Multiple sequence alignment - TraesCS1D01G121400

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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 TraesCS1D01G121400 chr1D 100.000 2908 0 0 1 2908 121242141 121239234 0.000000e+00 5371
1 TraesCS1D01G121400 chr1D 78.879 232 39 9 2391 2617 487197909 487198135 6.490000e-32 148
2 TraesCS1D01G121400 chr1B 94.967 2106 68 18 335 2422 184219841 184217756 0.000000e+00 3267
3 TraesCS1D01G121400 chr1B 97.129 209 6 0 1 209 184220043 184219835 1.280000e-93 353
4 TraesCS1D01G121400 chr1A 94.708 1285 40 13 1126 2395 132799017 132797746 0.000000e+00 1971
5 TraesCS1D01G121400 chr1A 96.310 813 21 5 335 1141 132799842 132799033 0.000000e+00 1327
6 TraesCS1D01G121400 chr1A 89.593 221 11 4 1 209 132800056 132799836 1.330000e-68 270
7 TraesCS1D01G121400 chr6A 83.109 521 57 22 2407 2908 272122367 272121859 2.060000e-121 446
8 TraesCS1D01G121400 chr6D 83.660 459 50 13 2462 2908 209918035 209917590 2.700000e-110 409
9 TraesCS1D01G121400 chr6D 98.519 135 2 0 204 338 296196552 296196686 3.750000e-59 239
10 TraesCS1D01G121400 chr6D 97.015 134 4 0 203 336 346959683 346959816 2.920000e-55 226
11 TraesCS1D01G121400 chr6B 82.566 304 27 9 2609 2908 399738482 399738201 8.050000e-61 244
12 TraesCS1D01G121400 chr6B 91.176 136 11 1 201 336 95972696 95972562 1.780000e-42 183
13 TraesCS1D01G121400 chr7B 93.478 138 9 0 203 340 174671103 174671240 3.800000e-49 206
14 TraesCS1D01G121400 chr5B 93.382 136 9 0 204 339 547830481 547830616 4.910000e-48 202
15 TraesCS1D01G121400 chr2B 93.284 134 9 0 203 336 677357569 677357702 6.360000e-47 198
16 TraesCS1D01G121400 chr2B 93.233 133 8 1 206 338 697119141 697119010 8.220000e-46 195
17 TraesCS1D01G121400 chr2B 91.736 121 8 2 197 316 714501574 714501455 1.790000e-37 167
18 TraesCS1D01G121400 chrUn 92.029 138 10 1 204 340 101542581 101542718 2.960000e-45 193
19 TraesCS1D01G121400 chr5D 81.860 215 35 4 2396 2606 540230565 540230779 8.280000e-41 178
20 TraesCS1D01G121400 chr2D 83.784 185 27 2 2396 2577 332335133 332335317 3.850000e-39 172
21 TraesCS1D01G121400 chr2D 80.569 211 30 10 2387 2590 618309702 618309908 5.020000e-33 152
22 TraesCS1D01G121400 chr3B 83.243 185 28 2 2396 2577 812616710 812616894 1.790000e-37 167
23 TraesCS1D01G121400 chr4A 81.132 212 33 6 2394 2600 321899575 321899366 2.320000e-36 163
24 TraesCS1D01G121400 chr4A 80.365 219 39 4 2394 2609 368567559 368567342 2.320000e-36 163


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 TraesCS1D01G121400 chr1D 121239234 121242141 2907 True 5371.000000 5371 100.000 1 2908 1 chr1D.!!$R1 2907
1 TraesCS1D01G121400 chr1B 184217756 184220043 2287 True 1810.000000 3267 96.048 1 2422 2 chr1B.!!$R1 2421
2 TraesCS1D01G121400 chr1A 132797746 132800056 2310 True 1189.333333 1971 93.537 1 2395 3 chr1A.!!$R1 2394
3 TraesCS1D01G121400 chr6A 272121859 272122367 508 True 446.000000 446 83.109 2407 2908 1 chr6A.!!$R1 501

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
229 242 0.535553 TTGTTCGGTTACACCCTGCC 60.536 55.0 0.0 0.0 33.75 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2172 0.111061 AACAGGTTCATCTGCCAGCA 59.889 50.0 0.0 0.0 38.26 4.41 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
103 116 3.194005 TCAGTTGAACCCACTTCAGAC 57.806 47.619 0.00 0.00 40.12 3.51
177 190 2.954684 GCGGGTGTCCATGAGGTGA 61.955 63.158 0.00 0.00 35.89 4.02
185 198 4.099419 GGTGTCCATGAGGTGAAAACTTTT 59.901 41.667 0.00 0.00 35.89 2.27
207 220 9.884465 CTTTTAGTTTGTCACAATTCTCTTAGG 57.116 33.333 0.00 0.00 0.00 2.69
208 221 5.948992 AGTTTGTCACAATTCTCTTAGGC 57.051 39.130 0.00 0.00 0.00 3.93
