Multiple sequence alignment - TraesCS4D01G203000

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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 TraesCS4D01G203000 chr4D 100.000 2849 0 0 1 2849 349574669 349577517 0.000000e+00 5262.0
1 TraesCS4D01G203000 chr4D 96.875 32 1 0 2010 2041 507889170 507889201 1.000000e-03 54.7
2 TraesCS4D01G203000 chr4B 88.945 2578 110 56 317 2837 432822890 432825349 0.000000e+00 3020.0
3 TraesCS4D01G203000 chr4B 93.976 166 4 4 1 160 432822728 432822893 2.190000e-61 246.0
4 TraesCS4D01G203000 chr4B 96.875 32 1 0 2010 2041 586585394 586585425 1.000000e-03 54.7
5 TraesCS4D01G203000 chr4A 92.690 1368 37 24 660 1996 115282859 115281524 0.000000e+00 1914.0
6 TraesCS4D01G203000 chr4A 86.056 502 25 16 2363 2837 115281005 115280522 5.480000e-137 497.0
7 TraesCS4D01G203000 chr4A 96.319 163 6 0 1 163 115283313 115283151 4.680000e-68 268.0
8 TraesCS4D01G203000 chr4A 83.062 307 32 10 327 629 115283149 115282859 7.830000e-66 261.0
9 TraesCS4D01G203000 chr4A 77.826 230 24 14 2061 2278 115281257 115281043 1.790000e-22 117.0
10 TraesCS4D01G203000 chr7D 95.122 164 8 0 157 320 414094770 414094933 2.820000e-65 259.0
11 TraesCS4D01G203000 chr3A 93.333 165 11 0 156 320 523738638 523738474 7.880000e-61 244.0
12 TraesCS4D01G203000 chr3D 92.353 170 13 0 155 324 46578038 46577869 2.840000e-60 243.0
13 TraesCS4D01G203000 chr3D 92.262 168 12 1 153 320 426479791 426479957 1.320000e-58 237.0
14 TraesCS4D01G203000 chr6B 92.814 167 11 1 155 320 601199600 601199434 1.020000e-59 241.0
15 TraesCS4D01G203000 chr2B 93.252 163 11 0 159 321 291855168 291855006 1.020000e-59 241.0
16 TraesCS4D01G203000 chr3B 92.262 168 12 1 153 320 540174924 540175090 1.320000e-58 237.0
17 TraesCS4D01G203000 chr3B 100.000 32 0 0 2010 2041 414494765 414494796 3.070000e-05 60.2
18 TraesCS4D01G203000 chr5B 90.164 183 14 4 153 334 474318341 474318520 4.750000e-58 235.0
19 TraesCS4D01G203000 chr1B 92.216 167 12 1 159 325 183877361 183877196 4.750000e-58 235.0


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 TraesCS4D01G203000 chr4D 349574669 349577517 2848 False 5262.0 5262 100.0000 1 2849 1 chr4D.!!$F1 2848
1 TraesCS4D01G203000 chr4B 432822728 432825349 2621 False 1633.0 3020 91.4605 1 2837 2 chr4B.!!$F2 2836
2 TraesCS4D01G203000 chr4A 115280522 115283313 2791 True 611.4 1914 87.1906 1 2837 5 chr4A.!!$R1 2836


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
668 691 0.516877 CAGCACACATACAACCACGG 59.483 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2534 0.108329 ACCACTAAATGAGCGACCGG 60.108 55.0 0.0 0.0 0.0 5.28 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
47 48 5.066593 GGAAAGAAGAAAAGAAGCTCTCCA 58.933 41.667 0.00 0.00 0.00 3.86
54 55 2.869101 AAGAAGCTCTCCACCCTTTC 57.131 50.000 0.00 0.00 0.00 2.62
164 171 9.939802 TTTCTTCAAAGAGTAAATAGTACTCCC 57.060 33.333 0.00 0.00 43.61 4.30
165 172 8.896722 TCTTCAAAGAGTAAATAGTACTCCCT 57.103 34.615 0.00 0.00 43.61 4.20
166 173 8.968969 TCTTCAAAGAGTAAATAGTACTCCCTC 58.031 37.037 0.00 0.00 43.61 4.30
167 174 7.657023 TCAAAGAGTAAATAGTACTCCCTCC 57.343 40.000 0.00 0.00 43.61 4.30
168 175 6.320672 TCAAAGAGTAAATAGTACTCCCTCCG 59.679 42.308 0.00 0.00 43.61 4.63
169 176 5.385628 AGAGTAAATAGTACTCCCTCCGT 57.614 43.478 0.00 0.00 43.61 4.69
