Multiple sequence alignment - TraesCS5A01G217100

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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 TraesCS5A01G217100 chr5A 100.000 2613 0 0 1 2613 433729603 433726991 0.000000e+00 4826
1 TraesCS5A01G217100 chr6A 97.208 2615 71 1 1 2613 601158358 601155744 0.000000e+00 4423
2 TraesCS5A01G217100 chr6A 96.980 2616 73 4 1 2613 447840084 447842696 0.000000e+00 4388
3 TraesCS5A01G217100 chr6A 89.035 228 16 4 1979 2197 20168101 20168328 9.210000e-70 274
4 TraesCS5A01G217100 chrUn 95.840 2620 82 9 1 2613 33219332 33216733 0.000000e+00 4209
5 TraesCS5A01G217100 chrUn 85.554 623 53 15 39 633 221036483 221037096 3.690000e-173 617
6 TraesCS5A01G217100 chrUn 91.358 81 3 3 2280 2358 221037141 221037219 9.890000e-20 108
7 TraesCS5A01G217100 chr5B 94.789 1919 74 9 1 1912 387891543 387889644 0.000000e+00 2966
8 TraesCS5A01G217100 chr5B 84.251 781 110 10 661 1434 259727914 259728688 0.000000e+00 749
9 TraesCS5A01G217100 chr3B 91.503 1836 117 16 3 1831 328598079 328599882 0.000000e+00 2490
10 TraesCS5A01G217100 chr3B 87.793 213 26 0 1 213 817790129 817790341 1.550000e-62 250
11 TraesCS5A01G217100 chr3B 95.775 71 3 0 2543 2613 328599883 328599953 5.910000e-22 115
12 TraesCS5A01G217100 chr1A 85.185 648 78 8 3 642 373587845 373587208 0.000000e+00 649
13 TraesCS5A01G217100 chr1A 88.312 231 18 4 1979 2200 388526040 388525810 4.290000e-68 268
14 TraesCS5A01G217100 chr2B 85.233 623 55 15 39 633 788440963 788441576 8.000000e-170 606
15 TraesCS5A01G217100 chr2B 91.358 81 3 3 2280 2358 788441621 788441699 9.890000e-20 108
16 TraesCS5A01G217100 chr7B 84.060 596 55 11 1790 2351 704819986 704820575 2.960000e-149 538
17 TraesCS5A01G217100 chr7B 84.868 456 35 14 1935 2358 704889106 704889559 1.860000e-116 429
18 TraesCS5A01G217100 chr5D 85.529 539 49 10 1 531 239195363 239195880 1.060000e-148 536
19 TraesCS5A01G217100 chr5D 86.813 91 12 0 529 619 535919781 535919871 4.600000e-18 102
20 TraesCS5A01G217100 chr4B 87.701 374 41 5 656 1025 429721548 429721176 5.170000e-117 431
21 TraesCS5A01G217100 chr7D 88.854 314 33 2 1484 1795 613791753 613792066 4.080000e-103 385
22 TraesCS5A01G217100 chr7D 88.158 228 16 5 1979 2197 87182631 87182856 7.170000e-66 261
23 TraesCS5A01G217100 chr7D 89.683 126 10 2 1793 1918 116821635 116821513 9.680000e-35 158
24 TraesCS5A01G217100 chr1D 87.446 231 19 5 1979 2200 386406286 386406057 9.280000e-65 257
25 TraesCS5A01G217100 chr1D 90.476 126 9 2 1793 1918 386406712 386406590 2.080000e-36 163
26 TraesCS5A01G217100 chr6D 90.052 191 19 0 76 266 126022565 126022375 5.580000e-62 248
27 TraesCS5A01G217100 chr3A 88.636 176 12 4 177 352 469500439 469500606 9.480000e-50 207
