Multiple sequence alignment - TraesCS6D01G364700

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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 TraesCS6D01G364700 chr6D 100.000 2473 0 0 1 2473 454294395 454296867 0.000000e+00 4567.0
1 TraesCS6D01G364700 chr6D 92.933 566 36 3 1653 2216 427067717 427067154 0.000000e+00 821.0
2 TraesCS6D01G364700 chr6D 86.275 102 8 6 70 168 407787303 407787401 3.360000e-19 106.0
3 TraesCS6D01G364700 chr6D 85.149 101 11 4 70 168 380669265 380669167 1.560000e-17 100.0
4 TraesCS6D01G364700 chr6D 85.567 97 9 5 74 168 446805699 446805792 2.020000e-16 97.1
5 TraesCS6D01G364700 chr6D 82.727 110 12 7 72 177 232312191 232312085 9.420000e-15 91.6
6 TraesCS6D01G364700 chr2D 96.643 834 18 1 1650 2473 312054398 312053565 0.000000e+00 1376.0
7 TraesCS6D01G364700 chr2D 93.391 575 34 4 1643 2216 604060261 604060832 0.000000e+00 848.0
8 TraesCS6D01G364700 chr2D 85.965 114 12 2 58 168 49259638 49259526 4.320000e-23 119.0
9 TraesCS6D01G364700 chr6B 94.286 770 31 4 887 1650 690756996 690757758 0.000000e+00 1166.0
10 TraesCS6D01G364700 chr6B 93.651 567 35 1 1650 2216 65854866 65854301 0.000000e+00 846.0
11 TraesCS6D01G364700 chr6B 91.259 572 45 2 298 864 543844510 543845081 0.000000e+00 774.0
12 TraesCS6D01G364700 chr6B 95.087 346 14 3 546 888 704955061 704955406 2.160000e-150 542.0
13 TraesCS6D01G364700 chr6B 80.882 680 118 7 974 1650 689996531 689995861 2.180000e-145 525.0
14 TraesCS6D01G364700 chr6B 87.129 101 9 4 70 168 531747252 531747154 7.230000e-21 111.0
15 TraesCS6D01G364700 chr3B 94.386 570 27 2 1649 2216 806968746 806968180 0.000000e+00 870.0
16 TraesCS6D01G364700 chr3B 92.807 570 36 2 1649 2216 56905511 56906077 0.000000e+00 821.0
17 TraesCS6D01G364700 chr3B 99.020 306 2 1 584 888 767495886 767496191 4.650000e-152 547.0
18 TraesCS6D01G364700 chr3B 88.889 90 7 3 70 157 510462307 510462395 9.350000e-20 108.0
19 TraesCS6D01G364700 chr3B 95.000 40 1 1 286 325 29150098 29150136 7.380000e-06 62.1
20 TraesCS6D01G364700 chr3B 94.737 38 2 0 288 325 56982432 56982395 2.660000e-05 60.2
21 TraesCS6D01G364700 chr3B 92.308 39 2 1 287 325 766028818 766028781 1.000000e-03 54.7
22 TraesCS6D01G364700 chr4B 92.530 589 36 5 1632 2216 636704253 636704837 0.000000e+00 837.0
23 TraesCS6D01G364700 chr7A 93.829 551 34 0 1666 2216 38803586 38803036 0.000000e+00 830.0
24 TraesCS6D01G364700 chr7A 92.657 572 39 2 1648 2216 155208536 155207965 0.000000e+00 821.0
25 TraesCS6D01G364700 chr7A 92.171 281 19 2 308 588 584035686 584035963 6.410000e-106 394.0
26 TraesCS6D01G364700 chr7A 89.744 273 18 2 2211 2473 509806978 509806706 8.470000e-90 340.0
27 TraesCS6D01G364700 chr6A 91.597 595 43 6 298 889 54490306 54490896 0.000000e+00 815.0
28 TraesCS6D01G364700 chr6A 95.908 391 16 0 1257 1647 600527434 600527824 3.470000e-178 634.0
29 TraesCS6D01G364700 chr6A 96.543 376 13 0 887 1262 600513567 600513942 7.510000e-175 623.0
