Multiple sequence alignment - TraesCS5B01G286700

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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 TraesCS5B01G286700 chr5B 100.000 2969 0 0 1 2969 472747780 472750748 0.000000e+00 5483
1 TraesCS5B01G286700 chr5B 92.544 456 32 2 2512 2965 475991164 475991619 0.000000e+00 652
2 TraesCS5B01G286700 chr5B 89.921 506 40 9 1969 2468 475990661 475991161 2.490000e-180 641
3 TraesCS5B01G286700 chr5D 98.456 2980 31 7 2 2969 391985892 391988868 0.000000e+00 5234
4 TraesCS5B01G286700 chr5D 91.972 984 63 12 1969 2945 395726001 395726975 0.000000e+00 1365
5 TraesCS5B01G286700 chr5D 90.737 1004 81 7 1969 2965 395924269 395925267 0.000000e+00 1328
6 TraesCS5B01G286700 chr5A 89.672 1007 91 9 1969 2968 501819228 501820228 0.000000e+00 1271
7 TraesCS5B01G286700 chr5A 89.741 1004 90 9 1969 2965 501827584 501828581 0.000000e+00 1271
8 TraesCS5B01G286700 chr2D 89.942 517 44 5 2458 2968 549927970 549927456 0.000000e+00 660
9 TraesCS5B01G286700 chr2D 90.000 500 41 7 2478 2968 549737338 549736839 3.230000e-179 638
10 TraesCS5B01G286700 chr2D 90.000 500 41 7 2478 2968 550250097 550249598 3.230000e-179 638
11 TraesCS5B01G286700 chr2D 87.287 527 42 20 1969 2481 549928520 549928005 1.980000e-161 579
12 TraesCS5B01G286700 chr2B 87.214 524 48 15 1969 2481 656237731 656237216 1.980000e-161 579
13 TraesCS5B01G286700 chr2B 86.266 466 53 8 1969 2428 691008735 691008275 2.060000e-136 496


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 TraesCS5B01G286700 chr5B 472747780 472750748 2968 False 5483.0 5483 100.0000 1 2969 1 chr5B.!!$F1 2968
1 TraesCS5B01G286700 chr5B 475990661 475991619 958 False 646.5 652 91.2325 1969 2965 2 chr5B.!!$F2 996
2 TraesCS5B01G286700 chr5D 391985892 391988868 2976 False 5234.0 5234 98.4560 2 2969 1 chr5D.!!$F1 2967
3 TraesCS5B01G286700 chr5D 395726001 395726975 974 False 1365.0 1365 91.9720 1969 2945 1 chr5D.!!$F2 976
4 TraesCS5B01G286700 chr5D 395924269 395925267 998 False 1328.0 1328 90.7370 1969 2965 1 chr5D.!!$F3 996
5 TraesCS5B01G286700 chr5A 501819228 501820228 1000 False 1271.0 1271 89.6720 1969 2968 1 chr5A.!!$F1 999
6 TraesCS5B01G286700 chr5A 501827584 501828581 997 False 1271.0 1271 89.7410 1969 2965 1 chr5A.!!$F2 996
7 TraesCS5B01G286700 chr2D 549927456 549928520 1064 True 619.5 660 88.6145 1969 2968 2 chr2D.!!$R3 999
8 TraesCS5B01G286700 chr2B 656237216 656237731 515 True 579.0 579 87.2140 1969 2481 1 chr2B.!!$R1 512

