Multiple sequence alignment - TraesCS5B01G454800

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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 TraesCS5B01G454800 chr5B 100.000 2903 0 0 1 2903 629081459 629078557 0.000000e+00 5361.0
1 TraesCS5B01G454800 chr5B 100.000 2813 0 0 3015 5827 629078445 629075633 0.000000e+00 5195.0
2 TraesCS5B01G454800 chr5B 98.542 2813 19 1 3015 5827 625450323 625447533 0.000000e+00 4948.0
3 TraesCS5B01G454800 chr5B 98.151 2812 38 4 3015 5824 632807851 632810650 0.000000e+00 4892.0
4 TraesCS5B01G454800 chr5B 97.075 2906 66 12 2 2902 632804950 632807841 0.000000e+00 4878.0
5 TraesCS5B01G454800 chr5B 99.130 2528 14 5 379 2903 625452847 625450325 0.000000e+00 4540.0
6 TraesCS5B01G454800 chr5B 95.023 1929 68 7 990 2903 604719190 604717275 0.000000e+00 3005.0
7 TraesCS5B01G454800 chr5B 94.245 1251 31 7 3433 4672 604717014 604715794 0.000000e+00 1873.0
8 TraesCS5B01G454800 chr5B 89.853 749 52 11 4732 5457 604715791 604715044 0.000000e+00 941.0
9 TraesCS5B01G454800 chr5B 95.724 304 13 0 5524 5827 604715046 604714743 1.890000e-134 490.0
10 TraesCS5B01G454800 chr5B 99.240 263 2 0 3015 3277 604717273 604717011 5.280000e-130 475.0
11 TraesCS5B01G454800 chr5B 90.517 232 6 8 855 1085 604355269 604355485 5.710000e-75 292.0
12 TraesCS5B01G454800 chr5B 77.987 318 64 3 1147 1458 622977742 622977425 1.660000e-45 195.0
13 TraesCS5B01G454800 chr5B 99.065 107 0 1 855 960 604719774 604719668 2.140000e-44 191.0
14 TraesCS5B01G454800 chr5B 85.987 157 10 8 4598 4744 632809612 632809458 2.170000e-34 158.0
15 TraesCS5B01G454800 chr5B 75.758 330 69 10 2198 2520 626803335 626803010 7.820000e-34 156.0
16 TraesCS5B01G454800 chr5B 86.111 144 18 2 2708 2850 394253475 394253617 2.810000e-33 154.0
17 TraesCS5B01G454800 chr5B 90.435 115 5 6 4627 4739 625448616 625448726 4.710000e-31 147.0
18 TraesCS5B01G454800 chr5B 89.565 115 6 6 4627 4739 629076716 629076826 2.190000e-29 141.0
19 TraesCS5B01G454800 chr5B 77.637 237 36 12 2445 2677 627470593 627470370 1.700000e-25 128.0
20 TraesCS5B01G454800 chr5B 72.840 486 87 27 2198 2643 629281355 629281835 2.200000e-24 124.0
21 TraesCS5B01G454800 chr5B 72.840 486 87 27 2198 2643 629363649 629364129 2.200000e-24 124.0
22 TraesCS5B01G454800 chr5B 77.215 237 37 12 2445 2677 623866298 623866075 7.930000e-24 122.0
23 TraesCS5B01G454800 chr5B 92.958 71 1 1 4673 4739 604715762 604715832 3.720000e-17 100.0
24 TraesCS5B01G454800 chr5B 83.810 105 10 3 4302 4403 633281230 633281330 6.220000e-15 93.5
25 TraesCS5B01G454800 chr5B 95.000 40 2 0 4598 4637 697609499 697609460 4.870000e-06 63.9
26 TraesCS5B01G454800 chr5D 98.259 2815 40 3 3015 5827 501709065 501706258 0.000000e+00 4918.0
