Multiple sequence alignment - TraesCS6B01G131500

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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 TraesCS6B01G131500 chr6B 100.000 2663 0 0 1 2663 128887564 128884902 0 4918
1 TraesCS6B01G131500 chrUn 98.952 1717 11 1 947 2663 223705988 223704279 0 3064
2 TraesCS6B01G131500 chrUn 98.746 877 11 0 1 877 233522849 233521973 0 1559
3 TraesCS6B01G131500 chr2A 98.893 1717 11 2 947 2663 605911931 605910223 0 3059
4 TraesCS6B01G131500 chr7B 98.779 1720 13 2 944 2663 698141103 698142814 0 3053
5 TraesCS6B01G131500 chr7B 96.624 1718 52 3 947 2663 47203801 47202089 0 2846
6 TraesCS6B01G131500 chr7B 98.860 877 10 0 1 877 698124515 698123639 0 1565
7 TraesCS6B01G131500 chr7B 98.404 877 13 1 1 877 716793419 716792544 0 1541
8 TraesCS6B01G131500 chr1B 98.719 1717 13 2 947 2663 683733196 683731489 0 3040
9 TraesCS6B01G131500 chr1B 98.314 1720 23 1 944 2663 338893761 338895474 0 3011
10 TraesCS6B01G131500 chr5B 97.838 1711 28 3 944 2653 508012600 508014302 0 2946
11 TraesCS6B01G131500 chr5D 96.690 1722 39 5 944 2663 3135832 3137537 0 2848
12 TraesCS6B01G131500 chr3A 95.515 1717 65 5 947 2663 401676230 401674526 0 2734
13 TraesCS6B01G131500 chr4A 95.407 1720 63 6 944 2663 295224118 295225821 0 2724
14 TraesCS6B01G131500 chr2D 98.518 877 13 0 1 877 637306283 637305407 0 1548
15 TraesCS6B01G131500 chr7D 98.733 868 11 0 1 868 578993170 578994037 0 1543
16 TraesCS6B01G131500 chr4D 98.618 868 12 0 1 868 123691386 123692253 0 1537
17 TraesCS6B01G131500 chr7A 98.176 877 16 0 1 877 60093779 60092903 0 1531
18 TraesCS6B01G131500 chr1D 98.502 868 12 1 1 868 212431293 212432159 0 1530
19 TraesCS6B01G131500 chr4B 98.062 877 16 1 1 877 495535356 495534481 0 1524


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 TraesCS6B01G131500 chr6B 128884902 128887564 2662 True 4918 4918 100.000 1 2663 1 chr6B.!!$R1 2662
1 TraesCS6B01G131500 chrUn 223704279 223705988 1709 True 3064 3064 98.952 947 2663 1 chrUn.!!$R1 1716
2 TraesCS6B01G131500 chrUn 233521973 233522849 876 True 1559 1559 98.746 1 877 1 chrUn.!!$R2 876
3 TraesCS6B01G131500 chr2A 605910223 605911931 1708 True 3059 3059 98.893 947 2663 1 chr2A.!!$R1 1716
4 TraesCS6B01G131500 chr7B 698141103 698142814 1711 False 3053 3053 98.779 944 2663 1 chr7B.!!$F1 1719
