Multiple sequence alignment - TraesCS5D01G543500

Loading Multiple Alignment...

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 TraesCS5D01G543500 chr5D 100.000 7064 0 0 1 7064 553678093 553671030 0.000000e+00 13045.0
1 TraesCS5D01G543500 chr5D 94.286 105 5 1 1 104 553658544 553658440 7.330000e-35 159.0
2 TraesCS5D01G543500 chr4A 84.098 1635 223 23 3843 5460 615039703 615041317 0.000000e+00 1544.0
3 TraesCS5D01G543500 chr4A 80.352 341 46 12 5979 6314 615042127 615042451 9.160000e-59 239.0
4 TraesCS5D01G543500 chr4A 85.484 186 19 6 1 179 614871131 614871315 3.360000e-43 187.0
5 TraesCS5D01G543500 chr5B 84.137 1431 169 34 4020 5440 697293924 697295306 0.000000e+00 1332.0
6 TraesCS5D01G543500 chr5B 84.661 1017 131 17 4564 5566 697125070 697126075 0.000000e+00 990.0
7 TraesCS5D01G543500 chr5B 81.989 1066 155 25 1481 2531 697287694 697288737 0.000000e+00 870.0
8 TraesCS5D01G543500 chr5B 89.509 591 43 10 1 577 697118035 697118620 0.000000e+00 730.0
9 TraesCS5D01G543500 chr5B 83.714 700 94 15 3800 4490 697124024 697124712 1.660000e-180 643.0
10 TraesCS5D01G543500 chr5B 78.554 401 72 12 3630 4021 697290036 697290431 1.180000e-62 252.0
11 TraesCS5D01G543500 chr5B 82.979 188 23 7 6435 6620 577082583 577082763 2.040000e-35 161.0
12 TraesCS5D01G543500 chr7B 76.043 1749 313 71 3868 5576 709559127 709560809 0.000000e+00 811.0
13 TraesCS5D01G543500 chr7B 81.732 843 131 12 4559 5383 709524952 709525789 0.000000e+00 682.0
14 TraesCS5D01G543500 chr7B 75.517 1499 293 55 3894 5349 746051886 746053353 0.000000e+00 667.0
15 TraesCS5D01G543500 chr7D 76.000 1750 287 78 3898 5587 616310755 616312431 0.000000e+00 782.0
16 TraesCS5D01G543500 chr7D 93.258 178 11 1 6426 6603 381000225 381000401 1.950000e-65 261.0
17 TraesCS5D01G543500 chr7D 95.890 146 5 1 6888 7033 71982515 71982371 1.180000e-57 235.0
18 TraesCS5D01G543500 chr7D 93.631 157 8 2 6877 7033 570276796 570276642 4.260000e-57 233.0
19 TraesCS5D01G543500 chr7D 87.709 179 21 1 6445 6622 483890736 483890558 2.580000e-49 207.0
20 TraesCS5D01G543500 chr7D 82.857 70 10 2 1426 1495 520390475 520390408 2.130000e-05 62.1
21 TraesCS5D01G543500 chr2B 79.134 1016 185 20 4556 5553 17594574 17593568 0.000000e+00 676.0
22 TraesCS5D01G543500 chr2B 79.395 859 141 25 4549 5387 17396122 17395280 2.210000e-159 573.0
23 TraesCS5D01G543500 chr2B 78.978 509 90 14 3854 4352 17595255 17594754 1.470000e-86 331.0
24 TraesCS5D01G543500 chr2B 73.684 513 112 15 4556 5051 787800957 787800451 2.020000e-40 178.0
25 TraesCS5D01G543500 chr2B 82.514 183 20 10 6435 6611 94807985 94808161 4.410000e-32 150.0
26 TraesCS5D01G543500 chr2B 82.243 107 15 2 1371 1477 418269890 418269788 9.760000e-14 89.8
