56444308 GCCACTCGGCCCTATCACATATAT
64 GCCACTCGGCCCTATCACATATAT
56444332 ATACTTGTAC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 32 0.39
96 50 0.61
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (94 bp):
CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATTGGC
CACTCGGCCCTATCACATATATGCATGTT
Found at i:56451529 original size:43 final size:44
Alignment explanation
Indices: 56451467--56451587 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 44
56451457 CATGTATCGC
* *
56451467 ATCCATCATGAACTCGGACCACTCAACGAGCTCAGATG-CTCAT
1 ATCCATCATGAACTTGGACCACTCAACGAGCTCAGATGCCACAT
* *
56451510 ATCCATAATGAACTTGGACCTCTCAACGAGCTCAGATGCCACAT
1 ATCCATCATGAACTTGGACCACTCAACGAGCTCAGATGCCACAT
** * *
56451554 AT--ATCACAAACCTGGACCACTCAACGAGTTCAGA
1 ATCCATCATGAACTTGGACCACTCAACGAGCTCAGA
56451588 CTTCTTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 26 0.39
43 35 0.52
44 6 0.09
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.21
Consensus pattern (44 bp):
ATCCATCATGAACTTGGACCACTCAACGAGCTCAGATGCCACAT
Found at i:56451587 original size:42 final size:42
Alignment explanation
Indices: 56451482--56451587 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
56451472 TCATGAACTC
* ** *
56451482 GGACCACTCAACGAGCTCAGATGCTCATATCCATAATGAACTT
1 GGACCACTCAACGAGCTCAGATGCACATAT-CATAACAAACCT
* *
56451525 GGACCTCTCAACGAGCTCAGATGCCACATAT-ATCACAAACCT
1 GGACCACTCAACGAGCTCAGATG-CACATATCATAACAAACCT
*
56451567 GGACCACTCAACGAGTTCAGA
1 GGACCACTCAACGAGCTCAGA
56451588 CTTCTTAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 26 0.48
43 22 0.41
44 6 0.11
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (42 bp):
GGACCACTCAACGAGCTCAGATGCACATATCATAACAAACCT
Found at i:56458780 original size:10 final size:10
Alignment explanation
Indices: 56458765--56458790 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56458755 AAACCCAAGT
56458765 TCTCTTTCTC
1 TCTCTTTCTC
56458775 TCTCTTTCTC
1 TCTCTTTCTC
56458785 TCTCTT
1 TCTCTT
56458791 ATTGGCTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TCTCTTTCTC
Found at i:56462393 original size:28 final size:29
Alignment explanation
Indices: 56462356--56462428 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
56462346 AAGTCTACAT
*
56462356 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
56462384 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
56462413 ACATTCATATAGCCCA
1 ACATTCATATGGCCCA
56462429 TGTGGCCCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:56462422 original size:29 final size:28
Alignment explanation
Indices: 56462356--56462446 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
56462346 AAGTCTACAT
* *
56462356 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCCAATC
*
56462384 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCC-AATC
*
56462413 ACATTCATATAGCCCATGT-GGCCCGAATC
1 ACATTCATATGGCCCAT-TAGGCCC-AATC
56462442 A-ATTC
1 ACATTC
56462447 CAAGCCATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.45
29 29 0.53
30 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAATC
Found at i:56462690 original size:16 final size:16
Alignment explanation
Indices: 56462669--56462699 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56462659 AGACTTTCAG
56462669 CTTTTCGGCACTTCGA
1 CTTTTCGGCACTTCGA
*
56462685 CTTTTCGGCATTTCG
1 CTTTTCGGCACTTCG
56462700 GGATTTGCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.42
Consensus pattern (16 bp):
CTTTTCGGCACTTCGA
Found at i:56466307 original size:29 final size:29
Alignment explanation
Indices: 56466241--56466331 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
56466231 AAGTCTACAT
* **
56466241 ACATGCATATGGCCCGCTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
56466269 ACATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
56466298 ACATTCATATGGCCCATCT-GGCCCAAATC
1 ACATTCATATGGCCCAT-TAGGCCCAAATC
56466327 A-ATTC
1 ACATTC
56466332 CAAGCAATGT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 25 0.43
29 32 0.55
30 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:56466579 original size:16 final size:16
Alignment explanation
Indices: 56466554--56466584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56466544 AGACTTTTGG
56466554 CTTTTCAGCATTTCGA
1 CTTTTCAGCATTTCGA
*
56466570 CTTTTTAGCATTTCG
1 CTTTTCAGCATTTCG
56466585 GGATTTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.23, G:0.13, T:0.48
Consensus pattern (16 bp):
CTTTTCAGCATTTCGA
Found at i:56470172 original size:28 final size:29
Alignment explanation
Indices: 56470140--56470204 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
56470130 ATACATGCAT
*
56470140 ATGGCCCACTAGGCCC-AATCTCATTCAA
1 ATGGCCCACTAGGCCCAAATCACATTCAA
* *
56470168 ATGGCCCATTAGGCCCAAATCACATTCAT
1 ATGGCCCACTAGGCCCAAATCACATTCAA
56470197 ATGGCCCA
1 ATGGCCCA
56470205 TCTGACCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.29, C:0.34, G:0.15, T:0.22
Consensus pattern (29 bp):
ATGGCCCACTAGGCCCAAATCACATTCAA
Found at i:56470200 original size:29 final size:28
Alignment explanation
Indices: 56470132--56470205 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
56470122 AAGTCTACAT
* *
56470132 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCCAATC
* *
56470160 TCATTCAAATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCC-AATC
56470189 ACATTCATATGGCCCAT
1 ACATTCATATGGCCCAT
56470206 CTGACCCGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 20 0.51
29 19 0.49
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAATC
Found at i:56471228 original size:5 final size:5
Alignment explanation
Indices: 56471218--56471256 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
56471208 CTATTTGCAA
*
56471218 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC GAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
56471257 GAGTCAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:56472579 original size:90 final size:90
Alignment explanation
Indices: 56472409--56472581 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 90
56472399 CATTGTCAGA
* * *
56472409 TGAACCACCAAGTTTGCAGGTTAATACGCTTCCAGATGGTTGTAAATACACAACATAATTGCATA
1 TGAACCACCAAGGTTGCAGGTTAATACGCTTCCAAATGGTTGTAAATACACAACATAATTGCAGA
**
56472474 TAAAAGCTACCAGATAATGGATGGG
66 TAAAAAATACCAGATAATGGATGGG
* * *
56472499 TGAACCACCAAGGTTGCAGGTTAATACG-TTGCCAAATGGTTGTGAATACACAACATATTTGTAG
1 TGAACCACCAAGGTTGCAGGTTAATACGCTT-CCAAATGGTTGTAAATACACAACATAATTGCAG
**
56472563 ATAAAAAATAGTAGATAAT
65 ATAAAAAATACCAGATAAT
56472582 ATGTGGATGG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 2 0.03
90 70 0.97
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (90 bp):
TGAACCACCAAGGTTGCAGGTTAATACGCTTCCAAATGGTTGTAAATACACAACATAATTGCAGA
TAAAAAATACCAGATAATGGATGGG
Found at i:56472999 original size:171 final size:173
Alignment explanation
Indices: 56472713--56473057 Score: 534
Period size: 171 Copynumber: 2.0 Consensus size: 173
56472703 TTTATAAATA
* *
56472713 ATTCTTCCTATAAAGACCAAAACAAAACTTTAAGTTCTCAATTAATTGTCACTGTAAATTAAGTT
1 ATTCTTCCTAAAAAGACCAAAACAAAACTTTAAGTTCTCAAGTAATTGTCACTGTAAATTAAGTT
* *
56472778 TGAGGTTTTCATTAAAAATAATTTCAGCGGGTACATTTATAAGAGAATTTAACTTGATATTTTGA
66 TGAGGTTTTCATTAAAAATAATTTCAACGAGTACATTTATAAGAGAATTTAACTTGATATTTTGA
*
56472843 CATATTTG-AAT-TTTTCTTTTAAAAAGGAGACAATAAAGTTTT
131 CATATTTGAAATGTTTT-TTTTAAAAACGAGACAATAAAGTTTT
** * *
56472885 ATTCTTCCTAAAAAGACCAAAATGAAACTTTAAGTTTTCAAGTAATTGTCACTG-CAATTAAGTT
1 ATTCTTCCTAAAAAGACCAAAACAAAACTTTAAGTTCTCAAGTAATTGTCACTGTAAATTAAGTT
*
56472949 TGAGGTTTTCATTAAAAATAATTTCAACGAGTACGTTTATAAGAGAATTTAACTTGATATTTTGA
66 TGAGGTTTTCATTAAAAATAATTTCAACGAGTACATTTATAAGAGAATTTAACTTGATATTTTGA
* * * *
56473014 CATGTTTGAAATGTTTTTTTTTAAAACGAGATAATGAAGTTTT
131 CATATTTGAAATGTTTTTTTTAAAAACGAGACAATAAAGTTTT
56473057 A
1 A
56473058 ACCTGCTGGA
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
171 78 0.50
172 75 0.48
173 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (173 bp):
ATTCTTCCTAAAAAGACCAAAACAAAACTTTAAGTTCTCAAGTAATTGTCACTGTAAATTAAGTT
TGAGGTTTTCATTAAAAATAATTTCAACGAGTACATTTATAAGAGAATTTAACTTGATATTTTGA
CATATTTGAAATGTTTTTTTTAAAAACGAGACAATAAAGTTTT
Found at i:56473661 original size:10 final size:10
Alignment explanation
Indices: 56473622--56473658 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
56473612 TGTTATAAAG
56473622 TTAACAACAA
1 TTAACAACAA
56473632 TTAACAACAA
1 TTAACAACAA
56473642 TTAACAA-AA
1 TTAACAACAA
56473651 TTGAACAA
1 TT-AACAA
56473659 AATAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (10 bp):
TTAACAACAA
Found at i:56475468 original size:21 final size:21
Alignment explanation
Indices: 56475431--56475482 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
56475421 GGTATCTACA
* *
56475431 AATCAAATC-TCTTAGATTAC
1 AATCATATCTTCTAAGATTAC