170 177 5.764432 AGAGTAAATAGTACTCCCTCCGTT 58.236 41.667 0.00 0.00 43.61 4.44
171 178 5.827267 AGAGTAAATAGTACTCCCTCCGTTC 59.173 44.000 0.00 0.00 43.61 3.95
172 179 4.892345 AGTAAATAGTACTCCCTCCGTTCC 59.108 45.833 0.00 0.00 0.00 3.62
173 180 3.684408 AATAGTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
174 181 4.803329 AATAGTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
175 182 4.803329 ATAGTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
176 183 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
177 184 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
178 185 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
179 186 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
180 187 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
181 188 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
182 189 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
183 190 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
184 191 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
185 192 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
186 193 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
187 194 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
188 195 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
189 196 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
192 199 8.762426 CCGTTCCTAAATATAAGTCTTTGTAGC 58.238 37.037 0.00 0.00 0.00 3.58
193 200 9.309516 CGTTCCTAAATATAAGTCTTTGTAGCA 57.690 33.333 0.00 0.00 0.00 3.49
201 208 9.686683 AATATAAGTCTTTGTAGCAATTCCACT 57.313 29.630 0.00 0.00 0.00 4.00
205 212 8.723942 AAGTCTTTGTAGCAATTCCACTATAG 57.276 34.615 0.00 0.00 0.00 1.31
206 213 8.079211 AGTCTTTGTAGCAATTCCACTATAGA 57.921 34.615 6.78 0.00 0.00 1.98
207 214 7.982354 AGTCTTTGTAGCAATTCCACTATAGAC 59.018 37.037 6.78 0.00 31.41 2.59
208 215 7.224949 GTCTTTGTAGCAATTCCACTATAGACC 59.775 40.741 6.78 0.00 0.00 3.85
209 216 6.553953 TTGTAGCAATTCCACTATAGACCA 57.446 37.500 6.78 0.00 0.00 4.02
210 217 5.914033 TGTAGCAATTCCACTATAGACCAC 58.086 41.667 6.78 0.00 0.00 4.16
211 218 5.423931 TGTAGCAATTCCACTATAGACCACA 59.576 40.000 6.78 0.00 0.00 4.17
212 219 5.636903 AGCAATTCCACTATAGACCACAT 57.363 39.130 6.78 0.00 0.00 3.21
213 220 6.747414 AGCAATTCCACTATAGACCACATA 57.253 37.500 6.78 0.00 0.00 2.29
214 221 6.525629 AGCAATTCCACTATAGACCACATAC 58.474 40.000 6.78 0.00 0.00 2.39
215 222 5.405571 GCAATTCCACTATAGACCACATACG 59.594 44.000 6.78 0.00 0.00 3.06
216 223 5.723672 ATTCCACTATAGACCACATACGG 57.276 43.478 6.78 0.00 0.00 4.02
217 224 4.442401 TCCACTATAGACCACATACGGA 57.558 45.455 6.78 0.00 0.00 4.69
218 225 4.994282 TCCACTATAGACCACATACGGAT 58.006 43.478 6.78 0.00 0.00 4.18
219 226 4.765339 TCCACTATAGACCACATACGGATG 59.235 45.833 5.94 5.94 39.16 3.51
221 228 5.708697 CCACTATAGACCACATACGGATGTA 59.291 44.000 14.23 0.00 44.82 2.29
222 229 6.377429 CCACTATAGACCACATACGGATGTAT 59.623 42.308 14.23 4.48 44.82 2.29
223 230 7.555195 CCACTATAGACCACATACGGATGTATA 59.445 40.741 14.23 6.48 44.82 1.47
224 231 9.121658 CACTATAGACCACATACGGATGTATAT 57.878 37.037 14.23 11.61 44.82 0.86
229 236 8.226819 AGACCACATACGGATGTATATAGATG 57.773 38.462 14.23 0.00 44.82 2.90
230 237 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
231 238 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
