Multiple sequence alignment - TraesCS5D01G203300

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 TraesCS5D01G203300 chr5D 100.000 3438 0 0 1 3438 308624760 308628197 0.000000e+00 6349.0
1 TraesCS5D01G203300 chr5D 99.576 943 4 0 1 943 217725305 217726247 0.000000e+00 1720.0
2 TraesCS5D01G203300 chr5D 89.538 1147 107 7 1296 2431 308344812 308345956 0.000000e+00 1441.0
3 TraesCS5D01G203300 chr5D 80.936 299 41 9 3016 3304 268878469 268878177 4.470000e-54 222.0
4 TraesCS5D01G203300 chr5A 96.047 2226 40 16 465 2674 389167810 389165617 0.000000e+00 3579.0
5 TraesCS5D01G203300 chr5A 89.208 1149 107 11 1296 2431 389637057 389635913 0.000000e+00 1419.0
6 TraesCS5D01G203300 chr5A 92.683 738 48 5 2707 3438 389165614 389164877 0.000000e+00 1059.0
7 TraesCS5D01G203300 chr5A 97.645 467 11 0 1 467 389168465 389167999 0.000000e+00 802.0
8 TraesCS5D01G203300 chr5A 96.653 478 16 0 1 478 12017267 12016790 0.000000e+00 795.0
9 TraesCS5D01G203300 chr5A 97.253 182 5 0 475 656 12016710 12016529 3.330000e-80 309.0
10 TraesCS5D01G203300 chr5A 87.031 293 9 8 654 942 12016255 12015988 1.550000e-78 303.0
11 TraesCS5D01G203300 chr5B 98.791 1654 12 2 881 2526 353919915 353921568 0.000000e+00 2937.0
12 TraesCS5D01G203300 chr5B 88.811 1144 115 7 1296 2428 353043812 353044953 0.000000e+00 1391.0
13 TraesCS5D01G203300 chr5B 97.241 725 18 2 1 724 353919188 353919911 0.000000e+00 1227.0
14 TraesCS5D01G203300 chr5B 88.943 814 79 7 134 942 507635374 507636181 0.000000e+00 994.0
15 TraesCS5D01G203300 chr5B 94.945 633 27 3 2570 3199 353922095 353922725 0.000000e+00 987.0
16 TraesCS5D01G203300 chr5B 89.425 539 51 5 406 942 81555239 81554705 0.000000e+00 675.0
17 TraesCS5D01G203300 chr5B 93.750 192 10 2 3248 3438 353922727 353922917 1.560000e-73 287.0
18 TraesCS5D01G203300 chr2B 97.931 725 13 2 1 724 629976480 629975757 0.000000e+00 1254.0
19 TraesCS5D01G203300 chr2B 84.910 444 34 8 1 415 780783398 780783837 5.310000e-113 418.0
20 TraesCS5D01G203300 chr2B 88.024 167 17 3 2686 2849 714466836 714466670 9.740000e-46 195.0
21 TraesCS5D01G203300 chr2B 96.429 56 2 0 890 945 629975746 629975691 3.650000e-15 93.5
22 TraesCS5D01G203300 chr6B 94.016 752 18 5 1 751 50069405 50068680 0.000000e+00 1114.0
23 TraesCS5D01G203300 chr6B 97.059 170 5 0 773 942 50068687 50068518 1.560000e-73 287.0
24 TraesCS5D01G203300 chr3A 86.495 970 93 13 1 942 712496495 712495536 0.000000e+00 1031.0
25 TraesCS5D01G203300 chr3A 84.406 699 85 13 2686 3372 632612474 632611788 0.000000e+00 665.0
26 TraesCS5D01G203300 chr3A 83.656 465 39 12 1 440 744570981 744571433 1.490000e-108 403.0
27 TraesCS5D01G203300 chr3A 89.474 95 10 0 2765 2859 739123049 739123143 1.680000e-23 121.0
28 TraesCS5D01G203300 chr3A 83.636 110 17 1 2757 2866 154028660 154028552 6.070000e-18 102.0
29 TraesCS5D01G203300 chr7B 85.109 826 99 14 2613 3419 162991247 162990427 0.000000e+00 822.0
30 TraesCS5D01G203300 chr3D 85.518 801 91 15 2642 3419 489529365 489528567 0.000000e+00 813.0
31 TraesCS5D01G203300 chr2A 83.521 801 101 20 2645 3419 129106822 129106027 0.000000e+00 719.0
32 TraesCS5D01G203300 chr1A 90.293 443 41 2 2612 3053 512857865 512858306 2.300000e-161 579.0
33 TraesCS5D01G203300 chr4A 82.222 540 81 10 2888 3416 298708172 298708707 5.230000e-123 451.0
34 TraesCS5D01G203300 chr4B 83.763 388 50 10 2990 3368 671680454 671680837 4.220000e-94 355.0
35 TraesCS5D01G203300 chr7D 81.429 140 17 2 2624 2755 121948732 121948594 4.690000e-19 106.0
36 TraesCS5D01G203300 chr7A 80.882 136 20 5 2620 2752 708353962 708354094 6.070000e-18 102.0


