Multiple sequence alignment - TraesCS5A01G430300

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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 TraesCS5A01G430300 chr5A 100.000 2597 0 0 1 2597 614333023 614335619 0.000000e+00 4796
1 TraesCS5A01G430300 chr5A 98.492 1061 14 2 524 1583 667732158 667731099 0.000000e+00 1869
2 TraesCS5A01G430300 chr5A 97.556 982 21 3 1618 2597 157781163 157780183 0.000000e+00 1677
3 TraesCS5A01G430300 chr5A 96.884 995 27 3 1603 2597 667731049 667730059 0.000000e+00 1663
4 TraesCS5A01G430300 chr7D 98.870 1062 10 2 524 1583 381881487 381880426 0.000000e+00 1893
5 TraesCS5A01G430300 chr7D 98.387 124 2 0 2474 2597 626710518 626710395 4.350000e-53 219
6 TraesCS5A01G430300 chr7D 97.581 124 3 0 2474 2597 382090476 382090599 2.020000e-51 213
7 TraesCS5A01G430300 chrUn 98.777 1063 10 2 524 1583 223716069 223717131 0.000000e+00 1888
8 TraesCS5A01G430300 chrUn 98.684 1064 10 3 524 1583 257855053 257853990 0.000000e+00 1884
9 TraesCS5A01G430300 chrUn 99.055 529 4 1 1 529 189420497 189419970 0.000000e+00 948
10 TraesCS5A01G430300 chrUn 98.677 529 6 1 1 529 86468668 86468141 0.000000e+00 937
11 TraesCS5A01G430300 chrUn 97.581 124 3 0 2474 2597 369464835 369464712 2.020000e-51 213
12 TraesCS5A01G430300 chr2A 98.776 1062 11 2 524 1583 755520494 755519433 0.000000e+00 1888
13 TraesCS5A01G430300 chr2A 98.584 1059 13 2 527 1583 397655287 397654229 0.000000e+00 1871
14 TraesCS5A01G430300 chr2A 97.778 585 11 2 1603 2186 423418770 423418187 0.000000e+00 1007
15 TraesCS5A01G430300 chr5B 98.588 1062 13 2 524 1583 127797750 127796689 0.000000e+00 1877
16 TraesCS5A01G430300 chr5B 97.607 585 11 3 1603 2186 34118643 34118061 0.000000e+00 1000
17 TraesCS5A01G430300 chr4D 98.492 1061 14 2 524 1583 123730675 123729616 0.000000e+00 1869
18 TraesCS5A01G430300 chr4D 97.581 124 3 0 2474 2597 134963690 134963813 2.020000e-51 213
19 TraesCS5A01G430300 chr1A 98.398 1061 15 2 524 1583 94525302 94524243 0.000000e+00 1864
20 TraesCS5A01G430300 chr1A 98.092 996 18 1 1603 2597 94597331 94596336 0.000000e+00 1733
21 TraesCS5A01G430300 chr1A 97.289 996 24 3 1603 2597 94709702 94710695 0.000000e+00 1687
22 TraesCS5A01G430300 chr1A 95.525 648 22 2 1603 2250 115889541 115888901 0.000000e+00 1029
23 TraesCS5A01G430300 chr1A 98.299 529 8 1 1 529 94734713 94735240 0.000000e+00 926
24 TraesCS5A01G430300 chr4A 95.011 882 37 4 1603 2478 295168093 295167213 0.000000e+00 1378
25 TraesCS5A01G430300 chr4A 91.176 306 27 0 2173 2478 79634684 79634989 1.440000e-112 416
26 TraesCS5A01G430300 chr4A 91.176 306 27 0 2173 2478 79644159 79643854 1.440000e-112 416
27 TraesCS5A01G430300 chr3A 97.833 646 12 2 1603 2247 51885586 51884942 0.000000e+00 1114
28 TraesCS5A01G430300 chr3A 98.488 529 7 1 1 529 633121088 633121615 0.000000e+00 931
29 TraesCS5A01G430300 chr2D 98.677 529 6 1 1 529 200932886 200932359 0.000000e+00 937
30 TraesCS5A01G430300 chr7A 98.488 529 7 1 1 529 60252422 60252949 0.000000e+00 931
31 TraesCS5A01G430300 chr6D 98.488 529 7 1 1 529 102372695 102373222 0.000000e+00 931
32 TraesCS5A01G430300 chr6A 98.488 529 7 1 1 529 64688209 64687682 0.000000e+00 931
33 TraesCS5A01G430300 chr3D 98.488 529 7 1 1 529 523716373 523715846 0.000000e+00 931
34 TraesCS5A01G430300 chr6B 91.176 306 27 0 2173 2478 596601242 596600937 1.440000e-112 416
35 TraesCS5A01G430300 chr6B 91.176 306 27 0 2173 2478 715990455 715990150 1.440000e-112 416
36 TraesCS5A01G430300 chr1D 97.581 124 3 0 2474 2597 212444040 212443917 2.020000e-51 213


