Multiple sequence alignment - TraesCS6D01G387600

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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 TraesCS6D01G387600 chr6D 100.000 2513 0 0 1 2513 464482023 464484535 0.000000e+00 4641.0
1 TraesCS6D01G387600 chr6D 81.013 316 53 7 2047 2359 432362856 432362545 6.940000e-61 244.0
2 TraesCS6D01G387600 chr6A 90.818 1797 104 25 405 2173 610984305 610986068 0.000000e+00 2348.0
3 TraesCS6D01G387600 chr6A 91.539 1702 100 15 486 2173 610959915 610961586 0.000000e+00 2305.0
4 TraesCS6D01G387600 chr6A 90.105 1435 93 19 405 1814 610954931 610956341 0.000000e+00 1818.0
5 TraesCS6D01G387600 chr6A 92.952 454 26 3 1906 2359 610956369 610956816 0.000000e+00 656.0
6 TraesCS6D01G387600 chr6A 93.734 383 23 1 1977 2359 611037563 611037944 7.800000e-160 573.0
7 TraesCS6D01G387600 chr6A 91.155 407 30 2 682 1088 611035743 611036143 4.730000e-152 547.0
8 TraesCS6D01G387600 chr6A 95.395 152 7 0 2360 2511 610956848 610956999 2.500000e-60 243.0
9 TraesCS6D01G387600 chr6A 95.395 152 7 0 2360 2511 611037976 611038127 2.500000e-60 243.0
10 TraesCS6D01G387600 chr6A 95.556 135 4 1 276 408 610954741 610954875 5.440000e-52 215.0
11 TraesCS6D01G387600 chr6A 92.913 127 5 2 2 127 610954638 610954761 5.520000e-42 182.0
12 TraesCS6D01G387600 chr6B 89.544 1339 107 13 405 1726 708227345 708228667 0.000000e+00 1666.0
13 TraesCS6D01G387600 chr6B 90.046 864 65 13 870 1726 708233044 708233893 0.000000e+00 1099.0
14 TraesCS6D01G387600 chr6B 91.003 778 49 12 758 1529 708255785 708256547 0.000000e+00 1029.0
15 TraesCS6D01G387600 chr6B 88.009 442 33 12 405 829 708232595 708233033 2.880000e-139 505.0
16 TraesCS6D01G387600 chr6B 86.452 310 24 9 1731 2029 708240992 708241294 8.670000e-85 324.0
17 TraesCS6D01G387600 chr6B 84.242 330 51 1 2031 2359 437797124 437797453 1.120000e-83 320.0
18 TraesCS6D01G387600 chr6B 83.601 311 30 8 1731 2029 708260024 708260325 3.190000e-69 272.0
19 TraesCS6D01G387600 chr6B 93.038 158 11 0 129 286 537827503 537827660 5.410000e-57 231.0
20 TraesCS6D01G387600 chr6B 97.015 134 4 0 275 408 708227157 708227290 2.520000e-55 226.0
21 TraesCS6D01G387600 chr6B 97.521 121 3 0 288 408 708232421 708232541 9.110000e-50 207.0
22 TraesCS6D01G387600 chr6B 95.312 128 5 1 1 127 708227051 708227178 4.240000e-48 202.0
23 TraesCS6D01G387600 chrUn 88.688 1052 76 18 405 1440 404582920 404583944 0.000000e+00 1243.0
24 TraesCS6D01G387600 chrUn 93.769 642 24 8 1545 2173 426112849 426113487 0.000000e+00 950.0
25 TraesCS6D01G387600 chrUn 95.556 135 4 1 276 408 404582730 404582864 5.440000e-52 215.0
26 TraesCS6D01G387600 chrUn 92.913 127 5 2 2 127 404582627 404582750 5.520000e-42 182.0
27 TraesCS6D01G387600 chr2D 81.892 740 62 34 856 1569 145683505 145682812 2.180000e-155 558.0
28 TraesCS6D01G387600 chr2A 81.935 703 62 36 887 1572 156514481 156515135 3.680000e-148 534.0
29 TraesCS6D01G387600 chr2B 89.873 237 18 3 1297 1527 121382908 121382672 1.460000e-77 300.0
30 TraesCS6D01G387600 chr2B 83.492 315 49 3 2046 2359 405288385 405288697 8.790000e-75 291.0
