Multiple sequence alignment - TraesCS5A01G157600

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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 TraesCS5A01G157600 chr5A 100.000 4041 0 0 1 4041 337831683 337835723 0.000000e+00 7463
1 TraesCS5A01G157600 chr5B 95.325 1583 51 14 234 1808 288307136 288305569 0.000000e+00 2492
2 TraesCS5A01G157600 chr5B 95.007 761 28 7 2355 3113 288304588 288303836 0.000000e+00 1186
3 TraesCS5A01G157600 chr5B 95.667 577 14 7 1795 2369 288305182 288304615 0.000000e+00 917
4 TraesCS5A01G157600 chr5B 85.229 589 79 4 3450 4033 288303292 288302707 2.080000e-167 599
5 TraesCS5A01G157600 chr5B 90.400 125 7 3 27 146 288307284 288307160 4.180000e-35 159
6 TraesCS5A01G157600 chr5D 92.026 928 22 23 110 1036 254570711 254571587 0.000000e+00 1256
7 TraesCS5A01G157600 chr5D 95.109 777 33 4 2355 3130 254575696 254576468 0.000000e+00 1219
8 TraesCS5A01G157600 chr5D 92.329 730 35 12 1649 2369 254574952 254575669 0.000000e+00 1018
9 TraesCS5A01G157600 chr5D 88.718 585 53 9 1070 1652 254571583 254572156 0.000000e+00 702
10 TraesCS5A01G157600 chr5D 84.106 604 83 5 3436 4033 254577270 254577866 4.530000e-159 571
11 TraesCS5A01G157600 chr5D 93.750 80 5 0 3 82 254570637 254570716 1.970000e-23 121


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 TraesCS5A01G157600 chr5A 337831683 337835723 4040 False 7463.0 7463 100.000000 1 4041 1 chr5A.!!$F1 4040
1 TraesCS5A01G157600 chr5B 288302707 288307284 4577 True 1070.6 2492 92.325600 27 4033 5 chr5B.!!$R1 4006
2 TraesCS5A01G157600 chr5D 254570637 254577866 7229 False 814.5 1256 91.006333 3 4033 6 chr5D.!!$F1 4030

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
198 203 1.535028 TGCTACCAACGCATCAAAGTG 59.465 47.619 0.00 0.0 31.40 3.16 F
255 264 1.686587 TGTTGAGGCTCGTCTTTCTGA 59.313 47.619 10.42 0.0 0.00 3.27 F
1279 1297 1.906574 TGGAGCCCTTCAAACTACGAT 59.093 47.619 0.00 0.0 0.00 3.73 F
2250 5476 1.234821 CCATGTGCAAGGTTACGTGT 58.765 50.000 0.00 0.0 33.13 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1547 1.538047 TCAGCACAGAGGCCATTTTC 58.462 50.000 5.01 0.0 0.0 2.29 R
1683 4502 1.675641 GCCGGTGCCTGAGAACAAT 60.676 57.895 1.90 0.0 0.0 2.71 R
2914 6179 0.413832 TCCCTGGGTAGAGCTTCAGT 59.586 55.000 13.56 0.0 0.0 3.41 R
3925 7724 0.681175 GTGCCCAACAAAAGCCATCT 59.319 50.000 0.00 0.0 0.0 2.90 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
50 51 5.070001 TCCTCCATAACCACTGAAAACAAG 58.930 41.667 0.00 0.00 0.00 3.16
52 53 4.211125 TCCATAACCACTGAAAACAAGCA 58.789 39.130 0.00 0.00 0.00 3.91
77 78 3.543680 TCTTAATCTGCTGGTGCCTAC 57.456 47.619 0.00 0.00 38.71 3.18
172 177 6.978080 TGTTTTCCTGACAATAAAGCAGAAAC 59.022 34.615 0.00 0.00 31.97 2.78
195 200 2.621055 ACTTTGCTACCAACGCATCAAA 59.379 40.909 0.00 0.00 37.22 2.69
196 201 2.987413 TTGCTACCAACGCATCAAAG 57.013 45.000 0.00 0.00 37.22 2.77
197 202 1.890876 TGCTACCAACGCATCAAAGT 58.109 45.000 0.00 0.00 31.40 2.66
198 203 1.535028 TGCTACCAACGCATCAAAGTG 59.465 47.619 0.00 0.00 31.40 3.16
199 204 1.804151 GCTACCAACGCATCAAAGTGA 59.196 47.619 0.00 0.00 0.00 3.41
200 205 2.420022 GCTACCAACGCATCAAAGTGAT 59.580 45.455 0.00 0.00 37.65 3.06
201 206 3.119849 GCTACCAACGCATCAAAGTGATT 60.120 43.478 0.00 0.00 34.28 2.57
202 207 4.615912 GCTACCAACGCATCAAAGTGATTT 60.616 41.667 0.00 0.00 34.28 2.17
