Multiple sequence alignment - TraesCS6B01G245700

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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 TraesCS6B01G245700 chr6B 100.000 3005 0 0 1 3005 438387910 438384906 0.000000e+00 5550
1 TraesCS6B01G245700 chr6B 82.422 256 36 7 2220 2472 540603904 540604153 6.520000e-52 215
2 TraesCS6B01G245700 chr6B 81.641 256 37 6 2220 2472 560180815 560180567 1.410000e-48 204
3 TraesCS6B01G245700 chr6D 93.232 1980 76 23 236 2197 276457635 276455696 0.000000e+00 2861
4 TraesCS6B01G245700 chr6D 74.433 485 85 26 2551 3005 84647540 84647065 3.980000e-39 172
5 TraesCS6B01G245700 chr6A 93.693 1871 58 22 357 2214 399721375 399723198 0.000000e+00 2747
6 TraesCS6B01G245700 chr6A 89.737 799 64 15 2220 3005 399723245 399724038 0.000000e+00 1005
7 TraesCS6B01G245700 chr6A 80.000 335 53 9 2220 2548 71663675 71663349 5.010000e-58 235
8 TraesCS6B01G245700 chr6A 93.388 121 8 0 1 121 399721057 399721177 2.380000e-41 180
9 TraesCS6B01G245700 chr6A 90.566 106 7 2 255 360 399721193 399721295 1.450000e-28 137
10 TraesCS6B01G245700 chr3B 85.829 995 91 25 1118 2098 766631403 766632361 0.000000e+00 1011
11 TraesCS6B01G245700 chr3B 81.360 1191 150 36 992 2135 769056382 769055217 0.000000e+00 904
12 TraesCS6B01G245700 chr3B 81.642 670 82 20 2274 2932 801187521 801186882 4.440000e-143 518
13 TraesCS6B01G245700 chr3B 79.784 742 102 34 2274 3001 169333216 169333923 2.080000e-136 496
14 TraesCS6B01G245700 chr3A 84.774 1018 98 26 1118 2118 711217980 711218957 0.000000e+00 968
15 TraesCS6B01G245700 chr3A 83.268 1022 113 30 1118 2122 711203103 711204083 0.000000e+00 887
16 TraesCS6B01G245700 chr3A 87.365 554 48 8 1459 2002 712571794 712571253 1.530000e-172 616
17 TraesCS6B01G245700 chr3A 83.425 543 55 20 1145 1667 712572319 712571792 3.510000e-129 472
18 TraesCS6B01G245700 chr3A 74.178 426 47 32 698 1075 711217458 711217868 5.260000e-23 119
19 TraesCS6B01G245700 chr3D 85.000 1000 91 33 1118 2094 575726010 575726973 0.000000e+00 961
20 TraesCS6B01G245700 chr3D 85.155 869 93 21 1145 2002 577255686 577254843 0.000000e+00 857
21 TraesCS6B01G245700 chr3D 92.331 326 19 1 1468 1787 577264186 577263861 2.730000e-125 459
22 TraesCS6B01G245700 chr3D 78.373 467 74 20 2551 3005 580329773 580329322 8.200000e-71 278
23 TraesCS6B01G245700 chr3D 76.033 242 38 8 1908 2134 577263863 577263627 1.140000e-19 108
24 TraesCS6B01G245700 chr5A 88.150 346 33 6 1661 2002 85164426 85164085 3.610000e-109 405
25 TraesCS6B01G245700 chr7D 84.597 422 47 13 2593 3005 490439317 490439729 1.300000e-108 403
26 TraesCS6B01G245700 chr5D 87.861 346 34 6 1661 2002 91405841 91405500 1.680000e-107 399
27 TraesCS6B01G245700 chr5D 82.405 449 64 13 2274 2713 524330637 524330195 7.860000e-101 377
28 TraesCS6B01G245700 chr5D 83.372 427 48 14 2594 3005 449947740 449947322 1.020000e-99 374
29 TraesCS6B01G245700 chr5B 87.283 346 36 6 1661 2002 96764631 96764290 3.630000e-104 388
