Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 69 of 214
Found at i:19674247 original size:22 final size:21
Alignment explanation
Indices: 19674198--19674249 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
19674188 AATAATTATG
*
19674198 TTAA-ATTATATTTTATAGTA
1 TTAATATTATATTTTATAATA
19674218 TTATATATTATGATTTTAGTAAT-
1 TTA-ATATTAT-ATTTTA-TAATA
19674241 TTAATATTA
1 TTAATATTA
19674250 AGAATATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTAATATTATATTTTATAATA
Found at i:19674305 original size:121 final size:118
Alignment explanation
Indices: 19674038--19674323 Score: 465
Period size: 121 Copynumber: 2.4 Consensus size: 118
19674028 CAAATTTTAG
19674038 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAA-T-T-TTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
* *
19674100 TTATATATTATGATTTTAGTACATATAAGAATATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATATAAGAATATATCTAATATTAAGAATTTT
19674153 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
19674218 TTATATATTATGATTTTAGTAATTTAATATTAAG-A-ATATCTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGT-A---AATA-TAAGAATATATCTAATATTAAGAATTTT
*
19674274 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
19674324 ATATGATTAA
Statistics
Matches: 160, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
115 40 0.25
116 1 0.01
117 1 0.01
118 40 0.25
119 1 0.01
121 69 0.43
122 4 0.03
123 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (118 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATATAAGAATATATCTAATATTAAGAATTTT
Found at i:19674396 original size:121 final size:119
Alignment explanation
Indices: 19674038--19674358 Score: 351
Period size: 121 Copynumber: 2.7 Consensus size: 119
19674028 CAAATTTTAG
*
19674038 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAAT--T-TTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAA-TATATATTATAG-A
* * **
19674100 TTATATATTATGAT-TT--T-A-GTACATAT-AAGAATATATTTAATATTAAGAATTTT
64 TTATATATTATGATATTAATAATTTA-ATATAAAGAATA-A-CTAATAACAAGAATTTT
* *
19674153 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAA-TATATATTATAG-A
* * * * **
19674218 TTATATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTT
64 TTATATATTATGATATTAATAATTTAATATAAAGAATAACTAATAACAAGAATTTT
19674274 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAA-ATATGATTA-A-AT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAATATAT-ATTATAGAT
*
19674336 TATTTATTACTGATATTAATAAT
65 TATATATTA-TGATATTAATAAT
19674359 CTTATTAAAA
Statistics
Matches: 187, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
115 41 0.22
117 11 0.06
118 45 0.24
119 7 0.04
120 3 0.02
121 66 0.35
122 5 0.03
123 9 0.05
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (119 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAATGTTAAATATATATTATAGATT
ATATATTATGATATTAATAATTTAATATAAAGAATAACTAATAACAAGAATTTT
Found at i:19683572 original size:30 final size:31
Alignment explanation
Indices: 19683533--19683592 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19683523 GGAGGTGGGA
*
19683533 TGGGAAGGGAATAAAAGTTTTAGGGG-AAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGGCAAAAG
*
19683564 TGGG-AGGGAGTAAAAATTTTGGGGCAAAA
1 TGGGAAGGGAATAAAAATTTTGGGGCAAAA
19683593 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGGCAAAAG
Found at i:19683902 original size:9 final size:9
Alignment explanation
Indices: 19683885--19683915 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19683875 TCGAGTTGAT
19683885 TCGAATAAC
1 TCGAATAAC
*
19683894 TCGATTAAC
1 TCGAATAAC
19683903 TCGAATAAC
1 TCGAATAAC
19683912 TCGA
1 TCGA
19683916 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19689766 original size:20 final size:19
Alignment explanation
Indices: 19689722--19689773 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
19689712 AATATATGTT
19689722 TATTT-AATATATTATAAA
1 TATTTAAATATATTATAAA
* *
19689740 T-TATAAATATATTTTAAA
1 TATTTAAATATATTATAAA
*
19689758 TAATTTAAAAATATTA
1 T-ATTTAAATATATTA
19689774 AATTAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 14 0.54
20 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTAAATATATTATAAA
Found at i:19692494 original size:5 final size:5
Alignment explanation
Indices: 19692484--19692508 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19692474 GAACAAGTTT
19692484 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
19692509 ATGAATAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:19692768 original size:12 final size:12
Alignment explanation
Indices: 19692751--19692788 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
19692741 TGAAAAGTTT
19692751 AATAATAATATA
1 AATAATAATATA
19692763 AATAATAATATA
1 AATAATAATATA
* *
19692775 TATAATGATATA
1 AATAATAATATA
19692787 AA
1 AA
19692789 AGTTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
AATAATAATATA
Found at i:19692773 original size:43 final size:42
Alignment explanation
Indices: 19692717--19692810 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 42
19692707 TACATTAGTC
19692717 TAAATAAGTAATATATAT-ATAAAATGAAAAGTTTAATAATAATA
1 TAAATAA-TAATATATATAATAAAAT-AAAAGTTTAATAA-AATA
* * *
19692761 TAAATAATAATATATATAATGATATAAAAGTTTAATAACATA
1 TAAATAATAATATATATAATAAAATAAAAGTTTAATAAAATA
19692803 T-AATAATA
1 TAAATAATA
19692811 TGTATAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 7 0.15
42 4 0.09
43 23 0.50
44 12 0.26
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (42 bp):
TAAATAATAATATATATAATAAAATAAAAGTTTAATAAAATA
Found at i:19700719 original size:17 final size:17
Alignment explanation
Indices: 19700687--19700723 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
19700677 ATTTTTTAAA
19700687 AATTATATTTTCAAAAT
1 AATTATATTTTCAAAAT
*
19700704 AATTAATATTTTAAAAAT
1 AATT-ATATTTTCAAAAT
19700722 AA
1 AA
19700724 AAATATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATATTTTCAAAAT
Found at i:19700728 original size:17 final size:18
Alignment explanation
Indices: 19700691--19700729 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19700681 TTTAAAAATT
* *
19700691 ATATTTTCAAAATAATTA
1 ATATTTTAAAAATAATAA
19700709 ATATTTTAAAAATAA-AA
1 ATATTTTAAAAATAATAA
19700726 ATAT
1 ATAT
19700730 AAGATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATTTTAAAAATAATAA
Found at i:19703781 original size:19 final size:18
Alignment explanation
Indices: 19703728--19703777 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
19703718 CGTGTTGTTC
*
19703728 ATTTCCAAAACATTATTA
1 ATTTACAAAACATTATTA
* *
19703746 ATTTACAAATCGTTATTCA
1 ATTTACAAAACATTATT-A
19703765 ATTT-CAAAACATT
1 ATTTACAAAACATT
19703778 TATTTTATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTTACAAAACATTATTA
Found at i:19703781 original size:37 final size:36
Alignment explanation
Indices: 19703706--19703777 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
19703696 TTACTTTATG
*
19703706 TTAATTTCAAATCGTGTTGTTCATTTCCAAAACATTA
1 TTAATTTCAAATCG-GTTATTCATTTCCAAAACATTA
19703743 TTAATTTACAAATC-GTTATTCAATTT-CAAAACATT
1 TTAATTT-CAAATCGGTTATTC-ATTTCCAAAACATT
19703778 TATTTTATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 15 0.47
37 11 0.34
38 6 0.19
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (36 bp):
TTAATTTCAAATCGGTTATTCATTTCCAAAACATTA
Found at i:19709004 original size:50 final size:49
Alignment explanation
Indices: 19708816--19709004 Score: 152
Period size: 50 Copynumber: 3.8 Consensus size: 49
19708806 GATAATAACA
* * ** *
19708816 TGCCAAAGCCATGTCCCAGACTTGGTCTTACATGGGATGTTTCTTGTC-C-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--CCTCTTATCTCG
* * * ** * *
19708865 TGCCAATGCCATATCCCAGATACGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTC-G
* * *
19708915 TGCCCATGCTATGTCCTAGACATGGTCTTAC--GGAAGACCTCTTATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG--GACCTCTTATCTC-G
*
19708965 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT
19709005 TTCATAATCT
Statistics
Matches: 109, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
47 5 0.05
48 3 0.03
49 32 0.29
50 67 0.61
52 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
Found at i:19710214 original size:10 final size:10
Alignment explanation
Indices: 19710199--19710223 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19710189 TCCTCATTGG
19710199 ATTTTCTAAA
1 ATTTTCTAAA
19710209 ATTTTCTAAA
1 ATTTTCTAAA
19710219 ATTTT
1 ATTTT
19710224 TTTATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTCTAAA
Found at i:19723059 original size:27 final size:27
Alignment explanation
Indices: 19723029--19723206 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
19723019 ATATTGAGTC
* *
19723029 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
19723056 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
19723083 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
19723111 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
19723138 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
19723165 TGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
19723192 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19723207 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:19723170 original size:82 final size:81
Alignment explanation
Indices: 19723050--19723205 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19723040 TGCTATATAA
*
19723050 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19723115 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
19723132 TCAATTCGCACACTTAGTGC-ATCATATTCATTTTGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19723196 CACTTAGTGC
65 CACTTAGTGC
19723206 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19729664 original size:16 final size:16
Alignment explanation
Indices: 19729643--19729675 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19729633 ACACTTAAGT
19729643 TGTTCACACTAAAACA
1 TGTTCACACTAAAACA
19729659 TGTTCACACTAAAACA
1 TGTTCACACTAAAACA
19729675 T
1 T
19729676 CAATGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (16 bp):
TGTTCACACTAAAACA
Found at i:19733705 original size:19 final size:20
Alignment explanation
Indices: 19733646--19733703 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
19733636 AATAAAAACC
19733646 AAAAAAA-ATTTTAGAAAATTA
1 AAAAAAATATTTTA-AAAA-TA
19733667 AAAAAAATATTTTAAAAATA
1 AAAAAAATATTTTAAAAATA
*
19733687 AAAAAAGTATTTTAAAA
1 AAAAAAATATTTTAAAA
19733704 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 18 0.51
21 11 0.31
22 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAAAATATTTTAAAAATA
Found at i:19738928 original size:18 final size:19
Alignment explanation
Indices: 19738905--19738948 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
19738895 TTTAGAAATT
*
19738905 ATTTTTATCGT-ATTAATA
1 ATTTTTATAGTAATTAATA
*
19738923 ATTTTTGTAGTAATTAATA
1 ATTTTTATAGTAATTAATA
*
19738942 TTTTTTA
1 ATTTTTA
19738949 AATTATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (19 bp):
ATTTTTATAGTAATTAATA
Found at i:19749157 original size:42 final size:42
Alignment explanation
Indices: 19749111--19749194 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
