Multiple sequence alignment - TraesCS4A01G293100

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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 TraesCS4A01G293100 chr4A 100.000 4051 0 0 1 4051 595377903 595373853 0.000000e+00 7481.0
1 TraesCS4A01G293100 chr4A 99.683 315 1 0 3112 3426 595374484 595374170 9.760000e-161 577.0
2 TraesCS4A01G293100 chr4A 99.683 315 1 0 3420 3734 595374792 595374478 9.760000e-161 577.0
3 TraesCS4A01G293100 chr4A 100.000 31 0 0 3557 3587 595374259 595374229 1.570000e-04 58.4
4 TraesCS4A01G293100 chr4A 100.000 31 0 0 3249 3279 595374259 595374229 1.570000e-04 58.4
5 TraesCS4A01G293100 chr4A 100.000 31 0 0 3645 3675 595374347 595374317 1.570000e-04 58.4
6 TraesCS4A01G293100 chr4A 100.000 31 0 0 3337 3367 595374347 595374317 1.570000e-04 58.4
7 TraesCS4A01G293100 chr4A 100.000 31 0 0 3557 3587 595374567 595374537 1.570000e-04 58.4
8 TraesCS4A01G293100 chr4A 100.000 31 0 0 3249 3279 595374567 595374537 1.570000e-04 58.4
9 TraesCS4A01G293100 chr4A 100.000 31 0 0 3645 3675 595374655 595374625 1.570000e-04 58.4
10 TraesCS4A01G293100 chr4A 100.000 31 0 0 3337 3367 595374655 595374625 1.570000e-04 58.4
11 TraesCS4A01G293100 chr4D 92.541 1877 91 23 1391 3244 7902440 7904290 0.000000e+00 2645.0
12 TraesCS4A01G293100 chr4D 82.452 775 88 28 3 749 550130 549376 5.710000e-178 634.0
13 TraesCS4A01G293100 chr4D 88.995 418 23 7 862 1272 7901853 7902254 2.810000e-136 496.0
14 TraesCS4A01G293100 chr4D 83.071 254 22 10 3718 3962 7904966 7905207 1.140000e-50 211.0
15 TraesCS4A01G293100 chr4D 89.552 134 12 2 3420 3552 7904158 7904290 6.960000e-38 169.0
16 TraesCS4A01G293100 chr4D 92.500 80 6 0 3249 3328 7904504 7904583 9.200000e-22 115.0
17 TraesCS4A01G293100 chr4D 92.500 80 6 0 3557 3636 7904504 7904583 9.200000e-22 115.0
18 TraesCS4A01G293100 chr4D 97.561 41 1 0 3328 3368 7904495 7904535 2.020000e-08 71.3
19 TraesCS4A01G293100 chr4D 97.561 41 1 0 3636 3676 7904495 7904535 2.020000e-08 71.3
20 TraesCS4A01G293100 chr4D 100.000 35 0 0 3334 3368 7904935 7904969 9.400000e-07 65.8
21 TraesCS4A01G293100 chr4D 100.000 35 0 0 3642 3676 7904935 7904969 9.400000e-07 65.8
22 TraesCS4A01G293100 chr4D 100.000 31 0 0 3249 3279 7904938 7904968 1.570000e-04 58.4
23 TraesCS4A01G293100 chr4D 100.000 31 0 0 3557 3587 7904938 7904968 1.570000e-04 58.4
24 TraesCS4A01G293100 chr4B 89.693 1106 64 20 2159 3236 14341789 14342872 0.000000e+00 1365.0
25 TraesCS4A01G293100 chr4B 85.542 996 58 35 727 1680 14340189 14341140 0.000000e+00 963.0
26 TraesCS4A01G293100 chr4B 86.792 212 25 2 3700 3908 14343196 14343407 2.430000e-57 233.0
27 TraesCS4A01G293100 chr4B 91.200 125 9 2 3420 3544 14342750 14342872 6.960000e-38 169.0
