Multiple sequence alignment - TraesCS3A01G252400

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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 TraesCS3A01G252400 chr3A 100.000 2195 0 0 1 2195 472907363 472905169 0.000000e+00 4054.0
1 TraesCS3A01G252400 chr3A 84.715 386 53 5 1 384 34045537 34045156 4.420000e-102 381.0
2 TraesCS3A01G252400 chr3B 90.784 1823 78 27 422 2195 454877395 454875614 0.000000e+00 2353.0
3 TraesCS3A01G252400 chr3B 85.117 383 50 7 1 380 725850596 725850974 3.420000e-103 385.0
4 TraesCS3A01G252400 chr3D 86.416 1119 61 33 475 1542 354275505 354274427 0.000000e+00 1140.0
5 TraesCS3A01G252400 chr3D 93.272 654 27 3 1543 2195 354274388 354273751 0.000000e+00 948.0
6 TraesCS3A01G252400 chr3D 86.592 358 42 5 3 356 52918322 52918677 7.350000e-105 390.0
7 TraesCS3A01G252400 chr3D 90.000 60 5 1 435 494 354277154 354277096 2.340000e-10 76.8
8 TraesCS3A01G252400 chr7D 86.082 388 46 7 1 384 100306313 100305930 5.640000e-111 411.0
9 TraesCS3A01G252400 chr2A 85.751 386 50 4 1 384 496834674 496835056 9.440000e-109 403.0
10 TraesCS3A01G252400 chr2D 85.013 387 53 4 1 384 87664277 87664661 2.640000e-104 388.0
11 TraesCS3A01G252400 chr7A 84.755 387 53 5 1 384 39471120 39470737 1.230000e-102 383.0
12 TraesCS3A01G252400 chr6B 84.856 383 50 7 2 380 64679592 64679214 1.590000e-101 379.0
13 TraesCS3A01G252400 chr5A 84.496 387 54 5 1 384 28756147 28755764 5.720000e-101 377.0


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 TraesCS3A01G252400 chr3A 472905169 472907363 2194 True 4054.0 4054 100.000 1 2195 1 chr3A.!!$R2 2194
1 TraesCS3A01G252400 chr3B 454875614 454877395 1781 True 2353.0 2353 90.784 422 2195 1 chr3B.!!$R1 1773
2 TraesCS3A01G252400 chr3D 354273751 354277154 3403 True 721.6 1140 89.896 435 2195 3 chr3D.!!$R1 1760

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
596 2208 0.108377 TCACCCGATCAACACATCCG 60.108 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 3355 0.179129 GTGGATGATTTTGCTGCCCG 60.179 55.0 0.0 0.0 0.0 6.13 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
19 20 1.783071 GGGGTGTTTGTTTTCAGGGA 58.217 50.000 0.00 0.00 0.00 4.20
20 21 2.325484 GGGGTGTTTGTTTTCAGGGAT 58.675 47.619 0.00 0.00 0.00 3.85
21 22 2.703536 GGGGTGTTTGTTTTCAGGGATT 59.296 45.455 0.00 0.00 0.00 3.01
22 23 3.135712 GGGGTGTTTGTTTTCAGGGATTT 59.864 43.478 0.00 0.00 0.00 2.17
23 24 4.384757 GGGGTGTTTGTTTTCAGGGATTTT 60.385 41.667 0.00 0.00 0.00 1.82
24 25 5.189928 GGGTGTTTGTTTTCAGGGATTTTT 58.810 37.500 0.00 0.00 0.00 1.94
109 110 7.696992 TTTAAGGGCTAAACTAGTCATTTGG 57.303 36.000 0.00 0.00 35.81 3.28
110 111 4.236527 AGGGCTAAACTAGTCATTTGGG 57.763 45.455 0.00 0.00 30.24 4.12
111 112 3.850173 AGGGCTAAACTAGTCATTTGGGA 59.150 43.478 0.00 0.00 30.24 4.37
112 113 4.478686 AGGGCTAAACTAGTCATTTGGGAT 59.521 41.667 0.00 0.00 30.24 3.85
113 114 5.044105 AGGGCTAAACTAGTCATTTGGGATT 60.044 40.000 0.00 0.00 30.24 3.01
114 115 6.159751 AGGGCTAAACTAGTCATTTGGGATTA 59.840 38.462 0.00 0.00 30.24 1.75
115 116 6.831868 GGGCTAAACTAGTCATTTGGGATTAA 59.168 38.462 0.00 0.00 30.24 1.40
116 117 7.340999 GGGCTAAACTAGTCATTTGGGATTAAA 59.659 37.037 0.00 0.00 30.24 1.52
117 118 8.914011 GGCTAAACTAGTCATTTGGGATTAAAT 58.086 33.333 0.00 0.00 0.00 1.40
118 119 9.736023 GCTAAACTAGTCATTTGGGATTAAATG 57.264 33.333 0.00 0.00 45.14 2.32
119 120 9.736023 CTAAACTAGTCATTTGGGATTAAATGC 57.264 33.333 0.00 3.19 44.04 3.56
120 121 7.716799 AACTAGTCATTTGGGATTAAATGCA 57.283 32.000 0.00 0.00 44.04 3.96
121 122 7.716799 ACTAGTCATTTGGGATTAAATGCAA 57.283 32.000 0.00 0.00 44.04 4.08
122 123 8.133024 ACTAGTCATTTGGGATTAAATGCAAA 57.867 30.769 0.00 0.00 44.04 3.68
123 124 8.592809 ACTAGTCATTTGGGATTAAATGCAAAA 58.407 29.630 0.00 0.00 44.04 2.44
124 125 7.910441 AGTCATTTGGGATTAAATGCAAAAG 57.090 32.000 0.00 0.00 44.04 2.27
125 126 7.678837 AGTCATTTGGGATTAAATGCAAAAGA 58.321 30.769 0.00 0.00 44.04 2.52
126 127 7.603784 AGTCATTTGGGATTAAATGCAAAAGAC 59.396 33.333 0.00 0.00 44.04 3.01
127 128 7.603784 GTCATTTGGGATTAAATGCAAAAGACT 59.396 33.333 0.00 0.00 44.04 3.24
128 129 8.811017 TCATTTGGGATTAAATGCAAAAGACTA 58.189 29.630 0.00 0.00 44.04 2.59
129 130 9.603921 CATTTGGGATTAAATGCAAAAGACTAT 57.396 29.630 0.00 0.00 40.09 2.12
134 135 9.750125 GGGATTAAATGCAAAAGACTATTAAGG 57.250 33.333 0.00 0.00 0.00 2.69
139 140 8.870075 AAATGCAAAAGACTATTAAGGAGAGT 57.130 30.769 0.00 0.00 0.00 3.24
140 141 8.499403 AATGCAAAAGACTATTAAGGAGAGTC 57.501 34.615 0.00 0.00 39.96 3.36
148 149 7.548967 AGACTATTAAGGAGAGTCTTTTTCGG 58.451 38.462 0.00 0.00 46.06 4.30
149 150 7.396623 AGACTATTAAGGAGAGTCTTTTTCGGA 59.603 37.037 0.00 0.00 46.06 4.55
150 151 7.321908 ACTATTAAGGAGAGTCTTTTTCGGAC 58.678 38.462 0.00 0.00 0.00 4.79
151 152 5.803237 TTAAGGAGAGTCTTTTTCGGACT 57.197 39.130 0.00 0.00 45.37 3.85
152 153 4.691326 AAGGAGAGTCTTTTTCGGACTT 57.309 40.909 0.00 0.00 43.13 3.01
153 154 4.691326 AGGAGAGTCTTTTTCGGACTTT 57.309 40.909 0.00 0.00 43.13 2.66
