Multiple sequence alignment - TraesCS3A01G477200

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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 TraesCS3A01G477200 chr3A 100.000 4995 0 0 1 4995 709071945 709066951 0.000000e+00 9225.0
1 TraesCS3A01G477200 chr3A 87.097 93 9 3 168 258 177112487 177112396 8.850000e-18 102.0
2 TraesCS3A01G477200 chr3D 94.991 2935 106 12 992 3924 573921648 573918753 0.000000e+00 4567.0
3 TraesCS3A01G477200 chr3D 88.563 682 35 10 263 911 573922323 573921652 0.000000e+00 787.0
4 TraesCS3A01G477200 chr3D 94.316 475 24 3 3993 4466 573912230 573911758 0.000000e+00 725.0
5 TraesCS3A01G477200 chr3D 84.211 247 39 0 1649 1895 514680942 514680696 1.800000e-59 241.0
6 TraesCS3A01G477200 chr3B 96.195 2129 76 4 1326 3452 763226839 763228964 0.000000e+00 3478.0
7 TraesCS3A01G477200 chr3B 91.160 871 46 6 3516 4366 763229058 763229917 0.000000e+00 1153.0
8 TraesCS3A01G477200 chr3B 89.346 413 30 5 4443 4849 763230257 763230661 1.600000e-139 507.0
9 TraesCS3A01G477200 chr3B 84.685 444 23 14 263 687 763225702 763226119 7.790000e-108 401.0
10 TraesCS3A01G477200 chr3B 81.731 520 29 20 779 1292 763226379 763226838 1.700000e-99 374.0
11 TraesCS3A01G477200 chr3B 89.524 105 8 2 4891 4995 763230783 763230884 4.060000e-26 130.0
12 TraesCS3A01G477200 chr3B 78.395 162 20 13 4628 4782 17036588 17036741 1.910000e-14 91.6
13 TraesCS3A01G477200 chr3B 96.226 53 1 1 4369 4420 763230206 763230258 8.910000e-13 86.1
14 TraesCS3A01G477200 chr2B 80.123 488 77 12 1431 1899 785984549 785984063 3.700000e-91 346.0
15 TraesCS3A01G477200 chr2B 81.081 111 16 5 4661 4770 523080696 523080590 3.200000e-12 84.2
16 TraesCS3A01G477200 chr2B 97.826 46 1 0 134 179 769490320 769490365 4.150000e-11 80.5
17 TraesCS3A01G477200 chr2B 80.180 111 17 4 4661 4770 523078456 523078350 1.490000e-10 78.7
18 TraesCS3A01G477200 chr1D 86.312 263 36 0 1644 1906 7372271 7372533 2.280000e-73 287.0
19 TraesCS3A01G477200 chr1D 90.000 90 9 0 4842 4931 482101126 482101215 3.160000e-22 117.0
20 TraesCS3A01G477200 chr1D 88.372 86 8 2 175 258 464288588 464288673 8.850000e-18 102.0
21 TraesCS3A01G477200 chr1D 87.273 55 7 0 68 122 87066400 87066346 4.170000e-06 63.9
22 TraesCS3A01G477200 chr1A 85.878 262 37 0 1645 1906 9532815 9532554 3.810000e-71 279.0
23 TraesCS3A01G477200 chr1A 86.957 92 10 2 168 258 588010744 588010654 8.850000e-18 102.0
24 TraesCS3A01G477200 chr1A 82.301 113 13 5 30 137 120378395 120378505 1.910000e-14 91.6
25 TraesCS3A01G477200 chr1B 85.171 263 39 0 1644 1906 9647615 9647877 2.290000e-68 270.0
26 TraesCS3A01G477200 chr6D 76.891 476 85 11 1443 1895 426109778 426109305 3.860000e-61 246.0
27 TraesCS3A01G477200 chr6D 94.118 51 2 1 134 183 472504271 472504321 5.360000e-10 76.8
28 TraesCS3A01G477200 chr6D 95.000 40 2 0 4083 4122 12560094 12560055 4.170000e-06 63.9
29 TraesCS3A01G477200 chr7B 80.986 284 54 0 1644 1927 745446456 745446739 5.030000e-55 226.0
30 TraesCS3A01G477200 chr5B 81.683 202 22 9 1 187 223958701 223958500 2.410000e-33 154.0
31 TraesCS3A01G477200 chr5B 93.103 58 2 2 132 187 223957663 223957606 3.200000e-12 84.2
32 TraesCS3A01G477200 chr5B 97.561 41 1 0 68 108 610296140 610296100 2.490000e-08 71.3
33 TraesCS3A01G477200 chr5B 100.000 35 0 0 224 258 337159873 337159839 1.160000e-06 65.8
34 TraesCS3A01G477200 chr6A 80.180 222 19 16 4430 4629 13785502 13785284 5.210000e-30 143.0
35 TraesCS3A01G477200 chr6A 79.508 122 21 3 4661 4781 33916169 33916051 3.200000e-12 84.2
36 TraesCS3A01G477200 chr6A 78.689 122 22 3 4661 4781 33918290 33918172 1.490000e-10 78.7
37 TraesCS3A01G477200 chr2A 83.453 139 20 2 1 137 651135639 651135776 5.250000e-25 126.0
38 TraesCS3A01G477200 chr2A 96.000 50 2 0 132 181 10978613 10978662 1.150000e-11 82.4
39 TraesCS3A01G477200 chr2A 93.617 47 2 1 141 186 724591193 724591147 8.970000e-08 69.4
40 TraesCS3A01G477200 chr4A 83.333 126 20 1 2 127 89019914 89020038 1.140000e-21 115.0
41 TraesCS3A01G477200 chr4A 81.034 116 17 4 4661 4775 715943693 715943582 2.480000e-13 87.9
42 TraesCS3A01G477200 chr4A 81.707 82 11 4 4843 4923 106101399 106101477 1.160000e-06 65.8
43 TraesCS3A01G477200 chr7D 87.778 90 11 0 4842 4931 623354303 623354214 6.840000e-19 106.0
44 TraesCS3A01G477200 chr6B 88.372 86 8 2 175 258 537452708 537452623 8.850000e-18 102.0
45 TraesCS3A01G477200 chr6B 86.585 82 5 4 4085 4161 21009070 21009150 8.910000e-13 86.1
46 TraesCS3A01G477200 chr6B 75.926 162 24 13 4629 4783 706024434 706024587 8.970000e-08 69.4
47 TraesCS3A01G477200 chr6B 75.625 160 24 11 4631 4783 706025228 706025379 1.160000e-06 65.8
48 TraesCS3A01G477200 chrUn 88.095 84 9 1 4842 4925 87112775 87112857 1.140000e-16 99.0
49 TraesCS3A01G477200 chr5D 85.417 96 12 2 175 268 558966819 558966914 1.140000e-16 99.0
50 TraesCS3A01G477200 chr7A 97.917 48 1 0 132 179 682268284 682268237 3.200000e-12 84.2
51 TraesCS3A01G477200 chr7A 95.918 49 2 0 132 180 569392764 569392716 4.150000e-11 80.5
52 TraesCS3A01G477200 chr4B 95.918 49 2 0 132 180 621846166 621846214 4.150000e-11 80.5
53 TraesCS3A01G477200 chr2D 85.897 78 8 3 4847 4923 467181318 467181243 4.150000e-11 80.5
54 TraesCS3A01G477200 chr2D 95.238 42 1 1 218 258 492711675 492711634 1.160000e-06 65.8
55 TraesCS3A01G477200 chr4D 88.060 67 6 2 4848 4913 137275279 137275214 1.490000e-10 78.7
56 TraesCS3A01G477200 chr4D 84.337 83 9 4 4842 4923 360836450 360836529 1.490000e-10 78.7
57 TraesCS3A01G477200 chr4D 84.932 73 7 4 4842 4913 191160211 191160280 2.490000e-08 71.3


