Multiple sequence alignment - TraesCS5D01G431100

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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 TraesCS5D01G431100 chr5D 100.000 2732 0 0 1 2732 488202794 488205525 0.000000e+00 5046.0
1 TraesCS5D01G431100 chr5D 89.823 226 18 5 2510 2732 332567822 332567599 4.450000e-73 285.0
2 TraesCS5D01G431100 chr5A 96.238 1462 45 5 409 1865 608949686 608951142 0.000000e+00 2386.0
3 TraesCS5D01G431100 chr5A 96.594 411 14 0 1 411 608949092 608949502 0.000000e+00 682.0
4 TraesCS5D01G431100 chr5B 95.137 1460 65 3 409 1865 600727396 600728852 0.000000e+00 2298.0
5 TraesCS5D01G431100 chr5B 95.110 409 19 1 3 411 600726807 600727214 0.000000e+00 643.0
6 TraesCS5D01G431100 chr1B 81.164 1375 193 41 520 1856 63201664 63203010 0.000000e+00 1044.0
7 TraesCS5D01G431100 chr1B 79.271 1317 189 51 520 1789 63888743 63890022 0.000000e+00 843.0
8 TraesCS5D01G431100 chr1B 81.317 926 91 52 1866 2732 131272773 131273675 0.000000e+00 676.0
9 TraesCS5D01G431100 chr1B 88.441 571 53 12 1866 2430 253428175 253427612 0.000000e+00 676.0
10 TraesCS5D01G431100 chr1B 88.021 576 55 13 1864 2432 261847190 261847758 0.000000e+00 669.0
11 TraesCS5D01G431100 chr1B 80.065 923 108 49 1864 2732 131266363 131267263 1.390000e-172 616.0
12 TraesCS5D01G431100 chr1B 85.795 352 34 10 2393 2732 131025314 131025661 2.590000e-95 359.0
13 TraesCS5D01G431100 chr1B 93.548 186 12 0 2547 2732 130695863 130696048 7.450000e-71 278.0
14 TraesCS5D01G431100 chr1A 80.786 1374 201 35 520 1856 42670184 42671531 0.000000e+00 1016.0
15 TraesCS5D01G431100 chr1A 82.359 1009 145 21 877 1856 42685948 42686952 0.000000e+00 846.0
16 TraesCS5D01G431100 chr1A 81.944 1008 151 17 877 1856 42721111 42722115 0.000000e+00 824.0
17 TraesCS5D01G431100 chr1A 83.249 197 26 5 1666 1856 42696080 42696275 1.010000e-39 174.0
18 TraesCS5D01G431100 chr1A 77.689 251 43 7 520 761 42692914 42693160 1.020000e-29 141.0
19 TraesCS5D01G431100 chr1A 90.164 61 6 0 1806 1866 43389753 43389693 2.260000e-11 80.5
20 TraesCS5D01G431100 chr1D 80.582 1375 201 40 520 1856 43305634 43306980 0.000000e+00 1000.0
21 TraesCS5D01G431100 chr1D 81.599 1038 145 26 782 1789 44628959 44629980 0.000000e+00 817.0
22 TraesCS5D01G431100 chr1D 91.667 516 35 6 1866 2377 308766737 308766226 0.000000e+00 708.0
23 TraesCS5D01G431100 chr1D 88.462 572 49 16 1866 2430 13236259 13235698 0.000000e+00 675.0
24 TraesCS5D01G431100 chr4D 84.081 892 96 38 1866 2732 125016390 125017260 0.000000e+00 819.0
25 TraesCS5D01G431100 chr4D 80.655 672 53 27 2099 2732 125010047 125010679 1.490000e-122 449.0
26 TraesCS5D01G431100 chr6D 91.913 507 29 11 1866 2365 211704954 211705455 0.000000e+00 699.0
27 TraesCS5D01G431100 chr6D 89.493 552 37 18 1865 2405 211698127 211698668 0.000000e+00 678.0
28 TraesCS5D01G431100 chr6D 88.215 577 55 12 1862 2432 224961262 224960693 0.000000e+00 676.0
29 TraesCS5D01G431100 chr2B 89.711 554 42 14 1864 2409 308961518 308962064 0.000000e+00 693.0
30 TraesCS5D01G431100 chr4B 89.837 551 39 14 1866 2409 299205304 299205844 0.000000e+00 691.0
31 TraesCS5D01G431100 chr3B 82.953 657 54 29 2099 2732 352811096 352810475 8.610000e-150 540.0
