Multiple sequence alignment - TraesCS2D01G172200

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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 TraesCS2D01G172200 chr2D 100.000 3176 0 0 1 3176 115960248 115957073 0.000000e+00 5866
1 TraesCS2D01G172200 chr2A 95.034 2537 88 16 328 2855 117404556 117402049 0.000000e+00 3952
2 TraesCS2D01G172200 chr2A 91.617 334 22 4 2848 3176 117401652 117401320 1.040000e-124 457
3 TraesCS2D01G172200 chr2B 95.381 2165 76 9 697 2855 166612694 166610548 0.000000e+00 3422
4 TraesCS2D01G172200 chr2B 86.228 334 19 8 2848 3176 166610145 166609834 1.410000e-88 337
5 TraesCS2D01G172200 chr3B 87.021 339 42 2 1168 1506 467068558 467068222 6.430000e-102 381
6 TraesCS2D01G172200 chr7A 86.970 330 41 2 1168 1497 64595519 64595192 1.390000e-98 370
7 TraesCS2D01G172200 chr6A 86.970 330 41 2 1168 1497 580187120 580187447 1.390000e-98 370


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 TraesCS2D01G172200 chr2D 115957073 115960248 3175 True 5866.0 5866 100.0000 1 3176 1 chr2D.!!$R1 3175
1 TraesCS2D01G172200 chr2A 117401320 117404556 3236 True 2204.5 3952 93.3255 328 3176 2 chr2A.!!$R1 2848
2 TraesCS2D01G172200 chr2B 166609834 166612694 2860 True 1879.5 3422 90.8045 697 3176 2 chr2B.!!$R1 2479

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
279 280 0.038159 AGAGCTCAACGTACTGCACC 60.038 55.0 17.77 1.75 0.0 5.01 F
333 334 0.111253 GGATCCAGGCCCTGTTATGG 59.889 60.0 10.47 0.00 0.0 2.74 F
1645 1652 0.687757 TCCTAAGCCCGCTGATCTGT 60.688 55.0 1.27 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1652 0.111061 AATGGCTTCCAGTCAGTGCA 59.889 50.000 0.00 0.00 36.75 4.57 R
1662 1669 1.153168 CCGTGGCATCGGGAAGAAT 60.153 57.895 17.20 0.00 45.88 2.40 R
2889 3322 0.174845 TAGTCCACGCAATTCGAGGG 59.825 55.000 11.53 8.89 46.81 4.30 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 0.848942 GATGCAGTAGTCGTCATGCG 59.151 55.000 0.00 3.55 41.58 4.73
29 30 3.576356 GTCATGCGACGGGCCATG 61.576 66.667 4.39 7.40 42.61 3.66
86 87 2.202946 GGCTAGCCAGGCGAAGAC 60.203 66.667 29.33 13.07 37.63 3.01
87 88 2.202946 GCTAGCCAGGCGAAGACC 60.203 66.667 18.39 0.95 31.70 3.85
88 89 2.501610 CTAGCCAGGCGAAGACCC 59.498 66.667 5.55 0.00 31.70 4.46
89 90 3.432051 CTAGCCAGGCGAAGACCCG 62.432 68.421 5.55 0.00 31.70 5.28
90 91 3.949885 TAGCCAGGCGAAGACCCGA 62.950 63.158 5.55 0.00 31.70 5.14
91 92 4.821589 GCCAGGCGAAGACCCGAG 62.822 72.222 0.00 0.00 31.70 4.63
92 93 3.382832 CCAGGCGAAGACCCGAGT 61.383 66.667 0.00 0.00 31.70 4.18
93 94 2.050350 CCAGGCGAAGACCCGAGTA 61.050 63.158 0.00 0.00 31.70 2.59
94 95 1.139095 CAGGCGAAGACCCGAGTAC 59.861 63.158 0.00 0.00 31.70 2.73
95 96 2.101770 GGCGAAGACCCGAGTACG 59.898 66.667 0.00 0.00 39.43 3.67
105 106 4.253257 CGAGTACGGAGAGGCGCC 62.253 72.222 21.89 21.89 35.72 6.53
106 107 3.902086 GAGTACGGAGAGGCGCCC 61.902 72.222 26.15 15.34 0.00 6.13
107 108 4.753662 AGTACGGAGAGGCGCCCA 62.754 66.667 26.15 0.00 0.00 5.36
108 109 3.766691 GTACGGAGAGGCGCCCAA 61.767 66.667 26.15 0.00 0.00 4.12
109 110 3.458163 TACGGAGAGGCGCCCAAG 61.458 66.667 26.15 13.16 0.00 3.61
120 121 4.424566 GCCCAAGTGCGCCATGTG 62.425 66.667 4.18 0.00 0.00 3.21
121 122 2.672651 CCCAAGTGCGCCATGTGA 60.673 61.111 4.18 0.00 0.00 3.58
122 123 2.693762 CCCAAGTGCGCCATGTGAG 61.694 63.158 4.18 0.00 0.00 3.51
123 124 2.177531 CAAGTGCGCCATGTGAGC 59.822 61.111 4.18 3.58 0.00 4.26
124 125 2.033141 AAGTGCGCCATGTGAGCT 59.967 55.556 4.18 0.00 0.00 4.09
125 126 1.601759 AAGTGCGCCATGTGAGCTT 60.602 52.632 4.18 0.00 0.00 3.74
126 127 1.580845 AAGTGCGCCATGTGAGCTTC 61.581 55.000 4.18 5.18 0.00 3.86
127 128 2.747460 TGCGCCATGTGAGCTTCC 60.747 61.111 4.18 0.00 0.00 3.46
128 129 2.747460 GCGCCATGTGAGCTTCCA 60.747 61.111 0.00 0.00 0.00 3.53
129 130 2.758089 GCGCCATGTGAGCTTCCAG 61.758 63.158 0.00 0.00 0.00 3.86
130 131 1.376424 CGCCATGTGAGCTTCCAGT 60.376 57.895 0.00 0.00 0.00 4.00
131 132 1.642037 CGCCATGTGAGCTTCCAGTG 61.642 60.000 0.00 0.00 0.00 3.66
132 133 1.310933 GCCATGTGAGCTTCCAGTGG 61.311 60.000 1.40 1.40 0.00 4.00
133 134 0.679002 CCATGTGAGCTTCCAGTGGG 60.679 60.000 9.92 0.00 0.00 4.61
134 135 0.679002 CATGTGAGCTTCCAGTGGGG 60.679 60.000 9.92 3.97 38.37 4.96
135 136 2.360475 GTGAGCTTCCAGTGGGGC 60.360 66.667 9.92 14.09 36.21 5.80
136 137 4.020617 TGAGCTTCCAGTGGGGCG 62.021 66.667 9.92 0.00 36.21 6.13
152 153 2.740826 CGCCGTTGTGGAACCGAT 60.741 61.111 0.00 0.00 42.00 4.18
