Multiple sequence alignment - TraesCS3A01G167400

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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 TraesCS3A01G167400 chr3A 100.000 5585 0 0 1 5585 173948526 173942942 0.000000e+00 10314.0
1 TraesCS3A01G167400 chr3A 82.090 134 18 6 4646 4774 198297013 198296881 5.920000e-20 110.0
2 TraesCS3A01G167400 chr3B 95.529 4854 151 25 394 5216 226478699 226483517 0.000000e+00 7701.0
3 TraesCS3A01G167400 chr3B 82.286 175 14 10 5202 5372 404830479 404830318 9.760000e-28 135.0
4 TraesCS3A01G167400 chr3B 81.679 131 16 7 4647 4770 556930595 556930724 9.900000e-18 102.0
5 TraesCS3A01G167400 chr3D 96.420 3017 62 17 2269 5266 154616348 154613359 0.000000e+00 4931.0
6 TraesCS3A01G167400 chr3D 97.476 1902 33 7 394 2286 154618411 154616516 0.000000e+00 3232.0
7 TraesCS3A01G167400 chr3D 95.918 294 11 1 5293 5585 154613363 154613070 5.060000e-130 475.0
8 TraesCS3A01G167400 chr3D 94.886 176 5 4 1 173 154618587 154618413 7.130000e-69 272.0
9 TraesCS3A01G167400 chrUn 99.002 401 4 0 4046 4446 478601153 478601553 0.000000e+00 719.0
10 TraesCS3A01G167400 chr7D 93.274 223 15 0 177 399 105360817 105360595 4.170000e-86 329.0
11 TraesCS3A01G167400 chr2D 92.793 222 16 0 174 395 393072267 393072488 6.980000e-84 322.0
12 TraesCS3A01G167400 chr5D 91.150 226 20 0 171 396 316247295 316247520 1.950000e-79 307.0
13 TraesCS3A01G167400 chr5D 91.818 220 18 0 176 395 383858662 383858881 1.950000e-79 307.0
14 TraesCS3A01G167400 chr5A 91.228 228 17 2 173 400 355515782 355516006 1.950000e-79 307.0
15 TraesCS3A01G167400 chr5A 91.228 228 17 2 173 400 355539665 355539889 1.950000e-79 307.0
16 TraesCS3A01G167400 chr5B 90.789 228 21 0 173 400 295166493 295166266 7.030000e-79 305.0
17 TraesCS3A01G167400 chr1A 90.129 233 22 1 168 400 244240602 244240833 9.090000e-78 302.0
18 TraesCS3A01G167400 chr1A 81.343 134 19 6 4646 4774 415124956 415125088 2.750000e-18 104.0
19 TraesCS3A01G167400 chr6A 90.393 229 20 2 173 400 297778535 297778762 3.270000e-77 300.0
20 TraesCS3A01G167400 chr6A 83.140 172 14 10 5211 5379 366029611 366029452 5.830000e-30 143.0
21 TraesCS3A01G167400 chr6A 81.538 130 17 7 4646 4769 75546177 75546305 3.560000e-17 100.0
22 TraesCS3A01G167400 chr6D 84.211 171 14 8 5211 5379 256728450 256728609 2.690000e-33 154.0
23 TraesCS3A01G167400 chr6D 84.211 171 14 8 5211 5379 256729247 256729406 2.690000e-33 154.0
24 TraesCS3A01G167400 chr6D 82.787 122 16 1 4653 4769 366003727 366003606 2.750000e-18 104.0
25 TraesCS3A01G167400 chr4B 84.756 164 13 7 5211 5373 106227409 106227561 2.690000e-33 154.0
26 TraesCS3A01G167400 chr4B 83.537 164 15 8 5211 5373 544041903 544041751 5.830000e-30 143.0
27 TraesCS3A01G167400 chr2B 84.146 164 14 7 5211 5373 190023043 190022891 1.250000e-31 148.0
28 TraesCS3A01G167400 chr2A 83.929 168 14 8 5208 5373 141506474 141506318 1.250000e-31 148.0
29 TraesCS3A01G167400 chr6B 82.456 171 17 8 5211 5379 372579606 372579765 2.710000e-28 137.0
30 TraesCS3A01G167400 chr4D 84.375 128 11 6 4648 4769 13372985 13372861 3.540000e-22 117.0
31 TraesCS3A01G167400 chr4D 83.333 126 16 4 4648 4769 456266732 456266856 1.640000e-20 111.0
32 TraesCS3A01G167400 chr7A 84.112 107 10 5 4653 4753 132649112 132649217 4.610000e-16 97.1


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 TraesCS3A01G167400 chr3A 173942942 173948526 5584 True 10314.0 10314 100.000 1 5585 1 chr3A.!!$R1 5584
1 TraesCS3A01G167400 chr3B 226478699 226483517 4818 False 7701.0 7701 95.529 394 5216 1 chr3B.!!$F1 4822
