Multiple sequence alignment - TraesCS4A01G069700

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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 TraesCS4A01G069700 chr4A 100.000 2528 0 0 1 2528 67554908 67552381 0 4669
1 TraesCS4A01G069700 chr2D 97.904 2529 42 4 1 2528 635037269 635039787 0 4366
2 TraesCS4A01G069700 chr7B 97.787 2531 43 5 1 2528 743066314 743068834 0 4351
3 TraesCS4A01G069700 chr7A 97.745 2528 45 4 1 2528 120828839 120826324 0 4342
4 TraesCS4A01G069700 chr7A 97.629 2531 45 8 1 2528 671960559 671958041 0 4327
5 TraesCS4A01G069700 chr3B 97.706 2528 46 5 1 2528 201635794 201633279 0 4337
6 TraesCS4A01G069700 chr2A 97.707 2529 43 6 1 2525 735172808 735175325 0 4335
7 TraesCS4A01G069700 chr3D 97.667 2529 48 4 1 2528 202611955 202614473 0 4333
8 TraesCS4A01G069700 chr5A 97.631 2533 45 6 1 2528 16623266 16620744 0 4331
9 TraesCS4A01G069700 chr4D 97.472 2532 48 7 1 2528 123367651 123370170 0 4307
10 TraesCS4A01G069700 chr4B 96.922 2534 61 12 1 2528 209149598 209147076 0 4231
11 TraesCS4A01G069700 chr7D 96.638 2528 70 6 1 2528 307064885 307062373 0 4183
12 TraesCS4A01G069700 chr1B 97.457 2320 45 10 1 2319 583500744 583498438 0 3945
13 TraesCS4A01G069700 chrUn 98.081 1511 16 7 1 1508 273238806 273240306 0 2617
14 TraesCS4A01G069700 chr3A 96.588 762 16 6 1 762 725792030 725792781 0 1254


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 TraesCS4A01G069700 chr4A 67552381 67554908 2527 True 4669 4669 100.000 1 2528 1 chr4A.!!$R1 2527
1 TraesCS4A01G069700 chr2D 635037269 635039787 2518 False 4366 4366 97.904 1 2528 1 chr2D.!!$F1 2527
2 TraesCS4A01G069700 chr7B 743066314 743068834 2520 False 4351 4351 97.787 1 2528 1 chr7B.!!$F1 2527
3 TraesCS4A01G069700 chr7A 120826324 120828839 2515 True 4342 4342 97.745 1 2528 1 chr7A.!!$R1 2527
4 TraesCS4A01G069700 chr7A 671958041 671960559 2518 True 4327 4327 97.629 1 2528 1 chr7A.!!$R2 2527
5 TraesCS4A01G069700 chr3B 201633279 201635794 2515 True 4337 4337 97.706 1 2528 1 chr3B.!!$R1 2527
6 TraesCS4A01G069700 chr2A 735172808 735175325 2517 False 4335 4335 97.707 1 2525 1 chr2A.!!$F1 2524
7 TraesCS4A01G069700 chr3D 202611955 202614473 2518 False 4333 4333 97.667 1 2528 1 chr3D.!!$F1 2527
8 TraesCS4A01G069700 chr5A 16620744 16623266 2522 True 4331 4331 97.631 1 2528 1 chr5A.!!$R1 2527
9 TraesCS4A01G069700 chr4D 123367651 123370170 2519 False 4307 4307 97.472 1 2528 1 chr4D.!!$F1 2527
10 TraesCS4A01G069700 chr4B 209147076 209149598 2522 True 4231 4231 96.922 1 2528 1 chr4B.!!$R1 2527
11 TraesCS4A01G069700 chr7D 307062373 307064885 2512 True 4183 4183 96.638 1 2528 1 chr7D.!!$R1 2527
12 TraesCS4A01G069700 chr1B 583498438 583500744 2306 True 3945 3945 97.457 1 2319 1 chr1B.!!$R1 2318
13 TraesCS4A01G069700 chrUn 273238806 273240306 1500 False 2617 2617 98.081 1 1508 1 chrUn.!!$F1 1507
14 TraesCS4A01G069700 chr3A 725792030 725792781 751 False 1254 1254 96.588 1 762 1 chr3A.!!$F1 761

