Multiple sequence alignment - TraesCS3D01G427400

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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 TraesCS3D01G427400 chr3D 100.000 1741 0 0 795 2535 540904049 540902309 0.000000e+00 3216
1 TraesCS3D01G427400 chr3D 100.000 312 0 0 1 312 540904843 540904532 6.080000e-161 577
2 TraesCS3D01G427400 chr3A 95.683 1691 44 9 862 2535 676072151 676070473 0.000000e+00 2691


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 TraesCS3D01G427400 chr3D 540902309 540904843 2534 True 1896.5 3216 100.000 1 2535 2 chr3D.!!$R1 2534
1 TraesCS3D01G427400 chr3A 676070473 676072151 1678 True 2691.0 2691 95.683 862 2535 1 chr3A.!!$R1 1673

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
297 298 0.035176 CAACCCCACCAATTGCCAAG 59.965 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1952 0.340208 GGGAGGAAGAGGAGGAGGAA 59.66 60.0 0.0 0.0 0.0 3.36 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
24 25 6.922389 GTACAGATTTGTTTTCTTGCACAAC 58.078 36.000 0.00 0.00 38.76 3.32
25 26 5.723295 ACAGATTTGTTTTCTTGCACAACT 58.277 33.333 0.00 0.00 32.28 3.16
26 27 5.807011 ACAGATTTGTTTTCTTGCACAACTC 59.193 36.000 0.00 0.00 34.42 3.01
27 28 5.036737 AGATTTGTTTTCTTGCACAACTCG 58.963 37.500 0.00 0.00 37.54 4.18
28 29 3.840890 TTGTTTTCTTGCACAACTCGT 57.159 38.095 0.00 0.00 0.00 4.18
29 30 4.948608 TTGTTTTCTTGCACAACTCGTA 57.051 36.364 0.00 0.00 0.00 3.43
30 31 4.948608 TGTTTTCTTGCACAACTCGTAA 57.051 36.364 0.00 0.00 0.00 3.18
31 32 5.298197 TGTTTTCTTGCACAACTCGTAAA 57.702 34.783 0.00 0.00 0.00 2.01
32 33 5.885881 TGTTTTCTTGCACAACTCGTAAAT 58.114 33.333 0.00 0.00 0.00 1.40
33 34 6.326375 TGTTTTCTTGCACAACTCGTAAATT 58.674 32.000 0.00 0.00 0.00 1.82
34 35 7.473366 TGTTTTCTTGCACAACTCGTAAATTA 58.527 30.769 0.00 0.00 0.00 1.40
35 36 7.968956 TGTTTTCTTGCACAACTCGTAAATTAA 59.031 29.630 0.00 0.00 0.00 1.40
36 37 7.901874 TTTCTTGCACAACTCGTAAATTAAC 57.098 32.000 0.00 0.00 0.00 2.01
37 38 6.606234 TCTTGCACAACTCGTAAATTAACA 57.394 33.333 0.00 0.00 0.00 2.41
38 39 7.197071 TCTTGCACAACTCGTAAATTAACAT 57.803 32.000 0.00 0.00 0.00 2.71
39 40 8.312896 TCTTGCACAACTCGTAAATTAACATA 57.687 30.769 0.00 0.00 0.00 2.29
40 41 8.440059 TCTTGCACAACTCGTAAATTAACATAG 58.560 33.333 0.00 0.00 0.00 2.23
41 42 7.661127 TGCACAACTCGTAAATTAACATAGT 57.339 32.000 0.00 0.00 0.00 2.12
42 43 8.090250 TGCACAACTCGTAAATTAACATAGTT 57.910 30.769 0.00 0.00 0.00 2.24
43 44 8.561212 TGCACAACTCGTAAATTAACATAGTTT 58.439 29.630 0.00 0.00 0.00 2.66
44 45 8.837059 GCACAACTCGTAAATTAACATAGTTTG 58.163 33.333 0.00 0.00 0.00 2.93
45 46 9.872757 CACAACTCGTAAATTAACATAGTTTGT 57.127 29.630 0.00 0.00 41.53 2.83
109 110 9.699703 TTTATACAAAAATCTTTAGGGTTGTGC 57.300 29.630 0.00 0.00 31.95 4.57
110 111 4.616953 ACAAAAATCTTTAGGGTTGTGCG 58.383 39.130 0.00 0.00 0.00 5.34
111 112 3.934457 AAAATCTTTAGGGTTGTGCGG 57.066 42.857 0.00 0.00 0.00 5.69
112 113 2.579410 AATCTTTAGGGTTGTGCGGT 57.421 45.000 0.00 0.00 0.00 5.68
113 114 3.706600 AATCTTTAGGGTTGTGCGGTA 57.293 42.857 0.00 0.00 0.00 4.02
114 115 2.460757 TCTTTAGGGTTGTGCGGTAC 57.539 50.000 0.00 0.00 0.00 3.34
115 116 1.693062 TCTTTAGGGTTGTGCGGTACA 59.307 47.619 0.00 0.00 37.56 2.90
116 117 2.303600 TCTTTAGGGTTGTGCGGTACAT 59.696 45.455 0.00 0.00 39.48 2.29
117 118 2.102070 TTAGGGTTGTGCGGTACATG 57.898 50.000 0.00 0.00 39.48 3.21
118 119 0.978151 TAGGGTTGTGCGGTACATGT 59.022 50.000 2.69 2.69 39.48 3.21
119 120 0.109723 AGGGTTGTGCGGTACATGTT 59.890 50.000 2.30 0.00 39.48 2.71
120 121 0.955905 GGGTTGTGCGGTACATGTTT 59.044 50.000 2.30 0.00 39.48 2.83
121 122 1.338655 GGGTTGTGCGGTACATGTTTT 59.661 47.619 2.30 0.00 39.48 2.43
122 123 2.223852 GGGTTGTGCGGTACATGTTTTT 60.224 45.455 2.30 0.00 39.48 1.94
123 124 2.792116 GGTTGTGCGGTACATGTTTTTG 59.208 45.455 2.30 0.00 39.48 2.44
124 125 2.126914 TGTGCGGTACATGTTTTTGC 57.873 45.000 2.30 4.34 33.42 3.68
125 126 1.269309 TGTGCGGTACATGTTTTTGCC 60.269 47.619 2.30 0.00 33.42 4.52
126 127 1.032794 TGCGGTACATGTTTTTGCCA 58.967 45.000 2.30 0.00 0.00 4.92
127 128 1.615883 TGCGGTACATGTTTTTGCCAT 59.384 42.857 2.30 0.00 0.00 4.40
128 129 2.036475 TGCGGTACATGTTTTTGCCATT 59.964 40.909 2.30 0.00 0.00 3.16
129 130 3.063485 GCGGTACATGTTTTTGCCATTT 58.937 40.909 2.30 0.00 0.00 2.32
130 131 3.496507 GCGGTACATGTTTTTGCCATTTT 59.503 39.130 2.30 0.00 0.00 1.82
131 132 4.610231 GCGGTACATGTTTTTGCCATTTTG 60.610 41.667 2.30 0.00 0.00 2.44
132 133 4.747108 CGGTACATGTTTTTGCCATTTTGA 59.253 37.500 2.30 0.00 0.00 2.69
133 134 5.107530 CGGTACATGTTTTTGCCATTTTGAG 60.108 40.000 2.30 0.00 0.00 3.02
134 135 5.179182 GGTACATGTTTTTGCCATTTTGAGG 59.821 40.000 2.30 0.00 0.00 3.86
135 136 4.136051 ACATGTTTTTGCCATTTTGAGGG 58.864 39.130 0.00 0.00 0.00 4.30
136 137 3.922171 TGTTTTTGCCATTTTGAGGGT 57.078 38.095 0.00 0.00 0.00 4.34
137 138 5.163258 ACATGTTTTTGCCATTTTGAGGGTA 60.163 36.000 0.00 0.00 0.00 3.69
138 139 5.559148 TGTTTTTGCCATTTTGAGGGTAT 57.441 34.783 0.00 0.00 0.00 2.73