31 TraesCS6D01G387600 chr2B 93.252 163 10 1 121 282 550810587 550810425 3.230000e-59 239.0
32 TraesCS6D01G387600 chr2B 91.667 144 11 1 143 285 160280298 160280441 5.480000e-47 198.0
33 TraesCS6D01G387600 chr2B 92.537 134 10 0 149 282 104941223 104941090 2.550000e-45 193.0
34 TraesCS6D01G387600 chr7B 81.873 331 39 11 2032 2358 703319683 703319996 2.480000e-65 259.0
35 TraesCS6D01G387600 chr5B 95.484 155 7 0 129 283 597296150 597296304 5.370000e-62 248.0
36 TraesCS6D01G387600 chr4B 94.268 157 7 2 129 284 340859018 340859173 3.230000e-59 239.0
37 TraesCS6D01G387600 chr1D 93.506 154 10 0 128 281 36626017 36626170 1.940000e-56 230.0
38 TraesCS6D01G387600 chr5D 89.937 159 12 2 129 287 557040106 557039952 4.240000e-48 202.0
39 TraesCS6D01G387600 chr5D 94.231 52 3 0 285 336 443834838 443834889 2.070000e-11 80.5
40 TraesCS6D01G387600 chr3B 90.789 152 8 2 129 274 56063473 56063322 5.480000e-47 198.0


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 TraesCS6D01G387600 chr6D 464482023 464484535 2512 False 4641.000000 4641 100.000000 1 2513 1 chr6D.!!$F1 2512
1 TraesCS6D01G387600 chr6A 610984305 610986068 1763 False 2348.000000 2348 90.818000 405 2173 1 chr6A.!!$F1 1768
2 TraesCS6D01G387600 chr6A 610954638 610961586 6948 False 903.166667 2305 93.076667 2 2511 6 chr6A.!!$F2 2509
3 TraesCS6D01G387600 chr6A 611035743 611038127 2384 False 454.333333 573 93.428000 682 2511 3 chr6A.!!$F3 1829
4 TraesCS6D01G387600 chr6B 708227051 708233893 6842 False 650.833333 1666 92.907833 1 1726 6 chr6B.!!$F4 1725
5 TraesCS6D01G387600 chr6B 708255785 708260325 4540 False 650.500000 1029 87.302000 758 2029 2 chr6B.!!$F5 1271
6 TraesCS6D01G387600 chrUn 426112849 426113487 638 False 950.000000 950 93.769000 1545 2173 1 chrUn.!!$F1 628
7 TraesCS6D01G387600 chrUn 404582627 404583944 1317 False 546.666667 1243 92.385667 2 1440 3 chrUn.!!$F2 1438
8 TraesCS6D01G387600 chr2D 145682812 145683505 693 True 558.000000 558 81.892000 856 1569 1 chr2D.!!$R1 713
9 TraesCS6D01G387600 chr2A 156514481 156515135 654 False 534.000000 534 81.935000 887 1572 1 chr2A.!!$F1 685

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
241 243 0.471211 CCGGGTGGGCTTCTCCTATA 60.471 60.0 0.0 0.0 34.39 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 15328 0.321653 AGCGGATCCAAGGTCAACAC 60.322 55.0 13.41 0.0 0.0 3.32 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
49 50 2.062971 TAAGTCCTACCTAGTGGCCG 57.937 55.000 0.00 0.00 36.63 6.13
56 57 2.036862 CCTACCTAGTGGCCGGTTATTC 59.963 54.545 1.90 0.00 36.63 1.75
108 110 2.107950 TGCAGGGTATTTTGTCCTCG 57.892 50.000 0.00 0.00 0.00 4.63
115 117 3.335579 GGTATTTTGTCCTCGCTTGTCT 58.664 45.455 0.00 0.00 0.00 3.41
116 118 4.501071 GGTATTTTGTCCTCGCTTGTCTA 58.499 43.478 0.00 0.00 0.00 2.59
117 119 4.567159 GGTATTTTGTCCTCGCTTGTCTAG 59.433 45.833 0.00 0.00 0.00 2.43
118 120 3.746045 TTTTGTCCTCGCTTGTCTAGT 57.254 42.857 0.00 0.00 0.00 2.57
119 121 3.746045 TTTGTCCTCGCTTGTCTAGTT 57.254 42.857 0.00 0.00 0.00 2.24
120 122 2.724977 TGTCCTCGCTTGTCTAGTTG 57.275 50.000 0.00 0.00 0.00 3.16
