Multiple sequence alignment - TraesCS2D01G268500

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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 TraesCS2D01G268500 chr2D 100.000 2765 0 0 1 2765 329147559 329150323 0.000000e+00 5107.0
1 TraesCS2D01G268500 chr2A 93.189 2496 132 18 290 2758 435577639 435580123 0.000000e+00 3633.0
2 TraesCS2D01G268500 chr2B 93.308 2391 130 12 291 2658 397919078 397921461 0.000000e+00 3502.0
3 TraesCS2D01G268500 chr2B 85.246 244 30 5 53 292 266120194 266120435 2.130000e-61 246.0
4 TraesCS2D01G268500 chr5D 89.083 229 22 3 291 517 448852486 448852259 5.830000e-72 281.0
5 TraesCS2D01G268500 chr5D 87.179 234 25 4 290 521 355098316 355098546 7.600000e-66 261.0
6 TraesCS2D01G268500 chr5D 84.810 237 34 2 53 287 456379205 456379441 1.280000e-58 237.0
7 TraesCS2D01G268500 chr6B 87.149 249 26 5 291 536 656290839 656291084 7.540000e-71 278.0
8 TraesCS2D01G268500 chr7D 87.660 235 24 5 290 521 233875942 233876174 4.540000e-68 268.0
9 TraesCS2D01G268500 chr7D 100.000 28 0 0 2731 2758 568069184 568069211 5.000000e-03 52.8
10 TraesCS2D01G268500 chr4A 87.179 234 27 3 290 522 645106775 645107006 2.110000e-66 263.0
11 TraesCS2D01G268500 chr3B 85.156 256 32 6 292 543 458404248 458404501 9.830000e-65 257.0
12 TraesCS2D01G268500 chr7B 85.892 241 32 2 49 287 572370561 572370801 3.530000e-64 255.0
13 TraesCS2D01G268500 chr4D 85.200 250 33 4 47 292 49821588 49821339 1.270000e-63 254.0
14 TraesCS2D01G268500 chr4D 84.298 242 36 2 53 292 439383021 439382780 4.600000e-58 235.0
15 TraesCS2D01G268500 chr6D 85.477 241 34 1 53 292 365625628 365625388 1.640000e-62 250.0
16 TraesCS2D01G268500 chr1D 84.921 252 32 5 291 540 36531986 36532233 1.640000e-62 250.0
17 TraesCS2D01G268500 chr5A 85.654 237 32 2 53 287 123677858 123678094 5.910000e-62 248.0
18 TraesCS2D01G268500 chr4B 84.937 239 34 2 53 289 283064948 283064710 9.900000e-60 241.0
19 TraesCS2D01G268500 chr4B 84.810 237 33 3 53 287 471671102 471671337 4.600000e-58 235.0


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 TraesCS2D01G268500 chr2D 329147559 329150323 2764 False 5107 5107 100.000 1 2765 1 chr2D.!!$F1 2764
1 TraesCS2D01G268500 chr2A 435577639 435580123 2484 False 3633 3633 93.189 290 2758 1 chr2A.!!$F1 2468
2 TraesCS2D01G268500 chr2B 397919078 397921461 2383 False 3502 3502 93.308 291 2658 1 chr2B.!!$F2 2367

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
217 218 0.035439 AGTGGCCCATTAGTGAACCG 60.035 55.0 0.0 0.0 0.0 4.44 F
218 219 0.035820 GTGGCCCATTAGTGAACCGA 60.036 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1176 0.253327 GGGTGGTCTCCTTCATGGAC 59.747 60.0 0.0 0.0 40.56 4.02 R
1794 1818 0.719465 GGATGTACAACGGTTCTGCG 59.281 55.0 0.0 0.0 0.00 5.18 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
21 22 4.981806 ATTACAATTCAACCGATGTGGG 57.018 40.909 0.00 0.00 44.64 4.61
22 23 1.544724 ACAATTCAACCGATGTGGGG 58.455 50.000 0.00 0.00 44.64 4.96
23 24 0.173255 CAATTCAACCGATGTGGGGC 59.827 55.000 0.00 0.00 44.64 5.80
24 25 0.251564 AATTCAACCGATGTGGGGCA 60.252 50.000 0.00 0.00 44.64 5.36
25 26 0.965363 ATTCAACCGATGTGGGGCAC 60.965 55.000 0.00 0.00 44.64 5.01
94 95 7.757941 TCAGATGATCTATCAACTAGTCTGG 57.242 40.000 15.43 0.00 37.77 3.86
95 96 6.208402 TCAGATGATCTATCAACTAGTCTGGC 59.792 42.308 15.43 0.00 37.77 4.85
96 97 5.480073 AGATGATCTATCAACTAGTCTGGCC 59.520 44.000 0.00 0.00 38.03 5.36
97 98 4.809193 TGATCTATCAACTAGTCTGGCCT 58.191 43.478 3.32 0.00 33.08 5.19
98 99 4.830046 TGATCTATCAACTAGTCTGGCCTC 59.170 45.833 3.32 0.00 33.08 4.70
99 100 3.215151 TCTATCAACTAGTCTGGCCTCG 58.785 50.000 3.32 0.00 0.00 4.63
100 101 1.115467 ATCAACTAGTCTGGCCTCGG 58.885 55.000 3.32 0.00 0.00 4.63
101 102 0.251653 TCAACTAGTCTGGCCTCGGT 60.252 55.000 3.32 0.00 0.00 4.69
102 103 0.608640 CAACTAGTCTGGCCTCGGTT 59.391 55.000 3.32 3.52 0.00 4.44
103 104 1.002087 CAACTAGTCTGGCCTCGGTTT 59.998 52.381 3.32 0.00 0.00 3.27
104 105 2.226962 ACTAGTCTGGCCTCGGTTTA 57.773 50.000 3.32 0.00 0.00 2.01
105 106 2.748388 ACTAGTCTGGCCTCGGTTTAT 58.252 47.619 3.32 0.00 0.00 1.40
106 107 3.907221 ACTAGTCTGGCCTCGGTTTATA 58.093 45.455 3.32 0.00 0.00 0.98
107 108 4.481072 ACTAGTCTGGCCTCGGTTTATAT 58.519 43.478 3.32 0.00 0.00 0.86
108 109 5.638133 ACTAGTCTGGCCTCGGTTTATATA 58.362 41.667 3.32 0.00 0.00 0.86
109 110 6.073314 ACTAGTCTGGCCTCGGTTTATATAA 58.927 40.000 3.32 0.00 0.00 0.98
110 111 6.724905 ACTAGTCTGGCCTCGGTTTATATAAT 59.275 38.462 3.32 0.00 0.00 1.28
111 112 7.892241 ACTAGTCTGGCCTCGGTTTATATAATA 59.108 37.037 3.32 0.00 0.00 0.98
112 113 6.932947 AGTCTGGCCTCGGTTTATATAATAC 58.067 40.000 3.32 0.00 0.00 1.89
