Multiple sequence alignment - TraesCS3A01G458600

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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 TraesCS3A01G458600 chr3A 100.000 2273 0 0 1 2273 695636380 695638652 0.000000e+00 4198.0
1 TraesCS3A01G458600 chr3A 98.080 2240 41 2 1 2240 672883048 672880811 0.000000e+00 3897.0
2 TraesCS3A01G458600 chr7B 98.259 2240 38 1 1 2240 662732894 662735132 0.000000e+00 3919.0
3 TraesCS3A01G458600 chr7B 98.338 1625 27 0 1 1625 622431988 622430364 0.000000e+00 2852.0
4 TraesCS3A01G458600 chr7B 100.000 30 0 0 2244 2273 105229471 105229442 3.150000e-04 56.5
5 TraesCS3A01G458600 chr1D 98.214 2240 39 1 1 2240 254531578 254533816 0.000000e+00 3914.0
6 TraesCS3A01G458600 chr1D 100.000 28 0 0 2246 2273 176207977 176208004 4.000000e-03 52.8
7 TraesCS3A01G458600 chr1D 100.000 28 0 0 2246 2273 254383784 254383757 4.000000e-03 52.8
8 TraesCS3A01G458600 chr1D 100.000 28 0 0 2246 2273 257436398 257436425 4.000000e-03 52.8
9 TraesCS3A01G458600 chr1D 100.000 28 0 0 2246 2273 260390603 260390576 4.000000e-03 52.8
10 TraesCS3A01G458600 chr1D 100.000 28 0 0 2246 2273 263935421 263935394 4.000000e-03 52.8
11 TraesCS3A01G458600 chr3B 97.991 2240 45 0 1 2240 201565401 201563162 0.000000e+00 3888.0
12 TraesCS3A01G458600 chr3B 100.000 30 0 0 2244 2273 201537756 201537785 3.150000e-04 56.5
13 TraesCS3A01G458600 chr1B 97.813 2241 46 3 1 2240 633733490 633731252 0.000000e+00 3864.0
14 TraesCS3A01G458600 chr6B 96.925 2244 49 9 1 2240 615601610 615599383 0.000000e+00 3744.0
15 TraesCS3A01G458600 chr6B 98.154 1625 28 1 1 1625 515380591 515378969 0.000000e+00 2833.0
16 TraesCS3A01G458600 chr2A 98.447 2125 33 0 1 2125 543187641 543189765 0.000000e+00 3742.0
17 TraesCS3A01G458600 chr2A 97.561 369 8 1 1872 2240 394050572 394050939 4.120000e-177 630.0
18 TraesCS3A01G458600 chr2A 98.361 183 2 1 2006 2188 707075343 707075524 1.010000e-83 320.0
19 TraesCS3A01G458600 chr4A 100.000 30 0 0 2244 2273 310785796 310785767 3.150000e-04 56.5
20 TraesCS3A01G458600 chr2B 100.000 30 0 0 2244 2273 784236554 784236583 3.150000e-04 56.5


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 TraesCS3A01G458600 chr3A 695636380 695638652 2272 False 4198 4198 100.000 1 2273 1 chr3A.!!$F1 2272
1 TraesCS3A01G458600 chr3A 672880811 672883048 2237 True 3897 3897 98.080 1 2240 1 chr3A.!!$R1 2239
2 TraesCS3A01G458600 chr7B 662732894 662735132 2238 False 3919 3919 98.259 1 2240 1 chr7B.!!$F1 2239
3 TraesCS3A01G458600 chr7B 622430364 622431988 1624 True 2852 2852 98.338 1 1625 1 chr7B.!!$R2 1624
4 TraesCS3A01G458600 chr1D 254531578 254533816 2238 False 3914 3914 98.214 1 2240 1 chr1D.!!$F2 2239
5 TraesCS3A01G458600 chr3B 201563162 201565401 2239 True 3888 3888 97.991 1 2240 1 chr3B.!!$R1 2239
6 TraesCS3A01G458600 chr1B 633731252 633733490 2238 True 3864 3864 97.813 1 2240 1 chr1B.!!$R1 2239
7 TraesCS3A01G458600 chr6B 615599383 615601610 2227 True 3744 3744 96.925 1 2240 1 chr6B.!!$R2 2239
8 TraesCS3A01G458600 chr6B 515378969 515380591 1622 True 2833 2833 98.154 1 1625 1 chr6B.!!$R1 1624
9 TraesCS3A01G458600 chr2A 543187641 543189765 2124 False 3742 3742 98.447 1 2125 1 chr2A.!!$F2 2124

