Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 62 of 279
Found at i:20805878 original size:29 final size:28
Alignment explanation
Indices: 20805834--20805888 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
20805824 CCTTCACCCC
*
20805834 AACCCTTAAACCATAAATC-ATAAACCAT
1 AACCCCTAAACCAT-AATCTATAAACCAT
20805862 AACCCCTAAACCCATAATCTATAAACC
1 AACCCCTAAA-CCATAATCTATAAACC
20805889 TTAAACTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (28 bp):
AACCCCTAAACCATAATCTATAAACCAT
Found at i:20805937 original size:14 final size:14
Alignment explanation
Indices: 20805840--20805956 Score: 74
Period size: 14 Copynumber: 8.2 Consensus size: 14
20805830 CCCCAACCCT
* *
20805840 TAAACCATAAATCA
1 TAAACCCTAAACCA
* * *
20805854 TAAACCATAACCCC
1 TAAACCCTAAACCA
* *
20805868 TAAACCCATAATCTA
1 TAAACCC-TAAACCA
* *
20805883 TAAACCTTAAACTA
1 TAAACCCTAAACCA
*
20805897 GT-AACTCCTAAACCT
1 -TAAAC-CCTAAACCA
*
20805912 TAAACCCCAAACCA
1 TAAACCCTAAACCA
* *
20805926 TATACTCTAAACCA
1 TAAACCCTAAACCA
*
20805940 TAAACCCTAAACTA
1 TAAACCCTAAACCA
20805954 TAA
1 TAA
20805957 TGATAATTAA
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
14 59 0.75
15 20 0.25
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:20806336 original size:40 final size:40
Alignment explanation
Indices: 20806261--20806346 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
20806251 TGTTTGTGGG
* ** * *
20806261 GTTTTTCAAAAAGCGCCACTAATGCTTTATTTATAGTAGC
1 GTTTTTCAAAAACCGCCACTAATGCTCGATCTATAGCAGC
* * *
20806301 GTTTTTCAAAAACCGCCGCTACTGCTCGATCTATAGCGGC
1 GTTTTTCAAAAACCGCCACTAATGCTCGATCTATAGCAGC
20806341 GTTTTT
1 GTTTTT
20806347 TGAAAAACAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (40 bp):
GTTTTTCAAAAACCGCCACTAATGCTCGATCTATAGCAGC
Found at i:20806491 original size:40 final size:40
Alignment explanation
Indices: 20806447--20806525 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
20806437 ATAGTTGACC
* *
20806447 TATAGC-AGCGTTTTTCAAAAAGCGCTGCTAATGCTCGATT
1 TATAGCGA-CGTTTTTCAAAAAGCACCGCTAATGCTCGATT
*
20806487 TATAGCGACGTTTTTCAAAAAGCACCGTTAATGCTCGAT
1 TATAGCGACGTTTTTCAAAAAGCACCGCTAATGCTCGAT
20806526 CTACAGTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (40 bp):
TATAGCGACGTTTTTCAAAAAGCACCGCTAATGCTCGATT
Found at i:20806541 original size:40 final size:40
Alignment explanation
Indices: 20806457--20806541 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
20806447 TATAGCAGCG
* * * * *
20806457 TTTTTCAAAAAGCGCTGCTAATGCTCGATTTATAGCGACG
1 TTTTTCAAAAAGCACCGCTAATGCTCGATCTACAGCGACA
* * *
20806497 TTTTTCAAAAAGCACCGTTAATGCTCGATCTACAGTGGCA
1 TTTTTCAAAAAGCACCGCTAATGCTCGATCTACAGCGACA
20806537 TTTTT
1 TTTTT
20806542 TTATCTAAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (40 bp):
TTTTTCAAAAAGCACCGCTAATGCTCGATCTACAGCGACA
Found at i:20811902 original size:44 final size:41
Alignment explanation
Indices: 20811849--20811999 Score: 135
Period size: 43 Copynumber: 3.5 Consensus size: 41
20811839 TCTGATATGC
* *
20811849 GATTTCGTGTAAGACCACGTTTAAGACATTGGCATCGATTT
1 GATTTCATGTAAGACCACGTCTAAGACATTGGCATCGATTT
* * * *
20811890 GAGATTTACGTGTAAGACCATGTCTGAGAC-TTCAGCATCGTATTT
1 --GATTT-CATGTAAGACCACGTCTAAGACATT-GGCATCG-ATTT
* *
20811935 GATTTCATGTAAGACC-CTGTCTAGGACAGTGGCATCGATATTT
1 GATTTCATGTAAGACCAC-GTCTAAGACATTGGCATCG--ATTT
*
20811978 GATTACATGTAAGACCACGTCT
1 GATTTCATGTAAGACCACGTCT
20812000 GGGACGTTGC
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
42 23 0.26
43 37 0.41
44 26 0.29
45 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (41 bp):
GATTTCATGTAAGACCACGTCTAAGACATTGGCATCGATTT
Found at i:20816727 original size:57 final size:57
Alignment explanation
Indices: 20816639--20816749 Score: 222
Period size: 57 Copynumber: 1.9 Consensus size: 57
20816629 GGTAGTATGA
20816639 AAATGTATAATGATCTGAAACATCATTACTGGTGGTCTGGAATGAAAAGAGATACGG
1 AAATGTATAATGATCTGAAACATCATTACTGGTGGTCTGGAATGAAAAGAGATACGG
20816696 AAATGTATAATGATCTGAAACATCATTACTGGTGGTCTGGAATGAAAAGAGATA
1 AAATGTATAATGATCTGAAACATCATTACTGGTGGTCTGGAATGAAAAGAGATA
20816750 TCTCTGACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (57 bp):
AAATGTATAATGATCTGAAACATCATTACTGGTGGTCTGGAATGAAAAGAGATACGG
Found at i:20817963 original size:170 final size:170
Alignment explanation
Indices: 20817506--20818063 Score: 728
Period size: 170 Copynumber: 3.2 Consensus size: 170
20817496 AAGTAGCAAG
* * *
20817506 AGTCTTATCTTTCTAAGGTAGCAAGAAAG-TAGACTGAAGATCTTATCTCCGTGAAGTTGCAATG
1 AGTCTTATCTTTCTGAGGTAGCAAGAAAGCT-GACTGAAGATCTTATCTCCTTGAAGTTGCAGTG
* * * *
20817570 GAGTAGATCAAAGATGGTGAATCTTATCTCCATGTATCGAAAATGGAG-TAGATTT-TACCACCA
65 GAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCT-GATTTAAACCACCA
* * *
20817633 GCCTTATCTCTTTGAGGTAGCAAGAGAGTAGGTTGAAGAATG
129 GCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAATA
*
20817675 AGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGATTGATGATTGAAGATCTTATCTCCTTGAAGTT
1 AGTCTTATCTTTCTGAGGTAGCAAGAAAGC-------TGACTGAAGATCTTATCTCCTTGAAGTT
* *
20817740 GCAGCGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGACAATGGAGCTGATTTAAAC
59 GCAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCTGATTTAAAC
* * *
20817805 CACCAACCTTATCTCTCTGAGGTAGAAAGAGAGCATGTTGAAGAATA
124 CACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAATA
*
20817852 AGTCTTATCTTTCTGAGGTAGAAAGAAAGCTGACTGAAGATCTTATCTCCTTGAAGTTGCAGTGG
1 AGTCTTATCTTTCTGAGGTAGCAAGAAAGCTGACTGAAGATCTTATCTCCTTGAAGTTGCAGTGG
** * *
20817917 AGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGGAATGGAGCAGATTTAAGCCACCAGC
66 AGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCTGATTTAAACCACCAGC
* * *
20817982 CTTATCTCTCTGCGATAGCAAGAGAGCAGGTTGAAGAATTG
131 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAA-TA
* * * **
20818023 AGTTTTATC-TTCTTGAGGAAGCAAGGAAGCAAACTGAAGAT
1 AGTCTTATCTTTC-TGAGGTAGCAAGAAAGCTGACTGAAGAT
20818064 TAAAGATTTT
Statistics
Matches: 342, Mismatches: 35, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
169 28 0.08
170 130 0.38
171 32 0.09
176 78 0.23
177 74 0.22
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (170 bp):
AGTCTTATCTTTCTGAGGTAGCAAGAAAGCTGACTGAAGATCTTATCTCCTTGAAGTTGCAGTGG
AGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGAAAATGGAGCTGATTTAAACCACCAGC
CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAATA
Found at i:20818187 original size:175 final size:177
Alignment explanation
Indices: 20817574--20818234 Score: 416
Period size: 170 Copynumber: 3.8 Consensus size: 177
20817564 GCAATGGAGT
* * * * *
20817574 AGATCAAAGATGGTGAATCTTATCTCCATGTATCGAA--AATGGAGTAGATTTTA-CCACCAGCC
1 AGATCGAAGATGGCGAATCTTATCTCCATGTAT--AAGCAATGGAGCAGATTTAAGCCACCAGAC
* * * * * * * * *
20817636 TTATCTCTTTGAGGTAGCAAGAGAGTAGGTTGAAG-AA-TG-AGTCTTATCTTTCTGAGGTAGCA
64 TTATCTCTCTGCGATAGCAAGAAAGCAGGTTG--GCAATTGTAGTCTCATCTTCCTGAAGAAGCA
* * * * * * * ** * *
20817698 AGAAAGCAGATTGATGATTGAAGATCTTATCTCCTTGAAGTTGCAGCGGAGC
127 AGGAAGCAAACTGAAGATTAAAGATTTTATCTCCCT-AAGCAGTAGCGAAGC
* * *
20817750 AGATCGAAGATGGCGAATCTTATCTCCATGTAT-CGACAATGGAGCTGATTTAAACCACCA-ACC
1 AGATCGAAGATGGCGAATCTTATCTCCATGTATAAG-CAATGGAGCAGATTTAAGCCACCAGA-C
* * * * * * * * *
20817813 TTATCTCTCTGAGGTAGAAAGAGAGCATGTTGAAG-AA-T-AAGTCTTATCTTTCTG-AG--G-T
64 TTATCTCTCTGCGATAGCAAGAAAGCAGGTTG--GCAATTGTAGTCTCATCTTCCTGAAGAAGCA
* * * * * ** * * *
20817871 AGAAAG-AAAGCT---GACTGAAGATCTTATCTCCTTGAAGTTGCAGTGGAGC
127 AGGAAGCAAA-CTGAAGATTAAAGATTTTATCTCCCT-AAGCAGTAGCGAAGC
** * *
20817920 AGATCGAAGATGGCGAATCTTATCTCCATGTATCGGGAATGGAGCAGATTTAAGCCACCAGCCTT
1 AGATCGAAGATGGCGAATCTTATCTCCATGTATAAGCAATGGAGCAGATTTAAGCCACCAGACTT
* * * * *
20817985 ATCTCTCTGCGATAGCAAGAGAGCAGGTTGAAG-AATTG-AGTTTTATCTTCTTGAGGAAGCAAG
66 ATCTCTCTGCGATAGCAAGAAAGCAGGTTG--GCAATTGTAGTCTCATCTTCCTGAAGAAGCAAG
20818048 GAAGCAAACTGAAGATTAAAGATTTTATCTCCCTAAGCAGTAGCGAAGC
129 GAAGCAAACTGAAGATTAAAGATTTTATCTCCCTAAGCAGTAGCGAAGC
* * * * * *
20818097 AGATTGAA-A-GGCGGATCTTATGTCCATGTATAAGCAATGGAGCAGATTTTAGCCACTAGATTT
1 AGATCGAAGATGGCGAATCTTATCTCCATGTATAAGCAATGGAGCAGATTTAAGCCACCAGACTT
* * * * *
20818160 ATCTTTTTGAGGA-AGTAAGAAAGCAGGTTGGCAATTGTAGTCTCATCTTCCTGAAGTAGCAAGG
66 ATCTCTCTG-CGATAGCAAGAAAGCAGGTTGGCAATTGTAGTCTCATCTTCCTGAAGAAGCAAGG
*
20818224 AAGCAGACTGA
130 AAGCAAACTGA
20818235 TTGTTATCTC
Statistics
Matches: 401, Mismatches: 62, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
170 123 0.31
171 14 0.03
172 3 0.01
173 8 0.02
174 7 0.02
175 105 0.26
176 51 0.13
177 73 0.18
178 17 0.04
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (177 bp):
AGATCGAAGATGGCGAATCTTATCTCCATGTATAAGCAATGGAGCAGATTTAAGCCACCAGACTT
ATCTCTCTGCGATAGCAAGAAAGCAGGTTGGCAATTGTAGTCTCATCTTCCTGAAGAAGCAAGGA
AGCAAACTGAAGATTAAAGATTTTATCTCCCTAAGCAGTAGCGAAGC
Found at i:20818508 original size:14 final size:15
Alignment explanation
Indices: 20818476--20818508 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20818466 CAATAAAACC
20818476 AAAA-AAATAAATTA
1 AAAATAAATAAATTA
20818490 AAAATAAATAAA-TA
1 AAAATAAATAAATTA
20818504 AAAAT
1 AAAAT
20818509 TCTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAATTA
Found at i:20820926 original size:24 final size:24
Alignment explanation
Indices: 20820899--20820945 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
20820889 CAAAAACAAC
*
20820899 GCAATGTTCAGTATTTAGAAATTG
1 GCAATGTTCAATATTTAGAAATTG
20820923 GCAATGTTCAATATTTAGAAATT
1 GCAATGTTCAATATTTAGAAATT
20820946 CGAGAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (24 bp):
GCAATGTTCAATATTTAGAAATTG
Found at i:20827922 original size:25 final size:25
Alignment explanation
Indices: 20827888--20827982 Score: 136
Period size: 25 Copynumber: 3.8 Consensus size: 25
20827878 CTCTTTTAAT
*
20827888 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
20827913 AACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* * *
20827938 AACCGGGGCAAAGTCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
20827963 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20827983 ATCACTTCCT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20827956 original size:50 final size:48
Alignment explanation
Indices: 20827875--20827983 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 48
20827865 CTAGAGGCCT
* *
20827875 AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTTGATAAACTGGGGCAA
1 AGCC-CTTTTAATAACCGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
* * *
20827924 AGCCCTTTTCAATAAACCGGGGCAAAGTCCTTTTCGGTAAACTGGGGCAT
1 AGCCCTTTT-AAT-AACCGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
20827974 AGCCCTTTTA
1 AGCCCTTTTA
20827984 TCACTTCCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
48 5 0.09
49 8 0.15
50 40 0.75
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (48 bp):
AGCCCTTTTAATAACCGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
Found at i:20828221 original size:27 final size:27
Alignment explanation
Indices: 20828183--20828425 Score: 315
Period size: 27 Copynumber: 9.0 Consensus size: 27
20828173 TGGGCAAAAT
* * * *
20828183 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20828210 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
20828237 GGTATTTCTATCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20828264 GGTAATTCTACGCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
20828291 AGTAATTCAAATCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20828318 GGTAATTCTACCCTATAGGGTTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20828345 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20828372 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20828399 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20828426 AATATTTTAC