2 TraesCS3A01G167400 chr3D 154613070 154618587 5517 True 2227.5 4931 96.175 1 5585 4 chr3D.!!$R1 5584

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
208 212 0.034337 TCGGTTTAGAGGGTGTGTGC 59.966 55.0 0.00 0.0 0.00 4.57 F
710 723 0.179004 CCCAAAAGGCCAAAAACCCC 60.179 55.0 5.01 0.0 0.00 4.95 F
731 744 0.249996 GCAAATGCTGTTGGCCTGTT 60.250 50.0 3.32 0.0 40.92 3.16 F
892 905 0.326927 TGGATTTCTGGTCCGGGTTC 59.673 55.0 0.00 0.0 38.64 3.62 F
2170 2191 0.818040 GGTTTCTGGTCGTGTGCCTT 60.818 55.0 0.00 0.0 0.00 4.35 F
3491 3718 0.755698 GGTGCTCGACCCTGGAGATA 60.756 60.0 0.00 0.0 39.10 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2191 0.401356 TCTTCTGCACCATCAGGCAA 59.599 50.000 0.00 0.00 39.93 4.52 R
2416 2626 2.091555 AGGCCAACAAAAGTCCTGGTTA 60.092 45.455 5.01 0.00 0.00 2.85 R
2722 2932 0.040067 AGCTGCTTAGCACGCAAAAC 60.040 50.000 22.97 2.40 36.88 2.43 R
2822 3032 5.048224 GCTTAGTACCTCACACAGACAGTTA 60.048 44.000 0.00 0.00 0.00 2.24 R
3797 4024 1.294659 CGTGGCAGAGAAAGGAGCAC 61.295 60.000 0.00 0.00 0.00 4.40 R
5176 5405 1.066605 CAATCTTGCATGGTAGCTGCC 59.933 52.381 14.87 14.87 38.89 4.85 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
39 41 9.362151 AGTTTTGTAGAAATGATAAAACCAGGA 57.638 29.630 0.00 0.00 40.33 3.86
88 90 8.736244 GGAGCGGAATATAGAGGAGATATAATC 58.264 40.741 0.00 0.00 0.00 1.75
119 121 9.712359 GTTAAAGAGTATAATACCGCAAAAAGG 57.288 33.333 0.00 0.00 0.00 3.11
141 145 6.989659 AGGAAAATATTGCAGGATTAGCATG 58.010 36.000 0.00 0.00 42.33 4.06
165 169 0.822121 AAAGGGCCGGTGAAGTTCAC 60.822 55.000 25.00 25.00 46.23 3.18
180 184 8.325367 GTGAAGTTCACGAACATATACTACTC 57.675 38.462 19.71 0.00 43.47 2.59
181 185 7.431668 GTGAAGTTCACGAACATATACTACTCC 59.568 40.741 19.71 0.00 43.47 3.85
182 186 6.388435 AGTTCACGAACATATACTACTCCC 57.612 41.667 12.21 0.00 43.47 4.30
183 187 6.127793 AGTTCACGAACATATACTACTCCCT 58.872 40.000 12.21 0.00 43.47 4.20
184 188 6.262720 AGTTCACGAACATATACTACTCCCTC 59.737 42.308 12.21 0.00 43.47 4.30
185 189 5.068636 TCACGAACATATACTACTCCCTCC 58.931 45.833 0.00 0.00 0.00 4.30
186 190 4.070716 ACGAACATATACTACTCCCTCCG 58.929 47.826 0.00 0.00 0.00 4.63
187 191 4.070716 CGAACATATACTACTCCCTCCGT 58.929 47.826 0.00 0.00 0.00 4.69
188 192 4.153835 CGAACATATACTACTCCCTCCGTC 59.846 50.000 0.00 0.00 0.00 4.79
189 193 4.997545 ACATATACTACTCCCTCCGTCT 57.002 45.455 0.00 0.00 0.00 4.18
190 194 4.909001 ACATATACTACTCCCTCCGTCTC 58.091 47.826 0.00 0.00 0.00 3.36
191 195 2.547299 ATACTACTCCCTCCGTCTCG 57.453 55.000 0.00 0.00 0.00 4.04
202 206 2.576298 CCGTCTCGGTTTAGAGGGT 58.424 57.895 4.77 0.00 43.49 4.34
203 207 0.172803 CCGTCTCGGTTTAGAGGGTG 59.827 60.000 4.77 0.00 43.49 4.61
204 208 0.886563 CGTCTCGGTTTAGAGGGTGT 59.113 55.000 0.00 0.00 38.71 4.16
205 209 1.402456 CGTCTCGGTTTAGAGGGTGTG 60.402 57.143 0.00 0.00 38.71 3.82
206 210 1.617357 GTCTCGGTTTAGAGGGTGTGT 59.383 52.381 0.00 0.00 38.71 3.72
207 211 1.616865 TCTCGGTTTAGAGGGTGTGTG 59.383 52.381 0.00 0.00 38.71 3.82
208 212 0.034337 TCGGTTTAGAGGGTGTGTGC 59.966 55.000 0.00 0.00 0.00 4.57
209 213 1.289109 CGGTTTAGAGGGTGTGTGCG 61.289 60.000 0.00 0.00 0.00 5.34
210 214 0.250166 GGTTTAGAGGGTGTGTGCGT 60.250 55.000 0.00 0.00 0.00 5.24
211 215 1.001181 GGTTTAGAGGGTGTGTGCGTA 59.999 52.381 0.00 0.00 0.00 4.42
212 216 2.334838 GTTTAGAGGGTGTGTGCGTAG 58.665 52.381 0.00 0.00 0.00 3.51
213 217 1.624336 TTAGAGGGTGTGTGCGTAGT 58.376 50.000 0.00 0.00 0.00 2.73
214 218 1.624336 TAGAGGGTGTGTGCGTAGTT 58.376 50.000 0.00 0.00 0.00 2.24