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
150 151 3.132824 TGCACGATCTTCACAGGTATCAT 59.867 43.478 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1774 2.224066 CGAGATCCGCCATAAAAGGTCT 60.224 50.0 0.0 0.0 0.0 3.85 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
150 151 3.132824 TGCACGATCTTCACAGGTATCAT 59.867 43.478 0.00 0.00 0.00 2.45
205 206 8.609176 CGATTTTCGAACCATTTCCTATAAGAA 58.391 33.333 0.00 0.00 43.74 2.52
1223 1225 7.066163 GCTGGCTTATTTGGCAAAGAAAAATAT 59.934 33.333 19.29 2.91 41.92 1.28
1286 1288 6.238374 CGGGAGCAGTAATTTAATCGTTCAAT 60.238 38.462 0.00 0.00 0.00 2.57
1772 1774 3.198635 AGCTTCTCACTTGCTATGGCTTA 59.801 43.478 1.68 0.00 39.59 3.09
1811 1813 1.869690 GGCGCACAGACTCCTTTTC 59.130 57.895 10.83 0.00 0.00 2.29
1871 1877 7.500141 TCTATTTGAAGCTGCTACATGTATGA 58.500 34.615 5.91 0.00 0.00 2.15
2188 2194 2.969628 TGGCAAAAAGAAGGGGATTCA 58.030 42.857 0.00 0.00 40.67 2.57
2207 2213 7.982354 GGGATTCATTAGCTCGCTATTTAGTAT 59.018 37.037 0.00 0.00 0.00 2.12
2240 2246 8.139989 GTGAAATGAGGGAATCCATCAAAATAG 58.860 37.037 20.94 0.00 34.83 1.73
2241 2247 8.060689 TGAAATGAGGGAATCCATCAAAATAGA 58.939 33.333 20.94 0.61 34.83 1.98
2242 2248 8.843308 AAATGAGGGAATCCATCAAAATAGAA 57.157 30.769 20.94 0.00 34.83 2.10
2243 2249 7.830099 ATGAGGGAATCCATCAAAATAGAAC 57.170 36.000 20.94 0.00 34.83 3.01
2244 2250 6.973642 TGAGGGAATCCATCAAAATAGAACT 58.026 36.000 14.82 0.00 34.83 3.01
2245 2251 6.830324 TGAGGGAATCCATCAAAATAGAACTG 59.170 38.462 14.82 0.00 34.83 3.16
2246 2252 6.131961 AGGGAATCCATCAAAATAGAACTGG 58.868 40.000 0.09 0.00 34.83 4.00
2247 2253 5.893824 GGGAATCCATCAAAATAGAACTGGT 59.106 40.000 0.09 0.00 0.00 4.00
2248 2254 6.183360 GGGAATCCATCAAAATAGAACTGGTG 60.183 42.308 0.09 0.00 0.00 4.17
2249 2255 6.183360 GGAATCCATCAAAATAGAACTGGTGG 60.183 42.308 0.00 0.00 41.87 4.61
2250 2256 5.512942 TCCATCAAAATAGAACTGGTGGA 57.487 39.130 0.00 0.00 45.93 4.02
2251 2257 5.500234 TCCATCAAAATAGAACTGGTGGAG 58.500 41.667 0.00 0.00 43.81 3.86
2252 2258 4.096984 CCATCAAAATAGAACTGGTGGAGC 59.903 45.833 0.00 0.00 42.95 4.70
2253 2259 3.334691 TCAAAATAGAACTGGTGGAGCG 58.665 45.455 0.00 0.00 0.00 5.03
2254 2260 2.403252 AAATAGAACTGGTGGAGCGG 57.597 50.000 0.00 0.00 0.00 5.52
2255 2261 1.276622 AATAGAACTGGTGGAGCGGT 58.723 50.000 0.00 0.00 0.00 5.68
2256 2262 0.537188 ATAGAACTGGTGGAGCGGTG 59.463 55.000 0.00 0.00 0.00 4.94
2257 2263 0.541063 TAGAACTGGTGGAGCGGTGA 60.541 55.000 0.00 0.00 0.00 4.02
2258 2264 1.070786 GAACTGGTGGAGCGGTGAA 59.929 57.895 0.00 0.00 0.00 3.18
2259 2265 0.534203 GAACTGGTGGAGCGGTGAAA 60.534 55.000 0.00 0.00 0.00 2.69
2260 2266 0.110486 AACTGGTGGAGCGGTGAAAT 59.890 50.000 0.00 0.00 0.00 2.17
