Multiple sequence alignment - TraesCS7D01G514100

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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 TraesCS7D01G514100 chr7D 100.000 2726 0 0 1 2726 614890173 614887448 0.000000e+00 5035.0
1 TraesCS7D01G514100 chr7D 97.090 378 9 2 1 376 102567920 102567543 1.060000e-178 636.0
2 TraesCS7D01G514100 chr7A 91.560 2429 74 42 381 2726 710757102 710759482 0.000000e+00 3229.0
3 TraesCS7D01G514100 chr7A 92.658 1866 62 23 381 2204 707620315 707618483 0.000000e+00 2617.0
4 TraesCS7D01G514100 chr7A 88.462 52 6 0 2666 2717 721389754 721389703 2.270000e-06 63.9
5 TraesCS7D01G514100 chr7B 80.360 1502 200 55 730 2187 707623975 707625425 0.000000e+00 1051.0
6 TraesCS7D01G514100 chr6D 98.177 384 4 3 1 382 34523671 34524053 0.000000e+00 667.0
7 TraesCS7D01G514100 chr6D 96.382 387 11 3 1 385 247625207 247624822 3.830000e-178 634.0
8 TraesCS7D01G514100 chr4D 97.638 381 8 1 1 380 10921092 10921472 0.000000e+00 652.0
9 TraesCS7D01G514100 chr4D 97.113 381 10 1 1 380 33237533 33237153 2.290000e-180 641.0
10 TraesCS7D01G514100 chrUn 97.638 381 6 3 1 379 126995501 126995122 0.000000e+00 651.0
11 TraesCS7D01G514100 chr5D 96.875 384 10 2 1 382 19111418 19111035 2.290000e-180 641.0
12 TraesCS7D01G514100 chr5D 96.183 393 10 3 1 391 440319577 440319966 2.960000e-179 638.0
13 TraesCS7D01G514100 chr1D 96.859 382 10 2 1 380 416482200 416482581 2.960000e-179 638.0


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 TraesCS7D01G514100 chr7D 614887448 614890173 2725 True 5035 5035 100.000 1 2726 1 chr7D.!!$R2 2725
1 TraesCS7D01G514100 chr7A 710757102 710759482 2380 False 3229 3229 91.560 381 2726 1 chr7A.!!$F1 2345
2 TraesCS7D01G514100 chr7A 707618483 707620315 1832 True 2617 2617 92.658 381 2204 1 chr7A.!!$R1 1823
3 TraesCS7D01G514100 chr7B 707623975 707625425 1450 False 1051 1051 80.360 730 2187 1 chr7B.!!$F1 1457

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
85 86 0.115745 ACGGGAGGGACTGTTTAGGA 59.884 55.0 0.0 0.0 41.55 2.94 F
175 176 0.189574 TTTCCAACAATGCCCCTCCA 59.810 50.0 0.0 0.0 0.00 3.86 F
177 178 0.324552 TCCAACAATGCCCCTCCATG 60.325 55.0 0.0 0.0 0.00 3.66 F
181 182 0.757935 ACAATGCCCCTCCATGCATC 60.758 55.0 0.0 0.0 46.97 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1240 0.035534 TGCTGATGTACCCACGCATT 60.036 50.0 0.0 0.0 0.00 3.56 R
1505 1539 0.523966 CTTCTCGTCGGTGAAGAGCT 59.476 55.0 17.8 0.0 43.24 4.09 R
1647 1681 1.380524 TGCAAACCGAAAAGAACCGA 58.619 45.0 0.0 0.0 0.00 4.69 R
2145 2225 1.485124 TCCTCCGTCACACAGCATAT 58.515 50.0 0.0 0.0 0.00 1.78 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
42 43 7.797038 TTTTGTGTAGGGACTAGAAAAAGTC 57.203 36.000 0.00 0.00 41.46 3.01
53 54 7.706100 GACTAGAAAAAGTCCCTCTTAGAGA 57.294 40.000 11.32 0.00 40.06 3.10
54 55 7.470935 ACTAGAAAAAGTCCCTCTTAGAGAC 57.529 40.000 11.32 2.08 35.02 3.36
55 56 7.243091 ACTAGAAAAAGTCCCTCTTAGAGACT 58.757 38.462 11.32 4.57 42.58 3.24
76 77 2.275134 TTTTACCAAACGGGAGGGAC 57.725 50.000 0.00 0.00 41.15 4.46
78 79 0.688487 TTACCAAACGGGAGGGACTG 59.312 55.000 0.00 0.00 41.55 3.51
79 80 0.472352 TACCAAACGGGAGGGACTGT 60.472 55.000 0.00 0.00 41.55 3.55
80 81 1.350310 ACCAAACGGGAGGGACTGTT 61.350 55.000 0.00 0.00 41.55 3.16
82 83 1.072648 CCAAACGGGAGGGACTGTTTA 59.927 52.381 3.15 0.00 45.49 2.01
83 84 2.423577 CAAACGGGAGGGACTGTTTAG 58.576 52.381 3.15 0.00 45.49 1.85
84 85 0.981943 AACGGGAGGGACTGTTTAGG 59.018 55.000 0.00 0.00 41.55 2.69
85 86 0.115745 ACGGGAGGGACTGTTTAGGA 59.884 55.000 0.00 0.00 41.55 2.94
86 87 1.272807 CGGGAGGGACTGTTTAGGAA 58.727 55.000 0.00 0.00 41.55 3.36
87 88 1.066358 CGGGAGGGACTGTTTAGGAAC 60.066 57.143 0.00 0.00 41.55 3.62
88 89 2.267192 GGGAGGGACTGTTTAGGAACT 58.733 52.381 0.00 0.00 41.55 3.01
89 90 3.447950 GGGAGGGACTGTTTAGGAACTA 58.552 50.000 0.00 0.00 41.55 2.24
90 91 3.842436 GGGAGGGACTGTTTAGGAACTAA 59.158 47.826 0.00 0.00 45.97 2.24
107 108 8.196378 AGGAACTAAACTAGACATTTGAGACT 57.804 34.615 0.00 0.00 36.02 3.24
108 109 9.310449 AGGAACTAAACTAGACATTTGAGACTA 57.690 33.333 0.00 0.00 36.02 2.59
109 110 9.924650 GGAACTAAACTAGACATTTGAGACTAA 57.075 33.333 0.00 0.00 0.00 2.24
120 121 9.213799 AGACATTTGAGACTAAATGAAGAAGAC 57.786 33.333 15.67 0.00 46.13 3.01
121 122 9.213799 GACATTTGAGACTAAATGAAGAAGACT 57.786 33.333 15.67 0.00 46.13 3.24
122 123 9.213799 ACATTTGAGACTAAATGAAGAAGACTC 57.786 33.333 15.67 0.00 46.13 3.36
123 124 9.434420 CATTTGAGACTAAATGAAGAAGACTCT 57.566 33.333 5.52 0.00 46.13 3.24
124 125 9.651913 ATTTGAGACTAAATGAAGAAGACTCTC 57.348 33.333 0.00 0.00 34.51 3.20
125 126 7.767250 TGAGACTAAATGAAGAAGACTCTCA 57.233 36.000 0.00 0.00 34.51 3.27
126 127 8.183104 TGAGACTAAATGAAGAAGACTCTCAA 57.817 34.615 0.00 0.00 34.51 3.02
127 128 8.303156 TGAGACTAAATGAAGAAGACTCTCAAG 58.697 37.037 0.00 0.00 34.51 3.02
128 129 7.610865 AGACTAAATGAAGAAGACTCTCAAGG 58.389 38.462 0.00 0.00 0.00 3.61
129 130 7.453126 AGACTAAATGAAGAAGACTCTCAAGGA 59.547 37.037 0.00 0.00 0.00 3.36
130 131 7.610865 ACTAAATGAAGAAGACTCTCAAGGAG 58.389 38.462 0.00 0.00 46.87 3.69
131 132 6.678568 AAATGAAGAAGACTCTCAAGGAGA 57.321 37.500 0.00 0.00 44.45 3.71