203 208 4.320608 ACCAACGCATCAAAGTGATTTT 57.679 36.364 0.00 0.00 34.28 1.82
204 209 4.298332 ACCAACGCATCAAAGTGATTTTC 58.702 39.130 0.00 0.00 34.28 2.29
205 210 4.202101 ACCAACGCATCAAAGTGATTTTCA 60.202 37.500 0.00 0.00 34.28 2.69
206 211 4.925054 CCAACGCATCAAAGTGATTTTCAT 59.075 37.500 0.00 0.00 34.28 2.57
207 212 5.061311 CCAACGCATCAAAGTGATTTTCATC 59.939 40.000 0.00 0.00 34.28 2.92
208 213 5.633830 ACGCATCAAAGTGATTTTCATCT 57.366 34.783 0.00 0.00 34.28 2.90
209 214 6.741992 ACGCATCAAAGTGATTTTCATCTA 57.258 33.333 0.00 0.00 34.28 1.98
210 215 7.325660 ACGCATCAAAGTGATTTTCATCTAT 57.674 32.000 0.00 0.00 34.28 1.98
211 216 7.765307 ACGCATCAAAGTGATTTTCATCTATT 58.235 30.769 0.00 0.00 34.28 1.73
212 217 8.892723 ACGCATCAAAGTGATTTTCATCTATTA 58.107 29.630 0.00 0.00 34.28 0.98
213 218 9.378597 CGCATCAAAGTGATTTTCATCTATTAG 57.621 33.333 0.00 0.00 34.28 1.73
239 248 5.219343 TGTCCTGGATAGATAGCATGTTG 57.781 43.478 0.00 0.00 0.00 3.33
240 249 4.901250 TGTCCTGGATAGATAGCATGTTGA 59.099 41.667 0.00 0.00 0.00 3.18
243 252 4.252073 CTGGATAGATAGCATGTTGAGGC 58.748 47.826 0.00 0.00 0.00 4.70
255 264 1.686587 TGTTGAGGCTCGTCTTTCTGA 59.313 47.619 10.42 0.00 0.00 3.27
285 294 5.278660 GCACTGAATAATTCAATAGGCTGGG 60.279 44.000 0.00 0.00 39.58 4.45
353 362 4.860802 TTGTGGGTATCTGGATGTTCAT 57.139 40.909 0.00 0.00 0.00 2.57
380 390 3.281727 AAGAACAGACTTGCTTGGACA 57.718 42.857 0.00 0.00 0.00 4.02
410 420 7.866393 GCTGATTCTTGCATATATTCTGCTTTT 59.134 33.333 10.29 0.00 40.34 2.27
414 424 7.182361 TCTTGCATATATTCTGCTTTTCTCG 57.818 36.000 10.29 0.00 40.34 4.04
663 675 3.576078 TCCTGACCAAACAATGACAGT 57.424 42.857 0.00 0.00 34.10 3.55
922 938 4.331168 GGACGTATATATAACGACCGCTCT 59.669 45.833 18.15 1.62 43.15 4.09
1041 1059 8.561738 TCAAATATCAAGAGGTTAGTTGGTTC 57.438 34.615 0.00 0.00 31.17 3.62
1059 1077 3.335579 GTTCCATACAGAAACGAAGCCT 58.664 45.455 0.00 0.00 0.00 4.58
1154 1172 9.722056 AGTTCTTTATTTATGTTTGATCGATGC 57.278 29.630 0.54 0.00 0.00 3.91
1167 1185 7.850492 TGTTTGATCGATGCGATACTTTAATTG 59.150 33.333 0.54 0.00 47.00 2.32
1257 1275 3.065371 GGATTGAACCTCTTTACATGCCG 59.935 47.826 0.00 0.00 0.00 5.69
1279 1297 1.906574 TGGAGCCCTTCAAACTACGAT 59.093 47.619 0.00 0.00 0.00 3.73
1419 1438 7.512579 CGTCATATAGTTTAACTGTACACGTGC 60.513 40.741 17.22 0.00 32.10 5.34
1850 5070 4.202000 TGCAAGTGTTTGTGGTATGTTCTG 60.202 41.667 0.00 0.00 36.65 3.02
1852 5072 5.678616 GCAAGTGTTTGTGGTATGTTCTGTT 60.679 40.000 0.00 0.00 36.65 3.16
2035 5256 6.889301 ATTGGCAGATATAGGTGATTTGTG 57.111 37.500 0.00 0.00 0.00 3.33
2052 5273 8.017946 GTGATTTGTGGATGTCTAGAAAACTTC 58.982 37.037 0.00 0.00 0.00 3.01
2056 5277 7.259290 TGTGGATGTCTAGAAAACTTCAAAC 57.741 36.000 0.00 0.00 0.00 2.93
2246 5472 1.604147 GCCCCCATGTGCAAGGTTAC 61.604 60.000 0.00 0.00 0.00 2.50
2250 5476 1.234821 CCATGTGCAAGGTTACGTGT 58.765 50.000 0.00 0.00 33.13 4.49
2329 5555 4.864916 TTTTGAGATCTACAATCTGCGC 57.135 40.909 0.00 0.00 0.00 6.09
2584 5849 5.693555 TCACTGAATCGTCTGCATCATTATC 59.306 40.000 0.00 0.00 0.00 1.75
2585 5850 5.695363 CACTGAATCGTCTGCATCATTATCT 59.305 40.000 0.00 0.00 0.00 1.98
2587 5852 7.544915 CACTGAATCGTCTGCATCATTATCTAT 59.455 37.037 0.00 0.00 0.00 1.98
2588 5853 8.743714 ACTGAATCGTCTGCATCATTATCTATA 58.256 33.333 0.00 0.00 0.00 1.31