2261 2267 0.606401 ACTGGTGGAGCGGTGAAATG 60.606 55.000 0.00 0.00 0.00 2.32
2262 2268 1.926511 CTGGTGGAGCGGTGAAATGC 61.927 60.000 0.00 0.00 0.00 3.56
2263 2269 1.971167 GGTGGAGCGGTGAAATGCA 60.971 57.895 0.00 0.00 0.00 3.96
2264 2270 1.315257 GGTGGAGCGGTGAAATGCAT 61.315 55.000 0.00 0.00 0.00 3.96
2265 2271 0.527565 GTGGAGCGGTGAAATGCATT 59.472 50.000 5.99 5.99 0.00 3.56
2266 2272 0.527113 TGGAGCGGTGAAATGCATTG 59.473 50.000 13.82 0.58 0.00 2.82
2267 2273 0.810648 GGAGCGGTGAAATGCATTGA 59.189 50.000 13.82 0.00 0.00 2.57
2268 2274 1.202222 GGAGCGGTGAAATGCATTGAG 60.202 52.381 13.82 4.28 0.00 3.02
2269 2275 1.739466 GAGCGGTGAAATGCATTGAGA 59.261 47.619 13.82 0.00 0.00 3.27
2270 2276 2.357009 GAGCGGTGAAATGCATTGAGAT 59.643 45.455 13.82 0.00 0.00 2.75
2271 2277 2.357009 AGCGGTGAAATGCATTGAGATC 59.643 45.455 13.82 7.30 0.00 2.75
2272 2278 2.852143 GCGGTGAAATGCATTGAGATCG 60.852 50.000 13.82 12.59 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 6.618811 GTGCATTTCAGTCAAATTCAGATCT 58.381 36.000 0.00 0.00 31.79 2.75
659 660 7.362142 CGAGAATTTCACGGGATAGAGATATGA 60.362 40.741 8.16 0.00 0.00 2.15
1150 1152 3.777465 TCGTAGACCTCTTTTCGATGG 57.223 47.619 0.00 0.00 0.00 3.51
1772 1774 2.224066 CGAGATCCGCCATAAAAGGTCT 60.224 50.000 0.00 0.00 0.00 3.85
1865 1871 8.510243 AAGTAATTGTGCATCATTCTCATACA 57.490 30.769 0.00 0.00 0.00 2.29
1871 1877 5.106197 TGCGAAAGTAATTGTGCATCATTCT 60.106 36.000 0.00 0.00 0.00 2.40
2188 2194 9.155975 CCAATTCATACTAAATAGCGAGCTAAT 57.844 33.333 9.00 0.00 31.73 1.73
2207 2213 4.711355 GGATTCCCTCATTTCACCAATTCA 59.289 41.667 0.00 0.00 0.00 2.57
2240 2246 0.534203 TTTCACCGCTCCACCAGTTC 60.534 55.000 0.00 0.00 0.00 3.01
2241 2247 0.110486 ATTTCACCGCTCCACCAGTT 59.890 50.000 0.00 0.00 0.00 3.16
2242 2248 0.606401 CATTTCACCGCTCCACCAGT 60.606 55.000 0.00 0.00 0.00 4.00
2243 2249 1.926511 GCATTTCACCGCTCCACCAG 61.927 60.000 0.00 0.00 0.00 4.00
2244 2250 1.971167 GCATTTCACCGCTCCACCA 60.971 57.895 0.00 0.00 0.00 4.17
2245 2251 1.315257 ATGCATTTCACCGCTCCACC 61.315 55.000 0.00 0.00 0.00 4.61
2246 2252 0.527565 AATGCATTTCACCGCTCCAC 59.472 50.000 5.99 0.00 0.00 4.02
2247 2253 0.527113 CAATGCATTTCACCGCTCCA 59.473 50.000 9.83 0.00 0.00 3.86
2248 2254 0.810648 TCAATGCATTTCACCGCTCC 59.189 50.000 9.83 0.00 0.00 4.70
2249 2255 1.739466 TCTCAATGCATTTCACCGCTC 59.261 47.619 9.83 0.00 0.00 5.03
2250 2256 1.825090 TCTCAATGCATTTCACCGCT 58.175 45.000 9.83 0.00 0.00 5.52
2251 2257 2.724349 GATCTCAATGCATTTCACCGC 58.276 47.619 9.83 0.00 0.00 5.68
2252 2258 2.978013 CGATCTCAATGCATTTCACCG 58.022 47.619 9.83 6.42 0.00 4.94


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

AutoCloner maintained by Alex Coulton.