Multiple sequence alignment - TraesCS2D01G160500

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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 TraesCS2D01G160500 chr2D 100.000 2282 0 0 1 2282 103241505 103239224 0.000000e+00 4215.0
1 TraesCS2D01G160500 chr2D 96.445 844 30 0 1439 2282 189872981 189872138 0.000000e+00 1393.0
2 TraesCS2D01G160500 chr2D 96.327 844 31 0 1439 2282 384797628 384798471 0.000000e+00 1387.0
3 TraesCS2D01G160500 chr2D 84.245 457 43 2 445 872 573649703 573650159 3.510000e-113 418.0
4 TraesCS2D01G160500 chr3D 98.275 1449 16 6 1 1441 49966323 49964876 0.000000e+00 2529.0
5 TraesCS2D01G160500 chr3D 96.682 844 28 0 1439 2282 177565984 177566827 0.000000e+00 1404.0
6 TraesCS2D01G160500 chr3D 88.087 596 43 18 871 1442 134640366 134640957 0.000000e+00 682.0
7 TraesCS2D01G160500 chr3D 85.996 457 35 2 445 872 134639833 134640289 1.600000e-126 462.0
8 TraesCS2D01G160500 chr3D 85.455 440 51 7 1 430 134638086 134638522 1.610000e-121 446.0
9 TraesCS2D01G160500 chr3D 84.187 449 42 2 451 870 14356590 14356142 2.110000e-110 409.0
10 TraesCS2D01G160500 chr3D 83.258 442 54 15 24 446 55371868 55372308 2.750000e-104 388.0
11 TraesCS2D01G160500 chr1A 95.712 1446 52 7 1 1441 571865714 571864274 0.000000e+00 2318.0
12 TraesCS2D01G160500 chr5B 93.089 1447 79 10 3 1442 178915614 178914182 0.000000e+00 2098.0
13 TraesCS2D01G160500 chr5B 86.214 457 51 6 1 446 607480692 607481147 3.410000e-133 484.0
14 TraesCS2D01G160500 chr5B 86.433 457 33 4 445 872 607482454 607482910 7.380000e-130 473.0
15 TraesCS2D01G160500 chr5B 83.193 357 30 4 445 772 333604717 333604362 1.330000e-77 300.0
16 TraesCS2D01G160500 chr5B 85.766 274 21 2 620 875 5103769 5103496 8.030000e-70 274.0
17 TraesCS2D01G160500 chr5D 96.445 844 30 0 1439 2282 222085363 222086206 0.000000e+00 1393.0
18 TraesCS2D01G160500 chr5D 90.588 510 45 3 874 1381 292726617 292726109 0.000000e+00 673.0
19 TraesCS2D01G160500 chr5D 86.304 460 33 3 445 875 292727152 292726694 7.380000e-130 473.0
20 TraesCS2D01G160500 chr5D 85.526 456 49 9 1 446 403889680 403890128 5.740000e-126 460.0
21 TraesCS2D01G160500 chr5D 91.746 315 20 3 138 446 292765467 292765153 1.250000e-117 433.0
22 TraesCS2D01G160500 chr5D 83.964 449 43 2 451 870 354744524 354744076 9.820000e-109 403.0
23 TraesCS2D01G160500 chr5D 83.445 447 44 3 453 870 547845835 547846280 2.750000e-104 388.0
24 TraesCS2D01G160500 chr5D 77.401 354 58 14 99 446 354746177 354745840 8.320000e-45 191.0
25 TraesCS2D01G160500 chr4D 96.327 844 31 0 1439 2282 276046628 276045785 0.000000e+00 1387.0
26 TraesCS2D01G160500 chr4D 91.837 490 39 1 871 1359 398867666 398868155 0.000000e+00 682.0
27 TraesCS2D01G160500 chr4D 86.463 458 32 3 445 872 398867132 398867589 2.050000e-130 475.0
28 TraesCS2D01G160500 chr1D 96.090 844 33 0 1439 2282 399377837 399376994 0.000000e+00 1376.0
29 TraesCS2D01G160500 chr1D 91.331 496 38 5 871 1364 481612242 481612734 0.000000e+00 673.0
30 TraesCS2D01G160500 chr1D 83.742 449 44 2 451 870 417747385 417746937 4.570000e-107 398.0
