Multiple sequence alignment - TraesCS6B01G232300

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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 TraesCS6B01G232300 chr6B 100.000 2407 0 0 1 2407 388038749 388041155 0 4446
1 TraesCS6B01G232300 chrUn 97.640 2415 45 8 1 2407 45100792 45098382 0 4133
2 TraesCS6B01G232300 chrUn 97.558 2416 47 8 1 2407 261513064 261515476 0 4124
3 TraesCS6B01G232300 chr5B 97.640 2415 46 7 1 2407 130614901 130612490 0 4133
4 TraesCS6B01G232300 chr5B 97.475 2416 48 9 1 2407 130609877 130607466 0 4111
5 TraesCS6B01G232300 chr5B 97.229 2418 54 7 1 2407 130568755 130571170 0 4082
6 TraesCS6B01G232300 chr3A 97.516 2415 49 7 1 2407 66030313 66032724 0 4117
7 TraesCS6B01G232300 chr3A 97.271 1319 34 2 1 1318 725775877 725777194 0 2235
8 TraesCS6B01G232300 chr3A 96.415 1088 28 7 1327 2407 725777379 725778462 0 1783
9 TraesCS6B01G232300 chr7B 97.393 2417 51 7 1 2407 743033700 743036114 0 4104
10 TraesCS6B01G232300 chr2B 97.266 2414 56 6 1 2407 112869113 112866703 0 4084


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 TraesCS6B01G232300 chr6B 388038749 388041155 2406 False 4446 4446 100.0000 1 2407 1 chr6B.!!$F1 2406
1 TraesCS6B01G232300 chrUn 45098382 45100792 2410 True 4133 4133 97.6400 1 2407 1 chrUn.!!$R1 2406
2 TraesCS6B01G232300 chrUn 261513064 261515476 2412 False 4124 4124 97.5580 1 2407 1 chrUn.!!$F1 2406
3 TraesCS6B01G232300 chr5B 130607466 130614901 7435 True 4122 4133 97.5575 1 2407 2 chr5B.!!$R1 2406
4 TraesCS6B01G232300 chr5B 130568755 130571170 2415 False 4082 4082 97.2290 1 2407 1 chr5B.!!$F1 2406
5 TraesCS6B01G232300 chr3A 66030313 66032724 2411 False 4117 4117 97.5160 1 2407 1 chr3A.!!$F1 2406
6 TraesCS6B01G232300 chr3A 725775877 725778462 2585 False 2009 2235 96.8430 1 2407 2 chr3A.!!$F2 2406
7 TraesCS6B01G232300 chr7B 743033700 743036114 2414 False 4104 4104 97.3930 1 2407 1 chr7B.!!$F1 2406
8 TraesCS6B01G232300 chr2B 112866703 112869113 2410 True 4084 4084 97.2660 1 2407 1 chr2B.!!$R1 2406