154 155 5.037383 AGGAGAGTCTTTTTCGGACTTTT 57.963 39.130 0.00 0.00 43.13 2.27
155 156 5.437946 AGGAGAGTCTTTTTCGGACTTTTT 58.562 37.500 0.00 0.00 43.13 1.94
156 157 5.297029 AGGAGAGTCTTTTTCGGACTTTTTG 59.703 40.000 0.00 0.00 43.13 2.44
157 158 5.500645 AGAGTCTTTTTCGGACTTTTTGG 57.499 39.130 0.00 0.00 43.13 3.28
158 159 4.338400 AGAGTCTTTTTCGGACTTTTTGGG 59.662 41.667 0.00 0.00 43.13 4.12
159 160 4.274978 AGTCTTTTTCGGACTTTTTGGGA 58.725 39.130 0.00 0.00 40.65 4.37
160 161 4.097437 AGTCTTTTTCGGACTTTTTGGGAC 59.903 41.667 0.00 0.00 40.65 4.46
161 162 4.097437 GTCTTTTTCGGACTTTTTGGGACT 59.903 41.667 0.00 0.00 0.00 3.85
162 163 4.707934 TCTTTTTCGGACTTTTTGGGACTT 59.292 37.500 0.00 0.00 0.00 3.01
163 164 5.186215 TCTTTTTCGGACTTTTTGGGACTTT 59.814 36.000 0.00 0.00 0.00 2.66
164 165 5.408880 TTTTCGGACTTTTTGGGACTTTT 57.591 34.783 0.00 0.00 0.00 2.27
165 166 5.408880 TTTCGGACTTTTTGGGACTTTTT 57.591 34.783 0.00 0.00 0.00 1.94
166 167 4.642445 TCGGACTTTTTGGGACTTTTTC 57.358 40.909 0.00 0.00 0.00 2.29
167 168 4.017808 TCGGACTTTTTGGGACTTTTTCA 58.982 39.130 0.00 0.00 0.00 2.69
168 169 4.463186 TCGGACTTTTTGGGACTTTTTCAA 59.537 37.500 0.00 0.00 0.00 2.69
169 170 4.565166 CGGACTTTTTGGGACTTTTTCAAC 59.435 41.667 0.00 0.00 0.00 3.18
170 171 5.483811 GGACTTTTTGGGACTTTTTCAACA 58.516 37.500 0.00 0.00 0.00 3.33
171 172 5.935206 GGACTTTTTGGGACTTTTTCAACAA 59.065 36.000 0.00 0.00 0.00 2.83
172 173 6.597672 GGACTTTTTGGGACTTTTTCAACAAT 59.402 34.615 0.00 0.00 0.00 2.71
173 174 7.376435 ACTTTTTGGGACTTTTTCAACAATG 57.624 32.000 0.00 0.00 0.00 2.82
174 175 5.809719 TTTTGGGACTTTTTCAACAATGC 57.190 34.783 0.00 0.00 0.00 3.56
175 176 4.751767 TTGGGACTTTTTCAACAATGCT 57.248 36.364 0.00 0.00 0.00 3.79
176 177 4.751767 TGGGACTTTTTCAACAATGCTT 57.248 36.364 0.00 0.00 0.00 3.91
177 178 4.692228 TGGGACTTTTTCAACAATGCTTC 58.308 39.130 0.00 0.00 0.00 3.86
178 179 4.405358 TGGGACTTTTTCAACAATGCTTCT 59.595 37.500 0.00 0.00 0.00 2.85
179 180 4.984785 GGGACTTTTTCAACAATGCTTCTC 59.015 41.667 0.00 0.00 0.00 2.87
180 181 4.984785 GGACTTTTTCAACAATGCTTCTCC 59.015 41.667 0.00 0.00 0.00 3.71
181 182 5.451798 GGACTTTTTCAACAATGCTTCTCCA 60.452 40.000 0.00 0.00 0.00 3.86
182 183 6.165700 ACTTTTTCAACAATGCTTCTCCAT 57.834 33.333 0.00 0.00 0.00 3.41
183 184 5.987347 ACTTTTTCAACAATGCTTCTCCATG 59.013 36.000 0.00 0.00 0.00 3.66
184 185 3.581024 TTCAACAATGCTTCTCCATGC 57.419 42.857 0.00 0.00 0.00 4.06
185 186 2.516906 TCAACAATGCTTCTCCATGCA 58.483 42.857 0.00 0.00 43.67 3.96
186 187 2.229543 TCAACAATGCTTCTCCATGCAC 59.770 45.455 0.00 0.00 42.26 4.57
187 188 2.211250 ACAATGCTTCTCCATGCACT 57.789 45.000 0.00 0.00 42.26 4.40
188 189 2.522185 ACAATGCTTCTCCATGCACTT 58.478 42.857 0.00 0.00 42.26 3.16
189 190 3.689347 ACAATGCTTCTCCATGCACTTA 58.311 40.909 0.00 0.00 42.26 2.24
190 191 4.275810 ACAATGCTTCTCCATGCACTTAT 58.724 39.130 0.00 0.00 42.26 1.73
191 192 4.708421 ACAATGCTTCTCCATGCACTTATT 59.292 37.500 0.00 0.00 42.26 1.40
192 193 5.887598 ACAATGCTTCTCCATGCACTTATTA 59.112 36.000 0.00 0.00 42.26 0.98
193 194 6.039047 ACAATGCTTCTCCATGCACTTATTAG 59.961 38.462 0.00 0.00 42.26 1.73
194 195 5.102953 TGCTTCTCCATGCACTTATTAGT 57.897 39.130 0.00 0.00 33.94 2.24
195 196 5.118990 TGCTTCTCCATGCACTTATTAGTC 58.881 41.667 0.00 0.00 33.94 2.59
196 197 4.513318 GCTTCTCCATGCACTTATTAGTCC 59.487 45.833 0.00 0.00 30.26 3.85
197 198 4.322080 TCTCCATGCACTTATTAGTCCG 57.678 45.455 0.00 0.00 30.26 4.79
198 199 2.802816 CTCCATGCACTTATTAGTCCGC 59.197 50.000 0.00 0.00 30.26 5.54
199 200 1.873591 CCATGCACTTATTAGTCCGCC 59.126 52.381 0.00 0.00 30.26 6.13
200 201 2.560504 CATGCACTTATTAGTCCGCCA 58.439 47.619 0.00 0.00 30.26 5.69
201 202 2.018542 TGCACTTATTAGTCCGCCAC 57.981 50.000 0.00 0.00 30.26 5.01
202 203 1.296727 GCACTTATTAGTCCGCCACC 58.703 55.000 0.00 0.00 30.26 4.61
203 204 1.949465 CACTTATTAGTCCGCCACCC 58.051 55.000 0.00 0.00 30.26 4.61
204 205 0.835276 ACTTATTAGTCCGCCACCCC 59.165 55.000 0.00 0.00 0.00 4.95
205 206 0.834612 CTTATTAGTCCGCCACCCCA 59.165 55.000 0.00 0.00 0.00 4.96
206 207 1.420138 CTTATTAGTCCGCCACCCCAT 59.580 52.381 0.00 0.00 0.00 4.00
207 208 2.402182 TATTAGTCCGCCACCCCATA 57.598 50.000 0.00 0.00 0.00 2.74
208 209 1.513858 ATTAGTCCGCCACCCCATAA 58.486 50.000 0.00 0.00 0.00 1.90
209 210 1.513858 TTAGTCCGCCACCCCATAAT 58.486 50.000 0.00 0.00 0.00 1.28
210 211 0.762418 TAGTCCGCCACCCCATAATG 59.238 55.000 0.00 0.00 0.00 1.90
211 212 1.226262 GTCCGCCACCCCATAATGT 59.774 57.895 0.00 0.00 0.00 2.71
212 213 0.395173 GTCCGCCACCCCATAATGTT 60.395 55.000 0.00 0.00 0.00 2.71
213 214 0.395036 TCCGCCACCCCATAATGTTG 60.395 55.000 0.00 0.00 0.00 3.33
214 215 0.682855 CCGCCACCCCATAATGTTGT 60.683 55.000 0.00 0.00 0.00 3.32
215 216 1.181786 CGCCACCCCATAATGTTGTT 58.818 50.000 0.00 0.00 0.00 2.83
216 217 1.548269 CGCCACCCCATAATGTTGTTT 59.452 47.619 0.00 0.00 0.00 2.83
217 218 2.673610 CGCCACCCCATAATGTTGTTTG 60.674 50.000 0.00 0.00 0.00 2.93
218 219 2.564947 GCCACCCCATAATGTTGTTTGA 59.435 45.455 0.00 0.00 0.00 2.69
