Multiple sequence alignment - TraesCS2A01G186500

Loading Multiple Alignment...

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 TraesCS2A01G186500 chr2A 100.000 2900 0 0 1 2900 148155534 148158433 0 5356
1 TraesCS2A01G186500 chr2A 85.714 1911 247 14 4 1912 147542783 147540897 0 1993
2 TraesCS2A01G186500 chr2A 78.237 1452 270 33 13 1452 43282077 43280660 0 889
3 TraesCS2A01G186500 chr2D 94.836 2285 88 14 4 2286 153002964 153000708 0 3539
4 TraesCS2A01G186500 chr2D 92.985 613 41 1 2284 2896 31475081 31474471 0 893
5 TraesCS2A01G186500 chr2B 94.496 2253 91 17 4 2248 210932595 210930368 0 3443
6 TraesCS2A01G186500 chr2B 86.663 1897 231 10 4 1900 211187471 211189345 0 2082
7 TraesCS2A01G186500 chr2B 92.775 609 41 2 2288 2896 90448275 90447670 0 878
8 TraesCS2A01G186500 chr2B 79.224 1160 211 13 13 1155 67217634 67216488 0 780
9 TraesCS2A01G186500 chr4A 80.129 1711 317 15 122 1815 662202226 662200522 0 1254
10 TraesCS2A01G186500 chr7A 79.778 1711 323 15 122 1815 49991007 49989303 0 1221
11 TraesCS2A01G186500 chr3D 93.322 614 36 4 2285 2896 151428304 151427694 0 902
12 TraesCS2A01G186500 chr3D 93.092 608 40 1 2289 2896 573155552 573156157 0 889
13 TraesCS2A01G186500 chr3D 92.928 608 41 1 2289 2896 573151312 573150707 0 883
14 TraesCS2A01G186500 chr7D 93.268 609 38 2 2288 2896 116824665 116825270 0 894
15 TraesCS2A01G186500 chr4D 93.103 609 40 2 2289 2896 360790065 360790672 0 891
16 TraesCS2A01G186500 chr5B 92.951 610 39 2 2289 2896 430151092 430150485 0 885
17 TraesCS2A01G186500 chr1D 92.939 609 40 2 2288 2896 326240685 326240080 0 883


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 TraesCS2A01G186500 chr2A 148155534 148158433 2899 False 5356 5356 100.000 1 2900 1 chr2A.!!$F1 2899
1 TraesCS2A01G186500 chr2A 147540897 147542783 1886 True 1993 1993 85.714 4 1912 1 chr2A.!!$R2 1908
2 TraesCS2A01G186500 chr2A 43280660 43282077 1417 True 889 889 78.237 13 1452 1 chr2A.!!$R1 1439
3 TraesCS2A01G186500 chr2D 153000708 153002964 2256 True 3539 3539 94.836 4 2286 1 chr2D.!!$R2 2282
4 TraesCS2A01G186500 chr2D 31474471 31475081 610 True 893 893 92.985 2284 2896 1 chr2D.!!$R1 612
5 TraesCS2A01G186500 chr2B 210930368 210932595 2227 True 3443 3443 94.496 4 2248 1 chr2B.!!$R3 2244
6 TraesCS2A01G186500 chr2B 211187471 211189345 1874 False 2082 2082 86.663 4 1900 1 chr2B.!!$F1 1896
7 TraesCS2A01G186500 chr2B 90447670 90448275 605 True 878 878 92.775 2288 2896 1 chr2B.!!$R2 608
8 TraesCS2A01G186500 chr2B 67216488 67217634 1146 True 780 780 79.224 13 1155 1 chr2B.!!$R1 1142
9 TraesCS2A01G186500 chr4A 662200522 662202226 1704 True 1254 1254 80.129 122 1815 1 chr4A.!!$R1 1693
10 TraesCS2A01G186500 chr7A 49989303 49991007 1704 True 1221 1221 79.778 122 1815 1 chr7A.!!$R1 1693
