Multiple sequence alignment - TraesCS3B01G192600

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 TraesCS3B01G192600 chr3B 100.000 2585 0 0 1 2585 207196834 207194250 0 4774
1 TraesCS3B01G192600 chr3B 97.667 986 22 1 1600 2585 132601302 132602286 0 1692
2 TraesCS3B01G192600 chr3B 97.183 994 28 0 1592 2585 423829492 423828499 0 1681
3 TraesCS3B01G192600 chr5B 97.972 986 20 0 1600 2585 438009423 438010408 0 1711
4 TraesCS3B01G192600 chr6B 97.769 986 22 0 1600 2585 445900020 445901005 0 1700
5 TraesCS3B01G192600 chr6B 97.566 986 24 0 1600 2585 445907054 445908039 0 1688
6 TraesCS3B01G192600 chr2B 97.566 986 24 0 1600 2585 454171714 454170729 0 1688
7 TraesCS3B01G192600 chr2B 98.016 857 16 1 1 856 18887150 18888006 0 1487
8 TraesCS3B01G192600 chr2B 97.900 857 16 2 1 857 706770878 706770024 0 1482
9 TraesCS3B01G192600 chr1B 97.566 986 24 0 1600 2585 112151314 112150329 0 1688
10 TraesCS3B01G192600 chr1B 97.566 986 24 0 1600 2585 181064077 181063092 0 1688
11 TraesCS3B01G192600 chr1B 97.566 986 24 0 1600 2585 461280383 461281368 0 1688
12 TraesCS3B01G192600 chr1B 97.902 858 14 4 1 856 370359793 370360648 0 1482
13 TraesCS3B01G192600 chr4A 98.019 858 15 2 1 857 500553114 500553970 0 1489
14 TraesCS3B01G192600 chr7A 97.902 858 16 2 1 857 542367559 542366703 0 1483
15 TraesCS3B01G192600 chr7A 93.636 660 34 7 943 1600 700256708 700257361 0 979
16 TraesCS3B01G192600 chr2A 97.793 861 17 2 1 859 387548151 387547291 0 1483
17 TraesCS3B01G192600 chr2A 97.905 859 15 3 1 857 412350017 412350874 0 1483
18 TraesCS3B01G192600 chr5A 97.900 857 16 2 1 856 593207257 593206402 0 1482
19 TraesCS3B01G192600 chr5A 94.554 661 29 3 945 1600 283620008 283619350 0 1014
20 TraesCS3B01G192600 chr7B 97.791 860 16 3 1 858 576411730 576412588 0 1480
21 TraesCS3B01G192600 chr1D 93.691 745 35 3 865 1600 491908024 491907283 0 1105
22 TraesCS3B01G192600 chr5D 94.048 672 30 4 934 1600 497305385 497304719 0 1011
23 TraesCS3B01G192600 chr5D 93.275 684 31 4 930 1600 53756522 53757203 0 994
24 TraesCS3B01G192600 chr5D 90.986 710 50 11 895 1600 84407546 84408245 0 944
25 TraesCS3B01G192600 chr6D 94.453 649 26 6 944 1584 424649069 424648423 0 990
26 TraesCS3B01G192600 chr3D 93.333 675 34 6 934 1600 486147212 486146541 0 987
27 TraesCS3B01G192600 chr2D 92.857 686 34 7 928 1600 543183520 543184203 0 981


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 TraesCS3B01G192600 chr3B 207194250 207196834 2584 True 4774 4774 100.000 1 2585 1 chr3B.!!$R1 2584
1 TraesCS3B01G192600 chr3B 132601302 132602286 984 False 1692 1692 97.667 1600 2585 1 chr3B.!!$F1 985
2 TraesCS3B01G192600 chr3B 423828499 423829492 993 True 1681 1681 97.183 1592 2585 1 chr3B.!!$R2 993
3 TraesCS3B01G192600 chr5B 438009423 438010408 985 False 1711 1711 97.972 1600 2585 1 chr5B.!!$F1 985
