Multiple sequence alignment - TraesCS6B01G248900

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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 TraesCS6B01G248900 chr6B 100.000 2257 0 0 1 2257 446834890 446837146 0.000000e+00 4169
1 TraesCS6B01G248900 chr6D 95.627 2264 74 11 1 2257 285868347 285870592 0.000000e+00 3609
2 TraesCS6B01G248900 chr6A 93.791 2271 103 15 4 2257 407084226 407086475 0.000000e+00 3378
3 TraesCS6B01G248900 chr2B 82.222 855 152 0 1399 2253 531466730 531467584 0.000000e+00 737
4 TraesCS6B01G248900 chr2B 82.877 146 18 4 994 1138 531466328 531466467 8.460000e-25 124
5 TraesCS6B01G248900 chr2A 81.839 859 152 4 1399 2255 598162350 598161494 0.000000e+00 719
6 TraesCS6B01G248900 chr2D 82.877 146 18 4 994 1138 451287397 451287536 8.460000e-25 124


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 TraesCS6B01G248900 chr6B 446834890 446837146 2256 False 4169.0 4169 100.0000 1 2257 1 chr6B.!!$F1 2256
1 TraesCS6B01G248900 chr6D 285868347 285870592 2245 False 3609.0 3609 95.6270 1 2257 1 chr6D.!!$F1 2256
2 TraesCS6B01G248900 chr6A 407084226 407086475 2249 False 3378.0 3378 93.7910 4 2257 1 chr6A.!!$F1 2253
3 TraesCS6B01G248900 chr2B 531466328 531467584 1256 False 430.5 737 82.5495 994 2253 2 chr2B.!!$F1 1259
4 TraesCS6B01G248900 chr2A 598161494 598162350 856 True 719.0 719 81.8390 1399 2255 1 chr2A.!!$R1 856

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
399 410 0.100682 GACAGATCCGTCGCTTGCTA 59.899 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2234 1.224592 CCAGGTCACCATAGGCCAC 59.775 63.158 5.01 0.0 0.0 5.01 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
51 52 4.453892 GCCCTCCCAGCCAAGCAT 62.454 66.667 0.00 0.00 0.00 3.79
207 208 2.232941 TCGCTCGGCCCCTTATAAATAG 59.767 50.000 0.00 0.00 0.00 1.73
246 247 3.181440 TGACTTTCCCATCTTGCAAGTCT 60.181 43.478 25.19 11.89 42.55 3.24
255 260 4.142447 CCATCTTGCAAGTCTCCTCATTTG 60.142 45.833 25.19 8.80 0.00 2.32
278 288 1.657181 GCACAAACGCAAACTCCGG 60.657 57.895 0.00 0.00 0.00 5.14
279 289 1.657181 CACAAACGCAAACTCCGGC 60.657 57.895 0.00 0.00 0.00 6.13
344 354 3.737266 GTGAGATTGTGTTCGTCCGTTTA 59.263 43.478 0.00 0.00 0.00 2.01
399 410 0.100682 GACAGATCCGTCGCTTGCTA 59.899 55.000 0.00 0.00 0.00 3.49
407 418 0.666274 CGTCGCTTGCTACCTGTTCA 60.666 55.000 0.00 0.00 0.00 3.18
422 442 1.068588 TGTTCAAGGTCTGTGACGAGG 59.931 52.381 0.00 0.00 32.65 4.63