121 123 1.272490 TGTCCTCGCTTGTCTAGTTGG 59.728 52.381 0.00 0.00 0.00 3.77
122 124 1.272769 GTCCTCGCTTGTCTAGTTGGT 59.727 52.381 0.00 0.00 0.00 3.67
123 125 1.968493 TCCTCGCTTGTCTAGTTGGTT 59.032 47.619 0.00 0.00 0.00 3.67
124 126 2.069273 CCTCGCTTGTCTAGTTGGTTG 58.931 52.381 0.00 0.00 0.00 3.77
125 127 1.461127 CTCGCTTGTCTAGTTGGTTGC 59.539 52.381 0.00 0.00 0.00 4.17
126 128 0.517316 CGCTTGTCTAGTTGGTTGCC 59.483 55.000 0.00 0.00 0.00 4.52
127 129 1.604604 GCTTGTCTAGTTGGTTGCCA 58.395 50.000 0.00 0.00 0.00 4.92
128 130 1.537202 GCTTGTCTAGTTGGTTGCCAG 59.463 52.381 0.00 0.00 33.81 4.85
129 131 2.810400 GCTTGTCTAGTTGGTTGCCAGA 60.810 50.000 0.00 0.00 33.81 3.86
130 132 2.839486 TGTCTAGTTGGTTGCCAGAG 57.161 50.000 0.00 0.00 33.81 3.35
131 133 1.347707 TGTCTAGTTGGTTGCCAGAGG 59.652 52.381 0.00 0.00 33.81 3.69
132 134 1.623811 GTCTAGTTGGTTGCCAGAGGA 59.376 52.381 0.00 0.00 33.81 3.71
133 135 1.623811 TCTAGTTGGTTGCCAGAGGAC 59.376 52.381 0.00 0.00 33.81 3.85
134 136 1.625818 CTAGTTGGTTGCCAGAGGACT 59.374 52.381 0.00 0.00 33.81 3.85
135 137 1.729586 AGTTGGTTGCCAGAGGACTA 58.270 50.000 0.00 0.00 33.81 2.59
136 138 1.625818 AGTTGGTTGCCAGAGGACTAG 59.374 52.381 0.00 0.00 33.81 2.57
137 139 0.984230 TTGGTTGCCAGAGGACTAGG 59.016 55.000 0.00 0.00 33.81 3.02
141 143 4.042251 GCCAGAGGACTAGGCTGT 57.958 61.111 0.00 0.00 44.92 4.40
142 144 3.209091 GCCAGAGGACTAGGCTGTA 57.791 57.895 0.00 0.00 44.92 2.74
143 145 1.036707 GCCAGAGGACTAGGCTGTAG 58.963 60.000 0.00 0.00 44.92 2.74
144 146 1.036707 CCAGAGGACTAGGCTGTAGC 58.963 60.000 0.00 0.00 41.14 3.58
161 163 2.125106 CCTAGTGGCAAGGGACGC 60.125 66.667 0.00 0.00 0.00 5.19
162 164 2.509336 CTAGTGGCAAGGGACGCG 60.509 66.667 3.53 3.53 37.72 6.01
163 165 4.077184 TAGTGGCAAGGGACGCGG 62.077 66.667 12.47 0.00 37.72 6.46
170 172 4.572571 AAGGGACGCGGTGGCAAA 62.573 61.111 12.47 0.00 39.92 3.68
184 186 2.262292 CAAACCTTGCGGCCATGG 59.738 61.111 7.63 7.63 40.97 3.66
187 189 2.203625 ACCTTGCGGCCATGGTTT 60.204 55.556 14.67 0.00 44.53 3.27
188 190 2.262292 CCTTGCGGCCATGGTTTG 59.738 61.111 14.67 4.59 32.94 2.93
189 191 2.274645 CCTTGCGGCCATGGTTTGA 61.275 57.895 14.67 0.00 32.94 2.69
190 192 1.080569 CTTGCGGCCATGGTTTGAC 60.081 57.895 14.67 0.00 0.00 3.18
191 193 1.526575 CTTGCGGCCATGGTTTGACT 61.527 55.000 14.67 0.00 0.00 3.41
192 194 1.523154 TTGCGGCCATGGTTTGACTC 61.523 55.000 14.67 0.00 0.00 3.36
193 195 2.700773 GCGGCCATGGTTTGACTCC 61.701 63.158 14.67 2.71 0.00 3.85
194 196 2.046285 CGGCCATGGTTTGACTCCC 61.046 63.158 14.67 1.90 0.00 4.30
195 197 2.046285 GGCCATGGTTTGACTCCCG 61.046 63.158 14.67 0.00 0.00 5.14
196 198 1.303317 GCCATGGTTTGACTCCCGT 60.303 57.895 14.67 0.00 0.00 5.28
197 199 1.305930 GCCATGGTTTGACTCCCGTC 61.306 60.000 14.67 0.00 40.64 4.79
198 200 1.019278 CCATGGTTTGACTCCCGTCG 61.019 60.000 2.57 0.00 43.21 5.12
199 201 1.019278 CATGGTTTGACTCCCGTCGG 61.019 60.000 3.60 3.60 43.21 4.79
200 202 2.047560 GGTTTGACTCCCGTCGGG 60.048 66.667 25.31 25.31 46.11 5.14
210 212 3.089784 CCGTCGGGAGCGAATTTG 58.910 61.111 2.34 0.00 34.06 2.32