159 160 7.899178 TTTTTGGGACTTTTTGAGACTTTTC 57.101 32.000 0.00 0.00 0.00 2.29
160 161 5.592104 TTGGGACTTTTTGAGACTTTTCC 57.408 39.130 0.00 0.00 0.00 3.13
161 162 4.605183 TGGGACTTTTTGAGACTTTTCCA 58.395 39.130 0.00 0.00 0.00 3.53
162 163 5.020132 TGGGACTTTTTGAGACTTTTCCAA 58.980 37.500 0.00 0.00 0.00 3.53
163 164 5.105513 TGGGACTTTTTGAGACTTTTCCAAC 60.106 40.000 0.00 0.00 0.00 3.77
164 165 5.105513 GGGACTTTTTGAGACTTTTCCAACA 60.106 40.000 0.00 0.00 0.00 3.33
165 166 6.394809 GGACTTTTTGAGACTTTTCCAACAA 58.605 36.000 0.00 0.00 0.00 2.83
166 167 7.041721 GGACTTTTTGAGACTTTTCCAACAAT 58.958 34.615 0.00 0.00 0.00 2.71
167 168 7.010460 GGACTTTTTGAGACTTTTCCAACAATG 59.990 37.037 0.00 0.00 0.00 2.82
168 169 6.313658 ACTTTTTGAGACTTTTCCAACAATGC 59.686 34.615 0.00 0.00 0.00 3.56
169 170 4.320608 TTGAGACTTTTCCAACAATGCC 57.679 40.909 0.00 0.00 0.00 4.40
170 171 2.627699 TGAGACTTTTCCAACAATGCCC 59.372 45.455 0.00 0.00 0.00 5.36
171 172 1.970640 AGACTTTTCCAACAATGCCCC 59.029 47.619 0.00 0.00 0.00 5.80
172 173 1.970640 GACTTTTCCAACAATGCCCCT 59.029 47.619 0.00 0.00 0.00 4.79
173 174 1.970640 ACTTTTCCAACAATGCCCCTC 59.029 47.619 0.00 0.00 0.00 4.30
174 175 1.276138 CTTTTCCAACAATGCCCCTCC 59.724 52.381 0.00 0.00 0.00 4.30
175 176 0.189574 TTTCCAACAATGCCCCTCCA 59.810 50.000 0.00 0.00 0.00 3.86
176 177 0.413037 TTCCAACAATGCCCCTCCAT 59.587 50.000 0.00 0.00 0.00 3.41
177 178 0.324552 TCCAACAATGCCCCTCCATG 60.325 55.000 0.00 0.00 0.00 3.66
178 179 1.518774 CAACAATGCCCCTCCATGC 59.481 57.895 0.00 0.00 0.00 4.06
179 180 1.078891 AACAATGCCCCTCCATGCA 59.921 52.632 0.00 0.00 42.52 3.96
181 182 0.757935 ACAATGCCCCTCCATGCATC 60.758 55.000 0.00 0.00 46.97 3.91
182 183 1.152398 AATGCCCCTCCATGCATCC 60.152 57.895 0.00 0.00 46.97 3.51
183 184 1.951923 AATGCCCCTCCATGCATCCA 61.952 55.000 0.00 0.00 46.97 3.41
184 185 1.736491 ATGCCCCTCCATGCATCCAT 61.736 55.000 0.00 0.00 44.58 3.41
185 186 1.152398 GCCCCTCCATGCATCCATT 60.152 57.895 0.00 0.00 0.00 3.16
186 187 1.469335 GCCCCTCCATGCATCCATTG 61.469 60.000 0.00 0.00 0.00 2.82
187 188 0.830444 CCCCTCCATGCATCCATTGG 60.830 60.000 0.00 0.00 0.00 3.16
188 189 1.469335 CCCTCCATGCATCCATTGGC 61.469 60.000 0.00 0.00 0.00 4.52
189 190 1.469335 CCTCCATGCATCCATTGGCC 61.469 60.000 0.00 0.00 0.00 5.36
190 191 1.458020 TCCATGCATCCATTGGCCC 60.458 57.895 0.00 0.00 0.00 5.80
191 192 2.732016 CATGCATCCATTGGCCCG 59.268 61.111 0.00 0.00 0.00 6.13
192 193 3.228759 ATGCATCCATTGGCCCGC 61.229 61.111 0.00 0.90 0.00 6.13
212 213 3.935371 ACCCCATGGTGTTGTTTGA 57.065 47.368 11.73 0.00 45.58 2.69
213 214 2.397044 ACCCCATGGTGTTGTTTGAT 57.603 45.000 11.73 0.00 45.58 2.57
214 215 2.688477 ACCCCATGGTGTTGTTTGATT 58.312 42.857 11.73 0.00 45.58 2.57
215 216 2.368221 ACCCCATGGTGTTGTTTGATTG 59.632 45.455 11.73 0.00 45.58 2.67
216 217 2.368221 CCCCATGGTGTTGTTTGATTGT 59.632 45.455 11.73 0.00 0.00 2.71
217 218 3.181456 CCCCATGGTGTTGTTTGATTGTT 60.181 43.478 11.73 0.00 0.00 2.83
218 219 4.039730 CCCCATGGTGTTGTTTGATTGTTA 59.960 41.667 11.73 0.00 0.00 2.41
219 220 5.279910 CCCCATGGTGTTGTTTGATTGTTAT 60.280 40.000 11.73 0.00 0.00 1.89
220 221 6.229733 CCCATGGTGTTGTTTGATTGTTATT 58.770 36.000 11.73 0.00 0.00 1.40
221 222 6.709846 CCCATGGTGTTGTTTGATTGTTATTT 59.290 34.615 11.73 0.00 0.00 1.40
222 223 7.228308 CCCATGGTGTTGTTTGATTGTTATTTT 59.772 33.333 11.73 0.00 0.00 1.82
223 224 8.619546 CCATGGTGTTGTTTGATTGTTATTTTT 58.380 29.630 2.57 0.00 0.00 1.94
224 225 9.649024 CATGGTGTTGTTTGATTGTTATTTTTC 57.351 29.630 0.00 0.00 0.00 2.29
225 226 9.612066 ATGGTGTTGTTTGATTGTTATTTTTCT 57.388 25.926 0.00 0.00 0.00 2.52
244 245 8.918202 TTTTTCTATATACTAGGGGCAACATG 57.082 34.615 0.00 0.00 39.74 3.21
245 246 6.620877 TTCTATATACTAGGGGCAACATGG 57.379 41.667 0.00 0.00 39.74 3.66
246 247 5.661565 TCTATATACTAGGGGCAACATGGT 58.338 41.667 0.00 0.00 39.74 3.55
247 248 4.910458 ATATACTAGGGGCAACATGGTC 57.090 45.455 0.00 0.00 39.74 4.02
248 249 1.959710 TACTAGGGGCAACATGGTCA 58.040 50.000 0.00 0.00 39.74 4.02
249 250 1.298953 ACTAGGGGCAACATGGTCAT 58.701 50.000 0.00 0.00 39.74 3.06
250 251 1.640670 ACTAGGGGCAACATGGTCATT 59.359 47.619 0.00 0.00 39.74 2.57
251 252 2.042979 ACTAGGGGCAACATGGTCATTT 59.957 45.455 0.00 0.00 39.74 2.32
252 253 2.917713 AGGGGCAACATGGTCATTTA 57.082 45.000 0.00 0.00 39.74 1.40
253 254 3.182887 AGGGGCAACATGGTCATTTAA 57.817 42.857 0.00 0.00 39.74 1.52
254 255 3.723325 AGGGGCAACATGGTCATTTAAT 58.277 40.909 0.00 0.00 39.74 1.40
255 256 4.877773 AGGGGCAACATGGTCATTTAATA 58.122 39.130 0.00 0.00 39.74 0.98
256 257 5.276440 AGGGGCAACATGGTCATTTAATAA 58.724 37.500 0.00 0.00 39.74 1.40
257 258 5.128663 AGGGGCAACATGGTCATTTAATAAC 59.871 40.000 0.00 0.00 39.74 1.89
258 259 5.356426 GGGCAACATGGTCATTTAATAACC 58.644 41.667 0.00 0.00 39.74 2.85
259 260 5.128663 GGGCAACATGGTCATTTAATAACCT 59.871 40.000 0.00 0.00 39.74 3.50
260 261 6.273071 GGCAACATGGTCATTTAATAACCTC 58.727 40.000 0.00 0.00 34.05 3.85
261 262 6.096846 GGCAACATGGTCATTTAATAACCTCT 59.903 38.462 0.00 0.00 34.05 3.69
262 263 7.284489 GGCAACATGGTCATTTAATAACCTCTA 59.716 37.037 0.00 0.00 34.05 2.43
263 264 8.345565 GCAACATGGTCATTTAATAACCTCTAG 58.654 37.037 0.00 0.00 34.05 2.43