32 TraesCS5D01G431100 chr3D 76.724 696 94 38 2094 2732 274500552 274501236 2.620000e-85 326.0


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 TraesCS5D01G431100 chr5D 488202794 488205525 2731 False 5046.0 5046 100.0000 1 2732 1 chr5D.!!$F1 2731
1 TraesCS5D01G431100 chr5A 608949092 608951142 2050 False 1534.0 2386 96.4160 1 1865 2 chr5A.!!$F1 1864
2 TraesCS5D01G431100 chr5B 600726807 600728852 2045 False 1470.5 2298 95.1235 3 1865 2 chr5B.!!$F1 1862
3 TraesCS5D01G431100 chr1B 63201664 63203010 1346 False 1044.0 1044 81.1640 520 1856 1 chr1B.!!$F1 1336
4 TraesCS5D01G431100 chr1B 63888743 63890022 1279 False 843.0 843 79.2710 520 1789 1 chr1B.!!$F2 1269
5 TraesCS5D01G431100 chr1B 131272773 131273675 902 False 676.0 676 81.3170 1866 2732 1 chr1B.!!$F6 866
6 TraesCS5D01G431100 chr1B 253427612 253428175 563 True 676.0 676 88.4410 1866 2430 1 chr1B.!!$R1 564
7 TraesCS5D01G431100 chr1B 261847190 261847758 568 False 669.0 669 88.0210 1864 2432 1 chr1B.!!$F7 568
8 TraesCS5D01G431100 chr1B 131266363 131267263 900 False 616.0 616 80.0650 1864 2732 1 chr1B.!!$F5 868
9 TraesCS5D01G431100 chr1A 42670184 42671531 1347 False 1016.0 1016 80.7860 520 1856 1 chr1A.!!$F1 1336
10 TraesCS5D01G431100 chr1A 42685948 42686952 1004 False 846.0 846 82.3590 877 1856 1 chr1A.!!$F2 979
11 TraesCS5D01G431100 chr1A 42721111 42722115 1004 False 824.0 824 81.9440 877 1856 1 chr1A.!!$F3 979
12 TraesCS5D01G431100 chr1D 43305634 43306980 1346 False 1000.0 1000 80.5820 520 1856 1 chr1D.!!$F1 1336
13 TraesCS5D01G431100 chr1D 44628959 44629980 1021 False 817.0 817 81.5990 782 1789 1 chr1D.!!$F2 1007
14 TraesCS5D01G431100 chr1D 308766226 308766737 511 True 708.0 708 91.6670 1866 2377 1 chr1D.!!$R2 511
15 TraesCS5D01G431100 chr1D 13235698 13236259 561 True 675.0 675 88.4620 1866 2430 1 chr1D.!!$R1 564
16 TraesCS5D01G431100 chr4D 125016390 125017260 870 False 819.0 819 84.0810 1866 2732 1 chr4D.!!$F2 866
17 TraesCS5D01G431100 chr4D 125010047 125010679 632 False 449.0 449 80.6550 2099 2732 1 chr4D.!!$F1 633
18 TraesCS5D01G431100 chr6D 211704954 211705455 501 False 699.0 699 91.9130 1866 2365 1 chr6D.!!$F2 499
19 TraesCS5D01G431100 chr6D 211698127 211698668 541 False 678.0 678 89.4930 1865 2405 1 chr6D.!!$F1 540
20 TraesCS5D01G431100 chr6D 224960693 224961262 569 True 676.0 676 88.2150 1862 2432 1 chr6D.!!$R1 570
21 TraesCS5D01G431100 chr2B 308961518 308962064 546 False 693.0 693 89.7110 1864 2409 1 chr2B.!!$F1 545
22 TraesCS5D01G431100 chr4B 299205304 299205844 540 False 691.0 691 89.8370 1866 2409 1 chr4B.!!$F1 543
23 TraesCS5D01G431100 chr3B 352810475 352811096 621 True 540.0 540 82.9530 2099 2732 1 chr3B.!!$R1 633
24 TraesCS5D01G431100 chr3D 274500552 274501236 684 False 326.0 326 76.7240 2094 2732 1 chr3D.!!$F1 638

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
331 332 4.300803 CACTGAATTTTGTGTGGTCATGG 58.699 43.478 0.0 0.0 0.0 3.66 F
1082 1303 1.422402 AGGGAAAAGAAGGCGGTGTAA 59.578 47.619 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1397 0.83640 ATGTCCTGTCGGTCACCCTT 60.836 55.000 0.0 0.0 31.18 3.95 R
2455 2820 1.00444 GTGCTCGGCCTCTTCAGTT 60.004 57.895 0.0 0.0 0.00 3.16 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
