Multiple sequence alignment - TraesCS6B01G454100

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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 TraesCS6B01G454100 chr6B 100.000 2528 0 0 1 2528 712026736 712024209 0.000000e+00 4669
1 TraesCS6B01G454100 chr6B 96.516 775 23 2 1 771 712038893 712038119 0.000000e+00 1279
2 TraesCS6B01G454100 chr6B 95.914 465 19 0 1510 1974 710883750 710884214 0.000000e+00 754
3 TraesCS6B01G454100 chr6D 97.316 1975 33 3 1 1974 471958895 471960850 0.000000e+00 3336
4 TraesCS6B01G454100 chr6D 98.955 861 9 0 1114 1974 472010199 472011059 0.000000e+00 1541
5 TraesCS6B01G454100 chr6D 96.993 898 24 3 1 897 472009309 472010204 0.000000e+00 1506
6 TraesCS6B01G454100 chr6D 97.280 772 16 3 1 768 471946788 471947558 0.000000e+00 1304
7 TraesCS6B01G454100 chr6D 97.021 772 19 2 1 768 471994917 471995688 0.000000e+00 1295
8 TraesCS6B01G454100 chr6D 95.271 571 14 6 1969 2528 428348523 428349091 0.000000e+00 893
9 TraesCS6B01G454100 chr6D 91.921 557 32 9 1975 2528 333080031 333080577 0.000000e+00 767
10 TraesCS6B01G454100 chr6D 95.914 465 19 0 1510 1974 377211671 377212135 0.000000e+00 754
11 TraesCS6B01G454100 chr6D 90.714 560 37 9 1975 2528 69204284 69203734 0.000000e+00 732
12 TraesCS6B01G454100 chr7A 90.883 702 56 4 810 1511 65946287 65946980 0.000000e+00 935
13 TraesCS6B01G454100 chr3B 89.918 734 58 9 783 1511 417719031 417719753 0.000000e+00 931
14 TraesCS6B01G454100 chr7D 89.481 751 55 13 767 1511 72149814 72150546 0.000000e+00 928
15 TraesCS6B01G454100 chr7D 85.455 605 76 11 1 600 83900532 83901129 9.930000e-174 619
16 TraesCS6B01G454100 chr4A 89.452 730 60 9 783 1511 535877875 535878588 0.000000e+00 905
17 TraesCS6B01G454100 chr4D 95.079 569 12 5 1975 2528 64572948 64572381 0.000000e+00 881
18 TraesCS6B01G454100 chr4D 89.347 704 64 6 809 1511 166923052 166922359 0.000000e+00 874
19 TraesCS6B01G454100 chr4D 91.829 563 32 9 1978 2528 236363680 236363120 0.000000e+00 773
20 TraesCS6B01G454100 chr4D 96.129 465 18 0 1510 1974 450519698 450520162 0.000000e+00 760
21 TraesCS6B01G454100 chr4D 96.129 465 18 0 1510 1974 470197172 470196708 0.000000e+00 760
22 TraesCS6B01G454100 chr4D 89.894 564 43 12 1975 2528 2916291 2915732 0.000000e+00 713
23 TraesCS6B01G454100 chr4D 89.027 565 44 18 1975 2528 51335407 51334850 0.000000e+00 684
24 TraesCS6B01G454100 chr4D 86.161 607 75 8 1 603 360570533 360569932 0.000000e+00 647
25 TraesCS6B01G454100 chr4D 85.406 603 80 8 1 600 392791472 392792069 9.930000e-174 619
26 TraesCS6B01G454100 chr1D 93.939 561 34 0 951 1511 414934380 414933820 0.000000e+00 848