211 213 1.740296 CCGTCGGGAGCGAATTTGT 60.740 57.895 2.34 0.00 34.06 2.83
212 214 1.419922 CGTCGGGAGCGAATTTGTG 59.580 57.895 0.00 0.00 0.00 3.33
213 215 1.794222 GTCGGGAGCGAATTTGTGG 59.206 57.895 0.00 0.00 0.00 4.17
214 216 2.038269 TCGGGAGCGAATTTGTGGC 61.038 57.895 0.00 0.00 0.00 5.01
215 217 2.485122 GGGAGCGAATTTGTGGCG 59.515 61.111 0.00 0.00 35.80 5.69
219 221 2.202479 GCGAATTTGTGGCGCCTC 60.202 61.111 29.70 25.38 44.55 4.70
220 222 2.976840 GCGAATTTGTGGCGCCTCA 61.977 57.895 29.70 27.99 44.55 3.86
221 223 1.154225 CGAATTTGTGGCGCCTCAC 60.154 57.895 29.62 19.88 38.09 3.51
222 224 1.212751 GAATTTGTGGCGCCTCACC 59.787 57.895 29.62 15.37 36.87 4.02
223 225 2.212900 GAATTTGTGGCGCCTCACCC 62.213 60.000 29.62 15.04 36.87 4.61
239 241 2.365105 CCGGGTGGGCTTCTCCTA 60.365 66.667 0.00 0.00 34.39 2.94
240 242 1.766461 CCGGGTGGGCTTCTCCTAT 60.766 63.158 0.00 0.00 34.39 2.57
241 243 0.471211 CCGGGTGGGCTTCTCCTATA 60.471 60.000 0.00 0.00 34.39 1.31
242 244 1.420430 CGGGTGGGCTTCTCCTATAA 58.580 55.000 0.00 0.00 34.39 0.98
243 245 1.766496 CGGGTGGGCTTCTCCTATAAA 59.234 52.381 0.00 0.00 34.39 1.40
244 246 2.171870 CGGGTGGGCTTCTCCTATAAAA 59.828 50.000 0.00 0.00 34.39 1.52
245 247 3.371166 CGGGTGGGCTTCTCCTATAAAAA 60.371 47.826 0.00 0.00 34.39 1.94
246 248 4.688874 CGGGTGGGCTTCTCCTATAAAAAT 60.689 45.833 0.00 0.00 34.39 1.82
247 249 5.455612 CGGGTGGGCTTCTCCTATAAAAATA 60.456 44.000 0.00 0.00 34.39 1.40
248 250 6.552932 GGGTGGGCTTCTCCTATAAAAATAT 58.447 40.000 0.00 0.00 34.39 1.28
249 251 6.434340 GGGTGGGCTTCTCCTATAAAAATATG 59.566 42.308 0.00 0.00 34.39 1.78
250 252 7.004691 GGTGGGCTTCTCCTATAAAAATATGT 58.995 38.462 0.00 0.00 34.39 2.29
251 253 7.175119 GGTGGGCTTCTCCTATAAAAATATGTC 59.825 40.741 0.00 0.00 34.39 3.06
252 254 7.175119 GTGGGCTTCTCCTATAAAAATATGTCC 59.825 40.741 0.00 0.00 34.39 4.02
253 255 7.073725 TGGGCTTCTCCTATAAAAATATGTCCT 59.926 37.037 0.00 0.00 34.39 3.85
254 256 7.391833 GGGCTTCTCCTATAAAAATATGTCCTG 59.608 40.741 0.00 0.00 34.39 3.86
255 257 7.391833 GGCTTCTCCTATAAAAATATGTCCTGG 59.608 40.741 0.00 0.00 0.00 4.45
256 258 7.391833 GCTTCTCCTATAAAAATATGTCCTGGG 59.608 40.741 0.00 0.00 0.00 4.45
257 259 7.947782 TCTCCTATAAAAATATGTCCTGGGT 57.052 36.000 0.00 0.00 0.00 4.51
258 260 7.745717 TCTCCTATAAAAATATGTCCTGGGTG 58.254 38.462 0.00 0.00 0.00 4.61
259 261 6.303839 TCCTATAAAAATATGTCCTGGGTGC 58.696 40.000 0.00 0.00 0.00 5.01
260 262 6.102615 TCCTATAAAAATATGTCCTGGGTGCT 59.897 38.462 0.00 0.00 0.00 4.40
261 263 7.293771 TCCTATAAAAATATGTCCTGGGTGCTA 59.706 37.037 0.00 0.00 0.00 3.49
262 264 7.607991 CCTATAAAAATATGTCCTGGGTGCTAG 59.392 40.741 0.00 0.00 0.00 3.42
263 265 4.862641 AAAATATGTCCTGGGTGCTAGT 57.137 40.909 0.00 0.00 0.00 2.57
264 266 3.845781 AATATGTCCTGGGTGCTAGTG 57.154 47.619 0.00 0.00 0.00 2.74
265 267 0.830648 TATGTCCTGGGTGCTAGTGC 59.169 55.000 0.00 0.00 40.20 4.40
266 268 1.915078 ATGTCCTGGGTGCTAGTGCC 61.915 60.000 0.00 0.00 38.71 5.01
267 269 3.009115 TCCTGGGTGCTAGTGCCC 61.009 66.667 14.48 14.48 45.04 5.36
271 273 2.124151 GGGTGCTAGTGCCCATGG 60.124 66.667 15.91 4.14 44.23 3.66