264 265 8.840321 CAACATGGTCATTTAATAACCTCTAGG 58.160 37.037 0.00 0.00 42.17 3.02
265 266 8.331931 ACATGGTCATTTAATAACCTCTAGGA 57.668 34.615 2.23 0.00 38.94 2.94
266 267 8.778059 ACATGGTCATTTAATAACCTCTAGGAA 58.222 33.333 2.23 0.00 38.94 3.36
267 268 9.277783 CATGGTCATTTAATAACCTCTAGGAAG 57.722 37.037 2.23 0.00 38.94 3.46
268 269 7.802117 TGGTCATTTAATAACCTCTAGGAAGG 58.198 38.462 2.23 0.00 42.55 3.46
269 270 7.147373 TGGTCATTTAATAACCTCTAGGAAGGG 60.147 40.741 2.23 0.00 41.04 3.95
270 271 7.072076 GGTCATTTAATAACCTCTAGGAAGGGA 59.928 40.741 2.23 0.00 41.04 4.20
271 272 7.932491 GTCATTTAATAACCTCTAGGAAGGGAC 59.068 40.741 2.23 0.00 41.04 4.46
272 273 7.849904 TCATTTAATAACCTCTAGGAAGGGACT 59.150 37.037 2.23 0.00 41.04 3.85
273 274 9.155785 CATTTAATAACCTCTAGGAAGGGACTA 57.844 37.037 2.23 0.00 41.04 2.59
274 275 8.779096 TTTAATAACCTCTAGGAAGGGACTAG 57.221 38.462 2.23 0.00 41.04 2.57
275 276 3.691698 AACCTCTAGGAAGGGACTAGG 57.308 52.381 2.23 0.00 41.04 3.02
276 277 1.860906 ACCTCTAGGAAGGGACTAGGG 59.139 57.143 2.23 0.00 41.04 3.53
277 278 2.145298 CCTCTAGGAAGGGACTAGGGA 58.855 57.143 1.08 0.00 40.69 4.20
278 279 2.158430 CCTCTAGGAAGGGACTAGGGAC 60.158 59.091 1.08 0.00 40.69 4.46
279 280 2.787035 CTCTAGGAAGGGACTAGGGACT 59.213 54.545 0.00 0.00 40.69 3.85
280 281 3.205733 CTCTAGGAAGGGACTAGGGACTT 59.794 52.174 0.00 0.00 40.69 3.01
281 282 3.601537 TCTAGGAAGGGACTAGGGACTTT 59.398 47.826 0.00 0.00 38.49 2.66
282 283 3.293215 AGGAAGGGACTAGGGACTTTT 57.707 47.619 0.00 0.00 38.49 2.27
283 284 3.610260 AGGAAGGGACTAGGGACTTTTT 58.390 45.455 0.00 0.00 38.49 1.94
284 285 4.771338 AGGAAGGGACTAGGGACTTTTTA 58.229 43.478 0.00 0.00 38.49 1.52
285 286 4.783763 AGGAAGGGACTAGGGACTTTTTAG 59.216 45.833 0.00 0.00 38.49 1.85
286 287 4.535294 GGAAGGGACTAGGGACTTTTTAGT 59.465 45.833 0.00 0.00 38.49 2.24
287 288 5.338219 GGAAGGGACTAGGGACTTTTTAGTC 60.338 48.000 0.00 3.01 38.49 2.59
288 289 5.026093 AGGGACTAGGGACTTTTTAGTCT 57.974 43.478 9.84 0.00 41.77 3.24
289 290 5.024785 AGGGACTAGGGACTTTTTAGTCTC 58.975 45.833 9.84 6.72 42.56 3.36
293 294 5.652324 ACTAGGGACTTTTTAGTCTCTGGA 58.348 41.667 20.87 2.39 46.69 3.86
294 295 6.082707 ACTAGGGACTTTTTAGTCTCTGGAA 58.917 40.000 20.87 1.77 46.69 3.53
295 296 5.906772 AGGGACTTTTTAGTCTCTGGAAA 57.093 39.130 6.89 0.00 46.88 3.13
296 297 5.622180 AGGGACTTTTTAGTCTCTGGAAAC 58.378 41.667 6.89 0.00 46.88 2.78
297 298 5.132144 AGGGACTTTTTAGTCTCTGGAAACA 59.868 40.000 6.89 0.00 46.88 2.83
298 299 5.826208 GGGACTTTTTAGTCTCTGGAAACAA 59.174 40.000 5.40 0.00 38.28 2.83
299 300 6.320418 GGGACTTTTTAGTCTCTGGAAACAAA 59.680 38.462 5.40 0.00 38.28 2.83
300 301 7.194278 GGACTTTTTAGTCTCTGGAAACAAAC 58.806 38.462 5.40 0.00 38.28 2.93
301 302 7.148137 GGACTTTTTAGTCTCTGGAAACAAACA 60.148 37.037 5.40 0.00 38.28 2.83
302 303 7.762382 ACTTTTTAGTCTCTGGAAACAAACAG 58.238 34.615 0.00 0.00 42.06 3.16
303 304 6.693315 TTTTAGTCTCTGGAAACAAACAGG 57.307 37.500 0.00 0.00 42.06 4.00
304 305 3.214696 AGTCTCTGGAAACAAACAGGG 57.785 47.619 0.00 0.00 42.06 4.45
305 306 2.777692 AGTCTCTGGAAACAAACAGGGA 59.222 45.455 0.00 0.00 41.67 4.20
306 307 3.142174 GTCTCTGGAAACAAACAGGGAG 58.858 50.000 0.00 0.00 44.32 4.30
307 308 3.045634 TCTCTGGAAACAAACAGGGAGA 58.954 45.455 0.00 0.00 39.19 3.71
308 309 3.071602 TCTCTGGAAACAAACAGGGAGAG 59.928 47.826 0.00 0.00 39.19 3.20
309 310 3.045634 TCTGGAAACAAACAGGGAGAGA 58.954 45.455 0.00 0.00 42.06 3.10
310 311 3.142174 CTGGAAACAAACAGGGAGAGAC 58.858 50.000 0.00 0.00 42.06 3.36
311 312 2.777692 TGGAAACAAACAGGGAGAGACT 59.222 45.455 0.00 0.00 37.44 3.24
312 313 3.202151 TGGAAACAAACAGGGAGAGACTT 59.798 43.478 0.00 0.00 37.44 3.01
313 314 4.207955 GGAAACAAACAGGGAGAGACTTT 58.792 43.478 0.00 0.00 0.00 2.66
314 315 4.645136 GGAAACAAACAGGGAGAGACTTTT 59.355 41.667 0.00 0.00 0.00 2.27
315 316 5.127194 GGAAACAAACAGGGAGAGACTTTTT 59.873 40.000 0.00 0.00 0.00 1.94
316 317 6.320418 GGAAACAAACAGGGAGAGACTTTTTA 59.680 38.462 0.00 0.00 0.00 1.52
317 318 6.944234 AACAAACAGGGAGAGACTTTTTAG 57.056 37.500 0.00 0.00 0.00 1.85
318 319 5.377478 ACAAACAGGGAGAGACTTTTTAGG 58.623 41.667 0.00 0.00 0.00 2.69
319 320 5.132144 ACAAACAGGGAGAGACTTTTTAGGA 59.868 40.000 0.00 0.00 0.00 2.94
320 321 4.893829 ACAGGGAGAGACTTTTTAGGAC 57.106 45.455 0.00 0.00 0.00 3.85
321 322 4.494591 ACAGGGAGAGACTTTTTAGGACT 58.505 43.478 0.00 0.00 0.00 3.85
322 323 5.652324 ACAGGGAGAGACTTTTTAGGACTA 58.348 41.667 0.00 0.00 0.00 2.59
323 324 5.717654 ACAGGGAGAGACTTTTTAGGACTAG 59.282 44.000 0.00 0.00 0.00 2.57
324 325 5.128008 CAGGGAGAGACTTTTTAGGACTAGG 59.872 48.000 0.00 0.00 0.00 3.02
325 326 5.016459 AGGGAGAGACTTTTTAGGACTAGGA 59.984 44.000 0.00 0.00 0.00 2.94
326 327 5.720520 GGGAGAGACTTTTTAGGACTAGGAA 59.279 44.000 0.00 0.00 0.00 3.36
327 328 6.351202 GGGAGAGACTTTTTAGGACTAGGAAC 60.351 46.154 0.00 0.00 0.00 3.62
328 329 6.438108 GGAGAGACTTTTTAGGACTAGGAACT 59.562 42.308 0.00 0.00 46.37 3.01
329 330 7.038870 GGAGAGACTTTTTAGGACTAGGAACTT 60.039 40.741 0.00 0.00 41.75 2.66
330 331 8.265108 AGAGACTTTTTAGGACTAGGAACTTT 57.735 34.615 0.00 0.00 41.75 2.66
331 332 8.715842 AGAGACTTTTTAGGACTAGGAACTTTT 58.284 33.333 0.00 0.00 41.75 2.27