31 TraesCS2D01G160500 chr1D 80.755 265 38 8 175 433 392493814 392494071 6.430000e-46 195.0
32 TraesCS2D01G160500 chr1D 100.000 56 0 0 1386 1441 481612789 481612844 1.120000e-18 104.0
33 TraesCS2D01G160500 chr7D 95.972 844 30 2 1439 2282 130694801 130695640 0.000000e+00 1367.0
34 TraesCS2D01G160500 chr7D 83.778 450 43 3 451 870 449769330 449768881 1.270000e-107 399.0
35 TraesCS2D01G160500 chr6D 95.853 844 35 0 1439 2282 154418873 154418030 0.000000e+00 1365.0
36 TraesCS2D01G160500 chr6D 95.853 844 35 0 1439 2282 211411612 211410769 0.000000e+00 1365.0
37 TraesCS2D01G160500 chr3B 87.427 859 63 12 56 871 775177186 775176330 0.000000e+00 946.0
38 TraesCS2D01G160500 chr3B 90.253 513 38 9 1 508 769386476 769385971 0.000000e+00 660.0
39 TraesCS2D01G160500 chr3B 87.895 570 42 12 887 1441 769385729 769385172 0.000000e+00 645.0
40 TraesCS2D01G160500 chr4A 89.766 684 53 5 1 667 709876027 709875344 0.000000e+00 859.0
41 TraesCS2D01G160500 chr4A 86.918 451 30 4 451 872 718008531 718008081 1.590000e-131 479.0
42 TraesCS2D01G160500 chr4A 86.547 446 47 7 13 446 718010288 718009844 1.590000e-131 479.0
43 TraesCS2D01G160500 chr4A 88.514 296 20 7 1160 1441 709875355 709875060 1.680000e-91 346.0
44 TraesCS2D01G160500 chr6B 88.759 685 57 8 1 667 203463246 203462564 0.000000e+00 821.0
45 TraesCS2D01G160500 chr6B 87.090 457 30 6 445 872 132658482 132658026 7.330000e-135 490.0
46 TraesCS2D01G160500 chr6B 85.906 447 49 8 13 446 132660235 132659790 4.440000e-127 464.0
47 TraesCS2D01G160500 chr5A 94.141 495 28 1 871 1364 697889952 697890446 0.000000e+00 752.0
48 TraesCS2D01G160500 chr5A 87.090 457 30 8 445 872 697889419 697889875 7.330000e-135 490.0
49 TraesCS2D01G160500 chr5A 86.801 447 44 9 13 446 651583285 651582841 3.410000e-133 484.0
50 TraesCS2D01G160500 chr5A 86.918 451 30 4 451 872 651581528 651581078 1.590000e-131 479.0
51 TraesCS2D01G160500 chr2B 92.227 476 34 1 874 1349 138737314 138736842 0.000000e+00 671.0
52 TraesCS2D01G160500 chr2B 90.741 54 4 1 1 53 227898169 227898116 1.130000e-08 71.3
53 TraesCS2D01G160500 chr1B 86.401 603 45 17 874 1441 46156484 46155884 1.920000e-175 625.0
54 TraesCS2D01G160500 chr1B 86.871 457 31 6 445 872 414556747 414557203 3.410000e-133 484.0
55 TraesCS2D01G160500 chr1B 86.918 451 30 6 451 872 494554990 494554540 1.590000e-131 479.0
56 TraesCS2D01G160500 chr1B 86.067 445 50 6 13 446 494556746 494556303 3.430000e-128 468.0
57 TraesCS2D01G160500 chr1B 85.339 457 54 7 1 446 414554986 414555440 5.740000e-126 460.0
58 TraesCS2D01G160500 chr1B 100.000 56 0 0 1388 1443 494553886 494553831 1.120000e-18 104.0
59 TraesCS2D01G160500 chr7B 85.643 599 60 20 871 1443 686804742 686805340 6.970000e-170 606.0
60 TraesCS2D01G160500 chr7A 90.385 416 28 8 43 446 729166743 729167158 9.280000e-149 536.0
61 TraesCS2D01G160500 chr7A 88.989 445 28 11 16 446 729165213 729164776 4.320000e-147 531.0
62 TraesCS2D01G160500 chr7A 85.339 457 38 2 445 872 729168459 729168915 1.610000e-121 446.0