219 220 3.197549 GCCACCCCATAATGTTGTTTGAT 59.802 43.478 0.00 0.00 0.00 2.57
220 221 4.323409 GCCACCCCATAATGTTGTTTGATT 60.323 41.667 0.00 0.00 0.00 2.57
221 222 5.105146 GCCACCCCATAATGTTGTTTGATTA 60.105 40.000 0.00 0.00 0.00 1.75
222 223 6.407979 GCCACCCCATAATGTTGTTTGATTAT 60.408 38.462 0.00 0.00 0.00 1.28
223 224 7.563906 CCACCCCATAATGTTGTTTGATTATT 58.436 34.615 0.00 0.00 0.00 1.40
224 225 8.700051 CCACCCCATAATGTTGTTTGATTATTA 58.300 33.333 0.00 0.00 0.00 0.98
253 254 9.654919 ATTTTATATACTAAGGGCAACATGGTT 57.345 29.630 0.00 0.00 39.74 3.67
260 261 7.971368 ACTAAGGGCAACATGGTTATTTAAT 57.029 32.000 0.00 0.00 39.74 1.40
262 263 9.482175 ACTAAGGGCAACATGGTTATTTAATAA 57.518 29.630 0.00 0.00 39.74 1.40
265 266 8.782137 AGGGCAACATGGTTATTTAATAATCT 57.218 30.769 9.08 0.00 39.74 2.40
266 267 8.860088 AGGGCAACATGGTTATTTAATAATCTC 58.140 33.333 9.08 0.79 39.74 2.75
267 268 8.860088 GGGCAACATGGTTATTTAATAATCTCT 58.140 33.333 9.08 0.00 39.74 3.10
284 285 6.987403 AATCTCTAGGAAAGGACTATGGAC 57.013 41.667 0.00 0.00 0.00 4.02
285 286 5.735733 TCTCTAGGAAAGGACTATGGACT 57.264 43.478 0.00 0.00 0.00 3.85
286 287 6.093617 TCTCTAGGAAAGGACTATGGACTT 57.906 41.667 0.00 0.00 0.00 3.01
287 288 6.503944 TCTCTAGGAAAGGACTATGGACTTT 58.496 40.000 3.94 3.94 37.16 2.66
288 289 6.960542 TCTCTAGGAAAGGACTATGGACTTTT 59.039 38.462 5.38 0.00 34.82 2.27
289 290 7.458170 TCTCTAGGAAAGGACTATGGACTTTTT 59.542 37.037 5.38 1.96 34.82 1.94
290 291 8.674925 TCTAGGAAAGGACTATGGACTTTTTA 57.325 34.615 5.38 2.72 34.82 1.52
291 292 8.759782 TCTAGGAAAGGACTATGGACTTTTTAG 58.240 37.037 5.38 9.25 34.82 1.85
292 293 7.331089 AGGAAAGGACTATGGACTTTTTAGT 57.669 36.000 5.38 0.00 34.82 2.24
293 294 7.756614 AGGAAAGGACTATGGACTTTTTAGTT 58.243 34.615 5.38 0.00 34.82 2.24
294 295 8.225416 AGGAAAGGACTATGGACTTTTTAGTTT 58.775 33.333 5.38 0.00 34.82 2.66
295 296 8.857098 GGAAAGGACTATGGACTTTTTAGTTTT 58.143 33.333 5.38 0.00 34.82 2.43
298 299 8.990163 AGGACTATGGACTTTTTAGTTTTTGA 57.010 30.769 0.00 0.00 0.00 2.69
299 300 9.416284 AGGACTATGGACTTTTTAGTTTTTGAA 57.584 29.630 0.00 0.00 0.00 2.69
332 333 8.502047 AGGAAGTAACTTTTTAGGACTAAGGA 57.498 34.615 0.00 0.00 0.00 3.36
333 334 8.373981 AGGAAGTAACTTTTTAGGACTAAGGAC 58.626 37.037 0.00 0.00 0.00 3.85
334 335 8.373981 GGAAGTAACTTTTTAGGACTAAGGACT 58.626 37.037 0.00 0.00 0.00 3.85
335 336 9.775854 GAAGTAACTTTTTAGGACTAAGGACTT 57.224 33.333 0.00 0.00 34.58 3.01
344 345 8.913487 TTTAGGACTAAGGACTTTTTAGTTGG 57.087 34.615 0.00 0.00 40.46 3.77
345 346 5.877491 AGGACTAAGGACTTTTTAGTTGGG 58.123 41.667 0.00 0.00 40.46 4.12
346 347 5.609708 AGGACTAAGGACTTTTTAGTTGGGA 59.390 40.000 0.00 0.00 40.46 4.37
347 348 5.704515 GGACTAAGGACTTTTTAGTTGGGAC 59.295 44.000 0.00 0.00 40.46 4.46
348 349 6.465464 GGACTAAGGACTTTTTAGTTGGGACT 60.465 42.308 0.00 0.00 40.46 3.85
349 350 7.256439 GGACTAAGGACTTTTTAGTTGGGACTA 60.256 40.741 0.00 0.00 40.46 2.59
350 351 7.677892 ACTAAGGACTTTTTAGTTGGGACTAG 58.322 38.462 0.00 0.00 37.95 2.57
351 352 6.758806 AAGGACTTTTTAGTTGGGACTAGA 57.241 37.500 0.00 0.00 39.43 2.43
352 353 6.758806 AGGACTTTTTAGTTGGGACTAGAA 57.241 37.500 0.00 0.00 39.43 2.10
353 354 7.145474 AGGACTTTTTAGTTGGGACTAGAAA 57.855 36.000 0.00 3.34 39.04 2.52
354 355 7.580007 AGGACTTTTTAGTTGGGACTAGAAAA 58.420 34.615 0.00 5.68 40.10 2.29
355 356 8.057011 AGGACTTTTTAGTTGGGACTAGAAAAA 58.943 33.333 0.00 0.00 40.10 1.94
378 379 8.942338 AAAATTTTAGAACCAGAGAACCAAAC 57.058 30.769 0.37 0.00 0.00 2.93
379 380 7.654022 AATTTTAGAACCAGAGAACCAAACA 57.346 32.000 0.00 0.00 0.00 2.83
380 381 6.445357 TTTTAGAACCAGAGAACCAAACAC 57.555 37.500 0.00 0.00 0.00 3.32
381 382 2.932261 AGAACCAGAGAACCAAACACC 58.068 47.619 0.00 0.00 0.00 4.16
382 383 2.241176 AGAACCAGAGAACCAAACACCA 59.759 45.455 0.00 0.00 0.00 4.17
383 384 2.052782 ACCAGAGAACCAAACACCAC 57.947 50.000 0.00 0.00 0.00 4.16
384 385 1.564348 ACCAGAGAACCAAACACCACT 59.436 47.619 0.00 0.00 0.00 4.00
385 386 1.949525 CCAGAGAACCAAACACCACTG 59.050 52.381 0.00 0.00 0.00 3.66
386 387 2.643551 CAGAGAACCAAACACCACTGT 58.356 47.619 0.00 0.00 0.00 3.55
387 388 3.433031 CCAGAGAACCAAACACCACTGTA 60.433 47.826 0.00 0.00 0.00 2.74
388 389 3.809832 CAGAGAACCAAACACCACTGTAG 59.190 47.826 0.00 0.00 0.00 2.74
389 390 3.454812 AGAGAACCAAACACCACTGTAGT 59.545 43.478 0.00 0.00 0.00 2.73
390 391 4.652421 AGAGAACCAAACACCACTGTAGTA 59.348 41.667 0.00 0.00 0.00 1.82
391 392 5.307196 AGAGAACCAAACACCACTGTAGTAT 59.693 40.000 0.00 0.00 0.00 2.12
392 393 5.305585 AGAACCAAACACCACTGTAGTATG 58.694 41.667 0.00 0.00 0.00 2.39
393 394 4.015872 ACCAAACACCACTGTAGTATGG 57.984 45.455 4.37 4.37 42.13 2.74
394 395 3.649023 ACCAAACACCACTGTAGTATGGA 59.351 43.478 10.38 0.00 39.46 3.41
395 396 4.000988 CCAAACACCACTGTAGTATGGAC 58.999 47.826 0.00 0.00 39.46 4.02
396 397 3.587797 AACACCACTGTAGTATGGACG 57.412 47.619 0.00 0.00 39.46 4.79
397 398 1.822990 ACACCACTGTAGTATGGACGG 59.177 52.381 0.00 0.00 39.46 4.79
398 399 2.097036 CACCACTGTAGTATGGACGGA 58.903 52.381 0.00 0.00 39.46 4.69
