Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 65 of 129
Found at i:12382927 original size:10 final size:10
Alignment explanation
Indices: 12382886--12382930 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
12382876 ACCTCATTTA
12382886 TTCTTTTTTT
1 TTCTTTTTTT
12382896 TTCTTCTCTTTCT
1 TTCTT-T-TTT-T
12382909 TTCCTTTTTTT
1 TT-CTTTTTTT
12382920 TTCTTTTTTT
1 TTCTTTTTTT
12382930 T
1 T
12382931 CCTTCTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 14 0.45
11 4 0.13
12 6 0.19
13 4 0.13
14 3 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:12383163 original size:20 final size:21
Alignment explanation
Indices: 12383123--12383169 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
12383113 AATCCATTTA
12383123 AAAAATTACAATATAATTTTT
1 AAAAATTACAATATAATTTTT
* * *
12383144 GAAAATTATATTAT-ATTTTT
1 AAAAATTACAATATAATTTTT
12383164 AAAAAT
1 AAAAAT
12383170 GAATTTCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AAAAATTACAATATAATTTTT
Found at i:12385602 original size:407 final size:407
Alignment explanation
Indices: 12384847--12385656 Score: 1557
Period size: 407 Copynumber: 2.0 Consensus size: 407
12384837 GCGCACTGAA
* *
12384847 TATGATATTTGATGGATGTCAAATGAGCTAATCATGTTAGGATTGATGCAAATGCTAGTGGTTAC
1 TATGATATTTGATGGAGGCCAAATGAGCTAATCATGTTAGGATTGATGCAAATGCTAGTGGTTAC
*
12384912 TTAATTAGAAGCACGCATGGATTATCTTATGCTTATGAAATTGCAGAGCATATAAGGGTGAGAAG
66 TTAATTAGAAGCACGCATGGATTATCTTATACTTATGAAATTGCAGAGCATATAAGGGTGAGAAG
* *
12384977 TCTAATTTTTTTATTTGAATTATATCTGCATTGAAAGAAGTTTGATTTAATGAAGAGCCAAGGTA
131 TCTAATTTTTTTATCTGAATTATATCCGCATTGAAAGAAGTTTGATTTAATGAAGAGCCAAGGTA
12385042 ATTATATCTCTAAAGAGTTGTACATCCAGTCCAAAGTTGACTGAATCATAAAATGCTTTAACTAA
196 ATTATATCTCTAAAGAGTTGTACATCCAGTCCAAAGTTGACTGAATCATAAAATGCTTTAACTAA
12385107 TGGATGAGTTCGGTAAATTGGCCATAAATAGAAAGTTATGAGAATTTGGTGATCCGTCAACAACT
261 TGGATGAGTTCGGTAAATTGGCCATAAATAGAAAGTTATGAGAATTTGGTGATCCGTCAACAACT
*
12385172 ATGTTAATTCCATTATTAGAGATGACTAAGACAAAAGATCGCAAAGCTATAAAAGTAGATACCTC
326 ATGTTAATTCCATTATTAGAGATGACTAAGACAAAAGATCGCAAAGCTATAAAAGTAAATACCTC
12385237 CACATAATGTGACTCAT
391 CACATAATGTGACTCAT
12385254 TATGATATTTGATGGAGGCCAAATGAGCTAATCATGTTAGGATTGATGCAAATGCTAGTGGTTAC
1 TATGATATTTGATGGAGGCCAAATGAGCTAATCATGTTAGGATTGATGCAAATGCTAGTGGTTAC
12385319 TTAATTAGAAGCACGCATGGATTATCTTATACTTATGAAATTGCAGAGCATATAAGGGTGAGAAG
66 TTAATTAGAAGCACGCATGGATTATCTTATACTTATGAAATTGCAGAGCATATAAGGGTGAGAAG
12385384 TCTAATTTTTTTATCTGAATTATATCCGCATTGAAAGAAGTTTGATTTAATGAAGAGCCAAGGTA
131 TCTAATTTTTTTATCTGAATTATATCCGCATTGAAAGAAGTTTGATTTAATGAAGAGCCAAGGTA
12385449 ATTATATCTCTAAAGAGTTGTACATCCAGTCCAAAGTTGACTGAATCATAAAATGCTTTAACTAA
196 ATTATATCTCTAAAGAGTTGTACATCCAGTCCAAAGTTGACTGAATCATAAAATGCTTTAACTAA
*
12385514 TGGATGAGTTCGGTAAATTGGCCATGAATAGAAAGTTATGAGAATTTGGTGATCCGTCAACAACT
261 TGGATGAGTTCGGTAAATTGGCCATAAATAGAAAGTTATGAGAATTTGGTGATCCGTCAACAACT
12385579 ATGTTAATTCCATTATTAGAGATGACTAAGACAAAAGATCGCAAAGCTATAAAAGTAAATACCTC
326 ATGTTAATTCCATTATTAGAGATGACTAAGACAAAAGATCGCAAAGCTATAAAAGTAAATACCTC
12385644 CACATAATGTGAC
391 CACATAATGTGAC
12385657 CCATCACACT
Statistics
Matches: 396, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
407 396 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (407 bp):
TATGATATTTGATGGAGGCCAAATGAGCTAATCATGTTAGGATTGATGCAAATGCTAGTGGTTAC
TTAATTAGAAGCACGCATGGATTATCTTATACTTATGAAATTGCAGAGCATATAAGGGTGAGAAG
TCTAATTTTTTTATCTGAATTATATCCGCATTGAAAGAAGTTTGATTTAATGAAGAGCCAAGGTA
ATTATATCTCTAAAGAGTTGTACATCCAGTCCAAAGTTGACTGAATCATAAAATGCTTTAACTAA
TGGATGAGTTCGGTAAATTGGCCATAAATAGAAAGTTATGAGAATTTGGTGATCCGTCAACAACT
ATGTTAATTCCATTATTAGAGATGACTAAGACAAAAGATCGCAAAGCTATAAAAGTAAATACCTC
CACATAATGTGACTCAT
Found at i:12386661 original size:31 final size:30
Alignment explanation
Indices: 12386612--12386671 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
12386602 GACGAGTGTT
* *
12386612 ATATTGAACATGTTATCTAACAAGATGTTTA
1 ATATTGAACAGGTAATCTAA-AAGATGTTTA
* *
12386643 ATATTGAATAGGTAATCTAATAGATGTTT
1 ATATTGAACAGGTAATCTAAAAGATGTTT
12386672 TATAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (30 bp):
ATATTGAACAGGTAATCTAAAAGATGTTTA
Found at i:12390616 original size:24 final size:25
Alignment explanation
Indices: 12390570--12390616 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
12390560 ATTAGTGTTT
*
12390570 TATGATTTTTATTTCTTTGATTTAG
1 TATGATTTTTATTTCTTTAATTTAG
12390595 TATG-TTTTTA-TTCTTTTAATTT
1 TATGATTTTTATTTC-TTTAATTT
12390617 GGTGATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 13 0.65
25 4 0.20
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (25 bp):
TATGATTTTTATTTCTTTAATTTAG
Found at i:12393883 original size:42 final size:42
Alignment explanation
Indices: 12393831--12393917 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
12393821 ACCTATTTGC
12393831 CAACCATTTATGGTCCATATTCTATTGGCATACTCTTTGCAG
1 CAACCATTTATGGTCCATATTCTATTGGCATACTCTTTGCAG
12393873 CAACCATTTATGGTCCATATTCTATTGGCATACTCTTTGCAG
1 CAACCATTTATGGTCCATATTCTATTGGCATACTCTTTGCAG
12393915 CAA
1 CAA
12393918 GAATGCTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (42 bp):
CAACCATTTATGGTCCATATTCTATTGGCATACTCTTTGCAG
Found at i:12395468 original size:16 final size:17
Alignment explanation
Indices: 12395447--12395480 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12395437 AGCAAGAATA
*
12395447 ATAAATAA-CCAAAATT
1 ATAAATAATACAAAATT
12395463 ATAAATAATACAAAATT
1 ATAAATAATACAAAATT
12395480 A
1 A
12395481 GCAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAATACAAAATT
Found at i:12398100 original size:17 final size:18
Alignment explanation
Indices: 12398060--12398100 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12398050 AAAATATGAT
*
12398060 AATTTATTTATTGATCAA
1 AATTTATTTATTCATCAA
*
12398078 AA-TTATTT-TTCCTCAA
1 AATTTATTTATTCATCAA
12398094 AATTTAT
1 AATTTAT
12398101 ATAATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
AATTTATTTATTCATCAA
Found at i:12408438 original size:12 final size:12
Alignment explanation
Indices: 12408421--12408445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12408411 CTTGCCTAAG
12408421 AATATTAAATGT
1 AATATTAAATGT
12408433 AATATTAAATGT
1 AATATTAAATGT
12408445 A
1 A
12408446 GTTCACAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATATTAAATGT
Found at i:12414016 original size:101 final size:101
Alignment explanation
Indices: 12413698--12414107 Score: 412
Period size: 101 Copynumber: 4.0 Consensus size: 101
12413688 ACAAAATAAC
* ** ** * * * ** *
12413698 CAACCATCATCATAATGCAAAATATGCAATAGTTTTCACATTTCACCTATCTGATGTCATCGT-G
1 CAACCATCATCACAATGCAAAATACACAATAGTTTTCACA-TTCACAAATGTAATCTCATTATAA
* * * *
12413762 TATTCTATTAAGATAGTTCATCAAGAATCACAATACA
65 TATACTATAAAGATAGTTGATCAACAATCACAATACA
* * * *
12413799 CAACTATCATCACAATGCAAAATACACAATAGTTTTCACATTTCACAAATGTGATTTCATCATAA
1 CAACCATCATCACAATGCAAAATACACAATAGTTTTCACA-TTCACAAATGTAATCTCATTATAA
* *
12413864 TATACTATAAAGATAGTTGATCAACAATCGCAATAGA
65 TATACTATAAAGATAGTTGATCAACAATCACAATACA
* * * * * *
12413901 CAATCATAAACACAATGCAAAATACACTATAGTTTTTACA-ACACCAAA-GTTAATCTCATTATA
1 CAACCATCATCACAATGCAAAATACACAATAGTTTTCACATTCA-CAAATG-TAATCTCATTATA
* * * *
12413964 ATATACTATAAAGATAATTGATTAATAATCATAATACA
64 ATATACTATAAAGATAGTTGATCAACAATCACAATACA
* * * * *
12414002 CAACCATCATCACAATGTAAAACACGCAATAGTTTTCACATTTCACAAATGTAATCTTATTACAA
1 CAACCATCATCACAATGCAAAATACACAATAGTTTTCACA-TTCACAAATGTAATCTCATTATAA
* *
12414067 TATACTATAAAGATGGTTGATCAACAATCATAATACA
65 TATACTATAAAGATAGTTGATCAACAATCACAATACA
12414104 CAAC
1 CAAC
12414108 TATTATACTA
Statistics
Matches: 256, Mismatches: 47, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
100 3 0.01
101 132 0.52
102 118 0.46
103 3 0.01
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (101 bp):
CAACCATCATCACAATGCAAAATACACAATAGTTTTCACATTCACAAATGTAATCTCATTATAAT
ATACTATAAAGATAGTTGATCAACAATCACAATACA
Found at i:12414139 original size:44 final size:44
Alignment explanation
Indices: 12414067--12414151 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
12414057 CTTATTACAA
* * * *
12414067 TATACTATAAAGATGGTTGATCAACAATCATAATACACAACTAT
1 TATACTATAAAGATAGTTAAACAACAATCACAATACACAACTAT
*
12414111 TATACTATAAAGATAGTTAAACAGCAATCACAATACACAAC
1 TATACTATAAAGATAGTTAAACAACAATCACAATACACAAC
12414152 CTGAATCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (44 bp):
TATACTATAAAGATAGTTAAACAACAATCACAATACACAACTAT
Found at i:12418469 original size:24 final size:24
Alignment explanation
Indices: 12418431--12418484 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12418421 CATGCCAAGT
* * *
12418431 CATATATTTAGTAGTTTTAGTTTA
1 CATATATTCAATAGTTTTAGTTAA
12418455 CATATATTCAATAGTTTTAGTTAA
1 CATATATTCAATAGTTTTAGTTAA
12418479 CATATA
1 CATATA
12418485 AAGTTTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (24 bp):
CATATATTCAATAGTTTTAGTTAA
Found at i:12420098 original size:23 final size:24
Alignment explanation
Indices: 12420055--12420101 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12420045 AATTATTAAT
12420055 AAATTTTATAAAATATCAAATATA
1 AAATTTTATAAAATATCAAATATA
*
12420079 AAATTTTTTCAAAA-AT-AAATATA
1 AAATTTTAT-AAAATATCAAATATA
12420102 GATCTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATTTTATAAAATATCAAATATA
Found at i:12424700 original size:62 final size:61
Alignment explanation
Indices: 12424626--12424815 Score: 160
Period size: 62 Copynumber: 3.2 Consensus size: 61
12424616 TTTTTTATAA
* * *
12424626 AAATTAAAAATAATACTACTGTAATAAAAATAATTATGAACTTTAAATAATTAAAATTATTG
1 AAATAAAAAATAATACGA-TGTAATAAAAATAATTATGAATTTTAAATAATTAAAATTATTG
* * * * * *** * * *
12424688 AAATAAAAAAT-A-A-GAT-T-ATATATATTATT-T-ATTTTTCAAACAACTTTTCATCAATA
1 AAATAAAAAATAATACGATGTAATAAAAATAATTATGAATTTT-AAATAA-TTAAAATTATTG
*
12424744 AAATTAAAAATAATACGATTGTAATAAAAATAATTATGAATTTTAAATAATTAAAATTATTG
1 AAATAAAAAATAATACGA-TGTAATAAAAATAATTATGAATTTTAAATAATTAAAATTATTG
12424806 AAATAAAAAA
1 AAATAAAAAA
12424816 ATAAGATTAT
Statistics
Matches: 91, Mismatches: 27, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
54 4 0.04
55 6 0.07
56 25 0.27
57 2 0.02
58 2 0.02
59 3 0.03
60 2 0.02
61 2 0.02
62 34 0.37
63 6 0.07
64 5 0.05
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (61 bp):
AAATAAAAAATAATACGATGTAATAAAAATAATTATGAATTTTAAATAATTAAAATTATTG
Found at i:12424837 original size:118 final size:118
Alignment explanation
Indices: 12424625--12424838 Score: 385
Period size: 118 Copynumber: 1.8 Consensus size: 118
12424615 ATTTTTTATA
*
12424625 AAAATTAAAAATAATACTACTGTAATAAAAATAATTATGAACTTTAAATAATTAAAATTATTGAA
1 AAAATTAAAAATAATACGACTGTAATAAAAATAATTATGAACTTTAAATAATTAAAATTATTGAA
12424690 ATAAAAAATAAGATTATATATATTATTTATTTTTCAAACAACTTTTCATCAAT
66 ATAAAAAATAAGATTATATATATTATTTATTTTTCAAACAACTTTTCATCAAT
* *
12424743 AAAATTAAAAATAATACGATTGTAATAAAAATAATTATGAATTTTAAATAATTAAAATTATTGAA
1 AAAATTAAAAATAATACGACTGTAATAAAAATAATTATGAACTTTAAATAATTAAAATTATTGAA
12424808 ATAAAAAAATAAGATTATATATATT-TTTATT
66 AT-AAAAAATAAGATTATATATATTATTTATT
12424839 ATATATTTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 70 0.76
119 22 0.24
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (118 bp):
