Multiple sequence alignment - TraesCS3A01G451800

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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 TraesCS3A01G451800 chr3A 100.000 2504 0 0 1 2504 689866527 689869030 0.000000e+00 4625.0
1 TraesCS3A01G451800 chr3A 97.686 2506 30 4 1 2504 689846212 689848691 0.000000e+00 4281.0
2 TraesCS3A01G451800 chr3A 93.116 857 42 3 1 856 689659362 689660202 0.000000e+00 1240.0
3 TraesCS3A01G451800 chr3A 93.116 857 42 3 1 856 689666014 689666854 0.000000e+00 1240.0
4 TraesCS3A01G451800 chr3A 89.724 798 70 5 656 1452 689659952 689660738 0.000000e+00 1009.0
5 TraesCS3A01G451800 chr3A 89.724 798 70 5 656 1452 689662789 689663575 0.000000e+00 1009.0
6 TraesCS3A01G451800 chr3A 87.606 823 78 9 847 1661 690027356 690028162 0.000000e+00 933.0
7 TraesCS3A01G451800 chr3A 86.198 797 90 10 656 1452 689608590 689609366 0.000000e+00 845.0
8 TraesCS3A01G451800 chr3A 86.073 797 91 10 656 1452 689523684 689524460 0.000000e+00 839.0
9 TraesCS3A01G451800 chr3A 94.972 537 23 2 321 856 689662506 689663039 0.000000e+00 839.0
10 TraesCS3A01G451800 chr3A 85.445 797 96 10 656 1452 689578812 689579588 0.000000e+00 811.0
11 TraesCS3A01G451800 chr3A 88.268 537 53 5 322 855 689608304 689608833 3.510000e-178 634.0
12 TraesCS3A01G451800 chr3A 88.082 537 54 5 322 855 689578526 689579055 1.630000e-176 628.0
13 TraesCS3A01G451800 chr3A 87.963 540 54 6 322 856 689523395 689523928 5.880000e-176 627.0
14 TraesCS3A01G451800 chr3A 85.932 263 33 3 2125 2386 690033737 690033996 6.820000e-71 278.0
15 TraesCS3A01G451800 chr3A 88.000 100 12 0 220 319 689523254 689523353 4.380000e-23 119.0
16 TraesCS3A01G451800 chr3A 88.172 93 10 1 226 318 686281566 686281475 2.630000e-20 110.0
17 TraesCS3A01G451800 chr3A 84.158 101 11 5 2379 2476 733529693 733529791 2.650000e-15 93.5
18 TraesCS3A01G451800 chr3D 94.782 824 39 2 847 1667 553440890 553441712 0.000000e+00 1280.0
19 TraesCS3A01G451800 chr3D 92.622 759 39 7 111 856 553356924 553357678 0.000000e+00 1075.0
20 TraesCS3A01G451800 chr3D 89.711 797 72 3 656 1452 553357428 553358214 0.000000e+00 1009.0
21 TraesCS3A01G451800 chr3D 87.867 750 77 6 706 1452 553405894 553406632 0.000000e+00 869.0
22 TraesCS3A01G451800 chr3D 88.906 631 26 9 1918 2504 553474022 553474652 0.000000e+00 737.0
23 TraesCS3A01G451800 chr3D 92.807 431 25 4 371 798 553405658 553406085 9.840000e-174 619.0
24 TraesCS3A01G451800 chr3D 92.278 259 19 1 1665 1922 553455053 553455311 1.420000e-97 366.0
25 TraesCS3A01G451800 chr3D 84.360 211 30 3 111 319 549000136 548999927 1.170000e-48 204.0
26 TraesCS3A01G451800 chr5D 84.444 270 37 4 1662 1930 487015208 487014943 6.870000e-66 261.0
27 TraesCS3A01G451800 chr4D 83.871 279 40 4 1662 1938 47492877 47492602 6.870000e-66 261.0
28 TraesCS3A01G451800 chr4D 100.000 31 0 0 13 43 502652086 502652116 9.670000e-05 58.4
29 TraesCS3A01G451800 chr4D 100.000 30 0 0 16 45 502647340 502647369 3.480000e-04 56.5
30 TraesCS3A01G451800 chr2B 84.980 253 34 3 1662 1914 365263728 365263480 1.150000e-63 254.0
31 TraesCS3A01G451800 chr2B 86.784 227 27 3 1662 1888 1203060 1202837 1.490000e-62 250.0
32 TraesCS3A01G451800 chr2D 87.054 224 22 6 1662 1884 180540285 180540068 1.920000e-61 246.0
33 TraesCS3A01G451800 chr2D 83.333 114 18 1 204 317 650651783 650651895 1.230000e-18 104.0
34 TraesCS3A01G451800 chr7D 83.026 271 35 7 1662 1930 419093947 419094208 4.160000e-58 235.0
35 TraesCS3A01G451800 chr5A 82.824 262 38 5 1662 1923 523998683 523998937 6.970000e-56 228.0
36 TraesCS3A01G451800 chr5A 86.486 111 12 3 2387 2495 604933226 604933117 4.380000e-23 119.0
37 TraesCS3A01G451800 chr5A 86.486 111 12 3 2387 2495 604951535 604951426 4.380000e-23 119.0
38 TraesCS3A01G451800 chr5A 82.569 109 17 2 208 316 652653577 652653471 7.370000e-16 95.3
39 TraesCS3A01G451800 chr7A 87.156 109 12 2 2383 2490 97255256 97255363 3.380000e-24 122.0
40 TraesCS3A01G451800 chr1B 88.710 62 7 0 2415 2476 642093020 642093081 2.670000e-10 76.8
41 TraesCS3A01G451800 chr2A 81.720 93 14 3 2379 2469 142740126 142740217 9.610000e-10 75.0