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
439 445 0.249699 CAACACCACCGTCTGCTACA 60.250 55.0 0.00 0.00 0.00 2.74 F
534 540 0.387239 TGTCACGATCGACTGCTGTG 60.387 55.0 24.34 7.76 36.82 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1254 1.406898 GCCACATCTCTCTCATCGTCA 59.593 52.381 0.0 0.0 0.00 4.35 R
2235 2253 2.223665 GCATGAGCTTTACATTCTGGGC 60.224 50.000 0.0 0.0 37.91 5.36 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
290 291 1.446272 CGACTTCTCGGTTGAGGCC 60.446 63.158 0.00 0.00 42.79 5.19
364 370 1.531840 AGAGCAGTCCACCGTCTGT 60.532 57.895 0.00 0.00 34.57 3.41
391 397 2.262471 CTGCTGCAAACCGCCTCATC 62.262 60.000 3.02 0.00 41.33 2.92
415 421 0.323178 CTTCAGAGCTTGCCACCCAT 60.323 55.000 0.00 0.00 0.00 4.00
438 444 1.566018 GCAACACCACCGTCTGCTAC 61.566 60.000 0.00 0.00 0.00 3.58
439 445 0.249699 CAACACCACCGTCTGCTACA 60.250 55.000 0.00 0.00 0.00 2.74
505 511 1.001641 ATGAGCAAGGGTGGCTGTC 60.002 57.895 0.00 0.00 42.78 3.51
534 540 0.387239 TGTCACGATCGACTGCTGTG 60.387 55.000 24.34 7.76 36.82 3.66
601 607 4.164087 TGTTGTGGTCGCCGGTGT 62.164 61.111 16.01 0.00 0.00 4.16
619 625 3.339353 TAGCGTCGTCGTCGTCGTG 62.339 63.158 19.72 7.05 46.29 4.35
1000 1012 8.423906 AGTTCTCTCTAGGAATTGACTTACAA 57.576 34.615 0.00 0.00 42.95 2.41
1136 1148 4.428209 AGACGTCTTATCTTGACATGCTG 58.572 43.478 13.58 0.00 34.37 4.41
1152 1164 3.371097 CTGCCATGTCGTAGCGGGT 62.371 63.158 0.00 0.00 0.00 5.28
1242 1254 2.752030 TCTGGCCAGATACTACTTGCT 58.248 47.619 32.00 0.00 31.41 3.91
1350 1362 2.571653 TGATCGGGTTGTCAAGAAGGAT 59.428 45.455 0.00 0.00 0.00 3.24
1372 1384 6.777580 GGATATGGAATTAGTCATGTTGGGTT 59.222 38.462 0.00 0.00 0.00 4.11
1374 1386 9.520515 GATATGGAATTAGTCATGTTGGGTTAT 57.479 33.333 0.00 0.00 0.00 1.89
1413 1425 6.008331 GGGTGTAATTAAAGAACCAGGAACT 58.992 40.000 0.00 0.00 43.88 3.01
1583 1595 3.071023 CGGTGTCATATGTATCAACCCCT 59.929 47.826 1.90 0.00 0.00 4.79
1810 1822 3.564225 CCGTGTATATTTTCAGAAGGGCC 59.436 47.826 0.00 0.00 0.00 5.80
1850 1862 4.630644 TTGAGAAGATCCTTTCAGCAGT 57.369 40.909 0.00 0.00 0.00 4.40
2235 2253 7.630026 TCTAATATGTCGCTGCACTTAAATTG 58.370 34.615 0.00 0.00 0.00 2.32
2402 2423 6.716284 TGGAATCATGTATGTGGTTCACTTA 58.284 36.000 2.75 0.00 35.11 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.363306 ACCAGCAAACAATCCTGACA 57.637 45.000 0.00 0.00 0.00 3.58
76 77 6.310149 AGAAAAATCTCTCCATCACCACTTT 58.690 36.000 0.00 0.00 0.00 2.66
364 370 2.901339 TTTGCAGCAGCTCGCACA 60.901 55.556 16.27 9.50 46.13 4.57
415 421 1.078072 AGACGGTGGTGTTGCAACA 60.078 52.632 27.96 27.96 36.38 3.33
438 444 2.110967 CAGCACTCGCATCCCCTTG 61.111 63.158 0.00 0.00 42.27 3.61
439 445 2.270205 CAGCACTCGCATCCCCTT 59.730 61.111 0.00 0.00 42.27 3.95
511 517 0.435008 GCAGTCGATCGTGACACAAC 59.565 55.000 15.94 3.77 41.41 3.32
1136 1148 1.299926 CTACCCGCTACGACATGGC 60.300 63.158 0.00 0.00 0.00 4.40
1242 1254 1.406898 GCCACATCTCTCTCATCGTCA 59.593 52.381 0.00 0.00 0.00 4.35
1372 1384 9.875708 AATTACACCCTTAGGCATGAAAATATA 57.124 29.630 0.00 0.00 36.11 0.86
1374 1386 9.702253 TTAATTACACCCTTAGGCATGAAAATA 57.298 29.630 0.00 0.00 36.11 1.40
1413 1425 6.090129 GCATTACTTTGATTTGCCGTAAGAA 58.910 36.000 0.00 0.00 43.02 2.52
1583 1595 3.319198 GGTGCTCCCGAAGTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
1810 1822 7.860918 TCTCAATCATTTCAGGAATTGAGAG 57.139 36.000 17.97 14.16 44.92 3.20
1850 1862 5.123186 CACAAGAACACTTTTACTCACCACA 59.877 40.000 0.00 0.00 0.00 4.17
1894 1906 5.756347 CCATGAGTATTTGGGAAATGCATTG 59.244 40.000 13.82 0.00 36.15 2.82
1938 1950 5.238650 CCTTCGACTGAAAACAGTTGGTATT 59.761 40.000 14.87 0.00 37.23 1.89
1961 1973 5.675538 AGTGTATGAGCAATTCCTACTTCC 58.324 41.667 0.00 0.00 30.74 3.46
2235 2253 2.223665 GCATGAGCTTTACATTCTGGGC 60.224 50.000 0.00 0.00 37.91 5.36


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

AutoCloner maintained by Alex Coulton.