153 154 2.867472 GCCGTTGTGGAACCGATG 59.133 61.111 0.00 0.00 42.00 3.84
154 155 1.669760 GCCGTTGTGGAACCGATGA 60.670 57.895 0.00 0.00 42.00 2.92
155 156 1.231958 GCCGTTGTGGAACCGATGAA 61.232 55.000 0.00 0.00 42.00 2.57
156 157 0.515564 CCGTTGTGGAACCGATGAAC 59.484 55.000 0.00 0.00 42.00 3.18
157 158 1.222300 CGTTGTGGAACCGATGAACA 58.778 50.000 0.00 0.00 34.36 3.18
158 159 1.804151 CGTTGTGGAACCGATGAACAT 59.196 47.619 0.00 0.00 34.36 2.71
159 160 2.412716 CGTTGTGGAACCGATGAACATG 60.413 50.000 0.00 0.00 34.36 3.21
160 161 1.819928 TGTGGAACCGATGAACATGG 58.180 50.000 0.00 0.00 34.36 3.66
161 162 0.451783 GTGGAACCGATGAACATGGC 59.548 55.000 0.00 0.00 0.00 4.40
162 163 0.679640 TGGAACCGATGAACATGGCC 60.680 55.000 0.00 0.00 0.00 5.36
163 164 0.394352 GGAACCGATGAACATGGCCT 60.394 55.000 3.32 0.00 0.00 5.19
164 165 1.463674 GAACCGATGAACATGGCCTT 58.536 50.000 3.32 0.00 0.00 4.35
165 166 1.133025 GAACCGATGAACATGGCCTTG 59.867 52.381 16.76 16.76 0.00 3.61
166 167 0.038166 ACCGATGAACATGGCCTTGT 59.962 50.000 18.18 18.18 0.00 3.16
167 168 1.280710 ACCGATGAACATGGCCTTGTA 59.719 47.619 23.40 10.44 0.00 2.41
168 169 1.942657 CCGATGAACATGGCCTTGTAG 59.057 52.381 23.40 12.59 0.00 2.74
169 170 1.331756 CGATGAACATGGCCTTGTAGC 59.668 52.381 23.40 18.13 0.00 3.58
170 171 2.368439 GATGAACATGGCCTTGTAGCA 58.632 47.619 23.40 22.38 0.00 3.49
171 172 1.825090 TGAACATGGCCTTGTAGCAG 58.175 50.000 23.40 0.00 0.00 4.24
172 173 1.098050 GAACATGGCCTTGTAGCAGG 58.902 55.000 23.40 0.00 36.95 4.85
173 174 0.698238 AACATGGCCTTGTAGCAGGA 59.302 50.000 23.40 0.00 35.71 3.86
174 175 0.921896 ACATGGCCTTGTAGCAGGAT 59.078 50.000 22.02 0.00 35.71 3.24
175 176 1.285962 ACATGGCCTTGTAGCAGGATT 59.714 47.619 22.02 0.00 35.71 3.01
176 177 2.291800 ACATGGCCTTGTAGCAGGATTT 60.292 45.455 22.02 0.00 35.71 2.17
177 178 2.128771 TGGCCTTGTAGCAGGATTTC 57.871 50.000 3.32 0.00 35.71 2.17
178 179 1.354031 TGGCCTTGTAGCAGGATTTCA 59.646 47.619 3.32 0.00 35.71 2.69
179 180 1.745653 GGCCTTGTAGCAGGATTTCAC 59.254 52.381 0.00 0.00 35.71 3.18
180 181 1.398390 GCCTTGTAGCAGGATTTCACG 59.602 52.381 0.00 0.00 35.71 4.35
181 182 2.009774 CCTTGTAGCAGGATTTCACGG 58.990 52.381 0.00 0.00 35.71 4.94
182 183 2.354704 CCTTGTAGCAGGATTTCACGGA 60.355 50.000 0.00 0.00 35.71 4.69
183 184 2.672961 TGTAGCAGGATTTCACGGAG 57.327 50.000 0.00 0.00 0.00 4.63
184 185 6.661647 CCTTGTAGCAGGATTTCACGGAGT 62.662 50.000 0.00 0.00 37.40 3.85
185 186 3.093814 TGTAGCAGGATTTCACGGAGTA 58.906 45.455 0.00 0.00 41.61 2.59
186 187 2.969628 AGCAGGATTTCACGGAGTAG 57.030 50.000 0.00 0.00 41.61 2.57
187 188 1.482593 AGCAGGATTTCACGGAGTAGG 59.517 52.381 0.00 0.00 41.61 3.18
188 189 1.941325 CAGGATTTCACGGAGTAGGC 58.059 55.000 0.00 0.00 41.61 3.93
189 190 1.482593 CAGGATTTCACGGAGTAGGCT 59.517 52.381 0.00 0.00 41.61 4.58
190 191 1.757699 AGGATTTCACGGAGTAGGCTC 59.242 52.381 0.00 0.00 41.61 4.70
209 210 2.661866 GGATTCGGTCCATCGCCG 60.662 66.667 3.29 0.00 46.96 6.46
220 221 4.819761 ATCGCCGACGCAGCACAT 62.820 61.111 0.00 0.00 39.84 3.21
223 224 3.857854 GCCGACGCAGCACATCAG 61.858 66.667 0.00 0.00 34.03 2.90
224 225 3.190849 CCGACGCAGCACATCAGG 61.191 66.667 0.00 0.00 0.00 3.86
225 226 3.190849 CGACGCAGCACATCAGGG 61.191 66.667 0.00 0.00 0.00 4.45
226 227 2.046892 GACGCAGCACATCAGGGT 60.047 61.111 0.00 0.00 0.00 4.34
227 228 2.046892 ACGCAGCACATCAGGGTC 60.047 61.111 0.00 0.00 0.00 4.46
228 229 2.821366 CGCAGCACATCAGGGTCC 60.821 66.667 0.00 0.00 0.00 4.46
229 230 2.821366 GCAGCACATCAGGGTCCG 60.821 66.667 0.00 0.00 0.00 4.79
230 231 2.124983 CAGCACATCAGGGTCCGG 60.125 66.667 0.00 0.00 0.00 5.14
231 232 2.284625 AGCACATCAGGGTCCGGA 60.285 61.111 0.00 0.00 0.00 5.14
232 233 2.187946 GCACATCAGGGTCCGGAG 59.812 66.667 3.06 0.00 0.00 4.63
233 234 2.660064 GCACATCAGGGTCCGGAGT 61.660 63.158 3.06 0.00 0.00 3.85
234 235 1.327690 GCACATCAGGGTCCGGAGTA 61.328 60.000 3.06 0.00 0.00 2.59
235 236 1.191535 CACATCAGGGTCCGGAGTAA 58.808 55.000 3.06 0.00 0.00 2.24
236 237 1.137086 CACATCAGGGTCCGGAGTAAG 59.863 57.143 3.06 0.00 0.00 2.34
237 238 1.006758 ACATCAGGGTCCGGAGTAAGA 59.993 52.381 3.06 0.97 0.00 2.10
238 239 2.108168 CATCAGGGTCCGGAGTAAGAA 58.892 52.381 3.06 0.00 0.00 2.52
239 240 2.544844 TCAGGGTCCGGAGTAAGAAT 57.455 50.000 3.06 0.00 0.00 2.40
240 241 2.108168 TCAGGGTCCGGAGTAAGAATG 58.892 52.381 3.06 0.00 0.00 2.67
241 242 2.108168 CAGGGTCCGGAGTAAGAATGA 58.892 52.381 3.06 0.00 0.00 2.57