399 400 2.693591 CACCACTGTAGTATGGACGGAT 59.306 50.000 0.00 0.00 39.46 4.18
400 401 2.693591 ACCACTGTAGTATGGACGGATG 59.306 50.000 0.00 0.00 39.46 3.51
401 402 2.545952 CCACTGTAGTATGGACGGATGC 60.546 54.545 0.00 0.00 38.34 3.91
402 403 2.362397 CACTGTAGTATGGACGGATGCT 59.638 50.000 0.00 0.00 0.00 3.79
403 404 3.031736 ACTGTAGTATGGACGGATGCTT 58.968 45.455 0.00 0.00 0.00 3.91
404 405 3.181475 ACTGTAGTATGGACGGATGCTTG 60.181 47.826 0.00 0.00 0.00 4.01
405 406 2.102420 TGTAGTATGGACGGATGCTTGG 59.898 50.000 0.00 0.00 0.00 3.61
406 407 1.204146 AGTATGGACGGATGCTTGGT 58.796 50.000 0.00 0.00 0.00 3.67
407 408 1.139058 AGTATGGACGGATGCTTGGTC 59.861 52.381 0.00 0.00 0.00 4.02
408 409 1.134521 GTATGGACGGATGCTTGGTCA 60.135 52.381 0.00 0.00 32.39 4.02
409 410 0.392998 ATGGACGGATGCTTGGTCAC 60.393 55.000 0.00 0.00 32.39 3.67
410 411 1.003839 GGACGGATGCTTGGTCACA 60.004 57.895 0.00 0.00 32.39 3.58
411 412 0.605319 GGACGGATGCTTGGTCACAA 60.605 55.000 0.00 0.00 34.87 3.33
448 449 1.464997 CTTCAAGTAAACCTCTGCGGC 59.535 52.381 0.00 0.00 35.61 6.53
500 2110 4.897509 TGCTCCTCTTTCTTTCTGATGA 57.102 40.909 0.00 0.00 0.00 2.92
501 2111 5.432680 TGCTCCTCTTTCTTTCTGATGAT 57.567 39.130 0.00 0.00 0.00 2.45
502 2112 5.183969 TGCTCCTCTTTCTTTCTGATGATG 58.816 41.667 0.00 0.00 0.00 3.07
503 2113 4.575645 GCTCCTCTTTCTTTCTGATGATGG 59.424 45.833 0.00 0.00 0.00 3.51
554 2166 0.111089 GATCGACGAATGATTGCGCC 60.111 55.000 4.18 0.00 0.00 6.53
575 2187 3.618780 CTGCTCGCTTCCAGGGCTT 62.619 63.158 0.00 0.00 0.00 4.35
596 2208 0.108377 TCACCCGATCAACACATCCG 60.108 55.000 0.00 0.00 0.00 4.18
637 2250 0.732571 CACCGCATTTCCGCTGTAAT 59.267 50.000 0.00 0.00 0.00 1.89
638 2251 1.014352 ACCGCATTTCCGCTGTAATC 58.986 50.000 0.00 0.00 0.00 1.75
728 2341 2.288213 CCAACTCACTAGTCGCAGAACA 60.288 50.000 0.00 0.00 39.69 3.18
813 2437 1.959899 GCCGTTGATCGTGAGCTGTG 61.960 60.000 0.00 0.00 37.94 3.66
847 2483 0.171007 CTGTAAAATGCAGGCCACCG 59.829 55.000 5.01 0.00 0.00 4.94
865 2501 1.153005 GCATTCCCCAGCTCCTCTG 60.153 63.158 0.00 0.00 42.49 3.35
866 2502 1.919600 GCATTCCCCAGCTCCTCTGT 61.920 60.000 0.00 0.00 41.25 3.41
867 2503 0.622665 CATTCCCCAGCTCCTCTGTT 59.377 55.000 0.00 0.00 41.25 3.16
893 2529 1.065928 AGCTATAAGAACGCGCGCT 59.934 52.632 32.58 20.41 0.00 5.92
1005 2664 1.670406 CGCAGCTAGGATCATGGCC 60.670 63.158 12.37 0.00 0.00 5.36
1006 2665 1.759881 GCAGCTAGGATCATGGCCT 59.240 57.895 12.37 11.89 39.56 5.19
1007 2666 0.321475 GCAGCTAGGATCATGGCCTC 60.321 60.000 12.37 0.66 36.96 4.70
1008 2667 0.324285 CAGCTAGGATCATGGCCTCC 59.676 60.000 12.37 1.59 36.96 4.30
1009 2668 0.104777 AGCTAGGATCATGGCCTCCA 60.105 55.000 12.37 0.00 36.96 3.86
1010 2669 0.767375 GCTAGGATCATGGCCTCCAA 59.233 55.000 11.14 0.00 36.95 3.53
1196 2857 4.175489 CAGCATGCGCCACTGAGC 62.175 66.667 13.01 5.34 39.83 4.26
1259 2920 0.331278 ATGCCGGATTTCAGGGTGAA 59.669 50.000 5.05 0.00 34.03 3.18
1260 2921 0.322456 TGCCGGATTTCAGGGTGAAG 60.322 55.000 5.05 0.00 37.70 3.02
1265 2928 2.027385 GGATTTCAGGGTGAAGATGGC 58.973 52.381 0.00 0.00 37.70 4.40
1291 2954 1.860423 CTTGCGTCATCTTTGCGCG 60.860 57.895 0.00 0.00 45.22 6.86
1295 2958 1.204062 CGTCATCTTTGCGCGTTGT 59.796 52.632 8.43 0.00 0.00 3.32
1296 2959 0.384230 CGTCATCTTTGCGCGTTGTT 60.384 50.000 8.43 0.00 0.00 2.83
1297 2960 1.318251 GTCATCTTTGCGCGTTGTTC 58.682 50.000 8.43 0.00 0.00 3.18
1298 2961 0.110867 TCATCTTTGCGCGTTGTTCG 60.111 50.000 8.43 0.00 43.12 3.95
1299 2962 0.384230 CATCTTTGCGCGTTGTTCGT 60.384 50.000 8.43 0.00 42.13 3.85
1300 2963 0.306533 ATCTTTGCGCGTTGTTCGTT 59.693 45.000 8.43 0.00 42.13 3.85
1301 2964 0.097325 TCTTTGCGCGTTGTTCGTTT 59.903 45.000 8.43 0.00 42.13 3.60
1302 2965 1.326852 TCTTTGCGCGTTGTTCGTTTA 59.673 42.857 8.43 0.00 42.13 2.01
1303 2966 2.032722 TCTTTGCGCGTTGTTCGTTTAT 60.033 40.909 8.43 0.00 42.13 1.40
1304 2967 3.183976 TCTTTGCGCGTTGTTCGTTTATA 59.816 39.130 8.43 0.00 42.13 0.98
1305 2968 2.490697 TGCGCGTTGTTCGTTTATAC 57.509 45.000 8.43 0.00 42.13 1.47
1306 2969 2.060284 TGCGCGTTGTTCGTTTATACT 58.940 42.857 8.43 0.00 42.13 2.12
1307 2970 3.240884 TGCGCGTTGTTCGTTTATACTA 58.759 40.909 8.43 0.00 42.13 1.82
1308 2971 3.059306 TGCGCGTTGTTCGTTTATACTAC 59.941 43.478 8.43 0.00 42.13 2.73
1330 2993 5.995446 ACCTCCTTGATTTGATAGTCTTCC 58.005 41.667 0.00 0.00 0.00 3.46
1333 2996 7.570607 ACCTCCTTGATTTGATAGTCTTCCTAT 59.429 37.037 0.00 0.00 39.14 2.57
1357 3033 0.108804 ACCCGTCGATGCTGTTAGTG 60.109 55.000 0.00 0.00 0.00 2.74
1390 3066 4.238514 AGAAAGTCGATGCTGTTAGTGTC 58.761 43.478 0.00 0.00 0.00 3.67
1472 3148 8.668353 TGTCAGAATTTGTTCTACTAATCATGC 58.332 33.333 0.00 0.00 0.00 4.06
1593 3308 6.796705 AACGATTATCGACACCTTCTTTTT 57.203 33.333 21.93 0.00 43.74 1.94
1621 3336 0.934496 TTTCTGCACGAAGTTGACCG 59.066 50.000 0.00 0.00 41.61 4.79
1627 3342 1.596220 GCACGAAGTTGACCGGTTTTC 60.596 52.381 9.42 10.04 41.61 2.29
1666 3381 3.057104 CAGCAAAATCATCCACTCAGCAA 60.057 43.478 0.00 0.00 0.00 3.91
1702 3422 3.068024 TGTTTTTCTGCATCCCAACAGAC 59.932 43.478 0.00 0.00 42.42 3.51
