Multiple sequence alignment - TraesCS1D01G163600

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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 TraesCS1D01G163600 chr1D 100.000 3089 0 0 1 3089 233920805 233923893 0.000000e+00 5705.0
1 TraesCS1D01G163600 chr1A 95.158 2747 91 23 366 3089 313594968 313592241 0.000000e+00 4298.0
2 TraesCS1D01G163600 chr1A 91.549 213 13 4 6 218 313595152 313594945 3.900000e-74 289.0
3 TraesCS1D01G163600 chr1B 92.854 2603 125 29 404 2990 368674836 368677393 0.000000e+00 3720.0
4 TraesCS1D01G163600 chr1B 99.083 109 1 0 2981 3089 368678978 368679086 2.430000e-46 196.0
5 TraesCS1D01G163600 chr1B 94.444 54 2 1 366 419 368673353 368673405 7.100000e-12 82.4
6 TraesCS1D01G163600 chr3B 95.205 146 7 0 228 373 745722552 745722697 6.660000e-57 231.0
7 TraesCS1D01G163600 chr3B 90.000 150 10 3 228 374 349275336 349275483 4.070000e-44 189.0
8 TraesCS1D01G163600 chr3A 94.595 148 7 1 228 374 272794096 272793949 8.620000e-56 228.0
9 TraesCS1D01G163600 chr7B 92.617 149 9 1 228 374 678852531 678852383 2.410000e-51 213.0
10 TraesCS1D01G163600 chr7B 92.254 142 11 0 232 373 520117079 520117220 5.220000e-48 202.0
11 TraesCS1D01G163600 chr6B 91.892 148 9 2 230 374 42759117 42758970 1.450000e-48 204.0
12 TraesCS1D01G163600 chr5B 91.096 146 11 1 232 375 341549927 341549782 2.430000e-46 196.0
13 TraesCS1D01G163600 chr5D 90.411 146 14 0 228 373 188388642 188388787 3.140000e-45 193.0
14 TraesCS1D01G163600 chr5A 89.510 143 14 1 228 370 242841306 242841165 2.450000e-41 180.0


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 TraesCS1D01G163600 chr1D 233920805 233923893 3088 False 5705.0 5705 100.000000 1 3089 1 chr1D.!!$F1 3088
1 TraesCS1D01G163600 chr1A 313592241 313595152 2911 True 2293.5 4298 93.353500 6 3089 2 chr1A.!!$R1 3083
2 TraesCS1D01G163600 chr1B 368673353 368679086 5733 False 1332.8 3720 95.460333 366 3089 3 chr1B.!!$F1 2723

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
225 226 0.036875 GGGCAGCAGTTAGGACAGTT 59.963 55.0 0.00 0.0 0.0 3.16 F
229 230 0.036875 AGCAGTTAGGACAGTTGGGC 59.963 55.0 0.00 0.0 0.0 5.36 F
325 326 0.108186 TCGGACACTGTGGATGATGC 60.108 55.0 13.09 0.0 0.0 3.91 F
326 327 0.391528 CGGACACTGTGGATGATGCA 60.392 55.0 13.09 0.0 0.0 3.96 F
728 2182 0.452184 AGACGTCACAGGCGATACAG 59.548 55.0 19.50 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 2686 0.395862 TTCCAAGTCCAACGGGCAAA 60.396 50.000 0.0 0.0 0.00 3.68 R
1228 2687 0.821711 CTTCCAAGTCCAACGGGCAA 60.822 55.000 0.0 0.0 0.00 4.52 R
1230 2689 0.822121 AACTTCCAAGTCCAACGGGC 60.822 55.000 0.0 0.0 38.57 6.13 R
1565 3027 1.133823 TGTGGCTCTGTTGAATGGTGT 60.134 47.619 0.0 0.0 0.00 4.16 R
2300 3768 1.407979 AGCTGAGCATTTTAGGCATGC 59.592 47.619 9.9 9.9 46.39 4.06 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
93 94 0.763986 AACAAGCAGGTGCCCCATTT 60.764 50.000 0.00 0.00 43.38 2.32
120 121 3.782244 CGAGCAGCCGCACAGTTC 61.782 66.667 0.00 0.00 42.27 3.01
127 128 2.030562 CCGCACAGTTCCGTTCCT 59.969 61.111 0.00 0.00 0.00 3.36
135 136 3.087781 ACAGTTCCGTTCCTAGTAGACC 58.912 50.000 0.00 0.00 0.00 3.85
139 140 3.278668 TCCGTTCCTAGTAGACCTGAG 57.721 52.381 0.00 0.00 0.00 3.35
189 190 0.861837 GACGTGAACAGTTGAGCCAG 59.138 55.000 0.00 0.00 0.00 4.85
