Multiple sequence alignment - TraesCS4A01G443200

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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 TraesCS4A01G443200 chr4A 100.000 4727 0 0 1 4727 711777749 711782475 0.000000e+00 8730.0
1 TraesCS4A01G443200 chr4A 99.577 4728 19 1 1 4727 711838974 711843701 0.000000e+00 8619.0
2 TraesCS4A01G443200 chr4A 94.529 2486 121 8 1927 4404 704301349 704298871 0.000000e+00 3823.0
3 TraesCS4A01G443200 chr4A 92.722 1058 66 4 876 1928 704302658 704301607 0.000000e+00 1517.0
4 TraesCS4A01G443200 chr4A 85.083 362 49 5 4046 4404 740607746 740608105 9.670000e-97 364.0
5 TraesCS4A01G443200 chr4A 89.706 136 9 4 731 865 727842887 727843018 8.140000e-38 169.0
6 TraesCS4A01G443200 chr4A 88.732 71 7 1 533 603 704303317 704303248 8.430000e-13 86.1
7 TraesCS4A01G443200 chr4A 91.071 56 5 0 1972 2027 708242194 708242249 5.070000e-10 76.8
8 TraesCS4A01G443200 chr7D 92.538 2506 146 17 1937 4404 21938949 21936447 0.000000e+00 3554.0
9 TraesCS4A01G443200 chr7D 92.171 1967 139 9 1934 3892 22039817 22041776 0.000000e+00 2765.0
10 TraesCS4A01G443200 chr7D 93.367 995 66 0 880 1874 21939965 21938971 0.000000e+00 1472.0
11 TraesCS4A01G443200 chr7D 91.825 1003 76 5 876 1874 22038798 22039798 0.000000e+00 1393.0
12 TraesCS4A01G443200 chr7D 88.571 140 11 5 727 864 530907354 530907490 1.050000e-36 165.0
13 TraesCS4A01G443200 chr7D 95.000 60 3 0 533 592 21940216 21940157 1.400000e-15 95.3
14 TraesCS4A01G443200 chr7D 85.366 82 12 0 1972 2053 23525161 23525080 8.430000e-13 86.1
15 TraesCS4A01G443200 chr7A 91.411 2119 149 20 1950 4045 22666891 22668999 0.000000e+00 2874.0
16 TraesCS4A01G443200 chr7A 86.908 2131 228 29 1950 4045 22867626 22869740 0.000000e+00 2342.0
17 TraesCS4A01G443200 chr7A 92.369 878 63 3 998 1874 22665978 22666852 0.000000e+00 1247.0
18 TraesCS4A01G443200 chr7A 88.310 864 84 12 1003 1865 22866728 22867575 0.000000e+00 1020.0
19 TraesCS4A01G443200 chr7A 81.930 653 115 1 1175 1827 23895190 23895839 2.490000e-152 549.0
20 TraesCS4A01G443200 chr7A 84.848 528 64 8 2 514 251472787 251473313 7.010000e-143 518.0
21 TraesCS4A01G443200 chr7A 90.840 262 20 2 4466 4727 66933642 66933385 9.740000e-92 348.0
22 TraesCS4A01G443200 chrUn 96.032 1764 64 3 1927 3686 313746280 313744519 0.000000e+00 2865.0
23 TraesCS4A01G443200 chrUn 95.687 1507 59 3 2184 3686 50547720 50546216 0.000000e+00 2418.0
24 TraesCS4A01G443200 chrUn 93.094 1057 63 3 876 1928 313747589 313746539 0.000000e+00 1539.0
25 TraesCS4A01G443200 chrUn 92.904 1057 65 3 876 1928 50554953 50553903 0.000000e+00 1528.0
26 TraesCS4A01G443200 chrUn 98.573 771 11 0 1927 2697 50553644 50552874 0.000000e+00 1363.0
27 TraesCS4A01G443200 chrUn 91.364 660 49 4 3749 4404 50551951 50551296 0.000000e+00 896.0
28 TraesCS4A01G443200 chrUn 91.364 660 49 4 3749 4404 352755403 352756058 0.000000e+00 896.0
29 TraesCS4A01G443200 chrUn 95.142 494 22 1 3193 3686 50552456 50551965 0.000000e+00 778.0
30 TraesCS4A01G443200 chrUn 93.822 259 10 2 876 1134 401383364 401383112 7.420000e-103 385.0
31 TraesCS4A01G443200 chrUn 82.530 166 23 6 533 697 50555585 50555425 1.770000e-29 141.0