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 TraesCS5A01G430300 chr5A 614333023 614335619 2596 False 4796 4796 100.000 1 2597 1 chr5A.!!$F1 2596
1 TraesCS5A01G430300 chr5A 667730059 667732158 2099 True 1766 1869 97.688 524 2597 2 chr5A.!!$R2 2073
2 TraesCS5A01G430300 chr5A 157780183 157781163 980 True 1677 1677 97.556 1618 2597 1 chr5A.!!$R1 979
3 TraesCS5A01G430300 chr7D 381880426 381881487 1061 True 1893 1893 98.870 524 1583 1 chr7D.!!$R1 1059
4 TraesCS5A01G430300 chrUn 223716069 223717131 1062 False 1888 1888 98.777 524 1583 1 chrUn.!!$F1 1059
5 TraesCS5A01G430300 chrUn 257853990 257855053 1063 True 1884 1884 98.684 524 1583 1 chrUn.!!$R3 1059
6 TraesCS5A01G430300 chrUn 189419970 189420497 527 True 948 948 99.055 1 529 1 chrUn.!!$R2 528
7 TraesCS5A01G430300 chrUn 86468141 86468668 527 True 937 937 98.677 1 529 1 chrUn.!!$R1 528
8 TraesCS5A01G430300 chr2A 755519433 755520494 1061 True 1888 1888 98.776 524 1583 1 chr2A.!!$R3 1059
9 TraesCS5A01G430300 chr2A 397654229 397655287 1058 True 1871 1871 98.584 527 1583 1 chr2A.!!$R1 1056
10 TraesCS5A01G430300 chr2A 423418187 423418770 583 True 1007 1007 97.778 1603 2186 1 chr2A.!!$R2 583
11 TraesCS5A01G430300 chr5B 127796689 127797750 1061 True 1877 1877 98.588 524 1583 1 chr5B.!!$R2 1059
12 TraesCS5A01G430300 chr5B 34118061 34118643 582 True 1000 1000 97.607 1603 2186 1 chr5B.!!$R1 583
13 TraesCS5A01G430300 chr4D 123729616 123730675 1059 True 1869 1869 98.492 524 1583 1 chr4D.!!$R1 1059
14 TraesCS5A01G430300 chr1A 94524243 94525302 1059 True 1864 1864 98.398 524 1583 1 chr1A.!!$R1 1059
15 TraesCS5A01G430300 chr1A 94596336 94597331 995 True 1733 1733 98.092 1603 2597 1 chr1A.!!$R2 994
16 TraesCS5A01G430300 chr1A 94709702 94710695 993 False 1687 1687 97.289 1603 2597 1 chr1A.!!$F1 994
17 TraesCS5A01G430300 chr1A 115888901 115889541 640 True 1029 1029 95.525 1603 2250 1 chr1A.!!$R3 647
18 TraesCS5A01G430300 chr1A 94734713 94735240 527 False 926 926 98.299 1 529 1 chr1A.!!$F2 528
19 TraesCS5A01G430300 chr4A 295167213 295168093 880 True 1378 1378 95.011 1603 2478 1 chr4A.!!$R2 875
20 TraesCS5A01G430300 chr3A 51884942 51885586 644 True 1114 1114 97.833 1603 2247 1 chr3A.!!$R1 644
21 TraesCS5A01G430300 chr3A 633121088 633121615 527 False 931 931 98.488 1 529 1 chr3A.!!$F1 528
22 TraesCS5A01G430300 chr2D 200932359 200932886 527 True 937 937 98.677 1 529 1 chr2D.!!$R1 528
23 TraesCS5A01G430300 chr7A 60252422 60252949 527 False 931 931 98.488 1 529 1 chr7A.!!$F1 528
24 TraesCS5A01G430300 chr6D 102372695 102373222 527 False 931 931 98.488 1 529 1 chr6D.!!$F1 528
25 TraesCS5A01G430300 chr6A 64687682 64688209 527 True 931 931 98.488 1 529 1 chr6A.!!$R1 528
26 TraesCS5A01G430300 chr3D 523715846 523716373 527 True 931 931 98.488 1 529 1 chr3D.!!$R1 528