AAAATTAAAAATAATACGACTGTAATAAAAATAATTATGAACTTTAAATAATTAAAATTATTGAA
ATAAAAAATAAGATTATATATATTATTTATTTTTCAAACAACTTTTCATCAAT
Found at i:12426716 original size:96 final size:96
Alignment explanation
Indices: 12426606--12426792 Score: 322
Period size: 96 Copynumber: 1.9 Consensus size: 96
12426596 GATATCATTG
*
12426606 ACTCCTATATTCTTTGAAATTTGAATTTTGTAAATAAA-TATTCATATATTTTGCATTAATGTTG
1 ACTCCTATATTCTTTGAAATTTGAATTTTGTAAATAAATTA-TCATATATTTTGCATTAATCTTG
*
12426670 GCCATTAATGGAGGATATTCAGGATTGTAATT
65 GCCATTAACGGAGGATATTCAGGATTGTAATT
*
12426702 ACTCCTATATTCTTTGAAATTTGAATTTTGTAAGTAAATTATCATATATTTTGCATTAATCTTGG
1 ACTCCTATATTCTTTGAAATTTGAATTTTGTAAATAAATTATCATATATTTTGCATTAATCTTGG
*
12426767 CCATTAACGGAGGATATTTAGGATTG
66 CCATTAACGGAGGATATTCAGGATTG
12426793 GAATGAAATT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
96 84 0.98
97 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (96 bp):
ACTCCTATATTCTTTGAAATTTGAATTTTGTAAATAAATTATCATATATTTTGCATTAATCTTGG
CCATTAACGGAGGATATTCAGGATTGTAATT
Found at i:12431089 original size:12 final size:13
Alignment explanation
Indices: 12431060--12431088 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12431050 GCTATCACTT
12431060 AAAACAAAAAAAA
1 AAAACAAAAAAAA
12431073 AAAACAAAAAAAA
1 AAAACAAAAAAAA
12431086 AAA
1 AAA
12431089 CTGTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:12435090 original size:32 final size:32
Alignment explanation
Indices: 12435041--12435139 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 32
12435031 GGCAAATGTC
* *
12435041 AAAGAT-AAGAGTGACCAAACTAAGCTAAAGTA
1 AAAGATAAAG-GTAACCAAATTAAGCTAAAGTA
* * *
12435073 AAAGATAAAGGTAACCAAATTGAA-CCAATGTC
1 AAAGATAAAGGTAACCAAATT-AAGCTAAAGTA
* *
12435105 AAA-ATAAAGGTAACCAGATTGAGCTAAAGTCA
1 AAAGATAAAGGTAACCAAATTAAGCTAAAGT-A
12435137 AAA
1 AAA
12435140 ATGAGGATGA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
30 1 0.02
31 21 0.40
32 26 0.49
33 5 0.09
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (32 bp):
AAAGATAAAGGTAACCAAATTAAGCTAAAGTA
Found at i:12435137 original size:31 final size:31
Alignment explanation
Indices: 12435054--12435139 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
12435044 GATAAGAGTG
* * *
12435054 ACCAAACTAAGCTAAAGTAAAAGATAAAGGTA
1 ACCAAATTGAGCTAAAGTCAAA-ATAAAGGTA
* * *
12435086 ACCAAATTGAACCAATGTCAAAATAAAGGTA
1 ACCAAATTGAGCTAAAGTCAAAATAAAGGTA
*
12435117 ACCAGATTGAGCTAAAGTCAAAA
1 ACCAAATTGAGCTAAAGTCAAAA
12435140 ATGAGGATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 28 0.64
32 16 0.36
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.17
Consensus pattern (31 bp):
ACCAAATTGAGCTAAAGTCAAAATAAAGGTA
Found at i:12435226 original size:37 final size:37
Alignment explanation
Indices: 12435185--12435284 Score: 137
Period size: 37 Copynumber: 2.7 Consensus size: 37
12435175 ATTTGGTCTG
* *
12435185 AGCCTACAAGTCGAAATGAAGATGATGACTTGGTGTA
1 AGCCTATAAGTCGAAATAAAGATGATGACTTGGTGTA
* * *
12435222 AGCCTATAAGTCAAAATAAAGATGATGACTTGGTTTG
1 AGCCTATAAGTCGAAATAAAGATGATGACTTGGTGTA
* *
12435259 AGCTTATAAGTCGAAATTAAGATGAT
1 AGCCTATAAGTCGAAATAAAGATGAT
12435285 CAAACTGAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (37 bp):
AGCCTATAAGTCGAAATAAAGATGATGACTTGGTGTA
Found at i:12435802 original size:20 final size:20
Alignment explanation
Indices: 12435777--12435819 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
12435767 GTGTGTAAGT
12435777 AATGCCAT-TAAAATAATGCA
1 AATGCCATCTAAAAT-ATGCA
*
12435797 AATGCCTTCTAAAATATGCA
1 AATGCCATCTAAAATATGCA
12435817 AAT
1 AAT
12435820 ACAACAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (20 bp):
AATGCCATCTAAAATATGCA
Found at i:12436930 original size:3 final size:3
Alignment explanation
Indices: 12436922--12437103 Score: 121
Period size: 3 Copynumber: 60.7 Consensus size: 3
12436912 GTTTTTCATC
* * * *
12436922 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTG TTA TTG TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * *
12436970 TTA TTA TCA TTA TTA TTA TTG TTA TTG TCA TTG TTA CTG TTA TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * *
12437018 TTA TTA CTA TTG TTA TTA TTG TTG TTG TTG TTA TTG TTG TTG TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
12437066 CTG TTG TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12437104 TTGTGTGCTT
Statistics
Matches: 141, Mismatches: 38, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 141 1.00
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:12440174 original size:37 final size:37
Alignment explanation
Indices: 12440133--12440205 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
12440123 AAATTAATTT
* * *
12440133 TCAAAAATATCTTTCAATATGTTGGTAAGACTTTCTA
1 TCAAAAATATCCTCCAATATGTTGATAAGACTTTCTA
* *
12440170 TCAAAATTATCCTCCAATATGTTGATAAGATTTTCT
1 TCAAAAATATCCTCCAATATGTTGATAAGACTTTCT
12440206 TGCAAATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (37 bp):
TCAAAAATATCCTCCAATATGTTGATAAGACTTTCTA
Found at i:12441337 original size:21 final size:21
Alignment explanation
Indices: 12441308--12441349 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12441298 GTAGCAGAAA
*
12441308 GAGTTTGGTTATGGT-TGGAT
1 GAGTTTGGTAATGGTATGGAT
12441328 GAGTCTTGGTAATGGTATGGAT
1 GAGT-TTGGTAATGGTATGGAT
12441350 AGTGGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.19, C:0.02, G:0.38, T:0.40
Consensus pattern (21 bp):
GAGTTTGGTAATGGTATGGAT
Found at i:12442228 original size:17 final size:16
Alignment explanation
Indices: 12442200--12442262 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
12442190 GATTTAAAAC
*
12442200 AAATAATGAAAAGGATA
1 AAATAAT-AAAAAGATA
*
12442217 AAATAATAAAAAAATA
1 AAATAATAAAAAGATA
*
12442233 AATTAAATAAAAAAGATA
1 AAAT-AAT-AAAAAGATA
*
12442251 AATACAATAAAA
1 AA-ATAATAAAA
12442263 GTAAGTACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.27
17 14 0.38
18 13 0.35
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (16 bp):
AAATAATAAAAAGATA
Found at i:12442245 original size:18 final size:18
Alignment explanation
Indices: 12442224--12442262 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12442214 ATAAAATAAT
12442224 AAAAAAATAAATTA-AATA
1 AAAAAAATAAA-TACAATA
*
12442242 AAAAAGATAAATACAATA
1 AAAAAAATAAATACAATA
12442260 AAA
1 AAA
12442263 GTAAGTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAAATAAATACAATA
Found at i:12447121 original size:18 final size:18
Alignment explanation
Indices: 12447100--12447153 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
12447090 TCATGTTTTT
*
12447100 CTATTCAAATAGTTATAA
1 CTATTCAAATAATTATAA
*
12447118 CTATTTAAATAATTAT--
1 CTATTCAAATAATTATAA
12447134 CTATTTCAAATAATTATAA
1 CTA-TTCAAATAATTATAA
12447153 C
1 C
12447154 ATTTTATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 3 0.10
17 12 0.40
18 14 0.47
19 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (18 bp):
CTATTCAAATAATTATAA
Found at i:12447753 original size:22 final size:22
Alignment explanation
Indices: 12447713--12447754 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12447703 TCTCTTTAAT
* *
12447713 TTTATTGATAAAATTTAAAAAA
1 TTTATTGACAAAATATAAAAAA
*
12447735 TTTATTGACAAAGTATAAAA
1 TTTATTGACAAAATATAAAA
12447755 TAAGTTTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
TTTATTGACAAAATATAAAAAA
Found at i:12451328 original size:21 final size:21
Alignment explanation
Indices: 12451304--12451344 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12451294 TATTTGAAAC
12451304 TTATTT-TTTCTATCATTTTAT
1 TTATTTCTTT-TATCATTTTAT
*
12451325 TTATTTCTTTTATTATTTTA
1 TTATTTCTTTTATCATTTTA
12451345 AAATTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTCTTTTATCATTTTAT
Found at i:12452351 original size:20 final size:20
Alignment explanation
Indices: 12452323--12452375 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
12452313 ATATTAATAC
* *
12452323 ATAATAAAAATAAAAATAAA
1 ATAAAAAAAATAAAAAGAAA
*
12452343 ATAAAAAAAATACAAAAGAAG
1 ATAAAAAAAATA-AAAAGAAA
12452364 A-AAAAAAAATAA
1 ATAAAAAAAATAA
12452376 CACAAGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 21 0.72
21 7 0.24
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (20 bp):
ATAAAAAAAATAAAAAGAAA
Found at i:12452359 original size:11 final size:10
Alignment explanation
Indices: 12452328--12452375 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
12452318 AATACATAAT
12452328 AAAAATAAAA
1 AAAAATAAAA
12452338 ATAAAAT-AAA
1 A-AAAATAAAA
*
12452348 AAAAATACAA
1 AAAAATAAAA
* *
12452358 AAGAAGAAAA
1 AAAAATAAAA
12452368 AAAAATAA
1 AAAAATAA
12452376 CACAAGATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 5 0.17
10 20 0.67
11 5 0.17
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.10
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:12455057 original size:16 final size:17
Alignment explanation
Indices: 12455021--12455059 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
12455011 ATTTGACAAA
*
12455021 AAGAAAAAATTTGTTAG
1 AAGAAAAAATTTGTAAG
*
12455038 AAGAAAAAATTT-TAAT
1 AAGAAAAAATTTGTAAG
12455054 AAGAAA
1 AAGAAA
12455060 TTCAAGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
AAGAAAAAATTTGTAAG
Found at i:12461870 original size:26 final size:25
Alignment explanation
Indices: 12461833--12461883 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
12461823 AACATTTTTG
*
12461833 CTTTTGAAAAACAAGCTCCCCCTGA
1 CTTTTGAAAAACAAACTCCCCCTGA
12461858 CTTTATGAAAAACAAACTCCCCCTGA
1 CTTT-TGAAAAACAAACTCCCCCTGA
12461884 GTAACAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (25 bp):
CTTTTGAAAAACAAACTCCCCCTGA
Found at i:12465156 original size:16 final size:16
Alignment explanation
Indices: 12465123--12465156 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12465113 CCTTCCCTCT
**
12465123 ATTAAAAAATTTTTCA
1 ATTAAAAAATTTGACA
12465139 ATTAAAAAATTTGACA
1 ATTAAAAAATTTGACA
12465155 AT
1 AT
12465157 CTTTCATACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTAAAAAATTTGACA
Found at i:12468628 original size:14 final size:14
Alignment explanation
Indices: 12468609--12468636 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12468599 ACTCACTTGG
12468609 CCTCAATGCACAAA
1 CCTCAATGCACAAA
12468623 CCTCAATGCACAAA
1 CCTCAATGCACAAA
12468637 AGAATGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.36, G:0.07, T:0.14
Consensus pattern (14 bp):
CCTCAATGCACAAA
Found at i:12475026 original size:19 final size:19
Alignment explanation
Indices: 12475004--12475064 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
12474994 TTGTCTTCTG
*
12475004 TTTTCTTTTTTTTGGTATT
1 TTTTATTTTTTTTGGTATT
*
12475023 TTTTGTTTTTTTT-GT-TT
1 TTTTATTTTTTTTGGTATT
*
12475040 ATTTGTATTATTTTTGGTATT
1 -TTT-TATTTTTTTTGGTATT
12475061 TTTT
1 TTTT
12475065 GTATTTCGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 21 0.60
20 5 0.14
21 2 0.06
ACGTcount: A:0.08, C:0.02, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTTTTGGTATT
Found at i:12475905 original size:141 final size:142
Alignment explanation
Indices: 12475498--12476045 Score: 813
Period size: 141 Copynumber: 3.9 Consensus size: 142
12475488 GAAGATCGAA
* * * * ** * * *
