Multiple sequence alignment - TraesCS6D01G405100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G405100 chr6D 100.000 3092 0 0 1 3092 472510684 472513775 0.000000e+00 5710
1 TraesCS6D01G405100 chr6D 98.403 2818 38 5 280 3092 51499464 51502279 0.000000e+00 4948
2 TraesCS6D01G405100 chr7D 98.617 2820 33 4 278 3092 245402433 245399615 0.000000e+00 4987
3 TraesCS6D01G405100 chr7D 98.297 2818 40 6 280 3092 54583766 54580952 0.000000e+00 4931
4 TraesCS6D01G405100 chr7D 98.226 2818 44 4 280 3092 115100272 115103088 0.000000e+00 4922
5 TraesCS6D01G405100 chr5D 98.614 2813 38 1 280 3092 480824254 480821443 0.000000e+00 4977
6 TraesCS6D01G405100 chr5D 98.546 2819 34 5 279 3092 565815801 565818617 0.000000e+00 4972
7 TraesCS6D01G405100 chr5D 98.403 2818 38 5 280 3092 260689962 260687147 0.000000e+00 4948
8 TraesCS6D01G405100 chr3D 98.436 2813 43 1 280 3092 574856805 574853994 0.000000e+00 4950
9 TraesCS6D01G405100 chr4D 98.264 2822 41 3 278 3092 398986369 398983549 0.000000e+00 4933
10 TraesCS6D01G405100 chr1D 91.864 295 6 3 1 279 210229133 210229425 2.230000e-106 396
11 TraesCS6D01G405100 chr1D 85.849 106 11 4 112 217 251296076 251295975 3.260000e-20 110
12 TraesCS6D01G405100 chr5B 88.475 295 16 9 1 279 199657349 199657057 1.060000e-89 340
13 TraesCS6D01G405100 chr4B 100.000 68 0 0 212 279 663807512 663807579 3.240000e-25 126
14 TraesCS6D01G405100 chr1A 87.736 106 10 3 112 217 244501169 244501271 1.510000e-23 121
15 TraesCS6D01G405100 chr7A 86.792 106 11 3 112 217 56200535 56200637 7.010000e-22 115
16 TraesCS6D01G405100 chr5A 86.792 106 11 3 112 217 381550581 381550683 7.010000e-22 115
17 TraesCS6D01G405100 chr3B 86.792 106 11 3 112 217 697164721 697164823 7.010000e-22 115
18 TraesCS6D01G405100 chr3B 86.792 106 11 3 112 217 736482203 736482101 7.010000e-22 115
19 TraesCS6D01G405100 chr6B 85.849 106 12 3 112 217 159798392 159798290 3.260000e-20 110


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G405100 chr6D 472510684 472513775 3091 False 5710 5710 100.000 1 3092 1 chr6D.!!$F2 3091
1 TraesCS6D01G405100 chr6D 51499464 51502279 2815 False 4948 4948 98.403 280 3092 1 chr6D.!!$F1 2812
2 TraesCS6D01G405100 chr7D 245399615 245402433 2818 True 4987 4987 98.617 278 3092 1 chr7D.!!$R2 2814
3 TraesCS6D01G405100 chr7D 54580952 54583766 2814 True 4931 4931 98.297 280 3092 1 chr7D.!!$R1 2812
4 TraesCS6D01G405100 chr7D 115100272 115103088 2816 False 4922 4922 98.226 280 3092 1 chr7D.!!$F1 2812
5 TraesCS6D01G405100 chr5D 480821443 480824254 2811 True 4977 4977 98.614 280 3092 1 chr5D.!!$R2 2812
6 TraesCS6D01G405100 chr5D 565815801 565818617 2816 False 4972 4972 98.546 279 3092 1 chr5D.!!$F1 2813
7 TraesCS6D01G405100 chr5D 260687147 260689962 2815 True 4948 4948 98.403 280 3092 1 chr5D.!!$R1 2812
8 TraesCS6D01G405100 chr3D 574853994 574856805 2811 True 4950 4950 98.436 280 3092 1 chr3D.!!$R1 2812
9 TraesCS6D01G405100 chr4D 398983549 398986369 2820 True 4933 4933 98.264 278 3092 1 chr4D.!!$R1 2814

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
270 271 0.320771 CGCCTCCTACACCCATATGC 60.321 60.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2186 2.027837 AGCTTCACATTCCCCAAAATGC 60.028 45.455 0.0 0.0 39.72 3.56 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.723298 ACAATGTGGAATTGTTAGTGGAAA 57.277 33.333 0.00 0.00 38.97 3.13
24 25 7.301868 ACAATGTGGAATTGTTAGTGGAAAT 57.698 32.000 0.00 0.00 38.97 2.17
25 26 8.415950 ACAATGTGGAATTGTTAGTGGAAATA 57.584 30.769 0.00 0.00 38.97 1.40
26 27 9.034800 ACAATGTGGAATTGTTAGTGGAAATAT 57.965 29.630 0.00 0.00 38.97 1.28
27 28 9.304731 CAATGTGGAATTGTTAGTGGAAATATG 57.695 33.333 0.00 0.00 0.00 1.78
28 29 8.821686 ATGTGGAATTGTTAGTGGAAATATGA 57.178 30.769 0.00 0.00 0.00 2.15
29 30 8.642935 TGTGGAATTGTTAGTGGAAATATGAA 57.357 30.769 0.00 0.00 0.00 2.57
30 31 9.083422 TGTGGAATTGTTAGTGGAAATATGAAA 57.917 29.630 0.00 0.00 0.00 2.69
31 32 9.353999 GTGGAATTGTTAGTGGAAATATGAAAC 57.646 33.333 0.00 0.00 0.00 2.78
32 33 9.083422 TGGAATTGTTAGTGGAAATATGAAACA 57.917 29.630 0.00 0.00 0.00 2.83
37 38 9.689976 TTGTTAGTGGAAATATGAAACATGTTG 57.310 29.630 12.82 0.00 0.00 3.33
38 39 9.072375 TGTTAGTGGAAATATGAAACATGTTGA 57.928 29.630 12.82 2.16 0.00 3.18
39 40 9.341899 GTTAGTGGAAATATGAAACATGTTGAC 57.658 33.333 12.82 10.19 0.00 3.18