27 TraesCS5D01G543500 chr3D 78.049 1066 165 41 1500 2546 539909599 539908584 6.060000e-170 608.0
28 TraesCS5D01G543500 chr3D 95.376 173 7 1 6427 6599 472443017 472442846 2.510000e-69 274.0
29 TraesCS5D01G543500 chr3D 96.364 165 6 0 6435 6599 2350724 2350560 9.030000e-69 272.0
30 TraesCS5D01G543500 chr3D 94.253 174 8 2 6431 6604 250054187 250054016 1.510000e-66 265.0
31 TraesCS5D01G543500 chr3D 96.479 142 4 1 6888 7029 604800440 604800300 4.260000e-57 233.0
32 TraesCS5D01G543500 chr3D 83.333 210 29 6 6434 6641 59924215 59924420 9.350000e-44 189.0
33 TraesCS5D01G543500 chr3D 97.297 37 1 0 1426 1462 236232984 236232948 5.920000e-06 63.9
34 TraesCS5D01G543500 chr2D 76.775 831 147 31 4572 5370 11257567 11258383 2.360000e-114 424.0
35 TraesCS5D01G543500 chr2D 77.279 691 123 26 4753 5426 11292141 11292814 6.690000e-100 375.0
36 TraesCS5D01G543500 chr2D 95.238 168 8 0 6435 6602 120100091 120099924 4.200000e-67 267.0
37 TraesCS5D01G543500 chr2D 95.775 142 5 1 6888 7029 136380372 136380512 1.980000e-55 228.0
38 TraesCS5D01G543500 chr2D 90.654 107 8 2 3261 3366 622352010 622351905 2.660000e-29 141.0
39 TraesCS5D01G543500 chr7A 82.150 493 76 9 4556 5042 709296236 709296722 5.100000e-111 412.0
40 TraesCS5D01G543500 chr7A 87.295 244 29 2 5139 5380 709296795 709297038 1.940000e-70 278.0
41 TraesCS5D01G543500 chr7A 95.105 143 7 0 6888 7030 495505227 495505369 7.130000e-55 226.0
42 TraesCS5D01G543500 chr7A 77.679 112 23 2 1370 1480 315296362 315296252 4.570000e-07 67.6
43 TraesCS5D01G543500 chr4B 95.455 176 8 0 6434 6609 97895048 97894873 1.500000e-71 281.0
44 TraesCS5D01G543500 chr1D 95.833 168 7 0 6435 6602 403044476 403044309 9.030000e-69 272.0
45 TraesCS5D01G543500 chr1D 82.857 210 31 4 6435 6641 315034929 315035136 4.350000e-42 183.0
46 TraesCS5D01G543500 chr1D 91.262 103 9 0 3269 3371 31154862 31154760 2.660000e-29 141.0
47 TraesCS5D01G543500 chr1D 89.720 107 9 2 3270 3375 258092058 258091953 1.240000e-27 135.0
48 TraesCS5D01G543500 chr6D 93.889 180 10 1 6424 6602 119803528 119803707 3.250000e-68 270.0
49 TraesCS5D01G543500 chr6D 95.804 143 6 0 6888 7030 426639432 426639290 1.530000e-56 231.0
50 TraesCS5D01G543500 chr6D 78.723 94 17 3 1370 1462 223454552 223454461 7.650000e-05 60.2
51 TraesCS5D01G543500 chr5A 93.785 177 11 0 6434 6610 436260735 436260559 4.200000e-67 267.0
52 TraesCS5D01G543500 chr5A 83.684 190 26 4 6435 6623 37590761 37590946 2.620000e-39 174.0
53 TraesCS5D01G543500 chr5A 80.000 95 12 7 1370 1461 95672442 95672352 5.920000e-06 63.9
54 TraesCS5D01G543500 chr4D 97.183 142 4 0 6888 7029 17560313 17560454 2.550000e-59 241.0
55 TraesCS5D01G543500 chr4D 97.183 142 3 1 6888 7029 507858228 507858368 9.160000e-59 239.0
56 TraesCS5D01G543500 chr4D 79.787 94 16 3 1370 1462 152155305 152155214 1.640000e-06 65.8