423 443 1.340248 GTTCAAGGTCTGTGACGAGGA 59.660 52.381 0.00 0.00 32.65 3.71
424 444 1.248486 TCAAGGTCTGTGACGAGGAG 58.752 55.000 0.00 0.00 32.65 3.69
425 445 0.244994 CAAGGTCTGTGACGAGGAGG 59.755 60.000 0.00 0.00 32.65 4.30
426 446 0.112606 AAGGTCTGTGACGAGGAGGA 59.887 55.000 0.00 0.00 32.65 3.71
427 447 0.322997 AGGTCTGTGACGAGGAGGAG 60.323 60.000 0.00 0.00 32.65 3.69
436 456 1.361993 CGAGGAGGAGCAGATTCGG 59.638 63.158 0.00 0.00 0.00 4.30
606 629 9.027202 GGGTTGGATAGGAAAAGTAAATAAACA 57.973 33.333 0.00 0.00 0.00 2.83
658 681 7.243487 ACAGACTTTGTGAAATATATGCAACG 58.757 34.615 0.00 0.00 38.99 4.10
659 682 6.688385 CAGACTTTGTGAAATATATGCAACGG 59.312 38.462 0.00 0.00 0.00 4.44
664 687 4.506288 TGTGAAATATATGCAACGGAGTCG 59.494 41.667 0.00 0.00 45.00 4.18
713 736 5.643379 ATGCTGTTCGGTACATCAATTTT 57.357 34.783 0.00 0.00 36.55 1.82
729 752 7.938490 ACATCAATTTTTGGTAGATTTTGGCTT 59.062 29.630 0.00 0.00 0.00 4.35
770 793 8.183536 TGATGTCAATTCGTTTCTATTTCATGG 58.816 33.333 0.00 0.00 0.00 3.66
795 818 4.593956 CTTTCCTCCCTTTCTGTTATGCT 58.406 43.478 0.00 0.00 0.00 3.79
796 819 3.634397 TCCTCCCTTTCTGTTATGCTG 57.366 47.619 0.00 0.00 0.00 4.41
797 820 2.019984 CCTCCCTTTCTGTTATGCTGC 58.980 52.381 0.00 0.00 0.00 5.25
798 821 1.667724 CTCCCTTTCTGTTATGCTGCG 59.332 52.381 0.00 0.00 0.00 5.18
799 822 0.734889 CCCTTTCTGTTATGCTGCGG 59.265 55.000 0.00 0.00 0.00 5.69
800 823 1.678728 CCCTTTCTGTTATGCTGCGGA 60.679 52.381 0.00 0.00 0.00 5.54
1144 1169 4.603985 TGCCTACTCAAACGTATGTATCG 58.396 43.478 0.00 0.00 0.00 2.92
1176 1201 3.139077 GCTCCTCCTTTCTTTTCGTTGA 58.861 45.455 0.00 0.00 0.00 3.18
1204 1229 6.647229 TCTTGTTGATGATTAGATGCTCACT 58.353 36.000 0.00 0.00 0.00 3.41
1301 1328 4.888626 AATTGCTTAGAATTCCCTCCCT 57.111 40.909 0.65 0.00 0.00 4.20
1397 1431 0.527565 CCTTCTGAAACAATGGCCGG 59.472 55.000 0.00 0.00 0.00 6.13
1611 1651 5.809001 TCTGAATCAAGCCTCTTTGTGTAT 58.191 37.500 0.00 0.00 0.00 2.29
1917 1957 2.433446 CCTGAGCAGCCTGTGGTT 59.567 61.111 0.00 0.00 36.87 3.67
2046 2086 3.047857 TGGCATCTCTGACATAATCCCA 58.952 45.455 0.00 0.00 34.67 4.37
2194 2234 4.410400 GGTTGGACCCTGCCTCCG 62.410 72.222 0.00 0.00 30.04 4.63
2215 2255 1.144057 GCCTATGGTGACCTGGTCG 59.856 63.158 21.15 6.80 34.95 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 260 2.787129 GGAGTTTGCGTTTGTGCTAAAC 59.213 45.455 6.97 6.97 36.75 2.01
