Multiple sequence alignment - TraesCS4A01G443300

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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 TraesCS4A01G443300 chr4A 100.000 4870 0 0 1 4870 711838832 711843701 0.000000e+00 8994.0
1 TraesCS4A01G443300 chr4A 99.589 4870 19 1 1 4870 711777607 711782475 0.000000e+00 8881.0
2 TraesCS4A01G443300 chr4A 94.529 2486 121 8 2070 4547 704301349 704298871 0.000000e+00 3823.0
3 TraesCS4A01G443300 chr4A 92.722 1058 66 4 1019 2071 704302658 704301607 0.000000e+00 1517.0
4 TraesCS4A01G443300 chr4A 85.359 362 48 5 4189 4547 740607746 740608105 2.140000e-98 370.0
5 TraesCS4A01G443300 chr4A 90.441 136 8 4 874 1008 727842887 727843018 1.800000e-39 174.0
6 TraesCS4A01G443300 chr4A 89.041 73 7 1 673 745 704303319 704303248 6.710000e-14 89.8
7 TraesCS4A01G443300 chr4A 91.071 56 5 0 2115 2170 708242194 708242249 5.230000e-10 76.8
8 TraesCS4A01G443300 chr7D 92.498 2506 147 17 2080 4547 21938949 21936447 0.000000e+00 3548.0
9 TraesCS4A01G443300 chr7D 92.120 1967 140 9 2077 4035 22039817 22041776 0.000000e+00 2760.0
10 TraesCS4A01G443300 chr7D 93.367 995 66 0 1023 2017 21939965 21938971 0.000000e+00 1472.0
11 TraesCS4A01G443300 chr7D 91.825 1003 76 5 1019 2017 22038798 22039798 0.000000e+00 1393.0
12 TraesCS4A01G443300 chr7D 89.286 140 10 5 870 1007 530907354 530907490 2.330000e-38 171.0
13 TraesCS4A01G443300 chr7D 95.082 61 3 0 674 734 21940217 21940157 4.010000e-16 97.1
14 TraesCS4A01G443300 chr7D 85.366 82 12 0 2115 2196 23525161 23525080 8.680000e-13 86.1
15 TraesCS4A01G443300 chr7A 91.411 2119 149 20 2093 4188 22666891 22668999 0.000000e+00 2874.0
16 TraesCS4A01G443300 chr7A 86.908 2131 228 29 2093 4188 22867626 22869740 0.000000e+00 2342.0
17 TraesCS4A01G443300 chr7A 92.483 878 62 3 1141 2017 22665978 22666852 0.000000e+00 1253.0
18 TraesCS4A01G443300 chr7A 88.426 864 83 12 1146 2008 22866728 22867575 0.000000e+00 1026.0
19 TraesCS4A01G443300 chr7A 83.929 672 73 14 1 656 251472661 251473313 1.160000e-170 610.0
20 TraesCS4A01G443300 chr7A 82.236 653 113 1 1318 1970 23895190 23895839 1.180000e-155 560.0
21 TraesCS4A01G443300 chr7A 91.221 262 19 2 4609 4870 66933642 66933385 2.160000e-93 353.0
22 TraesCS4A01G443300 chrUn 95.918 1764 66 3 2070 3829 313746280 313744519 0.000000e+00 2854.0
23 TraesCS4A01G443300 chrUn 95.554 1507 61 3 2327 3829 50547720 50546216 0.000000e+00 2407.0
24 TraesCS4A01G443300 chrUn 93.094 1057 63 3 1019 2071 313747589 313746539 0.000000e+00 1539.0
25 TraesCS4A01G443300 chrUn 92.904 1057 65 3 1019 2071 50554953 50553903 0.000000e+00 1528.0
26 TraesCS4A01G443300 chrUn 98.444 771 12 0 2070 2840 50553644 50552874 0.000000e+00 1358.0
27 TraesCS4A01G443300 chrUn 91.667 660 47 4 3892 4547 50551951 50551296 0.000000e+00 907.0
28 TraesCS4A01G443300 chrUn 91.667 660 47 4 3892 4547 352755403 352756058 0.000000e+00 907.0
29 TraesCS4A01G443300 chrUn 94.939 494 23 1 3336 3829 50552456 50551965 0.000000e+00 773.0
30 TraesCS4A01G443300 chrUn 93.050 259 12 2 1019 1277 401383364 401383112 1.660000e-99 374.0
31 TraesCS4A01G443300 chrUn 82.840 169 22 7 673 840 50555587 50555425 1.410000e-30 145.0
32 TraesCS4A01G443300 chrUn 82.840 169 22 7 673 840 401383998 401383836 1.410000e-30 145.0
33 TraesCS4A01G443300 chrUn 89.041 73 7 1 673 745 436529945 436529874 6.710000e-14 89.8
34 TraesCS4A01G443300 chr1D 86.715 685 73 10 1 668 8743407 8744090 0.000000e+00 745.0
35 TraesCS4A01G443300 chr1D 86.054 631 72 7 46 661 255026671 255027300 0.000000e+00 664.0