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 TraesCS5D01G203300 chr5D 308624760 308628197 3437 False 6349.000000 6349 100.000000 1 3438 1 chr5D.!!$F3 3437
1 TraesCS5D01G203300 chr5D 217725305 217726247 942 False 1720.000000 1720 99.576000 1 943 1 chr5D.!!$F1 942
2 TraesCS5D01G203300 chr5D 308344812 308345956 1144 False 1441.000000 1441 89.538000 1296 2431 1 chr5D.!!$F2 1135
3 TraesCS5D01G203300 chr5A 389164877 389168465 3588 True 1813.333333 3579 95.458333 1 3438 3 chr5A.!!$R3 3437
4 TraesCS5D01G203300 chr5A 389635913 389637057 1144 True 1419.000000 1419 89.208000 1296 2431 1 chr5A.!!$R1 1135
5 TraesCS5D01G203300 chr5A 12015988 12017267 1279 True 469.000000 795 93.645667 1 942 3 chr5A.!!$R2 941
6 TraesCS5D01G203300 chr5B 353043812 353044953 1141 False 1391.000000 1391 88.811000 1296 2428 1 chr5B.!!$F1 1132
7 TraesCS5D01G203300 chr5B 353919188 353922917 3729 False 1359.500000 2937 96.181750 1 3438 4 chr5B.!!$F3 3437
8 TraesCS5D01G203300 chr5B 507635374 507636181 807 False 994.000000 994 88.943000 134 942 1 chr5B.!!$F2 808
9 TraesCS5D01G203300 chr5B 81554705 81555239 534 True 675.000000 675 89.425000 406 942 1 chr5B.!!$R1 536
10 TraesCS5D01G203300 chr2B 629975691 629976480 789 True 673.750000 1254 97.180000 1 945 2 chr2B.!!$R2 944
11 TraesCS5D01G203300 chr6B 50068518 50069405 887 True 700.500000 1114 95.537500 1 942 2 chr6B.!!$R1 941
12 TraesCS5D01G203300 chr3A 712495536 712496495 959 True 1031.000000 1031 86.495000 1 942 1 chr3A.!!$R3 941
13 TraesCS5D01G203300 chr3A 632611788 632612474 686 True 665.000000 665 84.406000 2686 3372 1 chr3A.!!$R2 686
14 TraesCS5D01G203300 chr7B 162990427 162991247 820 True 822.000000 822 85.109000 2613 3419 1 chr7B.!!$R1 806
15 TraesCS5D01G203300 chr3D 489528567 489529365 798 True 813.000000 813 85.518000 2642 3419 1 chr3D.!!$R1 777
16 TraesCS5D01G203300 chr2A 129106027 129106822 795 True 719.000000 719 83.521000 2645 3419 1 chr2A.!!$R1 774
17 TraesCS5D01G203300 chr4A 298708172 298708707 535 False 451.000000 451 82.222000 2888 3416 1 chr4A.!!$F1 528