5 TraesCS6B01G131500 chr7B 47202089 47203801 1712 True 2846 2846 96.624 947 2663 1 chr7B.!!$R1 1716
6 TraesCS6B01G131500 chr7B 698123639 698124515 876 True 1565 1565 98.860 1 877 1 chr7B.!!$R2 876
7 TraesCS6B01G131500 chr7B 716792544 716793419 875 True 1541 1541 98.404 1 877 1 chr7B.!!$R3 876
8 TraesCS6B01G131500 chr1B 683731489 683733196 1707 True 3040 3040 98.719 947 2663 1 chr1B.!!$R1 1716
9 TraesCS6B01G131500 chr1B 338893761 338895474 1713 False 3011 3011 98.314 944 2663 1 chr1B.!!$F1 1719
10 TraesCS6B01G131500 chr5B 508012600 508014302 1702 False 2946 2946 97.838 944 2653 1 chr5B.!!$F1 1709
11 TraesCS6B01G131500 chr5D 3135832 3137537 1705 False 2848 2848 96.690 944 2663 1 chr5D.!!$F1 1719
12 TraesCS6B01G131500 chr3A 401674526 401676230 1704 True 2734 2734 95.515 947 2663 1 chr3A.!!$R1 1716
13 TraesCS6B01G131500 chr4A 295224118 295225821 1703 False 2724 2724 95.407 944 2663 1 chr4A.!!$F1 1719
14 TraesCS6B01G131500 chr2D 637305407 637306283 876 True 1548 1548 98.518 1 877 1 chr2D.!!$R1 876
15 TraesCS6B01G131500 chr7D 578993170 578994037 867 False 1543 1543 98.733 1 868 1 chr7D.!!$F1 867
16 TraesCS6B01G131500 chr4D 123691386 123692253 867 False 1537 1537 98.618 1 868 1 chr4D.!!$F1 867
17 TraesCS6B01G131500 chr7A 60092903 60093779 876 True 1531 1531 98.176 1 877 1 chr7A.!!$R1 876
18 TraesCS6B01G131500 chr1D 212431293 212432159 866 False 1530 1530 98.502 1 868 1 chr1D.!!$F1 867
19 TraesCS6B01G131500 chr4B 495534481 495535356 875 True 1524 1524 98.062 1 877 1 chr4B.!!$R1 876

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
398 399 0.043183 TCAGCCCTCTTCTCCCATGA 59.957 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2246 3.479203 CTATGCTGACCCGGGCCA 61.479 66.667 24.08 16.92 0.0 5.36 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
398 399 0.043183 TCAGCCCTCTTCTCCCATGA 59.957 55.000 0.00 0.00 0.00 3.07
430 431 0.179045 AGCGCCTCGGATAAAAGCAT 60.179 50.000 2.29 0.00 0.00 3.79
606 607 7.201893 GGTTATGTTCCTTATTCCTCGTCTAGT 60.202 40.741 0.00 0.00 0.00 2.57
715 716 5.235850 TCCTTAATAGTTCACTGTTGGCA 57.764 39.130 0.00 0.00 0.00 4.92
868 870 1.546099 GGGTCGGAGGTTTTTGCCTTA 60.546 52.381 0.00 0.00 39.34 2.69
871 873 3.257375 GGTCGGAGGTTTTTGCCTTATTT 59.743 43.478 0.00 0.00 39.34 1.40
873 875 5.294356 GTCGGAGGTTTTTGCCTTATTTTT 58.706 37.500 0.00 0.00 39.34 1.94
877 879 7.438757 TCGGAGGTTTTTGCCTTATTTTTAAAC 59.561 33.333 0.00 0.00 39.34 2.01
