Multiple sequence alignment - TraesCS2D01G458000

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 TraesCS2D01G458000 chr2D 100.000 6429 0 0 1 6429 565178320 565171892 0.000000e+00 11873.0
1 TraesCS2D01G458000 chr2D 80.451 133 25 1 415 546 469887926 469887794 4.100000e-17 100.0
2 TraesCS2D01G458000 chr6D 98.263 1324 22 1 2161 3483 18703699 18705022 0.000000e+00 2316.0
3 TraesCS2D01G458000 chr6D 90.854 831 68 6 5600 6429 408146915 408146092 0.000000e+00 1107.0
4 TraesCS2D01G458000 chr6D 95.588 272 7 1 3462 3733 18708184 18708450 1.280000e-116 431.0
5 TraesCS2D01G458000 chr6D 82.437 279 41 6 3879 4157 381360656 381360926 3.000000e-58 237.0
6 TraesCS2D01G458000 chr2B 93.546 1131 61 8 4414 5540 677200815 677199693 0.000000e+00 1674.0
7 TraesCS2D01G458000 chr2B 88.635 1355 90 32 3 1325 677208973 677207651 0.000000e+00 1591.0
8 TraesCS2D01G458000 chr2B 90.892 1054 52 15 974 2019 677049290 677048273 0.000000e+00 1375.0
9 TraesCS2D01G458000 chr2B 92.693 698 34 4 3733 4413 677047553 677046856 0.000000e+00 990.0
10 TraesCS2D01G458000 chr2B 90.846 721 26 13 1313 2019 677207492 677206798 0.000000e+00 929.0
11 TraesCS2D01G458000 chr2B 90.883 691 35 5 3735 4413 677204636 677203962 0.000000e+00 902.0
12 TraesCS2D01G458000 chr2B 88.368 533 31 10 5061 5578 677046076 677045560 4.260000e-171 612.0
13 TraesCS2D01G458000 chr2B 81.503 346 35 12 4450 4787 677046397 677046073 2.300000e-64 257.0
14 TraesCS2D01G458000 chr2B 97.727 132 3 0 2018 2149 677204771 677204640 1.800000e-55 228.0
15 TraesCS2D01G458000 chr2B 97.143 105 3 0 2018 2122 677047695 677047591 1.840000e-40 178.0
16 TraesCS2D01G458000 chr2B 94.231 52 3 0 5527 5578 677199676 677199625 5.340000e-11 80.5
17 TraesCS2D01G458000 chr2B 100.000 36 0 0 2114 2149 677047587 677047552 4.160000e-07 67.6
18 TraesCS2D01G458000 chr2A 90.828 1014 57 11 4481 5486 705769116 705768131 0.000000e+00 1325.0
19 TraesCS2D01G458000 chr2A 91.063 828 72 2 5604 6429 733579302 733578475 0.000000e+00 1118.0
20 TraesCS2D01G458000 chr2A 94.255 557 22 2 3733 4279 705769671 705769115 0.000000e+00 843.0
21 TraesCS2D01G458000 chr2A 88.468 633 36 13 88 686 705778984 705778355 0.000000e+00 730.0
22 TraesCS2D01G458000 chr2A 91.182 499 17 7 1521 2019 705771130 705770659 0.000000e+00 652.0
23 TraesCS2D01G458000 chr2A 92.621 393 17 7 974 1366 705776970 705776590 7.280000e-154 555.0
24 TraesCS2D01G458000 chr2A 86.914 405 38 7 974 1366 705771538 705771137 2.130000e-119 440.0
25 TraesCS2D01G458000 chr2A 76.367 622 94 32 2464 3036 755778114 755778731 1.050000e-72 285.0
26 TraesCS2D01G458000 chr2A 97.727 132 3 0 2018 2149 705769801 705769670 1.800000e-55 228.0
27 TraesCS2D01G458000 chr2A 77.778 135 26 4 415 546 589500201 589500068 5.340000e-11 80.5