27 TraesCS6B01G454100 chr1D 93.673 569 20 6 1975 2528 227624865 227625432 0.000000e+00 837
28 TraesCS6B01G454100 chr1D 95.484 465 21 0 1510 1974 446418774 446419238 0.000000e+00 743
29 TraesCS6B01G454100 chr1A 87.978 732 62 13 783 1511 403723997 403723289 0.000000e+00 841
30 TraesCS6B01G454100 chr2B 86.991 761 69 10 769 1511 15224690 15223942 0.000000e+00 830
31 TraesCS6B01G454100 chr3D 91.697 554 38 6 1975 2525 85424428 85424976 0.000000e+00 761
32 TraesCS6B01G454100 chr3D 96.129 465 17 1 1510 1974 116061003 116061466 0.000000e+00 758
33 TraesCS6B01G454100 chr3D 95.484 465 21 0 1510 1974 446921890 446922354 0.000000e+00 743
34 TraesCS6B01G454100 chr5D 96.129 465 18 0 1510 1974 348340709 348341173 0.000000e+00 760
35 TraesCS6B01G454100 chr2D 90.664 557 39 9 1975 2528 317764834 317765380 0.000000e+00 728
36 TraesCS6B01G454100 chr2D 92.141 509 16 11 2027 2528 484103123 484102632 0.000000e+00 697
37 TraesCS6B01G454100 chr5B 86.050 595 71 10 1 592 191121077 191120492 1.650000e-176 628


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 TraesCS6B01G454100 chr6B 712024209 712026736 2527 True 4669.0 4669 100.000 1 2528 1 chr6B.!!$R1 2527
1 TraesCS6B01G454100 chr6B 712038119 712038893 774 True 1279.0 1279 96.516 1 771 1 chr6B.!!$R2 770
2 TraesCS6B01G454100 chr6D 471958895 471960850 1955 False 3336.0 3336 97.316 1 1974 1 chr6D.!!$F5 1973
3 TraesCS6B01G454100 chr6D 472009309 472011059 1750 False 1523.5 1541 97.974 1 1974 2 chr6D.!!$F7 1973
4 TraesCS6B01G454100 chr6D 471946788 471947558 770 False 1304.0 1304 97.280 1 768 1 chr6D.!!$F4 767
5 TraesCS6B01G454100 chr6D 471994917 471995688 771 False 1295.0 1295 97.021 1 768 1 chr6D.!!$F6 767
6 TraesCS6B01G454100 chr6D 428348523 428349091 568 False 893.0 893 95.271 1969 2528 1 chr6D.!!$F3 559
7 TraesCS6B01G454100 chr6D 333080031 333080577 546 False 767.0 767 91.921 1975 2528 1 chr6D.!!$F1 553
8 TraesCS6B01G454100 chr6D 69203734 69204284 550 True 732.0 732 90.714 1975 2528 1 chr6D.!!$R1 553
9 TraesCS6B01G454100 chr7A 65946287 65946980 693 False 935.0 935 90.883 810 1511 1 chr7A.!!$F1 701
10 TraesCS6B01G454100 chr3B 417719031 417719753 722 False 931.0 931 89.918 783 1511 1 chr3B.!!$F1 728
11 TraesCS6B01G454100 chr7D 72149814 72150546 732 False 928.0 928 89.481 767 1511 1 chr7D.!!$F1 744
12 TraesCS6B01G454100 chr7D 83900532 83901129 597 False 619.0 619 85.455 1 600 1 chr7D.!!$F2 599
13 TraesCS6B01G454100 chr4A 535877875 535878588 713 False 905.0 905 89.452 783 1511 1 chr4A.!!$F1 728