193 194 2.970974 GAACAGTTGAGCCAGCGCC 61.971 63.158 2.29 0.00 34.57 6.53
198 199 2.518112 TTGAGCCAGCGCCAAACA 60.518 55.556 2.29 0.00 34.57 2.83
199 200 2.124060 TTGAGCCAGCGCCAAACAA 61.124 52.632 2.29 1.89 34.57 2.83
200 201 1.670949 TTGAGCCAGCGCCAAACAAA 61.671 50.000 2.29 0.00 34.57 2.83
201 202 1.372128 GAGCCAGCGCCAAACAAAG 60.372 57.895 2.29 0.00 34.57 2.77
202 203 1.795170 GAGCCAGCGCCAAACAAAGA 61.795 55.000 2.29 0.00 34.57 2.52
203 204 1.372128 GCCAGCGCCAAACAAAGAG 60.372 57.895 2.29 0.00 0.00 2.85
204 205 1.286880 CCAGCGCCAAACAAAGAGG 59.713 57.895 2.29 0.00 0.00 3.69
205 206 1.372128 CAGCGCCAAACAAAGAGGC 60.372 57.895 2.29 0.00 44.89 4.70
208 209 2.650778 GCCAAACAAAGAGGCGGG 59.349 61.111 0.00 0.00 38.86 6.13
209 210 2.650778 CCAAACAAAGAGGCGGGC 59.349 61.111 0.00 0.00 0.00 6.13
210 211 2.199652 CCAAACAAAGAGGCGGGCA 61.200 57.895 3.78 0.00 0.00 5.36
211 212 1.286880 CAAACAAAGAGGCGGGCAG 59.713 57.895 3.78 0.00 0.00 4.85
222 223 2.662596 CGGGCAGCAGTTAGGACA 59.337 61.111 0.00 0.00 0.00 4.02
223 224 1.448540 CGGGCAGCAGTTAGGACAG 60.449 63.158 0.00 0.00 0.00 3.51
224 225 1.679898 GGGCAGCAGTTAGGACAGT 59.320 57.895 0.00 0.00 0.00 3.55
225 226 0.036875 GGGCAGCAGTTAGGACAGTT 59.963 55.000 0.00 0.00 0.00 3.16
226 227 1.160137 GGCAGCAGTTAGGACAGTTG 58.840 55.000 0.00 0.00 0.00 3.16
227 228 1.160137 GCAGCAGTTAGGACAGTTGG 58.840 55.000 0.00 0.00 0.00 3.77
228 229 1.813513 CAGCAGTTAGGACAGTTGGG 58.186 55.000 0.00 0.00 0.00 4.12
229 230 0.036875 AGCAGTTAGGACAGTTGGGC 59.963 55.000 0.00 0.00 0.00 5.36
230 231 1.298859 GCAGTTAGGACAGTTGGGCG 61.299 60.000 0.00 0.00 0.00 6.13
231 232 1.003718 AGTTAGGACAGTTGGGCGC 60.004 57.895 0.00 0.00 0.00 6.53
232 233 1.302192 GTTAGGACAGTTGGGCGCA 60.302 57.895 10.83 0.00 0.00 6.09
233 234 1.302192 TTAGGACAGTTGGGCGCAC 60.302 57.895 10.83 6.04 0.00 5.34
234 235 2.046009 TTAGGACAGTTGGGCGCACA 62.046 55.000 9.15 9.15 0.00 4.57
235 236 2.046009 TAGGACAGTTGGGCGCACAA 62.046 55.000 23.74 23.74 0.00 3.33
236 237 2.268076 GGACAGTTGGGCGCACAAT 61.268 57.895 30.28 13.38 32.24 2.71
237 238 1.210155 GACAGTTGGGCGCACAATC 59.790 57.895 30.28 18.64 32.24 2.67
238 239 1.228245 ACAGTTGGGCGCACAATCT 60.228 52.632 30.28 22.99 32.24 2.40
239 240 0.823356 ACAGTTGGGCGCACAATCTT 60.823 50.000 30.28 14.65 32.24 2.40
240 241 0.387622 CAGTTGGGCGCACAATCTTG 60.388 55.000 30.28 22.01 32.24 3.02
241 242 1.734117 GTTGGGCGCACAATCTTGC 60.734 57.895 30.28 11.64 39.28 4.01
242 243 1.902918 TTGGGCGCACAATCTTGCT 60.903 52.632 23.74 0.00 40.62 3.91
243 244 0.607762 TTGGGCGCACAATCTTGCTA 60.608 50.000 23.74 0.00 40.62 3.49
244 245 1.026182 TGGGCGCACAATCTTGCTAG 61.026 55.000 11.60 0.00 40.62 3.42
245 246 0.744414 GGGCGCACAATCTTGCTAGA 60.744 55.000 10.83 0.00 40.62 2.43
246 247 0.375106 GGCGCACAATCTTGCTAGAC 59.625 55.000 10.83 0.00 40.62 2.59
247 248 1.078709 GCGCACAATCTTGCTAGACA 58.921 50.000 0.30 0.00 40.62 3.41
248 249 1.667724 GCGCACAATCTTGCTAGACAT 59.332 47.619 0.30 0.00 40.62 3.06
249 250 2.866156 GCGCACAATCTTGCTAGACATA 59.134 45.455 0.30 0.00 40.62 2.29
250 251 3.060003 GCGCACAATCTTGCTAGACATAG 60.060 47.826 0.30 0.00 40.62 2.23
251 252 4.115516 CGCACAATCTTGCTAGACATAGT 58.884 43.478 0.00 0.00 40.62 2.12