242 243 2.700897 CAGGGTCCGGAGTAAGAATGAT 59.299 50.000 3.06 0.00 0.00 2.45
243 244 2.700897 AGGGTCCGGAGTAAGAATGATG 59.299 50.000 3.06 0.00 0.00 3.07
244 245 2.434702 GGGTCCGGAGTAAGAATGATGT 59.565 50.000 3.06 0.00 0.00 3.06
245 246 3.458189 GGTCCGGAGTAAGAATGATGTG 58.542 50.000 3.06 0.00 0.00 3.21
246 247 2.866762 GTCCGGAGTAAGAATGATGTGC 59.133 50.000 3.06 0.00 0.00 4.57
247 248 2.766263 TCCGGAGTAAGAATGATGTGCT 59.234 45.455 0.00 0.00 0.00 4.40
248 249 2.868583 CCGGAGTAAGAATGATGTGCTG 59.131 50.000 0.00 0.00 0.00 4.41
249 250 3.430790 CCGGAGTAAGAATGATGTGCTGA 60.431 47.826 0.00 0.00 0.00 4.26
250 251 4.183865 CGGAGTAAGAATGATGTGCTGAA 58.816 43.478 0.00 0.00 0.00 3.02
251 252 4.269603 CGGAGTAAGAATGATGTGCTGAAG 59.730 45.833 0.00 0.00 0.00 3.02
252 253 4.574013 GGAGTAAGAATGATGTGCTGAAGG 59.426 45.833 0.00 0.00 0.00 3.46
253 254 5.423015 GAGTAAGAATGATGTGCTGAAGGA 58.577 41.667 0.00 0.00 0.00 3.36
254 255 5.181748 AGTAAGAATGATGTGCTGAAGGAC 58.818 41.667 0.00 0.00 36.87 3.85
255 256 2.625737 AGAATGATGTGCTGAAGGACG 58.374 47.619 0.00 0.00 39.39 4.79
256 257 1.063174 GAATGATGTGCTGAAGGACGC 59.937 52.381 0.00 0.00 39.39 5.19
257 258 1.086067 ATGATGTGCTGAAGGACGCG 61.086 55.000 3.53 3.53 39.39 6.01
258 259 3.088500 GATGTGCTGAAGGACGCGC 62.089 63.158 5.73 0.00 39.39 6.86
262 263 4.742201 GCTGAAGGACGCGCCAGA 62.742 66.667 19.30 4.31 40.02 3.86
263 264 2.507992 CTGAAGGACGCGCCAGAG 60.508 66.667 19.30 9.32 40.02 3.35
264 265 4.742201 TGAAGGACGCGCCAGAGC 62.742 66.667 19.30 7.78 40.02 4.09
265 266 4.443266 GAAGGACGCGCCAGAGCT 62.443 66.667 19.30 0.00 40.02 4.09
266 267 4.443266 AAGGACGCGCCAGAGCTC 62.443 66.667 19.30 5.27 40.02 4.09
268 269 4.742201 GGACGCGCCAGAGCTCAA 62.742 66.667 17.77 0.00 36.60 3.02
269 270 3.482783 GACGCGCCAGAGCTCAAC 61.483 66.667 17.77 3.41 36.60 3.18
272 273 2.126071 GCGCCAGAGCTCAACGTA 60.126 61.111 17.77 0.00 36.60 3.57
273 274 2.445438 GCGCCAGAGCTCAACGTAC 61.445 63.158 17.77 1.09 36.60 3.67
274 275 1.213013 CGCCAGAGCTCAACGTACT 59.787 57.895 17.77 0.00 36.60 2.73
275 276 1.073216 CGCCAGAGCTCAACGTACTG 61.073 60.000 17.77 3.01 36.60 2.74
276 277 1.355066 GCCAGAGCTCAACGTACTGC 61.355 60.000 17.77 2.49 35.50 4.40
277 278 0.038251 CCAGAGCTCAACGTACTGCA 60.038 55.000 17.77 0.00 0.00 4.41
278 279 1.063806 CAGAGCTCAACGTACTGCAC 58.936 55.000 17.77 3.41 0.00 4.57
279 280 0.038159 AGAGCTCAACGTACTGCACC 60.038 55.000 17.77 1.75 0.00 5.01
280 281 0.319555 GAGCTCAACGTACTGCACCA 60.320 55.000 9.40 0.00 0.00 4.17
281 282 0.321671 AGCTCAACGTACTGCACCAT 59.678 50.000 8.81 0.00 0.00 3.55
282 283 0.721718 GCTCAACGTACTGCACCATC 59.278 55.000 0.00 0.00 0.00 3.51
283 284 0.992072 CTCAACGTACTGCACCATCG 59.008 55.000 0.00 0.00 0.00 3.84
284 285 1.011968 TCAACGTACTGCACCATCGC 61.012 55.000 0.00 0.00 0.00 4.58
285 286 1.740296 AACGTACTGCACCATCGCC 60.740 57.895 0.00 0.00 0.00 5.54
286 287 3.254654 CGTACTGCACCATCGCCG 61.255 66.667 0.00 0.00 0.00 6.46
287 288 3.564027 GTACTGCACCATCGCCGC 61.564 66.667 0.00 0.00 0.00 6.53
288 289 3.770040 TACTGCACCATCGCCGCT 61.770 61.111 0.00 0.00 0.00 5.52
296 297 4.552365 CATCGCCGCTGGTCCCAT 62.552 66.667 0.00 0.00 0.00 4.00
297 298 4.552365 ATCGCCGCTGGTCCCATG 62.552 66.667 0.00 0.00 0.00 3.66
304 305 2.440796 CTGGTCCCATGGCGCATT 60.441 61.111 10.83 0.00 0.00 3.56
305 306 2.755064 TGGTCCCATGGCGCATTG 60.755 61.111 10.83 5.69 0.00 2.82
306 307 3.530260 GGTCCCATGGCGCATTGG 61.530 66.667 18.23 18.23 0.00 3.16
307 308 2.440065 GTCCCATGGCGCATTGGA 60.440 61.111 24.71 16.12 34.01 3.53
308 309 1.829533 GTCCCATGGCGCATTGGAT 60.830 57.895 24.71 0.00 37.85 3.41
309 310 1.829096 TCCCATGGCGCATTGGATG 60.829 57.895 24.71 12.07 31.89 3.51
310 311 2.129146 CCCATGGCGCATTGGATGT 61.129 57.895 24.71 0.00 29.30 3.06
311 312 1.361271 CCATGGCGCATTGGATGTC 59.639 57.895 19.96 0.00 0.00 3.06
312 313 1.361271 CATGGCGCATTGGATGTCC 59.639 57.895 10.83 0.00 0.00 4.02
313 314 1.076850 ATGGCGCATTGGATGTCCA 60.077 52.632 10.83 0.00 45.94 4.02
322 323 2.935348 TGGATGTCCAGGATCCAGG 58.065 57.895 17.08 17.08 43.71 4.45
323 324 1.348008 TGGATGTCCAGGATCCAGGC 61.348 60.000 18.31 13.39 43.71 4.85
324 325 1.453669 GATGTCCAGGATCCAGGCC 59.546 63.158 18.31 7.89 0.00 5.19
325 326 2.061790 GATGTCCAGGATCCAGGCCC 62.062 65.000 18.31 11.35 0.00 5.80
326 327 2.367512 GTCCAGGATCCAGGCCCT 60.368 66.667 18.31 0.00 0.00 5.19
333 334 0.111253 GGATCCAGGCCCTGTTATGG 59.889 60.000 10.47 0.00 0.00 2.74
