Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 60 of 182
Found at i:19459625 original size:18 final size:18
Alignment explanation
Indices: 19459580--19459627 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
19459570 ATAATATAAA
* *
19459580 TTAAATAGTAAATTATTT
1 TTAAATATTAAAATATTT
**
19459598 GGAAAT-TTAAAATATTT
1 TTAAATATTAAAATATTT
19459615 TTAAATATTAAAA
1 TTAAATATTAAAA
19459628 ATTCGATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAAATATTAAAATATTT
Found at i:19459755 original size:34 final size:34
Alignment explanation
Indices: 19459701--19459765 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
19459691 ATCGTTAGGG
*
19459701 TTTTTATAATTTATTTTATT-AATAATAAAAACTT
1 TTTTTATAATTTATTATATTAAATAA-AAAAACTT
19459735 TTTTTA-AATTATATTATATTAAATAAAAAAA
1 TTTTTATAATT-TATTATATTAAATAAAAAAA
19459766 TTATTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 19 0.68
35 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (34 bp):
TTTTTATAATTTATTATATTAAATAAAAAAACTT
Found at i:19460056 original size:14 final size:15
Alignment explanation
Indices: 19460037--19460065 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19460027 ATTTAAATAT
19460037 ATATTTTAAA-AACA
1 ATATTTTAAATAACA
19460051 ATATTTTAAATAACA
1 ATATTTTAAATAACA
19460066 GAATTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATTTTAAATAACA
Found at i:19460710 original size:141 final size:140
Alignment explanation
Indices: 19460475--19460740 Score: 430
Period size: 141 Copynumber: 1.9 Consensus size: 140
19460465 AACAACAACT
*
19460475 TCTCAACTTTCAAGTCCAAGATTCAACACATTTTGAAGTCCAAGATCCAACTTCAAATGTAACTA
1 TCTCAACTTTCAAGTCCAAGATTCAACAAATTTTGAAGTCCAAGATCCAACTTCAAATGTAACTA
*
19460540 CTTATTCAACTAGCTCATGCAATTTTTGTAATTTTACACTTCATATACTAATATTTTTGTTTAAA
66 CTTATTCAACTAACTCATGCAATTTTTGTAA-TTT-CACTTCATATACTAATATTTTTGTTTAAA
19460605 ACAAATGCAGCC
129 ACAAATGCAGCC
* *
19460617 TCTCAACTCTT-AAGTCTAAGATTCAACAAATTCTT-AAGTCCAAGAT-CTACTTCAAATGTAAC
1 TCTCAACT-TTCAAGTCCAAGATTCAACAAATT-TTGAAGTCCAAGATCCAACTTCAAATGTAAC
*
19460679 TACTTATTCAACTAACTCATGCAATTTTTGTAATTTCACTTCATATACTAGTATTTTTGTTT
64 TACTTATTCAACTAACTCATGCAATTTTTGTAATTTCACTTCATATACTAATATTTTTGTTT
19460741 TAACCAAGTG
Statistics
Matches: 117, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
139 25 0.21
140 3 0.03
141 47 0.40
142 38 0.32
143 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (140 bp):
TCTCAACTTTCAAGTCCAAGATTCAACAAATTTTGAAGTCCAAGATCCAACTTCAAATGTAACTA
CTTATTCAACTAACTCATGCAATTTTTGTAATTTCACTTCATATACTAATATTTTTGTTTAAAAC
AAATGCAGCC
Found at i:19463800 original size:13 final size:14
Alignment explanation
Indices: 19463782--19463811 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19463772 TATAAAATCA
19463782 CCAAAATT-AAAGT
1 CCAAAATTCAAAGT
19463795 CCAAAATTCAAAGT
1 CCAAAATTCAAAGT
19463809 CCA
1 CCA
19463812 TTACAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (14 bp):
CCAAAATTCAAAGT
Found at i:19470932 original size:30 final size:29
Alignment explanation
Indices: 19470887--19470977 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
19470877 GGGGTCAAAA
* * *
19470887 TGAAATTTTGGAAAGTTTAGGGGCTAAATT
1 TGAATTTTTGGAAAGTTTAAGGG-TAAATC
*
19470917 TGAATTTTTGTAAAGTTTAAGGGTCAAATC
1 TGAATTTTTGGAAAGTTTAAGGGT-AAATC
* *
19470947 TGAATATTTGGGAAGTTTAAGGGTTAAATC
1 TGAATTTTTGGAAAGTTTAAGGG-TAAATC
19470977 T
1 T
19470978 AAAATTTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.02
30 50 0.96
31 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
TGAATTTTTGGAAAGTTTAAGGGTAAATC
Found at i:19470993 original size:30 final size:30
Alignment explanation
Indices: 19470928--19471004 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
19470918 GAATTTTTGT
* * **
19470928 AAAGTTTAAGGGTCAAATCTGAATATTTGG
1 AAAGTTTAAGGGTTAAATCTAAATATTTAA
*
19470958 GAAGTTTAAGGGTTAAATCTAAA-ATTTTAA
1 AAAGTTTAAGGGTTAAATCTAAATA-TTTAA
**
19470988 AAAGTTCGAGGGTTAAA
1 AAAGTTTAAGGGTTAAA
19471005 ATGAGATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.32
Consensus pattern (30 bp):
AAAGTTTAAGGGTTAAATCTAAATATTTAA
Found at i:19471670 original size:23 final size:23
Alignment explanation
Indices: 19471644--19471693 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
19471634 TTCTCTTTAG
* *
19471644 TTTTTCTTTACTT-CATATAT-A
1 TTTTTATTTAATTACATATATAA
19471665 TATTTTATTTAATTACATATATAA
1 T-TTTTATTTAATTACATATATAA
19471689 TTTTT
1 TTTTT
19471694 GAAATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 10 0.42
23 11 0.46
24 2 0.08
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTATTTAATTACATATATAA
Found at i:19472822 original size:121 final size:122
Alignment explanation
Indices: 19472565--19472832 Score: 344
Period size: 121 Copynumber: 2.2 Consensus size: 122
19472555 TTTTGGTCCT
* * *
19472565 CTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTTAAGCTTCGCTTTATT
1 CTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAAGCTTCGCTTCATT
* * * * * *
19472630 ATCTTGGTCCACTTCTCTGTATCTTATCAAGAAGATGACCGTTTTATTGCCTTGACCCA
66 ATCTTGGT-C-CTACTCTGTATCTCATCAAGAAGATGACCGCTTCATTGACTTAACCCA
* *
19472689 CTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTTACATTGAA-CTTTGCTTCAT
1 CTTCTCTGTATCTCATCAAGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAAGCTTCGCTTCAT
* * * *
19472753 TGAT-TTGGT-CTACTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCA
65 T-ATCTTGGTCCTACTCTGTATCTCATCAAGAAGATGACCGCTTCATTGACTTAACCCA
19472810 CTTCTCTGTATCTCATCAAGAAG
1 CTTCTCTGTATCTCATCAAGAAG
19472833 GCGAATTTGG
Statistics
Matches: 127, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
121 61 0.48
124 39 0.31
125 27 0.21
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (122 bp):
CTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAAGCTTCGCTTCATT
ATCTTGGTCCTACTCTGTATCTCATCAAGAAGATGACCGCTTCATTGACTTAACCCA
Found at i:19472927 original size:206 final size:208
Alignment explanation
Indices: 19472633--19473078 Score: 680
Period size: 206 Copynumber: 2.1 Consensus size: 208
19472623 CTTTATTATC
* * **
19472633 TTGGTCCACTTCTCTGTATCTTATCAAGAAGATGACCGTTTTATTGCCTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTAA
* *
19472698 ATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTTACATTGAACTTTGCTTCATTGATTTGGTC
66 ATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTGGTC
*
19472763 TAC-T-CTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
131 TACTTACTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCCGTATCTCAT
19472826 CAAGAAGGCGAAT
196 CAAGAAGGCGAAT
* * * * * *
19472839 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACTCACTTCTCTAA
1 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTAA
* *
19472904 ATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTC
66 ATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTGGTC
* *
19472969 TACTTTACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTCCGTATCTCA
131 TAC-TTACTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCCGTATCTCA
* * *
19473034 TTAGGAAGGTGAAT
195 TCAAGAAGGCGAAT
*
19473048 TTGGTCCACTTCTTTGTATCTCATCAAGAAG
1 TTGGTCCACTTCTCTGTATCTCATCAAGAAG
19473079 GCGGATTTAG
Statistics
Matches: 213, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
206 119 0.56
208 1 0.00
209 93 0.44
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (208 bp):
TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTAA
ATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTGGTC
TACTTACTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCCGTATCTCAT
CAAGAAGGCGAAT
Found at i:19473079 original size:37 final size:37
Alignment explanation
Indices: 19473026--19473115 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
19473016 CCACTTTTCC
* * * *
19473026 GTATCTCATTAGGAAGGTGAATTTGGTCCACTTCTTT
1 GTATCTCATCAGGAAGGCGAATTTAGCCCACTTCTTT
* * *
19473063 GTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTT
1 GTATCTCATCAGGAAGGCGAATTTAGCCCACTTCTTT
* *
19473100 ATATCTTATCAGGAAG
1 GTATCTCATCAGGAAG
19473116 ATGATCGCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (37 bp):
GTATCTCATCAGGAAGGCGAATTTAGCCCACTTCTTT
Found at i:19473105 original size:246 final size:246
Alignment explanation
Indices: 19472806--19473324 Score: 808
Period size: 246 Copynumber: 2.1 Consensus size: 246
19472796 ATTGATTTAA
* * *
19472806 TCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGGTCTACTTCTCTATATCTCATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTAGCCCACTTCTCTATATCTCATCAGGAAGA
*
19472871 TGA-CTGCTTTATTGCTTTGACTCACTTCTCTAAATCTCATCAGGAAGATAGGGGTTTGAAGTTT
66 TGATC-GCTTTATTGCTTTGACCCACTTCTCTAAATCTCATCAGGAAGATAGGGGTTTGAAGTTT
* * * *
19472935 CACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTT-TACTGTATCTTATCAGGAAGATGAT
130 CACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCT-CTGTATCTCATCAAGAAGATGAC
* * * * *
19472999 CGCTTCATTGATTTAATCCACTTTTCCGTATCTCATTAGGAAGGTGAATTTGG
194 CGCTTCATTGATTTAATCCACTTCTCCATATCTCATCAAGAAGGCGAATTTGG
* * * * *
19473052 TCCACTTCTTTGTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTTATATCTTATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTAGCCCACTTCTCTATATCTCATCAGGAAGA
* *
19473117 TGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAGGAAGATAGGGGTTTGAAGTTTC
66 TGATCGCTTTATTGCTTTGACCCACTTCTCTAAATCTCATCAGGAAGATAGGGGTTTGAAGTTTC
19473182 ACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCG
131 ACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCG
*
19473247 CTTCATTGATTTAATCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGG
196 CTTCATTGATTTAATCCACTTCTCCATATCTCATCAAGAAGGCGAATTTGG
*
19473298 TCCACTTCTCTGTATCTCACCAAGAAG
1 TCCACTTCTCTGTATCTCATCAAGAAG
19473325 ATGACCGCTT
Statistics
Matches: 248, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
246 246 0.99
247 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (246 bp):
TCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTAGCCCACTTCTCTATATCTCATCAGGAAGA
TGATCGCTTTATTGCTTTGACCCACTTCTCTAAATCTCATCAGGAAGATAGGGGTTTGAAGTTTC
ACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCG
CTTCATTGATTTAATCCACTTCTCCATATCTCATCAAGAAGGCGAATTTGG
Found at i:19473272 original size:124 final size:124
Alignment explanation
Indices: 19472837--19473280 Score: 411
Period size: 124 Copynumber: 3.6 Consensus size: 124
19472827 AAGAAGGCGA
* * * * *
19472837 ATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCTTTATTGCTTTGA-CTCACTTCTC
1 ATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATC-CACTTCTC
* *
19472901 TAAATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
65 TATATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
* * * * *
19472961 ATTTGGTCTACTT-TACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTC
1 ATTTAGTCTACTTCT-CTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
** * ** * * * * * *** **
19473025 CGTATCTCATTAGGAAGGT--GAATTTG--G-TCCACT-TCTTTGTATCTCAT-CAAGAAGGCGG
65 TATATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTG-AGCT-TTGC-TTCA--TTG
* * * * * * * * * *
19473083 ATTTAGCCCACTTTTTTATATCTTATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
19473148 ATATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
66 ATATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