272 274 2.679342 GGGTGCTAGTGCCCATGGA 61.679 63.158 15.22 0.00 44.23 3.41
273 275 1.533711 GGTGCTAGTGCCCATGGAT 59.466 57.895 15.22 0.00 38.71 3.41
274 276 0.536006 GGTGCTAGTGCCCATGGATC 60.536 60.000 15.22 5.06 38.71 3.36
275 277 0.471617 GTGCTAGTGCCCATGGATCT 59.528 55.000 15.22 10.66 38.71 2.75
276 278 0.761187 TGCTAGTGCCCATGGATCTC 59.239 55.000 15.22 5.64 38.71 2.75
277 279 0.761187 GCTAGTGCCCATGGATCTCA 59.239 55.000 15.22 2.44 0.00 3.27
278 280 1.350351 GCTAGTGCCCATGGATCTCAT 59.650 52.381 15.22 0.00 36.31 2.90
279 281 2.224719 GCTAGTGCCCATGGATCTCATT 60.225 50.000 15.22 5.04 32.92 2.57
280 282 3.749954 GCTAGTGCCCATGGATCTCATTT 60.750 47.826 15.22 1.75 32.92 2.32
281 283 3.393426 AGTGCCCATGGATCTCATTTT 57.607 42.857 15.22 0.00 32.92 1.82
282 284 3.716431 AGTGCCCATGGATCTCATTTTT 58.284 40.909 15.22 0.00 32.92 1.94
425 488 1.761449 TGCTGCCTCAAAACTTGTGA 58.239 45.000 0.00 0.00 0.00 3.58
433 496 3.188460 CCTCAAAACTTGTGATGTACGGG 59.812 47.826 0.00 0.00 0.00 5.28
435 498 1.153353 AAACTTGTGATGTACGGGCG 58.847 50.000 0.00 0.00 0.00 6.13
465 528 6.698329 AGTTGATTTACGCACGCTACAATATA 59.302 34.615 0.00 0.00 0.00 0.86
526 606 5.105310 GCTTAGAGGTCAGTGGTATCTTCAA 60.105 44.000 0.00 0.00 0.00 2.69
534 614 2.714250 AGTGGTATCTTCAACCCACCAA 59.286 45.455 4.15 0.00 46.84 3.67
535 615 3.139397 AGTGGTATCTTCAACCCACCAAA 59.861 43.478 4.15 0.00 46.84 3.28
539 619 4.587262 GGTATCTTCAACCCACCAAAGTTT 59.413 41.667 0.00 0.00 0.00 2.66
544 624 7.189079 TCTTCAACCCACCAAAGTTTAAATT 57.811 32.000 0.00 0.00 0.00 1.82
607 5574 2.564947 ACGCTCAGTCTCTTGAAGGATT 59.435 45.455 0.00 0.00 0.00 3.01
609 5576 3.999663 CGCTCAGTCTCTTGAAGGATTTT 59.000 43.478 0.00 0.00 0.00 1.82
634 5601 3.519510 AGAAGTAGGGTGTGCATATGTGT 59.480 43.478 4.29 0.00 0.00 3.72
673 5640 2.561733 TGCGCGTATATATGAGGCTC 57.438 50.000 8.43 7.79 0.00 4.70
679 5646 3.489229 GCGTATATATGAGGCTCGCATCA 60.489 47.826 10.42 8.77 41.06 3.07
688 5655 2.554462 GAGGCTCGCATCAGTACTATGA 59.446 50.000 0.00 2.62 0.00 2.15
689 5656 2.556189 AGGCTCGCATCAGTACTATGAG 59.444 50.000 13.33 10.93 31.44 2.90
819 5795 1.068474 GGAAATCTGTGTCCGTGTCG 58.932 55.000 0.00 0.00 0.00 4.35
949 5943 1.861971 GAAGAGGAACCAAACGACGT 58.138 50.000 0.00 0.00 0.00 4.34
1083 6083 1.153429 GAACGGCTGCGGGTTCTAT 60.153 57.895 20.85 0.00 39.48 1.98
1092 6092 2.111251 GGGTTCTATGGGAGCGCC 59.889 66.667 2.29 0.00 33.32 6.53
1293 6298 3.680786 CTGACCGCCGAGACACCA 61.681 66.667 0.00 0.00 0.00 4.17
1529 11772 2.260844 TGAAGGCACAAGGAGTTCAG 57.739 50.000 0.00 0.00 0.00 3.02
1805 15328 5.798125 TCTAGTCCTAAGCTTGATGATGG 57.202 43.478 9.86 1.97 0.00 3.51
1812 15344 4.095483 CCTAAGCTTGATGATGGTGTTGAC 59.905 45.833 9.86 0.00 0.00 3.18
1878 15411 2.893637 CGAGATGGTGTGAACCTTAGG 58.106 52.381 0.00 0.00 0.00 2.69
1930 15463 0.682532 TTGTGCACCAAGTTGGCTCA 60.683 50.000 22.25 16.16 42.67 4.26
2003 15537 6.928202 TCTTCTAGGATCTCTTAGAACCCAT 58.072 40.000 7.48 0.00 37.86 4.00
2278 15815 0.260523 GTCTCTGCTACTCCCTCCCT 59.739 60.000 0.00 0.00 0.00 4.20
2288 15825 3.917760 CCCTCCCTCGCCGTCATC 61.918 72.222 0.00 0.00 0.00 2.92