332 333 9.339850 GAGACTTTTTAGGACTAGGAACTTTTT 57.660 33.333 0.00 0.00 41.75 1.94
338 339 8.913487 TTTAGGACTAGGAACTTTTTAGTTGG 57.087 34.615 0.00 0.00 41.75 3.77
339 340 5.877491 AGGACTAGGAACTTTTTAGTTGGG 58.123 41.667 0.00 0.00 41.75 4.12
340 341 5.609708 AGGACTAGGAACTTTTTAGTTGGGA 59.390 40.000 0.00 0.00 41.75 4.37
341 342 5.704515 GGACTAGGAACTTTTTAGTTGGGAC 59.295 44.000 0.00 0.00 41.75 4.46
342 343 6.465464 GGACTAGGAACTTTTTAGTTGGGACT 60.465 42.308 0.00 0.00 41.75 3.85
343 344 7.256439 GGACTAGGAACTTTTTAGTTGGGACTA 60.256 40.741 0.00 0.00 41.75 2.59
344 345 7.677892 ACTAGGAACTTTTTAGTTGGGACTAG 58.322 38.462 0.00 0.00 38.69 2.57
345 346 6.758806 AGGAACTTTTTAGTTGGGACTAGA 57.241 37.500 0.00 0.00 35.67 2.43
346 347 7.145474 AGGAACTTTTTAGTTGGGACTAGAA 57.855 36.000 0.00 0.00 35.67 2.10
347 348 7.580007 AGGAACTTTTTAGTTGGGACTAGAAA 58.420 34.615 0.00 3.34 39.04 2.52
348 349 8.057011 AGGAACTTTTTAGTTGGGACTAGAAAA 58.943 33.333 0.00 5.68 40.10 2.29
349 350 8.689061 GGAACTTTTTAGTTGGGACTAGAAAAA 58.311 33.333 0.00 0.00 40.10 1.94
350 351 9.731819 GAACTTTTTAGTTGGGACTAGAAAAAG 57.268 33.333 17.36 17.36 45.76 2.27
351 352 8.818622 ACTTTTTAGTTGGGACTAGAAAAAGT 57.181 30.769 18.18 18.18 46.80 2.66
374 375 7.365840 GTCCTAAGACTTATGAACCAAACAG 57.634 40.000 2.20 0.00 40.10 3.16
375 376 6.371825 GTCCTAAGACTTATGAACCAAACAGG 59.628 42.308 2.20 0.00 40.95 4.00
376 377 7.958807 GTCCTAAGACTTATGAACCAAACAGGT 60.959 40.741 2.20 0.00 46.29 4.00
484 490 8.299990 TCCTTCTGAAAAGTATTGGACAAAAA 57.700 30.769 0.00 0.00 0.00 1.94
537 548 3.119990 GGCGTACAAGTACAACGTAGGTA 60.120 47.826 10.63 0.00 38.81 3.08
601 612 3.132925 GCGAGGAGTAGTGGAGTAGTAG 58.867 54.545 0.00 0.00 0.00 2.57
695 706 5.880332 GCCATCCTTCTGAAAATGTGTAGTA 59.120 40.000 10.01 0.00 0.00 1.82
799 814 1.104577 AGCGGTCCAGTAGCTAGCTC 61.105 60.000 23.26 13.06 39.74 4.09
850 865 2.010497 CTGTAGCTGTCGAGTAGCAGA 58.990 52.381 20.09 7.88 43.53 4.26
928 961 4.203012 CCCTCCCCTCCCCTATATAAGAAA 60.203 50.000 0.00 0.00 0.00 2.52
929 962 5.033522 CCTCCCCTCCCCTATATAAGAAAG 58.966 50.000 0.00 0.00 0.00 2.62
930 963 5.222780 CCTCCCCTCCCCTATATAAGAAAGA 60.223 48.000 0.00 0.00 0.00 2.52
931 964 6.317531 TCCCCTCCCCTATATAAGAAAGAA 57.682 41.667 0.00 0.00 0.00 2.52
932 965 6.331846 TCCCCTCCCCTATATAAGAAAGAAG 58.668 44.000 0.00 0.00 0.00 2.85
933 966 6.107252 TCCCCTCCCCTATATAAGAAAGAAGA 59.893 42.308 0.00 0.00 0.00 2.87
934 967 6.442244 CCCCTCCCCTATATAAGAAAGAAGAG 59.558 46.154 0.00 0.00 0.00 2.85
935 968 7.020009 CCCTCCCCTATATAAGAAAGAAGAGT 58.980 42.308 0.00 0.00 0.00 3.24
936 969 8.178132 CCCTCCCCTATATAAGAAAGAAGAGTA 58.822 40.741 0.00 0.00 0.00 2.59
937 970 9.027202 CCTCCCCTATATAAGAAAGAAGAGTAC 57.973 40.741 0.00 0.00 0.00 2.73
938 971 9.816787 CTCCCCTATATAAGAAAGAAGAGTACT 57.183 37.037 0.00 0.00 0.00 2.73
1078 1111 1.956477 GTGTTGAAATCCACACTGGCT 59.044 47.619 9.76 0.00 37.47 4.75
1206 1240 1.684386 CTGCCTGCAACCCAACCAAA 61.684 55.000 0.00 0.00 0.00 3.28
1308 1342 2.101185 CTCGTCGAGAGTGCGCAT 59.899 61.111 15.91 1.95 41.99 4.73
1466 1500 4.704833 TGAGCAGCCGCACCTTCC 62.705 66.667 0.00 0.00 42.27 3.46
1468 1502 3.909086 GAGCAGCCGCACCTTCCTT 62.909 63.158 0.00 0.00 42.27 3.36
1505 1539 2.343758 GCAGGAGGAGCACGACAA 59.656 61.111 0.00 0.00 0.00 3.18
1646 1680 4.281941 GGTTCTTTGCTCCCAGATTTCTTT 59.718 41.667 0.00 0.00 0.00 2.52
1647 1681 5.221521 GGTTCTTTGCTCCCAGATTTCTTTT 60.222 40.000 0.00 0.00 0.00 2.27
1648 1682 5.712152 TCTTTGCTCCCAGATTTCTTTTC 57.288 39.130 0.00 0.00 0.00 2.29
1649 1683 4.216257 TCTTTGCTCCCAGATTTCTTTTCG 59.784 41.667 0.00 0.00 0.00 3.46
1650 1684 2.436417 TGCTCCCAGATTTCTTTTCGG 58.564 47.619 0.00 0.00 0.00 4.30
1651 1685 2.224769 TGCTCCCAGATTTCTTTTCGGT 60.225 45.455 0.00 0.00 0.00 4.69
1652 1686 2.820197 GCTCCCAGATTTCTTTTCGGTT 59.180 45.455 0.00 0.00 0.00 4.44
1653 1687 3.119814 GCTCCCAGATTTCTTTTCGGTTC 60.120 47.826 0.00 0.00 0.00 3.62
1654 1688 4.327680 CTCCCAGATTTCTTTTCGGTTCT 58.672 43.478 0.00 0.00 0.00 3.01
1655 1689 4.725490 TCCCAGATTTCTTTTCGGTTCTT 58.275 39.130 0.00 0.00 0.00 2.52
1656 1690 5.137551 TCCCAGATTTCTTTTCGGTTCTTT 58.862 37.500 0.00 0.00 0.00 2.52
1657 1691 5.596772 TCCCAGATTTCTTTTCGGTTCTTTT 59.403 36.000 0.00 0.00 0.00 2.27
1658 1692 5.920840 CCCAGATTTCTTTTCGGTTCTTTTC 59.079 40.000 0.00 0.00 0.00 2.29
1702 1736 2.836636 ACTCCAGGCAGATAGAGTCA 57.163 50.000 0.00 0.00 34.53 3.41
1765 1799 0.468226 TTGGAGTCGTTTCACTGCCT 59.532 50.000 0.00 0.00 33.92 4.75
1811 1845 0.459585 TCTGCGCGGGAACTAATGAC 60.460 55.000 17.88 0.00 0.00 3.06
1833 1867 4.929211 ACGTCGATGATGAGTTTCAAATCA 59.071 37.500 12.58 0.00 37.42 2.57
1862 1896 5.818678 TTGTTAGGCTAGGTCTTCAAAGA 57.181 39.130 0.00 0.00 0.00 2.52
1930 1965 2.194271 GATTCCGTGTGTGCTAGTAGC 58.806 52.381 15.56 15.56 42.82 3.58
2112 2186 3.991773 TGTGTGTCGAGCAACTATTTACC 59.008 43.478 0.00 0.00 0.00 2.85
2127 2207 9.612620 CAACTATTTACCTCACTGTTTCAAATC 57.387 33.333 0.00 0.00 0.00 2.17
2128 2208 8.336801 ACTATTTACCTCACTGTTTCAAATCC 57.663 34.615 0.00 0.00 0.00 3.01
2131 2211 7.595819 TTTACCTCACTGTTTCAAATCCATT 57.404 32.000 0.00 0.00 0.00 3.16
2132 2212 8.698973 TTTACCTCACTGTTTCAAATCCATTA 57.301 30.769 0.00 0.00 0.00 1.90
