Multiple sequence alignment - TraesCS5B01G472100

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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 TraesCS5B01G472100 chr5B 100.000 2812 0 0 818 3629 645558004 645555193 0.000000e+00 5193
1 TraesCS5B01G472100 chr5B 95.177 1949 46 15 820 2728 646375665 646377605 0.000000e+00 3035
2 TraesCS5B01G472100 chr5B 87.976 1314 143 13 1120 2430 646229733 646231034 0.000000e+00 1537
3 TraesCS5B01G472100 chr5B 100.000 624 0 0 1 624 645558821 645558198 0.000000e+00 1153
4 TraesCS5B01G472100 chr5B 83.736 1199 192 3 1262 2458 645993188 645991991 0.000000e+00 1131
5 TraesCS5B01G472100 chr5B 83.927 927 146 3 1533 2458 645981257 645980333 0.000000e+00 883
6 TraesCS5B01G472100 chr5B 95.768 449 18 1 1 449 61083075 61082628 0.000000e+00 723
7 TraesCS5B01G472100 chr5B 98.294 293 4 1 2969 3261 646378062 646378353 2.500000e-141 512
8 TraesCS5B01G472100 chr5B 84.916 358 41 8 34 387 616965928 616966276 2.070000e-92 350
9 TraesCS5B01G472100 chr5B 96.094 128 4 1 450 577 646375577 646375703 1.320000e-49 207
10 TraesCS5B01G472100 chr5B 96.330 109 4 0 2714 2822 646377957 646378065 2.880000e-41 180
11 TraesCS5B01G472100 chr5B 93.478 92 6 0 359 450 616966275 616966366 1.760000e-28 137
12 TraesCS5B01G472100 chr5B 97.436 78 2 0 3552 3629 646378363 646378440 2.270000e-27 134
13 TraesCS5B01G472100 chr5B 94.737 76 2 1 537 610 645558004 645557929 2.290000e-22 117
14 TraesCS5B01G472100 chr5B 94.737 76 2 1 818 893 645558285 645558212 2.290000e-22 117
15 TraesCS5B01G472100 chr5B 85.047 107 5 3 900 995 646229540 646229646 8.290000e-17 99
16 TraesCS5B01G472100 chr5D 93.393 1801 92 9 1040 2816 514423999 514425796 0.000000e+00 2641
17 TraesCS5B01G472100 chr5D 86.379 1439 164 19 1036 2466 514413041 514411627 0.000000e+00 1543
18 TraesCS5B01G472100 chr5D 84.365 1196 183 4 1262 2455 514294622 514295815 0.000000e+00 1170
19 TraesCS5B01G472100 chr5D 96.375 662 23 1 2969 3629 514425799 514426460 0.000000e+00 1088
20 TraesCS5B01G472100 chr5D 85.890 978 137 1 1268 2245 514515220 514516196 0.000000e+00 1040
21 TraesCS5B01G472100 chr5D 95.683 139 5 1 2835 2973 521027268 521027131 4.720000e-54 222
22 TraesCS5B01G472100 chr5A 83.866 1190 187 5 1262 2448 642502735 642503922 0.000000e+00 1129
23 TraesCS5B01G472100 chr3B 88.117 446 20 13 34 451 700780628 700781068 1.950000e-137 499
24 TraesCS5B01G472100 chr2B 88.345 429 26 11 34 442 73297248 73296824 9.050000e-136 494
25 TraesCS5B01G472100 chr2B 94.175 309 16 2 34 342 484109947 484109641 1.530000e-128 470
26 TraesCS5B01G472100 chr2B 91.241 137 8 3 309 442 73296501 73296366 2.230000e-42 183
27 TraesCS5B01G472100 chr6D 80.529 416 51 19 17 425 61010302 61010694 3.540000e-75 292
28 TraesCS5B01G472100 chr7D 94.406 143 7 1 2832 2974 597300831 597300972 6.100000e-53 219
29 TraesCS5B01G472100 chr7D 93.750 144 8 1 2832 2975 39001312 39001454 7.890000e-52 215
30 TraesCS5B01G472100 chr4D 94.406 143 7 1 2832 2974 75782080 75782221 6.100000e-53 219
31 TraesCS5B01G472100 chr4D 92.667 150 8 3 2821 2970 476310383 476310237 2.840000e-51 213
32 TraesCS5B01G472100 chr1D 94.406 143 7 1 2832 2974 178466333 178466474 6.100000e-53 219
33 TraesCS5B01G472100 chr6B 93.793 145 8 1 2832 2976 211161506 211161649 2.190000e-52 217
34 TraesCS5B01G472100 chr6A 92.105 152 10 2 2832 2982 338087423 338087273 2.840000e-51 213
35 TraesCS5B01G472100 chr1A 92.053 151 9 3 2821 2970 537089624 537089772 3.670000e-50 209
36 TraesCS5B01G472100 chr3D 86.885 183 20 3 265 444 61934058 61933877 6.140000e-48 202


