Multiple sequence alignment - TraesCS3B01G264700

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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 TraesCS3B01G264700 chr3B 100.000 3797 0 0 1 3797 423541466 423537670 0.000000e+00 7012.0
1 TraesCS3B01G264700 chr3B 98.608 862 12 0 1 862 197769164 197770025 0.000000e+00 1526.0
2 TraesCS3B01G264700 chr3B 97.912 862 18 0 1 862 828646252 828645391 0.000000e+00 1493.0
3 TraesCS3B01G264700 chr3B 96.984 862 24 2 1 861 170762609 170761749 0.000000e+00 1447.0
4 TraesCS3B01G264700 chr3D 96.908 2911 80 5 894 3797 326131744 326128837 0.000000e+00 4868.0
5 TraesCS3B01G264700 chr3A 96.819 2892 57 16 862 3731 438775895 438778773 0.000000e+00 4798.0
6 TraesCS3B01G264700 chr3A 96.970 99 3 0 3699 3797 438778775 438778873 2.350000e-37 167.0
7 TraesCS3B01G264700 chr3A 90.000 70 7 0 3533 3602 596167304 596167235 1.450000e-14 91.6
8 TraesCS3B01G264700 chr7A 98.394 872 12 2 1 870 12308491 12307620 0.000000e+00 1531.0
9 TraesCS3B01G264700 chr7A 96.181 864 30 3 2 863 214680016 214680878 0.000000e+00 1410.0
10 TraesCS3B01G264700 chr7B 98.262 863 14 1 1 862 729447340 729446478 0.000000e+00 1509.0
11 TraesCS3B01G264700 chr5A 97.914 863 18 0 1 863 32715910 32715048 0.000000e+00 1495.0
12 TraesCS3B01G264700 chr4A 97.572 865 20 1 1 864 382432349 382431485 0.000000e+00 1480.0
13 TraesCS3B01G264700 chr4A 97.106 864 24 1 1 864 550413393 550412531 0.000000e+00 1456.0


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 TraesCS3B01G264700 chr3B 423537670 423541466 3796 True 7012.0 7012 100.0000 1 3797 1 chr3B.!!$R2 3796
1 TraesCS3B01G264700 chr3B 197769164 197770025 861 False 1526.0 1526 98.6080 1 862 1 chr3B.!!$F1 861
2 TraesCS3B01G264700 chr3B 828645391 828646252 861 True 1493.0 1493 97.9120 1 862 1 chr3B.!!$R3 861
3 TraesCS3B01G264700 chr3B 170761749 170762609 860 True 1447.0 1447 96.9840 1 861 1 chr3B.!!$R1 860
4 TraesCS3B01G264700 chr3D 326128837 326131744 2907 True 4868.0 4868 96.9080 894 3797 1 chr3D.!!$R1 2903
5 TraesCS3B01G264700 chr3A 438775895 438778873 2978 False 2482.5 4798 96.8945 862 3797 2 chr3A.!!$F1 2935
6 TraesCS3B01G264700 chr7A 12307620 12308491 871 True 1531.0 1531 98.3940 1 870 1 chr7A.!!$R1 869
7 TraesCS3B01G264700 chr7A 214680016 214680878 862 False 1410.0 1410 96.1810 2 863 1 chr7A.!!$F1 861
8 TraesCS3B01G264700 chr7B 729446478 729447340 862 True 1509.0 1509 98.2620 1 862 1 chr7B.!!$R1 861
9 TraesCS3B01G264700 chr5A 32715048 32715910 862 True 1495.0 1495 97.9140 1 863 1 chr5A.!!$R1 862
10 TraesCS3B01G264700 chr4A 382431485 382432349 864 True 1480.0 1480 97.5720 1 864 1 chr4A.!!$R1 863
11 TraesCS3B01G264700 chr4A 550412531 550413393 862 True 1456.0 1456 97.1060 1 864 1 chr4A.!!$R2 863