2133 2213 6.575162 ACCTCACTGTTTCAAATCCATTAC 57.425 37.500 0.00 0.00 0.00 1.89
2161 2247 5.784578 ACTTATATATGCTGTGTGACGGA 57.215 39.130 0.00 0.00 0.00 4.69
2287 2386 3.989698 AACCGAGAGCGATGCACGG 62.990 63.158 15.98 15.98 43.11 4.94
2364 2463 7.208080 TGTTCTCTGTTCTGTAGTAGGAAAAC 58.792 38.462 0.00 0.00 0.00 2.43
2388 2487 6.027749 CCGGATTCTTGTTTGCTTATGTTAC 58.972 40.000 0.00 0.00 0.00 2.50
2415 2514 8.589338 GTGTGATGGAATACTATACTCTGGAAT 58.411 37.037 0.00 0.00 0.00 3.01
2463 2562 4.464597 AGAGAGAACGCCTAGAATTTCTGT 59.535 41.667 9.22 0.00 0.00 3.41
2482 2581 6.308371 TCTGTTATCATCGCATCGTACTAA 57.692 37.500 0.00 0.00 0.00 2.24
2551 2650 1.636003 GTGGGGAATGAAGGGAAGAGT 59.364 52.381 0.00 0.00 0.00 3.24
2573 2672 2.031870 TGACCATAGTGCTAGTGCGAT 58.968 47.619 0.00 0.00 43.34 4.58
2612 2711 9.907576 CAGTGTGAAGAATAGAAAATATCGTTC 57.092 33.333 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.217131 GACTTTTTCTAGTCCCTACACAAAAA 57.783 34.615 0.00 0.00 38.88 1.94
18 19 7.797038 GACTTTTTCTAGTCCCTACACAAAA 57.203 36.000 0.00 0.00 38.88 2.44
29 30 7.395206 AGTCTCTAAGAGGGACTTTTTCTAGTC 59.605 40.741 3.06 0.00 41.55 2.59
30 31 7.243091 AGTCTCTAAGAGGGACTTTTTCTAGT 58.757 38.462 3.06 0.00 41.55 2.57
31 32 7.712204 AGTCTCTAAGAGGGACTTTTTCTAG 57.288 40.000 3.06 0.00 41.55 2.43
56 57 2.175284 AGTCCCTCCCGTTTGGTAAAAA 59.825 45.455 0.00 0.00 34.77 1.94
57 58 1.776063 AGTCCCTCCCGTTTGGTAAAA 59.224 47.619 0.00 0.00 34.77 1.52
58 59 1.072648 CAGTCCCTCCCGTTTGGTAAA 59.927 52.381 0.00 0.00 34.77 2.01
59 60 0.688487 CAGTCCCTCCCGTTTGGTAA 59.312 55.000 0.00 0.00 34.77 2.85
60 61 0.472352 ACAGTCCCTCCCGTTTGGTA 60.472 55.000 0.00 0.00 34.77 3.25
61 62 1.350310 AACAGTCCCTCCCGTTTGGT 61.350 55.000 0.00 0.00 34.77 3.67
62 63 0.179001 AAACAGTCCCTCCCGTTTGG 60.179 55.000 0.00 0.00 30.70 3.28
63 64 2.423577 CTAAACAGTCCCTCCCGTTTG 58.576 52.381 0.00 0.00 33.79 2.93
64 65 1.350019 CCTAAACAGTCCCTCCCGTTT 59.650 52.381 0.00 0.00 35.79 3.60
65 66 0.981943 CCTAAACAGTCCCTCCCGTT 59.018 55.000 0.00 0.00 0.00 4.44
66 67 0.115745 TCCTAAACAGTCCCTCCCGT 59.884 55.000 0.00 0.00 0.00 5.28
67 68 1.066358 GTTCCTAAACAGTCCCTCCCG 60.066 57.143 0.00 0.00 35.36 5.14
68 69 2.267192 AGTTCCTAAACAGTCCCTCCC 58.733 52.381 0.00 0.00 37.88 4.30
69 70 5.494390 TTTAGTTCCTAAACAGTCCCTCC 57.506 43.478 0.00 0.00 37.88 4.30
80 81 9.924650 GTCTCAAATGTCTAGTTTAGTTCCTAA 57.075 33.333 0.00 0.00 0.00 2.69
81 82 9.310449 AGTCTCAAATGTCTAGTTTAGTTCCTA 57.690 33.333 0.00 0.00 0.00 2.94
82 83 8.196378 AGTCTCAAATGTCTAGTTTAGTTCCT 57.804 34.615 0.00 0.00 0.00 3.36
83 84 9.924650 TTAGTCTCAAATGTCTAGTTTAGTTCC 57.075 33.333 0.00 0.00 0.00 3.62
94 95 9.213799 GTCTTCTTCATTTAGTCTCAAATGTCT 57.786 33.333 8.07 0.00 43.40 3.41
95 96 9.213799 AGTCTTCTTCATTTAGTCTCAAATGTC 57.786 33.333 8.07 0.00 43.40 3.06
96 97 9.213799 GAGTCTTCTTCATTTAGTCTCAAATGT 57.786 33.333 8.07 0.00 43.40 2.71
97 98 9.434420 AGAGTCTTCTTCATTTAGTCTCAAATG 57.566 33.333 2.83 2.83 44.00 2.32
98 99 9.651913 GAGAGTCTTCTTCATTTAGTCTCAAAT 57.348 33.333 0.00 0.00 36.87 2.32
99 100 8.642432 TGAGAGTCTTCTTCATTTAGTCTCAAA 58.358 33.333 0.00 0.00 41.38 2.69
100 101 8.183104 TGAGAGTCTTCTTCATTTAGTCTCAA 57.817 34.615 0.00 0.00 41.38 3.02
101 102 7.767250 TGAGAGTCTTCTTCATTTAGTCTCA 57.233 36.000 0.00 0.00 41.83 3.27
102 103 7.759433 CCTTGAGAGTCTTCTTCATTTAGTCTC 59.241 40.741 0.00 0.00 37.23 3.36
103 104 7.453126 TCCTTGAGAGTCTTCTTCATTTAGTCT 59.547 37.037 0.00 0.00 32.53 3.24
104 105 7.607250 TCCTTGAGAGTCTTCTTCATTTAGTC 58.393 38.462 0.00 0.00 32.53 2.59
105 106 7.453126 TCTCCTTGAGAGTCTTCTTCATTTAGT 59.547 37.037 0.00 0.00 43.71 2.24
106 107 7.835822 TCTCCTTGAGAGTCTTCTTCATTTAG 58.164 38.462 0.00 0.00 43.71 1.85
107 108 7.782897 TCTCCTTGAGAGTCTTCTTCATTTA 57.217 36.000 0.00 0.00 43.71 1.40
108 109 6.678568 TCTCCTTGAGAGTCTTCTTCATTT 57.321 37.500 0.00 0.00 43.71 2.32
135 136 6.876789 GGAAAAGTCTCAAAAAGTCCCAAAAA 59.123 34.615 0.00 0.00 0.00 1.94
136 137 6.014156 TGGAAAAGTCTCAAAAAGTCCCAAAA 60.014 34.615 0.00 0.00 0.00 2.44
137 138 5.482175 TGGAAAAGTCTCAAAAAGTCCCAAA 59.518 36.000 0.00 0.00 0.00 3.28
138 139 5.020132 TGGAAAAGTCTCAAAAAGTCCCAA 58.980 37.500 0.00 0.00 0.00 4.12
139 140 4.605183 TGGAAAAGTCTCAAAAAGTCCCA 58.395 39.130 0.00 0.00 0.00 4.37
140 141 5.105513 TGTTGGAAAAGTCTCAAAAAGTCCC 60.106 40.000 0.00 0.00 0.00 4.46
141 142 5.961272 TGTTGGAAAAGTCTCAAAAAGTCC 58.039 37.500 0.00 0.00 0.00 3.85
142 143 7.464577 GCATTGTTGGAAAAGTCTCAAAAAGTC 60.465 37.037 0.00 0.00 0.00 3.01
143 144 6.313658 GCATTGTTGGAAAAGTCTCAAAAAGT 59.686 34.615 0.00 0.00 0.00 2.66
144 145 6.238184 GGCATTGTTGGAAAAGTCTCAAAAAG 60.238 38.462 0.00 0.00 0.00 2.27
145 146 5.584251 GGCATTGTTGGAAAAGTCTCAAAAA 59.416 36.000 0.00 0.00 0.00 1.94
146 147 5.115480 GGCATTGTTGGAAAAGTCTCAAAA 58.885 37.500 0.00 0.00 0.00 2.44
147 148 4.442753 GGGCATTGTTGGAAAAGTCTCAAA 60.443 41.667 0.00 0.00 0.00 2.69
148 149 3.069443 GGGCATTGTTGGAAAAGTCTCAA 59.931 43.478 0.00 0.00 0.00 3.02
149 150 2.627699 GGGCATTGTTGGAAAAGTCTCA 59.372 45.455 0.00 0.00 0.00 3.27
150 151 2.029020 GGGGCATTGTTGGAAAAGTCTC 60.029 50.000 0.00 0.00 0.00 3.36