27 TraesCS5B01G454800 chr5D 97.298 2813 43 10 3015 5827 498927529 498924750 0.000000e+00 4743.0
28 TraesCS5B01G454800 chr5D 96.072 2877 80 10 56 2903 498930403 498927531 0.000000e+00 4656.0
29 TraesCS5B01G454800 chr5D 98.266 2191 33 4 216 2404 501711699 501709512 0.000000e+00 3831.0
30 TraesCS5B01G454800 chr5D 99.553 447 2 0 2457 2903 501709513 501709067 0.000000e+00 815.0
31 TraesCS5B01G454800 chr5D 81.151 817 133 13 1148 1946 501430235 501429422 2.290000e-178 636.0
32 TraesCS5B01G454800 chr5D 90.244 246 19 3 5584 5827 249522095 249521853 3.390000e-82 316.0
33 TraesCS5B01G454800 chr5D 88.755 249 23 4 5582 5827 294617126 294617372 3.410000e-77 300.0
34 TraesCS5B01G454800 chr5D 95.758 165 7 0 3270 3434 478161355 478161191 3.460000e-67 267.0
35 TraesCS5B01G454800 chr5D 88.571 140 12 4 5446 5584 249522824 249522688 3.610000e-37 167.0
36 TraesCS5B01G454800 chr5D 86.667 150 10 6 4598 4739 501707299 501707446 2.170000e-34 158.0
37 TraesCS5B01G454800 chr5D 73.672 433 98 14 2101 2522 501439421 501438994 2.810000e-33 154.0
38 TraesCS5B01G454800 chr5D 82.000 150 19 5 4257 4403 501427950 501427806 2.850000e-23 121.0
39 TraesCS5B01G454800 chr5D 100.000 64 0 0 4698 4761 498925820 498925883 1.030000e-22 119.0
40 TraesCS5B01G454800 chr3D 90.083 847 65 17 14 855 90351885 90351053 0.000000e+00 1081.0
41 TraesCS5B01G454800 chr3D 89.336 844 75 12 14 852 182343030 182343863 0.000000e+00 1046.0
42 TraesCS5B01G454800 chr3D 98.077 52 0 1 4739 4789 119114446 119114497 8.040000e-14 89.8
43 TraesCS5B01G454800 chr6D 89.941 845 63 16 14 852 422221015 422220187 0.000000e+00 1070.0
44 TraesCS5B01G454800 chr7D 89.413 869 63 24 3 855 434163615 434162760 0.000000e+00 1068.0
45 TraesCS5B01G454800 chr7D 95.758 165 7 0 3279 3443 174342341 174342177 3.460000e-67 267.0
46 TraesCS5B01G454800 chr2D 89.336 844 72 13 18 852 119370253 119371087 0.000000e+00 1044.0
47 TraesCS5B01G454800 chr2D 88.799 866 65 24 3 852 497917491 497918340 0.000000e+00 1033.0
48 TraesCS5B01G454800 chr2D 98.137 161 3 0 3275 3435 519335227 519335067 1.240000e-71 281.0
49 TraesCS5B01G454800 chr2D 92.350 183 10 4 3272 3453 56541158 56540979 2.080000e-64 257.0
50 TraesCS5B01G454800 chr3B 80.920 870 142 14 1111 1959 462100099 462099233 0.000000e+00 665.0
51 TraesCS5B01G454800 chr3B 83.240 179 23 7 3106 3283 462097574 462097402 2.170000e-34 158.0
52 TraesCS5B01G454800 chr2B 84.370 627 82 10 1144 1754 667422781 667422155 8.350000e-168 601.0
53 TraesCS5B01G454800 chr2B 77.551 539 81 17 2011 2524 667421976 667421453 7.390000e-74 289.0
54 TraesCS5B01G454800 chr2B 81.957 327 55 4 5260 5584 669452794 669452470 2.070000e-69 274.0