40 41 7.523293 AGTGGAAATATGAAACATGTTGACA 57.477 32.000 12.82 15.45 0.00 3.58
41 42 8.125978 AGTGGAAATATGAAACATGTTGACAT 57.874 30.769 24.53 24.53 36.96 3.06
42 43 8.587608 AGTGGAAATATGAAACATGTTGACATT 58.412 29.630 25.57 15.19 33.61 2.71
43 44 9.206870 GTGGAAATATGAAACATGTTGACATTT 57.793 29.630 25.57 20.33 33.61 2.32
44 45 9.775854 TGGAAATATGAAACATGTTGACATTTT 57.224 25.926 25.57 22.00 33.61 1.82
48 49 6.847956 ATGAAACATGTTGACATTTTGTGG 57.152 33.333 12.82 0.00 33.61 4.17
49 50 5.970592 TGAAACATGTTGACATTTTGTGGA 58.029 33.333 12.82 0.00 33.61 4.02
50 51 6.401394 TGAAACATGTTGACATTTTGTGGAA 58.599 32.000 12.82 0.00 33.61 3.53
51 52 6.534436 TGAAACATGTTGACATTTTGTGGAAG 59.466 34.615 12.82 0.00 33.61 3.46
52 53 4.370917 ACATGTTGACATTTTGTGGAAGC 58.629 39.130 0.00 0.00 33.61 3.86
53 54 3.451141 TGTTGACATTTTGTGGAAGCC 57.549 42.857 0.00 0.00 0.00 4.35
54 55 2.762887 TGTTGACATTTTGTGGAAGCCA 59.237 40.909 0.00 0.00 0.00 4.75
55 56 3.196469 TGTTGACATTTTGTGGAAGCCAA 59.804 39.130 0.00 0.00 34.18 4.52
56 57 4.187694 GTTGACATTTTGTGGAAGCCAAA 58.812 39.130 0.00 0.00 34.18 3.28
57 58 3.791245 TGACATTTTGTGGAAGCCAAAC 58.209 40.909 0.00 0.00 34.18 2.93
58 59 3.196469 TGACATTTTGTGGAAGCCAAACA 59.804 39.130 0.00 0.00 34.18 2.83
59 60 4.187694 GACATTTTGTGGAAGCCAAACAA 58.812 39.130 0.00 0.00 34.18 2.83
60 61 3.938334 ACATTTTGTGGAAGCCAAACAAC 59.062 39.130 0.00 0.00 34.18 3.32
61 62 3.971245 TTTTGTGGAAGCCAAACAACT 57.029 38.095 0.00 0.00 34.18 3.16
62 63 5.105146 ACATTTTGTGGAAGCCAAACAACTA 60.105 36.000 0.00 0.00 34.18 2.24
63 64 4.647424 TTTGTGGAAGCCAAACAACTAG 57.353 40.909 0.00 0.00 34.18 2.57
64 65 3.569194 TGTGGAAGCCAAACAACTAGA 57.431 42.857 0.00 0.00 34.18 2.43
65 66 3.476552 TGTGGAAGCCAAACAACTAGAG 58.523 45.455 0.00 0.00 34.18 2.43
66 67 2.814336 GTGGAAGCCAAACAACTAGAGG 59.186 50.000 0.00 0.00 34.18 3.69
67 68 2.224769 TGGAAGCCAAACAACTAGAGGG 60.225 50.000 0.00 0.00 0.00 4.30
68 69 2.039879 GGAAGCCAAACAACTAGAGGGA 59.960 50.000 0.00 0.00 0.00 4.20
69 70 2.861147 AGCCAAACAACTAGAGGGAC 57.139 50.000 0.00 0.00 0.00 4.46
70 71 1.351350 AGCCAAACAACTAGAGGGACC 59.649 52.381 0.00 0.00 0.00 4.46
71 72 1.613520 GCCAAACAACTAGAGGGACCC 60.614 57.143 0.59 0.59 0.00 4.46
72 73 1.702957 CCAAACAACTAGAGGGACCCA 59.297 52.381 14.60 0.00 0.00 4.51
73 74 2.552373 CCAAACAACTAGAGGGACCCAC 60.552 54.545 14.60 6.57 0.00 4.61
74 75 2.105821 CAAACAACTAGAGGGACCCACA 59.894 50.000 14.60 0.00 0.00 4.17
75 76 1.349067 ACAACTAGAGGGACCCACAC 58.651 55.000 14.60 3.69 0.00 3.82
76 77 1.348064 CAACTAGAGGGACCCACACA 58.652 55.000 14.60 0.00 0.00 3.72
77 78 1.909302 CAACTAGAGGGACCCACACAT 59.091 52.381 14.60 0.00 0.00 3.21
78 79 3.104512 CAACTAGAGGGACCCACACATA 58.895 50.000 14.60 0.00 0.00 2.29
79 80 3.033659 ACTAGAGGGACCCACACATAG 57.966 52.381 14.60 7.20 0.00 2.23
80 81 1.689273 CTAGAGGGACCCACACATAGC 59.311 57.143 14.60 0.00 0.00 2.97
81 82 1.144057 GAGGGACCCACACATAGCG 59.856 63.158 14.60 0.00 0.00 4.26
82 83 2.513897 GGGACCCACACATAGCGC 60.514 66.667 5.33 0.00 0.00 5.92
83 84 2.267642 GGACCCACACATAGCGCA 59.732 61.111 11.47 0.00 0.00 6.09
84 85 2.106683 GGACCCACACATAGCGCAC 61.107 63.158 11.47 0.00 0.00 5.34
85 86 1.375396 GACCCACACATAGCGCACA 60.375 57.895 11.47 0.00 0.00 4.57
86 87 1.361668 GACCCACACATAGCGCACAG 61.362 60.000 11.47 0.00 0.00 3.66
104 105 3.359523 CAGCAGCGCACCACACAT 61.360 61.111 11.47 0.00 0.00 3.21
105 106 2.034317 CAGCAGCGCACCACACATA 61.034 57.895 11.47 0.00 0.00 2.29
106 107 1.078214 AGCAGCGCACCACACATAT 60.078 52.632 11.47 0.00 0.00 1.78
107 108 1.091771 AGCAGCGCACCACACATATC 61.092 55.000 11.47 0.00 0.00 1.63
108 109 1.368345 GCAGCGCACCACACATATCA 61.368 55.000 11.47 0.00 0.00 2.15
109 110 0.654160 CAGCGCACCACACATATCAG 59.346 55.000 11.47 0.00 0.00 2.90
110 111 0.462581 AGCGCACCACACATATCAGG 60.463 55.000 11.47 0.00 0.00 3.86
111 112 2.016961 CGCACCACACATATCAGGC 58.983 57.895 0.00 0.00 0.00 4.85
112 113 0.744057 CGCACCACACATATCAGGCA 60.744 55.000 0.00 0.00 0.00 4.75
113 114 1.462616 GCACCACACATATCAGGCAA 58.537 50.000 0.00 0.00 0.00 4.52
114 115 1.402968 GCACCACACATATCAGGCAAG 59.597 52.381 0.00 0.00 0.00 4.01
115 116 2.940971 GCACCACACATATCAGGCAAGA 60.941 50.000 0.00 0.00 0.00 3.02
116 117 2.679837 CACCACACATATCAGGCAAGAC 59.320 50.000 0.00 0.00 0.00 3.01