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 TraesCS3A01G477200 chr3A 709066951 709071945 4994 True 9225.000000 9225 100.000000 1 4995 1 chr3A.!!$R2 4994
1 TraesCS3A01G477200 chr3D 573918753 573922323 3570 True 2677.000000 4567 91.777000 263 3924 2 chr3D.!!$R3 3661
2 TraesCS3A01G477200 chr3B 763225702 763230884 5182 False 875.585714 3478 89.838143 263 4995 7 chr3B.!!$F2 4732


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
127 128 0.107214 TTGGACTGGGAATGGATCGC 60.107 55.0 0.00 0.00 41.21 4.58 F
175 176 0.255890 GCCCCATTGGAGTTGCTCTA 59.744 55.0 3.62 0.00 35.39 2.43 F
1911 2175 0.112412 TGGGAGCTTTGAAACCCTCC 59.888 55.0 7.39 10.04 42.49 4.30 F
2364 2628 0.179215 GTTGAAGATGCGAAGGTGCG 60.179 55.0 0.00 0.00 37.81 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2175 0.182537 TGTTGTCCAGTGGAACCCTG 59.817 55.000 15.09 0.0 37.80 4.45 R
2150 2414 3.004106 GCAATATGATGCCACTCCTTGTC 59.996 47.826 0.00 0.0 40.49 3.18 R
3400 3664 0.031857 CCTCTAGATGTCAGCTGCGG 59.968 60.000 9.47 0.0 0.00 5.69 R
4030 4371 0.178998 GCCAGGGACATGATGATGCT 60.179 55.000 0.00 0.0 32.14 3.79 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.