30 TraesCS6D01G364700 chr6A 94.118 238 13 1 1 237 600513261 600513498 6.500000e-96 361.0
31 TraesCS6D01G364700 chr6A 86.408 103 9 5 72 173 254324950 254324852 9.350000e-20 108.0
32 TraesCS6D01G364700 chr3D 96.629 445 5 1 2039 2473 67540752 67540308 0.000000e+00 730.0
33 TraesCS6D01G364700 chr3D 96.642 268 9 0 319 586 340147368 340147635 1.740000e-121 446.0
34 TraesCS6D01G364700 chr1A 88.571 595 48 13 298 888 220985338 220985916 0.000000e+00 704.0
35 TraesCS6D01G364700 chr1A 96.642 268 9 0 319 586 11240103 11240370 1.740000e-121 446.0
36 TraesCS6D01G364700 chr1A 89.091 110 11 1 60 168 69398143 69398034 4.290000e-28 135.0
37 TraesCS6D01G364700 chr5D 85.925 611 64 20 295 888 518286709 518287314 1.250000e-177 632.0
38 TraesCS6D01G364700 chr5D 86.364 110 11 4 65 173 207522863 207522757 1.550000e-22 117.0
39 TraesCS6D01G364700 chr5D 83.784 111 14 4 70 178 165036072 165036180 4.350000e-18 102.0
40 TraesCS6D01G364700 chr2B 84.288 611 65 28 298 886 213340510 213339909 3.570000e-158 568.0
41 TraesCS6D01G364700 chr2B 94.100 339 16 4 553 888 460963561 460963898 1.700000e-141 512.0
42 TraesCS6D01G364700 chr2B 86.364 352 43 5 322 668 116792499 116792148 1.790000e-101 379.0
43 TraesCS6D01G364700 chr1D 97.508 321 4 4 572 888 469385345 469385665 1.670000e-151 545.0
44 TraesCS6D01G364700 chr1D 98.693 306 3 1 584 888 267863081 267863386 2.160000e-150 542.0
45 TraesCS6D01G364700 chr1D 88.172 93 7 4 86 178 470584902 470584990 9.350000e-20 108.0
46 TraesCS6D01G364700 chr1D 84.404 109 11 5 65 171 157156222 157156118 4.350000e-18 102.0
47 TraesCS6D01G364700 chr1D 88.235 85 8 2 84 168 385187934 385187852 1.560000e-17 100.0
48 TraesCS6D01G364700 chr1D 85.149 101 10 4 70 168 8943821 8943918 5.630000e-17 99.0
49 TraesCS6D01G364700 chr1D 84.158 101 12 4 70 168 150904770 150904868 7.280000e-16 95.3
50 TraesCS6D01G364700 chr1D 82.692 104 14 4 70 171 362239424 362239323 3.390000e-14 89.8
51 TraesCS6D01G364700 chr1D 83.333 102 12 5 70 168 473257822 473257921 3.390000e-14 89.8
52 TraesCS6D01G364700 chr1D 87.179 78 8 2 86 163 91078411 91078336 1.220000e-13 87.9
53 TraesCS6D01G364700 chr3A 96.642 268 9 0 319 586 505743478 505743745 1.740000e-121 446.0
54 TraesCS6D01G364700 chr3A 92.150 293 23 0 298 590 587389775 587390067 4.920000e-112 414.0
55 TraesCS6D01G364700 chr3A 86.080 352 46 3 319 668 587390061 587390411 2.320000e-100 375.0
56 TraesCS6D01G364700 chr3A 90.323 279 23 4 308 584 564439743 564440019 1.810000e-96 363.0
57 TraesCS6D01G364700 chr2A 96.310 271 10 0 316 586 717765596 717765866 1.740000e-121 446.0
58 TraesCS6D01G364700 chr2A 94.595 37 1 1 289 325 293936767 293936802 3.440000e-04 56.5
59 TraesCS6D01G364700 chr7D 93.115 305 18 3 321 622 571322712 571323016 6.280000e-121 444.0
60 TraesCS6D01G364700 chr5A 96.970 264 8 0 321 584 281586630 281586893 6.280000e-121 444.0
61 TraesCS6D01G364700 chr5A 85.714 112 10 6 59 168 374690169 374690276 2.010000e-21 113.0
62 TraesCS6D01G364700 chr5A 90.909 44 3 1 283 325 399773646 399773689 9.550000e-05 58.4