392 393 8.579682 AAGAAACAAACAAAGACAAGATATGC 57.420 30.769 0.00 0.00 0.00 3.14
426 427 8.126871 TCTTAATTCGATTCCAACTTCATACG 57.873 34.615 0.00 0.00 0.00 3.06
488 489 4.928615 GCAACAATTTAGGCACATGCTTTA 59.071 37.500 3.48 0.00 41.70 1.85
493 494 8.010733 ACAATTTAGGCACATGCTTTATACAT 57.989 30.769 3.48 0.00 41.70 2.29
548 549 6.147821 TCAAAGATTTCAAAGAGGCGTCTTAG 59.852 38.462 21.14 3.37 42.59 2.18
569 570 3.100817 GCATTAACACATTGCTAGCACG 58.899 45.455 19.17 14.37 33.61 5.34
592 593 5.446473 CGTTAGCATGATCAAAGTGGAAGAC 60.446 44.000 0.00 0.00 0.00 3.01
613 614 3.748048 ACTCATGTCTGAAAATGTGGTCG 59.252 43.478 0.00 0.00 0.00 4.79
618 619 4.062293 TGTCTGAAAATGTGGTCGGTAAG 58.938 43.478 0.00 0.00 0.00 2.34
637 638 7.011482 TCGGTAAGAAATAGTACTCCGTTAGAC 59.989 40.741 13.19 1.33 38.21 2.59
650 651 3.194116 TCCGTTAGACGTGGAATAAAGCT 59.806 43.478 0.00 0.00 40.58 3.74
678 679 1.287425 CGAACCGTTGGAATAGAGCC 58.713 55.000 0.00 0.00 0.00 4.70
679 680 1.404986 CGAACCGTTGGAATAGAGCCA 60.405 52.381 0.00 0.00 0.00 4.75
732 736 6.400940 CGTTGGTATTGTAACCGTTACGAAAT 60.401 38.462 14.12 11.97 42.91 2.17
792 799 7.647715 CGCTGTAAATAGGGGTGATTAAAAATG 59.352 37.037 0.00 0.00 0.00 2.32
821 828 4.155462 GGAAATCTTTTTAGACGGTGGTCC 59.845 45.833 0.00 0.00 44.54 4.46
906 913 1.123077 AACACTCACCAGCTGTCTCA 58.877 50.000 13.81 0.00 0.00 3.27
909 916 1.294780 CTCACCAGCTGTCTCACCC 59.705 63.158 13.81 0.00 0.00 4.61
923 930 3.396951 CACCCAAACGAGAAGGTGT 57.603 52.632 10.06 0.00 43.91 4.16
952 959 2.527624 TCTGACAGCTGTGCCCCT 60.528 61.111 27.27 0.00 0.00 4.79
977 984 1.841556 ACTCGCTGACTTCCCCCAA 60.842 57.895 0.00 0.00 0.00 4.12
1623 1630 3.709834 GGGTTTCATCCCAATGGGT 57.290 52.632 19.28 2.65 46.30 4.51
1645 1652 0.687757 TCCTAAGCCCGCTGATCTGT 60.688 55.000 1.27 0.00 0.00 3.41
1662 1669 1.227943 GTGCACTGACTGGAAGCCA 60.228 57.895 10.32 0.00 37.60 4.75
1978 1988 3.760151 TGATTGGAGTGAAAATGCAGAGG 59.240 43.478 0.00 0.00 30.98 3.69
2269 2279 3.207265 TGCTCCTTTGCTGTCACTTTA 57.793 42.857 0.00 0.00 0.00 1.85
2274 2284 3.815401 TCCTTTGCTGTCACTTTAGCTTC 59.185 43.478 0.00 0.00 40.52 3.86
2291 2301 3.921021 AGCTTCTAATTTCGTGTCTGTCG 59.079 43.478 0.00 0.00 0.00 4.35
2368 2378 8.470657 AATCTGTTGTAGCATCTAGATGAGTA 57.529 34.615 32.38 20.32 41.20 2.59
2374 2384 3.417101 AGCATCTAGATGAGTACTCCCG 58.583 50.000 32.38 6.01 41.20 5.14
2404 2416 6.657541 GTCTGTAGACTAGAATATCCCCAGAG 59.342 46.154 0.00 0.00 41.65 3.35
2430 2442 9.185680 GTAGTTTGGGGATTCATAGTATTTGTT 57.814 33.333 0.00 0.00 0.00 2.83
2566 2579 7.485810 CAATTAACTCCTGATTGCATGATTCA 58.514 34.615 0.00 0.00 0.00 2.57
2588 2601 5.920312 CAGTTTGCACTGTTCATACTACAG 58.080 41.667 3.64 0.00 44.96 2.74
2619 2632 7.324935 TGATTATGTGATGCTTTTGATTTGCT 58.675 30.769 0.00 0.00 0.00 3.91
2634 2647 1.076632 TGCTGATGCATGCCCATGA 60.077 52.632 16.68 0.00 45.31 3.07
2682 2695 4.021192 ACAATTCACCAGCCTTATTGTTGG 60.021 41.667 0.00 0.00 36.35 3.77
2709 2722 7.609760 TGATCATCATGTTGTTGTTAGTACC 57.390 36.000 3.76 0.00 0.00 3.34
2713 2726 8.402798 TCATCATGTTGTTGTTAGTACCATTT 57.597 30.769 3.76 0.00 0.00 2.32
2715 2728 9.773328 CATCATGTTGTTGTTAGTACCATTTAG 57.227 33.333 0.00 0.00 0.00 1.85
2765 2778 9.669353 CCTGTTTATCAAAATAAATCTCCATCG 57.331 33.333 0.00 0.00 39.06 3.84
2815 2828 4.892655 TCAGAAAAGCACATTATTACGCG 58.107 39.130 3.53 3.53 0.00 6.01
2825 2838 3.554324 ACATTATTACGCGTTCGCTTGAT 59.446 39.130 20.78 10.26 39.84 2.57
2826 2839 4.033587 ACATTATTACGCGTTCGCTTGATT 59.966 37.500 20.78 0.00 39.84 2.57
2827 2840 4.587211 TTATTACGCGTTCGCTTGATTT 57.413 36.364 20.78 0.00 39.84 2.17
2828 2841 2.953640 TTACGCGTTCGCTTGATTTT 57.046 40.000 20.78 0.00 39.84 1.82
2829 2842 2.953640 TACGCGTTCGCTTGATTTTT 57.046 40.000 20.78 0.00 39.84 1.94
2869 3302 2.109126 GCGTGCACTGGATCCCTTC 61.109 63.158 16.19 0.00 0.00 3.46
2878 3311 1.484240 CTGGATCCCTTCCTCTGTGTC 59.516 57.143 9.90 0.00 45.68 3.67
2889 3322 4.371855 TCCTCTGTGTCGTTCATCATAC 57.628 45.455 0.00 0.00 0.00 2.39
2926 3359 4.333926 GGACTATCTACTGGCTTTTTGCTG 59.666 45.833 0.00 0.00 42.39 4.41
2952 3388 7.227512 GGGATGAATATCGAGTTTGAACTGATT 59.772 37.037 0.30 0.00 39.88 2.57
2962 3398 3.926821 TTGAACTGATTTTTACGCCCC 57.073 42.857 0.00 0.00 0.00 5.80
3034 3470 0.890683 GCCTTCACCACCCATCAAAG 59.109 55.000 0.00 0.00 0.00 2.77
3039 3475 0.890683 CACCACCCATCAAAGAAGCC 59.109 55.000 0.00 0.00 0.00 4.35
3056 3492 1.751924 AGCCGAATAAGAAGAGCGAGT 59.248 47.619 0.00 0.00 0.00 4.18
