Multiple sequence alignment - TraesCS6A01G091100

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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 TraesCS6A01G091100 chr6A 100.000 5832 0 0 319 6150 59782631 59788462 0.000000e+00 10770.0
1 TraesCS6A01G091100 chr6A 87.874 2573 239 39 3382 5890 59708729 59711292 0.000000e+00 2955.0
2 TraesCS6A01G091100 chr6A 84.611 1787 222 33 3317 5060 59676069 59677845 0.000000e+00 1727.0
3 TraesCS6A01G091100 chr6A 91.421 373 25 3 991 1362 59808223 59808589 7.110000e-139 505.0
4 TraesCS6A01G091100 chr6A 86.970 330 26 7 2016 2330 59809306 59809633 7.580000e-94 355.0
5 TraesCS6A01G091100 chr6A 84.118 340 32 10 1450 1767 59708108 59708447 5.990000e-80 309.0
6 TraesCS6A01G091100 chr6A 86.047 258 27 6 2349 2605 59809700 59809949 1.020000e-67 268.0
7 TraesCS6A01G091100 chr6A 91.912 136 11 0 5900 6035 59711358 59711493 2.260000e-44 191.0
8 TraesCS6A01G091100 chr6A 100.000 82 0 0 1 82 59782313 59782394 1.070000e-32 152.0
9 TraesCS6A01G091100 chr6A 87.611 113 14 0 6038 6150 582917329 582917217 1.390000e-26 132.0
10 TraesCS6A01G091100 chr6A 92.000 50 3 1 5610 5659 59814590 59814638 1.110000e-07 69.4
11 TraesCS6A01G091100 chr6A 82.667 75 6 6 5258 5326 59346430 59346503 6.660000e-05 60.2
12 TraesCS6A01G091100 chr6D 96.200 2842 90 6 2881 5705 45208346 45211186 0.000000e+00 4634.0
13 TraesCS6A01G091100 chr6D 88.442 2561 242 34 3382 5892 45203446 45206002 0.000000e+00 3040.0
14 TraesCS6A01G091100 chr6D 85.003 1667 206 27 3426 5060 44505976 44507630 0.000000e+00 1653.0
15 TraesCS6A01G091100 chr6D 84.754 1666 211 26 3426 5060 44736206 44737859 0.000000e+00 1629.0
16 TraesCS6A01G091100 chr6D 94.000 900 47 3 3589 4487 45479905 45480798 0.000000e+00 1356.0
17 TraesCS6A01G091100 chr6D 92.282 596 32 5 921 1504 45206238 45206831 0.000000e+00 833.0
18 TraesCS6A01G091100 chr6D 92.759 580 20 7 2231 2810 45207454 45208011 0.000000e+00 819.0
19 TraesCS6A01G091100 chr6D 92.290 428 28 3 5612 6035 45211653 45212079 2.450000e-168 603.0
20 TraesCS6A01G091100 chr6D 95.860 314 12 1 1871 2184 45207135 45207447 1.980000e-139 507.0
21 TraesCS6A01G091100 chr6D 90.860 372 28 1 991 1362 45478087 45478452 1.540000e-135 494.0
22 TraesCS6A01G091100 chr6D 87.147 389 45 3 933 1317 45202264 45202651 2.630000e-118 436.0
23 TraesCS6A01G091100 chr6D 87.915 331 24 5 2016 2330 45479174 45479504 5.820000e-100 375.0
24 TraesCS6A01G091100 chr6D 86.826 334 28 8 1450 1767 45202831 45203164 5.860000e-95 359.0
25 TraesCS6A01G091100 chr6D 94.860 214 11 0 1554 1767 45206923 45207136 9.880000e-88 335.0
26 TraesCS6A01G091100 chr6D 86.047 258 27 6 2349 2605 45479571 45479820 1.020000e-67 268.0
27 TraesCS6A01G091100 chr6D 90.299 134 13 0 660 793 459356285 459356152 6.340000e-40 176.0
28 TraesCS6A01G091100 chr6D 86.331 139 12 3 511 647 45212546 45212679 1.790000e-30 145.0
29 TraesCS6A01G091100 chr6D 83.908 87 8 6 5612 5695 45482067 45482150 1.840000e-10 78.7
30 TraesCS6A01G091100 chr6D 84.375 64 4 5 5258 5315 44507824 44507887 2.390000e-04 58.4
31 TraesCS6A01G091100 chr6D 84.375 64 4 5 5258 5315 44738052 44738115 2.390000e-04 58.4
