Multiple sequence alignment - TraesCS7B01G128200

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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 TraesCS7B01G128200 chr7B 100.000 2296 0 0 1 2296 153451806 153449511 0.000000e+00 4241.0
1 TraesCS7B01G128200 chr7B 100.000 2001 0 0 2707 4707 153449100 153447100 0.000000e+00 3696.0
2 TraesCS7B01G128200 chr7B 85.130 269 34 3 2707 2972 153449776 153449511 2.160000e-68 270.0
3 TraesCS7B01G128200 chr7B 90.404 198 19 0 2069 2266 153448954 153448757 1.300000e-65 261.0
4 TraesCS7B01G128200 chr7B 90.404 198 19 0 2853 3050 153449738 153449541 1.300000e-65 261.0
5 TraesCS7B01G128200 chr7B 92.982 171 12 0 2707 2877 153448884 153448714 2.810000e-62 250.0
6 TraesCS7B01G128200 chr7B 92.982 171 12 0 2923 3093 153449100 153448930 2.810000e-62 250.0
7 TraesCS7B01G128200 chr7B 94.340 159 9 0 2030 2188 153449669 153449511 1.310000e-60 244.0
8 TraesCS7B01G128200 chr7B 94.340 159 9 0 2138 2296 153449777 153449619 1.310000e-60 244.0
9 TraesCS7B01G128200 chr7B 91.473 129 11 0 2030 2158 153448885 153448757 1.350000e-40 178.0
10 TraesCS7B01G128200 chr7B 91.473 129 11 0 2922 3050 153449777 153449649 1.350000e-40 178.0
11 TraesCS7B01G128200 chr7B 90.756 119 11 0 2716 2834 153449659 153449541 4.880000e-35 159.0
12 TraesCS7B01G128200 chr7D 95.545 2020 67 6 2707 4707 184198097 184196082 0.000000e+00 3210.0
13 TraesCS7B01G128200 chr7D 95.324 1946 77 10 358 2296 184200094 184198156 0.000000e+00 3077.0
14 TraesCS7B01G128200 chr7D 84.635 384 47 9 2716 3093 184198304 184197927 5.750000e-99 372.0
15 TraesCS7B01G128200 chr7D 88.060 268 30 2 2030 2296 184198314 184198048 2.730000e-82 316.0
16 TraesCS7B01G128200 chr7D 81.609 348 56 5 2707 3050 184198421 184198078 9.970000e-72 281.0
17 TraesCS7B01G128200 chr7D 94.611 167 8 1 3 168 184200262 184200096 1.680000e-64 257.0
18 TraesCS7B01G128200 chr7D 89.899 198 20 0 2069 2266 184197951 184197754 6.040000e-64 255.0
19 TraesCS7B01G128200 chr7D 84.074 270 37 3 2030 2296 184198098 184197832 6.040000e-64 255.0
20 TraesCS7B01G128200 chr7D 91.713 181 15 0 2870 3050 184198366 184198186 7.820000e-63 252.0
21 TraesCS7B01G128200 chr7D 89.529 191 17 1 2716 2906 184197872 184197685 6.090000e-59 239.0
22 TraesCS7B01G128200 chr7D 93.082 159 11 0 2138 2296 184198422 184198264 2.830000e-57 233.0
23 TraesCS7B01G128200 chr7D 85.116 215 30 2 2036 2249 184198200 184197987 7.930000e-53 219.0
24 TraesCS7B01G128200 chr7D 77.551 343 61 10 2716 3050 184198196 184197862 4.810000e-45 193.0
25 TraesCS7B01G128200 chr7D 82.000 200 26 7 2748 2942 184197948 184197754 1.360000e-35 161.0
26 TraesCS7B01G128200 chr7D 88.372 129 15 0 2030 2158 184197882 184197754 6.310000e-34 156.0
27 TraesCS7B01G128200 chr7D 88.372 129 15 0 2922 3050 184198422 184198294 6.310000e-34 156.0
28 TraesCS7B01G128200 chr7D 96.552 58 2 0 167 224 479128424 479128367 3.880000e-16 97.1
29 TraesCS7B01G128200 chr7D 89.041 73 8 0 152 224 634378643 634378715 1.800000e-14 91.6
30 TraesCS7B01G128200 chr7A 92.944 1984 72 24 358 2296 186513325 186515285 0.000000e+00 2826.0
31 TraesCS7B01G128200 chr7A 95.476 1481 48 5 2807 4272 186515703 186517179 0.000000e+00 2346.0
32 TraesCS7B01G128200 chr7A 96.847 444 14 0 4264 4707 186522208 186522651 0.000000e+00 743.0
33 TraesCS7B01G128200 chr7A 84.561 285 38 3 2707 2988 186515020 186515301 1.290000e-70 278.0
34 TraesCS7B01G128200 chr7A 90.909 198 18 0 2069 2266 186515749 186515946 2.790000e-67 267.0
35 TraesCS7B01G128200 chr7A 89.848 197 20 0 2853 3049 186515058 186515254 2.170000e-63 254.0