11 TraesCS2A01G186500 chr3D 151427694 151428304 610 True 902 902 93.322 2285 2896 1 chr3D.!!$R1 611
12 TraesCS2A01G186500 chr3D 573155552 573156157 605 False 889 889 93.092 2289 2896 1 chr3D.!!$F1 607
13 TraesCS2A01G186500 chr3D 573150707 573151312 605 True 883 883 92.928 2289 2896 1 chr3D.!!$R2 607
14 TraesCS2A01G186500 chr7D 116824665 116825270 605 False 894 894 93.268 2288 2896 1 chr7D.!!$F1 608
15 TraesCS2A01G186500 chr4D 360790065 360790672 607 False 891 891 93.103 2289 2896 1 chr4D.!!$F1 607
16 TraesCS2A01G186500 chr5B 430150485 430151092 607 True 885 885 92.951 2289 2896 1 chr5B.!!$R1 607
17 TraesCS2A01G186500 chr1D 326240080 326240685 605 True 883 883 92.939 2288 2896 1 chr1D.!!$R1 608

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
36 37 0.322277 CCTGCTCATGCTGACCAACT 60.322 55.000 0.0 0.0 40.01 3.16 F
565 577 1.301293 CCAAGAAGCCCCTCCTCAC 59.699 63.158 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1816 0.319211 TGGTGAAACTGAGGTACGCG 60.319 55.0 3.53 3.53 36.74 6.01 R
2286 2330 0.172127 GCTTTTCTTGCAGCCCTAGC 59.828 55.0 0.00 0.00 40.32 3.42 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
36 37 0.322277 CCTGCTCATGCTGACCAACT 60.322 55.000 0.00 0.00 40.01 3.16
565 577 1.301293 CCAAGAAGCCCCTCCTCAC 59.699 63.158 0.00 0.00 0.00 3.51
585 597 4.477975 CCACCGTCGACCTCTCGC 62.478 72.222 10.58 0.00 39.96 5.03
590 602 2.104859 CGTCGACCTCTCGCCTGTA 61.105 63.158 10.58 0.00 39.96 2.74
663 681 4.373116 GCCACTTCGTCCTCGGCA 62.373 66.667 0.00 0.00 42.50 5.69
837 864 2.066262 ACATCTTTGTACGACGGCTTG 58.934 47.619 0.00 0.00 33.16 4.01
904 931 2.434336 CCCACCGATTCTCATACAAGGA 59.566 50.000 0.00 0.00 0.00 3.36
946 973 1.865865 GTTCAGCGACAAGAACCTGA 58.134 50.000 0.00 0.00 38.49 3.86
1274 1310 4.141482 GGCTTCTGGGTTATTGTATCTCCA 60.141 45.833 0.00 0.00 0.00 3.86
1275 1311 5.456763 GGCTTCTGGGTTATTGTATCTCCAT 60.457 44.000 0.00 0.00 0.00 3.41
1276 1312 5.471456 GCTTCTGGGTTATTGTATCTCCATG 59.529 44.000 0.00 0.00 0.00 3.66
1499 1536 1.445410 CCGATGTGTTCGCCTTCGA 60.445 57.895 0.00 0.00 46.71 3.71
1850 1887 3.417101 ACCAGAAAATGTTGCCATACGA 58.583 40.909 0.00 0.00 0.00 3.43
1893 1930 5.012458 TGCAGTTTCTGATATATCTGGAGGG 59.988 44.000 16.85 5.78 32.44 4.30
1979 2016 8.528044 TCCTATACACACATCTATGTTGTACA 57.472 34.615 14.60 0.00 39.39 2.90
2026 2069 7.287810 ACCTGATGGTTACCTAATTTATGGTC 58.712 38.462 2.07 0.00 46.05 4.02
2081 2124 1.953686 AGTGACATGTGTTTTTCCCCG 59.046 47.619 1.15 0.00 0.00 5.73
2082 2125 0.671251 TGACATGTGTTTTTCCCCGC 59.329 50.000 1.15 0.00 0.00 6.13
2083 2126 0.671251 GACATGTGTTTTTCCCCGCA 59.329 50.000 1.15 0.00 0.00 5.69
2084 2127 0.387565 ACATGTGTTTTTCCCCGCAC 59.612 50.000 0.00 0.00 0.00 5.34