209 222 5.625150 AGTTTGTCACAATTCTCTTAGGCT 58.375 37.500 0.00 0.00 0.00 4.58
210 223 6.064717 AGTTTGTCACAATTCTCTTAGGCTT 58.935 36.000 0.00 0.00 0.00 4.35
211 224 6.547510 AGTTTGTCACAATTCTCTTAGGCTTT 59.452 34.615 0.00 0.00 0.00 3.51
212 225 5.947228 TGTCACAATTCTCTTAGGCTTTG 57.053 39.130 0.00 0.00 0.00 2.77
213 226 5.376625 TGTCACAATTCTCTTAGGCTTTGT 58.623 37.500 0.00 0.00 0.00 2.83
214 227 5.827797 TGTCACAATTCTCTTAGGCTTTGTT 59.172 36.000 0.00 0.00 0.00 2.83
215 228 6.017109 TGTCACAATTCTCTTAGGCTTTGTTC 60.017 38.462 0.00 0.00 0.00 3.18
216 229 5.179368 TCACAATTCTCTTAGGCTTTGTTCG 59.821 40.000 0.00 0.00 0.00 3.95
217 230 4.455877 ACAATTCTCTTAGGCTTTGTTCGG 59.544 41.667 0.00 0.00 0.00 4.30
218 231 3.764237 TTCTCTTAGGCTTTGTTCGGT 57.236 42.857 0.00 0.00 0.00 4.69
219 232 3.764237 TCTCTTAGGCTTTGTTCGGTT 57.236 42.857 0.00 0.00 0.00 4.44
220 233 4.877378 TCTCTTAGGCTTTGTTCGGTTA 57.123 40.909 0.00 0.00 0.00 2.85
221 234 4.563061 TCTCTTAGGCTTTGTTCGGTTAC 58.437 43.478 0.00 0.00 0.00 2.50
222 235 4.039488 TCTCTTAGGCTTTGTTCGGTTACA 59.961 41.667 0.00 0.00 0.00 2.41
223 236 4.060205 TCTTAGGCTTTGTTCGGTTACAC 58.940 43.478 0.00 0.00 0.00 2.90
224 237 1.601166 AGGCTTTGTTCGGTTACACC 58.399 50.000 0.00 0.00 34.05 4.16
225 238 0.594602 GGCTTTGTTCGGTTACACCC 59.405 55.000 0.00 0.00 33.75 4.61
226 239 1.601166 GCTTTGTTCGGTTACACCCT 58.399 50.000 0.00 0.00 33.75 4.34
227 240 1.265905 GCTTTGTTCGGTTACACCCTG 59.734 52.381 0.00 0.00 33.75 4.45
228 241 1.265905 CTTTGTTCGGTTACACCCTGC 59.734 52.381 0.00 0.00 33.75 4.85
229 242 0.535553 TTGTTCGGTTACACCCTGCC 60.536 55.000 0.00 0.00 33.75 4.85
230 243 1.373812 GTTCGGTTACACCCTGCCT 59.626 57.895 0.00 0.00 33.75 4.75
231 244 0.953960 GTTCGGTTACACCCTGCCTG 60.954 60.000 0.00 0.00 33.75 4.85
232 245 2.046314 CGGTTACACCCTGCCTGG 60.046 66.667 0.00 0.00 33.75 4.45
233 246 2.589157 CGGTTACACCCTGCCTGGA 61.589 63.158 0.00 0.00 38.35 3.86
234 247 1.299976 GGTTACACCCTGCCTGGAG 59.700 63.158 0.00 0.00 38.35 3.86
235 248 1.299976 GTTACACCCTGCCTGGAGG 59.700 63.158 0.00 1.27 38.35 4.30
241 254 4.052518 CCTGCCTGGAGGGGGTTG 62.053 72.222 0.00 0.00 38.35 3.77
242 255 4.052518 CTGCCTGGAGGGGGTTGG 62.053 72.222 0.00 0.00 35.18 3.77
243 256 4.608514 TGCCTGGAGGGGGTTGGA 62.609 66.667 0.00 0.00 35.18 3.53
244 257 3.732849 GCCTGGAGGGGGTTGGAG 61.733 72.222 0.00 0.00 35.18 3.86
245 258 3.017581 CCTGGAGGGGGTTGGAGG 61.018 72.222 0.00 0.00 0.00 4.30
246 259 3.017581 CTGGAGGGGGTTGGAGGG 61.018 72.222 0.00 0.00 0.00 4.30
247 260 4.693915 TGGAGGGGGTTGGAGGGG 62.694 72.222 0.00 0.00 0.00 4.79
248 261 4.364686 GGAGGGGGTTGGAGGGGA 62.365 72.222 0.00 0.00 0.00 4.81
249 262 2.044620 GAGGGGGTTGGAGGGGAT 59.955 66.667 0.00 0.00 0.00 3.85
250 263 1.622752 GAGGGGGTTGGAGGGGATT 60.623 63.158 0.00 0.00 0.00 3.01
251 264 1.151131 AGGGGGTTGGAGGGGATTT 60.151 57.895 0.00 0.00 0.00 2.17
252 265 1.001631 GGGGGTTGGAGGGGATTTG 59.998 63.158 0.00 0.00 0.00 2.32
253 266 1.001631 GGGGTTGGAGGGGATTTGG 59.998 63.158 0.00 0.00 0.00 3.28
254 267 1.001631 GGGTTGGAGGGGATTTGGG 59.998 63.158 0.00 0.00 0.00 4.12
255 268 1.001631 GGTTGGAGGGGATTTGGGG 59.998 63.158 0.00 0.00 0.00 4.96
256 269 1.001631 GTTGGAGGGGATTTGGGGG 59.998 63.158 0.00 0.00 0.00 5.40
273 286 2.437085 GGGGGATTTGACTTACAGGG 57.563 55.000 0.00 0.00 0.00 4.45
274 287 1.063942 GGGGGATTTGACTTACAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
275 288 1.920351 GGGGATTTGACTTACAGGGGA 59.080 52.381 0.00 0.00 0.00 4.81
276 289 2.310647 GGGGATTTGACTTACAGGGGAA 59.689 50.000 0.00 0.00 0.00 3.97
277 290 3.052869 GGGGATTTGACTTACAGGGGAAT 60.053 47.826 0.00 0.00 0.00 3.01
