Multiple sequence alignment - TraesCS5B01G184500

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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 TraesCS5B01G184500 chr5B 100.000 2291 0 0 1 2291 335743290 335741000 0.000000e+00 4231.0
1 TraesCS5B01G184500 chr3A 89.878 2292 220 8 1 2291 579144508 579146788 0.000000e+00 2937.0
2 TraesCS5B01G184500 chr3A 83.215 1978 289 23 321 2290 633809031 633807089 0.000000e+00 1773.0
3 TraesCS5B01G184500 chr1D 86.582 2057 269 6 237 2290 236522759 236520707 0.000000e+00 2263.0
4 TraesCS5B01G184500 chr7B 83.406 2302 361 17 1 2290 239383761 239381469 0.000000e+00 2115.0
5 TraesCS5B01G184500 chr7B 82.916 2277 352 28 34 2290 205362430 205360171 0.000000e+00 2015.0
6 TraesCS5B01G184500 chr7B 81.589 1586 265 20 33 1607 240396397 240394828 0.000000e+00 1286.0
7 TraesCS5B01G184500 chr5D 86.510 1868 216 24 426 2290 231685280 231683446 0.000000e+00 2021.0
8 TraesCS5B01G184500 chr6A 84.591 1908 282 12 387 2290 468469163 468467264 0.000000e+00 1884.0
9 TraesCS5B01G184500 chr6A 81.661 2192 346 37 28 2200 178034942 178037096 0.000000e+00 1770.0
10 TraesCS5B01G184500 chr6A 78.930 299 46 11 31 317 99401885 99401592 1.080000e-43 187.0
11 TraesCS5B01G184500 chr7A 85.291 1686 225 15 1 1673 545905827 545907502 0.000000e+00 1718.0
12 TraesCS5B01G184500 chr6B 86.339 1464 184 15 834 2290 257587340 257588794 0.000000e+00 1581.0
13 TraesCS5B01G184500 chr7D 82.986 911 150 4 1382 2290 108408638 108407731 0.000000e+00 819.0
14 TraesCS5B01G184500 chr7D 89.091 55 6 0 100 154 58741207 58741261 4.080000e-08 69.4


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 TraesCS5B01G184500 chr5B 335741000 335743290 2290 True 4231 4231 100.000 1 2291 1 chr5B.!!$R1 2290
1 TraesCS5B01G184500 chr3A 579144508 579146788 2280 False 2937 2937 89.878 1 2291 1 chr3A.!!$F1 2290
2 TraesCS5B01G184500 chr3A 633807089 633809031 1942 True 1773 1773 83.215 321 2290 1 chr3A.!!$R1 1969
3 TraesCS5B01G184500 chr1D 236520707 236522759 2052 True 2263 2263 86.582 237 2290 1 chr1D.!!$R1 2053
4 TraesCS5B01G184500 chr7B 239381469 239383761 2292 True 2115 2115 83.406 1 2290 1 chr7B.!!$R2 2289
5 TraesCS5B01G184500 chr7B 205360171 205362430 2259 True 2015 2015 82.916 34 2290 1 chr7B.!!$R1 2256
6 TraesCS5B01G184500 chr7B 240394828 240396397 1569 True 1286 1286 81.589 33 1607 1 chr7B.!!$R3 1574
7 TraesCS5B01G184500 chr5D 231683446 231685280 1834 True 2021 2021 86.510 426 2290 1 chr5D.!!$R1 1864
8 TraesCS5B01G184500 chr6A 468467264 468469163 1899 True 1884 1884 84.591 387 2290 1 chr6A.!!$R2 1903
9 TraesCS5B01G184500 chr6A 178034942 178037096 2154 False 1770 1770 81.661 28 2200 1 chr6A.!!$F1 2172
10 TraesCS5B01G184500 chr7A 545905827 545907502 1675 False 1718 1718 85.291 1 1673 1 chr7A.!!$F1 1672
11 TraesCS5B01G184500 chr6B 257587340 257588794 1454 False 1581 1581 86.339 834 2290 1 chr6B.!!$F1 1456
12 TraesCS5B01G184500 chr7D 108407731 108408638 907 True 819 819 82.986 1382 2290 1 chr7D.!!$R1 908