Statistics
Matches: 187, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 187 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:20828512 original size:54 final size:52
Alignment explanation
Indices: 20828429--20828628 Score: 202
Period size: 54 Copynumber: 3.7 Consensus size: 52
20828419 GTATTTCAAT
* * * * *
20828429 ATTTTACAAATCGAGAGTATTTCGATAATTTCACAAATTAGGGGTATTTTGGTA
1 ATTTTACAAA-CCAGGGTATTTTGGTAATTTTACAAA-TAGGGGTATTTTGGTA
* *
20828483 ATTTTACAAGCCAGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTA
1 ATTTTACAAACCAG-GGTATTTTGGTAATTTTACAAA-TAGGGGTATTTTGGTA
* ** *
20828537 ATTTTACAAACTAGGGGTATTTTGGTAATTTTACTGATCGGAGGTATTTTGGTA
1 ATTTTACAAACCA-GGGTATTTTGGTAATTTTACAAATAGG-GGTATTTTGGTA
** * *
20828591 ATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAAT
1 ATTTTACAAACC-AGGGTATTTTGGTAATTTTACAAAT
20828629 CGAGGGTAAA
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
53 6 0.05
54 113 0.93
55 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (52 bp):
ATTTTACAAACCAGGGTATTTTGGTAATTTTACAAATAGGGGTATTTTGGTA
Found at i:20828546 original size:81 final size:81
Alignment explanation
Indices: 20828454--20828628 Score: 235
Period size: 81 Copynumber: 2.2 Consensus size: 81
20828444 AGTATTTCGA
* *
20828454 TAATTTCACAAATTAGGGGTATTTTGGTAATTTTACA-AGCCAGTGGTATTTTGGTAATTTTACA
1 TAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAGA-CCAGAGGTATTTTGGTAATTTTACA
* *
20828518 AACTAGGGGTATTTTAG
65 AACCAAGGGTATTTTAG
* * * * **
20828535 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTACTGATCGGAGGTATTTTGGTAATTTTGTAA
1 TAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAGACCAGAGGTATTTTGGTAATTTTACAA
20828600 ACCAAGGGTATTTTAG
66 ACCAAGGGTATTTTAG
*
20828616 TAATTTTATAAAT
1 TAATTTTACAAAT
20828629 CGAGGGTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 80 0.99
82 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (81 bp):
TAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAGACCAGAGGTATTTTGGTAATTTTACAA
ACCAAGGGTATTTTAG
Found at i:20828627 original size:27 final size:27
Alignment explanation
Indices: 20828429--20828623 Score: 160
Period size: 27 Copynumber: 7.2 Consensus size: 27
20828419 GTATTTCAAT
* * * * *
20828429 ATTTTACAAATCGAGAGTATTTCGATA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* ** *
20828456 ATTTCACAAATTAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
*
20828483 ATTTTACAAGCC-AGTGGTATTTTGGTA
1 ATTTTACAAACCAAG-GGTATTTTGGTA
* * *
20828510 ATTTTACAAACTAGGGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
* *
20828537 ATTTTACAAACTAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
** * *
20828564 ATTTTACTGATC-GGAGGTATTTTGGTA
1 ATTTTACAAACCAAG-GGTATTTTGGTA
** *
20828591 ATTTTGTAAACCAAGGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
20828618 ATTTTA
1 ATTTTA
20828624 TAAATCGAGG
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
26 3 0.02
27 130 0.96
28 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACAAACCAAGGGTATTTTGGTA
Found at i:20828647 original size:81 final size:81
Alignment explanation
Indices: 20828498--20828647 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
20828488 ACAAGCCAGT
* * * **** *
20828498 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGT
1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAACGAGGGGTAAAACGAT
20828563 AATTTTACTGATCGGA
66 AATTTTACTGATCGGA
** *
20828579 GGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGA-GGGTAAAACGA
1 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAA-CGAGGGGTAAAACGA
20828643 TAATT
65 TAATT
20828648 CTGTAAATCG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 55 0.96
82 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAAACGAGGGGTAAAACGAT
AATTTTACTGATCGGA
Found at i:20828674 original size:81 final size:81
Alignment explanation
Indices: 20828615--20828879 Score: 386
Period size: 81 Copynumber: 3.3 Consensus size: 81
20828605 GGGTATTTTA
* * *
20828615 GTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTATA
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATAATTCTGTA
*
20828680 AGTCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* *
20828696 GTAATTCTACAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATAATTTTGTA
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATAATTCTGTA
* * *
20828761 AATCTAGAGTAAAACG
66 AATCGAGGGTAAAATG
* * * * *
20828777 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTA
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATAATTCTGTA
20828842 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* *
20828858 GTAATTCTGTAAATCGATGGTA
1 GTAATTCTATAAATCGAGGGTA
20828880 CTTTGGTAAT
Statistics
Matches: 163, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 163 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGATAATTCTGTA
AATCGAGGGTAAAATG
Found at i:20828890 original size:27 final size:27
Alignment explanation
Indices: 20828615--20828879 Score: 341
Period size: 27 Copynumber: 9.8 Consensus size: 27
20828605 GGGTATTTTA
* *
20828615 GTAATTTTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
20828642 ATAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
20828669 ATAATTCTATAAGTCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
20828696 GTAATTCTACAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
20828723 ATAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * * * * *
20828750 ATAATTTTGTAAATCTAGAGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
20828777 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
20828804 GTAATTCTATAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
20828831 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
20828858 GTAATTCTGTAAATCGATGGTA
1 GTAATTCTATAAATCGAGGGTA
20828880 CTTTGGTAAT
Statistics
Matches: 210, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 210 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:20832093 original size:27 final size:27
Alignment explanation
Indices: 20832063--20832121 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
20832053 CAAATTGTAA
*
20832063 AATTACCAAAGTACCCTCGATTTATAG
1 AATTACCAAAGTACCCTCGATTTACAG
****
20832090 AATTACCGTTTTACCCTCGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
20832117 AATTA
1 AATTA
20832122 TTGTAGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (27 bp):
AATTACCAAAGTACCCTCGATTTACAG
Found at i:20832129 original size:38 final size:38
Alignment explanation
Indices: 20832087--20832159 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
20832077 CCTCGATTTA
* *
20832087 TAGAATTACCGTTTTACCCTCGATTTACAGAATTATTG
1 TAGAATTACCATTTTACCCTCGATTGACAGAATTATTG
* *
20832125 TAGAATTACTATTTTACCCTTGATTGACAGAATTA
1 TAGAATTACCATTTTACCCTCGATTGACAGAATTA
20832160 CTGTTTTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (38 bp):
TAGAATTACCATTTTACCCTCGATTGACAGAATTATTG
Found at i:20832156 original size:27 final size:27
Alignment explanation
Indices: 20832126--20832189 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
20832116 GAATTATTGT
*
20832126 AGAATTACTATTTTACCCTTGATTGAC
1 AGAATTACTATTTTACCCTCGATTGAC
* * *
20832153 AGAATTACTGTTTTTCCCTCGATTTAC
1 AGAATTACTATTTTACCCTCGATTGAC
*
20832180 AAAATTACTA
1 AGAATTACTA
20832190 AAATACCCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (27 bp):
AGAATTACTATTTTACCCTCGATTGAC
Found at i:20832198 original size:27 final size:27
Alignment explanation
Indices: 20832168--20832229 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
20832158 TACTGTTTTT
*
20832168 CCCTCGATTTACAAAATTACTAAAATA
1 CCCTCGATTTACAAAATTACCAAAATA
* *
20832195 CCCTTGGTTTACAAAATTACCAAAATA
1 CCCTCGATTTACAAAATTACCAAAATA
20832222 CCCTCGAT
1 CCCTCGAT
20832230 CAGTAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCAAAATA
Found at i:20833464 original size:25 final size:25
Alignment explanation
Indices: 20833426--20833482 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
20833416 AGGAAGTGCT
* *
20833426 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTATGCCCAAGTTTACCA
* *
20833451 AAAAGGGCTTTGCCCAAGTTTATCA
1 AAAAGGGCTATGCCCAAGTTTACCA
20833476 AAAAGGG
1 AAAAGGG
20833483 TTTTACCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (25 bp):
AAAAGGGCTATGCCCAAGTTTACCA
Found at i:20833502 original size:24 final size:25
Alignment explanation
Indices: 20833426--20833495 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
20833416 AGGAAGTGCT
* * * * *
20833426 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTACCCAAGTTTATCA
*
20833451 AAAAGGGCTTTGCCCAAGTTTATCA
1 AAAAGGGCTTTACCCAAGTTTATCA
* *
20833476 AAAAGGGTTTTACCCCAGTT
1 AAAAGGGCTTTACCCAAGTT
20833496 ATTAAAAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTACCCAAGTTTATCA
Found at i:20833702 original size:42 final size:42
Alignment explanation
Indices: 20833643--20833734 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
20833633 TAGTCTCCCC
* ** *
20833643 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
20833685 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
20833727 AAATGGGC
1 AAATGGGC
20833735 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:20833793 original size:31 final size:31
Alignment explanation
Indices: 20833758--20833836 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
20833748 CGTTTACAGT
20833758 AAAGGCTTCGGCCCAATGATATAATTTATGA
1 AAAGGCTTCGGCCCAATGATATAATTTATGA
* * *
20833789 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATAATTTATGA
20833820 AAAGGCTTCGGCCCAAT
1 AAAGGCTTCGGCCCAAT
20833837 AACCGTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATAATTTATGA
Found at i:20837277 original size:60 final size:64
Alignment explanation
Indices: 20837176--20837337 Score: 217
Period size: 60 Copynumber: 2.6 Consensus size: 64
20837166 AGGGGAAGAA
* * *
20837176 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGGCCTAATAAAAATG-GAAAAG-ATAA-AG-G
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACCTAATAAAAATGAAAAAAGAAAAAGAGAG
*
20837236 GCCAAAGTGAAAACCCGCAGAGGGCGCTTTGAGA-CTCAATAAAAATGAAAAAAGAAAAAAAGAG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACCT-AATAAAAATGAAAAAAG--AAAAAGAG
20837300 AG
63 AG
*
20837302 GCCAACGTGAAAACCCGCAAAGGGCGCTTTGAGACC
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACC
20837338 AAAGGGGATT
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
59 2 0.02
60 42 0.48
61 5 0.06
64 3 0.03
65 2 0.02
66 33 0.38
67 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (64 bp):
GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACCTAATAAAAATGAAAAAAGAAAAAGAGAG
Found at i:20838936 original size:170 final size:171
Alignment explanation
Indices: 20838407--20839123 Score: 865
Period size: 170 Copynumber: 4.2 Consensus size: 171
20838397 TTATGAAGTC
* *
20838407 AGCAGATTTTA-CCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGATTGAAGAATGAGTCT
1 AGCAGATTTAAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAGTCT
*
20838471 TATCTTTCTAAGGTAGCAAGAAAG-AAGACTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCA
66 TATCTTTCTAAGGTAGCAAGAAAGCAAGACTAAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCA
* * *
20838535 GATCGAAGATGGTGAATCTCATCTCCATGTATCAGCAATGG
131 GATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
* * * *