215 219 0.317479 AGAGGGTGTGTGCGTAGTTC 59.683 55.000 0.00 0.00 0.00 3.01
216 220 0.317479 GAGGGTGTGTGCGTAGTTCT 59.683 55.000 0.00 0.00 0.00 3.01
217 221 1.542915 GAGGGTGTGTGCGTAGTTCTA 59.457 52.381 0.00 0.00 0.00 2.10
218 222 1.544691 AGGGTGTGTGCGTAGTTCTAG 59.455 52.381 0.00 0.00 0.00 2.43
219 223 1.403780 GGGTGTGTGCGTAGTTCTAGG 60.404 57.143 0.00 0.00 0.00 3.02
220 224 1.271656 GGTGTGTGCGTAGTTCTAGGT 59.728 52.381 0.00 0.00 0.00 3.08
221 225 2.593257 GTGTGTGCGTAGTTCTAGGTC 58.407 52.381 0.00 0.00 0.00 3.85
222 226 2.030540 GTGTGTGCGTAGTTCTAGGTCA 60.031 50.000 0.00 0.00 0.00 4.02
223 227 2.823747 TGTGTGCGTAGTTCTAGGTCAT 59.176 45.455 0.00 0.00 0.00 3.06
224 228 3.119602 TGTGTGCGTAGTTCTAGGTCATC 60.120 47.826 0.00 1.43 0.00 2.92
225 229 2.426024 TGTGCGTAGTTCTAGGTCATCC 59.574 50.000 0.00 0.00 0.00 3.51
226 230 2.426024 GTGCGTAGTTCTAGGTCATCCA 59.574 50.000 0.00 0.00 35.89 3.41
227 231 3.068307 GTGCGTAGTTCTAGGTCATCCAT 59.932 47.826 0.00 0.00 35.89 3.41
228 232 3.704566 TGCGTAGTTCTAGGTCATCCATT 59.295 43.478 0.00 0.00 35.89 3.16
229 233 4.161565 TGCGTAGTTCTAGGTCATCCATTT 59.838 41.667 0.00 0.00 35.89 2.32
230 234 5.361571 TGCGTAGTTCTAGGTCATCCATTTA 59.638 40.000 0.00 0.00 35.89 1.40
231 235 6.127281 TGCGTAGTTCTAGGTCATCCATTTAA 60.127 38.462 0.00 0.00 35.89 1.52
232 236 6.200475 GCGTAGTTCTAGGTCATCCATTTAAC 59.800 42.308 0.00 0.00 35.89 2.01
233 237 7.490000 CGTAGTTCTAGGTCATCCATTTAACT 58.510 38.462 0.00 0.00 35.89 2.24
234 238 8.627403 CGTAGTTCTAGGTCATCCATTTAACTA 58.373 37.037 0.00 0.00 35.89 2.24
237 241 9.047947 AGTTCTAGGTCATCCATTTAACTAACT 57.952 33.333 0.00 0.00 35.89 2.24
286 290 9.965824 AAAGTATATCATTGGATTTTTAAGCGG 57.034 29.630 0.00 0.00 34.89 5.52
287 291 8.918202 AGTATATCATTGGATTTTTAAGCGGA 57.082 30.769 0.00 0.00 34.89 5.54
288 292 9.520515 AGTATATCATTGGATTTTTAAGCGGAT 57.479 29.630 0.00 0.00 34.89 4.18
289 293 9.559958 GTATATCATTGGATTTTTAAGCGGATG 57.440 33.333 0.00 0.00 34.89 3.51
290 294 5.913137 TCATTGGATTTTTAAGCGGATGT 57.087 34.783 0.00 0.00 0.00 3.06
291 295 7.581213 ATCATTGGATTTTTAAGCGGATGTA 57.419 32.000 0.00 0.00 0.00 2.29
292 296 7.026631 TCATTGGATTTTTAAGCGGATGTAG 57.973 36.000 0.00 0.00 0.00 2.74
293 297 6.601613 TCATTGGATTTTTAAGCGGATGTAGT 59.398 34.615 0.00 0.00 0.00 2.73
294 298 6.827586 TTGGATTTTTAAGCGGATGTAGTT 57.172 33.333 0.00 0.00 0.00 2.24
295 299 6.827586 TGGATTTTTAAGCGGATGTAGTTT 57.172 33.333 0.00 0.00 0.00 2.66
296 300 6.848451 TGGATTTTTAAGCGGATGTAGTTTC 58.152 36.000 0.00 0.00 0.00 2.78
297 301 6.657541 TGGATTTTTAAGCGGATGTAGTTTCT 59.342 34.615 0.00 0.00 0.00 2.52
298 302 7.825270 TGGATTTTTAAGCGGATGTAGTTTCTA 59.175 33.333 0.00 0.00 0.00 2.10
299 303 8.671028 GGATTTTTAAGCGGATGTAGTTTCTAA 58.329 33.333 0.00 0.00 0.00 2.10
372 376 8.792830 TTAACCTAGAACCACATATATGTCCT 57.207 34.615 15.60 12.07 39.39 3.85
373 377 6.672266 ACCTAGAACCACATATATGTCCTG 57.328 41.667 15.60 9.67 39.39 3.86
374 378 6.143915 ACCTAGAACCACATATATGTCCTGT 58.856 40.000 15.60 10.27 39.39 4.00
375 379 7.302948 ACCTAGAACCACATATATGTCCTGTA 58.697 38.462 15.60 5.48 39.39 2.74
376 380 7.787904 ACCTAGAACCACATATATGTCCTGTAA 59.212 37.037 15.60 0.62 39.39 2.41
377 381 8.647796 CCTAGAACCACATATATGTCCTGTAAA 58.352 37.037 15.60 0.00 39.39 2.01
378 382 9.477484 CTAGAACCACATATATGTCCTGTAAAC 57.523 37.037 15.60 8.55 39.39 2.01
379 383 7.280356 AGAACCACATATATGTCCTGTAAACC 58.720 38.462 15.60 4.95 39.39 3.27
380 384 5.607477 ACCACATATATGTCCTGTAAACCG 58.393 41.667 15.60 0.95 39.39 4.44