28 TraesCS5A01G217100 chr4A 92.308 130 9 1 1789 1918 553276417 553276289 1.600000e-42 183


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 TraesCS5A01G217100 chr5A 433726991 433729603 2612 True 4826.0 4826 100.0000 1 2613 1 chr5A.!!$R1 2612
1 TraesCS5A01G217100 chr6A 601155744 601158358 2614 True 4423.0 4423 97.2080 1 2613 1 chr6A.!!$R1 2612
2 TraesCS5A01G217100 chr6A 447840084 447842696 2612 False 4388.0 4388 96.9800 1 2613 1 chr6A.!!$F2 2612
3 TraesCS5A01G217100 chrUn 33216733 33219332 2599 True 4209.0 4209 95.8400 1 2613 1 chrUn.!!$R1 2612
4 TraesCS5A01G217100 chrUn 221036483 221037219 736 False 362.5 617 88.4560 39 2358 2 chrUn.!!$F1 2319
5 TraesCS5A01G217100 chr5B 387889644 387891543 1899 True 2966.0 2966 94.7890 1 1912 1 chr5B.!!$R1 1911
6 TraesCS5A01G217100 chr5B 259727914 259728688 774 False 749.0 749 84.2510 661 1434 1 chr5B.!!$F1 773
7 TraesCS5A01G217100 chr3B 328598079 328599953 1874 False 1302.5 2490 93.6390 3 2613 2 chr3B.!!$F2 2610
8 TraesCS5A01G217100 chr1A 373587208 373587845 637 True 649.0 649 85.1850 3 642 1 chr1A.!!$R1 639
9 TraesCS5A01G217100 chr2B 788440963 788441699 736 False 357.0 606 88.2955 39 2358 2 chr2B.!!$F1 2319
10 TraesCS5A01G217100 chr7B 704819986 704820575 589 False 538.0 538 84.0600 1790 2351 1 chr7B.!!$F1 561
11 TraesCS5A01G217100 chr5D 239195363 239195880 517 False 536.0 536 85.5290 1 531 1 chr5D.!!$F1 530
12 TraesCS5A01G217100 chr1D 386406057 386406712 655 True 210.0 257 88.9610 1793 2200 2 chr1D.!!$R1 407

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
105 111 0.105142 CGAAGGATTAGGGGAGGGGA 60.105 60.000 0.00 0.0 0.0 4.81 F
254 260 2.690497 CGTGTGGATGTAGATGAGACCT 59.310 50.000 0.00 0.0 0.0 3.85 F
1068 1116 1.228154 GTGGCAACCGGACCTTCTT 60.228 57.895 9.46 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1049 0.681564 ACCTCGCTTCTGATCGGTCT 60.682 55.000 0.42 0.0 0.0 3.85 R
1149 1199 1.153549 CGAGTAACTGGGAGCTGGC 60.154 63.158 0.00 0.0 0.0 4.85 R
2536 2874 5.353123 GCGTAATGTGAATTCCCTACTTTGA 59.647 40.000 2.27 0.0 0.0 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
35 36 0.902984 TTGGAGACGCAGCCTTAGGA 60.903 55.000 0.69 0.0 0.00 2.94
105 111 0.105142 CGAAGGATTAGGGGAGGGGA 60.105 60.000 0.00 0.0 0.00 4.81
201 207 2.882876 GCCATGGCTGCACTTCAG 59.117 61.111 29.98 0.0 45.62 3.02
254 260 2.690497 CGTGTGGATGTAGATGAGACCT 59.310 50.000 0.00 0.0 0.00 3.85
286 292 8.803235 TGATGAACAAATAGTAGTAGACTGTGT 58.197 33.333 0.00 0.0 39.39 3.72
580 598 6.974622 GTGCTTCTTTCATTTTCTCTGTTCAA 59.025 34.615 0.00 0.0 0.00 2.69
1005 1049 2.029110 GCCTTTGTAAGCAGCCATGAAA 60.029 45.455 0.00 0.0 0.00 2.69
1067 1115 2.430367 GTGGCAACCGGACCTTCT 59.570 61.111 9.46 0.0 0.00 2.85
1068 1116 1.228154 GTGGCAACCGGACCTTCTT 60.228 57.895 9.46 0.0 0.00 2.52