20838576 AGCATATTTTA-CCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTTAAGAATGAGTCT
1 AGCAGATTTAAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAGTCT
* *
20838640 TGTCTTTCTGAGGTAGCAAGAAAGC-AGACTGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAG
66 TATCTTTCTAAGGTAGCAAGAAAGCAAGACT----A---AAGATCTTATCTCCCTGAAGTTGCAG
* *
20838704 TGGAGTAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
124 CGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
* * *
20838752 AGCAGATATAAGCCACCAGCTTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAATCT
1 AGCAGATTTAAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAGTCT
* * * *
20838817 TATCTTTCTGAGGTAGTAAGAAAGCAA-ACTAAAGATCTTATCTCCCTGAAGTTGCAACAGAGCA
66 TATCTTTCTAAGGTAGCAAGAAAGCAAGACTAAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCA
* * *
20838881 GATAGAATATGGCGAATCTTATCTCCATGTATTGGCAATGG
131 GATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
* * * *
20838922 AGCAGAGTTAAGCCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCAGGTTGAAGAATTGAGTT
1 AGCAGATTTAAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAA-TGAGTC
* * * * ** *
20838987 TTATCTTCCTAAGGTAACAAGGAAGCAGACAGAAGATTAAAGATTTTATCTCCCT-AAGCAGTAG
65 TTATCTTTCTAAGGTAGCAA-GAA--AG-C--AAGACTAAAGATCTTATCTCCCTGAAGTTGCAG
* * * * *
20839051 CGGAGCAGATTGAA-A-GGCGGATCTTATCTCTATGTATTGGTAATGG
124 CGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
* * *
20839097 AGCAGATTTTAGCCACTAGACTTATCT
1 AGCAGATTTAAGCCACCAGCCTTATCT
20839124 TTTTCAGGAA
Statistics
Matches: 476, Mismatches: 54, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
169 87 0.18
170 120 0.25
171 20 0.04
172 3 0.01
173 1 0.00
174 2 0.00
175 52 0.11
176 78 0.16
177 94 0.20
178 19 0.04
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (171 bp):
AGCAGATTTAAGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAGTCT
TATCTTTCTAAGGTAGCAAGAAAGCAAGACTAAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCA
GATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGG
Found at i:20839190 original size:346 final size:344
Alignment explanation
Indices: 20838407--20839192 Score: 974
Period size: 346 Copynumber: 2.3 Consensus size: 344
20838397 TTATGAAGTC
20838407 AGCAGATTTTA-CCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAGATTGAAGAATGAGTCT
1 AGCAGATTTTAGCCACCAG-CTTATCTCTCTAAGGTAGCAAGAGAGCAGATTG-AGAATGAGTCT
* * *
20838471 TATCTTTCT-AAGGTAGCAAGAAAG-AAGACTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGC
64 TATCTTTCTGAA-GTAGCAAGAAAGCAA-ACTAAAGATCTTATCTCCCTGAAGTTGCAACAGAGC
* * * * *
20838534 AGATCGAAGATGGTGAATCTCATCTCCATGTATCAGCAATGGAGCATATTTTACCACCAGCCTTA
127 AGATAGAAGATGGCGAATCTCATCTCCATGTATCAGCAATGGAGCAGAGTTAACCACCAGCCTTA
* * * * * *
20838599 TCTCTCTGAGGTAGCAAGAGAGCAGGTTTAAGAATGAGTCTTGTCTTTCTGAGGTAGCAAGAAAG
192 TCTCTCTGAGATAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTAAGGTAACAAGAAAG
* * ** * *
20838664 CAGACTGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATGGCGAATC
257 CAGACAGAAGATTAAAGATCTTATCTCCCTGAAGCAGCAGCGGAGCAGATCGAAGATGGCGAATC
20838729 TTATCTCCATGTATCGGCAATGG
322 TTATCTCCATGTATCGGCAATGG
* * * *
20838752 AGCAGATATAAGCCACCAGCTTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGAATGAATCT
1 AGCAGATTTTAGCCACCAGC-TTATCTCTCTAAGGTAGCAAGAGAGCAGATTG-AGAATGAGTCT
* *
20838817 TATCTTTCTGAGGTAGTAAGAAAGCAAACTAAAGATCTTATCTCCCTGAAGTTGCAACAGAGCAG
64 TATCTTTCTGAAGTAGCAAGAAAGCAAACTAAAGATCTTATCTCCCTGAAGTTGCAACAGAGCAG
* * **
20838882 ATAGAATATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGAGTTAAGCCACCAGCCTTAT
129 ATAGAAGATGGCGAATCTCATCTCCATGTATCAGCAATGGAGCAGAGTTAA-CCACCAGCCTTAT
* *
20838947 CTCTCTGAGATAGCAAGAGAGCAGGTTGAAGAATTGAGTTTTATCTTCCTAAGGTAACAAGGAAG
193 CTCTCTGAGATAGCAAGAGAGCAGGTTGAAGAA-TGAGTCTTATCTTCCTAAGGTAACAAGAAAG
* * * *
20839012 CAGACAGAAGATTAAAGATTTTATCTCCCT-AAGCAGTAGCGGAGCAGATTGAA-A-GGCGGATC
257 CAGACAGAAGATTAAAGATCTTATCTCCCTGAAGCAGCAGCGGAGCAGATCGAAGATGGCGAATC
* * *
20839074 TTATCTCTATGTATTGGTAATGG
322 TTATCTCCATGTATCGGCAATGG
* * * * * * *
20839097 AGCAGATTTTAGCCACTAGACTTATCTTTTTCAGGAAGCAAGAAAGCTGATTG-GCAATTGTAGT
1 AGCAGATTTTAGCCACCAG-CTTATCTCTCTAAGGTAGCAAGAGAGCAGATTGAG-AA-TG-AGT
* * *
20839161 CTCATCTTCCTGAAGTAGCAAGGAAGCAAACT
62 CTTATCTTTCTGAAGTAGCAAGAAAGCAAACT
20839193 GATTGTTATC
Statistics
Matches: 376, Mismatches: 55, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
343 1 0.00
344 2 0.01
345 80 0.21
346 177 0.47
347 64 0.17
348 52 0.14
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (344 bp):
AGCAGATTTTAGCCACCAGCTTATCTCTCTAAGGTAGCAAGAGAGCAGATTGAGAATGAGTCTTA
TCTTTCTGAAGTAGCAAGAAAGCAAACTAAAGATCTTATCTCCCTGAAGTTGCAACAGAGCAGAT
AGAAGATGGCGAATCTCATCTCCATGTATCAGCAATGGAGCAGAGTTAACCACCAGCCTTATCTC
TCTGAGATAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTAAGGTAACAAGAAAGCAGA
CAGAAGATTAAAGATCTTATCTCCCTGAAGCAGCAGCGGAGCAGATCGAAGATGGCGAATCTTAT
CTCCATGTATCGGCAATGG
Found at i:20844817 original size:21 final size:22
Alignment explanation
Indices: 20844780--20844840 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
20844770 GTGTGTGCCC
*
20844780 CCTCCATAA-GGGTGTGTAG-GG
1 CCTCCA-AACGGGCGTGTAGTGG
*
20844801 CCTTCAAACGGGCGTGT-GTGG
1 CCTCCAAACGGGCGTGTAGTGG
* *
20844822 CCTCCACATGGGCGTGTAG
1 CCTCCAAACGGGCGTGTAG
20844841 ACACCCACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.09
21 28 0.88
22 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.23
Consensus pattern (22 bp):
CCTCCAAACGGGCGTGTAGTGG
Found at i:20847624 original size:39 final size:39
Alignment explanation
Indices: 20847570--20847661 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
20847560 GCATGATATT
20847570 TGGAAACATATCCGGACTTGAGGTCCACAGGCGACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCACAGGCGACGTGC
* *
20847609 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCACAGGCGACGTGC
*
20847648 TGG-AATATATCCGG
1 TGGAAACATATCCGG
20847662 GCCTAAAGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
38 10 0.20
39 40 0.80
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.21
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCACAGGCGACGTGC
Found at i:20847676 original size:39 final size:39
Alignment explanation
Indices: 20847570--20847672 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 39
20847560 GCATGATATT
* * * *
20847570 TGGAAACATATCCGGACTTGAGGTCCACAGGCGACGTGC
1 TGGAAACATATCCGGACCTAAAGTCCGCAGGCGACGTGC
* * * *
20847609 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACCTAAAGTCCGCAGGCGACGTGC
* *
20847648 TGG-AATATATCCGGGCCTAAAGTCC
1 TGGAAACATATCCGGACCTAAAGTCC
20847673 CGCATGCTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 17 0.30
39 40 0.70
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (39 bp):
TGGAAACATATCCGGACCTAAAGTCCGCAGGCGACGTGC
Found at i:20851470 original size:42 final size:43
Alignment explanation
Indices: 20851410--20851495 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
20851400 AGAGTTACAC
* *
20851410 GGGCTATTCACATGGGCGTGTGCT-CCCTCCACACGGGTGTGTA
1 GGGCTATTCACACGGGCGTGTG-TGCCCTCCACACGGGCGTGTA
* *
20851453 GGGCT-TTCACACGGGCGTGTGTGGCCTCCACATGGGCGTGTA
1 GGGCTATTCACACGGGCGTGTGTGCCCTCCACACGGGCGTGTA
20851495 G
1 G
20851496 ACACCCACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.03
42 32 0.84
43 5 0.13
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (43 bp):
GGGCTATTCACACGGGCGTGTGTGCCCTCCACACGGGCGTGTA
Found at i:20851484 original size:21 final size:21
Alignment explanation
Indices: 20851418--20851493 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
20851408 ACGGGCTATT
* *
20851418 CACATGGGCGTGTGCT-CCCTC
1 CACACGGGCGTGTG-TGGCCTC
* * *
20851439 CACACGGGTGTGTAG-GGCTTT
1 CACACGGGCGTGT-GTGGCCTC
20851460 CACACGGGCGTGTGTGGCCTC
1 CACACGGGCGTGTGTGGCCTC
*
20851481 CACATGGGCGTGT
1 CACACGGGCGTGT
20851494 AGACACCCAC
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.12, C:0.29, G:0.36, T:0.24
Consensus pattern (21 bp):
CACACGGGCGTGTGTGGCCTC
Found at i:20855035 original size:30 final size:30
Alignment explanation
Indices: 20854963--20855037 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
20854953 TATAAGGATG
* * *
20854963 TTCAAAAGCTTGAGAAGACTCGTTATCTCA
1 TTCAAGAGCTTGGGAAGACTCGATATCTCA
*
20854993 TTCAAGAGCTTGGGAAGACTCGATATCTCC
1 TTCAAGAGCTTGGGAAGACTCGATATCTCA
*
20855023 TTCAAGATCTTGGGA
1 TTCAAGAGCTTGGGA
20855038 TTGAGAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (30 bp):
TTCAAGAGCTTGGGAAGACTCGATATCTCA
Found at i:20855081 original size:66 final size:66
Alignment explanation
Indices: 20854986--20855151 Score: 210
Period size: 66 Copynumber: 2.5 Consensus size: 66
20854976 GAAGACTCGT
*
20854986 TATCTCATTCAAGAGCTTGGGAAGACTCGATATCT-CCTTCAAGATCTTGGGATTGAGAAGACCT
1 TATCTCATTCAAGAGCTTGGGAAGACTCGATAT-TGCCTTCAAGAGCTTGGGATTGAGAAGACCT
20855050 AA
65 AA
* * * * * * *
20855052 TATCCCATTCAGGAGCTTGGGAAGGCTCGATATTGCGTTCAGGAGCTTGGGATTGAGAAGACTTG
1 TATCTCATTCAAGAGCTTGGGAAGACTCGATATTGCCTTCAAGAGCTTGGGATTGAGAAGACCTA
20855117 A
66 A
**
20855118 TATCTTGTTCAAGAGCTTGGGAAGA-TCTGATATT
1 TATCTCATTCAAGAGCTTGGGAAGACTC-GATATT
20855152 TTATTTTTCT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 3 0.04
66 82 0.96
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (66 bp):
TATCTCATTCAAGAGCTTGGGAAGACTCGATATTGCCTTCAAGAGCTTGGGATTGAGAAGACCTA
A
Found at i:20856174 original size:21 final size:22
Alignment explanation
Indices: 20856132--20856179 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
20856122 CGTCAACATT
20856132 TAATTATTTTTTACAATATAAA
1 TAATTATTTTTTACAATATAAA
* * *
20856154 -AATTATTTTTTATATTTTAAA
1 TAATTATTTTTTACAATATAAA
20856175 TAATT
1 TAATT
20856180 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATTATTTTTTACAATATAAA
Found at i:20856192 original size:17 final size:18
Alignment explanation
Indices: 20856161--20856197 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
20856151 AAAAATTATT
20856161 TTTTATATTTTAAA-TAA
1 TTTTATATTTTAAATTAA
20856178 TTTTA-ATTTTAAAATTAA
1 TTTTATATTTT-AAATTAA
20856196 TT
1 TT
20856198 AAATGCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 8 0.44
18 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATATTTTAAATTAA
Found at i:20867301 original size:26 final size:26
Alignment explanation
Indices: 20867272--20867379 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
20867262 TGGTACAAAT
20867272 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
20867298 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20867324 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
20867350 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20867376 TGAT
1 TGAT
20867380 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:20871065 original size:12 final size:12
Alignment explanation
Indices: 20871048--20871074 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20871038 CATATAACAA
20871048 TAGTTATCAATC
1 TAGTTATCAATC
20871060 TAGTTATCAATC
1 TAGTTATCAATC
20871072 TAG
1 TAG
20871075 AACAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (12 bp):
TAGTTATCAATC
Found at i:20873237 original size:42 final size:42
Alignment explanation
Indices: 20873157--20873296 Score: 122
Period size: 42 Copynumber: 3.4 Consensus size: 42
20873147 AGCTTTAATC
* * *
20873157 AACTCATATGAGTTTC-AGTTTAACCCTAAT-GGTTTCCGTTT
1 AACTCTTATGAGCTTCTA-TTTAACCCTTATGGGTTTCCGTTT
* * * * *
20873198 AACTTTTTTGAGGTTTTATTTAACCCTTATGGGTTTCCGTTC
1 AACTCTTATGAGCTTCTATTTAACCCTTATGGGTTTCCGTTT
* * * *