1703 3423 2.957402 TTTCTGCATCCCAACAGACT 57.043 45.000 0.00 0.00 42.42 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.783071 TCCCTGAAAACAAACACCCC 58.217 50.000 0.00 0.00 0.00 4.95
1 2 4.415881 AAATCCCTGAAAACAAACACCC 57.584 40.909 0.00 0.00 0.00 4.61
83 84 8.581578 CCAAATGACTAGTTTAGCCCTTAAAAA 58.418 33.333 0.00 0.00 33.22 1.94
84 85 7.177744 CCCAAATGACTAGTTTAGCCCTTAAAA 59.822 37.037 0.00 0.00 33.22 1.52
85 86 6.661805 CCCAAATGACTAGTTTAGCCCTTAAA 59.338 38.462 0.00 0.00 0.00 1.52
86 87 6.012333 TCCCAAATGACTAGTTTAGCCCTTAA 60.012 38.462 0.00 0.00 0.00 1.85
87 88 5.489637 TCCCAAATGACTAGTTTAGCCCTTA 59.510 40.000 0.00 0.00 0.00 2.69
88 89 4.291249 TCCCAAATGACTAGTTTAGCCCTT 59.709 41.667 0.00 0.00 0.00 3.95
89 90 3.850173 TCCCAAATGACTAGTTTAGCCCT 59.150 43.478 0.00 0.00 0.00 5.19
90 91 4.230745 TCCCAAATGACTAGTTTAGCCC 57.769 45.455 0.00 0.00 0.00 5.19
91 92 7.875327 TTAATCCCAAATGACTAGTTTAGCC 57.125 36.000 0.00 0.00 0.00 3.93
92 93 9.736023 CATTTAATCCCAAATGACTAGTTTAGC 57.264 33.333 0.00 0.00 44.96 3.09
93 94 9.736023 GCATTTAATCCCAAATGACTAGTTTAG 57.264 33.333 11.66 0.00 44.96 1.85
94 95 9.249053 TGCATTTAATCCCAAATGACTAGTTTA 57.751 29.630 11.66 0.00 44.96 2.01
95 96 8.133024 TGCATTTAATCCCAAATGACTAGTTT 57.867 30.769 11.66 0.00 44.96 2.66
96 97 7.716799 TGCATTTAATCCCAAATGACTAGTT 57.283 32.000 11.66 0.00 44.96 2.24
97 98 7.716799 TTGCATTTAATCCCAAATGACTAGT 57.283 32.000 11.66 0.00 44.96 2.57
98 99 9.090692 CTTTTGCATTTAATCCCAAATGACTAG 57.909 33.333 11.66 0.00 44.96 2.57
99 100 8.811017 TCTTTTGCATTTAATCCCAAATGACTA 58.189 29.630 11.66 0.15 44.96 2.59
100 101 7.603784 GTCTTTTGCATTTAATCCCAAATGACT 59.396 33.333 22.21 0.00 44.96 3.41
101 102 7.603784 AGTCTTTTGCATTTAATCCCAAATGAC 59.396 33.333 22.12 22.12 44.96 3.06
102 103 7.678837 AGTCTTTTGCATTTAATCCCAAATGA 58.321 30.769 11.66 6.04 44.96 2.57
103 104 7.910441 AGTCTTTTGCATTTAATCCCAAATG 57.090 32.000 4.58 4.58 44.95 2.32
108 109 9.750125 CCTTAATAGTCTTTTGCATTTAATCCC 57.250 33.333 0.00 0.00 0.00 3.85
113 114 9.959721 ACTCTCCTTAATAGTCTTTTGCATTTA 57.040 29.630 0.00 0.00 0.00 1.40
114 115 8.870075 ACTCTCCTTAATAGTCTTTTGCATTT 57.130 30.769 0.00 0.00 0.00 2.32
115 116 8.325046 AGACTCTCCTTAATAGTCTTTTGCATT 58.675 33.333 0.00 0.00 45.94 3.56
116 117 7.856415 AGACTCTCCTTAATAGTCTTTTGCAT 58.144 34.615 0.00 0.00 45.94 3.96
117 118 7.246171 AGACTCTCCTTAATAGTCTTTTGCA 57.754 36.000 0.00 0.00 45.94 4.08
124 125 7.488792 GTCCGAAAAAGACTCTCCTTAATAGTC 59.511 40.741 0.00 0.00 39.95 2.59
125 126 7.178805 AGTCCGAAAAAGACTCTCCTTAATAGT 59.821 37.037 0.00 0.00 40.61 2.12
126 127 7.548967 AGTCCGAAAAAGACTCTCCTTAATAG 58.451 38.462 0.00 0.00 40.61 1.73
127 128 7.477945 AGTCCGAAAAAGACTCTCCTTAATA 57.522 36.000 0.00 0.00 40.61 0.98
128 129 6.361768 AGTCCGAAAAAGACTCTCCTTAAT 57.638 37.500 0.00 0.00 40.61 1.40
129 130 5.803237 AGTCCGAAAAAGACTCTCCTTAA 57.197 39.130 0.00 0.00 40.61 1.85
130 131 5.803237 AAGTCCGAAAAAGACTCTCCTTA 57.197 39.130 0.00 0.00 43.77 2.69
131 132 4.691326 AAGTCCGAAAAAGACTCTCCTT 57.309 40.909 0.00 0.00 43.77 3.36
132 133 4.691326 AAAGTCCGAAAAAGACTCTCCT 57.309 40.909 0.00 0.00 43.77 3.69
133 134 5.505819 CCAAAAAGTCCGAAAAAGACTCTCC 60.506 44.000 0.00 0.00 43.77 3.71
134 135 5.505819 CCCAAAAAGTCCGAAAAAGACTCTC 60.506 44.000 0.00 0.00 43.77 3.20
135 136 4.338400 CCCAAAAAGTCCGAAAAAGACTCT 59.662 41.667 0.00 0.00 43.77 3.24
136 137 4.337274 TCCCAAAAAGTCCGAAAAAGACTC 59.663 41.667 0.00 0.00 43.77 3.36
137 138 4.097437 GTCCCAAAAAGTCCGAAAAAGACT 59.903 41.667 0.00 0.00 46.50 3.24
138 139 4.097437 AGTCCCAAAAAGTCCGAAAAAGAC 59.903 41.667 0.00 0.00 34.31 3.01
139 140 4.274978 AGTCCCAAAAAGTCCGAAAAAGA 58.725 39.130 0.00 0.00 0.00 2.52
140 141 4.649088 AGTCCCAAAAAGTCCGAAAAAG 57.351 40.909 0.00 0.00 0.00 2.27
141 142 5.408880 AAAGTCCCAAAAAGTCCGAAAAA 57.591 34.783 0.00 0.00 0.00 1.94
142 143 5.408880 AAAAGTCCCAAAAAGTCCGAAAA 57.591 34.783 0.00 0.00 0.00 2.29
143 144 5.047235 TGAAAAAGTCCCAAAAAGTCCGAAA 60.047 36.000 0.00 0.00 0.00 3.46
144 145 4.463186 TGAAAAAGTCCCAAAAAGTCCGAA 59.537 37.500 0.00 0.00 0.00 4.30
145 146 4.017808 TGAAAAAGTCCCAAAAAGTCCGA 58.982 39.130 0.00 0.00 0.00 4.55
146 147 4.379339 TGAAAAAGTCCCAAAAAGTCCG 57.621 40.909 0.00 0.00 0.00 4.79
147 148 5.483811 TGTTGAAAAAGTCCCAAAAAGTCC 58.516 37.500 0.00 0.00 0.00 3.85
148 149 7.463544 CATTGTTGAAAAAGTCCCAAAAAGTC 58.536 34.615 0.00 0.00 0.00 3.01
149 150 6.128035 GCATTGTTGAAAAAGTCCCAAAAAGT 60.128 34.615 0.00 0.00 0.00 2.66
150 151 6.093909 AGCATTGTTGAAAAAGTCCCAAAAAG 59.906 34.615 0.00 0.00 0.00 2.27
151 152 5.942826 AGCATTGTTGAAAAAGTCCCAAAAA 59.057 32.000 0.00 0.00 0.00 1.94
152 153 5.495640 AGCATTGTTGAAAAAGTCCCAAAA 58.504 33.333 0.00 0.00 0.00 2.44
153 154 5.096443 AGCATTGTTGAAAAAGTCCCAAA 57.904 34.783 0.00 0.00 0.00 3.28
154 155 4.751767 AGCATTGTTGAAAAAGTCCCAA 57.248 36.364 0.00 0.00 0.00 4.12
155 156 4.405358 AGAAGCATTGTTGAAAAAGTCCCA 59.595 37.500 0.00 0.00 0.00 4.37
