Multiple sequence alignment - TraesCS4A01G454000

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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 TraesCS4A01G454000 chr4A 100.000 2683 0 0 455 3137 718079152 718076470 0.000000e+00 4955.0
1 TraesCS4A01G454000 chr4A 99.397 2654 14 1 484 3137 718185263 718182612 0.000000e+00 4811.0
2 TraesCS4A01G454000 chr4A 80.067 1495 229 47 821 2256 717051389 717049905 0.000000e+00 1046.0
3 TraesCS4A01G454000 chr4A 78.298 1539 245 66 831 2298 717045870 717044350 0.000000e+00 909.0
4 TraesCS4A01G454000 chr4A 79.047 1322 227 31 948 2225 716955547 716954232 0.000000e+00 861.0
5 TraesCS4A01G454000 chr4A 100.000 303 0 0 1 303 718079606 718079304 7.600000e-156 560.0
6 TraesCS4A01G454000 chr4A 99.650 286 1 0 18 303 718185632 718185347 9.970000e-145 523.0
7 TraesCS4A01G454000 chr4A 76.696 339 63 14 2557 2881 717049594 717049258 1.160000e-39 174.0
8 TraesCS4A01G454000 chr4A 81.522 92 17 0 1100 1191 714137529 714137438 3.350000e-10 76.8
9 TraesCS4A01G454000 chr4A 97.143 35 1 0 1769 1803 624983273 624983307 3.380000e-05 60.2
10 TraesCS4A01G454000 chr7D 92.341 1828 92 14 1241 3031 16571985 16573801 0.000000e+00 2556.0
11 TraesCS4A01G454000 chr7D 78.880 1321 203 43 948 2225 17344801 17346088 0.000000e+00 824.0
12 TraesCS4A01G454000 chr7D 79.681 940 146 31 831 1734 17214548 17215478 1.230000e-178 636.0
13 TraesCS4A01G454000 chr7D 83.709 577 85 3 1167 1734 17207121 17207697 1.280000e-148 536.0
14 TraesCS4A01G454000 chr7D 76.838 272 49 12 2557 2816 17208299 17208568 1.170000e-29 141.0
15 TraesCS4A01G454000 chr7D 97.222 36 1 0 1941 1976 549537821 549537786 9.390000e-06 62.1
16 TraesCS4A01G454000 chr7A 84.672 1494 190 26 922 2395 15534694 15533220 0.000000e+00 1454.0
17 TraesCS4A01G454000 chr7A 84.083 578 83 4 1091 1659 16596821 16597398 1.640000e-152 549.0
18 TraesCS4A01G454000 chr7A 81.395 430 62 13 816 1230 16596392 16596818 5.010000e-88 335.0
19 TraesCS4A01G454000 chr7A 77.126 341 59 16 2557 2881 16598572 16598909 2.490000e-41 180.0
20 TraesCS4A01G454000 chr7A 76.752 314 56 12 1413 1722 667984569 667984269 3.240000e-35 159.0
21 TraesCS4A01G454000 chr7A 85.000 160 14 4 563 713 15535199 15535041 1.510000e-33 154.0
22 TraesCS4A01G454000 chr7A 100.000 34 0 0 1941 1974 634979645 634979612 2.610000e-06 63.9
23 TraesCS4A01G454000 chr7A 88.889 45 4 1 2905 2948 15528679 15528635 2.000000e-03 54.7
24 TraesCS4A01G454000 chr7B 75.969 129 29 2 1847 1974 593913098 593912971 7.260000e-07 65.8
25 TraesCS4A01G454000 chr6A 100.000 35 0 0 455 489 88851348 88851382 7.260000e-07 65.8
26 TraesCS4A01G454000 chr5D 100.000 35 0 0 455 489 271849124 271849158 7.260000e-07 65.8
27 TraesCS4A01G454000 chr5D 95.000 40 2 0 1764 1803 544285246 544285207 2.610000e-06 63.9
28 TraesCS4A01G454000 chr3B 100.000 34 0 0 1941 1974 2993148 2993181 2.610000e-06 63.9