381 385 5.364446 ACCACATATATGTCCTGTAAACCGA 59.636 40.000 15.60 0.00 39.39 4.69
382 386 5.926542 CCACATATATGTCCTGTAAACCGAG 59.073 44.000 15.60 0.26 39.39 4.63
383 387 6.239204 CCACATATATGTCCTGTAAACCGAGA 60.239 42.308 15.60 0.00 39.39 4.04
384 388 6.641314 CACATATATGTCCTGTAAACCGAGAC 59.359 42.308 15.60 0.00 39.39 3.36
385 389 2.649331 ATGTCCTGTAAACCGAGACG 57.351 50.000 0.00 0.00 0.00 4.18
386 390 9.336850 ACATATATGTCCTGTAAACCGAGACGG 62.337 44.444 12.75 8.67 45.08 4.79
446 451 8.482852 AAGGCATCCTAAAAATAGTGCAATAT 57.517 30.769 0.00 0.00 34.45 1.28
552 561 2.159282 CCTGTCTCCGCTTACGTATTGT 60.159 50.000 0.00 0.00 37.70 2.71
710 723 0.179004 CCCAAAAGGCCAAAAACCCC 60.179 55.000 5.01 0.00 0.00 4.95
720 733 1.202794 CCAAAAACCCCTGCAAATGCT 60.203 47.619 6.97 0.00 42.66 3.79
731 744 0.249996 GCAAATGCTGTTGGCCTGTT 60.250 50.000 3.32 0.00 40.92 3.16
848 861 1.484653 TCGACGTCCCATTTGATCCAT 59.515 47.619 10.58 0.00 0.00 3.41
859 872 0.739462 TTGATCCATCGTCGTGCCAC 60.739 55.000 0.00 0.00 0.00 5.01
892 905 0.326927 TGGATTTCTGGTCCGGGTTC 59.673 55.000 0.00 0.00 38.64 3.62
914 931 1.535896 GGGAAAGGTGAGTCTTTTCGC 59.464 52.381 12.72 12.72 43.43 4.70
932 949 2.076863 CGCTCCTCTTTCGGTGATTTT 58.923 47.619 0.00 0.00 0.00 1.82
1572 1593 1.251251 GGTGTGGAATTCTTGCAGCT 58.749 50.000 5.23 0.00 0.00 4.24
1623 1644 3.812053 CAGATAGAGTGGCCATGTTTAGC 59.188 47.826 9.72 1.96 0.00 3.09
1635 1656 4.019174 CCATGTTTAGCCCAGAAGACATT 58.981 43.478 0.00 0.00 0.00 2.71
1665 1686 7.587757 CCTTTAGTTTTCGATGACACAGAAAAG 59.412 37.037 15.86 7.61 42.29 2.27
2141 2162 6.595326 TGCTTCATTTTCTGTAGATGTACCTG 59.405 38.462 0.00 0.00 0.00 4.00
2145 2166 7.323420 TCATTTTCTGTAGATGTACCTGTCTG 58.677 38.462 0.00 0.00 0.00 3.51
2170 2191 0.818040 GGTTTCTGGTCGTGTGCCTT 60.818 55.000 0.00 0.00 0.00 4.35
2206 2228 4.037208 CAGAAGATCATTTACCCATGTGCC 59.963 45.833 0.00 0.00 0.00 5.01
2593 2803 2.686405 CACACACCAATATGCAGCATCT 59.314 45.455 12.38 0.00 0.00 2.90
2605 2815 8.752254 CAATATGCAGCATCTTAATGAGTTTTG 58.248 33.333 12.38 0.00 34.61 2.44
2822 3032 9.077885 TGATGAGAAGCAAAAGGTAAACTAAAT 57.922 29.630 0.00 0.00 0.00 1.40
2877 3089 7.283354 CGAATATAGTCTCCTATCATGCCTACA 59.717 40.741 0.00 0.00 35.49 2.74
3403 3630 4.139859 AGAACAGCAGAGGAATGATCAG 57.860 45.455 0.09 0.00 0.00 2.90
3491 3718 0.755698 GGTGCTCGACCCTGGAGATA 60.756 60.000 0.00 0.00 39.10 1.98
3797 4024 6.438763 GCCCGAAAAGAATTGATAATGGTAG 58.561 40.000 0.00 0.00 0.00 3.18
3814 4041 1.276421 GTAGTGCTCCTTTCTCTGCCA 59.724 52.381 0.00 0.00 0.00 4.92
3890 4117 9.733556 TGGCTTTCTTTCATTGAATAGTTACTA 57.266 29.630 0.00 0.00 0.00 1.82
4015 4242 9.408069 GCAAGAGAAAATATGGAAATGATGATC 57.592 33.333 0.00 0.00 0.00 2.92
4623 4850 2.361610 GGGCTTTGGCTGCTAGCA 60.362 61.111 18.22 18.22 44.75 3.49
4625 4852 0.466189 GGGCTTTGGCTGCTAGCATA 60.466 55.000 19.72 5.06 44.75 3.14
4972 5200 8.047310 AGAGAAAGAGAAGGTACTGAAAACAAA 58.953 33.333 0.00 0.00 40.86 2.83
5037 5265 4.224991 TCTGATGCATTGACATTCCTCA 57.775 40.909 0.00 0.00 0.00 3.86
5176 5405 9.064706 AGATATCAAAATGCTCTAGGATGTTTG 57.935 33.333 5.32 10.17 31.84 2.93
5219 5448 5.163237 TGCACCTTTATATGTTACTCCCTCC 60.163 44.000 0.00 0.00 0.00 4.30
5220 5449 5.163237 GCACCTTTATATGTTACTCCCTCCA 60.163 44.000 0.00 0.00 0.00 3.86
5287 5516 9.914131 TGTACTACATAGATATACGTACGTTCT 57.086 33.333 27.92 23.87 31.08 3.01
5292 5521 8.824159 ACATAGATATACGTACGTTCTAGTGT 57.176 34.615 27.92 23.70 0.00 3.55
5293 5522 8.706936 ACATAGATATACGTACGTTCTAGTGTG 58.293 37.037 27.92 21.27 0.00 3.82