36 TraesCS4A01G443300 chr6D 85.714 686 79 10 1 668 154340068 154340752 0.000000e+00 706.0
37 TraesCS4A01G443300 chr3D 85.871 637 73 7 43 664 450871336 450870702 0.000000e+00 662.0
38 TraesCS4A01G443300 chr3D 87.705 122 11 3 874 994 22233923 22233805 6.570000e-29 139.0
39 TraesCS4A01G443300 chr3B 86.371 609 58 11 63 655 739657318 739657917 4.110000e-180 641.0
40 TraesCS4A01G443300 chr3B 90.370 135 13 0 874 1008 814738844 814738978 1.390000e-40 178.0
41 TraesCS4A01G443300 chr1A 84.663 652 81 14 35 669 463285929 463286578 2.470000e-177 632.0
42 TraesCS4A01G443300 chr1A 87.407 135 15 2 874 1007 2989342 2989475 2.350000e-33 154.0
43 TraesCS4A01G443300 chr5A 83.041 684 81 11 1 668 1905407 1906071 5.430000e-164 588.0
44 TraesCS4A01G443300 chr5A 73.157 529 128 11 2787 3308 607594894 607594373 1.390000e-40 178.0
45 TraesCS4A01G443300 chr5A 96.875 32 1 0 4455 4486 24431155 24431124 2.000000e-03 54.7
46 TraesCS4A01G443300 chr2D 82.969 640 84 12 46 669 142021161 142020531 5.510000e-154 555.0
47 TraesCS4A01G443300 chr7B 96.951 328 7 3 4545 4870 700883836 700884162 9.220000e-152 547.0
48 TraesCS4A01G443300 chr7B 91.718 326 24 1 4545 4870 474472682 474473004 2.670000e-122 449.0
49 TraesCS4A01G443300 chr7B 96.875 32 0 1 4456 4486 1294277 1294308 9.000000e-03 52.8
50 TraesCS4A01G443300 chr2A 92.366 262 16 2 4609 4870 684469509 684469766 2.140000e-98 370.0
51 TraesCS4A01G443300 chr2A 92.366 262 16 2 4609 4870 767591161 767591418 2.140000e-98 370.0
52 TraesCS4A01G443300 chr2A 92.857 112 7 1 870 981 713668738 713668848 1.400000e-35 161.0
53 TraesCS4A01G443300 chr2A 86.667 135 12 5 870 1002 610059694 610059824 1.410000e-30 145.0
54 TraesCS4A01G443300 chr3A 91.985 262 17 2 4609 4870 723494540 723494283 9.960000e-97 364.0
55 TraesCS4A01G443300 chr2B 90.503 179 13 2 4545 4723 729517341 729517167 2.930000e-57 233.0
56 TraesCS4A01G443300 chr2B 95.495 111 5 0 4760 4870 729517170 729517060 1.390000e-40 178.0
57 TraesCS4A01G443300 chr5D 88.000 175 20 1 4546 4720 321858869 321859042 6.390000e-49 206.0
58 TraesCS4A01G443300 chr5B 77.101 345 65 10 4189 4531 16202283 16201951 2.310000e-43 187.0
59 TraesCS4A01G443300 chr5B 96.875 32 0 1 4456 4486 711547320 711547289 9.000000e-03 52.8
60 TraesCS4A01G443300 chr6A 91.667 108 5 2 874 981 175657756 175657859 3.930000e-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 TraesCS4A01G443300 chr4A 711838832 711843701 4869 False 8994.000000 8994 100.000000 1 4870 1 chr4A.!!$F3 4869
1 TraesCS4A01G443300 chr4A 711777607 711782475 4868 False 8881.000000 8881 99.589000 1 4870 1 chr4A.!!$F2 4869
2 TraesCS4A01G443300 chr4A 704298871 704303319 4448 True 1809.933333 3823 92.097333 673 4547 3 chr4A.!!$R1 3874
3 TraesCS4A01G443300 chr7D 22038798 22041776 2978 False 2076.500000 2760 91.972500 1019 4035 2 chr7D.!!$F2 3016
4 TraesCS4A01G443300 chr7D 21936447 21940217 3770 True 1705.700000 3548 93.649000 674 4547 3 chr7D.!!$R2 3873
5 TraesCS4A01G443300 chr7A 22665978 22668999 3021 False 2063.500000 2874 91.947000 1141 4188 2 chr7A.!!$F3 3047
6 TraesCS4A01G443300 chr7A 22866728 22869740 3012 False 1684.000000 2342 87.667000 1146 4188 2 chr7A.!!$F4 3042
7 TraesCS4A01G443300 chr7A 251472661 251473313 652 False 610.000000 610 83.929000 1 656 1 chr7A.!!$F2 655
8 TraesCS4A01G443300 chr7A 23895190 23895839 649 False 560.000000 560 82.236000 1318 1970 1 chr7A.!!$F1 652
9 TraesCS4A01G443300 chrUn 313744519 313747589 3070 True 2196.500000 2854 94.506000 1019 3829 2 chrUn.!!$R3 2810