2594 5859 9.927668 TCGTCTGCATCATTATCTATAAATGAA 57.072 29.630 2.91 0.00 44.25 2.57
2650 5915 4.706842 TTGCTATAAAGGAAGGCCTAGG 57.293 45.455 5.16 3.67 46.28 3.02
2718 5983 3.437049 AGCAATCTTGAAAAGGTACGAGC 59.563 43.478 0.00 0.00 46.24 5.03
2762 6027 7.106239 ACATTGAACTGGTAATCCTGAAGTAG 58.894 38.462 0.00 0.00 36.65 2.57
2765 6030 7.074653 TGAACTGGTAATCCTGAAGTAGTTT 57.925 36.000 0.00 0.00 36.65 2.66
2771 6036 9.099454 CTGGTAATCCTGAAGTAGTTTCATAAC 57.901 37.037 0.00 0.00 44.48 1.89
2839 6104 4.354987 ACCCTGCCATTCATTATAGTCCAT 59.645 41.667 0.00 0.00 0.00 3.41
2891 6156 6.495181 AGCAGTAAGTGAGGCACTATATACAT 59.505 38.462 0.00 0.00 44.62 2.29
2914 6179 6.650427 TTAGCTGAGAGTAAAGACAAGACA 57.350 37.500 0.00 0.00 0.00 3.41
2915 6180 4.877282 AGCTGAGAGTAAAGACAAGACAC 58.123 43.478 0.00 0.00 0.00 3.67
2989 6254 5.947503 ACAACATTGACATTGTGTTTTCG 57.052 34.783 3.84 0.00 37.64 3.46
3000 6265 6.486248 ACATTGTGTTTTCGGATATCATTCG 58.514 36.000 4.83 0.00 0.00 3.34
3031 6296 3.509442 TGAGAGGGCATTGGTTCAAAAT 58.491 40.909 0.00 0.00 0.00 1.82
3040 6305 6.480981 GGGCATTGGTTCAAAATGAATCATAG 59.519 38.462 6.86 4.56 45.77 2.23
3076 6342 9.220767 CAGAGCCTAAAATGTTAATATACTCCC 57.779 37.037 0.00 0.00 0.00 4.30
3086 6352 6.486056 TGTTAATATACTCCCTGTTGCCAAA 58.514 36.000 0.00 0.00 0.00 3.28
3102 6368 2.356069 GCCAAAGCAGTGAGTATAAGGC 59.644 50.000 0.00 0.00 39.53 4.35
3110 6376 2.029623 GTGAGTATAAGGCGACCCAGA 58.970 52.381 0.00 0.00 0.00 3.86
3113 6379 3.117776 TGAGTATAAGGCGACCCAGAGTA 60.118 47.826 0.00 0.00 0.00 2.59
3115 6381 5.221986 TGAGTATAAGGCGACCCAGAGTATA 60.222 44.000 0.00 0.00 0.00 1.47
3118 6384 6.827762 AGTATAAGGCGACCCAGAGTATATAC 59.172 42.308 4.60 4.60 0.00 1.47
3163 6471 6.405278 ACCAATAGCTTAGTGCAAGTTTTT 57.595 33.333 0.00 0.00 45.94 1.94
3222 6530 4.712476 AGCATTGGATAGCAACCTTCTAG 58.288 43.478 0.00 0.00 0.00 2.43
3247 6556 7.492344 AGTTTTCTTGTTGTATCTTTTTGGCAG 59.508 33.333 0.00 0.00 0.00 4.85
3291 6625 8.497554 ACGTTGTACATGTAAATAACAATTCGT 58.502 29.630 20.02 17.89 42.70 3.85
3316 6650 4.881157 AGTTTACTCATATTGGGGGCTT 57.119 40.909 0.00 0.00 0.00 4.35
3328 6662 1.216678 TGGGGGCTTTCTCTTCAACAA 59.783 47.619 0.00 0.00 0.00 2.83
3342 6676 6.485313 TCTCTTCAACAAATTGTTCACGGTAT 59.515 34.615 8.59 0.00 38.77 2.73
3347 6681 5.862924 ACAAATTGTTCACGGTATGAGAG 57.137 39.130 0.00 0.00 38.99 3.20
3358 6692 4.690748 CACGGTATGAGAGTCATGTGTTTT 59.309 41.667 0.00 0.00 37.70 2.43
3377 6711 8.892723 TGTGTTTTACTATGGAGAAATATGCAG 58.107 33.333 0.00 0.00 0.00 4.41
3396 6730 9.783081 ATATGCAGACATCATAAGTTTGTCATA 57.217 29.630 7.88 0.00 41.71 2.15
3401 6735 9.538508 CAGACATCATAAGTTTGTCATATGAGA 57.461 33.333 5.42 1.05 41.71 3.27
3420 6754 3.572584 AGACCGCACTAGTAGAAAAACG 58.427 45.455 3.59 0.22 0.00 3.60
3431 6765 5.638596 AGTAGAAAAACGGGCATTAAAGG 57.361 39.130 0.00 0.00 0.00 3.11
3432 6766 5.074804 AGTAGAAAAACGGGCATTAAAGGT 58.925 37.500 0.00 0.00 0.00 3.50
3457 7253 2.657297 CCCCCAAGTGGTTGTGATG 58.343 57.895 0.00 0.00 30.95 3.07
3472 7268 4.350368 TGTGATGCAGAGGAACAAAGTA 57.650 40.909 0.00 0.00 0.00 2.24
3497 7293 6.708054 AGTATGTAATGCTGAACAATAGAGGC 59.292 38.462 0.00 0.00 38.08 4.70
3513 7309 2.234908 AGAGGCAGTTCCACATGAGTAC 59.765 50.000 0.00 0.00 37.29 2.73
3516 7312 2.500098 GGCAGTTCCACATGAGTACCTA 59.500 50.000 0.00 0.00 34.01 3.08