151 152 1.970640 GGGGCATTGTTGGAAAAGTCT 59.029 47.619 0.00 0.00 0.00 3.24
152 153 1.970640 AGGGGCATTGTTGGAAAAGTC 59.029 47.619 0.00 0.00 0.00 3.01
153 154 1.970640 GAGGGGCATTGTTGGAAAAGT 59.029 47.619 0.00 0.00 0.00 2.66
154 155 1.276138 GGAGGGGCATTGTTGGAAAAG 59.724 52.381 0.00 0.00 0.00 2.27
155 156 1.347062 GGAGGGGCATTGTTGGAAAA 58.653 50.000 0.00 0.00 0.00 2.29
156 157 0.189574 TGGAGGGGCATTGTTGGAAA 59.810 50.000 0.00 0.00 0.00 3.13
157 158 0.413037 ATGGAGGGGCATTGTTGGAA 59.587 50.000 0.00 0.00 0.00 3.53
158 159 0.324552 CATGGAGGGGCATTGTTGGA 60.325 55.000 0.00 0.00 0.00 3.53
159 160 1.963464 GCATGGAGGGGCATTGTTGG 61.963 60.000 0.00 0.00 0.00 3.77
160 161 1.259142 TGCATGGAGGGGCATTGTTG 61.259 55.000 0.00 0.00 34.58 3.33
161 162 1.078891 TGCATGGAGGGGCATTGTT 59.921 52.632 0.00 0.00 34.58 2.83
162 163 2.772224 TGCATGGAGGGGCATTGT 59.228 55.556 0.00 0.00 34.58 2.71
166 167 1.951923 AATGGATGCATGGAGGGGCA 61.952 55.000 2.46 0.00 45.23 5.36
167 168 1.152398 AATGGATGCATGGAGGGGC 60.152 57.895 2.46 0.00 0.00 5.80
168 169 0.830444 CCAATGGATGCATGGAGGGG 60.830 60.000 2.46 0.00 36.27 4.79
169 170 1.469335 GCCAATGGATGCATGGAGGG 61.469 60.000 2.46 10.22 36.27 4.30
170 171 1.469335 GGCCAATGGATGCATGGAGG 61.469 60.000 2.46 12.51 36.27 4.30
171 172 1.469335 GGGCCAATGGATGCATGGAG 61.469 60.000 2.46 4.05 36.27 3.86
172 173 1.458020 GGGCCAATGGATGCATGGA 60.458 57.895 2.46 0.00 36.27 3.41
173 174 2.863346 CGGGCCAATGGATGCATGG 61.863 63.158 2.46 0.11 37.29 3.66
174 175 2.732016 CGGGCCAATGGATGCATG 59.268 61.111 2.46 0.00 0.00 4.06
175 176 3.228759 GCGGGCCAATGGATGCAT 61.229 61.111 2.05 0.00 0.00 3.96
195 196 2.368221 ACAATCAAACAACACCATGGGG 59.632 45.455 14.08 14.08 41.29 4.96
196 197 3.749665 ACAATCAAACAACACCATGGG 57.250 42.857 18.09 7.72 0.00 4.00
197 198 7.727331 AAATAACAATCAAACAACACCATGG 57.273 32.000 11.19 11.19 0.00 3.66
198 199 9.649024 GAAAAATAACAATCAAACAACACCATG 57.351 29.630 0.00 0.00 0.00 3.66
199 200 9.612066 AGAAAAATAACAATCAAACAACACCAT 57.388 25.926 0.00 0.00 0.00 3.55
218 219 9.520515 CATGTTGCCCCTAGTATATAGAAAAAT 57.479 33.333 0.00 0.00 0.00 1.82
219 220 7.942341 CCATGTTGCCCCTAGTATATAGAAAAA 59.058 37.037 0.00 0.00 0.00 1.94
220 221 7.073215 ACCATGTTGCCCCTAGTATATAGAAAA 59.927 37.037 0.00 0.00 0.00 2.29
221 222 6.561070 ACCATGTTGCCCCTAGTATATAGAAA 59.439 38.462 0.00 0.00 0.00 2.52
222 223 6.088819 ACCATGTTGCCCCTAGTATATAGAA 58.911 40.000 0.00 0.00 0.00 2.10
223 224 5.661565 ACCATGTTGCCCCTAGTATATAGA 58.338 41.667 0.00 0.00 0.00 1.98
224 225 5.483937 TGACCATGTTGCCCCTAGTATATAG 59.516 44.000 0.00 0.00 0.00 1.31
225 226 5.407936 TGACCATGTTGCCCCTAGTATATA 58.592 41.667 0.00 0.00 0.00 0.86
226 227 4.239495 TGACCATGTTGCCCCTAGTATAT 58.761 43.478 0.00 0.00 0.00 0.86
227 228 3.659841 TGACCATGTTGCCCCTAGTATA 58.340 45.455 0.00 0.00 0.00 1.47
228 229 2.487775 TGACCATGTTGCCCCTAGTAT 58.512 47.619 0.00 0.00 0.00 2.12
229 230 1.959710 TGACCATGTTGCCCCTAGTA 58.040 50.000 0.00 0.00 0.00 1.82
230 231 1.298953 ATGACCATGTTGCCCCTAGT 58.701 50.000 0.00 0.00 0.00 2.57
231 232 2.442236 AATGACCATGTTGCCCCTAG 57.558 50.000 0.00 0.00 0.00 3.02
232 233 2.917713 AAATGACCATGTTGCCCCTA 57.082 45.000 0.00 0.00 0.00 3.53
233 234 2.917713 TAAATGACCATGTTGCCCCT 57.082 45.000 0.00 0.00 0.00 4.79
234 235 5.356426 GTTATTAAATGACCATGTTGCCCC 58.644 41.667 0.00 0.00 0.00 5.80
235 236 5.128663 AGGTTATTAAATGACCATGTTGCCC 59.871 40.000 6.26 0.00 41.10 5.36
236 237 6.096846 AGAGGTTATTAAATGACCATGTTGCC 59.903 38.462 6.26 0.00 41.10 4.52
237 238 7.100458 AGAGGTTATTAAATGACCATGTTGC 57.900 36.000 6.26 0.00 41.10 4.17
238 239 8.840321 CCTAGAGGTTATTAAATGACCATGTTG 58.160 37.037 6.26 0.00 41.10 3.33
239 240 8.778059 TCCTAGAGGTTATTAAATGACCATGTT 58.222 33.333 6.26 0.00 41.10 2.71
240 241 8.331931 TCCTAGAGGTTATTAAATGACCATGT 57.668 34.615 6.26 0.00 41.10 3.21
241 242 9.277783 CTTCCTAGAGGTTATTAAATGACCATG 57.722 37.037 6.26 0.00 41.10 3.66
242 243 8.440771 CCTTCCTAGAGGTTATTAAATGACCAT 58.559 37.037 6.26 0.00 41.10 3.55
243 244 7.147373 CCCTTCCTAGAGGTTATTAAATGACCA 60.147 40.741 6.26 0.00 41.10 4.02
244 245 7.072076 TCCCTTCCTAGAGGTTATTAAATGACC 59.928 40.741 0.00 0.00 39.09 4.02
245 246 7.932491 GTCCCTTCCTAGAGGTTATTAAATGAC 59.068 40.741 0.00 0.00 34.88 3.06
246 247 7.849904 AGTCCCTTCCTAGAGGTTATTAAATGA 59.150 37.037 0.00 0.00 34.88 2.57
247 248 8.035448 AGTCCCTTCCTAGAGGTTATTAAATG 57.965 38.462 0.00 0.00 34.88 2.32
248 249 9.382307 CTAGTCCCTTCCTAGAGGTTATTAAAT 57.618 37.037 0.00 0.00 35.01 1.40
249 250 7.788385 CCTAGTCCCTTCCTAGAGGTTATTAAA 59.212 40.741 0.00 0.00 35.01 1.52
250 251 7.303713 CCTAGTCCCTTCCTAGAGGTTATTAA 58.696 42.308 0.00 0.00 35.01 1.40
251 252 6.183361 CCCTAGTCCCTTCCTAGAGGTTATTA 60.183 46.154 0.00 0.00 35.01 0.98
252 253 5.401587 CCCTAGTCCCTTCCTAGAGGTTATT 60.402 48.000 0.00 0.00 35.01 1.40
253 254 4.108287 CCCTAGTCCCTTCCTAGAGGTTAT 59.892 50.000 0.00 0.00 35.01 1.89
254 255 3.466344 CCCTAGTCCCTTCCTAGAGGTTA 59.534 52.174 0.00 0.00 35.01 2.85
255 256 2.247897 CCCTAGTCCCTTCCTAGAGGTT 59.752 54.545 0.00 0.00 35.01 3.50
256 257 1.860906 CCCTAGTCCCTTCCTAGAGGT 59.139 57.143 0.00 0.00 35.01 3.85
257 258 2.145298 TCCCTAGTCCCTTCCTAGAGG 58.855 57.143 0.00 0.00 35.01 3.69