139 140 5.934781 TGTTTTTGCCATTTTGAGGGTATT 58.065 33.333 0.00 0.00 0.00 1.89
140 141 5.994668 TGTTTTTGCCATTTTGAGGGTATTC 59.005 36.000 0.00 0.00 0.00 1.75
141 142 5.815233 TTTTGCCATTTTGAGGGTATTCA 57.185 34.783 0.00 0.00 0.00 2.57
142 143 4.799564 TTGCCATTTTGAGGGTATTCAC 57.200 40.909 0.00 0.00 0.00 3.18
143 144 3.772387 TGCCATTTTGAGGGTATTCACA 58.228 40.909 0.00 0.00 0.00 3.58
144 145 4.352009 TGCCATTTTGAGGGTATTCACAT 58.648 39.130 0.00 0.00 0.00 3.21
145 146 4.776837 TGCCATTTTGAGGGTATTCACATT 59.223 37.500 0.00 0.00 0.00 2.71
146 147 5.954752 TGCCATTTTGAGGGTATTCACATTA 59.045 36.000 0.00 0.00 0.00 1.90
147 148 6.096705 TGCCATTTTGAGGGTATTCACATTAG 59.903 38.462 0.00 0.00 0.00 1.73
148 149 6.507023 CCATTTTGAGGGTATTCACATTAGC 58.493 40.000 0.00 0.00 0.00 3.09
149 150 6.096705 CCATTTTGAGGGTATTCACATTAGCA 59.903 38.462 0.00 0.00 0.00 3.49
150 151 7.201938 CCATTTTGAGGGTATTCACATTAGCAT 60.202 37.037 0.00 0.00 0.00 3.79
151 152 7.716799 TTTTGAGGGTATTCACATTAGCATT 57.283 32.000 0.00 0.00 0.00 3.56
152 153 7.716799 TTTGAGGGTATTCACATTAGCATTT 57.283 32.000 0.00 0.00 0.00 2.32
153 154 6.942532 TGAGGGTATTCACATTAGCATTTC 57.057 37.500 0.00 0.00 0.00 2.17
154 155 5.827797 TGAGGGTATTCACATTAGCATTTCC 59.172 40.000 0.00 0.00 0.00 3.13
155 156 6.018433 AGGGTATTCACATTAGCATTTCCT 57.982 37.500 0.00 0.00 0.00 3.36
156 157 6.435164 AGGGTATTCACATTAGCATTTCCTT 58.565 36.000 0.00 0.00 0.00 3.36
157 158 7.582719 AGGGTATTCACATTAGCATTTCCTTA 58.417 34.615 0.00 0.00 0.00 2.69
158 159 7.502561 AGGGTATTCACATTAGCATTTCCTTAC 59.497 37.037 0.00 0.00 0.00 2.34
159 160 7.255486 GGGTATTCACATTAGCATTTCCTTACC 60.255 40.741 0.00 0.00 0.00 2.85
160 161 7.502561 GGTATTCACATTAGCATTTCCTTACCT 59.497 37.037 0.00 0.00 0.00 3.08
161 162 7.961326 ATTCACATTAGCATTTCCTTACCTT 57.039 32.000 0.00 0.00 0.00 3.50
163 164 7.859325 TCACATTAGCATTTCCTTACCTTAC 57.141 36.000 0.00 0.00 0.00 2.34
164 165 6.826741 TCACATTAGCATTTCCTTACCTTACC 59.173 38.462 0.00 0.00 0.00 2.85
165 166 6.828785 CACATTAGCATTTCCTTACCTTACCT 59.171 38.462 0.00 0.00 0.00 3.08
166 167 7.339466 CACATTAGCATTTCCTTACCTTACCTT 59.661 37.037 0.00 0.00 0.00 3.50
167 168 8.554011 ACATTAGCATTTCCTTACCTTACCTTA 58.446 33.333 0.00 0.00 0.00 2.69
168 169 9.574516 CATTAGCATTTCCTTACCTTACCTTAT 57.425 33.333 0.00 0.00 0.00 1.73
169 170 9.794719 ATTAGCATTTCCTTACCTTACCTTATC 57.205 33.333 0.00 0.00 0.00 1.75
170 171 6.289064 AGCATTTCCTTACCTTACCTTATCG 58.711 40.000 0.00 0.00 0.00 2.92
171 172 5.049612 GCATTTCCTTACCTTACCTTATCGC 60.050 44.000 0.00 0.00 0.00 4.58
172 173 5.680594 TTTCCTTACCTTACCTTATCGCA 57.319 39.130 0.00 0.00 0.00 5.10
173 174 4.931661 TCCTTACCTTACCTTATCGCAG 57.068 45.455 0.00 0.00 0.00 5.18
174 175 3.640029 TCCTTACCTTACCTTATCGCAGG 59.360 47.826 0.00 0.00 40.23 4.85
175 176 3.244112 CCTTACCTTACCTTATCGCAGGG 60.244 52.174 0.87 0.00 38.42 4.45
176 177 2.170012 ACCTTACCTTATCGCAGGGA 57.830 50.000 0.00 0.00 38.42 4.20
177 178 2.690840 ACCTTACCTTATCGCAGGGAT 58.309 47.619 5.16 5.16 38.42 3.85
178 179 2.368875 ACCTTACCTTATCGCAGGGATG 59.631 50.000 10.23 0.00 38.42 3.51
179 180 2.289694 CCTTACCTTATCGCAGGGATGG 60.290 54.545 10.23 6.29 38.42 3.51
180 181 2.391926 TACCTTATCGCAGGGATGGA 57.608 50.000 10.23 0.00 38.42 3.41
181 182 1.734655 ACCTTATCGCAGGGATGGAT 58.265 50.000 10.23 0.00 38.42 3.41
182 183 2.057922 ACCTTATCGCAGGGATGGATT 58.942 47.619 10.23 0.00 38.42 3.01
183 184 2.224621 ACCTTATCGCAGGGATGGATTG 60.225 50.000 10.23 0.00 38.42 2.67
184 185 2.430465 CTTATCGCAGGGATGGATTGG 58.570 52.381 10.23 0.00 36.55 3.16
185 186 1.434188 TATCGCAGGGATGGATTGGT 58.566 50.000 10.23 0.00 36.55 3.67
186 187 0.109342 ATCGCAGGGATGGATTGGTC 59.891 55.000 0.00 0.00 32.92 4.02
187 188 0.982852 TCGCAGGGATGGATTGGTCT 60.983 55.000 0.00 0.00 0.00 3.85
188 189 0.758734 CGCAGGGATGGATTGGTCTA 59.241 55.000 0.00 0.00 0.00 2.59
189 190 1.349026 CGCAGGGATGGATTGGTCTAT 59.651 52.381 0.00 0.00 0.00 1.98
190 191 2.613977 CGCAGGGATGGATTGGTCTATC 60.614 54.545 0.00 0.00 40.52 2.08
191 192 2.373169 GCAGGGATGGATTGGTCTATCA 59.627 50.000 4.55 0.00 42.37 2.15
192 193 3.009916 GCAGGGATGGATTGGTCTATCAT 59.990 47.826 4.55 0.00 42.37 2.45
193 194 4.586884 CAGGGATGGATTGGTCTATCATG 58.413 47.826 4.55 0.00 42.37 3.07
194 195 4.042560 CAGGGATGGATTGGTCTATCATGT 59.957 45.833 4.55 0.00 42.37 3.21
195 196 4.666907 AGGGATGGATTGGTCTATCATGTT 59.333 41.667 4.55 0.00 42.37 2.71
196 197 5.135020 AGGGATGGATTGGTCTATCATGTTT 59.865 40.000 4.55 0.00 42.37 2.83
197 198 5.835280 GGGATGGATTGGTCTATCATGTTTT 59.165 40.000 4.55 0.00 42.37 2.43
198 199 7.004086 GGGATGGATTGGTCTATCATGTTTTA 58.996 38.462 4.55 0.00 42.37 1.52
199 200 7.671398 GGGATGGATTGGTCTATCATGTTTTAT 59.329 37.037 4.55 0.00 42.37 1.40
200 201 8.517878 GGATGGATTGGTCTATCATGTTTTATG 58.482 37.037 4.55 0.00 42.37 1.90
201 202 7.275888 TGGATTGGTCTATCATGTTTTATGC 57.724 36.000 0.00 0.00 0.00 3.14