232 239 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
233 240 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
234 241 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
235 242 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
239 246 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
240 247 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
251 258 9.624373 AGATGCATTTTAGAGTGTAGATTCATT 57.376 29.630 0.00 0.00 0.00 2.57
252 259 9.875675 GATGCATTTTAGAGTGTAGATTCATTC 57.124 33.333 0.00 0.00 0.00 2.67
253 260 8.791327 TGCATTTTAGAGTGTAGATTCATTCA 57.209 30.769 0.00 0.00 0.00 2.57
254 261 9.399797 TGCATTTTAGAGTGTAGATTCATTCAT 57.600 29.630 0.00 0.00 0.00 2.57
262 269 8.734386 AGAGTGTAGATTCATTCATTTTGTTCC 58.266 33.333 0.00 0.00 0.00 3.62
263 270 7.530010 AGTGTAGATTCATTCATTTTGTTCCG 58.470 34.615 0.00 0.00 0.00 4.30
264 271 7.174946 AGTGTAGATTCATTCATTTTGTTCCGT 59.825 33.333 0.00 0.00 0.00 4.69
265 272 8.447833 GTGTAGATTCATTCATTTTGTTCCGTA 58.552 33.333 0.00 0.00 0.00 4.02
266 273 9.173021 TGTAGATTCATTCATTTTGTTCCGTAT 57.827 29.630 0.00 0.00 0.00 3.06
267 274 9.438291 GTAGATTCATTCATTTTGTTCCGTATG 57.562 33.333 0.00 0.00 0.00 2.39
268 275 8.055279 AGATTCATTCATTTTGTTCCGTATGT 57.945 30.769 0.00 0.00 0.00 2.29
269 276 9.173021 AGATTCATTCATTTTGTTCCGTATGTA 57.827 29.630 0.00 0.00 0.00 2.29
270 277 9.438291 GATTCATTCATTTTGTTCCGTATGTAG 57.562 33.333 0.00 0.00 0.00 2.74
271 278 7.915293 TCATTCATTTTGTTCCGTATGTAGT 57.085 32.000 0.00 0.00 0.00 2.73
272 279 8.330466 TCATTCATTTTGTTCCGTATGTAGTT 57.670 30.769 0.00 0.00 0.00 2.24
273 280 8.788806 TCATTCATTTTGTTCCGTATGTAGTTT 58.211 29.630 0.00 0.00 0.00 2.66
280 287 9.926158 TTTTGTTCCGTATGTAGTTTATAGTGA 57.074 29.630 0.00 0.00 0.00 3.41
281 288 9.926158 TTTGTTCCGTATGTAGTTTATAGTGAA 57.074 29.630 0.00 0.00 0.00 3.18
282 289 9.926158 TTGTTCCGTATGTAGTTTATAGTGAAA 57.074 29.630 0.00 0.00 0.00 2.69
428 436 4.731773 GCACTGGTAGCTTTATTCATGCAC 60.732 45.833 0.00 0.00 0.00 4.57
484 507 5.221581 ACCCTACTACCTTTGGCAATATACG 60.222 44.000 0.00 0.00 0.00 3.06
491 514 1.021202 TTGGCAATATACGCAGGCAC 58.979 50.000 0.00 0.00 36.22 5.01
514 537 7.466996 GCACGAGTACATACATCTAGTTACTGT 60.467 40.741 0.00 0.00 0.00 3.55
515 538 8.396390 CACGAGTACATACATCTAGTTACTGTT 58.604 37.037 0.00 0.00 0.00 3.16
553 576 3.990318 AGTTACTGTTTGCTTTGCTCC 57.010 42.857 0.00 0.00 0.00 4.70
582 605 4.906423 AGCGTGAATTGTACTCTACTACG 58.094 43.478 0.00 0.00 0.00 3.51
583 606 4.394300 AGCGTGAATTGTACTCTACTACGT 59.606 41.667 0.00 0.00 0.00 3.57
584 607 5.582269 AGCGTGAATTGTACTCTACTACGTA 59.418 40.000 0.00 0.00 0.00 3.57
585 608 5.674580 GCGTGAATTGTACTCTACTACGTAC 59.325 44.000 0.00 0.00 37.19 3.67
635 658 7.941795 AGTGTACTACAACTTCAATACACAC 57.058 36.000 13.17 0.00 43.03 3.82
650 673 5.748670 ATACACACCCACATAACAGTACA 57.251 39.130 0.00 0.00 0.00 2.90
664 687 3.399330 ACAGTACAGCACACATACAACC 58.601 45.455 0.00 0.00 0.00 3.77
668 691 0.516877 CAGCACACATACAACCACGG 59.483 55.000 0.00 0.00 0.00 4.94
695 718 5.922960 AGGTCATCTGATCTACTAGGAGT 57.077 43.478 0.78 0.00 32.86 3.85
732 756 1.401552 GAGTGAGCACAACTGCACAAA 59.598 47.619 3.19 0.00 44.37 2.83
743 767 2.233271 ACTGCACAAAGACAATCCCTG 58.767 47.619 0.00 0.00 0.00 4.45
823 851 2.749621 CTGTTTTCTTGGATTCCTCCCG 59.250 50.000 3.95 0.00 41.29 5.14
928 956 3.536434 TCCTCTATTAACTCACTCCCCCT 59.464 47.826 0.00 0.00 0.00 4.79