156 157 4.948847 AGAAGCATTGTTGAAAAAGTCCC 58.051 39.130 0.00 0.00 0.00 4.46
157 158 4.984785 GGAGAAGCATTGTTGAAAAAGTCC 59.015 41.667 0.00 0.00 0.00 3.85
158 159 5.591099 TGGAGAAGCATTGTTGAAAAAGTC 58.409 37.500 0.00 0.00 0.00 3.01
159 160 5.596836 TGGAGAAGCATTGTTGAAAAAGT 57.403 34.783 0.00 0.00 0.00 2.66
160 161 5.107220 GCATGGAGAAGCATTGTTGAAAAAG 60.107 40.000 0.00 0.00 0.00 2.27
161 162 4.751098 GCATGGAGAAGCATTGTTGAAAAA 59.249 37.500 0.00 0.00 0.00 1.94
162 163 4.202233 TGCATGGAGAAGCATTGTTGAAAA 60.202 37.500 0.00 0.00 35.51 2.29
163 164 3.321396 TGCATGGAGAAGCATTGTTGAAA 59.679 39.130 0.00 0.00 35.51 2.69
164 165 2.892215 TGCATGGAGAAGCATTGTTGAA 59.108 40.909 0.00 0.00 35.51 2.69
165 166 2.229543 GTGCATGGAGAAGCATTGTTGA 59.770 45.455 0.00 0.00 43.44 3.18
166 167 2.230508 AGTGCATGGAGAAGCATTGTTG 59.769 45.455 0.00 0.00 43.44 3.33
167 168 2.522185 AGTGCATGGAGAAGCATTGTT 58.478 42.857 0.00 0.00 43.44 2.83
168 169 2.211250 AGTGCATGGAGAAGCATTGT 57.789 45.000 0.00 0.00 43.44 2.71
169 170 4.913335 ATAAGTGCATGGAGAAGCATTG 57.087 40.909 0.00 0.00 43.44 2.82
170 171 6.125029 ACTAATAAGTGCATGGAGAAGCATT 58.875 36.000 0.00 0.00 43.44 3.56
171 172 5.688807 ACTAATAAGTGCATGGAGAAGCAT 58.311 37.500 0.00 0.00 43.44 3.79
172 173 5.102953 ACTAATAAGTGCATGGAGAAGCA 57.897 39.130 0.00 0.00 38.65 3.91
173 174 4.513318 GGACTAATAAGTGCATGGAGAAGC 59.487 45.833 0.00 0.00 43.18 3.86
174 175 4.747108 CGGACTAATAAGTGCATGGAGAAG 59.253 45.833 0.00 0.00 43.83 2.85
175 176 4.693283 CGGACTAATAAGTGCATGGAGAA 58.307 43.478 0.00 0.00 43.83 2.87
176 177 3.492656 GCGGACTAATAAGTGCATGGAGA 60.493 47.826 0.00 0.00 43.83 3.71
177 178 2.802816 GCGGACTAATAAGTGCATGGAG 59.197 50.000 0.00 0.00 43.83 3.86
178 179 2.484770 GGCGGACTAATAAGTGCATGGA 60.485 50.000 0.00 0.00 43.83 3.41
179 180 1.873591 GGCGGACTAATAAGTGCATGG 59.126 52.381 0.00 0.00 43.83 3.66
180 181 2.287915 GTGGCGGACTAATAAGTGCATG 59.712 50.000 0.00 0.00 43.83 4.06
181 182 2.561569 GTGGCGGACTAATAAGTGCAT 58.438 47.619 0.00 0.00 43.83 3.96
182 183 1.406341 GGTGGCGGACTAATAAGTGCA 60.406 52.381 0.00 0.00 43.83 4.57
183 184 1.296727 GGTGGCGGACTAATAAGTGC 58.703 55.000 0.00 0.00 40.47 4.40
184 185 1.474498 GGGGTGGCGGACTAATAAGTG 60.474 57.143 0.00 0.00 35.56 3.16
185 186 0.835276 GGGGTGGCGGACTAATAAGT 59.165 55.000 0.00 0.00 39.21 2.24
186 187 0.834612 TGGGGTGGCGGACTAATAAG 59.165 55.000 0.00 0.00 0.00 1.73
187 188 1.513858 ATGGGGTGGCGGACTAATAA 58.486 50.000 0.00 0.00 0.00 1.40
188 189 2.402182 TATGGGGTGGCGGACTAATA 57.598 50.000 0.00 0.00 0.00 0.98
189 190 1.513858 TTATGGGGTGGCGGACTAAT 58.486 50.000 0.00 0.00 0.00 1.73
190 191 1.142060 CATTATGGGGTGGCGGACTAA 59.858 52.381 0.00 0.00 0.00 2.24
191 192 0.762418 CATTATGGGGTGGCGGACTA 59.238 55.000 0.00 0.00 0.00 2.59
192 193 1.279025 ACATTATGGGGTGGCGGACT 61.279 55.000 0.00 0.00 0.00 3.85
193 194 0.395173 AACATTATGGGGTGGCGGAC 60.395 55.000 0.00 0.00 0.00 4.79
194 195 0.395036 CAACATTATGGGGTGGCGGA 60.395 55.000 0.00 0.00 0.00 5.54
195 196 0.682855 ACAACATTATGGGGTGGCGG 60.683 55.000 0.00 0.00 0.00 6.13
196 197 1.181786 AACAACATTATGGGGTGGCG 58.818 50.000 0.00 0.00 0.00 5.69
197 198 2.564947 TCAAACAACATTATGGGGTGGC 59.435 45.455 0.00 0.00 0.00 5.01
198 199 5.419239 AATCAAACAACATTATGGGGTGG 57.581 39.130 0.00 0.00 0.00 4.61
227 228 9.654919 AACCATGTTGCCCTTAGTATATAAAAT 57.345 29.630 0.00 0.00 0.00 1.82
234 235 9.654919 ATTAAATAACCATGTTGCCCTTAGTAT 57.345 29.630 0.00 0.00 0.00 2.12
236 237 7.971368 ATTAAATAACCATGTTGCCCTTAGT 57.029 32.000 0.00 0.00 0.00 2.24
239 240 9.212593 AGATTATTAAATAACCATGTTGCCCTT 57.787 29.630 0.00 0.00 0.00 3.95
240 241 8.782137 AGATTATTAAATAACCATGTTGCCCT 57.218 30.769 0.00 0.00 0.00 5.19
241 242 8.860088 AGAGATTATTAAATAACCATGTTGCCC 58.140 33.333 0.00 0.00 0.00 5.36
258 259 9.095700 GTCCATAGTCCTTTCCTAGAGATTATT 57.904 37.037 0.00 0.00 0.00 1.40
259 260 8.461033 AGTCCATAGTCCTTTCCTAGAGATTAT 58.539 37.037 0.00 0.00 0.00 1.28
260 261 7.827787 AGTCCATAGTCCTTTCCTAGAGATTA 58.172 38.462 0.00 0.00 0.00 1.75
261 262 6.688554 AGTCCATAGTCCTTTCCTAGAGATT 58.311 40.000 0.00 0.00 0.00 2.40
262 263 6.288096 AGTCCATAGTCCTTTCCTAGAGAT 57.712 41.667 0.00 0.00 0.00 2.75
263 264 5.735733 AGTCCATAGTCCTTTCCTAGAGA 57.264 43.478 0.00 0.00 0.00 3.10
264 265 6.800072 AAAGTCCATAGTCCTTTCCTAGAG 57.200 41.667 0.00 0.00 0.00 2.43
265 266 7.569599 AAAAAGTCCATAGTCCTTTCCTAGA 57.430 36.000 0.00 0.00 0.00 2.43
266 267 8.541234 ACTAAAAAGTCCATAGTCCTTTCCTAG 58.459 37.037 0.00 0.00 0.00 3.02
267 268 8.445361 ACTAAAAAGTCCATAGTCCTTTCCTA 57.555 34.615 0.00 0.00 0.00 2.94
268 269 7.331089 ACTAAAAAGTCCATAGTCCTTTCCT 57.669 36.000 0.00 0.00 0.00 3.36
269 270 7.997773 AACTAAAAAGTCCATAGTCCTTTCC 57.002 36.000 0.00 0.00 0.00 3.13
272 273 9.416284 TCAAAAACTAAAAAGTCCATAGTCCTT 57.584 29.630 0.00 0.00 0.00 3.36
273 274 8.990163 TCAAAAACTAAAAAGTCCATAGTCCT 57.010 30.769 0.00 0.00 0.00 3.85
306 307 9.605951 TCCTTAGTCCTAAAAAGTTACTTCCTA 57.394 33.333 0.00 0.00 0.00 2.94