30 TraesCS6B01G245700 chr5B 82.596 339 43 5 2220 2553 54463704 54463377 4.900000e-73 285
31 TraesCS6B01G245700 chr5B 82.188 320 49 6 2220 2533 322558171 322558488 4.940000e-68 268
32 TraesCS6B01G245700 chr4A 81.674 442 58 17 2552 2980 467154078 467154509 2.220000e-91 346
33 TraesCS6B01G245700 chr1A 80.430 465 66 16 2551 3005 531655715 531655266 6.210000e-87 331
34 TraesCS6B01G245700 chr2D 82.597 385 47 14 2552 2925 636127231 636126856 3.740000e-84 322
35 TraesCS6B01G245700 chr2D 83.082 331 48 6 2222 2546 55317612 55317940 8.150000e-76 294
36 TraesCS6B01G245700 chr2D 80.997 321 52 6 2233 2547 572258433 572258750 2.310000e-61 246
37 TraesCS6B01G245700 chr1B 77.448 337 67 6 1661 1997 406037241 406037568 3.060000e-45 193
38 TraesCS6B01G245700 chr2B 77.812 329 57 13 2220 2545 16879928 16879613 3.950000e-44 189


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 TraesCS6B01G245700 chr6B 438384906 438387910 3004 True 5550.00 5550 100.000 1 3005 1 chr6B.!!$R1 3004
1 TraesCS6B01G245700 chr6D 276455696 276457635 1939 True 2861.00 2861 93.232 236 2197 1 chr6D.!!$R2 1961
2 TraesCS6B01G245700 chr6A 399721057 399724038 2981 False 1017.25 2747 91.846 1 3005 4 chr6A.!!$F1 3004
3 TraesCS6B01G245700 chr3B 766631403 766632361 958 False 1011.00 1011 85.829 1118 2098 1 chr3B.!!$F2 980
4 TraesCS6B01G245700 chr3B 769055217 769056382 1165 True 904.00 904 81.360 992 2135 1 chr3B.!!$R1 1143
5 TraesCS6B01G245700 chr3B 801186882 801187521 639 True 518.00 518 81.642 2274 2932 1 chr3B.!!$R2 658
6 TraesCS6B01G245700 chr3B 169333216 169333923 707 False 496.00 496 79.784 2274 3001 1 chr3B.!!$F1 727
7 TraesCS6B01G245700 chr3A 711203103 711204083 980 False 887.00 887 83.268 1118 2122 1 chr3A.!!$F1 1004
8 TraesCS6B01G245700 chr3A 712571253 712572319 1066 True 544.00 616 85.395 1145 2002 2 chr3A.!!$R1 857
9 TraesCS6B01G245700 chr3A 711217458 711218957 1499 False 543.50 968 79.476 698 2118 2 chr3A.!!$F2 1420
10 TraesCS6B01G245700 chr3D 575726010 575726973 963 False 961.00 961 85.000 1118 2094 1 chr3D.!!$F1 976
11 TraesCS6B01G245700 chr3D 577254843 577255686 843 True 857.00 857 85.155 1145 2002 1 chr3D.!!$R1 857
12 TraesCS6B01G245700 chr3D 577263627 577264186 559 True 283.50 459 84.182 1468 2134 2 chr3D.!!$R3 666

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
977 1095 0.250166 AACCACCAGAGTACGGCAAC 60.25 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2485 0.179 GATGCCTTCCACGGATGAGT 59.821 55.0 0.65 0.0 0.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.792830 TCAAGGATTAATACCACAAAGAAGAG 57.207 34.615 0.00 0.00 0.00 2.85
45 46 7.496263 GGATTAATACCACAAAGAAGAGGTCTC 59.504 40.741 0.00 0.00 34.56 3.36
128 129 7.161404 TGTATCCATATCATTACACTCAAGCC 58.839 38.462 0.00 0.00 0.00 4.35
129 130 4.973168 TCCATATCATTACACTCAAGCCC 58.027 43.478 0.00 0.00 0.00 5.19