63 TraesCS2D01G160500 chr4B 86.214 457 51 6 1 446 502274614 502275069 3.410000e-133 484.0
64 TraesCS2D01G160500 chr4B 85.808 458 35 11 445 872 502276375 502276832 2.070000e-125 459.0
65 TraesCS2D01G160500 chr4B 75.836 269 59 3 169 434 38752474 38752739 5.120000e-27 132.0
66 TraesCS2D01G160500 chr4B 75.564 266 59 3 175 437 63041744 63041482 2.380000e-25 126.0
67 TraesCS2D01G160500 chr4B 93.939 66 4 0 792 857 582376345 582376410 1.440000e-17 100.0
68 TraesCS2D01G160500 chr6A 82.314 458 47 4 445 870 610215424 610215879 1.290000e-97 366.0


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 TraesCS2D01G160500 chr2D 103239224 103241505 2281 True 4215.000000 4215 100.000000 1 2282 1 chr2D.!!$R1 2281
1 TraesCS2D01G160500 chr2D 189872138 189872981 843 True 1393.000000 1393 96.445000 1439 2282 1 chr2D.!!$R2 843
2 TraesCS2D01G160500 chr2D 384797628 384798471 843 False 1387.000000 1387 96.327000 1439 2282 1 chr2D.!!$F1 843
3 TraesCS2D01G160500 chr3D 49964876 49966323 1447 True 2529.000000 2529 98.275000 1 1441 1 chr3D.!!$R2 1440
4 TraesCS2D01G160500 chr3D 177565984 177566827 843 False 1404.000000 1404 96.682000 1439 2282 1 chr3D.!!$F2 843
5 TraesCS2D01G160500 chr3D 134638086 134640957 2871 False 530.000000 682 86.512667 1 1442 3 chr3D.!!$F3 1441
6 TraesCS2D01G160500 chr1A 571864274 571865714 1440 True 2318.000000 2318 95.712000 1 1441 1 chr1A.!!$R1 1440
7 TraesCS2D01G160500 chr5B 178914182 178915614 1432 True 2098.000000 2098 93.089000 3 1442 1 chr5B.!!$R2 1439
8 TraesCS2D01G160500 chr5B 607480692 607482910 2218 False 478.500000 484 86.323500 1 872 2 chr5B.!!$F1 871
9 TraesCS2D01G160500 chr5D 222085363 222086206 843 False 1393.000000 1393 96.445000 1439 2282 1 chr5D.!!$F1 843
10 TraesCS2D01G160500 chr5D 292726109 292727152 1043 True 573.000000 673 88.446000 445 1381 2 chr5D.!!$R2 936
11 TraesCS2D01G160500 chr5D 354744076 354746177 2101 True 297.000000 403 80.682500 99 870 2 chr5D.!!$R3 771
12 TraesCS2D01G160500 chr4D 276045785 276046628 843 True 1387.000000 1387 96.327000 1439 2282 1 chr4D.!!$R1 843
13 TraesCS2D01G160500 chr4D 398867132 398868155 1023 False 578.500000 682 89.150000 445 1359 2 chr4D.!!$F1 914
14 TraesCS2D01G160500 chr1D 399376994 399377837 843 True 1376.000000 1376 96.090000 1439 2282 1 chr1D.!!$R1 843
15 TraesCS2D01G160500 chr1D 481612242 481612844 602 False 388.500000 673 95.665500 871 1441 2 chr1D.!!$F2 570
16 TraesCS2D01G160500 chr7D 130694801 130695640 839 False 1367.000000 1367 95.972000 1439 2282 1 chr7D.!!$F1 843
17 TraesCS2D01G160500 chr6D 154418030 154418873 843 True 1365.000000 1365 95.853000 1439 2282 1 chr6D.!!$R1 843
18 TraesCS2D01G160500 chr6D 211410769 211411612 843 True 1365.000000 1365 95.853000 1439 2282 1 chr6D.!!$R2 843
19 TraesCS2D01G160500 chr3B 775176330 775177186 856 True 946.000000 946 87.427000 56 871 1 chr3B.!!$R1 815
20 TraesCS2D01G160500 chr3B 769385172 769386476 1304 True 652.500000 660 89.074000 1 1441 2 chr3B.!!$R2 1440
