Multiple sequence alignment - TraesCS6A01G238200

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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 TraesCS6A01G238200 chr6A 100.000 2613 0 0 1 2613 447840086 447842698 0.000000e+00 4826.0
1 TraesCS6A01G238200 chr6A 98.089 2617 44 4 1 2613 601158356 601155742 0.000000e+00 4551.0
2 TraesCS6A01G238200 chr6A 89.103 312 33 1 1484 1794 20167320 20167631 1.130000e-103 387.0
3 TraesCS6A01G238200 chr6A 88.158 228 18 5 1980 2198 20168101 20168328 1.990000e-66 263.0
4 TraesCS6A01G238200 chr5A 96.980 2616 73 4 1 2613 433729601 433726989 0.000000e+00 4388.0
5 TraesCS6A01G238200 chrUn 96.599 2617 62 7 4 2613 33219327 33216731 0.000000e+00 4314.0
6 TraesCS6A01G238200 chrUn 85.285 666 54 13 1 631 221036440 221037096 0.000000e+00 647.0
7 TraesCS6A01G238200 chrUn 88.889 81 5 3 2281 2359 221037141 221037219 2.140000e-16 97.1
8 TraesCS6A01G238200 chr5B 95.881 1918 54 7 1 1913 387891541 387889644 0.000000e+00 3081.0
9 TraesCS6A01G238200 chr5B 85.275 781 103 9 660 1434 259727914 259728688 0.000000e+00 795.0
10 TraesCS6A01G238200 chr3B 92.709 1838 94 15 1 1832 328598079 328599882 0.000000e+00 2615.0
11 TraesCS6A01G238200 chr3B 87.234 235 30 0 1 235 817790131 817790365 4.290000e-68 268.0
12 TraesCS6A01G238200 chr3B 97.260 73 2 0 2541 2613 328599883 328599955 9.820000e-25 124.0
13 TraesCS6A01G238200 chr2B 85.135 666 55 12 1 631 788440920 788441576 2.190000e-180 641.0
14 TraesCS6A01G238200 chr2B 88.889 81 5 3 2281 2359 788441621 788441699 2.140000e-16 97.1
15 TraesCS6A01G238200 chr1A 84.722 648 81 8 1 640 373587845 373587208 1.320000e-177 632.0
16 TraesCS6A01G238200 chr1A 88.498 313 31 5 1484 1794 388526819 388526510 8.830000e-100 374.0
17 TraesCS6A01G238200 chr1A 87.446 231 20 4 1980 2201 388526040 388525810 9.280000e-65 257.0
18 TraesCS6A01G238200 chr1A 87.654 81 6 3 2280 2359 373587173 373587096 9.960000e-15 91.6
19 TraesCS6A01G238200 chr5D 85.847 537 47 15 1 529 239195365 239195880 6.360000e-151 544.0
20 TraesCS6A01G238200 chr7B 86.680 488 53 7 1791 2268 704819986 704820471 4.950000e-147 531.0
21 TraesCS6A01G238200 chr7B 89.676 339 29 4 1936 2268 704889106 704889444 6.680000e-116 427.0
22 TraesCS6A01G238200 chr4B 88.076 369 41 3 660 1025 429721544 429721176 3.990000e-118 435.0
23 TraesCS6A01G238200 chr7D 90.127 314 30 1 1484 1796 613791753 613792066 8.710000e-110 407.0
24 TraesCS6A01G238200 chr7D 87.281 228 18 6 1980 2198 87182631 87182856 1.550000e-62 250.0
25 TraesCS6A01G238200 chr7D 88.889 126 11 2 1794 1919 116821635 116821513 4.500000e-33 152.0