113 114 6.495872 AGTCTGGCCTCGGTTTATATAATACA 59.504 38.462 3.32 0.00 0.00 2.29
114 115 6.589139 GTCTGGCCTCGGTTTATATAATACAC 59.411 42.308 3.32 0.00 0.00 2.90
115 116 5.797051 TGGCCTCGGTTTATATAATACACC 58.203 41.667 3.32 5.15 0.00 4.16
116 117 5.307456 TGGCCTCGGTTTATATAATACACCA 59.693 40.000 3.32 5.68 0.00 4.17
117 118 5.873164 GGCCTCGGTTTATATAATACACCAG 59.127 44.000 13.00 9.66 0.00 4.00
118 119 6.295462 GGCCTCGGTTTATATAATACACCAGA 60.295 42.308 13.00 10.26 0.00 3.86
119 120 6.812160 GCCTCGGTTTATATAATACACCAGAG 59.188 42.308 18.15 18.15 32.55 3.35
120 121 7.321153 CCTCGGTTTATATAATACACCAGAGG 58.679 42.308 23.39 23.39 39.60 3.69
121 122 6.694447 TCGGTTTATATAATACACCAGAGGC 58.306 40.000 13.00 0.00 0.00 4.70
122 123 5.873164 CGGTTTATATAATACACCAGAGGCC 59.127 44.000 13.00 0.00 0.00 5.19
123 124 6.295688 CGGTTTATATAATACACCAGAGGCCT 60.296 42.308 3.86 3.86 0.00 5.19
124 125 7.093640 CGGTTTATATAATACACCAGAGGCCTA 60.094 40.741 4.42 0.00 0.00 3.93
125 126 8.258708 GGTTTATATAATACACCAGAGGCCTAG 58.741 40.741 4.42 0.20 0.00 3.02
126 127 7.973048 TTATATAATACACCAGAGGCCTAGG 57.027 40.000 19.66 19.66 0.00 3.02
127 128 1.807814 AATACACCAGAGGCCTAGGG 58.192 55.000 23.75 21.20 0.00 3.53
128 129 0.642710 ATACACCAGAGGCCTAGGGT 59.357 55.000 23.75 21.80 0.00 4.34
129 130 0.416231 TACACCAGAGGCCTAGGGTT 59.584 55.000 22.16 16.16 0.00 4.11
130 131 0.475828 ACACCAGAGGCCTAGGGTTT 60.476 55.000 22.16 15.07 0.00 3.27
131 132 1.203389 ACACCAGAGGCCTAGGGTTTA 60.203 52.381 22.16 0.00 0.00 2.01
132 133 1.486726 CACCAGAGGCCTAGGGTTTAG 59.513 57.143 22.16 10.11 0.00 1.85
133 134 1.132500 CCAGAGGCCTAGGGTTTAGG 58.868 60.000 4.42 0.00 37.75 2.69
134 135 1.344087 CCAGAGGCCTAGGGTTTAGGA 60.344 57.143 4.42 0.00 36.85 2.94
135 136 2.043227 CAGAGGCCTAGGGTTTAGGAG 58.957 57.143 4.42 0.00 36.85 3.69
136 137 1.938069 AGAGGCCTAGGGTTTAGGAGA 59.062 52.381 4.42 0.00 36.85 3.71
137 138 2.090999 AGAGGCCTAGGGTTTAGGAGAG 60.091 54.545 4.42 0.00 36.85 3.20
138 139 1.652306 AGGCCTAGGGTTTAGGAGAGT 59.348 52.381 1.29 0.00 36.85 3.24
139 140 2.046025 AGGCCTAGGGTTTAGGAGAGTT 59.954 50.000 1.29 0.00 36.85 3.01
140 141 3.274153 AGGCCTAGGGTTTAGGAGAGTTA 59.726 47.826 1.29 0.00 36.85 2.24
141 142 4.077923 AGGCCTAGGGTTTAGGAGAGTTAT 60.078 45.833 1.29 0.00 36.85 1.89
142 143 4.659368 GGCCTAGGGTTTAGGAGAGTTATT 59.341 45.833 11.72 0.00 36.85 1.40
143 144 5.454897 GGCCTAGGGTTTAGGAGAGTTATTG 60.455 48.000 11.72 0.00 36.85 1.90
144 145 5.454897 GCCTAGGGTTTAGGAGAGTTATTGG 60.455 48.000 11.72 0.00 36.85 3.16
145 146 4.505324 AGGGTTTAGGAGAGTTATTGGC 57.495 45.455 0.00 0.00 0.00 4.52
146 147 4.112331 AGGGTTTAGGAGAGTTATTGGCT 58.888 43.478 0.00 0.00 0.00 4.75
147 148 4.540502 AGGGTTTAGGAGAGTTATTGGCTT 59.459 41.667 0.00 0.00 0.00 4.35
148 149 4.640647 GGGTTTAGGAGAGTTATTGGCTTG 59.359 45.833 0.00 0.00 0.00 4.01
149 150 4.640647 GGTTTAGGAGAGTTATTGGCTTGG 59.359 45.833 0.00 0.00 0.00 3.61
150 151 5.497474 GTTTAGGAGAGTTATTGGCTTGGA 58.503 41.667 0.00 0.00 0.00 3.53
151 152 3.636153 AGGAGAGTTATTGGCTTGGAC 57.364 47.619 0.00 0.00 0.00 4.02
152 153 2.093447 AGGAGAGTTATTGGCTTGGACG 60.093 50.000 0.00 0.00 0.00 4.79
153 154 1.666189 GAGAGTTATTGGCTTGGACGC 59.334 52.381 0.00 0.00 0.00 5.19
166 167 4.771127 GACGCCAAGTCTTGTGGA 57.229 55.556 11.61 0.00 46.13 4.02
167 168 2.533318 GACGCCAAGTCTTGTGGAG 58.467 57.895 11.61 2.49 46.13 3.86
168 169 1.830145 ACGCCAAGTCTTGTGGAGT 59.170 52.632 11.61 3.13 43.43 3.85
169 170 0.180406 ACGCCAAGTCTTGTGGAGTT 59.820 50.000 11.61 0.00 45.63 3.01
170 171 1.308998 CGCCAAGTCTTGTGGAGTTT 58.691 50.000 11.61 0.00 38.54 2.66
171 172 1.676006 CGCCAAGTCTTGTGGAGTTTT 59.324 47.619 11.61 0.00 38.54 2.43
172 173 2.287009 CGCCAAGTCTTGTGGAGTTTTC 60.287 50.000 11.61 0.00 38.54 2.29
173 174 2.034685 GCCAAGTCTTGTGGAGTTTTCC 59.965 50.000 11.61 0.00 44.31 3.13
174 175 3.555966 CCAAGTCTTGTGGAGTTTTCCT 58.444 45.455 11.61 0.00 44.36 3.36
175 176 3.954258 CCAAGTCTTGTGGAGTTTTCCTT 59.046 43.478 11.61 0.00 44.36 3.36
176 177 4.202050 CCAAGTCTTGTGGAGTTTTCCTTG 60.202 45.833 11.61 0.00 44.36 3.61
177 178 4.236527 AGTCTTGTGGAGTTTTCCTTGT 57.763 40.909 0.00 0.00 44.36 3.16
178 179 5.367945 AGTCTTGTGGAGTTTTCCTTGTA 57.632 39.130 0.00 0.00 44.36 2.41
179 180 5.941788 AGTCTTGTGGAGTTTTCCTTGTAT 58.058 37.500 0.00 0.00 44.36 2.29
180 181 7.074653 AGTCTTGTGGAGTTTTCCTTGTATA 57.925 36.000 0.00 0.00 44.36 1.47
181 182 7.690256 AGTCTTGTGGAGTTTTCCTTGTATAT 58.310 34.615 0.00 0.00 44.36 0.86
182 183 7.607991 AGTCTTGTGGAGTTTTCCTTGTATATG 59.392 37.037 0.00 0.00 44.36 1.78
183 184 7.390718 GTCTTGTGGAGTTTTCCTTGTATATGT 59.609 37.037 0.00 0.00 44.36 2.29
