Multiple sequence alignment - TraesCS5A01G476300

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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 TraesCS5A01G476300 chr5A 100.000 2507 0 0 1 2507 650824208 650826714 0.000000e+00 4630.0
1 TraesCS5A01G476300 chr5D 96.695 2511 67 11 4 2507 524577188 524579689 0.000000e+00 4163.0
2 TraesCS5A01G476300 chr5D 87.195 164 20 1 4 166 503522403 503522240 4.260000e-43 185.0
3 TraesCS5A01G476300 chr5D 86.517 89 10 2 74 162 520299470 520299556 2.050000e-16 97.1
4 TraesCS5A01G476300 chr6D 88.672 1589 154 18 299 1867 7994325 7992743 0.000000e+00 1914.0
5 TraesCS5A01G476300 chr6D 88.419 1347 141 10 528 1867 7715858 7717196 0.000000e+00 1609.0
6 TraesCS5A01G476300 chr6D 82.246 1487 234 25 334 1805 8967568 8969039 0.000000e+00 1256.0
7 TraesCS5A01G476300 chr6D 89.920 377 33 5 1868 2242 7717380 7717753 4.850000e-132 481.0
8 TraesCS5A01G476300 chr6D 88.918 379 31 8 1868 2245 7992561 7992193 8.170000e-125 457.0
9 TraesCS5A01G476300 chr6D 83.500 200 29 4 2049 2246 7719800 7719997 1.530000e-42 183.0
10 TraesCS5A01G476300 chr6D 79.545 220 33 7 2270 2485 7997369 7997158 2.010000e-31 147.0
11 TraesCS5A01G476300 chr6D 84.375 128 19 1 1924 2051 9545017 9544891 9.420000e-25 124.0
12 TraesCS5A01G476300 chr6A 87.131 1593 173 19 299 1867 8202388 8200804 0.000000e+00 1777.0
13 TraesCS5A01G476300 chr6A 86.493 1651 181 17 240 1867 7986676 7988307 0.000000e+00 1775.0
14 TraesCS5A01G476300 chr6A 79.762 168 24 4 1868 2027 23890383 23890548 2.040000e-21 113.0
15 TraesCS5A01G476300 chr6A 84.211 114 18 0 2343 2456 8447246 8447133 7.330000e-21 111.0
16 TraesCS5A01G476300 chr6B 86.547 1561 160 20 324 1867 14622763 14621236 0.000000e+00 1674.0
17 TraesCS5A01G476300 chr6B 86.498 1459 170 17 299 1736 14330391 14331843 0.000000e+00 1578.0
18 TraesCS5A01G476300 chr6B 84.347 1316 196 8 427 1736 14550128 14548817 0.000000e+00 1280.0
19 TraesCS5A01G476300 chr6B 91.534 378 30 2 1868 2244 14548476 14548100 1.030000e-143 520.0
20 TraesCS5A01G476300 chr6B 89.153 378 30 8 1868 2244 14621054 14620687 6.320000e-126 460.0
21 TraesCS5A01G476300 chr6B 85.676 377 28 8 1868 2244 14332165 14332515 8.470000e-100 374.0
22 TraesCS5A01G476300 chr6B 87.786 131 9 6 1741 1867 14548781 14548654 2.010000e-31 147.0
23 TraesCS5A01G476300 chr6B 78.539 219 37 7 2270 2485 14627891 14627680 4.350000e-28 135.0
24 TraesCS5A01G476300 chr6B 82.812 128 21 1 1924 2051 17497073 17496947 2.040000e-21 113.0
25 TraesCS5A01G476300 chr6B 92.188 64 1 2 2252 2311 14332593 14332656 1.240000e-13 87.9
26 TraesCS5A01G476300 chr1B 84.556 1677 182 41 240 1867 27678218 27676570 0.000000e+00 1591.0
27 TraesCS5A01G476300 chr1B 85.547 256 30 2 2252 2507 27675806 27675558 6.880000e-66 261.0
28 TraesCS5A01G476300 chr1B 92.073 164 13 0 2253 2416 27750844 27750681 5.390000e-57 231.0
29 TraesCS5A01G476300 chr1B 87.368 190 20 1 1996 2185 27751145 27750960 5.430000e-52 215.0
