Multiple sequence alignment - TraesCS2A01G050500

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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 TraesCS2A01G050500 chr2A 100.000 2661 0 0 1 2661 19565921 19568581 0.000000e+00 4915.0
1 TraesCS2A01G050500 chr2A 91.667 552 37 7 2 545 772332251 772331701 0.000000e+00 756.0
2 TraesCS2A01G050500 chr2A 87.143 560 58 7 839 1384 19586968 19587527 8.090000e-175 623.0
3 TraesCS2A01G050500 chr2A 88.652 141 11 4 546 684 19586260 19586397 1.640000e-37 167.0
4 TraesCS2A01G050500 chr2A 84.962 133 15 1 2527 2654 19588726 19588858 2.150000e-26 130.0
5 TraesCS2A01G050500 chr2D 96.925 2081 40 3 581 2661 18373330 18375386 0.000000e+00 3467.0
6 TraesCS2A01G050500 chr2D 88.626 633 42 7 776 1384 18611572 18612198 0.000000e+00 743.0
7 TraesCS2A01G050500 chr2D 88.095 126 12 2 546 668 18610210 18610335 2.130000e-31 147.0
8 TraesCS2A01G050500 chr2D 90.698 86 8 0 2569 2654 18613439 18613524 6.020000e-22 115.0
9 TraesCS2A01G050500 chr2D 100.000 30 0 0 720 749 18611540 18611569 3.700000e-04 56.5
10 TraesCS2A01G050500 chr2B 84.051 1417 163 30 1130 2524 30468097 30469472 0.000000e+00 1306.0
11 TraesCS2A01G050500 chr5A 97.436 546 13 1 1 545 551430494 551429949 0.000000e+00 929.0
12 TraesCS2A01G050500 chr4A 91.091 550 41 8 1 545 610123824 610124370 0.000000e+00 737.0
13 TraesCS2A01G050500 chr6B 90.182 550 45 7 1 545 59832173 59831628 0.000000e+00 708.0
14 TraesCS2A01G050500 chr6B 88.288 555 48 13 1 545 567778102 567777555 0.000000e+00 649.0
15 TraesCS2A01G050500 chr1B 89.649 541 46 9 1 536 684065257 684065792 0.000000e+00 680.0
16 TraesCS2A01G050500 chrUn 87.703 553 52 13 2 545 37156579 37157124 4.830000e-177 630.0
17 TraesCS2A01G050500 chrUn 87.161 553 50 16 1 545 77597524 77596985 2.270000e-170 608.0
18 TraesCS2A01G050500 chr4D 87.184 554 58 8 1 545 118340044 118339495 3.760000e-173 617.0
19 TraesCS2A01G050500 chr7D 82.136 515 78 12 882 1384 621172817 621173329 1.890000e-116 429.0


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 TraesCS2A01G050500 chr2A 19565921 19568581 2660 False 4915.000000 4915 100.00000 1 2661 1 chr2A.!!$F1 2660
1 TraesCS2A01G050500 chr2A 772331701 772332251 550 True 756.000000 756 91.66700 2 545 1 chr2A.!!$R1 543
2 TraesCS2A01G050500 chr2A 19586260 19588858 2598 False 306.666667 623 86.91900 546 2654 3 chr2A.!!$F2 2108
3 TraesCS2A01G050500 chr2D 18373330 18375386 2056 False 3467.000000 3467 96.92500 581 2661 1 chr2D.!!$F1 2080
4 TraesCS2A01G050500 chr2D 18610210 18613524 3314 False 265.375000 743 91.85475 546 2654 4 chr2D.!!$F2 2108
5 TraesCS2A01G050500 chr2B 30468097 30469472 1375 False 1306.000000 1306 84.05100 1130 2524 1 chr2B.!!$F1 1394
6 TraesCS2A01G050500 chr5A 551429949 551430494 545 True 929.000000 929 97.43600 1 545 1 chr5A.!!$R1 544
7 TraesCS2A01G050500 chr4A 610123824 610124370 546 False 737.000000 737 91.09100 1 545 1 chr4A.!!$F1 544
8 TraesCS2A01G050500 chr6B 59831628 59832173 545 True 708.000000 708 90.18200 1 545 1 chr6B.!!$R1 544
9 TraesCS2A01G050500 chr6B 567777555 567778102 547 True 649.000000 649 88.28800 1 545 1 chr6B.!!$R2 544
10 TraesCS2A01G050500 chr1B 684065257 684065792 535 False 680.000000 680 89.64900 1 536 1 chr1B.!!$F1 535
11 TraesCS2A01G050500 chrUn 37156579 37157124 545 False 630.000000 630 87.70300 2 545 1 chrUn.!!$F1 543
12 TraesCS2A01G050500 chrUn 77596985 77597524 539 True 608.000000 608 87.16100 1 545 1 chrUn.!!$R1 544
13 TraesCS2A01G050500 chr4D 118339495 118340044 549 True 617.000000 617 87.18400 1 545 1 chr4D.!!$R1 544
14 TraesCS2A01G050500 chr7D 621172817 621173329 512 False 429.000000 429 82.13600 882 1384 1 chr7D.!!$F1 502