* *
19473207 ATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
19473272 ATATCTCAT
66 ATATCTCAT
19473281 CAAGAAGGCG
Statistics
Matches: 243, Mismatches: 62, Indels: 30
0.73 0.19 0.09
Matches are distributed among these distances:
118 4 0.02
119 9 0.04
120 3 0.01
122 74 0.30
123 2 0.01
124 134 0.55
125 1 0.00
126 3 0.01
127 9 0.04
128 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (124 bp):
ATTTAGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
ATATCTCATTAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
Found at i:19473362 original size:85 final size:85
Alignment explanation
Indices: 19473207--19473372 Score: 251
Period size: 85 Copynumber: 2.0 Consensus size: 85
19473197 TGCTTCATTG
* * *
19473207 ATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTAGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
19473272 ATATCTCATCAAGAAGGCGA
66 ATATCTCATCAAGAAGGCGA
* * * *
19473292 ATTTGGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTAGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
* *
19473357 GTATCTCATTAAGAAG
66 ATATCTCATCAAGAAG
19473373 ATAGGGGTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (85 bp):
ATTTAGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
ATATCTCATCAAGAAGGCGA
Found at i:19473412 original size:209 final size:209
Alignment explanation
Indices: 19473052--19473668 Score: 898
Period size: 209 Copynumber: 3.0 Consensus size: 209
19473042 GTGAATTTGG
* * * * * * * * *
19473052 TCCACTTCTTTGTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTTATATCTTATCAGGAAGA
1 TCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
* *
19473117 TGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAGGAAGATAGGGGTTTGAAGTTTC
66 TGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAAGAAGATAGGGGTTTGAAGTTTC
* * *
19473182 ACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAAGAAGATGACCG
131 ACTCACATTAAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACCG
19473247 CTTCATTGATTTAA
196 CTTCATTGATTTAA
* *
19473261 TCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCACCAAGAAGA
1 TCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
*
19473326 TGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATTAAGAAGATAGGGGTTTGAAGTTTC
66 TGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAAGAAGATAGGGGTTTGAAGTTTC
* * * *
19473391 ACTCACATTAAGCTTTGCTTCATTGATTTGGCCTACTTCTCTGTATCTTATCAGGAAGTTGATCG
131 ACTCACATTAAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACCG
19473456 CTTCATTGATTTAA
196 CTTCATTGATTTAA
* *
19473470 TCCACTTTTCTATATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
1 TCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
* * * *
19473535 TGACCGCCTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGGTGGGGGTTTGAAGTTTC
66 TGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAAGAAGATAGGGGTTTGAAGTTTC
* * *** * *
19473600 ACTCAAACTAAGCTTCATTTCATT-ATTTTGGTCCAC-T-TCTGTATCTTATCATGAAGATGACC
131 ACTCACATTAAGCTTTGCTTCATTGA-TTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACC
19473662 GCTTCAT
195 GCTTCAT
19473669 CATTTTGATC
Statistics
Matches: 367, Mismatches: 40, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
207 29 0.08
208 2 0.01
209 336 0.92
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (209 bp):
TCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
TGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAAGAAGATAGGGGTTTGAAGTTTC
ACTCACATTAAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTTATCAAGAAGATGACCG
CTTCATTGATTTAA
Found at i:19473497 original size:455 final size:452
Alignment explanation
Indices: 19472649--19473533 Score: 1430
Period size: 455 Copynumber: 2.0 Consensus size: 452
19472639 CACTTCTCTG
* *
19472649 TATCTTATCAAGAAGATGACCGTTTTATTGCCTTGACCCACTTCTCTGTATCTCATCAAGAAGAT
1 TATCTTATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTATATCTCATCAAGAAGAT
* * *
19472714 GGGGGTTTGAAGTTTCACTTACATTGAACTTTGCTTCATTGATTTGGTCTACTCTGTATCTCATC
66 AGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTAGTCTACTCTGTATCTCATC
* * *
19472779 AGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGGT
131 AAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGT
* * * * *
19472844 CTACTTCTCTATATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACTCACTTCTCTAAATCTC
196 CCACTTCTCTATATCTCACCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTAAATCTC
* * *
19472909 ATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTT
261 ATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATTGATTTGGCCTACTT
* *
19472974 TACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTCCGTATCTCATTAGG
326 TACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTCCATATCTCATCAGG
* *
19473039 AAGGTGAATTTGGTCCACTTCTTTGTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTTA
391 AAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTTA
* * * * *
19473101 TATCTTATCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATTAGGAAGAT
1 TATCTTATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTATATCTCATCAAGAAGAT
*
19473166 AGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTAGTCTACTTCTCTGTATCTC
66 AGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTAGTCTA---CTCTGTATCTC
19473231 ATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCATCAAGAAGGCGAATTT
128 ATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCATCAAGAAGGCGAATTT
* **
19473296 GGTCCACTTCTCTGTATCTCACCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTGTAT
193 GGTCCACTTCTCTATATCTCACCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTAAAT
*
19473361 CTCATTAAGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATTGATTTGGCCTA
258 CTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATTGATTTGGCCTA
* *
19473426 CTTCT-CTGTATCTTATCAGGAAGTTGATCGCTTCATTGATTTAATCCACTTTTCTATATCTCAT
323 CTT-TACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTCCATATCTCAT
*
19473490 CAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
387 CAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAAGAAG
19473534 ATGACCGCCT
Statistics
Matches: 396, Mismatches: 33, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
452 105 0.27
455 290 0.73
456 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (452 bp):
TATCTTATCAAGAAGATGACCGCTTTATTGCCTTGACCCACTTCTCTATATCTCATCAAGAAGAT
AGGGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCATTGATTTAGTCTACTCTGTATCTCATC
AAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCATCAAGAAGGCGAATTTGGT
CCACTTCTCTATATCTCACCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTAAATCTC
ATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATTGATTTGGCCTACTT
TACTGTATCTTATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTTTCCATATCTCATCAGG
AAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAAGAAGGCGGATTTAGCCCACTTTTTTA
Found at i:19473560 original size:85 final size:85
Alignment explanation
Indices: 19473416--19473582 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
19473406 TGCTTCATTG
* * * * *
19473416 ATTTGGCCTACTTCTCTGTATCTTATCAGGAAGTTGATCGCTTCATTGATTTAATCCACTTTTCT
1 ATTTGGCCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
*
19473481 ATATCTCATCAGGAAGGCGA
66 ATATCTCATCAAGAAGGCGA
* *
19473501 ATTTGGTCC-ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTT-ATTGCTTTGACCCACTTCT
1 ATTTGG-CCTACTTCTCTGTATCTCATCAGGAAGATGACCG-CTTCATTGATTTAACCCACTTCT
19473564 CTATATCTCATCAAGAAGG
64 CTATATCTCATCAAGAAGG
19473583 TGGGGGTTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
85 67 0.93
86 5 0.07
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (85 bp):
ATTTGGCCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
ATATCTCATCAAGAAGGCGA
Found at i:19473940 original size:45 final size:42
Alignment explanation
Indices: 19473734--19473991 Score: 140
Period size: 45 Copynumber: 5.9 Consensus size: 42
19473724 CTTATGATGG
* * * *
19473734 CTTCAATCTGCCCCATATTGACTTAGGGGTAAAAGATTGGATGATGA
1 CTTCAATCTACCCC-TCTTGAC-TAGGGGTAAAAAATT--A-GACGA
* * * * * * *
19473781 CTTCAATTTGCCCCTCTGGATTAGTGGTAAAAGATTGGACAGTAA
1 CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTAGAC-G--A
* * *** * *
19473826 CTTCAATCT-GCCCTCTTGACTGGGGGTAAATGTTTGGAATGA
1 CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTAG-ACGA
* * * * * *
19473868 GTTCAACCTACCCCTCTAGATTAGGGGTAAAAAGTTGGACGGTGA
1 CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTAGAC---GA
* *
19473913 CTTTAATCTACCTCTCTTGACTAGGGGTAAAAAATTAGACGA
1 CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTAGACGA
* * *
19473955 CTTCAATCTGCCCCTCTTGACTAGGTGTAAAAGATTA
1 CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTA
19473992 AATGATGGCT
Statistics
Matches: 164, Mismatches: 39, Indels: 21
0.73 0.17 0.09
Matches are distributed among these distances:
42 45 0.27
43 22 0.13
44 22 0.13
45 58 0.35
46 4 0.02
47 13 0.08
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (42 bp):
CTTCAATCTACCCCTCTTGACTAGGGGTAAAAAATTAGACGA
Found at i:19473960 original size:87 final size:88
Alignment explanation
Indices: 19473791--19473990 Score: 201
Period size: 87 Copynumber: 2.3 Consensus size: 88
19473781 CTTCAATTTG
* * * *
19473791 CCCCTCTGGATTAGTGGT-AAAAGATTGGACAGTAACTTCAATCTGCCCTCTTGACTGGGGGTAA
1 CCCCTCTAGATTAGGGGTAAAAAGATTGGACAGTAACTTCAATCTACCCTCTTGACTAGGGGTAA
*** * * *
19473855 ATGTTTGGAATGAGTTCAACCTA
66 AAAATTAGAACGACTTCAACCTA
* * *
19473878 CCCCTCTAGATTAGGGGTAAAAAG-TTGGACGGTGACTTTAATCTACCTCTCTTGACTAGGGGTA
1 CCCCTCTAGATTAGGGGTAAAAAGATTGGACAGTAACTTCAATCTACC-CTCTTGACTAGGGGTA
* *
19473942 AAAAATTAG-ACGACTTCAATCTG
65 AAAAATTAGAACGACTTCAACCTA
* * *
19473965 CCCCTCTTGACTAGGTGT-AAAAGATT
1 CCCCTCTAGATTAGGGGTAAAAAGATT
19473991 AAATGATGGC
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
86 5 0.05
87 62 0.67
88 25 0.27
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (88 bp):
CCCCTCTAGATTAGGGGTAAAAAGATTGGACAGTAACTTCAATCTACCCTCTTGACTAGGGGTAA
AAAATTAGAACGACTTCAACCTA
Found at i:19474005 original size:132 final size:136
Alignment explanation
Indices: 19473727--19474015 Score: 290
Period size: 132 Copynumber: 2.2 Consensus size: 136
19473717 CTCTTAACTT
* * * * * *
19473727 ATGATGGCTTCAATCTGCCCCATATTGACTTAGGGGTAAAAGATTGGATGATGACTTCAATTTGC
1 ATGATGGCTTCAACCTACCCCATATAGACTTAGGGGTAAAAGATTGGACGATGACTTCAATCTAC
* * * * * *
19473792 CCCTCTGGATTAGTGGTAAAAGATTGGACAGTAACTTCAATCTGCCCTCTTGACTGGGGGTAAAT
66 CCCTCTGGACTAGGGGTAAAAAATTAGACAG-AACTTCAATCTGCCCTCTTGACTAGGGGTAAAA
* *
19473857 GTTTGGA
130 GATTGAA
* * *
19473864 ATGA--G-TTCAACCTACCCC-TCTAGA-TTAGGGGTAAAA-AGTTGGACGGTGACTTTAATCTA
1 ATGATGGCTTCAACCTACCCCATATAGACTTAGGGGTAAAAGA-TTGGACGATGACTTCAATCTA
* * *
19473923 CCTCTCTTGACTAGGGGTAAAAAATTAGAC-G-ACTTCAATCTGCCCCTCTTGACTAGGTGTAAA
65 CCCCTCTGGACTAGGGGTAAAAAATTAGACAGAACTTCAATCTG-CCCTCTTGACTAGGGGTAAA
19473986 AGATT-AA
129 AGATTGAA
* *
19473993 ATGATGGCTTCAATCTGCCCCAT
1 ATGATGGCTTCAACCTACCCCAT
19474016 GGTCGGGGTA
Statistics
Matches: 124, Mismatches: 22, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
129 16 0.13
130 21 0.17
131 3 0.02
132 63 0.51
133 5 0.04
134 11 0.09
135 1 0.01
137 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (136 bp):
