Multiple sequence alignment - TraesCS4A01G453700

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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 TraesCS4A01G453700 chr4A 100.000 2825 0 0 1 2825 718009417 718006593 0.000000e+00 5217
1 TraesCS4A01G453700 chr1B 98.434 2044 29 1 1 2041 494555876 494553833 0.000000e+00 3594
2 TraesCS4A01G453700 chr1B 97.979 1880 38 0 1 1880 414555867 414557746 0.000000e+00 3262
3 TraesCS4A01G453700 chr1B 89.975 788 71 8 2042 2825 364514876 364515659 0.000000e+00 1011
4 TraesCS4A01G453700 chr1B 84.800 125 9 8 1922 2037 414557743 414557866 1.780000e-22 117
5 TraesCS4A01G453700 chr6B 97.844 2041 13 5 1 2041 132659362 132657353 0.000000e+00 3496
6 TraesCS4A01G453700 chr5A 98.806 1926 23 0 1 1926 651582414 651580489 0.000000e+00 3430
7 TraesCS4A01G453700 chr5A 91.489 2068 136 29 5 2041 697888543 697890601 0.000000e+00 2808
8 TraesCS4A01G453700 chr5A 92.500 120 9 0 1922 2041 651580538 651580419 3.740000e-39 172
9 TraesCS4A01G453700 chr4B 96.915 2042 31 8 1 2041 502275495 502277505 0.000000e+00 3393
10 TraesCS4A01G453700 chr4B 89.734 789 75 6 2042 2825 384024231 384025018 0.000000e+00 1003
11 TraesCS4A01G453700 chr2B 98.631 1899 26 0 1 1899 138738730 138736832 0.000000e+00 3363
12 TraesCS4A01G453700 chr2B 89.734 789 73 8 2042 2825 411174621 411175406 0.000000e+00 1002
13 TraesCS4A01G453700 chr2B 97.500 120 3 0 1922 2041 235597422 235597303 3.690000e-49 206
14 TraesCS4A01G453700 chr3D 96.543 1880 64 1 1 1880 134638953 134640831 0.000000e+00 3110
15 TraesCS4A01G453700 chr2D 93.652 2048 107 21 1 2048 573648823 573650847 0.000000e+00 3040
16 TraesCS4A01G453700 chr3B 90.665 782 67 6 2042 2818 401778343 401777563 0.000000e+00 1035
17 TraesCS4A01G453700 chr3B 89.773 792 72 9 2042 2825 351975528 351974738 0.000000e+00 1005
18 TraesCS4A01G453700 chr3B 89.660 793 67 14 2042 2825 388575671 388574885 0.000000e+00 996
19 TraesCS4A01G453700 chrUn 90.228 788 71 6 2042 2825 249573611 249574396 0.000000e+00 1024
20 TraesCS4A01G453700 chrUn 89.975 788 73 6 2042 2825 249580318 249581103 0.000000e+00 1013
21 TraesCS4A01G453700 chr7B 90.114 789 71 7 2042 2825 460484466 460485252 0.000000e+00 1018
22 TraesCS4A01G453700 chr6A 85.949 790 69 28 1254 2041 153659985 153659236 0.000000e+00 806
23 TraesCS4A01G453700 chr6A 85.063 790 73 28 1254 2042 18459053 18458308 0.000000e+00 763
24 TraesCS4A01G453700 chr5B 95.146 103 4 1 1940 2041 607483419 607483521 8.100000e-36 161


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 TraesCS4A01G453700 chr4A 718006593 718009417 2824 True 5217.0 5217 100.0000 1 2825 1 chr4A.!!$R1 2824
1 TraesCS4A01G453700 chr1B 494553833 494555876 2043 True 3594.0 3594 98.4340 1 2041 1 chr1B.!!$R1 2040
2 TraesCS4A01G453700 chr1B 414555867 414557866 1999 False 1689.5 3262 91.3895 1 2037 2 chr1B.!!$F2 2036
3 TraesCS4A01G453700 chr1B 364514876 364515659 783 False 1011.0 1011 89.9750 2042 2825 1 chr1B.!!$F1 783
