Multiple sequence alignment - TraesCS6B01G348500

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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 TraesCS6B01G348500 chr6B 100.000 2255 0 0 1 2255 613164120 613161866 0 4165
1 TraesCS6B01G348500 chr6B 97.029 2255 67 0 1 2255 306997806 306995552 0 3794
2 TraesCS6B01G348500 chr1D 97.694 2255 51 1 1 2255 141314951 141312698 0 3875
3 TraesCS6B01G348500 chr7B 97.473 2256 56 1 1 2255 644465627 644467882 0 3849
4 TraesCS6B01G348500 chr7A 97.472 2255 57 0 1 2255 60150103 60147849 0 3849
5 TraesCS6B01G348500 chr7A 96.538 2253 77 1 3 2255 46399060 46396809 0 3727
6 TraesCS6B01G348500 chr3A 97.428 2255 58 0 1 2255 633109438 633111692 0 3843
7 TraesCS6B01G348500 chr1B 97.206 2255 63 0 1 2255 672477345 672479599 0 3816
8 TraesCS6B01G348500 chr1B 97.074 2256 64 2 1 2255 638702482 638700228 0 3799


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 TraesCS6B01G348500 chr6B 613161866 613164120 2254 True 4165 4165 100.000 1 2255 1 chr6B.!!$R2 2254
1 TraesCS6B01G348500 chr6B 306995552 306997806 2254 True 3794 3794 97.029 1 2255 1 chr6B.!!$R1 2254
2 TraesCS6B01G348500 chr1D 141312698 141314951 2253 True 3875 3875 97.694 1 2255 1 chr1D.!!$R1 2254
3 TraesCS6B01G348500 chr7B 644465627 644467882 2255 False 3849 3849 97.473 1 2255 1 chr7B.!!$F1 2254
4 TraesCS6B01G348500 chr7A 60147849 60150103 2254 True 3849 3849 97.472 1 2255 1 chr7A.!!$R2 2254
5 TraesCS6B01G348500 chr7A 46396809 46399060 2251 True 3727 3727 96.538 3 2255 1 chr7A.!!$R1 2252
6 TraesCS6B01G348500 chr3A 633109438 633111692 2254 False 3843 3843 97.428 1 2255 1 chr3A.!!$F1 2254
7 TraesCS6B01G348500 chr1B 672477345 672479599 2254 False 3816 3816 97.206 1 2255 1 chr1B.!!$F1 2254
8 TraesCS6B01G348500 chr1B 638700228 638702482 2254 True 3799 3799 97.074 1 2255 1 chr1B.!!$R1 2254

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
128 129 0.467804 TTTTGCCTTGTTTCAGCCCC 59.532 50.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1638 0.179043 TCAAAACTACAGGGCGTGCA 60.179 50.0 7.17 0.0 0.0 4.57 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
128 129 0.467804 TTTTGCCTTGTTTCAGCCCC 59.532 50.000 0.00 0.00 0.00 5.80
137 138 1.272092 TGTTTCAGCCCCTCCTTCATG 60.272 52.381 0.00 0.00 0.00 3.07
193 194 1.079490 AGACCCTTCATCTGACCTCCA 59.921 52.381 0.00 0.00 0.00 3.86
262 263 5.184671 GGAGCAAAAAGAGTGAAATGAGGAT 59.815 40.000 0.00 0.00 0.00 3.24