958 986 4.287781 TTGCGACCGTCGGAGCAA 62.288 61.111 31.89 31.89 42.14 3.91
1425 1468 2.915659 ACCTGGTGCTCCGACGAA 60.916 61.111 0.00 0.00 36.30 3.85
1911 1971 5.467063 TGTAGTACGTGTGCATGAAAAATGA 59.533 36.000 0.00 0.00 0.00 2.57
1978 2272 2.755836 ATTGCATTATCGGCGTCAAC 57.244 45.000 6.85 0.00 0.00 3.18
1982 2276 2.799978 TGCATTATCGGCGTCAACTATG 59.200 45.455 6.85 4.98 0.00 2.23
1984 2278 3.985279 GCATTATCGGCGTCAACTATGTA 59.015 43.478 6.85 0.00 0.00 2.29
1991 2285 3.000925 CGGCGTCAACTATGTATGTTTCC 59.999 47.826 0.00 0.00 0.00 3.13
1993 2287 4.270325 GGCGTCAACTATGTATGTTTCCTC 59.730 45.833 0.00 0.00 0.00 3.71
2004 2298 1.497991 TGTTTCCTCTTCTTCGCGTG 58.502 50.000 5.77 0.00 0.00 5.34
2005 2299 1.202486 TGTTTCCTCTTCTTCGCGTGT 60.202 47.619 5.77 0.00 0.00 4.49
2006 2300 1.456165 GTTTCCTCTTCTTCGCGTGTC 59.544 52.381 5.77 0.00 0.00 3.67
2007 2301 0.959553 TTCCTCTTCTTCGCGTGTCT 59.040 50.000 5.77 0.00 0.00 3.41
2008 2302 1.817357 TCCTCTTCTTCGCGTGTCTA 58.183 50.000 5.77 0.00 0.00 2.59
2015 2309 0.377554 CTTCGCGTGTCTATCCGTCT 59.622 55.000 5.77 0.00 0.00 4.18
2024 2318 5.462398 GCGTGTCTATCCGTCTCAAAATAAT 59.538 40.000 0.00 0.00 0.00 1.28
2029 2323 8.258007 TGTCTATCCGTCTCAAAATAATTGTCT 58.742 33.333 0.00 0.00 0.00 3.41
2033 2327 7.129109 TCCGTCTCAAAATAATTGTCTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
2048 2343 6.241207 TGTCTCAACTTTATACAAAGCAGC 57.759 37.500 0.00 0.00 44.27 5.25
2050 2345 6.430925 TGTCTCAACTTTATACAAAGCAGCAT 59.569 34.615 0.00 0.00 44.27 3.79
2054 2349 9.624697 CTCAACTTTATACAAAGCAGCATAAAA 57.375 29.630 0.00 0.00 44.27 1.52
2202 2521 0.889186 AAGTGCCGGTCGCTCATTTT 60.889 50.000 1.90 0.00 38.78 1.82
2203 2522 0.889186 AGTGCCGGTCGCTCATTTTT 60.889 50.000 1.90 0.00 38.78 1.94
2221 2540 2.281900 TTTTTGAGGGGCCGGTCG 60.282 61.111 1.90 0.00 0.00 4.79
2228 2547 4.796495 GGGGCCGGTCGCTCATTT 62.796 66.667 17.03 0.00 41.20 2.32
2246 2565 5.437060 TCATTTAGTGGTGATTAAGGAGGC 58.563 41.667 0.00 0.00 0.00 4.70
2344 2687 0.999406 CGGGAACACGAGCTGTATTG 59.001 55.000 0.00 0.00 35.47 1.90
2354 2697 2.409715 CGAGCTGTATTGCGATATGTGG 59.590 50.000 0.00 0.00 38.13 4.17
2397 2740 0.391395 GCTGCTGATCTGCTGTGACT 60.391 55.000 25.05 0.00 36.79 3.41
2416 2759 1.339929 CTCCAAAACAAAACCTCCCGG 59.660 52.381 0.00 0.00 0.00 5.73
2457 2802 2.120232 CGATGTGTTGGAGTATCTCGC 58.880 52.381 0.00 0.00 33.73 5.03
2610 2975 4.104417 GCGCGAGGTGAGACGAGT 62.104 66.667 12.10 0.00 0.00 4.18
2644 3012 3.542676 AACCACCCGCACTCGTGA 61.543 61.111 0.39 0.00 31.36 4.35
2645 3013 3.515316 AACCACCCGCACTCGTGAG 62.515 63.158 0.39 0.00 31.36 3.51
2650 3028 4.803426 CCGCACTCGTGAGCCTCC 62.803 72.222 0.39 0.00 0.00 4.30
2662 3040 2.740055 GCCTCCTGCTGTGTCGTG 60.740 66.667 0.00 0.00 36.87 4.35
2670 3048 4.329545 CTGTGTCGTGGGGGTGGG 62.330 72.222 0.00 0.00 0.00 4.61
2788 3170 0.456221 CAGGCAGTACCACTCCTACG 59.544 60.000 0.00 0.00 43.14 3.51
2820 3202 4.074970 TCTTCATTCTTGCTTTGACCTCC 58.925 43.478 0.00 0.00 0.00 4.30
2821 3203 3.795688 TCATTCTTGCTTTGACCTCCT 57.204 42.857 0.00 0.00 0.00 3.69
2822 3204 3.679389 TCATTCTTGCTTTGACCTCCTC 58.321 45.455 0.00 0.00 0.00 3.71
2823 3205 2.568623 TTCTTGCTTTGACCTCCTCC 57.431 50.000 0.00 0.00 0.00 4.30
2837 3219 2.281345 CTCCCCTGATGCGATGCC 60.281 66.667 0.00 0.00 0.00 4.40
