Multiple sequence alignment - TraesCS5D01G280500

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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 TraesCS5D01G280500 chr5D 100.000 5736 0 0 1 5736 381917290 381911555 0.000000e+00 10593.0
1 TraesCS5D01G280500 chr5B 96.698 3634 73 14 1 3610 458151983 458148373 0.000000e+00 6002.0
2 TraesCS5D01G280500 chr5B 92.956 2229 93 30 3532 5709 458148331 458146116 0.000000e+00 3188.0
3 TraesCS5D01G280500 chr5B 95.918 49 2 0 3562 3610 458148451 458148403 4.760000e-11 80.5
4 TraesCS5D01G280500 chr5A 93.433 3274 131 33 344 3580 482125519 482122293 0.000000e+00 4778.0
5 TraesCS5D01G280500 chr5A 91.533 1063 50 16 4195 5239 482121527 482120487 0.000000e+00 1428.0
6 TraesCS5D01G280500 chr5A 91.252 663 25 15 3563 4201 482122340 482121687 0.000000e+00 872.0
7 TraesCS5D01G280500 chr5A 94.375 480 24 3 5260 5736 482120305 482119826 0.000000e+00 734.0
8 TraesCS5D01G280500 chr5A 94.813 347 14 2 1 343 482125955 482125609 6.540000e-149 538.0
9 TraesCS5D01G280500 chr2A 96.364 55 2 0 2803 2857 115452893 115452839 2.200000e-14 91.6
10 TraesCS5D01G280500 chr1A 96.226 53 2 0 2803 2855 568396161 568396109 2.850000e-13 87.9
11 TraesCS5D01G280500 chr3B 91.803 61 3 1 2802 2862 149467873 149467815 3.680000e-12 84.2
12 TraesCS5D01G280500 chr3B 94.340 53 3 0 2800 2852 25431130 25431182 1.320000e-11 82.4
13 TraesCS5D01G280500 chr6D 100.000 44 0 0 2812 2855 437788106 437788063 1.320000e-11 82.4
14 TraesCS5D01G280500 chr6A 94.340 53 1 1 2803 2853 586040378 586040326 4.760000e-11 80.5
15 TraesCS5D01G280500 chr3D 95.833 48 2 0 2805 2852 98889591 98889544 1.710000e-10 78.7


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 TraesCS5D01G280500 chr5D 381911555 381917290 5735 True 10593.000000 10593 100.000000 1 5736 1 chr5D.!!$R1 5735
1 TraesCS5D01G280500 chr5B 458146116 458151983 5867 True 3090.166667 6002 95.190667 1 5709 3 chr5B.!!$R1 5708
2 TraesCS5D01G280500 chr5A 482119826 482125955 6129 True 1670.000000 4778 93.081200 1 5736 5 chr5A.!!$R1 5735

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
530 631 4.036971 TCCGTTCTAAATTTGTGTGGGTTG 59.963 41.667 0.00 0.0 0.0 3.77 F
1694 1800 5.585820 TTTTTCTACACCACACCTTTTCC 57.414 39.130 0.00 0.0 0.0 3.13 F
2236 2344 0.109342 AGGTTTCAGTGCTGTCCTGG 59.891 55.000 10.42 0.0 0.0 4.45 F
3309 3441 0.687354 ACGAGAACTGGGAGTGCAAT 59.313 50.000 0.00 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2024 0.394216 TGCACCGCCAAAGATGCTAT 60.394 50.000 0.00 0.00 38.90 2.97 R
3521 3659 1.338973 GATCCCATTACCGTACGCTCA 59.661 52.381 10.49 0.00 0.00 4.26 R