32 TraesCS4A01G443200 chrUn 82.530 166 23 6 533 697 401383996 401383836 1.770000e-29 141.0
33 TraesCS4A01G443200 chrUn 88.732 71 7 1 533 603 436529943 436529874 8.430000e-13 86.1
34 TraesCS4A01G443200 chr1D 86.322 541 57 9 2 526 8743551 8744090 1.480000e-159 573.0
35 TraesCS4A01G443200 chr1D 85.581 534 61 7 1 519 255026768 255027300 3.220000e-151 545.0
36 TraesCS4A01G443200 chr3B 86.948 521 53 8 1 506 169423865 169424385 5.310000e-159 571.0
37 TraesCS4A01G443200 chr3B 85.219 548 58 11 1 532 739657395 739657935 4.160000e-150 542.0
38 TraesCS4A01G443200 chr3B 89.630 135 14 0 731 865 814738844 814738978 6.290000e-39 172.0
39 TraesCS4A01G443200 chr3D 86.434 516 51 8 14 514 585939934 585940445 8.940000e-152 547.0
40 TraesCS4A01G443200 chr3D 87.705 122 11 3 731 851 22233923 22233805 6.380000e-29 139.0
41 TraesCS4A01G443200 chr7B 96.646 328 8 3 4402 4727 700883836 700884162 4.160000e-150 542.0
42 TraesCS4A01G443200 chr7B 91.411 326 25 1 4402 4727 474472682 474473004 1.210000e-120 444.0
43 TraesCS4A01G443200 chr7B 96.875 32 0 1 4313 4343 1294277 1294308 9.000000e-03 52.8
44 TraesCS4A01G443200 chr2A 85.300 517 58 6 17 522 474798163 474797654 7.010000e-143 518.0
45 TraesCS4A01G443200 chr2A 91.985 262 17 2 4466 4727 684469509 684469766 9.670000e-97 364.0
46 TraesCS4A01G443200 chr2A 91.985 262 17 2 4466 4727 767591161 767591418 9.670000e-97 364.0
47 TraesCS4A01G443200 chr2A 92.857 112 7 1 727 838 713668738 713668848 1.360000e-35 161.0
48 TraesCS4A01G443200 chr2A 86.567 134 12 5 727 858 610059694 610059823 4.930000e-30 143.0
49 TraesCS4A01G443200 chr6D 84.346 543 67 9 1 526 154340211 154340752 2.520000e-142 516.0
50 TraesCS4A01G443200 chr3A 91.603 262 18 2 4466 4727 723494540 723494283 4.500000e-95 359.0
51 TraesCS4A01G443200 chr2B 89.944 179 14 2 4402 4580 729517341 729517167 1.320000e-55 228.0
52 TraesCS4A01G443200 chr2B 95.495 111 5 0 4617 4727 729517170 729517060 1.350000e-40 178.0
53 TraesCS4A01G443200 chr5D 87.429 175 21 1 4403 4577 321858869 321859042 2.880000e-47 200.0
54 TraesCS4A01G443200 chr5B 77.429 350 65 11 4046 4393 16202283 16201946 3.730000e-46 196.0
55 TraesCS4A01G443200 chr5B 96.875 32 0 1 4313 4343 711547320 711547289 9.000000e-03 52.8
56 TraesCS4A01G443200 chr5A 73.157 529 128 11 2644 3165 607594894 607594373 1.350000e-40 178.0
57 TraesCS4A01G443200 chr5A 96.875 32 1 0 4312 4343 24431155 24431124 2.000000e-03 54.7
58 TraesCS4A01G443200 chr1A 86.667 135 16 2 731 864 2989342 2989475 1.060000e-31 148.0
59 TraesCS4A01G443200 chr6A 91.667 108 5 2 731 838 175657756 175657859 3.810000e-31 147.0


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 TraesCS4A01G443200 chr4A 711777749 711782475 4726 False 8730.000000 8730 100.000000 1 4727 1 chr4A.!!$F2 4726
1 TraesCS4A01G443200 chr4A 711838974 711843701 4727 False 8619.000000 8619 99.577000 1 4727 1 chr4A.!!$F3 4726
2 TraesCS4A01G443200 chr4A 704298871 704303317 4446 True 1808.700000 3823 91.994333 533 4404 3 chr4A.!!$R1 3871
3 TraesCS4A01G443200 chr7D 22038798 22041776 2978 False 2079.000000 2765 91.998000 876 3892 2 chr7D.!!$F2 3016