258 259 2.787035 AGTCCCTAGTCCCTTCCTAGAG 59.213 54.545 0.00 0.00 35.01 2.43
259 260 2.874447 AGTCCCTAGTCCCTTCCTAGA 58.126 52.381 0.00 0.00 35.01 2.43
260 261 3.691698 AAGTCCCTAGTCCCTTCCTAG 57.308 52.381 0.00 0.00 33.23 3.02
261 262 4.431158 AAAAGTCCCTAGTCCCTTCCTA 57.569 45.455 0.00 0.00 0.00 2.94
262 263 3.293215 AAAAGTCCCTAGTCCCTTCCT 57.707 47.619 0.00 0.00 0.00 3.36
263 264 4.535294 ACTAAAAAGTCCCTAGTCCCTTCC 59.465 45.833 0.00 0.00 0.00 3.46
264 265 5.484644 AGACTAAAAAGTCCCTAGTCCCTTC 59.515 44.000 2.00 0.00 41.59 3.46
265 266 5.413277 AGACTAAAAAGTCCCTAGTCCCTT 58.587 41.667 2.00 0.00 41.59 3.95
266 267 5.024785 GAGACTAAAAAGTCCCTAGTCCCT 58.975 45.833 2.00 0.00 41.59 4.20
267 268 5.024785 AGAGACTAAAAAGTCCCTAGTCCC 58.975 45.833 2.00 0.00 41.59 4.46
268 269 5.105269 CCAGAGACTAAAAAGTCCCTAGTCC 60.105 48.000 2.00 0.00 41.59 3.85
269 270 5.715753 TCCAGAGACTAAAAAGTCCCTAGTC 59.284 44.000 2.00 0.00 41.17 2.59
270 271 5.652324 TCCAGAGACTAAAAAGTCCCTAGT 58.348 41.667 2.00 0.00 39.50 2.57
271 272 6.607004 TTCCAGAGACTAAAAAGTCCCTAG 57.393 41.667 2.00 0.00 39.50 3.02
272 273 6.328148 TGTTTCCAGAGACTAAAAAGTCCCTA 59.672 38.462 2.00 0.00 39.50 3.53
273 274 5.132144 TGTTTCCAGAGACTAAAAAGTCCCT 59.868 40.000 2.00 0.00 39.50 4.20
274 275 5.374071 TGTTTCCAGAGACTAAAAAGTCCC 58.626 41.667 2.00 0.00 39.50 4.46
275 276 6.937436 TTGTTTCCAGAGACTAAAAAGTCC 57.063 37.500 2.00 0.00 39.50 3.85
276 277 7.758495 TGTTTGTTTCCAGAGACTAAAAAGTC 58.242 34.615 0.00 0.00 39.00 3.01
277 278 7.148069 CCTGTTTGTTTCCAGAGACTAAAAAGT 60.148 37.037 0.00 0.00 0.00 2.66
278 279 7.196331 CCTGTTTGTTTCCAGAGACTAAAAAG 58.804 38.462 0.00 0.00 0.00 2.27
279 280 6.096282 CCCTGTTTGTTTCCAGAGACTAAAAA 59.904 38.462 0.00 0.00 0.00 1.94
280 281 5.592688 CCCTGTTTGTTTCCAGAGACTAAAA 59.407 40.000 0.00 0.00 0.00 1.52
281 282 5.104277 TCCCTGTTTGTTTCCAGAGACTAAA 60.104 40.000 0.00 0.00 0.00 1.85
282 283 4.410883 TCCCTGTTTGTTTCCAGAGACTAA 59.589 41.667 0.00 0.00 0.00 2.24
283 284 3.971305 TCCCTGTTTGTTTCCAGAGACTA 59.029 43.478 0.00 0.00 0.00 2.59
284 285 2.777692 TCCCTGTTTGTTTCCAGAGACT 59.222 45.455 0.00 0.00 0.00 3.24
285 286 3.142174 CTCCCTGTTTGTTTCCAGAGAC 58.858 50.000 0.00 0.00 0.00 3.36
286 287 3.045634 TCTCCCTGTTTGTTTCCAGAGA 58.954 45.455 0.00 0.00 0.00 3.10
287 288 3.071602 TCTCTCCCTGTTTGTTTCCAGAG 59.928 47.826 0.00 0.00 0.00 3.35
288 289 3.045634 TCTCTCCCTGTTTGTTTCCAGA 58.954 45.455 0.00 0.00 0.00 3.86
289 290 3.142174 GTCTCTCCCTGTTTGTTTCCAG 58.858 50.000 0.00 0.00 0.00 3.86
290 291 2.777692 AGTCTCTCCCTGTTTGTTTCCA 59.222 45.455 0.00 0.00 0.00 3.53
291 292 3.493767 AGTCTCTCCCTGTTTGTTTCC 57.506 47.619 0.00 0.00 0.00 3.13
292 293 5.836821 AAAAGTCTCTCCCTGTTTGTTTC 57.163 39.130 0.00 0.00 0.00 2.78
293 294 6.321435 CCTAAAAAGTCTCTCCCTGTTTGTTT 59.679 38.462 0.00 0.00 0.00 2.83
294 295 5.828328 CCTAAAAAGTCTCTCCCTGTTTGTT 59.172 40.000 0.00 0.00 0.00 2.83
295 296 5.132144 TCCTAAAAAGTCTCTCCCTGTTTGT 59.868 40.000 0.00 0.00 0.00 2.83
296 297 5.470437 GTCCTAAAAAGTCTCTCCCTGTTTG 59.530 44.000 0.00 0.00 0.00 2.93
297 298 5.369993 AGTCCTAAAAAGTCTCTCCCTGTTT 59.630 40.000 0.00 0.00 0.00 2.83
298 299 4.908481 AGTCCTAAAAAGTCTCTCCCTGTT 59.092 41.667 0.00 0.00 0.00 3.16
299 300 4.494591 AGTCCTAAAAAGTCTCTCCCTGT 58.505 43.478 0.00 0.00 0.00 4.00
300 301 5.128008 CCTAGTCCTAAAAAGTCTCTCCCTG 59.872 48.000 0.00 0.00 0.00 4.45
301 302 5.016459 TCCTAGTCCTAAAAAGTCTCTCCCT 59.984 44.000 0.00 0.00 0.00 4.20
302 303 5.270794 TCCTAGTCCTAAAAAGTCTCTCCC 58.729 45.833 0.00 0.00 0.00 4.30
303 304 6.438108 AGTTCCTAGTCCTAAAAAGTCTCTCC 59.562 42.308 0.00 0.00 0.00 3.71
304 305 7.470935 AGTTCCTAGTCCTAAAAAGTCTCTC 57.529 40.000 0.00 0.00 0.00 3.20
305 306 7.859026 AAGTTCCTAGTCCTAAAAAGTCTCT 57.141 36.000 0.00 0.00 0.00 3.10
306 307 8.905660 AAAAGTTCCTAGTCCTAAAAAGTCTC 57.094 34.615 0.00 0.00 0.00 3.36
312 313 9.346005 CCAACTAAAAAGTTCCTAGTCCTAAAA 57.654 33.333 0.00 0.00 0.00 1.52
313 314 7.940688 CCCAACTAAAAAGTTCCTAGTCCTAAA 59.059 37.037 0.00 0.00 0.00 1.85
314 315 7.293062 TCCCAACTAAAAAGTTCCTAGTCCTAA 59.707 37.037 0.00 0.00 0.00 2.69
315 316 6.788957 TCCCAACTAAAAAGTTCCTAGTCCTA 59.211 38.462 0.00 0.00 0.00 2.94
316 317 5.609708 TCCCAACTAAAAAGTTCCTAGTCCT 59.390 40.000 0.00 0.00 0.00 3.85
317 318 5.704515 GTCCCAACTAAAAAGTTCCTAGTCC 59.295 44.000 0.00 0.00 0.00 3.85
318 319 6.531923 AGTCCCAACTAAAAAGTTCCTAGTC 58.468 40.000 0.00 0.00 32.59 2.59
319 320 6.511017 AGTCCCAACTAAAAAGTTCCTAGT 57.489 37.500 0.00 0.00 32.59 2.57
320 321 7.904205 TCTAGTCCCAACTAAAAAGTTCCTAG 58.096 38.462 0.00 0.00 37.53 3.02
321 322 7.860649 TCTAGTCCCAACTAAAAAGTTCCTA 57.139 36.000 0.00 0.00 37.53 2.94
322 323 6.758806 TCTAGTCCCAACTAAAAAGTTCCT 57.241 37.500 0.00 0.00 37.53 3.36
323 324 7.812690 TTTCTAGTCCCAACTAAAAAGTTCC 57.187 36.000 0.00 0.00 37.53 3.62
324 325 9.731819 CTTTTTCTAGTCCCAACTAAAAAGTTC 57.268 33.333 13.30 0.00 41.21 3.01
326 327 8.818622 ACTTTTTCTAGTCCCAACTAAAAAGT 57.181 30.769 17.77 17.77 46.78 2.66
350 351 6.371825 CCTGTTTGGTTCATAAGTCTTAGGAC 59.628 42.308 6.47 0.00 42.41 3.85
351 352 6.472887 CCTGTTTGGTTCATAAGTCTTAGGA 58.527 40.000 2.85 2.85 0.00 2.94