3518 7314 3.933332 GCAGTTCCACATGAGTACCTAAC 59.067 47.826 0.00 0.00 0.00 2.34
3520 7316 5.105473 GCAGTTCCACATGAGTACCTAACTA 60.105 44.000 0.00 0.00 39.07 2.24
3533 7329 7.504911 TGAGTACCTAACTACAGTTCAGAAACT 59.495 37.037 0.00 0.00 41.89 2.66
3581 7377 8.670135 CATACGATTATGAAACAAAACCACCTA 58.330 33.333 0.00 0.00 37.86 3.08
3592 7388 8.650143 AAACAAAACCACCTATGAGAATACAT 57.350 30.769 0.00 0.00 0.00 2.29
3595 7391 4.357918 ACCACCTATGAGAATACATGGC 57.642 45.455 0.00 0.00 0.00 4.40
3610 7406 0.671163 ATGGCGGCAGTTGCAATTTG 60.671 50.000 19.29 5.96 44.36 2.32
3615 7411 2.415776 CGGCAGTTGCAATTTGGAAAT 58.584 42.857 0.59 1.06 44.36 2.17
3617 7413 3.401182 GGCAGTTGCAATTTGGAAATCA 58.599 40.909 0.59 0.00 44.36 2.57
3619 7415 4.060205 GCAGTTGCAATTTGGAAATCACT 58.940 39.130 0.59 0.00 41.59 3.41
3677 7475 4.079253 GGAAACTGCCTCCAATACTTTGA 58.921 43.478 0.00 0.00 34.60 2.69
3680 7478 6.038714 GGAAACTGCCTCCAATACTTTGATAG 59.961 42.308 0.00 0.00 34.60 2.08
3683 7481 2.808543 GCCTCCAATACTTTGATAGCCG 59.191 50.000 0.00 0.00 34.60 5.52
3685 7483 4.058817 CCTCCAATACTTTGATAGCCGAC 58.941 47.826 0.00 0.00 34.60 4.79
3688 7486 4.058817 CCAATACTTTGATAGCCGACCTC 58.941 47.826 0.00 0.00 34.60 3.85
3689 7487 4.442893 CCAATACTTTGATAGCCGACCTCA 60.443 45.833 0.00 0.00 34.60 3.86
3691 7489 2.180276 ACTTTGATAGCCGACCTCACT 58.820 47.619 0.00 0.00 0.00 3.41
3696 7494 2.092592 TGATAGCCGACCTCACTGACTA 60.093 50.000 0.00 0.00 0.00 2.59
3703 7501 4.363999 CCGACCTCACTGACTATGATTTC 58.636 47.826 0.00 0.00 0.00 2.17
3712 7510 3.797039 TGACTATGATTTCGCTGGGAAG 58.203 45.455 7.24 0.00 35.70 3.46
3740 7538 1.531423 TCACTCGAGTGGGTAGTGTC 58.469 55.000 37.82 0.00 45.65 3.67
3757 7555 2.050351 CGTCGCTCTTGACCGTGT 60.050 61.111 0.00 0.00 35.40 4.49
3758 7556 1.660575 CGTCGCTCTTGACCGTGTT 60.661 57.895 0.00 0.00 35.40 3.32
3774 7572 4.424711 TTGAGTGGGATGGCGGCC 62.425 66.667 13.32 13.32 0.00 6.13
3804 7602 2.177016 TCATCGATCTAAGGTGGAGGGA 59.823 50.000 0.00 0.00 0.00 4.20
3810 7608 1.286849 TCTAAGGTGGAGGGATGTCGA 59.713 52.381 0.00 0.00 0.00 4.20
3811 7609 1.409427 CTAAGGTGGAGGGATGTCGAC 59.591 57.143 9.11 9.11 0.00 4.20
3813 7611 2.050350 GGTGGAGGGATGTCGACGA 61.050 63.158 11.62 0.00 0.00 4.20
3817 7615 1.679680 TGGAGGGATGTCGACGATAAC 59.320 52.381 11.62 0.00 0.00 1.89
3818 7616 1.955080 GGAGGGATGTCGACGATAACT 59.045 52.381 11.62 5.21 0.00 2.24
3834 7633 1.529744 AACTGTTTTGAGGGGGAGGA 58.470 50.000 0.00 0.00 0.00 3.71
3836 7635 1.355720 ACTGTTTTGAGGGGGAGGATG 59.644 52.381 0.00 0.00 0.00 3.51
3837 7636 1.355720 CTGTTTTGAGGGGGAGGATGT 59.644 52.381 0.00 0.00 0.00 3.06
3845 7644 0.404040 GGGGGAGGATGTTGTTGTCA 59.596 55.000 0.00 0.00 0.00 3.58
3846 7645 1.005924 GGGGGAGGATGTTGTTGTCAT 59.994 52.381 0.00 0.00 0.00 3.06
3847 7646 2.369394 GGGGAGGATGTTGTTGTCATC 58.631 52.381 0.00 0.00 40.38 2.92
3852 7651 5.227238 GAGGATGTTGTTGTCATCATCAC 57.773 43.478 13.18 9.11 45.94 3.06
3860 7659 6.072893 TGTTGTTGTCATCATCACTGATTCAG 60.073 38.462 12.17 12.17 40.20 3.02
3874 7673 2.239654 TGATTCAGGATGGAGGGTTGTC 59.760 50.000 0.00 0.00 36.16 3.18
3892 7691 0.953471 TCGCCGGACACCATTTTGAG 60.953 55.000 5.05 0.00 0.00 3.02
3914 7713 1.546323 GGATGGATGCCACCGATCATT 60.546 52.381 0.00 0.00 35.80 2.57
