Multiple sequence alignment - TraesCS1A01G293600

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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 TraesCS1A01G293600 chr1A 100.000 2843 0 0 1 2843 488775418 488778260 0.000000e+00 5251.0
1 TraesCS1A01G293600 chr1A 87.770 1619 184 9 947 2555 117810616 117809002 0.000000e+00 1881.0
2 TraesCS1A01G293600 chr1A 94.737 38 2 0 2624 2661 488778007 488778044 3.060000e-05 60.2
3 TraesCS1A01G293600 chr1A 94.737 38 2 0 2590 2627 488778041 488778078 3.060000e-05 60.2
4 TraesCS1A01G293600 chr4A 99.157 1898 15 1 138 2035 709879034 709880930 0.000000e+00 3415.0
5 TraesCS1A01G293600 chr4A 87.591 1644 193 6 947 2581 541424175 541425816 0.000000e+00 1895.0
6 TraesCS1A01G293600 chr4A 98.742 159 2 0 22 180 709878877 709879035 1.670000e-72 283.0
7 TraesCS1A01G293600 chr4A 97.368 38 1 0 2590 2627 709881386 709881423 6.570000e-07 65.8
8 TraesCS1A01G293600 chr7A 96.797 1998 63 1 592 2589 707593029 707591033 0.000000e+00 3334.0
9 TraesCS1A01G293600 chr7A 91.982 449 21 3 22 455 707593431 707592983 1.450000e-172 616.0
10 TraesCS1A01G293600 chr7A 87.313 268 24 9 2584 2843 707590875 707590610 5.950000e-77 298.0
11 TraesCS1A01G293600 chr7A 94.737 38 2 0 2624 2661 707590869 707590832 3.060000e-05 60.2
12 TraesCS1A01G293600 chr6A 87.373 2368 254 26 239 2581 435780422 435782769 0.000000e+00 2675.0
13 TraesCS1A01G293600 chr6A 88.660 1799 182 12 792 2581 319174405 319172620 0.000000e+00 2172.0
14 TraesCS1A01G293600 chr6A 88.537 410 47 0 321 730 319174935 319174526 5.470000e-137 497.0
15 TraesCS1A01G293600 chr6A 88.136 413 46 2 318 730 593364251 593364660 3.290000e-134 488.0
16 TraesCS1A01G293600 chr2A 85.337 2612 309 48 22 2579 190206385 190208976 0.000000e+00 2634.0
17 TraesCS1A01G293600 chr2A 88.874 1456 154 3 1133 2581 708667246 708668700 0.000000e+00 1784.0
18 TraesCS1A01G293600 chr2A 90.552 688 52 5 792 1471 93190392 93189710 0.000000e+00 898.0
19 TraesCS1A01G293600 chr2A 80.896 759 89 31 21 730 708641059 708641810 5.350000e-152 547.0
20 TraesCS1A01G293600 chr2A 83.273 550 41 16 21 534 70756319 70756853 2.580000e-125 459.0
21 TraesCS1A01G293600 chr2A 80.806 620 62 35 22 589 93191166 93190552 1.560000e-117 433.0
22 TraesCS1A01G293600 chr3B 86.742 1765 197 21 818 2581 499925260 499926988 0.000000e+00 1929.0
23 TraesCS1A01G293600 chr3B 96.975 595 16 1 22 616 790184286 790183694 0.000000e+00 998.0
24 TraesCS1A01G293600 chr3B 94.417 412 8 1 2432 2843 19988045 19988441 1.120000e-173 619.0
25 TraesCS1A01G293600 chr3B 99.410 339 2 0 688 1026 19987712 19988050 1.450000e-172 616.0
26 TraesCS1A01G293600 chr3B 100.000 35 0 0 2590 2624 19988237 19988271 6.570000e-07 65.8
27 TraesCS1A01G293600 chr4B 87.189 1608 188 10 947 2543 634418191 634416591 0.000000e+00 1812.0
28 TraesCS1A01G293600 chr6B 97.106 864 25 0 22 885 290171314 290172177 0.000000e+00 1458.0
29 TraesCS1A01G293600 chr6B 94.729 645 14 2 2218 2843 290172174 290172817 0.000000e+00 985.0
30 TraesCS1A01G293600 chr6B 100.000 33 0 0 2590 2622 290172613 290172645 8.500000e-06 62.1
31 TraesCS1A01G293600 chr6B 94.737 38 2 0 2624 2661 290172545 290172582 3.060000e-05 60.2
32 TraesCS1A01G293600 chr5B 88.394 1077 92 17 602 1661 595297581 595298641 0.000000e+00 1266.0
33 TraesCS1A01G293600 chr5B 87.931 1102 85 23 25 1109 445762400 445761330 0.000000e+00 1254.0
34 TraesCS1A01G293600 chr5B 95.556 45 2 0 2584 2628 595227302 595227346 3.930000e-09 73.1
35 TraesCS1A01G293600 chr5B 94.595 37 2 0 2625 2661 595227309 595227345 1.100000e-04 58.4
36 TraesCS1A01G293600 chr2B 96.577 672 22 1 22 692 772448669 772449340 0.000000e+00 1112.0
37 TraesCS1A01G293600 chr2B 88.735 506 37 5 818 1317 381501079 381500588 4.050000e-168 601.0
38 TraesCS1A01G293600 chr7B 86.427 501 56 6 239 730 88968654 88969151 3.220000e-149 538.0
39 TraesCS1A01G293600 chr3D 85.859 495 64 5 239 730 14087397 14087888 3.250000e-144 521.0
40 TraesCS1A01G293600 chr3D 84.444 270 29 11 2585 2842 501600306 501600038 1.310000e-63 254.0
41 TraesCS1A01G293600 chr3D 92.982 171 9 2 2676 2843 147502767 147502937 2.190000e-61 246.0
42 TraesCS1A01G293600 chr5A 85.185 270 27 12 2585 2843 508560357 508560624 6.040000e-67 265.0
43 TraesCS1A01G293600 chr5A 84.758 269 30 10 2585 2843 508535469 508535736 2.810000e-65 259.0
44 TraesCS1A01G293600 chr1B 83.704 270 30 12 2586 2843 681861599 681861866 2.830000e-60 243.0
45 TraesCS1A01G293600 chr7D 88.024 167 17 3 22 186 498492495 498492330 8.040000e-46 195.0