30 TraesCS5A01G476300 chr1B 90.816 98 6 3 1868 1965 27751238 27751144 7.280000e-26 128.0
31 TraesCS5A01G476300 chr1B 86.957 92 10 2 74 165 667234744 667234655 4.410000e-18 102.0
32 TraesCS5A01G476300 chr2D 91.139 158 13 1 4 160 592109270 592109427 1.950000e-51 213.0
33 TraesCS5A01G476300 chr2D 88.550 131 14 1 37 166 585077626 585077756 9.280000e-35 158.0
34 TraesCS5A01G476300 chr2B 89.506 162 14 2 4 162 362246737 362246898 4.230000e-48 202.0
35 TraesCS5A01G476300 chr2B 90.476 126 12 0 37 162 707260001 707260126 1.540000e-37 167.0
36 TraesCS5A01G476300 chr3D 89.313 131 13 1 37 166 316544760 316544630 2.000000e-36 163.0


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 TraesCS5A01G476300 chr5A 650824208 650826714 2506 False 4630.000000 4630 100.000000 1 2507 1 chr5A.!!$F1 2506
1 TraesCS5A01G476300 chr5D 524577188 524579689 2501 False 4163.000000 4163 96.695000 4 2507 1 chr5D.!!$F2 2503
2 TraesCS5A01G476300 chr6D 8967568 8969039 1471 False 1256.000000 1256 82.246000 334 1805 1 chr6D.!!$F1 1471
3 TraesCS5A01G476300 chr6D 7992193 7997369 5176 True 839.333333 1914 85.711667 299 2485 3 chr6D.!!$R2 2186
4 TraesCS5A01G476300 chr6D 7715858 7719997 4139 False 757.666667 1609 87.279667 528 2246 3 chr6D.!!$F2 1718
5 TraesCS5A01G476300 chr6A 8200804 8202388 1584 True 1777.000000 1777 87.131000 299 1867 1 chr6A.!!$R1 1568
6 TraesCS5A01G476300 chr6A 7986676 7988307 1631 False 1775.000000 1775 86.493000 240 1867 1 chr6A.!!$F1 1627
7 TraesCS5A01G476300 chr6B 14620687 14622763 2076 True 1067.000000 1674 87.850000 324 2244 2 chr6B.!!$R4 1920
8 TraesCS5A01G476300 chr6B 14330391 14332656 2265 False 679.966667 1578 88.120667 299 2311 3 chr6B.!!$F1 2012
9 TraesCS5A01G476300 chr6B 14548100 14550128 2028 True 649.000000 1280 87.889000 427 2244 3 chr6B.!!$R3 1817
10 TraesCS5A01G476300 chr1B 27675558 27678218 2660 True 926.000000 1591 85.051500 240 2507 2 chr1B.!!$R2 2267

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
230 235 0.107831 CCACTTCACTTGGGGTCGAA 59.892 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 4292 6.43 AGTCATACACAGTTACCAATTTCCAC 59.57 38.462 0.0 0.0 0.0 4.02 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
109 111 9.787435 TGTTCTATTAACTTGACCATTACTTGT 57.213 29.630 0.00 0.00 0.00 3.16
125 127 2.425312 ACTTGTTTTGCCACATCGTTGA 59.575 40.909 0.00 0.00 0.00 3.18
128 130 2.032799 TGTTTTGCCACATCGTTGAGAC 59.967 45.455 0.00 0.00 0.00 3.36
173 178 5.470368 CGATTCCGATCTTGTACATGGTAT 58.530 41.667 8.74 0.91 38.22 2.73
192 197 2.110627 GGCCAGCGAGCATGAGAT 59.889 61.111 0.00 0.00 0.00 2.75
228 233 4.379174 CCACTTCACTTGGGGTCG 57.621 61.111 0.00 0.00 0.00 4.79
230 235 0.107831 CCACTTCACTTGGGGTCGAA 59.892 55.000 0.00 0.00 0.00 3.71
234 239 0.107831 TTCACTTGGGGTCGAACCAG 59.892 55.000 23.64 13.89 41.02 4.00
236 241 0.320771 CACTTGGGGTCGAACCAGAG 60.321 60.000 23.64 19.82 41.02 3.35
237 242 1.376037 CTTGGGGTCGAACCAGAGC 60.376 63.158 23.64 3.86 41.02 4.09
238 243 2.111999 CTTGGGGTCGAACCAGAGCA 62.112 60.000 23.64 6.99 41.02 4.26