4 TraesCS3B01G192600 chr6B 445900020 445901005 985 False 1700 1700 97.769 1600 2585 1 chr6B.!!$F1 985
5 TraesCS3B01G192600 chr6B 445907054 445908039 985 False 1688 1688 97.566 1600 2585 1 chr6B.!!$F2 985
6 TraesCS3B01G192600 chr2B 454170729 454171714 985 True 1688 1688 97.566 1600 2585 1 chr2B.!!$R1 985
7 TraesCS3B01G192600 chr2B 18887150 18888006 856 False 1487 1487 98.016 1 856 1 chr2B.!!$F1 855
8 TraesCS3B01G192600 chr2B 706770024 706770878 854 True 1482 1482 97.900 1 857 1 chr2B.!!$R2 856
9 TraesCS3B01G192600 chr1B 112150329 112151314 985 True 1688 1688 97.566 1600 2585 1 chr1B.!!$R1 985
10 TraesCS3B01G192600 chr1B 181063092 181064077 985 True 1688 1688 97.566 1600 2585 1 chr1B.!!$R2 985
11 TraesCS3B01G192600 chr1B 461280383 461281368 985 False 1688 1688 97.566 1600 2585 1 chr1B.!!$F2 985
12 TraesCS3B01G192600 chr1B 370359793 370360648 855 False 1482 1482 97.902 1 856 1 chr1B.!!$F1 855
13 TraesCS3B01G192600 chr4A 500553114 500553970 856 False 1489 1489 98.019 1 857 1 chr4A.!!$F1 856
14 TraesCS3B01G192600 chr7A 542366703 542367559 856 True 1483 1483 97.902 1 857 1 chr7A.!!$R1 856
15 TraesCS3B01G192600 chr7A 700256708 700257361 653 False 979 979 93.636 943 1600 1 chr7A.!!$F1 657
16 TraesCS3B01G192600 chr2A 387547291 387548151 860 True 1483 1483 97.793 1 859 1 chr2A.!!$R1 858
17 TraesCS3B01G192600 chr2A 412350017 412350874 857 False 1483 1483 97.905 1 857 1 chr2A.!!$F1 856
18 TraesCS3B01G192600 chr5A 593206402 593207257 855 True 1482 1482 97.900 1 856 1 chr5A.!!$R2 855
19 TraesCS3B01G192600 chr5A 283619350 283620008 658 True 1014 1014 94.554 945 1600 1 chr5A.!!$R1 655
20 TraesCS3B01G192600 chr7B 576411730 576412588 858 False 1480 1480 97.791 1 858 1 chr7B.!!$F1 857
21 TraesCS3B01G192600 chr1D 491907283 491908024 741 True 1105 1105 93.691 865 1600 1 chr1D.!!$R1 735
22 TraesCS3B01G192600 chr5D 497304719 497305385 666 True 1011 1011 94.048 934 1600 1 chr5D.!!$R1 666
23 TraesCS3B01G192600 chr5D 53756522 53757203 681 False 994 994 93.275 930 1600 1 chr5D.!!$F1 670
24 TraesCS3B01G192600 chr5D 84407546 84408245 699 False 944 944 90.986 895 1600 1 chr5D.!!$F2 705
25 TraesCS3B01G192600 chr6D 424648423 424649069 646 True 990 990 94.453 944 1584 1 chr6D.!!$R1 640
26 TraesCS3B01G192600 chr3D 486146541 486147212 671 True 987 987 93.333 934 1600 1 chr3D.!!$R1 666
27 TraesCS3B01G192600 chr2D 543183520 543184203 683 False 981 981 92.857 928 1600 1 chr2D.!!$F1 672

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
818 825 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.0 15.81 0.0 43.2 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2481 1.002624 GGGTTCGGGAGACATGCAA 60.003 57.895 0.0 0.0 39.59 4.08 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
649 656 0.249073 GGTGCGTCATCGAGCTGTAT 60.249 55.000 0.00 0.00 39.71 2.29
734 741 2.161012 CGACTACTTCCTCTACGTTGCA 59.839 50.000 0.00 0.00 0.00 4.08