20873240 AGCTCTTATGAGCTTCTGTTCAACCCTTACGGGTTTCCGTTT
1 AACTCTTATGAGCTTCTATTTAACCCTTATGGGTTTCCGTTT
* * *
20873282 AGCACTTATGTGCTT
1 AACTCTTATGAGCTT
20873297 TTTGCAGCCT
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
41 22 0.28
42 57 0.72
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
AACTCTTATGAGCTTCTATTTAACCCTTATGGGTTTCCGTTT
Found at i:20873248 original size:21 final size:21
Alignment explanation
Indices: 20873223--20873291 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
20873213 TTATTTAACC
*
20873223 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCGTTCAGCA
* * * * *
20873244 CTTATGAGCTTCTGTTCAACC
1 CTTATGGGTTTCCGTTCAGCA
* *
20873265 CTTACGGGTTTCCGTTTAGCA
1 CTTATGGGTTTCCGTTCAGCA
20873286 CTTATG
1 CTTATG
20873292 TGCTTTTTGC
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTCAGCA
Found at i:20877501 original size:52 final size:52
Alignment explanation
Indices: 20877439--20877540 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
20877429 TTGGATAGAT
** *
20877439 TGTTTATATGTTTATATCGGCTGTTACATAACACTTCTAATTTTAGCTTAAC
1 TGTTTATATGTTTATATCAACTGTTACATAACACTTCTAATTTTAACTTAAC
*
20877491 TGTTTATATGTTTATATCAACTGTTACATAGCACTTCTAATTTTAACTTA
1 TGTTTATATGTTTATATCAACTGTTACATAACACTTCTAATTTTAACTTA
20877541 GCCTCCCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (52 bp):
TGTTTATATGTTTATATCAACTGTTACATAACACTTCTAATTTTAACTTAAC
Found at i:20877924 original size:34 final size:34
Alignment explanation
Indices: 20877881--20877948 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
20877871 GAAAAATATT
20877881 ATATTAAACAAATTATATCACATTTATTCGCTTA
1 ATATTAAACAAATTATATCACATTTATTCGCTTA
* *
20877915 ATATTAAACAAATTATATTACATTTATTTGCTTA
1 ATATTAAACAAATTATATCACATTTATTCGCTTA
20877949 CTTCATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (34 bp):
ATATTAAACAAATTATATCACATTTATTCGCTTA
Found at i:20879311 original size:14 final size:13
Alignment explanation
Indices: 20879293--20879317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20879283 AGAAGAAGTT
20879293 TTTTTTTAAATGA
1 TTTTTTTAAATGA
20879306 TTTTTTTAAATG
1 TTTTTTTAAATG
20879318 GGCTTTAAAT
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTTTTAAATGA
Found at i:20883408 original size:61 final size:61
Alignment explanation
Indices: 20883337--20883461 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
20883327 TTGAAGGCTA
* * *
20883337 GAATAACAGAACTAGAAAAATCACTTCATTAGTATCGTAGTCATAACTCTGCAATGGAGCT
1 GAATAACAGAACTAGAAAAATCACTTCATCAATATCGTAGTCACAACTCTGCAATGGAGCT
* *
20883398 GAATAGCAGAACTAGAAAAATCACTTTATCAATATCGTAGTCACAACTCTGCAATGGAGCT
1 GAATAACAGAACTAGAAAAATCACTTCATCAATATCGTAGTCACAACTCTGCAATGGAGCT
20883459 GAA
1 GAA
20883462 GGCGAGTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (61 bp):
GAATAACAGAACTAGAAAAATCACTTCATCAATATCGTAGTCACAACTCTGCAATGGAGCT
Found at i:20887546 original size:4 final size:4
Alignment explanation
Indices: 20887529--20887567 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
20887519 TTACTACCAA
* *
20887529 TATG TATA TATG TATG TATG TACG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
20887568 ATTTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:20887593 original size:23 final size:23
Alignment explanation
Indices: 20887563--20887608 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20887553 TATGTATGTA
20887563 TGTATATTTTTTTTCTTTTTTTT
1 TGTATATTTTTTTTCTTTTTTTT
20887586 TGTATATTTTTTTTCTTTTTTTT
1 TGTATATTTTTTTTCTTTTTTTT
20887609 CTTTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.83
Consensus pattern (23 bp):
TGTATATTTTTTTTCTTTTTTTT
Found at i:20890596 original size:248 final size:247
Alignment explanation
Indices: 20890152--20890632 Score: 782
Period size: 248 Copynumber: 1.9 Consensus size: 247
20890142 TAATAATAAA
20890152 TAAAAAAAATTAAGTAATAAAAGAATATAATAAAGAACTAAAGAAAAATAAAGGTTAAAAAGGGA
1 TAAAAAAAATTAAGTAATAAAAGAATATAATAAAGAACTAAAGAAAAATAAAGGTTAAAAAGGGA
*
20890217 ATAAGGGGGAACCAATGGTGGTTGGTGGTGGGTTGAAGTGTAACGGCGGTGGAAGGGGTCGGTCA
66 ATAAGGGGGAACCAATGGTGGTTGGTGGTGGGTTGAAGTGTAACAGCGGTGGAAGGGGTCGGTCA
* * * * * *
20890282 GCTGGTGAGGCGATGGTGGCAAGGGAGGTGGGTTGGACAAATGGGGAGTGCGGTTCTTGGTGGCT
131 GCTGGCGAGGCGACGGTGGCAAGAGAGGTAGGTTGGACAAACGGGGAGTGCGGCTCTTGGTGGCT
* *
20890347 AAGGAGAGGGGCAAGGTGTGGGAAGGAAAGAAATGGAGGGGGAAGGAAAGAT
196 AAGGAGAGGGGCAAGGTGTGGAAAGGAAAGAAAGGGAGGGGGAAGGAAAGAT
* *
20890399 TAAAAATAAATTAAGTAATAAAAGAATATAATAAAGAACTAAAGAAAAATGAAGTTTAAAAAGGG
1 TAAAAA-AAATTAAGTAATAAAAGAATATAATAAAGAACTAAAGAAAAATAAAGGTTAAAAAGGG
* * * *
20890464 AATAAGGGGGAATCGATGGTGGTTGGTGGTGGGTTGAAGTGTAACAGCGGTGGAGGGGGTCGGTT
65 AATAAGGGGGAACCAATGGTGGTTGGTGGTGGGTTGAAGTGTAACAGCGGTGGAAGGGGTCGGTC
* * **
20890529 GGCTGGCGAGGCGACGGTGGCGAGAGAGGTAGGTTGGACGGACGGGGAGTGCGGCTCTTGGTGGC
130 AGCTGGCGAGGCGACGGTGGCAAGAGAGGTAGGTTGGACAAACGGGGAGTGCGGCTCTTGGTGGC
20890594 TAAGGAGAGGGGCAAGGTGTGGAAAGGAAAGAAAGGGAG
195 TAAGGAGAGGGGCAAGGTGTGGAAAGGAAAGAAAGGGAG
20890633 AAGGTCGGTC
Statistics
Matches: 214, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
247 6 0.03
248 208 0.97
ACGTcount: A:0.35, C:0.07, G:0.40, T:0.18
Consensus pattern (247 bp):
TAAAAAAAATTAAGTAATAAAAGAATATAATAAAGAACTAAAGAAAAATAAAGGTTAAAAAGGGA
ATAAGGGGGAACCAATGGTGGTTGGTGGTGGGTTGAAGTGTAACAGCGGTGGAAGGGGTCGGTCA
GCTGGCGAGGCGACGGTGGCAAGAGAGGTAGGTTGGACAAACGGGGAGTGCGGCTCTTGGTGGCT
AAGGAGAGGGGCAAGGTGTGGAAAGGAAAGAAAGGGAGGGGGAAGGAAAGAT
Found at i:20897015 original size:44 final size:43
Alignment explanation
Indices: 20896877--20897021 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 43
20896867 ATCTGGTCTT
* *
20896877 CCTAAAGTTGCAGTGGAGCAGATTGAAGAAAACGAGTCTCAT-CTC
1 CCTAAAGTTGCAGTGGAGCAGATTGAA-ACAACAAGTCT-ATAC-C
* *
20896922 CCTAAAGTTGCAGTGGAGCAGA-TCAAAGCTACAAGTCTA-ATCC
1 CCTAAAGTTGCAGTGGAGCAGATTGAAA-CAACAAGTCTATA-CC
* * *
20896965 CTCTAAAGATGCAGTGGAGCAGATTGAAACAATAATTCCTATACC
1 C-CTAAAGTTGCAGTGGAGCAGATTGAAACAACAAGT-CTATACC
20897010 CCTAAAGTTGCA
1 CCTAAAGTTGCA
20897022 ATGGGTTGGA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
43 4 0.05
44 46 0.55
45 32 0.39
46 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (43 bp):
CCTAAAGTTGCAGTGGAGCAGATTGAAACAACAAGTCTATACC
Found at i:20897601 original size:5 final size:5
Alignment explanation
Indices: 20897591--20897617 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20897581 ATTAGTTAGG
20897591 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
20897618 CTTTCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:20900684 original size:23 final size:23
Alignment explanation
Indices: 20900658--20900732 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
20900648 AGGCACTTTA
20900658 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
20900681 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
20900702 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
20900723 TGTGTCGTAT
1 TGTGTCGTAT
20900733 ACTGATCAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:20900915 original size:18 final size:19
Alignment explanation
Indices: 20900894--20900934 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20900884 AATGAAATGA
20900894 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
20900912 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
20900931 GAAA
1 GAAA
20900935 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:20906891 original size:15 final size:15
Alignment explanation
Indices: 20906871--20906927 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
20906861 NNNNNNNTTT
20906871 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
20906886 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
20906901 ATTGAATTTATATTG
1 ATTGAATTTATATTG
20906916 ATTGAA-TTATAT
1 ATTGAATTTATAT
20906928 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:20908126 original size:5 final size:5
Alignment explanation
Indices: 20908116--20908141 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20908106 TTTTTCTTGC
20908116 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
20908142 TTATTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:20923519 original size:26 final size:26
Alignment explanation
Indices: 20923488--20923595 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
20923478 TGAAATGCCC
*
20923488 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
20923514 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
20923540 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
20923566 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20923592 ATCA
1 ATCA
20923596 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20926161 original size:116 final size:116
Alignment explanation
Indices: 20925955--20926182 Score: 393
Period size: 116 Copynumber: 2.0 Consensus size: 116
20925945 CACCCGATTC
*
20925955 ATCAGATCCATAAATACTGCAGGAGCGTTCGTCAGTCCAAATGGCATAACCAGAAACTCGTAATG
1 ATCAGATCCATAAATACTGCAGGAGCGTTCGTCAGTCCAAATGGCATAACCAAAAACTCGTAATG
*
20926020 ACCATACCGAGTCCTGAATGCCGTCTTATAGATATCTGCCTCCTTGAAGTT
66 ACCATACCGAGTCCTGAATGCCGTCTTATAGATATCCGCCTCCTTGAAGTT
* * *
20926071 ATCAGATCCATAAATGCTGCAGGAGCGTTTGTCAGTCCAAATGGCATAACCAAAAACTTGTAATG
1 ATCAGATCCATAAATACTGCAGGAGCGTTCGTCAGTCCAAATGGCATAACCAAAAACTCGTAATG
* *
20926136 ACCATACCGAGTCCTGAATGTCGTCTTATGGATATCCGCCTCCTTGA
66 ACCATACCGAGTCCTGAATGCCGTCTTATAGATATCCGCCTCCTTGA
20926183 CCCTTAACTG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (116 bp):
ATCAGATCCATAAATACTGCAGGAGCGTTCGTCAGTCCAAATGGCATAACCAAAAACTCGTAATG
ACCATACCGAGTCCTGAATGCCGTCTTATAGATATCCGCCTCCTTGAAGTT
Found at i:20929852 original size:26 final size:26
Alignment explanation
Indices: 20929821--20929927 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
20929811 TGAAATGCCC
*
20929821 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
20929847 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
20929873 ATCATAGAATATTTA-CTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
20929898 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20929924 ATCA
1 ATCA
20929928 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
25 22 0.30
26 51 0.70
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20929903 original size:51 final size:52
Alignment explanation
Indices: 20929821--20929927 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 52
20929811 TGAAATGCCC
*
20929821 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
* *
20929873 ATCATAGAATATTTA-CTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
20929924 ATCA
1 ATCA
20929928 ATTTGTACCA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 39 0.75
52 13 0.25
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATAGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:20936085 original size:30 final size:30
Alignment explanation
Indices: 20936051--20936118 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
20936041 GTGTGTCTCA
*
20936051 GCCGTGTGCGACACACGGTCATGTTACACG
1 GCCGTGTGCCACACACGGTCATGTTACACG
* * *
20936081 GCCGTGTACCTCACACGGTCATGTTACATG
1 GCCGTGTGCCACACACGGTCATGTTACACG
*
20936111 GCTGTGTG
1 GCCGTGTG
20936119 TCCTCTAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (30 bp):
GCCGTGTGCCACACACGGTCATGTTACACG
Found at i:20947383 original size:29 final size:29
Alignment explanation
Indices: 20947317--20947431 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 29
20947307 TACATAGGTG
* *
20947317 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCATTAGGCCCAATTCATATT
* * *
20947345 CAAATGGCCCATTTGGCCCAGTTCATATT