32 TraesCS6A01G091100 chr6B 93.526 2873 106 20 2881 5705 113846091 113848931 0.000000e+00 4202.0
33 TraesCS6A01G091100 chr6B 88.660 1896 179 22 4166 6035 113783435 113785320 0.000000e+00 2278.0
34 TraesCS6A01G091100 chr6B 85.210 1359 168 20 3727 5060 113771078 113772428 0.000000e+00 1365.0
35 TraesCS6A01G091100 chr6B 90.370 540 27 3 1125 1664 113843649 113844163 0.000000e+00 686.0
36 TraesCS6A01G091100 chr6B 92.947 397 21 3 5640 6033 113849362 113849754 6.920000e-159 571.0
37 TraesCS6A01G091100 chr6B 83.291 395 49 12 5612 5999 114028276 114028660 1.270000e-91 348.0
38 TraesCS6A01G091100 chr6B 85.928 334 31 8 1450 1767 113781771 113782104 5.900000e-90 342.0
39 TraesCS6A01G091100 chr6B 84.308 325 35 6 937 1258 113780910 113781221 2.790000e-78 303.0
40 TraesCS6A01G091100 chr6B 96.154 130 5 0 984 1113 113843464 113843593 4.830000e-51 213.0
41 TraesCS6A01G091100 chr6B 88.182 110 13 0 511 620 113850120 113850229 1.390000e-26 132.0
42 TraesCS6A01G091100 chr6B 97.101 69 1 1 2460 2527 113844192 113844260 1.400000e-21 115.0
43 TraesCS6A01G091100 chr6B 84.375 64 4 5 5258 5315 113657787 113657850 2.390000e-04 58.4
44 TraesCS6A01G091100 chr5D 96.491 114 4 0 1763 1876 521523688 521523801 8.140000e-44 189.0
45 TraesCS6A01G091100 chr5D 88.889 135 15 0 660 794 330702999 330703133 3.810000e-37 167.0
46 TraesCS6A01G091100 chr4A 91.241 137 12 0 660 796 140763864 140764000 2.930000e-43 187.0
47 TraesCS6A01G091100 chr4A 94.872 117 5 1 1765 1880 720526580 720526696 1.360000e-41 182.0
48 TraesCS6A01G091100 chrUn 94.872 117 5 1 1765 1880 51053148 51053032 1.360000e-41 182.0
49 TraesCS6A01G091100 chrUn 94.872 117 5 1 1765 1880 342353519 342353403 1.360000e-41 182.0
50 TraesCS6A01G091100 chrUn 94.828 116 5 1 1757 1872 77885381 77885267 4.900000e-41 180.0
51 TraesCS6A01G091100 chrUn 86.842 114 14 1 6038 6150 42175456 42175343 6.470000e-25 126.0
52 TraesCS6A01G091100 chr7B 95.575 113 5 0 1763 1875 297402183 297402295 1.360000e-41 182.0
53 TraesCS6A01G091100 chr7B 94.783 115 6 0 1765 1879 730205113 730205227 4.900000e-41 180.0
54 TraesCS6A01G091100 chr7B 89.552 134 14 0 661 794 96812038 96812171 2.950000e-38 171.0
55 TraesCS6A01G091100 chr7B 97.297 37 1 0 991 1027 684367701 684367737 5.150000e-06 63.9
56 TraesCS6A01G091100 chr2D 94.783 115 5 1 1758 1872 111321520 111321407 1.760000e-40 178.0
57 TraesCS6A01G091100 chr2D 94.017 117 7 0 1764 1880 593429590 593429706 1.760000e-40 178.0
58 TraesCS6A01G091100 chr7D 89.630 135 14 0 661 795 577917702 577917836 8.200000e-39 172.0
59 TraesCS6A01G091100 chr7D 88.889 135 15 0 660 794 315668054 315667920 3.810000e-37 167.0
60 TraesCS6A01G091100 chr7D 86.842 114 15 0 6037 6150 400297895 400298008 1.800000e-25 128.0
61 TraesCS6A01G091100 chr7D 85.714 56 8 0 790 845 111749196 111749251 6.660000e-05 60.2
62 TraesCS6A01G091100 chr3D 90.698 129 12 0 666 794 452657885 452658013 8.200000e-39 172.0
63 TraesCS6A01G091100 chr3D 90.000 130 13 0 666 795 424623475 424623604 1.060000e-37 169.0
64 TraesCS6A01G091100 chr3D 87.500 112 14 0 6039 6150 500223179 500223068 5.000000e-26 130.0
65 TraesCS6A01G091100 chr2B 87.500 144 15 3 660 803 105905975 105905835 4.930000e-36 163.0