14 TraesCS6B01G454100 chr4D 64572381 64572948 567 True 881.0 881 95.079 1975 2528 1 chr4D.!!$R3 553
15 TraesCS6B01G454100 chr4D 166922359 166923052 693 True 874.0 874 89.347 809 1511 1 chr4D.!!$R4 702
16 TraesCS6B01G454100 chr4D 236363120 236363680 560 True 773.0 773 91.829 1978 2528 1 chr4D.!!$R5 550
17 TraesCS6B01G454100 chr4D 2915732 2916291 559 True 713.0 713 89.894 1975 2528 1 chr4D.!!$R1 553
18 TraesCS6B01G454100 chr4D 51334850 51335407 557 True 684.0 684 89.027 1975 2528 1 chr4D.!!$R2 553
19 TraesCS6B01G454100 chr4D 360569932 360570533 601 True 647.0 647 86.161 1 603 1 chr4D.!!$R6 602
20 TraesCS6B01G454100 chr4D 392791472 392792069 597 False 619.0 619 85.406 1 600 1 chr4D.!!$F1 599
21 TraesCS6B01G454100 chr1D 414933820 414934380 560 True 848.0 848 93.939 951 1511 1 chr1D.!!$R1 560
22 TraesCS6B01G454100 chr1D 227624865 227625432 567 False 837.0 837 93.673 1975 2528 1 chr1D.!!$F1 553
23 TraesCS6B01G454100 chr1A 403723289 403723997 708 True 841.0 841 87.978 783 1511 1 chr1A.!!$R1 728
24 TraesCS6B01G454100 chr2B 15223942 15224690 748 True 830.0 830 86.991 769 1511 1 chr2B.!!$R1 742
25 TraesCS6B01G454100 chr3D 85424428 85424976 548 False 761.0 761 91.697 1975 2525 1 chr3D.!!$F1 550
26 TraesCS6B01G454100 chr2D 317764834 317765380 546 False 728.0 728 90.664 1975 2528 1 chr2D.!!$F1 553
27 TraesCS6B01G454100 chr5B 191120492 191121077 585 True 628.0 628 86.050 1 592 1 chr5B.!!$R1 591

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
149 153 0.548989 ATAAATAGCCACCCGCACCA 59.451 50.0 0.0 0.0 41.38 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2140 0.620556 GATGCACTCCTTTCCCCTCA 59.379 55.0 0.0 0.0 0.0 3.86 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
149 153 0.548989 ATAAATAGCCACCCGCACCA 59.451 50.000 0.00 0.00 41.38 4.17
257 261 5.045578 CCAATCAAGAGAAAACCCCTAGAGA 60.046 44.000 0.00 0.00 0.00 3.10
268 272 6.809976 AAACCCCTAGAGACGAAGAATTAT 57.190 37.500 0.00 0.00 0.00 1.28
345 349 3.582998 AGAGCTGCAGACTCTCTAGAT 57.417 47.619 25.57 10.54 40.52 1.98
662 669 9.860898 GATATATCTTGTTGCTTGTTTTCCTTT 57.139 29.630 5.42 0.00 0.00 3.11
768 782 5.356190 TGGTAGACATACTTCGTTCCTACAG 59.644 44.000 0.00 0.00 32.12 2.74
769 783 5.356470 GGTAGACATACTTCGTTCCTACAGT 59.644 44.000 0.00 0.00 32.12 3.55
770 784 5.979288 AGACATACTTCGTTCCTACAGTT 57.021 39.130 0.00 0.00 0.00 3.16
771 785 7.066284 GGTAGACATACTTCGTTCCTACAGTTA 59.934 40.741 0.00 0.00 32.12 2.24
772 786 7.642082 AGACATACTTCGTTCCTACAGTTAT 57.358 36.000 0.00 0.00 0.00 1.89
773 787 8.064336 AGACATACTTCGTTCCTACAGTTATT 57.936 34.615 0.00 0.00 0.00 1.40
774 788 7.974501 AGACATACTTCGTTCCTACAGTTATTG 59.025 37.037 0.00 0.00 0.00 1.90