2297 15834 2.264794 GCCGTCATCGTTGGAGGT 59.735 61.111 8.98 0.00 35.01 3.85
2300 15837 1.211969 CGTCATCGTTGGAGGTCGT 59.788 57.895 0.00 0.00 32.41 4.34
2302 15839 0.242825 GTCATCGTTGGAGGTCGTCA 59.757 55.000 0.00 0.00 0.00 4.35
2306 15843 2.932234 CGTTGGAGGTCGTCAGGCT 61.932 63.158 0.00 0.00 0.00 4.58
2332 15869 4.873129 CGGAGGATGGTGACGGCG 62.873 72.222 4.80 4.80 0.00 6.46
2406 15974 1.026182 TGTGATGACCTTGCGATGGC 61.026 55.000 0.00 0.00 40.52 4.40
2427 15995 2.741985 TTGCACTCATCACCGCCG 60.742 61.111 0.00 0.00 0.00 6.46
2467 16035 0.385751 CCGACGTGGATGCTACATCT 59.614 55.000 0.00 0.00 42.00 2.90
2499 16067 4.221422 GCCGCCGCTGATCTACCA 62.221 66.667 0.00 0.00 0.00 3.25
2511 16079 4.567971 CTGATCTACCATGCTCAAGATCC 58.432 47.826 15.99 5.57 42.35 3.36
2512 16080 3.006217 TGATCTACCATGCTCAAGATCCG 59.994 47.826 15.99 0.00 42.35 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.487299 AAATACCCTGCAACTGGTTTTTAA 57.513 33.333 13.03 0.00 35.09 1.52
108 110 1.537202 CTGGCAACCAACTAGACAAGC 59.463 52.381 0.00 0.00 30.80 4.01
115 117 1.729586 AGTCCTCTGGCAACCAACTA 58.270 50.000 0.00 0.00 30.80 2.24
116 118 1.625818 CTAGTCCTCTGGCAACCAACT 59.374 52.381 0.00 0.00 30.80 3.16
117 119 1.339151 CCTAGTCCTCTGGCAACCAAC 60.339 57.143 0.00 0.00 30.80 3.77
118 120 0.984230 CCTAGTCCTCTGGCAACCAA 59.016 55.000 0.00 0.00 30.80 3.67
119 121 1.553690 GCCTAGTCCTCTGGCAACCA 61.554 60.000 0.00 0.00 45.46 3.67
120 122 1.222113 GCCTAGTCCTCTGGCAACC 59.778 63.158 0.00 0.00 45.46 3.77
121 123 4.943822 GCCTAGTCCTCTGGCAAC 57.056 61.111 0.00 0.00 45.46 4.17
124 126 1.036707 CTACAGCCTAGTCCTCTGGC 58.963 60.000 0.00 0.00 46.42 4.85
125 127 1.036707 GCTACAGCCTAGTCCTCTGG 58.963 60.000 0.00 0.00 34.31 3.86
144 146 2.125106 GCGTCCCTTGCCACTAGG 60.125 66.667 0.00 0.00 38.23 3.02
145 147 2.509336 CGCGTCCCTTGCCACTAG 60.509 66.667 0.00 0.00 0.00 2.57
146 148 4.077184 CCGCGTCCCTTGCCACTA 62.077 66.667 4.92 0.00 0.00 2.74
153 155 4.572571 TTTGCCACCGCGTCCCTT 62.573 61.111 4.92 0.00 38.08 3.95
172 174 1.080569 GTCAAACCATGGCCGCAAG 60.081 57.895 13.04 0.00 0.00 4.01
173 175 1.523154 GAGTCAAACCATGGCCGCAA 61.523 55.000 13.04 0.00 32.58 4.85
174 176 1.971167 GAGTCAAACCATGGCCGCA 60.971 57.895 13.04 0.00 32.58 5.69
175 177 2.700773 GGAGTCAAACCATGGCCGC 61.701 63.158 13.04 0.00 32.58 6.53
176 178 2.046285 GGGAGTCAAACCATGGCCG 61.046 63.158 13.04 0.00 32.58 6.13
177 179 2.046285 CGGGAGTCAAACCATGGCC 61.046 63.158 13.04 2.27 32.58 5.36
178 180 1.303317 ACGGGAGTCAAACCATGGC 60.303 57.895 13.04 0.00 40.62 4.40
192 194 2.125269 AAATTCGCTCCCGACGGG 60.125 61.111 27.86 27.86 44.30 5.28
193 195 1.740296 ACAAATTCGCTCCCGACGG 60.740 57.895 6.99 6.99 44.30 4.79
194 196 1.419922 CACAAATTCGCTCCCGACG 59.580 57.895 0.00 0.00 44.30 5.12
195 197 1.794222 CCACAAATTCGCTCCCGAC 59.206 57.895 0.00 0.00 44.30 4.79
196 198 2.038269 GCCACAAATTCGCTCCCGA 61.038 57.895 0.00 0.00 42.66 5.14
197 199 2.485122 GCCACAAATTCGCTCCCG 59.515 61.111 0.00 0.00 0.00 5.14
198 200 2.485122 CGCCACAAATTCGCTCCC 59.515 61.111 0.00 0.00 0.00 4.30
199 201 2.202479 GCGCCACAAATTCGCTCC 60.202 61.111 0.00 0.00 44.79 4.70