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
130 131 0.389391 ACCTGGAGAACGTGTGACAG 59.611 55.0 0.0 0.0 0.00 3.51 F
1238 1240 0.250124 ATGTTCGACTTCGGTTGCCA 60.250 50.0 0.0 0.0 40.29 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 1321 0.541863 GATATCGGGTGGGGCATAGG 59.458 60.0 0.0 0.0 0.0 2.57 R
2321 7531 1.131303 TCGGAGAAAAGGAAGGGGCA 61.131 55.0 0.0 0.0 0.0 5.36 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
59 60 1.147153 GCTATTCCTGGCTCGGCTT 59.853 57.895 0.00 0.00 0.00 4.35
75 76 1.668751 GGCTTCGATAACGCAATTCCA 59.331 47.619 0.00 0.00 39.58 3.53
130 131 0.389391 ACCTGGAGAACGTGTGACAG 59.611 55.000 0.00 0.00 0.00 3.51
165 166 1.070786 GAACCAACAGGTCGCTCCA 59.929 57.895 0.00 0.00 39.02 3.86
324 325 2.011122 AGACCCATACCATAGGACCG 57.989 55.000 0.00 0.00 0.00 4.79
326 327 0.399376 ACCCATACCATAGGACCGCA 60.399 55.000 0.00 0.00 0.00 5.69
369 370 1.400846 GCGTAGGAGATCGAGACACAA 59.599 52.381 0.00 0.00 0.00 3.33
397 398 1.543429 GCTATGGGGAAAGTGGATCGG 60.543 57.143 0.00 0.00 0.00 4.18
537 538 7.416664 GCACCTAAGATCAAATATTTTGAGCCA 60.417 37.037 12.98 3.31 35.61 4.75
640 641 6.778834 ACATGGCAATTAAATCATGAGTCA 57.221 33.333 0.09 0.00 39.27 3.41
747 748 6.817765 ATCGAAACACATTGAAATGGTACT 57.182 33.333 7.87 0.00 40.70 2.73
1048 1050 2.772191 TGGGCGCCACTATCCCAT 60.772 61.111 30.85 0.00 44.62 4.00
1112 1114 3.650942 ACAGTTGTATCTTGTCTTGGGGA 59.349 43.478 0.00 0.00 0.00 4.81
1163 1165 2.176140 CGGCACCCTTTCGCATTAA 58.824 52.632 0.00 0.00 0.00 1.40
1238 1240 0.250124 ATGTTCGACTTCGGTTGCCA 60.250 50.000 0.00 0.00 40.29 4.92
1319 1321 3.009584 ACCCTCCTCCAAGAAGAATTGTC 59.990 47.826 0.00 0.00 0.00 3.18
1329 1506 2.852449 AGAAGAATTGTCCTATGCCCCA 59.148 45.455 0.00 0.00 0.00 4.96
1388 1566 2.486636 CTAGGTTGCAGCACGTCCGA 62.487 60.000 2.05 0.00 0.00 4.55
1479 1657 0.792640 CGTAGTGTAGTGTCGGTCGT 59.207 55.000 0.00 0.00 0.00 4.34
1504 1682 3.263602 TCATAATAGCGTTCGGACTCG 57.736 47.619 0.00 0.00 37.82 4.18
1568 1746 3.750373 GATTAGCCGGCCTTGCGGA 62.750 63.158 26.15 1.16 0.00 5.54
1583 1761 2.038387 GCGGAGGCAAAAGGATTAGA 57.962 50.000 0.00 0.00 39.62 2.10
1654 1833 1.002544 GCTGGGCGATAATAGCTCCTT 59.997 52.381 0.00 0.00 33.29 3.36
1884 2064 7.079451 ACTTCTTCTACTTTCATTTCCTCCA 57.921 36.000 0.00 0.00 0.00 3.86
1909 2089 5.354234 TCTTCCAAATCGCAGAGTTAATTCC 59.646 40.000 0.00 0.00 45.61 3.01
1935 2115 5.455872 AGCCTAGGTGTTATTACTGAGCTA 58.544 41.667 11.31 0.00 0.00 3.32
1938 2118 6.183360 GCCTAGGTGTTATTACTGAGCTACTT 60.183 42.308 11.31 0.00 0.00 2.24
1942 2122 6.893005 AGGTGTTATTACTGAGCTACTTCTCT 59.107 38.462 0.00 0.00 34.29 3.10
2009 2189 6.127703 CCTTATCCTACTCACTCGAAGTTTCA 60.128 42.308 0.00 0.00 0.00 2.69
2261 7471 2.030363 TGTGTTCATGTTGGCGATTTCC 60.030 45.455 0.00 0.00 0.00 3.13
2321 7531 1.272092 CCCCAGTGACACATCAACCAT 60.272 52.381 8.59 0.00 36.31 3.55
2352 7562 9.109393 CTTCCTTTTCTCCGATCATAAATAACA 57.891 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.483013 CCTCCTGGAATTGCGTTATCGA 60.483 50.000 0.00 0.00 35.64 3.59
75 76 0.324460 CCCAACTACCGACTCCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
130 131 0.106419 TTCACCAAACCCTGACCCAC 60.106 55.000 0.00 0.00 0.00 4.61
165 166 2.105993 GGGGCCCGATACTTCAACTAAT 59.894 50.000 17.79 0.00 0.00 1.73
281 282 1.280998 ACCCTTGGTCTAATTCCACGG 59.719 52.381 1.28 1.28 41.96 4.94
324 325 4.859798 CGAAAGATAAGATACGGGAGATGC 59.140 45.833 0.00 0.00 0.00 3.91
326 327 4.379603 CGCGAAAGATAAGATACGGGAGAT 60.380 45.833 0.00 0.00 36.20 2.75
369 370 2.136026 CTTTCCCCATAGCCCTAAGGT 58.864 52.381 0.00 0.00 34.57 3.50
397 398 5.173664 ACGTAGTTGTAATTCTAGGGCAAC 58.826 41.667 0.00 0.00 37.78 4.17
537 538 2.814336 GTCTGAATTTTCCACGGAAGCT 59.186 45.455 0.00 0.00 35.38 3.74
1112 1114 7.094592 GCTTGATAGTAAAGCCAAAGAAAGACT 60.095 37.037 0.00 0.00 43.45 3.24
1149 1151 4.196971 GGTAGATGTTAATGCGAAAGGGT 58.803 43.478 0.00 0.00 0.00 4.34
1163 1165 2.355818 GGAAAGAAAGGGCGGTAGATGT 60.356 50.000 0.00 0.00 0.00 3.06
1238 1240 1.064758 TCCCGCCAATTCTATTGCACT 60.065 47.619 0.00 0.00 0.00 4.40
1319 1321 0.541863 GATATCGGGTGGGGCATAGG 59.458 60.000 0.00 0.00 0.00 2.57
1329 1506 1.567649 TCGCCTATAGGGATATCGGGT 59.432 52.381 20.58 0.00 37.23 5.28
1388 1566 2.033550 CAGCTAGCGAGGAGTTAACGAT 59.966 50.000 9.55 0.00 0.00 3.73
1479 1657 6.080648 AGTCCGAACGCTATTATGAATGTA 57.919 37.500 0.00 0.00 0.00 2.29
1504 1682 2.633860 CTGGTTCAGGAAGGCACAC 58.366 57.895 0.00 0.00 0.00 3.82
1539 1717 1.143373 CGGCTAATCGTACGCAGCAA 61.143 55.000 26.47 7.25 35.69 3.91
1568 1746 3.344515 GGACGTTCTAATCCTTTTGCCT 58.655 45.455 0.00 0.00 31.75 4.75
1583 1761 1.205460 ACCTTAGCATGGGGGACGTT 61.205 55.000 0.00 0.00 0.00 3.99
1884 2064 6.038714 GGAATTAACTCTGCGATTTGGAAGAT 59.961 38.462 0.00 0.00 0.00 2.40
1909 2089 5.294552 GCTCAGTAATAACACCTAGGCTTTG 59.705 44.000 9.30 1.99 0.00 2.77
2261 7471 1.153369 ACCGGCCTCATTCACATCG 60.153 57.895 0.00 0.00 0.00 3.84
2321 7531 1.131303 TCGGAGAAAAGGAAGGGGCA 61.131 55.000 0.00 0.00 0.00 5.36
2352 7562 9.571816 GGGATGAATTAGAAAGAAAGAGATCAT 57.428 33.333 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.