36 TraesCS7B01G128200 chr7A 94.340 159 9 0 2138 2296 186515019 186515177 1.310000e-60 244.0
37 TraesCS7B01G128200 chr7A 92.398 171 13 0 2707 2877 186515819 186515989 1.310000e-60 244.0
38 TraesCS7B01G128200 chr7A 92.357 157 12 0 5 161 186513157 186513313 1.700000e-54 224.0
39 TraesCS7B01G128200 chr7A 90.780 141 12 1 226 365 105574039 105573899 2.240000e-43 187.0
40 TraesCS7B01G128200 chr7A 83.744 203 23 7 2745 2942 186515749 186515946 2.890000e-42 183.0
41 TraesCS7B01G128200 chr7A 92.500 120 9 0 2177 2296 186515749 186515868 6.260000e-39 172.0
42 TraesCS7B01G128200 chr7A 89.922 129 13 0 2922 3050 186515019 186515147 2.910000e-37 167.0
43 TraesCS7B01G128200 chr7A 88.189 127 15 0 2707 2833 186515128 186515254 8.160000e-33 152.0
44 TraesCS7B01G128200 chr7A 92.929 99 6 1 1741 1839 186514700 186514797 4.910000e-30 143.0
45 TraesCS7B01G128200 chr7A 87.778 90 11 0 2961 3050 186515749 186515838 6.440000e-19 106.0
46 TraesCS7B01G128200 chr7A 92.958 71 5 0 1230 1300 186514255 186514325 2.320000e-18 104.0
47 TraesCS7B01G128200 chr7A 96.552 58 2 0 167 224 490865565 490865622 3.880000e-16 97.1
48 TraesCS7B01G128200 chr6A 91.489 141 11 1 226 365 168617128 168617268 4.810000e-45 193.0
49 TraesCS7B01G128200 chr6A 91.791 134 11 0 226 359 300069548 300069681 2.240000e-43 187.0
50 TraesCS7B01G128200 chr6A 90.580 138 10 2 226 363 35481485 35481619 3.740000e-41 180.0
51 TraesCS7B01G128200 chr6A 88.235 85 9 1 276 359 605215278 605215362 3.000000e-17 100.0
52 TraesCS7B01G128200 chr4A 92.537 134 10 0 226 359 357789064 357789197 4.810000e-45 193.0
53 TraesCS7B01G128200 chr4A 96.552 58 2 0 167 224 30396539 30396596 3.880000e-16 97.1
54 TraesCS7B01G128200 chr3B 90.972 144 12 1 226 369 537423053 537423195 4.810000e-45 193.0
55 TraesCS7B01G128200 chr3B 89.189 74 7 1 152 224 571539896 571539969 1.800000e-14 91.6
56 TraesCS7B01G128200 chr3A 92.537 134 10 0 226 359 733260615 733260748 4.810000e-45 193.0
57 TraesCS7B01G128200 chr1B 90.972 144 12 1 226 369 323683383 323683525 4.810000e-45 193.0
58 TraesCS7B01G128200 chr1D 89.510 143 15 0 226 368 6522617 6522475 1.040000e-41 182.0
59 TraesCS7B01G128200 chr1D 86.869 99 9 3 276 374 356932548 356932642 1.790000e-19 108.0
60 TraesCS7B01G128200 chr4D 86.607 112 11 1 252 359 335779197 335779308 2.300000e-23 121.0
61 TraesCS7B01G128200 chr2A 78.866 194 13 12 166 359 31439972 31440137 6.440000e-19 106.0


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 TraesCS7B01G128200 chr7B 153447100 153451806 4706 True 852.666667 4241 92.857000 1 4707 12 chr7B.!!$R1 4706
1 TraesCS7B01G128200 chr7D 184196082 184200262 4180 True 602.000000 3210 88.093250 3 4707 16 chr7D.!!$R2 4704
2 TraesCS7B01G128200 chr7A 186513157 186517179 4022 False 514.000000 2826 90.723533 5 4272 15 chr7A.!!$F3 4267

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
106 108 0.174845 GGCAGCTACCACACGATACA 59.825 55.000 0.0 0.0 0.00 2.29 F
1203 1227 0.169672 GCGTCATGTTCAGCAATGCT 59.830 50.000 0.0 0.0 40.77 3.79 F
2250 2301 0.393537 CCCTTGTGGAGATGGCAGTC 60.394 60.000 0.0 0.0 35.39 3.51 F
3084 3135 1.877680 CGGTTCTGTTGCAGTGATGGA 60.878 52.381 0.0 0.0 32.61 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1810 0.602905 GGCAGTGGCGACAGTTTAGT 60.603 55.000 0.00 0.00 42.89 2.24 R
3100 3151 0.109827 CATTGCCATGTTCGTTGCGA 60.110 50.000 0.00 0.00 0.00 5.10 R
3332 3386 0.994247 TTCTGATGTGCCTCCCATGT 59.006 50.000 0.00 0.00 0.00 3.21 R
4598 4673 3.246301 AGACAGGCTGTATGATATGGCT 58.754 45.455 22.11 7.02 35.69 4.75 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
