Multiple sequence alignment - TraesCS2B01G331900

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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 TraesCS2B01G331900 chr2B 100.000 2240 0 0 1 2240 474923427 474925666 0 4137
1 TraesCS2B01G331900 chr2A 97.812 2240 48 1 1 2240 726903962 726901724 0 3864
2 TraesCS2B01G331900 chr3B 97.321 2240 59 1 1 2240 201572294 201570056 0 3803
3 TraesCS2B01G331900 chr3B 97.054 2240 62 2 1 2240 201542013 201544248 0 3768
4 TraesCS2B01G331900 chr5D 97.321 2240 57 3 1 2240 503247765 503250001 0 3801
5 TraesCS2B01G331900 chr5D 97.189 2241 59 4 1 2240 503262283 503260046 0 3786
6 TraesCS2B01G331900 chr3D 97.277 2240 59 2 1 2240 589261034 589258797 0 3797
7 TraesCS2B01G331900 chr7B 97.054 2240 64 1 1 2240 662729407 662731644 0 3770
8 TraesCS2B01G331900 chr7B 96.964 2240 66 1 1 2240 663096932 663094695 0 3759
9 TraesCS2B01G331900 chr2D 97.054 2240 61 4 1 2240 272809753 272807519 0 3766


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 TraesCS2B01G331900 chr2B 474923427 474925666 2239 False 4137 4137 100.000 1 2240 1 chr2B.!!$F1 2239
1 TraesCS2B01G331900 chr2A 726901724 726903962 2238 True 3864 3864 97.812 1 2240 1 chr2A.!!$R1 2239
2 TraesCS2B01G331900 chr3B 201570056 201572294 2238 True 3803 3803 97.321 1 2240 1 chr3B.!!$R1 2239
3 TraesCS2B01G331900 chr3B 201542013 201544248 2235 False 3768 3768 97.054 1 2240 1 chr3B.!!$F1 2239
4 TraesCS2B01G331900 chr5D 503247765 503250001 2236 False 3801 3801 97.321 1 2240 1 chr5D.!!$F1 2239
5 TraesCS2B01G331900 chr5D 503260046 503262283 2237 True 3786 3786 97.189 1 2240 1 chr5D.!!$R1 2239
6 TraesCS2B01G331900 chr3D 589258797 589261034 2237 True 3797 3797 97.277 1 2240 1 chr3D.!!$R1 2239
7 TraesCS2B01G331900 chr7B 662729407 662731644 2237 False 3770 3770 97.054 1 2240 1 chr7B.!!$F1 2239
8 TraesCS2B01G331900 chr7B 663094695 663096932 2237 True 3759 3759 96.964 1 2240 1 chr7B.!!$R1 2239
9 TraesCS2B01G331900 chr2D 272807519 272809753 2234 True 3766 3766 97.054 1 2240 1 chr2D.!!$R1 2239