778 785 3.002791 CGAGGGTACGTAGACAACACTA 58.997 50.000 0.00 0.00 0.00 2.74
779 786 3.624861 CGAGGGTACGTAGACAACACTAT 59.375 47.826 0.00 0.00 0.00 2.12
780 787 4.260538 CGAGGGTACGTAGACAACACTATC 60.261 50.000 0.00 0.00 0.00 2.08
781 788 3.950395 AGGGTACGTAGACAACACTATCC 59.050 47.826 0.00 0.00 0.00 2.59
782 789 3.067320 GGGTACGTAGACAACACTATCCC 59.933 52.174 0.00 0.00 0.00 3.85
783 790 3.067320 GGTACGTAGACAACACTATCCCC 59.933 52.174 0.00 0.00 0.00 4.81
784 791 3.097342 ACGTAGACAACACTATCCCCT 57.903 47.619 0.00 0.00 0.00 4.79
785 792 3.022406 ACGTAGACAACACTATCCCCTC 58.978 50.000 0.00 0.00 0.00 4.30
786 793 2.033049 CGTAGACAACACTATCCCCTCG 59.967 54.545 0.00 0.00 0.00 4.63
787 794 2.233305 AGACAACACTATCCCCTCGT 57.767 50.000 0.00 0.00 0.00 4.18
788 795 2.537143 AGACAACACTATCCCCTCGTT 58.463 47.619 0.00 0.00 0.00 3.85
789 796 2.233922 AGACAACACTATCCCCTCGTTG 59.766 50.000 0.00 0.00 42.04 4.10
790 797 1.338769 ACAACACTATCCCCTCGTTGC 60.339 52.381 0.00 0.00 40.42 4.17
791 798 1.066143 CAACACTATCCCCTCGTTGCT 60.066 52.381 0.00 0.00 31.53 3.91
792 799 2.154567 ACACTATCCCCTCGTTGCTA 57.845 50.000 0.00 0.00 0.00 3.49
793 800 2.679082 ACACTATCCCCTCGTTGCTAT 58.321 47.619 0.00 0.00 0.00 2.97
794 801 3.840991 ACACTATCCCCTCGTTGCTATA 58.159 45.455 0.00 0.00 0.00 1.31
795 802 4.417437 ACACTATCCCCTCGTTGCTATAT 58.583 43.478 0.00 0.00 0.00 0.86
796 803 4.463186 ACACTATCCCCTCGTTGCTATATC 59.537 45.833 0.00 0.00 0.00 1.63
797 804 4.462834 CACTATCCCCTCGTTGCTATATCA 59.537 45.833 0.00 0.00 0.00 2.15
798 805 5.127845 CACTATCCCCTCGTTGCTATATCAT 59.872 44.000 0.00 0.00 0.00 2.45
799 806 4.744795 ATCCCCTCGTTGCTATATCATC 57.255 45.455 0.00 0.00 0.00 2.92
800 807 3.506398 TCCCCTCGTTGCTATATCATCA 58.494 45.455 0.00 0.00 0.00 3.07
801 808 3.258372 TCCCCTCGTTGCTATATCATCAC 59.742 47.826 0.00 0.00 0.00 3.06
802 809 3.589988 CCCTCGTTGCTATATCATCACC 58.410 50.000 0.00 0.00 0.00 4.02
803 810 3.006859 CCCTCGTTGCTATATCATCACCA 59.993 47.826 0.00 0.00 0.00 4.17
804 811 4.323028 CCCTCGTTGCTATATCATCACCAT 60.323 45.833 0.00 0.00 0.00 3.55
805 812 4.628766 CCTCGTTGCTATATCATCACCATG 59.371 45.833 0.00 0.00 0.00 3.66
806 813 5.467035 TCGTTGCTATATCATCACCATGA 57.533 39.130 0.00 0.00 43.45 3.07
808 815 6.101997 TCGTTGCTATATCATCACCATGATC 58.898 40.000 0.00 0.00 45.26 2.92
809 816 6.071165 TCGTTGCTATATCATCACCATGATCT 60.071 38.462 0.00 0.00 45.26 2.75
810 817 6.592994 CGTTGCTATATCATCACCATGATCTT 59.407 38.462 0.00 0.00 45.26 2.40
811 818 7.412672 CGTTGCTATATCATCACCATGATCTTG 60.413 40.741 0.00 1.60 45.26 3.02
812 819 5.878669 TGCTATATCATCACCATGATCTTGC 59.121 40.000 3.07 5.56 45.26 4.01
813 820 5.006455 GCTATATCATCACCATGATCTTGCG 59.994 44.000 3.07 0.30 45.26 4.85
814 821 2.696989 TCATCACCATGATCTTGCGT 57.303 45.000 3.07 0.87 34.28 5.24
815 822 2.282407 TCATCACCATGATCTTGCGTG 58.718 47.619 17.02 17.02 34.28 5.34