12475498 ATTAAACCACGAATCAAATATTAACGATGACTGGGACTGAACCGTAAATCAAAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCACAAGTC--AGA-GAATGAAAT
* * *
12475563 GATC-GGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCA-AAAATT
63 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATT
12475626 AATGAAATGATC-GG
128 AATGAAATGATCGGG
* *
12475640 ATTAAACCACGAGTCAAAGATTGAAGATGACTGAGATTGAA--ACAAGTCAGAGAATGAAATGAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCACAAGTCAGAGAATGAAATGAT
* *
12475703 CGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGA-AATTAAT
66 CGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATTAAT
12475767 GAAATGATCGGG
131 GAAATGATCGGG
* *
12475779 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAC
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCACAAGTCAGAGAATGAAATGAT
12475844 CGGGATTAAACCACGAGTCAAAGATTAAA-ATGACTGAGATTGAACCGCAAGTCAGAGAATTAAT
66 CGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATTAAT
* *
12475908 GAAATGACCGAG
131 GAAATGATCGGG
* *
12475920 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACTACAAGTCAGAGAATGAAATGAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCACAAGTCAGAGAATGAAATGAT
*
12475985 CGGGATTAAACCACGAGTTAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAAT
66 CGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAAT
12476046 GAAATGACCG
Statistics
Matches: 373, Mismatches: 26, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
137 12 0.03
138 69 0.18
139 42 0.11
140 29 0.08
141 155 0.42
142 66 0.18
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (142 bp):
ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCACAAGTCAGAGAATGAAATGAT
CGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATTAAT
GAAATGATCGGG
Found at i:12475980 original size:210 final size:207
Alignment explanation
Indices: 12475498--12476087 Score: 769
Period size: 210 Copynumber: 2.8 Consensus size: 207
12475488 GAAGATCGAA
* * * * * ** * * *
12475498 ATTAAACCACGAATCAAATATTAACGATGACTGGGACTGAACCGTAAATCAAAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACCACAAGTC-AGAATGAATGAAAT
* * *
12475563 GATC-GGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAATTA
65 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC--AGA-GA
* *
12475627 ATGAAATGATC-GGATTAAACCACGAGTCAAAGATTGAAGATGACTGAGATTGAAACAAGTCAGA
127 ATGAAATGACCGGGATTAAACCACGAGTCAAAGATTGAAAATGACTGAGATTGAAACAAGTCAGA
* *
12475691 GAATGAAATGATCGGG
192 GAATGAAATGACCGAG
* ** *
12475707 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACCACAAGTCAG-AATGAATGAAAT
12475772 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATG
65 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATG
*
12475837 AAATGACCGGGATTAAACCACGAGTCAAAGATT-AAAATGACTGAGATTGAACCGCAAGTCAGAG
130 AAATGACCGGGATTAAACCACGAGTCAAAGATTGAAAATGACTGAGATTGAA--ACAAGTCAGAG
12475901 AATTAATGAAATGACCGAG
193 ----AATGAAATGACCGAG
*
12475920 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACTACAAGTCAG-A-GAATGAAATG
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACCACAAGTCAGAATGAATGAAATG
* *
12475983 ATCGGGATTAAACCACGAGTTAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATGA
66 ATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGA
* * * * *
12476048 AATGACCGGGATTGAACCGCAAGTCAGAGAATG-AAATGAC
131 AATGACCGGGATTAAACCACGAGTCAAAGATTGAAAATGAC
12476088 CGGATTAAAC
Statistics
Matches: 345, Mismatches: 26, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
207 28 0.08
208 27 0.08
209 71 0.21
210 157 0.46
211 1 0.00
213 61 0.18
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (207 bp):
ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACCACAAGTCAGAATGAATGAAATG
ATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGA
AATGACCGGGATTAAACCACGAGTCAAAGATTGAAAATGACTGAGATTGAAACAAGTCAGAGAAT
GAAATGACCGAG
Found at i:12476008 original size:69 final size:69
Alignment explanation
Indices: 12475498--12476065 Score: 741
Period size: 69 Copynumber: 8.1 Consensus size: 69
12475488 GAAGATCGAA
* * * * * * * *
12475498 ATTAAACCACGAATCAAATATTAACGATGACTGGGACTGAACCGTAAATCAAAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC--AGA-GAATGAAAT
12475563 GATC-GG
63 GATCGGG
* * *
12475569 ATTAAACCACGAGCCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC--AGA-GAATGAAAT
12475634 GATC-GG
63 GATCGGG
* * *
12475640 ATTAAACCACGAGTCAAAGATTGAAGATGACTGAGATTGAA--ACAAGTCAGAGAATGAAATGAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAT
12475703 CGGG
66 CGGG
* *
12475707 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGAAATTAATGAAAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAG--A-GAATGAAAT
12475772 GATCGGG
63 GATCGGG
*
12475779 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAC
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAT
12475844 CGGG
66 CGGG
*
12475848 ATTAAACCACGAGTCAAAGATTAAA-ATGACTGAGATTGAACCGCAAGTCAGAGAATTAATGAAA
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAG----AATGAAA
* *
12475912 TGACCGAG
62 TGATCGGG
* **
12475920 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTAAACTACAAGTCAGAGAATGAAATGAT
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAT
12475985 CGGG
66 CGGG
* * *
12475989 ATTAAACCACGAGTTAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGAGAATGAAATGAC
1 ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAT
12476054 CGGG
66 CGGG
*
12476058 ATTGAACC
1 ATTAAACC
12476066 GCAAGTCAGA
Statistics
Matches: 450, Mismatches: 36, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
66 12 0.03
67 43 0.10
68 27 0.06
69 135 0.30
70 1 0.00
71 103 0.23
72 105 0.23
73 24 0.05
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (69 bp):
ATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAATGAAATGAT
CGGG
Found at i:12477156 original size:8 final size:8
Alignment explanation
Indices: 12477143--12477189 Score: 76
Period size: 8 Copynumber: 5.8 Consensus size: 8
12477133 CTTTATCATT
12477143 TTTTTTCA
1 TTTTTTCA
*
12477151 TTTTTTTA
1 TTTTTTCA
12477159 TTTTTTCA
1 TTTTTTCA
12477167 TTTTTTTCA
1 -TTTTTTCA
12477176 TTTTTTCA
1 TTTTTTCA
12477184 TTTTTT
1 TTTTTT
12477190 TTGTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 28 0.78
9 8 0.22
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:12477156 original size:9 final size:9
Alignment explanation
Indices: 12477142--12477190 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
12477132 CCTTTATCAT
12477142 TTTTTTTCA
1 TTTTTTTCA
12477151 TTTTTTT-A
1 TTTTTTTCA
12477159 -TTTTTTCA
1 TTTTTTTCA
12477167 TTTTTTTCA
1 TTTTTTTCA
12477176 -TTTTTTCA
1 TTTTTTTCA
12477184 TTTTTTT
1 TTTTTTT
12477191 TGTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.16
8 10 0.27
9 21 0.57
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:12477164 original size:17 final size:17
Alignment explanation
Indices: 12477143--12477190 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
12477133 CTTTATCATT
12477143 TTTTTTCATTTTTTT-A
1 TTTTTTCATTTTTTTCA
12477159 TTTTTTCATTTTTTTCA
1 TTTTTTCATTTTTTTCA
12477176 TTTTTTCATTTTTTT
1 TTTTTTCATTTTTTT
12477191 TGTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCATTTTTTTCA
Found at i:12477176 original size:25 final size:25
Alignment explanation
Indices: 12477142--12477189 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12477132 CCTTTATCAT
*
12477142 TTTTTTTCATTTTTTTATTTTTTCA
1 TTTTTTTCATTTTTTCATTTTTTCA
12477167 TTTTTTTCATTTTTTCATTTTTT
1 TTTTTTTCATTTTTTCATTTTTT
12477190 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTTTCATTTTTTCATTTTTTCA
Found at i:12477196 original size:17 final size:17
Alignment explanation
Indices: 12477143--12477198 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
12477133 CTTTATCATT
12477143 TTTTTTCA-TTTTTTTA
1 TTTTTTCATTTTTTTTA
*
12477159 TTTTTTCATTTTTTTCA
1 TTTTTTCATTTTTTTTA
*
12477176 TTTTTTCATTTTTTTTG
1 TTTTTTCATTTTTTTTA
12477193 TTTTTT
1 TTTTTT
12477199 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 8 0.22
17 28 0.78
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTCATTTTTTTTA
Found at i:12477207 original size:8 final size:8
Alignment explanation
Indices: 12477142--12477210 Score: 65
Period size: 8 Copynumber: 8.9 Consensus size: 8
12477132 CCTTTATCAT
12477142 TTTTTTTCA
1 TTTTTTT-A
12477151 TTTTTTTA
1 TTTTTTTA
*
12477159 TTTTTTCA
1 TTTTTTTA
12477167 TTTTTTTCA
1 TTTTTTT-A
*
12477176 TTTTTTCA
1 TTTTTTTA
12477184 --TTTTT-
1 TTTTTTTA
*
12477189 TTTGTTT-
1 TTTTTTTA
12477196 TTTTTTTA
1 TTTTTTTA
12477204 TTTTTTT
1 TTTTTTT
12477211 GCCTCTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
6 4 0.08
7 10 0.20
8 22 0.44
9 14 0.28
ACGTcount: A:0.09, C:0.06, G:0.01, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12477207 original size:17 final size:16
Alignment explanation
Indices: 12477141--12477224 Score: 82
Period size: 17 Copynumber: 5.2 Consensus size: 16
12477131 TCCTTTATCA
12477141 TTTTTTTTCATTTTTT
1 TTTTTTTTCATTTTTT
*
12477157 TATTTTTTCATTTTTT
1 TTTTTTTTCATTTTTT
*
12477173 TCATTTTTTCATTTTTT
1 T-TTTTTTTCATTTTTT
* *
12477190 TTGTTTTT--TTTTTA
1 TTTTTTTTCATTTTTT
* *
12477204 TTTTTTTGCCTCTTTTT
1 TTTTTTTTCAT-TTTTT
12477221 TTTT
1 TTTT
12477225 AAGCAAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.19
16 22 0.39
17 24 0.42
ACGTcount: A:0.07, C:0.08, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTTTTCATTTTTT
Found at i:12488516 original size:17 final size:17
Alignment explanation
Indices: 12488491--12488539 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
12488481 TAGGATTTTT
*
12488491 AGGACTTTGGATTTTAAG
1 AGGATTTTGGATTTT-AG
*
12488509 AGG-TTTTGAATTTTAG
1 AGGATTTTGGATTTTAG
*
12488525 GGGATTTTGGATTTT
1 AGGATTTTGGATTTT
12488540 TAGGGGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 4 0.15
17 19 0.73
18 3 0.12
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (17 bp):
AGGATTTTGGATTTTAG
Found at i:12488542 original size:18 final size:18
Alignment explanation
Indices: 12488483--12488550 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 18
12488473 CGTGTCTTTA
*
12488483 GGATTTTTA--GGACTTT
1 GGATTTTTAGGGGATTTT
* *
12488499 GGATTTTAAGAGG-TTTT
1 GGATTTTTAGGGGATTTT
*
12488516 -GAATTTTAGGGGATTTT
1 GGATTTTTAGGGGATTTT
*
12488533 GGATTTTTAGGGGGTTTT
1 GGATTTTTAGGGGATTTT
12488551 AAAAACTTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
16 17 0.41
17 7 0.17
18 17 0.41
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (18 bp):
GGATTTTTAGGGGATTTT
Found at i:12489978 original size:12 final size:11
Alignment explanation
Indices: 12489956--12490022 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
12489946 TTTTTTTGTC
*
12489956 TTTTGTTTTTT
1 TTTTGTATTTT
12489967 TTTTGGTA--TT
1 TTTT-GTATTTT
12489977 TTTTGT-TTTGT
1 TTTTGTATTT-T
12489988 ATTTTGTATTATT
1 -TTTTGTATT-TT
*
12490001 TTTGGTATTTTT
1 TTTTGTA-TTTT
12490013 TTTTGTATTT
1 TTTTGTATTT
12490023 CGTATTTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
9 2 0.04
10 7 0.16
11 8 0.18
12 22 0.49
13 5 0.11
14 1 0.02
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.78
Consensus pattern (11 bp):
TTTTGTATTTT
Found at i:12489980 original size:21 final size:20
Alignment explanation