252 253 4.568359 CGCACAATCTTGCTAGACATAGTT 59.432 41.667 0.00 0.00 40.62 2.24
253 254 5.063944 CGCACAATCTTGCTAGACATAGTTT 59.936 40.000 0.00 0.00 40.62 2.66
254 255 6.481984 GCACAATCTTGCTAGACATAGTTTC 58.518 40.000 0.00 0.00 39.59 2.78
255 256 6.092670 GCACAATCTTGCTAGACATAGTTTCA 59.907 38.462 0.00 0.00 39.59 2.69
256 257 7.361201 GCACAATCTTGCTAGACATAGTTTCAA 60.361 37.037 0.00 0.00 39.59 2.69
257 258 8.671921 CACAATCTTGCTAGACATAGTTTCAAT 58.328 33.333 0.00 0.00 31.99 2.57
258 259 9.236006 ACAATCTTGCTAGACATAGTTTCAATT 57.764 29.630 0.00 0.00 31.99 2.32
292 293 7.601705 TTTTTATTTGGGATGATGATCCTCC 57.398 36.000 11.26 8.09 46.88 4.30
296 297 0.327591 GGGATGATGATCCTCCCAGC 59.672 60.000 25.30 3.85 46.73 4.85
297 298 1.360185 GGATGATGATCCTCCCAGCT 58.640 55.000 3.60 0.00 44.58 4.24
298 299 1.704070 GGATGATGATCCTCCCAGCTT 59.296 52.381 3.60 0.00 44.58 3.74
299 300 2.107901 GGATGATGATCCTCCCAGCTTT 59.892 50.000 3.60 0.00 44.58 3.51
300 301 3.436180 GGATGATGATCCTCCCAGCTTTT 60.436 47.826 3.60 0.00 44.58 2.27
301 302 3.744940 TGATGATCCTCCCAGCTTTTT 57.255 42.857 0.00 0.00 0.00 1.94
302 303 4.860802 TGATGATCCTCCCAGCTTTTTA 57.139 40.909 0.00 0.00 0.00 1.52
303 304 5.191727 TGATGATCCTCCCAGCTTTTTAA 57.808 39.130 0.00 0.00 0.00 1.52
304 305 5.769835 TGATGATCCTCCCAGCTTTTTAAT 58.230 37.500 0.00 0.00 0.00 1.40
305 306 6.197168 TGATGATCCTCCCAGCTTTTTAATT 58.803 36.000 0.00 0.00 0.00 1.40
306 307 6.669154 TGATGATCCTCCCAGCTTTTTAATTT 59.331 34.615 0.00 0.00 0.00 1.82
307 308 6.530019 TGATCCTCCCAGCTTTTTAATTTC 57.470 37.500 0.00 0.00 0.00 2.17
308 309 5.125417 TGATCCTCCCAGCTTTTTAATTTCG 59.875 40.000 0.00 0.00 0.00 3.46
309 310 3.761752 TCCTCCCAGCTTTTTAATTTCGG 59.238 43.478 0.00 0.00 0.00 4.30
310 311 3.761752 CCTCCCAGCTTTTTAATTTCGGA 59.238 43.478 0.00 0.00 0.00 4.55
311 312 4.380550 CCTCCCAGCTTTTTAATTTCGGAC 60.381 45.833 0.00 0.00 0.00 4.79
312 313 4.145807 TCCCAGCTTTTTAATTTCGGACA 58.854 39.130 0.00 0.00 0.00 4.02
313 314 4.022676 TCCCAGCTTTTTAATTTCGGACAC 60.023 41.667 0.00 0.00 0.00 3.67
314 315 4.022329 CCCAGCTTTTTAATTTCGGACACT 60.022 41.667 0.00 0.00 0.00 3.55
315 316 4.917415 CCAGCTTTTTAATTTCGGACACTG 59.083 41.667 0.00 0.00 0.00 3.66
316 317 5.507315 CCAGCTTTTTAATTTCGGACACTGT 60.507 40.000 0.00 0.00 0.00 3.55
317 318 5.399301 CAGCTTTTTAATTTCGGACACTGTG 59.601 40.000 6.19 6.19 0.00 3.66
318 319 4.679654 GCTTTTTAATTTCGGACACTGTGG 59.320 41.667 13.09 0.00 0.00 4.17
319 320 5.506649 GCTTTTTAATTTCGGACACTGTGGA 60.507 40.000 13.09 0.00 0.00 4.02
320 321 6.642707 TTTTTAATTTCGGACACTGTGGAT 57.357 33.333 13.09 0.00 0.00 3.41
321 322 5.621197 TTTAATTTCGGACACTGTGGATG 57.379 39.130 13.09 1.04 0.00 3.51
322 323 3.417069 AATTTCGGACACTGTGGATGA 57.583 42.857 13.09 3.52 0.00 2.92
323 324 3.634397 ATTTCGGACACTGTGGATGAT 57.366 42.857 13.09 0.00 0.00 2.45
324 325 2.385013 TTCGGACACTGTGGATGATG 57.615 50.000 13.09 0.00 0.00 3.07
325 326 0.108186 TCGGACACTGTGGATGATGC 60.108 55.000 13.09 0.00 0.00 3.91
326 327 0.391528 CGGACACTGTGGATGATGCA 60.392 55.000 13.09 0.00 0.00 3.96
327 328 1.825090 GGACACTGTGGATGATGCAA 58.175 50.000 13.09 0.00 0.00 4.08
328 329 1.470098 GGACACTGTGGATGATGCAAC 59.530 52.381 13.09 0.00 0.00 4.17
329 330 2.430465 GACACTGTGGATGATGCAACT 58.570 47.619 13.09 0.00 0.00 3.16