28 TraesCS2D01G458000 chr7D 91.336 831 60 4 5605 6429 207552114 207551290 0.000000e+00 1125.0
29 TraesCS2D01G458000 chr7D 91.029 836 70 4 5597 6429 564199800 564200633 0.000000e+00 1123.0
30 TraesCS2D01G458000 chr5D 91.262 824 71 1 5605 6428 430971327 430970505 0.000000e+00 1122.0
31 TraesCS2D01G458000 chr5D 90.678 826 74 3 5605 6429 411744422 411745245 0.000000e+00 1096.0
32 TraesCS2D01G458000 chr5D 79.938 324 46 13 415 735 409440487 409440180 3.020000e-53 220.0
33 TraesCS2D01G458000 chr3D 91.041 826 71 3 5605 6429 562356464 562357287 0.000000e+00 1112.0
34 TraesCS2D01G458000 chr3D 91.041 826 71 3 5605 6429 562438058 562438881 0.000000e+00 1112.0
35 TraesCS2D01G458000 chr3D 90.700 828 76 1 5603 6429 607413212 607412385 0.000000e+00 1101.0
36 TraesCS2D01G458000 chr3D 82.243 107 19 0 2148 2254 597456930 597456824 6.860000e-15 93.5
37 TraesCS2D01G458000 chr3B 83.841 953 87 29 34 932 171820525 171819586 0.000000e+00 845.0
38 TraesCS2D01G458000 chr3B 80.925 692 64 23 3 661 22589912 22590568 9.690000e-133 484.0
39 TraesCS2D01G458000 chr3B 96.875 32 1 0 215 246 823859215 823859184 3.000000e-03 54.7
40 TraesCS2D01G458000 chr3B 96.970 33 0 1 215 247 825520669 825520638 3.000000e-03 54.7
41 TraesCS2D01G458000 chr7B 83.295 868 105 23 3 851 670101961 670102807 0.000000e+00 763.0
42 TraesCS2D01G458000 chr7B 84.137 788 83 19 186 935 158540119 158539336 0.000000e+00 725.0
43 TraesCS2D01G458000 chr7B 80.779 822 86 37 2259 3014 568967663 568966848 1.550000e-160 577.0
44 TraesCS2D01G458000 chr7B 80.559 823 87 38 2259 3014 568964317 568963501 3.360000e-157 566.0
45 TraesCS2D01G458000 chr7B 85.782 211 23 5 3 208 158540267 158540059 3.900000e-52 217.0
46 TraesCS2D01G458000 chr7B 75.632 435 67 17 2406 2838 655572766 655573163 5.120000e-41 180.0
47 TraesCS2D01G458000 chr7B 84.713 157 16 6 2259 2408 658745483 658745638 4.020000e-32 150.0
48 TraesCS2D01G458000 chr7B 83.439 157 18 6 2259 2408 658878012 658878167 8.690000e-29 139.0
49 TraesCS2D01G458000 chr3A 84.539 802 70 23 3 758 20782489 20781696 0.000000e+00 745.0
50 TraesCS2D01G458000 chr3A 80.874 183 12 9 769 933 20780724 20780547 8.750000e-24 122.0
51 TraesCS2D01G458000 chr6B 80.947 824 86 31 2259 3014 522507367 522506547 2.580000e-163 586.0
52 TraesCS2D01G458000 chr6B 82.339 436 62 6 2412 2838 408409250 408408821 1.320000e-96 364.0
53 TraesCS2D01G458000 chr6B 91.139 158 11 2 3499 3653 522431221 522431064 1.820000e-50 211.0
54 TraesCS2D01G458000 chr6B 80.488 287 45 8 3879 4163 569885951 569885674 6.530000e-50 209.0
55 TraesCS2D01G458000 chr6B 72.371 970 160 63 4 924 663656094 663657004 2.350000e-49 207.0