279 289 3.638592 GATGGTGGGTGGGGAACGG 62.639 68.421 0.00 0.00 0.00 4.44
291 301 2.080286 AGGTTTTCGACGAGATGGTG 57.920 50.000 0.00 0.00 0.00 4.17
344 354 3.243336 CGGATCTCGAAGAAACGAAAGT 58.757 45.455 0.00 0.00 45.19 2.66
373 383 1.777030 CGACGGATCTGTCTCTCCCG 61.777 65.000 27.81 13.70 45.09 5.14
407 418 0.112606 TCCTCCTCGTCACAGACCTT 59.887 55.000 0.00 0.00 0.00 3.50
412 423 0.962855 TCTGCTCCTCCTCGTCACAG 60.963 60.000 0.00 0.00 0.00 3.66
422 442 2.964389 GCGCCGAATCTGCTCCTC 60.964 66.667 0.00 0.00 0.00 3.71
423 443 4.880537 CGCGCCGAATCTGCTCCT 62.881 66.667 0.00 0.00 0.00 3.69
425 445 3.918220 CACGCGCCGAATCTGCTC 61.918 66.667 5.73 0.00 0.00 4.26
441 461 3.388841 GGAAGAACCTCGGAGGCA 58.611 61.111 23.84 0.00 39.63 4.75
606 629 9.828852 GAAATTACAGATAATCTAGACGACGAT 57.171 33.333 0.00 0.00 30.27 3.73
664 687 4.741676 CGTACAGTTACACGGATAATTCCC 59.258 45.833 0.00 0.00 39.01 3.97
679 702 3.863424 CCGAACAGCATATTCGTACAGTT 59.137 43.478 13.65 0.00 45.88 3.16
713 736 5.249780 TCAGGTAAGCCAAAATCTACCAA 57.750 39.130 0.00 0.00 37.19 3.67
729 752 8.523915 AATTGACATCAAGCAATATTCAGGTA 57.476 30.769 0.23 0.00 39.47 3.08
770 793 2.278332 ACAGAAAGGGAGGAAAGCAC 57.722 50.000 0.00 0.00 0.00 4.40
800 823 6.037786 TGATTTGAAGACGACTATTCCAGT 57.962 37.500 0.00 0.00 41.47 4.00
812 835 7.225538 ACATGATATTCGACCTGATTTGAAGAC 59.774 37.037 0.00 0.00 0.00 3.01
857 880 7.584122 AAGTAGAGGAATAGTTCGCTAATCA 57.416 36.000 0.00 0.00 32.58 2.57
864 887 8.848182 AGGTACATAAAGTAGAGGAATAGTTCG 58.152 37.037 0.00 0.00 32.19 3.95
868 891 8.361139 CACCAGGTACATAAAGTAGAGGAATAG 58.639 40.741 0.00 0.00 32.19 1.73
923 947 7.903431 CAGAACATATTGCGAGGTAAAAAGTAC 59.097 37.037 0.00 0.00 0.00 2.73
1144 1169 5.192176 AGAAAGGAGGAGCTCAATTGATTC 58.808 41.667 17.19 11.82 31.08 2.52
1176 1201 9.788889 TGAGCATCTAATCATCAACAAGATATT 57.211 29.630 0.00 0.00 32.67 1.28
1204 1229 5.827797 ACAGAAGCAATTGGAAGTAGAAACA 59.172 36.000 7.72 0.00 0.00 2.83
1397 1431 1.424493 CTCGAACCCAATCGCAGAGC 61.424 60.000 0.00 0.00 43.63 4.09
1611 1651 3.322541 TCTTGATCACAACCTTGTACGGA 59.677 43.478 0.00 0.00 39.91 4.69
1917 1957 4.256110 CAGTCATGCACATCTCAAGGTTA 58.744 43.478 0.00 0.00 0.00 2.85
2046 2086 2.363306 AGTCGCAGATCTCCATCTCT 57.637 50.000 0.00 0.00 37.25 3.10
2194 2234 1.224592 CCAGGTCACCATAGGCCAC 59.775 63.158 5.01 0.00 0.00 5.01
2215 2255 1.494960 AAGGATCTCAGCACCCTCTC 58.505 55.000 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.