3921 7720 2.720915 TGCCACCGATCATTGATTTGA 58.279 42.857 0.00 0.00 0.00 2.69
3925 7724 4.450976 CCACCGATCATTGATTTGAGGTA 58.549 43.478 13.11 0.00 0.00 3.08
3933 7732 5.759059 TCATTGATTTGAGGTAGATGGCTT 58.241 37.500 0.00 0.00 0.00 4.35
3938 7737 5.774690 TGATTTGAGGTAGATGGCTTTTGTT 59.225 36.000 0.00 0.00 0.00 2.83
3939 7738 5.452078 TTTGAGGTAGATGGCTTTTGTTG 57.548 39.130 0.00 0.00 0.00 3.33
3966 7765 4.512914 GTGAGGGGGATGGCTGCC 62.513 72.222 12.87 12.87 0.00 4.85
3977 7776 4.408821 GGCTGCCACCGGTCATCA 62.409 66.667 15.17 1.38 0.00 3.07
4004 7803 2.107546 GGTGTGTTGTCGTCGGGT 59.892 61.111 0.00 0.00 0.00 5.28
4017 7816 0.608035 GTCGGGTGCCATTTTGAGGA 60.608 55.000 0.00 0.00 0.00 3.71
4033 7835 2.119495 GAGGAGGGGCTTCTGTTATCA 58.881 52.381 0.00 0.00 0.00 2.15
4034 7836 2.708325 GAGGAGGGGCTTCTGTTATCAT 59.292 50.000 0.00 0.00 0.00 2.45
4035 7837 3.126453 AGGAGGGGCTTCTGTTATCATT 58.874 45.455 0.00 0.00 0.00 2.57
4036 7838 3.137360 AGGAGGGGCTTCTGTTATCATTC 59.863 47.826 0.00 0.00 0.00 2.67
4037 7839 3.137360 GGAGGGGCTTCTGTTATCATTCT 59.863 47.826 0.00 0.00 0.00 2.40
4038 7840 4.348168 GGAGGGGCTTCTGTTATCATTCTA 59.652 45.833 0.00 0.00 0.00 2.10
4039 7841 5.013599 GGAGGGGCTTCTGTTATCATTCTAT 59.986 44.000 0.00 0.00 0.00 1.98
4040 7842 6.213600 GGAGGGGCTTCTGTTATCATTCTATA 59.786 42.308 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.199078 TCTTGATCGATCAGCTACATATATGC 58.801 38.462 25.95 0.00 38.19 3.14
1 2 9.747293 AATCTTGATCGATCAGCTACATATATG 57.253 33.333 25.95 11.29 38.19 1.78
13 14 6.459066 GTTATGGAGGAATCTTGATCGATCA 58.541 40.000 23.99 23.99 34.44 2.92
50 51 3.084786 ACCAGCAGATTAAGAACCTTGC 58.915 45.455 0.00 0.00 0.00 4.01
52 53 3.084786 GCACCAGCAGATTAAGAACCTT 58.915 45.455 0.00 0.00 41.58 3.50
102 103 6.711277 TGGGAGAAGAATATGTATGTATGCC 58.289 40.000 0.00 0.00 0.00 4.40
147 152 6.707440 TTCTGCTTTATTGTCAGGAAAACA 57.293 33.333 0.00 0.00 0.00 2.83
172 177 2.326222 TGCGTTGGTAGCAAAGTGG 58.674 52.632 19.30 7.06 42.18 4.00
208 213 9.990868 TGCTATCTATCCAGGACAATACTAATA 57.009 33.333 0.00 0.00 0.00 0.98
209 214 8.901472 TGCTATCTATCCAGGACAATACTAAT 57.099 34.615 0.00 0.00 0.00 1.73
210 215 8.753133 CATGCTATCTATCCAGGACAATACTAA 58.247 37.037 0.00 0.00 0.00 2.24
211 216 7.895962 ACATGCTATCTATCCAGGACAATACTA 59.104 37.037 0.00 0.00 0.00 1.82
212 217 6.728164 ACATGCTATCTATCCAGGACAATACT 59.272 38.462 0.00 0.00 0.00 2.12
213 218 6.940739 ACATGCTATCTATCCAGGACAATAC 58.059 40.000 0.00 0.00 0.00 1.89
214 219 7.235399 TCAACATGCTATCTATCCAGGACAATA 59.765 37.037 0.00 0.00 0.00 1.90
215 220 6.043590 TCAACATGCTATCTATCCAGGACAAT 59.956 38.462 0.00 0.00 0.00 2.71
216 221 5.366477 TCAACATGCTATCTATCCAGGACAA 59.634 40.000 0.00 0.00 0.00 3.18
217 222 4.901250 TCAACATGCTATCTATCCAGGACA 59.099 41.667 0.00 0.00 0.00 4.02
218 223 5.474578 TCAACATGCTATCTATCCAGGAC 57.525 43.478 0.00 0.00 0.00 3.85
219 224 4.529769 CCTCAACATGCTATCTATCCAGGA 59.470 45.833 0.00 0.00 0.00 3.86
220 225 4.829968 CCTCAACATGCTATCTATCCAGG 58.170 47.826 0.00 0.00 0.00 4.45
221 226 4.020396 AGCCTCAACATGCTATCTATCCAG 60.020 45.833 0.00 0.00 35.69 3.86
222 227 3.906218 AGCCTCAACATGCTATCTATCCA 59.094 43.478 0.00 0.00 35.69 3.41
223 228 4.502962 GAGCCTCAACATGCTATCTATCC 58.497 47.826 0.00 0.00 38.11 2.59
224 229 4.172505 CGAGCCTCAACATGCTATCTATC 58.827 47.826 0.00 0.00 38.11 2.08