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 TraesCS1A01G293600 chr1A 488775418 488778260 2842 False 1790.466667 5251 96.491333 1 2843 3 chr1A.!!$F1 2842
1 TraesCS1A01G293600 chr1A 117809002 117810616 1614 True 1881.000000 1881 87.770000 947 2555 1 chr1A.!!$R1 1608
2 TraesCS1A01G293600 chr4A 541424175 541425816 1641 False 1895.000000 1895 87.591000 947 2581 1 chr4A.!!$F1 1634
3 TraesCS1A01G293600 chr4A 709878877 709881423 2546 False 1254.600000 3415 98.422333 22 2627 3 chr4A.!!$F2 2605
4 TraesCS1A01G293600 chr7A 707590610 707593431 2821 True 1077.050000 3334 92.707250 22 2843 4 chr7A.!!$R1 2821
5 TraesCS1A01G293600 chr6A 435780422 435782769 2347 False 2675.000000 2675 87.373000 239 2581 1 chr6A.!!$F1 2342
6 TraesCS1A01G293600 chr6A 319172620 319174935 2315 True 1334.500000 2172 88.598500 321 2581 2 chr6A.!!$R1 2260
7 TraesCS1A01G293600 chr2A 190206385 190208976 2591 False 2634.000000 2634 85.337000 22 2579 1 chr2A.!!$F2 2557
8 TraesCS1A01G293600 chr2A 708667246 708668700 1454 False 1784.000000 1784 88.874000 1133 2581 1 chr2A.!!$F4 1448
9 TraesCS1A01G293600 chr2A 93189710 93191166 1456 True 665.500000 898 85.679000 22 1471 2 chr2A.!!$R1 1449
10 TraesCS1A01G293600 chr2A 708641059 708641810 751 False 547.000000 547 80.896000 21 730 1 chr2A.!!$F3 709
11 TraesCS1A01G293600 chr2A 70756319 70756853 534 False 459.000000 459 83.273000 21 534 1 chr2A.!!$F1 513
12 TraesCS1A01G293600 chr3B 499925260 499926988 1728 False 1929.000000 1929 86.742000 818 2581 1 chr3B.!!$F1 1763
13 TraesCS1A01G293600 chr3B 790183694 790184286 592 True 998.000000 998 96.975000 22 616 1 chr3B.!!$R1 594
14 TraesCS1A01G293600 chr3B 19987712 19988441 729 False 433.600000 619 97.942333 688 2843 3 chr3B.!!$F2 2155
15 TraesCS1A01G293600 chr4B 634416591 634418191 1600 True 1812.000000 1812 87.189000 947 2543 1 chr4B.!!$R1 1596
16 TraesCS1A01G293600 chr6B 290171314 290172817 1503 False 641.325000 1458 96.643000 22 2843 4 chr6B.!!$F1 2821
17 TraesCS1A01G293600 chr5B 595297581 595298641 1060 False 1266.000000 1266 88.394000 602 1661 1 chr5B.!!$F1 1059
18 TraesCS1A01G293600 chr5B 445761330 445762400 1070 True 1254.000000 1254 87.931000 25 1109 1 chr5B.!!$R1 1084
19 TraesCS1A01G293600 chr2B 772448669 772449340 671 False 1112.000000 1112 96.577000 22 692 1 chr2B.!!$F1 670