ATGATGGCTTCAACCTACCCCATATAGACTTAGGGGTAAAAGATTGGACGATGACTTCAATCTAC
CCCTCTGGACTAGGGGTAAAAAATTAGACAGAACTTCAATCTGCCCTCTTGACTAGGGGTAAAAG
ATTGAA
Found at i:19474337 original size:49 final size:49
Alignment explanation
Indices: 19474284--19474431 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 49
19474274 CAATCTACTT
*
19474284 CTTTACATCTTCAGGGTATAAGATTCACCGTTGTGGTTTCAATCTTTCC
1 CTTTACATCTTCAAGGTATAAGATTCACCGTTGTGGTTTCAATCTTTCC
* * *
19474333 CTTTACATC-TCTAAGGTATAAGATTCACCATTGCAGCTTT-AATCTCTT-C
1 CTTTACATCTTC-AAGGTATAAGATTCACCGTTG-TGGTTTCAATCT-TTCC
* * * *
19474382 CTTTACATTCTT-ATGGTATAAGATTCACCGTTGTAGCTTCTATCTTTCC
1 CTTTACA-TCTTCAAGGTATAAGATTCACCGTTGTGGTTTCAATCTTTCC
19474431 C
1 C
19474432 ATCTCGTCTT
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
48 6 0.07
49 66 0.81
50 8 0.10
51 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (49 bp):
CTTTACATCTTCAAGGTATAAGATTCACCGTTGTGGTTTCAATCTTTCC
Found at i:19475298 original size:13 final size:13
Alignment explanation
Indices: 19475272--19475305 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19475262 TAACTTTTCC
*
19475272 TTTTTCTTTTTCT
1 TTTTTCTTTCTCT
19475285 TTTTTCTTTCTCT
1 TTTTTCTTTCTCT
19475298 TTTCTTCT
1 TTT-TTCT
19475306 CTTTCTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCTCT
Found at i:19475316 original size:20 final size:18
Alignment explanation
Indices: 19475279--19475325 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
19475269 TCCTTTTTCT
*
19475279 TTTTCTTTTTTCTTTCTC
1 TTTTCTTTTTTCTCTCTC
19475297 TTTTCTTCTCTTTCTCTCTC
1 TTTTCTT-T-TTTCTCTCTC
19475317 TTTT-TTTTT
1 TTTTCTTTTT
19475326 GGTAAAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
19 3 0.12
20 13 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTTCTCTCTC
Found at i:19477344 original size:28 final size:28
Alignment explanation
Indices: 19477291--19477344 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
19477281 CAAATTTAAA
*
19477291 TAATAAATAATATTTAAATATTAAATCC
1 TAATAAATAATATTTAAATATAAAATCC
19477319 TAATAAA-ATATATTTTAAA-ATAAAAT
1 TAATAAATA-ATA-TTTAAATATAAAAT
19477345 AAAGTAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 1 0.04
28 16 0.70
29 6 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
TAATAAATAATATTTAAATATAAAATCC
Found at i:19478107 original size:108 final size:108
Alignment explanation
Indices: 19477911--19478108 Score: 256
Period size: 108 Copynumber: 1.8 Consensus size: 108
19477901 TATATTGGAT
* **
19477911 CTTTTGACGCGAAATGAAATAACACCCAAGCACTCCATTCCGGTTACTCAGTCCAACATGCTCCC
1 CTTTTGACGCGAAATGAAATAACAACCAAGCACTCCATTCCGGTTACTCAGTCCAACACACTCCC
* * * *
19477976 AATCATTTTTTTCTTTTTCTTTTTTTTTTAGAATGTTTTAACC
66 AATCACTTATTTATTTCTCTTTTTTTTTTAGAATGTTTTAACC
* * *
19478019 CTTTTGACGTGAAATGAAATGACAACCAAGCACTCCA-TCCTGGTTACTCAGTCTAACACACTCC
1 CTTTTGACGCGAAATGAAATAACAACCAAGCACTCCATTCC-GGTTACTCAGTCCAACACACTCC
* *
19478083 GAATTTACTTATTTATTTCT-TTTTTT
65 CAA-TCACTTATTTATTTCTCTTTTTT
19478109 CTCTTGTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 3 0.04
108 62 0.82
109 11 0.14
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (108 bp):
CTTTTGACGCGAAATGAAATAACAACCAAGCACTCCATTCCGGTTACTCAGTCCAACACACTCCC
AATCACTTATTTATTTCTCTTTTTTTTTTAGAATGTTTTAACC
Found at i:19480220 original size:19 final size:19
Alignment explanation
Indices: 19480196--19480238 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19480186 AAACATAAAT
19480196 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
19480215 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
19480234 TAAAT
1 TAAAT
19480239 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:19485883 original size:30 final size:30
Alignment explanation
Indices: 19485821--19485937 Score: 153
Period size: 30 Copynumber: 3.9 Consensus size: 30
19485811 AGGAAAAACG
** * * *
19485821 GGGTCAAAAATGAAATTTTAGAAAGTTTGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTCGA
* *
19485851 GGGCCAAATTTGAATTTTTGGGAAGTTCGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTCGA
19485881 GGGTCAAATTTGAATTTTTGGAAAGTTCGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTCGA
* *
19485911 GGGTCAAATCTAAATTTTTGGAAAGTT
1 GGGTCAAATTTGAATTTTTGGAAAGTT
19485938 TAGGTGTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTCGA
Found at i:19485947 original size:30 final size:30
Alignment explanation
Indices: 19485836--19485963 Score: 141
Period size: 30 Copynumber: 4.3 Consensus size: 30
19485826 AAAAATGAAA
* * * * *
19485836 TTTTAGAAAGTTTGAGGGCCAAATTTGAAT
1 TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
* * *
19485866 TTTTGGGAAGTTCGAGGGTCAAATTTGAAT
1 TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
19485896 TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
1 TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
* *
19485926 TTTTGGAAAGTT-TAGGTGTCAAATCCAAAT
1 TTTTGGAAAGTTCGAGG-GTCAAATCTAAAT
*
19485956 TTTAGGAA
1 TTTTGGAA
19485964 TTTTAGGATT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 3 0.03
30 84 0.97
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
Found at i:19491725 original size:47 final size:48
Alignment explanation
Indices: 19491648--19491746 Score: 155
Period size: 47 Copynumber: 2.0 Consensus size: 48
19491638 TTAAAAAATC
* *
19491648 CAATAAGTTTGTAACACCAACATGAGAAGCTTCTCCGAAAATGAGGCAGT
1 CAATAAGTTTGT-A-ACCAACATGAAAAGCTTATCCGAAAATGAGGCAGT
19491698 CAATAAGTTTGT-ACCAACATGAAAAGCTTATCCGAAAATGAGGCAGT
1 CAATAAGTTTGTAACCAACATGAAAAGCTTATCCGAAAATGAGGCAGT
19491745 CA
1 CA
19491747 TCGGCAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 35 0.74
50 12 0.26
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (48 bp):
CAATAAGTTTGTAACCAACATGAAAAGCTTATCCGAAAATGAGGCAGT
Found at i:19501046 original size:16 final size:16
Alignment explanation
Indices: 19501003--19501069 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 16
19500993 TATAAAAAAA
19501003 AAAAACTTTAAAAATTATT
1 AAAAA-TTTAAAAA-TA-T
*
19501022 AATAA-TTAAAAATAT
1 AAAAATTTAAAAATAT
19501037 AAAAATTT--AAATAT
1 AAAAATTTAAAAATAT
*
19501051 GAAAACTTTCAAAAATAT
1 -AAAAATTT-AAAAATAT
19501069 A
1 A
19501070 TATAAATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.15
15 12 0.30
16 4 0.10
17 8 0.20
18 6 0.15
19 4 0.10
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (16 bp):
AAAAATTTAAAAATAT
Found at i:19505353 original size:15 final size:15
Alignment explanation
Indices: 19505333--19505365 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19505323 AATGTTATAT
19505333 AAAAATTAACAA-ATA
1 AAAAATTAA-AAGATA
19505348 AAAAATTAAAAGATA
1 AAAAATTAAAAGATA
19505363 AAA
1 AAA
19505366 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAATTAAAAGATA
Found at i:19505374 original size:22 final size:22
Alignment explanation
Indices: 19505349--19505390 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
19505339 TAACAAATAA
19505349 AAAATTAAAAGATAAAATTATT
1 AAAATTAAAAGATAAAATTATT
19505371 AAAATTAAAAGATAAAATTA
1 AAAATTAAAAGATAAAATTA
19505391 GCAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAATTAAAAGATAAAATTATT
Found at i:19505402 original size:22 final size:22
Alignment explanation
Indices: 19505349--19505401 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
19505339 TAACAAATAA
* **
19505349 AAAATTAAAAGATAAAATTATT
1 AAAATAAAAAGATAAAATTAGC
*
19505371 AAAATTAAAAGATAAAATTAGC
1 AAAATAAAAAGATAAAATTAGC
19505393 -AAATAAAAA
1 AAAATAAAAA
19505402 ATTACACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (22 bp):
AAAATAAAAAGATAAAATTAGC
Found at i:19507606 original size:27 final size:27
Alignment explanation
Indices: 19507547--19507622 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
19507537 TCTCTATCAG
*
19507547 AGATAGCCACGGAGGCG-CCATTCATA
1 AGATAGCCACGGAGGCGTCCAGTCATA
*
19507573 AGATAGCCACGAAGGCGTCCAGTCATA
1 AGATAGCCACGGAGGCGTCCAGTCATA
*
19507600 AGATAGCTACGGAGGCGTCCAGT
1 AGATAGCCACGGAGGCGTCCAGT
19507623 AACTATGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 16 0.36
27 29 0.64
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (27 bp):
AGATAGCCACGGAGGCGTCCAGTCATA
Found at i:19509931 original size:18 final size:18
Alignment explanation
Indices: 19509910--19509962 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
19509900 AATTTATTTT
* *
19509910 ATTTTAATATTCAAATAA
1 ATTTAAATATTAAAATAA
*
19509928 ATTTAAATTTTAAAATAA
1 ATTTAAATATTAAAATAA
* **
19509946 ATATATCTATTAAAATA
1 ATTTAAATATTAAAATA
19509963 CCTGAAACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTAAATATTAAAATAA
Found at i:19530007 original size:73 final size:72
Alignment explanation
Indices: 19529920--19530072 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 72
19529910 CTATTATTCG
* * * *
19529920 TAAATTTAAAATTTAATTTTTATATTTTTATTTTTAAAAATTTAGT-TTATTTATTTTTTAAATT
1 TAAA-TTAAAATTTAATCTTCATATATCTATTTTT-AAAATTTAGTATT-TTTATTTTTTAAATT
19529984 TTAAAATTAA
63 TTAAAATTAA
*
19529994 TAAATTAAAATTTAATCTTCATATATCTATTTTTAGAATTTAGTATTTTTATTTTTTAAATTTTA
1 TAAATTAAAATTTAATCTTCATATATCTATTTTTAAAATTTAGTATTTTTATTTTTTAAATTTTA
*
19530059 AAATTTA
66 AAATTAA
19530066 -AAATTAA
1 TAAATTAA
19530073 TTAGTAACAT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
71 7 0.10
72 33 0.46
73 28 0.39
74 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (72 bp):
TAAATTAAAATTTAATCTTCATATATCTATTTTTAAAATTTAGTATTTTTATTTTTTAAATTTTA
AAATTAA
Found at i:19542741 original size:21 final size:22
Alignment explanation
Indices: 19542716--19542776 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
19542706 TAAAACTTTG
19542716 ATTTTATTAATTCTTCGATTTT
1 ATTTTATTAATTCTTCGATTTT
* * *
19542738 -TTTTA-AAATCCTTTGATTTT
1 ATTTTATTAATTCTTCGATTTT
*
19542758 ATTTTATTAATTCGTCGAT
1 ATTTTATTAATTCTTCGAT
19542777 GGCATATCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 12 0.40
21 10 0.33
22 8 0.27
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTTATTAATTCTTCGATTTT
Found at i:19542919 original size:52 final size:51
Alignment explanation
Indices: 19542838--19542935 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 51
19542828 ATTACAATTA
* * * * *
19542838 TAAGAAAATATTATTATTTATTT-ATTTTTAATCCGTTAATTATTATTATGT
1 TAAGAAAAAATTATAAATTATTTAATTTTAAAT-AGTTAATTATTATTATGT
19542889 TAAGAAAAAATTATCAAATTATTTAATTTTAAATAGTTAATTATTAT
1 TAAGAAAAAATTAT-AAATTATTTAATTTTAAATAGTTAATTATTAT
19542936 GTTGTTCAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
51 13 0.32
52 19 0.47
53 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (51 bp):
TAAGAAAAAATTATAAATTATTTAATTTTAAATAGTTAATTATTATTATGT
Found at i:19557336 original size:28 final size:27
Alignment explanation
Indices: 19557307--19557512 Score: 211
Period size: 28 Copynumber: 7.5 Consensus size: 27
19557297 GATAATGTCT
* *
19557307 TTTTCA-AATATCCTTTCGGATATAACC
1 TTTTCATAATATCCTTACGGATAT-TCC
* * * *
19557334 TTTTCAATGATATCCTTTCGAATATCCC
1 TTTTC-ATAATATCCTTACGGATATTCC
*
19557362 TTTTCATAGTATCCTTACGGATATTCC
1 TTTTCATAATATCCTTACGGATATTCC
* *
19557389 TTTTCATTGATATCCTTGCGGATA-TCC
1 TTTTCA-TAATATCCTTACGGATATTCC
19557416 TTTTTCAATAATATCCTTACGGATATTCC
1 -TTTTC-ATAATATCCTTACGGATATTCC
** *
19557445 TTTTCATTGGTATCCTTACGGATATCCC
1 TTTTCA-TAATATCCTTACGGATATTCC
*
19557473 TTTTCAATAATATCCTTACGGATATTTC