1 CATATGGCCCATTAGGCCCAATTCATATT
* * **
20947374 CTTATGGCCCACTAGGCCCAATTCACCTT
1 CATATGGCCCATTAGGCCCAATTCATATT
*
20947403 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCATTAGGCCCAATTCATATT
20947432 ATACTCATGC
Statistics
Matches: 69, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
28 17 0.25
29 52 0.75
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCATATT
Found at i:20947429 original size:58 final size:57
Alignment explanation
Indices: 20947319--20947431 Score: 156
Period size: 58 Copynumber: 2.0 Consensus size: 57
20947309 CATAGGTGCA
* * **
20947319 TATGGCCCACTAGGCCCAATCTTATTCAAATGGCCCATTTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATTAGGCCCAAATCATATTCT
*
20947376 TATGGCCCACTAGGCCCAAT-TCACCTTCATATGGCCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAATCTCA--TTCAAATGGCCCATTAGGCCCAAATCATATT
20947432 ATACTCATGC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 2 0.04
57 20 0.41
58 27 0.55
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATTAGGCCCAAATCATATTCT
Found at i:20954196 original size:40 final size:39
Alignment explanation
Indices: 20954152--20954256 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
20954142 AGTGACCATA
*
20954152 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
20954192 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
20954230 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
20954257 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:20954213 original size:39 final size:40
Alignment explanation
Indices: 20954112--20954275 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
20954102 TTGAATGATG
* *
20954112 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
20954152 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
20954191 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
20954231 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
20954271 TCCGG
1 TCCGG
20954276 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:20954275 original size:79 final size:80
Alignment explanation
Indices: 20954112--20954262 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
20954102 TTGAATGATG
*
20954112 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
20954177 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
20954192 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
20954254 TTGAACGAG
64 TTGAACGAG
20954263 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:20961939 original size:79 final size:81
Alignment explanation
Indices: 20961803--20961987 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
20961793 TTGAATGATG
*
20961803 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
20961867 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
20961882 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20961944 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
20961962 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20961988 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:20962001 original size:40 final size:40
Alignment explanation
Indices: 20961804--20961987 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
20961794 TGAATGATGT
* * * *
20961804 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20961844 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
20961884 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20961922 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20961963 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20961988 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20962009 original size:79 final size:79
Alignment explanation
Indices: 20961856--20962020 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
20961846 GGACTAAGAT
* **
20961856 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20961921 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20961935 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20961998 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20962014 CCGAAGG
1 CCGAAGG
20962021 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:20963448 original size:21 final size:20
Alignment explanation
Indices: 20963423--20963491 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
20963413 TAATAAAATT
20963423 TATAAACAAAATATATAATGA
1 TATAAACAAAATATATAAT-A
*
20963444 TATAAACAATATGATAGATAATA
1 TATAAACAA-A--ATATATAATA
*
20963467 TATAAA-ATAATATAT-ATA
1 TATAAACAAAATATATAATA
20963485 TAGTAAA
1 TA-TAAA
20963492 ATGTATGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
21 10 0.24
22 2 0.05
23 7 0.17
24 8 0.20
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (20 bp):
TATAAACAAAATATATAATA
Found at i:20963522 original size:10 final size:10
Alignment explanation
Indices: 20963432--20963542 Score: 61
Period size: 10 Copynumber: 10.6 Consensus size: 10
20963422 TTATAAACAA
20963432 AATATATAAT
1 AATATATAAT
* *
20963442 GATATA-AAC
1 AATATATAAT
20963451 AATATGATAGAT
1 AATAT-ATA-AT
20963463 AATATATAA-
1 AATATATAAT
20963472 AATA-AT-AT
1 AATATATAAT
20963480 ATATATAGTAA-
1 A-ATATA-TAAT
*
20963491 AATGTATGTAATAT
1 AA--TATAT-A-AT
20963505 AATATATAAT
1 AATATATAAT
*
20963515 AATGTATAAT
1 AATATATAAT
20963525 AATATAATAAAT
1 AATAT-AT-AAT
20963537 AATATA
1 AATATA
20963543 CAAAGATAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
7 1 0.01
8 3 0.04
9 13 0.17
10 24 0.31
11 11 0.14
12 23 0.29
13 1 0.01
14 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AATATATAAT
Found at i:20965171 original size:44 final size:44
Alignment explanation
Indices: 20965091--20965387 Score: 330
Period size: 44 Copynumber: 6.8 Consensus size: 44
20965081 CACCCTACCT
** * *
20965091 AATACAGAGACGCCAAATCCGCTACCCTCGATCTGCTCTTTGAC
1 AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTTTGAC
** * * * *
20965135 AATACAGAGGTGCCAAATCTACCATTTTCGACCTGCTCTCTGAC
1 AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTTTGAC
** * * * *
20965179 AATACAGAGATACCAAATCTGCTATCTTCGATTTTCTCTTTAAC
1 AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTTTGAC
* *
20965223 AATATAGAGACGTC-AATCCTACTATCTTCGATCTGCTCTCTT-AC
1 AATACAGAGACGCCAAAT-CTACTATCTTCGATCTGCTCT-TTGAC
*
20965267 AATATAGAGACGCCAAATCTACTATCTTCGATCTGCT-TTCTGAC
1 AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTT-TGAC
* * * *
20965311 AATACAGTGACGCCAAATCTGCTATCTTCGGTCTGCTCTCTGAC
1 AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTTTGAC
*
20965355 AATACAGAGACGCCAAATCTACTATCTTTGATC
1 AATACAGAGACGCCAAATCTACTATCTTCGATC
20965388 AGAGACGCCA
Statistics
Matches: 210, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 198 0.94
45 6 0.03
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (44 bp):
AATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTTTGAC
Found at i:20965333 original size:132 final size:131
Alignment explanation
Indices: 20965091--20965880 Score: 768
Period size: 132 Copynumber: 6.1 Consensus size: 131
20965081 CACCCTACCT
* ** * * * **
20965091 AATACAGAGACGCCAAATCCGCTACCCTCGATCTGCTCTTTGACAATACAGAGGTGCCAAATCTA
1 AATACAGAGACGTC-AATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTA
* * * ** * * * *
20965156 CCATTTTCGACCTGCTCTCTGACAATACAGAGATACCAAATCTGCTATCTTCGATTTTCTCTTTA
65 CTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTG
20965221 AC
130 AC
* * *
20965223 AATATAGAGACGTCAATCCTACTATCTTCGATCTGCTCTCTTACAATATAGAGACGCCAAATCTA
1 AATACAGAGACGTCAAT-CTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTA
* * *
20965288 CTATCTTCGATCTGCTTTCTGACAATACAGTGACGCCAAATCTGCTATCTTCGGTCTGCTCTCTG
65 CTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTG
20965353 AC
130 AC
* *
20965355 AATACAGAGACGCCAA-AT-CTA-C-T--A--T-CT-T-TG---AT-CAGAGACGCCAAATCTAC
1 AATACAGAGACGTCAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTAC
* * * *
20965405 TATCTTTGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATCTTCGATCTGCTCCCTGA
66 TATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
20965470 C
131 C
* * * * * * *
20965471 AATACAGGGGCGCCAAATCTATTATCTTCGATCTGCTCTCTAACAATACAGGGACGCCAAATCTG
1 AATACAGAGACGTC-AATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTA
* ** * *
20965536 TTATCTTCGATCTGCTCTCTGACAATACAGAGACATCAAATCTACTAATCTTCGATATGCTCTCT
65 CTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCT
20965601 GAC
129 GAC
* * * * * **
20965604 AATATAGAGACGATAAATCTGCTAATCTCCGATCTGCTCTCTGATAATACAGAGACAACAAATCT
1 AATACAGAGACG-TCAATCTACT-ATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* * * * * * * * * *
20965669 GCTATC-GCTGATCTGCTCTCTGACCATACAGGGATGCCAAACCAGCTATTTTCAATCTGCTCTT
64 ACTATCTTC-GATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTC
20965733 TGAC
128 TGAC
* * * * *
20965737 AATACAGAGATGCTAAATCTGCTATCTTCGATTTGCTCTCTGACAATACAGAGACGCCAAATCTG
1 AATACAGAGACG-TCAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTA
* * * * *
20965802 CTATCTTTGATCTGCTCTTTGACAATACAGAGACGCCAAATCTGCCATCTTTC-ATCTGCCCTTT
65 CTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC-TTCGATCTGCTCTCT
20965866 GAC
129 GAC
20965869 AATACAGAGACG
1 AATACAGAGACG
20965881 CCAAATCGGC
Statistics
Matches: 538, Mismatches: 97, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
116 89 0.17
117 4 0.01
118 1 0.00
119 2 0.00
120 2 0.00
121 2 0.00
122 2 0.00
123 2 0.00
125 2 0.00
126 2 0.00
127 2 0.00
128 2 0.00
129 3 0.01
130 1 0.00
131 5 0.01
132 272 0.51
133 75 0.14
134 70 0.13
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (131 bp):
AATACAGAGACGTCAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTAC
TATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
C
Found at i:20965399 original size:28 final size:28
Alignment explanation
Indices: 20965359--20965415 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20965349 TCTGACAATA
20965359 CAGAGACGCCAAATCTACTATCTTTGAT
1 CAGAGACGCCAAATCTACTATCTTTGAT
20965387 CAGAGACGCCAAATCTACTATCTTTGAT
1 CAGAGACGCCAAATCTACTATCTTTGAT
20965415 C
1 C
20965416 TACTCTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (28 bp):
CAGAGACGCCAAATCTACTATCTTTGAT
Found at i:20965439 original size:72 final size:72
Alignment explanation
Indices: 20965319--20965459 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
20965309 ACAATACAGT
* * * *
20965319 GACGCCAAATCTGCTATCTTCGGTCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTTT
1 GACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTATCTTC
20965384 GATCAGA
66 GATCAGA
* * *
20965391 GACGCCAAATCTACTATCTTTGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATCTTC
1 GACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTATCTTC
20965456 GATC
66 GATC
20965460 TGCTCCCTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (72 bp):
GACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTATCTTC
GATCAGA
Found at i:20965441 original size:44 final size:44
Alignment explanation
Indices: 20965387--20965894 Score: 597
Period size: 44 Copynumber: 11.5 Consensus size: 44
20965377 TATCTTTGAT
* * *
20965387 CAGAGACGCCAAATCTACTATCTTTGATCTACTCTCTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* *
20965431 CAGGGACGCCAAATCTGCTATCTTCGATCTGCTCCCTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* * ** *
20965475 CAGGGGCGCCAAATCTATTATCTTCGATCTGCTCTCTAACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* *
20965519 CAGGGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
** * *
20965563 CAGAGACATCAAATCTACTAATCTTCGATATGCTCTCTGACAATA