27 28 3.142838 CCAATGGCTCCTTGGGCG 61.143 66.667 6.27 0.00 39.62 6.13
51 53 3.295093 TCTGATGGTCAAAGGCAAACAA 58.705 40.909 0.00 0.00 0.00 2.83
106 108 0.174845 GGCAGCTACCACACGATACA 59.825 55.000 0.00 0.00 0.00 2.29
168 173 4.732285 TCCCGTCGATAATAACTCGTAC 57.268 45.455 0.00 0.00 37.40 3.67
170 175 4.449068 TCCCGTCGATAATAACTCGTACTC 59.551 45.833 0.00 0.00 37.40 2.59
171 176 4.377841 CCCGTCGATAATAACTCGTACTCC 60.378 50.000 0.00 0.00 37.40 3.85
172 177 4.377841 CCGTCGATAATAACTCGTACTCCC 60.378 50.000 0.00 0.00 37.40 4.30
173 178 4.450419 CGTCGATAATAACTCGTACTCCCT 59.550 45.833 0.00 0.00 37.40 4.20
174 179 5.389307 CGTCGATAATAACTCGTACTCCCTC 60.389 48.000 0.00 0.00 37.40 4.30
175 180 5.700373 GTCGATAATAACTCGTACTCCCTCT 59.300 44.000 0.00 0.00 37.40 3.69
176 181 5.699915 TCGATAATAACTCGTACTCCCTCTG 59.300 44.000 0.00 0.00 37.40 3.35
177 182 5.469421 CGATAATAACTCGTACTCCCTCTGT 59.531 44.000 0.00 0.00 0.00 3.41
178 183 6.017275 CGATAATAACTCGTACTCCCTCTGTT 60.017 42.308 0.00 0.00 0.00 3.16
179 184 5.579564 AATAACTCGTACTCCCTCTGTTC 57.420 43.478 0.00 0.00 0.00 3.18
180 185 1.836802 ACTCGTACTCCCTCTGTTCC 58.163 55.000 0.00 0.00 0.00 3.62
181 186 1.355043 ACTCGTACTCCCTCTGTTCCT 59.645 52.381 0.00 0.00 0.00 3.36
182 187 2.575279 ACTCGTACTCCCTCTGTTCCTA 59.425 50.000 0.00 0.00 0.00 2.94
183 188 3.009916 ACTCGTACTCCCTCTGTTCCTAA 59.990 47.826 0.00 0.00 0.00 2.69
184 189 4.015084 CTCGTACTCCCTCTGTTCCTAAA 58.985 47.826 0.00 0.00 0.00 1.85
185 190 4.607239 TCGTACTCCCTCTGTTCCTAAAT 58.393 43.478 0.00 0.00 0.00 1.40
186 191 5.759059 TCGTACTCCCTCTGTTCCTAAATA 58.241 41.667 0.00 0.00 0.00 1.40
187 192 6.371278 TCGTACTCCCTCTGTTCCTAAATAT 58.629 40.000 0.00 0.00 0.00 1.28
188 193 7.520798 TCGTACTCCCTCTGTTCCTAAATATA 58.479 38.462 0.00 0.00 0.00 0.86
189 194 7.664731 TCGTACTCCCTCTGTTCCTAAATATAG 59.335 40.741 0.00 0.00 0.00 1.31
212 217 7.971183 AGGTCTTTCTAGAGATTTCAACAAC 57.029 36.000 0.00 0.00 0.00 3.32
213 218 7.740805 AGGTCTTTCTAGAGATTTCAACAACT 58.259 34.615 0.00 0.00 0.00 3.16
214 219 7.659390 AGGTCTTTCTAGAGATTTCAACAACTG 59.341 37.037 0.00 0.00 0.00 3.16
215 220 7.657761 GGTCTTTCTAGAGATTTCAACAACTGA 59.342 37.037 0.00 0.00 0.00 3.41
216 221 8.491950 GTCTTTCTAGAGATTTCAACAACTGAC 58.508 37.037 0.00 0.00 32.21 3.51
217 222 8.424918 TCTTTCTAGAGATTTCAACAACTGACT 58.575 33.333 0.00 0.00 32.21 3.41
218 223 9.698309 CTTTCTAGAGATTTCAACAACTGACTA 57.302 33.333 0.00 0.00 32.21 2.59
257 262 8.840833 TTCAACAACTGACTATATACAAAGCA 57.159 30.769 0.00 0.00 32.21 3.91
258 263 8.840833 TCAACAACTGACTATATACAAAGCAA 57.159 30.769 0.00 0.00 0.00 3.91
259 264 9.278978 TCAACAACTGACTATATACAAAGCAAA 57.721 29.630 0.00 0.00 0.00 3.68
260 265 9.891828 CAACAACTGACTATATACAAAGCAAAA 57.108 29.630 0.00 0.00 0.00 2.44
274 279 9.988350 ATACAAAGCAAAATAAGTGAATCTACG 57.012 29.630 0.00 0.00 0.00 3.51
275 280 6.801862 ACAAAGCAAAATAAGTGAATCTACGC 59.198 34.615 0.00 0.00 0.00 4.42
276 281 6.743575 AAGCAAAATAAGTGAATCTACGCT 57.256 33.333 0.00 0.00 0.00 5.07
277 282 6.351327 AGCAAAATAAGTGAATCTACGCTC 57.649 37.500 0.00 0.00 0.00 5.03
278 283 6.109359 AGCAAAATAAGTGAATCTACGCTCT 58.891 36.000 0.00 0.00 0.00 4.09
279 284 7.265673 AGCAAAATAAGTGAATCTACGCTCTA 58.734 34.615 0.00 0.00 0.00 2.43
280 285 7.764443 AGCAAAATAAGTGAATCTACGCTCTAA 59.236 33.333 0.00 0.00 0.00 2.10
281 286 8.388103 GCAAAATAAGTGAATCTACGCTCTAAA 58.612 33.333 0.00 0.00 0.00 1.85
288 293 8.804688 AGTGAATCTACGCTCTAAAATATGTC 57.195 34.615 0.00 0.00 0.00 3.06
289 294 8.634444 AGTGAATCTACGCTCTAAAATATGTCT 58.366 33.333 0.00 0.00 0.00 3.41
290 295 9.894783 GTGAATCTACGCTCTAAAATATGTCTA 57.105 33.333 0.00 0.00 0.00 2.59