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
1293 1578 5.805728 AGTGTCAACCGGAGATTAAAGAAT 58.194 37.5 9.46 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2800 3270 5.791336 TCTAAGTATGGCTGTGTATCCTG 57.209 43.478 0.0 0.0 0.0 3.86 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
1293 1578 5.805728 AGTGTCAACCGGAGATTAAAGAAT 58.194 37.50 9.46 0.0 0.00 2.40
1369 1654 0.955919 CGTTTGGAGGAGGGTGAAGC 60.956 60.00 0.00 0.0 0.00 3.86
2498 2786 0.750850 GGATGGCCTAGAGCGTACAA 59.249 55.00 3.32 0.0 45.17 2.41
2674 3144 9.550406 CCAAATATTTTCATGCCAAATCTGTAT 57.450 29.63 0.00 0.0 0.00 2.29
2759 3229 6.819284 TGCAACAGATCATCATAGTCATGTA 58.181 36.00 0.00 0.0 33.57 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.579709 ACGCATCTACTGAACTCAACAG 58.420 45.455 0.0 0.0 40.68 3.16
1 2 3.660501 ACGCATCTACTGAACTCAACA 57.339 42.857 0.0 0.0 0.00 3.33
2 3 4.734917 AGTACGCATCTACTGAACTCAAC 58.265 43.478 0.0 0.0 0.00 3.18
4 5 3.377485 GGAGTACGCATCTACTGAACTCA 59.623 47.826 0.0 0.0 34.69 3.41
5 6 3.243134 GGGAGTACGCATCTACTGAACTC 60.243 52.174 0.0 0.0 33.39 3.01
6 7 2.688958 GGGAGTACGCATCTACTGAACT 59.311 50.000 0.0 0.0 0.00 3.01
7 8 2.688958 AGGGAGTACGCATCTACTGAAC 59.311 50.000 0.0 0.0 0.00 3.18
8 9 2.950309 GAGGGAGTACGCATCTACTGAA 59.050 50.000 0.0 0.0 0.00 3.02
9 10 2.573369 GAGGGAGTACGCATCTACTGA 58.427 52.381 0.0 0.0 0.00 3.41
10 11 1.609555 GGAGGGAGTACGCATCTACTG 59.390 57.143 0.0 0.0 0.00 2.74
11 12 1.814634 CGGAGGGAGTACGCATCTACT 60.815 57.143 0.0 0.0 0.00 2.57
12 13 0.592148 CGGAGGGAGTACGCATCTAC 59.408 60.000 0.0 0.0 0.00 2.59
13 14 0.182061 ACGGAGGGAGTACGCATCTA 59.818 55.000 0.0 0.0 0.00 1.98
14 15 1.076923 ACGGAGGGAGTACGCATCT 60.077 57.895 0.0 0.0 0.00 2.90
15 16 1.359475 GACGGAGGGAGTACGCATC 59.641 63.158 0.0 0.0 0.00 3.91
16 17 2.125961 GGACGGAGGGAGTACGCAT 61.126 63.158 0.0 0.0 0.00 4.73
17 18 2.753043 GGACGGAGGGAGTACGCA 60.753 66.667 0.0 0.0 0.00 5.24
18 19 3.885521 CGGACGGAGGGAGTACGC 61.886 72.222 0.0 0.0 39.20 4.42
1293 1578 2.171659 TGCAACTTCTCTGGTTGTGGTA 59.828 45.455 8.1 0.0 43.93 3.25
2052 2340 3.149005 ACTCCCTCGATGTATCTCTCC 57.851 52.381 0.0 0.0 0.00 3.71
2498 2786 7.112779 CACCCTAAAACATCAGGTAGATTTCT 58.887 38.462 0.0 0.0 33.72 2.52
2674 3144 8.107729 TCTCTGAAGTGGTGACTATACTTTCTA 58.892 37.037 0.0 0.0 34.99 2.10
2759 3229 8.635765 AACAATCTGTAGTGGTTAAATGACAT 57.364 30.769 0.0 0.0 0.00 3.06
2800 3270 5.791336 TCTAAGTATGGCTGTGTATCCTG 57.209 43.478 0.0 0.0 0.00 3.86


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

AutoCloner maintained by Alex Coulton.