278 291 4.207955 GGGATTTGACTTACAGGGGAATC 58.792 47.826 0.00 0.00 0.00 2.52
279 292 4.325030 GGGATTTGACTTACAGGGGAATCA 60.325 45.833 0.00 0.00 0.00 2.57
280 293 5.261216 GGATTTGACTTACAGGGGAATCAA 58.739 41.667 0.00 0.00 0.00 2.57
281 294 5.893824 GGATTTGACTTACAGGGGAATCAAT 59.106 40.000 0.00 0.00 0.00 2.57
282 295 6.381133 GGATTTGACTTACAGGGGAATCAATT 59.619 38.462 0.00 0.00 0.00 2.32
283 296 7.093333 GGATTTGACTTACAGGGGAATCAATTT 60.093 37.037 0.00 0.00 0.00 1.82
284 297 8.893563 ATTTGACTTACAGGGGAATCAATTTA 57.106 30.769 0.00 0.00 0.00 1.40
285 298 7.696992 TTGACTTACAGGGGAATCAATTTAC 57.303 36.000 0.00 0.00 0.00 2.01
286 299 7.027874 TGACTTACAGGGGAATCAATTTACT 57.972 36.000 0.00 0.00 0.00 2.24
287 300 7.466804 TGACTTACAGGGGAATCAATTTACTT 58.533 34.615 0.00 0.00 0.00 2.24
288 301 7.610305 TGACTTACAGGGGAATCAATTTACTTC 59.390 37.037 0.00 0.00 0.00 3.01
289 302 7.466804 ACTTACAGGGGAATCAATTTACTTCA 58.533 34.615 0.00 0.00 0.00 3.02
290 303 7.947890 ACTTACAGGGGAATCAATTTACTTCAA 59.052 33.333 0.00 0.00 0.00 2.69
291 304 8.893563 TTACAGGGGAATCAATTTACTTCAAT 57.106 30.769 0.00 0.00 0.00 2.57
292 305 7.410120 ACAGGGGAATCAATTTACTTCAATC 57.590 36.000 0.00 0.00 0.00 2.67
293 306 6.381133 ACAGGGGAATCAATTTACTTCAATCC 59.619 38.462 0.00 0.00 0.00 3.01
294 307 5.899547 AGGGGAATCAATTTACTTCAATCCC 59.100 40.000 0.00 0.00 42.64 3.85
295 308 5.899547 GGGGAATCAATTTACTTCAATCCCT 59.100 40.000 6.94 0.00 42.88 4.20
296 309 6.183360 GGGGAATCAATTTACTTCAATCCCTG 60.183 42.308 6.94 0.00 42.88 4.45
297 310 6.381133 GGGAATCAATTTACTTCAATCCCTGT 59.619 38.462 0.00 0.00 40.66 4.00
298 311 7.416777 GGGAATCAATTTACTTCAATCCCTGTC 60.417 40.741 0.00 0.00 40.66 3.51
299 312 7.122650 GGAATCAATTTACTTCAATCCCTGTCA 59.877 37.037 0.00 0.00 0.00 3.58
300 313 8.421249 AATCAATTTACTTCAATCCCTGTCAA 57.579 30.769 0.00 0.00 0.00 3.18
301 314 7.831691 TCAATTTACTTCAATCCCTGTCAAA 57.168 32.000 0.00 0.00 0.00 2.69
302 315 7.657336 TCAATTTACTTCAATCCCTGTCAAAC 58.343 34.615 0.00 0.00 0.00 2.93
303 316 6.590234 ATTTACTTCAATCCCTGTCAAACC 57.410 37.500 0.00 0.00 0.00 3.27
304 317 2.876581 ACTTCAATCCCTGTCAAACCC 58.123 47.619 0.00 0.00 0.00 4.11
305 318 2.171003 CTTCAATCCCTGTCAAACCCC 58.829 52.381 0.00 0.00 0.00 4.95
306 319 1.455822 TCAATCCCTGTCAAACCCCT 58.544 50.000 0.00 0.00 0.00 4.79
307 320 1.786441 TCAATCCCTGTCAAACCCCTT 59.214 47.619 0.00 0.00 0.00 3.95
308 321 2.178984 TCAATCCCTGTCAAACCCCTTT 59.821 45.455 0.00 0.00 0.00 3.11
309 322 2.562738 CAATCCCTGTCAAACCCCTTTC 59.437 50.000 0.00 0.00 0.00 2.62
310 323 1.227249 TCCCTGTCAAACCCCTTTCA 58.773 50.000 0.00 0.00 0.00 2.69
311 324 1.571457 TCCCTGTCAAACCCCTTTCAA 59.429 47.619 0.00 0.00 0.00 2.69
312 325 2.178984 TCCCTGTCAAACCCCTTTCAAT 59.821 45.455 0.00 0.00 0.00 2.57
313 326 2.972021 CCCTGTCAAACCCCTTTCAATT 59.028 45.455 0.00 0.00 0.00 2.32
314 327 3.006859 CCCTGTCAAACCCCTTTCAATTC 59.993 47.826 0.00 0.00 0.00 2.17
315 328 3.006859 CCTGTCAAACCCCTTTCAATTCC 59.993 47.826 0.00 0.00 0.00 3.01
316 329 2.969262 TGTCAAACCCCTTTCAATTCCC 59.031 45.455 0.00 0.00 0.00 3.97
317 330 3.239449 GTCAAACCCCTTTCAATTCCCT 58.761 45.455 0.00 0.00 0.00 4.20
318 331 3.006859 GTCAAACCCCTTTCAATTCCCTG 59.993 47.826 0.00 0.00 0.00 4.45
319 332 2.972021 CAAACCCCTTTCAATTCCCTGT 59.028 45.455 0.00 0.00 0.00 4.00
320 333 2.604912 ACCCCTTTCAATTCCCTGTC 57.395 50.000 0.00 0.00 0.00 3.51
321 334 1.786441 ACCCCTTTCAATTCCCTGTCA 59.214 47.619 0.00 0.00 0.00 3.58
322 335 2.178984 ACCCCTTTCAATTCCCTGTCAA 59.821 45.455 0.00 0.00 0.00 3.18
323 336 2.562738 CCCCTTTCAATTCCCTGTCAAC 59.437 50.000 0.00 0.00 0.00 3.18