298 303 9.627395 ACGCTCTAAAATATGTCTATGTACATC 57.373 33.333 12.68 0.00 40.52 3.06
299 304 9.847706 CGCTCTAAAATATGTCTATGTACATCT 57.152 33.333 12.68 0.00 40.52 2.90
308 313 7.603180 ATGTCTATGTACATCTGTATGTGGT 57.397 36.000 12.68 0.00 45.99 4.16
309 314 8.706322 ATGTCTATGTACATCTGTATGTGGTA 57.294 34.615 12.68 0.00 45.99 3.25
310 315 8.166422 TGTCTATGTACATCTGTATGTGGTAG 57.834 38.462 12.68 0.00 45.99 3.18
311 316 7.778382 TGTCTATGTACATCTGTATGTGGTAGT 59.222 37.037 12.68 0.00 45.99 2.73
312 317 8.291032 GTCTATGTACATCTGTATGTGGTAGTC 58.709 40.741 12.68 0.00 45.99 2.59
313 318 5.847111 TGTACATCTGTATGTGGTAGTCC 57.153 43.478 0.00 0.00 45.99 3.85
314 319 5.265989 TGTACATCTGTATGTGGTAGTCCA 58.734 41.667 0.00 0.00 45.99 4.02
315 320 5.897250 TGTACATCTGTATGTGGTAGTCCAT 59.103 40.000 0.00 0.00 45.99 3.41
316 321 5.957771 ACATCTGTATGTGGTAGTCCATT 57.042 39.130 0.00 0.00 44.79 3.16
317 322 6.313519 ACATCTGTATGTGGTAGTCCATTT 57.686 37.500 0.00 0.00 44.79 2.32
318 323 6.115446 ACATCTGTATGTGGTAGTCCATTTG 58.885 40.000 0.00 0.00 44.79 2.32
319 324 6.070251 ACATCTGTATGTGGTAGTCCATTTGA 60.070 38.462 0.00 0.00 44.79 2.69
320 325 6.367374 TCTGTATGTGGTAGTCCATTTGAA 57.633 37.500 0.00 0.00 46.20 2.69
321 326 6.957631 TCTGTATGTGGTAGTCCATTTGAAT 58.042 36.000 0.00 0.00 46.20 2.57
322 327 7.402054 TCTGTATGTGGTAGTCCATTTGAATT 58.598 34.615 0.00 0.00 46.20 2.17
323 328 7.552687 TCTGTATGTGGTAGTCCATTTGAATTC 59.447 37.037 0.00 0.00 46.20 2.17
324 329 7.402054 TGTATGTGGTAGTCCATTTGAATTCT 58.598 34.615 7.05 0.00 46.20 2.40
325 330 7.552687 TGTATGTGGTAGTCCATTTGAATTCTC 59.447 37.037 7.05 0.00 46.20 2.87
326 331 5.875224 TGTGGTAGTCCATTTGAATTCTCA 58.125 37.500 7.05 0.00 46.20 3.27
327 332 6.303054 TGTGGTAGTCCATTTGAATTCTCAA 58.697 36.000 7.05 0.08 46.20 3.02
354 359 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
355 360 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
356 361 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
357 362 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
358 363 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
359 364 9.205513 ACTTATATTTAGAAACGGAGGGAGTAA 57.794 33.333 0.00 0.00 0.00 2.24
364 369 7.722949 TTTAGAAACGGAGGGAGTAATAAGA 57.277 36.000 0.00 0.00 0.00 2.10
365 370 7.909485 TTAGAAACGGAGGGAGTAATAAGAT 57.091 36.000 0.00 0.00 0.00 2.40
366 371 9.425248 TTTAGAAACGGAGGGAGTAATAAGATA 57.575 33.333 0.00 0.00 0.00 1.98
429 434 1.475280 GCAATAAAACCCCGAGAACCC 59.525 52.381 0.00 0.00 0.00 4.11
449 454 3.096495 GGATACCCAGCCAGGCCA 61.096 66.667 8.22 0.00 35.39 5.36
662 681 5.703876 CAGAAGAAACAGAAATAGCAACCC 58.296 41.667 0.00 0.00 0.00 4.11
747 766 4.475135 GGTGGGCTTCCTCCTCGC 62.475 72.222 0.00 0.00 40.23 5.03
751 770 4.214327 GGCTTCCTCCTCGCCTCG 62.214 72.222 0.00 0.00 40.62 4.63
793 812 2.618045 CCAGTTCCCACCACCATTACTC 60.618 54.545 0.00 0.00 0.00 2.59
862 884 2.622452 CCTACTCCTTACCACCCGAAGA 60.622 54.545 0.00 0.00 0.00 2.87
898 922 2.425592 CACTTCTCCACCACCGCA 59.574 61.111 0.00 0.00 0.00 5.69
923 947 1.001293 CCAGCTATAAGCAGCCATCGA 59.999 52.381 1.22 0.00 45.56 3.59
936 960 1.064296 CATCGACTTCGTCTCCCCG 59.936 63.158 0.00 0.00 40.80 5.73
957 981 1.303236 CAGCCACCAAACCGATCCA 60.303 57.895 0.00 0.00 0.00 3.41
995 1019 0.825840 CCTCCTCCTCTGATCCGTCC 60.826 65.000 0.00 0.00 0.00 4.79
1048 1072 2.031012 TGCTCTTGTCGCTGGTGG 59.969 61.111 0.00 0.00 0.00 4.61
1082 1106 3.764466 CTCTCTCCGCTTGCCCGT 61.764 66.667 0.00 0.00 0.00 5.28
1203 1227 0.169672 GCGTCATGTTCAGCAATGCT 59.830 50.000 0.00 0.00 40.77 3.79
1255 1306 3.365265 CTGCCGCCTTCACCCAAC 61.365 66.667 0.00 0.00 0.00 3.77