4 TraesCS4A01G443200 chr7D 21936447 21940216 3769 True 1707.100000 3554 93.635000 533 4404 3 chr7D.!!$R2 3871
5 TraesCS4A01G443200 chr7A 22665978 22668999 3021 False 2060.500000 2874 91.890000 998 4045 2 chr7A.!!$F3 3047
6 TraesCS4A01G443200 chr7A 22866728 22869740 3012 False 1681.000000 2342 87.609000 1003 4045 2 chr7A.!!$F4 3042
7 TraesCS4A01G443200 chr7A 23895190 23895839 649 False 549.000000 549 81.930000 1175 1827 1 chr7A.!!$F1 652
8 TraesCS4A01G443200 chr7A 251472787 251473313 526 False 518.000000 518 84.848000 2 514 1 chr7A.!!$F2 512
9 TraesCS4A01G443200 chrUn 313744519 313747589 3070 True 2202.000000 2865 94.563000 876 3686 2 chrUn.!!$R3 2810
10 TraesCS4A01G443200 chrUn 50546216 50555585 9369 True 1187.333333 2418 92.700000 533 4404 6 chrUn.!!$R2 3871
11 TraesCS4A01G443200 chrUn 352755403 352756058 655 False 896.000000 896 91.364000 3749 4404 1 chrUn.!!$F1 655
12 TraesCS4A01G443200 chrUn 401383112 401383996 884 True 263.000000 385 88.176000 533 1134 2 chrUn.!!$R4 601
13 TraesCS4A01G443200 chr1D 8743551 8744090 539 False 573.000000 573 86.322000 2 526 1 chr1D.!!$F1 524
14 TraesCS4A01G443200 chr1D 255026768 255027300 532 False 545.000000 545 85.581000 1 519 1 chr1D.!!$F2 518
15 TraesCS4A01G443200 chr3B 169423865 169424385 520 False 571.000000 571 86.948000 1 506 1 chr3B.!!$F1 505
16 TraesCS4A01G443200 chr3B 739657395 739657935 540 False 542.000000 542 85.219000 1 532 1 chr3B.!!$F2 531
17 TraesCS4A01G443200 chr3D 585939934 585940445 511 False 547.000000 547 86.434000 14 514 1 chr3D.!!$F1 500
18 TraesCS4A01G443200 chr2A 474797654 474798163 509 True 518.000000 518 85.300000 17 522 1 chr2A.!!$R1 505
19 TraesCS4A01G443200 chr6D 154340211 154340752 541 False 516.000000 516 84.346000 1 526 1 chr6D.!!$F1 525

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
858 1298 1.726853 AAGCTCCGTTGATGTAGCAC 58.273 50.0 0.0 0.0 37.44 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3909 4725 2.549992 CGATGAGGACAAGGGTGTGAAA 60.55 50.0 0.0 0.0 38.41 2.69 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
679 1119 4.398988 TCGACATCCAAATTCCAATTCCAG 59.601 41.667 0.0 0.0 0.00 3.86
858 1298 1.726853 AAGCTCCGTTGATGTAGCAC 58.273 50.000 0.0 0.0 37.44 4.40
1248 1723 2.805546 GACCGCCTCGTCTGCATA 59.194 61.111 0.0 0.0 0.00 3.14
1549 2024 4.351054 AGCACAAAGGAGGCCCCG 62.351 66.667 0.0 0.0 40.87 5.73
3764 4577 8.237811 AGGACAATTTCAGTTTCAACACTAAT 57.762 30.769 0.0 0.0 0.00 1.73
4159 4980 1.823899 CGGCAATAGGGGCAACTCC 60.824 63.158 0.0 0.0 38.59 3.85
4540 10180 4.457834 AGTACTGTGGTGAACTCATAGC 57.542 45.455 0.0 0.0 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
531 554 0.320771 ACAGACTAAACCTGCAGCCG 60.321 55.000 8.66 0.00 35.14 5.52
679 1119 2.293399 ACCACCTCTCGCAAATTTGAAC 59.707 45.455 22.31 4.10 0.00 3.18
1549 2024 1.153229 GGATGTTGGGGGCGTCTAC 60.153 63.158 0.00 0.00 0.00 2.59
3909 4725 2.549992 CGATGAGGACAAGGGTGTGAAA 60.550 50.000 0.00 0.00 38.41 2.69
4159 4980 5.334319 TCTCAGCAATATCATGTTTTTGCG 58.666 37.500 19.56 15.85 46.84 4.85
4540 10180 8.656806 TCTGTATTGGATAGGGTATGGTTTTAG 58.343 37.037 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.