26 TraesCS6A01G238200 chr4A 88.710 310 33 1 1485 1794 224885153 224884846 6.830000e-101 377.0
27 TraesCS6A01G238200 chr4A 91.538 130 10 1 1790 1919 553276417 553276289 7.430000e-41 178.0
28 TraesCS6A01G238200 chr2A 90.050 201 20 0 64 264 747150568 747150768 7.170000e-66 261.0
29 TraesCS6A01G238200 chr1D 86.580 231 21 6 1980 2201 386406286 386406057 2.010000e-61 246.0


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 TraesCS6A01G238200 chr6A 447840086 447842698 2612 False 4826.00 4826 100.0000 1 2613 1 chr6A.!!$F1 2612
1 TraesCS6A01G238200 chr6A 601155742 601158356 2614 True 4551.00 4551 98.0890 1 2613 1 chr6A.!!$R1 2612
2 TraesCS6A01G238200 chr6A 20167320 20168328 1008 False 325.00 387 88.6305 1484 2198 2 chr6A.!!$F2 714
3 TraesCS6A01G238200 chr5A 433726989 433729601 2612 True 4388.00 4388 96.9800 1 2613 1 chr5A.!!$R1 2612
4 TraesCS6A01G238200 chrUn 33216731 33219327 2596 True 4314.00 4314 96.5990 4 2613 1 chrUn.!!$R1 2609
5 TraesCS6A01G238200 chrUn 221036440 221037219 779 False 372.05 647 87.0870 1 2359 2 chrUn.!!$F1 2358
6 TraesCS6A01G238200 chr5B 387889644 387891541 1897 True 3081.00 3081 95.8810 1 1913 1 chr5B.!!$R1 1912
7 TraesCS6A01G238200 chr5B 259727914 259728688 774 False 795.00 795 85.2750 660 1434 1 chr5B.!!$F1 774
8 TraesCS6A01G238200 chr3B 328598079 328599955 1876 False 1369.50 2615 94.9845 1 2613 2 chr3B.!!$F2 2612
9 TraesCS6A01G238200 chr2B 788440920 788441699 779 False 369.05 641 87.0120 1 2359 2 chr2B.!!$F1 2358
10 TraesCS6A01G238200 chr1A 373587096 373587845 749 True 361.80 632 86.1880 1 2359 2 chr1A.!!$R1 2358
11 TraesCS6A01G238200 chr1A 388525810 388526819 1009 True 315.50 374 87.9720 1484 2201 2 chr1A.!!$R2 717
12 TraesCS6A01G238200 chr5D 239195365 239195880 515 False 544.00 544 85.8470 1 529 1 chr5D.!!$F1 528

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
126 142 0.034059 CTGTGGAGACTTTGAGGCGT 59.966 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2261 2.356313 CACAGCTCGTGCCTCGTT 60.356 61.111 5.73 0.0 39.19 3.85 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
126 142 0.034059 CTGTGGAGACTTTGAGGCGT 59.966 55.000 0.00 0.00 0.00 5.68
612 661 9.597170 CTGCAGCAGATAGATACATTTGTATAT 57.403 33.333 18.42 3.45 36.13 0.86
648 697 8.988064 TTTGTGTCTTGTCTGATATAGTTCTC 57.012 34.615 0.00 0.00 0.00 2.87
997 1050 2.276732 AGCTCTGCCTTTGTAAGCAA 57.723 45.000 0.00 0.00 38.82 3.91
1526 1587 5.893255 CCTTTTGTTTGGGATGATCCAGATA 59.107 40.000 14.36 0.00 38.64 1.98