131 132 5.843969 TCCATATCATTACACTCAAGCCCTA 59.156 40.000 0.00 0.00 0.00 3.53
132 133 6.014242 TCCATATCATTACACTCAAGCCCTAG 60.014 42.308 0.00 0.00 0.00 3.02
145 146 4.232878 CCTAGGCAGGCCGAGCTG 62.233 72.222 20.27 4.29 41.95 4.24
146 147 4.906792 CTAGGCAGGCCGAGCTGC 62.907 72.222 20.27 13.91 45.04 5.25
172 173 3.478540 GGCGTGGCCTAAAATCTCT 57.521 52.632 3.32 0.00 46.69 3.10
173 174 1.751437 GGCGTGGCCTAAAATCTCTT 58.249 50.000 3.32 0.00 46.69 2.85
174 175 2.092323 GGCGTGGCCTAAAATCTCTTT 58.908 47.619 3.32 0.00 46.69 2.52
175 176 2.159379 GGCGTGGCCTAAAATCTCTTTG 60.159 50.000 3.32 0.00 46.69 2.77
176 177 2.488153 GCGTGGCCTAAAATCTCTTTGT 59.512 45.455 3.32 0.00 0.00 2.83
177 178 3.057526 GCGTGGCCTAAAATCTCTTTGTT 60.058 43.478 3.32 0.00 0.00 2.83
178 179 4.155280 GCGTGGCCTAAAATCTCTTTGTTA 59.845 41.667 3.32 0.00 0.00 2.41
179 180 5.335348 GCGTGGCCTAAAATCTCTTTGTTAA 60.335 40.000 3.32 0.00 0.00 2.01
180 181 6.084277 CGTGGCCTAAAATCTCTTTGTTAAC 58.916 40.000 3.32 0.00 0.00 2.01
181 182 6.072673 CGTGGCCTAAAATCTCTTTGTTAACT 60.073 38.462 3.32 0.00 0.00 2.24
182 183 7.084486 GTGGCCTAAAATCTCTTTGTTAACTG 58.916 38.462 3.32 0.00 0.00 3.16
183 184 6.775629 TGGCCTAAAATCTCTTTGTTAACTGT 59.224 34.615 3.32 0.00 0.00 3.55
184 185 7.940137 TGGCCTAAAATCTCTTTGTTAACTGTA 59.060 33.333 3.32 0.00 0.00 2.74
185 186 8.451748 GGCCTAAAATCTCTTTGTTAACTGTAG 58.548 37.037 7.22 1.93 0.00 2.74
186 187 9.000486 GCCTAAAATCTCTTTGTTAACTGTAGT 58.000 33.333 7.22 0.00 0.00 2.73
193 194 8.345724 TCTCTTTGTTAACTGTAGTAGGTAGG 57.654 38.462 7.22 0.00 28.34 3.18
194 195 8.166061 TCTCTTTGTTAACTGTAGTAGGTAGGA 58.834 37.037 7.22 0.00 28.34 2.94
195 196 8.115490 TCTTTGTTAACTGTAGTAGGTAGGAC 57.885 38.462 7.22 0.00 28.34 3.85
196 197 7.725397 TCTTTGTTAACTGTAGTAGGTAGGACA 59.275 37.037 7.22 0.00 28.34 4.02
197 198 6.824305 TGTTAACTGTAGTAGGTAGGACAC 57.176 41.667 7.22 0.00 28.34 3.67
198 199 6.546484 TGTTAACTGTAGTAGGTAGGACACT 58.454 40.000 7.22 0.00 28.34 3.55
199 200 6.432162 TGTTAACTGTAGTAGGTAGGACACTG 59.568 42.308 7.22 0.00 28.34 3.66
200 201 4.654389 ACTGTAGTAGGTAGGACACTGT 57.346 45.455 0.00 0.00 0.00 3.55
201 202 4.995536 ACTGTAGTAGGTAGGACACTGTT 58.004 43.478 0.00 0.00 0.00 3.16
202 203 6.131972 ACTGTAGTAGGTAGGACACTGTTA 57.868 41.667 0.00 0.00 0.00 2.41
203 204 6.546484 ACTGTAGTAGGTAGGACACTGTTAA 58.454 40.000 0.00 0.00 0.00 2.01
204 205 7.006509 ACTGTAGTAGGTAGGACACTGTTAAA 58.993 38.462 0.00 0.00 0.00 1.52
205 206 7.673082 ACTGTAGTAGGTAGGACACTGTTAAAT 59.327 37.037 0.00 0.00 0.00 1.40
206 207 8.059798 TGTAGTAGGTAGGACACTGTTAAATC 57.940 38.462 0.00 0.00 0.00 2.17
207 208 7.892241 TGTAGTAGGTAGGACACTGTTAAATCT 59.108 37.037 0.00 0.00 0.00 2.40
208 209 7.793948 AGTAGGTAGGACACTGTTAAATCTT 57.206 36.000 0.00 0.00 0.00 2.40
209 210 7.612677 AGTAGGTAGGACACTGTTAAATCTTG 58.387 38.462 0.00 0.00 0.00 3.02
210 211 5.805728 AGGTAGGACACTGTTAAATCTTGG 58.194 41.667 0.00 0.00 0.00 3.61