202 203 7.062322 TGGATTGGTCTATCATGTTTTATGCT 58.938 34.615 0.00 0.00 0.00 3.79
203 204 7.560991 TGGATTGGTCTATCATGTTTTATGCTT 59.439 33.333 0.00 0.00 0.00 3.91
204 205 7.864379 GGATTGGTCTATCATGTTTTATGCTTG 59.136 37.037 0.00 0.00 0.00 4.01
205 206 6.135290 TGGTCTATCATGTTTTATGCTTGC 57.865 37.500 0.00 0.00 0.00 4.01
206 207 5.651576 TGGTCTATCATGTTTTATGCTTGCA 59.348 36.000 0.00 0.00 0.00 4.08
207 208 5.973565 GGTCTATCATGTTTTATGCTTGCAC 59.026 40.000 0.00 0.00 0.00 4.57
208 209 6.183360 GGTCTATCATGTTTTATGCTTGCACT 60.183 38.462 0.00 0.00 0.00 4.40
209 210 7.012327 GGTCTATCATGTTTTATGCTTGCACTA 59.988 37.037 0.00 0.00 0.00 2.74
210 211 8.066595 GTCTATCATGTTTTATGCTTGCACTAG 58.933 37.037 0.00 0.00 0.00 2.57
211 212 7.986889 TCTATCATGTTTTATGCTTGCACTAGA 59.013 33.333 0.00 0.00 0.00 2.43
212 213 7.578310 ATCATGTTTTATGCTTGCACTAGAT 57.422 32.000 0.00 0.00 0.00 1.98
213 214 7.395190 TCATGTTTTATGCTTGCACTAGATT 57.605 32.000 0.00 0.00 0.00 2.40
214 215 7.829725 TCATGTTTTATGCTTGCACTAGATTT 58.170 30.769 0.00 0.00 0.00 2.17
215 216 8.955388 TCATGTTTTATGCTTGCACTAGATTTA 58.045 29.630 0.00 0.00 0.00 1.40
216 217 9.229784 CATGTTTTATGCTTGCACTAGATTTAG 57.770 33.333 0.00 0.00 0.00 1.85
217 218 8.335532 TGTTTTATGCTTGCACTAGATTTAGT 57.664 30.769 0.00 0.00 40.79 2.24
218 219 9.443323 TGTTTTATGCTTGCACTAGATTTAGTA 57.557 29.630 0.00 0.00 38.05 1.82
219 220 9.704098 GTTTTATGCTTGCACTAGATTTAGTAC 57.296 33.333 0.00 0.00 38.05 2.73
220 221 9.443323 TTTTATGCTTGCACTAGATTTAGTACA 57.557 29.630 0.00 0.00 38.05 2.90
221 222 9.613428 TTTATGCTTGCACTAGATTTAGTACAT 57.387 29.630 0.00 0.00 38.05 2.29
258 259 9.778741 ACATATCTAACATTTTGATACATCGGT 57.221 29.630 0.00 0.00 0.00 4.69
261 262 8.731275 ATCTAACATTTTGATACATCGGTTCA 57.269 30.769 0.00 0.00 0.00 3.18
262 263 8.196802 TCTAACATTTTGATACATCGGTTCAG 57.803 34.615 0.00 0.00 0.00 3.02
263 264 5.818136 ACATTTTGATACATCGGTTCAGG 57.182 39.130 0.00 0.00 0.00 3.86
264 265 4.640201 ACATTTTGATACATCGGTTCAGGG 59.360 41.667 0.00 0.00 0.00 4.45
265 266 2.325583 TTGATACATCGGTTCAGGGC 57.674 50.000 0.00 0.00 0.00 5.19
266 267 1.496060 TGATACATCGGTTCAGGGCT 58.504 50.000 0.00 0.00 0.00 5.19
267 268 1.412710 TGATACATCGGTTCAGGGCTC 59.587 52.381 0.00 0.00 0.00 4.70
268 269 0.759346 ATACATCGGTTCAGGGCTCC 59.241 55.000 0.00 0.00 0.00 4.70
269 270 0.616395 TACATCGGTTCAGGGCTCCA 60.616 55.000 0.00 0.00 0.00 3.86
270 271 1.153289 CATCGGTTCAGGGCTCCAG 60.153 63.158 0.00 0.00 0.00 3.86
271 272 1.613630 ATCGGTTCAGGGCTCCAGT 60.614 57.895 0.00 0.00 0.00 4.00
272 273 1.903877 ATCGGTTCAGGGCTCCAGTG 61.904 60.000 0.00 0.00 0.00 3.66
273 274 2.360475 GGTTCAGGGCTCCAGTGC 60.360 66.667 0.00 0.00 0.00 4.40
274 275 2.431683 GTTCAGGGCTCCAGTGCA 59.568 61.111 0.00 0.00 34.04 4.57
275 276 1.228245 GTTCAGGGCTCCAGTGCAA 60.228 57.895 0.00 0.00 34.04 4.08
276 277 0.610232 GTTCAGGGCTCCAGTGCAAT 60.610 55.000 0.00 0.00 34.04 3.56
277 278 0.609957 TTCAGGGCTCCAGTGCAATG 60.610 55.000 7.29 7.29 34.04 2.82
278 279 2.362120 AGGGCTCCAGTGCAATGC 60.362 61.111 9.04 0.00 34.04 3.56
279 280 2.677524 GGGCTCCAGTGCAATGCA 60.678 61.111 9.04 2.72 35.60 3.96
280 281 2.277591 GGGCTCCAGTGCAATGCAA 61.278 57.895 10.44 0.00 41.47 4.08
281 282 1.080298 GGCTCCAGTGCAATGCAAC 60.080 57.895 10.44 4.51 41.47 4.17
282 283 1.080298 GCTCCAGTGCAATGCAACC 60.080 57.895 10.44 0.00 41.47 3.77
283 284 1.588082 CTCCAGTGCAATGCAACCC 59.412 57.895 10.44 0.00 41.47 4.11
284 285 1.880819 CTCCAGTGCAATGCAACCCC 61.881 60.000 10.44 0.00 41.47 4.95
285 286 2.208619 CCAGTGCAATGCAACCCCA 61.209 57.895 10.44 0.00 41.47 4.96
286 287 1.005867 CAGTGCAATGCAACCCCAC 60.006 57.895 10.44 0.00 41.47 4.61
287 288 2.209315 AGTGCAATGCAACCCCACC 61.209 57.895 10.44 0.00 41.47 4.61
288 289 2.123121 TGCAATGCAACCCCACCA 60.123 55.556 5.01 0.00 34.76 4.17
289 290 1.763655 TGCAATGCAACCCCACCAA 60.764 52.632 5.01 0.00 34.76 3.67
290 291 1.126329 TGCAATGCAACCCCACCAAT 61.126 50.000 5.01 0.00 34.76 3.16
291 292 0.036590 GCAATGCAACCCCACCAATT 59.963 50.000 0.00 0.00 0.00 2.32
292 293 1.810959 CAATGCAACCCCACCAATTG 58.189 50.000 0.00 0.00 0.00 2.32
294 295 1.840224 ATGCAACCCCACCAATTGCC 61.840 55.000 0.00 0.00 46.53 4.52
295 296 2.515071 GCAACCCCACCAATTGCCA 61.515 57.895 0.00 0.00 42.32 4.92
296 297 2.049627 GCAACCCCACCAATTGCCAA 62.050 55.000 0.00 0.00 42.32 4.52
297 298 0.035176 CAACCCCACCAATTGCCAAG 59.965 55.000 0.00 0.00 0.00 3.61
298 299 0.399806 AACCCCACCAATTGCCAAGT 60.400 50.000 0.00 0.00 0.00 3.16
299 300 0.485099 ACCCCACCAATTGCCAAGTA 59.515 50.000 0.00 0.00 0.00 2.24
300 301 1.133009 ACCCCACCAATTGCCAAGTAA 60.133 47.619 0.00 0.00 0.00 2.24
301 302 1.550072 CCCCACCAATTGCCAAGTAAG 59.450 52.381 0.00 0.00 0.00 2.34
302 303 2.247358 CCCACCAATTGCCAAGTAAGT 58.753 47.619 0.00 0.00 0.00 2.24
303 304 2.632512 CCCACCAATTGCCAAGTAAGTT 59.367 45.455 0.00 0.00 0.00 2.66
304 305 3.829601 CCCACCAATTGCCAAGTAAGTTA 59.170 43.478 0.00 0.00 0.00 2.24
305 306 4.082245 CCCACCAATTGCCAAGTAAGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