1 CAGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATA
* ** * *
20965608 TAGAGACGATAAATCTGCTAATCTCCGATCTGCTCTCTGATAATA
1 CAGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATA
** * *
20965653 CAGAGACAACAAATCTGCTATC-GCTGATCTGCTCTCTGACCATA
1 CAGAGACGCCAAATCTGCTATCTTC-GATCTGCTCTCTGACAATA
* * * * * * *
20965697 CAGGGATGCCAAACCAGCTATTTTCAATCTGCTCTTTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* * *
20965741 CAGAGATGCTAAATCTGCTATCTTCGATTTGCTCTCTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* *
20965785 CAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTTTGACAATA
1 CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
* * *
20965829 CAGAGACGCCAAATCTGCCATCTTTC-ATCTGCCCTTTGACAATA
1 CAGAGACGCCAAATCTGCTATC-TTCGATCTGCTCTCTGACAATA
*
20965873 CAGAGACGCCAAATCGGCTATC
1 CAGAGACGCCAAATCTGCTATC
20965895 GGTGATCTAC
Statistics
Matches: 398, Mismatches: 62, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
43 1 0.00
44 317 0.80
45 80 0.20
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (44 bp):
CAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATA
Found at i:20965476 original size:116 final size:116
Alignment explanation
Indices: 20965272--20965503 Score: 374
Period size: 116 Copynumber: 2.0 Consensus size: 116
20965262 CTTACAATAT
* * *
20965272 AGAGACGCCAAATCTACTATCTTCGATCTGCTTTCTGACAATACAGTGACGCCAAATCTGCTATC
1 AGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATC
* * *
20965337 TTCGGTCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTTTGATC
66 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTACTATCTTCGATC
*
20965388 AGAGACGCCAAATCTACTATCTTTGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATC
1 AGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATC
* * *
20965453 TTCGATCTGCTCCCTGACAATACAGGGGCGCCAAATCTATTATCTTCGATC
66 TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTACTATCTTCGATC
20965504 TGCTCTCTAA
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 106 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (116 bp):
AGAGACGCCAAATCTACTATCTTCGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATC
TTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCTACTATCTTCGATC
Found at i:20965499 original size:160 final size:160
Alignment explanation
Indices: 20965228--20965887 Score: 457
Period size: 160 Copynumber: 3.9 Consensus size: 160
20965218 TTAACAATAT
* * * *
20965228 AGAGACGTCAATCCTACTATCTTCGATCTGCTCTCTTACAATATAGAGACGCCAAATCTACTATC
1 AGAGACGCCAATCCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTATC
** * * * *
20965293 TTCGATCTGCTTTCTGACAATACAGTGACGCCAAATCTGCTATCTTCGGTCTGCTCTCTGACAAT
66 TTCGATCTGCTCCCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAAT
20965358 ACAGAGACGCCAAATCTACTATCTTTGATC
131 ACAGAGACGCCAAATCTACTATCTTTGATC
* * *
20965388 AGAGACGCCAAAT-CTACTATCTTTGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTAT
1 AGAGACGCC-AATCCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTAT
* *
20965452 CTTCGATCTGCTCCCTGACAATACAGGGGCGCCAAATCTATTATCTTCGATCTGCTCTCTAACAA
65 CTTCGATCTGCTCCCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAA
*
20965517 TACAGGGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATAC
130 TACAGAGACGCCAAATC---TA-C-T--A--T-CT-T-TG---AT-C
* * * * * ** *
20965564 AGAGACATCAAAT-CTACTAATCTTCGATATGCTCTCTGACAATATAGAGACGATAAATCTGCTA
1 AGAGAC-GCCAATCCTACT-ATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACT-
* * * * ** * * *
20965628 ATCTCCGATCTGCTCTCTGATAATACAGAGACAACAAATCTGCTATC-GCTGATCTGCTCTCTGA
63 ATCTTCGATCTGCTCCCTGACAATACAGGGACGCCAAATCTACTATCTTC-GATCTGCTCTCTAA
* * * * *
20965692 CCATACAGGGATGCCAAACCAGCTATTTTCAATCTGCTCTTTGACAATAC
127 CAATACAGAGACGCC--A--A---A---TCTA-CT-ATCTTTG---AT-C
* * * * * *
20965742 AGAGATGCTAAAT-CTGCTATCTTCGATTTGCTCTCTGACAATACAGAGACGCCAAATCTGCTAT
1 AGAGACGC-CAATCCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTAT
* ** * * * * * *
20965806 CTTTGATCTGCTCTTTGACAATACAGAGACGCCAAATCTGCCATCTTTC-ATCTGCCCTTTGACA
65 CTTCGATCTGCTCCCTGACAATACAGGGACGCCAAATCTACTATC-TTCGATCTGCTCTCTAACA
20965870 ATACAGAGACGCCAAATC
129 ATACAGAGACGCCAAATC
20965888 GGCTATCGGT
Statistics
Matches: 406, Mismatches: 60, Indels: 62
0.77 0.11 0.12
Matches are distributed among these distances:
160 126 0.31
161 3 0.01
163 2 0.00
164 1 0.00
165 1 0.00
166 2 0.00
167 1 0.00
169 2 0.00
170 2 0.00
171 1 0.00
172 3 0.01
174 1 0.00
175 2 0.00
176 78 0.19
177 80 0.20
178 87 0.21
179 1 0.00
180 3 0.01
181 1 0.00
182 1 0.00
183 1 0.00
184 1 0.00
185 4 0.01
188 2 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (160 bp):
AGAGACGCCAATCCTACTATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTACTATC
TTCGATCTGCTCCCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAAT
ACAGAGACGCCAAATCTACTATCTTTGATC
Found at i:20965543 original size:204 final size:204
Alignment explanation
Indices: 20965191--20965813 Score: 649
Period size: 204 Copynumber: 3.0 Consensus size: 204
20965181 TACAGAGATA
* * * * * * *
20965191 CCAAATCTGCTATCTTCGATTTTCTCTTTAACAATATAGAGACGTC-AATCCTACTATCTTCGAT
1 CCAAATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGACGACAAAT-CTGCTATCTTCGAT
* * * * *
20965255 CTGCTCTCTTACAATATAGAGACGCCAAATCTACTATCTTCGATCTGCTTTCTGACAATACAGTG
65 CTGCTCTCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAG
*
20965320 ACGCCAAATCTGCTATCTTCGGTCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTTTG
130 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTTTG
20965385 ATCAGAGACG
195 ATCAGAGACG
* * * *
20965395 CCAAATCTACTATCTTTGATCTACTCTCTGACAATACAGGGACGCCAAATCTGCTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGACGACAAATCTGCTATCTTCGATC
* * * * *
20965460 TGCTCCCTGACAATACAGGGGCGCCAAATCTATTATCTTCGATCTGCTCTCTAACAATACAGGGA
66 TGCTCTCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGA
* * *
20965525 CGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACATCAAATCTACTAATCTTCG
131 CGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAC-GC----C-A--AATCTAC-
*
20965590 ATATGCTCTCTGACAATATAGAGACG
187 -TAT-CT-T-TG---AT-CAGAGACG
** * * * * *
20965616 ATAAATCTGCTAATCTCCGATCTGCTCTCTGATAATACAGAGACAACAAATCTGCTATC-GCTGA
1 CCAAATCTGCT-ATCTTCGATCTACTCTCTGACAATACAGAGACGACAAATCTGCTATCTTC-GA
* * * * * *
20965680 TCTGCTCTCTGACCATACAGGGATGCCAAA-CCAGCTATTTTCAATCTGCTCTTTGACAATACAG
64 TCTGCTCTCTGACAATACAGGGACGCCAAATCTA-CTATCTTCGATCTGCTCTCTGACAATACAG
* * * *
20965744 AGATGCTAAATCTGCTATCTTCGATTTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCTT
128 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTT
20965809 TGATC
193 TGATC
20965814 TGCTCTTTGA
Statistics
Matches: 345, Mismatches: 53, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
204 150 0.43
205 4 0.01
206 2 0.01
209 3 0.01
210 2 0.01
211 2 0.01
212 9 0.03
214 9 0.03
215 2 0.01
216 2 0.01
217 3 0.01
220 2 0.01
221 19 0.06
222 136 0.39
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (204 bp):
CCAAATCTGCTATCTTCGATCTACTCTCTGACAATACAGAGACGACAAATCTGCTATCTTCGATC
TGCTCTCTGACAATACAGGGACGCCAAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGA
CGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTACTATCTTTGA
TCAGAGACG
Found at i:20972065 original size:76 final size:76
Alignment explanation
Indices: 20971973--20972120 Score: 296
Period size: 76 Copynumber: 1.9 Consensus size: 76
20971963 ATGAATAATG
20971973 ACTTTCGGTACCATTGGCATTTCAACTTCATTATTTCTTGGTAAAGAAATAATGATCTTTGGTCG
1 ACTTTCGGTACCATTGGCATTTCAACTTCATTATTTCTTGGTAAAGAAATAATGATCTTTGGTCG
20972038 GTTTTGAAGAA
66 GTTTTGAAGAA
20972049 ACTTTCGGTACCATTGGCATTTCAACTTCATTATTTCTTGGTAAAGAAATAATGATCTTTGGTCG
1 ACTTTCGGTACCATTGGCATTTCAACTTCATTATTTCTTGGTAAAGAAATAATGATCTTTGGTCG
20972114 GTTTTGA
66 GTTTTGA
20972121 TTCTTCAGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (76 bp):
ACTTTCGGTACCATTGGCATTTCAACTTCATTATTTCTTGGTAAAGAAATAATGATCTTTGGTCG
GTTTTGAAGAA
Found at i:20977279 original size:16 final size:16
Alignment explanation
Indices: 20977258--20977288 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20977248 ATGAGCTGGT
20977258 TAGCCATGTATAACAG
1 TAGCCATGTATAACAG
20977274 TAGCCATGTATAACA
1 TAGCCATGTATAACA
20977289 TATATTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (16 bp):
TAGCCATGTATAACAG
Found at i:20977340 original size:36 final size:38
Alignment explanation
Indices: 20977266--20977349 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 38
20977256 GTTAGCCATG
* * *
20977266 TATAACAGTAGCCATGTATAACATATATTAAGCAACAA
1 TATACCAGCAGCCATGTATAACATACATTAAGCAACAA
*
20977304 TATACCAGCAGCCATGTATACCA-ACA-TAAGCAACAA
1 TATACCAGCAGCCATGTATAACATACATTAAGCAACAA
20977340 TATACCAGCA
1 TATACCAGCA
20977350 ACAATATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 20 0.48
37 2 0.05
38 20 0.48
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (38 bp):
TATACCAGCAGCCATGTATAACATACATTAAGCAACAA
Found at i:20977367 original size:36 final size:36
Alignment explanation
Indices: 20977294--20977370 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
20977284 TAACATATAT
* * * *
20977294 TAAGCAACAATATACCAGCAGCCATGTATACCAACA
1 TAAGCAACAATATACCAGCAACAATATATACAAACA
20977330 TAAGCAACAATATACCAGCAACAATAT-TACAATACA
1 TAAGCAACAATATACCAGCAACAATATATACAA-ACA
20977366 TAAGC
1 TAAGC
20977371 TAGTTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 4 0.11
36 32 0.89
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (36 bp):
TAAGCAACAATATACCAGCAACAATATATACAAACA
Found at i:20977727 original size:3 final size:3
Alignment explanation
Indices: 20977712--20977762 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
20977702 CTATTTTTCC
* * * *
20977712 TCT TCT CCT TCT TCT TCT TCT TCT AC- TCC TCT TCT TCT TCT TCT TTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
20977759 TCT T
1 TCT T
20977763 TTTTTCTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:20977746 original size:20 final size:21
Alignment explanation
Indices: 20977716--20977755 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
20977706 TTTTCCTCTT
20977716 CTCCTTCTTCTTCTTCTTCTA
1 CTCCTTCTTCTTCTTCTTCTA
20977737 CTCC-TCTTCTTCTTCTTCT
1 CTCCTTCTTCTTCTTCTTCT
20977756 TTTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (21 bp):
CTCCTTCTTCTTCTTCTTCTA
Found at i:20983812 original size:30 final size:30
Alignment explanation
Indices: 20983778--20983838 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20983768 TCCTTAACTC
20983778 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
20983808 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
20983838 A
1 A
20983839 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:20989350 original size:217 final size:216
Alignment explanation
Indices: 20988974--20989387 Score: 519
Period size: 217 Copynumber: 1.9 Consensus size: 216
20988964 GAGAAAGATT
* * * * *
20988974 ATTGAAGAGATTCCATCTAAAGACTCATTTGATTTAACTGATGAATCAGAAACTAAATCAAACTC
1 ATTGAAGAGATTCCACCTAAAGACTCATCTAATTCAACTGATGAACCAGAAACTAAATCAAACTC
* * *
20989039 CACTTTATAGAGGACATACCTCTGAAGGAAATCATCGATAATAAAGCTCGATCCAAGAAGCCAAA
66 CACTTTATAGAAGACATACCTCTAAAGGAAATCATCGATAATAAACCTCGATCCAAGAAGCCAAA
* * * * * *
20989104 TGTTCCTATGACTGCACAACAACGTAACAATAGGATAAAGCAAGTAGGTGTACCTTCTTTGCTTG
131 TGTGCATATGACTGCACAACAACGTAACAAGAAGATAAAGCAAGCAAGTGTACCTTCTTTGCTTG
20989169 CTGAAGCTGCTGCCAAGGTAC
196 CTGAAGCTGCTGCCAAGGTAC
** *
20989190 ATTGAAGAGATTCCACCTAAAGACTCATCTAATTCAGTTGATGAACCAGAAAC-AGAATCAGAC-
1 ATTGAAGAGATTCCACCTAAAGACTCATCTAATTCAACTGATGAACCAGAAACTA-AATCAAACT