211 212 5.309806 AGGTAGGACACTGTTAAATCTTGGT 59.690 40.000 0.00 0.00 0.00 3.67
212 213 5.642491 GGTAGGACACTGTTAAATCTTGGTC 59.358 44.000 0.00 0.00 0.00 4.02
213 214 4.652822 AGGACACTGTTAAATCTTGGTCC 58.347 43.478 0.00 0.00 42.94 4.46
214 215 4.351111 AGGACACTGTTAAATCTTGGTCCT 59.649 41.667 0.00 0.00 46.63 3.85
215 216 5.801380 GGACACTGTTAAATCTTGGTCCTA 58.199 41.667 0.00 0.00 40.23 2.94
216 217 5.875359 GGACACTGTTAAATCTTGGTCCTAG 59.125 44.000 0.00 0.00 40.23 3.02
217 218 6.435292 ACACTGTTAAATCTTGGTCCTAGT 57.565 37.500 0.00 0.00 0.00 2.57
218 219 6.838382 ACACTGTTAAATCTTGGTCCTAGTT 58.162 36.000 0.00 0.00 0.00 2.24
219 220 7.970102 ACACTGTTAAATCTTGGTCCTAGTTA 58.030 34.615 0.00 0.00 0.00 2.24
220 221 8.434392 ACACTGTTAAATCTTGGTCCTAGTTAA 58.566 33.333 0.00 0.00 0.00 2.01
221 222 9.280174 CACTGTTAAATCTTGGTCCTAGTTAAA 57.720 33.333 0.00 0.00 0.00 1.52
227 228 8.581253 AAATCTTGGTCCTAGTTAAATCTTGG 57.419 34.615 0.00 0.00 0.00 3.61
228 229 5.497474 TCTTGGTCCTAGTTAAATCTTGGC 58.503 41.667 0.00 0.00 32.08 4.52
229 230 4.919774 TGGTCCTAGTTAAATCTTGGCA 57.080 40.909 0.00 0.00 32.08 4.92
230 231 4.585879 TGGTCCTAGTTAAATCTTGGCAC 58.414 43.478 0.00 0.00 32.08 5.01
231 232 3.945921 GGTCCTAGTTAAATCTTGGCACC 59.054 47.826 0.00 0.00 32.08 5.01
232 233 3.621715 GTCCTAGTTAAATCTTGGCACCG 59.378 47.826 0.00 0.00 32.08 4.94
233 234 2.354821 CCTAGTTAAATCTTGGCACCGC 59.645 50.000 0.00 0.00 0.00 5.68
293 295 4.848357 AGAAATGGTGAACTGACTATGGG 58.152 43.478 0.00 0.00 0.00 4.00
325 327 7.390440 TCCAACATTGTATCTTTCGATGTTCTT 59.610 33.333 8.11 0.00 43.67 2.52
420 505 6.238456 CGGTATCTTGTACGTAACCACTATCA 60.238 42.308 11.38 0.00 0.00 2.15
456 541 3.068064 TGATCCTCTGCCGACGCA 61.068 61.111 0.00 0.00 44.78 5.24
483 568 1.270550 ACTTTCAGCTGGGCATTTTCG 59.729 47.619 15.13 0.00 0.00 3.46
507 592 4.069304 AGCACTAGTTTGGTATTTTCGCA 58.931 39.130 0.00 0.00 0.00 5.10
513 598 6.707161 ACTAGTTTGGTATTTTCGCAGTACAA 59.293 34.615 0.00 0.00 0.00 2.41
516 601 7.430441 AGTTTGGTATTTTCGCAGTACAAAAT 58.570 30.769 0.00 1.41 36.43 1.82
517 602 8.569641 AGTTTGGTATTTTCGCAGTACAAAATA 58.430 29.630 0.00 0.43 34.68 1.40
519 604 9.745880 TTTGGTATTTTCGCAGTACAAAATAAA 57.254 25.926 9.28 2.81 36.61 1.40
557 642 1.718757 GCAAGACGGATCATGTGGCC 61.719 60.000 0.00 0.00 0.00 5.36
563 648 2.672961 CGGATCATGTGGCCGTATAT 57.327 50.000 13.03 0.00 40.17 0.86
564 649 2.270923 CGGATCATGTGGCCGTATATG 58.729 52.381 13.03 0.00 40.17 1.78
565 650 2.353704 CGGATCATGTGGCCGTATATGT 60.354 50.000 13.03 0.00 40.17 2.29
566 651 3.119280 CGGATCATGTGGCCGTATATGTA 60.119 47.826 13.03 0.00 40.17 2.29
567 652 4.181578 GGATCATGTGGCCGTATATGTAC 58.818 47.826 0.00 0.00 0.00 2.90
623 709 4.580868 AGATGCCTCTATGATCTGCAATG 58.419 43.478 0.00 0.00 35.30 2.82
852 964 3.813443 CCATCTCCGTTCATTCATTCCT 58.187 45.455 0.00 0.00 0.00 3.36
869 981 1.900486 TCCTTCGTCCTTTTCCTCCTC 59.100 52.381 0.00 0.00 0.00 3.71
888 1000 6.462768 CCTCCTCTTGATTTGATCTGGTAGAG 60.463 46.154 0.00 0.00 0.00 2.43