306 307 4.485163 CACCAATTGCCAAGTAAGTTAGC 58.515 43.478 0.00 0.00 0.00 3.09
307 308 4.022416 CACCAATTGCCAAGTAAGTTAGCA 60.022 41.667 0.00 0.00 0.00 3.49
308 309 4.022329 ACCAATTGCCAAGTAAGTTAGCAC 60.022 41.667 0.00 0.00 32.18 4.40
309 310 4.218417 CCAATTGCCAAGTAAGTTAGCACT 59.782 41.667 0.00 0.00 32.18 4.40
310 311 5.278957 CCAATTGCCAAGTAAGTTAGCACTT 60.279 40.000 0.00 0.00 45.73 3.16
814 815 2.861147 AAGAGTTAGCACCTCAACCC 57.139 50.000 0.00 0.00 0.00 4.11
815 816 1.729586 AGAGTTAGCACCTCAACCCA 58.270 50.000 0.00 0.00 0.00 4.51
816 817 2.054799 AGAGTTAGCACCTCAACCCAA 58.945 47.619 0.00 0.00 0.00 4.12
817 818 2.644798 AGAGTTAGCACCTCAACCCAAT 59.355 45.455 0.00 0.00 0.00 3.16
818 819 3.010420 GAGTTAGCACCTCAACCCAATC 58.990 50.000 0.00 0.00 0.00 2.67
819 820 2.375174 AGTTAGCACCTCAACCCAATCA 59.625 45.455 0.00 0.00 0.00 2.57
820 821 3.153919 GTTAGCACCTCAACCCAATCAA 58.846 45.455 0.00 0.00 0.00 2.57
821 822 1.620822 AGCACCTCAACCCAATCAAC 58.379 50.000 0.00 0.00 0.00 3.18
822 823 1.133513 AGCACCTCAACCCAATCAACA 60.134 47.619 0.00 0.00 0.00 3.33
823 824 1.686052 GCACCTCAACCCAATCAACAA 59.314 47.619 0.00 0.00 0.00 2.83
824 825 2.102252 GCACCTCAACCCAATCAACAAA 59.898 45.455 0.00 0.00 0.00 2.83
825 826 3.431486 GCACCTCAACCCAATCAACAAAA 60.431 43.478 0.00 0.00 0.00 2.44
826 827 4.764172 CACCTCAACCCAATCAACAAAAA 58.236 39.130 0.00 0.00 0.00 1.94
827 828 5.367302 CACCTCAACCCAATCAACAAAAAT 58.633 37.500 0.00 0.00 0.00 1.82
828 829 6.520272 CACCTCAACCCAATCAACAAAAATA 58.480 36.000 0.00 0.00 0.00 1.40
829 830 7.160726 CACCTCAACCCAATCAACAAAAATAT 58.839 34.615 0.00 0.00 0.00 1.28
830 831 8.310382 CACCTCAACCCAATCAACAAAAATATA 58.690 33.333 0.00 0.00 0.00 0.86
831 832 8.875168 ACCTCAACCCAATCAACAAAAATATAA 58.125 29.630 0.00 0.00 0.00 0.98
832 833 9.717942 CCTCAACCCAATCAACAAAAATATAAA 57.282 29.630 0.00 0.00 0.00 1.40
855 856 8.795842 AAATGATAATCACATGCAATTTGGTT 57.204 26.923 0.00 0.00 31.30 3.67
856 857 8.795842 AATGATAATCACATGCAATTTGGTTT 57.204 26.923 0.00 0.00 28.87 3.27
857 858 8.795842 ATGATAATCACATGCAATTTGGTTTT 57.204 26.923 0.00 0.00 28.87 2.43
858 859 8.254178 TGATAATCACATGCAATTTGGTTTTC 57.746 30.769 0.00 0.00 28.87 2.29
859 860 8.095792 TGATAATCACATGCAATTTGGTTTTCT 58.904 29.630 0.00 0.00 29.93 2.52
860 861 8.851541 ATAATCACATGCAATTTGGTTTTCTT 57.148 26.923 0.00 0.00 28.87 2.52
870 871 6.424812 GCAATTTGGTTTTCTTGCAGATACTT 59.575 34.615 0.00 0.00 42.66 2.24
890 891 1.413812 TGTAGATCATCGTGGCTGCAT 59.586 47.619 0.50 0.00 0.00 3.96
891 892 1.797046 GTAGATCATCGTGGCTGCATG 59.203 52.381 0.50 0.00 0.00 4.06
911 912 5.787380 CATGCTAGCTATCAAGGATGTACA 58.213 41.667 17.23 0.00 36.95 2.90
919 920 4.927267 ATCAAGGATGTACAGGTTCCAA 57.073 40.909 14.86 2.52 31.65 3.53
924 925 1.282157 GATGTACAGGTTCCAAGGGCT 59.718 52.381 0.33 0.00 0.00 5.19
1121 1122 1.210155 GAGTTGACGGCACAATGGC 59.790 57.895 0.00 0.00 39.85 4.40
1156 1157 5.300792 GGACAAACAATGTTTGAGGAAGGTA 59.699 40.000 36.28 0.00 44.12 3.08
1197 1198 5.516090 TCTGAACACGGCTTTAAAATGTTC 58.484 37.500 18.38 18.38 46.02 3.18
1243 1245 5.816955 ATGAGAAGCTAGTATCTTTCCCC 57.183 43.478 0.00 0.00 0.00 4.81
1244 1246 4.620723 TGAGAAGCTAGTATCTTTCCCCA 58.379 43.478 0.00 0.00 0.00 4.96
1357 1361 3.111484 TCATTATGCTGGTGAGGGTACA 58.889 45.455 0.00 0.00 0.00 2.90
1375 1379 2.653726 ACATCCAGTGCAAGAAACACA 58.346 42.857 0.00 0.00 40.59 3.72
1380 1384 2.164219 CCAGTGCAAGAAACACACAACT 59.836 45.455 0.00 0.00 40.59 3.16
1386 1390 3.181510 GCAAGAAACACACAACTCGAGTT 60.182 43.478 24.93 24.93 39.12 3.01
1410 1414 5.883115 TGATAATGAAAATACGGCTTGACCA 59.117 36.000 0.00 0.00 39.03 4.02
1412 1416 2.432444 TGAAAATACGGCTTGACCAGG 58.568 47.619 0.00 0.00 39.03 4.45
1564 1569 0.895530 ATGAACTCGATGGGTGACGT 59.104 50.000 0.00 0.00 0.00 4.34
1595 1600 3.250762 GCACGGCTAGATAAATGCATGAA 59.749 43.478 0.00 0.00 33.27 2.57
1629 1634 7.775397 ATTGTTTTCTCTTTGAAACATGGTG 57.225 32.000 0.00 0.00 43.55 4.17
1681 1695 7.042254 GGGTATATGTCTTGTGAAAATACGGTC 60.042 40.741 0.00 0.00 0.00 4.79
1751 1769 9.823647 ATTCATAAATATCGACAACAGAAGACT 57.176 29.630 0.00 0.00 0.00 3.24
1760 1778 6.867550 TCGACAACAGAAGACTGATATCATT 58.132 36.000 5.72 0.00 46.03 2.57
1771 1789 5.247110 AGACTGATATCATTCGTGGCCTATT 59.753 40.000 15.17 0.00 31.72 1.73
1940 1958 3.325806 GGGCTTCCCTCTTCCTCC 58.674 66.667 0.00 0.00 41.34 4.30
1941 1959 1.307430 GGGCTTCCCTCTTCCTCCT 60.307 63.158 0.00 0.00 41.34 3.69
2043 2061 1.153005 CCTCAATGGCTGCCTCTCC 60.153 63.158 21.03 0.00 0.00 3.71
2188 2206 1.151450 CTTGGCTCCTGGTGGTTGT 59.849 57.895 0.00 0.00 34.23 3.32
2301 2319 2.948720 GCTGCTCTGTTCCGTCCCT 61.949 63.158 0.00 0.00 0.00 4.20
2434 2452 2.282180 GCGAGGCTGGTTTTCCCA 60.282 61.111 0.00 0.00 42.51 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.751888 AGTTGTGCAAGAAAACAAATCTGTAC 59.248 34.615 0.00 0.00 37.99 2.90
1 2 6.862209 AGTTGTGCAAGAAAACAAATCTGTA 58.138 32.000 0.00 0.00 37.99 2.74