10 TraesCS4A01G443300 chrUn 50546216 50555587 9371 True 1186.333333 2407 92.724667 673 4547 6 chrUn.!!$R2 3874
11 TraesCS4A01G443300 chrUn 352755403 352756058 655 False 907.000000 907 91.667000 3892 4547 1 chrUn.!!$F1 655
12 TraesCS4A01G443300 chrUn 401383112 401383998 886 True 259.500000 374 87.945000 673 1277 2 chrUn.!!$R4 604
13 TraesCS4A01G443300 chr1D 8743407 8744090 683 False 745.000000 745 86.715000 1 668 1 chr1D.!!$F1 667
14 TraesCS4A01G443300 chr1D 255026671 255027300 629 False 664.000000 664 86.054000 46 661 1 chr1D.!!$F2 615
15 TraesCS4A01G443300 chr6D 154340068 154340752 684 False 706.000000 706 85.714000 1 668 1 chr6D.!!$F1 667
16 TraesCS4A01G443300 chr3D 450870702 450871336 634 True 662.000000 662 85.871000 43 664 1 chr3D.!!$R2 621
17 TraesCS4A01G443300 chr3B 739657318 739657917 599 False 641.000000 641 86.371000 63 655 1 chr3B.!!$F1 592
18 TraesCS4A01G443300 chr1A 463285929 463286578 649 False 632.000000 632 84.663000 35 669 1 chr1A.!!$F2 634
19 TraesCS4A01G443300 chr5A 1905407 1906071 664 False 588.000000 588 83.041000 1 668 1 chr5A.!!$F1 667
20 TraesCS4A01G443300 chr2D 142020531 142021161 630 True 555.000000 555 82.969000 46 669 1 chr2D.!!$R1 623

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
822 1264 4.769488 TCGACATCCAAATTCCAATTCCAA 59.231 37.500 0.00 0.0 0.00 3.53 F
1126 1603 0.610174 TGCAGTTGGAGAGCTCGATT 59.390 50.000 8.37 0.0 0.00 3.34 F
1263 1740 1.069668 AGTACGACAAACGCCCTTCTT 59.930 47.619 0.00 0.0 46.94 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3434 1.066752 CCGGTGAGACGTGACACAA 59.933 57.895 18.77 0.0 38.57 3.33 R
3641 4429 3.807071 TGTGTACATTACATGCCTATGCG 59.193 43.478 0.00 0.0 41.34 4.73 R
4449 5273 1.138247 GCTCTCGGCAAAGCATTGG 59.862 57.895 3.55 0.0 41.35 3.16 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
781 1223 5.461032 ACTTTTCTCCACACACACAAAAA 57.539 34.783 0.00 0.0 0.00 1.94
822 1264 4.769488 TCGACATCCAAATTCCAATTCCAA 59.231 37.500 0.00 0.0 0.00 3.53
1001 1443 2.472695 AAGCTCCGTTGATGTAGCAA 57.527 45.000 0.00 0.0 37.44 3.91
1126 1603 0.610174 TGCAGTTGGAGAGCTCGATT 59.390 50.000 8.37 0.0 0.00 3.34
1263 1740 1.069668 AGTACGACAAACGCCCTTCTT 59.930 47.619 0.00 0.0 46.94 2.52
2659 3434 5.012046 TGTCGGAATATGCTGATAGTGGATT 59.988 40.000 0.00 0.0 0.00 3.01
3641 4429 7.199541 AGAAAGATGCATGCTCATACATAAC 57.800 36.000 20.33 0.0 0.00 1.89
4449 5273 4.083324 CGAATAATGGCATGGTCATGGTAC 60.083 45.833 0.00 0.0 39.16 3.34
4532 5357 2.094026 CCTTGCCCAAAGATAAGCAACC 60.094 50.000 0.00 0.0 40.13 3.77
4683 10326 5.417894 TGTAGTACTGTGGTGAACTCATAGG 59.582 44.000 5.39 0.0 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
822 1264 3.157087 ACCACCTCTCGCAAATTTGAAT 58.843 40.909 22.31 0.0 0.00 2.57
1126 1603 8.756927 ACCACGACATAGCTACTATACTCTATA 58.243 37.037 0.00 0.0 0.00 1.31
1263 1740 3.638160 AGGAGTTCGTTGTAGTTGGTGTA 59.362 43.478 0.00 0.0 0.00 2.90
1378 1855 2.197250 CAGAGGATGCAGACGAGGT 58.803 57.895 0.00 0.0 0.00 3.85
2659 3434 1.066752 CCGGTGAGACGTGACACAA 59.933 57.895 18.77 0.0 38.57 3.33
3641 4429 3.807071 TGTGTACATTACATGCCTATGCG 59.193 43.478 0.00 0.0 41.34 4.73
4449 5273 1.138247 GCTCTCGGCAAAGCATTGG 59.862 57.895 3.55 0.0 41.35 3.16
4532 5357 2.160813 CACCAGAATTTAAACCGGTCCG 59.839 50.000 8.04 3.6 0.00 4.79
4683 10326 8.434392 TCTGTATTGGATAGGGTATGGTTTTAC 58.566 37.037 0.00 0.0 0.00 2.01


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

AutoCloner maintained by Alex Coulton.