3780 4047 1.527696 CTGCAAAAGCTTCATACGCG 58.472 50.000 3.53 3.53 0.00 6.01 R
5118 5588 1.237285 GGTGCCACTGCTACAACTGG 61.237 60.000 0.00 0.00 38.71 4.00 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
176 180 7.559897 TCTGTTGTAAAGGGAAAAGAAGATTGT 59.440 33.333 0.00 0.00 0.00 2.71
230 235 7.864108 TGCTGCATTATTGTTGAACTACTAT 57.136 32.000 0.00 0.00 0.00 2.12
247 252 7.691993 ACTACTATCCCCAGTTCACAAATAT 57.308 36.000 0.00 0.00 0.00 1.28
530 631 4.036971 TCCGTTCTAAATTTGTGTGGGTTG 59.963 41.667 0.00 0.00 0.00 3.77
722 823 7.379059 ACATGATCATTATGTACTTGGGAGA 57.621 36.000 5.16 0.00 37.02 3.71
727 828 7.345653 TGATCATTATGTACTTGGGAGAGTCTT 59.654 37.037 0.00 0.00 0.00 3.01
1694 1800 5.585820 TTTTTCTACACCACACCTTTTCC 57.414 39.130 0.00 0.00 0.00 3.13
1754 1860 5.793030 AGAGTTCAAGTCGGGAATATAGG 57.207 43.478 0.00 0.00 0.00 2.57
1887 1994 6.176896 TGTATGGATGCTTAGTTTGTGCTAA 58.823 36.000 0.00 0.00 0.00 3.09
1917 2024 6.116711 TCACATTAGTTGCTTAGTTACCCA 57.883 37.500 0.00 0.00 0.00 4.51
1980 2087 2.368548 TCTGCTGCCTCTTGTTACTTCA 59.631 45.455 0.00 0.00 0.00 3.02
2126 2233 8.812513 ATTTTCTTCATCAGTGAATCATACCA 57.187 30.769 0.00 0.00 43.08 3.25
2173 2281 1.133325 TGAAGTTTTGCCAGCCCCTTA 60.133 47.619 0.00 0.00 0.00 2.69
2177 2285 3.994317 AGTTTTGCCAGCCCCTTATTAT 58.006 40.909 0.00 0.00 0.00 1.28
2178 2286 3.960755 AGTTTTGCCAGCCCCTTATTATC 59.039 43.478 0.00 0.00 0.00 1.75
2236 2344 0.109342 AGGTTTCAGTGCTGTCCTGG 59.891 55.000 10.42 0.00 0.00 4.45
2469 2592 2.691409 TGGGAATTAAGGCGACAGAG 57.309 50.000 0.00 0.00 0.00 3.35
3197 3326 8.193438 GCTGCTTTCTTCTCCATATTTTGTAAT 58.807 33.333 0.00 0.00 0.00 1.89
3240 3369 7.961325 AGTATCTAGTTACTACTAACGGAGC 57.039 40.000 11.09 0.00 37.85 4.70
3309 3441 0.687354 ACGAGAACTGGGAGTGCAAT 59.313 50.000 0.00 0.00 0.00 3.56
3521 3659 3.910648 GCCTCTCTTTTATACGGCGTAT 58.089 45.455 32.14 32.14 33.05 3.06
3555 3693 5.472301 AATGGGATCCCTCTTATTTGTGT 57.528 39.130 31.05 0.00 36.94 3.72
3613 3871 5.665701 AGTAATGGGATCCCTCTTATAGCA 58.334 41.667 31.05 8.30 36.94 3.49
3871 4153 2.510613 CAACGGTGGATAAGGGTTTGT 58.489 47.619 0.00 0.00 0.00 2.83
3872 4154 3.677190 CAACGGTGGATAAGGGTTTGTA 58.323 45.455 0.00 0.00 0.00 2.41
3873 4155 3.622166 ACGGTGGATAAGGGTTTGTAG 57.378 47.619 0.00 0.00 0.00 2.74
3874 4156 2.285977 CGGTGGATAAGGGTTTGTAGC 58.714 52.381 0.00 0.00 0.00 3.58
3875 4157 2.093128 CGGTGGATAAGGGTTTGTAGCT 60.093 50.000 0.00 0.00 0.00 3.32
3876 4158 3.133362 CGGTGGATAAGGGTTTGTAGCTA 59.867 47.826 0.00 0.00 0.00 3.32
3877 4159 4.202326 CGGTGGATAAGGGTTTGTAGCTAT 60.202 45.833 0.00 0.00 0.00 2.97
