Multiple sequence alignment - TraesCS4A01G088300

Loading Multiple Alignment...

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 TraesCS4A01G088300 chr4A 100.000 6670 0 0 1 6670 93889896 93896565 0.000000e+00 12318.0
1 TraesCS4A01G088300 chr4A 97.619 42 1 0 584 625 617280305 617280346 9.280000e-09 73.1
2 TraesCS4A01G088300 chr4A 93.478 46 3 0 590 635 145883983 145883938 1.200000e-07 69.4
3 TraesCS4A01G088300 chr4D 94.034 2883 128 29 1179 4040 370537963 370535104 0.000000e+00 4331.0
4 TraesCS4A01G088300 chr4D 92.415 2004 103 26 4311 6294 370535102 370533128 0.000000e+00 2813.0
5 TraesCS4A01G088300 chr4D 94.759 477 14 6 624 1098 370538781 370538314 0.000000e+00 732.0
6 TraesCS4A01G088300 chr4D 85.455 440 38 8 40 479 370539314 370538901 1.030000e-117 435.0
7 TraesCS4A01G088300 chr4D 93.810 210 9 4 6410 6618 370532741 370532535 5.020000e-81 313.0
8 TraesCS4A01G088300 chr4D 92.623 122 8 1 464 584 370538885 370538764 2.470000e-39 174.0
9 TraesCS4A01G088300 chr4D 95.349 43 2 0 583 625 45710259 45710301 1.200000e-07 69.4
10 TraesCS4A01G088300 chr4D 97.500 40 1 0 1 40 160433688 160433649 1.200000e-07 69.4
11 TraesCS4A01G088300 chr4D 90.566 53 4 1 584 635 325358774 325358826 1.200000e-07 69.4
12 TraesCS4A01G088300 chr4B 91.478 2335 131 38 4311 6618 455619939 455617646 0.000000e+00 3147.0
13 TraesCS4A01G088300 chr4B 97.082 1508 40 4 2534 4040 455621445 455619941 0.000000e+00 2538.0
14 TraesCS4A01G088300 chr4B 90.668 1393 89 28 1181 2552 455623004 455621632 0.000000e+00 1814.0
15 TraesCS4A01G088300 chr4B 95.858 507 11 5 624 1129 455623890 455623393 0.000000e+00 811.0
16 TraesCS4A01G088300 chr4B 90.476 546 43 5 40 584 455624410 455623873 0.000000e+00 712.0
17 TraesCS4A01G088300 chrUn 96.739 276 7 2 4039 4313 2223225 2222951 6.100000e-125 459.0
18 TraesCS4A01G088300 chr7D 97.048 271 7 1 4037 4306 586466234 586465964 7.880000e-124 455.0
19 TraesCS4A01G088300 chr7A 96.337 273 10 0 4034 4306 164784414 164784686 3.670000e-122 449.0
20 TraesCS4A01G088300 chr7A 93.333 45 2 1 582 625 518506569 518506525 1.550000e-06 65.8
21 TraesCS4A01G088300 chr7A 85.938 64 6 3 589 650 720924291 720924229 1.550000e-06 65.8
22 TraesCS4A01G088300 chr3D 96.679 271 8 1 4037 4306 479240609 479240339 3.670000e-122 449.0
23 TraesCS4A01G088300 chr3D 90.000 60 5 1 589 648 85002974 85002916 7.170000e-10 76.8
24 TraesCS4A01G088300 chr1D 96.679 271 8 1 4037 4306 483179232 483178962 3.670000e-122 449.0
25 TraesCS4A01G088300 chr1D 97.500 40 1 0 1 40 280200675 280200714 1.200000e-07 69.4
26 TraesCS4A01G088300 chr1D 97.500 40 1 0 1 40 308070590 308070629 1.200000e-07 69.4
27 TraesCS4A01G088300 chr1D 97.500 40 1 0 1 40 346841539 346841578 1.200000e-07 69.4
28 TraesCS4A01G088300 chr2D 96.667 270 8 1 4041 4310 295804755 295804487 1.320000e-121 448.0
29 TraesCS4A01G088300 chr2D 96.667 270 8 1 4038 4306 340144317 340144048 1.320000e-121 448.0
30 TraesCS4A01G088300 chr2D 96.324 272 9 1 4034 4304 351507229 351507500 4.750000e-121 446.0
31 TraesCS4A01G088300 chr5D 96.296 270 10 0 4037 4306 264730402 264730133 1.710000e-120 444.0
32 TraesCS4A01G088300 chr5D 97.500 40 1 0 586 625 334244235 334244196 1.200000e-07 69.4
33 TraesCS4A01G088300 chr1A 92.308 117 8 1 1679 1795 209532766 209532881 1.490000e-36 165.0
34 TraesCS4A01G088300 chr2B 90.909 121 8 2 1676 1796 486955666 486955783 6.920000e-35 159.0
35 TraesCS4A01G088300 chr5A 93.069 101 6 1 1679 1779 675407604 675407505 5.390000e-31 147.0
36 TraesCS4A01G088300 chr3B 97.561 41 1 0 1 41 108912289 108912249 3.340000e-08 71.3
37 TraesCS4A01G088300 chr3B 97.561 41 1 0 1 41 418105819 418105779 3.340000e-08 71.3
38 TraesCS4A01G088300 chr7B 95.455 44 1 1 586 628 479202241 479202284 1.200000e-07 69.4
39 TraesCS4A01G088300 chr6D 97.500 40 1 0 1 40 268370908 268370947 1.200000e-07 69.4
40 TraesCS4A01G088300 chr6D 97.500 40 1 0 1 40 314095969 314096008 1.200000e-07 69.4
41 TraesCS4A01G088300 chr6D 97.500 40 1 0 1 40 371179911 371179950 1.200000e-07 69.4