5294 5523 8.706936 CATAGATATACGTACGTTCTAGTGTGT 58.293 37.037 27.92 9.18 0.00 3.72
5295 5524 7.545362 AGATATACGTACGTTCTAGTGTGTT 57.455 36.000 27.92 2.90 0.00 3.32
5380 5609 7.656707 TGTGAACGTAGGGAGTATTTTTAAC 57.343 36.000 0.00 0.00 0.00 2.01
5387 5616 7.814587 ACGTAGGGAGTATTTTTAACACTGTAC 59.185 37.037 0.00 0.00 0.00 2.90
5402 5631 6.619801 ACACTGTACCTTCATGAAAAGTTC 57.380 37.500 9.88 8.45 0.00 3.01
5413 5642 7.275560 CCTTCATGAAAAGTTCGTGTTTCTTTT 59.724 33.333 9.88 0.00 44.93 2.27
5504 5734 1.064017 AGCTTGGACCAAAACTCCACA 60.064 47.619 8.59 0.00 37.54 4.17
5542 5772 3.135225 CGAACAATATGACGGCCCAATA 58.865 45.455 0.00 0.00 0.00 1.90
5565 5795 2.898729 ATTCTCCACTCGGTGCATAG 57.101 50.000 0.00 0.00 31.34 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 3.333680 TCTTGCTTCCCACCTCCTTTATT 59.666 43.478 0.00 0.00 0.00 1.40
88 90 9.740239 TTGCGGTATTATACTCTTTAACTAGTG 57.260 33.333 0.00 0.00 0.00 2.74
119 121 6.985117 TCCATGCTAATCCTGCAATATTTTC 58.015 36.000 0.00 0.00 44.01 2.29
151 155 1.155424 TGTTCGTGAACTTCACCGGC 61.155 55.000 14.98 6.77 44.20 6.13
161 165 5.533903 GGAGGGAGTAGTATATGTTCGTGAA 59.466 44.000 0.00 0.00 0.00 3.18
165 169 4.070716 ACGGAGGGAGTAGTATATGTTCG 58.929 47.826 0.00 0.00 0.00 3.95
174 178 4.959399 CGAGACGGAGGGAGTAGT 57.041 61.111 0.00 0.00 0.00 2.73
185 189 0.886563 ACACCCTCTAAACCGAGACG 59.113 55.000 0.00 0.00 32.74 4.18
186 190 1.617357 ACACACCCTCTAAACCGAGAC 59.383 52.381 0.00 0.00 32.74 3.36
187 191 1.616865 CACACACCCTCTAAACCGAGA 59.383 52.381 0.00 0.00 32.74 4.04
188 192 1.939838 GCACACACCCTCTAAACCGAG 60.940 57.143 0.00 0.00 0.00 4.63
189 193 0.034337 GCACACACCCTCTAAACCGA 59.966 55.000 0.00 0.00 0.00 4.69
190 194 1.289109 CGCACACACCCTCTAAACCG 61.289 60.000 0.00 0.00 0.00 4.44
191 195 0.250166 ACGCACACACCCTCTAAACC 60.250 55.000 0.00 0.00 0.00 3.27
192 196 2.288640 ACTACGCACACACCCTCTAAAC 60.289 50.000 0.00 0.00 0.00 2.01
193 197 1.965643 ACTACGCACACACCCTCTAAA 59.034 47.619 0.00 0.00 0.00 1.85
194 198 1.624336 ACTACGCACACACCCTCTAA 58.376 50.000 0.00 0.00 0.00 2.10
195 199 1.542915 GAACTACGCACACACCCTCTA 59.457 52.381 0.00 0.00 0.00 2.43
196 200 0.317479 GAACTACGCACACACCCTCT 59.683 55.000 0.00 0.00 0.00 3.69
197 201 0.317479 AGAACTACGCACACACCCTC 59.683 55.000 0.00 0.00 0.00 4.30
198 202 1.544691 CTAGAACTACGCACACACCCT 59.455 52.381 0.00 0.00 0.00 4.34
199 203 1.403780 CCTAGAACTACGCACACACCC 60.404 57.143 0.00 0.00 0.00 4.61
200 204 1.271656 ACCTAGAACTACGCACACACC 59.728 52.381 0.00 0.00 0.00 4.16
201 205 2.030540 TGACCTAGAACTACGCACACAC 60.031 50.000 0.00 0.00 0.00 3.82
202 206 2.232399 TGACCTAGAACTACGCACACA 58.768 47.619 0.00 0.00 0.00 3.72
203 207 3.436496 GATGACCTAGAACTACGCACAC 58.564 50.000 0.00 0.00 0.00 3.82
204 208 2.426024 GGATGACCTAGAACTACGCACA 59.574 50.000 0.00 0.00 0.00 4.57
205 209 2.426024 TGGATGACCTAGAACTACGCAC 59.574 50.000 0.00 0.00 37.04 5.34
206 210 2.730382 TGGATGACCTAGAACTACGCA 58.270 47.619 0.00 0.00 37.04 5.24
207 211 4.323553 AATGGATGACCTAGAACTACGC 57.676 45.455 0.00 0.00 37.04 4.42
208 212 7.490000 AGTTAAATGGATGACCTAGAACTACG 58.510 38.462 0.00 0.00 37.04 3.51
211 215 9.047947 AGTTAGTTAAATGGATGACCTAGAACT 57.952 33.333 0.00 0.00 37.04 3.01
260 264 9.965824 CCGCTTAAAAATCCAATGATATACTTT 57.034 29.630 0.00 0.00 0.00 2.66
261 265 9.349713 TCCGCTTAAAAATCCAATGATATACTT 57.650 29.630 0.00 0.00 0.00 2.24
262 266 8.918202 TCCGCTTAAAAATCCAATGATATACT 57.082 30.769 0.00 0.00 0.00 2.12