117 118 2.305635 ACCACACATATCAGGCAAGACA 59.694 45.455 0.00 0.00 0.00 3.41
118 119 3.054139 ACCACACATATCAGGCAAGACAT 60.054 43.478 0.00 0.00 0.00 3.06
119 120 4.164030 ACCACACATATCAGGCAAGACATA 59.836 41.667 0.00 0.00 0.00 2.29
120 121 5.125356 CCACACATATCAGGCAAGACATAA 58.875 41.667 0.00 0.00 0.00 1.90
121 122 5.589855 CCACACATATCAGGCAAGACATAAA 59.410 40.000 0.00 0.00 0.00 1.40
122 123 6.095300 CCACACATATCAGGCAAGACATAAAA 59.905 38.462 0.00 0.00 0.00 1.52
123 124 6.968904 CACACATATCAGGCAAGACATAAAAC 59.031 38.462 0.00 0.00 0.00 2.43
124 125 6.183360 ACACATATCAGGCAAGACATAAAACG 60.183 38.462 0.00 0.00 0.00 3.60
125 126 5.880332 ACATATCAGGCAAGACATAAAACGT 59.120 36.000 0.00 0.00 0.00 3.99
126 127 7.011016 CACATATCAGGCAAGACATAAAACGTA 59.989 37.037 0.00 0.00 0.00 3.57
127 128 7.224753 ACATATCAGGCAAGACATAAAACGTAG 59.775 37.037 0.00 0.00 0.00 3.51
128 129 4.250464 TCAGGCAAGACATAAAACGTAGG 58.750 43.478 0.00 0.00 0.00 3.18
129 130 4.000988 CAGGCAAGACATAAAACGTAGGT 58.999 43.478 0.00 0.00 0.00 3.08
130 131 4.454504 CAGGCAAGACATAAAACGTAGGTT 59.545 41.667 0.00 0.00 38.22 3.50
132 133 5.048991 AGGCAAGACATAAAACGTAGGTTTG 60.049 40.000 13.87 5.73 45.35 2.93
133 134 5.278120 GGCAAGACATAAAACGTAGGTTTGT 60.278 40.000 13.87 8.78 45.35 2.83
134 135 6.203647 GCAAGACATAAAACGTAGGTTTGTT 58.796 36.000 13.87 2.78 45.35 2.83
135 136 7.354257 GCAAGACATAAAACGTAGGTTTGTTA 58.646 34.615 13.87 4.86 45.35 2.41
136 137 8.019094 GCAAGACATAAAACGTAGGTTTGTTAT 58.981 33.333 13.87 6.82 45.35 1.89
137 138 9.887406 CAAGACATAAAACGTAGGTTTGTTATT 57.113 29.630 13.87 5.96 45.35 1.40
139 140 9.275398 AGACATAAAACGTAGGTTTGTTATTCA 57.725 29.630 13.87 0.00 45.35 2.57
141 142 9.834628 ACATAAAACGTAGGTTTGTTATTCATG 57.165 29.630 13.87 10.61 45.35 3.07
142 143 9.834628 CATAAAACGTAGGTTTGTTATTCATGT 57.165 29.630 13.87 0.00 45.35 3.21
146 147 9.887406 AAACGTAGGTTTGTTATTCATGTAAAG 57.113 29.630 12.50 0.00 44.43 1.85
147 148 8.036273 ACGTAGGTTTGTTATTCATGTAAAGG 57.964 34.615 0.00 0.00 0.00 3.11
148 149 7.879160 ACGTAGGTTTGTTATTCATGTAAAGGA 59.121 33.333 0.00 0.00 0.00 3.36
149 150 8.723311 CGTAGGTTTGTTATTCATGTAAAGGAA 58.277 33.333 0.00 0.00 0.00 3.36
155 156 9.771534 TTTGTTATTCATGTAAAGGAAAAAGGG 57.228 29.630 0.00 0.00 0.00 3.95
156 157 7.382898 TGTTATTCATGTAAAGGAAAAAGGGC 58.617 34.615 0.00 0.00 0.00 5.19
157 158 7.015682 TGTTATTCATGTAAAGGAAAAAGGGCA 59.984 33.333 0.00 0.00 0.00 5.36
158 159 6.625532 ATTCATGTAAAGGAAAAAGGGCAT 57.374 33.333 0.00 0.00 0.00 4.40
159 160 5.404466 TCATGTAAAGGAAAAAGGGCATG 57.596 39.130 0.00 0.00 35.25 4.06
160 161 4.222588 TCATGTAAAGGAAAAAGGGCATGG 59.777 41.667 0.00 0.00 34.84 3.66
161 162 2.301583 TGTAAAGGAAAAAGGGCATGGC 59.698 45.455 11.56 11.56 0.00 4.40
162 163 1.733385 AAAGGAAAAAGGGCATGGCT 58.267 45.000 19.78 2.16 0.00 4.75
163 164 1.733385 AAGGAAAAAGGGCATGGCTT 58.267 45.000 19.78 9.00 0.00 4.35
164 165 0.978907 AGGAAAAAGGGCATGGCTTG 59.021 50.000 19.78 0.00 0.00 4.01
165 166 0.975887 GGAAAAAGGGCATGGCTTGA 59.024 50.000 19.78 0.00 0.00 3.02
166 167 1.066645 GGAAAAAGGGCATGGCTTGAG 60.067 52.381 19.78 0.00 0.00 3.02
167 168 1.895131 GAAAAAGGGCATGGCTTGAGA 59.105 47.619 19.78 0.00 0.00 3.27
168 169 2.242882 AAAAGGGCATGGCTTGAGAT 57.757 45.000 19.78 0.00 0.00 2.75
169 170 2.242882 AAAGGGCATGGCTTGAGATT 57.757 45.000 19.78 0.00 0.00 2.40
170 171 2.242882 AAGGGCATGGCTTGAGATTT 57.757 45.000 19.78 0.00 0.00 2.17
171 172 3.386932 AAGGGCATGGCTTGAGATTTA 57.613 42.857 19.78 0.00 0.00 1.40
172 173 3.607490 AGGGCATGGCTTGAGATTTAT 57.393 42.857 19.78 0.00 0.00 1.40
173 174 3.919834 AGGGCATGGCTTGAGATTTATT 58.080 40.909 19.78 0.00 0.00 1.40
174 175 5.065613 AGGGCATGGCTTGAGATTTATTA 57.934 39.130 19.78 0.00 0.00 0.98
175 176 4.829492 AGGGCATGGCTTGAGATTTATTAC 59.171 41.667 19.78 0.00 0.00 1.89
176 177 4.021981 GGGCATGGCTTGAGATTTATTACC 60.022 45.833 19.78 0.00 0.00 2.85
177 178 4.320494 GGCATGGCTTGAGATTTATTACCG 60.320 45.833 12.86 0.00 0.00 4.02
178 179 4.787598 CATGGCTTGAGATTTATTACCGC 58.212 43.478 0.00 0.00 0.00 5.68
179 180 3.879998 TGGCTTGAGATTTATTACCGCA 58.120 40.909 0.00 0.00 0.00 5.69
180 181 4.460263 TGGCTTGAGATTTATTACCGCAT 58.540 39.130 0.00 0.00 0.00 4.73
181 182 5.616270 TGGCTTGAGATTTATTACCGCATA 58.384 37.500 0.00 0.00 0.00 3.14
182 183 6.058833 TGGCTTGAGATTTATTACCGCATAA 58.941 36.000 0.00 0.00 0.00 1.90