1 TTTTC-ATAATATCCTTACGGATATTCC
19557501 TTTTCA-AATATC
1 TTTTCATAATATC
19557513 TATTTTGATA
Statistics
Matches: 151, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.04
27 33 0.22
28 92 0.61
29 20 0.13
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (27 bp):
TTTTCATAATATCCTTACGGATATTCC
Found at i:19557375 original size:56 final size:56
Alignment explanation
Indices: 19557313--19557506 Score: 282
Period size: 56 Copynumber: 3.5 Consensus size: 56
19557303 GTCTTTTTCA
* * * * *
19557313 AATATCCTTTCGGATATAACCTTTTCAATGATATCCTTTCGAATATCCCTTTTC-AT
1 AATATCCTTACGGATAT-TCCTTTTCATTGATATCCTTACGGATATCCCTTTTCAAT
* * *
19557369 AGTATCCTTACGGATATTCCTTTTCATTGATATCCTTGCGGATATCCTTTTTCAAT
1 AATATCCTTACGGATATTCCTTTTCATTGATATCCTTACGGATATCCCTTTTCAAT
*
19557425 AATATCCTTACGGATATTCCTTTTCATTGGTATCCTTACGGATATCCCTTTTCAAT
1 AATATCCTTACGGATATTCCTTTTCATTGATATCCTTACGGATATCCCTTTTCAAT
*
19557481 AATATCCTTACGGATATTTCTTTTCA
1 AATATCCTTACGGATATTCCTTTTCA
19557507 AATATCTATT
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
55 31 0.25
56 94 0.75
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (56 bp):
AATATCCTTACGGATATTCCTTTTCATTGATATCCTTACGGATATCCCTTTTCAAT
Found at i:19557505 original size:84 final size:83
Alignment explanation
Indices: 19557313--19557507 Score: 248
Period size: 84 Copynumber: 2.3 Consensus size: 83
19557303 GTCTTTTTCA
* * * *
19557313 AATATCCTTTCGGATATAACCTTTTCAATGATATCCTTTCGAATATCCCTTTTCATAGTATCCTT
1 AATATCCTTACGGATAT-TCCTTTTCAATAATATCCTTACGAATATCCCTTTTCATAGTATCCTT
* *
19557378 ACGGATATTCCTTTTCATT
65 ACGGATATCCCTTTTCAAT
* * * * *
19557397 GATATCCTTGCGGATA-TCCTTTTTCAATAATATCCTTACGGATATTCCTTTTCATTGGTATCCT
1 AATATCCTTACGGATATTCC-TTTTCAATAATATCCTTACGAATATCCCTTTTCA-TAGTATCCT
19557461 TACGGATATCCCTTTTCAAT
64 TACGGATATCCCTTTTCAAT
*
19557481 AATATCCTTACGGATATTTCTTTTCAA
1 AATATCCTTACGGATATTCCTTTTCAA
19557508 ATATCTATTT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
82 2 0.02
83 30 0.32
84 61 0.64
85 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (83 bp):
AATATCCTTACGGATATTCCTTTTCAATAATATCCTTACGAATATCCCTTTTCATAGTATCCTTA
CGGATATCCCTTTTCAAT
Found at i:19561045 original size:28 final size:28
Alignment explanation
Indices: 19561013--19561071 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
19561003 ATTGAACTAT
19561013 TGTACTCGATTATGAAATGAAATTACAA
1 TGTACTCGATTATGAAATGAAATTACAA
19561041 TGTACTCGATTATGAAATGAAATTACAA
1 TGTACTCGATTATGAAATGAAATTACAA
19561069 TGT
1 TGT
19561072 TTATTTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (28 bp):
TGTACTCGATTATGAAATGAAATTACAA
Found at i:19561179 original size:14 final size:14
Alignment explanation
Indices: 19561162--19561228 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
19561152 GCTTAGGTTT
*
19561162 TAAACCTTAAACCC
1 TAAACCATAAACCC
19561176 TAAACACAT-AACCC
1 TAAAC-CATAAACCC
* *
19561190 TAAACCATGAATCC
1 TAAACCATAAACCC
*
19561204 TAAA-CATATAACCT
1 TAAACCATA-AACCC
*
19561218 TAAACCTTAAA
1 TAAACCATAAA
19561229 ATGTATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.14
14 32 0.74
15 5 0.12
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:19561194 original size:28 final size:28
Alignment explanation
Indices: 19561162--19561228 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
19561152 GCTTAGGTTT
19561162 TAAACCTTAAACCCTAAACACATAACCC
1 TAAACCTTAAACCCTAAACACATAACCC
* * * * *
19561190 TAAACCATGAATCCTAAACATATAACCT
1 TAAACCTTAAACCCTAAACACATAACCC
19561218 TAAACCTTAAA
1 TAAACCTTAAA
19561229 ATGTATTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAACCTTAAACCCTAAACACATAACCC
Found at i:19561636 original size:6 final size:6
Alignment explanation
Indices: 19561625--19561682 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
19561615 CATCTGATGC
* * * *
19561625 CTCTTG CTCTTG CTCTGG CTCTGG CTCTTG CTCTAG CT-TTAG CTCTAG
1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTT-G CTCTTG
*
19561673 CTCTAG CTCT
1 CTCTTG CTCT
19561683 GGTGTAAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
5 1 0.02
6 43 0.96
7 1 0.02
ACGTcount: A:0.07, C:0.33, G:0.19, T:0.41
Consensus pattern (6 bp):
CTCTTG
Found at i:19561645 original size:12 final size:12
Alignment explanation
Indices: 19561625--19561682 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
19561615 CATCTGATGC
*
19561625 CTCTTGCTCTTG
1 CTCTTGCTCTAG
* *
19561637 CTCTGGCTCTGG
1 CTCTTGCTCTAG
19561649 CTCTTGCTCTAG
1 CTCTTGCTCTAG
19561661 CT-TTAGCTCTAG
1 CTCTT-GCTCTAG
*
19561673 CTCTAGCTCT
1 CTCTTGCTCT
19561683 GGTGTAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
11 2 0.05
12 36 0.92
13 1 0.03
ACGTcount: A:0.07, C:0.33, G:0.19, T:0.41
Consensus pattern (12 bp):
CTCTTGCTCTAG
Found at i:19561651 original size:18 final size:18
Alignment explanation
Indices: 19561625--19561684 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
19561615 CATCTGATGC
* *
19561625 CTCTTGCTCTTGCTCTGG
1 CTCTGGCTCTTGCTCTAG
19561643 CTCTGGCTCTTGCTCTAG
1 CTCTGGCTCTTGCTCTAG
* * *
19561661 CTTTAGCTCTAGCTCTAG
1 CTCTGGCTCTTGCTCTAG
19561679 CTCTGG
1 CTCTGG
19561685 TGTAAGAGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.07, C:0.32, G:0.22, T:0.40
Consensus pattern (18 bp):
CTCTGGCTCTTGCTCTAG
Found at i:19562401 original size:21 final size:22
Alignment explanation
Indices: 19562377--19562439 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
19562367 TGATAATAGC
19562377 ATACAAACTACCGATACAT-CA
1 ATACAAACTACCGATACATGCA
* *
19562398 ATACTAATAACTACCAATACTTGCA
1 ATAC--A-AACTACCGATACATGCA
*
19562423 ATTC-AACTACCGATACA
1 ATACAAACTACCGATACA
19562440 ACTCAAGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 15 0.45
23 1 0.03
24 12 0.36
25 5 0.15
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (22 bp):
ATACAAACTACCGATACATGCA
Found at i:19565139 original size:80 final size:80
Alignment explanation
Indices: 19565047--19565256 Score: 321
Period size: 80 Copynumber: 2.6 Consensus size: 80
19565037 AGTTTAACTG
* * * *
19565047 ACTAGAGCTGGGCTCAGTTTTGCGGTTTATACGCTAGACACTGGGTGCCAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATAT
*
19565112 TTGTTGGTTAATCCA
66 TTGTTAGTTAATCCA
* * * *
19565127 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCACTAGGTAGTGGGTGCTAAGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATAT
19565192 TTGTTAGTTAATCCA
66 TTGTTAGTTAATCCA
* *
19565207 ACAAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCATTGGGTGCCA
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
19565257 TGACTGCCAG
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 116 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATAT
TTGTTAGTTAATCCA
Found at i:19566821 original size:43 final size:43
Alignment explanation
Indices: 19566760--19566856 Score: 131
Period size: 43 Copynumber: 2.3 Consensus size: 43
19566750 GAATGCACAA
* * * **
19566760 TTAATAACATGTCACAATATTAACAGGGGCCCAGTAATATAAT
1 TTAATAACATGCCACAATATTAACACGAGCAAAGTAATATAAT
* *
19566803 TTAATAACTTGCCACAATATTAACACGAGTAAAGTAATATAAT
1 TTAATAACATGCCACAATATTAACACGAGCAAAGTAATATAAT
19566846 TTAATAACATG
1 TTAATAACATG
19566857 TCAAGGAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.30
Consensus pattern (43 bp):
TTAATAACATGCCACAATATTAACACGAGCAAAGTAATATAAT
Found at i:19567977 original size:20 final size:21
Alignment explanation
Indices: 19567933--19567977 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19567923 AAAAATTAAT
*
19567933 TTAATTAGTTCGGTACATAAA
1 TTAATTAGTTCGGTACAAAAA
*
19567954 -TAATTATTTCGGTA-AAAAA
1 TTAATTAGTTCGGTACAAAAA
19567973 TTAAT
1 TTAAT
19567978 AAAAACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (21 bp):
TTAATTAGTTCGGTACAAAAA
Found at i:19568655 original size:15 final size:14
Alignment explanation
Indices: 19568625--19568675 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
19568615 ATCTATTTAC
19568625 TAAACAAATAAAAT
1 TAAACAAATAAAAT
* *
19568639 TATAACAAATCAGAT
1 TA-AACAAATAAAAT
*
19568654 TAAAC-ATTAAAAT
1 TAAACAAATAAAAT
19568667 TAAA-AAATA
1 TAAACAAATA
19568676 TATTTTATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 12 0.41
14 5 0.17
15 12 0.41
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAACAAATAAAAT
Found at i:19571691 original size:23 final size:23
Alignment explanation
Indices: 19571659--19571702 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19571649 ACTACCATTT
19571659 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
19571682 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
19571703 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:19571695 original size:13 final size:11
Alignment explanation
Indices: 19571663--19571705 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19571653 CCATTTTCTA
*
19571663 AATAAAATAAT
1 AATAAAATATT
19571674 AAT-AAATATCT
1 AATAAAATAT-T
19571685 AAGTAAAATATT
1 AA-TAAAATATT
19571697 AATAAAATA
1 AATAAAATA
19571706 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:19574321 original size:28 final size:27
Alignment explanation
Indices: 19574262--19574331 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
19574252 TGGGTGGTCG
*
19574262 AATTTGGGGCTTTTAGGTAAGGGTTTT
1 AATTTGGGGATTTTAGGTAAGGGTTTT
* * * *
19574289 GATTTGGGGATTTTTGTTTAGGGTTTTT
1 AATTTGGGGATTTTAGGTAAGGG-TTTT
*
19574317 AATTTTGGAGATTTT
1 AA-TTTGGGGATTTT
19574332 GGGTTAGTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 18 0.53
28 5 0.15
29 11 0.32
ACGTcount: A:0.17, C:0.01, G:0.30, T:0.51
Consensus pattern (27 bp):
AATTTGGGGATTTTAGGTAAGGGTTTT
Found at i:19574946 original size:16 final size:14
Alignment explanation
Indices: 19574909--19574989 Score: 50
Period size: 16 Copynumber: 5.9 Consensus size: 14
19574899 ATGATGATGA
19574909 TTATAATTTTAAAA-
1 TTAT-ATTTTAAAAT
19574923 -TA-ATTTTAATAATT
1 TTATATTTTAA-AA-T
*
19574937 TTATATTTTAAAAA
1 TTATATTTTAAAAT
*
19574951 AT-TATTTT-AAA-
1 TTATATTTTAAAAT
19574962 TTA-ATTTTAATAATT
1 TTATATTTTAA-AA-T
19574977 TTATATTTTAAAA
1 TTATATTTTAAAA
19574990 AAATAATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
11 13 0.25
12 6 0.11
13 10 0.19
14 1 0.02
15 9 0.17
16 14 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATTTTAAAAT
Found at i:19574967 original size:40 final size:41
Alignment explanation
Indices: 19574911--19575009 Score: 164
Period size: 40 Copynumber: 2.4 Consensus size: 41
19574901 GATGATGATT
19574911 ATAATTTTAAAATAATTTTAATAATTTTATATTTT-AAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAA
* *
19574951 ATTATTTTAAATTAATTTTAATAATTTTATATTTTAAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAA
*
19574992 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
19575010 GCTGATGTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 33 0.62
41 20 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (41 bp):
ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAA
Found at i:19574977 original size:20 final size:20
Alignment explanation
Indices: 19574911--19574979 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
19574901 GATGATGATT
*
19574911 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAATTAATTTTA
* **
19574931 ATAATTTTATATT--TTAAAAA
1 ATAATTTTAAATTAATT--TTA
*
19574951 ATTATTTTAAATTAATTTTA