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
757 1957 1.078214 ACCGACGACCCGTGATCTA 60.078 57.895 0.0 0.0 41.37 1.98 F
759 1959 1.094073 CCGACGACCCGTGATCTACT 61.094 60.000 0.0 0.0 41.37 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 3371 2.203294 GGTCGGCTGGGTTGTGTT 60.203 61.111 0.0 0.00 0.00 3.32 R
2489 4246 3.876300 GACGTGTGGTCATGCCTC 58.124 61.111 0.0 4.92 45.36 4.70 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
71 72 3.479979 GAACTCAGGGTTCGGGGT 58.520 61.111 0.00 0.0 43.75 4.95
268 269 2.940994 TGAGGGGAACGAATTTGTGA 57.059 45.000 0.00 0.0 0.00 3.58
623 643 5.252969 TCATGATAATTTCAGTTGCCAGC 57.747 39.130 0.00 0.0 37.89 4.85
749 1949 3.998672 TGCCAAGACCGACGACCC 61.999 66.667 0.00 0.0 0.00 4.46
751 1951 3.677648 CCAAGACCGACGACCCGT 61.678 66.667 0.00 0.0 45.10 5.28
752 1952 2.430244 CAAGACCGACGACCCGTG 60.430 66.667 0.00 0.0 41.37 4.94
753 1953 2.595463 AAGACCGACGACCCGTGA 60.595 61.111 0.00 0.0 41.37 4.35
754 1954 1.975407 AAGACCGACGACCCGTGAT 60.975 57.895 0.00 0.0 41.37 3.06
755 1955 1.930908 AAGACCGACGACCCGTGATC 61.931 60.000 0.00 0.0 41.37 2.92
756 1956 2.360852 ACCGACGACCCGTGATCT 60.361 61.111 0.00 0.0 41.37 2.75
757 1957 1.078214 ACCGACGACCCGTGATCTA 60.078 57.895 0.00 0.0 41.37 1.98
758 1958 1.354506 CCGACGACCCGTGATCTAC 59.645 63.158 0.00 0.0 41.37 2.59
759 1959 1.094073 CCGACGACCCGTGATCTACT 61.094 60.000 0.00 0.0 41.37 2.57
760 1960 1.575244 CGACGACCCGTGATCTACTA 58.425 55.000 0.00 0.0 41.37 1.82
761 1961 2.141517 CGACGACCCGTGATCTACTAT 58.858 52.381 0.00 0.0 41.37 2.12
762 1962 3.320626 CGACGACCCGTGATCTACTATA 58.679 50.000 0.00 0.0 41.37 1.31
763 1963 3.742882 CGACGACCCGTGATCTACTATAA 59.257 47.826 0.00 0.0 41.37 0.98
764 1964 4.391216 CGACGACCCGTGATCTACTATAAT 59.609 45.833 0.00 0.0 41.37 1.28
765 1965 5.106791 CGACGACCCGTGATCTACTATAATT 60.107 44.000 0.00 0.0 41.37 1.40
766 1966 6.567321 CGACGACCCGTGATCTACTATAATTT 60.567 42.308 0.00 0.0 41.37 1.82
767 1967 6.675987 ACGACCCGTGATCTACTATAATTTC 58.324 40.000 0.00 0.0 39.18 2.17
768 1968 6.263842 ACGACCCGTGATCTACTATAATTTCA 59.736 38.462 0.00 0.0 39.18 2.69
769 1969 7.143340 CGACCCGTGATCTACTATAATTTCAA 58.857 38.462 0.00 0.0 0.00 2.69
770 1970 7.813148 CGACCCGTGATCTACTATAATTTCAAT 59.187 37.037 0.00 0.0 0.00 2.57
800 2000 4.401202 TCTTCCCTTTTCACACCAAGTTTC 59.599 41.667 0.00 0.0 0.00 2.78
867 2547 4.005650 ACTAGACTGATGCATGGTTTGTG 58.994 43.478 2.46 0.0 0.00 3.33
1195 2904 3.308402 CCAAGAAGTAATTCTGAGCCCCA 60.308 47.826 6.14 0.0 0.00 4.96