263 267 9.559958 CATCCGCTTAAAAATCCAATGATATAC 57.440 33.333 0.00 0.00 0.00 1.47
264 268 9.295825 ACATCCGCTTAAAAATCCAATGATATA 57.704 29.630 0.00 0.00 0.00 0.86
265 269 8.181904 ACATCCGCTTAAAAATCCAATGATAT 57.818 30.769 0.00 0.00 0.00 1.63
266 270 7.581213 ACATCCGCTTAAAAATCCAATGATA 57.419 32.000 0.00 0.00 0.00 2.15
267 271 6.469782 ACATCCGCTTAAAAATCCAATGAT 57.530 33.333 0.00 0.00 0.00 2.45
268 272 5.913137 ACATCCGCTTAAAAATCCAATGA 57.087 34.783 0.00 0.00 0.00 2.57
269 273 6.795399 ACTACATCCGCTTAAAAATCCAATG 58.205 36.000 0.00 0.00 0.00 2.82
270 274 7.404671 AACTACATCCGCTTAAAAATCCAAT 57.595 32.000 0.00 0.00 0.00 3.16
271 275 6.827586 AACTACATCCGCTTAAAAATCCAA 57.172 33.333 0.00 0.00 0.00 3.53
272 276 6.657541 AGAAACTACATCCGCTTAAAAATCCA 59.342 34.615 0.00 0.00 0.00 3.41
273 277 7.085052 AGAAACTACATCCGCTTAAAAATCC 57.915 36.000 0.00 0.00 0.00 3.01
346 350 9.393786 AGGACATATATGTGGTTCTAGGTTAAT 57.606 33.333 22.93 0.00 41.95 1.40
347 351 8.647796 CAGGACATATATGTGGTTCTAGGTTAA 58.352 37.037 22.93 0.00 41.95 2.01
348 352 7.787904 ACAGGACATATATGTGGTTCTAGGTTA 59.212 37.037 22.93 0.00 41.95 2.85
349 353 6.615726 ACAGGACATATATGTGGTTCTAGGTT 59.384 38.462 22.93 0.00 41.95 3.50
350 354 6.143915 ACAGGACATATATGTGGTTCTAGGT 58.856 40.000 22.93 6.83 41.95 3.08
351 355 6.672266 ACAGGACATATATGTGGTTCTAGG 57.328 41.667 22.93 6.27 41.95 3.02
352 356 9.477484 GTTTACAGGACATATATGTGGTTCTAG 57.523 37.037 22.93 7.97 41.95 2.43
353 357 8.426489 GGTTTACAGGACATATATGTGGTTCTA 58.574 37.037 22.93 3.46 41.95 2.10
354 358 7.280356 GGTTTACAGGACATATATGTGGTTCT 58.720 38.462 22.93 11.36 41.95 3.01
355 359 6.202188 CGGTTTACAGGACATATATGTGGTTC 59.798 42.308 22.93 8.28 41.95 3.62
356 360 6.053005 CGGTTTACAGGACATATATGTGGTT 58.947 40.000 22.93 5.43 41.95 3.67
357 361 5.364446 TCGGTTTACAGGACATATATGTGGT 59.636 40.000 22.93 18.11 41.95 4.16
358 362 5.849510 TCGGTTTACAGGACATATATGTGG 58.150 41.667 22.93 13.72 41.95 4.17
359 363 6.641314 GTCTCGGTTTACAGGACATATATGTG 59.359 42.308 22.93 11.19 41.95 3.21
360 364 6.514541 CGTCTCGGTTTACAGGACATATATGT 60.515 42.308 18.31 18.31 45.16 2.29
361 365 5.856986 CGTCTCGGTTTACAGGACATATATG 59.143 44.000 11.29 11.29 0.00 1.78
362 366 5.048224 CCGTCTCGGTTTACAGGACATATAT 60.048 44.000 0.00 0.00 42.73 0.86
363 367 4.276678 CCGTCTCGGTTTACAGGACATATA 59.723 45.833 0.00 0.00 42.73 0.86
364 368 3.067742 CCGTCTCGGTTTACAGGACATAT 59.932 47.826 0.00 0.00 42.73 1.78
365 369 2.424601 CCGTCTCGGTTTACAGGACATA 59.575 50.000 0.00 0.00 42.73 2.29
366 370 1.203994 CCGTCTCGGTTTACAGGACAT 59.796 52.381 0.00 0.00 42.73 3.06
367 371 0.599558 CCGTCTCGGTTTACAGGACA 59.400 55.000 0.00 0.00 42.73 4.02
368 372 3.413522 CCGTCTCGGTTTACAGGAC 57.586 57.895 0.00 0.00 42.73 3.85
379 383 3.937706 TCTTTACTACTTCCTCCGTCTCG 59.062 47.826 0.00 0.00 0.00 4.04
380 384 5.415389 ACTTCTTTACTACTTCCTCCGTCTC 59.585 44.000 0.00 0.00 0.00 3.36
381 385 5.183522 CACTTCTTTACTACTTCCTCCGTCT 59.816 44.000 0.00 0.00 0.00 4.18
382 386 5.400703 CACTTCTTTACTACTTCCTCCGTC 58.599 45.833 0.00 0.00 0.00 4.79
383 387 4.220163 CCACTTCTTTACTACTTCCTCCGT 59.780 45.833 0.00 0.00 0.00 4.69
384 388 4.745649 CCACTTCTTTACTACTTCCTCCG 58.254 47.826 0.00 0.00 0.00 4.63
385 389 4.020485 TGCCACTTCTTTACTACTTCCTCC 60.020 45.833 0.00 0.00 0.00 4.30
386 390 5.148651 TGCCACTTCTTTACTACTTCCTC 57.851 43.478 0.00 0.00 0.00 3.71
387 391 5.306394 GTTGCCACTTCTTTACTACTTCCT 58.694 41.667 0.00 0.00 0.00 3.36
388 392 4.151867 CGTTGCCACTTCTTTACTACTTCC 59.848 45.833 0.00 0.00 0.00 3.46
389 393 4.151867 CCGTTGCCACTTCTTTACTACTTC 59.848 45.833 0.00 0.00 0.00 3.01