183 184 6.204688 TGGCTTGAGATTTATTACCGCATAAG 59.795 38.462 0.00 0.00 0.00 1.73
184 185 6.348540 GGCTTGAGATTTATTACCGCATAAGG 60.349 42.308 0.00 0.00 37.30 2.69
185 186 6.348540 GCTTGAGATTTATTACCGCATAAGGG 60.349 42.308 0.00 0.00 35.02 3.95
186 187 6.428083 TGAGATTTATTACCGCATAAGGGA 57.572 37.500 0.00 0.00 35.02 4.20
187 188 6.464222 TGAGATTTATTACCGCATAAGGGAG 58.536 40.000 0.00 0.00 35.02 4.30
188 189 6.269077 TGAGATTTATTACCGCATAAGGGAGA 59.731 38.462 0.00 0.00 35.02 3.71
189 190 6.465084 AGATTTATTACCGCATAAGGGAGAC 58.535 40.000 0.00 0.00 35.02 3.36
190 191 5.881923 TTTATTACCGCATAAGGGAGACT 57.118 39.130 0.00 0.00 35.02 3.24
191 192 3.753294 ATTACCGCATAAGGGAGACTG 57.247 47.619 0.00 0.00 35.02 3.51
192 193 2.154567 TACCGCATAAGGGAGACTGT 57.845 50.000 0.00 0.00 35.02 3.55
193 194 1.276622 ACCGCATAAGGGAGACTGTT 58.723 50.000 0.00 0.00 35.02 3.16
194 195 1.066143 ACCGCATAAGGGAGACTGTTG 60.066 52.381 0.00 0.00 35.02 3.33
195 196 1.009829 CGCATAAGGGAGACTGTTGC 58.990 55.000 0.00 0.00 35.60 4.17
196 197 1.406069 CGCATAAGGGAGACTGTTGCT 60.406 52.381 0.00 0.00 36.35 3.91
197 198 2.012673 GCATAAGGGAGACTGTTGCTG 58.987 52.381 0.00 0.00 35.88 4.41
198 199 2.012673 CATAAGGGAGACTGTTGCTGC 58.987 52.381 0.00 0.00 0.00 5.25
199 200 0.324943 TAAGGGAGACTGTTGCTGCC 59.675 55.000 0.00 0.00 43.45 4.85
200 201 2.743928 GGGAGACTGTTGCTGCCG 60.744 66.667 0.00 0.00 34.11 5.69
201 202 2.343758 GGAGACTGTTGCTGCCGA 59.656 61.111 0.00 0.00 0.00 5.54
202 203 1.301716 GGAGACTGTTGCTGCCGAA 60.302 57.895 0.00 0.00 0.00 4.30
203 204 1.294659 GGAGACTGTTGCTGCCGAAG 61.295 60.000 0.00 0.00 0.00 3.79
217 218 3.650950 GAAGCACAGGGGCAGGGA 61.651 66.667 0.00 0.00 35.83 4.20
218 219 3.635268 GAAGCACAGGGGCAGGGAG 62.635 68.421 0.00 0.00 35.83 4.30
226 227 3.971702 GGGCAGGGAGGCACTGTT 61.972 66.667 0.00 0.00 46.44 3.16
227 228 2.674380 GGCAGGGAGGCACTGTTG 60.674 66.667 0.00 0.00 41.55 3.33
228 229 2.431683 GCAGGGAGGCACTGTTGA 59.568 61.111 0.00 0.00 41.55 3.18
229 230 1.673665 GCAGGGAGGCACTGTTGAG 60.674 63.158 0.00 0.00 41.55 3.02
230 231 1.673665 CAGGGAGGCACTGTTGAGC 60.674 63.158 0.00 0.00 41.55 4.26
231 232 1.845205 AGGGAGGCACTGTTGAGCT 60.845 57.895 0.00 0.00 41.55 4.09
232 233 0.545309 AGGGAGGCACTGTTGAGCTA 60.545 55.000 0.00 0.00 41.55 3.32
233 234 0.391793 GGGAGGCACTGTTGAGCTAC 60.392 60.000 0.00 0.00 41.55 3.58
234 235 0.391793 GGAGGCACTGTTGAGCTACC 60.392 60.000 0.00 0.00 41.55 3.18
235 236 0.737715 GAGGCACTGTTGAGCTACCG 60.738 60.000 0.00 0.00 41.55 4.02
236 237 1.741770 GGCACTGTTGAGCTACCGG 60.742 63.158 0.00 0.00 0.00 5.28
237 238 1.741770 GCACTGTTGAGCTACCGGG 60.742 63.158 6.32 0.00 0.00 5.73
238 239 1.741770 CACTGTTGAGCTACCGGGC 60.742 63.158 6.32 0.00 0.00 6.13
239 240 2.214216 ACTGTTGAGCTACCGGGCA 61.214 57.895 6.32 0.00 34.17 5.36
240 241 1.448540 CTGTTGAGCTACCGGGCAG 60.449 63.158 6.32 3.23 34.17 4.85
255 256 4.003788 CAGGTTGGGTCGTCGCCT 62.004 66.667 5.82 0.00 0.00 5.52
256 257 3.692406 AGGTTGGGTCGTCGCCTC 61.692 66.667 5.82 0.00 0.00 4.70
257 258 4.754667 GGTTGGGTCGTCGCCTCC 62.755 72.222 5.82 0.21 0.00 4.30
258 259 3.692406 GTTGGGTCGTCGCCTCCT 61.692 66.667 5.82 0.00 0.00 3.69
259 260 2.036098 TTGGGTCGTCGCCTCCTA 59.964 61.111 5.82 0.00 0.00 2.94
260 261 2.345760 TTGGGTCGTCGCCTCCTAC 61.346 63.158 5.82 0.00 0.00 3.18
261 262 2.753043 GGGTCGTCGCCTCCTACA 60.753 66.667 5.82 0.00 0.00 2.74
262 263 2.488820 GGTCGTCGCCTCCTACAC 59.511 66.667 0.00 0.00 0.00 2.90
263 264 2.488820 GTCGTCGCCTCCTACACC 59.511 66.667 0.00 0.00 0.00 4.16
264 265 2.753043 TCGTCGCCTCCTACACCC 60.753 66.667 0.00 0.00 0.00 4.61
265 266 3.066190 CGTCGCCTCCTACACCCA 61.066 66.667 0.00 0.00 0.00 4.51
266 267 2.423898 CGTCGCCTCCTACACCCAT 61.424 63.158 0.00 0.00 0.00 4.00
267 268 1.105167 CGTCGCCTCCTACACCCATA 61.105 60.000 0.00 0.00 0.00 2.74
268 269 1.339097 GTCGCCTCCTACACCCATAT 58.661 55.000 0.00 0.00 0.00 1.78
269 270 1.000955 GTCGCCTCCTACACCCATATG 59.999 57.143 0.00 0.00 0.00 1.78
270 271 0.320771 CGCCTCCTACACCCATATGC 60.321 60.000 0.00 0.00 0.00 3.14
271 272 0.764890 GCCTCCTACACCCATATGCA 59.235 55.000 0.00 0.00 0.00 3.96
272 273 1.352352 GCCTCCTACACCCATATGCAT 59.648 52.381 3.79 3.79 0.00 3.96
273 274 2.877300 GCCTCCTACACCCATATGCATG 60.877 54.545 10.16 0.00 0.00 4.06
