Multiple sequence alignment - TraesCS5D01G052000

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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 TraesCS5D01G052000 chr5D 100.000 4520 0 0 1 4520 49764866 49760347 0.000000e+00 8347.0
1 TraesCS5D01G052000 chr5D 96.990 4552 65 21 1 4520 50201523 50197012 0.000000e+00 7581.0
2 TraesCS5D01G052000 chr5D 98.526 3324 16 6 1222 4519 50039228 50035912 0.000000e+00 5836.0
3 TraesCS5D01G052000 chr5D 100.000 569 0 0 1 569 50040429 50039861 0.000000e+00 1051.0
4 TraesCS5D01G052000 chr5D 89.231 65 6 1 2129 2192 45487978 45487914 3.750000e-11 80.5
5 TraesCS5D01G052000 chr5A 96.039 4569 85 26 1 4520 39245493 39240972 0.000000e+00 7347.0
6 TraesCS5D01G052000 chr5A 88.318 214 15 5 4170 4373 708833762 708833549 9.710000e-62 248.0
7 TraesCS5D01G052000 chr5A 92.473 93 7 0 4428 4520 551344177 551344085 2.840000e-27 134.0
8 TraesCS5D01G052000 chr5A 77.990 209 36 7 2072 2278 36365651 36365451 6.140000e-24 122.0
9 TraesCS5D01G052000 chr5A 86.364 110 12 2 4012 4118 490149677 490149786 2.860000e-22 117.0
10 TraesCS5D01G052000 chr5B 97.729 3038 49 4 904 3939 52649891 52646872 0.000000e+00 5210.0
11 TraesCS5D01G052000 chr5B 97.607 3009 52 4 904 3910 52915053 52918043 0.000000e+00 5140.0
12 TraesCS5D01G052000 chr5B 96.139 518 7 7 4012 4520 52646625 52646112 0.000000e+00 833.0
13 TraesCS5D01G052000 chr5B 77.754 463 63 22 1028 1483 45539559 45539130 9.710000e-62 248.0
14 TraesCS5D01G052000 chr5B 88.517 209 14 7 698 904 52650843 52650643 1.260000e-60 244.0
15 TraesCS5D01G052000 chr5B 88.517 209 14 7 698 904 52914101 52914301 1.260000e-60 244.0
16 TraesCS5D01G052000 chr5B 92.143 140 11 0 4381 4520 676178044 676177905 9.920000e-47 198.0
17 TraesCS5D01G052000 chr5B 79.894 189 27 8 2072 2258 45538274 45538095 1.320000e-25 128.0
18 TraesCS5D01G052000 chr5B 100.000 53 0 0 3961 4013 52646698 52646646 1.030000e-16 99.0
19 TraesCS5D01G052000 chrUn 97.354 1814 31 3 2099 3910 371433358 371431560 0.000000e+00 3068.0
20 TraesCS5D01G052000 chrUn 99.781 915 2 0 918 1832 460220116 460221030 0.000000e+00 1679.0
21 TraesCS5D01G052000 chr4A 88.322 608 62 4 23 629 37772262 37771663 0.000000e+00 721.0
22 TraesCS5D01G052000 chr4A 88.839 224 19 4 4156 4373 261150484 261150707 2.070000e-68 270.0
23 TraesCS5D01G052000 chr2B 89.068 558 55 5 74 628 91033229 91033783 0.000000e+00 688.0
24 TraesCS5D01G052000 chr1B 91.411 326 27 1 23 347 554692032 554692357 3.210000e-121 446.0
25 TraesCS5D01G052000 chr1B 86.192 239 29 3 366 604 554692345 554692579 5.800000e-64 255.0
26 TraesCS5D01G052000 chr6A 90.233 215 15 2 4165 4373 15380607 15380821 4.450000e-70 276.0
27 TraesCS5D01G052000 chr6D 87.946 224 20 5 4156 4373 14025586 14025808 1.610000e-64 257.0
28 TraesCS5D01G052000 chr6D 92.941 85 5 1 2939 3022 90111901 90111817 6.140000e-24 122.0
29 TraesCS5D01G052000 chr2A 94.479 163 9 0 23 185 772955261 772955099 7.510000e-63 252.0
30 TraesCS5D01G052000 chr2A 95.000 100 5 0 4421 4520 527320832 527320931 1.680000e-34 158.0
31 TraesCS5D01G052000 chr2A 82.857 140 13 1 4381 4520 740649763 740649635 1.030000e-21 115.0
32 TraesCS5D01G052000 chr2A 84.545 110 14 2 4012 4118 720953656 720953765 6.180000e-19 106.0
33 TraesCS5D01G052000 chr2D 93.865 163 10 0 23 185 647525440 647525602 3.490000e-61 246.0
34 TraesCS5D01G052000 chr2D 91.765 85 7 0 2938 3022 425742653 425742569 7.940000e-23 119.0
35 TraesCS5D01G052000 chr1A 94.964 139 7 0 47 185 495450790 495450652 7.610000e-53 219.0
36 TraesCS5D01G052000 chr1A 94.406 143 6 2 3189 3330 547018797 547018656 7.610000e-53 219.0
37 TraesCS5D01G052000 chr1A 94.928 138 6 1 3191 3328 388684886 388685022 9.850000e-52 215.0
38 TraesCS5D01G052000 chr4B 93.151 146 6 3 3192 3334 13408963 13409107 1.270000e-50 211.0
39 TraesCS5D01G052000 chr7A 91.241 137 12 0 4384 4520 422041561 422041697 2.150000e-43 187.0
40 TraesCS5D01G052000 chr7A 84.733 131 18 2 4374 4502 599245358 599245488 3.670000e-26 130.0
41 TraesCS5D01G052000 chr7A 86.364 110 12 2 4012 4118 454755080 454755189 2.860000e-22 117.0
42 TraesCS5D01G052000 chr7D 83.420 193 28 4 141 329 154174059 154173867 4.650000e-40 176.0
43 TraesCS5D01G052000 chr3B 90.826 109 7 2 4013 4118 458277540 458277432 4.710000e-30 143.0
44 TraesCS5D01G052000 chr6B 91.765 85 6 1 2939 3022 172738845 172738929 2.860000e-22 117.0