1560 1621 1.264288 GTTGCTCACAGGAAGAAACCG 59.736 52.381 0.00 0.00 34.73 4.44
1931 2261 1.471119 AAATCTCGAGTAGTGCCGGA 58.529 50.000 13.13 0.00 0.00 5.14
1991 2344 6.372931 ACTGCCCCTTATGCTGAATTTAATA 58.627 36.000 0.00 0.00 0.00 0.98
2320 2682 3.346315 TGGATACACATGGCTCTGTTTG 58.654 45.455 0.00 0.00 46.17 2.93
2333 2695 4.142160 GGCTCTGTTTGAATAAATCCCCAC 60.142 45.833 0.00 0.00 0.00 4.61
2352 2714 9.749996 ATCCCCACTTTATCCTATATGATATGT 57.250 33.333 0.00 0.46 0.00 2.29
2442 2804 9.515226 TCTTTTAAATGCTATAGGTGTCTTTGT 57.485 29.630 1.04 0.00 0.00 2.83
2443 2805 9.559958 CTTTTAAATGCTATAGGTGTCTTTGTG 57.440 33.333 1.04 0.00 0.00 3.33
2444 2806 8.630054 TTTAAATGCTATAGGTGTCTTTGTGT 57.370 30.769 1.04 0.00 0.00 3.72
2445 2807 6.743575 AAATGCTATAGGTGTCTTTGTGTC 57.256 37.500 1.04 0.00 0.00 3.67
2446 2808 5.683876 ATGCTATAGGTGTCTTTGTGTCT 57.316 39.130 1.04 0.00 0.00 3.41
2448 2810 5.237815 TGCTATAGGTGTCTTTGTGTCTTG 58.762 41.667 1.04 0.00 0.00 3.02
2491 2856 8.727910 GTTTTGGTTAGGAAAGATTGTAGGTAG 58.272 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 142 4.329545 GCCAACGCCTCCACCAGA 62.330 66.667 0.00 0.00 0.00 3.86
495 529 6.530120 TGCTTGAAAATGAGAGTTAGTGGTA 58.470 36.000 0.00 0.00 0.00 3.25
648 697 7.661040 ACTGATGTTGTTCAATCCCTAAAAAG 58.339 34.615 0.00 0.00 0.00 2.27
997 1050 0.982852 TCTGATCGGCCCTTCATGGT 60.983 55.000 0.00 0.00 0.00 3.55
1560 1621 3.883669 AGAAGAGGATTCTCATTGTGGC 58.116 45.455 3.21 0.00 42.34 5.01
1625 1686 6.127225 ACAGTGCACAATGAGAGATACTACAT 60.127 38.462 21.04 0.00 0.00 2.29
1931 2261 2.356313 CACAGCTCGTGCCTCGTT 60.356 61.111 5.73 0.00 39.19 3.85
2007 2360 8.425703 TCAAATCATAATGGCATTCATGATTGT 58.574 29.630 31.25 24.40 43.73 2.71
2179 2541 1.619654 TGGCTTGCATAAACACTGCT 58.380 45.000 0.00 0.00 40.34 4.24
2333 2695 9.386122 AGGGCCTACATATCATATAGGATAAAG 57.614 37.037 2.82 9.24 38.20 1.85
2352 2714 2.635915 TGAGAAAAGAAACGAGGGCCTA 59.364 45.455 5.73 0.00 0.00 3.93
2441 2803 0.661020 CGGACCACCAAACAAGACAC 59.339 55.000 0.00 0.00 35.59 3.67
2442 2804 1.098712 GCGGACCACCAAACAAGACA 61.099 55.000 0.00 0.00 35.59 3.41
2443 2805 1.652563 GCGGACCACCAAACAAGAC 59.347 57.895 0.00 0.00 35.59 3.01
2444 2806 1.527380 GGCGGACCACCAAACAAGA 60.527 57.895 0.00 0.00 35.59 3.02
2445 2807 1.106944 AAGGCGGACCACCAAACAAG 61.107 55.000 0.32 0.00 39.06 3.16
2446 2808 1.076632 AAGGCGGACCACCAAACAA 60.077 52.632 0.32 0.00 39.06 2.83
2448 2810 1.388837 AACAAGGCGGACCACCAAAC 61.389 55.000 0.32 0.00 39.06 2.93
2491 2856 6.995511 ACATATATCTCCGAAGCTACTCTC 57.004 41.667 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.