324 337 2.562738 CCCTTTCAATTCCCTGTCAACC 59.437 50.000 0.00 0.00 0.00 3.77
325 338 2.228822 CCTTTCAATTCCCTGTCAACCG 59.771 50.000 0.00 0.00 0.00 4.44
326 339 2.940994 TTCAATTCCCTGTCAACCGA 57.059 45.000 0.00 0.00 0.00 4.69
327 340 2.940994 TCAATTCCCTGTCAACCGAA 57.059 45.000 0.00 0.00 0.00 4.30
328 341 2.500229 TCAATTCCCTGTCAACCGAAC 58.500 47.619 0.00 0.00 0.00 3.95
329 342 1.196808 CAATTCCCTGTCAACCGAACG 59.803 52.381 0.00 0.00 0.00 3.95
330 343 0.953960 ATTCCCTGTCAACCGAACGC 60.954 55.000 0.00 0.00 0.00 4.84
331 344 2.280524 CCCTGTCAACCGAACGCA 60.281 61.111 0.00 0.00 0.00 5.24
332 345 2.317609 CCCTGTCAACCGAACGCAG 61.318 63.158 0.00 0.00 0.00 5.18
333 346 2.551270 CTGTCAACCGAACGCAGC 59.449 61.111 0.00 0.00 0.00 5.25
378 392 2.453983 AAAATTGGTTCATGGCCACG 57.546 45.000 8.16 0.00 35.46 4.94
408 422 3.019799 TGCCCAAAGGTTTGTTGAGTA 57.980 42.857 1.94 0.00 36.45 2.59
449 463 5.180868 GCAATCTCAGAAACTCACTTGTGAT 59.819 40.000 3.79 0.00 29.18 3.06
565 579 6.437477 TGGATACAGTTCTACCCTGCTATATG 59.563 42.308 0.00 0.00 46.17 1.78
642 659 1.811965 CGTTGTGGGAATTGCTCATCA 59.188 47.619 0.00 0.00 0.00 3.07
734 755 6.047231 CAGAATCATCATCTCTGTAGTGCAA 58.953 40.000 0.00 0.00 33.39 4.08
758 779 7.165460 ACTACCTAAAACTGCTGTTTGTTTT 57.835 32.000 20.64 13.74 44.70 2.43
903 924 6.365789 GCTTGATGTGATGATAGCTCTTAGAC 59.634 42.308 0.00 0.00 0.00 2.59
1526 1580 4.083590 GCTTCTGCTCTTCTGGTTAGTTTG 60.084 45.833 0.00 0.00 36.03 2.93
1554 1615 1.258720 CATACACGTGCATCATGTCCG 59.741 52.381 17.22 0.00 30.47 4.79
1629 1694 5.818136 ACAAGTTAATCATTCATCGGTGG 57.182 39.130 0.00 0.00 0.00 4.61
1648 1713 6.149308 TCGGTGGACATTATCATAATTCATGC 59.851 38.462 0.00 0.00 34.35 4.06
1663 1728 1.619332 TCATGCTTGAATTGCCTGCAA 59.381 42.857 7.06 7.06 40.47 4.08
1690 1755 6.599638 GCCTTCTTTACTTCCTTGTGATGTAT 59.400 38.462 0.00 0.00 34.60 2.29
1706 1771 8.076910 TGTGATGTATGGGCATTTTAAATCTT 57.923 30.769 0.00 0.00 0.00 2.40
1782 1847 5.510671 ACACTGTTAGCAAATGAGTTTTCG 58.489 37.500 0.00 0.00 0.00 3.46
1873 1938 7.201785 CCTTTCTGTTTTACTGGTAATGTGTGT 60.202 37.037 0.00 0.00 0.00 3.72
1955 2020 5.814188 TGCAAGATATTCGATGCATATCCTC 59.186 40.000 0.00 0.00 38.50 3.71
1975 2041 5.892119 TCCTCGAGGAATGAAGTACTTACAT 59.108 40.000 31.91 10.81 42.18 2.29
2172 2238 8.782144 GCAACCAATTGGAATTTATTCTTTCAA 58.218 29.630 31.22 0.20 38.94 2.69
2320 2390 7.510549 AGTGTTTTAATGTATTGCTGTCTGT 57.489 32.000 0.00 0.00 0.00 3.41
2321 2391 7.362662 AGTGTTTTAATGTATTGCTGTCTGTG 58.637 34.615 0.00 0.00 0.00 3.66
2503 2575 6.287589 TGTTTGGTCACCAATAAAAACTGT 57.712 33.333 10.97 0.00 43.55 3.55
2505 2577 6.071334 TGTTTGGTCACCAATAAAAACTGTGA 60.071 34.615 10.97 0.00 43.55 3.58
2510 2582 8.519526 TGGTCACCAATAAAAACTGTGATATTC 58.480 33.333 0.00 0.00 38.14 1.75
2545 2617 6.648879 TTCCCAAAACCAAAGTATTCTCTG 57.351 37.500 0.00 0.00 0.00 3.35
2547 2619 5.768164 TCCCAAAACCAAAGTATTCTCTGTC 59.232 40.000 0.00 0.00 0.00 3.51
2549 2621 6.940298 CCCAAAACCAAAGTATTCTCTGTCTA 59.060 38.462 0.00 0.00 0.00 2.59
2550 2622 7.447238 CCCAAAACCAAAGTATTCTCTGTCTAA 59.553 37.037 0.00 0.00 0.00 2.10
2615 2688 1.967319 AAAATGAGCTGGTCACACGT 58.033 45.000 12.27 0.00 38.28 4.49
2616 2689 1.512926 AAATGAGCTGGTCACACGTC 58.487 50.000 12.27 0.00 38.28 4.34
2617 2690 0.320771 AATGAGCTGGTCACACGTCC 60.321 55.000 12.27 0.00 38.28 4.79
2618 2691 1.471829 ATGAGCTGGTCACACGTCCA 61.472 55.000 12.27 0.00 38.28 4.02
2620 2693 3.036084 GCTGGTCACACGTCCACG 61.036 66.667 0.00 0.00 46.33 4.94
2637 2710 4.267928 GTCCACGTTTATCTTCTTCGATGG 59.732 45.833 0.00 0.00 0.00 3.51
2654 2727 0.100325 TGGCTGTTTGCAACAACTCG 59.900 50.000 0.00 0.00 45.15 4.18