816 823 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
817 824 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
818 825 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
852 859 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
853 860 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
854 861 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
855 862 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
856 863 4.998672 TGAAATTACTACGTTCCCCAACAG 59.001 41.667 0.00 0.00 32.14 3.16
857 864 2.460757 TTACTACGTTCCCCAACAGC 57.539 50.000 0.00 0.00 32.14 4.40
858 865 1.636148 TACTACGTTCCCCAACAGCT 58.364 50.000 0.00 0.00 32.14 4.24
859 866 0.320697 ACTACGTTCCCCAACAGCTC 59.679 55.000 0.00 0.00 32.14 4.09
860 867 0.391263 CTACGTTCCCCAACAGCTCC 60.391 60.000 0.00 0.00 32.14 4.70
861 868 2.162338 TACGTTCCCCAACAGCTCCG 62.162 60.000 0.00 0.00 32.14 4.63
862 869 2.430367 GTTCCCCAACAGCTCCGT 59.570 61.111 0.00 0.00 32.14 4.69
863 870 1.671379 GTTCCCCAACAGCTCCGTC 60.671 63.158 0.00 0.00 32.14 4.79
1047 1073 3.063704 TCGGGCTTCTTCGGCGTA 61.064 61.111 6.85 0.00 0.00 4.42
1153 1179 2.125713 CCGCACATGCCTACGACA 60.126 61.111 0.00 0.00 37.91 4.35
1284 1315 3.314357 TCACGACGAAGAAGAAGAAGACA 59.686 43.478 0.00 0.00 0.00 3.41
1401 1432 2.490903 GGAGTACTACTGGAAGCGTGAA 59.509 50.000 0.00 0.00 37.60 3.18
1423 1454 1.557269 GGAGCAGAAGCAGAAGGGGA 61.557 60.000 0.00 0.00 45.49 4.81
1702 1769 9.988350 CATGCTATAATTGTATTATCCGGAAAC 57.012 33.333 9.01 5.40 0.00 2.78
1859 1926 7.903226 TCATTAGGAGAATGATGTGATGGACAC 60.903 40.741 0.00 0.00 39.34 3.67
1967 2034 2.425143 TCGTGTAACTCCCGGATACT 57.575 50.000 0.73 0.00 31.75 2.12
2090 2157 2.303022 GAGACTGGGATTTGTCACTCCA 59.697 50.000 3.62 0.00 35.81 3.86
2132 2199 1.498865 GCCCACTCGGTAATGCATCG 61.499 60.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 238 1.711375 GGGAAGGAGAAAGGAAAGGGT 59.289 52.381 0.00 0.00 0.00 4.34
589 596 4.649705 TGCCGAGGGGGAGTTCCA 62.650 66.667 0.00 0.00 38.47 3.53
649 656 0.318699 CTCCGAGTTCTTGACACGCA 60.319 55.000 0.00 0.00 40.39 5.24
708 715 3.929610 ACGTAGAGGAAGTAGTCGTACAC 59.070 47.826 0.00 0.00 0.00 2.90
778 785 4.081420 GTGATGATATAGCAACGAGGGGAT 60.081 45.833 0.00 0.00 0.00 3.85
779 786 3.258372 GTGATGATATAGCAACGAGGGGA 59.742 47.826 0.00 0.00 0.00 4.81
780 787 3.589988 GTGATGATATAGCAACGAGGGG 58.410 50.000 0.00 0.00 0.00 4.79
781 788 3.006859 TGGTGATGATATAGCAACGAGGG 59.993 47.826 0.00 0.00 34.34 4.30
782 789 4.257267 TGGTGATGATATAGCAACGAGG 57.743 45.455 0.00 0.00 34.34 4.63
783 790 5.473039 TCATGGTGATGATATAGCAACGAG 58.527 41.667 0.00 0.00 34.34 4.18
784 791 5.467035 TCATGGTGATGATATAGCAACGA 57.533 39.130 0.00 0.00 34.34 3.85
795 802 2.282407 CACGCAAGATCATGGTGATGA 58.718 47.619 11.70 0.00 37.20 2.92
796 803 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