56 TraesCS2D01G458000 chr7A 83.372 427 45 11 2654 3058 664515013 664514591 7.870000e-99 372.0
57 TraesCS2D01G458000 chr7A 91.566 83 7 0 3650 3732 664514161 664514079 1.460000e-21 115.0
58 TraesCS2D01G458000 chr7A 91.549 71 6 0 3650 3720 518589209 518589139 1.480000e-16 99.0
59 TraesCS2D01G458000 chr5B 74.453 685 102 30 183 824 523410529 523411183 1.800000e-55 228.0
60 TraesCS2D01G458000 chr5B 90.141 71 7 0 3650 3720 461875376 461875446 6.860000e-15 93.5
61 TraesCS2D01G458000 chrUn 84.713 157 16 6 2259 2408 354102775 354102620 4.020000e-32 150.0
62 TraesCS2D01G458000 chrUn 84.713 157 16 6 2259 2408 367767596 367767751 4.020000e-32 150.0
63 TraesCS2D01G458000 chrUn 84.713 157 16 6 2259 2408 424755796 424755641 4.020000e-32 150.0
64 TraesCS2D01G458000 chrUn 84.713 157 16 6 2259 2408 467081292 467081137 4.020000e-32 150.0
65 TraesCS2D01G458000 chrUn 83.439 157 18 6 2259 2408 336506177 336506022 8.690000e-29 139.0
66 TraesCS2D01G458000 chrUn 83.439 157 18 6 2259 2408 366298491 366298646 8.690000e-29 139.0
67 TraesCS2D01G458000 chr5A 89.130 92 10 0 2161 2252 330730506 330730597 1.460000e-21 115.0
68 TraesCS2D01G458000 chr5A 88.095 84 10 0 3650 3733 32942793 32942876 4.100000e-17 100.0
69 TraesCS2D01G458000 chr5A 91.549 71 6 0 3650 3720 577801119 577801189 1.480000e-16 99.0
70 TraesCS2D01G458000 chr5A 83.333 84 14 0 3650 3733 647586721 647586638 1.920000e-10 78.7


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 TraesCS2D01G458000 chr2D 565171892 565178320 6428 True 11873.000000 11873 100.000000 1 6429 1 chr2D.!!$R2 6428
1 TraesCS2D01G458000 chr6D 18703699 18708450 4751 False 1373.500000 2316 96.925500 2161 3733 2 chr6D.!!$F2 1572
2 TraesCS2D01G458000 chr6D 408146092 408146915 823 True 1107.000000 1107 90.854000 5600 6429 1 chr6D.!!$R1 829
3 TraesCS2D01G458000 chr2B 677199625 677208973 9348 True 900.750000 1674 92.644667 3 5578 6 chr2B.!!$R2 5575
4 TraesCS2D01G458000 chr2B 677045560 677049290 3730 True 579.933333 1375 91.766500 974 5578 6 chr2B.!!$R1 4604
5 TraesCS2D01G458000 chr2A 733578475 733579302 827 True 1118.000000 1118 91.063000 5604 6429 1 chr2A.!!$R2 825
6 TraesCS2D01G458000 chr2A 705768131 705771538 3407 True 697.600000 1325 92.181200 974 5486 5 chr2A.!!$R3 4512
7 TraesCS2D01G458000 chr2A 705776590 705778984 2394 True 642.500000 730 90.544500 88 1366 2 chr2A.!!$R4 1278
8 TraesCS2D01G458000 chr2A 755778114 755778731 617 False 285.000000 285 76.367000 2464 3036 1 chr2A.!!$F1 572
9 TraesCS2D01G458000 chr7D 207551290 207552114 824 True 1125.000000 1125 91.336000 5605 6429 1 chr7D.!!$R1 824
10 TraesCS2D01G458000 chr7D 564199800 564200633 833 False 1123.000000 1123 91.029000 5597 6429 1 chr7D.!!$F1 832