1274 1325 2.045536 GGGCTTCACTGCTCCTGG 60.046 66.667 0.00 0.00 0.00 4.45
1286 1337 3.551496 CTCCTGGTGCCGCCTTCAA 62.551 63.158 0.00 0.00 38.35 2.69
1359 1410 1.066858 GGTGACGAAGCCTTCTCATCA 60.067 52.381 2.49 1.27 0.00 3.07
1367 1418 1.980765 AGCCTTCTCATCAGGTGACAA 59.019 47.619 0.00 0.00 33.40 3.18
1428 1479 5.186603 TGATGGATATTCAAGAGATCCCGAG 59.813 44.000 9.37 0.00 38.75 4.63
1507 1558 1.871039 TGCTCAGCGTTAAACAAGGTC 59.129 47.619 0.00 0.00 0.00 3.85
1543 1594 4.445452 AGCAGCAACAACTATGAATTGG 57.555 40.909 0.00 0.00 0.00 3.16
1749 1800 0.882927 GTAAACTGTCGCCACTGCCA 60.883 55.000 0.00 0.00 0.00 4.92
1759 1810 3.594775 CACTGCCAAGCCGCAACA 61.595 61.111 0.00 0.00 38.56 3.33
1802 1853 0.652071 CGCAATGCTAATCTGTCGCA 59.348 50.000 2.94 0.00 38.14 5.10
2039 2090 1.661463 AGGAACCAAGCAGGAGATGA 58.339 50.000 1.83 0.00 41.22 2.92
2044 2095 1.911357 ACCAAGCAGGAGATGATGTCA 59.089 47.619 1.83 0.00 41.22 3.58
2058 2109 3.457234 TGATGTCATGCTCGGTGATAAC 58.543 45.455 0.00 0.00 0.00 1.89
2250 2301 0.393537 CCCTTGTGGAGATGGCAGTC 60.394 60.000 0.00 0.00 35.39 3.51
2856 2907 3.414700 CGAGCACCACGGTTCTGC 61.415 66.667 0.00 0.00 0.00 4.26
2860 2911 2.591429 CACCACGGTTCTGCTGCA 60.591 61.111 0.88 0.88 0.00 4.41
2878 2929 1.950828 CAGTGATGGCAGGAGATGAC 58.049 55.000 0.00 0.00 37.50 3.06
2936 2987 2.367894 GAGATGGCAGGAGATGATGTCA 59.632 50.000 0.00 0.00 35.14 3.58
3084 3135 1.877680 CGGTTCTGTTGCAGTGATGGA 60.878 52.381 0.00 0.00 32.61 3.41
3093 3144 1.911357 TGCAGTGATGGAAGGAGATGT 59.089 47.619 0.00 0.00 0.00 3.06
3100 3151 4.080863 GTGATGGAAGGAGATGTGGTAGTT 60.081 45.833 0.00 0.00 0.00 2.24
3622 3676 2.196742 ATAAGGATGGTGGCTCTCCA 57.803 50.000 0.00 0.00 40.85 3.86
3737 3791 6.212955 CACATACCTTTTGTGTGTTTTAGGG 58.787 40.000 0.00 0.00 45.86 3.53
3749 3803 4.098807 TGTGTTTTAGGGAAAAGCAGGAAC 59.901 41.667 0.00 0.00 38.74 3.62
3894 3960 2.290641 ACAGGTAAATTCGCCACCATGA 60.291 45.455 0.00 0.00 34.62 3.07
3895 3961 2.097466 CAGGTAAATTCGCCACCATGAC 59.903 50.000 0.00 0.00 34.62 3.06
4070 4138 5.818136 ACACTTGATTTATCGACCAATGG 57.182 39.130 0.00 0.00 0.00 3.16
4209 4277 9.888878 CCTGCAAATGAACATATTGAGTATTAG 57.111 33.333 0.00 0.00 0.00 1.73
4264 4332 5.163269 ACATGCATGCTAAAGGATAGTCAGA 60.163 40.000 26.53 0.00 0.00 3.27
4283 4351 8.151141 AGTCAGATACATACAAATCATGCTTG 57.849 34.615 5.98 5.98 0.00 4.01
4293 4361 4.022068 ACAAATCATGCTTGAACATCGGTT 60.022 37.500 6.36 0.00 40.76 4.44
4422 4491 4.671831 TGGACCTCATGCTTTAATTTCCA 58.328 39.130 0.00 0.00 0.00 3.53
4450 4519 4.373348 ACGTGCTCTCCAAGATACTAAC 57.627 45.455 0.00 0.00 0.00 2.34
4459 4528 5.127194 TCTCCAAGATACTAACGTGCTGAAT 59.873 40.000 0.00 0.00 0.00 2.57
4493 4562 8.861033 TTTCGCATAACGTATTGTAGTATTCT 57.139 30.769 0.00 0.00 44.19 2.40
4576 4651 9.890629 AAATTCTGTATGCATACTACTTGAAGA 57.109 29.630 31.35 22.16 34.41 2.87
4617 4692 4.443978 AAAGCCATATCATACAGCCTGT 57.556 40.909 1.54 1.54 0.00 4.00
4619 4694 3.246301 AGCCATATCATACAGCCTGTCT 58.754 45.455 0.00 0.00 0.00 3.41
4628 4703 9.809395 ATATCATACAGCCTGTCTACTAAACTA 57.191 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.051237 GTTTGCCTTTGACCATCAGAAAC 58.949 43.478 0.00 0.00 0.00 2.78
51 53 1.605738 AGCGGGAGGTTGTAGACGT 60.606 57.895 0.00 0.00 37.18 4.34
106 108 2.165437 ACCAACGATGTTGTTTGCTTGT 59.835 40.909 8.68 0.00 0.00 3.16
152 154 5.699915 CAGAGGGAGTACGAGTTATTATCGA 59.300 44.000 1.94 0.00 42.76 3.59
186 191 9.660180 GTTGTTGAAATCTCTAGAAAGACCTAT 57.340 33.333 0.00 0.00 0.00 2.57
187 192 8.871125 AGTTGTTGAAATCTCTAGAAAGACCTA 58.129 33.333 0.00 0.00 0.00 3.08