274 275 2.373169 CCTCCTACACCCATATGCATGT 59.627 50.000 10.16 12.93 0.00 3.21
275 276 3.405831 CTCCTACACCCATATGCATGTG 58.594 50.000 15.95 15.95 34.92 3.21
276 277 3.044894 TCCTACACCCATATGCATGTGA 58.955 45.455 23.52 3.50 33.08 3.58
400 401 1.005512 AAAAACCCAAATCGCCCGC 60.006 52.632 0.00 0.00 0.00 6.13
2174 2186 4.132336 CTGATGTGAAGATATGGGGTGTG 58.868 47.826 0.00 0.00 0.00 3.82
2808 2821 2.303022 CACCCTTCTACCAGAGCAAAGA 59.697 50.000 0.00 0.00 0.00 2.52
2895 2910 5.463154 AGAGTCTGAGCTATGTATCCCTTT 58.537 41.667 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.723298 TTTCCACTAACAATTCCACATTGT 57.277 33.333 0.00 0.00 43.35 2.71
1 2 9.304731 CATATTTCCACTAACAATTCCACATTG 57.695 33.333 0.00 0.00 35.29 2.82
2 3 9.253832 TCATATTTCCACTAACAATTCCACATT 57.746 29.630 0.00 0.00 0.00 2.71
3 4 8.821686 TCATATTTCCACTAACAATTCCACAT 57.178 30.769 0.00 0.00 0.00 3.21
4 5 8.642935 TTCATATTTCCACTAACAATTCCACA 57.357 30.769 0.00 0.00 0.00 4.17
5 6 9.353999 GTTTCATATTTCCACTAACAATTCCAC 57.646 33.333 0.00 0.00 0.00 4.02
6 7 9.083422 TGTTTCATATTTCCACTAACAATTCCA 57.917 29.630 0.00 0.00 0.00 3.53
11 12 9.689976 CAACATGTTTCATATTTCCACTAACAA 57.310 29.630 8.77 0.00 0.00 2.83
12 13 9.072375 TCAACATGTTTCATATTTCCACTAACA 57.928 29.630 8.77 0.00 0.00 2.41
13 14 9.341899 GTCAACATGTTTCATATTTCCACTAAC 57.658 33.333 8.77 0.00 0.00 2.34
14 15 9.072375 TGTCAACATGTTTCATATTTCCACTAA 57.928 29.630 8.77 0.00 0.00 2.24
15 16 8.628630 TGTCAACATGTTTCATATTTCCACTA 57.371 30.769 8.77 0.00 0.00 2.74
16 17 7.523293 TGTCAACATGTTTCATATTTCCACT 57.477 32.000 8.77 0.00 0.00 4.00
17 18 8.761575 AATGTCAACATGTTTCATATTTCCAC 57.238 30.769 19.69 3.62 36.56 4.02
18 19 9.775854 AAAATGTCAACATGTTTCATATTTCCA 57.224 25.926 19.69 5.04 36.56 3.53
22 23 8.991026 CCACAAAATGTCAACATGTTTCATATT 58.009 29.630 19.69 12.37 36.56 1.28
23 24 8.366401 TCCACAAAATGTCAACATGTTTCATAT 58.634 29.630 19.69 12.59 36.56 1.78
24 25 7.720442 TCCACAAAATGTCAACATGTTTCATA 58.280 30.769 19.69 6.39 36.56 2.15
25 26 6.580788 TCCACAAAATGTCAACATGTTTCAT 58.419 32.000 8.77 13.37 36.56 2.57
26 27 5.970592 TCCACAAAATGTCAACATGTTTCA 58.029 33.333 8.77 11.63 36.56 2.69
27 28 6.509997 GCTTCCACAAAATGTCAACATGTTTC 60.510 38.462 8.77 5.99 36.56 2.78
28 29 5.294060 GCTTCCACAAAATGTCAACATGTTT 59.706 36.000 8.77 0.00 36.56 2.83
29 30 4.810491 GCTTCCACAAAATGTCAACATGTT 59.190 37.500 4.92 4.92 36.56 2.71
30 31 4.370917 GCTTCCACAAAATGTCAACATGT 58.629 39.130 0.00 0.00 36.56 3.21
31 32 3.742369 GGCTTCCACAAAATGTCAACATG 59.258 43.478 0.00 0.00 36.56 3.21
32 33 3.387374 TGGCTTCCACAAAATGTCAACAT 59.613 39.130 0.00 0.00 38.41 2.71
33 34 2.762887 TGGCTTCCACAAAATGTCAACA 59.237 40.909 0.00 0.00 0.00 3.33
34 35 3.451141 TGGCTTCCACAAAATGTCAAC 57.549 42.857 0.00 0.00 0.00 3.18
35 36 4.187694 GTTTGGCTTCCACAAAATGTCAA 58.812 39.130 0.00 0.00 39.29 3.18
36 37 3.196469 TGTTTGGCTTCCACAAAATGTCA 59.804 39.130 0.00 0.00 39.29 3.58
37 38 3.791245 TGTTTGGCTTCCACAAAATGTC 58.209 40.909 0.00 0.00 39.29 3.06
38 39 3.902881 TGTTTGGCTTCCACAAAATGT 57.097 38.095 0.00 0.00 39.29 2.71
39 40 4.190772 AGTTGTTTGGCTTCCACAAAATG 58.809 39.130 0.00 0.00 39.29 2.32
40 41 4.486125 AGTTGTTTGGCTTCCACAAAAT 57.514 36.364 0.00 0.00 39.29 1.82
41 42 3.971245 AGTTGTTTGGCTTCCACAAAA 57.029 38.095 0.00 0.00 39.29 2.44
42 43 4.274147 TCTAGTTGTTTGGCTTCCACAAA 58.726 39.130 0.00 0.00 35.62 2.83
43 44 3.882888 CTCTAGTTGTTTGGCTTCCACAA 59.117 43.478 0.00 0.00 30.78 3.33
44 45 3.476552 CTCTAGTTGTTTGGCTTCCACA 58.523 45.455 0.00 0.00 30.78 4.17
45 46 2.814336 CCTCTAGTTGTTTGGCTTCCAC 59.186 50.000 0.00 0.00 30.78 4.02
46 47 2.224769 CCCTCTAGTTGTTTGGCTTCCA 60.225 50.000 0.00 0.00 0.00 3.53
47 48 2.039879 TCCCTCTAGTTGTTTGGCTTCC 59.960 50.000 0.00 0.00 0.00 3.46
48 49 3.075148 GTCCCTCTAGTTGTTTGGCTTC 58.925 50.000 0.00 0.00 0.00 3.86
49 50 2.224793 GGTCCCTCTAGTTGTTTGGCTT 60.225 50.000 0.00 0.00 0.00 4.35
50 51 1.351350 GGTCCCTCTAGTTGTTTGGCT 59.649 52.381 0.00 0.00 0.00 4.75
51 52 1.613520 GGGTCCCTCTAGTTGTTTGGC 60.614 57.143 0.00 0.00 0.00 4.52
52 53 1.702957 TGGGTCCCTCTAGTTGTTTGG 59.297 52.381 10.00 0.00 0.00 3.28
53 54 2.105821 TGTGGGTCCCTCTAGTTGTTTG 59.894 50.000 10.00 0.00 0.00 2.93
54 55 2.105993 GTGTGGGTCCCTCTAGTTGTTT 59.894 50.000 10.00 0.00 0.00 2.83
55 56 1.697982 GTGTGGGTCCCTCTAGTTGTT 59.302 52.381 10.00 0.00 0.00 2.83