* * * * **
20989253 CCTAGCTTTGTAGAAGACATACCTCTAAAGGAAATCATTGGTGGA-AAACCTCGATCCAAGTGGC
65 CC-A-CTTTATAGAAGACATACCTCTAAAGGAAATCATCGAT-AATAAACCTCGATCCAAGAAGC
* * * * *
20989317 CAAATGTGCATATGACTGCACAACAATGTAACAAGAAGATGAAGTAAGCAAGTGTACTTTCTTTT
127 CAAATGTGCATATGACTGCACAACAACGTAACAAGAAGATAAAGCAAGCAAGTGTACCTTCTTTG
20989382 CTTGCT
192 CTTGCT
20989388 AAAGATAAGG
Statistics
Matches: 166, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
215 3 0.02
216 54 0.33
217 108 0.65
218 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (216 bp):
ATTGAAGAGATTCCACCTAAAGACTCATCTAATTCAACTGATGAACCAGAAACTAAATCAAACTC
CACTTTATAGAAGACATACCTCTAAAGGAAATCATCGATAATAAACCTCGATCCAAGAAGCCAAA
TGTGCATATGACTGCACAACAACGTAACAAGAAGATAAAGCAAGCAAGTGTACCTTCTTTGCTTG
CTGAAGCTGCTGCCAAGGTAC
Found at i:21003082 original size:17 final size:17
Alignment explanation
Indices: 21003048--21003093 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
21003038 TGTTAAATTG
*
21003048 TTTTATTTGT-AA-TTA
1 TTTTATTTATAAATTTA
21003063 TTTTATTTATAAATTTA
1 TTTTATTTATAAATTTA
21003080 TTTT-TTTAATAAAT
1 TTTTATTT-ATAAAT
21003094 GAATTTCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 5 0.19
17 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATTTATAAATTTA
Found at i:21003161 original size:9 final size:9
Alignment explanation
Indices: 21003142--21003182 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
21003132 TTATAAATAT
21003142 TTTTATG-A
1 TTTTATGCA
21003150 TTTTATGCA
1 TTTTATGCA
21003159 TTTTATGCA
1 TTTTATGCA
21003168 TTTTATGCA
1 TTTTATGCA
21003177 TTTTAT
1 TTTTAT
21003183 AAAATCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (9 bp):
TTTTATGCA
Found at i:21008576 original size:33 final size:31
Alignment explanation
Indices: 21008491--21008576 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 31
21008481 AATATTTTTT
*
21008491 TTCTATTTAAAATAAATATAAGTTTAATATATA
1 TTCTATTT--AATATATATAAGTTTAATATATA
*
21008524 TTCTATTTAATATAAATATAAGTTTAATA-ATTT
1 TTCTATTTAATAT--ATATAAGTTTAATATA-TA
21008557 TTAACTATTTAATATATATA
1 TT--CTATTTAATATATATA
21008577 TAATTTTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
31 4 0.09
32 1 0.02
33 30 0.65
35 11 0.24
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (31 bp):
TTCTATTTAATATATATAAGTTTAATATATA
Found at i:21015701 original size:26 final size:26
Alignment explanation
Indices: 21015670--21015777 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
21015660 TGAAATGCCC
*
21015670 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
21015696 ATCATGGAACATTTACGTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21015722 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21015748 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21015774 ATCA
1 ATCA
21015778 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:21016722 original size:42 final size:42
Alignment explanation
Indices: 21016669--21016750 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
21016659 TATTTAACTC
21016669 TTTGATGTCATTTATAATTCTATACAACTCCCCATTTCTTTT
1 TTTGATGTCATTTATAATTCTATACAACTCCCCATTTCTTTT
* * * *
21016711 TTTGATGTCATTTATACTTCTATAGAACTTCTCATTTCTT
1 TTTGATGTCATTTATAATTCTATACAACTCCCCATTTCTT
21016751 ATCTTTGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTGATGTCATTTATAATTCTATACAACTCCCCATTTCTTTT
Found at i:21017363 original size:11 final size:11
Alignment explanation
Indices: 21017347--21017371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21017337 CTTACGAACC
21017347 CATTTCTCAAT
1 CATTTCTCAAT
21017358 CATTTCTCAAT
1 CATTTCTCAAT
21017369 CAT
1 CAT
21017372 GTCGTACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
CATTTCTCAAT
Found at i:21027542 original size:44 final size:44
Alignment explanation
Indices: 21027464--21027762 Score: 180
Period size: 44 Copynumber: 6.7 Consensus size: 44
21027454 ATTGAAGGCT
* **
21027464 TTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGTAGTAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGTC
* *
21027508 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAG-TAAGTC
* * * * * * *
21027553 TTATTTCCTTGAAGATACAGTGGAACAGATTG-AGCTATAAATAAATAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG---T-AGT--A-AG-TC
* * ** * * **
21027604 TTATCTCTCTGAAGTTGCAGTAGATTAGAC--CA-TAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGTC
* ** *
21027645 TTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTAGCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGTC
* *
21027689 TTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAG-A-TAACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGT-A-AG-TC
* *
21027734 TTATCTCCCTGAAGTCGCAATGGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
21027763 TCAAAGCCAT
Statistics
Matches: 193, Mismatches: 45, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
41 26 0.13
42 1 0.01
43 4 0.02
44 72 0.37
45 58 0.30
46 5 0.03
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 23 0.12
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGTC
Found at i:21027760 original size:89 final size:88
Alignment explanation
Indices: 21027644--21027940 Score: 234
Period size: 89 Copynumber: 3.3 Consensus size: 88
21027634 CATAGCAAAC
*
21027644 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTAGCAAGTCTTATCTCCTTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA-GTTGAAGTAGCAAGTCTTATCTCCTTGAAGTTGCAG
21027709 TGGAGCAAACTGAAGATAACAGAT
65 TGGAGCAAACTGAAGATAACAGAT
* * * * * * * *
21027733 CTTATCTCCCTGAAGTCGCAATGGAGCAGATCAA--AGCCATAATCCTTATCT-TTATAAAGTCG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGTTGAAGTAG-CA-AGT-CTTATCTCCT-TGAAGTTG
** * * * *
21027795 CAGTAAAG-AAGGA-TAAAAATACACAAAC
62 CAGTGGAGCAA--ACTGAAGATA-ACAGAT
*
21027823 CTTATCTCCCTGAAGTTGCAGTGGGGCAAGTTGAAGTTATG--AGTCTTATCTTCC-TGAAGTTG
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-AGTTGAAG-TA-GCAAGTCTTATC-TCCTTGAAGTTG
*
21027885 CAGTGGAGCAAACTGAAGATAGC-GAAT
62 CAGTGGAGCAAACTGAAGATAACAG-AT
* * *
21027912 CTTATCTCTCTGAAGTTGTAGTAGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
21027941 ATTAAAGCTA
Statistics
Matches: 156, Mismatches: 35, Indels: 35
0.69 0.15 0.15
Matches are distributed among these distances:
86 2 0.01
87 2 0.01
88 11 0.07
89 76 0.49
90 53 0.34
91 10 0.06
94 1 0.01
95 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (88 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGTTGAAGTAGCAAGTCTTATCTCCTTGAAGTTGCAGT
GGAGCAAACTGAAGATAACAGAT
Found at i:21028098 original size:44 final size:44
Alignment explanation
Indices: 21027639--21028169 Score: 149
Period size: 44 Copynumber: 11.8 Consensus size: 44
21027629 TAGACCATAG
* * * * *
21027639 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG-TA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* * * * * **
21027682 GCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGATAA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG-CCA
* * * * **
21027728 CAGATCTTATCTCCCTGAAGTCGCAATGGAGCAGATCAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* *** * * ** * ** **
21027772 -TAATCCTTATCTTTATAAAGTCGCAGTAAAGAAGGATAAAAATACA
1 CAAAT-CTTATCTCCCTGAAGTTGCAGTGGAGTA-GAT-TGAAGCCA
* * * **
21027818 CAAACCTTATCTCCCTGAAGTTGCAGTGGGGCA-AGTTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTGAAGCCA
** * * * * * **
21027862 TGAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAAACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* * * * * * *
21027906 GCGAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* * * * * * ** *
21027951 TAAATCCTATAC-CTCTAAAGTTGCAGTAG-GTCGGATCAAACCCA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAGT-AGATTGAAGCCA
*
21027995 CCATGGTGAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCA
1 -CA-----AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* * **
21028045 CAAACCTTATC-CCTCTGAAGTTGCAGTGGGGTA-AGTTGAAGTTA
1 CAAATCTTATCTCC-CTGAAGTTGCAGTGGAGTAGA-TTGAAGCCA
* * * * * * **
21028089 CAAGTCTTATTTCCCTGAAGTCGTAGTGGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
* * * *
21028133 GCAAATCTTATCTCCTTGAAGATGCAATGAAGTAGAT
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
21028170 CAAGCTACAA
Statistics
Matches: 353, Mismatches: 110, Indels: 47
0.69 0.22 0.09
Matches are distributed among these distances:
43 6 0.02
44 185 0.52
45 102 0.29
46 25 0.07
47 2 0.01
49 3 0.01
50 28 0.08
51 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCCA
Found at i:21028179 original size:88 final size:88
Alignment explanation
Indices: 21028005--21028179 Score: 192
Period size: 88 Copynumber: 2.0 Consensus size: 88
21027995 CCATGGTGAA
* * * * *
21028005 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCCCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTCGTAGTGGAGCAGACTGAAGACACAAACCTTATCCCTCTGAAGATGCA
* ** * * *
21028070 GTGGGGTAAGTTGAAGTTACAAG
66 ATGAAGTAAGATCAAGCTACAAG
* * *
21028093 TCTTATTTCCCTGAAGTCGTAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCT-TGAAGATG
1 TCTTATCTCCCTGAAGTCGTAGTGGAGCAGACTGAAGACA-CAAACCTTATC-CCTCTGAAGATG
21028157 CAATGAAGT-AGATCAAGCTACAA
64 CAATGAAGTAAGATCAAGCTACAA
21028180 TAGCAAAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
88 45 0.63
89 23 0.32
90 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTCGTAGTGGAGCAGACTGAAGACACAAACCTTATCCCTCTGAAGATGCA
ATGAAGTAAGATCAAGCTACAAG
Found at i:21030176 original size:21 final size:20
Alignment explanation
Indices: 21030135--21030178 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
21030125 CATCATTTGT
21030135 TTTAAATTTATTCATTATTA
1 TTTAAATTTATTCATTATTA
* * *
21030155 TTTAGATTCTATTTATTTTTA
1 TTTAAATT-TATTCATTATTA
21030176 TTT
1 TTT
21030179 TGCCTTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTAAATTTATTCATTATTA
Found at i:21031347 original size:36 final size:35
Alignment explanation
Indices: 21031271--21031347 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 35
21031261 TAAAGTAAAT
* *
21031271 AAAGAATTAAACAAATAAAGAAACAAAAGAAATAG
1 AAAGAATTAAACAAATAAAGAAACAAAACAAAGAG
* *
21031306 AAAGAA-TAAACAGAATAAGGAGAACGAAACAAAGAG
1 AAAGAATTAAACA-AATAAAGA-AACAAAACAAAGAG
21031342 AAAGAA
1 AAAGAA
21031348 AGTGGAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 6 0.17
35 13 0.36
36 17 0.47
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (35 bp):
AAAGAATTAAACAAATAAAGAAACAAAACAAAGAG
Found at i:21035132 original size:5 final size:5
Alignment explanation
Indices: 21035122--21035159 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
21035112 CTGTGTATTC
21035122 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
21035160 TCACAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:21040074 original size:39 final size:39
Alignment explanation
Indices: 21040020--21040111 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
21040010 CAAGACACTG
*
21040020 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTA
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTA
* *
21040059 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTA
21040098 GAAATGTATCCGGG
1 GAAATGTATCCGGG
21040112 ACTTTCCGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTA
Found at i:21047661 original size:12 final size:12
Alignment explanation
Indices: 21047644--21047673 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
21047634 GTGTTAACAG
21047644 ACTTAATTCATT
1 ACTTAATTCATT
21047656 ACTTAATTCATT
1 ACTTAATTCATT
21047668 ACTTAA
1 ACTTAA