203 204 5.333798 CGACCAAAATTGTGTGACGTTAGAT 60.334 40.000 0.00 0.00 0.00 1.98
204 205 6.385649 ACCAAAATTGTGTGACGTTAGATT 57.614 33.333 0.00 0.00 0.00 2.40
331 332 4.300803 CACTGAATTTTGTGTGGTCATGG 58.699 43.478 0.00 0.00 0.00 3.66
471 660 9.931210 TGTCTTATAGTGCAATATATACGATCG 57.069 33.333 14.88 14.88 0.00 3.69
483 672 9.471084 CAATATATACGATCGGGTGCATATTTA 57.529 33.333 20.98 6.88 0.00 1.40
518 707 4.363999 CAGTACTGTAGCCATTAGAGTGC 58.636 47.826 15.06 0.00 38.16 4.40
721 933 6.624352 ATGCATAACATGTAGATGTGGAAC 57.376 37.500 17.50 0.00 42.30 3.62
1082 1303 1.422402 AGGGAAAAGAAGGCGGTGTAA 59.578 47.619 0.00 0.00 0.00 2.41
1101 1333 5.995282 GTGTAACATAGTAATAGCCATGGCA 59.005 40.000 37.18 23.40 39.58 4.92
1165 1397 2.106074 GTGTCGGCCGATGAATGCA 61.106 57.895 33.58 20.60 0.00 3.96
1389 1621 1.064003 TCCCACATGGCTACAAGTGT 58.936 50.000 0.00 0.00 42.97 3.55
1662 1902 6.931281 CCTCACAACAACTTCTCTTTCAGATA 59.069 38.462 0.00 0.00 0.00 1.98
2010 2283 2.771943 TCCAAGAACACACAAGAGGTCT 59.228 45.455 0.00 0.00 33.56 3.85
2469 2836 0.321671 CTTGGAACTGAAGAGGCCGA 59.678 55.000 0.00 0.00 0.00 5.54
2635 3071 2.145865 CACCCAGAGTGTCCAGGTT 58.854 57.895 0.00 0.00 41.93 3.50
2678 3114 2.743131 TCCTTCCCTTCCTTTCCTCT 57.257 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
203 204 6.710295 AGTAACTTGTGAGTACATGCATGAAA 59.290 34.615 32.75 17.10 36.53 2.69
204 205 6.230472 AGTAACTTGTGAGTACATGCATGAA 58.770 36.000 32.75 13.48 36.53 2.57
331 332 2.102588 AGCGTCCACCACATATACCTTC 59.897 50.000 0.00 0.00 0.00 3.46
471 660 5.554822 TCGTTCTTTGTAAATATGCACCC 57.445 39.130 0.00 0.00 0.00 4.61
483 672 3.728845 ACAGTACTGCATCGTTCTTTGT 58.271 40.909 22.90 0.00 0.00 2.83
518 707 5.932303 ACACCTACAAGCTACAACATTACAG 59.068 40.000 0.00 0.00 0.00 2.74
655 857 8.420222 TCCTGAAGATATTGTTTTGCTTCAAAA 58.580 29.630 0.00 1.05 42.82 2.44
656 858 7.950512 TCCTGAAGATATTGTTTTGCTTCAAA 58.049 30.769 0.00 0.00 42.82 2.69
657 859 7.523293 TCCTGAAGATATTGTTTTGCTTCAA 57.477 32.000 0.00 0.00 42.82 2.69
967 1186 9.280174 GTTAGCTATGGTTTGGTTTATATAGCA 57.720 33.333 14.23 0.00 43.18 3.49
1082 1303 6.129179 AGTTTTGCCATGGCTATTACTATGT 58.871 36.000 35.53 11.67 42.51 2.29
1101 1333 7.660112 TGATGAAACATAAGCACATGAGTTTT 58.340 30.769 0.00 0.00 30.23 2.43
1165 1397 0.836400 ATGTCCTGTCGGTCACCCTT 60.836 55.000 0.00 0.00 31.18 3.95
1416 1648 2.224606 AGCAATGCCCATCATCGTAAG 58.775 47.619 0.00 0.00 33.40 2.34
1662 1902 6.319658 CCTAAGCACAACCTCATCAATTACAT 59.680 38.462 0.00 0.00 0.00 2.29
1777 2022 6.322201 CCATGAGCCATAAATAGAACCAAACT 59.678 38.462 0.00 0.00 0.00 2.66
1857 2104 4.753516 TCCACCCTACAACACATATGAG 57.246 45.455 10.38 3.79 0.00 2.90
1894 2141 1.638589 TCCCCCTCCAATTCGTGAAAT 59.361 47.619 0.00 0.00 0.00 2.17
2010 2283 7.345422 TCCTTTGTTGTCTTTGAATCATTGA 57.655 32.000 0.00 0.00 0.00 2.57
2232 2578 9.240125 CTAGACTATATATACCCCTTCCCTAGT 57.760 40.741 0.00 0.00 0.00 2.57
2455 2820 1.004440 GTGCTCGGCCTCTTCAGTT 60.004 57.895 0.00 0.00 0.00 3.16
2456 2821 2.659610 GTGCTCGGCCTCTTCAGT 59.340 61.111 0.00 0.00 0.00 3.41
2635 3071 6.364568 TCATGAAGAATGAAGAAGTGGAGA 57.635 37.500 0.00 0.00 42.49 3.71
2678 3114 2.614481 GGAGGTACAAGCGACAATGGAA 60.614 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.