225 230 3.576118 ACGAGCCTCAACATGCTATCTAT 59.424 43.478 0.00 0.00 38.11 1.98
226 231 2.959030 ACGAGCCTCAACATGCTATCTA 59.041 45.455 0.00 0.00 38.11 1.98
227 232 1.759445 ACGAGCCTCAACATGCTATCT 59.241 47.619 0.00 0.00 38.11 1.98
228 233 2.131183 GACGAGCCTCAACATGCTATC 58.869 52.381 0.00 0.00 38.11 2.08
229 234 1.759445 AGACGAGCCTCAACATGCTAT 59.241 47.619 0.00 0.00 38.11 2.97
232 241 1.129437 GAAAGACGAGCCTCAACATGC 59.871 52.381 0.00 0.00 0.00 4.06
239 248 2.070028 GGTTTCAGAAAGACGAGCCTC 58.930 52.381 0.00 0.00 0.00 4.70
240 249 1.694696 AGGTTTCAGAAAGACGAGCCT 59.305 47.619 0.00 0.00 0.00 4.58
243 252 2.221981 GTGCAGGTTTCAGAAAGACGAG 59.778 50.000 0.00 0.00 0.00 4.18
255 264 7.631377 GCCTATTGAATTATTCAGTGCAGGTTT 60.631 37.037 15.80 0.00 41.38 3.27
285 294 6.942886 TGTGTTGTTGATTCAGACAAAAAC 57.057 33.333 12.73 0.00 42.40 2.43
337 346 6.757897 TTGAACAATGAACATCCAGATACC 57.242 37.500 0.00 0.00 0.00 2.73
353 362 5.401550 CAAGCAAGTCTGTTCTTTGAACAA 58.598 37.500 13.12 3.80 0.00 2.83
380 390 6.430308 CAGAATATATGCAAGAATCAGCAGGT 59.570 38.462 6.55 1.22 44.94 4.00
410 420 2.295349 ACTGTAGCCTTTCGAAACGAGA 59.705 45.455 6.47 0.00 37.14 4.04
414 424 3.259902 CCCTACTGTAGCCTTTCGAAAC 58.740 50.000 6.47 0.00 0.00 2.78
542 554 1.271379 CATCATGATCGGCCCATTTGG 59.729 52.381 4.86 0.00 37.09 3.28
638 650 5.415221 TGTCATTGTTTGGTCAGGAAAAAC 58.585 37.500 0.00 0.00 34.97 2.43
663 675 7.894376 AGATAATCGGTTGTTTTCGTTCTAA 57.106 32.000 0.00 0.00 0.00 2.10
1041 1059 3.252974 AGAGGCTTCGTTTCTGTATGG 57.747 47.619 0.00 0.00 0.00 2.74
1149 1167 9.727403 CTAATACACAATTAAAGTATCGCATCG 57.273 33.333 0.00 0.00 29.59 3.84
1176 1194 8.408043 TTTCCAACAGATCATTCAGTAACATT 57.592 30.769 0.00 0.00 0.00 2.71
1257 1275 2.093658 TCGTAGTTTGAAGGGCTCCATC 60.094 50.000 0.00 0.00 0.00 3.51
1279 1297 5.190528 ACATAGGAAGATGAGAGCTTTTGGA 59.809 40.000 0.00 0.00 0.00 3.53
1528 1547 1.538047 TCAGCACAGAGGCCATTTTC 58.462 50.000 5.01 0.00 0.00 2.29
1678 4497 3.535561 CGGTGCCTGAGAACAATAAGAT 58.464 45.455 0.00 0.00 0.00 2.40
1683 4502 1.675641 GCCGGTGCCTGAGAACAAT 60.676 57.895 1.90 0.00 0.00 2.71
1984 5204 5.163302 TGAAAAACGCCGGTCATTATATG 57.837 39.130 1.90 0.00 0.00 1.78
2035 5256 7.511959 AAGGTTTGAAGTTTTCTAGACATCC 57.488 36.000 0.00 0.00 0.00 3.51
2559 5824 2.610433 TGATGCAGACGATTCAGTGAC 58.390 47.619 0.00 0.00 0.00 3.67
2591 5856 8.977412 TCTGACCTGATTACATGTATACTTTCA 58.023 33.333 6.36 5.16 0.00 2.69
2592 5857 9.817809 TTCTGACCTGATTACATGTATACTTTC 57.182 33.333 6.36 0.81 0.00 2.62
2594 5859 9.601217 GTTTCTGACCTGATTACATGTATACTT 57.399 33.333 6.36 0.00 0.00 2.24
2595 5860 8.758829 TGTTTCTGACCTGATTACATGTATACT 58.241 33.333 6.36 0.00 0.00 2.12
2596 5861 8.942338 TGTTTCTGACCTGATTACATGTATAC 57.058 34.615 6.36 4.77 0.00 1.47
2650 5915 9.836076 ATAAAAATTTCGTAACCAGTCTTTAGC 57.164 29.630 0.00 0.00 0.00 3.09
2762 6027 8.507249 AGATGAACTACAAGCAAGTTATGAAAC 58.493 33.333 0.00 0.00 37.31 2.78
2765 6030 9.719355 TTTAGATGAACTACAAGCAAGTTATGA 57.281 29.630 0.00 0.00 37.31 2.15
2771 6036 7.533426 AGCAATTTAGATGAACTACAAGCAAG 58.467 34.615 0.00 0.00 0.00 4.01
2839 6104 1.601477 CACAGCATCAGCACCACCA 60.601 57.895 0.00 0.00 45.49 4.17
2875 6140 6.948309 TCTCAGCTAATGTATATAGTGCCTCA 59.052 38.462 0.00 0.00 0.00 3.86
2891 6156 6.265649 AGTGTCTTGTCTTTACTCTCAGCTAA 59.734 38.462 0.00 0.00 0.00 3.09