1 ATAATTTTAAATTAATTTTA
19574971 ATAATTTTA
1 ATAATTTTA
19574980 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
18 2 0.06
20 32 0.89
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATTTTAAATTAATTTTA
Found at i:19577048 original size:27 final size:26
Alignment explanation
Indices: 19576986--19577049 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
19576976 TAACTAAAAA
*
19576986 ATAAAATAATGTAACTCATTCAAACTT
1 ATAAAAAAATGTAACTCATTCAAAC-T
*
19577013 ATCAAAAAATGTAACTCATTCAAAGC-
1 ATAAAAAAATGTAACTCATTCAAA-CT
19577039 ATAAATAAAAT
1 ATAAA-AAAAT
19577050 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 27 0.84
28 1 0.03
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAAAAAAATGTAACTCATTCAAACT
Found at i:19584063 original size:23 final size:23
Alignment explanation
Indices: 19584032--19584113 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
19584022 AGTGCTGGGC
*
19584032 AACAAAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAATGCTA
19584055 AACAGAGAGCACACA-AAGTGCTA
1 AACAGAGAGCACACACAA-TGCTA
* *
19584078 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAATGCT-A
19584102 TAACAGAGAGCA
1 -AACAGAGAGCA
19584114 TGAGACGTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
22 2 0.04
23 37 0.73
24 2 0.04
25 10 0.20
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:19584159 original size:25 final size:25
Alignment explanation
Indices: 19584095--19584151 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
19584085 AGCACACACA
*
19584095 GTGCTAATAACAGAGAGCATGAGAC
1 GTGCTAATAACAGAGAGCATGAAAC
19584120 GTGCTAATAACAGAGAGCATGAAAC
1 GTGCTAATAACAGAGAGCATGAAAC
19584145 GTGCTAA
1 GTGCTAA
19584152 ATAGAGAGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (25 bp):
GTGCTAATAACAGAGAGCATGAAAC
Found at i:19591240 original size:23 final size:23
Alignment explanation
Indices: 19591214--19591318 Score: 129
Period size: 23 Copynumber: 4.5 Consensus size: 23
19591204 GTGCTGGGCG
*
19591214 ACAGAGAGCACACACAGTGCTAA
1 ACAGAGAGCACACAAAGTGCTAA
* *
19591237 ACAGAGAGTACACAAAGTACTAA
1 ACAGAGAGCACACAAAGTGCTAA
* * *
19591260 TCAGAGAGCACACAAAATGTTAA
1 ACAGAGAGCACACAAAGTGCTAA
*
19591283 TCAGAGAGCACACAAAGTGCTAATA
1 ACAGAGAGCACACAAAGTGCT-A-A
19591308 ACAGAGAGCAC
1 ACAGAGAGCAC
19591319 GAGACGTGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
23 57 0.83
24 1 0.01
25 11 0.16
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (23 bp):
ACAGAGAGCACACAAAGTGCTAA
Found at i:19591265 original size:46 final size:47
Alignment explanation
Indices: 19591214--19591339 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 47
19591204 GTGCTGGGCG
*
19591214 ACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * * *
19591261 -CAGAGAGCACACAAAATGTTAATCAGAGAGCACACAAAGTGCTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* *
19591307 AACAGAGAGCACGAGAC-GTGCTAAATAGAGAGC
1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
19591340 GCGCTAGTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
46 40 0.62
48 22 0.34
49 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (47 bp):
ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:19603767 original size:15 final size:15
Alignment explanation
Indices: 19603743--19603775 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19603733 TAAGGTGTAA
19603743 TAAAAATGAATTTAT
1 TAAAAATGAATTTAT
*
19603758 TAAAATTGAATTTAT
1 TAAAAATGAATTTAT
19603773 TAA
1 TAA
19603776 GTTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAAAATGAATTTAT
Found at i:19608891 original size:21 final size:22
Alignment explanation
Indices: 19608865--19608914 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
19608855 CGACGTCATG
* *
19608865 TTATTTTATATCCTTT-TATAA
1 TTATTTTATATCATTTCAATAA
* *
19608886 TTATTTGATTTCATTTCAATAA
1 TTATTTTATATCATTTCAATAA
19608908 TTATTTT
1 TTATTTT
19608915 TATGCTATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTTATATCATTTCAATAA
Found at i:19609659 original size:33 final size:33
Alignment explanation
Indices: 19609620--19609689 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
19609610 ATAATAATTT
* * *
19609620 ATATTTAAATAATTTAATATAATGATACATGAA
1 ATATTTAAATAATTTAAAATAATGATAAATAAA
*
19609653 ATATTTAAATAATTTAAAATAATTATAAATAAA
1 ATATTTAAATAATTTAAAATAATGATAAATAAA
19609686 ATAT
1 ATAT
19609690 AAATTAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (33 bp):
ATATTTAAATAATTTAAAATAATGATAAATAAA
Found at i:19609682 original size:28 final size:28
Alignment explanation
Indices: 19609590--19609683 Score: 82
Period size: 33 Copynumber: 3.2 Consensus size: 28
19609580 ATTATACATA
* *
19609590 AAATATTTAAA-AACTTAAATATAATAAT
1 AAATATTTAAATAATTTAAA-ATAATTAT
** *
19609618 TTATATTTAAATAATTTAATATAATGATACAT
1 AAATATTTAAATAATTTAAAATAAT--T--AT
19609650 GAAATATTTAAATAATTTAAAATAATTAT
1 -AAATATTTAAATAATTTAAAATAATTAT
19609679 AAATA
1 AAATA
19609684 AAATATAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 19 0.37
29 8 0.15
31 1 0.02
32 2 0.04
33 22 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATATTTAAATAATTTAAAATAATTAT
Found at i:19610364 original size:60 final size:60
Alignment explanation
Indices: 19610271--19610466 Score: 234
Period size: 60 Copynumber: 3.2 Consensus size: 60
19610261 TTAATATAAC
* *
19610271 ATTTGGTACCTAAACTTGACATTTTTTCTTAATTTAGTACTTAAACCTTTTTTT-GACCTA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACTTAAACCTTTTTTTAGACC-A
* * *
19610331 ATTTGGTACGTTAACTTGACACTTTTTCCTAATTTGGTACTTAAA-CTTTTTTTAGACCA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACTTAAACCTTTTTTTAGACCA
* * * * * *
19610390 ATTTGATACCTGAACTTGACATTTTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTAGATTCA
1 ATTTGGTACCTAAACTTGACA--TTTTTTCCTAATTTGGTACTTAAACCTTTTTTTAGA-CCA
*
19610453 ATTTGATACCTAAA
1 ATTTGGTACCTAAA
19610467 TTTATTAAAT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 27 0.23
60 44 0.38
61 21 0.18
62 10 0.09
63 15 0.13
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTTCCTAATTTGGTACTTAAACCTTTTTTTAGACCA
Found at i:19610378 original size:31 final size:30
Alignment explanation
Indices: 19610271--19610378 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 30
19610261 TTAATATAAC
* *
19610271 ATTTGGTACCTAAACTTGACATTTTTTCTTA
1 ATTTGGTACTTAAACTTGACA-TTTTTCCTA
*
19610302 ATTTAGTACTTAAACCTT----TTTTTGACCTA
1 ATTTGGTACTTAAA-CTTGACATTTTT--CCTA
19610331 ATTTGGTACGTT-AACTTGACACTTTTTCCTA
1 ATTTGGTAC-TTAAACTTGACA-TTTTTCCTA
19610362 ATTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
19610379 TTTTTAGACC
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
27 5 0.08
28 3 0.05
29 13 0.21
30 4 0.06
31 30 0.48
32 3 0.05
33 5 0.08
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTGACATTTTTCCTA
Found at i:19610656 original size:31 final size:30
Alignment explanation
Indices: 19610619--19610807 Score: 90
Period size: 31 Copynumber: 6.3 Consensus size: 30
19610609 AAAAGAATAT
*
19610619 GTACCAAATTAGGAAAAAGAGTCAAGTTCAG
1 GTACCAAATTAAGAAAAAGA-TCAAGTTCAG
* ** * *
19610650 GTACCAAATT-GGACGCCAA-A--AAGTTTAA
1 GTACCAAATTAAGA--AAAAGATCAAGTTCAG
* * * * *
19610678 GTATCAATTTAAAAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAG-ATCAAGTTCAG
* *
19610709 GTACCAAATTAAGAAAAAGTGTCAAGTT-TG
1 GTACCAAATTAAGAAAAAG-ATCAAGTTCAG
* * *
19610739 AGTATCAAATT-GGACTAAAA-A--AAGTTAAG
1 -GTACCAAATTAAGA--AAAAGATCAAGTTCAG
19610768 GTACCAAATTAAGAAAAAGTATCAAGTTCAG
1 GTACCAAATTAAGAAAAAG-ATCAAGTTCAG
19610799 GTACCAAAT
1 GTACCAAAT
19610808 GTTATATTAA
Statistics
Matches: 119, Mismatches: 23, Indels: 32
0.68 0.13 0.18
Matches are distributed among these distances:
27 6 0.05
28 28 0.24
29 5 0.04
30 6 0.05
31 68 0.57
32 6 0.05
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (30 bp):
GTACCAAATTAAGAAAAAGATCAAGTTCAG
Found at i:19610785 original size:90 final size:90
Alignment explanation
Indices: 19610619--19610807 Score: 238
Period size: 90 Copynumber: 2.1 Consensus size: 90
19610609 AAAAGAATAT
* ** *
19610619 GTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACGCCAAAAAGTTTAAGTATCA
1 GTACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACGAAAAAAAGTTTAAGTACCA
* * *
19610684 ATTTAAAAAAAAGTGTCAAGTTTAG
66 AATTAAAAAAAAGTATCAAGTTCAG
* * * *
19610709 GTACCAAATTAAGAAAAAGTGTCAAGTT-TGAGTATCAAATTGGACTAAAAAAAG-TTAAGGTAC
1 GTACCAAATTAAGAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACGAAAAAAAGTTTAA-GTAC
*
19610772 CAAATTAAGAAAAAGTATCAAGTTCAG
64 CAAATTAAAAAAAAGTATCAAGTTCAG
19610799 GTACCAAAT
1 GTACCAAAT
19610808 GTTATATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 5 0.06
90 80 0.94
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (90 bp):
GTACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACGAAAAAAAGTTTAAGTACCA
AATTAAAAAAAAGTATCAAGTTCAG
Found at i:19611174 original size:83 final size:83
Alignment explanation
Indices: 19611035--19611222 Score: 376
Period size: 83 Copynumber: 2.3 Consensus size: 83
19611025 AAAGTAAGTT
19611035 CTTTTTTTCATAATTTCATTCCTGTATAAAAATAGGTTTTAATTATTGCGGATGACAACTTGGCA
1 CTTTTTTTCATAATTTCATTCCTGTATAAAAATAGGTTTTAATTATTGCGGATGACAACTTGGCA
19611100 ACTTTATTTTAGTTTTGA
66 ACTTTATTTTAGTTTTGA
19611118 CTTTTTTTCATAATTTCATTCCTGTATAAAAATAGGTTTTAATTATTGCGGATGACAACTTGGCA
1 CTTTTTTTCATAATTTCATTCCTGTATAAAAATAGGTTTTAATTATTGCGGATGACAACTTGGCA
19611183 ACTTTATTTTAGTTTTGA
66 ACTTTATTTTAGTTTTGA
19611201 CTTTTTTTCATAATTTCATTCC
1 CTTTTTTTCATAATTTCATTCC
19611223 GGTTTTTAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 105 1.00
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (83 bp):
CTTTTTTTCATAATTTCATTCCTGTATAAAAATAGGTTTTAATTATTGCGGATGACAACTTGGCA
ACTTTATTTTAGTTTTGA
Found at i:19623528 original size:30 final size:31
Alignment explanation
Indices: 19623487--19623549 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
19623477 CTAATTGGGT
* *
19623487 ACCCAAATTTTAGG-TATTTTCGTTTTGATC
1 ACCCAAATTTTAGGATATTTTCATTTTAATC
*
19623517 ACCCAATTTTTAGGATATTTTCATTTTAATC
1 ACCCAAATTTTAGGATATTTTCATTTTAATC
19623548 AC
1 AC
19623550 TCTAGCGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (31 bp):
ACCCAAATTTTAGGATATTTTCATTTTAATC
Found at i:19624127 original size:14 final size:15
Alignment explanation
Indices: 19624106--19624138 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19624096 TGCTACTATA
*
19624106 ATTTTAAATTTTAAT
1 ATTTAAAATTTTAAT
19624121 ATTTAAAATTTT-AT
1 ATTTAAAATTTTAAT
19624135 ATTT
1 ATTT
19624139 CCAAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTAAAATTTTAAT
Found at i:19624638 original size:23 final size:23
Alignment explanation
Indices: 19624612--19624657 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19624602 AAATTCGAAT
**
19624612 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
19624635 TTCGAGTTAAACGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
19624658 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:19624715 original size:9 final size:9
Alignment explanation
Indices: 19624701--19624729 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
19624691 TGAATTTTCG
19624701 AATTCGAAT
1 AATTCGAAT
19624710 AATTCGAAT
1 AATTCGAAT
19624719 AATTCGAAT
1 AATTCGAAT
19624728 AA
1 AA