2 3 5.723295 AGTTGTGCAAGAAAACAAATCTGT 58.277 33.333 0.00 0.00 37.99 3.41
3 4 5.052172 CGAGTTGTGCAAGAAAACAAATCTG 60.052 40.000 12.36 4.72 44.81 2.90
4 5 5.036737 CGAGTTGTGCAAGAAAACAAATCT 58.963 37.500 12.36 0.00 44.81 2.40
5 6 4.798387 ACGAGTTGTGCAAGAAAACAAATC 59.202 37.500 6.05 6.05 44.02 2.17
6 7 4.743493 ACGAGTTGTGCAAGAAAACAAAT 58.257 34.783 0.00 0.00 37.99 2.32
7 8 4.167554 ACGAGTTGTGCAAGAAAACAAA 57.832 36.364 0.00 0.00 37.99 2.83
8 9 3.840890 ACGAGTTGTGCAAGAAAACAA 57.159 38.095 0.00 0.00 34.01 2.83
9 10 4.948608 TTACGAGTTGTGCAAGAAAACA 57.051 36.364 0.00 0.00 0.00 2.83
10 11 6.806120 AATTTACGAGTTGTGCAAGAAAAC 57.194 33.333 0.00 0.00 0.00 2.43
11 12 7.968956 TGTTAATTTACGAGTTGTGCAAGAAAA 59.031 29.630 0.00 0.00 0.00 2.29
12 13 7.473366 TGTTAATTTACGAGTTGTGCAAGAAA 58.527 30.769 0.00 0.00 0.00 2.52
13 14 7.017498 TGTTAATTTACGAGTTGTGCAAGAA 57.983 32.000 0.00 0.00 0.00 2.52
14 15 6.606234 TGTTAATTTACGAGTTGTGCAAGA 57.394 33.333 0.00 0.00 0.00 3.02
15 16 8.227791 ACTATGTTAATTTACGAGTTGTGCAAG 58.772 33.333 0.00 0.00 0.00 4.01
16 17 8.090250 ACTATGTTAATTTACGAGTTGTGCAA 57.910 30.769 0.00 0.00 0.00 4.08
17 18 7.661127 ACTATGTTAATTTACGAGTTGTGCA 57.339 32.000 0.00 0.00 0.00 4.57
18 19 8.837059 CAAACTATGTTAATTTACGAGTTGTGC 58.163 33.333 12.65 0.00 31.24 4.57
19 20 9.872757 ACAAACTATGTTAATTTACGAGTTGTG 57.127 29.630 12.65 13.59 40.06 3.33
83 84 9.699703 GCACAACCCTAAAGATTTTTGTATAAA 57.300 29.630 0.00 0.00 0.00 1.40
84 85 8.024285 CGCACAACCCTAAAGATTTTTGTATAA 58.976 33.333 0.00 0.00 0.00 0.98
85 86 7.362229 CCGCACAACCCTAAAGATTTTTGTATA 60.362 37.037 0.00 0.00 0.00 1.47
86 87 6.386654 CGCACAACCCTAAAGATTTTTGTAT 58.613 36.000 0.00 0.00 0.00 2.29
87 88 5.278561 CCGCACAACCCTAAAGATTTTTGTA 60.279 40.000 0.00 0.00 0.00 2.41
88 89 4.500716 CCGCACAACCCTAAAGATTTTTGT 60.501 41.667 0.00 0.00 0.00 2.83
89 90 3.987220 CCGCACAACCCTAAAGATTTTTG 59.013 43.478 0.00 0.00 0.00 2.44
90 91 3.639561 ACCGCACAACCCTAAAGATTTTT 59.360 39.130 0.00 0.00 0.00 1.94
91 92 3.227614 ACCGCACAACCCTAAAGATTTT 58.772 40.909 0.00 0.00 0.00 1.82
92 93 2.871453 ACCGCACAACCCTAAAGATTT 58.129 42.857 0.00 0.00 0.00 2.17
93 94 2.579410 ACCGCACAACCCTAAAGATT 57.421 45.000 0.00 0.00 0.00 2.40
94 95 2.303600 TGTACCGCACAACCCTAAAGAT 59.696 45.455 0.00 0.00 32.95 2.40
95 96 1.693062 TGTACCGCACAACCCTAAAGA 59.307 47.619 0.00 0.00 32.95 2.52
96 97 2.172851 TGTACCGCACAACCCTAAAG 57.827 50.000 0.00 0.00 32.95 1.85
97 98 2.224572 ACATGTACCGCACAACCCTAAA 60.225 45.455 0.00 0.00 41.55 1.85
98 99 1.348366 ACATGTACCGCACAACCCTAA 59.652 47.619 0.00 0.00 41.55 2.69
99 100 0.978151 ACATGTACCGCACAACCCTA 59.022 50.000 0.00 0.00 41.55 3.53
100 101 0.109723 AACATGTACCGCACAACCCT 59.890 50.000 0.00 0.00 41.55 4.34
101 102 0.955905 AAACATGTACCGCACAACCC 59.044 50.000 0.00 0.00 41.55 4.11
102 103 2.785713 AAAACATGTACCGCACAACC 57.214 45.000 0.00 0.00 41.55 3.77
103 104 2.217620 GCAAAAACATGTACCGCACAAC 59.782 45.455 0.00 0.00 41.55 3.32
104 105 2.464865 GCAAAAACATGTACCGCACAA 58.535 42.857 0.00 0.00 41.55 3.33
105 106 1.269309 GGCAAAAACATGTACCGCACA 60.269 47.619 0.00 0.00 42.69 4.57
106 107 1.269309 TGGCAAAAACATGTACCGCAC 60.269 47.619 0.00 0.00 0.00 5.34
107 108 1.032794 TGGCAAAAACATGTACCGCA 58.967 45.000 0.00 0.00 0.00 5.69
108 109 2.362169 ATGGCAAAAACATGTACCGC 57.638 45.000 0.00 0.00 0.00 5.68
109 110 4.747108 TCAAAATGGCAAAAACATGTACCG 59.253 37.500 0.00 0.00 0.00 4.02
110 111 5.179182 CCTCAAAATGGCAAAAACATGTACC 59.821 40.000 0.00 0.00 0.00 3.34
111 112 5.179182 CCCTCAAAATGGCAAAAACATGTAC 59.821 40.000 0.00 0.00 0.00 2.90
112 113 5.163258 ACCCTCAAAATGGCAAAAACATGTA 60.163 36.000 0.00 0.00 0.00 2.29
113 114 4.136051 CCCTCAAAATGGCAAAAACATGT 58.864 39.130 0.00 0.00 0.00 3.21
114 115 4.136051 ACCCTCAAAATGGCAAAAACATG 58.864 39.130 0.00 0.00 0.00 3.21
115 116 4.436113 ACCCTCAAAATGGCAAAAACAT 57.564 36.364 0.00 0.00 0.00 2.71
116 117 3.922171 ACCCTCAAAATGGCAAAAACA 57.078 38.095 0.00 0.00 0.00 2.83
117 118 5.994668 TGAATACCCTCAAAATGGCAAAAAC 59.005 36.000 0.00 0.00 0.00 2.43
118 119 5.994668 GTGAATACCCTCAAAATGGCAAAAA 59.005 36.000 0.00 0.00 0.00 1.94
119 120 5.070981 TGTGAATACCCTCAAAATGGCAAAA 59.929 36.000 0.00 0.00 0.00 2.44
120 121 4.590647 TGTGAATACCCTCAAAATGGCAAA 59.409 37.500 0.00 0.00 0.00 3.68
121 122 4.155709 TGTGAATACCCTCAAAATGGCAA 58.844 39.130 0.00 0.00 0.00 4.52
122 123 3.772387 TGTGAATACCCTCAAAATGGCA 58.228 40.909 0.00 0.00 0.00 4.92
123 124 5.343307 AATGTGAATACCCTCAAAATGGC 57.657 39.130 0.00 0.00 0.00 4.40
124 125 6.096705 TGCTAATGTGAATACCCTCAAAATGG 59.903 38.462 0.00 0.00 0.00 3.16
125 126 7.099266 TGCTAATGTGAATACCCTCAAAATG 57.901 36.000 0.00 0.00 0.00 2.32
126 127 7.902920 ATGCTAATGTGAATACCCTCAAAAT 57.097 32.000 0.00 0.00 0.00 1.82
127 128 7.716799 AATGCTAATGTGAATACCCTCAAAA 57.283 32.000 0.00 0.00 0.00 2.44
128 129 7.147915 GGAAATGCTAATGTGAATACCCTCAAA 60.148 37.037 0.00 0.00 0.00 2.69