21047674 ACAGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (12 bp):
ACTTAATTCATT
Found at i:21065530 original size:13 final size:13
Alignment explanation
Indices: 21065511--21065543 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
21065501 AGGATTTTGA
21065511 TTATCTGA-TCTG
1 TTATCTGACTCTG
21065523 TATATCTGACTCTG
1 T-TATCTGACTCTG
21065537 TTATCTG
1 TTATCTG
21065544 GATTTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 13 0.68
14 5 0.26
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (13 bp):
TTATCTGACTCTG
Found at i:21070924 original size:46 final size:46
Alignment explanation
Indices: 21070868--21071043 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
21070858 TGGTTGAGCA
*
21070868 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *** * * * *
21070914 TCCGAACTCGTTGAGTTGAGCCCGAGTTCGAGAGATGTAT-CTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-ACG
* *
21070961 TCCGAGCTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
21071007 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21071044 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
46 71 0.68
47 34 0.32
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:21071024 original size:93 final size:93
Alignment explanation
Indices: 21070865--21071035 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
21070855 GGATGGTTGA
* * *
21070865 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
21070930 TGAGCCCGAGTTCGAGAGATGTATCTAG
66 TGAGCCCGAGTTCGAGAGATGTATCTAG
* * *
21070958 GCATCCGAGCTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
21071023 TGAGTCCGAGTTC
66 TGAGCCCGAGTTC
21071036 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGCCCGAGTTCGAGAGATGTATCTAG
Found at i:21076685 original size:31 final size:30
Alignment explanation
Indices: 21076636--21076703 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
21076626 TTTTTAAATG
* *
21076636 TGTATA-ATTGAATCAAAA-TCAAAGTTTCT
1 TGTATATATTGAACCAAAATTC-AAGTTTCA
21076665 TGTATATATATGAACCAAAATTCAAGTTTCA
1 TGTATATAT-TGAACCAAAATTCAAGTTTCA
*
21076696 TGTGTATA
1 TGTATATA
21076704 ACAAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.18
30 2 0.06
31 23 0.70
32 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (30 bp):
TGTATATATTGAACCAAAATTCAAGTTTCA
Found at i:21081723 original size:30 final size:30
Alignment explanation
Indices: 21081706--21081852 Score: 97
Period size: 30 Copynumber: 4.9 Consensus size: 30
21081696 TTTTTATAAT
*
21081706 TTGATAGTTGAAGCCATCCCTTTTCATAGA
1 TTGATAGTCGAAGCCATCCCTTTTCATAGA
**
21081736 TTGATAGTCGAAGCCATCCCAATTCATAG-
1 TTGATAGTCGAAGCCATCCCTTTTCATAGA
* * * *
21081765 TACGATAG-CTGAAGTCAACCCTTTACATA-A
1 T-TGATAGTC-GAAGCCATCCCTTTTCATAGA
* *
21081795 TTTGATGGTCGTCA-CCATCCCTTTTCATA-A
1 -TTGATAGTCG-AAGCCATCCCTTTTCATAGA
* * * *
21081825 TTTGATAGCCAAAGCTATTCCTTTTCAT
1 -TTGATAGTCGAAGCCATCCCTTTTCAT
21081853 TTGTCGAGGA
Statistics
Matches: 89, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
29 3 0.03
30 83 0.93
31 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (30 bp):
TTGATAGTCGAAGCCATCCCTTTTCATAGA
Found at i:21081832 original size:60 final size:60
Alignment explanation
Indices: 21081630--21081833 Score: 178
Period size: 60 Copynumber: 3.4 Consensus size: 60
21081620 AATAATAATA
* * * ** **
21081630 CATCCATTTTCATAATTCGATAACTGAAGTTATCCCTTTTCATTGTTCAATGGTCGTCAC
1 CATCCCTTTTCATAATTCGATAGCTGAAGTCATCCCTTTTCATAATTTGATGGTCGTCAC
** * * * * * *
21081690 CATCTTTTTTTATAATTTGATAGTTGAAGCCATCCCTTTTCATAGA-TTGATAGTCG-AAGC
1 CATCCCTTTTCATAATTCGATAGCTGAAGTCATCCCTTTTCATA-ATTTGATGGTCGTCA-C
** * * * *
21081750 CATCCCAATTCATAGTACGATAGCTGAAGTCAACCCTTTACATAATTTGATGGTCGTCAC
1 CATCCCTTTTCATAATTCGATAGCTGAAGTCATCCCTTTTCATAATTTGATGGTCGTCAC
*
21081810 CATCCCTTTTCATAATTTGATAGC
1 CATCCCTTTTCATAATTCGATAGC
21081834 CAAAGCTATT
Statistics
Matches: 107, Mismatches: 33, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
59 2 0.02
60 104 0.97
61 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (60 bp):
CATCCCTTTTCATAATTCGATAGCTGAAGTCATCCCTTTTCATAATTTGATGGTCGTCAC
Found at i:21084258 original size:29 final size:29
Alignment explanation
Indices: 21084216--21084291 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
21084206 GAACTATTAT
*
21084216 CATGGCCCGAAGCCAAATCATTCGATATG
1 CATGACCCGAAGCCAAATCATTCGATATG
*
21084245 CATGACCCGAAGCCAAATCATTCGGTATG
1 CATGACCCGAAGCCAAATCATTCGATATG
*
21084274 CTTGACCCGAAGCCAAAT
1 CATGACCCGAAGCCAAAT
21084292 GGTAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (29 bp):
CATGACCCGAAGCCAAATCATTCGATATG
Found at i:21084773 original size:17 final size:19
Alignment explanation
Indices: 21084751--21084787 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21084741 TAGTCTTTAT
21084751 TTCACA-AATAC-ATAAAA
1 TTCACACAATACAATAAAA
*
21084768 TTCACACAATTCAATAAAA
1 TTCACACAATACAATAAAA
21084787 T
1 T
21084788 CCATGCTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (19 bp):
TTCACACAATACAATAAAA
Found at i:21091423 original size:94 final size:93
Alignment explanation
Indices: 21091220--21091410 Score: 219
Period size: 94 Copynumber: 2.0 Consensus size: 93
21091210 GTAGCCGACG
* * *
21091220 CATGTCCTAGGCAT-GTCTTACACTGGCTCTCATAATGTGACTGATGCATATCCCAGACATGTCT
1 CATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGACTGATGCATATCCCAGACATGTCT
* ***
21091284 TGCACTAGCCCTCGTCTCAATGTCGATGC
66 TACACTAGCCCAAATCTCAATGTC-ATGC
* *
21091313 CATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTG-GTCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGACT-GATGCATATCCCAGACATGTC
*
21091377 TTACACTGGCACACAAATCTC-ATGT-ATTGC
65 TTACACTAGC-C-CAAATCTCAATGTCA-TGC
21091407 CATG
1 CATG
21091411 GTCCAACCAT
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
93 14 0.17
94 59 0.71
95 5 0.06
96 5 0.06
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGACTGATGCATATCCCAGACATGTCT
TACACTAGCCCAAATCTCAATGTCATGC
Found at i:21102772 original size:47 final size:47
Alignment explanation
Indices: 21102667--21103075 Score: 620
Period size: 47 Copynumber: 8.6 Consensus size: 47
21102657 CCCTTCGGGA
* * * * * *
21102667 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
21102714 CCTGTCGCATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21102761 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21102808 CTTATCAGATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21102855 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21102904 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21102951 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21103000 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21103047 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
21103076 TATTCAAATA
Statistics
Matches: 330, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
47 221 0.67
49 109 0.33
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:21102905 original size:96 final size:96
Alignment explanation
Indices: 21102667--21103075 Score: 691
Period size: 96 Copynumber: 4.3 Consensus size: 96
21102657 CCCTTCGGGA
* * * * * *
21102667 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCGCATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
21102730 ACTTTCACATTCATCACATCGACCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
21102761 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAGATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
21102824 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
21102855 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
21102920 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
21102951 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
21103016 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
21103047 CTTATCACATATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
21103076 TATTCAAATA
Statistics
Matches: 296, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
93 1 0.00
94 88 0.30
96 207 0.70
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:21102923 original size:143 final size:141
Alignment explanation
Indices: 21102667--21103075 Score: 638
Period size: 143 Copynumber: 2.9 Consensus size: 141
21102657 CCCTTCGGGA
* * * * * * *
21102667 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCGCATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
21102732 TTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
21102797 GGCTATTAGGC
131 GGCCATTAGGC
* * *
21102808 CTTATCAGATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
* *
21102873 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
21102938 TCGGCCATTAGGC
129 TCGGCCATTAGGC
21102951 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
21103016 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATT
21103076 TATTCAAATA
Statistics
Matches: 243, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
141 45 0.19
143 134 0.55
145 64 0.26
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:21106823 original size:40 final size:40
Alignment explanation
Indices: 21106777--21106856 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
21106767 GGGGTAATTT
21106777 CGTACTTACGCAACTACACAAGCTACTACAGTAATTTTTA
1 CGTACTTACGCAACTACACAAGCTACTACAGTAATTTTTA
*
21106817 CGTACTTACGCAACTACACAATCTACTACAGTAATTTTTA
1 CGTACTTACGCAACTACACAAGCTACTACAGTAATTTTTA
21106857 GTAGTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (40 bp):
CGTACTTACGCAACTACACAAGCTACTACAGTAATTTTTA
Found at i:21113295 original size:15 final size:16
Alignment explanation
Indices: 21113258--21113295 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21113248 ATAAAAAGAT
21113258 TTGATTTGAAAACATA
1 TTGATTTGAAAACATA
* *
21113274 TTTATTTTAAAAC-TA
1 TTGATTTGAAAACATA
21113289 TTGATTT
1 TTGATTT
21113296 AACCCCGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (16 bp):
TTGATTTGAAAACATA
Found at i:21118719 original size:24 final size:24
Alignment explanation
Indices: 21118692--21118764 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
21118682 ATTCAAGCCG
*
21118692 GCACACATAGTGCCATTCGACTTC
1 GCACACATAGTGCCATTCGACTCC
* *
21118716 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCGACTCC
*
21118740 GCACACTTAGTGCCAATATCGACTC
1 GCACACATAGTGCC-AT-TCGACTC
21118765 ATATGATAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 34 0.83
25 2 0.05
26 5 0.12
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (24 bp):
GCACACATAGTGCCATTCGACTCC
Found at i:21122707 original size:41 final size:41
Alignment explanation
Indices: 21122661--21122742 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
21122651 AACCGTTTGG
21122661 TTATGTCCATCTTAAGAAAATGATTAAGGTTGAAAACGTTT
1 TTATGTCCATCTTAAGAAAATGATTAAGGTTGAAAACGTTT
* *
21122702 TTATGTCCATCTTAAGAATATGATTATGGTTGAAAACGTTT
1 TTATGTCCATCTTAAGAAAATGATTAAGGTTGAAAACGTTT
21122743 GCTTAGCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (41 bp):
TTATGTCCATCTTAAGAAAATGATTAAGGTTGAAAACGTTT
Found at i:21126461 original size:48 final size:48
Alignment explanation
Indices: 21126408--21126501 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
21126398 TCCATTGTTA
*
21126408 CTCTTTCCAACTTCCATAGCGGAATTTTCACAGGTTGCAGTAATCCTG
1 CTCTTTCCAACTTCCATAACGGAATTTTCACAGGTTGCAGTAATCCTG
*
21126456 CTCTTTCCCACTTCCATAACGGAATTTTCACAGGTTGCAGTAATCC
1 CTCTTTCCAACTTCCATAACGGAATTTTCACAGGTTGCAGTAATCC
21126502 CGAAGGCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (48 bp):
CTCTTTCCAACTTCCATAACGGAATTTTCACAGGTTGCAGTAATCCTG
Done.