188 193 7.659390 CAGTTGTTGAAATCTCTAGAAAGACCT 59.341 37.037 0.00 0.00 0.00 3.85
189 194 7.657761 TCAGTTGTTGAAATCTCTAGAAAGACC 59.342 37.037 0.00 0.00 31.34 3.85
190 195 8.491950 GTCAGTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 37.61 3.01
191 196 8.424918 AGTCAGTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 37.61 2.52
192 197 8.600449 AGTCAGTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 37.61 2.62
231 236 9.278978 TGCTTTGTATATAGTCAGTTGTTGAAA 57.721 29.630 0.00 0.00 37.61 2.69
232 237 8.840833 TGCTTTGTATATAGTCAGTTGTTGAA 57.159 30.769 0.00 0.00 37.61 2.69
233 238 8.840833 TTGCTTTGTATATAGTCAGTTGTTGA 57.159 30.769 0.00 0.00 0.00 3.18
234 239 9.891828 TTTTGCTTTGTATATAGTCAGTTGTTG 57.108 29.630 0.00 0.00 0.00 3.33
248 253 9.988350 CGTAGATTCACTTATTTTGCTTTGTAT 57.012 29.630 0.00 0.00 0.00 2.29
249 254 7.960738 GCGTAGATTCACTTATTTTGCTTTGTA 59.039 33.333 0.00 0.00 0.00 2.41
250 255 6.801862 GCGTAGATTCACTTATTTTGCTTTGT 59.198 34.615 0.00 0.00 0.00 2.83
251 256 7.023575 AGCGTAGATTCACTTATTTTGCTTTG 58.976 34.615 0.00 0.00 0.00 2.77
252 257 7.119846 AGAGCGTAGATTCACTTATTTTGCTTT 59.880 33.333 0.00 0.00 0.00 3.51
253 258 6.595716 AGAGCGTAGATTCACTTATTTTGCTT 59.404 34.615 0.00 0.00 0.00 3.91
254 259 6.109359 AGAGCGTAGATTCACTTATTTTGCT 58.891 36.000 0.00 0.00 0.00 3.91
255 260 6.351327 AGAGCGTAGATTCACTTATTTTGC 57.649 37.500 0.00 0.00 0.00 3.68
262 267 9.250624 GACATATTTTAGAGCGTAGATTCACTT 57.749 33.333 0.00 0.00 0.00 3.16
263 268 8.634444 AGACATATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
264 269 8.804688 AGACATATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
272 277 9.627395 GATGTACATAGACATATTTTAGAGCGT 57.373 33.333 8.71 0.00 40.18 5.07
273 278 9.847706 AGATGTACATAGACATATTTTAGAGCG 57.152 33.333 8.71 0.00 40.18 5.03
282 287 9.314133 ACCACATACAGATGTACATAGACATAT 57.686 33.333 8.71 0.64 44.82 1.78
283 288 8.706322 ACCACATACAGATGTACATAGACATA 57.294 34.615 8.71 0.00 44.82 2.29
284 289 7.603180 ACCACATACAGATGTACATAGACAT 57.397 36.000 8.71 0.00 44.82 3.06
285 290 7.778382 ACTACCACATACAGATGTACATAGACA 59.222 37.037 8.71 0.00 44.82 3.41
286 291 8.167605 ACTACCACATACAGATGTACATAGAC 57.832 38.462 8.71 0.00 44.82 2.59
287 292 7.447545 GGACTACCACATACAGATGTACATAGA 59.552 40.741 8.71 0.00 44.82 1.98
288 293 7.230712 TGGACTACCACATACAGATGTACATAG 59.769 40.741 8.71 7.27 44.82 2.23
289 294 7.064229 TGGACTACCACATACAGATGTACATA 58.936 38.462 8.71 0.00 44.82 2.29
290 295 5.897250 TGGACTACCACATACAGATGTACAT 59.103 40.000 8.43 8.43 44.82 2.29
291 296 5.265989 TGGACTACCACATACAGATGTACA 58.734 41.667 0.00 0.00 44.82 2.90
292 297 5.847111 TGGACTACCACATACAGATGTAC 57.153 43.478 0.00 0.00 44.82 2.90
301 306 8.106462 TTGAGAATTCAAATGGACTACCACATA 58.894 33.333 8.44 0.00 42.50 2.29
302 307 6.947733 TTGAGAATTCAAATGGACTACCACAT 59.052 34.615 8.44 0.00 42.50 3.21
303 308 6.303054 TTGAGAATTCAAATGGACTACCACA 58.697 36.000 8.44 0.00 42.50 4.17
304 309 6.817765 TTGAGAATTCAAATGGACTACCAC 57.182 37.500 8.44 0.00 42.50 4.16
328 333 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
329 334 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
330 335 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
331 336 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
332 337 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
333 338 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
338 343 9.425248 TCTTATTACTCCCTCCGTTTCTAAATA 57.575 33.333 0.00 0.00 0.00 1.40
339 344 8.315220 TCTTATTACTCCCTCCGTTTCTAAAT 57.685 34.615 0.00 0.00 0.00 1.40