330 331 2.816087 GACACTGTGGATGATGCAACTT 59.184 45.455 13.09 0.00 0.00 2.66
331 332 3.225104 ACACTGTGGATGATGCAACTTT 58.775 40.909 13.09 0.00 0.00 2.66
332 333 3.005050 ACACTGTGGATGATGCAACTTTG 59.995 43.478 13.09 0.00 0.00 2.77
333 334 3.253921 CACTGTGGATGATGCAACTTTGA 59.746 43.478 0.00 0.00 0.00 2.69
334 335 4.082408 CACTGTGGATGATGCAACTTTGAT 60.082 41.667 0.00 0.00 0.00 2.57
335 336 4.525487 ACTGTGGATGATGCAACTTTGATT 59.475 37.500 0.00 0.00 0.00 2.57
336 337 5.011329 ACTGTGGATGATGCAACTTTGATTT 59.989 36.000 0.00 0.00 0.00 2.17
337 338 5.231702 TGTGGATGATGCAACTTTGATTTG 58.768 37.500 0.00 0.00 0.00 2.32
338 339 5.010820 TGTGGATGATGCAACTTTGATTTGA 59.989 36.000 0.00 0.00 0.00 2.69
339 340 5.575606 GTGGATGATGCAACTTTGATTTGAG 59.424 40.000 0.00 0.00 0.00 3.02
340 341 5.244402 TGGATGATGCAACTTTGATTTGAGT 59.756 36.000 0.00 0.00 0.00 3.41
341 342 6.161381 GGATGATGCAACTTTGATTTGAGTT 58.839 36.000 0.00 0.00 36.58 3.01
342 343 6.647895 GGATGATGCAACTTTGATTTGAGTTT 59.352 34.615 0.00 0.00 34.04 2.66
343 344 7.814107 GGATGATGCAACTTTGATTTGAGTTTA 59.186 33.333 0.00 0.00 34.04 2.01
344 345 9.195411 GATGATGCAACTTTGATTTGAGTTTAA 57.805 29.630 0.00 0.00 34.04 1.52
345 346 9.715121 ATGATGCAACTTTGATTTGAGTTTAAT 57.285 25.926 0.00 0.00 34.04 1.40
353 354 9.180678 ACTTTGATTTGAGTTTAATAAAGTGCG 57.819 29.630 0.00 0.00 36.22 5.34
354 355 7.561237 TTGATTTGAGTTTAATAAAGTGCGC 57.439 32.000 0.00 0.00 0.00 6.09
355 356 6.090129 TGATTTGAGTTTAATAAAGTGCGCC 58.910 36.000 4.18 0.00 0.00 6.53
356 357 5.440234 TTTGAGTTTAATAAAGTGCGCCA 57.560 34.783 4.18 0.00 0.00 5.69
357 358 5.440234 TTGAGTTTAATAAAGTGCGCCAA 57.560 34.783 4.18 0.00 0.00 4.52
358 359 5.041951 TGAGTTTAATAAAGTGCGCCAAG 57.958 39.130 4.18 0.00 0.00 3.61
359 360 4.517453 TGAGTTTAATAAAGTGCGCCAAGT 59.483 37.500 4.18 0.00 0.00 3.16
360 361 4.794169 AGTTTAATAAAGTGCGCCAAGTG 58.206 39.130 4.18 0.00 0.00 3.16
361 362 3.840890 TTAATAAAGTGCGCCAAGTGG 57.159 42.857 4.18 0.00 38.53 4.00
362 363 1.616159 AATAAAGTGCGCCAAGTGGT 58.384 45.000 4.18 0.00 37.57 4.16
363 364 1.616159 ATAAAGTGCGCCAAGTGGTT 58.384 45.000 4.18 0.00 37.57 3.67
364 365 1.394618 TAAAGTGCGCCAAGTGGTTT 58.605 45.000 4.18 0.00 37.57 3.27
365 366 1.394618 AAAGTGCGCCAAGTGGTTTA 58.605 45.000 4.18 0.00 37.57 2.01
366 367 1.394618 AAGTGCGCCAAGTGGTTTAA 58.605 45.000 4.18 0.00 37.57 1.52
367 368 1.394618 AGTGCGCCAAGTGGTTTAAA 58.605 45.000 4.18 0.00 37.57 1.52
368 369 1.751924 AGTGCGCCAAGTGGTTTAAAA 59.248 42.857 4.18 0.00 37.57 1.52
495 1941 1.165907 TCCAGCAAAGCAACAGGTCG 61.166 55.000 0.00 0.00 0.00 4.79
706 2158 2.203167 CAGCTGATGCGGGCAGAT 60.203 61.111 8.42 0.00 45.42 2.90
720 2172 1.354040 GCAGATTCAGACGTCACAGG 58.646 55.000 19.50 4.26 0.00 4.00
728 2182 0.452184 AGACGTCACAGGCGATACAG 59.548 55.000 19.50 0.00 0.00 2.74
743 2197 3.937079 CGATACAGGGGAAAGTAAACACC 59.063 47.826 0.00 0.00 0.00 4.16
744 2198 4.563993 CGATACAGGGGAAAGTAAACACCA 60.564 45.833 0.00 0.00 31.04 4.17
806 2260 1.010935 CATCGCTCAACGTCAGTGCT 61.011 55.000 11.51 0.00 44.19 4.40
933 2392 2.769095 GGCAGAGTATTCTCAACTCCCT 59.231 50.000 1.92 0.00 43.64 4.20
982 2441 4.135153 CTCCGCCCACTCCACTCG 62.135 72.222 0.00 0.00 0.00 4.18