63 TraesCS6D01G364700 chr1B 96.283 269 10 0 319 587 368956115 368956383 2.260000e-120 442.0
64 TraesCS6D01G364700 chr4A 90.657 289 27 0 307 595 470875135 470875423 3.860000e-103 385.0
65 TraesCS6D01G364700 chr4A 85.859 99 11 3 65 163 469238205 469238300 4.350000e-18 102.0
66 TraesCS6D01G364700 chr4D 90.406 271 16 5 2213 2473 19506366 19506096 5.060000e-92 348.0
67 TraesCS6D01G364700 chr4D 88.186 237 27 1 308 544 420921938 420922173 5.210000e-72 281.0
68 TraesCS6D01G364700 chr4D 84.348 115 15 3 65 178 490289463 490289575 2.600000e-20 110.0
69 TraesCS6D01G364700 chr4D 85.849 106 10 4 65 168 80171807 80171909 9.350000e-20 108.0
70 TraesCS6D01G364700 chr4D 85.149 101 12 3 70 168 219623409 219623310 1.560000e-17 100.0
71 TraesCS6D01G364700 chr5B 82.906 117 14 6 66 178 424528766 424528880 1.560000e-17 100.0


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 TraesCS6D01G364700 chr6D 454294395 454296867 2472 False 4567.0 4567 100.0000 1 2473 1 chr6D.!!$F3 2472
1 TraesCS6D01G364700 chr6D 427067154 427067717 563 True 821.0 821 92.9330 1653 2216 1 chr6D.!!$R3 563
2 TraesCS6D01G364700 chr2D 312053565 312054398 833 True 1376.0 1376 96.6430 1650 2473 1 chr2D.!!$R2 823
3 TraesCS6D01G364700 chr2D 604060261 604060832 571 False 848.0 848 93.3910 1643 2216 1 chr2D.!!$F1 573
4 TraesCS6D01G364700 chr6B 690756996 690757758 762 False 1166.0 1166 94.2860 887 1650 1 chr6B.!!$F2 763
5 TraesCS6D01G364700 chr6B 65854301 65854866 565 True 846.0 846 93.6510 1650 2216 1 chr6B.!!$R1 566
6 TraesCS6D01G364700 chr6B 543844510 543845081 571 False 774.0 774 91.2590 298 864 1 chr6B.!!$F1 566
7 TraesCS6D01G364700 chr6B 689995861 689996531 670 True 525.0 525 80.8820 974 1650 1 chr6B.!!$R3 676
8 TraesCS6D01G364700 chr3B 806968180 806968746 566 True 870.0 870 94.3860 1649 2216 1 chr3B.!!$R3 567
9 TraesCS6D01G364700 chr3B 56905511 56906077 566 False 821.0 821 92.8070 1649 2216 1 chr3B.!!$F2 567
10 TraesCS6D01G364700 chr4B 636704253 636704837 584 False 837.0 837 92.5300 1632 2216 1 chr4B.!!$F1 584
11 TraesCS6D01G364700 chr7A 38803036 38803586 550 True 830.0 830 93.8290 1666 2216 1 chr7A.!!$R1 550
12 TraesCS6D01G364700 chr7A 155207965 155208536 571 True 821.0 821 92.6570 1648 2216 1 chr7A.!!$R2 568
13 TraesCS6D01G364700 chr6A 54490306 54490896 590 False 815.0 815 91.5970 298 889 1 chr6A.!!$F1 591
14 TraesCS6D01G364700 chr6A 600513261 600513942 681 False 492.0 623 95.3305 1 1262 2 chr6A.!!$F3 1261
15 TraesCS6D01G364700 chr1A 220985338 220985916 578 False 704.0 704 88.5710 298 888 1 chr1A.!!$F2 590
16 TraesCS6D01G364700 chr5D 518286709 518287314 605 False 632.0 632 85.9250 295 888 1 chr5D.!!$F2 593
17 TraesCS6D01G364700 chr2B 213339909 213340510 601 True 568.0 568 84.2880 298 886 1 chr2B.!!$R2 588
18 TraesCS6D01G364700 chr3A 587389775 587390411 636 False 394.5 414 89.1150 298 668 2 chr3A.!!$F3 370

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