390 394 4.062991 CCGTTGCCACTTCTTTACTACTT 58.937 43.478 0.00 0.00 0.00 2.24
391 395 3.660865 CCGTTGCCACTTCTTTACTACT 58.339 45.455 0.00 0.00 0.00 2.57
392 396 2.159037 GCCGTTGCCACTTCTTTACTAC 59.841 50.000 0.00 0.00 0.00 2.73
393 397 2.224329 TGCCGTTGCCACTTCTTTACTA 60.224 45.455 0.00 0.00 36.33 1.82
394 398 1.235724 GCCGTTGCCACTTCTTTACT 58.764 50.000 0.00 0.00 0.00 2.24
395 399 0.948678 TGCCGTTGCCACTTCTTTAC 59.051 50.000 0.00 0.00 36.33 2.01
710 723 0.669318 CAGGCCAACAGCATTTGCAG 60.669 55.000 5.01 0.00 46.50 4.41
720 733 3.161866 GGGATTTAAGAACAGGCCAACA 58.838 45.455 5.01 0.00 0.00 3.33
731 744 3.133003 CGAGAGGAGCAAGGGATTTAAGA 59.867 47.826 0.00 0.00 0.00 2.10
848 861 1.532604 ATTCCAGAGTGGCACGACGA 61.533 55.000 12.71 3.87 37.47 4.20
859 872 3.201708 AGAAATCCACCCAGATTCCAGAG 59.798 47.826 0.00 0.00 35.40 3.35
892 905 2.808543 CGAAAAGACTCACCTTTCCCAG 59.191 50.000 0.00 0.00 35.50 4.45
914 931 4.870991 GGAGTAAAATCACCGAAAGAGGAG 59.129 45.833 0.00 0.00 34.73 3.69
932 949 4.601857 GGGAATCCATAAGATTGGGGAGTA 59.398 45.833 0.09 0.00 45.52 2.59
1290 1311 3.939939 TGCTTGCTGGAGACGCCA 61.940 61.111 0.00 0.00 46.96 5.69
1572 1593 1.153524 AGCATTGAACCCTGCACCA 59.846 52.632 0.00 0.00 40.88 4.17
1623 1644 1.915141 AAGGCACAATGTCTTCTGGG 58.085 50.000 0.00 0.00 37.92 4.45
1635 1656 4.024387 GTGTCATCGAAAACTAAAGGCACA 60.024 41.667 0.00 0.00 0.00 4.57
1665 1686 2.409378 CACAATTGCAAAGCATTCCGAC 59.591 45.455 1.71 0.00 38.76 4.79
1788 1809 1.302033 GTCCACAGCACCTCCACAG 60.302 63.158 0.00 0.00 0.00 3.66
2141 2162 2.993899 CGACCAGAAACCATGTACAGAC 59.006 50.000 0.33 0.00 0.00 3.51
2145 2166 2.478894 CACACGACCAGAAACCATGTAC 59.521 50.000 0.00 0.00 0.00 2.90
2149 2170 0.889186 GGCACACGACCAGAAACCAT 60.889 55.000 0.00 0.00 0.00 3.55
2170 2191 0.401356 TCTTCTGCACCATCAGGCAA 59.599 50.000 0.00 0.00 39.93 4.52
2206 2228 7.387948 AGTTTCAGTAACATTAGTAGCCAAGTG 59.612 37.037 0.00 0.00 39.30 3.16
2318 2528 3.693085 CACAAGAGTTGATCATTCAGGGG 59.307 47.826 0.00 0.00 32.27 4.79
2416 2626 2.091555 AGGCCAACAAAAGTCCTGGTTA 60.092 45.455 5.01 0.00 0.00 2.85
2461 2671 9.897744 CAATGTTAAAGCAGATAAGAGACAAAA 57.102 29.630 0.00 0.00 0.00 2.44
2498 2708 8.917655 GCATTGTAAAACGTAACCAACATTATT 58.082 29.630 0.00 0.00 0.00 1.40
2593 2803 4.342665 AGGGGAAAACGCAAAACTCATTAA 59.657 37.500 0.00 0.00 33.80 1.40
2605 2815 2.926586 GCATTTCTGAAGGGGAAAACGC 60.927 50.000 0.00 0.00 36.47 4.84
2722 2932 0.040067 AGCTGCTTAGCACGCAAAAC 60.040 50.000 22.97 2.40 36.88 2.43
2822 3032 5.048224 GCTTAGTACCTCACACAGACAGTTA 60.048 44.000 0.00 0.00 0.00 2.24
3385 3612 2.475155 TCCTGATCATTCCTCTGCTGT 58.525 47.619 0.00 0.00 0.00 4.40
3403 3630 5.692654 GTCCTCGACTAGCTTCAAAATATCC 59.307 44.000 0.00 0.00 0.00 2.59
3491 3718 4.710324 TGTTGTTCCCACGATTAGTTCTT 58.290 39.130 0.00 0.00 0.00 2.52
3797 4024 1.294659 CGTGGCAGAGAAAGGAGCAC 61.295 60.000 0.00 0.00 0.00 4.40
3890 4117 1.617804 CCAAACCCTGCTCATGGTGAT 60.618 52.381 0.00 0.00 34.34 3.06
4015 4242 1.521010 CTGCTGCCCTCGTCTCATG 60.521 63.158 0.00 0.00 0.00 3.07
4147 4374 7.103641 CAGTAGCCTCTAACAATACAAAGGAA 58.896 38.462 0.00 0.00 0.00 3.36
4148 4375 6.212791 ACAGTAGCCTCTAACAATACAAAGGA 59.787 38.462 0.00 0.00 0.00 3.36
4182 4409 2.213499 CTGCATTACCCGAGGATTGTC 58.787 52.381 0.00 0.00 0.00 3.18
4301 4528 1.180456 TTCCGCTCGGGTTGTACTCA 61.180 55.000 8.59 0.00 37.00 3.41
4623 4850 5.102953 ACACCTGCACAATCTACACATAT 57.897 39.130 0.00 0.00 0.00 1.78