56475451 AATCATATCTTCTAAGATTAC
1 AATCATATCTTCTAAGATTAC
56475472 ATATCATATCT
1 A-ATCATATCT
56475483 AAGATTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.29
21 11 0.39
22 9 0.32
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (21 bp):
AATCATATCTTCTAAGATTAC
Found at i:56488581 original size:22 final size:23
Alignment explanation
Indices: 56488564--56488608 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
56488554 AAATCAATTC
56488564 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTACAAAATCATATCT
*
56488587 TCTAAGATTAC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
56488609 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:56488592 original size:23 final size:22
Alignment explanation
Indices: 56488551--56488608 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
56488541 AAAGGGTATC
56488551 TACAAATCA-AT-TCTCTAAGAT
1 TACAAATCATATCT-TCTAAGAT
56488572 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
56488595 TACATATCATATCT
1 TACAAATCATATCT
56488609 AAGATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 3 0.09
22 16 0.48
23 13 0.39
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:56488602 original size:17 final size:17
Alignment explanation
Indices: 56488580--56488630 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
56488570 ATTACAAAAT
56488580 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
56488597 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
56488616 CATATCTTCGAAGAT
1 CATATCTTCTAAGAT
56488631 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:56488611 original size:19 final size:20
Alignment explanation
Indices: 56488564--56488621 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
56488554 AAATCAATTC
*
56488564 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
56488587 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
56488606 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
56488622 TTCGAAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:56502801 original size:94 final size:94
Alignment explanation
Indices: 56502640--56502827 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
56502630 CTTGTGTTTC
56502640 TTATTCTCAAGGAAAATTGATTATTAGATCATCACCGACTAAAGTTGGCATTGAATCTCCTACAT
1 TTATTCTCAAGGAAAATTGATTATTAGATCATCACCGACTAAAGTTGGCATTGAATCTCCTACAT
56502705 TTCTGAAACGTATTCAAGGTAATATATGT
66 TTCTGAAACGTATTCAAGGTAATATATGT
* *
56502734 TTATTCTCAAGGAAAATTGATTATTAGATCATCATCGACTAAAGTTGGGATTGAATCTCCTACAT
1 TTATTCTCAAGGAAAATTGATTATTAGATCATCACCGACTAAAGTTGGCATTGAATCTCCTACAT
* *
56502799 TTCTGGAACGTATTCAAGGTGATATATGT
66 TTCTGAAACGTATTCAAGGTAATATATGT
56502828 GGGCCCATTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (94 bp):
TTATTCTCAAGGAAAATTGATTATTAGATCATCACCGACTAAAGTTGGCATTGAATCTCCTACAT
TTCTGAAACGTATTCAAGGTAATATATGT
Found at i:56505905 original size:49 final size:49
Alignment explanation
Indices: 56505800--56505983 Score: 203
Period size: 49 Copynumber: 3.8 Consensus size: 49
56505790 GGGTTAAGAT
* * *
56505800 GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTTTCATATAGCGAG
1 GCCGATGCCATGTCCCAAATA-GGTCTTACACTAGCTCTCATATAGCGAG
* * * *
56505850 GCCGATGCCATGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCG-G
1 GCCGATGCCATGTCCCAAATAGGTCTTACACTAGCTCTCATATAGCGAG
* * *
56505898 TGTCGATGCCATGTCCCAAATAGGTCTTACACTAGCTTGTC-TATCGCGAG
1 -GCCGATGCCATGTCCCAAATAGGTCTTACACTAGC-TCTCATATAGCGAG
* * *
56505948 GCTGATG-CATGTCCCAAACATGTCTTACACTAGCTC
1 GCCGATGCCATGTCCCAAATAGGTCTTACACTAGCTC
56505984 CCGACCCAAT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
47 1 0.01
48 26 0.23
49 63 0.56
50 22 0.20
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAAATAGGTCTTACACTAGCTCTCATATAGCGAG
Found at i:56506042 original size:94 final size:94
Alignment explanation
Indices: 56505808--56506121 Score: 274
Period size: 94 Copynumber: 3.3 Consensus size: 94
56505798 ATGCCGACGC
* ** * * * * *
56505808 CATGTCCCAAACATGGTCTTACACTAGCTTTCATATAGCGAGGCCGATGCCATGTCCCAGATAGG
1 CATGTCCCAGACAT-GTCTTACACTAGCTTAAATATCGCGAGGCCTATG-CATGTCCCAAACATG
* * * * **
56505873 TCTTACACTGGCTCTCA-TCTATCGGTGTCGATG
64 TCTTACACTAGCTCCCACCCAAT--G-ACCGATG
* * * ***
56505906 CCATGTCCCAAATAGGTCTTACACTAGCTTGTCTATCGCGAGG-CTGATGCATGTCCCAAACATG
1 -CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCT-ATGCATGTCCCAAACATG
56505970 TCTTACACTAGCTCCCGACCCAAT-ACCGATG
64 TCTTACACTAGCTCCC-ACCCAATGACCGATG
* * *
56506001 CATGTCCCAGACATGTCTTACACTGGCTTAAATATCTCGAGGCCTATGCATGTCCCAAACATGTT
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCTATGCATGTCCCAAACATGTC
* * * * **
56506066 TTACACTAGCTCTCATCTAGTGGTCGATG
66 TTACACTAGCTCCCACCCAATGACCGATG
56506095 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
56506122 ACACAATCAC
Statistics
Matches: 178, Mismatches: 32, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
93 4 0.02
94 97 0.54
95 7 0.04
97 27 0.15
98 28 0.16
99 15 0.08
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCTATGCATGTCCCAAACATGTC
TTACACTAGCTCCCACCCAATGACCGATG
Found at i:56506109 original size:46 final size:46
Alignment explanation
Indices: 56505808--56506121 Score: 238
Period size: 46 Copynumber: 6.6 Consensus size: 46
56505798 ATGCCGACGC
* *
56505808 CATGTCCCAAACATGGTCTTACACTAGCTTTCATATAGCGAGGCCGATG
1 CATGTCCCAAACAT-GTCTTACACTAGCTCTCATCTA--GAGGCCGATG
* * * * *
56505857 CCATGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCG-GTGTCGATG
1 -CATGTCCCAAACATGTCTTACACTAGCTCTCATCTA--GAG-GCCGATG
* * * ** *
56505906 CCATGTCCCAAATAGGTCTTACACTAGCTTGTCTATCGCGAGGCTGATG
1 -CATGTCCCAAACATGTCTTACACTAGC-TCTC-ATCTAGAGGCCGATG
* * * **
56505955 CATGTCCCAAACATGTCTTACACTAGCTCCCGACCCA-ATACCGATG
1 CATGTCCCAAACATGTCTTACACTAGCTCTC-ATCTAGAGGCCGATG
* * * * *
56506001 CATGTCCCAGACATGTCTTACACTGGCT-TAAATATCTCGAGGCCTATG
1 CATGTCCCAAACATGTCTTACACTAGCTCT---CATCTAGAGGCCGATG
* * *
56506049 CATGTCCCAAACATGTTTTACACTAGCTCTCATCTAGTGGTCGATG
1 CATGTCCCAAACATGTCTTACACTAGCTCTCATCTAGAGGCCGATG
*
56506095 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAAACATGTCTTACACTAGC
56506122 ACACAATCAC
Statistics
Matches: 209, Mismatches: 46, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
46 68 0.33
47 6 0.03
48 57 0.27
49 60 0.29
50 15 0.07
51 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAAACATGTCTTACACTAGCTCTCATCTAGAGGCCGATG
Found at i:56510829 original size:22 final size:24
Alignment explanation
Indices: 56510781--56510826 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
56510771 GCATCACATT
* *
56510781 TCATATACCAAAATCAAACCATAA
1 TCATATACAAAAACCAAACCATAA
*
56510805 TCATA-ACAAAAACCAAGCCATA
1 TCATATACAAAAACCAAACCATA
56510827 TCACATGGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.17
Consensus pattern (24 bp):
TCATATACAAAAACCAAACCATAA
Found at i:56511461 original size:42 final size:41
Alignment explanation
Indices: 56511387--56511517 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 41
56511377 TAGATGTAAC
* * *
56511387 CAAATATCGATGCCACTGTCTCAGATAGGGTCTTACACGAAAT
1 CAAATA-CGATGCCAATGTC-CAGACATGGTCTTACACGAAAT
56511430 CAAATACGATGCCAATGTACCAGACATGGTCTTACACGTAAAT
1 CAAATACGATGCCAATGT-CCAGACATGGTCTTACACG-AAAT
* * *
56511473 CATAAGT-CGATGCCAACGTCCAAGACATGGTCGTACATGAAAT
1 CA-AA-TACGATGCCAATGTCC-AGACATGGTCTTACACGAAAT
56511516 CA
1 CA
56511518 CATATCGGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
42 27 0.35
43 21 0.27
44 28 0.36
45 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (41 bp):
CAAATACGATGCCAATGTCCAGACATGGTCTTACACGAAAT
Found at i:56512624 original size:13 final size:13
Alignment explanation
Indices: 56512606--56512632 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56512596 CACAAACGAT
56512606 AAAATTTTCACAC
1 AAAATTTTCACAC
56512619 AAAATTTTCACAC
1 AAAATTTTCACAC
56512632 A
1 A
56512633 TACTAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:56515560 original size:49 final size:48
Alignment explanation
Indices: 56515505--56515678 Score: 147
Period size: 49 Copynumber: 3.6 Consensus size: 48
56515495 GGTGTGTCAT
*
56515505 TGTAAGACCTATCTGGGACATGGCATCGACACAAATAAGTGAGAGCCAG
1 TGTAAGACCTATCTGGGACATGGCATCGACTCAAAT-AGTGAGAGCCAG
* * * ** *
56515554 TGTAAGATCTATCTGGGACATGTCATCGGCCTCGATGTA-TG-GAAGTCAG
1 TGTAAGACCTATCTGGGACATGGCATC-GACTC-AAATAGTGAG-AGCCAG
* * * * *
56515603 TGTAAGACTTGTCTGGGACATGACATCGACTTAGAT-GTGAGAGCCAG
1 TGTAAGACCTATCTGGGACATGGCATCGACTCAAATAGTGAGAGCCAG
* * *
56515650 TGTAAGACCATGTTTGGAACATGGCATCG
1 TGTAAGACC-TATCTGGGACATGGCATCG
56515679 GCATCGTACC
Statistics
Matches: 99, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
47 17 0.17
48 21 0.21
49 55 0.56
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (48 bp):
TGTAAGACCTATCTGGGACATGGCATCGACTCAAATAGTGAGAGCCAG
Found at i:56518871 original size:49 final size:48
Alignment explanation