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
547 549 2.625790 AGTTTCATTTTTGGCCGCTACA 59.374 40.909 0.0 0.0 0.00 2.74 F
661 664 5.127519 TGAATAGGCGTAACAAAGCTACCTA 59.872 40.000 0.0 0.0 33.12 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1526 0.850784 AGGGGGTTTACTGCACAAGT 59.149 50.000 0.0 0.0 43.4 3.16 R
2467 2484 1.078823 TGATGGTAGAGTCAGGGGTGT 59.921 52.381 0.0 0.0 0.0 4.16 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
218 220 8.707796 AGATATATTCGAGGTACCTTTTCTCA 57.292 34.615 17.53 0.58 0.00 3.27
327 329 7.348680 ACAGGCTTATCTATTTTATGGGGAT 57.651 36.000 0.00 0.00 0.00 3.85
330 332 9.401058 CAGGCTTATCTATTTTATGGGGATAAG 57.599 37.037 13.41 13.41 43.80 1.73
331 333 9.351572 AGGCTTATCTATTTTATGGGGATAAGA 57.648 33.333 18.93 0.00 43.74 2.10
338 340 9.405369 TCTATTTTATGGGGATAAGATCTTGGA 57.595 33.333 18.47 0.00 0.00 3.53
344 346 5.418654 TGGGGATAAGATCTTGGATGAGAT 58.581 41.667 18.47 1.12 39.04 2.75
547 549 2.625790 AGTTTCATTTTTGGCCGCTACA 59.374 40.909 0.00 0.00 0.00 2.74
661 664 5.127519 TGAATAGGCGTAACAAAGCTACCTA 59.872 40.000 0.00 0.00 33.12 3.08
942 952 7.705700 AGACCCCTATTGTTTAGTAATTTGGT 58.294 34.615 0.00 0.00 0.00 3.67
1050 1060 7.419711 TTTCGATCTAAGTGGTCCTATTCTT 57.580 36.000 0.00 0.00 0.00 2.52
1084 1094 5.770685 AGGAAGCATTACTCCTCTTTTCT 57.229 39.130 0.00 0.00 28.40 2.52
1444 1455 7.103641 ACTATTCTATGTTCTTTCCGAAAGCA 58.896 34.615 14.99 9.27 38.39 3.91
1515 1526 1.136329 AGCTTTTCCTCTGCAGGGGA 61.136 55.000 32.25 32.25 40.80 4.81
1579 1590 0.179127 GTAGTAAAGGTCCCCGCGAC 60.179 60.000 8.23 0.00 41.15 5.19
1598 1609 1.377333 GCTTTCGGGAAGAGGGGTG 60.377 63.158 0.00 0.00 37.57 4.61
1997 2013 0.250338 GTTGCCGGAGAGTTCTTGGT 60.250 55.000 5.05 0.00 0.00 3.67
2044 2061 0.546747 ACAAACGGAGGGGAGGATCA 60.547 55.000 0.00 0.00 36.25 2.92
2143 2160 2.801631 GCAGGGTAGAGCTCGGCAT 61.802 63.158 8.37 0.00 38.68 4.40
2144 2161 1.826024 CAGGGTAGAGCTCGGCATT 59.174 57.895 8.37 0.00 0.00 3.56
2171 2188 5.093849 TCGAGAATAGGGTAGGGTTTTTG 57.906 43.478 0.00 0.00 0.00 2.44
2236 2253 0.912486 AGGAAGCAGGCCTAAACGAT 59.088 50.000 3.98 0.00 32.92 3.73
2321 2338 1.801178 GAGTCAAGGCGGAAAAGACAG 59.199 52.381 0.00 0.00 0.00 3.51
2457 2474 2.290071 CCAACTACCACCGGTCAATTCT 60.290 50.000 2.59 0.00 37.09 2.40
2467 2484 1.886222 CGGTCAATTCTGCTTTGGGGA 60.886 52.381 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 332 8.359875 TCCAAGATAGTATCTCATCCAAGATC 57.640 38.462 13.10 0.00 39.08 2.75
331 333 8.760735 CATCCAAGATAGTATCTCATCCAAGAT 58.239 37.037 13.10 5.68 39.08 2.40
332 334 7.952368 TCATCCAAGATAGTATCTCATCCAAGA 59.048 37.037 13.10 3.96 39.08 3.02
333 335 8.131847 TCATCCAAGATAGTATCTCATCCAAG 57.868 38.462 13.10 1.86 39.08 3.61
334 336 7.952368 TCTCATCCAAGATAGTATCTCATCCAA 59.048 37.037 13.10 0.00 39.08 3.53
335 337 7.473593 TCTCATCCAAGATAGTATCTCATCCA 58.526 38.462 13.10 0.00 39.08 3.41
336 338 7.953005 TCTCATCCAAGATAGTATCTCATCC 57.047 40.000 13.10 0.00 39.08 3.51
547 549 3.613737 TCAAGAAGTTTTCGACGAACGTT 59.386 39.130 10.38 0.00 43.13 3.99
764 767 6.146510 CCACGTATGCGCCTTTATTTAGATTA 59.853 38.462 4.18 0.00 42.83 1.75
942 952 2.827322 CAGTCAATCAAAAGATGGGGCA 59.173 45.455 0.00 0.00 0.00 5.36
1050 1060 1.295423 GCTTCCTAGCACGGGACAA 59.705 57.895 0.00 0.00 46.95 3.18
1084 1094 7.753309 TCGGTCTTATTGAAGAATTTGGAAA 57.247 32.000 0.00 0.00 43.38 3.13
1159 1169 4.528596 AGGATCGAATTGTATCCGAGGAAT 59.471 41.667 9.11 0.00 45.35 3.01
1444 1455 2.034124 GCACAACATAGGGATTGGCAT 58.966 47.619 0.00 0.00 0.00 4.40
1515 1526 0.850784 AGGGGGTTTACTGCACAAGT 59.149 50.000 0.00 0.00 43.40 3.16
1579 1590 2.125106 CCCCTCTTCCCGAAAGCG 60.125 66.667 0.00 0.00 34.76 4.68
1949 1965 1.376466 CTAACCTGCCAGCAGTGGT 59.624 57.895 17.86 8.22 46.96 4.16
1957 1973 1.623811 GACAGAGGAACTAACCTGCCA 59.376 52.381 0.00 0.00 41.55 4.92
1997 2013 5.721960 AGCAACTTATCCTAAGGTCTCTTCA 59.278 40.000 0.00 0.00 34.59 3.02
2044 2061 4.884668 TCAGAATTCTACTGAACGGGTT 57.115 40.909 7.86 0.00 40.70 4.11
2143 2160 3.036091 CCTACCCTATTCTCGAACCCAA 58.964 50.000 0.00 0.00 0.00 4.12
2144 2161 2.674420 CCTACCCTATTCTCGAACCCA 58.326 52.381 0.00 0.00 0.00 4.51
2321 2338 4.130118 CCTTGTCATTAGACCACTATGCC 58.870 47.826 0.00 0.00 44.33 4.40
2467 2484 1.078823 TGATGGTAGAGTCAGGGGTGT 59.921 52.381 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.