3906 4188 3.071312 ACAACATTGGTGCATGGTCAATT 59.929 39.130 0.45 0.00 0.00 2.32
4157 4439 0.391597 CCAGTGGAAGGTGTGTACGT 59.608 55.000 1.68 0.00 0.00 3.57
4514 4971 5.829924 ACCATCTCATGTTGTGTTTTTCTCT 59.170 36.000 0.00 0.00 0.00 3.10
4606 5063 1.128692 GACGAAAAGCCAGTTGGATCG 59.871 52.381 1.45 8.15 37.39 3.69
4652 5118 1.349357 GGAAAGCAGAACCAGGAGAGT 59.651 52.381 0.00 0.00 0.00 3.24
4863 5332 4.624024 CGTAATGGCCTTATATGTGTACCG 59.376 45.833 3.32 0.00 0.00 4.02
4910 5380 2.762535 ATTCGACGATTTGGGACAGT 57.237 45.000 0.00 0.00 42.39 3.55
5031 5501 9.028185 GCAAGATTAGATGCCTTTTATTTTCTG 57.972 33.333 0.00 0.00 36.56 3.02
5061 5531 3.394940 AGATACAGAGATGTCGGTAGGGA 59.605 47.826 8.69 0.00 36.88 4.20
5118 5588 8.673711 ACTCTTCTATTATCTATCGAGACATGC 58.326 37.037 0.00 0.00 33.41 4.06
5135 5605 4.798433 CCAGTTGTAGCAGTGGCA 57.202 55.556 0.00 0.00 44.61 4.92
5136 5606 2.247790 CCAGTTGTAGCAGTGGCAC 58.752 57.895 10.29 10.29 44.61 5.01
5137 5607 1.237285 CCAGTTGTAGCAGTGGCACC 61.237 60.000 15.27 0.00 44.61 5.01
5166 5636 2.202716 CTGCGCTCGTGATGCTCT 60.203 61.111 9.73 0.00 0.00 4.09
5167 5637 1.064783 CTGCGCTCGTGATGCTCTA 59.935 57.895 9.73 0.00 0.00 2.43
5171 5641 1.268589 GCGCTCGTGATGCTCTACTAA 60.269 52.381 0.00 0.00 0.00 2.24
5184 5664 8.597167 TGATGCTCTACTAATATATTTGCCAGT 58.403 33.333 2.68 3.76 0.00 4.00
5197 5677 0.250424 TGCCAGTATGATCCATGCCG 60.250 55.000 0.00 0.00 39.69 5.69
5201 5681 2.485302 CCAGTATGATCCATGCCGTTCA 60.485 50.000 0.00 0.00 39.69 3.18
5206 5686 2.445427 TGATCCATGCCGTTCAACAAT 58.555 42.857 0.00 0.00 0.00 2.71
5217 5699 6.938542 TGCCGTTCAACAATTAAACAAAATC 58.061 32.000 0.00 0.00 0.00 2.17
5235 5717 8.563123 ACAAAATCTCCATATCTATGCATGAG 57.437 34.615 10.16 5.52 32.40 2.90
5252 5734 6.981762 GCATGAGCAAAGCTACTATATGAT 57.018 37.500 0.00 0.00 39.88 2.45
5253 5735 7.375106 GCATGAGCAAAGCTACTATATGATT 57.625 36.000 0.00 0.00 39.88 2.57
5254 5736 7.462731 GCATGAGCAAAGCTACTATATGATTC 58.537 38.462 0.00 0.00 39.88 2.52
5255 5737 7.673545 GCATGAGCAAAGCTACTATATGATTCG 60.674 40.741 0.00 0.00 39.88 3.34
5256 5738 6.981722 TGAGCAAAGCTACTATATGATTCGA 58.018 36.000 0.00 0.00 39.88 3.71
5257 5739 7.433680 TGAGCAAAGCTACTATATGATTCGAA 58.566 34.615 0.00 0.00 39.88 3.71
5268 5912 2.724977 TGATTCGAACAGAGCTTCGT 57.275 45.000 0.00 0.00 42.97 3.85
5273 5917 2.132762 TCGAACAGAGCTTCGTTTTCC 58.867 47.619 5.51 0.00 42.97 3.13
5280 5924 5.730550 ACAGAGCTTCGTTTTCCATACATA 58.269 37.500 0.00 0.00 0.00 2.29
5369 6019 4.688879 CACAATGATTCTGCAGCAAAACAT 59.311 37.500 9.47 6.95 0.00 2.71
5411 6061 2.165641 ACAACGGCTGTTCATAGATCGA 59.834 45.455 8.28 0.00 35.72 3.59