57 TraesCS5D01G543500 chr3A 85.586 222 24 5 2683 2902 674755095 674754880 7.130000e-55 226.0
58 TraesCS5D01G543500 chr3A 89.720 107 10 1 3262 3367 7126828 7126934 1.240000e-27 135.0
59 TraesCS5D01G543500 chr2A 95.105 143 6 1 6888 7030 207465078 207465219 2.560000e-54 224.0
60 TraesCS5D01G543500 chr2A 72.745 510 113 20 4556 5051 771805383 771804886 1.590000e-31 148.0
61 TraesCS5D01G543500 chr2A 97.297 37 1 0 1426 1462 106518122 106518086 5.920000e-06 63.9
62 TraesCS5D01G543500 chr3B 75.000 464 93 17 3895 4350 1372869 1373317 7.230000e-45 193.0
63 TraesCS5D01G543500 chr3B 89.286 140 15 0 2578 2717 715890897 715890758 7.280000e-40 176.0
64 TraesCS5D01G543500 chr3B 90.566 106 9 1 3262 3366 4219307 4219202 9.550000e-29 139.0
65 TraesCS5D01G543500 chr3B 89.623 106 10 1 3262 3366 5074752 5074647 4.450000e-27 134.0
66 TraesCS5D01G543500 chr3B 83.133 83 6 7 6539 6620 524326234 524326309 1.270000e-07 69.4
67 TraesCS5D01G543500 chr1B 82.857 210 31 4 6435 6641 426855320 426855527 4.350000e-42 183.0
68 TraesCS5D01G543500 chr1B 90.654 107 9 1 3270 3375 354987434 354987540 2.660000e-29 141.0
69 TraesCS5D01G543500 chr1A 92.784 97 7 0 3270 3366 489239018 489238922 2.660000e-29 141.0
70 TraesCS5D01G543500 chr1A 90.476 105 9 1 3267 3370 385895955 385896059 3.440000e-28 137.0
71 TraesCS5D01G543500 chr1A 81.111 90 13 4 1374 1461 478551102 478551015 1.270000e-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 TraesCS5D01G543500 chr5D 553671030 553678093 7063 True 13045.0 13045 100.0000 1 7064 1 chr5D.!!$R2 7063
1 TraesCS5D01G543500 chr4A 615039703 615042451 2748 False 891.5 1544 82.2250 3843 6314 2 chr4A.!!$F2 2471
2 TraesCS5D01G543500 chr5B 697287694 697295306 7612 False 818.0 1332 81.5600 1481 5440 3 chr5B.!!$F4 3959
3 TraesCS5D01G543500 chr5B 697124024 697126075 2051 False 816.5 990 84.1875 3800 5566 2 chr5B.!!$F3 1766
4 TraesCS5D01G543500 chr5B 697118035 697118620 585 False 730.0 730 89.5090 1 577 1 chr5B.!!$F2 576
5 TraesCS5D01G543500 chr7B 709559127 709560809 1682 False 811.0 811 76.0430 3868 5576 1 chr7B.!!$F2 1708
6 TraesCS5D01G543500 chr7B 709524952 709525789 837 False 682.0 682 81.7320 4559 5383 1 chr7B.!!$F1 824
7 TraesCS5D01G543500 chr7B 746051886 746053353 1467 False 667.0 667 75.5170 3894 5349 1 chr7B.!!$F3 1455
8 TraesCS5D01G543500 chr7D 616310755 616312431 1676 False 782.0 782 76.0000 3898 5587 1 chr7D.!!$F2 1689
9 TraesCS5D01G543500 chr2B 17395280 17396122 842 True 573.0 573 79.3950 4549 5387 1 chr2B.!!$R1 838
10 TraesCS5D01G543500 chr2B 17593568 17595255 1687 True 503.5 676 79.0560 3854 5553 2 chr2B.!!$R4 1699
11 TraesCS5D01G543500 chr3D 539908584 539909599 1015 True 608.0 608 78.0490 1500 2546 1 chr3D.!!$R5 1046