1076 2535 2.599645 ATTGCTCGCGCCTGATCCTT 62.600 55.000 0.00 0.00 34.43 3.36
1197 2656 3.304257 CGCGGATATCTACGGTAACAGTT 60.304 47.826 0.00 0.00 0.00 3.16
1225 2684 1.035139 CCACCTCTGCTGCTTGTTTT 58.965 50.000 0.00 0.00 0.00 2.43
1227 2686 1.406539 CACCTCTGCTGCTTGTTTTGT 59.593 47.619 0.00 0.00 0.00 2.83
1228 2687 2.102578 ACCTCTGCTGCTTGTTTTGTT 58.897 42.857 0.00 0.00 0.00 2.83
1229 2688 2.497273 ACCTCTGCTGCTTGTTTTGTTT 59.503 40.909 0.00 0.00 0.00 2.83
1230 2689 2.861935 CCTCTGCTGCTTGTTTTGTTTG 59.138 45.455 0.00 0.00 0.00 2.93
1231 2690 2.270047 TCTGCTGCTTGTTTTGTTTGC 58.730 42.857 0.00 0.00 0.00 3.68
1282 2742 7.147724 TGGTATTTCCATCGAAGAAGACAGTAT 60.148 37.037 13.17 3.77 43.58 2.12
1285 2745 3.447229 TCCATCGAAGAAGACAGTATGCA 59.553 43.478 0.00 0.00 43.58 3.96
1335 2795 6.790285 ATTCTTGCATCATTTGTTTTCCAC 57.210 33.333 0.00 0.00 0.00 4.02
1425 2885 6.055588 ACCATGTTAGGTGGAATTATTCTCG 58.944 40.000 4.87 0.00 41.30 4.04
1475 2936 5.994054 ACAGTTCAATAGAGCATCGCATATT 59.006 36.000 0.00 0.00 42.67 1.28
1482 2943 8.570488 TCAATAGAGCATCGCATATTTCAAATT 58.430 29.630 0.00 0.00 42.67 1.82
1503 2964 4.637771 GCCATCGGCTTTAGGTGT 57.362 55.556 0.00 0.00 46.69 4.16
2199 3667 9.787435 TGACTTTGTACCATTACATCTAAAGTT 57.213 29.630 0.00 0.00 36.40 2.66
2279 3747 4.094830 TCTATACACGCCTACCTCATCA 57.905 45.455 0.00 0.00 0.00 3.07
2402 3870 3.199727 TCATTGAAGGCATGCACCTACTA 59.800 43.478 21.36 3.38 39.93 1.82
2413 3881 5.409826 GCATGCACCTACTACCAGATTAATC 59.590 44.000 14.21 7.41 0.00 1.75
2683 4152 5.123936 CCTATTACTAGGGTTGGCAGAAAC 58.876 45.833 0.00 0.00 40.91 2.78
2799 4272 6.315393 GGTCGTCATTGAGTAAAACCATATGT 59.685 38.462 1.24 0.00 0.00 2.29
2828 4301 6.820335 TCTTGTACTGTGGATGAATATCTGG 58.180 40.000 0.00 0.00 33.68 3.86
2925 4398 7.285401 TGAATAGAGCTCAACAAAAGGAAAACT 59.715 33.333 17.77 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.367321 GCCAGTCTTCTACCTCCTAGTT 58.633 50.000 0.00 0.00 0.00 2.24
1 2 2.358405 GGCCAGTCTTCTACCTCCTAGT 60.358 54.545 0.00 0.00 0.00 2.57
2 3 2.312390 GGCCAGTCTTCTACCTCCTAG 58.688 57.143 0.00 0.00 0.00 3.02
3 4 1.644337 TGGCCAGTCTTCTACCTCCTA 59.356 52.381 0.00 0.00 0.00 2.94
4 5 0.413832 TGGCCAGTCTTCTACCTCCT 59.586 55.000 0.00 0.00 0.00 3.69
5 6 0.827368 CTGGCCAGTCTTCTACCTCC 59.173 60.000 25.53 0.00 0.00 4.30
6 7 1.562783 ACTGGCCAGTCTTCTACCTC 58.437 55.000 33.20 0.00 36.92 3.85
7 8 3.796866 ACTGGCCAGTCTTCTACCT 57.203 52.632 33.20 6.75 36.92 3.08
28 29 1.827969 CCACAAGTTGGTTGGGTTTGA 59.172 47.619 7.96 0.00 37.96 2.69
120 121 1.677052 GCTCAGGTCTACTAGGAACGG 59.323 57.143 0.00 0.00 0.00 4.44
160 161 6.103997 TCAACTGTTCACGTCTACTCTTTTT 58.896 36.000 0.00 0.00 0.00 1.94
161 162 5.657474 TCAACTGTTCACGTCTACTCTTTT 58.343 37.500 0.00 0.00 0.00 2.27
162 163 5.258456 TCAACTGTTCACGTCTACTCTTT 57.742 39.130 0.00 0.00 0.00 2.52
163 164 4.793353 GCTCAACTGTTCACGTCTACTCTT 60.793 45.833 0.00 0.00 0.00 2.85
182 183 2.074230 CTTTGTTTGGCGCTGGCTCA 62.074 55.000 7.64 0.00 39.81 4.26
193 194 1.286880 CTGCCCGCCTCTTTGTTTG 59.713 57.895 0.00 0.00 0.00 2.93
198 199 2.124507 TAACTGCTGCCCGCCTCTTT 62.125 55.000 0.00 0.00 38.05 2.52
199 200 2.527951 CTAACTGCTGCCCGCCTCTT 62.528 60.000 0.00 0.00 38.05 2.85
200 201 3.003173 TAACTGCTGCCCGCCTCT 61.003 61.111 0.00 0.00 38.05 3.69