273 291 0.881796 TTTTGGTGTGCACGTGTTGA 59.118 45.0 18.38 0.0 0.0 3.18 F
1399 1714 1.045407 AGAAGGCGAGTGTGTTACCA 58.955 50.0 0.00 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1743 0.321564 TTGATTGTCGTGGAGGCCAG 60.322 55.0 5.01 0.0 32.34 4.85 R
2261 2583 0.600057 GAAGCAAGCTTTGGGAGTGG 59.400 55.0 8.91 0.0 36.26 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.922305 GTCTCTTATCTTTCAAAAATATCACCG 57.078 33.333 0.00 0.00 0.00 4.94
110 112 7.617533 AAATTTTTATCACGTTTGGACTTCG 57.382 32.000 0.00 0.00 0.00 3.79
126 128 6.674066 TGGACTTCGTTTGGTATGATTTTTC 58.326 36.000 0.00 0.00 0.00 2.29
128 130 6.801862 GGACTTCGTTTGGTATGATTTTTCTG 59.198 38.462 0.00 0.00 0.00 3.02
130 132 7.138736 ACTTCGTTTGGTATGATTTTTCTGTG 58.861 34.615 0.00 0.00 0.00 3.66
168 170 5.645929 TGCAAAGAAACAGAAACTGACACTA 59.354 36.000 5.76 0.00 35.18 2.74
231 233 2.159282 AGTAACGCAACCACTATCTCCG 60.159 50.000 0.00 0.00 0.00 4.63
237 239 2.872858 GCAACCACTATCTCCGGAAATC 59.127 50.000 5.23 0.00 0.00 2.17
272 290 1.702886 TTTTTGGTGTGCACGTGTTG 58.297 45.000 18.38 0.00 0.00 3.33
273 291 0.881796 TTTTGGTGTGCACGTGTTGA 59.118 45.000 18.38 0.00 0.00 3.18
274 292 1.098869 TTTGGTGTGCACGTGTTGAT 58.901 45.000 18.38 0.00 0.00 2.57
527 559 7.706159 TCATTAATTACTTGCCACATAAGCAG 58.294 34.615 0.00 0.00 42.17 4.24
545 843 2.726066 GCAGAATTTTCTCGAAGTGCGG 60.726 50.000 0.00 0.00 41.33 5.69
759 1063 6.527423 ACATGCATTGGTCAATTTTCTCTTT 58.473 32.000 0.00 0.00 0.00 2.52
873 1179 9.487442 AAATTTTGAGATAAGCCCTATAAACCA 57.513 29.630 0.00 0.00 0.00 3.67
921 1227 3.598019 ATTGTGTGCATTGATGGGAAC 57.402 42.857 0.00 0.00 0.00 3.62
1046 1355 3.439154 TCTCCTTCAGAGCTCACAGATT 58.561 45.455 17.77 0.00 42.90 2.40
1330 1645 1.383456 GCCATCGCCAAAGCCATGTA 61.383 55.000 0.00 0.00 36.00 2.29
1374 1689 2.221169 TGCGTCGAACGTATAGGGTAT 58.779 47.619 0.00 0.00 44.73 2.73
1399 1714 1.045407 AGAAGGCGAGTGTGTTACCA 58.955 50.000 0.00 0.00 0.00 3.25
1428 1743 3.843510 GCAAGTGTACGTACTGCACAAAC 60.844 47.826 25.14 15.02 37.93 2.93
1488 1803 2.742428 AGGATGGGATGTCATGTTGG 57.258 50.000 0.00 0.00 0.00 3.77
1597 1912 7.869429 ACTTGCTTCTTGAATTATTTGAGGTTG 59.131 33.333 0.00 0.00 0.00 3.77
1622 1937 6.649141 GTGAGGTGAGTTATGTGATGTTTACA 59.351 38.462 0.00 0.00 0.00 2.41
1623 1938 6.649141 TGAGGTGAGTTATGTGATGTTTACAC 59.351 38.462 0.00 0.00 38.55 2.90
1725 2040 2.038033 CTCAAGTAACCCTTCCCGAACA 59.962 50.000 0.00 0.00 0.00 3.18
2269 2591 1.001764 CAGCATTCTGCCACTCCCA 60.002 57.895 0.00 0.00 46.52 4.37
2337 2659 1.368850 GAAACTTGTGTGCGGTCGC 60.369 57.895 8.54 8.54 42.35 5.19
2464 2796 4.022464 TGTAAGGCGAAAACAACACAAG 57.978 40.909 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.043625 CCACAAGCTTGCATGGTGT 58.956 52.632 26.27 2.31 0.00 4.16
44 45 2.516227 AGAGACCAGAAGATCCACGA 57.484 50.000 0.00 0.00 0.00 4.35
84 85 8.624028 CGAAGTCCAAACGTGATAAAAATTTAC 58.376 33.333 0.00 0.00 0.00 2.01
99 100 5.622770 ATCATACCAAACGAAGTCCAAAC 57.377 39.130 0.00 0.00 45.00 2.93