129 130 6.321181 GGAAATGCTAATGTGAATACCCTCAA 59.679 38.462 0.00 0.00 0.00 3.02
130 131 5.827797 GGAAATGCTAATGTGAATACCCTCA 59.172 40.000 0.00 0.00 0.00 3.86
131 132 6.064717 AGGAAATGCTAATGTGAATACCCTC 58.935 40.000 0.00 0.00 0.00 4.30
132 133 6.018433 AGGAAATGCTAATGTGAATACCCT 57.982 37.500 0.00 0.00 0.00 4.34
133 134 6.715347 AAGGAAATGCTAATGTGAATACCC 57.285 37.500 0.00 0.00 0.00 3.69
134 135 7.502561 AGGTAAGGAAATGCTAATGTGAATACC 59.497 37.037 0.00 0.00 0.00 2.73
135 136 8.451908 AGGTAAGGAAATGCTAATGTGAATAC 57.548 34.615 0.00 0.00 0.00 1.89
137 138 7.961326 AAGGTAAGGAAATGCTAATGTGAAT 57.039 32.000 0.00 0.00 0.00 2.57
138 139 7.338449 GGTAAGGTAAGGAAATGCTAATGTGAA 59.662 37.037 0.00 0.00 0.00 3.18
139 140 6.826741 GGTAAGGTAAGGAAATGCTAATGTGA 59.173 38.462 0.00 0.00 0.00 3.58
140 141 6.828785 AGGTAAGGTAAGGAAATGCTAATGTG 59.171 38.462 0.00 0.00 0.00 3.21
141 142 6.970191 AGGTAAGGTAAGGAAATGCTAATGT 58.030 36.000 0.00 0.00 0.00 2.71
142 143 7.881775 AAGGTAAGGTAAGGAAATGCTAATG 57.118 36.000 0.00 0.00 0.00 1.90
143 144 9.794719 GATAAGGTAAGGTAAGGAAATGCTAAT 57.205 33.333 0.00 0.00 0.00 1.73
144 145 7.929785 CGATAAGGTAAGGTAAGGAAATGCTAA 59.070 37.037 0.00 0.00 0.00 3.09
145 146 7.439381 CGATAAGGTAAGGTAAGGAAATGCTA 58.561 38.462 0.00 0.00 0.00 3.49
146 147 6.289064 CGATAAGGTAAGGTAAGGAAATGCT 58.711 40.000 0.00 0.00 0.00 3.79
147 148 5.049612 GCGATAAGGTAAGGTAAGGAAATGC 60.050 44.000 0.00 0.00 0.00 3.56
148 149 6.053005 TGCGATAAGGTAAGGTAAGGAAATG 58.947 40.000 0.00 0.00 0.00 2.32
149 150 6.243216 TGCGATAAGGTAAGGTAAGGAAAT 57.757 37.500 0.00 0.00 0.00 2.17
150 151 5.395990 CCTGCGATAAGGTAAGGTAAGGAAA 60.396 44.000 0.00 0.00 32.17 3.13
151 152 4.100498 CCTGCGATAAGGTAAGGTAAGGAA 59.900 45.833 0.00 0.00 32.17 3.36
152 153 3.640029 CCTGCGATAAGGTAAGGTAAGGA 59.360 47.826 0.00 0.00 32.17 3.36
153 154 3.244112 CCCTGCGATAAGGTAAGGTAAGG 60.244 52.174 0.00 0.00 35.34 2.69
154 155 3.640029 TCCCTGCGATAAGGTAAGGTAAG 59.360 47.826 0.00 0.00 35.34 2.34
155 156 3.645434 TCCCTGCGATAAGGTAAGGTAA 58.355 45.455 0.00 0.00 35.34 2.85
156 157 3.317455 TCCCTGCGATAAGGTAAGGTA 57.683 47.619 0.00 0.00 35.34 3.08
157 158 2.170012 TCCCTGCGATAAGGTAAGGT 57.830 50.000 0.00 0.00 35.34 3.50
158 159 2.289694 CCATCCCTGCGATAAGGTAAGG 60.290 54.545 0.00 0.00 35.34 2.69
159 160 2.632996 TCCATCCCTGCGATAAGGTAAG 59.367 50.000 0.00 0.00 35.34 2.34
160 161 2.684943 TCCATCCCTGCGATAAGGTAA 58.315 47.619 0.00 0.00 35.34 2.85
161 162 2.391926 TCCATCCCTGCGATAAGGTA 57.608 50.000 0.00 0.00 35.34 3.08
162 163 1.734655 ATCCATCCCTGCGATAAGGT 58.265 50.000 0.00 0.00 35.34 3.50
163 164 2.430465 CAATCCATCCCTGCGATAAGG 58.570 52.381 0.00 0.00 37.05 2.69
164 165 2.224621 ACCAATCCATCCCTGCGATAAG 60.225 50.000 0.00 0.00 0.00 1.73
165 166 1.774254 ACCAATCCATCCCTGCGATAA 59.226 47.619 0.00 0.00 0.00 1.75
166 167 1.347707 GACCAATCCATCCCTGCGATA 59.652 52.381 0.00 0.00 0.00 2.92
167 168 0.109342 GACCAATCCATCCCTGCGAT 59.891 55.000 0.00 0.00 0.00 4.58
168 169 0.982852 AGACCAATCCATCCCTGCGA 60.983 55.000 0.00 0.00 0.00 5.10
169 170 0.758734 TAGACCAATCCATCCCTGCG 59.241 55.000 0.00 0.00 0.00 5.18
170 171 2.373169 TGATAGACCAATCCATCCCTGC 59.627 50.000 0.00 0.00 0.00 4.85
171 172 4.042560 ACATGATAGACCAATCCATCCCTG 59.957 45.833 0.00 0.00 0.00 4.45
172 173 4.246143 ACATGATAGACCAATCCATCCCT 58.754 43.478 0.00 0.00 0.00 4.20
173 174 4.647564 ACATGATAGACCAATCCATCCC 57.352 45.455 0.00 0.00 0.00 3.85
174 175 6.966534 AAAACATGATAGACCAATCCATCC 57.033 37.500 0.00 0.00 0.00 3.51
175 176 8.025445 GCATAAAACATGATAGACCAATCCATC 58.975 37.037 0.00 0.00 0.00 3.51
176 177 7.727186 AGCATAAAACATGATAGACCAATCCAT 59.273 33.333 0.00 0.00 0.00 3.41
177 178 7.062322 AGCATAAAACATGATAGACCAATCCA 58.938 34.615 0.00 0.00 0.00 3.41
178 179 7.516198 AGCATAAAACATGATAGACCAATCC 57.484 36.000 0.00 0.00 0.00 3.01
179 180 7.380602 GCAAGCATAAAACATGATAGACCAATC 59.619 37.037 0.00 0.00 0.00 2.67
180 181 7.147863 TGCAAGCATAAAACATGATAGACCAAT 60.148 33.333 0.00 0.00 0.00 3.16
181 182 6.152492 TGCAAGCATAAAACATGATAGACCAA 59.848 34.615 0.00 0.00 0.00 3.67
182 183 5.651576 TGCAAGCATAAAACATGATAGACCA 59.348 36.000 0.00 0.00 0.00 4.02
183 184 5.973565 GTGCAAGCATAAAACATGATAGACC 59.026 40.000 0.00 0.00 0.00 3.85
184 185 6.789262 AGTGCAAGCATAAAACATGATAGAC 58.211 36.000 0.00 0.00 0.00 2.59
185 186 7.986889 TCTAGTGCAAGCATAAAACATGATAGA 59.013 33.333 0.00 0.00 0.00 1.98
186 187 8.146479 TCTAGTGCAAGCATAAAACATGATAG 57.854 34.615 0.00 0.00 0.00 2.08
187 188 8.681486 ATCTAGTGCAAGCATAAAACATGATA 57.319 30.769 0.00 0.00 0.00 2.15
188 189 7.578310 ATCTAGTGCAAGCATAAAACATGAT 57.422 32.000 0.00 0.00 0.00 2.45
189 190 7.395190 AATCTAGTGCAAGCATAAAACATGA 57.605 32.000 0.00 0.00 0.00 3.07
190 191 9.229784 CTAAATCTAGTGCAAGCATAAAACATG 57.770 33.333 0.00 0.00 0.00 3.21
191 192 8.960591 ACTAAATCTAGTGCAAGCATAAAACAT 58.039 29.630 0.00 0.00 36.98 2.71
192 193 8.335532 ACTAAATCTAGTGCAAGCATAAAACA 57.664 30.769 0.00 0.00 36.98 2.83