201 202 2.512515 CTAACTGCTGCCCGCCTC 60.513 66.667 0.00 0.00 38.05 4.70
202 203 4.101448 CCTAACTGCTGCCCGCCT 62.101 66.667 0.00 0.00 38.05 5.52
203 204 4.096003 TCCTAACTGCTGCCCGCC 62.096 66.667 0.00 0.00 38.05 6.13
204 205 2.820037 GTCCTAACTGCTGCCCGC 60.820 66.667 0.00 0.00 39.77 6.13
205 206 1.448540 CTGTCCTAACTGCTGCCCG 60.449 63.158 0.00 0.00 0.00 6.13
206 207 0.036875 AACTGTCCTAACTGCTGCCC 59.963 55.000 0.00 0.00 0.00 5.36
207 208 1.160137 CAACTGTCCTAACTGCTGCC 58.840 55.000 0.00 0.00 0.00 4.85
208 209 1.160137 CCAACTGTCCTAACTGCTGC 58.840 55.000 0.00 0.00 0.00 5.25
209 210 1.813513 CCCAACTGTCCTAACTGCTG 58.186 55.000 0.00 0.00 0.00 4.41
210 211 0.036875 GCCCAACTGTCCTAACTGCT 59.963 55.000 0.00 0.00 0.00 4.24
211 212 1.298859 CGCCCAACTGTCCTAACTGC 61.299 60.000 0.00 0.00 0.00 4.40
212 213 1.298859 GCGCCCAACTGTCCTAACTG 61.299 60.000 0.00 0.00 0.00 3.16
213 214 1.003718 GCGCCCAACTGTCCTAACT 60.004 57.895 0.00 0.00 0.00 2.24
214 215 1.302192 TGCGCCCAACTGTCCTAAC 60.302 57.895 4.18 0.00 0.00 2.34
215 216 1.302192 GTGCGCCCAACTGTCCTAA 60.302 57.895 4.18 0.00 0.00 2.69
216 217 2.046009 TTGTGCGCCCAACTGTCCTA 62.046 55.000 4.18 0.00 0.00 2.94
217 218 2.697147 ATTGTGCGCCCAACTGTCCT 62.697 55.000 7.66 0.00 0.00 3.85
218 219 2.200170 GATTGTGCGCCCAACTGTCC 62.200 60.000 7.66 0.00 0.00 4.02
219 220 1.210155 GATTGTGCGCCCAACTGTC 59.790 57.895 7.66 0.00 0.00 3.51
220 221 0.823356 AAGATTGTGCGCCCAACTGT 60.823 50.000 7.66 0.00 0.00 3.55
221 222 0.387622 CAAGATTGTGCGCCCAACTG 60.388 55.000 7.66 2.15 0.00 3.16
222 223 1.959085 CAAGATTGTGCGCCCAACT 59.041 52.632 7.66 4.73 0.00 3.16
223 224 1.734117 GCAAGATTGTGCGCCCAAC 60.734 57.895 7.66 2.31 34.21 3.77
224 225 2.650196 GCAAGATTGTGCGCCCAA 59.350 55.556 7.99 7.99 34.21 4.12
230 231 6.092670 TGAAACTATGTCTAGCAAGATTGTGC 59.907 38.462 0.00 0.00 45.28 4.57
231 232 7.601073 TGAAACTATGTCTAGCAAGATTGTG 57.399 36.000 0.00 0.00 33.30 3.33
232 233 8.798859 ATTGAAACTATGTCTAGCAAGATTGT 57.201 30.769 0.00 0.00 33.30 2.71
279 280 3.505480 AAAGCTGGGAGGATCATCATC 57.495 47.619 9.94 1.52 36.25 2.92
280 281 3.967467 AAAAGCTGGGAGGATCATCAT 57.033 42.857 9.94 0.00 36.25 2.45
281 282 3.744940 AAAAAGCTGGGAGGATCATCA 57.255 42.857 9.94 0.00 36.25 3.07
282 283 6.721704 AATTAAAAAGCTGGGAGGATCATC 57.278 37.500 0.00 0.00 36.25 2.92
283 284 6.183360 CGAAATTAAAAAGCTGGGAGGATCAT 60.183 38.462 0.00 0.00 36.25 2.45
284 285 5.125417 CGAAATTAAAAAGCTGGGAGGATCA 59.875 40.000 0.00 0.00 36.25 2.92
285 286 5.450550 CCGAAATTAAAAAGCTGGGAGGATC 60.451 44.000 0.00 0.00 0.00 3.36
286 287 4.402474 CCGAAATTAAAAAGCTGGGAGGAT 59.598 41.667 0.00 0.00 0.00 3.24
287 288 3.761752 CCGAAATTAAAAAGCTGGGAGGA 59.238 43.478 0.00 0.00 0.00 3.71
288 289 3.761752 TCCGAAATTAAAAAGCTGGGAGG 59.238 43.478 0.00 0.00 0.00 4.30
289 290 4.217550 TGTCCGAAATTAAAAAGCTGGGAG 59.782 41.667 0.00 0.00 0.00 4.30
290 291 4.022676 GTGTCCGAAATTAAAAAGCTGGGA 60.023 41.667 0.00 0.00 0.00 4.37
291 292 4.022329 AGTGTCCGAAATTAAAAAGCTGGG 60.022 41.667 0.00 0.00 0.00 4.45
292 293 4.917415 CAGTGTCCGAAATTAAAAAGCTGG 59.083 41.667 0.00 0.00 0.00 4.85
293 294 5.399301 CACAGTGTCCGAAATTAAAAAGCTG 59.601 40.000 0.00 0.00 0.00 4.24
294 295 5.507315 CCACAGTGTCCGAAATTAAAAAGCT 60.507 40.000 0.00 0.00 0.00 3.74