11 TraesCS2D01G458000 chr5D 430970505 430971327 822 True 1122.000000 1122 91.262000 5605 6428 1 chr5D.!!$R2 823
12 TraesCS2D01G458000 chr5D 411744422 411745245 823 False 1096.000000 1096 90.678000 5605 6429 1 chr5D.!!$F1 824
13 TraesCS2D01G458000 chr3D 562356464 562357287 823 False 1112.000000 1112 91.041000 5605 6429 1 chr3D.!!$F1 824
14 TraesCS2D01G458000 chr3D 562438058 562438881 823 False 1112.000000 1112 91.041000 5605 6429 1 chr3D.!!$F2 824
15 TraesCS2D01G458000 chr3D 607412385 607413212 827 True 1101.000000 1101 90.700000 5603 6429 1 chr3D.!!$R2 826
16 TraesCS2D01G458000 chr3B 171819586 171820525 939 True 845.000000 845 83.841000 34 932 1 chr3B.!!$R1 898
17 TraesCS2D01G458000 chr3B 22589912 22590568 656 False 484.000000 484 80.925000 3 661 1 chr3B.!!$F1 658
18 TraesCS2D01G458000 chr7B 670101961 670102807 846 False 763.000000 763 83.295000 3 851 1 chr7B.!!$F4 848
19 TraesCS2D01G458000 chr7B 568963501 568967663 4162 True 571.500000 577 80.669000 2259 3014 2 chr7B.!!$R2 755
20 TraesCS2D01G458000 chr7B 158539336 158540267 931 True 471.000000 725 84.959500 3 935 2 chr7B.!!$R1 932
21 TraesCS2D01G458000 chr3A 20780547 20782489 1942 True 433.500000 745 82.706500 3 933 2 chr3A.!!$R1 930
22 TraesCS2D01G458000 chr6B 522506547 522507367 820 True 586.000000 586 80.947000 2259 3014 1 chr6B.!!$R3 755
23 TraesCS2D01G458000 chr6B 663656094 663657004 910 False 207.000000 207 72.371000 4 924 1 chr6B.!!$F1 920
24 TraesCS2D01G458000 chr7A 664514079 664515013 934 True 243.500000 372 87.469000 2654 3732 2 chr7A.!!$R2 1078
25 TraesCS2D01G458000 chr5B 523410529 523411183 654 False 228.000000 228 74.453000 183 824 1 chr5B.!!$F2 641

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
778 1922 1.067142 TGCTAACAAGGTCGTGGCTAG 60.067 52.381 0.00 0.00 0.00 3.42 F
1261 3375 0.110328 ACAACGAGTACAGAGACGCG 60.110 55.000 3.53 3.53 46.42 6.01 F
2154 6788 0.102120 CTTCACTAGCCTGAGAGCGG 59.898 60.000 0.00 0.00 38.01 5.52 F
3059 7793 0.175302 CTGAATCTCTGTCGCCTGCT 59.825 55.000 0.00 0.00 0.00 4.24 F
3562 12381 0.036164 TGCCTCAGTGCAACGGTAAT 59.964 50.000 0.00 0.00 45.86 1.89 F
5068 18044 0.172578 TCTGGTGCTGTACGAATCGG 59.827 55.000 7.80 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 4254 0.034863 GTACCCGGAAGCAATGGGAA 60.035 55.000 0.73 0.0 46.41 3.97 R
2943 7677 1.207085 GCAACTCGAGACGACGACT 59.793 57.895 21.68 0.0 37.37 4.18 R
3562 12381 0.744874 CAGGGCGAGAGGACGAAATA 59.255 55.000 0.00 0.0 35.09 1.40 R
4784 17755 0.901827 TTCGCCCTCATGCTTACTCA 59.098 50.000 0.00 0.0 0.00 3.41 R
5145 18121 1.027357 CAGCACAATACCCTGGCATC 58.973 55.000 0.00 0.0 0.00 3.91 R
6301 19347 0.318120 CGAAGCAAAAAGGCCCACAT 59.682 50.000 0.00 0.0 0.00 3.21 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.