19624730 ACCAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19625044 original size:23 final size:23
Alignment explanation
Indices: 19625024--19625069 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19625014 TTGTATAATC
*
19625024 ATATTTAAAAACTTTAAATAAAA
1 ATATTTAAAAAATTTAAATAAAA
*
19625047 ATATTTAAAAAATTTACATAAAA
1 ATATTTAAAAAATTTAAATAAAA
19625070 TTAAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATTTAAAAAATTTAAATAAAA
Found at i:19631285 original size:27 final size:27
Alignment explanation
Indices: 19631255--19631309 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19631245 CAAAAAAGGG
*
19631255 TATACCTTGCCGATTTTGAATTTAACT
1 TATACCCTGCCGATTTTGAATTTAACT
19631282 TATACCCTGCCGATTTTGAATTTAACT
1 TATACCCTGCCGATTTTGAATTTAACT
19631309 T
1 T
19631310 CTTTGATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (27 bp):
TATACCCTGCCGATTTTGAATTTAACT
Found at i:19634980 original size:15 final size:15
Alignment explanation
Indices: 19634951--19634986 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19634941 TATAATTAAC
19634951 CACATA-ATATTTCT
1 CACATATATATTTCT
*
19634965 CACATATATTTTTCT
1 CACATATATATTTCT
19634980 CACATAT
1 CACATAT
19634987 TCATCATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (15 bp):
CACATATATATTTCT
Found at i:19637031 original size:90 final size:88
Alignment explanation
Indices: 19636963--19637220 Score: 247
Period size: 89 Copynumber: 2.9 Consensus size: 88
19636953 ACTCTCGAGC
* * *
19636963 TTTCTAAAAATTT-ATTTTTGACCC-CTAAATTTTCTAGAATTTCATTTTCGACCCCTGAACTTT
1 TTTCTAAAAATTTCATTTTCGACCCTC-AAACTTTCTAAAATTTCATTTT-GACCCCTGAACTTT
*
19637026 TTAAAATTTCATTTTCGACCCTCAAA
64 TTAAAAATTCATTTTC-ACCCTCAAA
* * *
19637052 TTTTTTATAATTTCATTTTCGACCCTCAAACTTTCTAAAATTTCATTTTGACCCCTGAACTTTAT
1 TTTCTAAAAATTTCATTTTCGACCCTCAAACTTTCTAAAATTTCATTTTGACCCCTGAACTTT-T
* * * *
19637117 GT-AAATTTCATTTTGACCCTTACAC
65 -TAAAAATTCATTTTCACCCTCA-AA
* * * * * *
19637142 TTTTTAAAAATTTCATTTT--AACCTCTAAACTTTTTAAAATTACATTTTAACCTCTGAACTTTT
1 TTTCTAAAAATTTCATTTTCGACCCTC-AAACTTTCTAAAATTTCATTTTGACCCCTGAACTTTT
19637205 TGAAAAATTGCATTTT
65 T-AAAAATT-CATTTT
19637221 AGCCTCTAAA
Statistics
Matches: 143, Mismatches: 17, Indels: 17
0.81 0.10 0.10
Matches are distributed among these distances:
87 1 0.01
88 6 0.04
89 67 0.47
90 67 0.47
91 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (88 bp):
TTTCTAAAAATTTCATTTTCGACCCTCAAACTTTCTAAAATTTCATTTTGACCCCTGAACTTTTT
AAAAATTCATTTTCACCCTCAAA
Found at i:19637064 original size:89 final size:89
Alignment explanation
Indices: 19636967--19637220 Score: 277
Period size: 90 Copynumber: 2.8 Consensus size: 89
19636957 TCGAGCTTTC
*
19636967 TAAAAATTT-ATTTTTGACCCCTAAATTTTCTAGAATTTCATTTTCGACCCCTGAACTTTTTAAA
1 TAAAAATTTCATTTTTGACCCCTAAATTTTCTAAAATTTCATTTT-GACCCCTGAACTTTTTAAA
19637031 ATTTCATTTTCGACCCTCA-AATTTT
65 ATTTCATTTT-GACCCTCACAATTTT
* * * *
19637056 TTATAATTTCATTTTCGA-CCCTCAAACTTTCTAAAATTTCATTTTGACCCCTGAACTTTATGT-
1 TAAAAATTTCATTTTTGACCCCT-AAATTTTCTAAAATTTCATTTTGACCCCTGAACTTT-T-TA
* *
19637119 AAATTTCATTTTGACCCTTACACTTTT
63 AAATTTCATTTTGACCCTCACAATTTT
* * * * *
19637146 TAAAAATTTCA-TTTTAACCTCTAAACTTTT-TAAAATTACATTTTAACCTCTGAACTTTTTGAA
1 TAAAAATTTCATTTTTGACCCCTAAA-TTTTCTAAAATTTCATTTTGACCCCTGAACTTTTT--A
*
19637209 AAATTGCATTTT
63 AAATTTCATTTT
19637221 AGCCTCTAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
87 1 0.01
88 1 0.01
89 64 0.46
90 71 0.51
91 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.45
Consensus pattern (89 bp):
TAAAAATTTCATTTTTGACCCCTAAATTTTCTAAAATTTCATTTTGACCCCTGAACTTTTTAAAA
TTTCATTTTGACCCTCACAATTTT
Found at i:19637204 original size:29 final size:28
Alignment explanation
Indices: 19636969--19637220 Score: 213
Period size: 30 Copynumber: 8.5 Consensus size: 28
19636959 GAGCTTTCTA
19636969 AAAATTT-ATTTTTGACCCCTAAA-TTTTCT
1 AAAATTTCA-TTTTGA-CCCTAAACTTTT-T
* *
19636998 AGAATTTCATTTTCGACCCCTGAACTTTTT
1 AAAATTTCATTTT-GA-CCCTAAACTTTTT
*
19637028 AAAATTTCATTTTCGACCCTCAAATTTTTT
1 AAAATTTCATTTT-GACCCT-AAACTTTTT
* *
19637058 ATAATTTCATTTTCGACCCTCAAACTTTCT
1 AAAATTTCATTTT-GACCCT-AAACTTTTT
*
19637088 AAAATTTCATTTTGACCCCTGAACTTTATGT
1 AAAATTTCATTTTGA-CCCTAAACTTT-T-T
*
19637119 -AAATTTCATTTTGACCCTTACACTTTTT
1 AAAATTTCATTTTGACCC-TAAACTTTTT
*
19637147 AAAAATTTCATTTTAACCTCTAAACTTTTT
1 -AAAATTTCATTTTGACC-CTAAACTTTTT
* * *
19637177 AAAATTACATTTTAACCTCTGAACTTTTT
1 AAAATTTCATTTTGACC-CTAAACTTTTT
*
19637206 GAAAAATTGCATTTT
1 --AAAATTTCATTTT
19637221 AGCCTCTAAA
Statistics
Matches: 192, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.01
29 53 0.28
30 120 0.62
31 18 0.09
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.45
Consensus pattern (28 bp):
AAAATTTCATTTTGACCCTAAACTTTTT
Found at i:19641997 original size:16 final size:15
Alignment explanation
Indices: 19641976--19642009 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19641966 CTGGCATAAG
19641976 CATTCATGAAACTGTA
1 CATTCATGAAACTG-A
*
19641992 CATTCATGTAACTGA
1 CATTCATGAAACTGA
19642007 CAT
1 CAT
19642010 GATACCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (15 bp):
CATTCATGAAACTGA
Found at i:19644957 original size:7 final size:7
Alignment explanation
Indices: 19644945--19644970 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19644935 ATGAAAGAAA
19644945 GATGAGG
1 GATGAGG
19644952 GATGAGG
1 GATGAGG
19644959 GATGAGG
1 GATGAGG
19644966 GATGA
1 GATGA
19644971 TTAGGAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:19645393 original size:23 final size:22
Alignment explanation
Indices: 19645362--19645405 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19645352 AAAAAAATAA
*
19645362 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
19645384 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
19645406 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:19647473 original size:18 final size:18
Alignment explanation
Indices: 19647450--19647488 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19647440 AAAAATCAAG
*
19647450 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
19647468 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
19647486 TTT
1 TTT
19647489 GGTCTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:19648544 original size:3 final size:3
Alignment explanation
Indices: 19648538--19648574 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
19648528 ATTATTTATT
*
19648538 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
19648575 TATCATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:19652415 original size:18 final size:18
Alignment explanation
Indices: 19652384--19652419 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19652374 TTGCCTCTAC
*
19652384 TATTGGCACCACCTTGAG
1 TATTGCCACCACCTTGAG
*
19652402 TATTGCCACGACCTTGAG
1 TATTGCCACCACCTTGAG
19652420 CTACAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (18 bp):
TATTGCCACCACCTTGAG
Found at i:19653576 original size:13 final size:13
Alignment explanation
Indices: 19653546--19653570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19653536 CAAATAAAGC
19653546 AATTTCAGCATCA
1 AATTTCAGCATCA
19653559 AATTTCAGCATC
1 AATTTCAGCATC
19653571 CGATTTTAGC
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
AATTTCAGCATCA
Found at i:19659065 original size:78 final size:76
Alignment explanation
Indices: 19658969--19659380 Score: 377
Period size: 78 Copynumber: 5.3 Consensus size: 76
19658959 ATTTTACAGG
* * *
19658969 TCTCTTACCTCGATCATGGGGTAGATCGAAGCATCCAAATCTCTTACCCTAATCAAAAGGCAGAT
1 TCTCTTACCTTGATCATGGGGCAGATCGAAGCATCC-AATCTCTTACCCTAATCAGAAGGCAGAT
19659034 TAAAGATCGCCAA
65 TAAAGA-CGCCAA
*
19659047 TCTCTTACCTTGATCATGGGGCAGATCGAAGCATCCAAATCTCTTACCCT-ATCAGAGGGCAGAT
1 TCTCTTACCTTGATCATGGGGCAGATCGAAGCATCC-AATCTCTTACCCTAATCAGAAGGCAGAT
19659111 TAAAGACCGCCAA
65 TAAAGA-CGCCAA
* * * * * *
19659124 TATCTCAGCC-CGATCAT-GGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAGAT
1 TCTCTTA-CCTTGATCATGGGGCAGATCGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGAT
* *
19659187 TGAAGACACACCAA
65 T-AA-AGACGCCAA
* * * * * *
19659201 TCTCTTACCCTGATCATGGGGAAAATTGAAGCATCCAATCTTTTACCCTAATCAGAAGGCTGATT
1 TCTCTTACCTTGATCATGGGGCAGATCGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
* *
19659266 GAAGACATCCAA
66 AAAGAC-GCCAA
* *** * ** * *
19659278 TCTCTTACCTTAATCAAAAGGCAGATTGAAGACATGTAATCTCTTA-CCTCGATCATG-GGGCAG
1 TCTCTTACCTTGATCATGGGGCAGATCGAAG-CATCCAATCTCTTACCCT-AATCA-GAAGGCAG
* *
19659341 ATTGAAG-CATCCAA
63 ATTAAAGAC-GCCAA
**
19659355 TCTCTTACCCCGATCATGGGGCAGAT
1 TCTCTTACCTTGATCATGGGGCAGAT
19659381 TAAAAATATC
Statistics
Matches: 281, Mismatches: 43, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
75 11 0.04
76 36 0.13
77 112 0.40
78 121 0.43
79 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (76 bp):
TCTCTTACCTTGATCATGGGGCAGATCGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
AAAGACGCCAA
Found at i:19659278 original size:154 final size:154
Alignment explanation
Indices: 19658975--19659375 Score: 418
Period size: 154 Copynumber: 2.6 Consensus size: 154
19658965 CAGGTCTCTT
* * * * *
19658975 ACCTCGATCATGGGGTAGATCGAAGCATCCAAATCTCTTACCCTAATCAAAAGGCAGATTAAAGA
1 ACCTCGATCAT-GGGCAGATTGAAGCATCC-AATCTCTTACCTTAATCAGAAGGCAGATTGAAGA
* * * * * *
19659040 -TCGCCAATCTCTTACCTTGATCATGGGGCAGATCGAAGCATCCAAATCTCTTACCCTATCAGAG
64 CACACCAATCTCTTACCCTGATCATGGGGAAAATCGAAGCATCCAAATCTCTTACCCTATCAGAA
*
19659104 GGCAGATTAAAGACCGCCAATATCTC
129 GGCAGATTAAAGACAGCCAATATCTC
*
19659130 AGCC-CGATCATGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAGATTGAAGAC
1 A-CCTCGATCATGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGAC
* *
19659194 ACACCAATCTCTTACCCTGATCATGGGGAAAATTGAAGCATCC-AATCTTTTACCCTAATCAGAA
65 ACACCAATCTCTTACCCTGATCATGGGGAAAATCGAAGCATCCAAATCTCTTACCCT-ATCAGAA
* * * * *
19659258 GGCTGATTGAAGACATCCAATCTCTT
129 GGCAGATTAAAGACAGCCAATATCTC
** ** ** ** *
19659284 ACCTTAATCAAAAGGCAGATTGAAGACATGTAATCTCTTACCTCGATCATG-GGGCAGATTGAAG
1 ACCTCGATC-ATGGGCAGATTGAAG-CATCCAATCTCTTACCTTAATCA-GAAGGCAGATTGAAG
* *
19659348 -CA-TCCAATCTCTTACCCCGATCATGGGG
63 ACACACCAATCTCTTACCCTGATCATGGGG
19659376 CAGATTAAAA
Statistics
Matches: 207, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
153 44 0.21
154 107 0.52
155 23 0.11
156 32 0.15
157 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (154 bp):
ACCTCGATCATGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGACA
CACCAATCTCTTACCCTGATCATGGGGAAAATCGAAGCATCCAAATCTCTTACCCTATCAGAAGG
CAGATTAAAGACAGCCAATATCTC
Found at i:19659310 original size:39 final size:38
Alignment explanation
Indices: 19658991--19659424 Score: 288
Period size: 39 Copynumber: 11.2 Consensus size: 38
19658981 ATCATGGGGT
* *
19658991 AGATCGAAGCATCCAAATCTCTTACCCTAATCAAAAGGC
1 AGATTGAAGCATCC-AATCTCTTACCCTAATCAAAGGGC
* * * **
19659030 AGATTAAAG-ATCGCCAATCTCTTACCTTGATCATGGGGC
1 AGATTGAAGCAT--CCAATCTCTTACCCTAATCAAAGGGC
* *
19659069 AGATCGAAGCATCCAAATCTCTTACCCT-ATCAGAGGGC
1 AGATTGAAGCATCC-AATCTCTTACCCTAATCAAAGGGC
* ** * * * *
19659107 AGATTAAAGACCGCCAATATCTCAGCCC-GATC-ATGGGC
1 AGATTGAAG-CATCCAATCTCTTA-CCCTAATCAAAGGGC
* *
19659145 AGATTGAAGCATCCAATCTTTTACCTTAATCAGAA-GGC
1 AGATTGAAGCATCCAATCTCTTACCCTAATCA-AAGGGC
* * ** *
19659183 AGATTGAAGACACACCAATCTCTTACCCTGATCATGGGGA
