Multiple sequence alignment - TraesCS6B01G301400

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 TraesCS6B01G301400 chr6B 100.000 3352 0 0 1 3352 539720220 539723571 0.000000e+00 6191
1 TraesCS6B01G301400 chr6B 78.365 416 74 12 185 592 49945929 49946336 4.290000e-64 255
2 TraesCS6B01G301400 chr6D 96.960 2401 73 0 952 3352 358321157 358323557 0.000000e+00 4030
3 TraesCS6B01G301400 chr6D 98.361 61 1 0 893 953 358321073 358321133 1.270000e-19 108
4 TraesCS6B01G301400 chr6A 96.454 2397 83 2 958 3352 500078003 500080399 0.000000e+00 3954
5 TraesCS6B01G301400 chr4B 84.685 888 115 12 2 889 11589180 11590046 0.000000e+00 867
6 TraesCS6B01G301400 chr7B 83.038 902 124 26 5 892 464346356 464345470 0.000000e+00 791
7 TraesCS6B01G301400 chr7B 82.793 895 136 14 2 891 586062116 586062997 0.000000e+00 784
8 TraesCS6B01G301400 chr2B 82.682 895 135 16 2 891 44266871 44265992 0.000000e+00 776
9 TraesCS6B01G301400 chr2B 84.956 678 96 5 8 683 465678619 465677946 0.000000e+00 682
10 TraesCS6B01G301400 chr2D 77.105 677 138 14 53 720 179551049 179551717 3.160000e-100 375
11 TraesCS6B01G301400 chr3B 72.097 663 155 25 52 704 65531413 65532055 4.450000e-39 172


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 TraesCS6B01G301400 chr6B 539720220 539723571 3351 False 6191 6191 100.0000 1 3352 1 chr6B.!!$F2 3351
1 TraesCS6B01G301400 chr6D 358321073 358323557 2484 False 2069 4030 97.6605 893 3352 2 chr6D.!!$F1 2459
2 TraesCS6B01G301400 chr6A 500078003 500080399 2396 False 3954 3954 96.4540 958 3352 1 chr6A.!!$F1 2394
3 TraesCS6B01G301400 chr4B 11589180 11590046 866 False 867 867 84.6850 2 889 1 chr4B.!!$F1 887
4 TraesCS6B01G301400 chr7B 464345470 464346356 886 True 791 791 83.0380 5 892 1 chr7B.!!$R1 887
5 TraesCS6B01G301400 chr7B 586062116 586062997 881 False 784 784 82.7930 2 891 1 chr7B.!!$F1 889
6 TraesCS6B01G301400 chr2B 44265992 44266871 879 True 776 776 82.6820 2 891 1 chr2B.!!$R1 889
7 TraesCS6B01G301400 chr2B 465677946 465678619 673 True 682 682 84.9560 8 683 1 chr2B.!!$R2 675
8 TraesCS6B01G301400 chr2D 179551049 179551717 668 False 375 375 77.1050 53 720 1 chr2D.!!$F1 667

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
704 715 0.246635 TAGGGCAGCGTGAAGAAGAC 59.753 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2658 2696 0.035056 CCTCTTCCAATTCACCGGCT 60.035 55.0 0.0 0.0 0.0 5.52 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
32 33 2.443255 CCATGGCTACCTTCCCATTACT 59.557 50.000 0.00 0.00 39.76 2.24
36 37 1.070289 GCTACCTTCCCATTACTCCCG 59.930 57.143 0.00 0.00 0.00 5.14
72 73 2.478292 TCCTCCTCATCCAGGGTAAAC 58.522 52.381 0.00 0.00 43.67 2.01