307 308 8.373981 GTCCTTAGTCCTAAAAAGTTACTTCCT 58.626 37.037 0.00 0.00 0.00 3.36
308 309 8.373981 AGTCCTTAGTCCTAAAAAGTTACTTCC 58.626 37.037 0.00 0.00 0.00 3.46
309 310 9.775854 AAGTCCTTAGTCCTAAAAAGTTACTTC 57.224 33.333 0.00 0.00 0.00 3.01
318 319 9.346005 CCAACTAAAAAGTCCTTAGTCCTAAAA 57.654 33.333 0.00 0.00 38.38 1.52
319 320 7.940688 CCCAACTAAAAAGTCCTTAGTCCTAAA 59.059 37.037 0.00 0.00 38.38 1.85
320 321 7.293062 TCCCAACTAAAAAGTCCTTAGTCCTAA 59.707 37.037 0.00 0.00 38.38 2.69
321 322 6.788957 TCCCAACTAAAAAGTCCTTAGTCCTA 59.211 38.462 0.00 0.00 38.38 2.94
322 323 5.609708 TCCCAACTAAAAAGTCCTTAGTCCT 59.390 40.000 0.00 0.00 38.38 3.85
323 324 5.704515 GTCCCAACTAAAAAGTCCTTAGTCC 59.295 44.000 0.00 0.00 38.38 3.85
324 325 6.531923 AGTCCCAACTAAAAAGTCCTTAGTC 58.468 40.000 0.00 0.00 38.38 2.59
325 326 6.511017 AGTCCCAACTAAAAAGTCCTTAGT 57.489 37.500 0.00 0.00 40.52 2.24
326 327 7.904205 TCTAGTCCCAACTAAAAAGTCCTTAG 58.096 38.462 0.00 0.00 37.53 2.18
327 328 7.860649 TCTAGTCCCAACTAAAAAGTCCTTA 57.139 36.000 0.00 0.00 37.53 2.69
328 329 6.758806 TCTAGTCCCAACTAAAAAGTCCTT 57.241 37.500 0.00 0.00 37.53 3.36
329 330 6.758806 TTCTAGTCCCAACTAAAAAGTCCT 57.241 37.500 0.00 0.00 37.53 3.85
330 331 7.812690 TTTTCTAGTCCCAACTAAAAAGTCC 57.187 36.000 0.00 0.00 37.53 3.85
352 353 9.378551 GTTTGGTTCTCTGGTTCTAAAATTTTT 57.621 29.630 9.06 0.00 0.00 1.94
353 354 8.536175 TGTTTGGTTCTCTGGTTCTAAAATTTT 58.464 29.630 8.75 8.75 0.00 1.82
354 355 7.979537 GTGTTTGGTTCTCTGGTTCTAAAATTT 59.020 33.333 0.00 0.00 0.00 1.82
355 356 7.417456 GGTGTTTGGTTCTCTGGTTCTAAAATT 60.417 37.037 0.00 0.00 0.00 1.82
356 357 6.040504 GGTGTTTGGTTCTCTGGTTCTAAAAT 59.959 38.462 0.00 0.00 0.00 1.82
357 358 5.358725 GGTGTTTGGTTCTCTGGTTCTAAAA 59.641 40.000 0.00 0.00 0.00 1.52
358 359 4.885325 GGTGTTTGGTTCTCTGGTTCTAAA 59.115 41.667 0.00 0.00 0.00 1.85
359 360 4.080243 TGGTGTTTGGTTCTCTGGTTCTAA 60.080 41.667 0.00 0.00 0.00 2.10
360 361 3.456644 TGGTGTTTGGTTCTCTGGTTCTA 59.543 43.478 0.00 0.00 0.00 2.10
361 362 2.241176 TGGTGTTTGGTTCTCTGGTTCT 59.759 45.455 0.00 0.00 0.00 3.01
362 363 2.357952 GTGGTGTTTGGTTCTCTGGTTC 59.642 50.000 0.00 0.00 0.00 3.62
363 364 2.025321 AGTGGTGTTTGGTTCTCTGGTT 60.025 45.455 0.00 0.00 0.00 3.67
364 365 1.564348 AGTGGTGTTTGGTTCTCTGGT 59.436 47.619 0.00 0.00 0.00 4.00
365 366 1.949525 CAGTGGTGTTTGGTTCTCTGG 59.050 52.381 0.00 0.00 0.00 3.86
366 367 2.643551 ACAGTGGTGTTTGGTTCTCTG 58.356 47.619 0.00 0.00 30.30 3.35
367 368 3.454812 ACTACAGTGGTGTTTGGTTCTCT 59.545 43.478 0.00 0.00 38.19 3.10
368 369 3.805207 ACTACAGTGGTGTTTGGTTCTC 58.195 45.455 0.00 0.00 38.19 2.87
369 370 3.926058 ACTACAGTGGTGTTTGGTTCT 57.074 42.857 0.00 0.00 38.19 3.01
370 371 4.454504 CCATACTACAGTGGTGTTTGGTTC 59.545 45.833 14.45 0.00 38.19 3.62
371 372 4.103469 TCCATACTACAGTGGTGTTTGGTT 59.897 41.667 18.81 0.00 38.19 3.67
372 373 3.649023 TCCATACTACAGTGGTGTTTGGT 59.351 43.478 18.81 1.11 38.19 3.67
373 374 4.000988 GTCCATACTACAGTGGTGTTTGG 58.999 47.826 15.71 15.71 38.19 3.28
374 375 3.678072 CGTCCATACTACAGTGGTGTTTG 59.322 47.826 0.00 0.00 38.19 2.93
375 376 3.306502 CCGTCCATACTACAGTGGTGTTT 60.307 47.826 0.00 0.00 38.19 2.83
376 377 2.232941 CCGTCCATACTACAGTGGTGTT 59.767 50.000 0.00 0.00 38.19 3.32
377 378 1.822990 CCGTCCATACTACAGTGGTGT 59.177 52.381 0.00 0.00 41.06 4.16
378 379 2.097036 TCCGTCCATACTACAGTGGTG 58.903 52.381 0.00 0.00 36.84 4.17
379 380 2.519771 TCCGTCCATACTACAGTGGT 57.480 50.000 0.00 0.00 36.84 4.16
380 381 2.545952 GCATCCGTCCATACTACAGTGG 60.546 54.545 0.00 0.00 36.82 4.00
381 382 2.362397 AGCATCCGTCCATACTACAGTG 59.638 50.000 0.00 0.00 0.00 3.66
382 383 2.667470 AGCATCCGTCCATACTACAGT 58.333 47.619 0.00 0.00 0.00 3.55
383 384 3.384668 CAAGCATCCGTCCATACTACAG 58.615 50.000 0.00 0.00 0.00 2.74
384 385 2.102420 CCAAGCATCCGTCCATACTACA 59.898 50.000 0.00 0.00 0.00 2.74
385 386 2.102588 ACCAAGCATCCGTCCATACTAC 59.897 50.000 0.00 0.00 0.00 2.73
386 387 2.364324 GACCAAGCATCCGTCCATACTA 59.636 50.000 0.00 0.00 0.00 1.82
387 388 1.139058 GACCAAGCATCCGTCCATACT 59.861 52.381 0.00 0.00 0.00 2.12
388 389 1.134521 TGACCAAGCATCCGTCCATAC 60.135 52.381 0.00 0.00 0.00 2.39
389 390 1.134521 GTGACCAAGCATCCGTCCATA 60.135 52.381 0.00 0.00 0.00 2.74
390 391 0.392998 GTGACCAAGCATCCGTCCAT 60.393 55.000 0.00 0.00 0.00 3.41
391 392 1.003839 GTGACCAAGCATCCGTCCA 60.004 57.895 0.00 0.00 0.00 4.02
392 393 0.605319 TTGTGACCAAGCATCCGTCC 60.605 55.000 0.00 0.00 0.00 4.79
393 394 0.798776 CTTGTGACCAAGCATCCGTC 59.201 55.000 0.00 0.00 41.51 4.79
394 395 2.932663 CTTGTGACCAAGCATCCGT 58.067 52.632 0.00 0.00 41.51 4.69
402 403 5.064962 CACGGTTTAGTTTACTTGTGACCAA 59.935 40.000 0.00 0.00 0.00 3.67
403 404 4.571580 CACGGTTTAGTTTACTTGTGACCA 59.428 41.667 0.00 0.00 0.00 4.02
404 405 4.024641 CCACGGTTTAGTTTACTTGTGACC 60.025 45.833 0.00 0.00 0.00 4.02
405 406 4.553351 GCCACGGTTTAGTTTACTTGTGAC 60.553 45.833 0.00 0.00 0.00 3.67
406 407 3.560896 GCCACGGTTTAGTTTACTTGTGA 59.439 43.478 0.00 0.00 0.00 3.58