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 TraesCS3A01G451800 chr3A 689866527 689869030 2503 False 4625.000000 4625 100.000000 1 2504 1 chr3A.!!$F2 2503
1 TraesCS3A01G451800 chr3A 689846212 689848691 2479 False 4281.000000 4281 97.686000 1 2504 1 chr3A.!!$F1 2503
2 TraesCS3A01G451800 chr3A 689659362 689666854 7492 False 1067.400000 1240 92.130400 1 1452 5 chr3A.!!$F9 1451
3 TraesCS3A01G451800 chr3A 690027356 690028162 806 False 933.000000 933 87.606000 847 1661 1 chr3A.!!$F3 814
4 TraesCS3A01G451800 chr3A 689608304 689609366 1062 False 739.500000 845 87.233000 322 1452 2 chr3A.!!$F8 1130
5 TraesCS3A01G451800 chr3A 689578526 689579588 1062 False 719.500000 811 86.763500 322 1452 2 chr3A.!!$F7 1130
6 TraesCS3A01G451800 chr3A 689523254 689524460 1206 False 528.333333 839 87.345333 220 1452 3 chr3A.!!$F6 1232
7 TraesCS3A01G451800 chr3D 553440890 553441712 822 False 1280.000000 1280 94.782000 847 1667 1 chr3D.!!$F1 820
8 TraesCS3A01G451800 chr3D 553356924 553358214 1290 False 1042.000000 1075 91.166500 111 1452 2 chr3D.!!$F4 1341
9 TraesCS3A01G451800 chr3D 553405658 553406632 974 False 744.000000 869 90.337000 371 1452 2 chr3D.!!$F5 1081
10 TraesCS3A01G451800 chr3D 553474022 553474652 630 False 737.000000 737 88.906000 1918 2504 1 chr3D.!!$F3 586

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
503 558 3.020274 TGTTTTGCTCTTACACTGCCAA 58.98 40.909 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 5518 0.946221 CTTGCGGTTGCTTCGTCTCT 60.946 55.0 0.0 0.0 43.34 3.1 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
503 558 3.020274 TGTTTTGCTCTTACACTGCCAA 58.980 40.909 0.00 0.0 0.0 4.52
1668 5247 5.303078 GTGTCTCTACCATGGATCATAGTGT 59.697 44.000 21.47 0.0 0.0 3.55
1676 5255 5.163301 ACCATGGATCATAGTGTGGAGTAAC 60.163 44.000 21.47 0.0 0.0 2.50
2041 5634 5.634859 CACACACTTCTCAAAAGCAAAAACT 59.365 36.000 0.00 0.0 0.0 2.66
2045 5638 8.375465 CACACTTCTCAAAAGCAAAAACTAAAG 58.625 33.333 0.00 0.0 0.0 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 219 4.709397 AGTCGAGTGAGATTCTGAAATCCT 59.291 41.667 0.00 0.00 41.97 3.24
213 225 3.013219 CCTCAGTCGAGTGAGATTCTGA 58.987 50.000 39.60 20.99 46.02 3.27
344 395 7.789273 TGTTTCGGTAAATAAAAGAGTGTGA 57.211 32.000 0.00 0.00 0.00 3.58
503 558 3.828451 AGCTCTTGGTGCAATTACATTGT 59.172 39.130 0.00 0.00 42.20 2.71
837 896 7.634671 TTGTGTAATGTCTTAGAGGATACGA 57.365 36.000 0.00 0.00 46.39 3.43
839 898 8.552034 GCATTTGTGTAATGTCTTAGAGGATAC 58.448 37.037 0.00 0.00 44.52 2.24
841 900 7.341805 AGCATTTGTGTAATGTCTTAGAGGAT 58.658 34.615 0.00 0.00 44.52 3.24
1641 5220 7.231519 CACTATGATCCATGGTAGAGACACTTA 59.768 40.741 12.58 0.00 33.40 2.24
1668 5247 7.395206 TGCATGTTACTAGTCTAAGTTACTCCA 59.605 37.037 0.00 0.00 31.82 3.86
1939 5518 0.946221 CTTGCGGTTGCTTCGTCTCT 60.946 55.000 0.00 0.00 43.34 3.10
2041 5634 1.153046 GGCGTGCCCATAGCCTTTA 60.153 57.895 0.00 0.00 46.83 1.85
2103 5696 3.319405 CAGGATGCTACCACGATCTAAGT 59.681 47.826 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.