284 285 3.530564 TGTAAGCCTCCTAGGTCTTCCTA 59.469 47.826 9.08 0.00 44.58 2.94
540 541 4.142227 TGCTCGGATTCAGGTAGAAAGTAC 60.142 45.833 0.00 0.00 40.22 2.73
709 710 4.070716 GCTTCGGGATCAGATCATTCAAT 58.929 43.478 12.66 0.00 0.00 2.57
722 723 7.825761 TCAGATCATTCAATTAAAGCTGTCAGA 59.174 33.333 3.32 0.00 0.00 3.27
764 765 4.044825 ACATTGGGGGTTCCTTATGTTGTA 59.955 41.667 0.00 0.00 37.86 2.41
912 914 3.856638 GCCGCTTGTGTGAATTTCATTGA 60.857 43.478 1.78 0.00 0.00 2.57
1006 1008 3.454375 CTGGTTATCGAGTTTATGGCGT 58.546 45.455 0.00 0.00 0.00 5.68
1035 1037 5.473066 CCATCCAAAAAGTCAAAGATGGT 57.527 39.130 8.37 0.00 43.71 3.55
1158 1160 9.528489 TGTAATGGCCTATCTTCTTTAAAAAGT 57.472 29.630 3.32 0.00 37.31 2.66
1188 1190 7.433680 AGATAAGGATTTCGCAAAACTTTTGT 58.566 30.769 14.36 0.00 0.00 2.83
1195 1197 3.765026 TCGCAAAACTTTTGTGTTCCTC 58.235 40.909 21.57 2.85 0.00 3.71
1209 1211 7.461182 TTGTGTTCCTCTTTCTTTGAAAAGA 57.539 32.000 1.31 1.31 41.70 2.52
1428 1431 4.881920 TGTCCATGGTATCATCATACGTG 58.118 43.478 12.58 0.00 36.45 4.49
1449 1452 5.293560 GTGCCTTCTACTATCAACCAGATC 58.706 45.833 0.00 0.00 38.19 2.75
1464 1467 3.135530 ACCAGATCAGATAGGGCTTTGAC 59.864 47.826 0.00 0.00 0.00 3.18
1519 1522 0.879090 GTTTAGCAGTTCCCCAACCG 59.121 55.000 0.00 0.00 32.22 4.44
1632 1635 1.366679 GGCTGAAAAGCCGTAGTACC 58.633 55.000 0.12 0.00 45.79 3.34
1635 1638 3.007635 GCTGAAAAGCCGTAGTACCAAT 58.992 45.455 0.00 0.00 0.00 3.16
1692 1695 3.411351 GCTCCGCGTCGAAAAGCA 61.411 61.111 4.92 0.00 0.00 3.91
1703 1706 0.109597 CGAAAAGCAAAGCGAGCCAT 60.110 50.000 0.00 0.00 0.00 4.40
1768 1771 6.870971 GATCTACTGATCTAAGAACTCCGT 57.129 41.667 0.00 0.00 44.19 4.69
1786 1789 2.180518 GAGCGAACTGAGCGAGCT 59.819 61.111 0.00 0.00 41.29 4.09
1789 1792 0.457851 AGCGAACTGAGCGAGCTATT 59.542 50.000 0.00 0.00 40.04 1.73
2101 2106 6.361768 AGAAAGAAGGGTCGAAGTTTAGAT 57.638 37.500 0.00 0.00 0.00 1.98
2177 2182 3.830744 ACCCGAATCCATTTACGATCA 57.169 42.857 0.00 0.00 0.00 2.92
2204 2209 0.036952 CCAGACACATCGCACTTCCT 60.037 55.000 0.00 0.00 0.00 3.36
2209 2214 0.171231 CACATCGCACTTCCTCTCGA 59.829 55.000 0.00 0.00 35.34 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 3.423539 TGGAAGGTTCACATGAAGGAG 57.576 47.619 0.00 0.00 34.27 3.69
137 138 8.697292 AGATAGATTAGTACTTGGAAGGTTCAC 58.303 37.037 0.00 0.00 0.00 3.18
193 194 8.838649 AATTTTTATAATTGACAGGGTAGCCT 57.161 30.769 7.93 7.93 0.00 4.58
