Multiple sequence alignment - TraesCS3A01G307600

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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 TraesCS3A01G307600 chr3A 100.000 3497 0 0 1 3497 545886822 545890318 0.000000e+00 6458
1 TraesCS3A01G307600 chr3A 91.698 265 19 3 3232 3495 545356739 545357001 7.130000e-97 364
2 TraesCS3A01G307600 chr3D 98.144 3503 44 10 1 3497 92212699 92216186 0.000000e+00 6089
3 TraesCS3A01G307600 chr3D 92.620 271 17 3 3227 3497 92358234 92358501 1.520000e-103 387
4 TraesCS3A01G307600 chr3D 92.251 271 19 2 3227 3497 92123342 92123610 1.970000e-102 383
5 TraesCS3A01G307600 chr3D 90.566 265 22 3 3232 3495 91800885 91801147 7.180000e-92 348
6 TraesCS3A01G307600 chr3D 88.848 269 26 3 3227 3495 92262057 92262321 9.360000e-86 327
7 TraesCS3A01G307600 chr7A 89.105 3084 273 27 1 3051 538770618 538773671 0.000000e+00 3775
8 TraesCS3A01G307600 chr7B 90.478 2825 239 17 4 2803 483796687 483793868 0.000000e+00 3699
9 TraesCS3A01G307600 chr7B 88.072 830 92 5 4 828 483789466 483788639 0.000000e+00 977
10 TraesCS3A01G307600 chr7D 90.372 2825 242 15 4 2803 461259309 461256490 0.000000e+00 3683
11 TraesCS3A01G307600 chr7D 90.105 2759 242 19 4 2736 461249583 461246830 0.000000e+00 3554
12 TraesCS3A01G307600 chr7D 83.962 106 15 2 2790 2894 461246833 461246729 2.220000e-17 100
13 TraesCS3A01G307600 chr6A 87.868 3124 301 46 4 3074 29614371 29617469 0.000000e+00 3598
14 TraesCS3A01G307600 chrUn 100.000 388 0 0 1973 2360 480303380 480302993 0.000000e+00 717
15 TraesCS3A01G307600 chr3B 93.644 236 13 2 3262 3497 141862569 141862802 5.550000e-93 351
16 TraesCS3A01G307600 chr3B 90.566 265 22 3 3232 3495 141745221 141745483 7.180000e-92 348
17 TraesCS3A01G307600 chr3B 89.811 265 24 3 3232 3495 141813794 141814056 1.560000e-88 337


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 TraesCS3A01G307600 chr3A 545886822 545890318 3496 False 6458 6458 100.0000 1 3497 1 chr3A.!!$F2 3496
1 TraesCS3A01G307600 chr3D 92212699 92216186 3487 False 6089 6089 98.1440 1 3497 1 chr3D.!!$F3 3496
2 TraesCS3A01G307600 chr7A 538770618 538773671 3053 False 3775 3775 89.1050 1 3051 1 chr7A.!!$F1 3050
3 TraesCS3A01G307600 chr7B 483793868 483796687 2819 True 3699 3699 90.4780 4 2803 1 chr7B.!!$R2 2799
4 TraesCS3A01G307600 chr7B 483788639 483789466 827 True 977 977 88.0720 4 828 1 chr7B.!!$R1 824
5 TraesCS3A01G307600 chr7D 461256490 461259309 2819 True 3683 3683 90.3720 4 2803 1 chr7D.!!$R1 2799
6 TraesCS3A01G307600 chr7D 461246729 461249583 2854 True 1827 3554 87.0335 4 2894 2 chr7D.!!$R2 2890
7 TraesCS3A01G307600 chr6A 29614371 29617469 3098 False 3598 3598 87.8680 4 3074 1 chr6A.!!$F1 3070