56 57 1.349067 GTGTGGGTCCCTCTAGTTGT 58.651 55.000 10.00 0.00 0.00 3.32
57 58 1.348064 TGTGTGGGTCCCTCTAGTTG 58.652 55.000 10.00 0.00 0.00 3.16
58 59 2.344093 ATGTGTGGGTCCCTCTAGTT 57.656 50.000 10.00 0.00 0.00 2.24
59 60 2.955461 GCTATGTGTGGGTCCCTCTAGT 60.955 54.545 10.00 0.00 0.00 2.57
60 61 1.689273 GCTATGTGTGGGTCCCTCTAG 59.311 57.143 10.00 5.06 0.00 2.43
61 62 1.789523 GCTATGTGTGGGTCCCTCTA 58.210 55.000 10.00 0.00 0.00 2.43
62 63 1.330655 CGCTATGTGTGGGTCCCTCT 61.331 60.000 10.00 0.00 0.00 3.69
63 64 1.144057 CGCTATGTGTGGGTCCCTC 59.856 63.158 10.00 6.20 0.00 4.30
64 65 3.031417 GCGCTATGTGTGGGTCCCT 62.031 63.158 10.00 0.00 0.00 4.20
65 66 2.513897 GCGCTATGTGTGGGTCCC 60.514 66.667 0.00 0.00 0.00 4.46
66 67 2.106683 GTGCGCTATGTGTGGGTCC 61.107 63.158 9.73 0.00 0.00 4.46
67 68 1.361668 CTGTGCGCTATGTGTGGGTC 61.362 60.000 9.73 0.00 0.00 4.46
68 69 1.375908 CTGTGCGCTATGTGTGGGT 60.376 57.895 9.73 0.00 0.00 4.51
69 70 2.753966 GCTGTGCGCTATGTGTGGG 61.754 63.158 9.73 0.00 35.14 4.61
70 71 1.974249 CTGCTGTGCGCTATGTGTGG 61.974 60.000 9.73 0.00 40.11 4.17
71 72 1.422662 CTGCTGTGCGCTATGTGTG 59.577 57.895 9.73 0.00 40.11 3.82
72 73 2.393768 GCTGCTGTGCGCTATGTGT 61.394 57.895 9.73 0.00 40.11 3.72
73 74 2.305826 CTGCTGCTGTGCGCTATGTG 62.306 60.000 9.73 0.00 40.11 3.21
74 75 2.046988 TGCTGCTGTGCGCTATGT 60.047 55.556 9.73 0.00 40.11 2.29
75 76 2.707646 CTGCTGCTGTGCGCTATG 59.292 61.111 9.73 0.00 40.11 2.23
76 77 3.200593 GCTGCTGCTGTGCGCTAT 61.201 61.111 9.73 0.00 40.11 2.97
87 88 1.371337 ATATGTGTGGTGCGCTGCTG 61.371 55.000 9.73 0.00 0.00 4.41
88 89 1.078214 ATATGTGTGGTGCGCTGCT 60.078 52.632 9.73 0.00 0.00 4.24
89 90 1.353103 GATATGTGTGGTGCGCTGC 59.647 57.895 9.73 0.69 0.00 5.25
90 91 0.654160 CTGATATGTGTGGTGCGCTG 59.346 55.000 9.73 0.00 0.00 5.18
91 92 0.462581 CCTGATATGTGTGGTGCGCT 60.463 55.000 9.73 0.00 0.00 5.92
92 93 2.016961 CCTGATATGTGTGGTGCGC 58.983 57.895 0.00 0.00 0.00 6.09
93 94 0.744057 TGCCTGATATGTGTGGTGCG 60.744 55.000 0.00 0.00 0.00 5.34
94 95 1.402968 CTTGCCTGATATGTGTGGTGC 59.597 52.381 0.00 0.00 0.00 5.01
95 96 2.679837 GTCTTGCCTGATATGTGTGGTG 59.320 50.000 0.00 0.00 0.00 4.17
96 97 2.305635 TGTCTTGCCTGATATGTGTGGT 59.694 45.455 0.00 0.00 0.00 4.16
97 98 2.989909 TGTCTTGCCTGATATGTGTGG 58.010 47.619 0.00 0.00 0.00 4.17
98 99 6.682423 TTTATGTCTTGCCTGATATGTGTG 57.318 37.500 0.00 0.00 0.00 3.82
99 100 6.183360 CGTTTTATGTCTTGCCTGATATGTGT 60.183 38.462 0.00 0.00 0.00 3.72
100 101 6.183360 ACGTTTTATGTCTTGCCTGATATGTG 60.183 38.462 0.00 0.00 0.00 3.21
101 102 5.880332 ACGTTTTATGTCTTGCCTGATATGT 59.120 36.000 0.00 0.00 0.00 2.29
102 103 6.363577 ACGTTTTATGTCTTGCCTGATATG 57.636 37.500 0.00 0.00 0.00 1.78
103 104 6.706270 CCTACGTTTTATGTCTTGCCTGATAT 59.294 38.462 0.00 0.00 0.00 1.63
104 105 6.046593 CCTACGTTTTATGTCTTGCCTGATA 58.953 40.000 0.00 0.00 0.00 2.15
105 106 4.876107 CCTACGTTTTATGTCTTGCCTGAT 59.124 41.667 0.00 0.00 0.00 2.90
106 107 4.250464 CCTACGTTTTATGTCTTGCCTGA 58.750 43.478 0.00 0.00 0.00 3.86
107 108 4.000988 ACCTACGTTTTATGTCTTGCCTG 58.999 43.478 0.00 0.00 0.00 4.85
108 109 4.281898 ACCTACGTTTTATGTCTTGCCT 57.718 40.909 0.00 0.00 0.00 4.75
109 110 5.151389 CAAACCTACGTTTTATGTCTTGCC 58.849 41.667 0.00 0.00 40.28 4.52
110 111 5.754778 ACAAACCTACGTTTTATGTCTTGC 58.245 37.500 0.00 0.00 40.28 4.01
111 112 9.887406 AATAACAAACCTACGTTTTATGTCTTG 57.113 29.630 0.00 0.00 40.28 3.02
113 114 9.275398 TGAATAACAAACCTACGTTTTATGTCT 57.725 29.630 0.00 0.00 40.28 3.41
115 116 9.834628 CATGAATAACAAACCTACGTTTTATGT 57.165 29.630 0.00 0.00 40.28 2.29
116 117 9.834628 ACATGAATAACAAACCTACGTTTTATG 57.165 29.630 0.00 0.00 40.28 1.90
120 121 9.887406 CTTTACATGAATAACAAACCTACGTTT 57.113 29.630 0.00 0.00 43.09 3.60
121 122 8.508875 CCTTTACATGAATAACAAACCTACGTT 58.491 33.333 0.00 0.00 0.00 3.99
122 123 7.879160 TCCTTTACATGAATAACAAACCTACGT 59.121 33.333 0.00 0.00 0.00 3.57
123 124 8.259049 TCCTTTACATGAATAACAAACCTACG 57.741 34.615 0.00 0.00 0.00 3.51
129 130 9.771534 CCCTTTTTCCTTTACATGAATAACAAA 57.228 29.630 0.00 0.00 0.00 2.83
130 131 7.875554 GCCCTTTTTCCTTTACATGAATAACAA 59.124 33.333 0.00 0.00 0.00 2.83
131 132 7.015682 TGCCCTTTTTCCTTTACATGAATAACA 59.984 33.333 0.00 0.00 0.00 2.41
132 133 7.382898 TGCCCTTTTTCCTTTACATGAATAAC 58.617 34.615 0.00 0.00 0.00 1.89