Indices: 12489956--12490022 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 20
12489946 TTTTTTTGTC
12489956 TTTTGTTTTTTTTTTGGTATT
1 TTTTGTTTTTTTTTT-GTATT
*
12489977 TTTTGTTTTGTATTTTGTATTAT
1 TTTTGTTTT-TTTTTTGTA-T-T
12490000 TTTTGGTATTTTTTTTTGTATT
1 TTTT-GT-TTTTTTTTTGTATT
12490022 T
1 T
12490023 CGTATTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 12 0.31
22 8 0.21
23 6 0.15
24 10 0.26
25 3 0.08
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTTTTTTGTATT
Found at i:12489995 original size:7 final size:7
Alignment explanation
Indices: 12489949--12490033 Score: 58
Period size: 7 Copynumber: 13.0 Consensus size: 7
12489939 CCTTAATTTT
*
12489949 TTTTGTC
1 TTTTGTA
12489956 TTTTGT-
1 TTTTGTA
12489962 TTTT-T-
1 TTTTGTA
12489967 TTTTGGTA
1 TTTT-GTA
* *
12489975 TTTTTTG
1 TTTTGTA
12489982 TTTTGTA
1 TTTTGTA
12489989 TTTTGTA
1 TTTTGTA
*
12489996 TTAT-T-
1 TTTTGTA
*
12490001 TTTGGTA
1 TTTTGTA
12490008 TTTT-T-
1 TTTTGTA
12490013 TTTTGTA
1 TTTTGTA
*
12490020 TTTCGTA
1 TTTTGTA
12490027 TTTTGTA
1 TTTTGTA
12490034 ATATTATTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 11 0.18
6 8 0.13
7 38 0.62
8 4 0.07
ACGTcount: A:0.09, C:0.02, G:0.14, T:0.74
Consensus pattern (7 bp):
TTTTGTA
Found at i:12490000 original size:24 final size:24
Alignment explanation
Indices: 12489973--12490021 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12489963 TTTTTTTTGG
*
12489973 TATTTTTTGT-TTTGTATTTTGTAT
1 TATTTTTGGTATTT-TATTTTGTAT
*
12489997 TATTTTTGGTATTTTTTTTTGTAT
1 TATTTTTGGTATTTTATTTTGTAT
12490021 T
1 T
12490022 TCGTATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (24 bp):
TATTTTTGGTATTTTATTTTGTAT
Found at i:12490020 original size:31 final size:32
Alignment explanation
Indices: 12489945--12490028 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
12489935 CCATCCTTAA
* * *
12489945 TTTTTTTTGTCTTTTGTTTTTTTTTTGGTATT
1 TTTTTTTTGTATTTTGTATTATTTTTGGTATT
12489977 TTTTGTTTTGTATTTTGTATTATTTTTGGTA-T
1 TTTT-TTTTGTATTTTGTATTATTTTTGGTATT
*
12490009 TTTTTTTTGTATTTCGTATT
1 TTTTTTTTGTATTTTGTATT
12490029 TTGTAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
31 15 0.32
32 9 0.19
33 23 0.49
ACGTcount: A:0.08, C:0.02, G:0.13, T:0.76
Consensus pattern (32 bp):
TTTTTTTTGTATTTTGTATTATTTTTGGTATT
Found at i:12490031 original size:45 final size:45
Alignment explanation
Indices: 12489962--12490047 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
12489952 TGTCTTTTGT
** * * *
12489962 TTTTTTTTTGGTATTTTTTGTTTTGTATTTTGTATTATTTTTGGTA
1 TTTTTTTTTGGTATTTCGTATTTTGTAATAT-TATTATTTTTGGTA
12490008 TTTTTTTTT-GTATTTCGTATTTTGTAATATTATTATTTTT
1 TTTTTTTTTGGTATTTCGTATTTTGTAATATTATTATTTTT
12490048 ATTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 10 0.29
45 16 0.46
46 9 0.26
ACGTcount: A:0.14, C:0.01, G:0.12, T:0.73
Consensus pattern (45 bp):
TTTTTTTTTGGTATTTCGTATTTTGTAATATTATTATTTTTGGTA
Found at i:12495836 original size:8 final size:8
Alignment explanation
Indices: 12495823--12495869 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
12495813 ATTATGCTTG
12495823 AAAAATGA
1 AAAAATGA
12495831 AAAAATGA
1 AAAAATGA
12495839 AAAAATGAA
1 AAAAATG-A
12495848 AAAAATG-
1 AAAAATGA
12495855 -AAAATG-
1 AAAAATGA
12495861 AAAAATGA
1 AAAAATGA
12495869 A
1 A
12495870 TGAAAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.17
7 6 0.17
8 16 0.44
9 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAATGA
Found at i:12495841 original size:15 final size:15
Alignment explanation
Indices: 12495821--12495869 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
12495811 ATATTATGCT
12495821 TGAAAAATGAAAAAA
1 TGAAAAATGAAAAAA
12495836 TGAAAAAATGAAAAAAA
1 TG-AAAAATG-AAAAAA
12495853 TG-AAAATG-AAAAA
1 TGAAAAATGAAAAAA
12495866 TGAA
1 TGAA
12495870 TGAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
15 8 0.26
16 7 0.23
17 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
TGAAAAATGAAAAAA
Found at i:12495843 original size:17 final size:17
Alignment explanation
Indices: 12495823--12495877 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
12495813 ATTATGCTTG
12495823 AAAAATG-AAAAAATGA
1 AAAAATGAAAAAAATGA
12495839 AAAAATGAAAAAAATG-
1 AAAAATGAAAAAAATGA
12495855 -AAAATGAAAAATGAATGA
1 AAAAATGAAAAA--AATGA
12495873 AAAAA
1 AAAAA
12495878 AGGACTCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.32
16 7 0.21
17 12 0.35
19 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (17 bp):
AAAAATGAAAAAAATGA
Found at i:12496889 original size:43 final size:41
Alignment explanation
Indices: 12496842--12497145 Score: 310
Period size: 42 Copynumber: 7.1 Consensus size: 41
12496832 ATGATTGTCA
*
12496842 AGGAGCATTTTACTTTTTCAAAAATCGTTGAGCCTCTGATTAG
1 AGGAGCATTTTA-TTTTTC-AAAGTCGTTGAGCCTCTGATTAG
*
12496885 AGGAGCCA-TTTATTTTTCCAAAGTCGTTGAACCTCTGATTAG
1 AGGAG-CATTTTATTTTT-CAAAGTCGTTGAGCCTCTGATTAG
* * *
12496927 AGGAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCGCTAATTAG
1 AGGAGC-AT-TTTATTTTT-CAAAGTCGTTGAGCCTCTGATTAG
* * *
12496971 AGGAG-ATTTATTTATTTTCCAAAGTTGTTGAGCTTCTGATTAG
1 AGGAGCA--T-TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAG
*
12497014 AAGAGCCA-TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAG
1 AGGAG-CATTTTA-TTTTTCAAAGTCGTTGAGCCTCTGATTAG
* *
12497056 AGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTGATTAG
1 AGGAGC-AT-TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAG
* * *
12497099 AGGAGCTTTATTCA-TTTTCAAAGTCGTTGAACCTCTGCTTAG
1 AGGAGCATT-TT-ATTTTTCAAAGTCGTTGAGCCTCTGATTAG
12497141 AGGAG
1 AGGAG
12497146 TTTTGATCAA
Statistics
Matches: 224, Mismatches: 22, Indels: 31
0.81 0.08 0.11
Matches are distributed among these distances:
41 7 0.03
42 95 0.42
43 69 0.31
44 52 0.23
45 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (41 bp):
AGGAGCATTTTATTTTTCAAAGTCGTTGAGCCTCTGATTAG
Found at i:12497055 original size:85 final size:85
Alignment explanation
Indices: 12496842--12497145 Score: 359
Period size: 85 Copynumber: 3.6 Consensus size: 85
12496832 ATGATTGTCA
* *
12496842 AGGAG-CATTTTACTTTTTCAAAAATCGTTGAGCCTCTGATTAGAGGAGCCATTTA--T-TTTTC
1 AGGAGCCA-TTTATTTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAG--ATTTATTTATTTTC
*
12496903 CAAAGTCGTTGAACCTCTGATTAG
62 CAAAGTCGTTGAGCCTCTGATTAG
* * * *
12496927 AGGAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCGCTAATTAGAGGAGATTTATTTATTTTCCA
1 AGGAGC--CATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGATTTATTTATTTTCCA
* *
12496992 AAGTTGTTGAGCTTCTGATTAG
64 AAGTCGTTGAGCCTCTGATTAG
* * *
12497014 AAGAGCCATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAA
1 AGGAGCCATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGATTTATTTATTTTCCAAA
*
12497079 GTCATTGAGCCTCTGATTAG
66 GTCGTTGAGCCTCTGATTAG
* *
12497099 AGGAG-C-TTTATTCATTTTCAAAGTCGTTGAACCTCTGCTTAGAGGAG
1 AGGAGCCATTTATT--TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAG
12497146 TTTTGATCAA
Statistics
Matches: 189, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
83 6 0.03
84 6 0.03
85 110 0.58
86 26 0.14
87 40 0.21
88 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (85 bp):
AGGAGCCATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGATTTATTTATTTTCCAAA
GTCGTTGAGCCTCTGATTAG
Found at i:12497072 original size:129 final size:127
Alignment explanation
Indices: 12496856--12497141 Score: 428
Period size: 129 Copynumber: 2.2 Consensus size: 127
12496846 GCATTTTACT
* *
12496856 TTTTCAAAAATCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCCAAAGTCGTTGAACCTCT
1 TTTTC-AAAGTCGTTGAGCCTCTGATTAGAAGAGCCATTTATTTTTCCAAAGTCGTTGAACCTCT
* *
12496921 GATTAGAGGAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCGCTAATTAGAGGAGATTTATTTA
65 GATTAGAGGAGCTTTATTTATTTTT-CAAAGTCATTGAGCCGCTAATTAGAGGAGATTTATTCA
* * * *
12496985 TTTTCCAAAGTTGTTGAGCTTCTGATTAGAAGAGCCATTTATTTTTTCAAAGTCGTTGAGCCTCT
1 TTTT-CAAAGTCGTTGAGCCTCTGATTAGAAGAGCCATTTATTTTTCCAAAGTCGTTGAACCTCT
* * *
12497050 GATTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTATTCA
65 GATTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCGCTAATTAGAGGAGATTTATTCA
* *
12497113 TTTTCAAAGTCGTTGAACCTCTGCTTAGA
1 TTTTCAAAGTCGTTGAGCCTCTGATTAGA
12497142 GGAGTTTTGA
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
127 21 0.15
128 37 0.26
129 82 0.58
130 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (127 bp):
TTTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCCATTTATTTTTCCAAAGTCGTTGAACCTCTG
ATTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCGCTAATTAGAGGAGATTTATTCA
Found at i:12497302 original size:13 final size:12
Alignment explanation
Indices: 12497286--12497420 Score: 71
Period size: 11 Copynumber: 10.7 Consensus size: 12
12497276 CCATTTTATT
12497286 TTTTTATTTTGTA
1 TTTTTATTTT-TA
12497299 TTTTATATTTTTA
1 TTTT-TATTTTTA
*
12497312 -TTTTATTTATA
1 TTTTTATTTTTA
*
12497323 -TTTTATTTATA
1 TTTTTATTTTTA
* *
12497334 TTTATATTTTTT
1 TTTTTATTTTTA
*
12497346 TTATTTATATATATA
1 TT-TTTAT-T-TTTA
*
12497361 TTTTTTTCTTTTA
1 TTTTTAT-TTTTA
*
12497374 TGTTTA-TTTTA
1 TTTTTATTTTTA
12497385 TGTATTTATTATTTA
1 T-T-TTTATT-TTTA
*
12497400 TTTATT-TATTTA
1 TTT-TTATTTTTA
12497412 TTTATTATT
1 TTT-TTATT
12497421 ACTATTTATT
Statistics
Matches: 96, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
11 24 0.25
12 23 0.24
13 24 0.25
14 16 0.17
15 9 0.09
ACGTcount: A:0.23, C:0.01, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:12497331 original size:4 final size:4
Alignment explanation
Indices: 12497280--12497458 Score: 85
Period size: 4 Copynumber: 45.8 Consensus size: 4
12497270 GTAAGCCCAT
* * *
12497280 TTTA TTTT TTTA TTT- TGTA TTTTA TATT- TTTA TTTTA TTTA TAT- TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA T-TTA TTTA -TTTA TTTA TTTA TTTA
* * * *
12497328 TTTA --TA TTTA TATT- TTT- TTTA TTTA TATA TATA TTTT TTTC TTT-
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
12497372 TATG TTTA TTTTA TGTA TTTA -TTA TTTA TTTA TTTA TTTA TTTA -TTA
1 TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
12497419 TTACTA TTTA TTAA TATA TATA TTTA -TTA -TTA TTATA TTT
1 TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTT
12497459 CTTTTCTTTT
Statistics
Matches: 138, Mismatches: 19, Indels: 36
0.72 0.10 0.19
Matches are distributed among these distances:
2 2 0.01
3 25 0.18
4 88 0.64
5 19 0.14
6 4 0.03
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12497350 original size:15 final size:16
Alignment explanation
Indices: 12497278--12497414 Score: 101
Period size: 15 Copynumber: 8.6 Consensus size: 16
12497268 GGGTAAGCCC
12497278 ATTTTATTTT-TTTAT
1 ATTTTATTTTATTTAT
12497293 -TTTGTATTTTA--TAT
1 ATTT-TATTTTATTTAT
12497307 -TTTTATTTTATTTAT
1 ATTTTATTTTATTTAT
12497322 ATTTTATTTATATTTAT
1 ATTTTATTT-TATTTAT
12497339 ATTTT-TTTTATTTAT
1 ATTTTATTTTATTTAT
* * *
12497354 ATATATATTTTTTTCTTTT
1 AT-TTTA-TTTTAT-TTAT
*
12497373 ATGTTTATTTTATGTAT
1 AT-TTTATTTTATTTAT
12497390 -TTATTA-TTTATTTAT
1 ATT-TTATTTTATTTAT
*
12497405 TTATTTATTT
1 AT-TTTATTT
12497415 ATTATTACTA
Statistics
Matches: 99, Mismatches: 9, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
13 7 0.07
14 9 0.09
15 27 0.27
16 21 0.21