184 185 7.606456 TCTTGTGGAGTTTTCCTTGTATATGTC 59.394 37.037 0.00 0.00 44.36 3.06
185 186 6.774673 TGTGGAGTTTTCCTTGTATATGTCA 58.225 36.000 0.00 0.00 44.36 3.58
186 187 7.402054 TGTGGAGTTTTCCTTGTATATGTCAT 58.598 34.615 0.00 0.00 44.36 3.06
187 188 7.336679 TGTGGAGTTTTCCTTGTATATGTCATG 59.663 37.037 0.00 0.00 44.36 3.07
188 189 6.828273 TGGAGTTTTCCTTGTATATGTCATGG 59.172 38.462 0.00 7.74 44.36 3.66
189 190 6.828785 GGAGTTTTCCTTGTATATGTCATGGT 59.171 38.462 0.00 0.00 40.58 3.55
190 191 7.012421 GGAGTTTTCCTTGTATATGTCATGGTC 59.988 40.741 0.00 0.00 40.58 4.02
191 192 7.633789 AGTTTTCCTTGTATATGTCATGGTCT 58.366 34.615 0.00 6.59 33.61 3.85
192 193 7.554118 AGTTTTCCTTGTATATGTCATGGTCTG 59.446 37.037 0.00 0.00 33.61 3.51
193 194 4.960938 TCCTTGTATATGTCATGGTCTGC 58.039 43.478 0.00 0.00 33.61 4.26
194 195 4.067896 CCTTGTATATGTCATGGTCTGCC 58.932 47.826 0.00 0.00 0.00 4.85
213 214 2.524306 CCAAAAGTGGCCCATTAGTGA 58.476 47.619 0.00 0.00 38.35 3.41
214 215 2.896685 CCAAAAGTGGCCCATTAGTGAA 59.103 45.455 0.00 0.00 38.35 3.18
215 216 3.306019 CCAAAAGTGGCCCATTAGTGAAC 60.306 47.826 0.00 0.00 38.35 3.18
216 217 2.215942 AAGTGGCCCATTAGTGAACC 57.784 50.000 0.00 0.00 0.00 3.62
217 218 0.035439 AGTGGCCCATTAGTGAACCG 60.035 55.000 0.00 0.00 0.00 4.44
218 219 0.035820 GTGGCCCATTAGTGAACCGA 60.036 55.000 0.00 0.00 0.00 4.69
219 220 0.035820 TGGCCCATTAGTGAACCGAC 60.036 55.000 0.00 0.00 0.00 4.79
220 221 0.035820 GGCCCATTAGTGAACCGACA 60.036 55.000 0.00 0.00 0.00 4.35
221 222 1.408266 GGCCCATTAGTGAACCGACAT 60.408 52.381 0.00 0.00 0.00 3.06
222 223 1.670811 GCCCATTAGTGAACCGACATG 59.329 52.381 0.00 0.00 0.00 3.21
223 224 2.288666 CCCATTAGTGAACCGACATGG 58.711 52.381 0.00 0.00 46.41 3.66
224 225 2.288666 CCATTAGTGAACCGACATGGG 58.711 52.381 0.00 0.00 44.64 4.00
225 226 2.288666 CATTAGTGAACCGACATGGGG 58.711 52.381 0.00 0.00 44.64 4.96
226 227 1.354101 TTAGTGAACCGACATGGGGT 58.646 50.000 4.98 4.98 44.64 4.95
227 228 0.899720 TAGTGAACCGACATGGGGTC 59.100 55.000 10.71 5.24 44.43 4.46
228 229 1.376812 GTGAACCGACATGGGGTCC 60.377 63.158 10.71 0.00 43.48 4.46
229 230 1.537889 TGAACCGACATGGGGTCCT 60.538 57.895 10.71 0.00 43.48 3.85
230 231 1.221021 GAACCGACATGGGGTCCTC 59.779 63.158 10.71 3.30 43.95 3.71
231 232 2.573609 GAACCGACATGGGGTCCTCG 62.574 65.000 10.71 2.96 43.95 4.63
232 233 2.758327 CCGACATGGGGTCCTCGA 60.758 66.667 0.00 0.00 43.95 4.04
233 234 2.494918 CGACATGGGGTCCTCGAC 59.505 66.667 0.00 0.00 43.95 4.20
241 242 2.441532 GGTCCTCGACCCGATCCA 60.442 66.667 0.00 0.00 46.19 3.41
242 243 2.783288 GGTCCTCGACCCGATCCAC 61.783 68.421 0.00 0.00 46.19 4.02
243 244 2.441532 TCCTCGACCCGATCCACC 60.442 66.667 0.00 0.00 34.61 4.61
244 245 2.442272 CCTCGACCCGATCCACCT 60.442 66.667 0.00 0.00 34.61 4.00
245 246 1.152819 CCTCGACCCGATCCACCTA 60.153 63.158 0.00 0.00 34.61 3.08
246 247 0.754217 CCTCGACCCGATCCACCTAA 60.754 60.000 0.00 0.00 34.61 2.69
247 248 1.329256 CTCGACCCGATCCACCTAAT 58.671 55.000 0.00 0.00 34.61 1.73
248 249 1.269998 CTCGACCCGATCCACCTAATC 59.730 57.143 0.00 0.00 34.61 1.75
249 250 0.039437 CGACCCGATCCACCTAATCG 60.039 60.000 0.00 0.00 44.29 3.34
266 267 2.851805 TCGGAAGATGACGTGATGAG 57.148 50.000 0.00 0.00 33.31 2.90
267 268 2.092323 TCGGAAGATGACGTGATGAGT 58.908 47.619 0.00 0.00 33.31 3.41
268 269 3.275999 TCGGAAGATGACGTGATGAGTA 58.724 45.455 0.00 0.00 33.31 2.59
269 270 3.064958 TCGGAAGATGACGTGATGAGTAC 59.935 47.826 0.00 0.00 33.31 2.73
270 271 3.707793 GGAAGATGACGTGATGAGTACC 58.292 50.000 0.00 0.00 0.00 3.34
271 272 3.491104 GGAAGATGACGTGATGAGTACCC 60.491 52.174 0.00 0.00 0.00 3.69
272 273 2.032620 AGATGACGTGATGAGTACCCC 58.967 52.381 0.00 0.00 0.00 4.95
273 274 2.032620 GATGACGTGATGAGTACCCCT 58.967 52.381 0.00 0.00 0.00 4.79
274 275 2.812836 TGACGTGATGAGTACCCCTA 57.187 50.000 0.00 0.00 0.00 3.53
275 276 2.651455 TGACGTGATGAGTACCCCTAG 58.349 52.381 0.00 0.00 0.00 3.02
276 277 2.025605 TGACGTGATGAGTACCCCTAGT 60.026 50.000 0.00 0.00 0.00 2.57
277 278 2.617774 GACGTGATGAGTACCCCTAGTC 59.382 54.545 0.00 0.00 0.00 2.59
278 279 1.955080 CGTGATGAGTACCCCTAGTCC 59.045 57.143 0.00 0.00 0.00 3.85
279 280 2.317973 GTGATGAGTACCCCTAGTCCC 58.682 57.143 0.00 0.00 0.00 4.46
280 281 1.133575 TGATGAGTACCCCTAGTCCCG 60.134 57.143 0.00 0.00 0.00 5.14
281 282 0.187851 ATGAGTACCCCTAGTCCCGG 59.812 60.000 0.00 0.00 0.00 5.73
282 283 0.920763 TGAGTACCCCTAGTCCCGGA 60.921 60.000 0.73 0.00 0.00 5.14
283 284 0.467106 GAGTACCCCTAGTCCCGGAC 60.467 65.000 9.81 9.81 0.00 4.79
284 285 1.217057 AGTACCCCTAGTCCCGGACA 61.217 60.000 19.95 5.08 34.60 4.02