203 205 1.154225 GTGAGGCGCCACAAATTCG 60.154 57.895 28.51 0.00 37.04 3.34
204 206 1.212751 GGTGAGGCGCCACAAATTC 59.787 57.895 28.51 16.06 38.74 2.17
205 207 2.275380 GGGTGAGGCGCCACAAATT 61.275 57.895 28.51 5.55 38.74 1.82
206 208 2.676471 GGGTGAGGCGCCACAAAT 60.676 61.111 28.51 6.46 38.74 2.32
222 224 0.471211 TATAGGAGAAGCCCACCCGG 60.471 60.000 0.00 0.00 37.37 5.73
223 225 1.420430 TTATAGGAGAAGCCCACCCG 58.580 55.000 0.00 0.00 37.37 5.28
224 226 3.945640 TTTTATAGGAGAAGCCCACCC 57.054 47.619 0.00 0.00 37.37 4.61
225 227 7.004691 ACATATTTTTATAGGAGAAGCCCACC 58.995 38.462 0.00 0.00 37.37 4.61
226 228 7.175119 GGACATATTTTTATAGGAGAAGCCCAC 59.825 40.741 0.00 0.00 37.37 4.61
227 229 7.073725 AGGACATATTTTTATAGGAGAAGCCCA 59.926 37.037 0.00 0.00 37.37 5.36
228 230 7.391833 CAGGACATATTTTTATAGGAGAAGCCC 59.608 40.741 0.00 0.00 37.37 5.19
229 231 7.391833 CCAGGACATATTTTTATAGGAGAAGCC 59.608 40.741 0.00 0.00 0.00 4.35
230 232 7.391833 CCCAGGACATATTTTTATAGGAGAAGC 59.608 40.741 0.00 0.00 0.00 3.86
231 233 8.440771 ACCCAGGACATATTTTTATAGGAGAAG 58.559 37.037 0.00 0.00 0.00 2.85
232 234 8.217799 CACCCAGGACATATTTTTATAGGAGAA 58.782 37.037 0.00 0.00 0.00 2.87
233 235 7.691791 GCACCCAGGACATATTTTTATAGGAGA 60.692 40.741 0.00 0.00 0.00 3.71
234 236 6.431234 GCACCCAGGACATATTTTTATAGGAG 59.569 42.308 0.00 0.00 0.00 3.69
235 237 6.102615 AGCACCCAGGACATATTTTTATAGGA 59.897 38.462 0.00 0.00 0.00 2.94
236 238 6.306987 AGCACCCAGGACATATTTTTATAGG 58.693 40.000 0.00 0.00 0.00 2.57
237 239 8.157476 ACTAGCACCCAGGACATATTTTTATAG 58.843 37.037 0.00 0.00 0.00 1.31
238 240 7.936847 CACTAGCACCCAGGACATATTTTTATA 59.063 37.037 0.00 0.00 0.00 0.98
239 241 6.772716 CACTAGCACCCAGGACATATTTTTAT 59.227 38.462 0.00 0.00 0.00 1.40
240 242 6.119536 CACTAGCACCCAGGACATATTTTTA 58.880 40.000 0.00 0.00 0.00 1.52
241 243 4.949856 CACTAGCACCCAGGACATATTTTT 59.050 41.667 0.00 0.00 0.00 1.94
242 244 4.526970 CACTAGCACCCAGGACATATTTT 58.473 43.478 0.00 0.00 0.00 1.82
243 245 3.685550 GCACTAGCACCCAGGACATATTT 60.686 47.826 0.00 0.00 41.58 1.40
244 246 2.158755 GCACTAGCACCCAGGACATATT 60.159 50.000 0.00 0.00 41.58 1.28
245 247 1.417890 GCACTAGCACCCAGGACATAT 59.582 52.381 0.00 0.00 41.58 1.78
246 248 0.830648 GCACTAGCACCCAGGACATA 59.169 55.000 0.00 0.00 41.58 2.29
247 249 1.604378 GCACTAGCACCCAGGACAT 59.396 57.895 0.00 0.00 41.58 3.06
248 250 2.592993 GGCACTAGCACCCAGGACA 61.593 63.158 0.00 0.00 44.61 4.02
249 251 2.269241 GGCACTAGCACCCAGGAC 59.731 66.667 0.00 0.00 44.61 3.85
250 252 3.009115 GGGCACTAGCACCCAGGA 61.009 66.667 14.48 0.00 46.22 3.86
254 256 1.999634 ATCCATGGGCACTAGCACCC 62.000 60.000 13.02 12.83 46.13 4.61
255 257 0.536006 GATCCATGGGCACTAGCACC 60.536 60.000 13.02 0.00 46.13 5.01
257 259 0.761187 GAGATCCATGGGCACTAGCA 59.239 55.000 13.02 0.00 44.61 3.49
258 260 0.761187 TGAGATCCATGGGCACTAGC 59.239 55.000 13.02 0.00 41.10 3.42
259 261 3.784511 AATGAGATCCATGGGCACTAG 57.215 47.619 13.02 0.00 35.24 2.57
260 262 4.524802 AAAATGAGATCCATGGGCACTA 57.475 40.909 13.02 0.00 35.24 2.74
261 263 3.393426 AAAATGAGATCCATGGGCACT 57.607 42.857 13.02 8.87 35.24 4.40
