Multiple sequence alignment - TraesCS2B01G403400

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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 TraesCS2B01G403400 chr2B 100.000 2899 0 0 1 2899 571833846 571830948 0.000000e+00 5354.0
1 TraesCS2B01G403400 chr2B 97.391 2875 51 5 1 2853 789358523 789355651 0.000000e+00 4872.0
2 TraesCS2B01G403400 chr2B 97.288 2876 56 4 1 2856 789375621 789372748 0.000000e+00 4859.0
3 TraesCS2B01G403400 chr2B 96.235 2895 53 15 1 2853 789406836 789403956 0.000000e+00 4691.0
4 TraesCS2B01G403400 chr2B 96.171 2899 58 12 1 2853 571994861 571991970 0.000000e+00 4689.0
5 TraesCS2B01G403400 chr2B 95.845 2888 80 11 1 2853 571964215 571961333 0.000000e+00 4632.0
6 TraesCS2B01G403400 chr2B 95.740 2887 81 15 1 2853 571851907 571849029 0.000000e+00 4612.0
7 TraesCS2B01G403400 chr2B 96.873 2654 40 7 1 2615 571877771 571875122 0.000000e+00 4401.0
8 TraesCS2B01G403400 chr2B 96.172 2482 51 12 49 2500 789425171 789422704 0.000000e+00 4017.0
9 TraesCS2B01G403400 chr2B 97.818 2246 37 6 611 2853 789326514 789324278 0.000000e+00 3866.0
10 TraesCS2B01G403400 chr2B 96.025 2365 73 8 505 2853 789296119 789293760 0.000000e+00 3827.0
11 TraesCS2B01G403400 chr2B 98.094 1679 27 3 1177 2854 571909381 571907707 0.000000e+00 2918.0
12 TraesCS2B01G403400 chr2B 94.925 867 23 8 1 849 571910241 571909378 0.000000e+00 1338.0
13 TraesCS2B01G403400 chr2B 93.290 462 13 1 1 444 789326971 789326510 0.000000e+00 665.0
14 TraesCS2B01G403400 chr2B 93.261 460 10 3 1 441 789296873 789296416 0.000000e+00 658.0
15 TraesCS2B01G403400 chr2B 98.693 153 2 0 2701 2853 571875106 571874954 3.680000e-69 272.0
16 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 571849012 571848964 5.150000e-13 86.1
17 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 571961316 571961268 5.150000e-13 86.1
18 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 571991953 571991905 5.150000e-13 86.1
19 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 789293743 789293695 5.150000e-13 86.1
20 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 789324261 789324213 5.150000e-13 86.1
21 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 789355634 789355586 5.150000e-13 86.1
22 TraesCS2B01G403400 chr2B 97.959 49 1 0 2851 2899 789403939 789403891 5.150000e-13 86.1
23 TraesCS2B01G403400 chr2D 90.748 2983 149 56 1 2899 646053690 646056629 0.000000e+00 3862.0
24 TraesCS2B01G403400 chr2A 90.935 695 42 9 1 682 773381059 773380373 0.000000e+00 915.0


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 TraesCS2B01G403400 chr2B 571830948 571833846 2898 True 5354.000000 5354 100.000000 1 2899 1 chr2B.!!$R1 2898
1 TraesCS2B01G403400 chr2B 789372748 789375621 2873 True 4859.000000 4859 97.288000 1 2856 1 chr2B.!!$R2 2855
2 TraesCS2B01G403400 chr2B 789422704 789425171 2467 True 4017.000000 4017 96.172000 49 2500 1 chr2B.!!$R3 2451
3 TraesCS2B01G403400 chr2B 789355586 789358523 2937 True 2479.050000 4872 97.675000 1 2899 2 chr2B.!!$R11 2898
4 TraesCS2B01G403400 chr2B 789403891 789406836 2945 True 2388.550000 4691 97.097000 1 2899 2 chr2B.!!$R12 2898
5 TraesCS2B01G403400 chr2B 571991905 571994861 2956 True 2387.550000 4689 97.065000 1 2899 2 chr2B.!!$R8 2898
6 TraesCS2B01G403400 chr2B 571961268 571964215 2947 True 2359.050000 4632 96.902000 1 2899 2 chr2B.!!$R7 2898
7 TraesCS2B01G403400 chr2B 571848964 571851907 2943 True 2349.050000 4612 96.849500 1 2899 2 chr2B.!!$R4 2898
8 TraesCS2B01G403400 chr2B 571874954 571877771 2817 True 2336.500000 4401 97.783000 1 2853 2 chr2B.!!$R5 2852
9 TraesCS2B01G403400 chr2B 571907707 571910241 2534 True 2128.000000 2918 96.509500 1 2854 2 chr2B.!!$R6 2853
10 TraesCS2B01G403400 chr2B 789324213 789326971 2758 True 1539.033333 3866 96.355667 1 2899 3 chr2B.!!$R10 2898
11 TraesCS2B01G403400 chr2B 789293695 789296873 3178 True 1523.700000 3827 95.748333 1 2899 3 chr2B.!!$R9 2898
12 TraesCS2B01G403400 chr2D 646053690 646056629 2939 False 3862.000000 3862 90.748000 1 2899 1 chr2D.!!$F1 2898
13 TraesCS2B01G403400 chr2A 773380373 773381059 686 True 915.000000 915 90.935000 1 682 1 chr2A.!!$R1 681