17 17 0.17
18 10 0.10
19 8 0.08
ACGTcount: A:0.23, C:0.01, G:0.02, T:0.74
Consensus pattern (16 bp):
ATTTTATTTTATTTAT
Found at i:12497358 original size:19 final size:19
Alignment explanation
Indices: 12497284--12497416 Score: 91
Period size: 19 Copynumber: 6.9 Consensus size: 19
12497274 GCCCATTTTA
* *
12497284 TTTTTTTATTT-TGTATTT
1 TTTTTTTATTTATTTATAT
12497302 TATATTTTTATTTTATTTATAT
1 T-T-TTTTTA-TTTATTTATAT
*
12497324 TTTATTTA--TATTTATAT
1 TTTTTTTATTTATTTATAT
12497341 TTTTTTTATTTATATATATAT
1 TTTTTTTATTTAT-T-TATAT
12497362 TTTTTTCT-TTTATGTT-TAT
1 TTTTTT-TATTTAT-TTATAT
* *
12497381 TTTATGTATTTA-TTAT-T
1 TTTTTTTATTTATTTATAT
12497398 TATTTATTTATTTATTTAT
1 T-TTT-TTTATTTATTTAT
12497417 TATTACTATT
Statistics
Matches: 92, Mismatches: 9, Indels: 26
0.72 0.07 0.20
Matches are distributed among these distances:
17 20 0.22
18 5 0.05
19 22 0.24
20 17 0.18
21 21 0.23
22 7 0.08
ACGTcount: A:0.23, C:0.01, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTTATTTATAT
Found at i:12497416 original size:36 final size:35
Alignment explanation
Indices: 12497278--12497431 Score: 110
Period size: 36 Copynumber: 4.5 Consensus size: 35
12497268 GGGTAAGCCC
*
12497278 ATTTTAT-T-TTT-TTATTT-TGTATTTTATATTT
1 ATTTTATCTATTTATTATTTATTTATTTTATATTT
12497309 -TTATT-T-TATTTA-TATTTTATTTATATTTATATTT
1 ATT-TTATCTATTTATTA-TTTATTTAT-TTTATATTT
* * * * * *
12497343 TTTTTATTTATATATATATTTTTTTCTTTTATGTTT
1 ATTTTATCTATTTAT-TATTTATTTATTTTATATTT
* *
12497379 ATTTTATGTATTTATTATTTATTTATTTATTTATTT
1 ATTTTATCTATTTATTATTTATTTATTT-TATATTT
12497415 ATTATTA-CTATTTATTA
1 ATT-TTATCTATTTATTA
12497432 ATATATATAT
Statistics
Matches: 97, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
30 4 0.04
31 7 0.07
32 3 0.03
33 4 0.04
34 11 0.11
35 14 0.14
36 42 0.43
37 10 0.10
38 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.02, T:0.73
Consensus pattern (35 bp):
ATTTTATCTATTTATTATTTATTTATTTTATATTT
Found at i:12497419 original size:19 final size:19
Alignment explanation
Indices: 12497308--12497446 Score: 74
Period size: 19 Copynumber: 7.1 Consensus size: 19
12497298 ATTTTATATT
12497308 TTTATTTTATTTA-TATTTTA
1 TTTA-TTTATTTATTA-TTTA
*
12497328 TTTA--TATTTA-TATTTTT
1 TTTATTTATTTATTA-TTTA
* *
12497345 TTTATTTATATATATATTTT
1 TTTATTTATTTAT-TATTTA
* *
12497365 TTTCTTTTATGT-TTATTTTA
1 TTT-ATTTATTTATTA-TTTA
*
12497385 TGTATTTA-TTATTTATTTA
1 TTTATTTATTTA-TTATTTA
12497404 TTTATTTATTTATTATTACTA
1 TTTATTTATTTATTATT--TA
* *
12497425 TTTATTAATATATATATTTA
1 TTTATTTATTTAT-TATTTA
12497445 TT
1 TT
12497447 ATTATTATAT
Statistics
Matches: 96, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
17 16 0.17
18 1 0.01
19 27 0.28
20 27 0.28
21 21 0.22
22 4 0.04
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (19 bp):
TTTATTTATTTATTATTTA
Found at i:12497526 original size:22 final size:19
Alignment explanation
Indices: 12497491--12497535 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 19
12497481 CTGTTAATAT
12497491 TTATATATATATTTATCTGA
1 TTATATATATATTTATCT-A
12497511 TTATATAGTATAATTTATCTA
1 TTATATA-TAT-ATTTATCTA
12497532 TTAT
1 TTAT
12497536 TTATTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (19 bp):
TTATATATATATTTATCTA
Found at i:12497581 original size:38 final size:42
Alignment explanation
Indices: 12497503--12497595 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
12497493 ATATATATAT
12497503 TTATCTGATTATATAGTATAATTTATCTATTATTTATTTTTAG
1 TTATCTGATTATATAGTATAATTTATC-ATTATTTATTTTTAG
* *
12497546 TTATCTG-TTA-ATATTATTATTTATCTTATTATTT-TTTTTA-
1 TTATCTGATTATATAGTATAATTTATC--ATTATTTATTTTTAG
12497586 TTATCT-ATTA
1 TTATCTGATTA
12497596 ACATTTTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
40 9 0.20
41 19 0.41
42 11 0.24
43 7 0.15
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.62
Consensus pattern (42 bp):
TTATCTGATTATATAGTATAATTTATCATTATTTATTTTTAG
Found at i:12497589 original size:20 final size:20
Alignment explanation
Indices: 12497525--12497595 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
12497515 ATAGTATAAT
12497525 TTATCTATTATTTATTTTTAG
1 TTATCTATTATTT-TTTTTAG
* * * * *
12497546 TTATCTGTTAATATTATTAT
1 TTATCTATTATTTTTTTTAG
12497566 TTATCTTATTATTTTTTTTA-
1 TTATC-TATTATTTTTTTTAG
12497586 TTATCTATTA
1 TTATCTATTA
12497596 ACATTTTTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 5 0.12
20 15 0.38
21 20 0.50
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (20 bp):
TTATCTATTATTTTTTTTAG
Found at i:12498435 original size:17 final size:17
Alignment explanation
Indices: 12498415--12498551 Score: 50
Period size: 17 Copynumber: 7.8 Consensus size: 17
12498405 TTTTTTTTTC
12498415 ATTTTATTTTTTTATAT
1 ATTTTATTTTTTTATAT
*
12498432 A-TTTATTTATTTAT-T
1 ATTTTATTTTTTTATAT
* * *
12498447 ATTAGTATTTATTTATTAG
1 ATT-TTATTTTTTTA-TAT
** *
12498466 ATTAGATTTGTTTAATAT
1 ATTTTATTT-TTTTATAT
* *
12498484 TTTTTATCTATTTTTATTT
1 ATTTTAT-T-TTTTTATAT
*
12498503 ATTTTCCTTTATTTT-TAT
1 ATTTT-ATTT-TTTTATAT
*
12498521 -TTTCATTTTTATTAT-T
1 ATTTTATTTTT-TTATAT
*
12498537 ATTTTGTTTTCTTTA
1 ATTTTATTTT-TTTA
12498552 AATAAAATTT
Statistics
Matches: 87, Mismatches: 20, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
15 4 0.05
16 19 0.22
17 25 0.29
18 15 0.17
19 22 0.25
20 2 0.02
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (17 bp):
ATTTTATTTTTTTATAT
Found at i:12498436 original size:16 final size:15
Alignment explanation
Indices: 12498417--12498506 Score: 67
Period size: 16 Copynumber: 5.7 Consensus size: 15
12498407 TTTTTTTCAT
*
12498417 TTTATTTTTTTATATA
1 TTTATTTATTTAT-TA
12498433 TTTATTTATTTATTA
1 TTTATTTATTTATTA
12498448 TTAGTATTTATTTATTAGA
1 TT--TATTTATTTATT--A
* * *
12498467 TTAGATTTGTTTAATA
1 TT-TATTTATTTATTA
*
12498483 TTT-TTTATCTATT-
1 TTTATTTATTTATTA
12498496 TTTATTTATTT
1 TTTATTTATTT
12498507 TCCTTTATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
13 3 0.05
14 13 0.22
15 4 0.07
16 15 0.25
17 12 0.20
18 9 0.15
19 3 0.05
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:12498440 original size:4 final size:4
Alignment explanation
Indices: 12498417--12498463 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
12498407 TTTTTTTCAT
* *
12498417 TTTA TTTT TTTA TATA TTTA TTTA TTTA -TTA TTAGTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TT
12498464 AGATTAGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 29 0.81
6 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12498507 original size:20 final size:21
Alignment explanation
Indices: 12498484--12498536 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
12498474 TGTTTAATAT
12498484 TTTTTATCTATTTTTA-TTT-A
1 TTTTTAT-TATTTTTATTTTCA
12498504 TTTTCCT-TTATTTTTATTTTCA
1 TTTT--TATTATTTTTATTTTCA
12498526 TTTTTATTATT
1 TTTTTATTATT
12498537 ATTTTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 6 0.21
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTATTTTTATTTTCA
Found at i:12498540 original size:12 final size:11
Alignment explanation
Indices: 12498492--12498541 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
12498482 ATTTTTTATC
12498492 TATTTTTA-TT
1 TATTTTTATTT
**
12498502 TA-TTTTCCTT
1 TATTTTTATTT
12498512 TATTTTTATTT
1 TATTTTTATTT
12498523 TCATTTTTATTAT
1 T-ATTTTTATT-T
12498536 TATTTT
1 TATTTT
12498542 GTTTTCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 4 0.12
10 6 0.18
11 7 0.21
12 14 0.42
13 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:12498616 original size:58 final size:59
Alignment explanation
Indices: 12498551--12499138 Score: 655
Period size: 60 Copynumber: 9.9 Consensus size: 59
12498541 TGTTTTCTTT
* *
12498551 AAATAAAATTT-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGA
1 AAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
*
12498609 AATTAAAATTTTC--AAAAAATATTTTTG-GAGAAAAGTTAAAAGTAAAGTATCAATTTTCCTTA
1 AAAT-AAATTTTCAAAAAAAATATTTTTGAG-GAAAAGTT----G-AAAGTATCAATTTTCCTTA
12498671 A
59 A
* *
12498672 AAATAAATTTTCAAAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATTAATTTTCCTTAA
1 AAATAAATTTTC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
** * *
12498732 AAATAAATTTTCGAAAAAAGTTTTTTTTTTGA-GAAAATGTTGAAAGTATCAATTTTCCTCAA
1 AAATAAATTTTC-AAAAAA--AATATTTTTGAGGAAAA-GTTGAAAGTATCAATTTTCCTTAA
* * **
12498794 AATTAAAGTTTC--AAAAAA-ATTTTTGA--AAAATGTTGAAAGTATCAATTTTCCGCAA
1 AAATAAATTTTCAAAAAAAATATTTTTGAGGAAAA-GTTGAAAGTATCAATTTTCCTTAA
* * *
12498849 AATTAAAGTTTC-AAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTGA
1 AAATAAATTTTCAAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAA
* * ** *
12498907 AATTAAAGTTTC-CGAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAACTTTCCTTAA
1 AAATAAATTTTCAAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
12498965 AAATAAACTTTCAAAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAATAAATTTTCAAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
** * * *
12499025 AAATAAATTTTCAAAAAAGGTTTTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAA
1 AAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AA
* *
12499085 AAATAAATTTTCAAAAAAAGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
1 AAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
12499139 TCTTGTACAA
Statistics
Matches: 465, Mismatches: 39, Indels: 50
0.84 0.07 0.09
Matches are distributed among these distances:
55 40 0.09
56 14 0.03
57 7 0.02
58 107 0.23
59 55 0.12
60 142 0.31
61 7 0.02
62 49 0.11
63 22 0.05
65 22 0.05
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (59 bp):
AAATAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:12499170 original size:119 final size:116
Alignment explanation
Indices: 12498572--12499138 Score: 435
Period size: 119 Copynumber: 4.8 Consensus size: 116
12498562 AAAAAAAATA
* * * * * *
12498572 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTCAAAAAATA--TTTTT
1 TTTTTGA-GAAAAGTTAAAAGTATCAACTTTCCTTAAAAAT-AAACTTTCAAAAAAAAGTTTTTT
* * ** *
12498635 GGA-GAAAAGTTAAAAGTAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAATA
64 TGAGGAAAAGTT----G-AAAGTATCAATTTTCCTTAAAAAGAAA--TTC-AAAAAAGCTT
* * * * *
12498695 TTTTTGAAGAAAAGTTGAAAGTATTAATTTTCCTTAAAAATAAATTTTC-GAAAAAAGTTTTTTT
1 TTTTTG-AGAAAAGTTAAAAGTATCAACTTTCCTTAAAAATAAACTTTCAAAAAAAAG---TTTT
* ** *
12498759 TTTGA-GAAAATGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCAAAAAA---A
62 TTTGAGGAAAA-GTTGAAAGTATCAATTTTCCTTAAAAAGAAA--TTCAAAAAAGCTT
* * ** * * *
12498813 TTTTTGA-AAAATGTTGAAAGTATCAATTTTCCGCAAAATTAAAGTTTC-AAAAAAA-TATTTTT
1 TTTTTGAGAAAA-GTTAAAAGTATCAACTTTCCTTAAAAATAAACTTTCAAAAAAAAGTTTTTTT
* ** *
12498875 -AGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCCGAAAAA--TAT
65 GAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAAGAAA--TT-CAAAAAAGCT-T
* * *
12498929 TTTTGGAGAAAAGTTGAAAGTATCAACTTTCCTTAAAAATAAACTTTCAAAAAAAATTTTTTTTG
1 TTTTTGAGAAAAGTTAAAAGTATCAACTTTCCTTAAAAATAAACTTTCAAAAAAAAGTTTTTTTG
* *
12498994 AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
66 AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAGAAA--TTCAAAAAAGCTT
* * *
12499047 TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAATTTTC-AAAAAAAGTTTTTT