29 TraesCS4A01G454000 chr5B 94.737 38 2 0 1766 1803 685950339 685950302 3.380000e-05 60.2
30 TraesCS4A01G454000 chr2D 90.244 41 4 0 1763 1803 84917723 84917763 2.000000e-03 54.7
31 TraesCS4A01G454000 chr2D 90.244 41 4 0 1763 1803 85674710 85674750 2.000000e-03 54.7
32 TraesCS4A01G454000 chr2A 100.000 29 0 0 1775 1803 84153021 84152993 2.000000e-03 54.7


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 TraesCS4A01G454000 chr4A 718076470 718079606 3136 True 2757.500000 4955 100.000000 1 3137 2 chr4A.!!$R4 3136
1 TraesCS4A01G454000 chr4A 718182612 718185632 3020 True 2667.000000 4811 99.523500 18 3137 2 chr4A.!!$R5 3119
2 TraesCS4A01G454000 chr4A 716954232 716955547 1315 True 861.000000 861 79.047000 948 2225 1 chr4A.!!$R2 1277
3 TraesCS4A01G454000 chr4A 717044350 717051389 7039 True 709.666667 1046 78.353667 821 2881 3 chr4A.!!$R3 2060
4 TraesCS4A01G454000 chr7D 16571985 16573801 1816 False 2556.000000 2556 92.341000 1241 3031 1 chr7D.!!$F1 1790
5 TraesCS4A01G454000 chr7D 17344801 17346088 1287 False 824.000000 824 78.880000 948 2225 1 chr7D.!!$F3 1277
6 TraesCS4A01G454000 chr7D 17214548 17215478 930 False 636.000000 636 79.681000 831 1734 1 chr7D.!!$F2 903
7 TraesCS4A01G454000 chr7D 17207121 17208568 1447 False 338.500000 536 80.273500 1167 2816 2 chr7D.!!$F4 1649
8 TraesCS4A01G454000 chr7A 15533220 15535199 1979 True 804.000000 1454 84.836000 563 2395 2 chr7A.!!$R4 1832
9 TraesCS4A01G454000 chr7A 16596392 16598909 2517 False 354.666667 549 80.868000 816 2881 3 chr7A.!!$F1 2065

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
86 87 1.379977 CGCTCTCTCCCCTACACCA 60.380 63.158 0.00 0.0 0.0 4.17 F
476 477 2.571653 ACCACTCAAATGAAGGATCCGA 59.428 45.455 5.98 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1974 5.163322 TGGCAATGAACTGACCTTTGAATTT 60.163 36.000 0.0 0.0 0.00 1.82 R
2526 3181 4.789095 TCGTACTTCTGTTTCAGCAAAC 57.211 40.909 0.0 0.0 42.16 2.93 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
86 87 1.379977 CGCTCTCTCCCCTACACCA 60.380 63.158 0.00 0.00 0.00 4.17
475 476 2.991250 ACCACTCAAATGAAGGATCCG 58.009 47.619 5.98 0.00 0.00 4.18
476 477 2.571653 ACCACTCAAATGAAGGATCCGA 59.428 45.455 5.98 0.00 0.00 4.55
477 478 3.201290 CCACTCAAATGAAGGATCCGAG 58.799 50.000 5.98 7.53 0.00 4.63
478 479 3.118629 CCACTCAAATGAAGGATCCGAGA 60.119 47.826 15.06 0.49 0.00 4.04
479 480 4.507710 CACTCAAATGAAGGATCCGAGAA 58.492 43.478 15.06 0.53 0.00 2.87
480 481 5.121811 CACTCAAATGAAGGATCCGAGAAT 58.878 41.667 15.06 2.73 0.00 2.40
481 482 5.587844 CACTCAAATGAAGGATCCGAGAATT 59.412 40.000 15.06 7.98 0.00 2.17
482 483 6.763135 CACTCAAATGAAGGATCCGAGAATTA 59.237 38.462 15.06 0.00 0.00 1.40
526 527 6.758593 AGCGTACGTTGTTGTATATATTGG 57.241 37.500 17.90 0.00 0.00 3.16
2637 3317 2.169978 GCGGGCTAAATATACCCCTAGG 59.830 54.545 0.06 0.06 40.86 3.02
2645 3325 6.070194 GCTAAATATACCCCTAGGAGCATCAA 60.070 42.308 11.48 0.00 36.25 2.57