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
1082 1675 4.292178 CGCCATCCTCCCTCTCGC 62.292 72.222 0.00 0.0 0.00 5.03 F
1293 1893 1.001641 GGCAGCAGGTGGTGAAGAT 60.002 57.895 13.25 0.0 45.66 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2635 0.109689 GCGAGAACGTAGTCAGCACT 60.110 55.0 0.00 0.0 45.0 4.40 R
2629 3746 0.179040 TTTCTCTTTGTCCGCCGGTT 60.179 50.0 1.63 0.0 0.0 4.44 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
1082 1675 4.292178 CGCCATCCTCCCTCTCGC 62.292 72.222 0.00 0.0 0.00 5.03
1293 1893 1.001641 GGCAGCAGGTGGTGAAGAT 60.002 57.895 13.25 0.0 45.66 2.40
2490 3104 7.050970 TGTGCGACTATCACTCCTATATTTT 57.949 36.000 0.00 0.0 35.58 1.82
2606 3723 9.844257 AATTTTGAAGGATTGTAATGTTTTCCA 57.156 25.926 0.00 0.0 0.00 3.53
2923 4053 2.686470 CCTCCTCTGCCTCAGCCA 60.686 66.667 0.00 0.0 38.69 4.75
2924 4054 2.071262 CCTCCTCTGCCTCAGCCAT 61.071 63.158 0.00 0.0 38.69 4.40
3007 4140 3.933332 GGTATTTTCTGCAACTAGAGCGT 59.067 43.478 0.00 0.0 33.85 5.07
3015 4148 4.812091 TCTGCAACTAGAGCGTTGTTTTTA 59.188 37.500 0.00 0.0 44.61 1.52
3202 4347 1.408969 TTTGAAACAAGACCCCTGCC 58.591 50.000 0.00 0.0 0.00 4.85
3422 4571 4.378459 GCTGAAAGGTAGTGTTTTCCGATG 60.378 45.833 0.00 0.0 33.43 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1082 1675 1.133294 GGGAGAGGTAGAAGAGGAGGG 60.133 61.905 0.00 0.0 0.00 4.30
2026 2635 0.109689 GCGAGAACGTAGTCAGCACT 60.110 55.000 0.00 0.0 45.00 4.40
2490 3104 9.913310 AAAAATTATTTTCCTTTCCTTGGTTCA 57.087 25.926 3.23 0.0 33.48 3.18
2606 3723 3.131478 GTAGCGCGGCCCACAATT 61.131 61.111 8.83 0.0 0.00 2.32
2629 3746 0.179040 TTTCTCTTTGTCCGCCGGTT 60.179 50.000 1.63 0.0 0.00 4.44
2763 3891 1.689273 GACTGGCTGGGACGATAGATT 59.311 52.381 0.00 0.0 41.38 2.40
3007 4140 5.411781 ACGTGAGGCATGTTTTAAAAACAA 58.588 33.333 1.31 0.0 33.42 2.83
3015 4148 0.743688 TGCAACGTGAGGCATGTTTT 59.256 45.000 5.79 0.0 40.99 2.43
3306 4453 2.567169 CCACAAGTCAGTCCTACATCCA 59.433 50.000 0.00 0.0 0.00 3.41
3307 4454 2.678190 GCCACAAGTCAGTCCTACATCC 60.678 54.545 0.00 0.0 0.00 3.51
3308 4455 2.622436 GCCACAAGTCAGTCCTACATC 58.378 52.381 0.00 0.0 0.00 3.06
3310 4457 0.685097 GGCCACAAGTCAGTCCTACA 59.315 55.000 0.00 0.0 0.00 2.74
3311 4458 0.685097 TGGCCACAAGTCAGTCCTAC 59.315 55.000 0.00 0.0 0.00 3.18


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

AutoCloner maintained by Alex Coulton.