1 TTTTTGA-GAAAAGTTAAAAGTATCAACTTTCCTT-AAAAATAAACTTTCAAAAAAAAGTTTTTT
12499111 TGAGGAAAAGTTGAAAGTATCAATTTTC
64 TGAGGAAAAGTTGAAAGTATCAATTTTC
12499139 TCTTGTACAA
Statistics
Matches: 386, Mismatches: 37, Indels: 46
0.82 0.08 0.10
Matches are distributed among these distances:
112 1 0.00
113 40 0.10
114 10 0.03
116 41 0.11
117 55 0.14
118 56 0.15
119 69 0.18
120 13 0.03
121 11 0.03
122 37 0.10
123 37 0.10
124 1 0.00
126 12 0.03
127 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (116 bp):
TTTTTGAGAAAAGTTAAAAGTATCAACTTTCCTTAAAAATAAACTTTCAAAAAAAAGTTTTTTTG
AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAGAAATTCAAAAAAGCTT
Found at i:12502908 original size:15 final size:14
Alignment explanation
Indices: 12502878--12502905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12502868 GTATGACTAA
12502878 AAAACATTTTTTTT
1 AAAACATTTTTTTT
12502892 AAAACATTTTTTTT
1 AAAACATTTTTTTT
12502906 TAATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
AAAACATTTTTTTT
Found at i:12503003 original size:18 final size:17
Alignment explanation
Indices: 12502975--12503009 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
12502965 GCAATAATGT
12502975 AATATATCATGCAATTA
1 AATATATCATGCAATTA
12502992 AATATCATCATGCAATTA
1 AATAT-ATCATGCAATTA
12503010 TGCAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (17 bp):
AATATATCATGCAATTA
Found at i:12504831 original size:37 final size:37
Alignment explanation
Indices: 12504776--12504852 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
12504766 AATTTGAGCA
12504776 AACTTAATATTTACAAGCAAAATCTCTTATATTCGAG
1 AACTTAATATTTACAAGCAAAATCTCTTATATTCGAG
*
12504813 AACTTAATATTTATAAGCAAAATCTCTTATATTCGAG
1 AACTTAATATTTACAAGCAAAATCTCTTATATTCGAG
12504850 AAC
1 AAC
12504853 ACCTTTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (37 bp):
AACTTAATATTTACAAGCAAAATCTCTTATATTCGAG
Found at i:12507516 original size:52 final size:52
Alignment explanation
Indices: 12507442--12507585 Score: 164
Period size: 52 Copynumber: 2.8 Consensus size: 52
12507432 CTTGCAAAAG
** *
12507442 AAGAATTCTAAGA-GAAAGGAGATTCTTAATAGGTAAGTTTAACTTAAAAGAA
1 AAGAATTCTAAGAGGAAA-GAGATTCTTAATAGACAAATTTAACTTAAAAGAA
* * * * *
12507494 AAGAATTCTAAAAGGAAAGAGATTTTTAATAGACAAATTTAACTTACAGGAG
1 AAGAATTCTAAGAGGAAAGAGATTCTTAATAGACAAATTTAACTTAAAAGAA
* * * *
12507546 AAGAATTTTAAGAGGAGAGAGATTCTTAATGGGCAAATTT
1 AAGAATTCTAAGAGGAAAGAGATTCTTAATAGACAAATTT
12507586 GTATGGTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
52 73 0.95
53 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (52 bp):
AAGAATTCTAAGAGGAAAGAGATTCTTAATAGACAAATTTAACTTAAAAGAA
Found at i:12507818 original size:74 final size:74
Alignment explanation
Indices: 12507697--12507838 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
12507687 GGGCTCTACG
* * * * *
12507697 TCTTATGGGTGTGTATGTTTGTTTGTGAGTAAACTAAAGGAGACTGAGATAGTTCACATAGGTAT
1 TCTTATGGGTATGTATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTAT
12507762 GATGTATGA
66 GATGTATGA
** * *
12507771 TCTTATGGGTATGTATGTTTGTTTGTAAGTGGACTAGAGGAGACTGAGAGGGTCCACATAAGTAT
1 TCTTATGGGTATGTATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTAT
12507836 GAT
66 GAT
12507839 ATATAAGAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (74 bp):
TCTTATGGGTATGTATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTAT
GATGTATGA
Found at i:12507864 original size:74 final size:73
Alignment explanation
Indices: 12507700--12507865 Score: 172
Period size: 74 Copynumber: 2.2 Consensus size: 73
12507690 CTCTACGTCT
* * * * *
12507700 TATGGGTGTGTATGTTTGTTTGTGAGTAAACTAAAGGAGACTGAGATAGTTCACATAGGTATGAT
1 TATGGGTATG-ATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTATGAT
* * *
12507765 GTATGATCT
65 ATATGAGCA
** * *
12507774 TATGGGTATGTATGTTTGTTTGTAAGTGGACTAGAGGAGACTGAGAGGGTCCACATAAGTATGAT
1 TATGGGTATG-ATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTATGAT
12507839 ATATAAGAGCA
65 ATAT--GAGCA
*
12507850 TATTGGTATG-TGTTTG
1 TATGGGTATGATGTTTG
12507866 GTTATGTTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
74 65 0.84
76 12 0.16
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.36
Consensus pattern (73 bp):
TATGGGTATGATGTTTGTTTGTAAGTAAACTAAAGGAGACTGAGAGAGTCCACATAAGTATGATA
TATGAGCA
Found at i:12512113 original size:15 final size:16
Alignment explanation
Indices: 12512093--12512124 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12512083 GATGAATTTA
12512093 TTTTAAATTT-ATATT
1 TTTTAAATTTAATATT
12512108 TTTTAAATTTAATATT
1 TTTTAAATTTAATATT
12512124 T
1 T
12512125 AAGTTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTAAATTTAATATT
Found at i:12512166 original size:29 final size:30
Alignment explanation
Indices: 12512131--12512211 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
12512121 ATTTAAGTTG
* *
12512131 TTTGAATTTGACATATTTAATTCAAAT-AA
1 TTTGAATTTAAAATATTTAATTCAAATCAA
** *
12512160 TTTGAATTTAAAATATTTGTTTCAAATCAT
1 TTTGAATTTAAAATATTTAATTCAAATCAA
* * *
12512190 TTTGAATGTAAATTATTAAATT
1 TTTGAATTTAAAATATTTAATT
12512212 TTATAAATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTGAATTTAAAATATTTAATTCAAATCAA
Found at i:12512255 original size:17 final size:16
Alignment explanation
Indices: 12512232--12512283 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
12512222 AATTAATTAA
*
12512232 ATTTAAAATTCAAATT
1 ATTTTAAATTCAAATT
12512248 ATTTTAAATTCAAATT
1 ATTTTAAATTCAAATT
* * * *
12512264 AATTTGAATTAAAATA
1 ATTTTAAATTCAAATT
12512280 ATTT
1 ATTT
12512284 GAATTGGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTTTAAATTCAAATT
Found at i:12512262 original size:22 final size:21
Alignment explanation
Indices: 12512198--12512276 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
12512188 ATTTTGAATG
12512198 TAAATT-ATTAAATTTTATAAAT
1 TAAATTAATTAAA-TTTA-AAAT
12512220 TAAATTAATTAAATTTAAAAT
1 TAAATTAATTAAATTTAAAAT
* *
12512241 TCAAATTATTTTAAA-TTCAAAT
1 T-AAATTA-ATTAAATTTAAAAT
*
12512263 TAATTTGAATTAAA
1 TAAATT-AATTAAA
12512277 ATAATTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
21 14 0.29
22 24 0.49
23 11 0.22
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
TAAATTAATTAAATTTAAAAT
Found at i:12512273 original size:16 final size:16
Alignment explanation
Indices: 12512238--12512288 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
12512228 TTAAATTTAA
* *
12512238 AATTCAAATTATTTTA
1 AATTCAAATTAATTTG
12512254 AATTCAAATTAATTTG
1 AATTCAAATTAATTTG
*
12512270 AATT-AAAATAATTTG
1 AATTCAAATTAATTTG
12512285 AATT
1 AATT
12512289 GGATAGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (16 bp):
AATTCAAATTAATTTG
Found at i:12512276 original size:38 final size:36
Alignment explanation
Indices: 12512180--12512278 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 36
12512170 AAATATTTGT
* *
12512180 TTCAAATCATTTTGAATGTAAATTATTAAATTTTATAAA
1 TTCAAATTAATTTGAAT-TAAA--ATTAAATTTTATAAA
* *
12512219 TT-AAATTAA-TTAAATTTAAAATTCAAATTATTTTAAA
1 TTCAAATTAATTTGAA-TTAAAATT-AAATT-TTATAAA
12512256 TTCAAATTAATTTGAATTAAAAT
1 TTCAAATTAATTTGAATTAAAAT
12512279 AATTTGAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
35 3 0.06
36 5 0.10
37 16 0.32
38 20 0.40
39 6 0.12
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
TTCAAATTAATTTGAATTAAAATTAAATTTTATAAA
Found at i:12512539 original size:2 final size:2
Alignment explanation
Indices: 12512534--12512562 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12512524 TGTGTGTGTT
12512534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12512563 GAAAGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12514108 original size:18 final size:19
Alignment explanation
Indices: 12514070--12514109 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12514060 ATTGAATATG
*
12514070 AATTCAAATAATTATATTA
1 AATTCAAATAAATATATTA
*
12514089 AATTTAAATAAATA-ATTA
1 AATTCAAATAAATATATTA
12514107 AAT
1 AAT
12514110 AAATTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCAAATAAATATATTA
Found at i:12514115 original size:22 final size:23
Alignment explanation
Indices: 12514075--12514120 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
12514065 ATATGAATTC
*
12514075 AAATAATTATATTAAATTTAAAT
1 AAATAATTATAATAAATTTAAAT
*
12514098 AAATAATTA-AATAAATTTGAAT
1 AAATAATTATAATAAATTTAAAT
12514120 A
1 A
12514121 TTGTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATAATTATAATAAATTTAAAT
Found at i:12515577 original size:218 final size:218
Alignment explanation
Indices: 12515321--12515792 Score: 761
Period size: 218 Copynumber: 2.2 Consensus size: 218
12515311 AATTTGAAGG
*
12515321 AAAAGTTGAATTATCAACTTTCCCTAAAAAGAAAATATCATTTTAGAAAAAATTTTCAGAAAAAA
1 AAAAGTTGAATTATCAACTTTCCTTAAAAAGAAAATATCATTTTAGAAAAAATTTTCAGAAAAAA
* *
12515386 GTTGGAATGCCTATTTTTCCTTAAATTAAATAAAATTTTTAAGAAAAAAATTGAAATATCAAAAT
66 GTTGGAATGCCTATTTTTCCTTAAATTAAATAAAATTTTTAAGAAAAAAATTGAAAGATCAAAAC
* * *
12515451 TTTCTCAAATAAAAATAATTTCAAAATTACAAGAAAGGGTTAAAGTATCAATTTTTTCCTAAATA
131 TTTCTCAAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCTAAATA
12515516 AAAATCATTTTAAAAAATG-AGAA
196 AAAATCATTTT-AAAAATGAAGAA
* * *
12515539 AAAAGTTGAATTATCAACTTTCCTTAAAAAGAAAATATCATTTTAGAAAAATTTTTGAGGAAAAA
1 AAAAGTTGAATTATCAACTTTCCTTAAAAAGAAAATATCATTTTAGAAAAAATTTTCAGAAAAAA
* *
12515604 GTTGGAATGCCTATTTTTCCTTACATTAAATAAAATTTTTAAGGAAAAAATTGAAAGATCAAAAC
66 GTTGGAATGCCTATTTTTCCTTAAATTAAATAAAATTTTTAAGAAAAAAATTGAAAGATCAAAAC
12515669 TTTCTCAAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCTAAATA
131 TTTCTCAAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCTAAATA
12515734 AAAATCATTTTAAAAATGAAGAA
196 AAAATCATTTTAAAAATGAAGAA
* * * * *
12515757 ACAA-TTAAAATATCAATTTTTCCTTAAACA-AAAATA
1 AAAAGTTGAATTATCAA-CTTTCCTTAAAAAGAAAATA
12515793 ATTTCAAAAT
Statistics
Matches: 236, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
217 23 0.10
218 213 0.90
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (218 bp):
AAAAGTTGAATTATCAACTTTCCTTAAAAAGAAAATATCATTTTAGAAAAAATTTTCAGAAAAAA
GTTGGAATGCCTATTTTTCCTTAAATTAAATAAAATTTTTAAGAAAAAAATTGAAAGATCAAAAC
TTTCTCAAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCTAAATA
AAAATCATTTTAAAAATGAAGAA
Found at i:12515765 original size:53 final size:53
Alignment explanation
Indices: 12515457--12516015 Score: 266
Period size: 54 Copynumber: 10.3 Consensus size: 53
12515447 AAATTTTCTC
* * * **
12515457 AAATAAAAATAATTTCAAAATTACAAGAAAGGGTTAAAGTATCAATTTTTTCC-T
1 AAATAAAAATAATTTTAAAAAT-GAAGAAAAAGTTAAAGTATCAA-TTTTTCCTT
* * * *
12515511 AAATAAAAATCATTTTAAAAAATG-AGAAAAAAGTTGAATTATCAA-CTTTCCTT
1 AAATAAAAATAATTTT-AAAAATGAAG-AAAAAGTTAAAGTATCAATTTTTCCTT
* * * ** *
12515564 AAAAAGAAAATATCATTTTAGAAAAATTTTTGAGGAAAAAGTTGGAA-TGCCTATTTTTCCTT
1 AAATA-AAAATA--ATTTT--AAAAA----TGAAGAAAAAGTT-AAAGTATCAATTTTTCCTT
* * * ** *
12515626 ACATTAAATAA-AATTTT--TAA-G--GAAAAAATTGAAAG-ATCAAAACTTT-CTC
1 A-AATAAA-AATAATTTTAAAAATGAAGAAAAAGTT-AAAGTATC-AATTTTTCCTT
* * * * * *
12515675 AAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCT
1 AAATAAAAATAATTTTAAAAAT-GAAGAAAAAGTTAAAGTATCAATTTTTCCTT
* *
12515729 AAATAAAAATCATTTTAAAAATGAAGAAACAA-TTAAAATATCAATTTTTCCTT
1 AAATAAAAATAATTTTAAAAATGAAGAAA-AAGTTAAAGTATCAATTTTTCCTT