28 TraesCS4A01G293100 chr4B 95.556 45 2 0 3249 3293 14343096 14343140 5.620000e-09 73.1
29 TraesCS4A01G293100 chr4B 95.556 45 2 0 3557 3601 14343096 14343140 5.620000e-09 73.1
30 TraesCS4A01G293100 chr4B 97.561 41 1 0 3328 3368 14343087 14343127 2.020000e-08 71.3
31 TraesCS4A01G293100 chr4B 97.561 41 1 0 3636 3676 14343087 14343127 2.020000e-08 71.3
32 TraesCS4A01G293100 chr7B 84.204 766 97 22 4 749 234915665 234914904 0.000000e+00 723.0
33 TraesCS4A01G293100 chr7B 90.732 410 15 10 2832 3223 682800192 682799788 3.590000e-145 525.0
34 TraesCS4A01G293100 chr7B 90.220 409 18 11 2833 3223 706366733 706366329 7.760000e-142 514.0
35 TraesCS4A01G293100 chr7B 89.928 417 17 12 2822 3219 706372959 706372549 7.760000e-142 514.0
36 TraesCS4A01G293100 chr7B 89.500 400 20 9 2833 3214 499385480 499385875 1.690000e-133 486.0
37 TraesCS4A01G293100 chr7B 87.826 115 5 5 3425 3531 682799901 682799788 4.250000e-25 126.0
38 TraesCS4A01G293100 chr7B 87.069 116 6 5 3420 3527 706372663 706372549 5.500000e-24 122.0
39 TraesCS4A01G293100 chr7B 93.846 65 4 0 3987 4051 1358650 1358714 9.270000e-17 99.0
40 TraesCS4A01G293100 chr3A 83.097 775 96 22 3 749 662617006 662617773 0.000000e+00 673.0
41 TraesCS4A01G293100 chr3A 82.500 760 100 25 3 749 510305018 510305757 1.590000e-178 636.0
42 TraesCS4A01G293100 chr2B 83.097 775 94 24 3 748 51080225 51079459 0.000000e+00 671.0
43 TraesCS4A01G293100 chr2B 85.663 558 71 9 3 554 518771630 518772184 2.710000e-161 579.0
44 TraesCS4A01G293100 chr2B 89.731 409 20 8 2833 3223 91294645 91295049 1.680000e-138 503.0
45 TraesCS4A01G293100 chr2B 87.500 120 6 5 3420 3531 91294931 91295049 3.290000e-26 130.0
46 TraesCS4A01G293100 chr2A 82.968 775 96 24 3 749 644223045 644222279 0.000000e+00 667.0
47 TraesCS4A01G293100 chr3B 85.423 638 79 11 6 637 457569749 457569120 0.000000e+00 651.0
48 TraesCS4A01G293100 chr3B 90.709 409 16 10 2833 3223 805916375 805915971 3.590000e-145 525.0
49 TraesCS4A01G293100 chr3B 89.891 366 15 9 2876 3223 49346230 49345869 6.170000e-123 451.0
50 TraesCS4A01G293100 chr3B 89.071 366 18 11 2876 3223 737253007 737253368 6.220000e-118 435.0
51 TraesCS4A01G293100 chr3B 87.500 120 6 4 3420 3531 805916089 805915971 3.290000e-26 130.0
52 TraesCS4A01G293100 chr3B 87.826 115 5 5 3425 3531 737253255 737253368 4.250000e-25 126.0
53 TraesCS4A01G293100 chr5B 82.219 658 81 22 127 756 532767371 532768020 5.960000e-148 534.0
54 TraesCS4A01G293100 chr5B 89.344 366 17 10 2876 3223 37720481 37720120 1.340000e-119 440.0
55 TraesCS4A01G293100 chr5B 97.647 85 0 2 3733 3817 5102032 5102114 1.170000e-30 145.0
56 TraesCS4A01G293100 chr5B 94.624 93 4 1 3734 3825 862907 862815 4.220000e-30 143.0