1 AGATTGAAG-CA-TCCAATCTCTTACCCTAATCAAAGGGC
* *
19659223 AAATTGAAGCATCCAATCTTTTACCCTAATCAGAA-GGC
1 AGATTGAAGCATCCAATCTCTTACCCTAATCA-AAGGGC
* * *
19659261 TGATTGAAGACATCCAATCTCTTACCTTAATCAAAAGGC
1 AGATTGAAG-CATCCAATCTCTTACCCTAATCAAAGGGC
** * **
19659300 AGATTGAAGACATGTAATCTCTTA-CCTCGATCATGGGGC
1 AGATTGAAG-CATCCAATCTCTTACCCT-AATCAAAGGGC
** **
19659339 AGATTGAAGCATCCAATCTCTTACCCCGATCATGGGGC
1 AGATTGAAGCATCCAATCTCTTACCCTAATCAAAGGGC
* ** * ** **
19659377 AGATTAAAAATATCTAATCTCTTACCCCGATCATGGGGC
1 AGATT-GAAGCATCCAATCTCTTACCCTAATCAAAGGGC
19659416 AGATTGAAG
1 AGATTGAAG
19659425 ATATATCAAT
Statistics
Matches: 312, Mismatches: 64, Indels: 39
0.75 0.15 0.09
Matches are distributed among these distances:
36 2 0.01
37 12 0.04
38 111 0.36
39 156 0.50
40 31 0.10
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (38 bp):
AGATTGAAGCATCCAATCTCTTACCCTAATCAAAGGGC
Found at i:19659354 original size:77 final size:78
Alignment explanation
Indices: 19659262--19659444 Score: 224
Period size: 77 Copynumber: 2.3 Consensus size: 78
19659252 TCAGAAGGCT
** * * * *
19659262 GATTGAAGACATCCAATCTCTTACCTTAATCAAAAGGCAGATTGAAGACATGTAATCTCTTACCT
1 GATTGAAGACATCCAATCTCTTACCCCAATCAAAAGGCAGATTAAAAACATCTAATCTCTTACCC
19659327 CGATCATGGGGCA
66 CGATCATGGGGCA
* *** *
19659340 GATTGAAG-CATCCAATCTCTTACCCCGATCATGGGGCAGATTAAAAATATCTAATCTCTTACCC
1 GATTGAAGACATCCAATCTCTTACCCCAATCAAAAGGCAGATTAAAAACATCTAATCTCTTACCC
19659404 CGATCATGGGGCA
66 CGATCATGGGGCA
* * *
19659417 GATTGAAGATATATCAATTTCTTACCCC
1 GATTGAAGACAT-CCAATCTCTTACCCC
19659445 GAATGTAGGG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
77 66 0.74
78 10 0.11
79 13 0.15
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (78 bp):
GATTGAAGACATCCAATCTCTTACCCCAATCAAAAGGCAGATTAAAAACATCTAATCTCTTACCC
CGATCATGGGGCA
Found at i:19661322 original size:30 final size:30
Alignment explanation
Indices: 19661269--19661533 Score: 301
Period size: 30 Copynumber: 8.9 Consensus size: 30
19661259 TTCAAAATTT
* *
19661269 ACCC-CAAGCTTTCTAAAAATTCATTTTTG
1 ACCCTCAAACTTTCTAAAATTTCATTTTTG
* * * *
19661298 ATCCCT-AAATTTTCTAGAATTTCATCTTCG
1 A-CCCTCAAACTTTCTAAAATTTCATTTTTG
*
19661328 ACCCTCAAACTTTCTAAAATTTCATTTTTA
1 ACCCTCAAACTTTCTAAAATTTCATTTTTG
* *
19661358 ACCGTCGAACTTTCTAAAATTTCATTTTTG
1 ACCCTCAAACTTTCTAAAATTTCATTTTTG
* *
19661388 ACCCTCAAATTTTCTAGAATTTCATTTTTG
1 ACCCTCAAACTTTCTAAAATTTCATTTTTG
19661418 ACCCTCAAACTTTCTAAAATTTCATTTTTG
1 ACCCTCAAACTTTCTAAAATTTCATTTTTG
* *
19661448 ACCCTTAAACTTTTTAGAAATTTCA-TTTTG
1 ACCCTCAAACTTTCTA-AAATTTCATTTTTG
* *
19661478 A-CCTCTAAACTTTTTTAAAA--TCA-TTTTA
1 ACCCTC-AAAC-TTTCTAAAATTTCATTTTTG
19661506 ACCCTCAAACTTTCTAAAAATTTCATTT
1 ACCCTCAAACTTTCT-AAAATTTCATTT
19661534 AACCCTTGAA
Statistics
Matches: 200, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.02
28 16 0.08
29 12 0.06
30 152 0.76
31 16 0.08
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (30 bp):
ACCCTCAAACTTTCTAAAATTTCATTTTTG
Found at i:19664050 original size:42 final size:41
Alignment explanation
Indices: 19663982--19664074 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 41
19663972 TGAACTGTAG
19663982 TATTAATTTTACTATGTAATTAATAATTAGTTATATTTACA
1 TATTAATTTTACTATGTAATTAATAATTAGTTATATTTACA
* *
19664023 TATTATTTTTACATATTTAATTAATAATTAGTTATATTT--A
1 TATTAATTTTAC-TATGTAATTAATAATTAGTTATATTTACA
19664063 TATTGAATTTTA
1 TATT-AATTTTA
19664075 TCTGAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 5 0.11
41 17 0.36
42 25 0.53
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (41 bp):
TATTAATTTTACTATGTAATTAATAATTAGTTATATTTACA
Found at i:19664059 original size:21 final size:21
Alignment explanation
Indices: 19663998--19664062 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
19663988 TTTTACTATG
19663998 TAATTAATAATTAGTTATATT
1 TAATTAATAATTAGTTATATT
* *
19664019 TACA-T-ATTATT-TTTACATATT
1 TA-ATTAATAATTAGTT--ATATT
19664040 TAATTAATAATTAGTTATATT
1 TAATTAATAATTAGTTATATT
19664061 TA
1 TA
19664063 TATTGAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 18 0.53
22 6 0.18
23 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
TAATTAATAATTAGTTATATT
Found at i:19664133 original size:40 final size:41
Alignment explanation
Indices: 19664079--19664166 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 41
19664069 ATTTTATCTG
* *
19664079 AATTTTTGTAAATATTTTGTAGTGTTAATTATAAGTTTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTAT
* * *
19664120 -ATTTTTGTGAATATTTTGTATTATTAATTATAGGTCTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTAT
19664160 AATTTTT
1 AATTTTT
19664167 TTCTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 35 0.85
41 6 0.15
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (41 bp):
AATTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTAT
Found at i:19668076 original size:49 final size:53
Alignment explanation
Indices: 19667975--19668079 Score: 141
Period size: 49 Copynumber: 2.0 Consensus size: 53
19667965 TTGAGTTCAA
19667975 AACAACTAATAAAATATTCATAAAAATGAAACAAAAATGATAAGACTTAAAACT
1 AACAACTAATAAAATATTCATAAAAATG-AACAAAAATGATAAGACTTAAAACT
19668029 AACAA-TAA-AAAATATTC-TCAAAAATG-A-AAAAATGATAA-AGCTTAAAACT
1 AACAACTAATAAAATATTCAT-AAAAATGAACAAAAATGATAAGA-CTTAAAACT
19668078 AA
1 AA
19668080 AAAATGAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
48 1 0.02
49 22 0.45
50 1 0.02
51 1 0.02
52 16 0.33
53 3 0.06
54 5 0.10
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (53 bp):
AACAACTAATAAAATATTCATAAAAATGAACAAAAATGATAAGACTTAAAACT
Found at i:19668107 original size:34 final size:34
Alignment explanation
Indices: 19668056--19668135 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
19668046 TCAAAAATGA
*
19668056 AAAAATGATAAAGCTTAAAACTAAAAAATGAAAC
1 AAAAATAATAAAGCTTAAAACTAAAAAATGAAAC
19668090 AAAAATAAT-AAGACTTAAAACTAAAAAATGAAAC
1 AAAAATAATAAAG-CTTAAAACTAAAAAATGAAAC
19668124 AAAAATAATAAA
1 AAAAATAATAAA
19668136 ACTCTAACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
33 3 0.07
34 38 0.88
35 2 0.05
ACGTcount: A:0.69, C:0.07, G:0.06, T:0.17
Consensus pattern (34 bp):
AAAAATAATAAAGCTTAAAACTAAAAAATGAAAC
Found at i:19668334 original size:21 final size:21
Alignment explanation
Indices: 19668310--19668349 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19668300 TAATTATTAA
19668310 TTAAATATGTAAAAATAATAT
1 TTAAATATGTAAAAATAATAT
* *
19668331 TTAAGTATGTAAATATAAT
1 TTAAATATGTAAAAATAAT
19668350 TAATTATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTAAATATGTAAAAATAATAT
Found at i:19679129 original size:15 final size:15
Alignment explanation
Indices: 19679066--19679130 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
19679056 TAACAATATT
*
19679066 TATAAATTTTTATAA
1 TATAAATTTTAATAA
* *
19679081 CATATATTTGTAATATA
1 TATAAATTT-TAATA-A
* *
19679098 TAAAAAAATTT-ATAA
1 T-ATAAATTTTAATAA
19679113 TATAAATTTTAATAA
1 TATAAATTTTAATAA
19679128 TAT
1 TAT
19679131 TTTTTGCGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
14 7 0.19
15 16 0.43
16 7 0.19
17 2 0.05
18 5 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TATAAATTTTAATAA
Found at i:19684651 original size:13 final size:11
Alignment explanation
Indices: 19684619--19684661 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19684609 CCATTTTTTA
*
19684619 AATAAAATAAT
1 AATAAAATATT
19684630 AAT-AAATATCT
1 AATAAAATAT-T
19684641 AAGTAAAATATT
1 AA-TAAAATATT
19684653 AATAAAATA
1 AATAAAATA
19684662 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:19693272 original size:6 final size:6
Alignment explanation
Indices: 19693263--19693295 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
19693253 ACCAAAAATA
*
19693263 AAATTT AAATTT AAAGTT -AATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
19693296 GTTCAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:19695052 original size:59 final size:59
Alignment explanation
Indices: 19694871--19695179 Score: 275
Period size: 59 Copynumber: 5.2 Consensus size: 59
19694861 GAACTTTTTA
* * * ** * **
19694871 AAAATCACATTTTAACCACTAAACTTTTACAAAATTACATTTTAACCCCCAAACTTTCTT
1 AAAATTACATTTTGACC-CCAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCC
* * * **
19694931 AAAATTACATTTTGACACCTAAAC-TTCTCTAAAATTACATTTTGACCTTTAAAC-TTCTCC
1 AAAATTACATTTTGAC-CCCAAACTTTC-CCAAAATTACATTTTAACCCCTAAACTTTC-CC
*
19694991 AAAATTACATTTTGACCCCAAGCTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCC
1 AAAATTACATTTTGACCCCAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCC
* * * * * * *
19695050 AAAATCATATTTTGATCTCAAAATTTTCCAAAATTACATTTTGACCCC-AAAC-TTCTCC
1 AAAATTACATTTTGACCCCAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTC-CC
* * * * * * * *
19695108 AATATCACATTTTAACCCTAAACTTTTCTAAAATTACATTTTTACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCC
*
19695167 AAAATTAAATTTT
1 AAAATTACATTTT
19695180 AACCTTGAAT
Statistics
Matches: 203, Mismatches: 38, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
57 3 0.01
58 45 0.22
59 90 0.44
60 64 0.32
61 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (59 bp):
AAAATTACATTTTGACCCCAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCC
Found at i:19695180 original size:29 final size:30
Alignment explanation
Indices: 19694862--19695179 Score: 313
Period size: 30 Copynumber: 10.7 Consensus size: 30
19694852 GCAGTCCCCG
** * * *
19694862 AACTTTTTAAAAATCACATTTTAACCACTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * *
19694892 AACTTTTACAAAATTACATTTTAACCCCCA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* *
19694922 AAC-TTTCTTAAAATTACATTTTGACACCTA
1 AACTTTTC-CAAAATTACATTTTGACCCCTA
* * **
19694952 AACTTCTCTAAAATTACATTTTGACCTTTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
*
19694982 AACTTCTCCAAAATTACATTTTGACCCC-A
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * *
19695011 AGCTTTCCCAAAATTACATTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * * * *
19695041 AACTTTCCCAAAATCATATTTTGATCTC-A
1 AACTTTTCCAAAATTACATTTTGACCCCTA
*
19695070 AAATTTTCCAAAATTACATTTTGACCCC-A
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * * *
19695099 AACTTCTCCAATATCACATTTT-AACCCTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* *
19695128 AACTTTTCTAAAATTACATTTTTACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
*
19695158 AACTTTTCCAAAATTAAATTTT
1 AACTTTTCCAAAATTACATTTT
19695180 AACCTTGAAT
Statistics
Matches: 238, Mismatches: 45, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
28 4 0.02
29 89 0.37
30 142 0.60
31 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTGACCCCTA
Found at i:19695289 original size:18 final size:20
Alignment explanation
Indices: 19695250--19695293 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
19695240 GTATATAAAA
19695250 TTTAATTATTATCCTTTCTTT
1 TTTAATTA-TATCCTTTCTTT
*
19695271 TTTAATTA-ATCCTTTTTTT
1 TTTAATTATATCCTTTCTTT
19695290 TTTA
1 TTTA
19695294 TTTTGATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTAATTATATCCTTTCTTT
Found at i:19708620 original size:18 final size:17
Alignment explanation
Indices: 19708589--19708623 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
19708579 AGTTTTGGGT
19708589 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