797 804 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
798 805 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
799 806 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
800 807 2.174334 GCACACGCAAGATCATGGT 58.826 52.632 0.00 0.00 43.62 3.55
829 836 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
830 837 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
831 838 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
832 839 5.374921 TGTTGGGGAACGTAGTAATTTCAA 58.625 37.500 0.00 0.00 45.00 2.69
833 840 4.970711 TGTTGGGGAACGTAGTAATTTCA 58.029 39.130 0.00 0.00 45.00 2.69
834 841 4.142752 GCTGTTGGGGAACGTAGTAATTTC 60.143 45.833 0.00 0.00 45.00 2.17
835 842 3.754850 GCTGTTGGGGAACGTAGTAATTT 59.245 43.478 0.00 0.00 45.00 1.82
836 843 3.008704 AGCTGTTGGGGAACGTAGTAATT 59.991 43.478 0.00 0.00 45.00 1.40
837 844 2.570302 AGCTGTTGGGGAACGTAGTAAT 59.430 45.455 0.00 0.00 45.00 1.89
838 845 1.972795 AGCTGTTGGGGAACGTAGTAA 59.027 47.619 0.00 0.00 45.00 2.24
839 846 1.547372 GAGCTGTTGGGGAACGTAGTA 59.453 52.381 0.00 0.00 45.00 1.82
841 848 0.391263 GGAGCTGTTGGGGAACGTAG 60.391 60.000 0.00 0.00 0.00 3.51
842 849 1.675219 GGAGCTGTTGGGGAACGTA 59.325 57.895 0.00 0.00 0.00 3.57
843 850 2.430367 GGAGCTGTTGGGGAACGT 59.570 61.111 0.00 0.00 0.00 3.99
844 851 2.742372 CGGAGCTGTTGGGGAACG 60.742 66.667 0.00 0.00 0.00 3.95
845 852 1.671379 GACGGAGCTGTTGGGGAAC 60.671 63.158 0.00 0.00 0.00 3.62
846 853 2.747686 GACGGAGCTGTTGGGGAA 59.252 61.111 0.00 0.00 0.00 3.97
847 854 3.319198 GGACGGAGCTGTTGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
848 855 4.760047 CGGACGGAGCTGTTGGGG 62.760 72.222 0.00 0.00 0.00 4.96
851 858 4.680237 TGGCGGACGGAGCTGTTG 62.680 66.667 0.00 0.00 34.52 3.33
852 859 4.681978 GTGGCGGACGGAGCTGTT 62.682 66.667 0.00 0.00 34.52 3.16
911 919 2.764128 GGGCGGAGGGAGACATGA 60.764 66.667 0.00 0.00 0.00 3.07
1284 1315 0.661020 CGACAACCAACGGCTTCTTT 59.339 50.000 0.00 0.00 0.00 2.52
1318 1349 2.356793 CATCGCCTCCTCATCGGC 60.357 66.667 0.00 0.00 42.86 5.54
1365 1396 2.038813 TCCATCTCGGCCTGGACA 59.961 61.111 7.35 0.00 36.63 4.02
1401 1432 1.079266 CTTCTGCTTCTGCTCCGCT 60.079 57.895 0.00 0.00 40.48 5.52
1423 1454 0.827368 GCCTCATCCTCCTTCTTCGT 59.173 55.000 0.00 0.00 0.00 3.85
1543 1610 0.689623 AACTGCTCCCAGAACTCCTG 59.310 55.000 0.00 0.00 41.77 3.86
1859 1926 2.224281 TGCTATGCTTAGGATTGGGTCG 60.224 50.000 8.57 0.00 0.00 4.79
1967 2034 1.136828 ACACCCAAAGCACTCCTACA 58.863 50.000 0.00 0.00 0.00 2.74
2090 2157 4.568804 CCCAGAGATACCTCTCCGTCATAT 60.569 50.000 0.00 0.00 46.38 1.78
2132 2199 4.937620 TGGTCACTTTGAGCTCATTATGAC 59.062 41.667 29.22 29.22 44.58 3.06
2414 2481 1.002624 GGGTTCGGGAGACATGCAA 60.003 57.895 0.00 0.00 39.59 4.08
2440 2507 3.737774 GTCACCGAACCTTAAGTGTGTAC 59.262 47.826 0.97 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.