285 286 1.039785 GTACCCCTAGTCCCGGACAC 61.040 65.000 19.95 3.39 34.60 3.67
286 287 2.228841 TACCCCTAGTCCCGGACACC 62.229 65.000 19.95 0.00 34.60 4.16
287 288 2.038329 CCCTAGTCCCGGACACCA 59.962 66.667 19.95 3.57 34.60 4.17
288 289 1.382695 CCCTAGTCCCGGACACCAT 60.383 63.158 19.95 1.25 34.60 3.55
360 361 8.204160 CCACTGGATTAGATTGTGTCTGTTATA 58.796 37.037 0.00 0.00 37.83 0.98
361 362 9.770097 CACTGGATTAGATTGTGTCTGTTATAT 57.230 33.333 0.00 0.00 37.83 0.86
369 370 7.795047 AGATTGTGTCTGTTATATGGACATGA 58.205 34.615 0.00 0.00 41.14 3.07
375 376 7.926018 GTGTCTGTTATATGGACATGACACATA 59.074 37.037 26.04 5.51 44.41 2.29
422 423 4.568152 TGTTTTGCTTAGAAAGTGGCTC 57.432 40.909 0.00 0.00 0.00 4.70
439 440 2.173569 GGCTCTGGGTTGATCCTTGTAT 59.826 50.000 0.00 0.00 36.25 2.29
457 459 6.599244 CCTTGTATTTATTTGTCAGGCTCTGA 59.401 38.462 1.25 1.25 38.25 3.27
492 494 5.654603 AAAGATGATTGTGTGCATCATGT 57.345 34.783 4.51 0.00 42.52 3.21
507 509 0.745486 CATGTTGATGCAGAGGCCGA 60.745 55.000 0.00 0.00 40.13 5.54
529 531 5.180810 AGGTAATCCTCCTTCTTGAAACC 57.819 43.478 0.00 0.00 40.58 3.27
587 611 8.938883 ACACTTCATATATTACTTGGGTGAGAT 58.061 33.333 0.00 0.00 0.00 2.75
618 642 3.415457 AATAGCTAGCATCCTCTTGGC 57.585 47.619 18.83 0.00 0.00 4.52
712 736 2.719531 TCCGGCATGGTTAGCATTTA 57.280 45.000 0.00 0.00 39.52 1.40
722 746 7.362574 GGCATGGTTAGCATTTAGAGTTTGTAA 60.363 37.037 0.00 0.00 0.00 2.41
758 782 5.526111 CGATCAATGAAACGGGGTTATACTT 59.474 40.000 5.56 0.00 0.00 2.24
982 1006 4.695396 ACACACATTACACCGTTACAGAA 58.305 39.130 0.00 0.00 0.00 3.02
986 1010 7.136119 CACACATTACACCGTTACAGAAAAAT 58.864 34.615 0.00 0.00 0.00 1.82
1056 1080 2.150719 ACGTCCCCCACCATTGTCA 61.151 57.895 0.00 0.00 0.00 3.58
1152 1176 0.524862 GGATGTTGTCCAAGCAGCTG 59.475 55.000 10.11 10.11 46.96 4.24
1173 1197 1.264749 CCATGAAGGAGACCACCCGA 61.265 60.000 0.00 0.00 41.22 5.14
1212 1236 2.514013 GCGGCGACAGATACAACGG 61.514 63.158 12.98 0.00 0.00 4.44
1221 1245 2.038557 ACAGATACAACGGCAAAGGAGT 59.961 45.455 0.00 0.00 0.00 3.85
1239 1263 0.529992 GTAGCATGGGCCTGTACGAC 60.530 60.000 4.53 0.00 42.56 4.34
1276 1300 2.604174 GCTAACACGCACGCCACTT 61.604 57.895 0.00 0.00 0.00 3.16
1404 1428 0.460311 CCCTCGACCTGTATTTCGCT 59.540 55.000 0.00 0.00 35.15 4.93
1611 1635 9.074576 ACGTTTCCTTTGTTAATTTCTTCCTAT 57.925 29.630 0.00 0.00 0.00 2.57
1669 1693 0.179040 TGGTCGGTTGTTTGGTCCTC 60.179 55.000 0.00 0.00 0.00 3.71
1758 1782 2.216898 GCTTGTTCAGTGAAGCACTCT 58.783 47.619 5.62 0.00 43.43 3.24
1794 1818 0.614415 TGCAATGAACCACCCATCCC 60.614 55.000 0.00 0.00 0.00 3.85
1832 1856 3.021695 TCCGAGTGTTCCATTAGACGAT 58.978 45.455 0.00 0.00 0.00 3.73
1835 1859 4.499865 CCGAGTGTTCCATTAGACGATGAT 60.500 45.833 0.00 0.00 0.00 2.45
1962 1986 0.179004 CATTAATGCACCGCCCCCTA 60.179 55.000 1.74 0.00 0.00 3.53
1992 2016 4.081862 CAGGACAACATTTGATGCAAGGAT 60.082 41.667 0.00 0.00 0.00 3.24
2050 2074 6.899393 AACTCTTGCTGAAACATTTCCATA 57.101 33.333 2.00 0.00 36.36 2.74
2186 2211 5.476091 AAAGTTGGGCCGATAAAATTTCA 57.524 34.783 0.00 0.00 0.00 2.69
2282 2307 4.500035 GCTATAGTACTTGCACCTCTGACC 60.500 50.000 0.00 0.00 0.00 4.02
2284 2309 0.317479 GTACTTGCACCTCTGACCGT 59.683 55.000 0.00 0.00 0.00 4.83
2296 2321 2.143122 TCTGACCGTTGAAGATGTTGC 58.857 47.619 0.00 0.00 0.00 4.17
2403 2428 3.342719 TGATTGGACTTAGCGCAAATCA 58.657 40.909 11.47 9.99 33.02 2.57
2412 2437 0.806868 AGCGCAAATCACTCATGTGG 59.193 50.000 11.47 0.00 43.94 4.17
2461 2486 5.316167 TCAAGCCTCAGATACAAAATGTGT 58.684 37.500 0.00 0.00 44.82 3.72
2487 2512 1.271871 TGGGCATCTCCAAACGTTGAT 60.272 47.619 0.00 0.00 36.21 2.57
2496 2521 6.438259 TCTCCAAACGTTGATGTTAAACAA 57.562 33.333 0.00 0.00 0.00 2.83
2683 2713 5.582689 AAACTAAACTAATGCTGGATGGC 57.417 39.130 0.00 0.00 0.00 4.40
2693 2723 1.284491 TGCTGGATGGCAACCTCATAA 59.716 47.619 15.31 0.00 39.43 1.90
2696 2726 1.284491 TGGATGGCAACCTCATAAGCA 59.716 47.619 15.31 0.00 32.06 3.91
2700 2730 0.386838 GGCAACCTCATAAGCATGGC 59.613 55.000 0.00 0.00 32.61 4.40
2701 2731 0.386838 GCAACCTCATAAGCATGGCC 59.613 55.000 0.00 0.00 32.61 5.36
2718 2748 1.381327 CCTCCGAGGCCACTAGGAA 60.381 63.158 5.01 0.00 46.10 3.36
2759 2789 4.785453 GGGAAGTCGGGCCAGCTG 62.785 72.222 6.78 6.78 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.699038 CCCCACATCGGTTGAATTGTAAT 59.301 43.478 0.00 0.00 0.00 1.89
1 2 3.085533 CCCCACATCGGTTGAATTGTAA 58.914 45.455 0.00 0.00 0.00 2.41
2 3 2.717390 CCCCACATCGGTTGAATTGTA 58.283 47.619 0.00 0.00 0.00 2.41
3 4 1.544724 CCCCACATCGGTTGAATTGT 58.455 50.000 0.00 0.00 0.00 2.71
4 5 0.173255 GCCCCACATCGGTTGAATTG 59.827 55.000 0.00 0.00 0.00 2.32