280 282 3.889520 AAACCGGCAACCAACTAAAAA 57.110 38.095 0.00 0.00 0.00 1.94
281 283 4.996788 TTAAACCGGCAACCAACTAAAA 57.003 36.364 0.00 0.00 0.00 1.52
282 284 5.532664 AATTAAACCGGCAACCAACTAAA 57.467 34.783 0.00 0.00 0.00 1.85
283 285 5.532664 AAATTAAACCGGCAACCAACTAA 57.467 34.783 0.00 0.00 0.00 2.24
425 488 0.459585 CAACTACAGCGCCCGTACAT 60.460 55.000 2.29 0.00 0.00 2.29
433 496 1.392168 TGCGTAAATCAACTACAGCGC 59.608 47.619 0.00 0.00 43.26 5.92
435 498 2.783316 GCGTGCGTAAATCAACTACAGC 60.783 50.000 0.00 0.00 0.00 4.40
503 583 6.334202 GTTGAAGATACCACTGACCTCTAAG 58.666 44.000 0.00 0.00 0.00 2.18
526 606 4.966168 ACCAGAATTTAAACTTTGGTGGGT 59.034 37.500 10.72 0.00 37.52 4.51
595 5562 9.771534 CCCTACTTCTATAAAATCCTTCAAGAG 57.228 37.037 0.00 0.00 0.00 2.85
601 5568 7.054751 GCACACCCTACTTCTATAAAATCCTT 58.945 38.462 0.00 0.00 0.00 3.36
607 5574 7.931407 CACATATGCACACCCTACTTCTATAAA 59.069 37.037 1.58 0.00 0.00 1.40
609 5576 6.553476 ACACATATGCACACCCTACTTCTATA 59.447 38.462 1.58 0.00 0.00 1.31
634 5601 4.421058 GCATACACTCACTCGTATGAACA 58.579 43.478 12.46 0.00 45.09 3.18
797 5773 3.074412 GACACGGACACAGATTTCCAAT 58.926 45.455 0.00 0.00 0.00 3.16
819 5795 2.736682 CGTGTCACCGGCGAATTCC 61.737 63.158 9.30 0.00 0.00 3.01
936 5912 0.382636 CGCTTGACGTCGTTTGGTTC 60.383 55.000 11.62 0.00 36.87 3.62
1092 6092 3.071459 GCACATGTTCTCGGTCGCG 62.071 63.158 0.00 0.00 0.00 5.87
1177 6182 0.537188 TCGGCCTTGATCTTGGTCTC 59.463 55.000 0.00 0.00 0.00 3.36
1182 6187 1.413767 CGTCGTCGGCCTTGATCTTG 61.414 60.000 0.00 0.00 0.00 3.02
1277 6282 3.680786 CTGGTGTCTCGGCGGTCA 61.681 66.667 7.21 0.88 0.00 4.02
1628 12724 1.135402 AGAAAAATCAACATCGGCGGC 60.135 47.619 7.21 0.00 0.00 6.53
1629 12725 2.916716 CAAGAAAAATCAACATCGGCGG 59.083 45.455 7.21 0.00 0.00 6.13
1630 12726 3.564511 ACAAGAAAAATCAACATCGGCG 58.435 40.909 0.00 0.00 0.00 6.46
1680 12776 6.036300 CACGATGGTACGTATTTACACCAATT 59.964 38.462 9.54 0.00 43.91 2.32
1805 15328 0.321653 AGCGGATCCAAGGTCAACAC 60.322 55.000 13.41 0.00 0.00 3.32
2003 15537 9.698309 GTAGCAGATTATTTCAGCTATAAGTCA 57.302 33.333 3.53 0.00 46.97 3.41
2069 15603 2.353958 AGCCACAGACATGGGCTG 59.646 61.111 11.18 12.78 45.69 4.85
2138 15675 2.057137 ATTGGCTTGCACATACCGAT 57.943 45.000 0.00 0.00 0.00 4.18
2252 15789 0.101579 GAGTAGCAGAGACGAAGGCC 59.898 60.000 0.00 0.00 0.00 5.19
2278 15815 2.180769 CTCCAACGATGACGGCGA 59.819 61.111 16.62 0.00 44.46 5.54
2286 15823 1.890894 CCTGACGACCTCCAACGAT 59.109 57.895 0.00 0.00 0.00 3.73
2288 15825 1.592400 TAGCCTGACGACCTCCAACG 61.592 60.000 0.00 0.00 0.00 4.10
2306 15843 2.443394 CCATCCTCCGCCAGGCTTA 61.443 63.158 10.54 0.00 43.08 3.09
2332 15869 2.433318 GAGGCAGCACACGTCCTC 60.433 66.667 3.26 3.26 38.40 3.71
2406 15974 0.445436 GCGGTGATGAGTGCAAGAAG 59.555 55.000 0.00 0.00 0.00 2.85
2485 16053 0.948141 GAGCATGGTAGATCAGCGGC 60.948 60.000 0.00 0.00 0.00 6.53
2490 16058 3.006217 CGGATCTTGAGCATGGTAGATCA 59.994 47.826 27.05 9.30 42.96 2.92


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

AutoCloner maintained by Alex Coulton.