368 3115 4.821589 CTGCCTCCGCCTCCGTTC 62.822 72.222 0.00 0.00 0.00 3.95
877 3646 1.887198 ACATTCTCTCGTCCAACGTCT 59.113 47.619 0.00 0.00 43.14 4.18
1051 3820 2.423926 CCGTAGATCTGGGATGTTCG 57.576 55.000 5.18 0.00 0.00 3.95
1575 4348 9.498176 GACAGAGTTTTTACCATTCCTAGTAAA 57.502 33.333 0.00 0.00 36.82 2.01
1768 4611 3.735237 TCGCCTACAATCTCTGGAATC 57.265 47.619 0.00 0.00 0.00 2.52
2079 5337 2.975489 AGTTCAGGCCCTGATACTATGG 59.025 50.000 15.62 0.00 40.39 2.74
2284 5618 1.393883 GGCGCTAGCTGTTTCTGTTAC 59.606 52.381 13.93 0.00 44.37 2.50
2285 5619 2.066262 GCGCTAGCTGTTTCTGTTACA 58.934 47.619 13.93 0.00 41.01 2.41
2328 5665 6.373216 CCACGGATACTCAGAATTTTGGTTAA 59.627 38.462 0.00 0.00 0.00 2.01
2357 5694 8.197439 CCCCTTTTGAAAGCCTTATATTACTTG 58.803 37.037 0.00 0.00 34.69 3.16
2445 5782 6.378661 TGCATTATATATCTTGAGGGCTGT 57.621 37.500 0.00 0.00 0.00 4.40
2470 5807 3.055094 GGACTGAAGTTCTAGCCATTGGA 60.055 47.826 6.95 0.00 0.00 3.53
2472 5809 5.163301 GGACTGAAGTTCTAGCCATTGGATA 60.163 44.000 6.95 3.19 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.331466 ACAATATATCTCCATAGTCACCAGAAT 57.669 33.333 0.00 0.00 0.00 2.40
11 12 9.955102 TCGTGTAGTACAATATATCTCCATAGT 57.045 33.333 4.11 0.00 0.00 2.12
24 25 7.724305 AGAACAAACATTCGTGTAGTACAAT 57.276 32.000 4.11 0.00 33.57 2.71
60 61 8.041143 ACACCAGGCTTTATTAGGATATAACA 57.959 34.615 0.00 0.00 0.00 2.41
61 62 8.919777 AACACCAGGCTTTATTAGGATATAAC 57.080 34.615 0.00 0.00 0.00 1.89
71 72 8.739972 CAAGTTAATAGAACACCAGGCTTTATT 58.260 33.333 0.00 0.00 0.00 1.40
109 111 1.606668 GGTCTCAACGATGTGGCAAAA 59.393 47.619 1.83 0.00 0.00 2.44
150 152 3.717707 ACCATGTACAAGATCGGAATCG 58.282 45.455 0.00 0.00 36.97 3.34
173 178 4.478371 CTCATGCTCGCTGGCCCA 62.478 66.667 0.00 0.00 0.00 5.36
192 197 2.867855 GCCCCACACGTCAGTCTCA 61.868 63.158 0.00 0.00 0.00 3.27
216 221 0.761323 TCTGGTTCGACCCCAAGTGA 60.761 55.000 0.00 0.00 37.50 3.41
227 232 1.294659 GGTGCTCTTGCTCTGGTTCG 61.295 60.000 0.00 0.00 40.48 3.95
228 233 0.957888 GGGTGCTCTTGCTCTGGTTC 60.958 60.000 0.00 0.00 40.48 3.62
230 235 2.149383 TGGGTGCTCTTGCTCTGGT 61.149 57.895 0.00 0.00 40.48 4.00
234 239 2.731691 TTCCGTGGGTGCTCTTGCTC 62.732 60.000 0.00 0.00 40.48 4.26
236 241 1.244019 ATTTCCGTGGGTGCTCTTGC 61.244 55.000 0.00 0.00 40.20 4.01
237 242 0.804989 GATTTCCGTGGGTGCTCTTG 59.195 55.000 0.00 0.00 0.00 3.02
238 243 0.693049 AGATTTCCGTGGGTGCTCTT 59.307 50.000 0.00 0.00 0.00 2.85
1521 4292 6.430000 AGTCATACACAGTTACCAATTTCCAC 59.570 38.462 0.00 0.00 0.00 4.02
1768 4611 7.953158 ACACAAATATATTCATGGACTCTCG 57.047 36.000 0.00 0.00 0.00 4.04
1820 4681 9.167311 AGAAAATTGGTCTACTCACATATTCAC 57.833 33.333 0.00 0.00 0.00 3.18
2328 5665 2.775490 AAGGCTTTCAAAAGGGGAGT 57.225 45.000 0.00 0.00 36.53 3.85
2357 5694 4.925068 TCTTTCTGTGCTTGAAAAAGCTC 58.075 39.130 11.39 8.47 45.66 4.09
2445 5782 5.338381 CCAATGGCTAGAACTTCAGTCCTAA 60.338 44.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.