Multiple sequence alignment - TraesCS6B01G161200

Loading Multiple Alignment...

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 TraesCS6B01G161200 chr6B 100.000 3857 0 0 1 3857 165124146 165128002 0 7123
1 TraesCS6B01G161200 chr6B 95.648 3860 162 4 1 3857 645419900 645416044 0 6192
2 TraesCS6B01G161200 chr6B 95.649 3861 159 5 1 3857 714971843 714975698 0 6191
3 TraesCS6B01G161200 chr4B 96.788 3860 120 3 1 3857 501373330 501377188 0 6438
4 TraesCS6B01G161200 chr5B 96.113 3859 145 5 1 3857 547375572 547379427 0 6290
5 TraesCS6B01G161200 chr5B 95.647 3859 162 6 1 3857 434636866 434640720 0 6191
6 TraesCS6B01G161200 chr2B 95.854 3859 154 6 1 3857 417666571 417670425 0 6235
7 TraesCS6B01G161200 chr7B 95.803 3860 157 4 1 3857 84605702 84601845 0 6226
8 TraesCS6B01G161200 chr7B 95.623 3861 164 2 1 3857 687520034 687516175 0 6189
9 TraesCS6B01G161200 chr3B 95.653 3865 156 8 1 3857 465995266 465999126 0 6196


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 TraesCS6B01G161200 chr6B 165124146 165128002 3856 False 7123 7123 100.000 1 3857 1 chr6B.!!$F1 3856
1 TraesCS6B01G161200 chr6B 645416044 645419900 3856 True 6192 6192 95.648 1 3857 1 chr6B.!!$R1 3856
2 TraesCS6B01G161200 chr6B 714971843 714975698 3855 False 6191 6191 95.649 1 3857 1 chr6B.!!$F2 3856
3 TraesCS6B01G161200 chr4B 501373330 501377188 3858 False 6438 6438 96.788 1 3857 1 chr4B.!!$F1 3856
4 TraesCS6B01G161200 chr5B 547375572 547379427 3855 False 6290 6290 96.113 1 3857 1 chr5B.!!$F2 3856
5 TraesCS6B01G161200 chr5B 434636866 434640720 3854 False 6191 6191 95.647 1 3857 1 chr5B.!!$F1 3856
6 TraesCS6B01G161200 chr2B 417666571 417670425 3854 False 6235 6235 95.854 1 3857 1 chr2B.!!$F1 3856
7 TraesCS6B01G161200 chr7B 84601845 84605702 3857 True 6226 6226 95.803 1 3857 1 chr7B.!!$R1 3856
8 TraesCS6B01G161200 chr7B 687516175 687520034 3859 True 6189 6189 95.623 1 3857 1 chr7B.!!$R2 3856
9 TraesCS6B01G161200 chr3B 465995266 465999126 3860 False 6196 6196 95.653 1 3857 1 chr3B.!!$F1 3856