19749101 TTTCACTTAG
19749111 ATTATAAAAACCAAACACAAAACACACTTA-AGAAAATACAAA
1 ATTATAAAAACCAAACACAAAACACACTTAGA-AAAATACAAA
19749153 ATTATAAAAACCAAACACAAAACACACTTAGAAAAATACAAA
1 ATTATAAAAACCAAACACAAAACACACTTAGAAAAATACAAA
19749195 TACACCAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.64, C:0.19, G:0.02, T:0.14
Consensus pattern (42 bp):
ATTATAAAAACCAAACACAAAACACACTTAGAAAAATACAAA
Found at i:19752074 original size:16 final size:16
Alignment explanation
Indices: 19752053--19752083 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19752043 TACATATATA
19752053 AAATATAAGTAAATAG
1 AAATATAAGTAAATAG
*
19752069 AAATATAATTAAATA
1 AAATATAAGTAAATA
19752084 TAATAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATATAAGTAAATAG
Found at i:19753659 original size:44 final size:43
Alignment explanation
Indices: 19753599--19753873 Score: 160
Period size: 44 Copynumber: 6.4 Consensus size: 43
19753589 TCTACTCTAA
* *
19753599 TGCAATTTCAGAGAGATAAGATCTGAAGTTTTAATCTGCTCCAA
1 TGCAACTTCAGAGAGATAAGATCT-AAGTTTTAATCTGCTCCAC
* **
19753643 TGCAACTTCA-AGGAGATAGGAT-T-AGATTCTTCTGTCTGCTCCAC
1 TGCAACTTCAGA-GAGATAAGATCTAAG-TT-TT-AATCTGCTCCAC
* ** *
19753687 TGCAACTTCAGCGAGATAAGA-CTATACG---CGATCTGCT-CTC
1 TGCAACTTCAGAGAGATAAGATCTA-A-GTTTTAATCTGCTCCAC
* * *
19753727 TGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCAT
1 TGCAACTTCAGAGAGATAAGATCTA-AGTTTTAATCTGCTCCAC
* * * * * * * *
19753771 TGCAACTTTAGGGGGAT-AGAAT-T-GGATGTGATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAG-ATCTAAGTTTTAATCTGCTCCAC
* *
19753812 TGCAACTTCAGAGAGATAAGATCTGAGGTTTTAACCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATCT-AAGTTTTAATCTGCTCCAC
*
19753856 TACAACTTCA-AGGAGATA
1 TGCAACTTCAGA-GAGATA
19753874 GGATTATTGG
Statistics
Matches: 175, Mismatches: 36, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
40 23 0.13
41 40 0.23
42 5 0.03
43 14 0.08
44 91 0.52
46 1 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAAGATCTAAGTTTTAATCTGCTCCAC
Found at i:19753768 original size:84 final size:84
Alignment explanation
Indices: 19753678--19753873 Score: 231
Period size: 85 Copynumber: 2.3 Consensus size: 84
19753668 ATTCTTCTGT
*
19753678 CTGCTCCACTGCAACTTCAGCGAGATAAGACTAT-ACGCGATCTGCTCT-CTGCAACTTCAGAGA
1 CTGCTCCACTGCAACTTCAG-GAGATAAGAAT-TGACGCGATCTGCTCTACTGCAACTTCAGAGA
19753741 GATAAGATCT-ATGGTTTTAATC
64 GATAAGATCTGA-GGTTTTAA-C
* * * * *
19753763 C-GCTCCATTGCAACTTTAGGGGGAT-AGAATTGGATGTGATCTGCTCTACTGCAACTTCAGAGA
1 CTGCTCCACTGCAACTTCA-GGAGATAAGAATT-GACGCGATCTGCTCTACTGCAACTTCAGAGA
19753826 GATAAGATCTGAGGTTTTAAC
64 GATAAGATCTGAGGTTTTAAC
*
19753847 CTGCTCCACTACAACTTCAAGGAGATA
1 CTGCTCCACTGCAACTTC-AGGAGATA
19753874 GGATTATTGG
Statistics
Matches: 93, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
82 1 0.01
83 4 0.04
84 33 0.35
85 53 0.57
86 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (84 bp):
CTGCTCCACTGCAACTTCAGGAGATAAGAATTGACGCGATCTGCTCTACTGCAACTTCAGAGAGA
TAAGATCTGAGGTTTTAAC
Found at i:19753775 original size:128 final size:129
Alignment explanation
Indices: 19753540--19753832 Score: 335
Period size: 128 Copynumber: 2.3 Consensus size: 129
19753530 TAGGACTGGT
* * * * *
19753540 TTCTTCTATTTGCTCTACTGCAACTTCAGGGAGATAAGACGGGACGCAATCTACTCTAATGCAAT
1 TTCTTCTATCTGCTCCACTGCAACTTCAGCGAGATAAGACGAGACGCAATCTACTCTAATGCAAC
*
19753605 TTCAGAGAGATAAGATCTGAAGTTTTAATCTGCTCCAATGCAACTTCAAGGAGATAGGATTAGA
66 TTCAGAGAGATAAGATCTGAAGTTTTAATCCGCTCCAATGCAACTTCAAGGAGATAGGATTAGA
* * * * * *
19753669 TTCTTCTGTCTGCTCCACTGCAACTTCAGCGAGATAAGACTATACGCGATCTGCTCT-CTGCAAC
1 TTCTTCTATCTGCTCCACTGCAACTTCAGCGAGATAAGACGAGACGCAATCTACTCTAATGCAAC
* * * * * * *
19753733 TTCAGAGAGATAAGATCT-ATGGTTTTAATCCGCTCCATTGCAACTTTAGGGGGATAGAATTGGA
66 TTCAGAGAGATAAGATCTGA-AGTTTTAATCCGCTCCAATGCAACTTCAAGGAGATAGGATTAGA
* * * *
19753797 -T-GT-GATCTGCTCTACTGCAACTTCAGAGAGATAAGA
1 TTCTTCTATCTGCTCCACTGCAACTTCAGCGAGATAAGA
19753833 TCTGAGGTTT
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
125 29 0.21
126 1 0.01
127 2 0.01
128 59 0.42
129 48 0.35
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (129 bp):
TTCTTCTATCTGCTCCACTGCAACTTCAGCGAGATAAGACGAGACGCAATCTACTCTAATGCAAC
TTCAGAGAGATAAGATCTGAAGTTTTAATCCGCTCCAATGCAACTTCAAGGAGATAGGATTAGA
Found at i:19753874 original size:85 final size:84
Alignment explanation
Indices: 19753716--19753874 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 84
19753706 GACTATACGC
* * *
19753716 GATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCATTGCAACTTTA
1 GATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCA
* *
19753781 GGGGGATAGAATTGGATGT
66 AGGAGATAGAATTGGATGT
19753800 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGA-GGTTTTAA-CCTGCTCCACTACAACT
1 GATCTGCTCT-CTGCAACTTCAGAGAGATAAGATCT-ATGGTTTTAATCC-GCTCCACTACAACT
19753863 TCAAGGAGATAG
63 TCAAGGAGATAG
19753875 GATTATTGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
84 12 0.18
85 54 0.81
86 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (84 bp):
GATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCA
AGGAGATAGAATTGGATGT
Found at i:19754063 original size:100 final size:100
Alignment explanation
Indices: 19753929--19754540 Score: 854
Period size: 100 Copynumber: 6.1 Consensus size: 100
19753919 GATTCGCCAT
* *
19753929 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
*
19753994 CTGCACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
66 CTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
* *
19754029 CTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
*
19754094 CTGCACCGCCAG-GAAAGTAAGATT-GACCGTTGTGG
66 CTACACCGCCAGAG-AAGTAAGATTCG-CCGTTGTGG
* *
19754129 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGTTTTAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
19754194 CTACACCACCAGGGAAGTAAGATTCACCATTGTGG
66 CTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
* * * *
19754229 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTTGCTGTCGTAGCTTCAATTTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
19754294 CTACACTGCTA-AGGAAGTAAGATTCGCCGTTGTGC
66 CTACACCGCCAGA-GAAGTAAGATTCGCCGTTGTGG
* *
19754329 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAACTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
19754394 CTACACCACCAGGGAAGTAAGATTCGTCGTTGTGG
66 CTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
* * * * * *
19754429 CTTCAATCTATTTAACTGCAACGTCAGGGAAATAAGATTCACCGTTGTGGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* ** *
19754494 CTGCACCGCCA-AGGAAGTAAGATTCGTTGTTGCGG
66 CTACACCGCCAGA-GAAGTAAGATTCGCCGTTGTGG
19754529 CTTCAATCTATT
1 CTTCAATCTATT
19754541 CCACTGTAAT
Statistics
Matches: 455, Mismatches: 50, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
99 2 0.00
100 452 0.99
101 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
Found at i:19754497 original size:50 final size:50
Alignment explanation
Indices: 19753929--19754546 Score: 398
Period size: 50 Copynumber: 12.4 Consensus size: 50
19753919 GATTCGCCAT
** * * * * ** *
19753929 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * * * *
19753979 CTTCAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
** * * * * * * *
19754029 CTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGATTCGCCATCGTAG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * *
19754079 CTTCAATCTGTTCCACTGCACCGCCA-GGAAAGTAAGATT-GACCGTTGTGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAA-TAAGATTCG-CCGTTGTGG
** * * * * *
19754129 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * * * * ** * * *
19754179 TTTTAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCACCATTGTGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
** * * * * * * * *
19754229 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTTGCTGTCGTAG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * * * * *
19754279 CTTCAATTTGTTCCACTAC-AC-TGCTAAGGAAGTAAGATTCGCCGTTGTGC
1 CTTCAATCTATTCCACTGCAACGT-C-AGGGAAATAAGATTCGCCGTTGTGG
** * * * ** **
19754329 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAA
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * * ** * *
19754379 CTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCGTCGTTGTGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
** *
19754429 CTTCAATCTATTTAACTGCAACGTCAGGGAAATAAGATTCACCGTTGTGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
* * * * * ** *
19754479 CTTCAATCTGTTCCACTGCACCGCCAAGGAAGTAAGATTCGTTGTTGCGG
1 CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
19754529 CTTCAATCTATTCCACTG
1 CTTCAATCTATTCCACTG
19754547 TAATACCAAA
Statistics
Matches: 409, Mismatches: 151, Indels: 16
0.71 0.26 0.03
Matches are distributed among these distances:
48 1 0.00
49 8 0.02
50 391 0.96
51 8 0.02
52 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATTCGCCGTTGTGG
Found at i:19754829 original size:88 final size:88
Alignment explanation
Indices: 19754680--19754849 Score: 250
Period size: 88 Copynumber: 1.9 Consensus size: 88
19754670 AAGACTGTTG
* * * *
19754680 TCTTCGATCTGCTTCGCTGCCACTACAAGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
19754745 TGCTCAGAGAGACAAGGCTGGTA
66 TGCTCAGAGAGACAAGGCTGGTA
* * * *
19754768 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGTTATTTTCAACCTACTCCACTGT
1 TCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
19754833 TGCTCAGGGAGATAAGG
66 TGCTCAGAGAGACAAGG
19754850 TTGGGGTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGAGAGACAAGGCTGGTA
Found at i:19759545 original size:26 final size:26
Alignment explanation
Indices: 19759489--19759552 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
19759479 GAATGATGTG
* *
19759489 GAAAAAGAATAAAAGAATAATTACTC
1 GAAAAAGAATAAAAAAATAATGACTC
*
19759515 GAAAAAGAATAAAAAAACTACTGACTC
1 GAAAAAGAATAAAAAAA-TAATGACTC
19759542 -AAAAATGAATA
1 GAAAAA-GAATA
19759553 CGAAAAGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.17
Consensus pattern (26 bp):
GAAAAAGAATAAAAAAATAATGACTC
Found at i:19765137 original size:31 final size:29
Alignment explanation
Indices: 19765102--19765160 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
19765092 GGAGGTGGGA
*
19765102 TGGGAAGAGAATAAAAGTTTTAGGGGGAAAG
1 TGGG-AGAGAATAAAAATTTT-GGGGGAAAG
*
19765133 TGGGAGGGAATAAAAATTTTGGGGGAAA
1 TGGGAGAGAATAAAAATTTTGGGGGAAA
19765161 ATAAAAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 14 0.54
31 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTGGGGGAAAG
Found at i:19765389 original size:9 final size:9
Alignment explanation
Indices: 19765375--19765402 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19765365 TATAGTTTGA
19765375 TATTCGAAT
1 TATTCGAAT
19765384 TATTCGAAT
1 TATTCGAAT
19765393 TATTCGAAT
1 TATTCGAAT
19765402 T
1 T
19765403 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19768529 original size:17 final size:17
Alignment explanation
Indices: 19768504--19768537 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19768494 GTATATGCAA
*
19768504 AACAGTTTAAAATAAAT
1 AACAATTTAAAATAAAT
19768521 AACAATTTAAAATAAAT
1 AACAATTTAAAATAAAT