295 296 4.679654 CCACAGTGTCCGAAATTAAAAAGC 59.320 41.667 0.00 0.00 0.00 3.51
296 297 6.067263 TCCACAGTGTCCGAAATTAAAAAG 57.933 37.500 0.00 0.00 0.00 2.27
297 298 6.263392 TCATCCACAGTGTCCGAAATTAAAAA 59.737 34.615 0.00 0.00 0.00 1.94
298 299 5.765677 TCATCCACAGTGTCCGAAATTAAAA 59.234 36.000 0.00 0.00 0.00 1.52
299 300 5.309638 TCATCCACAGTGTCCGAAATTAAA 58.690 37.500 0.00 0.00 0.00 1.52
300 301 4.900684 TCATCCACAGTGTCCGAAATTAA 58.099 39.130 0.00 0.00 0.00 1.40
301 302 4.545208 TCATCCACAGTGTCCGAAATTA 57.455 40.909 0.00 0.00 0.00 1.40
302 303 3.417069 TCATCCACAGTGTCCGAAATT 57.583 42.857 0.00 0.00 0.00 1.82
303 304 3.273434 CATCATCCACAGTGTCCGAAAT 58.727 45.455 0.00 0.00 0.00 2.17
304 305 2.698803 CATCATCCACAGTGTCCGAAA 58.301 47.619 0.00 0.00 0.00 3.46
305 306 1.675714 GCATCATCCACAGTGTCCGAA 60.676 52.381 0.00 0.00 0.00 4.30
306 307 0.108186 GCATCATCCACAGTGTCCGA 60.108 55.000 0.00 0.00 0.00 4.55
307 308 0.391528 TGCATCATCCACAGTGTCCG 60.392 55.000 0.00 0.00 0.00 4.79
308 309 1.470098 GTTGCATCATCCACAGTGTCC 59.530 52.381 0.00 0.00 0.00 4.02
309 310 2.430465 AGTTGCATCATCCACAGTGTC 58.570 47.619 0.00 0.00 0.00 3.67
310 311 2.574006 AGTTGCATCATCCACAGTGT 57.426 45.000 0.00 0.00 0.00 3.55
311 312 3.253921 TCAAAGTTGCATCATCCACAGTG 59.746 43.478 0.00 0.00 0.00 3.66
312 313 3.489355 TCAAAGTTGCATCATCCACAGT 58.511 40.909 0.00 0.00 0.00 3.55
313 314 4.713824 ATCAAAGTTGCATCATCCACAG 57.286 40.909 0.00 0.00 0.00 3.66
314 315 5.010820 TCAAATCAAAGTTGCATCATCCACA 59.989 36.000 0.00 0.00 0.00 4.17
315 316 5.472148 TCAAATCAAAGTTGCATCATCCAC 58.528 37.500 0.00 0.00 0.00 4.02
316 317 5.244402 ACTCAAATCAAAGTTGCATCATCCA 59.756 36.000 0.00 0.00 0.00 3.41
317 318 5.717119 ACTCAAATCAAAGTTGCATCATCC 58.283 37.500 0.00 0.00 0.00 3.51
318 319 7.647907 AAACTCAAATCAAAGTTGCATCATC 57.352 32.000 0.00 0.00 35.93 2.92
319 320 9.715121 ATTAAACTCAAATCAAAGTTGCATCAT 57.285 25.926 0.00 0.00 35.93 2.45
327 328 9.180678 CGCACTTTATTAAACTCAAATCAAAGT 57.819 29.630 0.00 0.00 35.86 2.66
328 329 8.155923 GCGCACTTTATTAAACTCAAATCAAAG 58.844 33.333 0.30 0.00 0.00 2.77
329 330 7.115663 GGCGCACTTTATTAAACTCAAATCAAA 59.884 33.333 10.83 0.00 0.00 2.69
330 331 6.584563 GGCGCACTTTATTAAACTCAAATCAA 59.415 34.615 10.83 0.00 0.00 2.57
331 332 6.090129 GGCGCACTTTATTAAACTCAAATCA 58.910 36.000 10.83 0.00 0.00 2.57
332 333 6.090129 TGGCGCACTTTATTAAACTCAAATC 58.910 36.000 10.83 0.00 0.00 2.17
333 334 6.019779 TGGCGCACTTTATTAAACTCAAAT 57.980 33.333 10.83 0.00 0.00 2.32
334 335 5.440234 TGGCGCACTTTATTAAACTCAAA 57.560 34.783 10.83 0.00 0.00 2.69
335 336 5.009210 ACTTGGCGCACTTTATTAAACTCAA 59.991 36.000 10.83 0.00 0.00 3.02
336 337 4.517453 ACTTGGCGCACTTTATTAAACTCA 59.483 37.500 10.83 0.00 0.00 3.41
337 338 4.851558 CACTTGGCGCACTTTATTAAACTC 59.148 41.667 10.83 0.00 0.00 3.01
338 339 4.320935 CCACTTGGCGCACTTTATTAAACT 60.321 41.667 10.83 0.00 0.00 2.66
339 340 3.917985 CCACTTGGCGCACTTTATTAAAC 59.082 43.478 10.83 0.00 0.00 2.01
340 341 3.570550 ACCACTTGGCGCACTTTATTAAA 59.429 39.130 10.83 0.00 39.32 1.52
341 342 3.150767 ACCACTTGGCGCACTTTATTAA 58.849 40.909 10.83 0.00 39.32 1.40
342 343 2.785562 ACCACTTGGCGCACTTTATTA 58.214 42.857 10.83 0.00 39.32 0.98