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 TraesCS5B01G472100 chr5B 645555193 645558821 3628 True 1645.0 5193 97.3685 1 3629 4 chr5B.!!$R4 3628
1 TraesCS5B01G472100 chr5B 645991991 645993188 1197 True 1131.0 1131 83.7360 1262 2458 1 chr5B.!!$R3 1196
2 TraesCS5B01G472100 chr5B 645980333 645981257 924 True 883.0 883 83.9270 1533 2458 1 chr5B.!!$R2 925
3 TraesCS5B01G472100 chr5B 646229540 646231034 1494 False 818.0 1537 86.5115 900 2430 2 chr5B.!!$F2 1530
4 TraesCS5B01G472100 chr5B 646375577 646378440 2863 False 813.6 3035 96.6662 450 3629 5 chr5B.!!$F3 3179
5 TraesCS5B01G472100 chr5D 514423999 514426460 2461 False 1864.5 2641 94.8840 1040 3629 2 chr5D.!!$F3 2589
6 TraesCS5B01G472100 chr5D 514411627 514413041 1414 True 1543.0 1543 86.3790 1036 2466 1 chr5D.!!$R1 1430
7 TraesCS5B01G472100 chr5D 514294622 514295815 1193 False 1170.0 1170 84.3650 1262 2455 1 chr5D.!!$F1 1193
8 TraesCS5B01G472100 chr5D 514515220 514516196 976 False 1040.0 1040 85.8900 1268 2245 1 chr5D.!!$F2 977
9 TraesCS5B01G472100 chr5A 642502735 642503922 1187 False 1129.0 1129 83.8660 1262 2448 1 chr5A.!!$F1 1186
10 TraesCS5B01G472100 chr2B 73296366 73297248 882 True 338.5 494 89.7930 34 442 2 chr2B.!!$R2 408


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
257 258 0.031857 CAAAGAAATGTGGTGGCGCA 59.968 50.0 10.83 0.0 0.00 6.09 F
291 292 0.038166 TTGTGAGGATGTTGGAGGGC 59.962 55.0 0.00 0.0 0.00 5.19 F
605 606 0.175760 ATCACGATTCGGTGTCCCTG 59.824 55.0 11.29 0.0 39.00 4.45 F
607 608 0.736325 CACGATTCGGTGTCCCTGTC 60.736 60.0 11.29 0.0 33.24 3.51 F
1266 1336 0.941542 TTTCGCCAAACGTCCTTCTG 59.058 50.0 0.00 0.0 44.19 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 1328 0.389166 CTCGTGACCAGCAGAAGGAC 60.389 60.000 0.00 0.0 0.00 3.85 R
1259 1329 0.539669 TCTCGTGACCAGCAGAAGGA 60.540 55.000 0.00 0.0 0.00 3.36 R
2123 2223 1.066858 TCCTTGTTCAGATCCTCGCAC 60.067 52.381 0.00 0.0 0.00 5.34 R
2332 2433 2.097142 CCTTTTGTAGCTGCTCATGCTC 59.903 50.000 4.91 0.0 41.46 4.26 R
3083 3551 1.133025 GAAATGGTTCACGGAGGCATG 59.867 52.381 0.00 0.0 33.61 4.06 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)



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AutoCloner maintained by Alex Coulton.