3079 3515 4.412199 TGGATTGGTTTAGGGACTATCAGG 59.588 45.833 0.00 0.00 42.38 3.86
3089 3525 2.564947 GGGACTATCAGGCATCAGTAGG 59.435 54.545 0.00 0.00 0.00 3.18
3098 3534 3.194116 CAGGCATCAGTAGGTTGCAAAAT 59.806 43.478 0.00 0.00 42.74 1.82
3117 3553 7.942908 GCAAAATATACTTGCTCTTTTGTGTC 58.057 34.615 12.88 0.00 44.66 3.67
3137 3573 0.714439 GTTCGCTTAGCTGTTCGTCC 59.286 55.000 1.76 0.00 0.00 4.79
3167 3603 3.125146 TGAATCGTGAGCGGAAAATTCTG 59.875 43.478 0.00 0.00 38.89 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.576356 CATGGCCCGTCGCATGAC 61.576 66.667 0.00 0.00 41.91 3.06
67 68 4.899239 CTTCGCCTGGCTAGCCGG 62.899 72.222 32.50 32.50 42.03 6.13
68 69 3.838271 TCTTCGCCTGGCTAGCCG 61.838 66.667 28.28 21.44 39.42 5.52
69 70 2.202946 GTCTTCGCCTGGCTAGCC 60.203 66.667 27.71 27.71 0.00 3.93
70 71 2.202946 GGTCTTCGCCTGGCTAGC 60.203 66.667 17.92 6.04 0.00 3.42
71 72 2.501610 GGGTCTTCGCCTGGCTAG 59.498 66.667 17.92 13.62 0.00 3.42
72 73 3.458163 CGGGTCTTCGCCTGGCTA 61.458 66.667 17.92 2.11 0.00 3.93
74 75 4.821589 CTCGGGTCTTCGCCTGGC 62.822 72.222 9.11 9.11 35.63 4.85
75 76 2.050350 TACTCGGGTCTTCGCCTGG 61.050 63.158 0.00 0.00 35.63 4.45
76 77 1.139095 GTACTCGGGTCTTCGCCTG 59.861 63.158 0.00 0.00 36.25 4.85
77 78 2.404995 CGTACTCGGGTCTTCGCCT 61.405 63.158 0.00 0.00 0.00 5.52
78 79 2.101770 CGTACTCGGGTCTTCGCC 59.898 66.667 0.00 0.00 0.00 5.54
88 89 4.253257 GGCGCCTCTCCGTACTCG 62.253 72.222 22.15 0.00 0.00 4.18
89 90 3.902086 GGGCGCCTCTCCGTACTC 61.902 72.222 28.56 0.41 0.00 2.59
90 91 4.753662 TGGGCGCCTCTCCGTACT 62.754 66.667 28.56 0.00 0.00 2.73
91 92 3.718210 CTTGGGCGCCTCTCCGTAC 62.718 68.421 28.56 7.32 0.00 3.67
92 93 3.458163 CTTGGGCGCCTCTCCGTA 61.458 66.667 28.56 3.02 0.00 4.02
104 105 2.672651 TCACATGGCGCACTTGGG 60.673 61.111 10.83 8.65 0.00 4.12
105 106 2.872557 CTCACATGGCGCACTTGG 59.127 61.111 10.83 0.00 0.00 3.61
106 107 1.859427 AAGCTCACATGGCGCACTTG 61.859 55.000 10.83 9.81 34.52 3.16
107 108 1.580845 GAAGCTCACATGGCGCACTT 61.581 55.000 10.83 0.00 34.52 3.16
108 109 2.033141 AAGCTCACATGGCGCACT 59.967 55.556 10.83 0.00 34.52 4.40
109 110 2.482374 GAAGCTCACATGGCGCAC 59.518 61.111 10.83 0.00 34.52 5.34
110 111 2.747460 GGAAGCTCACATGGCGCA 60.747 61.111 10.83 0.00 34.52 6.09
111 112 2.747460 TGGAAGCTCACATGGCGC 60.747 61.111 0.00 0.00 34.52 6.53
112 113 1.376424 ACTGGAAGCTCACATGGCG 60.376 57.895 0.00 0.00 37.60 5.69
113 114 1.310933 CCACTGGAAGCTCACATGGC 61.311 60.000 0.00 0.00 37.60 4.40
114 115 0.679002 CCCACTGGAAGCTCACATGG 60.679 60.000 0.00 0.00 37.60 3.66
115 116 0.679002 CCCCACTGGAAGCTCACATG 60.679 60.000 0.00 0.00 37.60 3.21
116 117 1.687612 CCCCACTGGAAGCTCACAT 59.312 57.895 0.00 0.00 37.60 3.21
117 118 3.160585 CCCCACTGGAAGCTCACA 58.839 61.111 0.00 0.00 37.60 3.58
118 119 2.360475 GCCCCACTGGAAGCTCAC 60.360 66.667 0.00 0.00 37.60 3.51
119 120 4.020617 CGCCCCACTGGAAGCTCA 62.021 66.667 0.00 0.00 37.60 4.26
135 136 2.740826 ATCGGTTCCACAACGGCG 60.741 61.111 4.80 4.80 33.79 6.46
136 137 1.231958 TTCATCGGTTCCACAACGGC 61.232 55.000 0.00 0.00 33.79 5.68
137 138 0.515564 GTTCATCGGTTCCACAACGG 59.484 55.000 0.00 0.00 34.82 4.44
138 139 1.222300 TGTTCATCGGTTCCACAACG 58.778 50.000 0.00 0.00 32.68 4.10
139 140 2.095263 CCATGTTCATCGGTTCCACAAC 60.095 50.000 0.00 0.00 0.00 3.32
140 141 2.158559 CCATGTTCATCGGTTCCACAA 58.841 47.619 0.00 0.00 0.00 3.33
141 142 1.819928 CCATGTTCATCGGTTCCACA 58.180 50.000 0.00 0.00 0.00 4.17
142 143 0.451783 GCCATGTTCATCGGTTCCAC 59.548 55.000 0.00 0.00 0.00 4.02
143 144 0.679640 GGCCATGTTCATCGGTTCCA 60.680 55.000 0.00 0.00 0.00 3.53
144 145 0.394352 AGGCCATGTTCATCGGTTCC 60.394 55.000 5.01 0.00 0.00 3.62
145 146 1.133025 CAAGGCCATGTTCATCGGTTC 59.867 52.381 5.01 0.00 0.00 3.62
146 147 1.176527 CAAGGCCATGTTCATCGGTT 58.823 50.000 5.01 0.00 0.00 4.44
147 148 0.038166 ACAAGGCCATGTTCATCGGT 59.962 50.000 8.06 0.00 0.00 4.69
148 149 1.942657 CTACAAGGCCATGTTCATCGG 59.057 52.381 20.29 0.00 34.75 4.18
149 150 1.331756 GCTACAAGGCCATGTTCATCG 59.668 52.381 20.29 4.53 34.75 3.84
150 151 2.357009 CTGCTACAAGGCCATGTTCATC 59.643 50.000 20.29 6.77 34.75 2.92
151 152 2.372264 CTGCTACAAGGCCATGTTCAT 58.628 47.619 20.29 0.00 34.75 2.57
152 153 1.614051 CCTGCTACAAGGCCATGTTCA 60.614 52.381 20.29 15.79 34.75 3.18
153 154 1.098050 CCTGCTACAAGGCCATGTTC 58.902 55.000 20.29 12.02 34.75 3.18