193 194 9.704098 GTACTAAATCTAGTGCAAGCATAAAAC 57.296 33.333 0.00 0.00 39.73 2.43
194 195 9.443323 TGTACTAAATCTAGTGCAAGCATAAAA 57.557 29.630 0.00 0.00 44.69 1.52
232 233 9.778741 ACCGATGTATCAAAATGTTAGATATGT 57.221 29.630 0.00 0.00 0.00 2.29
235 236 9.825109 TGAACCGATGTATCAAAATGTTAGATA 57.175 29.630 0.00 0.00 0.00 1.98
236 237 8.731275 TGAACCGATGTATCAAAATGTTAGAT 57.269 30.769 0.00 0.00 0.00 1.98
237 238 7.279981 CCTGAACCGATGTATCAAAATGTTAGA 59.720 37.037 0.00 0.00 0.00 2.10
238 239 7.409697 CCTGAACCGATGTATCAAAATGTTAG 58.590 38.462 0.00 0.00 0.00 2.34
239 240 6.317642 CCCTGAACCGATGTATCAAAATGTTA 59.682 38.462 0.00 0.00 0.00 2.41
240 241 5.125417 CCCTGAACCGATGTATCAAAATGTT 59.875 40.000 0.00 0.00 0.00 2.71
241 242 4.640201 CCCTGAACCGATGTATCAAAATGT 59.360 41.667 0.00 0.00 0.00 2.71
242 243 4.498009 GCCCTGAACCGATGTATCAAAATG 60.498 45.833 0.00 0.00 0.00 2.32
243 244 3.632145 GCCCTGAACCGATGTATCAAAAT 59.368 43.478 0.00 0.00 0.00 1.82
244 245 3.013921 GCCCTGAACCGATGTATCAAAA 58.986 45.455 0.00 0.00 0.00 2.44
245 246 2.238646 AGCCCTGAACCGATGTATCAAA 59.761 45.455 0.00 0.00 0.00 2.69
246 247 1.837439 AGCCCTGAACCGATGTATCAA 59.163 47.619 0.00 0.00 0.00 2.57
247 248 1.412710 GAGCCCTGAACCGATGTATCA 59.587 52.381 0.00 0.00 0.00 2.15
248 249 1.270358 GGAGCCCTGAACCGATGTATC 60.270 57.143 0.00 0.00 0.00 2.24
249 250 0.759346 GGAGCCCTGAACCGATGTAT 59.241 55.000 0.00 0.00 0.00 2.29
250 251 0.616395 TGGAGCCCTGAACCGATGTA 60.616 55.000 0.00 0.00 0.00 2.29
251 252 1.903877 CTGGAGCCCTGAACCGATGT 61.904 60.000 0.00 0.00 0.00 3.06
252 253 1.153289 CTGGAGCCCTGAACCGATG 60.153 63.158 0.00 0.00 0.00 3.84
253 254 1.613630 ACTGGAGCCCTGAACCGAT 60.614 57.895 5.36 0.00 0.00 4.18
254 255 2.203788 ACTGGAGCCCTGAACCGA 60.204 61.111 5.36 0.00 0.00 4.69
255 256 2.046892 CACTGGAGCCCTGAACCG 60.047 66.667 5.36 0.00 0.00 4.44
256 257 2.360475 GCACTGGAGCCCTGAACC 60.360 66.667 5.36 0.00 0.00 3.62
257 258 0.610232 ATTGCACTGGAGCCCTGAAC 60.610 55.000 0.00 0.00 0.00 3.18
258 259 0.609957 CATTGCACTGGAGCCCTGAA 60.610 55.000 0.00 0.00 0.00 3.02
259 260 1.001764 CATTGCACTGGAGCCCTGA 60.002 57.895 0.00 0.00 0.00 3.86
260 261 2.707849 GCATTGCACTGGAGCCCTG 61.708 63.158 6.16 0.00 0.00 4.45
261 262 2.362120 GCATTGCACTGGAGCCCT 60.362 61.111 6.16 0.00 0.00 5.19
262 263 2.277591 TTGCATTGCACTGGAGCCC 61.278 57.895 11.66 0.00 38.71 5.19
263 264 1.080298 GTTGCATTGCACTGGAGCC 60.080 57.895 11.66 0.00 38.71 4.70
264 265 1.080298 GGTTGCATTGCACTGGAGC 60.080 57.895 11.66 5.01 38.71 4.70
265 266 1.588082 GGGTTGCATTGCACTGGAG 59.412 57.895 11.66 0.00 38.71 3.86
266 267 1.907807 GGGGTTGCATTGCACTGGA 60.908 57.895 11.66 0.00 38.71 3.86
267 268 2.208619 TGGGGTTGCATTGCACTGG 61.209 57.895 11.66 0.00 38.71 4.00
268 269 1.005867 GTGGGGTTGCATTGCACTG 60.006 57.895 11.66 0.00 38.71 3.66
269 270 2.209315 GGTGGGGTTGCATTGCACT 61.209 57.895 11.66 0.00 38.71 4.40
270 271 2.037620 TTGGTGGGGTTGCATTGCAC 62.038 55.000 11.66 6.75 38.71 4.57
271 272 1.126329 ATTGGTGGGGTTGCATTGCA 61.126 50.000 7.38 7.38 36.47 4.08
272 273 0.036590 AATTGGTGGGGTTGCATTGC 59.963 50.000 0.46 0.46 0.00 3.56
273 274 1.810959 CAATTGGTGGGGTTGCATTG 58.189 50.000 0.00 0.00 0.00 2.82
274 275 0.036590 GCAATTGGTGGGGTTGCATT 59.963 50.000 7.72 0.00 45.57 3.56
275 276 1.678724 GCAATTGGTGGGGTTGCAT 59.321 52.632 7.72 0.00 45.57 3.96
276 277 3.146182 GCAATTGGTGGGGTTGCA 58.854 55.556 7.72 0.00 45.57 4.08
277 278 2.049627 TTGGCAATTGGTGGGGTTGC 62.050 55.000 7.72 0.97 45.54 4.17
278 279 0.035176 CTTGGCAATTGGTGGGGTTG 59.965 55.000 7.72 0.00 0.00 3.77
279 280 0.399806 ACTTGGCAATTGGTGGGGTT 60.400 50.000 7.72 0.00 0.00 4.11
280 281 0.485099 TACTTGGCAATTGGTGGGGT 59.515 50.000 7.72 0.00 0.00 4.95
281 282 1.550072 CTTACTTGGCAATTGGTGGGG 59.450 52.381 7.72 0.00 0.00 4.96
282 283 2.247358 ACTTACTTGGCAATTGGTGGG 58.753 47.619 7.72 0.00 0.00 4.61
283 284 4.618227 GCTAACTTACTTGGCAATTGGTGG 60.618 45.833 7.72 0.00 36.38 4.61
284 285 4.022416 TGCTAACTTACTTGGCAATTGGTG 60.022 41.667 7.72 0.00 42.93 4.17
285 286 4.022329 GTGCTAACTTACTTGGCAATTGGT 60.022 41.667 7.72 0.00 46.88 3.67
286 287 4.218417 AGTGCTAACTTACTTGGCAATTGG 59.782 41.667 7.72 0.00 46.88 3.16
287 288 5.376854 AGTGCTAACTTACTTGGCAATTG 57.623 39.130 0.00 0.00 46.88 2.32
289 290 5.376854 CAAGTGCTAACTTACTTGGCAAT 57.623 39.130 0.00 0.00 46.88 3.56
290 291 4.829064 CAAGTGCTAACTTACTTGGCAA 57.171 40.909 0.00 0.00 46.88 4.52
794 795 2.441750 TGGGTTGAGGTGCTAACTCTTT 59.558 45.455 3.43 0.00 35.98 2.52
795 796 2.054799 TGGGTTGAGGTGCTAACTCTT 58.945 47.619 3.43 0.00 35.98 2.85
796 797 1.729586 TGGGTTGAGGTGCTAACTCT 58.270 50.000 3.43 0.00 35.98 3.24
797 798 2.561478 TTGGGTTGAGGTGCTAACTC 57.439 50.000 0.00 0.00 35.55 3.01
798 799 2.375174 TGATTGGGTTGAGGTGCTAACT 59.625 45.455 0.00 0.00 0.00 2.24
799 800 2.790433 TGATTGGGTTGAGGTGCTAAC 58.210 47.619 0.00 0.00 0.00 2.34
800 801 3.153919 GTTGATTGGGTTGAGGTGCTAA 58.846 45.455 0.00 0.00 0.00 3.09