66 TraesCS6A01G091100 chr3A 89.474 114 12 0 6037 6150 725923636 725923749 1.790000e-30 145.0
67 TraesCS6A01G091100 chr4D 88.496 113 13 0 6038 6150 484720786 484720674 2.990000e-28 137.0
68 TraesCS6A01G091100 chr4D 89.623 106 10 1 6038 6143 484719539 484719643 3.870000e-27 134.0
69 TraesCS6A01G091100 chr1D 89.524 105 10 1 6038 6142 411190944 411190841 1.390000e-26 132.0
70 TraesCS6A01G091100 chr1D 85.455 55 8 0 791 845 81062712 81062658 2.390000e-04 58.4
71 TraesCS6A01G091100 chr1A 86.726 113 13 2 6039 6150 22538753 22538642 2.330000e-24 124.0
72 TraesCS6A01G091100 chr1A 90.909 55 5 0 791 845 59128239 59128293 2.380000e-09 75.0
73 TraesCS6A01G091100 chr5B 89.091 55 6 0 791 845 681782131 681782185 1.110000e-07 69.4


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 TraesCS6A01G091100 chr6A 59782313 59788462 6149 False 5461.000000 10770 100.000000 1 6150 2 chr6A.!!$F5 6149
1 TraesCS6A01G091100 chr6A 59676069 59677845 1776 False 1727.000000 1727 84.611000 3317 5060 1 chr6A.!!$F2 1743
2 TraesCS6A01G091100 chr6A 59708108 59711493 3385 False 1151.666667 2955 87.968000 1450 6035 3 chr6A.!!$F4 4585
3 TraesCS6A01G091100 chr6A 59808223 59809949 1726 False 376.000000 505 88.146000 991 2605 3 chr6A.!!$F6 1614
4 TraesCS6A01G091100 chr6D 45202264 45212679 10415 False 1171.100000 4634 91.299700 511 6035 10 chr6D.!!$F3 5524
5 TraesCS6A01G091100 chr6D 44505976 44507887 1911 False 855.700000 1653 84.689000 3426 5315 2 chr6D.!!$F1 1889
6 TraesCS6A01G091100 chr6D 44736206 44738115 1909 False 843.700000 1629 84.564500 3426 5315 2 chr6D.!!$F2 1889
7 TraesCS6A01G091100 chr6D 45478087 45482150 4063 False 514.340000 1356 88.546000 991 5695 5 chr6D.!!$F4 4704
8 TraesCS6A01G091100 chr6B 113771078 113772428 1350 False 1365.000000 1365 85.210000 3727 5060 1 chr6B.!!$F2 1333
9 TraesCS6A01G091100 chr6B 113843464 113850229 6765 False 986.500000 4202 93.046667 511 6033 6 chr6B.!!$F5 5522
10 TraesCS6A01G091100 chr6B 113780910 113785320 4410 False 974.333333 2278 86.298667 937 6035 3 chr6B.!!$F4 5098


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
424 425 0.038159 GGAGCATAGCGAGCCGTAAT 60.038 55.000 0.0 0.0 0.00 1.89 F
1720 5461 0.249868 TATATGTGCCGCTGCCTGTC 60.250 55.000 0.0 0.0 36.33 3.51 F
2126 6079 0.171455 GTGCTGACGTGTAGAGGAGG 59.829 60.000 0.0 0.0 0.00 4.30 F
2830 7250 0.734253 CGTGGCTTGGAAGTCTCTCG 60.734 60.000 0.0 0.0 0.00 4.04 F
3099 8590 1.067582 GTAGGGATTGACTCGGGCG 59.932 63.158 0.0 0.0 0.00 6.13 F
3258 8749 1.068055 GTTTTGCTGCACTCCCATCAG 60.068 52.381 0.0 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 5508 0.179065 GTAATTCCGAACGGAGGGGG 60.179 60.000 15.34 0.00 46.06 5.40 R
2876 7944 0.539986 TCGAAAGAAATCTCCCGGGG 59.460 55.000 23.50 12.05 37.03 5.73 R
3238 8729 0.961019 TGATGGGAGTGCAGCAAAAC 59.039 50.000 0.00 0.00 0.00 2.43 R
4631 10516 4.500603 AGATTTGCTGCAAAGACTCAAG 57.499 40.909 28.86 0.00 36.76 3.02 R
4684 10569 6.258507 TCATGACATTTGTTATCCTCATGTCG 59.741 38.462 0.00 0.00 39.59 4.35 R
5256 11145 2.303022 ACTTCATCCGGTGACATCAAGT 59.697 45.455 0.00 2.23 36.32 3.16 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.