55 TraesCS5B01G454800 chr2B 81.346 327 57 3 5259 5584 179147133 179147456 4.480000e-66 263.0
56 TraesCS5B01G454800 chr2A 88.500 400 34 8 1145 1533 699529840 699529442 1.900000e-129 473.0
57 TraesCS5B01G454800 chr2A 77.740 593 92 13 1955 2523 699527576 699527000 1.570000e-85 327.0
58 TraesCS5B01G454800 chr5A 75.259 869 171 28 1118 1953 599556959 599556102 1.980000e-99 374.0
59 TraesCS5B01G454800 chr5A 75.359 767 142 29 1193 1937 629372514 629373255 5.630000e-85 326.0
60 TraesCS5B01G454800 chr5A 74.713 609 114 26 2096 2678 629249618 629249024 9.760000e-58 235.0
61 TraesCS5B01G454800 chr5A 74.465 607 113 27 2096 2678 629373396 629373984 2.110000e-54 224.0
62 TraesCS5B01G454800 chr5A 90.840 131 12 0 2720 2850 571787548 571787678 6.000000e-40 176.0
63 TraesCS5B01G454800 chr5A 86.111 144 18 2 2708 2850 311019856 311019714 2.810000e-33 154.0
64 TraesCS5B01G454800 chr5A 81.935 155 21 5 2466 2613 599555671 599555517 2.200000e-24 124.0
65 TraesCS5B01G454800 chr5A 94.915 59 3 0 4735 4793 55159029 55158971 6.220000e-15 93.5
66 TraesCS5B01G454800 chr1A 89.113 248 25 1 5582 5827 576378470 576378717 2.040000e-79 307.0
67 TraesCS5B01G454800 chr1D 88.710 248 24 3 5582 5826 479896712 479896958 3.410000e-77 300.0
68 TraesCS5B01G454800 chr1D 96.894 161 5 0 3274 3434 458883508 458883668 2.680000e-68 270.0
69 TraesCS5B01G454800 chr1D 93.103 58 3 1 4735 4791 399819766 399819823 3.740000e-12 84.2
70 TraesCS5B01G454800 chr3A 83.699 319 45 4 5258 5570 746561016 746561333 1.590000e-75 294.0
71 TraesCS5B01G454800 chr3A 90.400 125 12 0 2717 2841 177109083 177108959 1.300000e-36 165.0
72 TraesCS5B01G454800 chr3A 83.871 62 8 2 5429 5490 578955264 578955323 2.270000e-04 58.4
73 TraesCS5B01G454800 chrUn 94.444 54 3 0 4735 4788 100236654 100236601 3.740000e-12 84.2
74 TraesCS5B01G454800 chr4D 86.567 67 7 2 4731 4795 362116451 362116517 8.100000e-09 73.1
75 TraesCS5B01G454800 chr7B 95.000 40 2 0 4598 4637 403298302 403298341 4.870000e-06 63.9


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 TraesCS5B01G454800 chr5B 629075633 629081459 5826 True 5278.0 5361 100.000000 1 5827 2 chr5B.!!$R9 5826
1 TraesCS5B01G454800 chr5B 632804950 632810650 5700 False 4885.0 4892 97.613000 2 5824 2 chr5B.!!$F9 5822
2 TraesCS5B01G454800 chr5B 625447533 625452847 5314 True 4744.0 4948 98.836000 379 5827 2 chr5B.!!$R8 5448
3 TraesCS5B01G454800 chr5B 604714743 604719774 5031 True 1162.5 3005 95.525000 855 5827 6 chr5B.!!$R7 4972
4 TraesCS5B01G454800 chr5D 498924750 498930403 5653 True 4699.5 4743 96.685000 56 5827 2 chr5D.!!$R4 5771
5 TraesCS5B01G454800 chr5D 501706258 501711699 5441 True 3188.0 4918 98.692667 216 5827 3 chr5D.!!$R6 5611