2658 2731 0.247894 TGTTTGCAACAACTCGCGTC 60.248 50.000 5.77 0.00 38.72 5.19
2660 2733 2.958137 TTTGCAACAACTCGCGTCGC 62.958 55.000 7.29 7.29 0.00 5.19
2661 2734 3.995669 GCAACAACTCGCGTCGCA 61.996 61.111 18.75 3.61 0.00 5.10
2676 2749 3.573491 GCACCGCCGTATTGCCTC 61.573 66.667 0.00 0.00 0.00 4.70
2686 2759 1.202533 CGTATTGCCTCCGGAGATGTT 60.203 52.381 33.39 16.37 0.00 2.71
2689 2762 0.984230 TTGCCTCCGGAGATGTTTCT 59.016 50.000 33.39 0.00 33.88 2.52
2699 2772 2.338500 GAGATGTTTCTGTCGGTGGAC 58.662 52.381 0.00 0.00 43.71 4.02
2713 2786 1.977009 TGGACGACCACAGCGAGAT 60.977 57.895 1.37 0.00 41.77 2.75
2720 2793 0.976641 ACCACAGCGAGATCAAAGGA 59.023 50.000 0.00 0.00 0.00 3.36
2722 2795 1.005340 CACAGCGAGATCAAAGGAGC 58.995 55.000 0.00 0.00 0.00 4.70
2753 2835 0.687354 TCTTCTCCCACCTCTTGCAC 59.313 55.000 0.00 0.00 0.00 4.57
2758 2840 2.358737 CCACCTCTTGCACCGGTC 60.359 66.667 2.59 0.00 0.00 4.79
2759 2841 2.738521 CACCTCTTGCACCGGTCG 60.739 66.667 2.59 1.09 0.00 4.79
2780 2862 2.359230 GCCTTGACTTCTGCGGCT 60.359 61.111 0.00 0.00 37.76 5.52
2781 2863 2.684843 GCCTTGACTTCTGCGGCTG 61.685 63.158 0.00 0.00 37.76 4.85
2782 2864 2.684843 CCTTGACTTCTGCGGCTGC 61.685 63.158 11.65 11.65 43.20 5.25
2783 2865 1.670406 CTTGACTTCTGCGGCTGCT 60.670 57.895 20.27 0.00 43.34 4.24
2784 2866 1.909141 CTTGACTTCTGCGGCTGCTG 61.909 60.000 20.27 18.90 43.34 4.41
2785 2867 3.123620 GACTTCTGCGGCTGCTGG 61.124 66.667 22.51 13.62 43.34 4.85
2816 2898 1.377333 GTACTCTTGCCTGGCCACC 60.377 63.158 17.53 0.00 0.00 4.61
2817 2899 1.845664 TACTCTTGCCTGGCCACCA 60.846 57.895 17.53 0.00 0.00 4.17
2818 2900 2.124507 TACTCTTGCCTGGCCACCAC 62.125 60.000 17.53 0.00 0.00 4.16
2820 2902 4.954970 CTTGCCTGGCCACCACGT 62.955 66.667 17.53 0.00 0.00 4.49
2864 2949 6.192970 AGTAGACCATGGATTATTGGAAGG 57.807 41.667 21.47 0.00 0.00 3.46
2870 2955 5.044179 ACCATGGATTATTGGAAGGAAGTGA 60.044 40.000 21.47 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.016555 AGGCCAATGTGGTTTTACTAAGAAT 58.983 36.000 5.01 0.00 40.46 2.40
103 116 3.932710 TGCTACTATTGGAAGCACTTTCG 59.067 43.478 3.09 0.00 41.15 3.46
185 198 6.769512 AGCCTAAGAGAATTGTGACAAACTA 58.230 36.000 0.62 0.00 0.00 2.24
202 215 4.400036 GTGTAACCGAACAAAGCCTAAG 57.600 45.455 0.00 0.00 0.00 2.18
217 230 1.299976 CCTCCAGGCAGGGTGTAAC 59.700 63.158 0.00 0.00 38.24 2.50
218 231 3.820425 CCTCCAGGCAGGGTGTAA 58.180 61.111 0.00 0.00 38.24 2.41
224 237 4.052518 CAACCCCCTCCAGGCAGG 62.053 72.222 0.00 0.00 39.47 4.85
225 238 4.052518 CCAACCCCCTCCAGGCAG 62.053 72.222 0.00 0.00 0.00 4.85
226 239 4.608514 TCCAACCCCCTCCAGGCA 62.609 66.667 0.00 0.00 0.00 4.75
227 240 3.732849 CTCCAACCCCCTCCAGGC 61.733 72.222 0.00 0.00 0.00 4.85
228 241 3.017581 CCTCCAACCCCCTCCAGG 61.018 72.222 0.00 0.00 0.00 4.45
229 242 3.017581 CCCTCCAACCCCCTCCAG 61.018 72.222 0.00 0.00 0.00 3.86
230 243 4.693915 CCCCTCCAACCCCCTCCA 62.694 72.222 0.00 0.00 0.00 3.86
231 244 3.677689 ATCCCCTCCAACCCCCTCC 62.678 68.421 0.00 0.00 0.00 4.30
232 245 1.221909 AAATCCCCTCCAACCCCCTC 61.222 60.000 0.00 0.00 0.00 4.30
233 246 1.151131 AAATCCCCTCCAACCCCCT 60.151 57.895 0.00 0.00 0.00 4.79
234 247 1.001631 CAAATCCCCTCCAACCCCC 59.998 63.158 0.00 0.00 0.00 5.40
235 248 1.001631 CCAAATCCCCTCCAACCCC 59.998 63.158 0.00 0.00 0.00 4.95
236 249 1.001631 CCCAAATCCCCTCCAACCC 59.998 63.158 0.00 0.00 0.00 4.11
237 250 1.001631 CCCCAAATCCCCTCCAACC 59.998 63.158 0.00 0.00 0.00 3.77
238 251 1.001631 CCCCCAAATCCCCTCCAAC 59.998 63.158 0.00 0.00 0.00 3.77
239 252 3.531961 CCCCCAAATCCCCTCCAA 58.468 61.111 0.00 0.00 0.00 3.53
