Multiple sequence alignment - TraesCS1A01G437900

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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 TraesCS1A01G437900 chr1A 100.000 2756 0 0 1 2756 587768449 587771204 0.000000e+00 5090.0
1 TraesCS1A01G437900 chr1A 98.917 1570 16 1 1181 2750 587739882 587741450 0.000000e+00 2804.0
2 TraesCS1A01G437900 chr1A 100.000 882 0 0 298 1179 587738801 587739682 0.000000e+00 1629.0
3 TraesCS1A01G437900 chr1A 91.509 212 16 1 1 210 443457228 443457439 9.660000e-75 291.0
4 TraesCS1A01G437900 chr1A 90.566 212 18 1 1 210 48324885 48324674 2.090000e-71 279.0
5 TraesCS1A01G437900 chr1A 90.141 213 18 2 1 210 100967920 100968132 9.720000e-70 274.0
6 TraesCS1A01G437900 chr1A 88.722 133 12 3 1415 1545 579977162 579977293 2.840000e-35 159.0
7 TraesCS1A01G437900 chrUn 99.309 2750 18 1 1 2750 2183185 2180437 0.000000e+00 4972.0
8 TraesCS1A01G437900 chrUn 99.830 1179 2 0 1 1179 358054219 358053041 0.000000e+00 2167.0
9 TraesCS1A01G437900 chrUn 92.925 212 13 1 1 210 2211434 2211223 9.590000e-80 307.0
10 TraesCS1A01G437900 chrUn 94.872 39 1 1 2161 2199 478657815 478657778 2.960000e-05 60.2
11 TraesCS1A01G437900 chr3D 78.309 899 144 31 545 1416 591624487 591625361 1.450000e-147 532.0
12 TraesCS1A01G437900 chr3D 78.671 858 133 29 587 1416 591654832 591653997 2.430000e-145 525.0
13 TraesCS1A01G437900 chr3D 96.739 92 3 0 1457 1548 611212497 611212406 1.320000e-33 154.0
14 TraesCS1A01G437900 chr3A 77.855 858 140 30 587 1416 722394868 722395703 1.150000e-133 486.0
15 TraesCS1A01G437900 chr3A 77.713 857 143 33 587 1416 722439404 722438569 5.340000e-132 481.0
16 TraesCS1A01G437900 chr3A 89.623 212 20 1 1 210 750659793 750660004 4.520000e-68 268.0
17 TraesCS1A01G437900 chr3A 89.565 115 11 1 1415 1528 681724533 681724419 7.950000e-31 145.0
18 TraesCS1A01G437900 chr7A 75.527 854 169 28 587 1416 47435946 47436783 1.550000e-102 383.0
19 TraesCS1A01G437900 chr7A 93.893 131 7 1 1415 1544 678930192 678930062 2.170000e-46 196.0
20 TraesCS1A01G437900 chr4A 91.943 211 15 1 1 209 20986810 20987020 7.460000e-76 294.0
21 TraesCS1A01G437900 chr6A 90.094 212 19 1 1 210 144557820 144557609 9.720000e-70 274.0
22 TraesCS1A01G437900 chr5B 78.125 384 69 6 1044 1416 515187598 515187977 2.130000e-56 230.0
23 TraesCS1A01G437900 chr6D 94.355 124 7 0 1417 1540 496625 496748 1.010000e-44 191.0
24 TraesCS1A01G437900 chr2B 84.058 69 9 2 2161 2229 53832512 53832446 6.370000e-07 65.8
25 TraesCS1A01G437900 chr2B 94.872 39 1 1 2161 2199 53834019 53833982 2.960000e-05 60.2
26 TraesCS1A01G437900 chr2B 94.872 39 1 1 2161 2199 53840045 53840008 2.960000e-05 60.2