Indices: 56518805--56519117 Score: 193
Period size: 49 Copynumber: 6.6 Consensus size: 48
56518795 CATCAAAGTT
* *
56518805 GATGTCATGTCCTAGACAGGTCTTACACTGACTTTCATATATCGAGACC
1 GATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-CC
* * * * * *
56518854 GATGCCGTGTCCCAGACAGGTCTTACGCTGGCTCTCATCTATCGATGTC
1 GATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGA-GCC
* * * * * *
56518903 GATGCCATGTCCCAGACAAGTCTTACATTGA--TACACA-A-CAAGCT
1 GATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGCC
* * *
56518947 GACGCCATGTCCCAGACAGGTCTTACACT-AGCTTGT-ATATCTCGAGATC
1 GATGCCATGTCCCAGACAGGTCTTACACTGA-CTT-TCATATATCGAG-CC
* * * * * * *
56518996 GATG-CATGTCCTAGACATGTCTTACACT-AGC--TCTTGTCTCAATGTC
1 GATGCCATGTCCCAGACAGGTCTTACACTGA-CTTTCATATATCGA-GCC
* * * *
56519042 GATG-CATGTCCCAGACATGTCTTACACTGGCTGGT-ATATCTCGAGGCC
1 GATGCCATGTCCCAGACAGGTCTTACACTGACT-TTCATATATCGA-GCC
*
56519090 GATG-CATGTCCCAGACATGTCTTACACT
1 GATGCCATGTCCCAGACAGGTCTTACACT
56519118 AGCACACATA
Statistics
Matches: 208, Mismatches: 42, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.00
44 27 0.13
45 3 0.01
46 40 0.19
47 3 0.01
48 64 0.31
49 69 0.33
50 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGCC
Found at i:56519012 original size:48 final size:47
Alignment explanation
Indices: 56518952--56519120 Score: 225
Period size: 48 Copynumber: 3.6 Consensus size: 47
56518942 AAGCTGACGC
*
56518952 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGATCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAG-TCGATG
* * * *
56519000 CATGTCCTAGACATGTCTTACACTAGC-TCT-TGTCTCAATGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGA-GTCGATG
* * *
56519046 CATGTCCCAGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGA-GTCGATG
56519094 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
56519121 ACACATATCA
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
46 37 0.36
47 4 0.04
48 63 0.61
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGTCGATG
Found at i:56525308 original size:20 final size:20
Alignment explanation
Indices: 56525279--56525335 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
56525269 ATAAACTATG
* *
56525279 TACCACTCCATTTACTTTCT
1 TACCATTCCATTTACTTACT
56525299 TACCATTCCATTTACTTACT
1 TACCATTCCATTTACTTACT
* *
56525319 TTCCATTTCATTTACTT
1 TACCATTCCATTTACTT
56525336 CACATAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (20 bp):
TACCATTCCATTTACTTACT
Found at i:56526795 original size:26 final size:26
Alignment explanation
Indices: 56526766--56526815 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
56526756 GAAAATGATG
*
56526766 TGAATGAATAAAAACCAATGGGCAGA
1 TGAATGAAGAAAAACCAATGGGCAGA
**
56526792 TGAATGAAGAAACTCCAATGGGCA
1 TGAATGAAGAAAAACCAATGGGCA
56526816 TACAATGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (26 bp):
TGAATGAAGAAAAACCAATGGGCAGA
Found at i:56528288 original size:26 final size:26
Alignment explanation
Indices: 56528259--56528308 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
56528249 CATTCTTGAT
56528259 TTAAATTAATAATTTCATTAAATTAA
1 TTAAATTAATAATTTCATTAAATTAA
*
56528285 TTAAATTAATAATTTTATTAAATT
1 TTAAATTAATAATTTCATTAAATT
56528309 CCACGATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAAATTAATAATTTCATTAAATTAA
Found at i:56528289 original size:9 final size:9
Alignment explanation
Indices: 56528259--56528308 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
56528249 CATTCTTGAT
56528259 TTAAATTAA
1 TTAAATTAA
* *
56528268 -TAATTTCA
1 TTAAATTAA
56528276 TTAAATTAA
1 TTAAATTAA
56528285 TTAAATTAA
1 TTAAATTAA
* *
56528294 -TAATTTTA
1 TTAAATTAA
56528302 TTAAATT
1 TTAAATT
56528309 CCACGATAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
8 12 0.38
9 20 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAAATTAA
Found at i:56534813 original size:19 final size:19
Alignment explanation
Indices: 56534789--56534825 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56534779 TTAATGTGCG
*
56534789 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
56534808 AATATATATATATGTGTG
1 AATATATATATATGTGTG
56534826 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:56535099 original size:41 final size:41
Alignment explanation
Indices: 56535037--56535212 Score: 280
Period size: 41 Copynumber: 4.3 Consensus size: 41
56535027 GTTTGGAATT
* *
56535037 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
56535078 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
56535119 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
56535160 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
56535201 GGTGATCCGAAT
1 GGTGATCTGAAT
56535213 ATGATGAATT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:56535174 original size:82 final size:82
Alignment explanation
Indices: 56535037--56535206 Score: 331
Period size: 82 Copynumber: 2.1 Consensus size: 82
56535027 GTTTGGAATT
56535037 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
56535102 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
56535119 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
56535184 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
56535201 GGTGAT
1 GGTGAT
56535207 CCGAATATGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:56542538 original size:41 final size:41
Alignment explanation
Indices: 56542476--56542604 Score: 231
Period size: 41 Copynumber: 3.1 Consensus size: 41
56542466 GTTTGGAATT
56542476 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
* * *
56542517 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
56542558 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
56542599 GGTGAT
1 GGTGAT
56542605 CCGAATATGA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (41 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
Found at i:56543450 original size:33 final size:33
Alignment explanation
Indices: 56543408--56543472 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
56543398 TCTTTTTGTT
56543408 TTGAATTTGGTATTAACGAATATGTTTTAATGG
1 TTGAATTTGGTATTAACGAATATGTTTTAATGG
56543441 TTGAATTTGGTATTAACGAATATGTTTTAATG
1 TTGAATTTGGTATTAACGAATATGTTTTAATG
56543473 TTTTATTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGAATTTGGTATTAACGAATATGTTTTAATGG
Found at i:56555641 original size:29 final size:29
Alignment explanation
Indices: 56555599--56555674 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
56555589 TGATATGAAT
56555599 TCTCAATGAACAAGTTCTTCATCGCGAAC
1 TCTCAATGAACAAGTTCTTCATCGCGAAC
56555628 TCTCAATGAACAAGTTCTTCATCGCGAAC
1 TCTCAATGAACAAGTTCTTCATCGCGAAC
56555657 TCTCAATGAACAAGTTCT
1 TCTCAATGAACAAGTTCT
56555675 CTACCTTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (29 bp):
TCTCAATGAACAAGTTCTTCATCGCGAAC
Found at i:56556248 original size:157 final size:157
Alignment explanation
Indices: 56555962--56556277 Score: 632
Period size: 157 Copynumber: 2.0 Consensus size: 157
56555952 GGACTTCATT
56555962 GAGTTCACTAAAAAGTCCCTTCAACCAAATAGCTTCTTTACAAGTCTCAGTAATCACCATGTACT
1 GAGTTCACTAAAAAGTCCCTTCAACCAAATAGCTTCTTTACAAGTCTCAGTAATCACCATGTACT
56556027 TAGCTTCAGTGGTAGACAAAGTGACTGTAGTTTGCAAAGTGGCTTTCCAACTGATTGTACAACTT
66 TAGCTTCAGTGGTAGACAAAGTGACTGTAGTTTGCAAAGTGGCTTTCCAACTGATTGTACAACTT
56556092 TTGATTGTAAAAACATAACCTATGAGA
131 TTGATTGTAAAAACATAACCTATGAGA
56556119 GAGTTCACTAAAAAGTCCCTTCAACCAAATAGCTTCTTTACAAGTCTCAGTAATCACCATGTACT
1 GAGTTCACTAAAAAGTCCCTTCAACCAAATAGCTTCTTTACAAGTCTCAGTAATCACCATGTACT
56556184 TAGCTTCAGTGGTAGACAAAGTGACTGTAGTTTGCAAAGTGGCTTTCCAACTGATTGTACAACTT
66 TAGCTTCAGTGGTAGACAAAGTGACTGTAGTTTGCAAAGTGGCTTTCCAACTGATTGTACAACTT
56556249 TTGATTGTAAAAACATAACCTATGAGA
131 TTGATTGTAAAAACATAACCTATGAGA
56556276 GA
1 GA
56556278 TCTTCTTCTA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 159 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (157 bp):
GAGTTCACTAAAAAGTCCCTTCAACCAAATAGCTTCTTTACAAGTCTCAGTAATCACCATGTACT
TAGCTTCAGTGGTAGACAAAGTGACTGTAGTTTGCAAAGTGGCTTTCCAACTGATTGTACAACTT
TTGATTGTAAAAACATAACCTATGAGA
Found at i:56562704 original size:18 final size:18
Alignment explanation
Indices: 56562681--56562718 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56562671 TAAAGCTTAG
* *
56562681 AAAGTTTTCATGTAAATA
1 AAAGTTTGCATATAAATA
56562699 AAAGTTTGCATATAAATA
1 AAAGTTTGCATATAAATA
56562717 AA
1 AA
56562719 TAACAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAGTTTGCATATAAATA
Found at i:56562997 original size:55 final size:53
Alignment explanation
Indices: 56562871--56563065 Score: 149
Period size: 55 Copynumber: 3.6 Consensus size: 53
56562861 CTTACCATTT
** * *
56562871 CCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTATGAACTCACTATTG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACTAATG
* * * ** *