974 1092 2.277084 CATTAACCACCAGAGTACGGC 58.723 52.381 0.00 0.00 0.00 5.68
976 1094 1.340088 TAACCACCAGAGTACGGCAA 58.660 50.000 0.00 0.00 0.00 4.52
977 1095 0.250166 AACCACCAGAGTACGGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
1047 1191 2.185608 GTCGCCCTCTTCTGCCTC 59.814 66.667 0.00 0.00 0.00 4.70
1391 1626 0.250510 TGTGGCCGACATTGCAGTTA 60.251 50.000 0.00 0.00 0.00 2.24
1974 2443 4.008933 GACTGGCAGCCCGACACT 62.009 66.667 15.89 0.00 0.00 3.55
2013 2485 1.003118 CAGTTCGATTGACCCCTTCCA 59.997 52.381 0.00 0.00 0.00 3.53
2021 2499 1.264749 TGACCCCTTCCACTCATCCG 61.265 60.000 0.00 0.00 0.00 4.18
2103 2601 2.105328 TGACGTCCGGTGTGTGTG 59.895 61.111 14.12 0.00 0.00 3.82
2209 2713 5.349061 TTTTAGCTACTAGTACAAGGGCC 57.651 43.478 0.00 0.00 0.00 5.80
2214 2718 0.613777 ACTAGTACAAGGGCCTGTGC 59.386 55.000 6.92 11.35 32.62 4.57
2217 2721 2.033194 GTACAAGGGCCTGTGCGTC 61.033 63.158 6.92 0.00 38.85 5.19
2218 2722 2.214216 TACAAGGGCCTGTGCGTCT 61.214 57.895 6.92 0.00 38.85 4.18
2254 2799 6.238869 GCATCACTGAGATACACTATCACTCA 60.239 42.308 0.00 0.00 37.65 3.41
2255 2800 7.682981 GCATCACTGAGATACACTATCACTCAA 60.683 40.741 0.00 0.00 37.20 3.02
2256 2801 7.888250 TCACTGAGATACACTATCACTCAAT 57.112 36.000 0.00 0.00 37.20 2.57
2257 2802 8.298729 TCACTGAGATACACTATCACTCAATT 57.701 34.615 0.00 0.00 37.20 2.32
2259 2804 9.029243 CACTGAGATACACTATCACTCAATTTC 57.971 37.037 0.00 0.00 37.20 2.17
2260 2805 8.753133 ACTGAGATACACTATCACTCAATTTCA 58.247 33.333 0.00 0.00 37.20 2.69
2261 2806 9.761504 CTGAGATACACTATCACTCAATTTCAT 57.238 33.333 0.00 0.00 37.20 2.57
2263 2808 9.755804 GAGATACACTATCACTCAATTTCATGA 57.244 33.333 0.00 0.00 37.65 3.07
2268 2813 9.234827 ACACTATCACTCAATTTCATGAAATCA 57.765 29.630 29.08 19.15 39.88 2.57
2361 2909 9.605275 TTCAAATCCATGAACACAATTACAAAA 57.395 25.926 0.00 0.00 34.50 2.44
2480 3029 7.111247 ACAACTTTCTTGAATCCATGAACAA 57.889 32.000 0.00 0.00 36.55 2.83
2569 3121 0.955428 CTAGCAAAAGGGCTCGTGCA 60.955 55.000 12.07 0.00 44.54 4.57
2583 3135 0.512518 CGTGCATTGCAACGAGAGAA 59.487 50.000 21.17 0.00 41.47 2.87
2722 3295 9.907576 CTAAAACTCGTGAACATATCTGAAATC 57.092 33.333 0.00 0.00 0.00 2.17
2723 3296 7.905604 AAACTCGTGAACATATCTGAAATCA 57.094 32.000 0.00 0.00 0.00 2.57
2724 3297 6.893958 ACTCGTGAACATATCTGAAATCAC 57.106 37.500 0.00 0.00 34.12 3.06
2726 3300 4.267690 TCGTGAACATATCTGAAATCACGC 59.732 41.667 21.54 3.42 45.55 5.34
2735 3309 7.485913 ACATATCTGAAATCACGCACATTTTTC 59.514 33.333 0.00 0.00 0.00 2.29
2736 3310 5.180367 TCTGAAATCACGCACATTTTTCA 57.820 34.783 0.00 0.00 35.61 2.69
2737 3311 5.586339 TCTGAAATCACGCACATTTTTCAA 58.414 33.333 0.00 0.00 36.27 2.69
2738 3312 6.038985 TCTGAAATCACGCACATTTTTCAAA 58.961 32.000 0.00 0.00 36.27 2.69
2739 3313 6.700960 TCTGAAATCACGCACATTTTTCAAAT 59.299 30.769 0.00 0.00 36.27 2.32
2740 3314 7.224362 TCTGAAATCACGCACATTTTTCAAATT 59.776 29.630 0.00 0.00 36.27 1.82