775 789 7.609056 ACATACTTCGTTCCTACAGTTATTGT 58.391 34.615 0.00 0.00 43.96 2.71
776 790 8.092687 ACATACTTCGTTCCTACAGTTATTGTT 58.907 33.333 0.00 0.00 41.29 2.83
777 791 9.577110 CATACTTCGTTCCTACAGTTATTGTTA 57.423 33.333 0.00 0.00 41.29 2.41
778 792 9.798994 ATACTTCGTTCCTACAGTTATTGTTAG 57.201 33.333 0.00 0.00 41.29 2.34
779 793 7.095270 ACTTCGTTCCTACAGTTATTGTTAGG 58.905 38.462 0.00 0.00 41.29 2.69
797 811 6.761518 TGTTAGGGTTAGGGTTAGGGTTATA 58.238 40.000 0.00 0.00 0.00 0.98
800 814 5.222086 AGGGTTAGGGTTAGGGTTATAGTG 58.778 45.833 0.00 0.00 0.00 2.74
801 815 4.349048 GGGTTAGGGTTAGGGTTATAGTGG 59.651 50.000 0.00 0.00 0.00 4.00
802 816 4.971282 GGTTAGGGTTAGGGTTATAGTGGT 59.029 45.833 0.00 0.00 0.00 4.16
803 817 5.429762 GGTTAGGGTTAGGGTTATAGTGGTT 59.570 44.000 0.00 0.00 0.00 3.67
804 818 6.615316 GGTTAGGGTTAGGGTTATAGTGGTTA 59.385 42.308 0.00 0.00 0.00 2.85
805 819 7.127186 GGTTAGGGTTAGGGTTATAGTGGTTAA 59.873 40.741 0.00 0.00 0.00 2.01
806 820 8.548025 GTTAGGGTTAGGGTTATAGTGGTTAAA 58.452 37.037 0.00 0.00 0.00 1.52
807 821 7.776291 AGGGTTAGGGTTATAGTGGTTAAAT 57.224 36.000 0.00 0.00 0.00 1.40
830 844 8.874743 AATTAGGGGTTAGTGTTAGGGTTATA 57.125 34.615 0.00 0.00 0.00 0.98
835 855 8.076251 AGGGGTTAGTGTTAGGGTTATAGTTAT 58.924 37.037 0.00 0.00 0.00 1.89
838 864 7.658982 GGTTAGTGTTAGGGTTATAGTTATGGC 59.341 40.741 0.00 0.00 0.00 4.40
1085 1171 1.847088 AGGGGAAGAGGCTATGGTTTC 59.153 52.381 0.00 0.00 0.00 2.78
1126 1212 9.875675 GATTTGATGATCTTATAGTGAAAGTGC 57.124 33.333 0.00 0.00 0.00 4.40
1222 1309 4.423625 AAGTCCCGATTAAAGGATCTGG 57.576 45.455 2.25 0.00 33.88 3.86
1403 1497 7.200434 AGGTGTATGTCTCCAATTGTTCTAT 57.800 36.000 4.43 0.00 32.63 1.98
1415 1509 5.469479 CAATTGTTCTATCCAACCACCAAC 58.531 41.667 0.00 0.00 0.00 3.77
1918 2012 4.700213 CCGGATAAAGAAAAGTGGTCACAT 59.300 41.667 0.00 0.00 0.00 3.21
1991 2085 2.799126 ATTGTTGGGGATCGTAGCAA 57.201 45.000 0.00 0.00 0.00 3.91
2126 2221 0.102481 CGGGGTTGATGGAGTCGTAG 59.898 60.000 0.00 0.00 0.00 3.51
2297 2394 0.032515 TGGAAGTAGCGGGGATCTCA 60.033 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 153 2.555547 GCAGCCACCGACAAAAGCT 61.556 57.895 0.00 0.00 0.00 3.74
257 261 7.497595 TGCTCAACCACTATATAATTCTTCGT 58.502 34.615 0.00 0.00 0.00 3.85
268 272 4.030216 TCCAGTGATGCTCAACCACTATA 58.970 43.478 0.00 0.00 38.93 1.31
345 349 4.782691 TCTGAGGAAATTGACACCTATCCA 59.217 41.667 0.00 0.00 33.89 3.41
662 669 2.936498 GCAGCGGAAATAAACTAGAGCA 59.064 45.455 0.00 0.00 0.00 4.26
768 782 6.069440 ACCCTAACCCTAACCCTAACAATAAC 60.069 42.308 0.00 0.00 0.00 1.89