2838 3220 3.089217 TCCCCTGATGCGATGCCA 61.089 61.111 0.00 0.00 0.00 4.92
2839 3221 2.114625 CCCCTGATGCGATGCCAT 59.885 61.111 0.00 0.00 0.00 4.40
2840 3222 2.265904 CCCCTGATGCGATGCCATG 61.266 63.158 0.00 0.00 0.00 3.66
2841 3223 2.643272 CCTGATGCGATGCCATGC 59.357 61.111 0.00 0.00 0.00 4.06
2842 3224 2.643272 CTGATGCGATGCCATGCC 59.357 61.111 0.00 0.00 0.00 4.40
2843 3225 2.124236 TGATGCGATGCCATGCCA 60.124 55.556 0.00 0.00 0.00 4.92
2844 3226 1.524008 CTGATGCGATGCCATGCCAT 61.524 55.000 0.00 0.00 0.00 4.40
2845 3227 1.080772 GATGCGATGCCATGCCATG 60.081 57.895 0.00 0.00 0.00 3.66
2846 3228 3.220999 ATGCGATGCCATGCCATGC 62.221 57.895 0.00 0.00 0.00 4.06
2847 3229 4.994201 GCGATGCCATGCCATGCG 62.994 66.667 0.00 0.00 0.00 4.73
2848 3230 3.281395 CGATGCCATGCCATGCGA 61.281 61.111 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.876303 AGCTTCTTTTCTTCTTTCCATTATCT 57.124 30.769 0.00 0.00 0.00 1.98
121 128 5.122239 TGAAGAAAAAGAGCACGTATGGATG 59.878 40.000 0.00 0.00 0.00 3.51
160 167 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
163 170 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
164 171 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
166 173 8.762426 GCTACAAAGACTTATATTTAGGAACGG 58.238 37.037 0.00 0.00 0.00 4.44
167 174 9.309516 TGCTACAAAGACTTATATTTAGGAACG 57.690 33.333 0.00 0.00 0.00 3.95
175 182 9.686683 AGTGGAATTGCTACAAAGACTTATATT 57.313 29.630 0.00 0.00 0.00 1.28
179 186 9.817809 CTATAGTGGAATTGCTACAAAGACTTA 57.182 33.333 0.00 0.00 0.00 2.24
180 187 8.540388 TCTATAGTGGAATTGCTACAAAGACTT 58.460 33.333 0.00 0.00 0.00 3.01
181 188 7.982354 GTCTATAGTGGAATTGCTACAAAGACT 59.018 37.037 0.00 0.00 34.01 3.24
182 189 7.224949 GGTCTATAGTGGAATTGCTACAAAGAC 59.775 40.741 0.00 6.22 35.01 3.01
183 190 7.093068 TGGTCTATAGTGGAATTGCTACAAAGA 60.093 37.037 0.00 0.00 0.00 2.52
184 191 7.011482 GTGGTCTATAGTGGAATTGCTACAAAG 59.989 40.741 0.00 0.00 0.00 2.77
185 192 6.821665 GTGGTCTATAGTGGAATTGCTACAAA 59.178 38.462 0.00 0.00 0.00 2.83
186 193 6.070481 TGTGGTCTATAGTGGAATTGCTACAA 60.070 38.462 0.00 0.00 0.00 2.41
187 194 5.423931 TGTGGTCTATAGTGGAATTGCTACA 59.576 40.000 0.00 0.00 0.00 2.74
188 195 5.914033 TGTGGTCTATAGTGGAATTGCTAC 58.086 41.667 0.00 0.00 0.00 3.58
189 196 6.747414 ATGTGGTCTATAGTGGAATTGCTA 57.253 37.500 0.00 0.00 0.00 3.49
190 197 5.636903 ATGTGGTCTATAGTGGAATTGCT 57.363 39.130 0.00 0.00 0.00 3.91
191 198 5.405571 CGTATGTGGTCTATAGTGGAATTGC 59.594 44.000 0.00 0.00 0.00 3.56
192 199 5.926542 CCGTATGTGGTCTATAGTGGAATTG 59.073 44.000 0.00 0.00 0.00 2.32
193 200 5.836898 TCCGTATGTGGTCTATAGTGGAATT 59.163 40.000 0.00 0.00 0.00 2.17
194 201 5.391256 TCCGTATGTGGTCTATAGTGGAAT 58.609 41.667 0.00 0.00 0.00 3.01
195 202 4.795469 TCCGTATGTGGTCTATAGTGGAA 58.205 43.478 0.00 0.00 0.00 3.53
196 203 4.442401 TCCGTATGTGGTCTATAGTGGA 57.558 45.455 0.00 0.00 0.00 4.02
197 204 4.523173 ACATCCGTATGTGGTCTATAGTGG 59.477 45.833 0.00 0.00 44.79 4.00
198 205 5.707242 ACATCCGTATGTGGTCTATAGTG 57.293 43.478 0.00 0.00 44.79 2.74
203 210 9.338622 CATCTATATACATCCGTATGTGGTCTA 57.661 37.037 3.56 0.00 45.99 2.59
204 211 7.201830 GCATCTATATACATCCGTATGTGGTCT 60.202 40.741 3.56 0.00 45.99 3.85
205 212 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
206 213 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
207 214 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