1096 1146 1.672854 CGACAGGCAGGAATCCGGTA 61.673 60.000 0.00 0.0 32.23 4.02
1264 1314 3.537506 TGGGTCCACCTCTCCCCA 61.538 66.667 0.00 0.0 44.84 4.96
1308 1358 1.003233 GTGGCCACTCCTCAGGTTC 60.003 63.158 29.12 0.0 35.26 3.62
1327 1377 2.267006 CTGGCTGATGTCACGCCT 59.733 61.111 17.96 0.0 39.37 5.52
1376 1426 0.544357 CTCCTGGGGTGTGTCCTACA 60.544 60.000 0.00 0.0 36.82 2.74
1471 1523 6.363626 ACTCACGCGATAGATCATTTATGTTC 59.636 38.462 15.93 0.0 39.76 3.18
1543 1595 5.835280 TCCAGATGAGATAGTGCATCAGTTA 59.165 40.000 0.00 0.0 42.52 2.24
1620 1672 8.041323 ACTATTCCTACTTGATTGACGAACATT 58.959 33.333 0.00 0.0 0.00 2.71
1729 1785 6.719829 TGTGTTAGGAACTGAGATTCACTAGA 59.280 38.462 0.00 0.0 41.52 2.43
2091 2402 8.215050 TCTGAACAATTAGTTTGAAAGGTCCTA 58.785 33.333 0.00 0.0 41.51 2.94
2201 2516 4.493547 GCAGTGTTTATGCAAGCCAATAA 58.506 39.130 0.00 0.0 43.31 1.40
2371 2709 2.230660 CAGGCCCTCGTTTCTTTTCTT 58.769 47.619 0.00 0.0 0.00 2.52
2559 2897 6.978343 TCAAAGTAGGGAATTCACATTACG 57.022 37.500 11.02 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 111 1.228894 TCGAAGTCTCCACAGCCCT 60.229 57.895 0.00 0.00 0.00 5.19
254 260 6.216801 ACTACTATTTGTTCATCACGGCTA 57.783 37.500 0.00 0.00 0.00 3.93
486 504 9.656323 ATGAGAGTTAGTGGTGATATTTACCTA 57.344 33.333 10.38 0.00 39.01 3.08
580 598 8.183104 TGTATCTATCTGCTGCAGTATAAGTT 57.817 34.615 27.24 16.56 32.61 2.66
882 924 9.337396 GGATTACATACCATGTTGATTCAGTTA 57.663 33.333 0.00 0.00 41.63 2.24
1005 1049 0.681564 ACCTCGCTTCTGATCGGTCT 60.682 55.000 0.42 0.00 0.00 3.85
1067 1115 2.669569 GCCTGTCGCTGGCAAGAA 60.670 61.111 18.09 0.00 45.75 2.52
1096 1146 2.089201 GTACTTATTTGGCGGCCACTT 58.911 47.619 23.78 14.55 30.78 3.16
1149 1199 1.153549 CGAGTAACTGGGAGCTGGC 60.154 63.158 0.00 0.00 0.00 4.85
1264 1314 3.010138 TGGGGAGAAAAGATCCAACGAAT 59.990 43.478 0.00 0.00 38.70 3.34
1308 1358 3.857854 GCGTGACATCAGCCAGCG 61.858 66.667 0.00 0.00 0.00 5.18
1327 1377 1.760029 GGAAAAACCTGCCTTGGAACA 59.240 47.619 0.00 0.00 35.41 3.18
1471 1523 6.483640 AGCAAGAAACTTCTACCTAAACACAG 59.516 38.462 0.00 0.00 36.28 3.66
1543 1595 1.843851 TGGTGGTTTCTTCCTGTGAGT 59.156 47.619 0.00 0.00 0.00 3.41
1609 1661 8.683615 AGATACTACAGATACAATGTTCGTCAA 58.316 33.333 0.00 0.00 32.02 3.18
1620 1672 7.285401 TGCACAATGAGAGATACTACAGATACA 59.715 37.037 0.00 0.00 0.00 2.29
1700 1756 7.721399 AGTGAATCTCAGTTCCTAACACAAAAT 59.279 33.333 0.00 0.00 0.00 1.82
2201 2516 9.469807 CTTCGTTTGCTTTCTAGTATCTCATAT 57.530 33.333 0.00 0.00 0.00 1.78
2328 2666 8.708378 CCTGCATATCATATAGGATAAACTGGA 58.292 37.037 19.91 12.13 33.90 3.86
2536 2874 5.353123 GCGTAATGTGAATTCCCTACTTTGA 59.647 40.000 2.27 0.00 0.00 2.69
2559 2897 6.497785 ACTGTCACCTACTCGTATATATGC 57.502 41.667 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.