210 211 8.391106 GCGAGACATGACTCAACTAATTTTTAT 58.609 33.333 22.07 0.00 36.80 1.40
217 218 3.367395 CCTGCGAGACATGACTCAACTAA 60.367 47.826 22.07 4.62 36.80 2.24
228 229 1.808945 CTTTTTGCTCCTGCGAGACAT 59.191 47.619 0.00 0.00 43.34 3.06
262 263 2.315155 AGGAAGACCTAGGAGGCTTACA 59.685 50.000 17.98 0.00 45.83 2.41
540 541 5.124617 TCTCCTATGAATATGCTACTGCTCG 59.875 44.000 0.00 0.00 40.48 5.03
709 710 1.053424 ACCCGGTCTGACAGCTTTAA 58.947 50.000 10.38 0.00 0.00 1.52
722 723 0.838987 TTCCTCAAAGCCTACCCGGT 60.839 55.000 0.00 0.00 34.25 5.28
764 765 5.757320 GCACAATAGACATATCTGCTCAGTT 59.243 40.000 0.00 0.00 36.29 3.16
912 914 2.429930 CACACACGGGACCCACAT 59.570 61.111 12.15 0.00 0.00 3.21
1006 1008 0.250553 ACTTTTTGGATGGTCGGCGA 60.251 50.000 4.99 4.99 0.00 5.54
1035 1037 6.288294 AGAGCATAATAAGTAAATGCCGACA 58.712 36.000 3.08 0.00 45.66 4.35
1069 1071 2.573463 ACCTGAATACCAAGGGACCAT 58.427 47.619 0.00 0.00 0.00 3.55
1209 1211 4.130857 CGGCCCAAAAATGGTAAGTTTTT 58.869 39.130 0.00 0.00 38.82 1.94
1428 1431 5.303078 TCTGATCTGGTTGATAGTAGAAGGC 59.697 44.000 0.00 0.00 35.14 4.35
1449 1452 2.237143 TGACCTGTCAAAGCCCTATCTG 59.763 50.000 0.00 0.00 36.53 2.90
1464 1467 2.091541 GAGGAGACTGACTCTGACCTG 58.908 57.143 7.06 0.00 44.43 4.00
1587 1590 5.361857 CCCTTTGCTGGTTCTGAATTATCAT 59.638 40.000 0.00 0.00 34.37 2.45
1593 1596 2.556114 CCTCCCTTTGCTGGTTCTGAAT 60.556 50.000 0.00 0.00 0.00 2.57
1597 1600 1.075659 GCCTCCCTTTGCTGGTTCT 59.924 57.895 0.00 0.00 0.00 3.01
1630 1633 1.377202 CTACAGGGCGTGCATTGGT 60.377 57.895 7.17 0.00 0.00 3.67
1632 1635 0.881118 AAACTACAGGGCGTGCATTG 59.119 50.000 7.17 0.00 0.00 2.82
1635 1638 0.179043 TCAAAACTACAGGGCGTGCA 60.179 50.000 7.17 0.00 0.00 4.57
1692 1695 0.465097 ATGCTAGCATGGCTCGCTTT 60.465 50.000 29.08 1.42 45.59 3.51
1703 1706 2.392662 AGGAAGAGTAGCATGCTAGCA 58.607 47.619 27.54 21.85 36.85 3.49
1710 1713 4.342378 TCGCTCATAAAGGAAGAGTAGCAT 59.658 41.667 0.00 0.00 0.00 3.79
1711 1714 3.699538 TCGCTCATAAAGGAAGAGTAGCA 59.300 43.478 0.00 0.00 0.00 3.49
1768 1771 1.305930 TAGCTCGCTCAGTTCGCTCA 61.306 55.000 0.00 0.00 32.49 4.26
1873 1876 7.604927 TCGTAAAGGAAAAATTAGCTAGCTCAA 59.395 33.333 23.26 14.13 0.00 3.02
1960 1963 3.366396 GGAAGTAGTCCCATCACTCTCA 58.634 50.000 0.00 0.00 41.10 3.27
2101 2106 2.089980 GGGTAGAACTACTGTGAGCGA 58.910 52.381 11.04 0.00 36.36 4.93
2177 2182 1.935300 GCGATGTGTCTGGAAACTCGT 60.935 52.381 11.35 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.