6 TraesCS5B01G454800 chr5D 501427806 501430235 2429 True 378.5 636 81.575500 1148 4403 2 chr5D.!!$R5 3255
7 TraesCS5B01G454800 chr5D 249521853 249522824 971 True 241.5 316 89.407500 5446 5827 2 chr5D.!!$R3 381
8 TraesCS5B01G454800 chr3D 90351053 90351885 832 True 1081.0 1081 90.083000 14 855 1 chr3D.!!$R1 841
9 TraesCS5B01G454800 chr3D 182343030 182343863 833 False 1046.0 1046 89.336000 14 852 1 chr3D.!!$F2 838
10 TraesCS5B01G454800 chr6D 422220187 422221015 828 True 1070.0 1070 89.941000 14 852 1 chr6D.!!$R1 838
11 TraesCS5B01G454800 chr7D 434162760 434163615 855 True 1068.0 1068 89.413000 3 855 1 chr7D.!!$R2 852
12 TraesCS5B01G454800 chr2D 119370253 119371087 834 False 1044.0 1044 89.336000 18 852 1 chr2D.!!$F1 834
13 TraesCS5B01G454800 chr2D 497917491 497918340 849 False 1033.0 1033 88.799000 3 852 1 chr2D.!!$F2 849
14 TraesCS5B01G454800 chr3B 462097402 462100099 2697 True 411.5 665 82.080000 1111 3283 2 chr3B.!!$R1 2172
15 TraesCS5B01G454800 chr2B 667421453 667422781 1328 True 445.0 601 80.960500 1144 2524 2 chr2B.!!$R2 1380
16 TraesCS5B01G454800 chr2A 699527000 699529840 2840 True 400.0 473 83.120000 1145 2523 2 chr2A.!!$R1 1378
17 TraesCS5B01G454800 chr5A 629372514 629373984 1470 False 275.0 326 74.912000 1193 2678 2 chr5A.!!$F2 1485
18 TraesCS5B01G454800 chr5A 599555517 599556959 1442 True 249.0 374 78.597000 1118 2613 2 chr5A.!!$R4 1495
19 TraesCS5B01G454800 chr5A 629249024 629249618 594 True 235.0 235 74.713000 2096 2678 1 chr5A.!!$R3 582

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
191 195 0.322456 TCCATTTCCAAGAGGCACGG 60.322 55.0 0.0 0.0 33.74 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4932 7503 2.139118 GAGACAAACACTGAGGCTGTC 58.861 52.381 0.0 0.0 37.3 3.51 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
129 133 1.266989 CCTCTCGTGAAAGCAAAACCC 59.733 52.381 0.00 0.0 0.00 4.11
189 193 4.335400 TTTTTCCATTTCCAAGAGGCAC 57.665 40.909 0.00 0.0 33.74 5.01
191 195 0.322456 TCCATTTCCAAGAGGCACGG 60.322 55.000 0.00 0.0 33.74 4.94
192 196 0.609131 CCATTTCCAAGAGGCACGGT 60.609 55.000 0.00 0.0 33.74 4.83
193 197 0.804989 CATTTCCAAGAGGCACGGTC 59.195 55.000 0.00 0.0 33.74 4.79
195 199 2.035237 TTTCCAAGAGGCACGGTCGT 62.035 55.000 0.00 0.0 33.74 4.34
371 393 3.854286 GTGACTCTCGCGAAAGAAAAA 57.146 42.857 17.91 0.0 0.00 1.94
793 866 0.866061 GCGAATGACTAAGAGCGCGA 60.866 55.000 12.10 0.0 35.02 5.87
1300 1861 1.952635 GACCGCCGTTGAAGTCGTT 60.953 57.895 0.00 0.0 0.00 3.85
4668 7237 7.490402 CCGTCCCATAATATAGGAACGTTATTC 59.510 40.741 0.00 0.0 0.00 1.75
4890 7461 6.206438 AGTTTGAGATTGAAAGCCTTCTCTTC 59.794 38.462 0.00 0.0 36.43 2.87
4932 7503 3.977244 AAGCGGGTTTTGCAGGCG 61.977 61.111 0.00 0.0 33.85 5.52