12 TraesCS5D01G543500 chr2D 11257567 11258383 816 False 424.0 424 76.7750 4572 5370 1 chr2D.!!$F1 798
13 TraesCS5D01G543500 chr2D 11292141 11292814 673 False 375.0 375 77.2790 4753 5426 1 chr2D.!!$F2 673
14 TraesCS5D01G543500 chr7A 709296236 709297038 802 False 345.0 412 84.7225 4556 5380 2 chr7A.!!$F2 824


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
717 729 0.039911 AGCCGAGTAGAGTGGACCTT 59.960 55.000 0.00 0.0 0.00 3.50 F
953 965 0.040058 TCCCTTGCTTGCATCCACAT 59.960 50.000 0.00 0.0 0.00 3.21 F
963 975 0.099436 GCATCCACATCTTGTTCCGC 59.901 55.000 0.00 0.0 0.00 5.54 F
966 978 0.109532 TCCACATCTTGTTCCGCCAA 59.890 50.000 0.00 0.0 0.00 4.52 F
970 982 0.109597 CATCTTGTTCCGCCAACTGC 60.110 55.000 0.00 0.0 35.79 4.40 F
2840 3065 0.178992 CTGGGGCAAAGAACCAGTGA 60.179 55.000 0.00 0.0 45.21 3.41 F
2936 3161 0.030773 TCACGTGCTCACTCACACTC 59.969 55.000 11.67 0.0 36.80 3.51 F
2937 3162 0.031314 CACGTGCTCACTCACACTCT 59.969 55.000 0.82 0.0 36.80 3.24 F
2938 3163 0.031314 ACGTGCTCACTCACACTCTG 59.969 55.000 0.00 0.0 36.80 3.35 F
2940 3165 0.033228 GTGCTCACTCACACTCTGCT 59.967 55.000 0.00 0.0 36.97 4.24 F
3384 3609 0.038744 ACATGTTCTTCAGCCCCAGG 59.961 55.000 0.00 0.0 0.00 4.45 F
3892 4761 0.463654 TGCAGACAACACCCACACTC 60.464 55.000 0.00 0.0 0.00 3.51 F
3893 4762 0.463654 GCAGACAACACCCACACTCA 60.464 55.000 0.00 0.0 0.00 3.41 F
5266 10053 1.446792 CTGCGTGAATCCTGAGCGT 60.447 57.895 0.00 0.0 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2032 0.251354 TCCAGCTCACCTGATTCAGC 59.749 55.000 8.23 0.00 44.64 4.26 R
2917 3142 0.030773 GAGTGTGAGTGAGCACGTGA 59.969 55.000 22.23 0.00 41.63 4.35 R
2918 3143 0.031314 AGAGTGTGAGTGAGCACGTG 59.969 55.000 12.28 12.28 41.63 4.49 R
2919 3144 0.031314 CAGAGTGTGAGTGAGCACGT 59.969 55.000 0.00 0.00 41.63 4.49 R
2921 3146 0.033228 AGCAGAGTGTGAGTGAGCAC 59.967 55.000 0.00 0.00 39.22 4.40 R
4609 9306 0.036875 GCCCATAGGAAATCCCCTCG 59.963 60.000 0.00 0.00 37.74 4.63 R
4627 9324 0.100861 GCTCGTGGAGGTACTGTAGC 59.899 60.000 8.91 8.91 41.55 3.58 R
4872 9601 5.662456 TGCATTAACATGAATGGGTGAATG 58.338 37.500 0.00 0.00 37.31 2.67 R
5053 9804 5.067805 GGGGCCTCAAAAGTTTATACAGATG 59.932 44.000 0.84 0.00 0.00 2.90 R
5075 9844 3.010138 TGACATGGTCTTTAGGAAAGGGG 59.990 47.826 0.00 0.00 39.01 4.79 R
5169 9953 3.525268 ACCTTGGTTCTTTTTGCAGTG 57.475 42.857 0.00 0.00 0.00 3.66 R
5648 10583 2.348472 TGGACTCTGAAACCATTCCCT 58.652 47.619 0.00 0.00 34.49 4.20 R
6028 11181 2.579873 CTGGATGTTGGGGCTTGATAG 58.420 52.381 0.00 0.00 0.00 2.08 R
6917 12073 0.033601 AATGGGACCATTTAGCGGCA 60.034 50.000 10.71 0.00 43.32 5.69 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)



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

AutoCloner maintained by Alex Coulton.