208 215 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
213 220 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
214 221 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
225 232 9.624373 AATGAATCTACACTCTAAAATGCATCT 57.376 29.630 0.00 0.00 0.00 2.90
226 233 9.875675 GAATGAATCTACACTCTAAAATGCATC 57.124 33.333 0.00 0.00 0.00 3.91
227 234 9.399797 TGAATGAATCTACACTCTAAAATGCAT 57.600 29.630 0.00 0.00 0.00 3.96
228 235 8.791327 TGAATGAATCTACACTCTAAAATGCA 57.209 30.769 0.00 0.00 0.00 3.96
236 243 8.734386 GGAACAAAATGAATGAATCTACACTCT 58.266 33.333 0.00 0.00 0.00 3.24
237 244 7.693951 CGGAACAAAATGAATGAATCTACACTC 59.306 37.037 0.00 0.00 0.00 3.51
238 245 7.174946 ACGGAACAAAATGAATGAATCTACACT 59.825 33.333 0.00 0.00 0.00 3.55
239 246 7.305474 ACGGAACAAAATGAATGAATCTACAC 58.695 34.615 0.00 0.00 0.00 2.90
240 247 7.447374 ACGGAACAAAATGAATGAATCTACA 57.553 32.000 0.00 0.00 0.00 2.74
241 248 9.438291 CATACGGAACAAAATGAATGAATCTAC 57.562 33.333 0.00 0.00 0.00 2.59
242 249 9.173021 ACATACGGAACAAAATGAATGAATCTA 57.827 29.630 0.00 0.00 0.00 1.98
243 250 8.055279 ACATACGGAACAAAATGAATGAATCT 57.945 30.769 0.00 0.00 0.00 2.40
244 251 9.438291 CTACATACGGAACAAAATGAATGAATC 57.562 33.333 0.00 0.00 0.00 2.52
245 252 8.956426 ACTACATACGGAACAAAATGAATGAAT 58.044 29.630 0.00 0.00 0.00 2.57
246 253 8.330466 ACTACATACGGAACAAAATGAATGAA 57.670 30.769 0.00 0.00 0.00 2.57
247 254 7.915293 ACTACATACGGAACAAAATGAATGA 57.085 32.000 0.00 0.00 0.00 2.57
248 255 8.964420 AAACTACATACGGAACAAAATGAATG 57.036 30.769 0.00 0.00 0.00 2.67
254 261 9.926158 TCACTATAAACTACATACGGAACAAAA 57.074 29.630 0.00 0.00 0.00 2.44
255 262 9.926158 TTCACTATAAACTACATACGGAACAAA 57.074 29.630 0.00 0.00 0.00 2.83
256 263 9.926158 TTTCACTATAAACTACATACGGAACAA 57.074 29.630 0.00 0.00 0.00 2.83
295 302 9.257651 CGTACTCCCTTTGTTCCTAAATATAAG 57.742 37.037 0.00 0.00 0.00 1.73
296 303 8.761689 ACGTACTCCCTTTGTTCCTAAATATAA 58.238 33.333 0.00 0.00 0.00 0.98
297 304 8.310122 ACGTACTCCCTTTGTTCCTAAATATA 57.690 34.615 0.00 0.00 0.00 0.86
298 305 7.191593 ACGTACTCCCTTTGTTCCTAAATAT 57.808 36.000 0.00 0.00 0.00 1.28
299 306 6.610075 ACGTACTCCCTTTGTTCCTAAATA 57.390 37.500 0.00 0.00 0.00 1.40
300 307 5.494390 ACGTACTCCCTTTGTTCCTAAAT 57.506 39.130 0.00 0.00 0.00 1.40
301 308 4.961438 ACGTACTCCCTTTGTTCCTAAA 57.039 40.909 0.00 0.00 0.00 1.85
302 309 4.082787 CGTACGTACTCCCTTTGTTCCTAA 60.083 45.833 22.55 0.00 0.00 2.69
303 310 3.440173 CGTACGTACTCCCTTTGTTCCTA 59.560 47.826 22.55 0.00 0.00 2.94
304 311 2.229784 CGTACGTACTCCCTTTGTTCCT 59.770 50.000 22.55 0.00 0.00 3.36
305 312 2.029918 ACGTACGTACTCCCTTTGTTCC 60.030 50.000 21.41 0.00 0.00 3.62
306 313 3.288809 ACGTACGTACTCCCTTTGTTC 57.711 47.619 21.41 0.00 0.00 3.18
307 314 3.191371 CCTACGTACGTACTCCCTTTGTT 59.809 47.826 23.60 0.00 0.00 2.83
308 315 2.749621 CCTACGTACGTACTCCCTTTGT 59.250 50.000 23.60 13.45 0.00 2.83
309 316 2.749621 ACCTACGTACGTACTCCCTTTG 59.250 50.000 23.60 11.40 0.00 2.77
310 317 3.073274 ACCTACGTACGTACTCCCTTT 57.927 47.619 23.60 0.00 0.00 3.11
311 318 2.789409 ACCTACGTACGTACTCCCTT 57.211 50.000 23.60 0.00 0.00 3.95
312 319 3.906720 TTACCTACGTACGTACTCCCT 57.093 47.619 23.60 7.28 0.00 4.20
313 320 6.803154 ATTATTACCTACGTACGTACTCCC 57.197 41.667 23.60 0.00 0.00 4.30