407 408 3.562557 AGCCACGGTTTAGTTTACTTGTG 59.437 43.478 0.00 0.00 0.00 3.33
408 409 3.812262 AGCCACGGTTTAGTTTACTTGT 58.188 40.909 0.00 0.00 0.00 3.16
409 410 4.273969 TGAAGCCACGGTTTAGTTTACTTG 59.726 41.667 0.00 0.00 0.00 3.16
410 411 4.453751 TGAAGCCACGGTTTAGTTTACTT 58.546 39.130 0.00 0.00 0.00 2.24
411 412 4.075963 TGAAGCCACGGTTTAGTTTACT 57.924 40.909 0.00 0.00 0.00 2.24
412 413 4.274214 ACTTGAAGCCACGGTTTAGTTTAC 59.726 41.667 0.00 0.00 0.00 2.01
413 414 4.453751 ACTTGAAGCCACGGTTTAGTTTA 58.546 39.130 0.00 0.00 0.00 2.01
414 415 3.284617 ACTTGAAGCCACGGTTTAGTTT 58.715 40.909 0.00 0.00 0.00 2.66
415 416 2.927028 ACTTGAAGCCACGGTTTAGTT 58.073 42.857 0.00 0.00 0.00 2.24
416 417 2.632987 ACTTGAAGCCACGGTTTAGT 57.367 45.000 0.00 0.00 0.00 2.24
417 418 4.319984 GGTTTACTTGAAGCCACGGTTTAG 60.320 45.833 0.00 0.00 38.29 1.85
418 419 3.565063 GGTTTACTTGAAGCCACGGTTTA 59.435 43.478 0.00 0.00 38.29 2.01
419 420 2.359848 GGTTTACTTGAAGCCACGGTTT 59.640 45.455 0.00 0.00 38.29 3.27
420 421 1.951602 GGTTTACTTGAAGCCACGGTT 59.048 47.619 0.00 0.00 38.29 4.44
448 449 2.584166 CAGCTTACAAGTTGCTGTCG 57.416 50.000 1.81 0.00 46.23 4.35
500 2110 1.827969 CGTCAGGAGAAGGAGAACCAT 59.172 52.381 0.00 0.00 38.94 3.55
501 2111 1.257743 CGTCAGGAGAAGGAGAACCA 58.742 55.000 0.00 0.00 38.94 3.67
502 2112 0.108567 GCGTCAGGAGAAGGAGAACC 60.109 60.000 0.00 0.00 0.00 3.62
503 2113 0.456995 CGCGTCAGGAGAAGGAGAAC 60.457 60.000 0.00 0.00 0.00 3.01
530 2141 0.033504 AATCATTCGTCGATCCCGGG 59.966 55.000 16.85 16.85 36.24 5.73
575 2187 1.338674 GGATGTGTTGATCGGGTGACA 60.339 52.381 0.00 0.00 0.00 3.58
610 2222 1.349234 GGAAATGCGGTGCAATGTTC 58.651 50.000 0.00 0.64 43.62 3.18
611 2223 0.388391 CGGAAATGCGGTGCAATGTT 60.388 50.000 0.00 0.00 43.62 2.71
658 2271 3.782244 CTTCCGTGACAGCAGCGC 61.782 66.667 0.00 0.00 0.00 5.92
672 2285 0.873743 CAGCCGCCTCGAGAATCTTC 60.874 60.000 15.71 0.00 0.00 2.87
728 2341 0.666913 CTGCAAGCAAAGCACTCTGT 59.333 50.000 0.00 0.00 37.02 3.41
813 2437 0.614979 TACAGTCTGGCCTCCTCCAC 60.615 60.000 3.32 0.00 31.74 4.02
847 2483 1.153005 CAGAGGAGCTGGGGAATGC 60.153 63.158 0.00 0.00 41.07 3.56
857 2493 2.093553 AGCTGATGAAGAACAGAGGAGC 60.094 50.000 0.00 0.00 36.38 4.70
866 2502 4.740205 CGCGTTCTTATAGCTGATGAAGAA 59.260 41.667 0.00 3.36 35.97 2.52
867 2503 4.290969 CGCGTTCTTATAGCTGATGAAGA 58.709 43.478 0.00 0.00 0.00 2.87
893 2529 1.220749 CGGAGGAAATCAGGGCGAA 59.779 57.895 0.00 0.00 0.00 4.70
1005 2664 2.898705 CGGAAGATCTTGGAGTTGGAG 58.101 52.381 14.00 0.00 0.00 3.86
1006 2665 1.066143 GCGGAAGATCTTGGAGTTGGA 60.066 52.381 14.00 0.00 0.00 3.53
1007 2666 1.373570 GCGGAAGATCTTGGAGTTGG 58.626 55.000 14.00 0.00 0.00 3.77
1008 2667 1.002366 CGCGGAAGATCTTGGAGTTG 58.998 55.000 14.00 0.00 0.00 3.16
1009 2668 0.741221 GCGCGGAAGATCTTGGAGTT 60.741 55.000 14.00 0.00 0.00 3.01
1010 2669 1.153549 GCGCGGAAGATCTTGGAGT 60.154 57.895 14.00 0.00 0.00 3.85
1259 2920 1.885871 GCAAGAAAAGCGGCCATCT 59.114 52.632 2.24 0.00 0.00 2.90
1260 2921 4.483711 GCAAGAAAAGCGGCCATC 57.516 55.556 2.24 0.00 0.00 3.51
1280 2943 0.384230 ACGAACAACGCGCAAAGATG 60.384 50.000 5.73 0.00 46.94 2.90
1291 2954 7.092716 TCAAGGAGGTAGTATAAACGAACAAC 58.907 38.462 0.00 0.00 0.00 3.32
1295 2958 8.533657 TCAAATCAAGGAGGTAGTATAAACGAA 58.466 33.333 0.00 0.00 0.00 3.85
1296 2959 8.070034 TCAAATCAAGGAGGTAGTATAAACGA 57.930 34.615 0.00 0.00 0.00 3.85
1297 2960 8.888579 ATCAAATCAAGGAGGTAGTATAAACG 57.111 34.615 0.00 0.00 0.00 3.60
1302 2965 9.440761 AAGACTATCAAATCAAGGAGGTAGTAT 57.559 33.333 0.00 0.00 0.00 2.12
1303 2966 8.840200 AAGACTATCAAATCAAGGAGGTAGTA 57.160 34.615 0.00 0.00 0.00 1.82
1304 2967 7.147637 GGAAGACTATCAAATCAAGGAGGTAGT 60.148 40.741 0.00 0.00 0.00 2.73
1305 2968 7.070571 AGGAAGACTATCAAATCAAGGAGGTAG 59.929 40.741 0.00 0.00 0.00 3.18
1306 2969 6.903534 AGGAAGACTATCAAATCAAGGAGGTA 59.096 38.462 0.00 0.00 0.00 3.08
1307 2970 5.728741 AGGAAGACTATCAAATCAAGGAGGT 59.271 40.000 0.00 0.00 0.00 3.85
1308 2971 6.245890 AGGAAGACTATCAAATCAAGGAGG 57.754 41.667 0.00 0.00 0.00 4.30
1330 2993 1.337071 AGCATCGACGGGTACACATAG 59.663 52.381 0.00 0.00 0.00 2.23
1333 2996 1.214325 CAGCATCGACGGGTACACA 59.786 57.895 0.00 0.00 0.00 3.72
1368 3044 4.238514 GACACTAACAGCATCGACTTTCT 58.761 43.478 0.00 0.00 0.00 2.52
1390 3066 4.026640 CACATGAAAAGAAAAACACAGCCG 60.027 41.667 0.00 0.00 0.00 5.52
1458 3134 8.363390 CCAATACAGAGAGCATGATTAGTAGAA 58.637 37.037 0.00 0.00 0.00 2.10
1593 3308 3.435327 ACTTCGTGCAGAAATTATGCGAA 59.565 39.130 8.12 5.59 46.87 4.70
1600 3315 2.032030 CGGTCAACTTCGTGCAGAAATT 60.032 45.455 0.00 0.00 38.57 1.82
1621 3336 4.174129 CGCGCCCGATGGAAAACC 62.174 66.667 0.00 0.00 36.29 3.27
1640 3355 0.179129 GTGGATGATTTTGCTGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
1679 3394 3.703556 TCTGTTGGGATGCAGAAAAACAA 59.296 39.130 8.55 0.00 38.61 2.83
2150 3871 3.499737 GACCATCAACAGCGCCGG 61.500 66.667 2.29 0.00 0.00 6.13
2154 3875 2.819595 CCCCGACCATCAACAGCG 60.820 66.667 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.