2741 3315 7.343691 TGAAATCACGCACATTTTTCAAATTC 58.656 30.769 0.00 0.00 34.39 2.17
2742 3316 6.841443 AATCACGCACATTTTTCAAATTCA 57.159 29.167 0.00 0.00 0.00 2.57
2743 3317 7.424227 AATCACGCACATTTTTCAAATTCAT 57.576 28.000 0.00 0.00 0.00 2.57
2744 3318 8.531622 AATCACGCACATTTTTCAAATTCATA 57.468 26.923 0.00 0.00 0.00 2.15
2745 3319 7.936950 TCACGCACATTTTTCAAATTCATAA 57.063 28.000 0.00 0.00 0.00 1.90
2746 3320 8.357796 TCACGCACATTTTTCAAATTCATAAA 57.642 26.923 0.00 0.00 0.00 1.40
2747 3321 8.820933 TCACGCACATTTTTCAAATTCATAAAA 58.179 25.926 0.00 0.00 0.00 1.52
2748 3322 8.881231 CACGCACATTTTTCAAATTCATAAAAC 58.119 29.630 0.00 0.00 0.00 2.43
2749 3323 8.607459 ACGCACATTTTTCAAATTCATAAAACA 58.393 25.926 0.00 0.00 0.00 2.83
2750 3324 9.430838 CGCACATTTTTCAAATTCATAAAACAA 57.569 25.926 0.00 0.00 0.00 2.83
2867 3445 9.098355 TGAATAGACAAACATTTCTAGAATCGG 57.902 33.333 5.89 1.71 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.610305 TCTTTGTGGTATTAATCCTTGAAGGTC 59.390 37.037 11.60 0.00 36.53 3.85
111 112 4.040461 GCCTAGGGCTTGAGTGTAATGATA 59.960 45.833 11.72 0.00 46.69 2.15
114 115 2.565841 GCCTAGGGCTTGAGTGTAATG 58.434 52.381 11.72 0.00 46.69 1.90
155 156 2.488153 ACAAAGAGATTTTAGGCCACGC 59.512 45.455 5.01 0.00 0.00 5.34
156 157 4.766404 AACAAAGAGATTTTAGGCCACG 57.234 40.909 5.01 0.00 0.00 4.94
157 158 7.084486 CAGTTAACAAAGAGATTTTAGGCCAC 58.916 38.462 5.01 0.00 0.00 5.01
158 159 6.775629 ACAGTTAACAAAGAGATTTTAGGCCA 59.224 34.615 5.01 0.00 0.00 5.36
159 160 7.215719 ACAGTTAACAAAGAGATTTTAGGCC 57.784 36.000 8.61 0.00 0.00 5.19
160 161 9.000486 ACTACAGTTAACAAAGAGATTTTAGGC 58.000 33.333 8.61 0.00 0.00 3.93
167 168 8.968969 CCTACCTACTACAGTTAACAAAGAGAT 58.031 37.037 8.61 0.00 0.00 2.75
168 169 8.166061 TCCTACCTACTACAGTTAACAAAGAGA 58.834 37.037 8.61 0.00 0.00 3.10
169 170 8.242739 GTCCTACCTACTACAGTTAACAAAGAG 58.757 40.741 8.61 2.15 0.00 2.85
170 171 7.725397 TGTCCTACCTACTACAGTTAACAAAGA 59.275 37.037 8.61 0.00 0.00 2.52
171 172 7.811713 GTGTCCTACCTACTACAGTTAACAAAG 59.188 40.741 8.61 4.50 0.00 2.77
172 173 7.506938 AGTGTCCTACCTACTACAGTTAACAAA 59.493 37.037 8.61 0.00 0.00 2.83
173 174 7.006509 AGTGTCCTACCTACTACAGTTAACAA 58.993 38.462 8.61 0.00 0.00 2.83
174 175 6.432162 CAGTGTCCTACCTACTACAGTTAACA 59.568 42.308 8.61 0.00 0.00 2.41
175 176 6.432472 ACAGTGTCCTACCTACTACAGTTAAC 59.568 42.308 0.00 0.00 0.00 2.01
176 177 6.546484 ACAGTGTCCTACCTACTACAGTTAA 58.454 40.000 0.00 0.00 0.00 2.01
177 178 6.131972 ACAGTGTCCTACCTACTACAGTTA 57.868 41.667 0.00 0.00 0.00 2.24
178 179 4.995536 ACAGTGTCCTACCTACTACAGTT 58.004 43.478 0.00 0.00 0.00 3.16
179 180 4.654389 ACAGTGTCCTACCTACTACAGT 57.346 45.455 0.00 0.00 0.00 3.55
180 181 7.458409 TTTAACAGTGTCCTACCTACTACAG 57.542 40.000 0.00 0.00 0.00 2.74
181 182 7.892241 AGATTTAACAGTGTCCTACCTACTACA 59.108 37.037 0.00 0.00 0.00 2.74
182 183 8.291191 AGATTTAACAGTGTCCTACCTACTAC 57.709 38.462 0.00 0.00 0.00 2.73