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
765 771 0.612453 AGGAAGACGAGGACCTGGTC 60.612 60.000 24.89 24.89 39.05 4.02 F
831 837 1.153127 TGGACCAGCCGAAACGTTT 60.153 52.632 14.57 14.57 40.66 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2742 2764 0.668096 CAAACCGGTGGAATCGACGA 60.668 55.000 8.52 0.0 0.0 4.20 R
2942 2971 4.257267 TCCATCACCTCACTATTATGCG 57.743 45.455 0.00 0.0 0.0 4.73 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
87 89 1.096386 TACGGTTGCAGCAAAACGGT 61.096 50.000 27.40 20.75 41.91 4.83
765 771 0.612453 AGGAAGACGAGGACCTGGTC 60.612 60.000 24.89 24.89 39.05 4.02
831 837 1.153127 TGGACCAGCCGAAACGTTT 60.153 52.632 14.57 14.57 40.66 3.60
892 898 2.045926 GGCAATGCTGTCCCTCGT 60.046 61.111 4.82 0.00 0.00 4.18
922 928 3.138304 GAGTAACAATATCATGCCGGCA 58.862 45.455 34.80 34.80 0.00 5.69
992 1012 1.891060 GCGGCAGTCAAGTCGAACTG 61.891 60.000 10.06 10.06 39.34 3.16
1119 1141 2.123854 CAGCAGCTCCATGGCCAT 60.124 61.111 14.09 14.09 0.00 4.40
1239 1261 3.905678 CTCCGCGCCTTCCTCGAT 61.906 66.667 0.00 0.00 0.00 3.59
1847 1869 1.468520 CCTTGTGGATTGTGCTTACCG 59.531 52.381 0.00 0.00 34.57 4.02
2560 2582 5.568825 GCAGTAGTTAAGGATGTGGACAGAA 60.569 44.000 0.00 0.00 0.00 3.02
2742 2764 4.785376 AGAGTTGTGGTTCTCAGGGATAAT 59.215 41.667 0.00 0.00 33.63 1.28
2862 2891 4.383173 CTCACATGGATTCATCGATTGGA 58.617 43.478 0.00 0.00 0.00 3.53
2923 2952 4.871933 TGTGAACTCAGAAGCTGATACA 57.128 40.909 0.00 0.12 39.92 2.29
2977 3006 6.091076 AGGTGATGGATTCAATTTTAGGGA 57.909 37.500 0.00 0.00 35.70 4.20
2981 3010 4.916983 TGGATTCAATTTTAGGGATGCG 57.083 40.909 0.00 0.00 0.00 4.73
3069 3098 7.364144 CCACATAGTGCTGCTATATATTCAGGA 60.364 40.741 0.00 9.53 38.28 3.86
3263 3293 2.926200 CTCACAGAGCGATCGAACATTT 59.074 45.455 21.57 0.00 0.00 2.32
3269 3299 4.327357 CAGAGCGATCGAACATTTAGTTGT 59.673 41.667 21.57 0.00 41.51 3.32
3270 3300 4.327357 AGAGCGATCGAACATTTAGTTGTG 59.673 41.667 21.57 0.00 41.51 3.33
3281 3311 8.751335 CGAACATTTAGTTGTGCTTGTTTATTT 58.249 29.630 0.00 0.00 41.51 1.40
3585 3615 0.315251 TGCTCTTGTGAGACAGGTCG 59.685 55.000 0.00 0.00 42.73 4.79
3630 3660 6.071728 GGTCAACCTCAGTTCAATGATTTGAT 60.072 38.462 5.31 0.00 41.38 2.57
3716 3746 4.346709 TGGACTAGTTTGAGTGATCCAACA 59.653 41.667 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 2.104132 CCCGCGATGACGATGACA 59.896 61.111 8.23 0.00 42.66 3.58
259 263 2.993937 ACAACCGGTGACAGAAAAAGA 58.006 42.857 8.52 0.00 0.00 2.52
419 424 0.248702 TCCCGCTTGCGAACAAAAAC 60.249 50.000 16.99 0.00 34.74 2.43
819 825 3.656045 CGGCCAAACGTTTCGGCT 61.656 61.111 33.31 8.63 45.50 5.52
866 872 3.306641 GGGACAGCATTGCCATTGTTTAA 60.307 43.478 4.70 0.00 0.00 1.52
899 905 3.433615 GCCGGCATGATATTGTTACTCTC 59.566 47.826 24.80 0.00 0.00 3.20
910 916 2.558617 GCATGATGCCGGCATGATA 58.441 52.632 44.96 29.47 44.49 2.15
911 917 3.362262 GCATGATGCCGGCATGAT 58.638 55.556 44.96 38.44 44.49 2.45
922 928 3.484407 GAAAGGATAGTGCTGGCATGAT 58.516 45.455 0.00 0.00 0.00 2.45
937 943 2.342279 CTGCGTGGACGGAAAGGA 59.658 61.111 0.71 0.00 39.68 3.36
955 961 3.242936 GCCGCTTGAACTTTTTGTGTAGA 60.243 43.478 0.00 0.00 0.00 2.59
992 1012 2.032681 GCGGGGTCATATGGCTCC 59.967 66.667 16.88 16.88 36.79 4.70
1119 1141 2.257409 GATGGCCGCCCTTGAGAAGA 62.257 60.000 7.03 0.00 0.00 2.87
1215 1237 3.607370 GAAGGCGCGGAGGGAAAGT 62.607 63.158 8.83 0.00 46.37 2.66
1311 1333 3.314388 GAAGGCGTCAAAGGCTGCG 62.314 63.158 0.00 0.00 46.87 5.18
1491 1513 0.670546 ACATGTCAAGAACCGCCGAG 60.671 55.000 0.00 0.00 0.00 4.63
1632 1654 2.236382 CGAGCGGAAGATGCAGAGC 61.236 63.158 0.00 0.00 33.85 4.09
1847 1869 1.956802 GGTGCTGCACTAAACACCC 59.043 57.895 29.54 9.20 45.56 4.61
2533 2555 3.055385 TCCACATCCTTAACTACTGCACC 60.055 47.826 0.00 0.00 0.00 5.01
2742 2764 0.668096 CAAACCGGTGGAATCGACGA 60.668 55.000 8.52 0.00 0.00 4.20
2942 2971 4.257267 TCCATCACCTCACTATTATGCG 57.743 45.455 0.00 0.00 0.00 4.73
2977 3006 5.237048 ACTTATTGCAAAATTTCCACGCAT 58.763 33.333 1.71 0.00 31.67 4.73
2981 3010 6.223120 ACCAGACTTATTGCAAAATTTCCAC 58.777 36.000 1.71 0.00 0.00 4.02
3069 3098 1.632409 AGGCCACAGAGTCATGTTGAT 59.368 47.619 5.01 0.00 0.00 2.57
3269 3299 7.038659 CCCGGATAAAATGAAATAAACAAGCA 58.961 34.615 0.73 0.00 0.00 3.91
3270 3300 7.262048 TCCCGGATAAAATGAAATAAACAAGC 58.738 34.615 0.73 0.00 0.00 4.01
3281 3311 5.887214 TGATCTTCTCCCGGATAAAATGA 57.113 39.130 0.73 0.00 0.00 2.57
3630 3660 1.970640 TCTGTGCAGAAGGAAGTAGCA 59.029 47.619 0.00 0.00 33.91 3.49
3716 3746 3.689347 TCTACCATGCTGCATCACTTTT 58.311 40.909 13.10 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.