154 155 0.698238 TCCTGCTACAAGGCCATGTT 59.302 50.000 20.29 3.61 37.24 2.71
155 156 0.921896 ATCCTGCTACAAGGCCATGT 59.078 50.000 18.99 18.99 37.24 3.21
156 157 2.062971 AATCCTGCTACAAGGCCATG 57.937 50.000 5.01 5.77 37.24 3.66
157 158 2.025037 TGAAATCCTGCTACAAGGCCAT 60.025 45.455 5.01 0.00 37.24 4.40
158 159 1.354031 TGAAATCCTGCTACAAGGCCA 59.646 47.619 5.01 0.00 37.24 5.36
159 160 1.745653 GTGAAATCCTGCTACAAGGCC 59.254 52.381 0.00 0.00 37.24 5.19
160 161 1.398390 CGTGAAATCCTGCTACAAGGC 59.602 52.381 0.00 0.00 37.24 4.35
161 162 2.009774 CCGTGAAATCCTGCTACAAGG 58.990 52.381 0.00 0.00 38.84 3.61
162 163 2.932614 CTCCGTGAAATCCTGCTACAAG 59.067 50.000 0.00 0.00 0.00 3.16
163 164 2.301870 ACTCCGTGAAATCCTGCTACAA 59.698 45.455 0.00 0.00 0.00 2.41
164 165 1.899814 ACTCCGTGAAATCCTGCTACA 59.100 47.619 0.00 0.00 0.00 2.74
165 166 2.674796 ACTCCGTGAAATCCTGCTAC 57.325 50.000 0.00 0.00 0.00 3.58
166 167 2.693591 CCTACTCCGTGAAATCCTGCTA 59.306 50.000 0.00 0.00 0.00 3.49
167 168 1.482593 CCTACTCCGTGAAATCCTGCT 59.517 52.381 0.00 0.00 0.00 4.24
168 169 1.941325 CCTACTCCGTGAAATCCTGC 58.059 55.000 0.00 0.00 0.00 4.85
169 170 1.482593 AGCCTACTCCGTGAAATCCTG 59.517 52.381 0.00 0.00 0.00 3.86
170 171 1.757699 GAGCCTACTCCGTGAAATCCT 59.242 52.381 0.00 0.00 36.90 3.24
171 172 2.226602 GAGCCTACTCCGTGAAATCC 57.773 55.000 0.00 0.00 36.90 3.01
203 204 4.819761 ATGTGCTGCGTCGGCGAT 62.820 61.111 16.53 0.00 44.10 4.58
206 207 3.857854 CTGATGTGCTGCGTCGGC 61.858 66.667 4.02 4.02 35.92 5.54
207 208 3.190849 CCTGATGTGCTGCGTCGG 61.191 66.667 0.00 0.00 38.83 4.79
208 209 3.190849 CCCTGATGTGCTGCGTCG 61.191 66.667 0.00 0.00 35.92 5.12
209 210 2.046892 ACCCTGATGTGCTGCGTC 60.047 61.111 0.00 0.00 0.00 5.19
210 211 2.046892 GACCCTGATGTGCTGCGT 60.047 61.111 0.00 0.00 0.00 5.24
211 212 2.821366 GGACCCTGATGTGCTGCG 60.821 66.667 0.00 0.00 0.00 5.18
212 213 2.821366 CGGACCCTGATGTGCTGC 60.821 66.667 0.00 0.00 0.00 5.25
213 214 2.124983 CCGGACCCTGATGTGCTG 60.125 66.667 0.00 0.00 0.00 4.41
214 215 2.284625 TCCGGACCCTGATGTGCT 60.285 61.111 0.00 0.00 0.00 4.40
215 216 1.327690 TACTCCGGACCCTGATGTGC 61.328 60.000 0.00 0.00 0.00 4.57
216 217 1.137086 CTTACTCCGGACCCTGATGTG 59.863 57.143 0.00 0.00 0.00 3.21
217 218 1.006758 TCTTACTCCGGACCCTGATGT 59.993 52.381 0.00 0.00 0.00 3.06
218 219 1.776662 TCTTACTCCGGACCCTGATG 58.223 55.000 0.00 0.00 0.00 3.07
219 220 2.544844 TTCTTACTCCGGACCCTGAT 57.455 50.000 0.00 0.00 0.00 2.90
220 221 2.108168 CATTCTTACTCCGGACCCTGA 58.892 52.381 0.00 0.00 0.00 3.86
221 222 2.108168 TCATTCTTACTCCGGACCCTG 58.892 52.381 0.00 0.00 0.00 4.45
222 223 2.544844 TCATTCTTACTCCGGACCCT 57.455 50.000 0.00 0.00 0.00 4.34
223 224 2.434702 ACATCATTCTTACTCCGGACCC 59.565 50.000 0.00 0.00 0.00 4.46
224 225 3.458189 CACATCATTCTTACTCCGGACC 58.542 50.000 0.00 0.00 0.00 4.46
225 226 2.866762 GCACATCATTCTTACTCCGGAC 59.133 50.000 0.00 0.00 0.00 4.79
226 227 2.766263 AGCACATCATTCTTACTCCGGA 59.234 45.455 2.93 2.93 0.00 5.14
227 228 2.868583 CAGCACATCATTCTTACTCCGG 59.131 50.000 0.00 0.00 0.00 5.14
228 229 3.785486 TCAGCACATCATTCTTACTCCG 58.215 45.455 0.00 0.00 0.00 4.63
229 230 4.574013 CCTTCAGCACATCATTCTTACTCC 59.426 45.833 0.00 0.00 0.00 3.85
230 231 5.293079 GTCCTTCAGCACATCATTCTTACTC 59.707 44.000 0.00 0.00 0.00 2.59
231 232 5.181748 GTCCTTCAGCACATCATTCTTACT 58.818 41.667 0.00 0.00 0.00 2.24
232 233 4.033358 CGTCCTTCAGCACATCATTCTTAC 59.967 45.833 0.00 0.00 0.00 2.34
233 234 4.183865 CGTCCTTCAGCACATCATTCTTA 58.816 43.478 0.00 0.00 0.00 2.10
234 235 3.005554 CGTCCTTCAGCACATCATTCTT 58.994 45.455 0.00 0.00 0.00 2.52
235 236 2.625737 CGTCCTTCAGCACATCATTCT 58.374 47.619 0.00 0.00 0.00 2.40
236 237 1.063174 GCGTCCTTCAGCACATCATTC 59.937 52.381 0.00 0.00 0.00 2.67
237 238 1.089920 GCGTCCTTCAGCACATCATT 58.910 50.000 0.00 0.00 0.00 2.57
238 239 1.086067 CGCGTCCTTCAGCACATCAT 61.086 55.000 0.00 0.00 0.00 2.45
239 240 1.737735 CGCGTCCTTCAGCACATCA 60.738 57.895 0.00 0.00 0.00 3.07
240 241 3.084579 CGCGTCCTTCAGCACATC 58.915 61.111 0.00 0.00 0.00 3.06
241 242 3.121030 GCGCGTCCTTCAGCACAT 61.121 61.111 8.43 0.00 0.00 3.21
245 246 4.742201 TCTGGCGCGTCCTTCAGC 62.742 66.667 8.89 0.00 35.26 4.26
246 247 2.507992 CTCTGGCGCGTCCTTCAG 60.508 66.667 8.89 8.59 35.26 3.02
247 248 4.742201 GCTCTGGCGCGTCCTTCA 62.742 66.667 8.89 0.00 35.26 3.02
248 249 4.443266 AGCTCTGGCGCGTCCTTC 62.443 66.667 8.89 0.00 44.37 3.46
