Multiple sequence alignment - TraesCS3D01G246000

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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 TraesCS3D01G246000 chr3D 100.000 7058 0 0 1 7058 342522973 342515916 0.000000e+00 13034.0
1 TraesCS3D01G246000 chr3A 98.277 6734 95 7 7 6736 459955038 459961754 0.000000e+00 11773.0
2 TraesCS3D01G246000 chr3B 98.291 5853 85 5 1 5852 441462080 441456242 0.000000e+00 10240.0
3 TraesCS3D01G246000 chr3B 95.955 890 29 4 5850 6736 441456149 441455264 0.000000e+00 1437.0
4 TraesCS3D01G246000 chr3B 94.864 331 8 7 6732 7058 441455228 441454903 6.320000e-140 508.0
5 TraesCS3D01G246000 chr2B 81.675 3056 460 41 251 3247 716053441 716050427 0.000000e+00 2449.0
6 TraesCS3D01G246000 chr2B 85.441 2198 305 9 3361 5555 716050337 716048152 0.000000e+00 2272.0
7 TraesCS3D01G246000 chr2A 80.768 3047 483 60 243 3220 725420685 725417673 0.000000e+00 2285.0
8 TraesCS3D01G246000 chr2A 83.600 2250 352 12 3320 5553 725417627 725415379 0.000000e+00 2095.0
9 TraesCS3D01G246000 chr7D 76.571 175 26 9 6342 6504 214364450 214364621 1.630000e-11 82.4


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 TraesCS3D01G246000 chr3D 342515916 342522973 7057 True 13034.000000 13034 100.000 1 7058 1 chr3D.!!$R1 7057
1 TraesCS3D01G246000 chr3A 459955038 459961754 6716 False 11773.000000 11773 98.277 7 6736 1 chr3A.!!$F1 6729
2 TraesCS3D01G246000 chr3B 441454903 441462080 7177 True 4061.666667 10240 96.370 1 7058 3 chr3B.!!$R1 7057
3 TraesCS3D01G246000 chr2B 716048152 716053441 5289 True 2360.500000 2449 83.558 251 5555 2 chr2B.!!$R1 5304
4 TraesCS3D01G246000 chr2A 725415379 725420685 5306 True 2190.000000 2285 82.184 243 5553 2 chr2A.!!$R1 5310