5 6 0.251564 TGCCCCACATCGGTTGAATT 60.252 50.000 0.00 0.00 0.00 2.17
6 7 0.965363 GTGCCCCACATCGGTTGAAT 60.965 55.000 0.00 0.00 34.08 2.57
7 8 1.602323 GTGCCCCACATCGGTTGAA 60.602 57.895 0.00 0.00 34.08 2.69
8 9 2.033448 GTGCCCCACATCGGTTGA 59.967 61.111 0.00 0.00 34.08 3.18
9 10 3.061848 GGTGCCCCACATCGGTTG 61.062 66.667 0.00 0.00 35.86 3.77
10 11 2.837031 GATGGTGCCCCACATCGGTT 62.837 60.000 0.00 0.00 45.65 4.44
11 12 3.338250 ATGGTGCCCCACATCGGT 61.338 61.111 0.00 0.00 45.65 4.69
12 13 2.516930 GATGGTGCCCCACATCGG 60.517 66.667 0.00 0.00 45.65 4.18
13 14 2.516930 GGATGGTGCCCCACATCG 60.517 66.667 0.00 0.00 45.65 3.84
14 15 2.516930 CGGATGGTGCCCCACATC 60.517 66.667 0.00 0.00 45.65 3.06
15 16 3.338250 ACGGATGGTGCCCCACAT 61.338 61.111 0.00 0.00 45.65 3.21
16 17 4.343323 CACGGATGGTGCCCCACA 62.343 66.667 0.00 0.00 45.65 4.17
68 69 9.460019 CCAGACTAGTTGATAGATCATCTGATA 57.540 37.037 16.41 0.00 39.50 2.15
69 70 7.093814 GCCAGACTAGTTGATAGATCATCTGAT 60.094 40.741 16.41 0.00 39.50 2.90
70 71 6.208402 GCCAGACTAGTTGATAGATCATCTGA 59.792 42.308 16.41 0.00 39.50 3.27
71 72 6.389091 GCCAGACTAGTTGATAGATCATCTG 58.611 44.000 11.67 11.28 38.07 2.90
72 73 5.480073 GGCCAGACTAGTTGATAGATCATCT 59.520 44.000 0.00 7.93 39.46 2.90
73 74 5.480073 AGGCCAGACTAGTTGATAGATCATC 59.520 44.000 5.01 0.00 36.56 2.92
74 75 5.401750 AGGCCAGACTAGTTGATAGATCAT 58.598 41.667 5.01 0.00 36.56 2.45
75 76 4.809193 AGGCCAGACTAGTTGATAGATCA 58.191 43.478 5.01 0.00 35.30 2.92
76 77 4.083003 CGAGGCCAGACTAGTTGATAGATC 60.083 50.000 5.01 0.00 35.30 2.75
77 78 3.823873 CGAGGCCAGACTAGTTGATAGAT 59.176 47.826 5.01 0.00 35.30 1.98
78 79 3.215151 CGAGGCCAGACTAGTTGATAGA 58.785 50.000 5.01 0.00 35.30 1.98
79 80 2.294791 CCGAGGCCAGACTAGTTGATAG 59.705 54.545 5.01 0.00 37.53 2.08
80 81 2.307768 CCGAGGCCAGACTAGTTGATA 58.692 52.381 5.01 0.00 0.00 2.15
81 82 1.115467 CCGAGGCCAGACTAGTTGAT 58.885 55.000 5.01 0.00 0.00 2.57
82 83 0.251653 ACCGAGGCCAGACTAGTTGA 60.252 55.000 5.01 0.00 0.00 3.18
83 84 0.608640 AACCGAGGCCAGACTAGTTG 59.391 55.000 5.01 0.00 0.00 3.16
84 85 1.349067 AAACCGAGGCCAGACTAGTT 58.651 50.000 5.01 0.00 0.00 2.24
85 86 2.226962 TAAACCGAGGCCAGACTAGT 57.773 50.000 5.01 0.00 0.00 2.57
86 87 6.585695 TTATATAAACCGAGGCCAGACTAG 57.414 41.667 5.01 0.00 0.00 2.57
87 88 7.670979 TGTATTATATAAACCGAGGCCAGACTA 59.329 37.037 5.01 0.00 0.00 2.59
88 89 6.495872 TGTATTATATAAACCGAGGCCAGACT 59.504 38.462 5.01 0.00 0.00 3.24
89 90 6.589139 GTGTATTATATAAACCGAGGCCAGAC 59.411 42.308 5.01 0.00 0.00 3.51
90 91 6.295462 GGTGTATTATATAAACCGAGGCCAGA 60.295 42.308 5.01 0.00 0.00 3.86
91 92 5.873164 GGTGTATTATATAAACCGAGGCCAG 59.127 44.000 5.01 0.00 0.00 4.85
92 93 5.307456 TGGTGTATTATATAAACCGAGGCCA 59.693 40.000 5.01 5.39 33.41 5.36
93 94 5.797051 TGGTGTATTATATAAACCGAGGCC 58.203 41.667 0.00 0.00 33.41 5.19
94 95 6.694447 TCTGGTGTATTATATAAACCGAGGC 58.306 40.000 9.32 0.00 33.41 4.70
95 96 7.321153 CCTCTGGTGTATTATATAAACCGAGG 58.679 42.308 23.39 23.39 41.14 4.63
96 97 6.812160 GCCTCTGGTGTATTATATAAACCGAG 59.188 42.308 18.15 18.15 34.37 4.63
97 98 6.295462 GGCCTCTGGTGTATTATATAAACCGA 60.295 42.308 0.00 8.62 33.41 4.69
98 99 5.873164 GGCCTCTGGTGTATTATATAAACCG 59.127 44.000 0.00 5.75 33.41 4.44
99 100 7.017319 AGGCCTCTGGTGTATTATATAAACC 57.983 40.000 0.00 7.59 0.00 3.27
100 101 8.258708 CCTAGGCCTCTGGTGTATTATATAAAC 58.741 40.741 9.68 0.88 0.00 2.01
101 102 7.402071 CCCTAGGCCTCTGGTGTATTATATAAA 59.598 40.741 9.68 0.00 0.00 1.40
102 103 6.901300 CCCTAGGCCTCTGGTGTATTATATAA 59.099 42.308 9.68 0.00 0.00 0.98
103 104 6.010111 ACCCTAGGCCTCTGGTGTATTATATA 60.010 42.308 22.10 0.00 0.00 0.86
104 105 5.222780 ACCCTAGGCCTCTGGTGTATTATAT 60.223 44.000 22.10 0.00 0.00 0.86
105 106 4.109106 ACCCTAGGCCTCTGGTGTATTATA 59.891 45.833 22.10 0.00 0.00 0.98
106 107 3.116317 ACCCTAGGCCTCTGGTGTATTAT 60.116 47.826 22.10 0.00 0.00 1.28
107 108 2.249214 ACCCTAGGCCTCTGGTGTATTA 59.751 50.000 22.10 0.00 0.00 0.98
108 109 1.009675 ACCCTAGGCCTCTGGTGTATT 59.990 52.381 22.10 0.69 0.00 1.89
109 110 0.642710 ACCCTAGGCCTCTGGTGTAT 59.357 55.000 22.10 1.04 0.00 2.29
110 111 0.416231 AACCCTAGGCCTCTGGTGTA 59.584 55.000 23.14 0.00 0.00 2.90
111 112 0.475828 AAACCCTAGGCCTCTGGTGT 60.476 55.000 23.14 16.81 0.00 4.16
112 113 1.486726 CTAAACCCTAGGCCTCTGGTG 59.513 57.143 23.14 15.75 0.00 4.17
113 114 1.625508 CCTAAACCCTAGGCCTCTGGT 60.626 57.143 18.23 18.23 0.00 4.00
114 115 1.132500 CCTAAACCCTAGGCCTCTGG 58.868 60.000 9.68 14.47 0.00 3.86
115 116 2.043227 CTCCTAAACCCTAGGCCTCTG 58.957 57.143 9.68 3.03 34.74 3.35
116 117 1.938069 TCTCCTAAACCCTAGGCCTCT 59.062 52.381 9.68 0.00 34.74 3.69