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 TraesCS4A01G088300 chr4A 93889896 93896565 6669 False 12318.000000 12318 100.000000 1 6670 1 chr4A.!!$F1 6669
1 TraesCS4A01G088300 chr4D 370532535 370539314 6779 True 1466.333333 4331 92.182667 40 6618 6 chr4D.!!$R2 6578
2 TraesCS4A01G088300 chr4B 455617646 455624410 6764 True 1804.400000 3147 93.112400 40 6618 5 chr4B.!!$R1 6578


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
301 302 0.035534 TGTGTGGACGATGGGGATTG 60.036 55.000 0.00 0.00 0.00 2.67 F
1421 1802 0.033366 GCATTCCGGTTTGCCAAGTT 59.967 50.000 17.14 0.00 32.66 2.66 F
1427 1808 0.385390 CGGTTTGCCAAGTTTGAGCT 59.615 50.000 0.00 0.00 34.09 4.09 F
2020 2421 0.464870 CAGAGCACCTGATCCAGAGG 59.535 60.000 0.33 0.00 45.78 3.69 F
2134 2535 1.628846 AGAGTGCCGGTGAGGTAATTT 59.371 47.619 1.90 0.00 43.70 1.82 F
3357 3965 2.869801 CGTATGCCGGATGTTGTGTTAT 59.130 45.455 5.05 0.00 0.00 1.89 F
4059 4670 0.038310 AGGGCTGTTTGGTTCTAGGC 59.962 55.000 0.00 0.00 35.24 3.93 F
4061 4672 0.038310 GGCTGTTTGGTTCTAGGCCT 59.962 55.000 11.78 11.78 35.73 5.19 F
4272 4883 0.109723 TAACCTGAGGTGTGGCAACC 59.890 55.000 4.15 9.86 40.85 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1891 0.248215 CACTTAGGTACGGGTACGCG 60.248 60.000 28.27 28.27 46.04 6.01 R
2637 3244 1.593196 ACATTTCACGCCCATATCCG 58.407 50.000 0.00 0.00 0.00 4.18 R
3234 3842 3.520290 TCAGGACGTATAAACTGCTGG 57.480 47.619 0.00 0.00 0.00 4.85 R
3757 4367 0.670162 GCTCCTTTTGTGCAAGCTGA 59.330 50.000 0.00 0.00 0.00 4.26 R
4040 4651 0.038310 GCCTAGAACCAAACAGCCCT 59.962 55.000 0.00 0.00 0.00 5.19 R
4262 4873 0.107945 TTTGCCAAAGGTTGCCACAC 60.108 50.000 0.00 0.00 0.00 3.82 R
5417 6028 0.116342 TCCCCTTGGAGAGTGCTACA 59.884 55.000 0.00 0.00 35.03 2.74 R
5615 6226 0.235665 CAGCGGCTTGTTGTGTACTG 59.764 55.000 0.00 0.00 0.00 2.74 R
5677 6318 0.250295 TTTCACCGGCTTGACCAGAG 60.250 55.000 0.00 0.00 39.03 3.35 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)



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

AutoCloner maintained by Alex Coulton.