249 250 4.443266 GAGCTCTGGCGCGTCCTT 62.443 66.667 8.89 0.00 44.37 3.36
251 252 4.742201 TTGAGCTCTGGCGCGTCC 62.742 66.667 16.19 10.74 44.37 4.79
252 253 3.482783 GTTGAGCTCTGGCGCGTC 61.483 66.667 16.19 2.29 44.37 5.19
254 255 3.964221 TACGTTGAGCTCTGGCGCG 62.964 63.158 16.19 0.00 44.37 6.86
255 256 2.126071 TACGTTGAGCTCTGGCGC 60.126 61.111 16.19 0.00 44.37 6.53
256 257 1.073216 CAGTACGTTGAGCTCTGGCG 61.073 60.000 16.19 17.53 44.37 5.69
257 258 1.355066 GCAGTACGTTGAGCTCTGGC 61.355 60.000 16.19 4.07 39.06 4.85
258 259 0.038251 TGCAGTACGTTGAGCTCTGG 60.038 55.000 16.19 6.49 0.00 3.86
259 260 1.063806 GTGCAGTACGTTGAGCTCTG 58.936 55.000 16.19 7.44 0.00 3.35
260 261 0.038159 GGTGCAGTACGTTGAGCTCT 60.038 55.000 16.19 0.00 0.00 4.09
261 262 0.319555 TGGTGCAGTACGTTGAGCTC 60.320 55.000 6.82 6.82 0.00 4.09
262 263 0.321671 ATGGTGCAGTACGTTGAGCT 59.678 50.000 0.00 0.00 0.00 4.09
263 264 0.721718 GATGGTGCAGTACGTTGAGC 59.278 55.000 0.00 0.00 0.00 4.26
264 265 0.992072 CGATGGTGCAGTACGTTGAG 59.008 55.000 0.00 0.00 0.00 3.02
265 266 1.011968 GCGATGGTGCAGTACGTTGA 61.012 55.000 0.00 0.00 34.15 3.18
266 267 1.419922 GCGATGGTGCAGTACGTTG 59.580 57.895 0.00 0.00 34.15 4.10
267 268 1.740296 GGCGATGGTGCAGTACGTT 60.740 57.895 0.00 0.00 36.28 3.99
268 269 2.125673 GGCGATGGTGCAGTACGT 60.126 61.111 0.00 0.00 36.28 3.57
269 270 3.254654 CGGCGATGGTGCAGTACG 61.255 66.667 0.00 0.00 36.28 3.67
270 271 3.564027 GCGGCGATGGTGCAGTAC 61.564 66.667 12.98 0.00 36.28 2.73
271 272 3.770040 AGCGGCGATGGTGCAGTA 61.770 61.111 12.98 0.00 36.28 2.74
279 280 4.552365 ATGGGACCAGCGGCGATG 62.552 66.667 19.62 19.62 0.00 3.84
280 281 4.552365 CATGGGACCAGCGGCGAT 62.552 66.667 12.98 0.00 0.00 4.58
287 288 2.440796 AATGCGCCATGGGACCAG 60.441 61.111 15.13 0.00 0.00 4.00
288 289 2.755064 CAATGCGCCATGGGACCA 60.755 61.111 15.13 0.00 0.00 4.02
289 290 3.530260 CCAATGCGCCATGGGACC 61.530 66.667 15.13 0.00 37.11 4.46
290 291 1.829533 ATCCAATGCGCCATGGGAC 60.830 57.895 23.55 0.00 45.60 4.46
291 292 1.829096 CATCCAATGCGCCATGGGA 60.829 57.895 23.55 19.48 46.66 4.37
292 293 2.079020 GACATCCAATGCGCCATGGG 62.079 60.000 23.55 15.48 36.32 4.00
293 294 1.361271 GACATCCAATGCGCCATGG 59.639 57.895 19.51 19.51 0.00 3.66
294 295 1.361271 GGACATCCAATGCGCCATG 59.639 57.895 4.18 3.31 35.64 3.66
295 296 1.076850 TGGACATCCAATGCGCCAT 60.077 52.632 4.18 0.00 44.35 4.40
296 297 1.750018 CTGGACATCCAATGCGCCA 60.750 57.895 4.18 0.00 46.97 5.69
297 298 2.484062 CCTGGACATCCAATGCGCC 61.484 63.158 4.18 0.00 46.97 6.53
298 299 0.820891 ATCCTGGACATCCAATGCGC 60.821 55.000 0.00 0.00 46.97 6.09
299 300 1.233019 GATCCTGGACATCCAATGCG 58.767 55.000 0.00 0.00 46.97 4.73
300 301 1.133699 TGGATCCTGGACATCCAATGC 60.134 52.381 15.14 0.00 45.73 3.56
304 305 1.348008 GCCTGGATCCTGGACATCCA 61.348 60.000 35.17 16.27 46.39 3.41
305 306 1.453669 GCCTGGATCCTGGACATCC 59.546 63.158 35.17 17.02 40.46 3.51
306 307 1.453669 GGCCTGGATCCTGGACATC 59.546 63.158 35.17 19.84 41.96 3.06
307 308 2.081161 GGGCCTGGATCCTGGACAT 61.081 63.158 36.76 0.00 43.87 3.06
308 309 2.692368 GGGCCTGGATCCTGGACA 60.692 66.667 36.76 7.19 43.87 4.02
309 310 2.367512 AGGGCCTGGATCCTGGAC 60.368 66.667 35.17 33.16 41.69 4.02
310 311 2.367377 CAGGGCCTGGATCCTGGA 60.367 66.667 35.17 5.96 44.99 3.86
313 314 1.143813 CATAACAGGGCCTGGATCCT 58.856 55.000 35.34 13.27 35.51 3.24
314 315 0.111253 CCATAACAGGGCCTGGATCC 59.889 60.000 35.34 4.20 35.51 3.36
315 316 1.140312 TCCATAACAGGGCCTGGATC 58.860 55.000 35.34 0.00 35.51 3.36
316 317 0.846693 GTCCATAACAGGGCCTGGAT 59.153 55.000 35.34 24.86 39.81 3.41
317 318 0.548926 TGTCCATAACAGGGCCTGGA 60.549 55.000 35.34 23.76 35.51 3.86
318 319 0.394352 GTGTCCATAACAGGGCCTGG 60.394 60.000 35.34 19.80 38.97 4.45
319 320 0.327924 TGTGTCCATAACAGGGCCTG 59.672 55.000 31.62 31.62 38.97 4.85
320 321 0.328258 GTGTGTCCATAACAGGGCCT 59.672 55.000 0.00 0.00 38.97 5.19
321 322 0.328258 AGTGTGTCCATAACAGGGCC 59.672 55.000 0.00 0.00 38.97 5.80
322 323 3.118408 TGATAGTGTGTCCATAACAGGGC 60.118 47.826 0.00 0.00 38.97 5.19
323 324 4.753516 TGATAGTGTGTCCATAACAGGG 57.246 45.455 0.00 0.00 38.97 4.45
324 325 5.674525 ACATGATAGTGTGTCCATAACAGG 58.325 41.667 0.00 0.00 38.97 4.00
325 326 8.893219 ATAACATGATAGTGTGTCCATAACAG 57.107 34.615 0.00 0.00 38.97 3.16
326 327 9.325198 GAATAACATGATAGTGTGTCCATAACA 57.675 33.333 0.00 0.00 34.78 2.41
392 393 8.552034 GTTGGAATCGAATTAAGAAGGTAGATG 58.448 37.037 0.00 0.00 0.00 2.90