801 802 2.107378 TGTTGATTGGGTTGAGGTGCTA 59.893 45.455 0.00 0.00 0.00 3.49
802 803 1.133513 TGTTGATTGGGTTGAGGTGCT 60.134 47.619 0.00 0.00 0.00 4.40
803 804 1.327303 TGTTGATTGGGTTGAGGTGC 58.673 50.000 0.00 0.00 0.00 5.01
804 805 4.399004 TTTTGTTGATTGGGTTGAGGTG 57.601 40.909 0.00 0.00 0.00 4.00
805 806 5.628797 ATTTTTGTTGATTGGGTTGAGGT 57.371 34.783 0.00 0.00 0.00 3.85
806 807 9.717942 TTTATATTTTTGTTGATTGGGTTGAGG 57.282 29.630 0.00 0.00 0.00 3.86
829 830 9.887629 AACCAAATTGCATGTGATTATCATTTA 57.112 25.926 0.00 0.00 0.00 1.40
830 831 8.795842 AACCAAATTGCATGTGATTATCATTT 57.204 26.923 0.00 0.00 0.00 2.32
831 832 8.795842 AAACCAAATTGCATGTGATTATCATT 57.204 26.923 0.00 0.00 0.00 2.57
832 833 8.795842 AAAACCAAATTGCATGTGATTATCAT 57.204 26.923 0.00 0.00 0.00 2.45
833 834 8.095792 AGAAAACCAAATTGCATGTGATTATCA 58.904 29.630 0.00 0.00 0.00 2.15
834 835 8.483307 AGAAAACCAAATTGCATGTGATTATC 57.517 30.769 0.00 0.00 0.00 1.75
835 836 8.723311 CAAGAAAACCAAATTGCATGTGATTAT 58.277 29.630 0.00 0.00 0.00 1.28
836 837 7.307870 GCAAGAAAACCAAATTGCATGTGATTA 60.308 33.333 4.02 0.00 45.66 1.75
837 838 6.513720 GCAAGAAAACCAAATTGCATGTGATT 60.514 34.615 4.02 0.00 45.66 2.57
838 839 5.049267 GCAAGAAAACCAAATTGCATGTGAT 60.049 36.000 4.02 0.00 45.66 3.06
839 840 4.272991 GCAAGAAAACCAAATTGCATGTGA 59.727 37.500 4.02 0.00 45.66 3.58
840 841 4.529446 GCAAGAAAACCAAATTGCATGTG 58.471 39.130 4.02 0.00 45.66 3.21
841 842 4.816786 GCAAGAAAACCAAATTGCATGT 57.183 36.364 4.02 0.00 45.66 3.21
858 859 6.143598 CACGATGATCTACAAGTATCTGCAAG 59.856 42.308 0.00 0.00 0.00 4.01
859 860 5.979517 CACGATGATCTACAAGTATCTGCAA 59.020 40.000 0.00 0.00 0.00 4.08
860 861 5.507985 CCACGATGATCTACAAGTATCTGCA 60.508 44.000 0.00 0.00 0.00 4.41
870 871 0.823460 TGCAGCCACGATGATCTACA 59.177 50.000 0.00 0.00 0.00 2.74
890 891 4.281941 CCTGTACATCCTTGATAGCTAGCA 59.718 45.833 18.83 7.80 0.00 3.49
891 892 4.282195 ACCTGTACATCCTTGATAGCTAGC 59.718 45.833 6.62 6.62 0.00 3.42
911 912 1.719063 TTCTGCAGCCCTTGGAACCT 61.719 55.000 9.47 0.00 0.00 3.50
919 920 3.285484 CTTCATACATTTCTGCAGCCCT 58.715 45.455 9.47 0.00 0.00 5.19
924 925 5.491070 ACTGTAGCTTCATACATTTCTGCA 58.509 37.500 0.00 0.00 35.21 4.41
1121 1122 4.142182 ACATTGTTTGTCCTCCAAGTTGTG 60.142 41.667 1.45 0.00 30.89 3.33
1197 1198 5.849357 TGTGCAAAGTTAATACGTACCTG 57.151 39.130 0.00 0.00 0.00 4.00
1250 1252 5.914033 TGATGGTGCAAAGATACTAGTACC 58.086 41.667 4.31 2.37 37.28 3.34
1251 1253 6.574350 ACTGATGGTGCAAAGATACTAGTAC 58.426 40.000 4.31 0.00 0.00 2.73
1252 1254 6.607600 AGACTGATGGTGCAAAGATACTAGTA 59.392 38.462 4.77 4.77 0.00 1.82
1357 1361 2.653726 TGTGTGTTTCTTGCACTGGAT 58.346 42.857 0.00 0.00 37.70 3.41
1380 1384 6.046593 AGCCGTATTTTCATTATCAACTCGA 58.953 36.000 0.00 0.00 0.00 4.04
1386 1390 5.883115 TGGTCAAGCCGTATTTTCATTATCA 59.117 36.000 0.00 0.00 41.21 2.15
1387 1391 6.371809 TGGTCAAGCCGTATTTTCATTATC 57.628 37.500 0.00 0.00 41.21 1.75
1388 1392 5.299279 CCTGGTCAAGCCGTATTTTCATTAT 59.701 40.000 0.00 0.00 41.21 1.28
1394 1398 1.173913 GCCTGGTCAAGCCGTATTTT 58.826 50.000 0.00 0.00 41.21 1.82
1400 1404 3.423154 GTTCGCCTGGTCAAGCCG 61.423 66.667 0.00 0.00 41.21 5.52
1410 1414 6.650807 CACCATCTTGTAATATATGTTCGCCT 59.349 38.462 0.00 0.00 0.00 5.52
1412 1416 6.649141 TCCACCATCTTGTAATATATGTTCGC 59.351 38.462 0.00 0.00 0.00 4.70
1447 1451 9.881773 ATGTCCATATTTCCTAATAACACCAAT 57.118 29.630 0.00 0.00 30.38 3.16
1578 1583 9.525409 ACAAAAATCTTCATGCATTTATCTAGC 57.475 29.630 0.00 0.00 0.00 3.42
1629 1634 2.488153 GCTATTATTGGAACGATGGGCC 59.512 50.000 0.00 0.00 0.00 5.80
1640 1653 8.103305 AGACATATACCCTTGTGCTATTATTGG 58.897 37.037 0.00 0.00 0.00 3.16
1751 1769 4.996758 CACAATAGGCCACGAATGATATCA 59.003 41.667 8.10 8.10 0.00 2.15
1760 1778 1.479323 GGAGTACACAATAGGCCACGA 59.521 52.381 5.01 0.00 0.00 4.35
1771 1789 4.282703 GGAACTGGAAACTAGGAGTACACA 59.717 45.833 0.00 0.00 0.00 3.72
1817 1835 4.553330 TGTTGAGTGGAGGATAAGGAAC 57.447 45.455 0.00 0.00 0.00 3.62
1933 1951 1.691163 GGGAGGAAGAGGAGGAGGAAG 60.691 61.905 0.00 0.00 0.00 3.46
1934 1952 0.340208 GGGAGGAAGAGGAGGAGGAA 59.660 60.000 0.00 0.00 0.00 3.36
1935 1953 1.939082 CGGGAGGAAGAGGAGGAGGA 61.939 65.000 0.00 0.00 0.00 3.71
1936 1954 1.456705 CGGGAGGAAGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1937 1955 2.131067 GCGGGAGGAAGAGGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
1938 1956 2.042843 GCGGGAGGAAGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
1939 1957 1.753368 GATGCGGGAGGAAGAGGAGG 61.753 65.000 0.00 0.00 0.00 4.30
1940 1958 0.758685 AGATGCGGGAGGAAGAGGAG 60.759 60.000 0.00 0.00 0.00 3.69
1941 1959 0.757188 GAGATGCGGGAGGAAGAGGA 60.757 60.000 0.00 0.00 0.00 3.71
1985 2003 3.843240 CTGAAGCTTCGCGCCGAC 61.843 66.667 21.11 0.00 40.39 4.79
2177 2195 1.172180 ACGAATGCACAACCACCAGG 61.172 55.000 0.00 0.00 42.21 4.45
2188 2206 1.561769 ATCCTCCACCCACGAATGCA 61.562 55.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.