133 134 7.546250 TGCCCTTTTTCCTTTACATGAATAA 57.454 32.000 0.00 0.00 0.00 1.40
134 135 7.364585 CCATGCCCTTTTTCCTTTACATGAATA 60.365 37.037 0.00 0.00 36.60 1.75
135 136 6.408869 CATGCCCTTTTTCCTTTACATGAAT 58.591 36.000 0.00 0.00 36.60 2.57
136 137 5.279910 CCATGCCCTTTTTCCTTTACATGAA 60.280 40.000 0.00 0.00 36.60 2.57
137 138 4.222588 CCATGCCCTTTTTCCTTTACATGA 59.777 41.667 0.00 0.00 36.60 3.07
138 139 4.506758 CCATGCCCTTTTTCCTTTACATG 58.493 43.478 0.00 0.00 34.78 3.21
139 140 3.055167 GCCATGCCCTTTTTCCTTTACAT 60.055 43.478 0.00 0.00 0.00 2.29
140 141 2.301583 GCCATGCCCTTTTTCCTTTACA 59.698 45.455 0.00 0.00 0.00 2.41
141 142 2.567169 AGCCATGCCCTTTTTCCTTTAC 59.433 45.455 0.00 0.00 0.00 2.01
142 143 2.901291 AGCCATGCCCTTTTTCCTTTA 58.099 42.857 0.00 0.00 0.00 1.85
143 144 1.733385 AGCCATGCCCTTTTTCCTTT 58.267 45.000 0.00 0.00 0.00 3.11
144 145 1.348696 CAAGCCATGCCCTTTTTCCTT 59.651 47.619 0.00 0.00 0.00 3.36
145 146 0.978907 CAAGCCATGCCCTTTTTCCT 59.021 50.000 0.00 0.00 0.00 3.36
146 147 0.975887 TCAAGCCATGCCCTTTTTCC 59.024 50.000 0.00 0.00 0.00 3.13
147 148 1.895131 TCTCAAGCCATGCCCTTTTTC 59.105 47.619 0.00 0.00 0.00 2.29
148 149 2.014010 TCTCAAGCCATGCCCTTTTT 57.986 45.000 0.00 0.00 0.00 1.94
149 150 2.242882 ATCTCAAGCCATGCCCTTTT 57.757 45.000 0.00 0.00 0.00 2.27
150 151 2.242882 AATCTCAAGCCATGCCCTTT 57.757 45.000 0.00 0.00 0.00 3.11
151 152 2.242882 AAATCTCAAGCCATGCCCTT 57.757 45.000 0.00 0.00 0.00 3.95
152 153 3.607490 ATAAATCTCAAGCCATGCCCT 57.393 42.857 0.00 0.00 0.00 5.19
153 154 4.021981 GGTAATAAATCTCAAGCCATGCCC 60.022 45.833 0.00 0.00 0.00 5.36
154 155 4.320494 CGGTAATAAATCTCAAGCCATGCC 60.320 45.833 0.00 0.00 0.00 4.40
155 156 4.787598 CGGTAATAAATCTCAAGCCATGC 58.212 43.478 0.00 0.00 0.00 4.06
156 157 4.275689 TGCGGTAATAAATCTCAAGCCATG 59.724 41.667 0.00 0.00 0.00 3.66
157 158 4.460263 TGCGGTAATAAATCTCAAGCCAT 58.540 39.130 0.00 0.00 0.00 4.40
158 159 3.879998 TGCGGTAATAAATCTCAAGCCA 58.120 40.909 0.00 0.00 0.00 4.75
159 160 6.348540 CCTTATGCGGTAATAAATCTCAAGCC 60.349 42.308 0.00 0.00 0.00 4.35
160 161 6.348540 CCCTTATGCGGTAATAAATCTCAAGC 60.349 42.308 0.00 0.00 0.00 4.01
161 162 6.934645 TCCCTTATGCGGTAATAAATCTCAAG 59.065 38.462 0.00 0.00 0.00 3.02
162 163 6.833041 TCCCTTATGCGGTAATAAATCTCAA 58.167 36.000 0.00 0.00 0.00 3.02
163 164 6.269077 TCTCCCTTATGCGGTAATAAATCTCA 59.731 38.462 0.00 0.00 0.00 3.27
164 165 6.590677 GTCTCCCTTATGCGGTAATAAATCTC 59.409 42.308 0.00 0.00 0.00 2.75
165 166 6.270231 AGTCTCCCTTATGCGGTAATAAATCT 59.730 38.462 0.00 0.00 0.00 2.40
166 167 6.369065 CAGTCTCCCTTATGCGGTAATAAATC 59.631 42.308 0.00 0.00 0.00 2.17
167 168 6.183361 ACAGTCTCCCTTATGCGGTAATAAAT 60.183 38.462 0.00 0.00 0.00 1.40
168 169 5.129815 ACAGTCTCCCTTATGCGGTAATAAA 59.870 40.000 0.00 0.00 0.00 1.40
169 170 4.652421 ACAGTCTCCCTTATGCGGTAATAA 59.348 41.667 0.00 0.00 0.00 1.40
170 171 4.220724 ACAGTCTCCCTTATGCGGTAATA 58.779 43.478 0.00 0.00 0.00 0.98
171 172 3.039011 ACAGTCTCCCTTATGCGGTAAT 58.961 45.455 0.00 0.00 0.00 1.89
172 173 2.463752 ACAGTCTCCCTTATGCGGTAA 58.536 47.619 0.00 0.00 0.00 2.85
173 174 2.154567 ACAGTCTCCCTTATGCGGTA 57.845 50.000 0.00 0.00 0.00 4.02
174 175 1.066143 CAACAGTCTCCCTTATGCGGT 60.066 52.381 0.00 0.00 0.00 5.68
175 176 1.656652 CAACAGTCTCCCTTATGCGG 58.343 55.000 0.00 0.00 0.00 5.69
176 177 1.009829 GCAACAGTCTCCCTTATGCG 58.990 55.000 0.00 0.00 0.00 4.73
177 178 2.012673 CAGCAACAGTCTCCCTTATGC 58.987 52.381 0.00 0.00 34.06 3.14
178 179 2.012673 GCAGCAACAGTCTCCCTTATG 58.987 52.381 0.00 0.00 0.00 1.90
179 180 1.065126 GGCAGCAACAGTCTCCCTTAT 60.065 52.381 0.00 0.00 0.00 1.73
180 181 0.324943 GGCAGCAACAGTCTCCCTTA 59.675 55.000 0.00 0.00 0.00 2.69
181 182 1.073897 GGCAGCAACAGTCTCCCTT 59.926 57.895 0.00 0.00 0.00 3.95
182 183 2.753029 GGCAGCAACAGTCTCCCT 59.247 61.111 0.00 0.00 0.00 4.20
183 184 2.731691 TTCGGCAGCAACAGTCTCCC 62.732 60.000 0.00 0.00 0.00 4.30
184 185 1.294659 CTTCGGCAGCAACAGTCTCC 61.295 60.000 0.00 0.00 0.00 3.71
185 186 2.157421 CTTCGGCAGCAACAGTCTC 58.843 57.895 0.00 0.00 0.00 3.36
186 187 4.368391 CTTCGGCAGCAACAGTCT 57.632 55.556 0.00 0.00 0.00 3.24
200 201 3.635268 CTCCCTGCCCCTGTGCTTC 62.635 68.421 0.00 0.00 0.00 3.86
201 202 3.655211 CTCCCTGCCCCTGTGCTT 61.655 66.667 0.00 0.00 0.00 3.91
209 210 3.971702 AACAGTGCCTCCCTGCCC 61.972 66.667 0.00 0.00 33.09 5.36