19768538 GATTTACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AACAATTTAAAATAAAT
Found at i:19768819 original size:4 final size:4
Alignment explanation
Indices: 19768797--19768836 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
19768787 TAACAAAGGA
*
19768797 AAAT AAAA AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
19768837 GATCTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:19770403 original size:44 final size:44
Alignment explanation
Indices: 19770235--19771541 Score: 209
Period size: 44 Copynumber: 30.3 Consensus size: 44
19770225 CACTGCAACT
** * * * *
19770235 TCAGGGAGATAAGA-CTGTAATATTCAATCTATTCCACTGCTAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* * ** * *
19770278 -CTAGGGAGAT-AGAACTACCGGCTTCAATATACTCCACTGTAAT-C
1 TC-AGGGAGATAAGATCTGCCATCTTCAATCTACTCCAC--TACTGC
* * * * * *
19770322 TCAGGGAGGTAAAATCCT-CCATCTTCGACCTGCTCCACTATTGC
1 TCAGGGAGATAAGAT-CTGCCATCTTCAATCTACTCCACTACTGC
* ** *
19770366 TTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGA-TGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACT-ACTGC
* * * ** * * *
19770410 -CTAGAGAGAT-AGAACTACCGGCTTCAATGTACTCTACTGTAAT-C
1 TC-AGGGAGATAAGATCTGCCATCTTCAATCTACTCCAC--TACTGC
* * * * *
19770454 TCAAGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* ** * * ** **
19770498 TTAGGGAGATAAGATCTGTAATCTTTAATCTATTTTACTGTTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* * * ** * * *
19770542 CCAGGGAGAT-AGAACTACCGGCTTCAATGTACTCCATTGTAAT-C
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCA--CTACTGC
* * ** * *
19770586 TCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* ** * * **
19770630 TTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACT-ACTGC
* * * *
19770675 -CAGGGAGAT-AGAAT-TATCGA-CTTCAATGTACTCCACT-GTAGTC
1 TCAGGGAGATAAG-ATCT-GCCATCTTCAATCTACTCCACTACT-G-C
* * * * *
19770718 ACAGGGAGGTAAAATCTGCCATTTTCAATCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* ** * * * **
19770762 TTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCATTGCCAAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACT-ACTGC
** ** * *
19770807 -CAGGGAGAT-AGAAT-TATCGGCTTCAATGTACTCCACCGTAAT-C
1 TCAGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCA-C-TACTGC
* * * * * ** *
19770850 TCAGGGAGGTAAAATCCGCCATCTTCGACCTGTTCCACTACTAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* ** * * **
19770894 TTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACT-ACTGC
** ** * *
19770939 -CAGGGAGAT-AGAAT-TATCGGCTTCAATGTACTCCACT-GTAGTC
1 TCAGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCACTACT-G-C
* * * * * * *
19770982 ACAGGGAGGTAAAATCTACCATCTTTAATCTGCTCCACTACTAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
** *** * * * **
19771026 TTGGGGAGATAAGATCTATAATATTCAATCTATTCCACTGCCAAC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACT-ACTGC
** ** * * *
19771071 -CAGGGAGAT-AGAGT-TATCGGCTTCAATGTACTTCACCGTAAT-C
1 TCAGGGAGATAAGA-TCTGCCATCTTCAATCTACTCCA-C-TACTGC
* * * * *
19771114 TCAGGGAGGTAAAAT-TCGCCATCTTCGACCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCT-GCCATCTTCAATCTACTCCACTACTGC
* * ** *
19771158 TCAGGGAGATAAGATTTG---TGGTTCTGTCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCAT-CTTCAATCTACTCCACTACTGC
* ** *
19771200 TTAGGGAGATAAGA-CTTG--A--GGCGATCTACTCCACTACTGC
1 TCAGGGAGATAAGATC-TGCCATCTTCAATCTACTCCACTACTGC
* * * ** *
19771240 TTAGGGAGATAAGATTTG---TGGTTCTGTCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCAT-CTTCAATCTACTCCACTACTGC
* * * *
19771282 TTAGGGAGATAAGA-CTTG--A--TGCGATCTGCTCCACTACTGC
1 TCAGGGAGATAAGATC-TGCCATCTTCAATCTACTCCACTACTGC
* * * ** * *
19771322 TTAGGGAGATAAGATCTG--TTGTTCTGTCTTCTCCACTATTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* ** *
19771364 TTAGGGAGATAAGA-CTTG--A--GGCGATCTACTCCACTACTGC
1 TCAGGGAGATAAGATC-TGCCATCTTCAATCTACTCCACTACTGC
* * ** *
19771404 TTAGGGAGATAAGATCTG---TGGTTCTGTCTGCTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCAT-CTTCAATCTACTCCACTACTGC
* * * *
19771446 TTAGGGAGATAAGA-CTTG--A--TGCGATCTGCTCCACTACTGC
1 TCAGGGAGATAAGATC-TGCCATCTTCAATCTACTCCACTACTGC
* * * **
19771486 TTAGGGAGATAAGATCTG--TTGTTCTGTCTACTCCACTACTGC
1 TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
* *
19771528 TTAGGAAGATAAGA
1 TCAGGGAGATAAGA
19771542 CTTGAGGCGA
Statistics
Matches: 906, Mismatches: 280, Indels: 157
0.67 0.21 0.12
Matches are distributed among these distances:
40 131 0.14
41 6 0.01
42 163 0.18
43 148 0.16
44 320 0.35
45 134 0.15
46 4 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGC
Found at i:19770413 original size:132 final size:131
Alignment explanation
Indices: 19770218--19771172 Score: 1320
Period size: 132 Copynumber: 7.2 Consensus size: 131
19770208 TTGGTTTTAG
* ** * *
19770218 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGTAATATTCAATCTATTCCACTGCTACCTAG
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCAACC-AG
* * * *
19770282 GGAGATAGAACTACCGGCTTCAATATACTCCACTGTAATCTCAGGGAGGTAAAATCCTCCATCTT
64 GGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTT
19770347 CGA
129 CGA
* * *
19770350 CCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-ATGCCTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCA-ACC-AG
* * * * *
19770414 AGAGATAGAACTACCGGCTTCAATGTACTCTACTGTAATCTCAAGGAGGTAAAATCCGCCATCTT
64 GGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTT
19770479 CGA
129 CGA
* * ** ***
19770482 TCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTTTACTGTTGCCCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CAACCAGG
* * * *
19770547 GAGATAGAACTACCGGCTTCAATGTACTCCATTGTAATCTCAGGGAGGTAAAATCCACCATCTTC
65 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
19770612 GA
130 GA
19770614 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CAACCAGG
* * * * *
19770679 GAGATAGAATTATCGACTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATTTTC
65 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
*
19770744 AA
130 GA
*
19770746 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCATTGCCAACCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CAACCAGG
*
19770811 GAGATAGAATTATCGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
65 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
19770876 GA
130 GA
* * *
19770878 CCTGTTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAACCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CAACCAGG
* * ** *
19770943 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTACCATCTTT
65 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
*
19771008 AA
130 GA
* * * *
19771010 TCTGCTCCACTACTACTTGGGGAGATAAGATCTATAATATTCAATCTATTCCACTGCCAACCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTG-CAACCAGG
* * * *
19771075 GAGATAGAGTTATCGGCTTCAATGTACTTCACCGTAATCTCAGGGAGGTAAAATTCGCCATCTTC
65 GAGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTC
19771140 GA
130 GA
* *
19771142 CCTGCTCCACTACTGCTCAGGGAGATAAGAT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAT
19771173 TTGTGGTTCT
Statistics
Matches: 737, Mismatches: 82, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
131 12 0.02
132 723 0.98
133 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (131 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCAACCAGGG
AGATAGAATTATCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCG
A
Found at i:19771246 original size:82 final size:82
Alignment explanation
Indices: 19771143--19771587 Score: 755
Period size: 82 Copynumber: 5.4 Consensus size: 82
19771133 CATCTTCGAC
* *
19771143 CTGCTCCACTACTGCTCAGGGAGATAAGATTTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
19771208 ATAAGACTTGAGGCGAT
66 ATAAGACTTGAGGCGAT
* *
19771225 CTACTCCACTACTGCTTAGGGAGATAAGATTTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
*
19771290 ATAAGACTTGATGCGAT
66 ATAAGACTTGAGGCGAT
* * *
19771307 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTGTTCTGTCTTCTCCACTATTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
19771372 ATAAGACTTGAGGCGAT
66 ATAAGACTTGAGGCGAT
*
19771389 CTACTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
*
19771454 ATAAGACTTGATGCGAT
66 ATAAGACTTGAGGCGAT
* * *
19771471 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTGTTCTGTCTACTCCACTACTGCTTAGGAAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
19771536 ATAAGACTTGAGGCGAT
66 ATAAGACTTGAGGCGAT
* *
19771553 CTGCTCCACTACTGCTAAGGGAGATATGATCTGTG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
19771588 ATGTATAGCT
Statistics
Matches: 341, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 341 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (82 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAG
ATAAGACTTGAGGCGAT
Found at i:19771652 original size:50 final size:49
Alignment explanation
Indices: 19771593--19771754 Score: 153
Period size: 50 Copynumber: 3.3 Consensus size: 49
19771583 CTGTGATGTA
**
19771593 TAGCTTCAATCTTTTTAAACTGCAATGTCGGGGAACCGGATTCGCCGTTG
1 TAGCTTCAATCTTTTT-AACTGCAATGTCGGGGAACAAGATTCGCCGTTG
* ** * * * * *
19771643 TAGCTTCAATCTGTTCCACTGTACTGCCAGGGAAGTAAGATTCGCCGTTG
1 TAGCTTCAATCTTTTTAACTGCAATGTCGGGGAA-CAAGATTCGCCGTTG
** * * *
19771693 CGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTCG
1 TAGCTTCAATCTTTTTAACTGCAATGTCGGGGAACAAGATTCGCCGTTG
* *
19771742 TATCTTTAATCTT
1 TAGCTTCAATCTT
19771755 CTCTATTGCA
Statistics
Matches: 84, Mismatches: 27, Indels: 3
0.74 0.24 0.03
Matches are distributed among these distances:
49 34 0.40
50 50 0.60
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (49 bp):
TAGCTTCAATCTTTTTAACTGCAATGTCGGGGAACAAGATTCGCCGTTG
Found at i:19771888 original size:44 final size:43
Alignment explanation
Indices: 19771830--19772177 Score: 347
Period size: 44 Copynumber: 8.0 Consensus size: 43
19771820 AGATCTGTTT
* * *
19771830 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * *
19771874 TCTTCGAT-TCACTTCCTAACAATATAGGAAGACAGGACCTGCTA
1 TCTTCGATCT-ACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * * **
19771918 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTG-CA
* * *
19771962 TCTTTGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * *
19772006 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGTA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * *
19772050 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
* ** *
19772093 TCTTCGATCCACTTCATACCAATATAGGAAGACAGGATCTGCTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * * *
19772137 TCTTCGATATACTTCACGCCAATACATGAAGACAAGATCTG
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTG
19772178 TTTTAATGAC
Statistics
Matches: 253, Mismatches: 45, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
43 86 0.34
44 146 0.58
45 21 0.08
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (43 bp):
TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
Found at i:19772052 original size:132 final size:131
Alignment explanation
Indices: 19771819--19772149 Score: 384
Period size: 132 Copynumber: 2.5 Consensus size: 131
19771809 TCAGAGAGAT
* *
19771819 AAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACATCTTCGATTC
1 AAGATCTGTTTTCTTCGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATT-
* * * * * *
19771884 ACTTCCTAACAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
65 ACTCCCCAACAATATAGGAAGACAAGACCTGCTATCTTCGATCCACTTC-CTACCAATACAGGAA
19771948 GAC
129 GAC
*
19771951 AAGATCTGTTTTCTTTGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCT
1 AAGATCTGTTTTCTTCGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT-T
* * * *
19772016 ACTCCGCCACCAATATGGGAAGACAAGATCTG-TATCTTCGATCCACTTCCTACCAATATAGGAA
65 ACTCC-CCAACAATATAGGAAGACAAGACCTGCTATCTTCGATCCACTTCCTACCAATACAGGAA
19772080 GAC
129 GAC
* ** * * * *
19772083 AGGATCTG-CATCTTCGATCCACTTCAT--ACCAATATAGGAAGACAGGATCTGCTATCTTCGAT
1 AAGATCTGTTTTCTTCGATCTACTTC-TCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGAT
19772145 ATACT
64 -TACT
19772150 TCACGCCAAT
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
130 22 0.13
131 27 0.16
132 101 0.59
133 22 0.13
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (131 bp):
AAGATCTGTTTTCTTCGATCTACTTCTCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATTA
CTCCCCAACAATATAGGAAGACAAGACCTGCTATCTTCGATCCACTTCCTACCAATACAGGAAGA
C
Found at i:19780823 original size:24 final size:22
Alignment explanation
Indices: 19780791--19780840 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
19780781 GGCCTCTCCT
*
19780791 TTTTCTTTTTTCATTCTTCTTTTC
1 TTTTCTTTTTTC-TT-TTCGTTTC
19780815 TTTTCTTTTTTCTTTTCGTTTC
1 TTTTCTTTTTTCTTTTCGTTTC
19780837 TTTT
1 TTTT
19780841 TTCGAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.44
23 2 0.08
24 12 0.48
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTTTCTTTTCGTTTC
Found at i:19780827 original size:17 final size:17
Alignment explanation
Indices: 19780807--19780843 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19780797 TTTTTCATTC
*
19780807 TTCTTTTCTTTTCTTTT
1 TTCTTTTCGTTTCTTTT
19780824 TTCTTTTCGTTTCTTTT
1 TTCTTTTCGTTTCTTTT
19780841 TTC
1 TTC
19780844 GAGTGAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (17 bp):
TTCTTTTCGTTTCTTTT
Found at i:19780844 original size:12 final size:12
Alignment explanation
Indices: 19780791--19780831 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
19780781 GGCCTCTCCT
19780791 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
19780803 -ATTCTTCTTTTC
1 TTTTCTT-TTTTC
19780815 TTTTCTTTTTTC
1 TTTTCTTTTTTC
19780827 TTTTC
1 TTTTC
19780832 GTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:19781320 original size:16 final size:15
Alignment explanation
Indices: 19781278--19781321 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
19781268 CAGTAGAGGT
19781278 TTTTTGTTTTTTTTC
1 TTTTTGTTTTTTTTC
19781293 -TTTTGTTCTTTTTTTC
1 TTTTTG-T-TTTTTTTC
19781309 TTTTTGTGTTTTT
1 TTTTTGT-TTTTT
19781322 GGTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 14 0.56
17 5 0.20
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (15 bp):
TTTTTGTTTTTTTTC
Found at i:19781321 original size:17 final size:17
Alignment explanation
Indices: 19781277--19781321 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
19781267 CCAGTAGAGG
19781277 TTTTT-TGTTTTTTTTC
1 TTTTTGTGTTTTTTTTC
19781293 -TTTTGT-TCTTTTTTTC
1 TTTTTGTGT-TTTTTTTC
19781309 TTTTTGTGTTTTT
1 TTTTTGTGTTTTT
19781322 GGTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
17 10 0.40
18 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (17 bp):
TTTTTGTGTTTTTTTTC
Found at i:19784612 original size:34 final size:34
Alignment explanation
Indices: 19784565--19784632 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
19784555 CCCAAGTATC
19784565 GAGTATTGCCTTTATTTCCAAAAATTTCTATTTT
1 GAGTATTGCCTTTATTTCCAAAAATTTCTATTTT
*
19784599 GAGTATTGTCTTTATTTCCAAAAATTTCTATTTT
1 GAGTATTGCCTTTATTTCCAAAAATTTCTATTTT
19784633 TTACTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.51
Consensus pattern (34 bp):
GAGTATTGCCTTTATTTCCAAAAATTTCTATTTT
Found at i:19784980 original size:17 final size:17
Alignment explanation
Indices: 19784955--19784988 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19784945 GTATATGCAA
*
19784955 AACAGTTTAAAATAAAT
1 AACAATTTAAAATAAAT
19784972 AACAATTTAAAATAAAT
1 AACAATTTAAAATAAAT
19784989 GATTTACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AACAATTTAAAATAAAT
Found at i:19785264 original size:4 final size:4
Alignment explanation
Indices: 19785248--19785285 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
19785238 TAACAAAGGA
19785248 AAAT AAA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
19785286 GATCTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:19786654 original size:13 final size:13
Alignment explanation
Indices: 19786636--19786660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19786626 CAATATGTTT
19786636 ATTAATTAAAAAC
1 ATTAATTAAAAAC
19786649 ATTAATTAAAAA
1 ATTAATTAAAAA
19786661 TAAAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:19787559 original size:14 final size:14
Alignment explanation
Indices: 19787540--19787566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19787530 ATTTTTCTAT
19787540 TTTATTTATTATTA
1 TTTATTTATTATTA
19787554 TTTATTTATTATT
1 TTTATTTATTATT
19787567 TGTTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:19787564 original size:11 final size:11
Alignment explanation
Indices: 19787541--19787573 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19787531 TTTTTCTATT
19787541 TTATTTA-TTA
1 TTATTTATTTA
19787551 TTATTTATTTA
1 TTATTTATTTA
*
19787562 TTATTTGTTTA
1 TTATTTATTTA
19787573 T
1 T
19787574 AATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:19787636 original size:9 final size:10
Alignment explanation
Indices: 19787618--19787642 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19787608 CACCAATTCA
19787618 TTTAATTTTT
1 TTTAATTTTT
19787628 TTTAATTTTT
1 TTTAATTTTT
19787638 TTTAA
1 TTTAA
19787643 AAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:19788686 original size:15 final size:17
Alignment explanation
Indices: 19788653--19788691 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
19788643 ATTAAAAGGT
19788653 TAAA-TAAGTAAATAAA
1 TAAAGTAAGTAAATAAA
19788669 TAAAGTAAGT-AA-AAA
1 TAAAGTAAGTAAATAAA
19788684 TAAAGTAA
1 TAAAGTAA
19788692 AACAAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
16 6 0.27
17 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (17 bp):
TAAAGTAAGTAAATAAA
Found at i:19789527 original size:30 final size:31
Alignment explanation
Indices: 19789459--19789806 Score: 128
Period size: 30 Copynumber: 11.6 Consensus size: 31
19789449 TCATCAACCA
19789459 ATGAAAAGGGATAGCTTCGACTACCAAAATT
1 ATGAAAAGGGATAGCTTCGACTACCAAAATT
* * * * *
19789490 -TGGAAAGGGATATCTTCGGCTATC-GAATT
1 ATGAAAAGGGATAGCTTCGACTACCAAAATT
* * * *
19789519 ATGAAAAGGGAT-GGTGACGACCATCAACAA-T
1 ATGAAAAGGGATAGCT-TCGACTACCAA-AATT
* * * **
19789550 A--AAAAGGGAT-G-AT-GACGACCATCAACA
1 ATGAAAAGGGATAGCTTCGACTACCA-AAATT
* * *
19789577 ATGAAAAGGGAT-G-AT-GACGACCATCGAATT
1 ATGAAAAGGGATAGCTTCGACTACCA--AAATT
* * *
19789607 ATGAAAAGGGATGGCTTCAACTATCAAATTATT
1 ATGAAAAGGGATAGCTTCGACTACCAAA--ATT
* * *
19789640 ATGAAAAGGGATAGCTTCGGCTATC-GAATT
1 ATGAAAAGGGATAGCTTCGACTACCAAAATT
* *
19789670 ATGAAAAGGGATAGCTTCGGCTATC-AAATT
1 ATGAAAAGGGATAGCTTCGACTACCAAAATT
* * * **
19789700 ATGAAAAGGGAT-G-GT-GACGACCATCAACA
1 ATGAAAAGGGATAGCTTCGACTACCA-AAATT
* * *
19789729 ATGAAAAGGGAT-G-GT-GACGACCATCGAATT
1 ATGAAAAGGGATAGCTTCGACTACCA--AAATT
*
19789759 ATGAAAAGGGAT-GACTTCGACTATCAAAA-T
1 ATGAAAAGGGATAG-CTTCGACTACCAAAATT
*
19789789 ATGGAAAGGGATAGCTTC
1 ATGAAAAGGGATAGCTTC
19789807 AGCTATCGAA
Statistics
Matches: 248, Mismatches: 48, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
26 8 0.03
27 5 0.02
28 1 0.00
29 61 0.25
30 125 0.50
31 7 0.03
32 5 0.02
33 36 0.15
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (31 bp):
ATGAAAAGGGATAGCTTCGACTACCAAAATT
Found at i:19789558 original size:29 final size:29
Alignment explanation
Indices: 19789519--19789772 Score: 165
Period size: 30 Copynumber: 8.5 Consensus size: 29
19789509 CTATCGAATT
*
19789519 ATGAAAAGGGATGGTGACGACCATCAACA
1 ATGAAAAGGGATGATGACGACCATCAACA
*
19789548 ATAAAAAGGGATGATGACGACCATCAACA
1 ATGAAAAGGGATGATGACGACCATCAACA
**
19789577 ATGAAAAGGGATGATGACGACCATCGAATT
1 ATGAAAAGGGATGATGACGACCATC-AACA
* * * * *
19789607 ATGAAAAGGGATGGCT-TCAACTATCAAATTA
1 ATGAAAAGGGAT-GATGACGACCATC-AA-CA
* * * * **
19789638 TTATGAAAAGGGATAGCT-TCGGCTATCGAATT
1 --ATGAAAAGGGAT-GATGACGACCATC-AACA
* * * *
19789670 ATGAAAAGGGATAGCT-TCGGCTATCAA-A
1 ATGAAAAGGGAT-GATGACGACCATCAACA
*
19789698 TTATGAAAAGGGATGGTGACGACCATCAACA
1 --ATGAAAAGGGATGATGACGACCATCAACA
* **
19789729 ATGAAAAGGGATGGTGACGACCATCGAATT
1 ATGAAAAGGGATGATGACGACCATC-AACA
19789759 ATGAAAAGGGATGA
1 ATGAAAAGGGATGA
19789773 CTTCGACTAT
Statistics
Matches: 191, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
29 80 0.42
30 82 0.43
31 4 0.02
32 1 0.01
33 24 0.13
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (29 bp):
ATGAAAAGGGATGATGACGACCATCAACA
Found at i:19789646 original size:33 final size:30
Alignment explanation
Indices: 19789603--19789825 Score: 177
Period size: 30 Copynumber: 7.4 Consensus size: 30
19789593 ACGACCATCG
* **
19789603 AATTATGAAAAGGGATGGCTTCAACTATCAA
1 AATTATGAAAAGGGATAGCTTCGGCTATC-A
*
19789634 ATTATTATGAAAAGGGATAGCTTCGGCTATCG
1 A--ATTATGAAAAGGGATAGCTTCGGCTATCA
19789666 AATTATGAAAAGGGATAGCTTCGGCTATCA
1 AATTATGAAAAGGGATAGCTTCGGCTATCA
* * * *
19789696 AATTATGAAAAGGGAT-GGTGACGACCATCA
1 AATTATGAAAAGGGATAGCT-TCGGCTATCA
* * * * *
19789726 ACA--ATGAAAAGGGAT-GGTGACGACCATCG
1 A-ATTATGAAAAGGGATAGCT-TCGGCTATCA
*
19789755 AATTATGAAAAGGGAT-GACTTCGACTATCA
1 AATTATGAAAAGGGATAG-CTTCGGCTATCA
* * * *
19789785 AAATATGGAAAGGGATAGCTTCAGCTATCG
1 AATTATGAAAAGGGATAGCTTCGGCTATCA
*
19789815 AACTATGAAAA
1 AATTATGAAAA
19789826 AGGGTGGTAA
Statistics
Matches: 163, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 28 0.17
30 104 0.64
31 4 0.02
32 1 0.01
33 25 0.15
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (30 bp):
AATTATGAAAAGGGATAGCTTCGGCTATCA
Found at i:19789801 original size:119 final size:122
Alignment explanation
Indices: 19789577--19789833 Score: 310
Period size: 119 Copynumber: 2.1 Consensus size: 122
19789567 ACCATCAACA
* ** * *
19789577 ATGAAAAGGGATGATGACGACCATCGAATTATGAAAAGGGATGGCTTCAACTATCAAATTATTAT
1 ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACAACCATCAAA-TATTAT
* * * * *
19789642 GAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGGATAGCTTCGGCTATCAAATT
65 GAAAAGGGATAGCTTCGACTATCAAAATATGAAAAGGGATAGCTTCAGCTATCAAACT
* *
19789700 ATGAAAAGGGATGGTGACGACCATC-AACAATGAAAAGGGATGG-TGACGACCATC-GA-ATTAT
1 ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCT-ACAACCATCAAATATTAT
* *
19789761 GAAAAGGGAT-GACTTCGACTATCAAAATATGGAAAGGGATAGCTTCAGCTATCGAACT
65 GAAAAGGGATAG-CTTCGACTATCAAAATATGAAAAGGGATAGCTTCAGCTATCAAACT
19789819 ATGAAAAAGGG-TGGT
1 ATG-AAAAGGGATGGT
19789834 AACAACTATC
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 1 0.01
119 61 0.52
120 7 0.06
121 2 0.02
122 22 0.19
123 24 0.21
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (122 bp):
ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACAACCATCAAATATTATG
AAAAGGGATAGCTTCGACTATCAAAATATGAAAAGGGATAGCTTCAGCTATCAAACT
Found at i:19797201 original size:30 final size:29
Alignment explanation
Indices: 19797167--19797466 Score: 205
Period size: 30 Copynumber: 10.1 Consensus size: 29
19797157 ATATCAATGG
19797167 AAAGGGATAGCTTCGACTATCGAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
* * * **
19797197 AAAGGGATGGTGACGACCATC-AACAATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* * * * *
19797226 AAAGGCATG-TGACAACCATTGAATTATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* *
19797255 AAAGGGATGACTTCGGCTATCAAATTATGA
1 AAAGGGATG-CTTCGACTATCGAATTATGA
* *
19797285 AAAGGGATGGCTTTGGCTATCGAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
* *
19797315 AAAGGGATAGCTTCAACTATCAAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
* * * *
19797345 AAAGGGATGGTGACGACCATC-AATAATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* * * * *
19797374 AAAGTGATGGTGACGACCATCAAATTATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* *
19797404 AAAGGGATGGCTTCGACTAT-GAAAATATGG
1 AAAGGGAT-GCTTCGACTATCG-AATTATGA
*
19797434 AAAGGGATAGCTTCGGA-TATCGAACTATGA
1 AAAGGGAT-GCTTC-GACTATCGAATTATGA
19797464 AAA
1 AAA
19797467 CGGGTGGTAA
Statistics
Matches: 218, Mismatches: 41, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
28 9 0.04
29 59 0.27
30 143 0.66
31 7 0.03
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (29 bp):
AAAGGGATGCTTCGACTATCGAATTATGA
Found at i:19797321 original size:60 final size:60
Alignment explanation
Indices: 19797167--19797466 Score: 235
Period size: 60 Copynumber: 5.0 Consensus size: 60
19797157 ATATCAATGG
* * * *
19797167 AAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGAT-GGTGACGACCATCAACA--ATGA
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCT-TCGACTATCAA-ATTATGA
* * * * * *
19797226 AAAGGCAT-G-TGACAACCATTGAATTATGAAAAGGGAT-GACTTCGGCTATCAAATTATGA
1 AAAGGGATGGCT-TCGACTATCGAATTATGAAAAGGGATAG-CTTCGACTATCAAATTATGA
* * *
19797285 AAAGGGATGGCTTTGGCTATCGAATTATGAAAAGGGATAGCTTCAACTATCAAATTATGA
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGACTATCAAATTATGA
* * * * * * *
19797345 AAAGGGATGG-TGACGACCATC-AATAATGAAAAGTGAT-GGTGACGACCATCAAATTATGA
1 AAAGGGATGGCT-TCGACTATCGAATTATGAAAAGGGATAGCT-TCGACTATCAAATTATGA
* * * *
19797404 AAAGGGATGGCTTCGACTAT-GAAAATATGGAAAGGGATAGCTTCGGA-TATCGAACTATGA
1 AAAGGGATGGCTTCGACTATCG-AATTATGAAAAGGGATAGCTTC-GACTATCAAATTATGA
19797464 AAA
1 AAA
19797467 CGGGTGGTAA
Statistics
Matches: 188, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
57 2 0.01
58 34 0.18
59 65 0.35
60 81 0.43
61 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (60 bp):
AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGACTATCAAATTATGA
Found at i:19802150 original size:25 final size:25
Alignment explanation
Indices: 19802122--19802216 Score: 118
Period size: 25 Copynumber: 3.8 Consensus size: 25
19802112 GATACTCCAC
*
19802122 AGCTTGTGAGAGCATACCGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
* *
19802147 AGCTAGTGAGAGCATATCGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
* * *
19802172 AGCTCGTGAGAGCATACTGATCTAA
1 AGCTCGTGAGAGCATACCGATTTAT
* *
19802197 AGCTCGAGTGAGCATACCGA
1 AGCTCGTGAGAGCATACCGA
19802217 ATCACAACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (25 bp):
AGCTCGTGAGAGCATACCGATTTAT
Found at i:19804842 original size:17 final size:17
Alignment explanation
Indices: 19804820--19804855 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19804810 GAACAACACA
* *
19804820 AAAAAAGTAAAACTGAG
1 AAAAAAGAAAAAATGAG
19804837 AAAAAAGAAAAAATGAG
1 AAAAAAGAAAAAATGAG
19804854 AA
1 AA
19804856 CCAGCCCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (17 bp):
AAAAAAGAAAAAATGAG
Found at i:19805132 original size:27 final size:27
Alignment explanation
Indices: 19805094--19805153 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
19805084 CAAGCTTCGA
*
19805094 ACCT-CAGTGTTTTTGCGTCTTGTTTT
1 ACCTACAGGGTTTTTGCGTCTTGTTTT
19805120 ACCTACAGGGTTTTTGCGTCTTGTTTT
1 ACCTACAGGGTTTTTGCGTCTTGTTTT
19805147 ACCTACA
1 ACCTACA
19805154 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (27 bp):
ACCTACAGGGTTTTTGCGTCTTGTTTT
Found at i:19811334 original size:11 final size:11
Alignment explanation
Indices: 19811318--19811342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19811308 TTACCAACAC
19811318 AATTCATATAT
1 AATTCATATAT
19811329 AATTCATATAT
1 AATTCATATAT
19811340 AAT
1 AAT
19811343 AACTCGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTCATATAT
Found at i:19815543 original size:7 final size:7
Alignment explanation
Indices: 19815525--19815555 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
19815515 TTTACCACTC
19815525 TAATTCCA
1 TAATT-CA
19815533 TAATTCA
1 TAATTCA
19815540 TAATTCA
1 TAATTCA
19815547 TAATTCA
1 TAATTCA
19815554 TA
1 TA
19815556 CCTTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATTCA
Found at i:19816031 original size:38 final size:38
Alignment explanation
Indices: 19815989--19816064 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
19815979 ATAACATGAG
*
19815989 TTGCATTGTAATGCCATGAATCTCATGAGTAACACAAA
1 TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
* *
19816027 TTGCATTGTAGTGCCACGAATGTCATGAGTAACACAAA
1 TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
19816065 CAACATGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (38 bp):
TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
Found at i:19822806 original size:18 final size:17
Alignment explanation
Indices: 19822783--19822826 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
19822773 ACATACGTAA
19822783 CTCTTTTTCTTTCTTTCT
1 CTCTTTTTCTTT-TTTCT
*
19822801 CTCTTTTCCTTTTTTCT
1 CTCTTTTTCTTTTTTCT
*
19822818 -TCTTATTCT
1 CTCTTTTTCT
19822827 ATTATCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 11 0.48
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (17 bp):
CTCTTTTTCTTTTTTCT
Found at i:19823571 original size:19 final size:19
Alignment explanation
Indices: 19823547--19823603 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
19823537 CTCACATGCC
19823547 AAAGTGAAAAATTGATTTT
1 AAAGTGAAAAATTGATTTT
* *
19823566 AAAGTGAAAATTTAATTTT
1 AAAGTGAAAAATTGATTTT
* *
19823585 AAAGTGGAAAAGTGATTTT
1 AAAGTGAAAAATTGATTTT
19823604 TGTTGCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.37
Consensus pattern (19 bp):
AAAGTGAAAAATTGATTTT
Found at i:19841464 original size:27 final size:27
Alignment explanation
Indices: 19841425--19841780 Score: 444
Period size: 27 Copynumber: 13.2 Consensus size: 27
19841415 AGAGGTTGAT
* * **
19841425 AAATTACCAAAATACCCCTGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
19841452 AAATGACTGAAATACCCCTGTAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
19841479 AAATAACTGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
19841505 GAATGACTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
19841532 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
19841559 GAATGACCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
**
19841586 AAATGGTCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
19841613 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
19841640 AAATAATCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
19841667 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
19841694 GAATGATCGAAATACCCCCGTAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
19841721 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
19841748 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
19841775 GAATGA
1 AAATGA
19841781 ATTTTATACC
Statistics
Matches: 289, Mismatches: 39, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
26 21 0.07
27 268 0.93
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:19843395 original size:51 final size:50
Alignment explanation
Indices: 19843230--19843416 Score: 164
Period size: 51 Copynumber: 3.7 Consensus size: 50
19843220 AGTGAAAGTG
* * * *
19843230 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGCACCAGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CAGGATGGT
* * * * * *
19843281 A-GGTCGCATGTGTAGTACTATGTGCAGGATACTATGCGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGATGGT
** * * *
19843330 -TCCAATCACGTGTGTAGTACTAGGTGCAGGCTACTACGTGTACGGGATGGT
1 AT--GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGATGGT
*
19843381 AATGGTCACATGTGTAGTACTACGTGC-GAGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAG-GCTACTA
19843417 TGTGAATCGA
Statistics
Matches: 106, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
49 5 0.05
50 34 0.32
51 66 0.62
53 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGATGGT
Found at i:19843478 original size:45 final size:45
Alignment explanation
Indices: 19843427--19843514 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
19843417 TGTGAATCGA
* * * * *
19843427 ACATCATTGATTAGTAATGTGGTTGTTATGGGCTGATTCCACCAG
1 ACATCATTGATCAATAAGGTGGTTGCTATGGGCTGAATCCACCAG
*
19843472 ACATCATTGATCAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ACATCATTGATCAATAAGGTGGTTGCTATGGGCTGAATCCACC
19843515 GAGTATCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATTGATCAATAAGGTGGTTGCTATGGGCTGAATCCACCAG
Found at i:19848796 original size:45 final size:45
Alignment explanation
Indices: 19848745--19848830 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
19848735 TGTGAACTGA
* *
19848745 ACATCATTGATTAGTAAGGTGGTTGCAATGTACTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCAATGTACTGAATCCACCAG
* *
19848790 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGTTGCAATGTACTGAATCCA
19848831 TCGAGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCAATGTACTGAATCCACCAG
Found at i:19853969 original size:6 final size:6
Alignment explanation
Indices: 19853960--19853984 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19853950 AAAAAGACTC
19853960 AGTGGA AGTGGA AGTGGA AGTGGA A
1 AGTGGA AGTGGA AGTGGA AGTGGA A
19853985 TAAACTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
AGTGGA
Found at i:19884969 original size:35 final size:35
Alignment explanation
Indices: 19884921--19885011 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
19884911 CTCTTTCAAG
* *
19884921 GTGTCGCCTTGAAGGACCTATATACCA-TTTACACA
1 GTGTCGCCCTGAAGAACCTATATA-CAGTTTACACA
* * *
19884956 GTGTTGCCCTGAAGAACCTATGTACAGTTTACACG
1 GTGTCGCCCTGAAGAACCTATATACAGTTTACACA
* *
19884991 GTGTCGCCCCGAAGAATCTAT
1 GTGTCGCCCTGAAGAACCTAT
19885012 CGATAATCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.04
35 45 0.96
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (35 bp):
GTGTCGCCCTGAAGAACCTATATACAGTTTACACA
Found at i:19889182 original size:5 final size:5
Alignment explanation
Indices: 19889174--19889198 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19889164 ATCAATCCCC
19889174 TTTGT TTTGT TTTGT TTTGT TTTGT
1 TTTGT TTTGT TTTGT TTTGT TTTGT
19889199 GCTTTTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTGT
Found at i:19890558 original size:16 final size:16
Alignment explanation