93 94 2.291800 CCCCCTCATCAATGGTTTGTCT 60.292 50.000 0.00 0.00 34.32 3.41
104 105 3.281727 TGGTTTGTCTATCTGCATCCC 57.718 47.619 0.00 0.00 0.00 3.85
168 169 1.134098 CCAGTATCCGCCTCCACAAAT 60.134 52.381 0.00 0.00 0.00 2.32
183 184 9.073475 GCCTCCACAAATACACCAATAATATTA 57.927 33.333 0.00 0.00 0.00 0.98
261 262 7.797617 ACCCTAACCTAGATTGGGATATTGTTA 59.202 37.037 17.49 2.21 40.23 2.41
360 361 1.209275 CCTCGATCGCCTTACGCTTG 61.209 60.000 11.09 0.00 43.23 4.01
438 439 1.279496 TCCCCTTGATCAGACACCAG 58.721 55.000 0.00 0.00 0.00 4.00
525 526 3.445518 CTGCATCGCCGCCTCCTTA 62.446 63.158 0.00 0.00 0.00 2.69
588 589 1.203013 TCCTCCTCCGACAACTTCAGA 60.203 52.381 0.00 0.00 0.00 3.27
609 610 2.359354 TTCAACATCCCGGCCACG 60.359 61.111 2.24 0.00 40.55 4.94
627 628 4.100084 CCCTCCAGCGCCATGACA 62.100 66.667 2.29 0.00 0.00 3.58
703 714 0.532573 CTAGGGCAGCGTGAAGAAGA 59.467 55.000 0.00 0.00 0.00 2.87
704 715 0.246635 TAGGGCAGCGTGAAGAAGAC 59.753 55.000 0.00 0.00 0.00 3.01
715 726 3.133003 CGTGAAGAAGACCTATGGTGGAT 59.867 47.826 0.00 0.00 35.25 3.41
720 731 2.587060 AGACCTATGGTGGATGGGAA 57.413 50.000 0.00 0.00 36.18 3.97
723 734 3.395941 AGACCTATGGTGGATGGGAATTC 59.604 47.826 0.00 0.00 36.18 2.17
727 738 2.346766 TGGTGGATGGGAATTCGATG 57.653 50.000 0.00 0.00 0.00 3.84
733 744 2.154462 GATGGGAATTCGATGCGGATT 58.846 47.619 0.00 0.00 37.82 3.01
734 745 2.051334 TGGGAATTCGATGCGGATTT 57.949 45.000 0.00 0.00 34.99 2.17
735 746 1.675483 TGGGAATTCGATGCGGATTTG 59.325 47.619 0.00 0.00 34.99 2.32
736 747 1.001378 GGGAATTCGATGCGGATTTGG 60.001 52.381 0.00 0.00 34.99 3.28
737 748 1.676006 GGAATTCGATGCGGATTTGGT 59.324 47.619 0.00 0.00 34.99 3.67
738 749 2.099098 GGAATTCGATGCGGATTTGGTT 59.901 45.455 0.00 0.00 34.99 3.67
743 754 0.682855 GATGCGGATTTGGTTGGGGA 60.683 55.000 0.00 0.00 0.00 4.81
744 755 0.252012 ATGCGGATTTGGTTGGGGAA 60.252 50.000 0.00 0.00 0.00 3.97
746 757 1.880186 CGGATTTGGTTGGGGAACG 59.120 57.895 0.00 0.00 0.00 3.95
793 804 4.530857 AAAGGCGGCGGATCTCGG 62.531 66.667 9.78 0.00 39.69 4.63
806 817 2.376109 GATCTCGGTGAACCCTAGACA 58.624 52.381 0.00 0.00 30.26 3.41
808 819 1.353358 TCTCGGTGAACCCTAGACAGA 59.647 52.381 0.00 0.00 0.00 3.41
809 820 2.168496 CTCGGTGAACCCTAGACAGAA 58.832 52.381 0.00 0.00 0.00 3.02
810 821 2.164624 CTCGGTGAACCCTAGACAGAAG 59.835 54.545 0.00 0.00 0.00 2.85
812 823 2.561419 CGGTGAACCCTAGACAGAAGAA 59.439 50.000 0.00 0.00 0.00 2.52
815 826 4.040584 GGTGAACCCTAGACAGAAGAAACT 59.959 45.833 0.00 0.00 0.00 2.66
829 840 1.730593 GAAACTCGGACGTGATCGCG 61.731 60.000 26.14 26.14 41.18 5.87
830 841 4.831307 ACTCGGACGTGATCGCGC 62.831 66.667 27.51 19.23 41.18 6.86