4625 4852 3.423539 ACACCTGCACAATCTACACAT 57.576 42.857 0.00 0.00 0.00 3.21
4690 4917 9.117183 TGTAATAACGTGTCTAGATACATCTGT 57.883 33.333 18.39 6.30 37.76 3.41
4746 4973 1.227556 CCCTCCGCCCTGAATTACG 60.228 63.158 0.00 0.00 0.00 3.18
4754 4981 3.778622 ATATAATACTCCCTCCGCCCT 57.221 47.619 0.00 0.00 0.00 5.19
4885 5113 6.767524 TTCACCAAACAGCTCTAAAAGAAA 57.232 33.333 0.00 0.00 0.00 2.52
4972 5200 3.076032 ACCCAGCAAAGTTCCCTTCTAAT 59.924 43.478 0.00 0.00 0.00 1.73
5037 5265 7.604545 GTGATTCTAAAGCTCTCCTACTTTTGT 59.395 37.037 0.00 0.00 37.33 2.83
5176 5405 1.066605 CAATCTTGCATGGTAGCTGCC 59.933 52.381 14.87 14.87 38.89 4.85
5203 5432 7.684317 TTGTGAATGGAGGGAGTAACATATA 57.316 36.000 0.00 0.00 0.00 0.86
5266 5495 9.914131 ACACTAGAACGTACGTATATCTATGTA 57.086 33.333 23.12 6.04 0.00 2.29
5267 5496 8.706936 CACACTAGAACGTACGTATATCTATGT 58.293 37.037 23.12 22.20 0.00 2.29
5268 5497 8.706936 ACACACTAGAACGTACGTATATCTATG 58.293 37.037 23.12 21.70 0.00 2.23
5269 5498 8.824159 ACACACTAGAACGTACGTATATCTAT 57.176 34.615 23.12 11.64 0.00 1.98
5270 5499 8.648557 AACACACTAGAACGTACGTATATCTA 57.351 34.615 23.12 21.85 0.00 1.98
5271 5500 7.515841 CGAACACACTAGAACGTACGTATATCT 60.516 40.741 23.12 21.91 0.00 1.98
5272 5501 6.567875 CGAACACACTAGAACGTACGTATATC 59.432 42.308 23.12 15.71 0.00 1.63
5273 5502 6.036083 ACGAACACACTAGAACGTACGTATAT 59.964 38.462 23.12 12.85 32.42 0.86
5274 5503 5.347635 ACGAACACACTAGAACGTACGTATA 59.652 40.000 23.12 16.11 32.42 1.47
5275 5504 4.152402 ACGAACACACTAGAACGTACGTAT 59.848 41.667 23.12 15.82 32.42 3.06
5276 5505 3.493129 ACGAACACACTAGAACGTACGTA 59.507 43.478 23.12 5.12 32.42 3.57
5277 5506 2.287915 ACGAACACACTAGAACGTACGT 59.712 45.455 16.72 16.72 32.42 3.57
5278 5507 2.908634 ACGAACACACTAGAACGTACG 58.091 47.619 15.01 15.01 32.42 3.67
5279 5508 4.145414 GTGAACGAACACACTAGAACGTAC 59.855 45.833 0.00 0.00 40.11 3.67
5280 5509 4.035558 AGTGAACGAACACACTAGAACGTA 59.964 41.667 15.83 0.00 44.06 3.57
5281 5510 3.111098 GTGAACGAACACACTAGAACGT 58.889 45.455 0.00 0.00 40.11 3.99
5282 5511 3.369385 AGTGAACGAACACACTAGAACG 58.631 45.455 15.83 0.00 44.06 3.95
5283 5512 4.357142 TGAGTGAACGAACACACTAGAAC 58.643 43.478 15.83 3.83 45.54 3.01
5284 5513 4.642445 TGAGTGAACGAACACACTAGAA 57.358 40.909 15.83 2.45 45.54 2.10
5285 5514 4.848562 ATGAGTGAACGAACACACTAGA 57.151 40.909 15.83 5.26 45.54 2.43
5286 5515 5.907197 AAATGAGTGAACGAACACACTAG 57.093 39.130 15.83 0.00 45.54 2.57
5287 5516 6.509656 ACTAAATGAGTGAACGAACACACTA 58.490 36.000 15.83 5.34 45.54 2.74
5289 5518 5.462398 AGACTAAATGAGTGAACGAACACAC 59.538 40.000 15.83 11.41 42.45 3.82
5290 5519 5.462068 CAGACTAAATGAGTGAACGAACACA 59.538 40.000 15.83 5.27 42.45 3.72
5291 5520 5.462398 ACAGACTAAATGAGTGAACGAACAC 59.538 40.000 8.22 8.22 39.06 3.32
5292 5521 5.597806 ACAGACTAAATGAGTGAACGAACA 58.402 37.500 0.00 0.00 39.06 3.18
5293 5522 7.813852 ATACAGACTAAATGAGTGAACGAAC 57.186 36.000 0.00 0.00 39.06 3.95
5360 5589 7.219322 ACAGTGTTAAAAATACTCCCTACGTT 58.781 34.615 0.00 0.00 29.72 3.99
5380 5609 5.236478 ACGAACTTTTCATGAAGGTACAGTG 59.764 40.000 8.41 0.00 0.00 3.66
5387 5616 5.821204 AGAAACACGAACTTTTCATGAAGG 58.179 37.500 8.41 8.39 34.68 3.46
5402 5631 7.273381 ACTTTTCAATGTCTCAAAAGAAACACG 59.727 33.333 10.55 0.00 38.77 4.49
5413 5642 7.121168 AGACAACAGAAACTTTTCAATGTCTCA 59.879 33.333 20.16 0.00 44.17 3.27
5542 5772 5.127845 CCTATGCACCGAGTGGAGAATATAT 59.872 44.000 0.00 0.00 37.30 0.86


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

AutoCloner maintained by Alex Coulton.