2085 2128 0.387202 CATGTGTTTTTCCCCGCACA 59.613 50.000 0.00 0.00 44.43 4.57
2157 2200 4.158579 AGCTCTGAAACACATCGTATCTCA 59.841 41.667 0.00 0.00 0.00 3.27
2158 2201 5.046529 GCTCTGAAACACATCGTATCTCAT 58.953 41.667 0.00 0.00 0.00 2.90
2159 2202 5.174761 GCTCTGAAACACATCGTATCTCATC 59.825 44.000 0.00 0.00 0.00 2.92
2160 2203 5.273944 TCTGAAACACATCGTATCTCATCG 58.726 41.667 0.00 0.00 0.00 3.84
2161 2204 4.993905 TGAAACACATCGTATCTCATCGT 58.006 39.130 0.00 0.00 0.00 3.73
2162 2205 6.037830 TCTGAAACACATCGTATCTCATCGTA 59.962 38.462 0.00 0.00 0.00 3.43
2163 2206 6.735130 TGAAACACATCGTATCTCATCGTAT 58.265 36.000 0.00 0.00 0.00 3.06
2164 2207 6.856426 TGAAACACATCGTATCTCATCGTATC 59.144 38.462 0.00 0.00 0.00 2.24
2165 2208 6.561737 AACACATCGTATCTCATCGTATCT 57.438 37.500 0.00 0.00 0.00 1.98
2166 2209 6.171932 ACACATCGTATCTCATCGTATCTC 57.828 41.667 0.00 0.00 0.00 2.75
2167 2210 5.122554 ACACATCGTATCTCATCGTATCTCC 59.877 44.000 0.00 0.00 0.00 3.71
2182 2225 2.662006 TCTCCATTCAGAACGCTCAG 57.338 50.000 0.00 0.00 0.00 3.35
2220 2264 9.710818 TCGCCTTAATTATAGGATCCTAATAGT 57.289 33.333 25.20 16.52 34.56 2.12
2231 2275 9.954992 ATAGGATCCTAATAGTATAAGGGGAAC 57.045 37.037 25.20 0.00 31.73 3.62
2236 2280 6.494835 TCCTAATAGTATAAGGGGAACGTTCC 59.505 42.308 34.71 34.71 46.82 3.62
2237 2281 6.496218 CCTAATAGTATAAGGGGAACGTTCCT 59.504 42.308 38.59 25.60 46.72 3.36
2254 2298 2.040254 TTCCCCTGATACCCCGGG 60.040 66.667 15.80 15.80 37.73 5.73
2286 2330 1.043116 TCCGCCAGGGTACATCAGAG 61.043 60.000 0.00 0.00 38.33 3.35
2338 2382 1.939785 CCGCTCGAAATCGACTCGG 60.940 63.158 20.01 20.01 45.65 4.63
2377 2424 6.396459 GAGATCGACTCGAAAAGAAACAAT 57.604 37.500 5.00 0.00 39.99 2.71
2435 2482 2.223611 CGAGATGATCTTGAGCCAATGC 59.776 50.000 3.50 0.00 37.95 3.56
2669 2717 6.260663 TCCTATATTTTTGGCAAAGGTTCCT 58.739 36.000 13.04 0.66 0.00 3.36
2670 2718 6.154363 TCCTATATTTTTGGCAAAGGTTCCTG 59.846 38.462 13.04 2.26 0.00 3.86
2675 2723 1.186917 TGGCAAAGGTTCCTGGCATG 61.187 55.000 14.57 0.00 42.56 4.06
2687 2735 5.127682 GGTTCCTGGCATGTTCATCTTAATT 59.872 40.000 0.00 0.00 0.00 1.40
2688 2736 6.351286 GGTTCCTGGCATGTTCATCTTAATTT 60.351 38.462 0.00 0.00 0.00 1.82
2741 2792 6.677781 TTTTTACCATCTCATTTAGCTCGG 57.322 37.500 0.00 0.00 0.00 4.63
2842 2893 3.251004 AGTTTGAGCTCGCTCGAATTTTT 59.749 39.130 20.94 8.05 45.11 1.94
2879 2930 1.593196 CCAACTCCAACTCGCTCAAA 58.407 50.000 0.00 0.00 0.00 2.69
2896 2947 1.593006 CAAACTCGACTCGTTTGCAGT 59.407 47.619 13.68 0.00 42.99 4.40
2897 2948 1.935933 AACTCGACTCGTTTGCAGTT 58.064 45.000 0.00 0.00 0.00 3.16
2898 2949 1.488527 ACTCGACTCGTTTGCAGTTC 58.511 50.000 0.00 0.00 0.00 3.01
2899 2950 1.067212 ACTCGACTCGTTTGCAGTTCT 59.933 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.321564 CCTTTCGTCTGGATGGTGCA 60.322 55.000 0.00 0.00 0.00 4.57