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
134 135 0.18135 CCGCCTTAGAGGGAAGCAAT 59.819 55.0 0.0 0.0 35.37 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1600 0.324943 AATGCTCTAACGCCCACACT 59.675 50.0 0.0 0.0 0.0 3.55 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
134 135 0.181350 CCGCCTTAGAGGGAAGCAAT 59.819 55.000 0.00 0.00 35.37 3.56
185 186 3.448686 CGAGAATGTCGGCTTGAGTAAT 58.551 45.455 0.00 0.00 45.58 1.89
297 298 0.870307 CGAAAGGCGTAGTCGATGGG 60.870 60.000 6.58 0.00 36.95 4.00
301 302 1.227556 GGCGTAGTCGATGGGCAAT 60.228 57.895 0.00 0.00 39.71 3.56
328 329 6.556116 GGTCAATATTCCTGTACTACCCCTTA 59.444 42.308 0.00 0.00 0.00 2.69
464 465 1.660560 GGTCCGAGTACCAAGCGCTA 61.661 60.000 12.05 0.00 39.50 4.26
735 736 3.224007 AAAAGGGGGCCGCAGTGAT 62.224 57.895 23.67 0.00 0.00 3.06
742 743 4.479993 GCCGCAGTGATCAGGCCT 62.480 66.667 11.71 0.00 43.54 5.19
751 752 3.453070 GATCAGGCCTGGGCGACTC 62.453 68.421 32.23 15.00 43.06 3.36
760 761 1.676014 CCTGGGCGACTCTTTACCAAG 60.676 57.143 0.00 0.00 0.00 3.61
863 864 3.329542 GATGACAGGGAAGCCGGCA 62.330 63.158 31.54 4.05 0.00 5.69
925 926 3.312697 CCTAAGGTAGCGAAATTCCTTGC 59.687 47.826 4.53 0.00 40.05 4.01
954 955 2.280524 CGACCCACACGAAAGGCA 60.281 61.111 0.00 0.00 0.00 4.75
976 977 0.900182 ACGATCTGGGCACTGTCTCA 60.900 55.000 0.00 0.00 0.00 3.27
1109 1110 1.002134 GCAGCTTAGGTGGAAGGCA 60.002 57.895 13.50 0.00 0.00 4.75
1158 1159 3.110705 AGCCATCAGTGAGATACCACTT 58.889 45.455 0.00 0.00 44.32 3.16
1236 1237 2.504175 GGTAGACAGTTTCTATGGGGCA 59.496 50.000 0.00 0.00 39.13 5.36
1279 1280 1.452145 GGCGTGCAAAGGTTTCCTCA 61.452 55.000 0.00 0.00 30.89 3.86
1573 1574 0.249868 CGTGAGCTGGGTTCAGAACA 60.250 55.000 15.36 0.00 43.49 3.18
1599 1600 2.693591 GAGACAGTTCGGTCCATATCCA 59.306 50.000 0.02 0.00 38.59 3.41
1805 1806 2.520069 CTAGAGCCTCCGGTATCACAT 58.480 52.381 0.00 0.00 0.00 3.21
1818 1819 1.035923 ATCACATCCGAGACAGCGAT 58.964 50.000 0.00 0.00 0.00 4.58
1850 1851 2.034104 CATATGGGGATGGAGCGATG 57.966 55.000 0.00 0.00 0.00 3.84
1884 1885 0.889306 GGATAAGGTAGCGGCGAGAT 59.111 55.000 12.98 0.00 0.00 2.75
2215 2218 0.622136 TGGTGTCCTAGGCGTAGAGA 59.378 55.000 14.94 7.62 0.00 3.10
2223 2226 2.431057 CCTAGGCGTAGAGAAACCACAT 59.569 50.000 14.94 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 2.126463 CTCGCTTCCGCTTCGTCA 60.126 61.111 0.00 0.00 0.00 4.35
297 298 7.603024 GGTAGTACAGGAATATTGACCTATTGC 59.397 40.741 2.06 0.00 34.87 3.56
301 302 6.080009 GGGGTAGTACAGGAATATTGACCTA 58.920 44.000 2.06 0.00 34.87 3.08
328 329 1.424638 CTCCATCCCTCCGTACCAAT 58.575 55.000 0.00 0.00 0.00 3.16
364 365 8.044908 TGTGTCCTTAAACCTATAACCATCTTC 58.955 37.037 0.00 0.00 0.00 2.87
464 465 1.473434 GGGCTCATACTTTAGCGCTGT 60.473 52.381 22.90 12.55 45.35 4.40
472 473 0.252197 GTCCACGGGGCTCATACTTT 59.748 55.000 0.00 0.00 0.00 2.66
613 614 2.111255 TCTCTACCTACCCACCTGTGTT 59.889 50.000 0.00 0.00 0.00 3.32
687 688 1.838077 CACCCCTTCTCCCGAAGTTAT 59.162 52.381 1.92 0.00 44.12 1.89
735 736 4.704103 AGAGTCGCCCAGGCCTGA 62.704 66.667 34.91 11.56 37.98 3.86
742 743 1.344065 TCTTGGTAAAGAGTCGCCCA 58.656 50.000 0.00 0.00 37.51 5.36
751 752 4.065789 GGAGACCTGTGTTCTTGGTAAAG 58.934 47.826 0.00 0.00 33.74 1.85
760 761 0.868406 CTTTGCGGAGACCTGTGTTC 59.132 55.000 0.00 0.00 0.00 3.18
837 838 2.289945 GCTTCCCTGTCATCAGTTCACT 60.290 50.000 0.00 0.00 39.82 3.41
925 926 2.580815 GGGTCGGAACTTACCCGG 59.419 66.667 0.00 0.00 45.73 5.73
943 944 2.930040 CAGATCGTTATGCCTTTCGTGT 59.070 45.455 0.00 0.00 0.00 4.49
954 955 2.101582 GAGACAGTGCCCAGATCGTTAT 59.898 50.000 0.00 0.00 0.00 1.89
976 977 1.859302 ATTTCACCGAGCCTCTCTCT 58.141 50.000 0.00 0.00 39.70 3.10
1158 1159 3.118738 GGTTAGAATCCGAGCTCTTCCAA 60.119 47.826 12.85 1.67 0.00 3.53
1236 1237 2.092592 CGTTACCTTTTGGGAGGCCTAT 60.093 50.000 4.42 0.00 46.08 2.57
1279 1280 2.185310 GACCAATGTCCGTCTGGCCT 62.185 60.000 3.32 0.00 35.34 5.19
1363 1364 0.683504 ACCGTCGGATCACTAAGGCT 60.684 55.000 20.51 0.00 0.00 4.58
1573 1574 0.526662 GGACCGAACTGTCTCACGAT 59.473 55.000 0.00 0.00 35.54 3.73
1599 1600 0.324943 AATGCTCTAACGCCCACACT 59.675 50.000 0.00 0.00 0.00 3.55
1666 1667 4.619863 CGTAGGCACAATAACTGGTACACT 60.620 45.833 0.00 0.00 0.00 3.55
1805 1806 1.945354 GAACCCATCGCTGTCTCGGA 61.945 60.000 0.00 0.00 0.00 4.55
1835 1836 1.692395 TTCCATCGCTCCATCCCCA 60.692 57.895 0.00 0.00 0.00 4.96
1850 1851 8.041919 GCTACCTTATCCTATTTCCATACTTCC 58.958 40.741 0.00 0.00 0.00 3.46
1884 1885 4.274602 TGACACCTATTTAAACGGCTCA 57.725 40.909 5.50 4.54 0.00 4.26
2054 2055 2.174360 GATGGAAGGGCAGAGCTTTTT 58.826 47.619 0.00 0.00 0.00 1.94
2215 2218 2.025416 TCGGGATGGATTGATGTGGTTT 60.025 45.455 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.