117 118 2.321719 CTCTCCTAAACCCTAGGCCTC 58.678 57.143 9.68 0.00 34.74 4.70
118 119 1.652306 ACTCTCCTAAACCCTAGGCCT 59.348 52.381 11.78 11.78 34.74 5.19
119 120 2.177811 ACTCTCCTAAACCCTAGGCC 57.822 55.000 2.05 0.00 34.74 5.19
120 121 5.454897 CCAATAACTCTCCTAAACCCTAGGC 60.455 48.000 2.05 0.00 34.74 3.93
121 122 5.454897 GCCAATAACTCTCCTAAACCCTAGG 60.455 48.000 0.06 0.06 36.06 3.02
122 123 5.367060 AGCCAATAACTCTCCTAAACCCTAG 59.633 44.000 0.00 0.00 0.00 3.02
123 124 5.286221 AGCCAATAACTCTCCTAAACCCTA 58.714 41.667 0.00 0.00 0.00 3.53
124 125 4.112331 AGCCAATAACTCTCCTAAACCCT 58.888 43.478 0.00 0.00 0.00 4.34
125 126 4.505324 AGCCAATAACTCTCCTAAACCC 57.495 45.455 0.00 0.00 0.00 4.11
126 127 4.640647 CCAAGCCAATAACTCTCCTAAACC 59.359 45.833 0.00 0.00 0.00 3.27
127 128 5.354513 GTCCAAGCCAATAACTCTCCTAAAC 59.645 44.000 0.00 0.00 0.00 2.01
128 129 5.497474 GTCCAAGCCAATAACTCTCCTAAA 58.503 41.667 0.00 0.00 0.00 1.85
129 130 4.382685 CGTCCAAGCCAATAACTCTCCTAA 60.383 45.833 0.00 0.00 0.00 2.69
130 131 3.132289 CGTCCAAGCCAATAACTCTCCTA 59.868 47.826 0.00 0.00 0.00 2.94
131 132 2.093447 CGTCCAAGCCAATAACTCTCCT 60.093 50.000 0.00 0.00 0.00 3.69
132 133 2.280628 CGTCCAAGCCAATAACTCTCC 58.719 52.381 0.00 0.00 0.00 3.71
133 134 1.666189 GCGTCCAAGCCAATAACTCTC 59.334 52.381 0.00 0.00 0.00 3.20
134 135 1.739067 GCGTCCAAGCCAATAACTCT 58.261 50.000 0.00 0.00 0.00 3.24
146 147 0.817634 CCACAAGACTTGGCGTCCAA 60.818 55.000 19.16 10.28 43.91 3.53
147 148 1.227823 CCACAAGACTTGGCGTCCA 60.228 57.895 19.16 0.00 43.91 4.02
148 149 0.951040 CTCCACAAGACTTGGCGTCC 60.951 60.000 19.16 0.00 43.91 4.79
149 150 0.249911 ACTCCACAAGACTTGGCGTC 60.250 55.000 19.16 0.00 43.17 5.19
150 151 0.180406 AACTCCACAAGACTTGGCGT 59.820 50.000 19.16 1.60 33.34 5.68
151 152 1.308998 AAACTCCACAAGACTTGGCG 58.691 50.000 19.16 9.62 33.71 5.69
152 153 2.034685 GGAAAACTCCACAAGACTTGGC 59.965 50.000 19.16 0.00 33.71 4.52
153 154 3.555966 AGGAAAACTCCACAAGACTTGG 58.444 45.455 19.16 3.43 35.18 3.61
154 155 4.399303 ACAAGGAAAACTCCACAAGACTTG 59.601 41.667 13.77 13.77 38.85 3.16
155 156 4.600062 ACAAGGAAAACTCCACAAGACTT 58.400 39.130 0.00 0.00 0.00 3.01
156 157 4.236527 ACAAGGAAAACTCCACAAGACT 57.763 40.909 0.00 0.00 0.00 3.24
157 158 7.390718 ACATATACAAGGAAAACTCCACAAGAC 59.609 37.037 0.00 0.00 0.00 3.01
158 159 7.458397 ACATATACAAGGAAAACTCCACAAGA 58.542 34.615 0.00 0.00 0.00 3.02
159 160 7.390440 TGACATATACAAGGAAAACTCCACAAG 59.610 37.037 0.00 0.00 0.00 3.16
160 161 7.227873 TGACATATACAAGGAAAACTCCACAA 58.772 34.615 0.00 0.00 0.00 3.33
161 162 6.774673 TGACATATACAAGGAAAACTCCACA 58.225 36.000 0.00 0.00 0.00 4.17
162 163 7.201732 CCATGACATATACAAGGAAAACTCCAC 60.202 40.741 0.00 0.00 0.00 4.02
163 164 6.828273 CCATGACATATACAAGGAAAACTCCA 59.172 38.462 0.00 0.00 0.00 3.86
164 165 6.828785 ACCATGACATATACAAGGAAAACTCC 59.171 38.462 0.00 0.00 31.67 3.85
165 166 7.770897 AGACCATGACATATACAAGGAAAACTC 59.229 37.037 0.00 0.00 31.67 3.01
166 167 7.554118 CAGACCATGACATATACAAGGAAAACT 59.446 37.037 0.00 0.00 31.67 2.66
167 168 7.679638 GCAGACCATGACATATACAAGGAAAAC 60.680 40.741 0.00 0.00 31.67 2.43
168 169 6.318648 GCAGACCATGACATATACAAGGAAAA 59.681 38.462 0.00 0.00 31.67 2.29
169 170 5.822519 GCAGACCATGACATATACAAGGAAA 59.177 40.000 0.00 0.00 31.67 3.13
170 171 5.368145 GCAGACCATGACATATACAAGGAA 58.632 41.667 0.00 0.00 31.67 3.36
171 172 4.202357 GGCAGACCATGACATATACAAGGA 60.202 45.833 0.00 0.00 36.67 3.36
172 173 4.067896 GGCAGACCATGACATATACAAGG 58.932 47.826 0.00 0.00 36.67 3.61
173 174 4.707105 TGGCAGACCATGACATATACAAG 58.293 43.478 0.00 0.00 44.15 3.16
174 175 4.769345 TGGCAGACCATGACATATACAA 57.231 40.909 0.00 0.00 44.15 2.41
194 195 3.306019 GGTTCACTAATGGGCCACTTTTG 60.306 47.826 9.28 3.80 0.00 2.44
195 196 2.897326 GGTTCACTAATGGGCCACTTTT 59.103 45.455 9.28 1.22 0.00 2.27
196 197 2.525368 GGTTCACTAATGGGCCACTTT 58.475 47.619 9.28 2.14 0.00 2.66
197 198 1.613255 CGGTTCACTAATGGGCCACTT 60.613 52.381 9.28 7.43 0.00 3.16
198 199 0.035439 CGGTTCACTAATGGGCCACT 60.035 55.000 9.28 0.00 0.00 4.00
199 200 0.035820 TCGGTTCACTAATGGGCCAC 60.036 55.000 9.28 0.00 0.00 5.01
200 201 0.035820 GTCGGTTCACTAATGGGCCA 60.036 55.000 9.61 9.61 0.00 5.36
201 202 0.035820 TGTCGGTTCACTAATGGGCC 60.036 55.000 0.00 0.00 0.00 5.80
202 203 1.670811 CATGTCGGTTCACTAATGGGC 59.329 52.381 0.00 0.00 0.00 5.36
203 204 2.288666 CCATGTCGGTTCACTAATGGG 58.711 52.381 0.00 0.00 32.61 4.00
204 205 2.288666 CCCATGTCGGTTCACTAATGG 58.711 52.381 0.00 0.00 35.39 3.16
205 206 2.288666 CCCCATGTCGGTTCACTAATG 58.711 52.381 0.00 0.00 0.00 1.90
206 207 1.913419 ACCCCATGTCGGTTCACTAAT 59.087 47.619 0.00 0.00 0.00 1.73