Indices: 19890514--19890560 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19890504 TACTATAAAA
*
19890514 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
19890530 TATTATT-AAATATAT
1 TATAATTAAAATATAT
19890545 TATAATTAAAATATAT
1 TATAATTAAAATATAT
19890561 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:19890678 original size:16 final size:16
Alignment explanation
Indices: 19890634--19890680 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19890624 TACTATAAAA
*
19890634 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
19890650 TATTATT-AAATATAT
1 TATAATTAAAATATAT
19890665 TATAATTAAAATATAT
1 TATAATTAAAATATAT
19890681 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:19890798 original size:16 final size:16
Alignment explanation
Indices: 19890754--19890800 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19890744 TACTATAAAA
*
19890754 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
19890770 TATTATT-AAATATAT
1 TATAATTAAAATATAT
19890785 TATAATTAAAATATAT
1 TATAATTAAAATATAT
19890801 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:19890987 original size:245 final size:241
Alignment explanation
Indices: 19890278--19891059 Score: 1322
Period size: 245 Copynumber: 3.2 Consensus size: 241
19890268 AGTTAATCAT
* *
19890278 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
19890343 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA-A
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT-AACA
* *
19890407 TAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATT
130 TAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAATATT
19890472 CTTA-ATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
195 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
19890518 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
19890582 ATTAATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAATTTAACAT
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACAT
* *
19890647 AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
131 AATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAATATTC
*
19890712 TTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATA
196 TTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
19890758 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
19890822 ATTAATATTCTTATATGAATTTACTCAAATCATATCATAATATATGATACTATAAAAGATAATTT
66 ATTAATATTCTTATATGAATTTACTC--A--A-ATCATAATATATGATACTATAAAAGATAATTT
*
19890887 AACATAATTATTATTAAATATATTTTAATTAAAATATATGGTTTAATAAAATTCTTAATAATTAA
126 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAA
* * *
19890952 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATA
191 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * * *
19891003 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
19891060 TAAAATAATT
Statistics
Matches: 514, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
238 2 0.00
239 182 0.35
240 134 0.26
242 1 0.00
244 1 0.00
245 192 0.37
246 2 0.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (241 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACAT
AATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAATATTC
TTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
Found at i:19891040 original size:365 final size:359
Alignment explanation
Indices: 19890278--19891059 Score: 1300
Period size: 365 Copynumber: 2.2 Consensus size: 359
19890268 AGTTAATCAT
*
19890278 ATTTAAACATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAAT
1 ATTT-AACATAATTAA-TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
19890342 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAAA
64 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAAA
* *
19890407 TAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATT
129 TAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATT
*
19890472 CTTAATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTAACATAATTATTATT
194 CTTAATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAATTTAACATAATTATTATT
*
19890537 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAAT
259 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATAAAT
* *
19890602 TTACTGAAATCATAATATATGATACTATAAAATATA
324 TTACTCAAATCATAATATATGATACTATAAAAGATA
*
19890638 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
19890703 TTAATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAATTT-AACAT
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA-AT
* *
19890767 AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
130 AATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTC
19890832 TTATATGAATTTACTCAAATCATATCATAATATATGATACTATAAAAGATAATTTAACATAATTA
195 TTA-ATGAATTTACT--AA--A-ATCATAATATATGATACTATAAAAGATAATTTAACATAATTA
* **
19890897 TTATTAAATATATTTTAATTAAAATATATGGTTTAATAAAATTCTTAATAATTAATATTCTTATA
254 TTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
19890962 TAAATTTACTCAAATCATAATATATGATACTATAAAAGATA
319 TAAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
19891003 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
19891060 TAAAATAATT
Statistics
Matches: 395, Mismatches: 18, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
358 2 0.01
359 179 0.45
360 17 0.04
362 2 0.01
364 1 0.00
365 192 0.49
366 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (359 bp):
ATTTAACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAAATA
ATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCT
TAATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAATTTAACATAATTATTATTAA
ATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATAAATTT
ACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:19891070 original size:120 final size:120
Alignment explanation
Indices: 19890278--19891059 Score: 1300
Period size: 120 Copynumber: 6.5 Consensus size: 120
19890268 AGTTAATCAT
* *
19890278 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
19890343 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
19890399 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
19890463 ATCAATATTCTTA-ATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
19890518 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
19890583 TTAATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
19890638 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
19890703 TTAATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
19890758 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
19890823 TTAATATTCTTATATGAATTTACTCAAATCATATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTC--A--A-ATCATAATATATGATACTATAAAAGATA
* **
19890883 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGGTTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
19890948 TTAATATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
19891003 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
19891060 TAAAATAATT
Statistics
Matches: 631, Mismatches: 22, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
118 2 0.00
119 110 0.17
120 394 0.62
121 9 0.01
122 1 0.00
123 1 0.00
124 1 0.00
125 113 0.18
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:19895816 original size:16 final size:18
Alignment explanation
Indices: 19895790--19895822 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19895780 TTAAACTAAC
19895790 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
19895807 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
19895823 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:19900229 original size:10 final size:11
Alignment explanation
Indices: 19900198--19900242 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
19900188 AAAATAGGCC
19900198 TTAGTTTAC-TT
1 TTAG-TTACTTT
19900209 TTAGTTA-TTT
1 TTAGTTACTTT
19900219 TTA-TTACTTT
1 TTAGTTACTTT
*
19900229 TTAGATACTTT
1 TTAGTTACTTT
19900240 TTA
1 TTA
19900243 TTTGATGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 3 0.10
10 14 0.47
11 13 0.43
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (11 bp):
TTAGTTACTTT
Found at i:19903034 original size:22 final size:22
Alignment explanation
Indices: 19903006--19903067 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
19902996 AAGTGAAGTA
19903006 ATATGATGTTGGAAATATTGTT
1 ATATGATGTTGGAAATATTGTT
* * *
19903028 ATATGATAAATTTGG-GATTTTGTT
1 ATATGAT---GTTGGAAATATTGTT
19903052 ATATGATGTTGGAAAT
1 ATATGATGTTGGAAAT
19903068 TGGTAGTGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
21 4 0.13
22 9 0.29
24 14 0.45
25 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (22 bp):
ATATGATGTTGGAAATATTGTT
Found at i:19903985 original size:15 final size:15
Alignment explanation
Indices: 19903965--19903994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19903955 TCAAAGAGAG
19903965 AAATTTCCAAATAAA
1 AAATTTCCAAATAAA
19903980 AAATTTCCAAATAAA
1 AAATTTCCAAATAAA
19903995 GTTTGCTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTTCCAAATAAA
Found at i:19904092 original size:15 final size:15
Alignment explanation
Indices: 19904069--19904102 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
19904059 ATTCCTAAAG
19904069 GTGCCCCCTTCCTAT
1 GTGCCCCCTTCCTAT
*
19904084 GTGCTCCCTTCCTAT
1 GTGCCCCCTTCCTAT
19904099 GTGC
1 GTGC
19904103 ATGACTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.41, G:0.18, T:0.35
Consensus pattern (15 bp):
GTGCCCCCTTCCTAT
Found at i:19905556 original size:27 final size:27
Alignment explanation
Indices: 19905526--19905637 Score: 98
Period size: 27 Copynumber: 4.1 Consensus size: 27
19905516 CTCCTTGGAT
*
19905526 TATCCCGTGTTTGACGTCCCATCAAAC
1 TATCCCGTGTTTAACGTCCCATCAAAC
* * * *
19905553 TATCTCGTGTTTAACGTTCCATAAAAG
1 TATCCCGTGTTTAACGTCCCATCAAAC
* * ** *
19905580 TATCCCATCTTTAACGTCCTGTCAGAC
1 TATCCCGTGTTTAACGTCCCATCAAAC
** * *
19905607 TATCTTGTGTTTAACATCCCGTCAAAC
1 TATCCCGTGTTTAACGTCCCATCAAAC
19905634 TATC
1 TATC
19905638 TATGATATCG
Statistics
Matches: 64, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (27 bp):
TATCCCGTGTTTAACGTCCCATCAAAC
Found at i:19905840 original size:45 final size:45
Alignment explanation
Indices: 19905776--19905955 Score: 200
Period size: 45 Copynumber: 4.0 Consensus size: 45
19905766 AGTACTTTCA
* *
19905776 CATGATGCCATAACATCTTTTAGTTATGGTCTTACTCAT-TTCTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTT-TAT
* * * *
19905821 CATGATGCCATAGCTTCTTTCAGCTATGGTATTACTTATCTTTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
** ** * * *
19905866 GGTGATTTCATAAAATCTTTCAGCTATGATGTTACTCATCTTTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
* * *
19905911 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTTTTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
19905956 GCATATAAGC
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
45 108 0.98
46 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (45 bp):
CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
Found at i:19905907 original size:23 final size:23
Alignment explanation
Indices: 19905880--19905949 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
19905870 ATTTCATAAA
19905880 ATCTTTCAGCTATGATGTTACTC