21 TraesCS2D01G160500 chr4A 709875060 709876027 967 True 602.500000 859 89.140000 1 1441 2 chr4A.!!$R1 1440
22 TraesCS2D01G160500 chr4A 718008081 718010288 2207 True 479.000000 479 86.732500 13 872 2 chr4A.!!$R2 859
23 TraesCS2D01G160500 chr6B 203462564 203463246 682 True 821.000000 821 88.759000 1 667 1 chr6B.!!$R1 666
24 TraesCS2D01G160500 chr6B 132658026 132660235 2209 True 477.000000 490 86.498000 13 872 2 chr6B.!!$R2 859
25 TraesCS2D01G160500 chr5A 697889419 697890446 1027 False 621.000000 752 90.615500 445 1364 2 chr5A.!!$F1 919
26 TraesCS2D01G160500 chr5A 651581078 651583285 2207 True 481.500000 484 86.859500 13 872 2 chr5A.!!$R1 859
27 TraesCS2D01G160500 chr1B 46155884 46156484 600 True 625.000000 625 86.401000 874 1441 1 chr1B.!!$R1 567
28 TraesCS2D01G160500 chr1B 414554986 414557203 2217 False 472.000000 484 86.105000 1 872 2 chr1B.!!$F1 871
29 TraesCS2D01G160500 chr1B 494553831 494556746 2915 True 350.333333 479 90.995000 13 1443 3 chr1B.!!$R2 1430
30 TraesCS2D01G160500 chr7B 686804742 686805340 598 False 606.000000 606 85.643000 871 1443 1 chr7B.!!$F1 572
31 TraesCS2D01G160500 chr7A 729166743 729168915 2172 False 491.000000 536 87.862000 43 872 2 chr7A.!!$F1 829
32 TraesCS2D01G160500 chr4B 502274614 502276832 2218 False 471.500000 484 86.011000 1 872 2 chr4B.!!$F3 871

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
706 4705 6.776094 AGTTTGAGCATCGCTAAAGTTATTC 58.224 36.0 0.0 0.0 39.88 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 6109 0.675837 GAAAGTACTTGCCGGGACCC 60.676 60.0 9.34 0.0 0.0 4.46 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
125 145 8.132362 GGCACCGTTCAATAATTGATACAATTA 58.868 33.333 15.82 15.82 39.84 1.40
126 146 9.677567 GCACCGTTCAATAATTGATACAATTAT 57.322 29.630 18.13 18.13 39.84 1.28
706 4705 6.776094 AGTTTGAGCATCGCTAAAGTTATTC 58.224 36.000 0.00 0.00 39.88 1.75
1561 5792 2.052690 GCTGAGTACGAGGGGCTGA 61.053 63.158 0.00 0.00 0.00 4.26
1611 5842 1.339151 GGGGTGAAGAAGCTCATCGTT 60.339 52.381 0.00 0.00 0.00 3.85
1659 5890 3.572255 GGCAAGTCAACAAGGATTACCAA 59.428 43.478 0.00 0.00 38.94 3.67
1878 6109 1.394917 CAGAACAAGCGGAGGAAATCG 59.605 52.381 0.00 0.00 0.00 3.34
2025 6256 1.542987 GCTCCCATGGCAGAAGAGATC 60.543 57.143 6.94 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 148 8.266392 TGAGAACAAACAAAATGCTGAAAAAT 57.734 26.923 0.00 0.0 0.00 1.82
706 4705 4.162320 TGGCTCTATTCCCACTTCAGTTAG 59.838 45.833 0.00 0.0 0.00 2.34
840 4843 1.400494 GTGGTCGCCATATCAACCAAC 59.600 52.381 1.90 0.0 43.09 3.77
1561 5792 0.811616 GCGATTCTGAGACCGGCAAT 60.812 55.000 0.00 0.0 0.00 3.56
1611 5842 1.609501 AAGCTGCGAGTCACCCCTA 60.610 57.895 0.00 0.0 0.00 3.53
1878 6109 0.675837 GAAAGTACTTGCCGGGACCC 60.676 60.000 9.34 0.0 0.00 4.46
1910 6141 4.431131 CCTTGCCGGCAGTCCCAT 62.431 66.667 30.75 0.0 0.00 4.00
2025 6256 1.971695 GACGGCAAGGACCAAAGGG 60.972 63.158 0.00 0.0 41.29 3.95
2069 6300 1.339151 GGAGGAATCGGATGGTATGCC 60.339 57.143 0.00 0.0 0.00 4.40


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

AutoCloner maintained by Alex Coulton.