254 267 1.063942 CCCCTGTAAGTCAAATCCCCC 60.064 57.143 0.00 0.00 0.00 5.40
255 268 1.920351 TCCCCTGTAAGTCAAATCCCC 59.080 52.381 0.00 0.00 0.00 4.81
256 269 3.732048 TTCCCCTGTAAGTCAAATCCC 57.268 47.619 0.00 0.00 0.00 3.85
257 270 4.855340 TGATTCCCCTGTAAGTCAAATCC 58.145 43.478 0.00 0.00 0.00 3.01
258 271 7.410120 AATTGATTCCCCTGTAAGTCAAATC 57.590 36.000 0.00 0.00 0.00 2.17
259 272 7.797121 AAATTGATTCCCCTGTAAGTCAAAT 57.203 32.000 0.00 0.00 0.00 2.32
260 273 7.947890 AGTAAATTGATTCCCCTGTAAGTCAAA 59.052 33.333 0.00 0.00 0.00 2.69
261 274 7.466804 AGTAAATTGATTCCCCTGTAAGTCAA 58.533 34.615 0.00 0.00 0.00 3.18
262 275 7.027874 AGTAAATTGATTCCCCTGTAAGTCA 57.972 36.000 0.00 0.00 0.00 3.41
263 276 7.610305 TGAAGTAAATTGATTCCCCTGTAAGTC 59.390 37.037 0.00 0.00 0.00 3.01
264 277 7.466804 TGAAGTAAATTGATTCCCCTGTAAGT 58.533 34.615 0.00 0.00 0.00 2.24
265 278 7.938140 TGAAGTAAATTGATTCCCCTGTAAG 57.062 36.000 0.00 0.00 0.00 2.34
266 279 8.893563 ATTGAAGTAAATTGATTCCCCTGTAA 57.106 30.769 0.00 0.00 0.00 2.41
267 280 7.559897 GGATTGAAGTAAATTGATTCCCCTGTA 59.440 37.037 0.00 0.00 0.00 2.74
268 281 6.381133 GGATTGAAGTAAATTGATTCCCCTGT 59.619 38.462 0.00 0.00 0.00 4.00
269 282 6.183360 GGGATTGAAGTAAATTGATTCCCCTG 60.183 42.308 0.00 0.00 38.23 4.45
270 283 5.899547 GGGATTGAAGTAAATTGATTCCCCT 59.100 40.000 0.00 0.00 38.23 4.79
271 284 5.899547 AGGGATTGAAGTAAATTGATTCCCC 59.100 40.000 0.00 0.00 42.51 4.81
272 285 6.381133 ACAGGGATTGAAGTAAATTGATTCCC 59.619 38.462 0.00 0.00 42.10 3.97
273 286 7.122650 TGACAGGGATTGAAGTAAATTGATTCC 59.877 37.037 0.00 0.00 0.00 3.01
274 287 8.055279 TGACAGGGATTGAAGTAAATTGATTC 57.945 34.615 0.00 0.00 0.00 2.52
275 288 8.421249 TTGACAGGGATTGAAGTAAATTGATT 57.579 30.769 0.00 0.00 0.00 2.57
276 289 8.306761 GTTTGACAGGGATTGAAGTAAATTGAT 58.693 33.333 0.00 0.00 0.00 2.57
277 290 7.255801 GGTTTGACAGGGATTGAAGTAAATTGA 60.256 37.037 0.00 0.00 0.00 2.57
278 291 6.868339 GGTTTGACAGGGATTGAAGTAAATTG 59.132 38.462 0.00 0.00 0.00 2.32
279 292 6.014584 GGGTTTGACAGGGATTGAAGTAAATT 60.015 38.462 0.00 0.00 0.00 1.82
280 293 5.480422 GGGTTTGACAGGGATTGAAGTAAAT 59.520 40.000 0.00 0.00 0.00 1.40
281 294 4.830600 GGGTTTGACAGGGATTGAAGTAAA 59.169 41.667 0.00 0.00 0.00 2.01
282 295 4.403734 GGGTTTGACAGGGATTGAAGTAA 58.596 43.478 0.00 0.00 0.00 2.24
283 296 3.245122 GGGGTTTGACAGGGATTGAAGTA 60.245 47.826 0.00 0.00 0.00 2.24
284 297 2.490902 GGGGTTTGACAGGGATTGAAGT 60.491 50.000 0.00 0.00 0.00 3.01
285 298 2.171003 GGGGTTTGACAGGGATTGAAG 58.829 52.381 0.00 0.00 0.00 3.02
286 299 1.786441 AGGGGTTTGACAGGGATTGAA 59.214 47.619 0.00 0.00 0.00 2.69
287 300 1.455822 AGGGGTTTGACAGGGATTGA 58.544 50.000 0.00 0.00 0.00 2.57
288 301 2.309136 AAGGGGTTTGACAGGGATTG 57.691 50.000 0.00 0.00 0.00 2.67
289 302 2.178984 TGAAAGGGGTTTGACAGGGATT 59.821 45.455 0.00 0.00 0.00 3.01
290 303 1.786441 TGAAAGGGGTTTGACAGGGAT 59.214 47.619 0.00 0.00 0.00 3.85
291 304 1.227249 TGAAAGGGGTTTGACAGGGA 58.773 50.000 0.00 0.00 0.00 4.20
292 305 2.080654 TTGAAAGGGGTTTGACAGGG 57.919 50.000 0.00 0.00 0.00 4.45
293 306 3.006859 GGAATTGAAAGGGGTTTGACAGG 59.993 47.826 0.00 0.00 0.00 4.00
294 307 3.006859 GGGAATTGAAAGGGGTTTGACAG 59.993 47.826 0.00 0.00 0.00 3.51
295 308 2.969262 GGGAATTGAAAGGGGTTTGACA 59.031 45.455 0.00 0.00 0.00 3.58
296 309 3.006859 CAGGGAATTGAAAGGGGTTTGAC 59.993 47.826 0.00 0.00 0.00 3.18
297 310 3.238597 CAGGGAATTGAAAGGGGTTTGA 58.761 45.455 0.00 0.00 0.00 2.69
298 311 2.972021 ACAGGGAATTGAAAGGGGTTTG 59.028 45.455 0.00 0.00 0.00 2.93
299 312 3.239449 GACAGGGAATTGAAAGGGGTTT 58.761 45.455 0.00 0.00 0.00 3.27
300 313 2.178984 TGACAGGGAATTGAAAGGGGTT 59.821 45.455 0.00 0.00 0.00 4.11