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
897 916 0.679960 TCATCCGCTCTGAGGTCGAA 60.680 55.000 6.83 0.0 0.00 3.71 F
2327 2403 1.227205 CTGATCGCAGGCTCTGGAC 60.227 63.158 4.65 0.0 38.51 4.02 F
2745 2836 1.211212 CCTGATGAGGAGAATGCCACA 59.789 52.381 0.00 0.0 42.93 4.17 F
3552 3667 2.058829 AAAAACACTCGGCTGGTGCG 62.059 55.000 12.44 0.0 40.82 5.34 F
4296 4426 2.678336 GGTTGTGCTAACTGTCTATGCC 59.322 50.000 4.78 0.0 0.00 4.40 F
5577 5710 2.158957 TGTGTCCTTGTCTTGTGTCTCC 60.159 50.000 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 2836 1.873903 CGCCGCACCTGCTTATAGAAT 60.874 52.381 0.00 0.0 39.32 2.40 R
3582 3703 0.319555 TCTGCAACTGCTGGTCGTAC 60.320 55.000 8.49 0.0 42.66 3.67 R
4296 4426 1.256812 AAAATCGCCCCCAGACAAAG 58.743 50.000 0.00 0.0 0.00 2.77 R
4731 4861 4.657013 TGTACACAAATGTATTCCCAGCA 58.343 39.130 0.00 0.0 43.21 4.41 R
5885 6114 0.874390 GATTGCAGGCGAGAACACAA 59.126 50.000 0.00 0.0 0.00 3.33 R
6739 7011 2.557317 ACGTATGGCGGGTAAAAGATG 58.443 47.619 0.00 0.0 46.52 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
196 197 2.407340 AACCCTAAACCCAAATGCCA 57.593 45.000 0.00 0.00 0.00 4.92
678 697 1.809619 CGATTTGCTCTTCGCGGGA 60.810 57.895 6.13 0.00 43.27 5.14
897 916 0.679960 TCATCCGCTCTGAGGTCGAA 60.680 55.000 6.83 0.00 0.00 3.71
1131 1150 1.299648 GTGGGTCATGCTGGTGCTA 59.700 57.895 0.00 0.00 40.48 3.49
1242 1267 1.670087 CGAGTGCTCACCGTCTTCATT 60.670 52.381 0.00 0.00 0.00 2.57
1260 1285 3.942377 TACCTGGGCGGCACTACGA 62.942 63.158 12.47 0.00 35.61 3.43
1884 1936 2.291089 TGCAATCTTCTCTTCCATGGCA 60.291 45.455 6.96 0.00 0.00 4.92
2327 2403 1.227205 CTGATCGCAGGCTCTGGAC 60.227 63.158 4.65 0.00 38.51 4.02
2745 2836 1.211212 CCTGATGAGGAGAATGCCACA 59.789 52.381 0.00 0.00 42.93 4.17
2969 3066 3.041946 ACAAGGACCAGCTCTATAAGGG 58.958 50.000 0.00 0.00 0.00 3.95
2982 3079 5.572475 GCTCTATAAGGGGAATGAAGATGGG 60.572 48.000 0.00 0.00 0.00 4.00
3387 3502 6.260271 GTGTGAGCTCTTTGTTTAAAGGTAGT 59.740 38.462 16.19 0.00 42.81 2.73
3552 3667 2.058829 AAAAACACTCGGCTGGTGCG 62.059 55.000 12.44 0.00 40.82 5.34
3582 3703 2.821991 ACTTCTCCGTCCTTGTGAAG 57.178 50.000 0.00 0.00 38.59 3.02
3771 3892 4.271533 GCTCTGAAGATGAGAAATCTGCTG 59.728 45.833 0.00 0.00 33.68 4.41
4296 4426 2.678336 GGTTGTGCTAACTGTCTATGCC 59.322 50.000 4.78 0.00 0.00 4.40
4731 4861 2.414994 ATGCATCTTACAGCAGCAGT 57.585 45.000 0.00 0.00 44.94 4.40
5245 5375 9.076781 TCCTGTTGATAGAATTCACAAATTTCA 57.923 29.630 8.44 5.04 35.21 2.69
5561 5691 7.985184 TGGAGTTTAAGGTATGATATGTGTGTC 59.015 37.037 0.00 0.00 0.00 3.67
5575 5708 2.236146 TGTGTGTCCTTGTCTTGTGTCT 59.764 45.455 0.00 0.00 0.00 3.41
5576 5709 2.866762 GTGTGTCCTTGTCTTGTGTCTC 59.133 50.000 0.00 0.00 0.00 3.36
5577 5710 2.158957 TGTGTCCTTGTCTTGTGTCTCC 60.159 50.000 0.00 0.00 0.00 3.71
5793 5927 7.575332 TGTTTAAAGCTCAGTGAAACAAAAC 57.425 32.000 3.83 6.95 41.43 2.43
5829 5963 4.201951 GCTAACGCAGCCTGCTTA 57.798 55.556 15.80 11.01 45.23 3.09
5885 6114 7.481275 AAAATCTGTTTGTTTGAATCGCAAT 57.519 28.000 0.00 0.00 36.15 3.56
5895 6124 3.454042 TGAATCGCAATTGTGTTCTCG 57.546 42.857 18.08 6.71 0.00 4.04
6070 6299 3.626217 TGTAGTGTAGGTACAGCTGATCG 59.374 47.826 23.35 0.00 36.78 3.69
6109 6338 3.169099 ACTACTCTGCAGGTTCACAGAT 58.831 45.455 15.13 0.00 41.84 2.90
6216 6445 5.107453 GGATTTCCGTAGTAGAAATGATGCG 60.107 44.000 3.62 0.00 0.00 4.73
6241 6470 7.165318 CGATCAAACTTAATGAGTCGTCGATTA 59.835 37.037 0.00 0.00 37.72 1.75