* * * * * *
12515782 AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTTCTT
1 AAATAAAAATAATTTTAAAA-ATGAAGAAAAAGTTAAAGTATCAATTTTTCCTT
* * * ** *
12515836 AAATAAAAATAATTTTAAAAAATGAGGAAAAAGTTAAAATATTAAAATTTCCTC
1 AAATAAAAATAATTTT-AAAAATGAAGAAAAAGTTAAAGTATCAATTTTTCCTT
* * ** * * *
12515890 AAGATCAAAATAATTTCAAATTTTGAAGAAAAAGTTGAAA-TATAAAATTTTCTTT
1 AA-ATAAAAATAATTTTAAA-AATGAAGAAAAAGTT-AAAGTATCAATTTTTCCTT
* * ** * *
12515945 AAATAAAAAATAATTTCTAAAATTTG-GGAAAATTTTCAAAGTATTAATTTTTTCTT
1 AAAT-AAAAATAATTT-TAAAA-ATGAAGAAAAAGTT-AAAGTATCAATTTTTCCTT
12516001 AAATAAAAATAATTT
1 AAATAAAAATAATTT
12516016 CAAATTTTTT
Statistics
Matches: 383, Mismatches: 84, Indels: 75
0.71 0.15 0.14
Matches are distributed among these distances:
47 2 0.01
48 9 0.02
49 15 0.04
50 5 0.01
51 1 0.00
52 5 0.01
53 60 0.16
54 136 0.36
55 77 0.20
56 31 0.08
57 5 0.01
60 5 0.01
61 13 0.03
62 15 0.04
63 4 0.01
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (53 bp):
AAATAAAAATAATTTTAAAAATGAAGAAAAAGTTAAAGTATCAATTTTTCCTT
Found at i:12515833 original size:55 final size:54
Alignment explanation
Indices: 12515675--12516059 Score: 305
Period size: 54 Copynumber: 7.1 Consensus size: 54
12515665 AAACTTTCTC
** * * * *
12515675 AAACAAAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCT
1 AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTCCTT
* * * * * * *
12515729 AAATAAAAATCATTTTAAAA-ATGAAGAAACAA-TTAAAATATCAATTTTTCCTT
1 AAACAAAAATAATTTCAAAATTTGAGGAAA-AAGTTAAAGTATTAATTTTTCCTT
*
12515782 AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTTCTT
1 AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTCCTT
* * ** * ** *
12515836 AAATAAAAATAATTTTAAAAAATGAGGAAAAAGTTAAAATATTAAAATTTCCTC
1 AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTCCTT
* * * * *
12515890 AAGATC-AAAATAATTTCAAATTTTGAAGAAAAAGTTGAAA-TATAAAATTTTCTTT
1 AA-A-CAAAAATAATTTCAAAATTTGAGGAAAAAGTT-AAAGTATTAATTTTTCCTT
* ** *
12515945 AAATAAAAAATAATTTCTAAAATTTG-GGAAAATTTTCAAAGTATTAATTTTTTCTT
1 AAA-CAAAAATAATTTC-AAAATTTGAGGAAAAAGTT-AAAGTATTAATTTTTCCTT
* * * * * *
12516001 AAATAAAAATAATTTCAAATTTTTTAGGGAGAAAGTTGAAGTATCAATATTTT-CTT
1 AAACAAAAATAATTTCAAA-ATTTGA-GGAAAAAGTTAAAGTATTAAT-TTTTCCTT
12516057 AAA
1 AAA
12516060 ATTAAAATTT
Statistics
Matches: 264, Mismatches: 54, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
53 44 0.17
54 95 0.36
55 75 0.28
56 39 0.15
57 11 0.04
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (54 bp):
AAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTCCTT
Found at i:12515950 original size:109 final size:106
Alignment explanation
Indices: 12515680--12516019 Score: 346
Period size: 107 Copynumber: 3.1 Consensus size: 106
12515670 TTCTCAAACA
** * * ** *
12515680 AAAATAATTTCAAAATTACAAGAAAGAGTTAAAGTATCAATTTTTCCCTAAATAAAAATCATTTT
1 AAAATAATTTCAAAATTTGAAGAAAAAGTTAAAGTAT-AAATTTTCTTTAAATAAAAATAATTTT
* *
12515745 -AAAAATGAAGAAACAATTAAAATATCAATTTTTCCTTAAA-C
65 AAAAAATGAGGAAA-AATTAAAATATTAATTTTTCCTTAAATC
* * *
12515786 AAAAATAATTTCAAAATTTGAGGAAAAAGTTAAAGTATTAATTTTTTCTTAAATAAAAATAATTT
1 -AAAATAATTTCAAAATTTGAAGAAAAAGTTAAAGTATAAATTTTCT-TTAAATAAAAATAATTT
** *
12515851 TAAAAAATGAGGAAAAAGTTAAAATATTAAAATTTCCTCAAGATC
64 TAAAAAATGAGGAAAAA-TTAAAATATTAATTTTTCCTTAA-ATC
*
12515896 AAAATAATTTCAAATTTTGAAGAAAAAGTTGAAA-TATAAAATTTTCTTTAAATAAAAAATAATT
1 AAAATAATTTCAAAATTTGAAGAAAAAGTT-AAAGTAT-AAATTTTCTTTAAAT-AAAAATAATT
** * * * *
12515960 TCTAAAATTTG-GGAAAATTTTCAAAGTATTAATTTTTTCTTAAATA
63 T-TAAAAAATGAGGAAAA-ATT-AAAATATTAATTTTTCCTTAAATC
12516006 AAAATAATTTCAAA
1 AAAATAATTTCAAA
12516020 TTTTTTAGGG
Statistics
Matches: 194, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
106 5 0.03
107 51 0.26
108 31 0.16
109 38 0.20
110 46 0.24
111 23 0.12
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (106 bp):
AAAATAATTTCAAAATTTGAAGAAAAAGTTAAAGTATAAATTTTCTTTAAATAAAAATAATTTTA
AAAAATGAGGAAAAATTAAAATATTAATTTTTCCTTAAATC
Found at i:12518188 original size:25 final size:25
Alignment explanation
Indices: 12518143--12518190 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12518133 ATAGATTTTA
*
12518143 ATATTTTTTTAAGGATTATTTTTGG
1 ATATTTTTTTAAGGATAATTTTTGG
*
12518168 ATATTTTTGTT-AGTATAATTTTT
1 ATATTTTT-TTAAGGATAATTTTT
12518191 AATTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (25 bp):
ATATTTTTTTAAGGATAATTTTTGG
Found at i:12521196 original size:27 final size:26
Alignment explanation
Indices: 12521160--12521285 Score: 79
Period size: 26 Copynumber: 4.9 Consensus size: 26
12521150 ATTGCTCAAT
* *
12521160 AAAAAT-AAATAA-ATAATAAAAGTTA
1 AAAAATAAAATAATAAAATAAAA-CTA
12521185 ATAAAATAAAATAATAAAATAAAACTA
1 A-AAAATAAAATAATAAAATAAAACTA
**
12521212 AAATAATAAAAT-ATAAAAT---TTTA
1 AAA-AATAAAATAATAAAATAAAACTA
*
12521235 AAATATAAAATAAATAAATATAAAA-TA
1 AAAAATAAAAT-AATAAA-ATAAAACTA
*
12521262 TAAAATATAAA-AATAAAATGAAAA
1 AAAAATA-AAATAATAAAAT-AAAA
12521286 AAGAAAAACC
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
22 7 0.09
23 5 0.06
24 5 0.06
25 5 0.06
26 24 0.30
27 24 0.30
28 11 0.14
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAATAAAATAATAAAATAAAACTA
Found at i:12521215 original size:19 final size:18
Alignment explanation
Indices: 12521184--12521285 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
12521174 AATAAAAGTT
12521184 AATAAAATAAAATAATAA
1 AATAAAATAAAATAATAA
12521202 AATAAAACTAAAATAATAAA
1 AATAAAA-TAAAATAAT-AA
12521222 ATATAAAATTTTAAAAT-ATAA
1 A-ATAAAA---TAAAATAATAA
12521243 AAT-AAATAAATATAA-AA
1 AATAAAATAAA-ATAATAA
*
12521260 TATAAAATATAAA-AATAA
1 AATAAAATA-AAATAATAA
12521278 AATGAAAA
1 AAT-AAAA
12521286 AAGAAAAACC
Statistics
Matches: 70, Mismatches: 3, Indels: 21
0.74 0.03 0.22
Matches are distributed among these distances:
16 4 0.06
17 8 0.11
18 18 0.26
19 18 0.26
20 5 0.07
21 9 0.13
22 2 0.03
23 6 0.09
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (18 bp):
AATAAAATAAAATAATAA
Found at i:12521229 original size:7 final size:7
Alignment explanation
Indices: 12521190--12521280 Score: 91
Period size: 7 Copynumber: 13.0 Consensus size: 7
12521180 AGTTAATAAA
12521190 ATAAAAT
1 ATAAAAT
12521197 A-ATAAA-
1 ATA-AAAT
12521203 ATAAAA-
1 ATAAAAT
*
12521209 CTAAAAT
1 ATAAAAT
12521216 AATAAAAT
1 -ATAAAAT
12521224 ATAAAATT
1 ATAAAA-T
*
12521232 TTAAAAT
1 ATAAAAT
12521239 ATAAAAT
1 ATAAAAT
*
12521246 AAATAAAT
1 ATA-AAAT
12521254 ATAAAAT
1 ATAAAAT
12521261 ATAAAAT
1 ATAAAAT
12521268 ATAAAA-
1 ATAAAAT
12521274 ATAAAAT
1 ATAAAAT
12521281 GAAAAAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
6 16 0.23
7 37 0.52
8 18 0.25
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (7 bp):
ATAAAAT
Found at i:12521230 original size:15 final size:15
Alignment explanation
Indices: 12521170--12521273 Score: 96
Period size: 15 Copynumber: 7.2 Consensus size: 15
12521160 AAAAATAAAT
12521170 AAATAATAAAAGT-TA
1 AAATAATAAAA-TATA
12521185 ATAA-AATAAAATA-A
1 A-AATAATAAAATATA
* *
12521199 TAA-AATAAAA-CTA
1 AAATAATAAAATATA
12521212 AAATAATAAAATATA
1 AAATAATAAAATATA
**
12521227 AAATTTTAAAATATA
1 AAATAATAAAATATA
12521242 AAATAA-ATAAATATA
1 AAATAATA-AAATATA
12521257 AAAT-ATAAAATATA
1 AAATAATAAAATATA
12521271 AAA
1 AAA
12521274 ATAAAATGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
13 12 0.16
14 21 0.28
15 39 0.53
16 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (15 bp):
AAATAATAAAATATA
Found at i:12521245 original size:22 final size:22
Alignment explanation
Indices: 12521210--12521276 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
12521200 AAAATAAAAC
* *
12521210 TAAAATAATAAAATATAAAATTT
1 TAAAAT-ATAAAATATAAAAATA
12521233 TAAAATATAAAATA-AATAAATA
1 TAAAATATAAAATATAA-AAATA
12521255 TAAAATATAAAATATAAAAATA
1 TAAAATATAAAATATAAAAATA
12521277 AAATGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.05
22 30 0.75
23 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATATAAAATATAAAAATA
Found at i:12521285 original size:6 final size:5
Alignment explanation
Indices: 12521184--12521285 Score: 54
Period size: 5 Copynumber: 20.4 Consensus size: 5
12521174 AATAAAAGTT
* **
12521184 AATAA AATAA AAT-- AATAA AATAA AACTAA AATAA TAA-AA TATAA AATTTT
1 AATAA AATAA AATAA AATAA AATAA AA-TAA AATAA -AATAA AATAA AA-TAA
* * *
12521234 AA-AA TATAA AAT-A AATAA ATATAA AATAT AA-AA TATAAA AATAA AATGAA
1 AATAA AATAA AATAA AATAA A-ATAA AATAA AATAA AAT-AA AATAA AAT-AA
12521284 AA
1 AA
12521286 AAGAAAAACC
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
3 3 0.04
4 8 0.11
5 39 0.53
6 23 0.32
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (5 bp):
AATAA
Found at i:12521704 original size:19 final size:21
Alignment explanation
Indices: 12521673--12521712 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12521663 ATTCTTCAAC
12521673 ACTTCCAAACTAAA-CTAGAA
1 ACTTCCAAACTAAACCTAGAA
12521693 ACTTCC-AACTAAACCTAGAA
1 ACTTCCAAACTAAACCTAGAA
12521713 TCTATAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.20
Consensus pattern (21 bp):
ACTTCCAAACTAAACCTAGAA
Found at i:12522075 original size:3 final size:3
Alignment explanation
Indices: 12522067--12522168 Score: 107
Period size: 3 Copynumber: 37.3 Consensus size: 3
12522057 ATAGGAAAGA
12522067 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
12522114 AA- GAT AAT -AT AA- GAT AAT -AT AAT AAT -AT AAT -AT AAT -AT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12522155 AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
12522169 TTATATATCA
Statistics
Matches: 84, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
2 18 0.21
3 66 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12522085 original size:15 final size:15
Alignment explanation
Indices: 12522067--12522168 Score: 107
Period size: 13 Copynumber: 7.5 Consensus size: 15
12522057 ATAGGAAAGA
12522067 AATAATAATAATAAT
1 AATAATAATAATAAT
12522082 AATAATAATAATAAT
1 AATAATAATAATAAT
12522097 AATAATAATAATAAT
1 AATAATAATAATAAT
*
12522112 -ATAA-GATAAT-AT
1 AATAATAATAATAAT
*
12522124 AA-GATAAT-ATAAT
1 AATAATAATAATAAT
12522137 AAT-ATAAT-ATAAT
1 AATAATAATAATAAT
*
12522150 -ATGATAAT-ATAAT
1 AATAATAATAATAAT
12522163 -ATAATA
1 AATAATA
12522169 TTATATATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
12 7 0.09
13 37 0.47
14 4 0.05
15 30 0.38
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:12522120 original size:5 final size:5
Alignment explanation
Indices: 12522071--12522175 Score: 92
Period size: 5 Copynumber: 20.6 Consensus size: 5
12522061 GAAAGAAATA
*
12522071 ATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT ATAAG ATAAT
1 ATAAT -ATAAT -ATAAT -ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT
* *
12522122 ATAAG ATAAT AT-A- ATAAT ATAAT ATAAT AT--G ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
12522168 ATTAT ATA
1 ATAAT ATA
12522176 TCATACTATA
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
3 4 0.05
4 2 0.02
5 46 0.53
6 35 0.40
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:12522575 original size:55 final size:55
Alignment explanation
Indices: 12522424--12522778 Score: 250
Period size: 55 Copynumber: 6.4 Consensus size: 55
12522414 ATGACTAGGA