343 344 1.616159 ACCACTTGGCGCACTTTATT 58.384 45.000 10.83 0.00 39.32 1.40
344 345 1.616159 AACCACTTGGCGCACTTTAT 58.384 45.000 10.83 0.00 39.32 1.40
345 346 1.394618 AAACCACTTGGCGCACTTTA 58.605 45.000 10.83 0.00 39.32 1.85
346 347 1.394618 TAAACCACTTGGCGCACTTT 58.605 45.000 10.83 0.00 39.32 2.66
347 348 1.394618 TTAAACCACTTGGCGCACTT 58.605 45.000 10.83 0.00 39.32 3.16
348 349 1.394618 TTTAAACCACTTGGCGCACT 58.605 45.000 10.83 0.00 39.32 4.40
349 350 2.211353 TTTTAAACCACTTGGCGCAC 57.789 45.000 10.83 0.00 39.32 5.34
350 351 2.961526 TTTTTAAACCACTTGGCGCA 57.038 40.000 10.83 0.00 39.32 6.09
372 373 1.207488 TCATACCTGCTGCCCACCTT 61.207 55.000 0.00 0.00 0.00 3.50
706 2158 1.135489 GTATCGCCTGTGACGTCTGAA 60.135 52.381 17.92 1.12 0.00 3.02
720 2172 3.373130 GTGTTTACTTTCCCCTGTATCGC 59.627 47.826 0.00 0.00 0.00 4.58
728 2182 1.241165 CGGTGGTGTTTACTTTCCCC 58.759 55.000 0.00 0.00 0.00 4.81
743 2197 2.202570 CGGAAGAGGTACGCGGTG 60.203 66.667 12.47 0.00 0.00 4.94
744 2198 4.125695 GCGGAAGAGGTACGCGGT 62.126 66.667 12.47 0.00 43.98 5.68
806 2260 2.353406 GCTCTTGCTGAACGGTAGGTTA 60.353 50.000 0.00 0.00 36.07 2.85
933 2392 2.606587 GGGAAGGGAAGGCTGAGCA 61.607 63.158 6.82 0.00 0.00 4.26
1028 2487 1.900245 TAACCCAAGAAAGAACCCGC 58.100 50.000 0.00 0.00 0.00 6.13
1076 2535 3.472652 GGCCGAACATACATACAATCCA 58.527 45.455 0.00 0.00 0.00 3.41
1197 2656 3.160585 CAGAGGTGGGAGGTGCAA 58.839 61.111 0.00 0.00 0.00 4.08
1225 2684 1.388065 CCAAGTCCAACGGGCAAACA 61.388 55.000 0.00 0.00 0.00 2.83
1227 2686 0.395862 TTCCAAGTCCAACGGGCAAA 60.396 50.000 0.00 0.00 0.00 3.68
1228 2687 0.821711 CTTCCAAGTCCAACGGGCAA 60.822 55.000 0.00 0.00 0.00 4.52
1229 2688 1.228124 CTTCCAAGTCCAACGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
1230 2689 0.822121 AACTTCCAAGTCCAACGGGC 60.822 55.000 0.00 0.00 38.57 6.13
1231 2690 1.687563 AAACTTCCAAGTCCAACGGG 58.312 50.000 0.00 0.00 38.57 5.28
1285 2745 2.295885 GCCAGCTTCTGCAACTATCAT 58.704 47.619 0.00 0.00 42.74 2.45
1335 2795 6.343703 TCAGATACATGAACCACAGATTGAG 58.656 40.000 0.00 0.00 0.00 3.02
1425 2885 3.469899 TCTTTATGTCAATGTGTGCGC 57.530 42.857 0.00 0.00 0.00 6.09
1503 2964 7.707624 AACATGATTTTTCCTCTCATGCTTA 57.292 32.000 0.00 0.00 46.51 3.09
1508 2969 6.604795 CCACCTAACATGATTTTTCCTCTCAT 59.395 38.462 0.00 0.00 0.00 2.90
1565 3027 1.133823 TGTGGCTCTGTTGAATGGTGT 60.134 47.619 0.00 0.00 0.00 4.16
1822 3285 5.329035 AGGTGTGTATTGCATCATTTTCC 57.671 39.130 0.00 0.00 0.00 3.13
2279 3747 7.705325 GCATGCATGAAGAACTGAAGATAATTT 59.295 33.333 30.64 0.00 0.00 1.82
2300 3768 1.407979 AGCTGAGCATTTTAGGCATGC 59.592 47.619 9.90 9.90 46.39 4.06
2429 3897 6.867293 ACGTCTGTTCCTCTGTTTCTTATAAC 59.133 38.462 0.00 0.00 0.00 1.89
2447 3915 2.691526 TGTCAACCTTCTGTACGTCTGT 59.308 45.455 0.00 0.00 0.00 3.41
2547 4015 8.057536 TGTTTTGCTTAGTGGTTCTCTTTTAA 57.942 30.769 0.00 0.00 0.00 1.52
2799 4272 5.497464 TTCATCCACAGTACAAGATGGAA 57.503 39.130 10.34 4.49 44.25 3.53
2828 4301 8.883731 ACTAGTCATCAATATTGTTTGTAGTGC 58.116 33.333 14.97 5.41 0.00 4.40
2925 4398 7.057894 AGTCCTAATTCCTACACACACAAAAA 58.942 34.615 0.00 0.00 0.00 1.94
2930 4403 7.553334 TCAATAGTCCTAATTCCTACACACAC 58.447 38.462 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.