4 TraesCS4A01G453700 chr6B 132657353 132659362 2009 True 3496.0 3496 97.8440 1 2041 1 chr6B.!!$R1 2040
5 TraesCS4A01G453700 chr5A 697888543 697890601 2058 False 2808.0 2808 91.4890 5 2041 1 chr5A.!!$F1 2036
6 TraesCS4A01G453700 chr5A 651580419 651582414 1995 True 1801.0 3430 95.6530 1 2041 2 chr5A.!!$R1 2040
7 TraesCS4A01G453700 chr4B 502275495 502277505 2010 False 3393.0 3393 96.9150 1 2041 1 chr4B.!!$F2 2040
8 TraesCS4A01G453700 chr4B 384024231 384025018 787 False 1003.0 1003 89.7340 2042 2825 1 chr4B.!!$F1 783
9 TraesCS4A01G453700 chr2B 138736832 138738730 1898 True 3363.0 3363 98.6310 1 1899 1 chr2B.!!$R1 1898
10 TraesCS4A01G453700 chr2B 411174621 411175406 785 False 1002.0 1002 89.7340 2042 2825 1 chr2B.!!$F1 783
11 TraesCS4A01G453700 chr3D 134638953 134640831 1878 False 3110.0 3110 96.5430 1 1880 1 chr3D.!!$F1 1879
12 TraesCS4A01G453700 chr2D 573648823 573650847 2024 False 3040.0 3040 93.6520 1 2048 1 chr2D.!!$F1 2047
13 TraesCS4A01G453700 chr3B 401777563 401778343 780 True 1035.0 1035 90.6650 2042 2818 1 chr3B.!!$R3 776
14 TraesCS4A01G453700 chr3B 351974738 351975528 790 True 1005.0 1005 89.7730 2042 2825 1 chr3B.!!$R1 783
15 TraesCS4A01G453700 chr3B 388574885 388575671 786 True 996.0 996 89.6600 2042 2825 1 chr3B.!!$R2 783
16 TraesCS4A01G453700 chrUn 249573611 249574396 785 False 1024.0 1024 90.2280 2042 2825 1 chrUn.!!$F1 783
17 TraesCS4A01G453700 chrUn 249580318 249581103 785 False 1013.0 1013 89.9750 2042 2825 1 chrUn.!!$F2 783
18 TraesCS4A01G453700 chr7B 460484466 460485252 786 False 1018.0 1018 90.1140 2042 2825 1 chr7B.!!$F1 783
19 TraesCS4A01G453700 chr6A 153659236 153659985 749 True 806.0 806 85.9490 1254 2041 1 chr6A.!!$R2 787
20 TraesCS4A01G453700 chr6A 18458308 18459053 745 True 763.0 763 85.0630 1254 2042 1 chr6A.!!$R1 788

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
230 231 5.045942 TGGTAATGCAAGATCACCTTAGACA 60.046 40.0 0.0 0.0 32.86 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2292 1.285578 GAGTGCTCTCGATCTTTGCC 58.714 55.0 0.0 0.0 0.0 4.52 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
230 231 5.045942 TGGTAATGCAAGATCACCTTAGACA 60.046 40.000 0.00 0.00 32.86 3.41
609 610 8.711170 TCTAATATGAAAGGAAAATACCGAGGT 58.289 33.333 0.00 0.00 34.73 3.85
2055 2152 0.036164 CCCTGGACATGGAAACGACA 59.964 55.000 0.00 0.00 0.00 4.35
2132 2229 3.444034 CCACTAACAAGAGATCTCGTCCA 59.556 47.826 16.97 2.47 34.09 4.02
2195 2292 6.018343 GGTGAAACAAGAACTCAAGAGAAGAG 60.018 42.308 3.73 0.00 39.98 2.85
2283 2381 8.971073 TCACTGAATCAGATAGACTATGAAACA 58.029 33.333 18.20 0.00 35.18 2.83
2335 2434 7.852945 CGAATAAGACTGAAAGGATTTATGCAC 59.147 37.037 0.00 0.00 39.27 4.57
2399 2498 3.589988 AGATGGAATGACACTTGACGAC 58.410 45.455 0.00 0.00 0.00 4.34
2404 2503 4.929211 TGGAATGACACTTGACGACATAAG 59.071 41.667 0.00 0.00 0.00 1.73
2409 2508 2.030185 ACACTTGACGACATAAGCGACT 60.030 45.455 0.00 0.00 0.00 4.18