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
894 924 1.070289 ACTGGGACGTTTTCTCCAGAC 59.93 52.381 21.12 0.0 41.71 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2546 2.005451 ACTGATCACAATGAAGCGAGC 58.995 47.619 0.0 0.0 0.0 5.03 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
578 582 3.450457 TGGAAACCTTGTCAACTTGCAAT 59.550 39.130 0.00 0.00 0.00 3.56
853 857 7.888250 ACCAAAAGAGATTTTCCTCATATCC 57.112 36.000 0.00 0.00 35.68 2.59
854 858 7.646884 ACCAAAAGAGATTTTCCTCATATCCT 58.353 34.615 0.00 0.00 35.68 3.24
855 859 7.559170 ACCAAAAGAGATTTTCCTCATATCCTG 59.441 37.037 0.00 0.00 35.68 3.86
856 860 7.014038 CCAAAAGAGATTTTCCTCATATCCTGG 59.986 40.741 0.00 0.00 35.68 4.45
857 861 5.839517 AGAGATTTTCCTCATATCCTGGG 57.160 43.478 0.00 0.00 35.68 4.45
860 864 4.977739 AGATTTTCCTCATATCCTGGGTGA 59.022 41.667 0.00 0.00 0.00 4.02
861 865 5.433051 AGATTTTCCTCATATCCTGGGTGAA 59.567 40.000 0.00 0.00 0.00 3.18
862 866 4.503714 TTTCCTCATATCCTGGGTGAAC 57.496 45.455 0.00 0.00 0.00 3.18
863 867 3.421394 TCCTCATATCCTGGGTGAACT 57.579 47.619 0.00 0.00 0.00 3.01
864 868 4.552883 TCCTCATATCCTGGGTGAACTA 57.447 45.455 0.00 0.00 0.00 2.24
865 869 5.093236 TCCTCATATCCTGGGTGAACTAT 57.907 43.478 0.00 0.00 0.00 2.12
866 870 6.227624 TCCTCATATCCTGGGTGAACTATA 57.772 41.667 0.00 0.00 0.00 1.31
867 871 6.017192 TCCTCATATCCTGGGTGAACTATAC 58.983 44.000 0.00 0.00 0.00 1.47
868 872 6.019748 CCTCATATCCTGGGTGAACTATACT 58.980 44.000 0.00 0.00 0.00 2.12
869 873 7.019254 TCCTCATATCCTGGGTGAACTATACTA 59.981 40.741 0.00 0.00 0.00 1.82
894 924 1.070289 ACTGGGACGTTTTCTCCAGAC 59.930 52.381 21.12 0.00 41.71 3.51
935 965 5.762218 GTCTTGGATATCTGGATTTGTCTGG 59.238 44.000 2.05 0.00 0.00 3.86
1147 1177 0.727398 GCTCGTTACCCTGAACATGC 59.273 55.000 0.00 0.00 0.00 4.06
1259 1289 5.741011 TGGAGGTATACCACAATTCAACTC 58.259 41.667 23.87 8.13 38.89 3.01
1264 1294 5.756347 GGTATACCACAATTCAACTCGCATA 59.244 40.000 17.44 0.00 35.64 3.14
1392 1422 3.002862 CACGACGGAAATTGAGAACCAAA 59.997 43.478 0.00 0.00 38.43 3.28
1470 1500 3.986572 CCTATGCTGAATTAGTGAGAGCG 59.013 47.826 0.00 0.00 32.05 5.03
1756 1786 6.111669 TGCCAAATGGAAATCTTGATCAAA 57.888 33.333 9.88 1.39 37.39 2.69
1757 1787 6.531923 TGCCAAATGGAAATCTTGATCAAAA 58.468 32.000 9.88 0.00 37.39 2.44
1788 1818 1.127343 GTCTCCTGGAAGATGGGAGG 58.873 60.000 0.00 0.00 44.72 4.30
2509 2546 3.278367 CCATCTAAATGCTTGATGGCG 57.722 47.619 8.08 0.00 46.88 5.69
2696 2743 0.693622 TAAGTCATCGGGCCACCAAA 59.306 50.000 4.39 0.00 36.13 3.28