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
984 990 1.954035 AGGGGGAAGAGGAGTTGTAC 58.046 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2386 2.084546 CTCAGGTTCCGGGAATGAAAC 58.915 52.381 13.48 0.0 0.0 2.78 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
89 90 7.906199 AAGACACTTAGCATAGGAGTAGATT 57.094 36.000 0.00 0.00 0.00 2.40
331 332 2.749076 TCTTTGCAGGATCCATTGTTCG 59.251 45.455 15.82 0.00 0.00 3.95
688 689 4.717279 TGAAAAGGGCTAGGTAGTTTGT 57.283 40.909 0.00 0.00 0.00 2.83
984 990 1.954035 AGGGGGAAGAGGAGTTGTAC 58.046 55.000 0.00 0.00 0.00 2.90
1118 1124 0.778720 TATTGGTGGGGGTTCGGTTT 59.221 50.000 0.00 0.00 0.00 3.27
1210 1216 3.244526 TGTGGATCTAGCTTTCAACAGCA 60.245 43.478 0.00 0.00 42.84 4.41
1338 1344 7.414208 CGTGGTCTATATCATGCGAGTTATAGT 60.414 40.741 10.58 0.00 30.84 2.12
1354 1360 8.858094 CGAGTTATAGTAGTCCTAGGGAATTTT 58.142 37.037 9.46 0.00 31.38 1.82
1555 1562 6.654582 GGACAATGCCACCTTAAATCATTTTT 59.345 34.615 0.00 0.00 0.00 1.94
1583 1590 6.443849 AGTCTCCATCATTTACTCCACCTTAA 59.556 38.462 0.00 0.00 0.00 1.85
1584 1591 7.037586 AGTCTCCATCATTTACTCCACCTTAAA 60.038 37.037 0.00 0.00 0.00 1.52
1586 1593 7.993183 TCTCCATCATTTACTCCACCTTAAATC 59.007 37.037 0.00 0.00 0.00 2.17
1587 1594 6.765989 TCCATCATTTACTCCACCTTAAATCG 59.234 38.462 0.00 0.00 0.00 3.34
1588 1595 6.542370 CCATCATTTACTCCACCTTAAATCGT 59.458 38.462 0.00 0.00 0.00 3.73
1590 1597 7.989416 TCATTTACTCCACCTTAAATCGTTT 57.011 32.000 0.00 0.00 0.00 3.60
1591 1598 8.398878 TCATTTACTCCACCTTAAATCGTTTT 57.601 30.769 0.00 0.00 0.00 2.43
1592 1599 8.852135 TCATTTACTCCACCTTAAATCGTTTTT 58.148 29.630 0.00 0.00 0.00 1.94
1760 1801 3.016736 GGGGCATCCCGACAATTATATG 58.983 50.000 0.00 0.00 46.66 1.78
1876 1917 0.462047 GGTGTAGCCGCAATAGCACT 60.462 55.000 0.00 0.00 42.27 4.40
2040 2082 6.068461 TGGAGGCACCATTTGTTACTATTA 57.932 37.500 0.00 0.00 44.64 0.98
2340 2386 5.070770 AGAGTGCAAGATAGACTCACTTG 57.929 43.478 13.72 13.72 42.33 3.16
2496 2542 1.152312 GCGGAGGGAGGGGAATCTA 60.152 63.158 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.201785 GGTGTTCTTTGTCTTAGTTTGATTCCA 60.202 37.037 0.00 0.00 0.00 3.53
331 332 4.965119 AACAACCAGTTGAGAAGTGTTC 57.035 40.909 17.06 0.00 42.93 3.18
522 523 2.603560 CTCGGAAACTCTTATTGGACGC 59.396 50.000 0.00 0.00 0.00 5.19
688 689 0.174389 TGAAAAGTTTTGCCTGCGCA 59.826 45.000 10.98 10.98 45.49 6.09
1118 1124 8.630054 AATGACTAAACAAATACCTGCTAACA 57.370 30.769 0.00 0.00 0.00 2.41
1354 1360 0.748450 ACAACTCCGAGACACCGAAA 59.252 50.000 1.33 0.00 0.00 3.46
1555 1562 6.443849 AGGTGGAGTAAATGATGGAGACTAAA 59.556 38.462 0.00 0.00 0.00 1.85
1592 1599 9.135189 CCAATGGATTATTTGATGGAGACTAAA 57.865 33.333 0.00 0.00 0.00 1.85
1593 1600 7.725397 CCCAATGGATTATTTGATGGAGACTAA 59.275 37.037 0.00 0.00 0.00 2.24
1594 1601 7.147141 ACCCAATGGATTATTTGATGGAGACTA 60.147 37.037 0.00 0.00 34.81 2.59
1595 1602 6.073314 CCCAATGGATTATTTGATGGAGACT 58.927 40.000 0.00 0.00 0.00 3.24
1596 1603 5.835280 ACCCAATGGATTATTTGATGGAGAC 59.165 40.000 0.00 0.00 34.81 3.36
1597 1604 5.834742 CACCCAATGGATTATTTGATGGAGA 59.165 40.000 0.00 0.00 34.81 3.71
1598 1605 5.599656 ACACCCAATGGATTATTTGATGGAG 59.400 40.000 0.00 0.00 34.81 3.86
1601 1608 7.345422 TGTACACCCAATGGATTATTTGATG 57.655 36.000 0.00 0.00 34.81 3.07
1760 1801 1.968540 GGGCATCGGATTAGCAGGC 60.969 63.158 3.17 0.00 0.00 4.85
2340 2386 2.084546 CTCAGGTTCCGGGAATGAAAC 58.915 52.381 13.48 0.00 0.00 2.78
2496 2542 8.701643 ATATAAGCAGGGTTATAGGAATCCTT 57.298 34.615 7.30 0.00 34.61 3.36


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

AutoCloner maintained by Alex Coulton.