314 321 7.010023 CGAATTATTACCTACGTACGTACTCC 58.990 42.308 23.60 0.00 0.00 3.85
315 322 7.564988 ACGAATTATTACCTACGTACGTACTC 58.435 38.462 23.60 3.08 32.42 2.59
316 323 7.438459 AGACGAATTATTACCTACGTACGTACT 59.562 37.037 23.60 13.87 34.26 2.73
317 324 7.564988 AGACGAATTATTACCTACGTACGTAC 58.435 38.462 23.60 15.90 34.26 3.67
318 325 7.095774 GGAGACGAATTATTACCTACGTACGTA 60.096 40.741 25.41 25.41 34.26 3.57
319 326 6.292919 GGAGACGAATTATTACCTACGTACGT 60.293 42.308 25.98 25.98 34.26 3.57
320 327 6.073548 AGGAGACGAATTATTACCTACGTACG 60.074 42.308 15.01 15.01 34.26 3.67
355 362 8.973228 CAGGAACTCAACTCAGGATGAAGCAT 62.973 46.154 0.00 0.00 41.80 3.79
356 363 7.766155 CAGGAACTCAACTCAGGATGAAGCA 62.766 48.000 0.00 0.00 41.80 3.91
428 436 2.746362 GAGCAGGTTCTGGATCAAAGTG 59.254 50.000 0.00 0.00 31.21 3.16
484 507 2.128035 GATGTATGTACTCGTGCCTGC 58.872 52.381 0.00 0.00 0.00 4.85
491 514 9.784680 AAAACAGTAACTAGATGTATGTACTCG 57.215 33.333 0.00 0.00 0.00 4.18
553 576 2.475111 AGTACAATTCACGCTTCACACG 59.525 45.455 0.00 0.00 0.00 4.49
582 605 4.392921 ACTCCTGTGCAGTATCATGTAC 57.607 45.455 0.00 0.00 36.46 2.90
583 606 4.341235 GGTACTCCTGTGCAGTATCATGTA 59.659 45.833 0.00 0.00 29.12 2.29
584 607 3.133003 GGTACTCCTGTGCAGTATCATGT 59.867 47.826 0.00 0.00 29.12 3.21
585 608 3.132824 TGGTACTCCTGTGCAGTATCATG 59.867 47.826 0.00 0.00 33.37 3.07
635 658 2.742053 GTGTGCTGTACTGTTATGTGGG 59.258 50.000 1.46 0.00 0.00 4.61
650 673 0.394938 TCCGTGGTTGTATGTGTGCT 59.605 50.000 0.00 0.00 0.00 4.40
664 687 0.526211 TCAGATGACCTTCGTCCGTG 59.474 55.000 0.00 0.00 38.32 4.94
668 691 5.180492 CCTAGTAGATCAGATGACCTTCGTC 59.820 48.000 0.00 0.00 39.66 4.20
695 718 1.227249 CTCACTCTCCCTCCCTCCTA 58.773 60.000 0.00 0.00 0.00 2.94
732 756 1.566298 GCCAGTCCCAGGGATTGTCT 61.566 60.000 25.64 10.10 37.68 3.41
743 767 1.064463 TGATTGATTCCAGCCAGTCCC 60.064 52.381 0.00 0.00 0.00 4.46
1026 1054 1.997928 CTCTCGCTCTCACCATCGCA 61.998 60.000 0.00 0.00 0.00 5.10
1936 2000 3.428870 ACGTAGAATGAAAGCGACACTTG 59.571 43.478 0.00 0.00 39.09 3.16
1944 2008 7.475565 CGATAATGCAATACGTAGAATGAAAGC 59.524 37.037 0.08 0.00 0.00 3.51
1978 2272 5.174035 CGCGAAGAAGAGGAAACATACATAG 59.826 44.000 0.00 0.00 0.00 2.23
1982 2276 3.060895 CACGCGAAGAAGAGGAAACATAC 59.939 47.826 15.93 0.00 0.00 2.39
1984 2278 2.069273 CACGCGAAGAAGAGGAAACAT 58.931 47.619 15.93 0.00 0.00 2.71
1991 2285 2.722071 GGATAGACACGCGAAGAAGAG 58.278 52.381 15.93 0.00 0.00 2.85
1993 2287 1.202154 ACGGATAGACACGCGAAGAAG 60.202 52.381 15.93 0.00 0.00 2.85
2004 2298 8.649973 AGACAATTATTTTGAGACGGATAGAC 57.350 34.615 0.00 0.00 0.00 2.59
2005 2299 8.474831 TGAGACAATTATTTTGAGACGGATAGA 58.525 33.333 0.00 0.00 0.00 1.98
2006 2300 8.648557 TGAGACAATTATTTTGAGACGGATAG 57.351 34.615 0.00 0.00 0.00 2.08
2007 2301 8.879759 GTTGAGACAATTATTTTGAGACGGATA 58.120 33.333 0.00 0.00 0.00 2.59
2008 2302 7.607991 AGTTGAGACAATTATTTTGAGACGGAT 59.392 33.333 0.00 0.00 0.00 4.18
2024 2318 6.262049 TGCTGCTTTGTATAAAGTTGAGACAA 59.738 34.615 12.82 0.00 44.11 3.18
2037 2331 7.829725 TGTCTCAATTTTATGCTGCTTTGTAT 58.170 30.769 0.00 0.00 0.00 2.29
2041 2335 6.336842 ACTGTCTCAATTTTATGCTGCTTT 57.663 33.333 0.00 0.00 0.00 3.51
2054 2349 7.310609 CCCCCATTTCAAAATAACTGTCTCAAT 60.311 37.037 0.00 0.00 0.00 2.57
2073 2368 6.980577 TCTATGAAACAAATACTCCCCCATT 58.019 36.000 0.00 0.00 0.00 3.16