3132 5485 8.542497 AGTATTAACTTTGCACGTTTATCTCA 57.458 30.769 5.95 0.00 29.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 4.282292 AGCTACCTAGGGTTTACAGGAT 57.718 45.455 14.81 0.00 37.09 3.24
454 455 3.772572 TCGGATCCTTCATTTGAGTGGTA 59.227 43.478 10.75 0.00 0.00 3.25
455 456 2.571653 TCGGATCCTTCATTTGAGTGGT 59.428 45.455 10.75 0.00 0.00 4.16
456 457 3.118629 TCTCGGATCCTTCATTTGAGTGG 60.119 47.826 10.75 0.00 0.00 4.00
457 458 4.128925 TCTCGGATCCTTCATTTGAGTG 57.871 45.455 10.75 0.00 0.00 3.51
458 459 4.826274 TTCTCGGATCCTTCATTTGAGT 57.174 40.909 10.75 0.00 0.00 3.41
459 460 6.763135 TGTAATTCTCGGATCCTTCATTTGAG 59.237 38.462 10.75 7.18 0.00 3.02
460 461 6.649155 TGTAATTCTCGGATCCTTCATTTGA 58.351 36.000 10.75 0.00 0.00 2.69
461 462 6.512415 GCTGTAATTCTCGGATCCTTCATTTG 60.512 42.308 10.75 0.00 0.00 2.32
462 463 5.529060 GCTGTAATTCTCGGATCCTTCATTT 59.471 40.000 10.75 1.00 0.00 2.32
463 464 5.059833 GCTGTAATTCTCGGATCCTTCATT 58.940 41.667 10.75 5.49 0.00 2.57
464 465 4.101585 TGCTGTAATTCTCGGATCCTTCAT 59.898 41.667 10.75 0.00 0.00 2.57
465 466 3.450817 TGCTGTAATTCTCGGATCCTTCA 59.549 43.478 10.75 0.00 0.00 3.02
466 467 4.054671 CTGCTGTAATTCTCGGATCCTTC 58.945 47.826 10.75 0.00 0.00 3.46
467 468 3.452627 ACTGCTGTAATTCTCGGATCCTT 59.547 43.478 10.75 0.00 0.00 3.36
468 469 3.034635 ACTGCTGTAATTCTCGGATCCT 58.965 45.455 10.75 0.00 0.00 3.24
469 470 3.460857 ACTGCTGTAATTCTCGGATCC 57.539 47.619 0.00 0.00 0.00 3.36
470 471 7.348201 CAAAATACTGCTGTAATTCTCGGATC 58.652 38.462 7.59 0.00 31.80 3.36
471 472 6.260936 CCAAAATACTGCTGTAATTCTCGGAT 59.739 38.462 7.59 0.00 31.80 4.18
472 473 5.584649 CCAAAATACTGCTGTAATTCTCGGA 59.415 40.000 7.59 0.00 31.80 4.55
473 474 5.354234 ACCAAAATACTGCTGTAATTCTCGG 59.646 40.000 7.59 9.44 31.80 4.63
474 475 6.422776 ACCAAAATACTGCTGTAATTCTCG 57.577 37.500 7.59 0.55 31.80 4.04
475 476 7.857885 GCATACCAAAATACTGCTGTAATTCTC 59.142 37.037 7.59 0.00 31.80 2.87
476 477 7.557719 AGCATACCAAAATACTGCTGTAATTCT 59.442 33.333 7.59 0.00 41.38 2.40
477 478 7.707104 AGCATACCAAAATACTGCTGTAATTC 58.293 34.615 7.59 0.00 41.38 2.17
478 479 7.645058 AGCATACCAAAATACTGCTGTAATT 57.355 32.000 7.59 2.90 41.38 1.40
479 480 7.041098 GCTAGCATACCAAAATACTGCTGTAAT 60.041 37.037 10.63 0.00 42.74 1.89
480 481 6.260050 GCTAGCATACCAAAATACTGCTGTAA 59.740 38.462 10.63 0.00 42.74 2.41
481 482 5.758296 GCTAGCATACCAAAATACTGCTGTA 59.242 40.000 10.63 5.87 42.74 2.74
482 483 4.576463 GCTAGCATACCAAAATACTGCTGT 59.424 41.667 10.63 0.66 42.74 4.40
526 527 5.073311 TCTAGTCTAGTGACAACAATGCC 57.927 43.478 6.77 0.00 45.20 4.40
1639 1974 5.163322 TGGCAATGAACTGACCTTTGAATTT 60.163 36.000 0.00 0.00 0.00 1.82
2526 3181 4.789095 TCGTACTTCTGTTTCAGCAAAC 57.211 40.909 0.00 0.00 42.16 2.93
2645 3325 5.457686 ACCACATATGCATCCAGGTAAATT 58.542 37.500 0.19 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.