Multiple sequence alignment - TraesCS5D01G412100

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 TraesCS5D01G412100 chr5D 100.000 4986 0 0 1 4986 475498786 475503771 0.000000e+00 9208.0
1 TraesCS5D01G412100 chr5B 91.326 2006 80 35 3016 4984 582834719 582836667 0.000000e+00 2654.0
2 TraesCS5D01G412100 chr5B 91.188 1725 67 28 846 2488 582832484 582834205 0.000000e+00 2265.0
3 TraesCS5D01G412100 chr5B 92.778 540 35 4 2482 3019 582834154 582834691 0.000000e+00 778.0
4 TraesCS5D01G412100 chr5A 91.065 1925 81 38 641 2483 594952785 594954700 0.000000e+00 2518.0
5 TraesCS5D01G412100 chr5A 88.533 1779 112 34 2576 4308 594954721 594956453 0.000000e+00 2071.0
6 TraesCS5D01G412100 chr5A 89.286 728 55 17 1 719 594952066 594952779 0.000000e+00 891.0
7 TraesCS5D01G412100 chr5A 89.588 461 33 9 4460 4912 594956731 594957184 5.600000e-159 571.0
8 TraesCS5D01G412100 chr5A 89.474 171 14 2 4297 4467 594956473 594956639 3.910000e-51 213.0
9 TraesCS5D01G412100 chr5A 84.564 149 15 5 2654 2799 594979436 594979579 1.870000e-29 141.0
10 TraesCS5D01G412100 chr5A 76.382 199 38 7 2138 2332 594978178 594978371 1.140000e-16 99.0
11 TraesCS5D01G412100 chr5A 88.158 76 9 0 4911 4986 594957290 594957365 1.910000e-14 91.6
12 TraesCS5D01G412100 chr1D 88.682 1184 96 23 3016 4171 409538005 409539178 0.000000e+00 1410.0
13 TraesCS5D01G412100 chr1D 80.278 1440 178 56 1635 3013 409536569 409537963 0.000000e+00 989.0
14 TraesCS5D01G412100 chr1D 88.401 569 47 10 972 1529 409535913 409536473 0.000000e+00 667.0
15 TraesCS5D01G412100 chr1B 87.638 1181 106 25 3017 4171 551723674 551724840 0.000000e+00 1336.0
16 TraesCS5D01G412100 chr1B 80.556 1440 174 64 1636 3015 551722248 551723641 0.000000e+00 1011.0
17 TraesCS5D01G412100 chr1B 86.092 568 58 5 972 1529 551721600 551722156 4.300000e-165 592.0
18 TraesCS5D01G412100 chr1A 91.162 792 50 9 3017 3788 505539797 505540588 0.000000e+00 1057.0
19 TraesCS5D01G412100 chr1A 82.008 1245 146 44 1809 3019 505538568 505539768 0.000000e+00 987.0
20 TraesCS5D01G412100 chr1A 87.698 569 51 5 972 1529 505537728 505538288 0.000000e+00 645.0
21 TraesCS5D01G412100 chr1A 88.197 305 33 2 3824 4127 505540881 505541183 1.320000e-95 361.0
22 TraesCS5D01G412100 chr7B 82.051 78 10 4 490 566 741399695 741399769 4.170000e-06 63.9
23 TraesCS5D01G412100 chr7B 100.000 30 0 0 469 498 21713664 21713693 6.970000e-04 56.5
24 TraesCS5D01G412100 chr2D 86.441 59 5 3 514 571 512138602 512138658 1.500000e-05 62.1
25 TraesCS5D01G412100 chr3D 85.965 57 6 2 512 566 76915130 76915186 5.390000e-05 60.2
26 TraesCS5D01G412100 chr2A 88.235 51 4 2 524 574 655421261 655421309 5.390000e-05 60.2
27 TraesCS5D01G412100 chr2A 100.000 28 0 0 538 565 144269507 144269480 9.000000e-03 52.8
28 TraesCS5D01G412100 chr6B 100.000 29 0 0 470 498 720527741 720527769 3.000000e-03 54.7


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 TraesCS5D01G412100 chr5D 475498786 475503771 4985 False 9208.000000 9208 100.000000 1 4986 1 chr5D.!!$F1 4985
1 TraesCS5D01G412100 chr5B 582832484 582836667 4183 False 1899.000000 2654 91.764000 846 4984 3 chr5B.!!$F1 4138
2 TraesCS5D01G412100 chr5A 594952066 594957365 5299 False 1059.266667 2518 89.350667 1 4986 6 chr5A.!!$F1 4985
3 TraesCS5D01G412100 chr1D 409535913 409539178 3265 False 1022.000000 1410 85.787000 972 4171 3 chr1D.!!$F1 3199
4 TraesCS5D01G412100 chr1B 551721600 551724840 3240 False 979.666667 1336 84.762000 972 4171 3 chr1B.!!$F1 3199
5 TraesCS5D01G412100 chr1A 505537728 505541183 3455 False 762.500000 1057 87.266250 972 4127 4 chr1A.!!$F1 3155


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
137 138 0.255033 CCTACTTAAGGTGCCACCCC 59.745 60.000 11.06 0.00 39.75 4.95 F
141 142 0.323451 CTTAAGGTGCCACCCCCTTC 60.323 60.000 11.06 0.00 41.30 3.46 F
897 995 0.394216 CGAGGCCCATTCCACATTCA 60.394 55.000 0.00 0.00 0.00 2.57 F
1106 1218 1.409427 CGAGAAGCAGGTAACCCTAGG 59.591 57.143 0.06 0.06 39.89 3.02 F
1619 1738 2.362717 CCCGTAGAAAAGCCCACAAAAA 59.637 45.455 0.00 0.00 0.00 1.94 F
2629 2876 0.387112 CCGCGAAATGCATGTTGTGT 60.387 50.000 8.23 0.00 46.97 3.72 F
3030 3329 1.078778 ATCGCAATGTACACGGGCA 60.079 52.632 13.58 3.96 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1701 0.680280 TACGGGACAGTCAGAGCTCC 60.680 60.000 10.93 0.0 0.00 4.70 R
1973 2161 3.055891 GGATCTTTGGGTTGGATGGTTTG 60.056 47.826 0.00 0.0 0.00 2.93 R
2462 2668 0.040058 TCTGTGGGCAGGCATGATTT 59.960 50.000 0.62 0.0 42.78 2.17 R
2470 2676 0.256752 TGAATCCATCTGTGGGCAGG 59.743 55.000 0.00 0.0 46.06 4.85 R
3012 3271 0.463654 ATGCCCGTGTACATTGCGAT 60.464 50.000 0.00 0.0 0.00 4.58 R
3646 3970 0.400213 AGGAAGATCGGGCAAACACA 59.600 50.000 0.00 0.0 0.00 3.72 R
4918 5768 0.321387 AGCACACTGGAGATGCACTG 60.321 55.000 0.00 0.0 41.97 3.66 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)



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

AutoCloner maintained by Alex Coulton.