340 345 7.722949 TCTTATTACTCCCTCCGTTTCTAAA 57.277 36.000 0.00 0.00 0.00 1.85
341 346 7.909485 ATCTTATTACTCCCTCCGTTTCTAA 57.091 36.000 0.00 0.00 0.00 2.10
342 347 9.075678 CTTATCTTATTACTCCCTCCGTTTCTA 57.924 37.037 0.00 0.00 0.00 2.10
343 348 7.783596 TCTTATCTTATTACTCCCTCCGTTTCT 59.216 37.037 0.00 0.00 0.00 2.52
344 349 7.949434 TCTTATCTTATTACTCCCTCCGTTTC 58.051 38.462 0.00 0.00 0.00 2.78
345 350 7.783596 TCTCTTATCTTATTACTCCCTCCGTTT 59.216 37.037 0.00 0.00 0.00 3.60
346 351 7.296098 TCTCTTATCTTATTACTCCCTCCGTT 58.704 38.462 0.00 0.00 0.00 4.44
347 352 6.850234 TCTCTTATCTTATTACTCCCTCCGT 58.150 40.000 0.00 0.00 0.00 4.69
348 353 7.169591 TCTCTCTTATCTTATTACTCCCTCCG 58.830 42.308 0.00 0.00 0.00 4.63
349 354 7.122204 GCTCTCTCTTATCTTATTACTCCCTCC 59.878 44.444 0.00 0.00 0.00 4.30
350 355 7.668052 TGCTCTCTCTTATCTTATTACTCCCTC 59.332 40.741 0.00 0.00 0.00 4.30
351 356 7.531317 TGCTCTCTCTTATCTTATTACTCCCT 58.469 38.462 0.00 0.00 0.00 4.20
352 357 7.768807 TGCTCTCTCTTATCTTATTACTCCC 57.231 40.000 0.00 0.00 0.00 4.30
353 358 9.691362 CTTTGCTCTCTCTTATCTTATTACTCC 57.309 37.037 0.00 0.00 0.00 3.85
354 359 9.691362 CCTTTGCTCTCTCTTATCTTATTACTC 57.309 37.037 0.00 0.00 0.00 2.59
355 360 9.427821 TCCTTTGCTCTCTCTTATCTTATTACT 57.572 33.333 0.00 0.00 0.00 2.24
356 361 9.691362 CTCCTTTGCTCTCTCTTATCTTATTAC 57.309 37.037 0.00 0.00 0.00 1.89
357 362 8.364142 GCTCCTTTGCTCTCTCTTATCTTATTA 58.636 37.037 0.00 0.00 0.00 0.98
358 363 7.071071 AGCTCCTTTGCTCTCTCTTATCTTATT 59.929 37.037 0.00 0.00 39.34 1.40
359 364 6.554605 AGCTCCTTTGCTCTCTCTTATCTTAT 59.445 38.462 0.00 0.00 39.34 1.73
360 365 5.896678 AGCTCCTTTGCTCTCTCTTATCTTA 59.103 40.000 0.00 0.00 39.34 2.10
361 366 4.716287 AGCTCCTTTGCTCTCTCTTATCTT 59.284 41.667 0.00 0.00 39.34 2.40
362 367 4.289245 AGCTCCTTTGCTCTCTCTTATCT 58.711 43.478 0.00 0.00 39.34 1.98
363 368 4.670896 AGCTCCTTTGCTCTCTCTTATC 57.329 45.455 0.00 0.00 39.34 1.75
364 369 5.434182 AAAGCTCCTTTGCTCTCTCTTAT 57.566 39.130 0.00 0.00 43.24 1.73
365 370 4.899352 AAAGCTCCTTTGCTCTCTCTTA 57.101 40.909 0.00 0.00 43.24 2.10
366 371 3.786368 AAAGCTCCTTTGCTCTCTCTT 57.214 42.857 0.00 0.00 43.24 2.85
404 409 4.289238 TCTCGGGGTTTTATTGCTTGTA 57.711 40.909 0.00 0.00 0.00 2.41
406 411 3.366985 GGTTCTCGGGGTTTTATTGCTTG 60.367 47.826 0.00 0.00 0.00 4.01
407 412 2.823747 GGTTCTCGGGGTTTTATTGCTT 59.176 45.455 0.00 0.00 0.00 3.91
408 413 2.443416 GGTTCTCGGGGTTTTATTGCT 58.557 47.619 0.00 0.00 0.00 3.91
409 414 1.475280 GGGTTCTCGGGGTTTTATTGC 59.525 52.381 0.00 0.00 0.00 3.56
410 415 2.490509 GTGGGTTCTCGGGGTTTTATTG 59.509 50.000 0.00 0.00 0.00 1.90
411 416 2.799017 GTGGGTTCTCGGGGTTTTATT 58.201 47.619 0.00 0.00 0.00 1.40
413 418 0.035176 CGTGGGTTCTCGGGGTTTTA 59.965 55.000 0.00 0.00 0.00 1.52
429 434 2.505982 CCTGGCTGGGTATCCGTG 59.494 66.667 1.84 0.00 35.24 4.94
662 681 2.222678 CGGCTCCGATCTGATTTTGATG 59.777 50.000 1.35 0.00 42.83 3.07
700 719 1.134580 AGGTTGTGATCATGGCTCTCG 60.135 52.381 0.00 0.00 0.00 4.04
751 770 2.724349 CAAGCGCAAATCCTTATCTGC 58.276 47.619 11.47 0.00 0.00 4.26
793 812 2.577593 GTTCCTTCCTCGGTCGGG 59.422 66.667 0.00 0.00 0.00 5.14
829 850 0.175073 GGAGTAGGAACGGACGCATT 59.825 55.000 0.00 0.00 0.00 3.56
936 960 4.966787 TCGGTTTGGTGGCTGGGC 62.967 66.667 0.00 0.00 0.00 5.36
952 976 1.834822 CGAGGGAGGGGAGTGGATC 60.835 68.421 0.00 0.00 0.00 3.36
957 981 4.467107 GGAGCGAGGGAGGGGAGT 62.467 72.222 0.00 0.00 0.00 3.85
995 1019 1.600663 CGCTCCGCTTACTCATGTAGG 60.601 57.143 0.00 0.00 0.00 3.18
1107 1131 4.731503 GCAGCAGCAGCAACGACG 62.732 66.667 4.63 0.00 45.49 5.12
1203 1227 4.426112 CTGCTGAGCTCGTCGCCA 62.426 66.667 9.64 0.62 40.39 5.69