878 880 7.307514 CGGAGGTTTTTGCCTTATTTTTAAACC 60.308 37.037 0.00 0.00 41.93 3.27
880 882 8.671384 AGGTTTTTGCCTTATTTTTAAACCTC 57.329 30.769 9.81 0.00 46.14 3.85
881 883 7.717875 AGGTTTTTGCCTTATTTTTAAACCTCC 59.282 33.333 9.81 0.00 46.14 4.30
882 884 7.499563 GGTTTTTGCCTTATTTTTAAACCTCCA 59.500 33.333 0.00 0.00 39.73 3.86
883 885 8.339714 GTTTTTGCCTTATTTTTAAACCTCCAC 58.660 33.333 0.00 0.00 0.00 4.02
884 886 6.732896 TTGCCTTATTTTTAAACCTCCACA 57.267 33.333 0.00 0.00 0.00 4.17
885 887 6.339587 TGCCTTATTTTTAAACCTCCACAG 57.660 37.500 0.00 0.00 0.00 3.66
886 888 5.245075 TGCCTTATTTTTAAACCTCCACAGG 59.755 40.000 0.00 0.00 46.87 4.00
896 898 2.930826 CCTCCACAGGTGTTGTTACT 57.069 50.000 0.00 0.00 38.16 2.24
898 900 3.926616 CCTCCACAGGTGTTGTTACTAG 58.073 50.000 0.00 0.00 38.16 2.57
899 901 3.323979 CCTCCACAGGTGTTGTTACTAGT 59.676 47.826 0.00 0.00 38.16 2.57
900 902 4.525487 CCTCCACAGGTGTTGTTACTAGTA 59.475 45.833 0.00 0.00 38.16 1.82
901 903 5.011329 CCTCCACAGGTGTTGTTACTAGTAA 59.989 44.000 11.38 11.38 38.16 2.24
902 904 6.463331 CCTCCACAGGTGTTGTTACTAGTAAA 60.463 42.308 16.82 5.34 38.16 2.01
903 905 7.069877 TCCACAGGTGTTGTTACTAGTAAAT 57.930 36.000 16.82 0.00 38.16 1.40
904 906 7.156673 TCCACAGGTGTTGTTACTAGTAAATC 58.843 38.462 16.82 10.50 38.16 2.17
905 907 6.370718 CCACAGGTGTTGTTACTAGTAAATCC 59.629 42.308 16.82 13.50 38.16 3.01
906 908 6.090358 CACAGGTGTTGTTACTAGTAAATCCG 59.910 42.308 16.82 12.07 38.16 4.18
907 909 6.161381 CAGGTGTTGTTACTAGTAAATCCGT 58.839 40.000 16.82 3.39 0.00 4.69
908 910 6.090358 CAGGTGTTGTTACTAGTAAATCCGTG 59.910 42.308 16.82 10.68 0.00 4.94
909 911 5.928264 GGTGTTGTTACTAGTAAATCCGTGT 59.072 40.000 16.82 0.00 0.00 4.49
910 912 6.424812 GGTGTTGTTACTAGTAAATCCGTGTT 59.575 38.462 16.82 0.00 0.00 3.32
911 913 7.041848 GGTGTTGTTACTAGTAAATCCGTGTTT 60.042 37.037 16.82 0.00 0.00 2.83
912 914 8.337532 GTGTTGTTACTAGTAAATCCGTGTTTT 58.662 33.333 16.82 0.00 0.00 2.43
913 915 9.539825 TGTTGTTACTAGTAAATCCGTGTTTTA 57.460 29.630 16.82 0.00 0.00 1.52
914 916 9.797473 GTTGTTACTAGTAAATCCGTGTTTTAC 57.203 33.333 16.82 1.65 38.99 2.01
915 917 9.762933 TTGTTACTAGTAAATCCGTGTTTTACT 57.237 29.630 16.82 16.96 46.37 2.24
922 924 7.578852 AGTAAATCCGTGTTTTACTAGTTTGC 58.421 34.615 0.00 0.00 44.18 3.68
923 925 6.628919 AAATCCGTGTTTTACTAGTTTGCT 57.371 33.333 0.00 0.00 0.00 3.91