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
811 818 1.064685 GGGATCCGAATTGTGGGAAGT 60.065 52.381 5.45 0.0 34.96 3.01 F
1754 1763 0.322997 CAGTCGACTGGTCTCCCTCT 60.323 60.000 33.36 0.0 40.20 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2297 0.179137 GTCATCGTCGTCAGCATCCA 60.179 55.0 0.0 0.0 0.00 3.41 R
2984 2996 0.753479 AGCACTCGACGATGGAGGAT 60.753 55.0 0.0 0.0 35.82 3.24 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
112 113 3.387050 GCCCTTCTCGGAGGAAGTAATAA 59.613 47.826 4.96 0.00 40.56 1.40
124 125 5.513233 AGGAAGTAATAACCCTACGTCTCA 58.487 41.667 0.00 0.00 31.08 3.27
246 247 1.207089 CTCCGACCCTCAGTTATGCAA 59.793 52.381 0.00 0.00 0.00 4.08
389 393 2.353704 CGAGTGGTTAGCTTCATGGTCA 60.354 50.000 0.00 0.00 0.00 4.02
589 593 6.013032 TGAGGAAGGAGTTGATGATTTTCTCT 60.013 38.462 0.00 0.00 0.00 3.10
616 620 5.180868 CCTATTTCCTGTGCTCTGATTATGC 59.819 44.000 0.00 0.00 0.00 3.14
617 621 3.920231 TTCCTGTGCTCTGATTATGCT 57.080 42.857 0.00 0.00 0.00 3.79
631 635 6.270695 TCTGATTATGCTGTATCCTGGATCAA 59.729 38.462 13.54 1.67 0.00 2.57
643 650 5.880054 TCCTGGATCAACGATTTTTCTTC 57.120 39.130 0.00 0.00 0.00 2.87
664 671 5.103290 TCTTTGGCGTTGACATTAACTTC 57.897 39.130 0.00 0.00 0.00 3.01
670 677 5.992829 TGGCGTTGACATTAACTTCTCTTTA 59.007 36.000 0.00 0.00 0.00 1.85
677 684 6.926826 TGACATTAACTTCTCTTTAAGTCGCA 59.073 34.615 0.00 0.00 38.76 5.10
803 810 4.989279 AGATTTTGTGGGATCCGAATTG 57.011 40.909 5.45 0.00 0.00 2.32
811 818 1.064685 GGGATCCGAATTGTGGGAAGT 60.065 52.381 5.45 0.00 34.96 3.01
820 827 2.665185 GTGGGAAGTGCGCGAAGT 60.665 61.111 12.10 0.00 0.00 3.01
914 921 2.892334 ATGCGTGCGCGACTGTTTT 61.892 52.632 26.19 0.00 45.51 2.43
955 962 1.282157 GGGCCTACTTGTCATCCACTT 59.718 52.381 0.84 0.00 0.00 3.16
957 964 2.027192 GGCCTACTTGTCATCCACTTGA 60.027 50.000 0.00 0.00 0.00 3.02
977 984 6.821665 ACTTGAAAGCGTCCTTATATAAAGCA 59.178 34.615 11.74 0.00 0.00 3.91
1033 1042 2.043115 TCTCCTCTCTGCCCTCTTTGTA 59.957 50.000 0.00 0.00 0.00 2.41
1142 1151 3.843240 GCGTGCGAAGAAGGCGAG 61.843 66.667 0.00 0.00 0.00 5.03
1312 1321 1.898574 CACGGGTCAGCAAGGCTTT 60.899 57.895 0.00 0.00 36.40 3.51
1429 1438 2.695359 TCCGAGGGTTTCTGAATTTCG 58.305 47.619 0.00 0.00 0.00 3.46
1444 1453 2.951475 TTTCGTTGGGGCGCAACTCT 62.951 55.000 34.68 0.00 0.00 3.24
1679 1688 0.329596 GCCATGACCCTTCCTGAGTT 59.670 55.000 0.00 0.00 0.00 3.01
1683 1692 0.764890 TGACCCTTCCTGAGTTGGTG 59.235 55.000 0.00 0.00 0.00 4.17
1700 1709 1.979155 TGAGAGGGTGGCAGTCGAG 60.979 63.158 0.00 0.00 0.00 4.04
1712 1721 2.490903 GGCAGTCGAGTTGGTTCTACTA 59.509 50.000 0.00 0.00 0.00 1.82
1754 1763 0.322997 CAGTCGACTGGTCTCCCTCT 60.323 60.000 33.36 0.00 40.20 3.69
1913 1922 0.460284 CTTAGACGGCGCATCCAACT 60.460 55.000 10.83 1.82 34.01 3.16
2179 2188 4.391140 GTCGATTGACCTTTGTCTTGTC 57.609 45.455 1.10 0.00 42.28 3.18
2381 2393 1.272536 ACCTCCTAGCTCGGAAAGACA 60.273 52.381 8.54 0.00 31.44 3.41
2952 2964 1.204941 GACAATGTCACTCGGCCTACT 59.795 52.381 8.74 0.00 32.09 2.57