831 842 4.538283 CTCGGACGTGATCGCGCT 62.538 66.667 27.51 15.10 41.18 5.92
848 859 4.207281 TCGCAATCGCCTCCGGAG 62.207 66.667 25.36 25.36 35.26 4.63
878 890 1.147600 GACACCAACCGTCACCCTT 59.852 57.895 0.00 0.00 33.43 3.95
912 924 0.609131 ATGAGGCCAGGTTTGGTTCG 60.609 55.000 5.01 0.00 46.80 3.95
1122 1160 1.307343 CCTCCACTCCTCCCACCAT 60.307 63.158 0.00 0.00 0.00 3.55
1584 1622 1.619654 TTGCAAGGAGTGTGATTGGG 58.380 50.000 0.00 0.00 0.00 4.12
1587 1625 0.883833 CAAGGAGTGTGATTGGGCAC 59.116 55.000 0.00 0.00 39.22 5.01
1588 1626 0.478072 AAGGAGTGTGATTGGGCACA 59.522 50.000 0.00 0.00 45.80 4.57
1652 1690 2.045926 GGCGCAGTTGAGGGATGT 60.046 61.111 10.83 0.00 0.00 3.06
1717 1755 4.348168 ACTTGGAGTATGACTTGGTTCTGT 59.652 41.667 0.00 0.00 0.00 3.41
1754 1792 3.372025 GGGCTTTACATGAGGATTGGAGT 60.372 47.826 0.00 0.00 0.00 3.85
1776 1814 3.411446 TGTACAATCTGCAAGGAGGTTG 58.589 45.455 12.26 12.26 39.41 3.77
1792 1830 1.401905 GGTTGTTCGAGGGAATGATGC 59.598 52.381 0.00 0.00 34.05 3.91
1886 1924 8.725405 TTGAGCGTATATAAGAAAATGGTTGA 57.275 30.769 0.00 0.00 0.00 3.18
1914 1952 3.490348 AGTGAAGCCAAATGCAGTTACT 58.510 40.909 0.00 0.00 44.83 2.24
1917 1955 3.636300 TGAAGCCAAATGCAGTTACTGTT 59.364 39.130 14.23 0.00 44.83 3.16
1941 1979 0.819259 GTGTTCTGCAGGCCTGTTCA 60.819 55.000 32.81 21.90 0.00 3.18
2312 2350 5.995282 TGGTTAACACTGGTTTCTGTGATAG 59.005 40.000 8.10 0.00 42.95 2.08
2315 2353 4.543590 ACACTGGTTTCTGTGATAGGAG 57.456 45.455 9.71 0.00 42.95 3.69
2340 2378 2.641559 GCAGCTGCACTTGTGGAC 59.358 61.111 33.36 0.00 41.59 4.02
2620 2658 5.934043 CGAGTCTATGGAATCATGCCAAATA 59.066 40.000 7.32 0.00 39.21 1.40
2658 2696 1.198094 TGGTTGATCTCCTTGGCCGA 61.198 55.000 0.00 0.00 0.00 5.54
2747 2785 2.522436 TGCCTTGCTTGCTGCCTT 60.522 55.556 0.00 0.00 42.00 4.35
2748 2786 2.135581 TGCCTTGCTTGCTGCCTTT 61.136 52.632 0.00 0.00 42.00 3.11
2829 2867 3.384168 TCCTGACCATGTTGGCTACTAT 58.616 45.455 0.01 0.00 42.67 2.12
2950 2988 5.494632 TTGCAGTGCAATAGAGATCAATG 57.505 39.130 26.36 0.00 43.99 2.82
2988 3026 1.081833 AGCTGGGGAGAGGTCACAT 59.918 57.895 0.00 0.00 0.00 3.21
3039 3077 3.385433 TCTGGGAGTTGTCACGAAAGTTA 59.615 43.478 0.00 0.00 46.40 2.24
3168 3206 7.713942 GGTGAGTTCCTAGAAGAAAGTAACAAA 59.286 37.037 0.00 0.00 0.00 2.83
3289 3327 7.097192 CACTTCCAAGAAGTGTATAGCTGTAA 58.903 38.462 23.22 0.00 41.90 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.613260 TAGCCATGGTGAGTGGTGAC 59.387 55.000 14.67 0.00 39.01 3.67
36 37 1.612739 GGATATCGGGGGAGGGGAC 60.613 68.421 0.00 0.00 0.00 4.46
48 49 3.197927 ACCCTGGATGAGGAGGATATC 57.802 52.381 0.00 0.00 46.33 1.63