924 926 5.607119 ATCCGTGTTTTACTAGTTTGCTG 57.393 39.130 0.00 0.00 0.00 4.41
925 927 4.695396 TCCGTGTTTTACTAGTTTGCTGA 58.305 39.130 0.00 0.00 0.00 4.26
926 928 5.117584 TCCGTGTTTTACTAGTTTGCTGAA 58.882 37.500 0.00 0.00 0.00 3.02
927 929 5.006941 TCCGTGTTTTACTAGTTTGCTGAAC 59.993 40.000 0.00 0.00 38.58 3.18
928 930 5.202640 CGTGTTTTACTAGTTTGCTGAACC 58.797 41.667 0.00 0.00 39.13 3.62
929 931 5.007332 CGTGTTTTACTAGTTTGCTGAACCT 59.993 40.000 0.00 0.00 39.13 3.50
930 932 6.201425 CGTGTTTTACTAGTTTGCTGAACCTA 59.799 38.462 0.00 0.00 39.13 3.08
931 933 7.568861 CGTGTTTTACTAGTTTGCTGAACCTAG 60.569 40.741 0.00 0.00 39.13 3.02
932 934 7.440255 GTGTTTTACTAGTTTGCTGAACCTAGA 59.560 37.037 0.00 0.00 39.13 2.43
933 935 8.154856 TGTTTTACTAGTTTGCTGAACCTAGAT 58.845 33.333 0.00 0.00 39.13 1.98
934 936 8.657729 GTTTTACTAGTTTGCTGAACCTAGATC 58.342 37.037 0.00 0.00 39.13 2.75
935 937 7.719871 TTACTAGTTTGCTGAACCTAGATCT 57.280 36.000 0.00 0.00 39.13 2.75
936 938 6.613153 ACTAGTTTGCTGAACCTAGATCTT 57.387 37.500 0.00 0.00 39.13 2.40
937 939 6.635755 ACTAGTTTGCTGAACCTAGATCTTC 58.364 40.000 0.00 0.00 39.13 2.87
938 940 4.837972 AGTTTGCTGAACCTAGATCTTCC 58.162 43.478 0.00 0.00 39.13 3.46
939 941 4.534103 AGTTTGCTGAACCTAGATCTTCCT 59.466 41.667 0.00 0.00 39.13 3.36
940 942 5.013599 AGTTTGCTGAACCTAGATCTTCCTT 59.986 40.000 0.00 0.00 39.13 3.36
941 943 4.478206 TGCTGAACCTAGATCTTCCTTG 57.522 45.455 0.00 0.00 0.00 3.61
942 944 3.198635 TGCTGAACCTAGATCTTCCTTGG 59.801 47.826 0.00 0.00 35.60 3.61
945 947 5.104900 GCTGAACCTAGATCTTCCTTGGTTA 60.105 44.000 0.00 0.00 46.80 2.85
1390 1393 5.724328 TCTGTGGTCTGCTCTATTTACAAG 58.276 41.667 0.00 0.00 0.00 3.16
2237 2246 0.895559 CTTCCCAAAAAGCGAGCCCT 60.896 55.000 0.00 0.00 0.00 5.19
2329 2343 2.333701 AAAAGCGGACGTGGGGACTT 62.334 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 4.234574 CGAACTAGTCATGTGCTGTGTTA 58.765 43.478 0.00 0.00 0.00 2.41
430 431 2.046988 CTGCATGTGGCTCGTCCA 60.047 61.111 0.00 0.00 45.15 4.02
491 492 9.839185 ATTACAGGGACCTACACATATTAGTAT 57.161 33.333 0.00 0.00 0.00 2.12
606 607 4.035324 CAGACGGAGCTCGATTAGTTTCTA 59.965 45.833 7.83 0.00 42.43 2.10
715 716 0.909610 TCCCCGAGACATTGGCTTCT 60.910 55.000 0.00 0.00 0.00 2.85
808 810 5.431765 GAATGAAGAATGAAGAGTGCCCTA 58.568 41.667 0.00 0.00 0.00 3.53
877 879 2.930826 AGTAACAACACCTGTGGAGG 57.069 50.000 1.91 0.00 46.21 4.30
878 880 4.602340 ACTAGTAACAACACCTGTGGAG 57.398 45.455 0.00 0.00 38.67 3.86