2984 2996 2.355837 GCCGTTGACGAGTGCTCA 60.356 61.111 4.91 0.00 43.02 4.26
3039 3051 1.214589 CTCAACCTACCACGTCCCG 59.785 63.158 0.00 0.00 0.00 5.14
3635 3653 5.759963 CCGTAGTCTTAGAAACGCTATGAT 58.240 41.667 11.41 0.00 36.17 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.959512 ACTACTCCATAGCTAGGATCTTGT 58.040 41.667 7.04 6.95 33.99 3.16
112 113 1.380112 GGGCTCTGAGACGTAGGGT 60.380 63.158 9.28 0.00 0.00 4.34
246 247 8.500238 CCCCCTATCTTAATGTACTTTAAACCT 58.500 37.037 13.21 5.68 0.00 3.50
389 393 2.230508 TCGACGTTGAAGATAGCCACTT 59.769 45.455 2.05 0.00 0.00 3.16
589 593 3.173151 TCAGAGCACAGGAAATAGGTCA 58.827 45.455 0.00 0.00 0.00 4.02
616 620 6.540189 AGAAAAATCGTTGATCCAGGATACAG 59.460 38.462 0.32 0.00 41.41 2.74
617 621 6.414732 AGAAAAATCGTTGATCCAGGATACA 58.585 36.000 0.32 0.00 41.41 2.29
631 635 3.982576 ACGCCAAAGAAGAAAAATCGT 57.017 38.095 0.00 0.00 0.00 3.73
643 650 5.049405 AGAGAAGTTAATGTCAACGCCAAAG 60.049 40.000 0.00 0.00 33.50 2.77
664 671 5.998454 ATGGATCAATGCGACTTAAAGAG 57.002 39.130 0.00 0.00 0.00 2.85
670 677 3.287867 AGGAATGGATCAATGCGACTT 57.712 42.857 0.00 0.00 0.00 3.01
677 684 5.587844 CGACAGAAGAAAGGAATGGATCAAT 59.412 40.000 0.00 0.00 0.00 2.57
781 788 4.772100 ACAATTCGGATCCCACAAAATCTT 59.228 37.500 6.06 0.00 0.00 2.40
782 789 4.158394 CACAATTCGGATCCCACAAAATCT 59.842 41.667 6.06 0.00 0.00 2.40
803 810 2.665185 ACTTCGCGCACTTCCCAC 60.665 61.111 8.75 0.00 0.00 4.61
914 921 2.981302 CGCTCCTGTCACATCCCA 59.019 61.111 0.00 0.00 0.00 4.37
955 962 5.526111 GGTGCTTTATATAAGGACGCTTTCA 59.474 40.000 8.68 0.00 39.16 2.69
957 964 4.510340 CGGTGCTTTATATAAGGACGCTTT 59.490 41.667 8.68 0.00 39.16 3.51
1128 1137 4.760047 GCCCTCGCCTTCTTCGCA 62.760 66.667 0.00 0.00 0.00 5.10
1444 1453 4.666412 TGGAATTGGGAGTGAAATGGTA 57.334 40.909 0.00 0.00 0.00 3.25
1679 1688 2.122413 ACTGCCACCCTCTCACCA 60.122 61.111 0.00 0.00 0.00 4.17
1683 1692 1.536943 AACTCGACTGCCACCCTCTC 61.537 60.000 0.00 0.00 0.00 3.20
1712 1721 2.254651 GCGTCGACTCGTCTTGGT 59.745 61.111 14.70 0.00 0.00 3.67
1754 1763 0.608130 CACTCGGTCCATGGAGAACA 59.392 55.000 16.81 0.00 34.40 3.18
1861 1870 0.689080 AGATCCATGCCCGTCACTCT 60.689 55.000 0.00 0.00 0.00 3.24
1913 1922 1.911269 TGGCCTCGGTACTGAAGCA 60.911 57.895 23.44 9.68 0.00 3.91
1945 1954 1.604693 GGTGTCTTCGGTACCACAGTG 60.605 57.143 13.54 0.00 34.61 3.66
2179 2188 0.947244 GTGGCCTGTCAGACAACAAG 59.053 55.000 3.32 0.00 0.00 3.16
2288 2297 0.179137 GTCATCGTCGTCAGCATCCA 60.179 55.000 0.00 0.00 0.00 3.41
2368 2380 0.959553 TTCGAGTGTCTTTCCGAGCT 59.040 50.000 0.00 0.00 32.41 4.09
2381 2393 2.419297 GGATCATGGACAAGCTTCGAGT 60.419 50.000 0.00 0.00 0.00 4.18
2984 2996 0.753479 AGCACTCGACGATGGAGGAT 60.753 55.000 0.00 0.00 35.82 3.24
3456 3468 4.662961 TGCCAGCAGTCGACCACG 62.663 66.667 13.01 2.08 41.26 4.94
3635 3653 5.286267 ACTTCCGAGTGACTAAGGAAAAA 57.714 39.130 18.46 2.61 41.59 1.94


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

AutoCloner maintained by Alex Coulton.