1255 1306 1.376942 CAGGAGCAGTGAAGCCCTG 60.377 63.158 0.00 8.37 42.40 4.45
1274 1325 1.856265 CTCTTGGTTGAAGGCGGCAC 61.856 60.000 13.08 5.41 31.85 5.01
1286 1337 1.073897 GCAGTGAAGCCCTCTTGGT 59.926 57.895 0.00 0.00 36.04 3.67
1359 1410 5.701224 TCTTCTTTTGGGTATTTGTCACCT 58.299 37.500 0.00 0.00 36.25 4.00
1367 1418 6.472887 TCGTCTTCATCTTCTTTTGGGTATT 58.527 36.000 0.00 0.00 0.00 1.89
1428 1479 3.938334 GCCCTTCTTCTTCAACAGATCTC 59.062 47.826 0.00 0.00 0.00 2.75
1507 1558 2.011046 GCTGCTAGGCTCAACTTGAGG 61.011 57.143 18.53 4.98 44.43 3.86
1543 1594 2.401766 CGTTGGCACTGCTCCCATC 61.402 63.158 0.00 0.00 0.00 3.51
1558 1609 2.281070 CTCAGGGCACTGCACGTT 60.281 61.111 12.37 0.00 44.54 3.99
1572 1623 1.293498 GAAGAGCTTCCCGCACTCA 59.707 57.895 0.00 0.00 38.68 3.41
1749 1800 1.602377 GACAGTTTAGTGTTGCGGCTT 59.398 47.619 0.00 0.00 0.00 4.35
1759 1810 0.602905 GGCAGTGGCGACAGTTTAGT 60.603 55.000 0.00 0.00 42.89 2.24
1788 1839 1.078709 GCAGTTGCGACAGATTAGCA 58.921 50.000 6.90 0.00 39.33 3.49
1790 1841 0.647410 CGGCAGTTGCGACAGATTAG 59.353 55.000 6.90 0.00 43.26 1.73
2026 2077 2.290916 GCATGACATCATCTCCTGCTTG 59.709 50.000 0.00 0.00 33.61 4.01
2039 2090 2.838736 GGTTATCACCGAGCATGACAT 58.161 47.619 0.00 0.00 31.60 3.06
2058 2109 1.303888 AGCAACAGAGGTGCCATGG 60.304 57.895 7.63 7.63 0.00 3.66
2714 2765 2.665649 TTATCACCGAGCACGACATT 57.334 45.000 4.70 0.00 42.66 2.71
2722 2773 2.870411 GGTACCATGTTTATCACCGAGC 59.130 50.000 7.15 0.00 0.00 5.03
2789 2840 2.956987 CGCAAGGGAACTGCCTTG 59.043 61.111 21.95 21.95 42.68 3.61
2860 2911 0.463204 CGTCATCTCCTGCCATCACT 59.537 55.000 0.00 0.00 0.00 3.41
2871 2922 2.094659 CGGTGCACCACGTCATCTC 61.095 63.158 34.16 4.51 34.83 2.75
2878 2929 4.710695 TCGCTACGGTGCACCACG 62.711 66.667 34.16 28.32 34.83 4.94
2936 2987 1.949525 GCCATGTTTATCACCGAGCAT 59.050 47.619 0.00 0.00 0.00 3.79
3023 3074 1.134580 CACGTCATCTCCTGCCATCTT 60.135 52.381 0.00 0.00 0.00 2.40
3084 3135 1.899814 TGCGAACTACCACATCTCCTT 59.100 47.619 0.00 0.00 0.00 3.36
3100 3151 0.109827 CATTGCCATGTTCGTTGCGA 60.110 50.000 0.00 0.00 0.00 5.10
3202 3253 2.034432 TGTGTAAGAACGCTTGACCGTA 59.966 45.455 0.00 0.00 41.16 4.02
3332 3386 0.994247 TTCTGATGTGCCTCCCATGT 59.006 50.000 0.00 0.00 0.00 3.21
3686 3740 4.222124 TCTATTCCTTTTCTGGAGCCAC 57.778 45.455 0.00 0.00 37.43 5.01
3737 3791 5.296748 TGGCTTTATTTGTTCCTGCTTTTC 58.703 37.500 0.00 0.00 0.00 2.29
3837 3903 2.214376 TTCTGCTGGGTATTGTTGGG 57.786 50.000 0.00 0.00 0.00 4.12
3944 4012 7.047891 ACTAATTCTGATCCATAGACGCAAAA 58.952 34.615 0.00 0.00 0.00 2.44
4042 4110 7.400599 TGGTCGATAAATCAAGTGTACTAGT 57.599 36.000 0.00 0.00 0.00 2.57
4209 4277 6.192360 GGATAACAAAGAATACGTCACATGC 58.808 40.000 0.00 0.00 0.00 4.06
4264 4332 8.071967 CGATGTTCAAGCATGATTTGTATGTAT 58.928 33.333 0.00 0.00 34.96 2.29
4439 4508 6.647212 TCAATTCAGCACGTTAGTATCTTG 57.353 37.500 0.00 0.00 0.00 3.02
4450 4519 4.260656 GCGAAAACTTATCAATTCAGCACG 59.739 41.667 0.00 0.00 0.00 5.34
4459 4528 8.444715 ACAATACGTTATGCGAAAACTTATCAA 58.555 29.630 0.00 0.00 44.77 2.57
4493 4562 5.762179 ACTGTCTTACTTTGATCATGGGA 57.238 39.130 0.00 0.00 0.00 4.37
4598 4673 3.246301 AGACAGGCTGTATGATATGGCT 58.754 45.455 22.11 7.02 35.69 4.75
4601 4676 8.580720 AGTTTAGTAGACAGGCTGTATGATATG 58.419 37.037 24.13 0.00 0.00 1.78
4654 4729 9.214957 AGTAGAACGTTGATTTTTGTATGATCA 57.785 29.630 5.00 0.00 0.00 2.92
4656 4731 7.962918 GCAGTAGAACGTTGATTTTTGTATGAT 59.037 33.333 5.00 0.00 0.00 2.45
4669 4744 4.744570 TCTTAGGATGCAGTAGAACGTTG 58.255 43.478 5.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.