879 881 6.482898 TTTACTAGTAACAACACCTGTGGA 57.517 37.500 14.96 0.00 38.67 4.02
880 882 6.370718 GGATTTACTAGTAACAACACCTGTGG 59.629 42.308 14.96 0.00 38.67 4.17
881 883 6.090358 CGGATTTACTAGTAACAACACCTGTG 59.910 42.308 14.96 0.00 38.67 3.66
882 884 6.161381 CGGATTTACTAGTAACAACACCTGT 58.839 40.000 14.96 0.00 41.27 4.00
883 885 6.090358 CACGGATTTACTAGTAACAACACCTG 59.910 42.308 14.96 0.00 0.00 4.00
884 886 6.161381 CACGGATTTACTAGTAACAACACCT 58.839 40.000 14.96 3.20 0.00 4.00
885 887 5.928264 ACACGGATTTACTAGTAACAACACC 59.072 40.000 14.96 12.00 0.00 4.16
886 888 7.412137 AACACGGATTTACTAGTAACAACAC 57.588 36.000 14.96 5.30 0.00 3.32
887 889 8.436046 AAAACACGGATTTACTAGTAACAACA 57.564 30.769 14.96 1.01 0.00 3.33
888 890 9.797473 GTAAAACACGGATTTACTAGTAACAAC 57.203 33.333 14.96 9.06 39.20 3.32
889 891 9.762933 AGTAAAACACGGATTTACTAGTAACAA 57.237 29.630 14.96 2.13 46.43 2.83
896 898 8.711457 GCAAACTAGTAAAACACGGATTTACTA 58.289 33.333 19.56 19.56 46.43 1.82
898 900 7.532884 CAGCAAACTAGTAAAACACGGATTTAC 59.467 37.037 0.00 10.29 41.42 2.01
899 901 7.441760 TCAGCAAACTAGTAAAACACGGATTTA 59.558 33.333 0.00 0.00 0.00 1.40
900 902 6.261381 TCAGCAAACTAGTAAAACACGGATTT 59.739 34.615 0.00 0.00 0.00 2.17
901 903 5.761234 TCAGCAAACTAGTAAAACACGGATT 59.239 36.000 0.00 0.00 0.00 3.01
902 904 5.302360 TCAGCAAACTAGTAAAACACGGAT 58.698 37.500 0.00 0.00 0.00 4.18
903 905 4.695396 TCAGCAAACTAGTAAAACACGGA 58.305 39.130 0.00 0.00 0.00 4.69
904 906 5.202640 GTTCAGCAAACTAGTAAAACACGG 58.797 41.667 0.00 0.00 34.85 4.94
905 907 5.007332 AGGTTCAGCAAACTAGTAAAACACG 59.993 40.000 0.00 0.00 38.02 4.49
906 908 6.373186 AGGTTCAGCAAACTAGTAAAACAC 57.627 37.500 0.00 0.00 38.02 3.32
907 909 7.502696 TCTAGGTTCAGCAAACTAGTAAAACA 58.497 34.615 8.32 0.00 46.47 2.83
908 910 7.958053 TCTAGGTTCAGCAAACTAGTAAAAC 57.042 36.000 8.32 0.00 46.47 2.43
909 911 8.594550 AGATCTAGGTTCAGCAAACTAGTAAAA 58.405 33.333 8.32 0.00 46.47 1.52
910 912 8.135382 AGATCTAGGTTCAGCAAACTAGTAAA 57.865 34.615 8.32 0.00 46.47 2.01
911 913 7.719871 AGATCTAGGTTCAGCAAACTAGTAA 57.280 36.000 8.32 0.00 46.47 2.24
912 914 7.147880 GGAAGATCTAGGTTCAGCAAACTAGTA 60.148 40.741 8.32 0.00 46.47 1.82
913 915 6.351456 GGAAGATCTAGGTTCAGCAAACTAGT 60.351 42.308 8.32 0.00 46.47 2.57
915 917 5.721960 AGGAAGATCTAGGTTCAGCAAACTA 59.278 40.000 0.00 0.00 38.02 2.24