5081 7652 6.696411 TGTCTGTTTTGTTTGGATTTTGTCT 58.304 32.000 0.00 0.0 0.00 3.41
5370 8024 7.277539 CACTAGCCAAACTTCAAAATGAACAAA 59.722 33.333 0.00 0.0 32.21 2.83
5459 8113 1.508632 GACGACAACAAAGCCAGCTA 58.491 50.000 0.00 0.0 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 133 2.209064 TTTCCTTCCGCGAGAGTCGG 62.209 60.000 8.23 5.60 46.94 4.79
168 172 3.243704 CGTGCCTCTTGGAAATGGAAAAA 60.244 43.478 0.00 0.00 34.57 1.94
173 177 0.609131 ACCGTGCCTCTTGGAAATGG 60.609 55.000 0.00 0.00 35.16 3.16
174 178 0.804989 GACCGTGCCTCTTGGAAATG 59.195 55.000 0.00 0.00 34.57 2.32
175 179 0.673644 CGACCGTGCCTCTTGGAAAT 60.674 55.000 0.00 0.00 34.57 2.17
180 184 2.022129 GTCACGACCGTGCCTCTTG 61.022 63.158 16.76 0.00 45.04 3.02
181 185 2.143594 GAGTCACGACCGTGCCTCTT 62.144 60.000 21.50 5.43 44.66 2.85
182 186 2.597805 AGTCACGACCGTGCCTCT 60.598 61.111 16.76 11.74 45.04 3.69
183 187 2.126424 GAGTCACGACCGTGCCTC 60.126 66.667 15.98 15.98 42.51 4.70
184 188 2.597805 AGAGTCACGACCGTGCCT 60.598 61.111 16.76 11.62 45.04 4.75
185 189 2.126424 GAGAGTCACGACCGTGCC 60.126 66.667 16.76 6.58 45.04 5.01
186 190 2.502080 CGAGAGTCACGACCGTGC 60.502 66.667 16.76 12.00 45.04 5.34
188 192 4.086178 CGCGAGAGTCACGACCGT 62.086 66.667 14.42 0.00 0.00 4.83
189 193 2.775359 TTTCGCGAGAGTCACGACCG 62.775 60.000 14.42 8.70 43.69 4.79
191 195 1.666446 GCTTTCGCGAGAGTCACGAC 61.666 60.000 25.34 6.27 43.69 4.34
192 196 1.442184 GCTTTCGCGAGAGTCACGA 60.442 57.895 25.34 6.50 43.69 4.35
193 197 1.729484 TGCTTTCGCGAGAGTCACG 60.729 57.895 25.34 5.53 43.69 4.35
195 199 0.249280 TTGTGCTTTCGCGAGAGTCA 60.249 50.000 25.34 20.22 43.69 3.41
196 200 0.161870 GTTGTGCTTTCGCGAGAGTC 59.838 55.000 25.34 18.16 43.69 3.36
199 203 2.307309 CGGTTGTGCTTTCGCGAGA 61.307 57.895 9.59 3.35 39.65 4.04
212 216 4.717629 TCGCGAGAGGCACGGTTG 62.718 66.667 3.71 0.00 43.84 3.77
213 217 3.509137 TTTCGCGAGAGGCACGGTT 62.509 57.895 9.59 0.00 43.84 4.44
215 219 3.181967 CTTTCGCGAGAGGCACGG 61.182 66.667 18.35 0.00 43.84 4.94
216 220 3.843240 GCTTTCGCGAGAGGCACG 61.843 66.667 25.84 3.72 43.84 5.34
217 221 1.841663 TTTGCTTTCGCGAGAGGCAC 61.842 55.000 25.84 11.56 45.26 5.01
218 222 1.163420 TTTTGCTTTCGCGAGAGGCA 61.163 50.000 25.84 23.78 44.45 4.75
219 223 0.726118 GTTTTGCTTTCGCGAGAGGC 60.726 55.000 25.84 21.76 43.69 4.70
391 418 3.756963 GTGCCTCTCGTAAAGGGAAAAAT 59.243 43.478 3.37 0.00 35.86 1.82
737 810 2.427506 GACGCTCCCTCTGAATTTTGT 58.572 47.619 0.00 0.00 0.00 2.83
793 866 0.606401 CAACGATCAGGGCCACTTGT 60.606 55.000 6.18 0.00 0.00 3.16
4932 7503 2.139118 GAGACAAACACTGAGGCTGTC 58.861 52.381 0.00 0.00 37.30 3.51
5081 7652 2.509548 CAGACATCCCCATCCCTAAACA 59.490 50.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.