2914 6179 0.413832 TCCCTGGGTAGAGCTTCAGT 59.586 55.000 13.56 0.00 0.00 3.41
2915 6180 1.415659 CATCCCTGGGTAGAGCTTCAG 59.584 57.143 13.56 0.00 0.00 3.02
2989 6254 3.126001 TCAAGCCACCGAATGATATCC 57.874 47.619 0.00 0.00 0.00 2.59
3000 6265 1.452833 GCCCTCTCATCAAGCCACC 60.453 63.158 0.00 0.00 0.00 4.61
3031 6296 9.040259 AGGCTCTGTAATATTAGCTATGATTCA 57.960 33.333 7.66 0.00 35.30 2.57
3086 6352 1.409427 GGTCGCCTTATACTCACTGCT 59.591 52.381 0.00 0.00 0.00 4.24
3093 6359 2.456073 ACTCTGGGTCGCCTTATACT 57.544 50.000 0.00 0.00 0.00 2.12
3163 6471 3.712016 TGCTCTGCCCTAACATGTAAA 57.288 42.857 0.00 0.00 0.00 2.01
3164 6472 3.544684 CATGCTCTGCCCTAACATGTAA 58.455 45.455 0.00 0.00 34.73 2.41
3165 6473 2.158769 CCATGCTCTGCCCTAACATGTA 60.159 50.000 0.00 0.00 37.10 2.29
3166 6474 1.409241 CCATGCTCTGCCCTAACATGT 60.409 52.381 0.00 0.00 37.10 3.21
3167 6475 1.315690 CCATGCTCTGCCCTAACATG 58.684 55.000 0.00 0.00 38.24 3.21
3168 6476 0.921896 ACCATGCTCTGCCCTAACAT 59.078 50.000 0.00 0.00 0.00 2.71
3169 6477 1.486310 CTACCATGCTCTGCCCTAACA 59.514 52.381 0.00 0.00 0.00 2.41
3170 6478 1.486726 ACTACCATGCTCTGCCCTAAC 59.513 52.381 0.00 0.00 0.00 2.34
3197 6505 3.370840 AGGTTGCTATCCAATGCTTCA 57.629 42.857 0.00 0.00 35.55 3.02
3222 6530 7.491048 TCTGCCAAAAAGATACAACAAGAAAAC 59.509 33.333 0.00 0.00 0.00 2.43
3243 6552 6.376056 GTGAATTTAAACACGAAATCTGCC 57.624 37.500 0.00 0.00 0.00 4.85
3291 6625 6.737608 AGCCCCCAATATGAGTAAACTTTTA 58.262 36.000 0.00 0.00 0.00 1.52
3316 6650 5.124776 ACCGTGAACAATTTGTTGAAGAGAA 59.875 36.000 19.03 0.00 41.28 2.87
3328 6662 5.147330 TGACTCTCATACCGTGAACAATT 57.853 39.130 0.00 0.00 36.14 2.32
3342 6676 7.178451 TCTCCATAGTAAAACACATGACTCTCA 59.822 37.037 0.00 0.00 0.00 3.27
3358 6692 8.193953 TGATGTCTGCATATTTCTCCATAGTA 57.806 34.615 0.00 0.00 35.07 1.82
3373 6707 7.769970 TCATATGACAAACTTATGATGTCTGCA 59.230 33.333 0.00 0.00 42.99 4.41
3377 6711 8.768955 GGTCTCATATGACAAACTTATGATGTC 58.231 37.037 0.00 10.29 41.47 3.06
3396 6730 5.169295 GTTTTTCTACTAGTGCGGTCTCAT 58.831 41.667 5.39 0.00 0.00 2.90
3401 6735 2.611224 CCCGTTTTTCTACTAGTGCGGT 60.611 50.000 5.39 0.00 36.63 5.68
3447 7243 1.142667 TGTTCCTCTGCATCACAACCA 59.857 47.619 0.00 0.00 0.00 3.67
3448 7244 1.896220 TGTTCCTCTGCATCACAACC 58.104 50.000 0.00 0.00 0.00 3.77
3456 7252 5.483685 ACATACTACTTTGTTCCTCTGCA 57.516 39.130 0.00 0.00 0.00 4.41
3457 7253 7.466050 GCATTACATACTACTTTGTTCCTCTGC 60.466 40.741 0.00 0.00 0.00 4.26
3472 7268 6.708054 GCCTCTATTGTTCAGCATTACATACT 59.292 38.462 0.00 0.00 0.00 2.12
3497 7293 5.407407 AGTTAGGTACTCATGTGGAACTG 57.593 43.478 7.85 0.00 41.75 3.16
3554 7350 6.750039 GGTGGTTTTGTTTCATAATCGTATGG 59.250 38.462 0.00 0.00 38.15 2.74
3558 7354 7.392113 TCATAGGTGGTTTTGTTTCATAATCGT 59.608 33.333 0.00 0.00 0.00 3.73
3561 7357 8.877864 TCTCATAGGTGGTTTTGTTTCATAAT 57.122 30.769 0.00 0.00 0.00 1.28
3571 7367 5.594317 GCCATGTATTCTCATAGGTGGTTTT 59.406 40.000 0.00 0.00 0.00 2.43
3581 7377 1.141657 ACTGCCGCCATGTATTCTCAT 59.858 47.619 0.00 0.00 0.00 2.90
3592 7388 1.300775 CAAATTGCAACTGCCGCCA 60.301 52.632 0.00 0.00 41.18 5.69
3595 7391 1.863267 TTTCCAAATTGCAACTGCCG 58.137 45.000 0.00 0.00 41.18 5.69
3632 7428 2.452295 TTGCGAACCACCGTGTATTA 57.548 45.000 0.00 0.00 0.00 0.98