183 184 8.746530 CAAGATTTAACAGTGTCCTACCTACTA 58.253 37.037 0.00 0.00 0.00 1.82
184 185 7.310485 CCAAGATTTAACAGTGTCCTACCTACT 60.310 40.741 0.00 0.00 0.00 2.57
185 186 6.817140 CCAAGATTTAACAGTGTCCTACCTAC 59.183 42.308 0.00 0.00 0.00 3.18
186 187 6.499350 ACCAAGATTTAACAGTGTCCTACCTA 59.501 38.462 0.00 0.00 0.00 3.08
187 188 5.309806 ACCAAGATTTAACAGTGTCCTACCT 59.690 40.000 0.00 0.00 0.00 3.08
188 189 5.557866 ACCAAGATTTAACAGTGTCCTACC 58.442 41.667 0.00 0.00 0.00 3.18
189 190 5.642491 GGACCAAGATTTAACAGTGTCCTAC 59.358 44.000 0.00 0.00 38.36 3.18
190 191 5.801380 GGACCAAGATTTAACAGTGTCCTA 58.199 41.667 0.00 0.00 38.36 2.94
191 192 4.351111 AGGACCAAGATTTAACAGTGTCCT 59.649 41.667 0.00 0.00 44.83 3.85
192 193 4.652822 AGGACCAAGATTTAACAGTGTCC 58.347 43.478 0.00 0.00 41.00 4.02
193 194 6.465084 ACTAGGACCAAGATTTAACAGTGTC 58.535 40.000 0.00 0.00 0.00 3.67
194 195 6.435292 ACTAGGACCAAGATTTAACAGTGT 57.565 37.500 0.00 0.00 0.00 3.55
195 196 8.842358 TTAACTAGGACCAAGATTTAACAGTG 57.158 34.615 0.00 0.00 0.00 3.66
201 202 9.681062 CCAAGATTTAACTAGGACCAAGATTTA 57.319 33.333 0.00 0.00 0.00 1.40
202 203 7.122799 GCCAAGATTTAACTAGGACCAAGATTT 59.877 37.037 0.00 0.00 0.00 2.17
203 204 6.603599 GCCAAGATTTAACTAGGACCAAGATT 59.396 38.462 0.00 0.00 0.00 2.40
204 205 6.122964 GCCAAGATTTAACTAGGACCAAGAT 58.877 40.000 0.00 0.00 0.00 2.40
205 206 5.013704 TGCCAAGATTTAACTAGGACCAAGA 59.986 40.000 0.00 0.00 0.00 3.02
206 207 5.123979 GTGCCAAGATTTAACTAGGACCAAG 59.876 44.000 0.00 0.00 0.00 3.61
207 208 5.007682 GTGCCAAGATTTAACTAGGACCAA 58.992 41.667 0.00 0.00 0.00 3.67
208 209 4.566907 GGTGCCAAGATTTAACTAGGACCA 60.567 45.833 0.00 0.00 36.00 4.02
209 210 3.945921 GGTGCCAAGATTTAACTAGGACC 59.054 47.826 0.00 0.00 31.67 4.46
210 211 3.621715 CGGTGCCAAGATTTAACTAGGAC 59.378 47.826 0.00 0.00 0.00 3.85
211 212 3.869065 CGGTGCCAAGATTTAACTAGGA 58.131 45.455 0.00 0.00 0.00 2.94
212 213 2.354821 GCGGTGCCAAGATTTAACTAGG 59.645 50.000 0.00 0.00 0.00 3.02
213 214 3.675467 GCGGTGCCAAGATTTAACTAG 57.325 47.619 0.00 0.00 0.00 2.57
232 233 3.978687 AGTTGTACTCGCATATAGTGGC 58.021 45.455 0.00 0.00 0.00 5.01
233 234 6.736123 ACTTAGTTGTACTCGCATATAGTGG 58.264 40.000 0.00 0.00 0.00 4.00
234 235 9.167239 GTAACTTAGTTGTACTCGCATATAGTG 57.833 37.037 8.00 0.00 0.00 2.74
240 241 6.395629 ACATGTAACTTAGTTGTACTCGCAT 58.604 36.000 8.00 0.00 0.00 4.73
241 242 5.775686 ACATGTAACTTAGTTGTACTCGCA 58.224 37.500 8.00 0.00 0.00 5.10
276 278 3.904965 TGTAACCCATAGTCAGTTCACCA 59.095 43.478 0.00 0.00 0.00 4.17
291 293 7.404671 AAAGATACAATGTTGGATGTAACCC 57.595 36.000 0.00 0.00 35.79 4.11
293 295 7.970384 TCGAAAGATACAATGTTGGATGTAAC 58.030 34.615 0.00 0.00 35.79 2.50
344 346 4.504461 CAGTGACATACTAACGAAGCATCC 59.496 45.833 0.00 0.00 37.60 3.51
456 541 1.878953 CCCAGCTGAAAGTTACGTGT 58.121 50.000 17.39 0.00 35.30 4.49
483 568 5.121142 TGCGAAAATACCAAACTAGTGCTAC 59.879 40.000 0.00 0.00 0.00 3.58