837 864 1.347817 CGCAGCTCCGAGAACTTGAC 61.348 60.000 0.00 0.00 0.00 3.18
904 931 3.381272 CCCTTGGTCGCATGATACAATTT 59.619 43.478 0.00 0.00 0.00 1.82
1218 1254 5.902613 TTATGTGAAATCTTTGAGGCCAG 57.097 39.130 5.01 0.00 0.00 4.85
1274 1310 1.424302 CCTGCTCCCAATCCTCATCAT 59.576 52.381 0.00 0.00 0.00 2.45
1275 1311 0.841961 CCTGCTCCCAATCCTCATCA 59.158 55.000 0.00 0.00 0.00 3.07
1276 1312 0.842635 ACCTGCTCCCAATCCTCATC 59.157 55.000 0.00 0.00 0.00 2.92
1779 1816 0.319211 TGGTGAAACTGAGGTACGCG 60.319 55.000 3.53 3.53 36.74 6.01
1850 1887 0.465705 ACCCATGCTCGTCGATGATT 59.534 50.000 7.99 0.00 0.00 2.57
1884 1921 1.842562 CATTGTCACCTCCCTCCAGAT 59.157 52.381 0.00 0.00 0.00 2.90
1893 1930 1.197721 CCGCAAGAACATTGTCACCTC 59.802 52.381 0.00 0.00 43.02 3.85
1948 1985 3.374764 AGATGTGTGTATAGGAGCCACA 58.625 45.455 0.00 0.00 40.02 4.17
1981 2018 8.877864 TCAGGTCATACATTTCAGGTAAAAAT 57.122 30.769 0.00 0.00 0.00 1.82
2026 2069 5.484173 TTGTTCTGCTTATAGGCAATTCG 57.516 39.130 11.03 0.00 41.94 3.34
2040 2083 4.508861 ACTTGTTTGATTGCATTGTTCTGC 59.491 37.500 0.00 0.00 42.62 4.26
2157 2200 3.319405 AGCGTTCTGAATGGAGATACGAT 59.681 43.478 11.32 0.00 32.74 3.73
2158 2201 2.688446 AGCGTTCTGAATGGAGATACGA 59.312 45.455 11.32 0.00 32.74 3.43
2159 2202 3.046390 GAGCGTTCTGAATGGAGATACG 58.954 50.000 11.32 1.20 33.45 3.06
2160 2203 4.046938 TGAGCGTTCTGAATGGAGATAC 57.953 45.455 11.32 0.00 0.00 2.24
2161 2204 3.491619 GCTGAGCGTTCTGAATGGAGATA 60.492 47.826 10.28 0.00 0.00 1.98
2162 2205 2.741228 GCTGAGCGTTCTGAATGGAGAT 60.741 50.000 10.28 0.00 0.00 2.75
2163 2206 1.404717 GCTGAGCGTTCTGAATGGAGA 60.405 52.381 10.28 0.00 0.00 3.71
2164 2207 1.005340 GCTGAGCGTTCTGAATGGAG 58.995 55.000 10.28 0.00 0.00 3.86
2165 2208 3.143675 GCTGAGCGTTCTGAATGGA 57.856 52.632 10.28 0.00 0.00 3.41
2231 2275 0.468648 GGGTATCAGGGGAAGGAACG 59.531 60.000 0.00 0.00 0.00 3.95
2236 2280 2.147387 CCCGGGGTATCAGGGGAAG 61.147 68.421 14.71 0.00 45.67 3.46
2237 2281 2.040254 CCCGGGGTATCAGGGGAA 60.040 66.667 14.71 0.00 45.67 3.97
2254 2298 3.544615 GGCGGAATGTTTATTCGCC 57.455 52.632 9.24 9.24 45.84 5.54
2286 2330 0.172127 GCTTTTCTTGCAGCCCTAGC 59.828 55.000 0.00 0.00 40.32 3.42
2377 2424 7.217200 AGCTACATAAAGTGTTCAAACTCAGA 58.783 34.615 0.00 0.00 42.29 3.27
2435 2482 0.579156 GCTAAAATCGAGCGAGCCAG 59.421 55.000 0.00 0.00 0.00 4.85
2566 2614 8.842280 ACTTAATTAAGTTTCCATGTTCGTTGA 58.158 29.630 22.49 0.00 43.57 3.18
2842 2893 4.406972 AGTTGGCTCAGCTCAACTCATATA 59.593 41.667 21.33 0.00 42.04 0.86
2879 2930 1.067212 AGAACTGCAAACGAGTCGAGT 59.933 47.619 21.50 8.87 0.00 4.18


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

AutoCloner maintained by Alex Coulton.