210 211 2.674380 CAACAGTGCCTCCCTGCC 60.674 66.667 0.00 0.00 33.09 4.85
211 212 1.673665 CTCAACAGTGCCTCCCTGC 60.674 63.158 0.00 0.00 33.09 4.85
212 213 1.673665 GCTCAACAGTGCCTCCCTG 60.674 63.158 0.00 0.00 36.01 4.45
213 214 0.545309 TAGCTCAACAGTGCCTCCCT 60.545 55.000 0.00 0.00 0.00 4.20
214 215 0.391793 GTAGCTCAACAGTGCCTCCC 60.392 60.000 0.00 0.00 0.00 4.30
215 216 0.391793 GGTAGCTCAACAGTGCCTCC 60.392 60.000 0.00 0.00 0.00 4.30
216 217 0.737715 CGGTAGCTCAACAGTGCCTC 60.738 60.000 0.00 0.00 0.00 4.70
217 218 1.293498 CGGTAGCTCAACAGTGCCT 59.707 57.895 0.00 0.00 0.00 4.75
218 219 1.741770 CCGGTAGCTCAACAGTGCC 60.742 63.158 0.00 0.00 0.00 5.01
219 220 1.741770 CCCGGTAGCTCAACAGTGC 60.742 63.158 0.00 0.00 0.00 4.40
220 221 1.741770 GCCCGGTAGCTCAACAGTG 60.742 63.158 0.00 0.00 0.00 3.66
221 222 2.172483 CTGCCCGGTAGCTCAACAGT 62.172 60.000 0.00 0.00 0.00 3.55
222 223 1.448540 CTGCCCGGTAGCTCAACAG 60.449 63.158 0.00 0.00 0.00 3.16
223 224 2.662596 CTGCCCGGTAGCTCAACA 59.337 61.111 0.00 0.00 0.00 3.33
224 225 2.125106 CCTGCCCGGTAGCTCAAC 60.125 66.667 0.00 0.00 0.00 3.18
225 226 2.606519 ACCTGCCCGGTAGCTCAA 60.607 61.111 0.00 0.00 46.73 3.02
238 239 3.934391 GAGGCGACGACCCAACCTG 62.934 68.421 0.00 0.00 0.00 4.00
239 240 3.692406 GAGGCGACGACCCAACCT 61.692 66.667 0.00 0.00 0.00 3.50
240 241 4.754667 GGAGGCGACGACCCAACC 62.755 72.222 0.00 0.00 0.00 3.77
241 242 2.345760 TAGGAGGCGACGACCCAAC 61.346 63.158 10.35 0.00 33.34 3.77
242 243 2.036098 TAGGAGGCGACGACCCAA 59.964 61.111 10.35 0.00 33.34 4.12
243 244 2.753043 GTAGGAGGCGACGACCCA 60.753 66.667 10.35 0.00 33.34 4.51
244 245 2.753043 TGTAGGAGGCGACGACCC 60.753 66.667 0.00 0.00 33.34 4.46
245 246 2.488820 GTGTAGGAGGCGACGACC 59.511 66.667 0.00 0.00 0.00 4.79
246 247 2.488820 GGTGTAGGAGGCGACGAC 59.511 66.667 0.00 0.00 0.00 4.34
247 248 2.753043 GGGTGTAGGAGGCGACGA 60.753 66.667 0.00 0.00 0.00 4.20
248 249 1.105167 TATGGGTGTAGGAGGCGACG 61.105 60.000 0.00 0.00 0.00 5.12
249 250 1.000955 CATATGGGTGTAGGAGGCGAC 59.999 57.143 0.00 0.00 0.00 5.19
250 251 1.338107 CATATGGGTGTAGGAGGCGA 58.662 55.000 0.00 0.00 0.00 5.54
251 252 0.320771 GCATATGGGTGTAGGAGGCG 60.321 60.000 4.56 0.00 0.00 5.52
252 253 0.764890 TGCATATGGGTGTAGGAGGC 59.235 55.000 4.56 0.00 0.00 4.70
253 254 2.373169 ACATGCATATGGGTGTAGGAGG 59.627 50.000 0.00 0.00 38.66 4.30
254 255 3.071457 TCACATGCATATGGGTGTAGGAG 59.929 47.826 4.88 0.00 38.86 3.69
255 256 3.044894 TCACATGCATATGGGTGTAGGA 58.955 45.455 4.88 0.00 38.86 2.94
256 257 3.490439 TCACATGCATATGGGTGTAGG 57.510 47.619 4.88 0.00 38.86 3.18
257 258 3.817084 CCTTCACATGCATATGGGTGTAG 59.183 47.826 4.88 9.38 38.86 2.74
258 259 3.457749 TCCTTCACATGCATATGGGTGTA 59.542 43.478 4.88 0.00 38.86 2.90
259 260 2.241941 TCCTTCACATGCATATGGGTGT 59.758 45.455 4.88 0.00 38.86 4.16
260 261 2.882761 CTCCTTCACATGCATATGGGTG 59.117 50.000 4.88 6.83 38.86 4.61
261 262 2.511218 ACTCCTTCACATGCATATGGGT 59.489 45.455 4.88 0.00 38.86 4.51
262 263 3.219176 ACTCCTTCACATGCATATGGG 57.781 47.619 4.88 0.00 39.14 4.00
263 264 6.889301 ATTTACTCCTTCACATGCATATGG 57.111 37.500 4.88 0.00 38.66 2.74
264 265 7.173735 TGCTATTTACTCCTTCACATGCATATG 59.826 37.037 0.00 0.00 40.24 1.78
265 266 7.226441 TGCTATTTACTCCTTCACATGCATAT 58.774 34.615 0.00 0.00 0.00 1.78
266 267 6.591001 TGCTATTTACTCCTTCACATGCATA 58.409 36.000 0.00 0.00 0.00 3.14
267 268 5.439721 TGCTATTTACTCCTTCACATGCAT 58.560 37.500 0.00 0.00 0.00 3.96
268 269 4.842574 TGCTATTTACTCCTTCACATGCA 58.157 39.130 0.00 0.00 0.00 3.96
269 270 7.496529 TTATGCTATTTACTCCTTCACATGC 57.503 36.000 0.00 0.00 0.00 4.06
270 271 9.722056 GTTTTATGCTATTTACTCCTTCACATG 57.278 33.333 0.00 0.00 0.00 3.21
271 272 9.686683 AGTTTTATGCTATTTACTCCTTCACAT 57.313 29.630 0.00 0.00 0.00 3.21
299 300 3.071892 TGGAACCATAGGACGAAAAGTGT 59.928 43.478 0.00 0.00 0.00 3.55
400 401 3.531262 AACGGTTTAAAACGCTAGCAG 57.469 42.857 24.87 10.16 0.00 4.24
1685 1697 5.179368 TCATTTTCAGTCTTAAGCTTGGTCG 59.821 40.000 9.86 0.00 0.00 4.79
1687 1699 5.827797 TGTCATTTTCAGTCTTAAGCTTGGT 59.172 36.000 9.86 0.00 0.00 3.67
2174 2186 2.027837 AGCTTCACATTCCCCAAAATGC 60.028 45.455 0.00 0.00 39.72 3.56
2808 2821 1.268899 ACGATCGAAGAAACGACACCT 59.731 47.619 24.34 0.00 44.84 4.00


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.