2410 2509 2.987149 CACTTGACGACATAAGCGACTT 59.013 45.455 0.00 0.00 0.00 3.01
2446 2546 9.662947 GGAAGAATTGAAAGAATGGAATGAAAT 57.337 29.630 0.00 0.00 0.00 2.17
2467 2567 6.824305 AATGAACGGAGAAGAAAATGACAT 57.176 33.333 0.00 0.00 0.00 3.06
2503 2603 9.643652 CGAATGAAATAGAAAGCATCTTTAGAC 57.356 33.333 0.00 0.00 39.71 2.59
2615 2719 1.187087 AACTGGCCACAAACGGAAAA 58.813 45.000 0.00 0.00 0.00 2.29
2620 2724 3.223435 TGGCCACAAACGGAAAAGATTA 58.777 40.909 0.00 0.00 0.00 1.75
2625 2729 6.309494 GGCCACAAACGGAAAAGATTAAATAC 59.691 38.462 0.00 0.00 0.00 1.89
2629 2733 7.540745 CACAAACGGAAAAGATTAAATACCTGG 59.459 37.037 0.00 0.00 0.00 4.45
2636 2740 9.031537 GGAAAAGATTAAATACCTGGGAAGAAA 57.968 33.333 0.00 0.00 0.00 2.52
2656 2760 7.059202 AGAAAGAAGAAATGCAAAACTCCAT 57.941 32.000 0.00 0.00 0.00 3.41
2754 2861 8.224389 TCTTGATGAACACTTGAAGAATGAAA 57.776 30.769 0.00 0.00 0.00 2.69
2777 2884 6.659745 ATAAATCATGATGAACCACCATGG 57.340 37.500 11.19 11.19 45.02 3.66
2796 2904 2.567985 GGAGAACTCCGGTGACAAAAA 58.432 47.619 11.17 0.00 40.36 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
230 231 3.909732 TGGGTTTCCTTGTTCTCAACAT 58.090 40.909 0.00 0.00 41.79 2.71
1299 1301 5.398603 TCGCCATATCAACCAAAACATTT 57.601 34.783 0.00 0.00 0.00 2.32
2055 2152 1.676014 GGTGTCTGCCAGTTATTCGCT 60.676 52.381 0.00 0.00 0.00 4.93
2132 2229 2.485835 CCGTCTCGGTCCTAAGATCTCT 60.486 54.545 0.00 0.00 42.73 3.10
2195 2292 1.285578 GAGTGCTCTCGATCTTTGCC 58.714 55.000 0.00 0.00 0.00 4.52
2283 2381 4.946157 TCTTATCTCGTTCTAACCGGAGTT 59.054 41.667 9.46 0.00 40.15 3.01
2331 2430 3.113514 TTTCAGCCGGAGTGGTGCA 62.114 57.895 5.05 0.00 41.21 4.57
2335 2434 1.308069 CCATGTTTCAGCCGGAGTGG 61.308 60.000 5.05 0.00 42.50 4.00
2399 2498 2.476619 CGGAGGCATTAAGTCGCTTATG 59.523 50.000 1.12 0.00 0.00 1.90
2404 2503 3.719214 CCGGAGGCATTAAGTCGC 58.281 61.111 0.00 0.00 46.14 5.19
2446 2546 5.551233 AGATGTCATTTTCTTCTCCGTTCA 58.449 37.500 0.00 0.00 0.00 3.18
2467 2567 4.574892 TCTATTTCATTCGTGGCACAAGA 58.425 39.130 19.09 4.66 46.62 3.02
2503 2603 2.874086 ACAACTCCGTTTAAACCTTCCG 59.126 45.455 12.66 0.63 0.00 4.30
2532 2633 6.791303 ACAAGCTTATTCTTTCGTTGTTGAA 58.209 32.000 0.00 0.00 0.00 2.69
2599 2702 1.698506 ATCTTTTCCGTTTGTGGCCA 58.301 45.000 0.00 0.00 0.00 5.36
2615 2719 8.836735 TCTTCTTTCTTCCCAGGTATTTAATCT 58.163 33.333 0.00 0.00 0.00 2.40
2620 2724 7.310052 GCATTTCTTCTTTCTTCCCAGGTATTT 60.310 37.037 0.00 0.00 0.00 1.40
2625 2729 3.828451 TGCATTTCTTCTTTCTTCCCAGG 59.172 43.478 0.00 0.00 0.00 4.45
2629 2733 6.422100 GGAGTTTTGCATTTCTTCTTTCTTCC 59.578 38.462 0.00 0.00 0.00 3.46
2656 2760 9.187455 GCATTTAATTCTCCGTAACTTTTGAAA 57.813 29.630 0.00 0.00 0.00 2.69
2765 2872 1.351017 GGAGTTCTCCATGGTGGTTCA 59.649 52.381 12.58 0.00 39.03 3.18
2777 2884 3.463944 TCTTTTTGTCACCGGAGTTCTC 58.536 45.455 9.46 0.00 0.00 2.87
2796 2904 9.599056 TTCTACCTTCATTCTATCTCATCATCT 57.401 33.333 0.00 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.