110 112 8.641499 TGTTTCACAGAAAAATCATACCAAAC 57.359 30.769 0.00 0.00 0.00 2.93
140 142 8.289618 GTGTCAGTTTCTGTTTCTTTGCATATA 58.710 33.333 0.00 0.00 32.61 0.86
154 156 6.529829 GCTCTAATGTCTAGTGTCAGTTTCTG 59.470 42.308 0.00 0.00 0.00 3.02
168 170 6.409704 TGCTTGTTTGATAGCTCTAATGTCT 58.590 36.000 0.00 0.00 38.22 3.41
216 218 2.396590 TTTCCGGAGATAGTGGTTGC 57.603 50.000 3.34 0.00 0.00 4.17
263 281 0.095245 CGTCATGGATCAACACGTGC 59.905 55.000 17.22 0.00 0.00 5.34
264 282 1.428448 ACGTCATGGATCAACACGTG 58.572 50.000 15.48 15.48 41.90 4.49
265 283 2.602878 GTACGTCATGGATCAACACGT 58.397 47.619 12.50 12.50 45.23 4.49
266 284 1.924524 GGTACGTCATGGATCAACACG 59.075 52.381 0.00 2.47 36.54 4.49
267 285 3.119101 AGAGGTACGTCATGGATCAACAC 60.119 47.826 17.27 0.00 0.00 3.32
268 286 3.096852 AGAGGTACGTCATGGATCAACA 58.903 45.455 17.27 0.00 0.00 3.33
269 287 3.802948 AGAGGTACGTCATGGATCAAC 57.197 47.619 17.27 0.00 0.00 3.18
270 288 4.274978 TGTAGAGGTACGTCATGGATCAA 58.725 43.478 17.27 0.00 30.95 2.57
271 289 3.893521 TGTAGAGGTACGTCATGGATCA 58.106 45.455 17.27 4.80 30.95 2.92
272 290 5.455056 AATGTAGAGGTACGTCATGGATC 57.545 43.478 17.27 2.60 30.95 3.36
273 291 6.069331 AGTAATGTAGAGGTACGTCATGGAT 58.931 40.000 17.27 3.90 30.95 3.41
274 292 5.443283 AGTAATGTAGAGGTACGTCATGGA 58.557 41.667 17.27 0.00 30.95 3.41
442 460 6.642950 ACTTTTCAAGACAAGATGAGTCTACG 59.357 38.462 3.20 0.00 45.11 3.51
527 559 4.092968 ACATACCGCACTTCGAGAAAATTC 59.907 41.667 0.00 0.00 41.67 2.17
545 843 8.134261 GTGGGAGTAACTTAGCTAGTAACATAC 58.866 40.741 0.00 0.00 35.54 2.39
759 1063 8.142551 TGCATTAAATCATTGCATGCAAGTATA 58.857 29.630 34.15 20.70 40.64 1.47
873 1179 3.261818 ACACACTACTCCCTCCTTTCT 57.738 47.619 0.00 0.00 0.00 2.52
921 1227 6.898912 AATCATGTAGCATGCAGATATACG 57.101 37.500 21.98 1.94 31.11 3.06
985 1294 5.971763 AGCCGTTTTATATTGAATTTGCCA 58.028 33.333 0.00 0.00 0.00 4.92
993 1302 6.767524 AATGGACAAGCCGTTTTATATTGA 57.232 33.333 0.00 0.00 43.47 2.57
1004 1313 2.091541 ACCAACATAATGGACAAGCCG 58.908 47.619 0.00 0.00 43.54 5.52
1046 1355 2.108168 AGACTTGCCGATAGTTGCCTA 58.892 47.619 0.00 0.00 0.00 3.93
1330 1645 4.822896 TGCCTTACGACAAGTTTGGTTATT 59.177 37.500 0.00 0.00 0.00 1.40
1374 1689 2.031012 CACTCGCCTTCTGTGCCA 59.969 61.111 0.00 0.00 0.00 4.92
1399 1714 1.050204 TACGTACACTTGCACCCCTT 58.950 50.000 0.00 0.00 0.00 3.95
1428 1743 0.321564 TTGATTGTCGTGGAGGCCAG 60.322 55.000 5.01 0.00 32.34 4.85
1560 1875 5.775686 TCAAGAAGCAAGTCCAAATTCATG 58.224 37.500 0.00 0.00 0.00 3.07
1597 1912 6.649141 TGTAAACATCACATAACTCACCTCAC 59.351 38.462 0.00 0.00 0.00 3.51
1675 1990 1.134848 GCAAATTTATTCGCTGGCCCA 60.135 47.619 0.00 0.00 0.00 5.36
1973 2289 6.037830 TGCCGCATTTTCTTACTATTTCTACC 59.962 38.462 0.00 0.00 0.00 3.18
2261 2583 0.600057 GAAGCAAGCTTTGGGAGTGG 59.400 55.000 8.91 0.00 36.26 4.00
2269 2591 4.635765 TCGCTACAATATGAAGCAAGCTTT 59.364 37.500 8.91 0.00 36.26 3.51


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

AutoCloner maintained by Alex Coulton.