50 51 4.232091 GTTTACCCTGGATGAGGAGGATA 58.768 47.826 0.00 0.00 46.33 2.59
72 73 2.102578 GACAAACCATTGATGAGGGGG 58.897 52.381 0.00 0.00 38.94 5.40
93 94 4.101585 AGAGTCAAAATCGGGATGCAGATA 59.898 41.667 0.00 0.00 0.00 1.98
104 105 7.240414 GGAAGATTCCTTAGAGTCAAAATCG 57.760 40.000 4.29 0.00 44.11 3.34
132 133 0.329261 CTGGACCAGATGGGAAAGCA 59.671 55.000 17.22 0.00 41.15 3.91
168 169 9.787435 GAGGACATTGGTAATATTATTGGTGTA 57.213 33.333 0.00 0.00 0.00 2.90
183 184 2.045926 GCCGCAGAGGACATTGGT 60.046 61.111 0.00 0.00 45.00 3.67
261 262 2.406559 AGGCCAGAAGACTATGCTCAT 58.593 47.619 5.01 0.00 0.00 2.90
360 361 1.671379 GTTCCACCAAGAGTCGGGC 60.671 63.158 4.03 0.00 0.00 6.13
405 406 0.324738 AGGGGATCGACTGCAGAGAA 60.325 55.000 23.35 4.83 0.00 2.87
430 431 0.109342 CTTGGCAAGGTCTGGTGTCT 59.891 55.000 19.55 0.00 0.00 3.41
543 544 6.273495 AGAAGAAGGGAGTCAAGGTTAGAATT 59.727 38.462 0.00 0.00 0.00 2.17
588 589 2.355115 GCCGGGATGTTGAAGGGT 59.645 61.111 2.18 0.00 0.00 4.34
643 649 1.717077 CTATACCTAGGAGGGGCTGGA 59.283 57.143 17.98 0.00 40.58 3.86
697 708 2.780010 CCCATCCACCATAGGTCTTCTT 59.220 50.000 0.00 0.00 31.02 2.52
703 714 2.106511 CGAATTCCCATCCACCATAGGT 59.893 50.000 0.00 0.00 35.62 3.08
704 715 2.371841 TCGAATTCCCATCCACCATAGG 59.628 50.000 0.00 0.00 0.00 2.57
715 726 1.675483 CAAATCCGCATCGAATTCCCA 59.325 47.619 0.00 0.00 0.00 4.37
720 731 1.405105 CCAACCAAATCCGCATCGAAT 59.595 47.619 0.00 0.00 0.00 3.34
723 734 1.433064 CCCAACCAAATCCGCATCG 59.567 57.895 0.00 0.00 0.00 3.84
727 738 1.589630 GTTCCCCAACCAAATCCGC 59.410 57.895 0.00 0.00 0.00 5.54
733 744 2.902846 CGTGCGTTCCCCAACCAA 60.903 61.111 0.00 0.00 0.00 3.67
734 745 4.939368 CCGTGCGTTCCCCAACCA 62.939 66.667 0.00 0.00 0.00 3.67
775 786 3.264897 CGAGATCCGCCGCCTTTG 61.265 66.667 0.00 0.00 0.00 2.77
793 804 5.216614 AGTTTCTTCTGTCTAGGGTTCAC 57.783 43.478 0.00 0.00 0.00 3.18
794 805 4.022242 CGAGTTTCTTCTGTCTAGGGTTCA 60.022 45.833 0.00 0.00 0.00 3.18
806 817 2.414293 CGATCACGTCCGAGTTTCTTCT 60.414 50.000 0.00 0.00 34.56 2.85
808 819 1.978542 CGATCACGTCCGAGTTTCTT 58.021 50.000 0.00 0.00 34.56 2.52
809 820 0.456312 GCGATCACGTCCGAGTTTCT 60.456 55.000 5.81 0.00 41.98 2.52
810 821 1.730593 CGCGATCACGTCCGAGTTTC 61.731 60.000 0.00 0.00 41.98 2.78
812 823 2.202440 CGCGATCACGTCCGAGTT 60.202 61.111 0.00 0.00 41.98 3.01
815 826 4.531912 GAGCGCGATCACGTCCGA 62.532 66.667 21.13 0.00 41.98 4.55
848 859 1.804748 GTTGGTGTCTGGTTCGGAATC 59.195 52.381 0.00 0.00 0.00 2.52
851 863 1.448497 GGTTGGTGTCTGGTTCGGA 59.552 57.895 0.00 0.00 0.00 4.55
855 867 0.463116 GTGACGGTTGGTGTCTGGTT 60.463 55.000 0.00 0.00 37.26 3.67