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 TraesCS1A01G437900 chr1A 587768449 587771204 2755 False 5090.0 5090 100.0000 1 2756 1 chr1A.!!$F4 2755
1 TraesCS1A01G437900 chr1A 587738801 587741450 2649 False 2216.5 2804 99.4585 298 2750 2 chr1A.!!$F5 2452
2 TraesCS1A01G437900 chrUn 2180437 2183185 2748 True 4972.0 4972 99.3090 1 2750 1 chrUn.!!$R1 2749
3 TraesCS1A01G437900 chrUn 358053041 358054219 1178 True 2167.0 2167 99.8300 1 1179 1 chrUn.!!$R3 1178
4 TraesCS1A01G437900 chr3D 591624487 591625361 874 False 532.0 532 78.3090 545 1416 1 chr3D.!!$F1 871
5 TraesCS1A01G437900 chr3D 591653997 591654832 835 True 525.0 525 78.6710 587 1416 1 chr3D.!!$R1 829
6 TraesCS1A01G437900 chr3A 722394868 722395703 835 False 486.0 486 77.8550 587 1416 1 chr3A.!!$F1 829
7 TraesCS1A01G437900 chr3A 722438569 722439404 835 True 481.0 481 77.7130 587 1416 1 chr3A.!!$R2 829
8 TraesCS1A01G437900 chr7A 47435946 47436783 837 False 383.0 383 75.5270 587 1416 1 chr7A.!!$F1 829

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
165 166 2.432628 CGTCGTTGAGGCTGACCC 60.433 66.667 0.00 0.0 36.11 4.46 F
1443 1678 2.899122 CCTGGGGCATGCACAATAA 58.101 52.632 23.88 2.8 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1678 1.961394 TGCTACACTGACCGAAGAACT 59.039 47.619 0.00 0.00 0.00 3.01 R
2425 2660 3.981212 ACAGGCATGCCCTAAAGTTAAT 58.019 40.909 33.14 7.61 44.09 1.40 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
165 166 2.432628 CGTCGTTGAGGCTGACCC 60.433 66.667 0.00 0.00 36.11 4.46
1443 1678 2.899122 CCTGGGGCATGCACAATAA 58.101 52.632 23.88 2.80 0.00 1.40
1595 1830 2.101582 AGCTGCCCTTTAGTCGTGATAG 59.898 50.000 0.00 0.00 0.00 2.08
1606 1841 2.292016 AGTCGTGATAGCCATCTTCTCG 59.708 50.000 0.00 0.00 31.93 4.04
1624 1859 3.214123 TATCGAGGGTCGGTGCCG 61.214 66.667 3.94 3.94 40.88 5.69
1639 1874 3.552890 CGGTGCCGATGAGAAGATAATCA 60.553 47.826 4.35 0.00 42.83 2.57
1867 2102 2.286365 ACGGAGCTTTCCAAATTGGA 57.714 45.000 11.23 11.23 46.61 3.53
2324 2559 4.278310 ACTTCACACTTTTGTAGGGCTTT 58.722 39.130 0.00 0.00 33.30 3.51
2337 2572 2.654863 AGGGCTTTAAATGGATGACGG 58.345 47.619 0.00 0.00 0.00 4.79
2387 2622 6.770785 ACATCGTATGCATGTATTAAGGGTTT 59.229 34.615 10.16 0.00 32.48 3.27
2549 2784 3.877508 AGGGTTTCTCTTTCAAGACAACG 59.122 43.478 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 0.251033 ACGGGTTACAAAAGGAGCCC 60.251 55.000 0.00 0.00 0.00 5.19
1443 1678 1.961394 TGCTACACTGACCGAAGAACT 59.039 47.619 0.00 0.00 0.00 3.01
1606 1841 2.416260 GGCACCGACCCTCGATAC 59.584 66.667 0.00 0.00 43.74 2.24
1624 1859 8.805175 TCTCATCTCCTTGATTATCTTCTCATC 58.195 37.037 0.00 0.00 32.05 2.92
1639 1874 3.796111 TCTTTGGACCTCTCATCTCCTT 58.204 45.455 0.00 0.00 0.00 3.36
1867 2102 3.671008 TGCTAGTATGAACACGGTGTT 57.329 42.857 25.33 25.33 44.37 3.32
1875 2110 6.455646 CGTGAGGTTTTGATGCTAGTATGAAC 60.456 42.308 0.00 0.99 0.00 3.18
2004 2239 5.449177 CCCGATTTGGATAGTTTTTCTCTGC 60.449 44.000 0.00 0.00 42.00 4.26
2210 2445 3.550233 CCATAATACTGTGTACGCTCGCT 60.550 47.826 8.10 0.00 0.00 4.93
2357 2592 5.929697 AATACATGCATACGATGTGGAAG 57.070 39.130 0.00 0.00 35.62 3.46
2425 2660 3.981212 ACAGGCATGCCCTAAAGTTAAT 58.019 40.909 33.14 7.61 44.09 1.40
2549 2784 5.880887 AGAGGTTCCTTTTTCGTTATGGATC 59.119 40.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.