207 208 1.276989 GACCCCATGTCGGTTCACTAA 59.723 52.381 3.39 0.00 33.49 2.24
208 209 0.899720 GACCCCATGTCGGTTCACTA 59.100 55.000 3.39 0.00 33.49 2.74
209 210 1.677552 GACCCCATGTCGGTTCACT 59.322 57.895 3.39 0.00 33.49 3.41
210 211 1.376812 GGACCCCATGTCGGTTCAC 60.377 63.158 3.39 0.00 45.46 3.18
211 212 1.537889 AGGACCCCATGTCGGTTCA 60.538 57.895 9.58 0.00 45.46 3.18
212 213 1.221021 GAGGACCCCATGTCGGTTC 59.779 63.158 3.39 1.67 45.46 3.62
213 214 2.656069 CGAGGACCCCATGTCGGTT 61.656 63.158 3.39 0.00 45.46 4.44
214 215 3.075005 CGAGGACCCCATGTCGGT 61.075 66.667 1.42 1.42 45.46 4.69
215 216 2.758327 TCGAGGACCCCATGTCGG 60.758 66.667 1.89 0.00 45.46 4.79
216 217 2.494918 GTCGAGGACCCCATGTCG 59.505 66.667 0.00 0.00 45.46 4.35
217 218 2.901042 GGTCGAGGACCCCATGTC 59.099 66.667 3.36 0.00 46.19 3.06
225 226 2.783288 GGTGGATCGGGTCGAGGAC 61.783 68.421 0.00 0.00 39.91 3.85
226 227 1.638679 TAGGTGGATCGGGTCGAGGA 61.639 60.000 0.00 0.00 39.91 3.71
227 228 0.754217 TTAGGTGGATCGGGTCGAGG 60.754 60.000 0.00 0.00 39.91 4.63
228 229 1.269998 GATTAGGTGGATCGGGTCGAG 59.730 57.143 0.00 0.00 39.91 4.04
229 230 1.325355 GATTAGGTGGATCGGGTCGA 58.675 55.000 0.00 0.00 41.13 4.20
230 231 0.039437 CGATTAGGTGGATCGGGTCG 60.039 60.000 0.00 0.00 41.89 4.79
231 232 3.888093 CGATTAGGTGGATCGGGTC 57.112 57.895 0.00 0.00 41.89 4.46
235 236 3.255888 TCATCTTCCGATTAGGTGGATCG 59.744 47.826 0.00 0.00 44.40 3.69
236 237 4.561105 GTCATCTTCCGATTAGGTGGATC 58.439 47.826 0.00 0.00 41.99 3.36
237 238 3.005897 CGTCATCTTCCGATTAGGTGGAT 59.994 47.826 0.00 0.00 41.99 3.41
238 239 2.361119 CGTCATCTTCCGATTAGGTGGA 59.639 50.000 0.00 0.00 41.99 4.02
239 240 2.100916 ACGTCATCTTCCGATTAGGTGG 59.899 50.000 0.00 0.00 41.99 4.61
240 241 3.116300 CACGTCATCTTCCGATTAGGTG 58.884 50.000 0.00 0.00 41.99 4.00
241 242 3.021695 TCACGTCATCTTCCGATTAGGT 58.978 45.455 0.00 0.00 41.99 3.08
242 243 3.710326 TCACGTCATCTTCCGATTAGG 57.290 47.619 0.00 0.00 42.97 2.69
243 244 4.860072 TCATCACGTCATCTTCCGATTAG 58.140 43.478 0.00 0.00 0.00 1.73
244 245 4.338400 ACTCATCACGTCATCTTCCGATTA 59.662 41.667 0.00 0.00 0.00 1.75
245 246 3.131223 ACTCATCACGTCATCTTCCGATT 59.869 43.478 0.00 0.00 0.00 3.34
246 247 2.690497 ACTCATCACGTCATCTTCCGAT 59.310 45.455 0.00 0.00 0.00 4.18
247 248 2.092323 ACTCATCACGTCATCTTCCGA 58.908 47.619 0.00 0.00 0.00 4.55
248 249 2.568696 ACTCATCACGTCATCTTCCG 57.431 50.000 0.00 0.00 0.00 4.30
249 250 3.491104 GGGTACTCATCACGTCATCTTCC 60.491 52.174 0.00 0.00 0.00 3.46
250 251 3.491104 GGGGTACTCATCACGTCATCTTC 60.491 52.174 0.00 0.00 0.00 2.87
251 252 2.431057 GGGGTACTCATCACGTCATCTT 59.569 50.000 0.00 0.00 0.00 2.40
252 253 2.032620 GGGGTACTCATCACGTCATCT 58.967 52.381 0.00 0.00 0.00 2.90
253 254 2.032620 AGGGGTACTCATCACGTCATC 58.967 52.381 0.00 0.00 0.00 2.92
254 255 2.160721 AGGGGTACTCATCACGTCAT 57.839 50.000 0.00 0.00 0.00 3.06
255 256 2.025605 ACTAGGGGTACTCATCACGTCA 60.026 50.000 0.00 0.00 0.00 4.35
256 257 2.617774 GACTAGGGGTACTCATCACGTC 59.382 54.545 0.00 0.00 0.00 4.34
257 258 2.652590 GACTAGGGGTACTCATCACGT 58.347 52.381 0.00 0.00 0.00 4.49
258 259 1.955080 GGACTAGGGGTACTCATCACG 59.045 57.143 0.00 0.00 0.00 4.35
259 260 2.317973 GGGACTAGGGGTACTCATCAC 58.682 57.143 0.00 0.00 0.00 3.06
260 261 1.133575 CGGGACTAGGGGTACTCATCA 60.134 57.143 0.00 0.00 0.00 3.07
261 262 1.618487 CGGGACTAGGGGTACTCATC 58.382 60.000 0.00 0.00 0.00 2.92
262 263 0.187851 CCGGGACTAGGGGTACTCAT 59.812 60.000 0.00 0.00 0.00 2.90
263 264 0.920763 TCCGGGACTAGGGGTACTCA 60.921 60.000 0.00 0.00 0.00 3.41
264 265 0.467106 GTCCGGGACTAGGGGTACTC 60.467 65.000 19.92 0.00 0.00 2.59
265 266 1.217057 TGTCCGGGACTAGGGGTACT 61.217 60.000 26.41 0.00 33.15 2.73
266 267 1.039785 GTGTCCGGGACTAGGGGTAC 61.040 65.000 26.41 11.67 33.15 3.34
267 268 1.307647 GTGTCCGGGACTAGGGGTA 59.692 63.158 26.41 2.84 33.15 3.69
268 269 2.038490 GTGTCCGGGACTAGGGGT 59.962 66.667 26.41 0.00 33.15 4.95
269 270 2.762875 GGTGTCCGGGACTAGGGG 60.763 72.222 26.41 0.00 33.15 4.79
270 271 0.981277 AATGGTGTCCGGGACTAGGG 60.981 60.000 26.41 0.00 33.15 3.53
271 272 1.687123 CTAATGGTGTCCGGGACTAGG 59.313 57.143 26.41 7.41 33.15 3.02
272 273 1.687123 CCTAATGGTGTCCGGGACTAG 59.313 57.143 26.41 18.16 33.15 2.57
273 274 1.784358 CCTAATGGTGTCCGGGACTA 58.216 55.000 26.41 13.98 33.15 2.59
274 275 1.623542 GCCTAATGGTGTCCGGGACT 61.624 60.000 26.41 9.70 33.15 3.85
275 276 1.153229 GCCTAATGGTGTCCGGGAC 60.153 63.158 20.36 20.36 35.27 4.46
276 277 2.727392 CGCCTAATGGTGTCCGGGA 61.727 63.158 0.00 0.00 38.95 5.14
277 278 2.203015 CGCCTAATGGTGTCCGGG 60.203 66.667 0.00 0.00 38.95 5.73