* * * * * *
12522424 TGAACCACAAGTCAGAAAGATGATATAGACTAAGCTAAGATCAAACGATCAAGAT
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCAAACGATCAAGAT
* ** * * * * *
12522479 TAAACCACATCTCTAGAAAACA--ATCTGGATTAAGCCGAGATCAAATGACCAAGAT
1 TGAACCACAAGTCT-GAAAA-ATGATCTGGACTGAGCCAAGATCAAACGATCAAGAT
* * *
12522534 TGAACCACAAGTTTGAAAAATGATTTGGACTGAGCCAAGATCGATTAAGCGATCGAGAT
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATC-A--AA-CGATCAAGAT
* * * * * * * **
12522593 TAAACCATAAGTCTGTAAAATAATTTGGATTGAGCCAAGCTCAAACGATTGAGAT
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCAAACGATCAAGAT
* * * * * * * **
12522648 TGAACTACAAGTCT-AGAAAATGATCTGTACTGAGTCGAGATCGAGCAATTGAGAT
1 TGAACCACAAGTCTGA-AAAATGATCTGGACTGAGCCAAGATCAAACGATCAAGAT
* * * * *
12522703 TAAATCACAAGTTTGAAAAATGATCTGGACTGAGCCAAGATCAAACAATC-GGAAT
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCAAACGATCAAG-AT
12522758 TGAACCACAAGTCTGAAAAAT
1 TGAACCACAAGTCTGAAAAAT
12522779 AATTGAACCA
Statistics
Matches: 230, Mismatches: 59, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
53 1 0.00
54 6 0.03
55 169 0.73
56 8 0.03
57 1 0.00
58 3 0.01
59 42 0.18
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (55 bp):
TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCAAACGATCAAGAT
Found at i:12522778 original size:110 final size:111
Alignment explanation
Indices: 12522424--12522778 Score: 279
Period size: 110 Copynumber: 3.2 Consensus size: 111
12522414 ATGACTAGGA
* * * * * * * * *
12522424 TGAACCACAAGTCAGAAAGATGATATAGACTAAGCTAAGATC-AAACGATCAAGATTAAACCACA
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCGAAGCAATCGAGATTAAACCACA
** * * * * ** ***
12522488 TCTCT-AGAAAACAATCTGGATTAAGCCGAGATCAAATGACCAAGAT
66 AGTCTGA-AAAATAATCTGGACTGAGCCAAGATCAAACAATGGAGAT
* * *
12522534 TGAACCACAAGTTTGAAAAATGATTTGGACTGAGCCAAGATCGATTAAGCGATCGAGATTAAACC
1 TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCG---AAGCAATCGAGATTAAACC
* * * * * * *
12522599 ATAAGTCTGTAAAATAATTTGGATTGAGCCAAGCTCAAACGATTGAGAT
63 ACAAGTCTGAAAAATAATCTGGACTGAGCCAAGATCAAACAATGGAGAT
* * * * * *
12522648 TGAACTACAAGTCT-AGAAAATGATCTGTACTGAGTCGAGATCG-AGCAATTGAGATTAAATCAC
1 TGAACCACAAGTCTGA-AAAATGATCTGGACTGAGCCAAGATCGAAGCAATCGAGATTAAACCAC
* *
12522711 AAGTTTGAAAAATGATCTGGACTGAGCCAAGATCAAACAATCGGA-AT
65 AAGTCTGAAAAATAATCTGGACTGAGCCAAGATCAAACAAT-GGAGAT
12522758 TGAACCACAAGTCTGAAAAAT
1 TGAACCACAAGTCTGAAAAAT
12522779 AATTGAACCA
Statistics
Matches: 196, Mismatches: 41, Indels: 16
0.77 0.16 0.06
Matches are distributed among these distances:
110 105 0.54
111 3 0.02
113 1 0.01
114 87 0.44
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (111 bp):
TGAACCACAAGTCTGAAAAATGATCTGGACTGAGCCAAGATCGAAGCAATCGAGATTAAACCACA
AGTCTGAAAAATAATCTGGACTGAGCCAAGATCAAACAATGGAGAT
Found at i:12522782 original size:24 final size:24
Alignment explanation
Indices: 12522755--12522802 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12522745 AAACAATCGG
12522755 AATTGAACCACAAGTCTGAAAAAT
1 AATTGAACCACAAGTCTGAAAAAT
* *
12522779 AATTGAACCACAAGTTTGGAAAAT
1 AATTGAACCACAAGTCTGAAAAAT
12522803 GATTTGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (24 bp):
AATTGAACCACAAGTCTGAAAAAT
Found at i:12522839 original size:79 final size:79
Alignment explanation
Indices: 12522708--12522857 Score: 210
Period size: 79 Copynumber: 1.9 Consensus size: 79
12522698 GAGATTAAAT
* * *
12522708 CACAAGTTTGAAAAATGATCTGGACTGAGCCAAGATCAAACAATCGGAATTGAACCACAAGTCTG
1 CACAAGTTTGAAAAATGATCTGGACTAAGCCAAGATCAAACAACCGAAATTGAACCACAAGTCTG
12522773 AAAAATAATTGAAC
66 AAAAATAATTGAAC
* * * * * * *
12522787 CACAAGTTTGGAAAATGATTTGGATTAAGCTAAGATCAAGCAACCGAAATTGAACCATAAGTTTG
1 CACAAGTTTGAAAAATGATCTGGACTAAGCCAAGATCAAACAACCGAAATTGAACCACAAGTCTG
12522852 AAAAAT
66 AAAAAT
12522858 GATATGGACT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (79 bp):
CACAAGTTTGAAAAATGATCTGGACTAAGCCAAGATCAAACAACCGAAATTGAACCACAAGTCTG
AAAAATAATTGAAC
Found at i:12524012 original size:18 final size:18
Alignment explanation
Indices: 12523986--12524037 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
12523976 TTCTTTTTCT
12523986 TTTTCCTTCATTTTTTTTA
1 TTTT-CTTCATTTTTTTTA
12524005 TTTTCTTCATTTTTTTTA
1 TTTTCTTCATTTTTTTTA
*
12524023 TTTTCATCATTTTTT
1 TTTTCTTCATTTTTT
12524038 AAGAAAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTTCATTTTTTTTA
Found at i:12529424 original size:3 final size:3
Alignment explanation
Indices: 12529416--12529612 Score: 106
Period size: 3 Copynumber: 70.3 Consensus size: 3
12529406 AATAGAAAGA
* *
12529416 AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- CAT AAT -AT AA- CAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12529460 -AT AAT -AT AAT AAT -AT GAT ACT -AC AAT AAT AAT AA- CAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12529502 AAT AAT -AT AAT ACGAT AAT AAT -AT AAT -AT GAT AAT -AT AAT AAT
1 AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12529545 -AT AAT ATAT CAT ACT -AT ACT -AT ACT AAT AAT AAT AAT AA- AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
12529587 AAT ACAA AAT AAT AAC AAT AAA AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT A
12529613 TACTCTAATT
Statistics
Matches: 146, Mismatches: 26, Indels: 44
0.68 0.12 0.20
Matches are distributed among these distances:
2 29 0.20
3 110 0.75
4 4 0.03
5 3 0.02
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12529448 original size:5 final size:5
Alignment explanation
Indices: 12529417--12529600 Score: 89
Period size: 5 Copynumber: 36.2 Consensus size: 5
12529407 ATAGAAAGAA
* *
12529417 ATAAT AATAAT AATAAT AATAAT ATAAC ATAAT ATAAC ATAAT ATAAT
1 ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
12529465 AT-A- ATAAT ATGAT ACTACA- ATAAT AATAAC ATAAT AT-A- ATAAT
1 ATAAT ATAAT ATAAT A-TA-AT ATAAT -ATAAT ATAAT ATAAT ATAAT
** *
12529508 ATAAT ACGAT AATAAT ATAAT ATGAT A-ATAT AATAAT ATAAT AT-AT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT
* * * * *
12529554 CATACT ATACT ATACT AATAAT AATAAT A-AA- ATAAT ACAAA ATAAT
1 -ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
12529600 A
1 A
12529601 ACAATAAAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
3 5 0.04
4 11 0.08
5 83 0.59
6 40 0.28
7 2 0.01
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (5 bp):
ATAAT
Found at i:12529473 original size:8 final size:8
Alignment explanation
Indices: 12529416--12529590 Score: 112
Period size: 8 Copynumber: 21.5 Consensus size: 8
12529406 AATAGAAAGA
12529416 AATAATAAT
1 AATAAT-AT
12529425 AATAATAAT
1 AATAAT-AT
12529434 AATAATAT
1 AATAATAT
12529442 AACATAATAT
1 -A-ATAATAT
*
12529452 AA-CATA-
1 AATAATAT
12529458 ATATAATAT
1 A-ATAATAT
12529467 AATAATAT
1 AATAATAT
* * *
12529475 GATACTAC
1 AATAATAT
12529483 AATAATAAT
1 AATAAT-AT
12529492 AACATAATAT
1 -A-ATAATAT
12529502 AATAATAT
1 AATAATAT
**
12529510 AATACGAT
1 AATAATAT
12529518 AAT-A-AT
1 AATAATAT
12529524 -ATAATAT
1 AATAATAT
*
12529531 GATAATAT
1 AATAATAT
12529539 AATAATAT
1 AATAATAT
12529547 AAT-ATAT
1 AATAATAT
* *
12529554 CATACTAT
1 AATAATAT
*
12529562 ACT-ATACT
1 AATAATA-T
12529570 AATAATAAT
1 AATAAT-AT
*
12529579 AATAAAAT
1 AATAATAT
12529587 AATA
1 AATA
12529591 CAAAATAATA
Statistics
Matches: 132, Mismatches: 19, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
5 2 0.02
6 4 0.03
7 14 0.11
8 68 0.52
9 28 0.21
10 11 0.08
11 5 0.04
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.34
Consensus pattern (8 bp):
AATAATAT
Found at i:12532069 original size:22 final size:22
Alignment explanation
Indices: 12532027--12532079 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
12532017 GCATGATTTT
*
12532027 TTAAGTCTTTTGAGCAAAATCA
1 TTAAGTCTTTAGAGCAAAATCA
*
12532049 TTAAGTCTTATAG-GCAGAATCA
1 TTAAGTCTT-TAGAGCAAAATCA
* *
12532071 CTAAATCTT
1 TTAAGTCTT
12532080 CCAGCCATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTAAGTCTTTAGAGCAAAATCA
Found at i:12534328 original size:54 final size:55
Alignment explanation
Indices: 12534183--12534431 Score: 197
Period size: 54 Copynumber: 4.5 Consensus size: 55
12534173 AAGTATCAAA
* * * * * * *
12534183 TTTTCCTCAAACAAAAATAATTCCAAAA-TTAAAGAAAAGGTTG-AATTATTAAA
1 TTTTCCTTAAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTGAAACTATTAAT
* * **
12534236 TTTTCCCTAAATACAAAAT-ATTTCAAAAAATGAGGAAAAAGTTGAAA-TATTAAT
1 TTTTCCTTAAACA-AAAATAATTTCAAAATTTGAGGAAAAAGTTGAAACTATTAAT
* *
12534290 TTTTCCTTAAACAAAAATAATTTCAAAATTTTGA-GAAAAAATTCAAACTATTAAT
1 TTTTCCTTAAACAAAAATAATTTCAAAA-TTTGAGGAAAAAGTTGAAACTATTAAT
* * * * * *
12534345 TTTT-TTACTAAATAAAAATAATTTCAAATTTTTTAGGAAAAAGTT-AAAGTATCAAT
1 TTTTCCT--TAAACAAAAATAATTTCAAA-ATTTGAGGAAAAAGTTGAAACTATTAAT
*
12534401 TTTTCCTTAAAATAAAAAAATAATTTCAAAA
1 TTTTCCTT--AA-ACAAAAATAATTTCAAAA
12534432 AAAAAAAAGA
Statistics
Matches: 157, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
53 23 0.15
54 54 0.34
55 17 0.11
56 36 0.23
57 11 0.07
58 16 0.10
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (55 bp):
TTTTCCTTAAACAAAAATAATTTCAAAATTTGAGGAAAAAGTTGAAACTATTAAT
Found at i:12534368 original size:56 final size:55
Alignment explanation
Indices: 12534242--12534431 Score: 169
Period size: 56 Copynumber: 3.4 Consensus size: 55
12534232 TAAATTTTCC
** *
12534242 CTAAATACAAAAT-ATTTCAAAA-AATGAGGAAAAAGTTGAAATATTAA--TTTTTC
1 CTAAATA-AAAATAATTTCAAAATTTTGAGGAAAAAGTT-AAATATTAATTTTTTTA
* *
12534295 CTTAAACAAAAATAATTTCAAAATTTTGA-GAAAAAATTCAAACTATTAATTTTTTTA
1 C-TAAATAAAAATAATTTCAAAATTTTGAGGAAAAAGTT-AAA-TATTAATTTTTTTA
* * *
12534352 CTAAATAAAAATAATTTCAAATTTTTTAGGAAAAAGTTAAAGTATCAATTTTTCCTTA
1 CTAAATAAAAATAATTTCAAAATTTTGAGGAAAAAGTTAAA-TATTAATTTTT--TTA
12534410 --AAATAAAAAAATAATTTCAAAA
1 CTAAAT--AAAAATAATTTCAAAA
12534432 AAAAAAAAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
53 6 0.05
54 25 0.22
55 9 0.08
56 41 0.36
57 14 0.12
58 18 0.16
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (55 bp):
CTAAATAAAAATAATTTCAAAATTTTGAGGAAAAAGTTAAATATTAATTTTTTTA
Found at i:12537585 original size:18 final size:16
Alignment explanation
Indices: 12537562--12537596 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12537552 ATTTTTTTTT
12537562 TCAATAAATGAAATAAAA
1 TCAATAAA--AAATAAAA
12537580 TCAATAAAAAATAAAA
1 TCAATAAAAAATAAAA
12537596 T
1 T
12537597 AAAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (16 bp):
TCAATAAAAAATAAAA
Found at i:12539624 original size:19 final size:19
Alignment explanation
Indices: 12539596--12539639 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
12539586 AGGTTATTAT
*
12539596 CTTTTACAATGAAAGTTAC
1 CTTTTCCAATGAAAGTTAC
12539615 CTTTTCCAATGAAAGTTAC
1 CTTTTCCAATGAAAGTTAC
12539634 CTTTTC
1 CTTTTC
12539640 TTGCTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (19 bp):
CTTTTCCAATGAAAGTTAC
Found at i:12542021 original size:15 final size:16
Alignment explanation
Indices: 12541997--12542029 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12541987 AACTTTAGAA
12541997 TTTTTAAAAATA-ATT
1 TTTTTAAAAATATATT
*
12542012 TTTTTCAAAATATATT
1 TTTTTAAAAATATATT
12542028 TT
1 TT
12542030 CAACTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAAAAATATATT
Done.