352 353 6.743575 CCTGTTTGGTTCATAAGTCTTAGG 57.256 41.667 0.00 0.00 0.00 2.69
367 368 2.779506 GTGGAGTAAGGACCTGTTTGG 58.220 52.381 0.00 0.00 42.93 3.28
368 369 2.413837 CGTGGAGTAAGGACCTGTTTG 58.586 52.381 0.00 0.00 0.00 2.93
369 370 1.346722 CCGTGGAGTAAGGACCTGTTT 59.653 52.381 0.00 0.00 0.00 2.83
370 371 0.974383 CCGTGGAGTAAGGACCTGTT 59.026 55.000 0.00 0.00 0.00 3.16
371 372 0.113776 TCCGTGGAGTAAGGACCTGT 59.886 55.000 0.00 0.00 31.58 4.00
372 373 0.818296 CTCCGTGGAGTAAGGACCTG 59.182 60.000 7.79 0.00 37.47 4.00
373 374 3.284711 CTCCGTGGAGTAAGGACCT 57.715 57.895 7.79 0.00 37.47 3.85
537 548 1.271840 ACATGGCAGGGATACGGTGT 61.272 55.000 3.46 0.00 37.60 4.16
601 612 6.591261 GGAGAAAGAATGAAACAACGAGTAC 58.409 40.000 0.00 0.00 0.00 2.73
614 625 1.281899 GGCGAGACGGAGAAAGAATG 58.718 55.000 0.00 0.00 0.00 2.67
727 738 0.466922 TAGCTACTACCCGACAGCCC 60.467 60.000 0.00 0.00 34.49 5.19
799 814 2.123428 CCCGTGGTACTAGTCCCCG 61.123 68.421 0.00 3.48 0.00 5.73
850 865 2.029964 CGCGTGGTGGTAGTGGTT 59.970 61.111 0.00 0.00 0.00 3.67
928 961 4.530161 ACAAGCTCATCCAAGTACTCTTCT 59.470 41.667 0.00 0.00 0.00 2.85
929 962 4.826556 ACAAGCTCATCCAAGTACTCTTC 58.173 43.478 0.00 0.00 0.00 2.87
930 963 4.899352 ACAAGCTCATCCAAGTACTCTT 57.101 40.909 0.00 0.00 0.00 2.85
931 964 4.142049 GCTACAAGCTCATCCAAGTACTCT 60.142 45.833 0.00 0.00 38.45 3.24
932 965 4.116238 GCTACAAGCTCATCCAAGTACTC 58.884 47.826 0.00 0.00 38.45 2.59
933 966 3.515502 TGCTACAAGCTCATCCAAGTACT 59.484 43.478 0.03 0.00 42.97 2.73
934 967 3.861840 TGCTACAAGCTCATCCAAGTAC 58.138 45.455 0.03 0.00 42.97 2.73
935 968 3.679917 GCTGCTACAAGCTCATCCAAGTA 60.680 47.826 0.03 0.00 42.97 2.24
936 969 2.938756 GCTGCTACAAGCTCATCCAAGT 60.939 50.000 0.03 0.00 42.97 3.16
937 970 1.669779 GCTGCTACAAGCTCATCCAAG 59.330 52.381 0.03 0.00 42.97 3.61
938 971 1.003464 TGCTGCTACAAGCTCATCCAA 59.997 47.619 0.00 0.00 42.97 3.53
1078 1111 3.357203 TGCCAAACAAGGTGTTCACTAA 58.643 40.909 2.98 0.00 40.14 2.24
1182 1216 4.284550 GGGTTGCAGGCAGGGTCA 62.285 66.667 0.00 0.00 0.00 4.02
1206 1240 0.035534 TGCTGATGTACCCACGCATT 60.036 50.000 0.00 0.00 0.00 3.56
1333 1367 1.630878 CTTGTACTTGGCCTCCTCCTT 59.369 52.381 3.32 0.00 0.00 3.36
1466 1500 2.817423 GCATTCAGAGCCGCCGAAG 61.817 63.158 0.00 0.00 0.00 3.79
1468 1502 4.838152 GGCATTCAGAGCCGCCGA 62.838 66.667 0.00 0.00 43.15 5.54
1505 1539 0.523966 CTTCTCGTCGGTGAAGAGCT 59.476 55.000 17.80 0.00 43.24 4.09
1646 1680 1.743958 TGCAAACCGAAAAGAACCGAA 59.256 42.857 0.00 0.00 0.00 4.30
1647 1681 1.380524 TGCAAACCGAAAAGAACCGA 58.619 45.000 0.00 0.00 0.00 4.69
1648 1682 1.849829 GTTGCAAACCGAAAAGAACCG 59.150 47.619 0.00 0.00 42.21 4.44
1702 1736 4.057428 GGACCGAGAGCACAGCGT 62.057 66.667 0.00 0.00 0.00 5.07
1765 1799 5.212745 ACCCAGAAAAGGAACAAATGGTAA 58.787 37.500 0.00 0.00 0.00 2.85
1811 1845 5.062683 ACTGATTTGAAACTCATCATCGACG 59.937 40.000 0.00 0.00 0.00 5.12
1833 1867 2.233186 GACCTAGCCTAACAAACCGACT 59.767 50.000 0.00 0.00 0.00 4.18
1994 2059 5.408604 ACACACAGATTCCGCTTAAACTAAG 59.591 40.000 0.00 0.00 38.80 2.18
2076 2147 7.872483 TGCTCGACACACAATATATCATACAAT 59.128 33.333 0.00 0.00 0.00 2.71
2090 2161 3.991773 GGTAAATAGTTGCTCGACACACA 59.008 43.478 0.00 0.00 0.00 3.72
2095 2166 4.563184 CAGTGAGGTAAATAGTTGCTCGAC 59.437 45.833 0.00 0.00 0.00 4.20
2145 2225 1.485124 TCCTCCGTCACACAGCATAT 58.515 50.000 0.00 0.00 0.00 1.78
2155 2241 2.203788 AGGGTGCTTCCTCCGTCA 60.204 61.111 0.00 0.00 36.25 4.35
2234 2333 8.251026 CAGAAAAGGAATTAAATACACCTTCCC 58.749 37.037 0.00 0.00 39.59 3.97
2266 2365 1.014044 GTGCATCGCTCTCGGTTTCA 61.014 55.000 0.00 0.00 36.13 2.69
2314 2413 7.119699 CAGAGTATGTTGGTGCTCTCAAATTAA 59.880 37.037 0.00 0.00 38.84 1.40
2316 2415 5.413833 CAGAGTATGTTGGTGCTCTCAAATT 59.586 40.000 0.00 0.00 38.84 1.82
2317 2416 4.940046 CAGAGTATGTTGGTGCTCTCAAAT 59.060 41.667 0.00 0.00 38.84 2.32
2318 2417 4.202357 ACAGAGTATGTTGGTGCTCTCAAA 60.202 41.667 0.00 0.00 39.96 2.69
2319 2418 3.324846 ACAGAGTATGTTGGTGCTCTCAA 59.675 43.478 0.00 0.00 39.96 3.02
2320 2419 2.899900 ACAGAGTATGTTGGTGCTCTCA 59.100 45.455 0.00 0.00 39.96 3.27
2364 2463 4.701956 ACATAAGCAAACAAGAATCCGG 57.298 40.909 0.00 0.00 0.00 5.14
2388 2487 6.206829 TCCAGAGTATAGTATTCCATCACACG 59.793 42.308 0.00 0.00 0.00 4.49
2415 2514 5.241949 TCGCTTGCTAATTTAACCTTTCCAA 59.758 36.000 0.00 0.00 0.00 3.53
2482 2581 2.973316 GATTTTTCACGGGCGGCGT 61.973 57.895 9.37 1.23 0.00 5.68
2484 2583 1.136774 GAGATTTTTCACGGGCGGC 59.863 57.895 0.00 0.00 0.00 6.53
2485 2584 2.018542 TAGAGATTTTTCACGGGCGG 57.981 50.000 0.00 0.00 0.00 6.13
2486 2585 3.788797 GCATTAGAGATTTTTCACGGGCG 60.789 47.826 0.00 0.00 0.00 6.13
2487 2586 3.378427 AGCATTAGAGATTTTTCACGGGC 59.622 43.478 0.00 0.00 0.00 6.13
2488 2587 6.677781 TTAGCATTAGAGATTTTTCACGGG 57.322 37.500 0.00 0.00 0.00 5.28
2489 2588 9.573133 AAAATTAGCATTAGAGATTTTTCACGG 57.427 29.630 0.00 0.00 28.54 4.94
2530 2629 1.918957 CTCTTCCCTTCATTCCCCACT 59.081 52.381 0.00 0.00 0.00 4.00
2551 2650 2.232696 TCGCACTAGCACTATGGTCAAA 59.767 45.455 0.00 0.00 42.27 2.69
2573 2672 1.031235 CACACTGCCACAATGAACCA 58.969 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.