56562924 CCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTA-TCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G-AACTCACT-AATG
*** * * * * *
56562979 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATA
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-GAACTCACTAATG
* * * *
56563033 CCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTT
56563066 AAACCGTAAT
Statistics
Matches: 111, Mismatches: 27, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
53 34 0.31
54 37 0.33
55 40 0.36
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACTAATG
Found at i:56572341 original size:53 final size:54
Alignment explanation
Indices: 56572261--56572466 Score: 202
Period size: 53 Copynumber: 3.8 Consensus size: 54
56572251 TTCCTTTTTA
* * *
56572261 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * * *
56572314 AACTCACCATTGTCATGCCTTGGCATGGTCTTACATGGGATCTTTGCGTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
56572368 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACAT-GTTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
56572422 AACTTACCAATACCATGCCTTGGCATGGTCTTAC-TCGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACAT-GGTATCCTT
56572467 ACACCCTAAT
Statistics
Matches: 120, Mismatches: 29, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
52 1 0.01
53 72 0.60
54 19 0.16
55 28 0.23
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:56578012 original size:95 final size:99
Alignment explanation
Indices: 56577891--56578128 Score: 254
Period size: 95 Copynumber: 2.4 Consensus size: 99
56577881 ATTAAAGTCG
* * * * * *
56577891 ATGCCATGTCCCAGACATAGTCTTACACTGA-ATCTCGTATATCGAGGTCGATCCCATGTCCCAG
1 ATGCCATGTCCCAAACATGGTCTTACACTGAGATCTCATATATCAAGGCCCATCCCATGTCCCAG
56577955 ACATGGTCTTACACT-G-ACACATATC-AAGCCC
66 ACATGGTCTTACACTAGCACACATATCTAAGCCC
* * * * *
56577986 ATGCCATGTCCCAAACATGGTCTTACA-TTAGCTCTCATGTCTCAAGGCCCATGCCATGTCCCAG
1 ATGCCATGTCCCAAACATGGTCTTACACTGAGATCTCATATATCAAGGCCCATCCCATGTCCCAG
* * * * *
56578050 ACATGGTTTTACACTAGCTCTCATATCTTGAGGCCG
66 ACATGGTCTTACACTAGCACACATATC-T-AAGCCC
* *
56578086 ATGTCATGTCCCAAACATGGTCTTACACT-AGCTCTCATATATC
1 ATGCCATGTCCCAAACATGGTCTTACACTGAGATCTCATATATC
56578129 CCTAGCATCA
Statistics
Matches: 117, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
94 2 0.02
95 64 0.55
96 1 0.01
97 7 0.06
100 42 0.36
101 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (99 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGAGATCTCATATATCAAGGCCCATCCCATGTCCCAG
ACATGGTCTTACACTAGCACACATATCTAAGCCC
Found at i:56578054 original size:50 final size:50
Alignment explanation
Indices: 56577891--56578128 Score: 245
Period size: 50 Copynumber: 4.9 Consensus size: 50
56577881 ATTAAAGTCG
* * * * * *
56577891 ATGCCATGTCCCAGACATAGTCTTACACT-GAATCTCGTATATCGAGGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATATATCAAGGCCC
* * *
56577941 ATCCCATGTCCCAGACATGGTCTTACACT-G---ACACATATCAA-GCCC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAGGCCC
* * * *
56577986 ATGCCATGTCCCAAACATGGTCTTACATTAGCTCTCATGTCTCAAGGCCC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAGGCCC
* * ** *
56578036 ATGCCATGTCCCAGACATGGTTTTACACTAGCTCTCATATCTTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAGGCCC
* *
56578086 ATGTCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATC
56578129 CCTAGCATCA
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
45 28 0.18
46 8 0.05
49 7 0.04
50 113 0.72
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCAAGGCCC
Found at i:56583492 original size:27 final size:27
Alignment explanation
Indices: 56583462--56583559 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
56583452 TTAGTTTACC
56583462 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
56583489 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
56583516 AAATTACTAAAATATCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
*
56583543 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
56583560 TCAACCTGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:56583570 original size:54 final size:54
Alignment explanation
Indices: 56583462--56583575 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
56583452 TTAGTTTACC
* ***
56583462 AAATTACCAAAATACCCCTGGTTTGTAAAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTATCAAAATACCCCTAACCTGTA
* * *
56583516 AAATTACTAAAATATCCCTGATTTGTGAAATTA-CTAAAATA-CCCTCAACCTGTA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTATC-AAAATACCCCT-AACCTGTA
56583570 AAATTA
1 AAATTA
56583576 TTGAAATACC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
53 5 0.10
54 46 0.90
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGATTTGTAAAATTATCAAAATACCCCTAACCTGTA
Found at i:56583573 original size:27 final size:27
Alignment explanation
Indices: 56583462--56583614 Score: 107
Period size: 27 Copynumber: 5.7 Consensus size: 27
56583452 TTAGTTTACC
* **
56583462 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GACTTGTA
* *
56583489 AAATTA-TCAAAATACCC-CTAGTTTGTA
1 AAATTACT-AAAATACCCTCGA-CTTGTA
* *
56583516 AAATTACTAAAATATCCCT-GATTTGTG
1 AAATTACTAAAATA-CCCTCGACTTGTA
* *
56583543 AAATTACTAAAATACCCTCAACCTGTA
1 AAATTACTAAAATACCCTCGACTTGTA
* * *
56583570 AAATTATTGAAATACCATCGACTTGTA
1 AAATTACTAAAATACCCTCGACTTGTA
* * *
56583597 AAGTTACCAAAGTACCCT
1 AAATTACTAAAATACCCT
56583615 TGATTTATAG
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
26 4 0.04
27 91 0.91
28 5 0.05
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGACTTGTA
Found at i:56583613 original size:54 final size:54
Alignment explanation
Indices: 56583512--56583614 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
56583502 ACCCCTAGTT
* * *
56583512 TGTAAAATTACTAAAATATCCCTGATTTGTGAAATTACTAAAATACCCTCAACC
1 TGTAAAATTACTAAAATATCCATGACTTGTGAAATTACCAAAATACCCTCAACC
* * *
56583566 TGTAAAATTATTGAAATA-CCATCGACTTGT-AAAGTTACCAAAGTACCCT
1 TGTAAAATTACTAAAATATCCAT-GACTTGTGAAA-TTACCAAAATACCCT
56583615 TGATTTATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
53 6 0.15
54 35 0.85
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (54 bp):
TGTAAAATTACTAAAATATCCATGACTTGTGAAATTACCAAAATACCCTCAACC
Found at i:56583630 original size:27 final size:26
Alignment explanation
Indices: 56583462--56583670 Score: 73
Period size: 27 Copynumber: 7.7 Consensus size: 26
56583452 TTAGTTTACC
* * *
56583462 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACC-AAATACCCTTGATTTATA
* * *
56583489 AAATTATCAAAATACCCCT-AGTTTGTA
1 AAATTA-CCAAATACCCTTGA-TTTATA
* * *
56583516 AAATTACTAAAATATCCC-TGATTTGTG
1 AAATTAC-CAAATA-CCCTTGATTTATA
* ** ** *
56583543 AAATTACTAAAATACCCTCAACCTGTA
1 AAATTAC-CAAATACCCTTGATTTATA
** * * * *
56583570 AAATTATTGAAATACCATCGACTTGTA
1 AAATTA-CCAAATACCCTTGATTTATA
*
56583597 AAGTTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAA-TACCCTTGATTTATA
* **
56583624 GAATTACCATTTTA-CCTTCGATTTATA
1 AAATTACCA-AATACCCTT-GATTTATA
56583651 AAATTACCGAAATACCCTTG
1 AAATTACC-AAATACCCTTG
56583671 TAGGGTAGAA
Statistics
Matches: 143, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
26 11 0.08
27 122 0.85
28 10 0.07
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (26 bp):
AAATTACCAAATACCCTTGATTTATA
Found at i:56583687 original size:27 final size:27
Alignment explanation
Indices: 56583655--56583897 Score: 326
Period size: 27 Copynumber: 9.0 Consensus size: 27
56583645 TTTATAAAAT
*
56583655 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
* * *
56583682 TGCCGAAATACCCTTATAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
56583709 TACCGAAATACCCCTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
56583736 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
** * *
56583763 TACTAAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
* *
56583790 TACCGAAATACCCTTGTAAGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
56583817 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
* *
56583844 TACTGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
* * *
56583871 TACCGAGATACCCTTGTGGGGTA-AAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
56583897 T
1 T
56583898 TACCATTTTA
Statistics
Matches: 192, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
26 3 0.02
27 189 0.98
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAA
Found at i:56583912 original size:81 final size:81
Alignment explanation
Indices: 56583655--56583897 Score: 371
Period size: 81 Copynumber: 3.0 Consensus size: 81
56583645 TTTATAAAAT
* * * * * *
56583655 TACCGAAATACCCTTGTAGGGTAGAAATGCCGAAATACCCTTATAGGGTAGAAATACCGAAATAC
1 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATAC
*
56583720 CCCTGTAGGGTAGAAA
66 CCTTGTAGGGTAGAAA
*
56583736 TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTACCGAAATAC
1 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATAC
*
56583801 CCTTGTAAGGTAGAAA
66 CCTTGTAGGGTAGAAA
* *
56583817 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATAC
1 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATAC
*
56583882 CCTTGTGGGGTA-AAA
66 CCTTGTAGGGTAGAAA
56583897 T
1 T
56583898 TACCATTTTA
Statistics
Matches: 148, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
80 4 0.03
81 144 0.97
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (81 bp):
TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATAC
CCTTGTAGGGTAGAAA
Found at i:56584439 original size:58 final size:57
Alignment explanation
Indices: 56584351--56584501 Score: 166
Period size: 57 Copynumber: 2.6 Consensus size: 57
56584341 CATTGACGTT
* * *
56584351 GTTATAGAAAGGATTTAGCCCAGACAGGTAATCCTGAAAT-AA-TACCTCTCGAGCATAC
1 GTTATATAAAGGATTTAGCCTAGACTGGTAATCCTG-AATCAACT-CCTCT-GAGCATAC
* *
56584409 GTTATGATTATGG-TTTAGCCTAGACTGGTAATCCT-AATCAAGCTCCTCTGAGCATAC
1 GTTAT-ATAAAGGATTTAGCCTAGACTGGTAATCCTGAATCAA-CTCCTCTGAGCATAC
* *
56584466 GTTATATAAAGGATTTAGCCTGGACTAGTAATCCTG
1 GTTATATAAAGGATTTAGCCTAGACTGGTAATCCTG
56584502 TTGTACGATA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
56 8 0.10
57 35 0.45
58 30 0.38
59 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (57 bp):
GTTATATAAAGGATTTAGCCTAGACTGGTAATCCTGAATCAACTCCTCTGAGCATAC
Found at i:56585871 original size:46 final size:46
Alignment explanation
Indices: 56585821--56585995 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
56585811 TGGTTGAGCA
56585821 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
56585867 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
56585913 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
56585959 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56585996 GCGGGTTACA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:56596068 original size:46 final size:46
Alignment explanation
Indices: 56596018--56596193 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
56596008 TGGTTGAGCA
56596018 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
56596064 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
56596109 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
56596157 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56596194 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:56596174 original size:93 final size:93
Alignment explanation
Indices: 56596015--56596186 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
56596005 GGATGGTTGA
* *
56596015 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
56596080 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
56596108 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
56596173 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
56596187 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:56598526 original size:125 final size:124
Alignment explanation
Indices: 56598323--56598548 Score: 289
Period size: 125 Copynumber: 1.8 Consensus size: 124
56598313 TCATTTTGTC
* * *
56598323 CACACGGGTAGACACACGGGCGTGTGTCTAGACCGTGTGTGACACATGCCTGGTAACACGGGCGT
1 CACACGGGTAGACACACGAGCGTGTGTCTAGACCGAGTGTGACACATGCCTAGTAACACGGGCGT
***
56598388 ATGGTTTGGCCGTGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCCTAGAATTGGG
66 ATGGTTTGGCCGTGTGAAACCTGCACC-TAATTTTGAGAAATAGAATGCCTAGAATTGGG
* * *
56598448 CACACGGGTAGAGACACGAGCGTGTGTCTCAG-CTGAGTGTGCCACACA-GCCTAG-CACACGGG
1 CACACGGGTAGACACACGAGCGTGTGTCT-AGACCGAGTGTG--ACACATGCCTAGTAACACGGG
*
56598510 CGTGT-GTCTTGGCCGTGTGAAACCTGCACCTAATTTTGA
63 CGTATGGT-TTGGCCGTGTGAAACCTGCACCTAATTTTGA
56598549 ATTGAATTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
124 11 0.13
125 64 0.74
126 7 0.08
127 5 0.06
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (124 bp):
CACACGGGTAGACACACGAGCGTGTGTCTAGACCGAGTGTGACACATGCCTAGTAACACGGGCGT
ATGGTTTGGCCGTGTGAAACCTGCACCTAATTTTGAGAAATAGAATGCCTAGAATTGGG
Found at i:56602413 original size:93 final size:93
Alignment explanation
Indices: 56602301--56602475 Score: 278
Period size: 93 Copynumber: 1.9 Consensus size: 93
56602291 CGCCCATAAG
* * ***
56602301 CGAACTTGGACTCAACTCAATGAGATCGGGTGTTCGCATCCACAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCA
56602366 ACGAGCTCGGATGCCCAGTTACATCTCT
66 ACGAGCTCGGATGCCCAGTTACATCTCT
* *
56602394 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCA
*
56602459 ACGAGTTCGGATGCCCA
66 ACGAGCTCGGATGCCCA
56602476 AATATCCTAG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCCAGTTACATCTCT
Found at i:56602462 original size:46 final size:45
Alignment explanation
Indices: 56602294--56602469 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
56602284 TGAAACCCGC
* * * * **
56602294 CCATAAGCGAACTTGGACTCAACTCAATGAGATCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGAATTCGCAT
* * * *
56602340 CCACAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGCCCAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATTCGCA--T
* ***
56602386 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGA-ATTCGCAT
56602433 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
56602470 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 62 0.59
47 32 0.30
49 5 0.05
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATTCGCAT
Found at i:56602488 original size:46 final size:44
Alignment explanation
Indices: 56602345--56602488 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 44
56602335 CGCATCCACA
*
56602345 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
56602394 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
56602437 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
56602484 AGTGA
1 AGTGA
56602489 CATGTCACTT
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 33 0.42
47 28 0.36
48 4 0.05
49 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:56610408 original size:52 final size:48
Alignment explanation
Indices: 56610305--56610561 Score: 352
Period size: 48 Copynumber: 5.2 Consensus size: 48
56610295 ATTGTATAAT
*
56610305 TTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGC
1 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGC
* * *
56610353 TTTACCACATATACATATCTCATATATATATATTTCACATTAACCATTCCGC
1 TTTACCACATATACATATCTC----ATACATATTTCACATTAGCCATTCGGC
* * *
56610405 TTTACCACATATACATATCTCATATATATATATTTCGCATTAGCCATTCGGA
1 TTTACCACATATACATATCTC----ATACATATTTCACATTAGCCATTCGGC
* *
56610457 TTTACCACATATACATATCTCATACATATTTCGCATTAGCCATTCGGA
1 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGC
*
56610505 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTTGGC
1 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGC
56610553 TTTACCACA
1 TTTACCACA
56610562 CACATATATA
Statistics
Matches: 193, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
48 101 0.52
52 92 0.48
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGC
Found at i:56610533 original size:104 final size:101
Alignment explanation
Indices: 56610305--56610561 Score: 307
Period size: 100 Copynumber: 2.6 Consensus size: 101
56610295 ATTGTATAAT
* *
56610305 TTTACCACATATACATATCTC----ATACATATTTCACACTAGCCATTCGGCTTTACCACATATA
1 TTTACCACATATACATATCTCATATATATATATTTCACACTAGCCATTCGGATTTACCACATATA
* *
56610366 CATATCTCATATATATATATTTCACATTAACCATTCCGC
66 CATATCTC--A-ATACATATTTCACATTAACCATTCCGA
* *
56610405 TTTACCACATATACATATCTCATATATATATATTTCGCATTAGCCATTCGGATTTACCACATATA
1 TTTACCACATATACATATCTCATATATATATATTTCACACTAGCCATTCGGATTTACCACATATA
* * *
56610470 CATATCTC-ATACATATTTCGCATTAGCCATTCGGA
66 CATATCTCAATACATATTTCACATTAACCATTCCGA
* * * *
56610505 TTTACCACATATACATATCTC----ATACATATTTCACATTAGCCATTTGGCTTTACCACA
1 TTTACCACATATACATATCTCATATATATATATTTCACACTAGCCATTCGGATTTACCACA
56610562 CACATATATA
Statistics
Matches: 140, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
96 32 0.23
100 64 0.46
104 44 0.31
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (101 bp):
TTTACCACATATACATATCTCATATATATATATTTCACACTAGCCATTCGGATTTACCACATATA
CATATCTCAATACATATTTCACATTAACCATTCCGA
Found at i:56613966 original size:40 final size:40
Alignment explanation
Indices: 56613922--56614002 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
56613912 GAATACACAT
* *
56613922 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACCTAGCCCGGATATAA
*
56613962 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACCTAGCCCGGATATAA
56614002 C
1 C
56614003 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACCTAGCCCGGATATAA
Found at i:56637045 original size:21 final size:21
Alignment explanation
Indices: 56637021--56637060 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56637011 CATTTGTACA
* *
56637021 TATATCATATTTTCTCAAACT
1 TATATCATATGTTCACAAACT
56637042 TATATCATATGTTCACAAA
1 TATATCATATGTTCACAAA
56637061 AGTACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (21 bp):