301 314 1.786441 TGACAGGGAATTGAAAGGGGT 59.214 47.619 0.00 0.00 0.00 4.95
302 315 2.562738 GTTGACAGGGAATTGAAAGGGG 59.437 50.000 0.00 0.00 0.00 4.79
303 316 2.562738 GGTTGACAGGGAATTGAAAGGG 59.437 50.000 0.00 0.00 0.00 3.95
304 317 2.228822 CGGTTGACAGGGAATTGAAAGG 59.771 50.000 0.00 0.00 0.00 3.11
305 318 3.146066 TCGGTTGACAGGGAATTGAAAG 58.854 45.455 0.00 0.00 0.00 2.62
306 319 3.216187 TCGGTTGACAGGGAATTGAAA 57.784 42.857 0.00 0.00 0.00 2.69
307 320 2.882137 GTTCGGTTGACAGGGAATTGAA 59.118 45.455 0.00 0.00 0.00 2.69
308 321 2.500229 GTTCGGTTGACAGGGAATTGA 58.500 47.619 0.00 0.00 0.00 2.57
309 322 1.196808 CGTTCGGTTGACAGGGAATTG 59.803 52.381 0.00 0.00 0.00 2.32
310 323 1.519408 CGTTCGGTTGACAGGGAATT 58.481 50.000 0.00 0.00 0.00 2.17
311 324 0.953960 GCGTTCGGTTGACAGGGAAT 60.954 55.000 0.00 0.00 0.00 3.01
312 325 1.595929 GCGTTCGGTTGACAGGGAA 60.596 57.895 0.00 0.00 0.00 3.97
313 326 2.029964 GCGTTCGGTTGACAGGGA 59.970 61.111 0.00 0.00 0.00 4.20
314 327 2.280524 TGCGTTCGGTTGACAGGG 60.281 61.111 0.00 0.00 0.00 4.45
315 328 2.954753 GCTGCGTTCGGTTGACAGG 61.955 63.158 0.00 0.00 0.00 4.00
316 329 2.551270 GCTGCGTTCGGTTGACAG 59.449 61.111 0.00 0.00 0.00 3.51
317 330 2.933878 AAGGCTGCGTTCGGTTGACA 62.934 55.000 1.08 0.00 0.00 3.58
318 331 0.947180 TAAGGCTGCGTTCGGTTGAC 60.947 55.000 11.22 0.00 0.00 3.18
319 332 0.669318 CTAAGGCTGCGTTCGGTTGA 60.669 55.000 11.22 0.00 0.00 3.18
320 333 1.635663 CCTAAGGCTGCGTTCGGTTG 61.636 60.000 11.22 0.00 0.00 3.77
321 334 1.375523 CCTAAGGCTGCGTTCGGTT 60.376 57.895 11.22 0.00 0.00 4.44
322 335 2.264794 CCTAAGGCTGCGTTCGGT 59.735 61.111 11.22 0.00 0.00 4.69
323 336 3.195698 GCCTAAGGCTGCGTTCGG 61.196 66.667 18.06 18.06 46.69 4.30
333 346 6.431234 ACTGACTTGATTAAACTTGCCTAAGG 59.569 38.462 0.00 0.00 38.26 2.69
347 360 8.090214 CCATGAACCAATTTTACTGACTTGATT 58.910 33.333 0.00 0.00 0.00 2.57
378 392 0.536724 CCTTTGGGCATGCCTAAACC 59.463 55.000 36.22 21.16 40.77 3.27
408 422 6.126940 TGAGATTGCCTAAGCTAATCTTGACT 60.127 38.462 9.49 0.00 42.12 3.41
449 463 5.487433 TGTCTCAGAGAAAAACAAGACACA 58.513 37.500 0.20 0.00 38.47 3.72
565 579 8.137437 TCTTTTCAGACCATTTTCATCAAGAAC 58.863 33.333 0.00 0.00 35.56 3.01
659 680 5.520288 TCGAGTGCAATTGAACTAGCTATTC 59.480 40.000 19.45 4.48 33.02 1.75
660 681 5.419542 TCGAGTGCAATTGAACTAGCTATT 58.580 37.500 19.45 0.00 33.02 1.73
661 682 5.011090 TCGAGTGCAATTGAACTAGCTAT 57.989 39.130 19.45 0.00 33.02 2.97
662 683 4.450082 TCGAGTGCAATTGAACTAGCTA 57.550 40.909 19.45 1.62 33.02 3.32
734 755 6.769134 AAACAAACAGCAGTTTTAGGTAGT 57.231 33.333 4.24 0.00 45.32 2.73
738 759 6.959671 TTCAAAACAAACAGCAGTTTTAGG 57.040 33.333 4.24 0.00 45.32 2.69
791 812 0.179129 GGCAGGAAAATCATGTGGCG 60.179 55.000 0.00 0.00 29.72 5.69
903 924 7.228507 TGCTGTAATGGCTAATGTAAACTATGG 59.771 37.037 0.00 0.00 0.00 2.74
1073 1094 7.928103 AGCATGCTTTTAATAAGATGAGAGTG 58.072 34.615 16.30 0.00 0.00 3.51
1074 1095 7.042187 CGAGCATGCTTTTAATAAGATGAGAGT 60.042 37.037 23.61 0.00 0.00 3.24
1597 1658 7.946207 TGAATGATTAACTTGTTAAACAGGCA 58.054 30.769 16.90 14.46 0.00 4.75
1613 1678 7.449247 TGATAATGTCCACCGATGAATGATTA 58.551 34.615 0.00 0.00 0.00 1.75
1663 1728 3.394606 TCACAAGGAAGTAAAGAAGGCCT 59.605 43.478 0.00 0.00 0.00 5.19
1755 1820 5.924475 ACTCATTTGCTAACAGTGTACAC 57.076 39.130 18.56 18.56 0.00 2.90
1782 1847 5.241728 ACCAAAGCAGAGGAAACATAAGAAC 59.758 40.000 0.00 0.00 0.00 3.01
1873 1938 6.649141 ACAGCTATTCAAGAATCGTTTGTGTA 59.351 34.615 0.00 0.00 32.50 2.90
2068 2134 3.934457 TCTACACTCGAGCAAATGACA 57.066 42.857 13.61 0.00 0.00 3.58