3182 3245 6.434340 GGGATTTGGTTGACTCTTGACTAATT 59.566 38.462 0.00 0.00 0.00 1.40
3416 3479 8.887036 TGTCAATATATCATGTACTGAACCAC 57.113 34.615 0.00 0.00 37.44 4.16
3453 3516 9.587772 CAAAAGGATTTCGATCTAGAGTTAAGA 57.412 33.333 0.00 0.00 37.28 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
578 582 6.434028 AGCAAATTATCTTCCAAGTGCAAGTA 59.566 34.615 0.00 0.00 0.00 2.24
861 865 7.709149 AAACGTCCCAGTTAACTAGTATAGT 57.291 36.000 8.04 2.22 43.39 2.12
862 866 8.465201 AGAAAACGTCCCAGTTAACTAGTATAG 58.535 37.037 8.04 1.60 38.02 1.31
863 867 8.353423 AGAAAACGTCCCAGTTAACTAGTATA 57.647 34.615 8.04 0.00 33.41 1.47
864 868 7.237209 AGAAAACGTCCCAGTTAACTAGTAT 57.763 36.000 8.04 0.00 33.41 2.12
865 869 6.294731 GGAGAAAACGTCCCAGTTAACTAGTA 60.295 42.308 8.04 0.00 33.41 1.82
866 870 5.510349 GGAGAAAACGTCCCAGTTAACTAGT 60.510 44.000 8.04 1.33 33.41 2.57
867 871 4.928020 GGAGAAAACGTCCCAGTTAACTAG 59.072 45.833 8.04 0.04 33.41 2.57
868 872 4.344679 TGGAGAAAACGTCCCAGTTAACTA 59.655 41.667 8.04 0.00 33.41 2.24
869 873 3.135167 TGGAGAAAACGTCCCAGTTAACT 59.865 43.478 1.12 1.12 33.41 2.24
894 924 5.103000 CCAAGACTCACTAGATTACCAACG 58.897 45.833 0.00 0.00 0.00 4.10
935 965 5.048434 GGAATTAAGCCAGATATCCTGTTGC 60.048 44.000 0.00 0.00 41.33 4.17
1147 1177 5.212532 TCACCCTCAAAATTGTTGAATGG 57.787 39.130 4.11 4.11 0.00 3.16
1212 1242 5.829924 ACATAAGCCATAGTTCCCTTCAATG 59.170 40.000 0.00 0.00 0.00 2.82
1264 1294 2.308570 TGGGTGTATGATTTGAGCAGGT 59.691 45.455 0.00 0.00 0.00 4.00
1392 1422 6.126409 TGGAACCTGTCTTGTCTTTGTAAAT 58.874 36.000 0.00 0.00 0.00 1.40
1470 1500 3.627577 TCTCAGAAGCAAAACCACTTGTC 59.372 43.478 0.00 0.00 0.00 3.18
2509 2546 2.005451 ACTGATCACAATGAAGCGAGC 58.995 47.619 0.00 0.00 0.00 5.03
2990 3053 8.928733 GTTGTCGGTATATACTTTCTTTTGTCA 58.071 33.333 12.54 0.00 0.00 3.58
3144 3207 3.756434 ACCAAATCCCAGAATACAACACG 59.244 43.478 0.00 0.00 0.00 4.49
3202 3265 3.072211 GCTTAGTTCACCCTACAACCAC 58.928 50.000 0.00 0.00 0.00 4.16
3313 3376 7.730364 ACTACTCTGAATTGTTTCATTCGTT 57.270 32.000 0.00 0.00 40.95 3.85
3337 3400 8.265055 AGTGCCTCAACTAGCTTTGTTAATATA 58.735 33.333 0.00 0.00 0.00 0.86
3416 3479 4.309933 GAAATCCTTTTGTTGCTCTTGGG 58.690 43.478 0.00 0.00 0.00 4.12
3453 3516 3.669536 CCGGCCAAACCAAATGTTTATT 58.330 40.909 2.24 0.00 45.35 1.40
3459 3522 0.534412 TATGCCGGCCAAACCAAATG 59.466 50.000 26.77 0.00 39.03 2.32


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

AutoCloner maintained by Alex Coulton.