493 494 6.094048 GTGCAGAGCATAAAGAAACAGGAATA 59.906 38.462 0.00 0.00 41.91 1.75
513 514 8.133754 TCTTTGAAATCTTTGAATTTGTGCAG 57.866 30.769 0.00 0.00 0.00 4.41
548 549 3.100817 CGTGCTAGCAATGTGTTAATGC 58.899 45.455 21.29 0.88 40.34 3.56
569 570 5.645497 AGTCTTCCACTTTGATCATGCTAAC 59.355 40.000 0.00 0.00 26.56 2.34
592 593 3.125829 CCGACCACATTTTCAGACATGAG 59.874 47.826 0.00 0.00 36.61 2.90
613 614 7.128976 CGTCTAACGGAGTACTATTTCTTACC 58.871 42.308 0.00 0.00 45.00 2.85
637 638 4.378616 CGTTTTCAACAGCTTTATTCCACG 59.621 41.667 0.00 0.00 0.00 4.94
792 799 6.311690 CACCGTCTAAAAAGATTTCCTCTCTC 59.688 42.308 0.00 0.00 31.03 3.20
821 828 6.775142 TCTCTCTCACCCTCTCTGTTTATATG 59.225 42.308 0.00 0.00 0.00 1.78
906 913 2.430248 AAACACCTTCTCGTTTGGGT 57.570 45.000 0.00 0.00 34.16 4.51
909 916 3.541711 CGCTTAAACACCTTCTCGTTTG 58.458 45.455 0.00 0.00 36.10 2.93
922 929 0.947180 TGTCAGACCGGCGCTTAAAC 60.947 55.000 7.64 0.00 0.00 2.01
923 930 0.669318 CTGTCAGACCGGCGCTTAAA 60.669 55.000 7.64 0.00 0.00 1.52
995 1002 2.974698 CGGAGGAATCCATGCGGC 60.975 66.667 0.61 0.00 0.00 6.53
1422 1429 0.530744 AGAACGTATCTTCTGCGGCA 59.469 50.000 1.29 1.29 37.27 5.69
1623 1630 1.559682 AGATCAGCGGGCTTAGGAAAA 59.440 47.619 0.00 0.00 0.00 2.29
1645 1652 0.111061 AATGGCTTCCAGTCAGTGCA 59.889 50.000 0.00 0.00 36.75 4.57
1662 1669 1.153168 CCGTGGCATCGGGAAGAAT 60.153 57.895 17.20 0.00 45.88 2.40
1978 1988 3.126001 TGAATTCTCAGTGTGTCCACC 57.874 47.619 7.05 0.00 42.88 4.61
2240 2250 5.887598 TGACAGCAAAGGAGCAATATATGTT 59.112 36.000 0.00 0.00 36.85 2.71
2246 2256 3.423539 AGTGACAGCAAAGGAGCAATA 57.576 42.857 0.00 0.00 36.85 1.90
2248 2258 2.057137 AAGTGACAGCAAAGGAGCAA 57.943 45.000 0.00 0.00 36.85 3.91
2269 2279 3.921021 CGACAGACACGAAATTAGAAGCT 59.079 43.478 0.00 0.00 0.00 3.74
2274 2284 4.966850 AACACGACAGACACGAAATTAG 57.033 40.909 0.00 0.00 34.70 1.73
2291 2301 7.718272 TTACCACACAACATAAGACTAACAC 57.282 36.000 0.00 0.00 0.00 3.32
2321 2331 2.292257 ACCAGCTACCCATAGACACAGA 60.292 50.000 0.00 0.00 0.00 3.41
2368 2378 3.938289 GTCTACAGACTTTTCGGGAGT 57.062 47.619 2.03 0.00 41.65 3.85
2404 2416 8.747538 ACAAATACTATGAATCCCCAAACTAC 57.252 34.615 0.00 0.00 0.00 2.73
2430 2442 1.152860 TTGCTTTGCTTCGGGGACA 60.153 52.632 0.00 0.00 0.00 4.02
2512 2524 7.619050 ACAATGGCCATACAAATAAATGTGAA 58.381 30.769 21.15 0.00 34.75 3.18
2513 2525 7.180322 ACAATGGCCATACAAATAAATGTGA 57.820 32.000 21.15 0.00 34.75 3.58
2514 2526 7.846644 AACAATGGCCATACAAATAAATGTG 57.153 32.000 21.15 11.34 34.75 3.21
2515 2527 7.148272 GCAAACAATGGCCATACAAATAAATGT 60.148 33.333 21.15 13.38 37.32 2.71
2516 2528 7.148289 TGCAAACAATGGCCATACAAATAAATG 60.148 33.333 21.15 12.67 0.00 2.32
2517 2529 6.883217 TGCAAACAATGGCCATACAAATAAAT 59.117 30.769 21.15 0.00 0.00 1.40
2528 2541 4.314121 GAGTTAATTGCAAACAATGGCCA 58.686 39.130 8.56 8.56 45.90 5.36
2566 2579 5.853936 TCTGTAGTATGAACAGTGCAAACT 58.146 37.500 0.00 0.00 43.88 2.66
2588 2601 8.746922 TCAAAAGCATCACATAATCAACTTTC 57.253 30.769 0.00 0.00 0.00 2.62
2619 2632 2.963599 ATAGTCATGGGCATGCATCA 57.036 45.000 21.36 17.16 38.65 3.07
2634 2647 9.574516 GTTGAATAGGGATCACCATTTAATAGT 57.425 33.333 0.00 0.00 43.89 2.12
2791 2804 6.256975 ACGCGTAATAATGTGCTTTTCTGATA 59.743 34.615 11.67 0.00 0.00 2.15
2869 3302 3.448686 GGTATGATGAACGACACAGAGG 58.551 50.000 0.00 0.00 0.00 3.69
2878 3311 3.059597 GCAATTCGAGGGTATGATGAACG 60.060 47.826 0.00 0.00 0.00 3.95
2889 3322 0.174845 TAGTCCACGCAATTCGAGGG 59.825 55.000 11.53 8.89 46.81 4.30
2926 3359 6.049149 TCAGTTCAAACTCGATATTCATCCC 58.951 40.000 0.00 0.00 37.08 3.85
2952 3388 3.288964 TCTGAAACAAAGGGGCGTAAAA 58.711 40.909 0.00 0.00 0.00 1.52
2962 3398 5.645067 TGCAGTCCAGATATCTGAAACAAAG 59.355 40.000 30.40 20.25 46.59 2.77
3034 3470 2.792116 CTCGCTCTTCTTATTCGGCTTC 59.208 50.000 0.00 0.00 0.00 3.86
3039 3475 3.422417 TCCACTCGCTCTTCTTATTCG 57.578 47.619 0.00 0.00 0.00 3.34
3056 3492 4.412199 CCTGATAGTCCCTAAACCAATCCA 59.588 45.833 0.00 0.00 0.00 3.41
3079 3515 7.264373 AGTATATTTTGCAACCTACTGATGC 57.736 36.000 0.00 0.00 40.45 3.91
3098 3534 5.118050 CGAACGACACAAAAGAGCAAGTATA 59.882 40.000 0.00 0.00 0.00 1.47
3113 3549 1.124477 GAACAGCTAAGCGAACGACAC 59.876 52.381 0.00 0.00 0.00 3.67
3117 3553 0.362512 GACGAACAGCTAAGCGAACG 59.637 55.000 8.06 0.00 0.00 3.95
3137 3573 0.249657 GCTCACGATTCAGGCTAGGG 60.250 60.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.