1 ATCTTTCAGCTATGATGTTACTC
* *
19905903 ATCTTT-ATC-ATGATGTCATA-GC
1 ATCTTTCAGCTATGATGT--TACTC
* *
19905925 ATCTTTCAGCTATGGTCTTACTC
1 ATCTTTCAGCTATGATGTTACTC
19905948 AT
1 AT
19905950 TTTTATGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
21 7 0.19
22 11 0.31
23 13 0.36
24 5 0.14
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (23 bp):
ATCTTTCAGCTATGATGTTACTC
Found at i:19905937 original size:90 final size:90
Alignment explanation
Indices: 19905784--19905956 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 90
19905774 CACATGATGC
* * * * *
19905784 CATAACATCTTTTAGTTATGGTCTTACTCATTTCTATCATGATGCCATAGCTTCTTTCAGCTATG
1 CATAAAATCTTTCAGCTATGATCTTACTCATTTCTATCATGATGCCATAGCATCTTTCAGCTATG
*
19905849 GTATTACTTATCTTTATGGTGATTT
66 GTATTACTCATCTTTATGGTGATTT
* *
19905874 CATAAAATCTTTCAGCTATGATGTTACTCATCTT-TATCATGATGTCATAGCATCTTTCAGCTAT
1 CATAAAATCTTTCAGCTATGATCTTACTCAT-TTCTATCATGATGCCATAGCATCTTTCAGCTAT
* *
19905938 GGTCTTACTCATTTTTATG
65 GGTATTACTCATCTTTATG
19905957 CATATAAGCC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 70 0.97
91 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (90 bp):
CATAAAATCTTTCAGCTATGATCTTACTCATTTCTATCATGATGCCATAGCATCTTTCAGCTATG
GTATTACTCATCTTTATGGTGATTT
Found at i:19912386 original size:99 final size:98
Alignment explanation
Indices: 19912229--19912453 Score: 269
Period size: 99 Copynumber: 2.3 Consensus size: 98
19912219 AAATTAAAGT
* * * * *
19912229 ATTTAGTTAAAATAAAAGTAT-TAGTAATAATATCAAAAGAAAAAAAAATCTTACTTTCAAGCTT
1 ATTTAGTTAAAATAAAAATATATAATAATAATATCAAAAGAAAAAAAAATCTCACTTTCAAGATG
* * *
19912293 ATGTATAAACTTAGGAATGTCTCCTTCTTCATA
66 ATGTATAAACTTAGGAATCTCTACTTCTTCAGA
* **
19912326 ATTTGGTTAAAATAAAAATAGTATAATAATAATA-CTAAACA-AAAAAAAAATCTCGTTTTCAAG
1 ATTTAGTTAAAATAAAAATA-TATAATAATAATATC-AAA-AGAAAAAAAAATCTCACTTTCAAG
* *
19912389 ATGATGTATAAACTTGGGAATCTCTACTTCTTGAGA
63 ATGATGTATAAACTTAGGAATCTCTACTTCTTCAGA
19912425 ATTTAGTT-AAATAAAAATATTATAATAAT
1 ATTTAGTTAAAATAAAAATA-TATAATAAT
19912454 GTATGATATA
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
97 18 0.17
98 22 0.20
99 68 0.62
100 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (98 bp):
ATTTAGTTAAAATAAAAATATATAATAATAATATCAAAAGAAAAAAAAATCTCACTTTCAAGATG
ATGTATAAACTTAGGAATCTCTACTTCTTCAGA
Found at i:19914936 original size:13 final size:14
Alignment explanation
Indices: 19914918--19914952 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
19914908 TAGAATTACT
19914918 TAATATATATAA-A
1 TAATATATATAATA
19914931 TAATATAATATAATA
1 TAATAT-ATATAATA
19914946 TAATATA
1 TAATATA
19914953 ATACTATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 7 0.35
15 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATATATAATA
Found at i:19914940 original size:5 final size:5
Alignment explanation
Indices: 19914918--19914955 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
19914908 TAGAATTACT
19914918 TAATA T-ATA TAA-A TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
19914956 CTATACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:19919097 original size:19 final size:19
Alignment explanation
Indices: 19919073--19919113 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19919063 ATGAATTACA
19919073 TTAATACCCTTTTTATATT
1 TTAATACCCTTTTTATATT
19919092 TTAATACCCTTTTTATATT
1 TTAATACCCTTTTTATATT
19919111 TTA
1 TTA
19919114 CTCAATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATACCCTTTTTATATT
Found at i:19925901 original size:23 final size:22
Alignment explanation
Indices: 19925875--19925918 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19925865 GGATTTACAT
*
19925875 AATCATCTAAGATTACAAAATCA
1 AATCATATAAGATTA-AAAATCA
*
19925898 AATCTTATAAGATTAAAAATC
1 AATCATATAAGATTAAAAATC
19925919 TTCTATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
AATCATATAAGATTAAAAATCA
Found at i:19929002 original size:14 final size:14
Alignment explanation
Indices: 19928983--19929022 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19928973 TTGATTGCCA
19928983 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19928997 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19929011 GGAAAATGTTTT
1 GTAAAATGTTTT
19929023 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19929031 original size:20 final size:20
Alignment explanation
Indices: 19929006--19929045 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19928996 CGTAAAATGA
*
19929006 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
19929026 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
19929046 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:19929035 original size:34 final size:35
Alignment explanation
Indices: 19928991--19929057 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19928981 CAGTAAAATG
*
19928991 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
19929025 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19929058 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:19929156 original size:10 final size:10
Alignment explanation
Indices: 19929141--19929174 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
19929131 TTTTTTTTAC
19929141 ATATATTAAT
1 ATATATTAAT
19929151 ATATATTAAT
1 ATATATTAAT
* *
19929161 AAATTTTAAT
1 ATATATTAAT
19929171 ATAT
1 ATAT
19929175 TAAATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATTAAT
Found at i:19943311 original size:39 final size:39
Alignment explanation
Indices: 19943257--19943334 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
19943247 CCAAAGAAAG
19943257 AATGCACACAAATGCACACAAAGTGTTTGAGTAAATGCT
1 AATGCACACAAATGCACACAAAGTGTTTGAGTAAATGCT
19943296 AATGCACACAAATGCACACAAAGTGTTTGAGTAAATGCT
1 AATGCACACAAATGCACACAAAGTGTTTGAGTAAATGCT
19943335 CAAAGAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (39 bp):
AATGCACACAAATGCACACAAAGTGTTTGAGTAAATGCT
Found at i:19949372 original size:23 final size:22
Alignment explanation
Indices: 19949329--19949372 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
19949319 TTCTAAGTCG
19949329 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
19949352 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
19949373 TTCGGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:19949551 original size:51 final size:50
Alignment explanation
Indices: 19949493--19949667 Score: 219
Period size: 51 Copynumber: 3.5 Consensus size: 50
19949483 TCAGTTCACA
*
19949493 TAGTAGCCTACACATAGTACTACACATGTGATCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCA-TACCATCCGATACACG
* * * * *
19949544 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGATC-ATACCATCCGATACACG
* * *
19949595 TAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCATTCC-AGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCATACCA-TCCGA-TACACG
19949645 TAGTAGCCTGCACATAGTACTAC
1 TAGTAGCCTGCACATAGTACTAC
19949668 GCACGTGACC
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.02
50 32 0.30
51 72 0.67
52 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGATCATACCATCCGATACACG
Found at i:19949673 original size:101 final size:102
Alignment explanation
Indices: 19949489--19949675 Score: 290
Period size: 101 Copynumber: 1.8 Consensus size: 102
19949479 ATGTTCAGTT
* *
19949489 CACATAGTAGCCTACACATAGTACTACACATGTGATCATTACCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCGATCACTACCATCCGATACACGTAGTAGCCTG
19949554 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
66 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
* *
19949591 CACATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCC-AGTACACGTAGTAGCC
1 CACATAGTAGCCTACACATAGTACTACACATGCGATCACTACCA-TCCGA-TACACGTAGTAGCC
*
19949653 TGCACATAGTACTACGCACGTGA
64 TGCACATAGTACTACACACGTGA
19949676 CCATCATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
100 5 0.06
101 40 0.51
102 33 0.42
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (102 bp):
CACATAGTAGCCTACACATAGTACTACACATGCGATCACTACCATCCGATACACGTAGTAGCCTG
CACATAGTACTACACACGTGATCGAAACTATCCGGTA
Found at i:19952395 original size:17 final size:17
Alignment explanation
Indices: 19952360--19952396 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19952350 TTGGAAAGTG
**
19952360 AAATAATAAAATATGAT
1 AAATAATAAAATAACAT
19952377 AAATAATAAAATAACAT
1 AAATAATAAAATAACAT
19952394 AAA
1 AAA
19952397 ATATCATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAATAAAATAACAT
Found at i:19953517 original size:24 final size:25
Alignment explanation
Indices: 19953471--19953517 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
19953461 CTCTCTGGAG
* *
19953471 CTTCCTGATATTAGCTTGCTTGAAC
1 CTTCCTAATATTAGCTTACTTGAAC
*
19953496 CTTCCTAATA-TAGCTTATTTGA
1 CTTCCTAATATTAGCTTACTTGA
19953518 GCTTCTCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (25 bp):
CTTCCTAATATTAGCTTACTTGAAC
Found at i:19960257 original size:30 final size:30
Alignment explanation
Indices: 19960221--19960283 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
19960211 ATTAGTCATC
*
19960221 ATTGGAAAATTAAATAA-AGAAA-ATGACTAA
1 ATTGGAAAATGAAATAATA-AAATATGA-TAA
*
19960251 ATTGGAAAGTGAAATAATAAAATATGATAA
1 ATTGGAAAATGAAATAATAAAATATGATAA
19960281 ATT
1 ATT
19960284 ATAAAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (30 bp):
ATTGGAAAATGAAATAATAAAATATGATAA
Found at i:19961201 original size:24 final size:25
Alignment explanation
Indices: 19961139--19961195 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
19961129 ATCCCATAAT
**
19961139 TAGCTCTCATGAGCTTCCCGTTATA
1 TAGCTCTTGTGAGCTTCCCGTTATA
* *
19961164 TGGTTCTTGTGAGCTTCCCGTTA-A
1 TAGCTCTTGTGAGCTTCCCGTTATA
19961188 TAGCTCTT
1 TAGCTCTT
19961196 CGGAGCATCC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (25 bp):
TAGCTCTTGTGAGCTTCCCGTTATA
Found at i:19963134 original size:2 final size:2
Alignment explanation
Indices: 19963127--19963182 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
19963117 AAATCACTAA
19963127 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19963169 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
19963183 TGTGTGTGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19963187 original size:2 final size:2
Alignment explanation
Indices: 19963182--19963230 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
19963172 GAGAGAGAGA
*
19963182 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT AT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
19963224 GT AT GT G
1 GT GT GT G
19963231 CGCACGGACG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.04, C:0.00, G:0.47, T:0.49
Consensus pattern (2 bp):
GT
Found at i:19980782 original size:11 final size:11
Alignment explanation
Indices: 19980768--19980843 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
19980758 GATAATCACT
19980768 TTAATATTAAA
1 TTAATATTAAA
19980779 TTAATA--AAA
1 TTAATATTAAA
*
19980788 -TACTATTAAGA
1 TTAATATTAA-A
19980799 -TAATTATTAAA
1 TTAA-TATTAAA
*
19980810 TTAATTTTAATA
1 TTAATATTAA-A
19980822 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
19980835 ATAATATTA
1 TTAATATTA
19980844 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 2 0.04
11 20 0.38
12 14 0.27