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
578 594 0.177373 GTGTTCCCGTCCCTATCCAC 59.823 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1926 1.982395 CTGCACGTCCACCCTAGGA 60.982 63.158 11.48 0.0 34.64 2.94 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
73 74 1.614824 CTGCCTCCTCCTGTTCCCT 60.615 63.158 0.00 0.00 0.00 4.20
214 219 1.474077 GATCCATTGTGGTTGTGCCTC 59.526 52.381 0.00 0.00 39.03 4.70
506 521 1.152030 AGGAGTGCCCTCAGAACCA 60.152 57.895 0.00 0.00 43.31 3.67
573 589 2.288025 GCTGGTGTTCCCGTCCCTA 61.288 63.158 0.00 0.00 35.15 3.53
574 590 1.623542 GCTGGTGTTCCCGTCCCTAT 61.624 60.000 0.00 0.00 35.15 2.57
578 594 0.177373 GTGTTCCCGTCCCTATCCAC 59.823 60.000 0.00 0.00 0.00 4.02
580 596 0.690077 GTTCCCGTCCCTATCCACCT 60.690 60.000 0.00 0.00 0.00 4.00
666 682 1.296392 CCACAAGGTGATCGCCTCA 59.704 57.895 27.69 0.00 38.03 3.86
758 781 4.394712 CGCGGCCAACCCTCTCTT 62.395 66.667 2.24 0.00 0.00 2.85
816 839 3.069980 GCATCTCCTCCGCGTCACT 62.070 63.158 4.92 0.00 0.00 3.41
874 897 1.514678 GCCGGCACACAAAGACATCA 61.515 55.000 24.80 0.00 0.00 3.07
1055 1078 2.813908 GGGCGACGTGGTCATCAC 60.814 66.667 4.13 0.00 42.74 3.06
1151 1181 2.440147 CCACATCCCCACCAAGCA 59.560 61.111 0.00 0.00 0.00 3.91
1289 1319 1.475280 CATCGACCGGGTTGAAGACTA 59.525 52.381 20.66 0.00 29.05 2.59
1897 1946 1.982395 CTCCTAGGGTGGACGTGCA 60.982 63.158 5.33 5.33 31.94 4.57
2142 2191 4.379243 CGGCCCAGCTGTTCGTCT 62.379 66.667 13.81 0.00 0.00 4.18
2261 2311 0.533531 GAAGAACCCGTCCACCGTTT 60.534 55.000 0.00 0.00 33.66 3.60
2273 2323 4.157607 CCGTTTTGGTCAGCCAGT 57.842 55.556 0.00 0.00 46.91 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.458163 CGCGGCTAGGGAACAGGA 61.458 66.667 0.00 0.0 34.27 3.86
118 119 3.842923 CGCCCTCGAGGTCAGCAT 61.843 66.667 29.25 0.0 38.26 3.79
193 198 1.076024 AGGCACAACCACAATGGATCT 59.924 47.619 0.84 0.0 40.96 2.75
261 267 0.325296 TCCTGCGGGACTGGAATAGT 60.325 55.000 11.27 0.0 42.93 2.12
498 513 0.761323 TCTGGTTCCGGTGGTTCTGA 60.761 55.000 0.00 0.0 0.00 3.27
506 521 2.933834 CCCCCTTCTGGTTCCGGT 60.934 66.667 0.00 0.0 0.00 5.28
573 589 2.444895 GGCGGAGGAGAGGTGGAT 60.445 66.667 0.00 0.0 0.00 3.41
613 629 3.770040 CCCATGGTCGACGCAGGA 61.770 66.667 11.73 0.0 0.00 3.86
749 772 2.427245 CGGCCGATGAAGAGAGGGT 61.427 63.158 24.07 0.0 0.00 4.34
775 798 1.627297 GGGATCTGGAACTCCCGCTT 61.627 60.000 0.00 0.0 41.74 4.68
816 839 0.033796 AGTCCTCCGGATCGTGGTTA 60.034 55.000 3.57 0.0 32.73 2.85
1063 1086 2.876879 CGAACGTGCGGCTGTCAAA 61.877 57.895 8.46 0.0 0.00 2.69
1151 1181 1.187567 GGCATGCTTCCACAGGGTTT 61.188 55.000 18.92 0.0 34.93 3.27
1246 1276 2.827190 CAGCACATCCCAGCGCAT 60.827 61.111 11.47 0.0 35.48 4.73
1533 1573 3.883744 CTTCCAAGACCGCCGCTGT 62.884 63.158 0.00 0.0 0.00 4.40
1880 1926 1.982395 CTGCACGTCCACCCTAGGA 60.982 63.158 11.48 0.0 34.64 2.94
1926 1975 2.264480 CGGCCTGTCGACCATTGA 59.736 61.111 14.12 0.0 0.00 2.57
1987 2036 2.588877 GGCCCATGTCGATGACGG 60.589 66.667 0.00 0.0 40.21 4.79
2273 2323 3.399046 AATGCGGAGTGTAGCCCA 58.601 55.556 0.00 0.0 0.00 5.36


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

AutoCloner maintained by Alex Coulton.