2076 2371 6.661805 TGTTTCTATGAAACAAATACTCCCCC 59.338 38.462 19.44 0.00 37.22 5.40
2113 2416 2.257371 CGCCGTCTTTGTCTCGGA 59.743 61.111 7.01 0.00 46.05 4.55
2204 2523 2.281900 CGACCGGCCCCTCAAAAA 60.282 61.111 0.00 0.00 0.00 1.94
2211 2530 3.394635 TAAATGAGCGACCGGCCCC 62.395 63.158 0.00 0.00 45.17 5.80
2212 2531 1.887707 CTAAATGAGCGACCGGCCC 60.888 63.158 0.00 0.00 45.17 5.80
2213 2532 1.153429 ACTAAATGAGCGACCGGCC 60.153 57.895 0.00 0.00 45.17 6.13
2214 2533 1.429148 CCACTAAATGAGCGACCGGC 61.429 60.000 0.00 0.00 44.05 6.13
2215 2534 0.108329 ACCACTAAATGAGCGACCGG 60.108 55.000 0.00 0.00 0.00 5.28
2216 2535 0.999406 CACCACTAAATGAGCGACCG 59.001 55.000 0.00 0.00 0.00 4.79
2217 2536 2.380084 TCACCACTAAATGAGCGACC 57.620 50.000 0.00 0.00 0.00 4.79
2218 2537 5.006746 CCTTAATCACCACTAAATGAGCGAC 59.993 44.000 0.00 0.00 0.00 5.19
2219 2538 5.105106 TCCTTAATCACCACTAAATGAGCGA 60.105 40.000 0.00 0.00 0.00 4.93
2220 2539 5.116180 TCCTTAATCACCACTAAATGAGCG 58.884 41.667 0.00 0.00 0.00 5.03
2221 2540 5.529060 CCTCCTTAATCACCACTAAATGAGC 59.471 44.000 0.00 0.00 0.00 4.26
2222 2541 5.529060 GCCTCCTTAATCACCACTAAATGAG 59.471 44.000 0.00 0.00 0.00 2.90
2223 2542 5.191722 AGCCTCCTTAATCACCACTAAATGA 59.808 40.000 0.00 0.00 0.00 2.57
2224 2543 5.297776 CAGCCTCCTTAATCACCACTAAATG 59.702 44.000 0.00 0.00 0.00 2.32
2225 2544 5.440610 CAGCCTCCTTAATCACCACTAAAT 58.559 41.667 0.00 0.00 0.00 1.40
2226 2545 4.843728 CAGCCTCCTTAATCACCACTAAA 58.156 43.478 0.00 0.00 0.00 1.85
2227 2546 3.370527 GCAGCCTCCTTAATCACCACTAA 60.371 47.826 0.00 0.00 0.00 2.24
2228 2547 2.170607 GCAGCCTCCTTAATCACCACTA 59.829 50.000 0.00 0.00 0.00 2.74
2246 2565 1.379044 GTTCAGGGGTGGATGGCAG 60.379 63.158 0.00 0.00 0.00 4.85
2322 2652 4.003788 CAGCTCGTGTTCCCGGGT 62.004 66.667 22.86 0.00 0.00 5.28
2323 2653 1.956629 ATACAGCTCGTGTTCCCGGG 61.957 60.000 16.85 16.85 40.94 5.73
2324 2654 0.108329 AATACAGCTCGTGTTCCCGG 60.108 55.000 0.00 0.00 40.94 5.73
2328 2671 1.346365 TCGCAATACAGCTCGTGTTC 58.654 50.000 0.00 0.00 40.94 3.18
2344 2687 1.797046 CAGATCAGCACCACATATCGC 59.203 52.381 0.00 0.00 0.00 4.58
2354 2697 2.476873 ATCGACGTACAGATCAGCAC 57.523 50.000 0.00 0.00 0.00 4.40
2432 2775 3.960755 AGATACTCCAACACATCGATCCA 59.039 43.478 0.00 0.00 0.00 3.41
2433 2776 4.551388 GAGATACTCCAACACATCGATCC 58.449 47.826 0.00 0.00 0.00 3.36
2474 2819 2.438434 CGTCAATCAGCCCACCCC 60.438 66.667 0.00 0.00 0.00 4.95
2605 2970 0.249489 GCACCTTCACTCACACTCGT 60.249 55.000 0.00 0.00 0.00 4.18
2610 2975 1.153269 TTGCGCACCTTCACTCACA 60.153 52.632 11.12 0.00 0.00 3.58
2645 3013 2.740055 CACGACACAGCAGGAGGC 60.740 66.667 0.00 0.00 45.30 4.70
2650 3028 3.941188 ACCCCCACGACACAGCAG 61.941 66.667 0.00 0.00 0.00 4.24
2695 3073 4.773117 GGCGGTCGAGTCGTGTCC 62.773 72.222 13.12 12.30 0.00 4.02
2713 3091 3.076621 CCGGTAAGGTAAGACCAAAACC 58.923 50.000 0.00 1.83 41.95 3.27
2788 3170 2.399916 AGAATGAAGACCAGCAGCTC 57.600 50.000 0.00 0.00 0.00 4.09
2820 3202 2.281345 GGCATCGCATCAGGGGAG 60.281 66.667 0.00 0.00 42.26 4.30
2821 3203 2.454688 ATGGCATCGCATCAGGGGA 61.455 57.895 0.00 0.00 43.25 4.81
2822 3204 2.114625 ATGGCATCGCATCAGGGG 59.885 61.111 0.00 0.00 0.00 4.79
2823 3205 2.916052 GCATGGCATCGCATCAGGG 61.916 63.158 14.33 0.00 0.00 4.45



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

AutoCloner maintained by Alex Coulton.