13 4 0.08
14 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:19980783 original size:20 final size:18
Alignment explanation
Indices: 19980731--19980829 Score: 63
Period size: 17 Copynumber: 5.8 Consensus size: 18
19980721 GTCTACAAGA
*
19980731 TTAACATTAAATTAA-AT
1 TTAATATTAAATTAATAT
19980748 TTAATATTAAGA-TAATCACT
1 TTAATATTAA-ATTAAT-A-T
19980768 TTAATATTAAATTAATA-
1 TTAATATTAAATTAATAT
* * *
19980785 -AAATACT--ATTAAGA-
1 TTAATATTAAATTAATAT
19980799 -TAATTATTAAATTAAT-T
1 TTAA-TATTAAATTAATAT
19980816 TTAATATTAAATTA
1 TTAATATTAAATTA
19980830 TTAAAATAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
14 8 0.12
15 3 0.05
16 5 0.08
17 27 0.42
18 4 0.06
19 3 0.05
20 15 0.23
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAATATTAAATTAATAT
Found at i:19984886 original size:18 final size:20
Alignment explanation
Indices: 19984851--19984890 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19984841 ACTTGCATGG
*
19984851 TTAGTGATTTTGTCATGTTT
1 TTAGTAATTTTGTCATGTTT
19984871 TTAGTAATTTT-T-ATGTTT
1 TTAGTAATTTTGTCATGTTT
19984889 TT
1 TT
19984891 GAGCTCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.17, C:0.03, G:0.15, T:0.65
Consensus pattern (20 bp):
TTAGTAATTTTGTCATGTTT
Found at i:19992214 original size:2 final size:2
Alignment explanation
Indices: 19992207--19992268 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
19992197 CTCAGAAACT
* * *
19992207 TA TA TA TA TA TA CA TA TA TA TA TA T- TC GA GTA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
19992248 CA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
19992269 TCATATCTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.94
3 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:19997635 original size:53 final size:53
Alignment explanation
Indices: 19997548--19997686 Score: 172
Period size: 53 Copynumber: 2.6 Consensus size: 53
19997538 AAATTCAAAA
* * * *
19997548 AAAAAGTTTTTAGGGTTTGGAGGGAAGTAAAAGTTTTATGGA-AAAGCAAAAGG
1 AAAAAGGTTTTGGGGTTTGG-GGGAAATAAAAGTTTTAGGGAGAAAGCAAAAGG
* *
19997601 AAAAAGGTTTTGGGGATTTGGGGGAAATATAAGTTTTAGGGAGAAAGTAAAAGG
1 AAAAAGGTTTTGGGG-TTTGGGGGAAATAAAAGTTTTAGGGAGAAAGCAAAAGG
*
19997655 AAAAAGGTTTTGGGGGTTTGTGGGTAAATAAA
1 AAAAAGGTTTT-GGGGTTTG-GGGGAAATAAA
19997687 TTTTTTTGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
53 31 0.42
54 30 0.41
55 13 0.18
ACGTcount: A:0.39, C:0.01, G:0.33, T:0.27
Consensus pattern (53 bp):
AAAAAGGTTTTGGGGTTTGGGGGAAATAAAAGTTTTAGGGAGAAAGCAAAAGG
Found at i:19997707 original size:54 final size:54
Alignment explanation
Indices: 19997548--19997684 Score: 170
Period size: 54 Copynumber: 2.5 Consensus size: 54
19997538 AAATTCAAAA
* * * * * *
19997548 AAAAAGTTTTTAGGG-TTTGGAGGGAAGTAAAAGTTTTATGGA-AAAGCAAAAGG
1 AAAAAGGTTTTGGGGATTTGG-GGGAAATATAAGTTTTAGGGAGAAAGTAAAAGG
19997601 AAAAAGGTTTTGGGGATTTGGGGGAAATATAAGTTTTAGGGAGAAAGTAAAAGG
1 AAAAAGGTTTTGGGGATTTGGGGGAAATATAAGTTTTAGGGAGAAAGTAAAAGG
* *
19997655 AAAAAGGTTTTGGGGGTTTGTGGGTAAATA
1 AAAAAGGTTTTGGGGATTTG-GGGGAAATA
19997685 AATTTTTTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 31 0.42
54 34 0.47
55 8 0.11
ACGTcount: A:0.38, C:0.01, G:0.34, T:0.28
Consensus pattern (54 bp):
AAAAAGGTTTTGGGGATTTGGGGGAAATATAAGTTTTAGGGAGAAAGTAAAAGG
Found at i:19997724 original size:19 final size:18
Alignment explanation
Indices: 19997690--19997726 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19997680 AAATAAATTT
*
19997690 TTTTGGGGGAAGTAAAAG
1 TTTTGGGGGAAATAAAAG
19997708 TTTTGGGGGAAAATAAAAG
1 TTTTGGGGG-AAATAAAAG
19997727 GAAAAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (18 bp):
TTTTGGGGGAAATAAAAG
Found at i:19997791 original size:126 final size:127
Alignment explanation
Indices: 19997563--19997859 Score: 356
Period size: 126 Copynumber: 2.3 Consensus size: 127
19997553 GTTTTTAGGG
** * **
19997563 TTTGGAGGGAAGTAAAAGTTTT-ATGGAAAAGCAAAAGGAAAAAGGTTTTGGGGATTTGGGGGAA
1 TTTGG-GGGAAGTAAAAGTTTTGGGGGAAAA-TAAAAGG-AAAAGAATTTGGGGATTTGGGGGAA
* * *
19997627 ATATAAGTTTTAGGGAGAAAGTAAAAGGAAAAAGGTTTTGGGGGTTTGTGGGTA-AA-T-AAATT
63 ATAAAAGTTTTAGGGAGAAAGTAAAAGGAAAAAAGTTTTGAGGGTTTG-GGG-AGAAGTAAAATT
19997689 TT
126 TT
*
19997691 TTTGGGGGAAGTAAAAGTTTTGGGGGAAAATAAAAGGAAAAGAATTTGGGTG-TTT-GGGGAAGG
1 TTTGGGGGAAGTAAAAGTTTTGGGGGAAAATAAAAGGAAAAGAATTTGGG-GATTTGGGGGAA-A
19997754 TAAAAGTTTT-GGGTAGAAAGTAAAAGGAAAAAAGTTTTGAGGGTTTGGGGAGAAGTAAAATTTT
64 TAAAAGTTTTAGGG-AGAAAGTAAAAGGAAAAAAGTTTTGAGGGTTTGGGGAGAAGTAAAATTTT
** *
19997818 TGAGGGGGAAGTAAAAGTTTTGTGGAGAAAATAAAAGGAAAA
1 TTTGGGGGAAGTAAAAGTTTTG-GGGGAAAATAAAAGGAAAA
19997860 ATGTTTTAAA
Statistics
Matches: 149, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
124 1 0.01
125 14 0.09
126 55 0.37
127 50 0.34
128 29 0.19
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (127 bp):
TTTGGGGGAAGTAAAAGTTTTGGGGGAAAATAAAAGGAAAAGAATTTGGGGATTTGGGGGAAATA
AAAGTTTTAGGGAGAAAGTAAAAGGAAAAAAGTTTTGAGGGTTTGGGGAGAAGTAAAATTTT
Found at i:19997830 original size:20 final size:21
Alignment explanation
Indices: 19997800--19997839 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19997790 TTGAGGGTTT
*
19997800 GGGGAGAAGTAAAATTTTTGA
1 GGGGAGAAGTAAAAGTTTTGA
19997821 GGGG-GAAGTAAAAGTTTTG
1 GGGGAGAAGTAAAAGTTTTG
19997840 TGGAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGAGAAGTAAAAGTTTTGA
Found at i:19997837 original size:75 final size:74
Alignment explanation
Indices: 19997746--19997900 Score: 224
Period size: 75 Copynumber: 2.1 Consensus size: 74
19997736 TTGGGTGTTT
* * *
19997746 GGGGAAGGTAAAAGTTTTG-GGTAGAAAGTAAAAGGAAAAAAGTTTTGAGGGTTTGGGGAGAAGT
1 GGGGAAGGTAAAAGTTTTGTGG-AGAAAATAAAAGGAAAAAAGTTTTAAAGGTTTGGGG-GAAGT
19997810 AAAATTTTTGAG
64 AAAA-TTTTGAG
*
19997822 GGGGAA-GTAAAAGTTTTGTGGAGAAAATAAAAGGAAAAATGTTTTAAAGGTTTGGGGGAAGTAA
1 GGGGAAGGTAAAAGTTTTGTGGAGAAAATAAAAGGAAAAAAGTTTTAAAGGTTTGGGGGAAGTAA
*
19997886 AATTTTGGG
66 AATTTTGAG
19997895 GGGGAA
1 GGGGAA
19997901 AATAAAAAGG
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
73 12 0.16
74 9 0.12
75 44 0.60
76 8 0.11
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (74 bp):
GGGGAAGGTAAAAGTTTTGTGGAGAAAATAAAAGGAAAAAAGTTTTAAAGGTTTGGGGGAAGTAA
AATTTTGAG
Found at i:20001738 original size:23 final size:24
Alignment explanation
Indices: 20001697--20002486 Score: 374
Period size: 23 Copynumber: 33.9 Consensus size: 24
20001687 TATACATCAG
20001697 AAATT-GAGCAGC-ATGTATATACC
1 AAATTGGA-CAGCAATGTATATACC
* * *
20001720 AATTTGGACAGCAAT-TATACACA
1 AAATTGGACAGCAATGTATATACC
* * *
20001743 AAATTTGACAAC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
*
20001766 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* *
20001789 AAAATTGGGCAGCATATATATATACC
1 -AAATTGGACAGCA-ATGTATATACC
* * * *
20001815 AATTTGGACAGCACT-TATACACA
1 AAATTGGACAGCAATGTATATACC
* *
20001838 AAATTTGACAGC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
*
20001861 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* *
20001884 AAAATTGGGCAGC-ATATATATACC
1 -AAATTGGACAGCAATGTATATACC
* * *
20001908 AATTTGGACAGCACT-TATACA-C
1 AAATTGGACAGCAATGTATATACC
* *
20001930 AGAATTTGACAG-AATGTATATACA
1 A-AATTGGACAGCAATGTATATACC
* *
20001954 AAATTGGACAGC-ATCTATTTACC
1 AAATTGGACAGCAATGTATATACC
* *
20001977 AACATTGGGCAGC-ATATATATACC
1 AA-ATTGGACAGCAATGTATATACC
* * * * *
20002001 AATTTGGGCAGCACT-TATACACA
1 AAATTGGACAGCAATGTATATACC
*
20002024 AAATTGGACAGC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
*
20002047 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* * * *
20002070 AAAATTGGGCAGC-ATATATGTAGC
1 -AAATTGGACAGCAATGTATATACC
** * * *
20002094 ACTTTGGACAGCACT-TATACACA
1 AAATTGGACAGCAATGTATATACC
* *
20002117 AAATTTGACAGC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
*
20002140 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* *
20002163 AAAATTGGGCAGC-ATATATATACC
1 -AAATTGGACAGCAATGTATATACC
* * * * *
20002187 AATTTGGACAGCACT-TAAACACA
1 AAATTGGACAGCAATGTATATACC
* *
20002210 AAATTTGACAGC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
*
20002233 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* * *
20002256 AAAATTGGGCAGC-ATATATGA-AGC
1 -AAATTGGACAGCAATGTAT-ATACC
* * * * *
20002280 AATTTGGATAGCACT-TATACACA
1 AAATTGGACAGCAATGTATATACC
*
20002303 AAATTGGACAGC-ATGTATATACA
1 AAATTGGACAGCAATGTATATACC
* *
20002326 AAATTTGACAGC-ATATATATA-C
1 AAATTGGACAGCAATGTATATACC
*
20002348 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
*
20002371 AAAATTGGGA-AGC-ATATATATACC
1 -AAATT-GGACAGCAATGTATATACC
* * * * *
20002395 AATTTGGACAACACT-TATACACA
1 AAATTGGACAGCAATGTATATACC
*
20002418 AAATTTGACAGC-ATGTATATA-C
1 AAATTGGACAGCAATGTATATACC
*
20002440 AAATTGGACAGC-ATTTAT-TCACC
1 AAATTGGACAGCAATGTATAT-ACC
* *
20002463 AAAATTGGGCAGCATATATATATA
1 -AAATTGGACAGCA-ATGTATATA
20002487 TACCAATTTT
Statistics
Matches: 594, Mismatches: 122, Indels: 99
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.00
22 55 0.09
23 359 0.60
24 144 0.24
25 18 0.03
26 14 0.02
27 2 0.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (24 bp):
AAATTGGACAGCAATGTATATACC
Found at i:20001809 original size:93 final size:93
Alignment explanation
Indices: 20001675--20002339 Score: 1082
Period size: 93 Copynumber: 7.1 Consensus size: 93
20001665 TCTACCCTGT
* * * * *
20001675 TTGGACAGC-TCTTATACATCAGAAATTGAGCAGCATGTATATACCAATTTGGACAGCAATTATA
1 TTGGACAGCAT-TTATTCACCA-AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATA
*
20001739 CACAAAATTTGACAACATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
20001769 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATATACCAATTTGGACAGCACTTATA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGC--ATATATATACCAATTTGGACAGCACTTATA
20001834 CACAAAATTTGACAGCATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
20001864 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
* *
20001929 CAGAATTTGACAGAATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
* * * *
20001957 TTGGACAGCATCTATTTACCAACATTGGGCAGCATATATATACCAATTTGGGCAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
*
20002022 CAAAATTGGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
* * *
20002050 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCACTTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
20002115 CAAAATTTGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
*
20002143 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTAAACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
20002208 CAAAATTTGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
* *
20002236 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGA-AGCAATTTGGATAGCACTTATAC
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATAT-ATACCAATTTGGACAGCACTTATAC
*
20002300 ACAAAATTGGACAGCATGTATATACAAAA
65 ACAAAATTTGACAGCATGTATATACAAAA
*
20002329 TTTGACAGCAT
1 TTGGACAGCAT
20002340 ATATATACAA
Statistics
Matches: 535, Mismatches: 32, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
93 426 0.80
94 18 0.03
95 91 0.17
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (93 bp):
TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
CAAAATTTGACAGCATGTATATACAAAA
Done.