TATATCATATGTTCACAAACT
Found at i:56640001 original size:21 final size:20
Alignment explanation
Indices: 56639955--56639993 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56639945 AGAGACTAAA
*
56639955 ATGAAAAGTTATAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
56639975 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTATAAAATTT
56639994 TATGGAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:56645328 original size:46 final size:44
Alignment explanation
Indices: 56645274--56645408 Score: 161
Period size: 46 Copynumber: 3.1 Consensus size: 44
56645264 ATTGAGACGA
* * *
56645274 GTGCCAGTGTAAGATATATCTGGGACATGCATCAGCCT-CGAGAT
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAG-CTACAAGAT
56645318 GTAAGCCAGTGTAAGACATGT-TCGGGACATGCATCAGCTACAAGAT
1 GT--GCCAGTGTAAGACATGTCT-GGGACATGCATCAGCTACAAGAT
* *
56645364 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-AC-AGAT
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACAAGAT
56645406 GTG
1 GTG
56645409 TGAGAACCAG
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
42 7 0.09
43 2 0.02
44 32 0.40
45 4 0.05
46 36 0.44
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (44 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACAAGAT
Found at i:56649202 original size:15 final size:16
Alignment explanation
Indices: 56649183--56649224 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
56649173 ATTTTCTTGT
56649183 TTTGGATTTCTTTATA
1 TTTGGATTTCTTTATA
56649199 -TTGGA-TT-TTTATA
1 TTTGGATTTCTTTATA
56649212 TTCTGGATTTCTT
1 TT-TGGATTTCTT
56649225 CGTTATGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 9 0.41
16 2 0.09
17 2 0.09
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (16 bp):
TTTGGATTTCTTTATA
Found at i:56649202 original size:30 final size:30
Alignment explanation
Indices: 56649168--56649224 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56649158 CGGTATCGTG
* *
56649168 ATTGGATTTTCT-TGTTTTGGATTTCTTTAT
1 ATTGGATTTT-TATATTCTGGATTTCTTTAT
56649198 ATTGGATTTTTATATTCTGGATTTCTT
1 ATTGGATTTTTATATTCTGGATTTCTT
56649225 CGTTATGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.61
Consensus pattern (30 bp):
ATTGGATTTTTATATTCTGGATTTCTTTAT
Found at i:56651935 original size:46 final size:44
Alignment explanation
Indices: 56651840--56652016 Score: 171
Period size: 46 Copynumber: 3.9 Consensus size: 44
56651830 ATGAAAGCCT
* *
56651840 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCCA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGA--TGTGCCA
* * *
56651888 GTGTAAGATATGTCTGGGACATGCATCGGCCTCGAGATGTCAACCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGT--GCCA
* * ** *
56651934 GTATAAGACATGTCCGGGACATGCATC-TAATACGAGATGTGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGATGTGCCA
*
56651978 GTGTAAGACATGCCTGGGACATGCATCGGCA-CG-GATGTG
1 GTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGTG
56652017 TGAGAGCCGG
Statistics
Matches: 107, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
42 6 0.06
43 2 0.02
44 28 0.26
45 2 0.02
46 48 0.45
47 13 0.12
48 8 0.07
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (44 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGTGCCA
Found at i:56666821 original size:27 final size:27
Alignment explanation
Indices: 56666329--56666848 Score: 664
Period size: 27 Copynumber: 19.3 Consensus size: 27
56666319 TAGTTTACCA
* *
56666329 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56666356 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666383 AATTACTGAAATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
56666410 AATTACCGAAATACCATTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666437 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666464 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
56666491 AATTAACGACATACCCCTCTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56666518 AATTACCGAAATGCCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56666545 AATTACCGAAATACCCCTGTAGAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* ** *
56666572 AATAACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666599 AATTATCGAATTACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
56666626 AATTACTAAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56666653 AATTACCGAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
56666680 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
56666707 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666734 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
56666761 AATTACCTACATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56666788 AAATACCGAAATGCCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
56666815 AATTACC-AAGATACCATTGTGGGGTAA
1 AATTACCGAA-ATACCCCTGTAGGGTAG
56666842 AATTACC
1 AATTACC
56666849 ATTTTGCCCC
Statistics
Matches: 420, Mismatches: 72, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
26 2 0.00
27 418 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:56667154 original size:20 final size:20
Alignment explanation
Indices: 56667131--56667177 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
56667121 CCAAAGGTTG
56667131 TGTGCCGTTACTGTGGGCTT
1 TGTGCCGTTACTGTGGGCTT
56667151 TGTGCCGTTACTGTGGGCTT
1 TGTGCCGTTACTGTGGGCTT
*
56667171 CGTGCCG
1 TGTGCCG
56667178 ATTATAGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.04, C:0.23, G:0.36, T:0.36
Consensus pattern (20 bp):
TGTGCCGTTACTGTGGGCTT
Found at i:56667221 original size:22 final size:22
Alignment explanation
Indices: 56667196--56667253 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
56667186 CCCATTATCA
*
56667196 ATGGCTCTGTGCCATCCTAAAT
1 ATGGCTTTGTGCCATCCTAAAT
* * *
56667218 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCATCCTAAAT
56667240 ATGGCTTTGTGCCA
1 ATGGCTTTGTGCCA
56667254 AACGTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.36
Consensus pattern (22 bp):
ATGGCTTTGTGCCATCCTAAAT
Found at i:56667375 original size:32 final size:32
Alignment explanation
Indices: 56667339--56667399 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
56667329 GTGCTAGTTA
*
56667339 TATTACCGTCA-CTGATGGCTATGTGCCAAAGT
1 TATTACAGTCATC-GATGGCTATGTGCCAAAGT
* *
56667371 TATTACAGTTATCGATGGCTTTGTGCCAA
1 TATTACAGTCATCGATGGCTATGTGCCAA
56667400 GTATTCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (32 bp):
TATTACAGTCATCGATGGCTATGTGCCAAAGT
Found at i:56669393 original size:40 final size:40
Alignment explanation
Indices: 56669344--56669472 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
56669334 CAGAATTTAA
* *
56669344 CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56669384 CCGGTTATAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56669424 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56669465 CCGGATAT
1 CCGGATAT
56669473 CATTCGAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
39 4 0.05
40 42 0.55
41 27 0.36
42 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56671929 original size:13 final size:13
Alignment explanation
Indices: 56671911--56671935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56671901 TAATGGTATA
56671911 TTGAATCCATGAT
1 TTGAATCCATGAT
56671924 TTGAATCCATGA
1 TTGAATCCATGA
56671936 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:56673840 original size:25 final size:25
Alignment explanation
Indices: 56673812--56673890 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
56673802 CTAATGGCCG
56673812 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * * *
56673837 ATGTGAT-AAGGCCGAATG-GCA-A-
1 ATGTGATGAATG-TGAAAGTGTATAT
56673859 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
56673884 ATGTGAT
1 ATGTGAT
56673891 AAGGCCTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.27
23 6 0.15
24 6 0.15
25 18 0.44
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:56673844 original size:47 final size:47
Alignment explanation
Indices: 56673790--56673940 Score: 266
Period size: 47 Copynumber: 3.2 Consensus size: 47
56673780 AGATATGTAC
56673790 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* **
56673837 ATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
56673884 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGGGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
56673931 ATGTGATAAG
1 ATGTGATAAG
56673941 TCCCGAAGGA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:56681029 original size:52 final size:52
Alignment explanation
Indices: 56680973--56681077 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
56680963 ACATACCTTC
*
56680973 GGAATTTAACCGGATATAGCTACTCGCTCAACTGCCTTCGAGACATAGCCCG
1 GGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGAGACATAGCCCG
*
56681025 GGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCG
1 GGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGAGACATAGCCCG
56681077 G
1 G
56681078 TTATAGTAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (52 bp):
GGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGAGACATAGCCCG
Found at i:56681083 original size:40 final size:40
Alignment explanation
Indices: 56681034--56681241 Score: 253
Period size: 40 Copynumber: 5.2 Consensus size: 40
56681024 GGGAATTTAA
* *
56681034 CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56681074 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56681114 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56681153 CC-GAAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56681193 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56681234 CCGGATAT
1 CCGGATAT
56681242 CATTCGAATA
Statistics
Matches: 144, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 4 0.03
39 30 0.21
40 77 0.53
41 30 0.21
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56681174 original size:79 final size:78
Alignment explanation
Indices: 56681030--56681241 Score: 241
Period size: 79 Copynumber: 2.7 Consensus size: 78
56681020 GCCCGGGAAT
* * **
56681030 TTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACA
1 TTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACA
56681095 AATGCCTTCGGGA-C
65 AATGCCTTC-GGATC
* *
56681109 TTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGAA-ATTAGTAACTCGCA
1 TTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCA
56681172 CAAATGCCTTCGGATC
63 CAAATGCCTTCGGATC
* * * *
56681188 TTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 TTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGAATAT
56681242 CATTCGAATA
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
78 4 0.04
79 52 0.46
80 44 0.39
81 11 0.10
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (78 bp):
TTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAA
ATGCCTTCGGATC
Found at i:56693415 original size:18 final size:18
Alignment explanation
Indices: 56693392--56693426 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56693382 TCAATTTGGC
56693392 TATGATGAAT-TATATGTT
1 TATGAT-AATGTATATGTT
56693410 TATGATAATGTATATGT
1 TATGATAATGTATATGT
56693427 GATAGTGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (18 bp):
TATGATAATGTATATGTT
Found at i:56701146 original size:25 final size:25
Alignment explanation
Indices: 56701118--56701181 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
56701108 CTGTTATTGA
* * *
56701118 TAGTATATCCTGAAACTACTATAGG
1 TAGTACATACTGAAACAACTATAGG
* *
56701143 TAGTACATACTGAGACAACTATAGA
1 TAGTACATACTGAAACAACTATAGG
*
56701168 TAG-ACTTACTGAAA
1 TAGTACATACTGAAA
56701182 ACACCCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (25 bp):
TAGTACATACTGAAACAACTATAGG
Found at i:56717733 original size:39 final size:39
Alignment explanation
Indices: 56717681--56717982 Score: 433
Period size: 39 Copynumber: 7.7 Consensus size: 39
56717671 TGTGTGAGAT
*
56717681 TTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717720 TTATATCCAGGCTAAGTCCCGAAGGTATTGGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717759 TTATGTCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717798 TTATATCCAGGCTAAGTCCCGAAGGTATTGGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717837 TTATGTCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717876 TTATATCCAGGCTAAGTCCCGAAGGTATTGGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
56717915 TTATGTCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
56717954 TTATATCCGGGCTAAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
56717983 TGTGTTGGAA
Statistics
Matches: 226, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 226 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:56717782 original size:78 final size:78
Alignment explanation
Indices: 56717689--56717978 Score: 571
Period size: 78 Copynumber: 3.7 Consensus size: 78
56717679 ATTTATATCC
56717689 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
1 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
56717754 TGGTGTTATGTCT
66 TGGTGTTATGTCT
56717767 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
1 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
56717832 TGGTGTTATGTCT
66 TGGTGTTATGTCT
56717845 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
1 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
56717910 TGGTGTTATGTCT
66 TGGTGTTATGTCT
*
56717923 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGG
1 GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGG
56717979 CATTTGTGTT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 211 1.00
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (78 bp):
GGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCAGGCTAAGTCCCGAAGGTATTGGTGC
TGGTGTTATGTCT
Found at i:56725073 original size:42 final size:42
Alignment explanation
Indices: 56724962--56725112 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 42
56724952 TACCACATCA
* *** *
56724962 ATGCCATATTCCAGATATGGTCTTACATGGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACATAAAATCTCATATCG
* * * *
56725004 ATACCAATAGCCCAGCTATGGCCTTACATAAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATAAAATCTCATATCG
* *
56725047 ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACATAAAATCTCAT-ATCG
*
56725089 ATGCCATATCCTAGATATGGTCTT
1 ATGCCATATCCCAGATATGGTCTT
56725113 CCACATAGTC
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 56 0.62
43 35 0.38
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATAAAATCTCATATCG
Found at i:56731673 original size:32 final size:32
Alignment explanation
Indices: 56731613--56731677 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
56731603 GAAGAGAAAT
56731613 TTAGAGTAATACGTGACTGCTTGAAGGCCACC
1 TTAGAGTAATACGTGACTGCTTGAAGGCCACC
*
56731645 TTAGAGTAATTCGTGACTGCTTGAAGGCCACC
1 TTAGAGTAATACGTGACTGCTTGAAGGCCACC
56731677 T
1 T
56731678 CAAATTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (32 bp):
TTAGAGTAATACGTGACTGCTTGAAGGCCACC
Found at i:56733495 original size:46 final size:47
Alignment explanation
Indices: 56733346--56733519 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 47
56733336 TCACTTGTGT
* * * *
56733346 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACAT-A
* * * *
56733392 GAGCCAATGTAAGACCATGTTTGGGACATGGCATCAACATCGAGACA-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGACATA
* * *
56733440 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGACCTCGAGACATA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACATA
56733487 -AGCCAGTGTAAGACATGTCTGGGACATGCATCG
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCG
56733520 GCACGGTTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
46 57 0.53
47 28 0.26
48 19 0.18
49 1 0.01
50 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (47 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACATA
Found at i:56738513 original size:39 final size:41
Alignment explanation
Indices: 56738409--56738592 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
56738399 TTGAATGATG
*
56738409 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
* *
56738448 TCCGGACTAAGAT-CCGGAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
56738488 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
56738527 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
56738567 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56738593 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
39 52 0.42
40 61 0.49
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:56738548 original size:79 final size:81
Alignment explanation
Indices: 56738409--56738592 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
56738399 TTGAATGATG
*
56738409 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGGAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
56738472 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
56738487 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
56738548 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
56738567 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56738593 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 11 0.12
79 57 0.63
80 23 0.25
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:56738614 original size:79 final size:79
Alignment explanation
Indices: 56738465--56738625 Score: 186
Period size: 79 Copynumber: 2.0 Consensus size: 79
56738455 TAAGATCCGG
* ** *
56738465 AGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 AGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCC
*
56738530 GGGTTAAGTCCCGA
66 GGGTTAAATCCCGA
* *
56738544 AGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTAT
1 AGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAA
*
56738606 ATCC-GGTTAAATTCCGA
62 ATCCGGGTTAAATCCCGA
56738623 AGG
1 AGG
56738626 TACGTGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 42 0.60
80 25 0.36
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
AGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCC
GGGTTAAATCCCGA
Found at i:56741975 original size:87 final size:87
Alignment explanation
Indices: 56741829--56742001 Score: 310
Period size: 87 Copynumber: 2.0 Consensus size: 87
56741819 GTATGTACTT
*
56741829 GATGATAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGGTTGTGAATACCCGGATGTTTT
1 GATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGGTTGTGAATACCCGGATGTTTT
56741894 TCCTGAAGAATTACCGGGTTTG
66 TCCTGAAGAATTACCGGGTTTG
* *
56741916 GATGACAAAGAATTAGACAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGATGTTTT
1 GATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGGTTGTGAATACCCGGATGTTTT
*
56741981 TCCTGAAGGATTACCGGGTTT
66 TCCTGAAGAATTACCGGGTTT
56742002 ACCACCTGTT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (87 bp):
GATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGGTTGTGAATACCCGGATGTTTT
TCCTGAAGAATTACCGGGTTTG
Found at i:56742359 original size:56 final size:56
Alignment explanation
Indices: 56742268--56742377 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
56742258 TATCCGTTGT
* *
56742268 CGCGCATCGATGATTTGTTTGACCAACTGAAGGGAGCCTCAGTGTTCTCAAAAAAC
1 CGCGCATCGATGATTTGTTCGACCAACTGAAGGGAGCCTCAATGTTCTCAAAAAAC
*
56742324 CGCGTATCGATGATTTGTTCGACCAACTGAAGGGAGCCTCAATGTTCTCAAAAA
1 CGCGCATCGATGATTTGTTCGACCAACTGAAGGGAGCCTCAATGTTCTCAAAAA
56742378 TAGATTTGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (56 bp):
CGCGCATCGATGATTTGTTCGACCAACTGAAGGGAGCCTCAATGTTCTCAAAAAAC
Found at i:56742746 original size:84 final size:84
Alignment explanation
Indices: 56742605--56742770 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 84
56742595 AGATGAGACC
* *
56742605 GAACATGCTGAGCACCTGAGATTAGTGTTGCAAATTTTGCGGGATAAGCAGTTATATGCTAAGTT
1 GAACATGCTGAGCACCTGAGACTAGTGTTGCAAATTTTGCGGGATAAGCAGTTATATGCCAAGTT
56742670 CAGTAAGTGTGAGTTCTCT
66 CAGTAAGTGTGAGTTCTCT
* *
56742689 GAACATGCTGAGCATCTGAGGCTAGTGTTGCAAATTTTGCGGGATAAGCAGTTATATGCCAAGTT
1 GAACATGCTGAGCACCTGAGACTAGTGTTGCAAATTTTGCGGGATAAGCAGTTATATGCCAAGTT
56742754 CAGTAAGTGTGAGTTCT
66 CAGTAAGTGTGAGTTCT
56742771 GGTTAAGAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (84 bp):
GAACATGCTGAGCACCTGAGACTAGTGTTGCAAATTTTGCGGGATAAGCAGTTATATGCCAAGTT
CAGTAAGTGTGAGTTCTCT
Found at i:56743159 original size:196 final size:197
Alignment explanation
Indices: 56742819--56743213 Score: 756
Period size: 196 Copynumber: 2.0 Consensus size: 197
56742809 GCATCGGGTA
56742819 TTCGAGCTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTACCGAA
1 TTCGAGCTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTACCGAA
*
56742884 GTTCGGAGCTTCCTGGGGCTCGCCGGTTATTACCGACGATTTGTAAAAGGTTTCTCGATGATAGC
66 GTTCGGAGCTTCCTGGGACTCGCCGGTTATTACCGACGATTTGTAAAAGGTTTCTCGATGATAGC
56742949 CACACCAATGACGAAGCTACTTCAAAAGGATGTTAAGTTCGAATGGACGGAGAAATGTCAGAAAA
131 CACACCAATGACGAAGCTACTTCAAAAGGATGTTAAGTTCGAATGGACGGAGAAATGTCAGAAAA
56743014 GT
196 GT
56743016 TTCGA-CTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTACCGAA
1 TTCGAGCTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTACCGAA
*
56743080 GTTCGGAGCTTCCTGGGACTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGC
66 GTTCGGAGCTTCCTGGGACTCGCCGGTTATTACCGACGATTTGTAAAAGGTTTCTCGATGATAGC
*
56743145 CACACCAATGACGAAGCTACTTCAAATGGATGTTAAGTTCGAATGGACGGAGAAATGTCAGAAAA
131 CACACCAATGACGAAGCTACTTCAAAAGGATGTTAAGTTCGAATGGACGGAGAAATGTCAGAAAA
56743210 GT
196 GT
56743212 TT
1 TT
56743214 TGATCAACTA
Statistics
Matches: 195, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
196 190 0.97
197 5 0.03
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (197 bp):
TTCGAGCTGACCCGAGCAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTACCGAA
GTTCGGAGCTTCCTGGGACTCGCCGGTTATTACCGACGATTTGTAAAAGGTTTCTCGATGATAGC
CACACCAATGACGAAGCTACTTCAAAAGGATGTTAAGTTCGAATGGACGGAGAAATGTCAGAAAA
GT
Found at i:56744096 original size:82 final size:81
Alignment explanation
Indices: 56743953--56744110 Score: 307
Period size: 82 Copynumber: 1.9 Consensus size: 81
56743943 TTGAAACGTC
56743953 GGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAA
1 GGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAA
56744018 CAAGTGAAAGCAGATT
66 CAAGTGAAAGCAGATT
56744034 GGTTTTAGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCA
1 GGTTTT-GGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCA
56744099 ACAAGTGAAAGC
65 ACAAGTGAAAGC
56744111 GGAACATCAA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 6 0.08
82 70 0.92
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (81 bp):
GGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAA
CAAGTGAAAGCAGATT
Found at i:56744481 original size:85 final size:85
Alignment explanation
Indices: 56744338--56744508 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 85
56744328 TTCACCTCAC
56744338 GATTTTGGAAGAAATTGCAAGAAGCTTTGGGTACCAAGCTGCACTTTAACACCACTTTTCACCCC
1 GATTTTGGAAGAAATTGCAAGAAGCTTTGGGTACCAAGCTGCACTTTAACACCACTTTTCACCCC
56744403 CAAACCGATGGTCAATCCGA
66 CAAACCGATGGTCAATCCGA
**
56744423 GATTTTGGAAGAAATTGCAAGAAGCTTTGGGTACCAAGCTGCA-TTTAAGCACTGCTTTTCACCC
1 GATTTTGGAAGAAATTGCAAGAAGCTTTGGGTACCAAGCTGCACTTTAA-CACCACTTTTCACCC
56744487 CCAAACCGATGGTCAATCCGA
65 CCAAACCGATGGTCAATCCGA
56744508 G
1 G
56744509 TGGATAATTC
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 5 0.06
85 78 0.94
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (85 bp):
GATTTTGGAAGAAATTGCAAGAAGCTTTGGGTACCAAGCTGCACTTTAACACCACTTTTCACCCC
CAAACCGATGGTCAATCCGA
Found at i:56744908 original size:81 final size:81
Alignment explanation
Indices: 56744773--56744933 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
56744763 AAGTCTGAAG
*
56744773 GCAGCCACAGATCGTCAGAAATCGTATGCGGACTTGAAACGAAAGGACATTGAATATCAGGTGGG
1 GCAGCCACAGATCGTCAAAAATCGTATGCGGACTTGAAACGAAAGGACATTGAATATCAGGTGGG
56744838 AGATAAAGTGTTCCTA
66 AGATAAAGTGTTCCTA
*
56744854 GCAGCCACAGATCGTCAAAAATCGTATGCGGATTTGAAACGAAAGGACATTGAATATCAGGTGGG
1 GCAGCCACAGATCGTCAAAAATCGTATGCGGACTTGAAACGAAAGGACATTGAATATCAGGTGGG
56744919 AGATAAAGTGTTCCT
66 AGATAAAGTGTTCCT
56744934 TAAAGTTTCA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (81 bp):
GCAGCCACAGATCGTCAAAAATCGTATGCGGACTTGAAACGAAAGGACATTGAATATCAGGTGGG
AGATAAAGTGTTCCTA
Found at i:56746506 original size:39 final size:40
Alignment explanation
Indices: 56746411--56746633 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
56746401 TTGAATGATG
*
56746411 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
56746449 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
56746490 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
56746529 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
56746568 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
56746607 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
56746634 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:56746597 original size:79 final size:81
Alignment explanation
Indices: 56746411--56746633 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
56746401 TTGAATGATG
* * *
56746411 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
56746473 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
56746490 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
56746551 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
56746568 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
56746632 TG
66 TG
56746634 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:56746655 original size:79 final size:79
Alignment explanation
Indices: 56746411--56746666 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
56746401 TTGAATGATG
* * * *
56746411 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
56746472 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
56746490 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
56746554 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
56746568 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
56746631 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
56746648 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
56746667 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:56749662 original size:11 final size:11
Alignment explanation
Indices: 56749646--56749674 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
56749636 GCCTGGACTG
56749646 ATAATCCTGAT
1 ATAATCCTGAT
56749657 ATAATCCTGAT
1 ATAATCCTGAT
56749668 ATAATCC
1 ATAATCC
56749675 CTCTCGAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (11 bp):
ATAATCCTGAT
Done.