1341 3050 3.429822 CCAATGGCTATGCTTGGTTTCTG 60.430 47.826 0.00 0.0 35.70 3.02
1591 3339 1.614903 CAGAGCAGCCCAAACATTGAA 59.385 47.619 0.00 0.0 0.00 2.69
1652 3401 3.739300 CCAGCCGACCGTAAGTATAATTG 59.261 47.826 0.00 0.0 0.00 2.32
2025 3776 9.268268 CCCTGCTAACGATTTATTTATCTGTTA 57.732 33.333 0.00 0.0 0.00 2.41
2175 3932 8.970691 ATGTCGGTGAAATCTTCTTTATTTTG 57.029 30.769 0.00 0.0 0.00 2.44
2340 4097 4.142600 GCATTTGTCCTTCGCTGTTCTTAT 60.143 41.667 0.00 0.0 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.028905 CGGCAAAACCAAGTCCAAGA 58.971 50.000 0.00 0.00 39.03 3.02
201 202 0.810016 AGCTTACGAGAGGGAACGAC 59.190 55.000 0.00 0.00 0.00 4.34
268 269 1.147824 CATCCATGGCGAGCTCCTT 59.852 57.895 6.96 0.00 0.00 3.36
763 1963 9.807921 TGAAAAGGGAAGACTAACTATTGAAAT 57.192 29.630 0.00 0.00 0.00 2.17
764 1964 9.063615 GTGAAAAGGGAAGACTAACTATTGAAA 57.936 33.333 0.00 0.00 0.00 2.69
765 1965 8.215050 TGTGAAAAGGGAAGACTAACTATTGAA 58.785 33.333 0.00 0.00 0.00 2.69
766 1966 7.660208 GTGTGAAAAGGGAAGACTAACTATTGA 59.340 37.037 0.00 0.00 0.00 2.57
767 1967 7.094762 GGTGTGAAAAGGGAAGACTAACTATTG 60.095 40.741 0.00 0.00 0.00 1.90
768 1968 6.940867 GGTGTGAAAAGGGAAGACTAACTATT 59.059 38.462 0.00 0.00 0.00 1.73
769 1969 6.043938 TGGTGTGAAAAGGGAAGACTAACTAT 59.956 38.462 0.00 0.00 0.00 2.12
770 1970 5.367352 TGGTGTGAAAAGGGAAGACTAACTA 59.633 40.000 0.00 0.00 0.00 2.24
771 1971 4.165372 TGGTGTGAAAAGGGAAGACTAACT 59.835 41.667 0.00 0.00 0.00 2.24
772 1972 4.457466 TGGTGTGAAAAGGGAAGACTAAC 58.543 43.478 0.00 0.00 0.00 2.34
773 1973 4.781775 TGGTGTGAAAAGGGAAGACTAA 57.218 40.909 0.00 0.00 0.00 2.24
774 1974 4.165372 ACTTGGTGTGAAAAGGGAAGACTA 59.835 41.667 0.00 0.00 0.00 2.59
800 2000 2.423926 AGAGTAATGCGTATGAGGCG 57.576 50.000 0.00 0.00 0.00 5.52
1011 2717 2.086869 AGGAAAATCACGACATGGCTG 58.913 47.619 0.00 0.00 0.00 4.85
1067 2773 1.307084 GGTGCTAAGGGAGGAGGGT 60.307 63.158 0.00 0.00 0.00 4.34
1195 2904 3.317993 ACACCAAACGAATTAGCAAAGCT 59.682 39.130 0.00 0.00 43.41 3.74
1341 3050 1.606668 TCAAAGACCATGTTGAACGGC 59.393 47.619 0.00 0.00 30.93 5.68
1622 3371 2.203294 GGTCGGCTGGGTTGTGTT 60.203 61.111 0.00 0.00 0.00 3.32
1691 3441 7.156876 TGAATATGATTTCCCAACTTGACAC 57.843 36.000 0.00 0.00 0.00 3.67
2175 3932 6.468956 CACGCCACAAACATCTACATTATTTC 59.531 38.462 0.00 0.00 0.00 2.17
2340 4097 8.655970 CCGTATATGCATCGAATATGAAAAAGA 58.344 33.333 0.19 0.00 0.00 2.52
2489 4246 3.876300 GACGTGTGGTCATGCCTC 58.124 61.111 0.00 4.92 45.36 4.70


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

AutoCloner maintained by Alex Coulton.