507 592 7.012044 AGTGACGAGCTTGTTTTATTTTGTACT 59.988 33.333 8.34 0.00 0.00 2.73
513 598 6.560253 ATCAGTGACGAGCTTGTTTTATTT 57.440 33.333 8.34 0.00 0.00 1.40
516 601 4.319477 GCAATCAGTGACGAGCTTGTTTTA 60.319 41.667 8.34 0.00 0.00 1.52
517 602 3.548818 GCAATCAGTGACGAGCTTGTTTT 60.549 43.478 8.34 0.00 0.00 2.43
519 604 1.532868 GCAATCAGTGACGAGCTTGTT 59.467 47.619 8.34 0.00 0.00 2.83
557 642 5.793952 GGAGTCGTAGCAATGTACATATACG 59.206 44.000 26.46 26.46 37.83 3.06
562 647 3.079960 CGGAGTCGTAGCAATGTACAT 57.920 47.619 1.41 1.41 0.00 2.29
563 648 2.554806 CGGAGTCGTAGCAATGTACA 57.445 50.000 0.00 0.00 0.00 2.90
591 677 6.065976 TCATAGAGGCATCTTTTTCTTGGA 57.934 37.500 6.05 0.00 36.96 3.53
807 911 0.117140 TGGAGAAAGGAGGAGCCAGA 59.883 55.000 0.00 0.00 40.02 3.86
852 964 2.969950 TCAAGAGGAGGAAAAGGACGAA 59.030 45.455 0.00 0.00 0.00 3.85
869 981 6.882656 TCTTCCTCTACCAGATCAAATCAAG 58.117 40.000 0.00 0.00 0.00 3.02
888 1000 4.319177 TCAAGTGCTAAGCTTCTTCTTCC 58.681 43.478 0.00 0.00 0.00 3.46
974 1092 1.136336 GCTTTCGCTGGTTACTCGTTG 60.136 52.381 0.00 0.00 0.00 4.10
976 1094 1.007336 CGCTTTCGCTGGTTACTCGT 61.007 55.000 0.00 0.00 0.00 4.18
977 1095 1.683790 CCGCTTTCGCTGGTTACTCG 61.684 60.000 0.00 0.00 0.00 4.18
1035 1179 2.498726 GCGAGGAGGCAGAAGAGG 59.501 66.667 0.00 0.00 0.00 3.69
1391 1626 2.293677 CACTCTACCGTCACTGTCAAGT 59.706 50.000 0.00 0.00 36.98 3.16
1974 2443 1.248785 GGACGAGGGAGCTGTACACA 61.249 60.000 0.00 0.00 0.00 3.72
2013 2485 0.179000 GATGCCTTCCACGGATGAGT 59.821 55.000 0.65 0.00 0.00 3.41
2052 2540 2.286294 CAGCTAGCTTGGCACGATTAAG 59.714 50.000 16.46 0.00 0.00 1.85
2103 2601 1.198637 ACGTAGTAGCACACGAAGACC 59.801 52.381 0.62 0.00 41.94 3.85
2200 2704 0.901114 TAGACGCACAGGCCCTTGTA 60.901 55.000 0.00 0.00 36.38 2.41
2201 2705 2.214216 TAGACGCACAGGCCCTTGT 61.214 57.895 0.00 0.00 36.38 3.16
2209 2713 2.843077 CAGCAAAATGTAGACGCACAG 58.157 47.619 0.00 0.00 0.00 3.66
2214 2718 3.125829 AGTGATGCAGCAAAATGTAGACG 59.874 43.478 6.05 0.00 0.00 4.18
2217 2721 4.393990 TCTCAGTGATGCAGCAAAATGTAG 59.606 41.667 6.05 6.27 0.00 2.74
2218 2722 4.325972 TCTCAGTGATGCAGCAAAATGTA 58.674 39.130 6.05 0.00 0.00 2.29
2460 3009 9.784680 CTAGAATTGTTCATGGATTCAAGAAAG 57.215 33.333 0.00 0.00 33.22 2.62
2563 3115 0.319469 TCTCTCGTTGCAATGCACGA 60.319 50.000 23.35 23.35 38.71 4.35
2599 3153 4.561123 GCAAAATGTGGTCATGTCCATTGA 60.561 41.667 20.32 8.37 39.81 2.57
2696 3250 9.907576 GATTTCAGATATGTTCACGAGTTTTAG 57.092 33.333 0.00 0.00 0.00 1.85
2722 3295 8.881231 GTTTTATGAATTTGAAAAATGTGCGTG 58.119 29.630 0.00 0.00 0.00 5.34
2723 3296 8.607459 TGTTTTATGAATTTGAAAAATGTGCGT 58.393 25.926 0.00 0.00 0.00 5.24
2724 3297 8.984482 TGTTTTATGAATTTGAAAAATGTGCG 57.016 26.923 0.00 0.00 0.00 5.34
2892 3470 6.813649 TCGTGAATTTCAAAATTTGTTCCACA 59.186 30.769 5.56 0.65 38.64 4.17
2965 3545 8.726650 TTGATTCATAGAATGTTCGTTGTTTG 57.273 30.769 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.