769 783 6.037949 ACCCTAACCCTAACCCTAACAATAA 58.962 40.000 0.00 0.00 0.00 1.40
770 784 5.612813 ACCCTAACCCTAACCCTAACAATA 58.387 41.667 0.00 0.00 0.00 1.90
771 785 4.451309 ACCCTAACCCTAACCCTAACAAT 58.549 43.478 0.00 0.00 0.00 2.71
772 786 3.885669 ACCCTAACCCTAACCCTAACAA 58.114 45.455 0.00 0.00 0.00 2.83
773 787 3.583296 ACCCTAACCCTAACCCTAACA 57.417 47.619 0.00 0.00 0.00 2.41
774 788 6.846505 ACTATAACCCTAACCCTAACCCTAAC 59.153 42.308 0.00 0.00 0.00 2.34
775 789 6.845975 CACTATAACCCTAACCCTAACCCTAA 59.154 42.308 0.00 0.00 0.00 2.69
776 790 6.384603 CACTATAACCCTAACCCTAACCCTA 58.615 44.000 0.00 0.00 0.00 3.53
777 791 5.222086 CACTATAACCCTAACCCTAACCCT 58.778 45.833 0.00 0.00 0.00 4.34
778 792 4.349048 CCACTATAACCCTAACCCTAACCC 59.651 50.000 0.00 0.00 0.00 4.11
779 793 4.971282 ACCACTATAACCCTAACCCTAACC 59.029 45.833 0.00 0.00 0.00 2.85
797 811 6.458630 ACACTAACCCCTAATTTAACCACT 57.541 37.500 0.00 0.00 0.00 4.00
800 814 6.830324 CCCTAACACTAACCCCTAATTTAACC 59.170 42.308 0.00 0.00 0.00 2.85
801 815 7.405292 ACCCTAACACTAACCCCTAATTTAAC 58.595 38.462 0.00 0.00 0.00 2.01
802 816 7.587375 ACCCTAACACTAACCCCTAATTTAA 57.413 36.000 0.00 0.00 0.00 1.52
803 817 7.587375 AACCCTAACACTAACCCCTAATTTA 57.413 36.000 0.00 0.00 0.00 1.40
804 818 6.473429 AACCCTAACACTAACCCCTAATTT 57.527 37.500 0.00 0.00 0.00 1.82
805 819 7.776291 ATAACCCTAACACTAACCCCTAATT 57.224 36.000 0.00 0.00 0.00 1.40
806 820 8.076251 ACTATAACCCTAACACTAACCCCTAAT 58.924 37.037 0.00 0.00 0.00 1.73
807 821 7.430007 ACTATAACCCTAACACTAACCCCTAA 58.570 38.462 0.00 0.00 0.00 2.69
830 844 6.729569 CCCTAACCCTAACTATAGCCATAACT 59.270 42.308 0.00 0.00 0.00 2.24
835 855 4.564616 ACCCTAACCCTAACTATAGCCA 57.435 45.455 0.00 0.00 0.00 4.75
838 864 6.628182 ACCCTAACCCTAACCCTAACTATAG 58.372 44.000 0.00 0.00 0.00 1.31
1085 1171 5.471116 TCATCAAATCTTGGACTTGTGTCAG 59.529 40.000 0.00 0.00 44.61 3.51
1126 1212 3.616821 TCATTCCAATGTAAGACGCTTCG 59.383 43.478 0.00 0.00 37.65 3.79
1222 1309 0.971959 TGCAATTGGGAGGTGATGGC 60.972 55.000 7.72 0.00 0.00 4.40
1403 1497 0.847373 TTGGCTAGTTGGTGGTTGGA 59.153 50.000 0.00 0.00 0.00 3.53
1415 1509 3.054065 AGGATCTTCTTTGGGTTGGCTAG 60.054 47.826 0.00 0.00 0.00 3.42
1809 1903 1.872388 TCGGCTTTTGAATGTGTCGA 58.128 45.000 0.00 0.00 0.00 4.20
1918 2012 3.492656 GCATACCTCCTTCATCGTTAGCA 60.493 47.826 0.00 0.00 0.00 3.49
2046 2140 0.620556 GATGCACTCCTTTCCCCTCA 59.379 55.000 0.00 0.00 0.00 3.86
2126 2221 2.762360 TGATTTGGATCACGGCGAC 58.238 52.632 16.62 1.47 37.37 5.19


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

AutoCloner maintained by Alex Coulton.