2106 2172 0.111061 AACAGGTTCATCTGCCAGCA 59.889 50.000 0.00 0.00 38.26 4.41
2172 2238 3.003068 GCATGTAATCTTCTGATTGCGCT 59.997 43.478 9.73 0.00 44.61 5.92
2203 2270 6.904463 TTCGGTGGTAGCTGATATATTACA 57.096 37.500 0.00 0.00 0.00 2.41
2396 2466 2.171003 ACTTTGCTATCAAACAGGGCC 58.829 47.619 0.00 0.00 37.28 5.80
2510 2582 9.423061 CTTTGGTTTTGGGAATATTCTAGTTTG 57.577 33.333 14.95 0.00 0.00 2.93
2519 2591 8.971073 CAGAGAATACTTTGGTTTTGGGAATAT 58.029 33.333 0.00 0.00 0.00 1.28
2524 2596 5.770162 AGACAGAGAATACTTTGGTTTTGGG 59.230 40.000 0.00 0.00 33.32 4.12
2599 2672 1.293498 GGACGTGTGACCAGCTCAT 59.707 57.895 0.00 0.00 0.00 2.90
2600 2673 2.131067 TGGACGTGTGACCAGCTCA 61.131 57.895 0.00 0.00 34.93 4.26
2601 2674 1.664965 GTGGACGTGTGACCAGCTC 60.665 63.158 0.00 0.00 40.62 4.09
2602 2675 2.421739 GTGGACGTGTGACCAGCT 59.578 61.111 0.00 0.00 40.62 4.24
2603 2676 3.036084 CGTGGACGTGTGACCAGC 61.036 66.667 0.00 0.00 40.62 4.85
2613 2686 3.495193 TCGAAGAAGATAAACGTGGACG 58.505 45.455 0.00 0.00 46.33 4.79
2614 2687 4.267928 CCATCGAAGAAGATAAACGTGGAC 59.732 45.833 0.00 0.00 43.58 4.02
2615 2688 4.430007 CCATCGAAGAAGATAAACGTGGA 58.570 43.478 0.00 0.00 43.58 4.02
2616 2689 3.001330 GCCATCGAAGAAGATAAACGTGG 59.999 47.826 0.00 0.00 43.58 4.94
2617 2690 3.865745 AGCCATCGAAGAAGATAAACGTG 59.134 43.478 0.00 0.00 43.58 4.49
2618 2691 3.865745 CAGCCATCGAAGAAGATAAACGT 59.134 43.478 0.00 0.00 43.58 3.99
2620 2693 5.803020 AACAGCCATCGAAGAAGATAAAC 57.197 39.130 0.00 0.00 43.58 2.01
2624 2697 2.421424 GCAAACAGCCATCGAAGAAGAT 59.579 45.455 0.00 0.00 37.41 2.40
2625 2698 1.806542 GCAAACAGCCATCGAAGAAGA 59.193 47.619 0.00 0.00 37.41 2.87
2626 2699 1.536766 TGCAAACAGCCATCGAAGAAG 59.463 47.619 0.00 0.00 42.00 2.85
2676 2749 0.246635 ACCGACAGAAACATCTCCGG 59.753 55.000 0.00 0.00 38.29 5.14
2679 2752 2.338500 GTCCACCGACAGAAACATCTC 58.662 52.381 0.00 0.00 38.99 2.75
2699 2772 0.994995 CTTTGATCTCGCTGTGGTCG 59.005 55.000 0.00 0.00 0.00 4.79
2703 2776 1.005340 GCTCCTTTGATCTCGCTGTG 58.995 55.000 0.00 0.00 0.00 3.66
2711 2784 1.506025 AGAGGGAGGCTCCTTTGATC 58.494 55.000 31.39 20.26 37.25 2.92
2713 2786 1.203364 AGAAGAGGGAGGCTCCTTTGA 60.203 52.381 31.39 0.00 37.25 2.69
2720 2793 2.466846 GAGAAGAAGAAGAGGGAGGCT 58.533 52.381 0.00 0.00 0.00 4.58
2722 2795 2.115427 GGGAGAAGAAGAAGAGGGAGG 58.885 57.143 0.00 0.00 0.00 4.30
2758 2840 2.383527 GCAGAAGTCAAGGCCGACG 61.384 63.158 0.00 0.00 40.98 5.12
2759 2841 2.383527 CGCAGAAGTCAAGGCCGAC 61.384 63.158 0.00 0.00 36.08 4.79
2786 2868 0.101399 AAGAGTACTGATCGGCGCAG 59.899 55.000 10.83 5.07 39.26 5.18
2787 2869 0.179137 CAAGAGTACTGATCGGCGCA 60.179 55.000 10.83 0.00 0.00 6.09
2790 2872 0.461961 AGGCAAGAGTACTGATCGGC 59.538 55.000 0.00 0.00 0.00 5.54
2797 2879 1.679898 GTGGCCAGGCAAGAGTACT 59.320 57.895 15.19 0.00 0.00 2.73
2816 2898 2.879462 GTAGCTTCCGCCGACGTG 60.879 66.667 0.00 0.00 37.70 4.49
2817 2899 3.048941 GAGTAGCTTCCGCCGACGT 62.049 63.158 0.00 0.00 37.70 4.34
2818 2900 1.434622 TAGAGTAGCTTCCGCCGACG 61.435 60.000 0.00 0.00 36.60 5.12
2820 2902 1.022735 CTTAGAGTAGCTTCCGCCGA 58.977 55.000 0.00 0.00 36.60 5.54
2833 2915 9.703892 CAATAATCCATGGTCTACTTCTTAGAG 57.296 37.037 12.58 0.00 37.51 2.43
2843 2925 6.389869 ACTTCCTTCCAATAATCCATGGTCTA 59.610 38.462 12.58 4.81 37.94 2.59
2846 2928 5.044179 TCACTTCCTTCCAATAATCCATGGT 60.044 40.000 12.58 0.00 37.94 3.55
2847 2929 5.300286 GTCACTTCCTTCCAATAATCCATGG 59.700 44.000 4.97 4.97 38.09 3.66
2856 2941 3.690460 GACATGGTCACTTCCTTCCAAT 58.310 45.455 0.00 0.00 33.55 3.16


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

AutoCloner maintained by Alex Coulton.