6299 6528 5.289595 TGTAGTGAAACAGAGCTGTACAAG 58.710 41.667 3.21 0.00 44.13 3.16
6351 6580 1.243342 TTTCTTCGGGTGCTGCCATG 61.243 55.000 0.00 0.00 39.65 3.66
6356 6585 1.080569 CGGGTGCTGCCATGTTTTC 60.081 57.895 0.00 0.00 39.65 2.29
6374 6603 5.163499 TGTTTTCGTTGTAAAGCTGGGAATT 60.163 36.000 0.00 0.00 0.00 2.17
6471 6700 0.250513 GTCATCGGCTGGGTCTTTCT 59.749 55.000 0.00 0.00 0.00 2.52
6515 6744 6.208797 TCCATATTGGGATGTACTACTTCTCG 59.791 42.308 0.00 0.00 38.32 4.04
6715 6948 1.141053 ACGGGTGAATTCTATGAGCCC 59.859 52.381 7.05 7.63 0.00 5.19
6722 6955 1.063183 ATTCTATGAGCCCTGGCCTC 58.937 55.000 3.32 0.00 43.17 4.70
6753 7025 2.125326 GGGCCATCTTTTACCCGCC 61.125 63.158 4.39 0.00 35.60 6.13
6754 7026 1.379309 GGCCATCTTTTACCCGCCA 60.379 57.895 0.00 0.00 36.38 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
678 697 1.304547 CCAGACGAGGAGGTGGAGT 60.305 63.158 0.00 0.00 31.64 3.85
1242 1267 3.454573 CGTAGTGCCGCCCAGGTA 61.455 66.667 0.00 0.00 43.70 3.08
1884 1936 1.909781 CAGCCCCACAAATGCACCT 60.910 57.895 0.00 0.00 0.00 4.00
2327 2403 7.530728 CGATAATCATTCTTGCAGATTTTCG 57.469 36.000 17.36 17.36 42.28 3.46
2745 2836 1.873903 CGCCGCACCTGCTTATAGAAT 60.874 52.381 0.00 0.00 39.32 2.40
3387 3502 4.878968 TCATAAGGACAGTCCCATACTCA 58.121 43.478 16.72 0.00 37.19 3.41
3552 3667 2.943449 CGGAGAAGTACTCTGGTTCC 57.057 55.000 0.00 0.00 45.42 3.62
3582 3703 0.319555 TCTGCAACTGCTGGTCGTAC 60.320 55.000 8.49 0.00 42.66 3.67
3705 3826 9.739276 TCTTGGTTCATATCAATAGTTTGAACT 57.261 29.630 12.26 1.60 44.70 3.01
3771 3892 4.023707 CCATAATGGCGATTGAACTCTTCC 60.024 45.833 3.95 0.00 0.00 3.46
4296 4426 1.256812 AAAATCGCCCCCAGACAAAG 58.743 50.000 0.00 0.00 0.00 2.77
4731 4861 4.657013 TGTACACAAATGTATTCCCAGCA 58.343 39.130 0.00 0.00 43.21 4.41
5245 5375 7.398024 AGACTAGTAAAGGCATCAATGAACTT 58.602 34.615 0.00 0.00 34.57 2.66
5561 5691 3.760580 AAGAGGAGACACAAGACAAGG 57.239 47.619 0.00 0.00 0.00 3.61
5575 5708 4.968719 TCATAGGCATCCTTACAAAGAGGA 59.031 41.667 0.00 0.00 46.73 3.71
5576 5709 5.296151 TCATAGGCATCCTTACAAAGAGG 57.704 43.478 0.00 0.00 34.61 3.69
5577 5710 6.037610 GTGTTCATAGGCATCCTTACAAAGAG 59.962 42.308 0.00 0.00 34.61 2.85
5793 5927 1.069906 GCAGGCGCTGTAATATTTCCG 60.070 52.381 7.64 0.00 33.43 4.30
5885 6114 0.874390 GATTGCAGGCGAGAACACAA 59.126 50.000 0.00 0.00 0.00 3.33
5895 6124 3.944015 AGAACAAGTATCTGATTGCAGGC 59.056 43.478 0.00 0.00 42.53 4.85
6067 6296 5.784177 AGTCTCAATGTTAGTGTGTTCGAT 58.216 37.500 0.00 0.00 0.00 3.59
6070 6299 7.327275 CAGAGTAGTCTCAATGTTAGTGTGTTC 59.673 40.741 0.00 0.00 42.66 3.18
6109 6338 5.023452 TCCATCTACTCTAAACCAGAAGCA 58.977 41.667 0.00 0.00 31.12 3.91
6216 6445 6.814076 ATCGACGACTCATTAAGTTTGATC 57.186 37.500 0.00 0.00 38.74 2.92
6241 6470 3.643320 TCTCGAACCATGAATATGAGCCT 59.357 43.478 0.00 0.00 36.36 4.58
6317 6546 2.839486 AGAAATGTCTGGCACGAGAA 57.161 45.000 0.00 0.00 30.83 2.87
6351 6580 3.974871 TCCCAGCTTTACAACGAAAAC 57.025 42.857 0.00 0.00 0.00 2.43
6356 6585 2.228822 AGCAATTCCCAGCTTTACAACG 59.771 45.455 0.00 0.00 38.01 4.10
6374 6603 2.229792 CAGGTAAAAGCAGGAACAGCA 58.770 47.619 0.00 0.00 45.86 4.41
6515 6744 7.008628 GCATAAAGCAGACACAATAATTGACAC 59.991 37.037 0.00 0.00 44.79 3.67
6614 6843 5.356190 GCTGAAGAACATGATCAGAATCCAA 59.644 40.000 19.30 0.00 42.48 3.53
6739 7011 2.557317 ACGTATGGCGGGTAAAAGATG 58.443 47.619 0.00 0.00 46.52 2.90


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

AutoCloner maintained by Alex Coulton.