916 918 4.534103 AGGAAGATCTAGGTTCAGCAAACT 59.466 41.667 0.00 0.00 38.02 2.66
917 919 4.837972 AGGAAGATCTAGGTTCAGCAAAC 58.162 43.478 0.00 0.00 37.12 2.93
918 920 5.248640 CAAGGAAGATCTAGGTTCAGCAAA 58.751 41.667 0.00 0.00 0.00 3.68
919 921 4.323792 CCAAGGAAGATCTAGGTTCAGCAA 60.324 45.833 0.00 0.00 0.00 3.91
920 922 3.198635 CCAAGGAAGATCTAGGTTCAGCA 59.801 47.826 0.00 0.00 0.00 4.41
921 923 3.198853 ACCAAGGAAGATCTAGGTTCAGC 59.801 47.826 0.00 0.00 0.00 4.26
922 924 5.428184 AACCAAGGAAGATCTAGGTTCAG 57.572 43.478 0.00 0.00 34.47 3.02
923 925 5.783360 TGTAACCAAGGAAGATCTAGGTTCA 59.217 40.000 15.39 11.98 39.77 3.18
924 926 6.295719 TGTAACCAAGGAAGATCTAGGTTC 57.704 41.667 15.39 2.49 39.77 3.62
925 927 6.893020 ATGTAACCAAGGAAGATCTAGGTT 57.107 37.500 15.91 15.91 41.74 3.50
926 928 6.893020 AATGTAACCAAGGAAGATCTAGGT 57.107 37.500 0.00 0.00 0.00 3.08
927 929 8.581253 AAAAATGTAACCAAGGAAGATCTAGG 57.419 34.615 0.00 0.00 0.00 3.02
929 931 9.174166 GCTAAAAATGTAACCAAGGAAGATCTA 57.826 33.333 0.00 0.00 0.00 1.98
930 932 7.148239 CGCTAAAAATGTAACCAAGGAAGATCT 60.148 37.037 0.00 0.00 0.00 2.75
931 933 6.967199 CGCTAAAAATGTAACCAAGGAAGATC 59.033 38.462 0.00 0.00 0.00 2.75
932 934 6.433093 ACGCTAAAAATGTAACCAAGGAAGAT 59.567 34.615 0.00 0.00 0.00 2.40
933 935 5.766174 ACGCTAAAAATGTAACCAAGGAAGA 59.234 36.000 0.00 0.00 0.00 2.87
934 936 6.009115 ACGCTAAAAATGTAACCAAGGAAG 57.991 37.500 0.00 0.00 0.00 3.46
935 937 5.766174 AGACGCTAAAAATGTAACCAAGGAA 59.234 36.000 0.00 0.00 0.00 3.36
936 938 5.310451 AGACGCTAAAAATGTAACCAAGGA 58.690 37.500 0.00 0.00 0.00 3.36
937 939 5.180492 TGAGACGCTAAAAATGTAACCAAGG 59.820 40.000 0.00 0.00 0.00 3.61
938 940 6.236017 TGAGACGCTAAAAATGTAACCAAG 57.764 37.500 0.00 0.00 0.00 3.61
939 941 6.653320 AGATGAGACGCTAAAAATGTAACCAA 59.347 34.615 0.00 0.00 0.00 3.67
940 942 6.170506 AGATGAGACGCTAAAAATGTAACCA 58.829 36.000 0.00 0.00 0.00 3.67
941 943 6.663944 AGATGAGACGCTAAAAATGTAACC 57.336 37.500 0.00 0.00 0.00 2.85
942 944 7.965045 AGAAGATGAGACGCTAAAAATGTAAC 58.035 34.615 0.00 0.00 0.00 2.50
945 947 6.312426 CAGAGAAGATGAGACGCTAAAAATGT 59.688 38.462 0.00 0.00 0.00 2.71
1390 1393 7.022979 GGTAAAGAGAAGAGAGTACGAAAGAC 58.977 42.308 0.00 0.00 0.00 3.01
2237 2246 3.479203 CTATGCTGACCCGGGCCA 61.479 66.667 24.08 16.92 0.00 5.36


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

AutoCloner maintained by Alex Coulton.