19708606 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
19708624 AAATATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:19713314 original size:33 final size:33
Alignment explanation
Indices: 19713277--19713343 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
19713267 AATCAGATAC
*
19713277 GCTTGATTCCTTCCCGATTTGTTCGAATCACTT
1 GCTTGATTCCTTCCCGATTTGGTCGAATCACTT
*
19713310 GCTTGATTCCTTCTCGATTTGGTCGAATCACTT
1 GCTTGATTCCTTCCCGATTTGGTCGAATCACTT
19713343 G
1 G
19713344 GACATGAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (33 bp):
GCTTGATTCCTTCCCGATTTGGTCGAATCACTT
Found at i:19724470 original size:90 final size:91
Alignment explanation
Indices: 19724347--19724907 Score: 713
Period size: 90 Copynumber: 6.2 Consensus size: 91
19724337 TTACCAGTAC
* * * *
19724347 ACGATGCTGCTCACATGAGCTATCGAGGACTCGCAACATATGCGGTACCTCTA-CCATCGATACG
1 ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
19724411 GTATCTGTGCATATAACTGTTCCCTA
66 GTATCTGTGCATATAACTGTTCCCTA
* ** * *
19724437 ACGATGTTGCTCACATAAGCTGTTAAGGACTCGCAACATATGCGGTACC-CCAGCCATTGATACG
1 ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
*
19724501 GTATCTGTGCATATAACTGTTCTCTA
66 GTATCTGTGCATATAACTGTTCCCTA
* * * * *
19724527 ACGATGCTACTCACACGAGTTGTCT-AGGACTTGTAACATATGCGGTA-CTCCAGCCATTGATAC
1 ACGATGCTGCTCACACGAGCTGT-TGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATAC
19724590 GGTATCTGTGCATATAACTGTTCCCTA
65 GGTATCTGTGCATATAACTGTTCCCTA
* * * * *
19724617 ACGATGCTACTTACACGATCTGTTGAGGACTCGTAACATATGCGGTACC-CCAACCATCGATACG
1 ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
*
19724681 GTATCTGTGCATATAACTGTACCCTA
66 GTATCTGTGCATATAACTGTTCCCTA
* * * * * *
19724707 ACGATGTTGCTCATACGAGTTGTTGAGGACTCGTAACATAGGAGGTA-CTCCAGCCATCGATACG
1 ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
* * *
19724771 ATATCTATGCATATAACTGTTCTCTA
66 GTATCTGTGCATATAACTGTTCCCTA
* * * * * *
19724797 ATGATGCTGCTCACACGATCTGTCGAGGACTCGCAACATACGCAGTA-CGCCAGCCATCGATACG
1 ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
* *
19724861 ATATCTGTGCATATAACTATTCCCTA
66 GTATCTGTGCATATAACTGTTCCCTA
*
19724887 ACGATGCTGCTTACACGAGCT
1 ACGATGCTGCTCACACGAGCT
19724908 ATCAAGAATA
Statistics
Matches: 412, Mismatches: 53, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
89 5 0.01
90 405 0.98
91 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (91 bp):
ACGATGCTGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCCAGCCATCGATACG
GTATCTGTGCATATAACTGTTCCCTA
Found at i:19724852 original size:270 final size:270
Alignment explanation
Indices: 19724371--19724904 Score: 800
Period size: 270 Copynumber: 2.0 Consensus size: 270
19724361 ATGAGCTATC
* * *
19724371 GAGGACTCGCAACATATGCGGTACCTCTACCATCGATACGGTATCTGTGCATATAACTGTTCCCT
1 GAGGACTCGCAACATATGCGGTACCCCAACCATCGATACGGTATCTGTGCATATAACTGTACCCT
* * * *
19724436 AACGATGTTGCTCACATAAGCTGTTAAGGACTCGCAACATATGCGGTACCCCAGCCATTGATACG
66 AACGATGTTGCTCACACAAGCTGTTAAGGACTCGCAACATAGGAGGTACCCCAGCCATCGATACG
* * * * *
19724501 GTATCTGTGCATATAACTGTTCTCTAACGATGCTACTCACACGAGTTGTCTAGGACTTGTAACAT
131 ATATCTATGCATATAACTGTTCTCTAACGATGCTACTCACACGAGTTGTCGAGGACTCGCAACAT
* * * * * *
19724566 ATGCGGTACTCCAGCCATTGATACGGTATCTGTGCATATAACTGTTCCCTAACGATGCTACTTAC
196 ACGCAGTACGCCAGCCATCGATACGATATCTGTGCATATAACTATTCCCTAACGATGCTACTTAC
19724631 ACGATCTGTT
261 ACGATCTGTT
*
19724641 GAGGACTCGTAACATATGCGGTACCCCAACCATCGATACGGTATCTGTGCATATAACTGTACCCT
1 GAGGACTCGCAACATATGCGGTACCCCAACCATCGATACGGTATCTGTGCATATAACTGTACCCT
* * * * * *
19724706 AACGATGTTGCTCATACGAGTTGTTGAGGACTCGTAACATAGGAGGTACTCCAGCCATCGATACG
66 AACGATGTTGCTCACACAAGCTGTTAAGGACTCGCAACATAGGAGGTACCCCAGCCATCGATACG
* *
19724771 ATATCTATGCATATAACTGTTCTCTAATGATGCTGCTCACACGA-TCTGTCGAGGACTCGCAACA
131 ATATCTATGCATATAACTGTTCTCTAACGATGCTACTCACACGAGT-TGTCGAGGACTCGCAACA
*
19724835 TACGCAGTACGCCAGCCATCGATACGATATCTGTGCATATAACTATTCCCTAACGATGCTGCTTA
195 TACGCAGTACGCCAGCCATCGATACGATATCTGTGCATATAACTATTCCCTAACGATGCTACTTA
19724900 CACGA
260 CACGA
19724905 GCTATCAAGA
Statistics
Matches: 235, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
269 1 0.00
270 234 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (270 bp):
GAGGACTCGCAACATATGCGGTACCCCAACCATCGATACGGTATCTGTGCATATAACTGTACCCT
AACGATGTTGCTCACACAAGCTGTTAAGGACTCGCAACATAGGAGGTACCCCAGCCATCGATACG
ATATCTATGCATATAACTGTTCTCTAACGATGCTACTCACACGAGTTGTCGAGGACTCGCAACAT
ACGCAGTACGCCAGCCATCGATACGATATCTGTGCATATAACTATTCCCTAACGATGCTACTTAC
ACGATCTGTT
Found at i:19729487 original size:29 final size:29
Alignment explanation
Indices: 19729457--19729584 Score: 95
Period size: 28 Copynumber: 4.4 Consensus size: 29
19729447 ATCGGGGTTA
*
19729457 AAAATGG-GATTTAGGGAAGTTTGAGGGT
1 AAAATGGTAATTTAGGGAAGTTTGAGGGT
* *
19729485 AAAATGGTAATTTTAGTGAA-ATT-AGGGTTT
1 AAAATGGTAA-TTTAGGGAAGTTTGAGGG--T
* * *
19729515 AAAATGG-GATTTAGGGAAGTTAGGGGGT
1 AAAATGGTAATTTAGGGAAGTTTGAGGGT
** * *
19729543 AAAATGGTAATTTTTGAAAGTTTCAGGGT
1 AAAATGGTAATTTAGGGAAGTTTGAGGGT
19729572 AAAAAT-GTAATTT
1 -AAAATGGTAATTT
19729585 TTTGGAAATT
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
28 27 0.35
29 26 0.34
30 24 0.31
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTAGGGAAGTTTGAGGGT
Found at i:19729519 original size:58 final size:58
Alignment explanation
Indices: 19729426--19729556 Score: 199
Period size: 58 Copynumber: 2.2 Consensus size: 58
19729416 ACTCGGGGAC
* * *
19729426 AAAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAATCAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
* * *
19729485 AAAATGGTAATTTTAGTGAAATTAGGGTTTAAAATGGGATTTAGGGAAGTTAGGGGGT
1 AAAATGGTAATTTTAGTGAAATCAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
19729543 AAAATGGTAATTTT
1 AAAATGGTAATTTT
19729557 TGAAAGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 57 0.86
59 9 0.14
ACGTcount: A:0.34, C:0.01, G:0.32, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAATCAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
Found at i:19729577 original size:58 final size:57
Alignment explanation
Indices: 19729426--19729578 Score: 184
Period size: 58 Copynumber: 2.6 Consensus size: 57
19729416 ACTCGGGGAC
* ** *
19729426 AAAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTT-ATGAAATTAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
* *
19729485 AAAATGGTAATTTTAGTGAAATTAGGGTTTAAAATGGGATTTAGGGAAGTTAGGGGGT
1 AAAATGGTAATTTTA-TGAAATTAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
19729543 AAAATGGTAATTTT-TGAAAGTTTCAGGG-TAAAAATG
1 AAAATGGTAATTTTATGAAA--TT-AGGGTTAAAAATG
19729579 TAATTTTTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
56 5 0.06
58 65 0.78
59 13 0.16
ACGTcount: A:0.35, C:0.01, G:0.31, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTATGAAATTAGGGTTAAAAATGGGATTTAGGGAAGTTAGAGGGT
Found at i:19729767 original size:30 final size:30
Alignment explanation
Indices: 19729539--19729766 Score: 236
Period size: 30 Copynumber: 7.6 Consensus size: 30
19729529 GGAAGTTAGG
*
19729539 GGGT-AAAATGGTAATTTTT-GAAAGTTTCA
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTTTA
* *
19729568 GGGTAAAAATGTAATTTTTTGGAAA-TTTTG
1 GGGTCAAAATGTAA-TTTTTGGAAAGTTTTA
* * *
19729598 GGGTCAAAATATGA-TTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTTGG-AAAGTTTTA
19729628 GGGTCAAAATGTAA-TTTTGGAAAAG-TTTA
1 GGGTCAAAATGTAATTTTTGG-AAAGTTTTA
** *
19729657 GGGGTCAAAATGTAATTTTTAAAAAGTTTTG
1 -GGGTCAAAATGTAATTTTTGGAAAGTTTTA
*
19729688 GGGTCAAAATATAA-TTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTTGG-AAAGTTTTA
*
19729718 GGGTCAAAATGTAATTTTTAGAAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAAGTTTTA
* *
19729748 GGGTTAACATGTAATTTTT
1 GGGTCAAAATGTAATTTTT
19729767 AAACAATTTA
Statistics
Matches: 170, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.04
29 18 0.11
30 130 0.76
31 16 0.09
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTTTA
Found at i:19729767 original size:90 final size:88
Alignment explanation
Indices: 19729539--19729775 Score: 316
Period size: 90 Copynumber: 2.6 Consensus size: 88
19729529 GGAAGTTAGG
* **
19729539 GGGT-AAAATGGTAATTTTTGAAAGTTTCAGGGTAAAAATGTAATTTTTTGGAAATTTTGGGGTC
1 GGGTCAAAAT-GTAATTTTTGAAAGTTTTAGGGTAAAAATGTAA-TTTTTAAAAATTTTGGGGTC
* *
19729603 AAAATATGATTTTGGAAAAGTTTTG
64 AAAATATAATTTTGGAAAAGTTTTA
* *
19729628 GGGTCAAAATGTAATTTTGGAAAAG-TTTAGGGGTCAAAATGTAATTTTTAAAAAGTTTTGGGGT
1 GGGTCAAAATGTAATTTTTG-AAAGTTTTA-GGGTAAAAATGTAATTTTTAAAAA-TTTTGGGGT
19729692 CAAAATATAATTTTGGAAAAGTTTTA
63 CAAAATATAATTTTGGAAAAGTTTTA
* *
19729718 GGGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTTAACATGTAATTTTTAAACAATTT
1 GGGTCAAAATGTAATTTTT-GAAAGTTTTAGGGTAAAAATGTAATTTTTAAA-AATTT
19729776 AGGGACTTAC
Statistics
Matches: 131, Mismatches: 10, Indels: 13
0.85 0.06 0.08
Matches are distributed among these distances:
89 24 0.18
90 100 0.76
91 7 0.05
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (88 bp):
GGGTCAAAATGTAATTTTTGAAAGTTTTAGGGTAAAAATGTAATTTTTAAAAATTTTGGGGTCAA
AATATAATTTTGGAAAAGTTTTA
Found at i:19731453 original size:20 final size:20
Alignment explanation
Indices: 19731415--19731454 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19731405 CAGGGTATGG
*
19731415 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
19731435 TGGAGC-TGGTGGATAGCAGA
1 TGGAGCTTGGTGG-TAGCAGA
19731455 ATGTGGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.20, C:0.10, G:0.47, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:19734246 original size:24 final size:24
Alignment explanation
Indices: 19734216--19734266 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
19734206 ACAAACAACA
* * *
19734216 TTAGCTCTCATGAGCCTAGAATGG
1 TTAGCTCTCACGAGCCCAAAATGG
*
19734240 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTCACGAGCCCAAAATGG
19734264 TTA
1 TTA
19734267 ACCAGTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
TTAGCTCTCACGAGCCCAAAATGG
Found at i:19738897 original size:24 final size:25
Alignment explanation
Indices: 19738867--19738941 Score: 86
Period size: 24 Copynumber: 3.1 Consensus size: 25
19738857 ACATACAACA
*
19738867 TTAGCTCTC-ATGAGCCTA-AGATGG
1 TTAGCTCTCTACGAGCCTAGA-ATGG
19738891 TTAGCTC-CTACGAGCCTAGAATGG
1 TTAGCTCTCTACGAGCCTAGAATGG
* *
19738915 TTAGCTCT-TACGAGCCCAGAATAG
1 TTAGCTCTCTACGAGCCTAGAATGG
19738939 TTA
1 TTA
19738942 ACCAATATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (25 bp):
TTAGCTCTCTACGAGCCTAGAATGG
Found at i:19748417 original size:19 final size:18
Alignment explanation
Indices: 19748373--19748409 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19748363 AATAACACTT
19748373 AGCATCTTCTTTTCTATA
1 AGCATCTTCTTTTCTATA
*
19748391 AGCATCTTCTTTTTTATA
1 AGCATCTTCTTTTCTATA
19748409 A
1 A
19748410 CTCCTCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (18 bp):
AGCATCTTCTTTTCTATA
Found at i:19759083 original size:21 final size:21
Alignment explanation
Indices: 19759059--19759108 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
19759049 GAATTTCAGT
*
19759059 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
* *
19759080 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
19759101 AGAAAACT
1 AGCAAACT
19759109 GAGGCATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Done.