3677 7475 2.730934 TAGTCAGTGAGGTCGGCTAT 57.269 50.000 0.00 0.00 0.00 2.97
3680 7478 1.103803 TCATAGTCAGTGAGGTCGGC 58.896 55.000 0.00 0.00 0.00 5.54
3683 7481 3.799420 GCGAAATCATAGTCAGTGAGGTC 59.201 47.826 0.00 0.00 0.00 3.85
3685 7483 3.801050 CAGCGAAATCATAGTCAGTGAGG 59.199 47.826 0.00 0.00 0.00 3.86
3688 7486 2.868583 CCCAGCGAAATCATAGTCAGTG 59.131 50.000 0.00 0.00 0.00 3.66
3689 7487 2.766263 TCCCAGCGAAATCATAGTCAGT 59.234 45.455 0.00 0.00 0.00 3.41
3691 7489 3.197766 ACTTCCCAGCGAAATCATAGTCA 59.802 43.478 0.00 0.00 0.00 3.41
3696 7494 2.749621 GACAACTTCCCAGCGAAATCAT 59.250 45.455 0.00 0.00 0.00 2.45
3703 7501 0.804989 GAATGGACAACTTCCCAGCG 59.195 55.000 0.00 0.00 45.17 5.18
3712 7510 2.069273 CCACTCGAGTGAATGGACAAC 58.931 52.381 40.21 0.00 44.34 3.32
3726 7524 1.134075 CGACGACACTACCCACTCG 59.866 63.158 0.00 0.00 0.00 4.18
3757 7555 4.424711 GGCCGCCATCCCACTCAA 62.425 66.667 3.91 0.00 0.00 3.02
3774 7572 3.243877 CCTTAGATCGATGACAAGCAACG 59.756 47.826 0.54 0.00 43.25 4.10
3804 7602 4.625742 CCTCAAAACAGTTATCGTCGACAT 59.374 41.667 17.16 10.63 0.00 3.06
3810 7608 2.640826 TCCCCCTCAAAACAGTTATCGT 59.359 45.455 0.00 0.00 0.00 3.73
3811 7609 3.270877 CTCCCCCTCAAAACAGTTATCG 58.729 50.000 0.00 0.00 0.00 2.92
3813 7611 3.265489 TCCTCCCCCTCAAAACAGTTAT 58.735 45.455 0.00 0.00 0.00 1.89
3817 7615 1.355720 ACATCCTCCCCCTCAAAACAG 59.644 52.381 0.00 0.00 0.00 3.16
3818 7616 1.455822 ACATCCTCCCCCTCAAAACA 58.544 50.000 0.00 0.00 0.00 2.83
3834 7633 6.431852 TGAATCAGTGATGATGACAACAACAT 59.568 34.615 6.34 0.00 41.10 2.71
3836 7635 6.245115 TGAATCAGTGATGATGACAACAAC 57.755 37.500 6.34 0.00 31.08 3.32
3837 7636 5.413523 CCTGAATCAGTGATGATGACAACAA 59.586 40.000 6.34 0.00 31.08 2.83
3845 7644 4.041815 CCTCCATCCTGAATCAGTGATGAT 59.958 45.833 27.76 14.93 39.34 2.45
3846 7645 3.390311 CCTCCATCCTGAATCAGTGATGA 59.610 47.826 27.76 18.49 39.34 2.92
3847 7646 3.496337 CCCTCCATCCTGAATCAGTGATG 60.496 52.174 23.14 23.14 38.10 3.07
3852 7651 2.240667 ACAACCCTCCATCCTGAATCAG 59.759 50.000 2.68 2.68 0.00 2.90
3860 7659 2.124695 GGCGACAACCCTCCATCC 60.125 66.667 0.00 0.00 0.00 3.51
3874 7673 1.501741 CTCAAAATGGTGTCCGGCG 59.498 57.895 0.00 0.00 0.00 6.46
3892 7691 2.754664 GATCGGTGGCATCCATCCCC 62.755 65.000 0.00 0.00 35.28 4.81
3914 7713 5.324409 ACAAAAGCCATCTACCTCAAATCA 58.676 37.500 0.00 0.00 0.00 2.57
3921 7720 2.807676 CCCAACAAAAGCCATCTACCT 58.192 47.619 0.00 0.00 0.00 3.08
3925 7724 0.681175 GTGCCCAACAAAAGCCATCT 59.319 50.000 0.00 0.00 0.00 2.90
3933 7732 1.411977 CTCACAATGGTGCCCAACAAA 59.588 47.619 0.00 0.00 44.87 2.83
3938 7737 2.440147 CCCTCACAATGGTGCCCA 59.560 61.111 0.00 0.00 44.87 5.36
3939 7738 2.362889 CCCCTCACAATGGTGCCC 60.363 66.667 0.00 0.00 44.87 5.36
3949 7748 4.512914 GGCAGCCATCCCCCTCAC 62.513 72.222 6.55 0.00 0.00 3.51
3966 7765 3.366273 CCACTTCAAATTGATGACCGGTG 60.366 47.826 14.63 0.00 0.00 4.94
3967 7766 2.819608 CCACTTCAAATTGATGACCGGT 59.180 45.455 6.92 6.92 0.00 5.28
3970 7769 4.037923 ACACACCACTTCAAATTGATGACC 59.962 41.667 14.60 0.00 0.00 4.02
3977 7776 3.442273 ACGACAACACACCACTTCAAATT 59.558 39.130 0.00 0.00 0.00 1.82
4004 7803 1.305213 GCCCCTCCTCAAAATGGCA 60.305 57.895 0.00 0.00 38.73 4.92


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

AutoCloner maintained by Alex Coulton.