57 TraesCS4A01G293100 chr5B 88.696 115 4 4 3425 3531 37720233 37720120 9.140000e-27 132.0
58 TraesCS4A01G293100 chr5D 96.667 90 1 2 3733 3821 544865456 544865368 9.070000e-32 148.0
59 TraesCS4A01G293100 chr5D 97.674 86 0 2 3733 3818 6822757 6822674 3.260000e-31 147.0
60 TraesCS4A01G293100 chr5D 97.619 84 2 0 3734 3817 3810211 3810128 1.170000e-30 145.0
61 TraesCS4A01G293100 chr5D 97.619 84 2 0 3734 3817 13909884 13909801 1.170000e-30 145.0
62 TraesCS4A01G293100 chr6D 97.647 85 1 1 3735 3818 456096949 456096865 1.170000e-30 145.0
63 TraesCS4A01G293100 chr2D 93.750 64 4 0 3987 4050 576279074 576279011 3.330000e-16 97.1
64 TraesCS4A01G293100 chr1B 98.077 52 0 1 2832 2883 171844119 171844169 5.580000e-14 89.8
65 TraesCS4A01G293100 chr5A 86.885 61 4 4 643 700 626190445 626190386 9.400000e-07 65.8


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 TraesCS4A01G293100 chr4A 595373853 595377903 4050 True 827.472727 7481 99.942364 1 4051 11 chr4A.!!$R1 4050
1 TraesCS4A01G293100 chr4D 549376 550130 754 True 634.000000 634 82.452000 3 749 1 chr4D.!!$R1 746
2 TraesCS4A01G293100 chr4D 7901853 7905207 3354 False 345.166667 2645 94.523417 862 3962 12 chr4D.!!$F1 3100
3 TraesCS4A01G293100 chr4B 14340189 14343407 3218 False 377.350000 1365 92.432625 727 3908 8 chr4B.!!$F1 3181
4 TraesCS4A01G293100 chr7B 234914904 234915665 761 True 723.000000 723 84.204000 4 749 1 chr7B.!!$R1 745
5 TraesCS4A01G293100 chr3A 662617006 662617773 767 False 673.000000 673 83.097000 3 749 1 chr3A.!!$F2 746
6 TraesCS4A01G293100 chr3A 510305018 510305757 739 False 636.000000 636 82.500000 3 749 1 chr3A.!!$F1 746
7 TraesCS4A01G293100 chr2B 51079459 51080225 766 True 671.000000 671 83.097000 3 748 1 chr2B.!!$R1 745
8 TraesCS4A01G293100 chr2B 518771630 518772184 554 False 579.000000 579 85.663000 3 554 1 chr2B.!!$F1 551
9 TraesCS4A01G293100 chr2A 644222279 644223045 766 True 667.000000 667 82.968000 3 749 1 chr2A.!!$R1 746
10 TraesCS4A01G293100 chr3B 457569120 457569749 629 True 651.000000 651 85.423000 6 637 1 chr3B.!!$R2 631
11 TraesCS4A01G293100 chr5B 532767371 532768020 649 False 534.000000 534 82.219000 127 756 1 chr5B.!!$F2 629


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
728 765 0.106868 TCGAGCCCCATCTTCGACTA 60.107 55.0 0.00 0.0 0.00 2.59 F
1656 1793 0.462789 CAAGATCTTTGCCATGGCCC 59.537 55.0 33.44 14.9 41.09 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1995 0.648441 GTGCAATTGCGGCATTCATG 59.352 50.000 24.58 2.02 44.11 3.07 R
3434 4029 1.133823 TGTGAAAGCACCACATCCAGT 60.134 47.619 0.00 0.00 44.51 4.00 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)



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AutoCloner maintained by Alex Coulton.