278 279 2.203015 CCGCCTAATGGTGTCCGG 60.203 66.667 0.00 0.00 42.08 5.14
279 280 2.582436 ACCGCCTAATGGTGTCCG 59.418 61.111 0.00 0.00 42.08 4.79
284 285 0.609662 AACGTACACCGCCTAATGGT 59.390 50.000 0.00 0.00 41.42 3.55
285 286 2.582728 TAACGTACACCGCCTAATGG 57.417 50.000 0.00 0.00 41.42 3.16
286 287 2.798283 CCATAACGTACACCGCCTAATG 59.202 50.000 0.00 0.00 41.42 1.90
287 288 2.224113 CCCATAACGTACACCGCCTAAT 60.224 50.000 0.00 0.00 41.42 1.73
288 289 1.136695 CCCATAACGTACACCGCCTAA 59.863 52.381 0.00 0.00 41.42 2.69
298 299 2.895404 GGTCTAGGCATCCCATAACGTA 59.105 50.000 0.00 0.00 0.00 3.57
360 361 8.432013 ACAAGTATACATATGTGTCATGTCCAT 58.568 33.333 18.81 3.11 39.77 3.41
361 362 7.791029 ACAAGTATACATATGTGTCATGTCCA 58.209 34.615 18.81 0.00 39.77 4.02
367 368 8.301252 ACACCTACAAGTATACATATGTGTCA 57.699 34.615 18.81 0.00 39.77 3.58
369 370 8.358148 GCTACACCTACAAGTATACATATGTGT 58.642 37.037 18.81 14.37 42.39 3.72
375 376 7.419711 AGTTGCTACACCTACAAGTATACAT 57.580 36.000 5.50 0.00 0.00 2.29
415 416 0.548682 AGGATCAACCCAGAGCCACT 60.549 55.000 0.83 0.00 46.36 4.00
422 423 8.066612 ACAAATAAATACAAGGATCAACCCAG 57.933 34.615 0.00 0.00 40.05 4.45
439 440 8.806429 TTATTCATCAGAGCCTGACAAATAAA 57.194 30.769 18.74 10.75 43.63 1.40
492 494 0.975556 TACCTCGGCCTCTGCATCAA 60.976 55.000 0.00 0.00 40.13 2.57
507 509 6.411554 TTTGGTTTCAAGAAGGAGGATTACCT 60.412 38.462 0.00 0.00 40.71 3.08
587 611 9.338622 GAGGATGCTAGCTATTTTAAGGTTTAA 57.661 33.333 17.23 0.00 0.00 1.52
712 736 4.932200 CGAGATGCCTCTTTTACAAACTCT 59.068 41.667 0.00 0.00 37.28 3.24
722 746 4.412796 TCATTGATCGAGATGCCTCTTT 57.587 40.909 0.00 0.00 37.28 2.52
758 782 5.303333 GGAGGAACAACAACCCAAAAATAGA 59.697 40.000 0.00 0.00 0.00 1.98
807 831 0.905357 ACGAGAAAGGGAGGTGATGG 59.095 55.000 0.00 0.00 0.00 3.51
946 970 1.737236 TGTGTGTTGGCTATCGAATGC 59.263 47.619 4.67 4.67 0.00 3.56
1044 1068 2.566833 TGAAGAGTGACAATGGTGGG 57.433 50.000 0.00 0.00 0.00 4.61
1056 1080 1.342076 TGCTCCCTACCGATGAAGAGT 60.342 52.381 0.00 0.00 0.00 3.24
1152 1176 0.253327 GGGTGGTCTCCTTCATGGAC 59.747 60.000 0.00 0.00 40.56 4.02
1173 1197 0.980423 GCTTCTCCCACTTGACCTCT 59.020 55.000 0.00 0.00 0.00 3.69
1200 1224 2.038557 ACTCCTTTGCCGTTGTATCTGT 59.961 45.455 0.00 0.00 0.00 3.41
1212 1236 1.387295 GGCCCATGCTACTCCTTTGC 61.387 60.000 0.00 0.00 37.74 3.68
1221 1245 1.820581 GTCGTACAGGCCCATGCTA 59.179 57.895 0.00 0.00 37.74 3.49
1248 1272 1.739929 CGTGTTAGCGCATCCCACA 60.740 57.895 11.47 1.15 0.00 4.17
1383 1407 0.870307 CGAAATACAGGTCGAGGGCG 60.870 60.000 0.00 0.00 39.64 6.13
1404 1428 2.280797 GACAGCTGCCGGTTGACA 60.281 61.111 15.27 0.00 0.00 3.58
1419 1443 2.956964 CGCATCTTCGGCTCGGAC 60.957 66.667 0.00 0.00 0.00 4.79
1452 1476 0.961753 CCACAGAAAGGGAAGGCAAC 59.038 55.000 0.00 0.00 0.00 4.17
1611 1635 6.706270 GCTGATGGTTCTTTCGGAATCTATAA 59.294 38.462 0.00 0.00 36.12 0.98
1669 1693 2.461945 CGCCTGCTGCATGAGTCAG 61.462 63.158 9.18 0.00 41.33 3.51
1758 1782 2.757508 AGCCAGCGCTCTCAGCTA 60.758 61.111 7.13 0.00 43.95 3.32
1794 1818 0.719465 GGATGTACAACGGTTCTGCG 59.281 55.000 0.00 0.00 0.00 5.18
1832 1856 1.114627 CGGTCATGTCCTCTCCATCA 58.885 55.000 7.41 0.00 0.00 3.07
1835 1859 1.078528 ACCGGTCATGTCCTCTCCA 59.921 57.895 0.00 0.00 0.00 3.86
1962 1986 6.153170 TGCATCAAATGTTGTCCTGTCAATAT 59.847 34.615 0.00 0.00 32.17 1.28
1992 2016 5.253330 AGAAGTTGGTGAACAAGAAGAACA 58.747 37.500 0.00 0.00 40.38 3.18
2186 2211 8.964772 CCCATCTAAAATCTCTGATTCAAAACT 58.035 33.333 0.00 0.00 0.00 2.66
2260 2285 4.261238 CGGTCAGAGGTGCAAGTACTATAG 60.261 50.000 0.00 0.00 0.00 1.31
2263 2288 1.816835 CGGTCAGAGGTGCAAGTACTA 59.183 52.381 0.00 0.00 0.00 1.82
2282 2307 6.746822 TGCATATTTAAGCAACATCTTCAACG 59.253 34.615 0.00 0.00 37.90 4.10
2461 2486 3.278574 CGTTTGGAGATGCCCAATAAGA 58.721 45.455 0.00 0.00 44.83 2.10
2487 2512 8.341903 CACAGACATATGAGTGTTTGTTTAACA 58.658 33.333 10.38 0.00 42.63 2.41
2522 2551 2.478335 TTTGATGGTGTCCTCCCGGC 62.478 60.000 0.00 0.00 0.00 6.13
2528 2557 3.846588 AGGATAGTGTTTGATGGTGTCCT 59.153 43.478 0.00 0.00 0.00 3.85
2683 2713 1.952296 GAGGCCATGCTTATGAGGTTG 59.048 52.381 5.01 0.00 0.00 3.77
2700 2730 0.760945 ATTCCTAGTGGCCTCGGAGG 60.761 60.000 19.95 19.95 34.32 4.30
2701 2731 0.390860 CATTCCTAGTGGCCTCGGAG 59.609 60.000 3.32 3.44 34.32 4.63
2718 2748 1.217585 CGTCGCGATGAGGATTGCAT 61.218 55.000 23.83 0.00 38.76 3.96
2729 2759 4.077184 TTCCCCAAGCGTCGCGAT 62.077 61.111 14.06 1.70 0.00 4.58
2732 2762 3.119096 GACTTCCCCAAGCGTCGC 61.119 66.667 9.80 9.80 32.09 5.19


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

AutoCloner maintained by Alex Coulton.