858 870 1.597027 GGGTGACGGTTGGTGTCTG 60.597 63.158 0.00 0.00 37.26 3.51
862 874 1.959226 CGAAGGGTGACGGTTGGTG 60.959 63.158 0.00 0.00 0.00 4.17
863 875 2.424302 CGAAGGGTGACGGTTGGT 59.576 61.111 0.00 0.00 0.00 3.67
912 924 0.956902 TTTCCGGCGCTTTTCTACCC 60.957 55.000 7.64 0.00 0.00 3.69
1122 1160 1.406898 GCGAGGACATGAGATGTGAGA 59.593 52.381 0.00 0.00 45.03 3.27
1202 1240 2.751436 GGAGCGCATTGGCAAGGA 60.751 61.111 17.10 0.00 41.24 3.36
1368 1406 4.271816 CAGGATCGGACGGCGAGG 62.272 72.222 16.62 1.48 0.00 4.63
1584 1622 0.166814 GACTCGGCATGAAACTGTGC 59.833 55.000 0.00 0.00 40.55 4.57
1587 1625 1.081892 CTGGACTCGGCATGAAACTG 58.918 55.000 0.00 0.00 0.00 3.16
1588 1626 0.687354 ACTGGACTCGGCATGAAACT 59.313 50.000 0.00 0.00 0.00 2.66
1652 1690 3.338250 AGGCCTGCCCATTTCGGA 61.338 61.111 3.11 0.00 36.56 4.55
1717 1755 5.714333 TGTAAAGCCCAAGAATAGCATTCAA 59.286 36.000 10.26 0.00 0.00 2.69
1754 1792 3.788227 ACCTCCTTGCAGATTGTACAA 57.212 42.857 11.41 11.41 0.00 2.41
1776 1814 2.159043 TCTCTGCATCATTCCCTCGAAC 60.159 50.000 0.00 0.00 0.00 3.95
1792 1830 1.403382 CCATGTGACCACGTCTCTCTG 60.403 57.143 0.00 0.00 33.15 3.35
1841 1879 1.953559 TGCTTCAGAGTTGTGTCCAC 58.046 50.000 0.00 0.00 0.00 4.02
1850 1888 3.533606 ATACGCTCAATGCTTCAGAGT 57.466 42.857 0.00 0.00 40.11 3.24
1886 1924 0.407139 ATTTGGCTTCACTCCTGCCT 59.593 50.000 0.00 0.00 46.23 4.75
1914 1952 1.667236 CCTGCAGAACACTCACAACA 58.333 50.000 17.39 0.00 0.00 3.33
1917 1955 1.227943 GGCCTGCAGAACACTCACA 60.228 57.895 17.39 0.00 0.00 3.58
1941 1979 3.777106 TCTTCAACATCCAGAGCAAGT 57.223 42.857 0.00 0.00 0.00 3.16
1981 2019 2.159653 CGCAACCTATCTTGACAGCAAC 60.160 50.000 0.00 0.00 0.00 4.17
2312 2350 2.924105 GCAGCTGCCACAAACCTCC 61.924 63.158 28.76 0.00 34.31 4.30
2315 2353 2.019897 AAGTGCAGCTGCCACAAACC 62.020 55.000 34.64 13.74 41.18 3.27
2340 2378 8.028938 CCCAAGTTTCCACATTTAGAATACAAG 58.971 37.037 0.00 0.00 0.00 3.16
2620 2658 0.826715 ATGGCACTACGATGCTCTGT 59.173 50.000 10.09 0.00 45.38 3.41
2658 2696 0.035056 CCTCTTCCAATTCACCGGCT 60.035 55.000 0.00 0.00 0.00 5.52
2671 2709 1.813337 GGAGCTTCGCTGCCTCTTC 60.813 63.158 0.00 0.00 41.12 2.87
2747 2785 2.953648 TCTGTGTCACGGTGTTCTCTAA 59.046 45.455 11.59 0.00 0.00 2.10
2748 2786 2.552743 CTCTGTGTCACGGTGTTCTCTA 59.447 50.000 11.59 0.00 0.00 2.43
2950 2988 2.921121 CTGTGAATGTGTGCATTGCATC 59.079 45.455 15.49 11.58 44.61 3.91
2988 3026 6.197903 TGTAGAGATCTTCTCCCAATCTTGA 58.802 40.000 0.00 0.00 44.42 3.02
3039 3077 5.644188 TGAAAGAAACAATCATCCCCTCTT 58.356 37.500 0.00 0.00 0.00 2.85
3289 3327 6.493166 TGACTGATTGTTAAATGAAGGGGAT 58.507 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.