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
742 1008 0.618458 TCGCCCCTATGAACTTTGCT 59.382 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 3046 1.542767 CCTAGCTATGGACGACCTCGA 60.543 57.143 5.33 0.0 43.02 4.04 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
522 786 7.443302 AATTTGGGAATCAGATAGACTCTCA 57.557 36.000 0.00 0.00 29.53 3.27
742 1008 0.618458 TCGCCCCTATGAACTTTGCT 59.382 50.000 0.00 0.00 0.00 3.91
765 1032 8.440059 TGCTAACAGAATATTGTACGTCTTTTG 58.560 33.333 0.00 0.00 0.00 2.44
917 1191 1.298157 CCGACTTGATTTGCCTCGCA 61.298 55.000 0.00 0.00 36.47 5.10
998 1291 7.619964 AAATAAAAAGATAACCACGGACGAT 57.380 32.000 0.00 0.00 0.00 3.73
1464 1849 2.435437 TGCTATGTTCTATCCTGCTGCA 59.565 45.455 0.88 0.88 0.00 4.41
1558 1943 2.501610 GACGGAGGGATGCCACTC 59.498 66.667 5.86 0.00 0.00 3.51
1769 2159 0.670546 GCTTCAAGAGTAGGTGCGCA 60.671 55.000 5.66 5.66 0.00 6.09
1931 2321 4.211374 ACTTAGCTAAGCACTGTTTTGTCG 59.789 41.667 29.39 5.82 36.79 4.35
2008 2399 5.614781 CGTAAGATAGCGTTGACGTTACTAG 59.385 44.000 5.36 0.00 37.84 2.57
2009 2400 5.557891 AAGATAGCGTTGACGTTACTAGT 57.442 39.130 0.00 0.00 37.84 2.57
2011 2402 4.394300 AGATAGCGTTGACGTTACTAGTGT 59.606 41.667 5.39 0.00 37.84 3.55
2534 2928 3.829026 GGTGATTTCTCCTGGAAAGCTTT 59.171 43.478 12.53 12.53 46.71 3.51
2652 3046 4.412075 GCCTTTGCCTTCAGAGCT 57.588 55.556 0.00 0.00 0.00 4.09
2805 3199 5.338463 GGCTAAGGTGTCAAAGGAACTATCT 60.338 44.000 0.00 0.00 38.49 1.98
2840 3234 6.014840 AGCAATTTCTTCACAACCTCATGATT 60.015 34.615 0.00 0.00 0.00 2.57
2868 3281 3.891366 TGTCAGCTCATTGGAGATATCGA 59.109 43.478 0.00 0.00 44.26 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.342819 GATATGCCGGCTCAGTCTCTT 59.657 52.381 29.70 1.60 0.00 2.85
522 786 9.123902 ACAAAAAGGGAAAATAAGTACGTAGTT 57.876 29.630 19.04 19.04 37.78 2.24
765 1032 7.333672 AGACGTACAATATTCTTCCCTCAAAAC 59.666 37.037 0.00 0.00 0.00 2.43
917 1191 7.455008 CCCTATATTATATATCTCGGGTTGGCT 59.545 40.741 6.27 0.00 0.00 4.75
998 1291 3.713764 GGAAGAGAAGAAGGATCCCATCA 59.286 47.826 8.55 0.00 0.00 3.07
1464 1849 2.679716 GGCACTTCCATGGGCTCT 59.320 61.111 13.02 0.00 34.01 4.09
1494 1879 3.706373 TCCTGCCTGAAGCCGACC 61.706 66.667 0.00 0.00 42.71 4.79
1558 1943 6.715464 AGAAGTACTTTTGTTCATTGTCGTG 58.285 36.000 10.02 0.00 0.00 4.35
1931 2321 6.093495 TGAACAAGCAATATACAGTACAAGGC 59.907 38.462 0.00 0.00 0.00 4.35
2534 2928 5.124457 GCTAATGCTTGTGAGAGAATTCCAA 59.876 40.000 0.65 0.00 36.03 3.53
2607 3001 4.810491 GCAATCTCTTCATCTGAGGAAGAC 59.190 45.833 25.72 14.77 44.21 3.01
2652 3046 1.542767 CCTAGCTATGGACGACCTCGA 60.543 57.143 5.33 0.00 43.02 4.04
2805 3199 4.997395 GTGAAGAAATTGCTGAGGTCACTA 59.003 41.667 8.26 0.00 33.12 2.74
2840 3234 4.026052 TCTCCAATGAGCTGACATCACTA 58.974 43.478 0.00 0.00 38.58 2.74
2868 3281 1.478510 ACAGACTTTCGATCGCCTCAT 59.521 47.619 11.09 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.