5413 6063 2.025155 ACGGCTGTTCATAGATCGACT 58.975 47.619 0.00 0.00 0.00 4.18
5447 6098 4.323417 TGGATCACGTTTGCTAAAGATGT 58.677 39.130 0.49 0.00 0.00 3.06
5570 6221 1.818642 AAGTTGAGCAGAGTCATGGC 58.181 50.000 0.00 0.00 0.00 4.40
5683 6335 1.429463 GTACACACACAGGCTACAGC 58.571 55.000 0.00 0.00 41.14 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 180 3.076621 CCTCAGCTAGCACACAAATTCA 58.923 45.455 18.83 0.00 0.00 2.57
207 212 7.355778 GGATAGTAGTTCAACAATAATGCAGC 58.644 38.462 0.00 0.00 0.00 5.25
230 235 3.380471 CCCATATTTGTGAACTGGGGA 57.620 47.619 0.00 0.00 42.41 4.81
500 601 7.362574 CCACACAAATTTAGAACGGATAACCAT 60.363 37.037 0.00 0.00 35.59 3.55
530 631 4.202305 CCAGATAGAGATGGACTTGTTCCC 60.202 50.000 0.00 0.00 45.17 3.97
722 823 6.349300 CAATACCAGTATTAGCCACAAGACT 58.651 40.000 2.82 0.00 34.27 3.24
727 828 3.201045 TGGCAATACCAGTATTAGCCACA 59.799 43.478 25.88 14.83 46.36 4.17
1584 1690 6.924913 AGCATATAGAGATAAAGTGGCAGA 57.075 37.500 0.00 0.00 0.00 4.26
1694 1800 0.590682 TGGTGTATGCGTGCAACTTG 59.409 50.000 13.45 0.00 31.75 3.16
1784 1890 4.322953 GGTCAACCCTAAGATCACCGTTAA 60.323 45.833 0.00 0.00 0.00 2.01
1899 2006 6.302535 TGCTATGGGTAACTAAGCAACTAA 57.697 37.500 0.65 0.00 37.90 2.24
1917 2024 0.394216 TGCACCGCCAAAGATGCTAT 60.394 50.000 0.00 0.00 38.90 2.97
2002 2109 8.995027 ATAATAAATGGGTTCTCATGCTTACA 57.005 30.769 0.00 0.00 0.00 2.41
2236 2344 5.911752 TGCTTCAGAATAGAATCAGGAGTC 58.088 41.667 0.00 0.00 0.00 3.36
2281 2389 3.118408 ACTGATAGGCCGTCAGCATAAAA 60.118 43.478 29.74 3.21 45.42 1.52
2469 2592 0.667453 TTTTACGTTTTCCACCGCCC 59.333 50.000 0.00 0.00 0.00 6.13
3126 3255 6.712095 TGCTACTTCATGTTTTGACTTCAGAT 59.288 34.615 0.00 0.00 32.84 2.90
3269 3401 4.849926 CGTGTACCACTCATACGCATATAC 59.150 45.833 0.00 0.00 33.51 1.47
3521 3659 1.338973 GATCCCATTACCGTACGCTCA 59.661 52.381 10.49 0.00 0.00 4.26
3555 3693 4.295905 AGAGGGGTCCCATTACTATCAA 57.704 45.455 10.98 0.00 38.92 2.57
3780 4047 1.527696 CTGCAAAAGCTTCATACGCG 58.472 50.000 3.53 3.53 0.00 6.01
3873 4155 5.163663 TGCACCAATGTTGTTAGCTAATAGC 60.164 40.000 9.88 9.75 42.84 2.97
3874 4156 6.435430 TGCACCAATGTTGTTAGCTAATAG 57.565 37.500 9.88 0.00 0.00 1.73
3875 4157 6.183360 CCATGCACCAATGTTGTTAGCTAATA 60.183 38.462 9.88 3.78 0.00 0.98
3876 4158 5.394443 CCATGCACCAATGTTGTTAGCTAAT 60.394 40.000 9.88 0.00 0.00 1.73
3877 4159 4.082300 CCATGCACCAATGTTGTTAGCTAA 60.082 41.667 0.86 0.86 0.00 3.09
4014 4296 2.012051 GCTAATGTTACACCCTGCGCT 61.012 52.381 9.73 0.00 0.00 5.92
4200 4482 9.284968 TCTAGCAAAGCAGTAAGAAAAAGTTAT 57.715 29.630 0.00 0.00 0.00 1.89
4201 4483 8.671384 TCTAGCAAAGCAGTAAGAAAAAGTTA 57.329 30.769 0.00 0.00 0.00 2.24