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 TraesCS5D01G052000 chr5D 49760347 49764866 4519 True 8347.0 8347 100.00000 1 4520 1 chr5D.!!$R2 4519
1 TraesCS5D01G052000 chr5D 50197012 50201523 4511 True 7581.0 7581 96.99000 1 4520 1 chr5D.!!$R3 4519
2 TraesCS5D01G052000 chr5D 50035912 50040429 4517 True 3443.5 5836 99.26300 1 4519 2 chr5D.!!$R4 4518
3 TraesCS5D01G052000 chr5A 39240972 39245493 4521 True 7347.0 7347 96.03900 1 4520 1 chr5A.!!$R2 4519
4 TraesCS5D01G052000 chr5B 52914101 52918043 3942 False 2692.0 5140 93.06200 698 3910 2 chr5B.!!$F1 3212
5 TraesCS5D01G052000 chr5B 52646112 52650843 4731 True 1596.5 5210 95.59625 698 4520 4 chr5B.!!$R3 3822
6 TraesCS5D01G052000 chrUn 371431560 371433358 1798 True 3068.0 3068 97.35400 2099 3910 1 chrUn.!!$R1 1811
7 TraesCS5D01G052000 chrUn 460220116 460221030 914 False 1679.0 1679 99.78100 918 1832 1 chrUn.!!$F1 914
8 TraesCS5D01G052000 chr4A 37771663 37772262 599 True 721.0 721 88.32200 23 629 1 chr4A.!!$R1 606
9 TraesCS5D01G052000 chr2B 91033229 91033783 554 False 688.0 688 89.06800 74 628 1 chr2B.!!$F1 554
10 TraesCS5D01G052000 chr1B 554692032 554692579 547 False 350.5 446 88.80150 23 604 2 chr1B.!!$F1 581

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
727 733 7.76824 AGAAAAGGAAAAAGAGTAAAAAGCGA 58.232 30.769 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4134 5102 2.151202 GGTGCAAGTCGATTTGGAAGA 58.849 47.619 20.52 0.0 29.97 2.87 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
727 733 7.768240 AGAAAAGGAAAAAGAGTAAAAAGCGA 58.232 30.769 0.00 0.00 0.00 4.93
728 734 8.248253 AGAAAAGGAAAAAGAGTAAAAAGCGAA 58.752 29.630 0.00 0.00 0.00 4.70
1220 1978 1.227380 GAGAGGTGCGCCGAATCAT 60.227 57.895 11.42 0.00 40.50 2.45
2881 3662 1.473258 TTGTTCTGTGGGGCATATGC 58.527 50.000 19.79 19.79 41.14 3.14
4134 5102 4.664150 TTTTCTGAATTCAACCGGCTTT 57.336 36.364 9.88 0.00 0.00 3.51
4214 5183 2.629137 TGTTGAGCATGCAGGTTTTGAT 59.371 40.909 21.98 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1220 1978 3.431922 AGACGACGAAAGACAAGTGAA 57.568 42.857 0.00 0.0 0.00 3.18
4134 5102 2.151202 GGTGCAAGTCGATTTGGAAGA 58.849 47.619 20.52 0.0 29.97 2.87
4214 5183 5.071788 GGGGATGGTGATAGTGATTAGACAA 59.928 44.000 0.00 0.0 0.00 3.18


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

AutoCloner maintained by Alex Coulton.