4202 4484 7.568199 TCTAGCAAAGCAGTAAGAAAAAGTT 57.432 32.000 0.00 0.00 0.00 2.66
4203 4485 7.751768 ATCTAGCAAAGCAGTAAGAAAAAGT 57.248 32.000 0.00 0.00 0.00 2.66
4245 4697 7.088272 TGGATAATCGTAATTCATGACTACCG 58.912 38.462 0.00 0.00 0.00 4.02
4309 4761 9.892130 CCAATACTTCTCAAGTAGATTAAAGGT 57.108 33.333 2.76 0.00 46.32 3.50
4354 4810 3.402628 AGTGTCTTGACCATGTGTACC 57.597 47.619 0.00 0.00 0.00 3.34
4452 4908 4.057406 TGGTTTTGAAAAGCACCTGATG 57.943 40.909 17.47 0.00 33.36 3.07
4606 5063 1.451028 GACCAGCTCCACATCTGCC 60.451 63.158 0.00 0.00 0.00 4.85
4652 5118 4.002982 GACACATGGTTGTTAGCATCTGA 58.997 43.478 0.00 0.00 40.37 3.27
4888 5357 3.818773 ACTGTCCCAAATCGTCGAATTTT 59.181 39.130 0.00 0.00 0.00 1.82
4910 5380 7.758076 CCGATACTACAACATTCAGTCAACTTA 59.242 37.037 0.00 0.00 0.00 2.24
5031 5501 5.460419 CCGACATCTCTGTATCTTACAAAGC 59.540 44.000 0.00 0.00 38.38 3.51
5048 5518 2.028385 ACAACAGTTCCCTACCGACATC 60.028 50.000 0.00 0.00 0.00 3.06
5061 5531 3.694072 ACATACAGCACAACACAACAGTT 59.306 39.130 0.00 0.00 0.00 3.16
5118 5588 1.237285 GGTGCCACTGCTACAACTGG 61.237 60.000 0.00 0.00 38.71 4.00
5135 5605 3.050703 CGCAGAGAATAACGCAGGT 57.949 52.632 0.00 0.00 0.00 4.00
5171 5641 6.548622 GGCATGGATCATACTGGCAAATATAT 59.451 38.462 0.00 0.00 34.59 0.86
5184 5664 3.274095 TGTTGAACGGCATGGATCATA 57.726 42.857 0.00 0.00 0.00 2.15
5235 5717 7.382488 TCTGTTCGAATCATATAGTAGCTTTGC 59.618 37.037 0.00 0.00 0.00 3.68
5239 5721 6.432783 AGCTCTGTTCGAATCATATAGTAGCT 59.567 38.462 0.00 3.62 0.00 3.32
5240 5722 6.616947 AGCTCTGTTCGAATCATATAGTAGC 58.383 40.000 0.00 1.38 0.00 3.58
5255 5737 4.451096 TGTATGGAAAACGAAGCTCTGTTC 59.549 41.667 4.23 0.00 0.00 3.18
5256 5738 4.385825 TGTATGGAAAACGAAGCTCTGTT 58.614 39.130 0.00 0.00 0.00 3.16
5257 5739 4.002906 TGTATGGAAAACGAAGCTCTGT 57.997 40.909 0.00 0.00 0.00 3.41
5295 5939 9.769093 GAAGCTTAACGAAATTTTGCTAGAATA 57.231 29.630 0.00 0.00 30.55 1.75
5369 6019 5.124645 TGTTTTGAACCTAGGAAAACGCTA 58.875 37.500 22.57 10.32 40.77 4.26
5409 6059 3.055819 TGATCCAAGGAAGGAAAGAGTCG 60.056 47.826 0.00 0.00 41.92 4.18
5411 6061 3.307059 CGTGATCCAAGGAAGGAAAGAGT 60.307 47.826 0.00 0.00 41.92 3.24
5413 6063 2.637872 ACGTGATCCAAGGAAGGAAAGA 59.362 45.455 0.00 0.00 41.92 2.52
5447 6098 0.776810 TTGAGCCATTTGTGAGGGGA 59.223 50.000 0.00 0.00 0.00 4.81
5570 6221 5.371526 ACTGAACATAGGCAACATATCCTG 58.628 41.667 0.00 0.00 41.41 3.86
5672 6324 1.133809 TTGGGGAAGCTGTAGCCTGT 61.134 55.000 0.00 0.00 43.38 4.00
5683 6335 3.629398 GCTCTGTATGTGAATTGGGGAAG 59.371 47.826 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.