Multiple sequence alignment - TraesCS5B01G250500

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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 TraesCS5B01G250500 chr5B 100.000 2213 0 0 1 2213 432875609 432877821 0.000000e+00 4087
1 TraesCS5B01G250500 chr3A 96.486 2220 69 6 1 2213 672879550 672877333 0.000000e+00 3659
2 TraesCS5B01G250500 chr3B 96.183 2227 70 7 1 2213 201561898 201559673 0.000000e+00 3627
3 TraesCS5B01G250500 chr3B 84.233 463 42 16 1750 2207 821762710 821763146 2.630000e-114 422
4 TraesCS5B01G250500 chr3B 83.153 463 40 16 1750 2207 821794088 821794517 2.660000e-104 388
5 TraesCS5B01G250500 chr3B 83.715 393 33 16 1820 2207 821778142 821778508 2.100000e-90 342
6 TraesCS5B01G250500 chr1B 96.090 2225 73 6 1 2213 633729987 633727765 0.000000e+00 3615
7 TraesCS5B01G250500 chr2D 96.133 2224 56 12 1 2211 272802780 272800574 0.000000e+00 3603
8 TraesCS5B01G250500 chr2D 97.466 1815 39 4 1 1808 630268106 630269920 0.000000e+00 3090
9 TraesCS5B01G250500 chr5D 95.770 2222 80 10 1 2213 432293834 432291618 0.000000e+00 3570
10 TraesCS5B01G250500 chr4A 95.090 2220 99 6 1 2213 310761291 310763507 0.000000e+00 3487
11 TraesCS5B01G250500 chr4A 94.144 2220 97 18 1 2213 219340979 219338786 0.000000e+00 3349
12 TraesCS5B01G250500 chr7A 93.699 2222 109 19 1 2213 352678563 352676364 0.000000e+00 3299


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 TraesCS5B01G250500 chr5B 432875609 432877821 2212 False 4087 4087 100.000 1 2213 1 chr5B.!!$F1 2212
1 TraesCS5B01G250500 chr3A 672877333 672879550 2217 True 3659 3659 96.486 1 2213 1 chr3A.!!$R1 2212
2 TraesCS5B01G250500 chr3B 201559673 201561898 2225 True 3627 3627 96.183 1 2213 1 chr3B.!!$R1 2212
3 TraesCS5B01G250500 chr1B 633727765 633729987 2222 True 3615 3615 96.090 1 2213 1 chr1B.!!$R1 2212
4 TraesCS5B01G250500 chr2D 272800574 272802780 2206 True 3603 3603 96.133 1 2211 1 chr2D.!!$R1 2210
5 TraesCS5B01G250500 chr2D 630268106 630269920 1814 False 3090 3090 97.466 1 1808 1 chr2D.!!$F1 1807
6 TraesCS5B01G250500 chr5D 432291618 432293834 2216 True 3570 3570 95.770 1 2213 1 chr5D.!!$R1 2212
7 TraesCS5B01G250500 chr4A 310761291 310763507 2216 False 3487 3487 95.090 1 2213 1 chr4A.!!$F1 2212
8 TraesCS5B01G250500 chr4A 219338786 219340979 2193 True 3349 3349 94.144 1 2213 1 chr4A.!!$R1 2212
9 TraesCS5B01G250500 chr7A 352676364 352678563 2199 True 3299 3299 93.699 1 2213 1 chr7A.!!$R1 2212

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
497 519 2.235402 TCTAGCGGACGGAATTCCTTTT 59.765 45.455 22.05 6.38 32.88 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 1357 5.241403 TGTTGACCATAACTCATGAACCT 57.759 39.13 0.0 0.0 36.69 3.5 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
251 256 2.313041 CCTCCCTGGGGAAAGAAGAATT 59.687 50.000 14.00 0.00 44.66 2.17
463 485 5.620738 AAGGATGAGATCAATTCGGAAGA 57.379 39.130 0.00 0.00 39.20 2.87
482 504 6.508721 CGGAAGAGCTTTTTCTTATTCTAGCG 60.509 42.308 10.56 1.49 37.53 4.26
497 519 2.235402 TCTAGCGGACGGAATTCCTTTT 59.765 45.455 22.05 6.38 32.88 2.27
844 871 5.044558 CAGAAGCGGAGGAAGAATTAGTAC 58.955 45.833 0.00 0.00 0.00 2.73
847 874 3.132467 AGCGGAGGAAGAATTAGTACCAC 59.868 47.826 0.00 0.00 0.00 4.16
848 875 3.118884 GCGGAGGAAGAATTAGTACCACA 60.119 47.826 0.00 0.00 0.00 4.17
857 884 9.185680 GGAAGAATTAGTACCACATTACCAAAT 57.814 33.333 0.00 0.00 0.00 2.32
1208 1237 4.200092 ACCTCTTCTCAACTTGTTTCACC 58.800 43.478 0.00 0.00 0.00 4.02
1381 1410 4.202121 CGTGCTACAAGGTACATAGGTCAT 60.202 45.833 0.00 0.00 0.00 3.06
1413 1442 6.388619 AACTACCTTATCCCACACAAATCT 57.611 37.500 0.00 0.00 0.00 2.40
1499 1528 7.330700 GGCGAATCCACTTTGAATTTGATAAAA 59.669 33.333 0.00 0.00 34.01 1.52
1763 1792 5.514834 CGGTTACCAATCTCCATAATGGGAT 60.515 44.000 1.13 0.00 38.32 3.85
1765 1794 7.112779 GGTTACCAATCTCCATAATGGGATAG 58.887 42.308 0.00 0.00 38.32 2.08
1766 1795 5.184892 ACCAATCTCCATAATGGGATAGC 57.815 43.478 0.00 0.00 38.32 2.97
2181 2215 4.903045 TTTGTTCTTCTACTAGGGGGTG 57.097 45.455 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
463 485 4.567159 CGTCCGCTAGAATAAGAAAAAGCT 59.433 41.667 0.00 0.00 0.00 3.74
482 504 6.510879 AATTAGACAAAAGGAATTCCGTCC 57.489 37.500 18.82 6.43 42.08 4.79
844 871 6.922957 CCGGAATATTCAATTTGGTAATGTGG 59.077 38.462 17.07 0.00 0.00 4.17
847 874 9.840427 GATACCGGAATATTCAATTTGGTAATG 57.160 33.333 17.07 0.00 34.67 1.90
848 875 9.581289 TGATACCGGAATATTCAATTTGGTAAT 57.419 29.630 17.07 9.69 34.67 1.89
857 884 9.581289 AACCATATTTGATACCGGAATATTCAA 57.419 29.630 17.07 6.82 0.00 2.69
938 965 1.517832 CACCCGCCCAAGTAGAGAG 59.482 63.158 0.00 0.00 0.00 3.20
1328 1357 5.241403 TGTTGACCATAACTCATGAACCT 57.759 39.130 0.00 0.00 36.69 3.50
1381 1410 8.480501 GTGTGGGATAAGGTAGTTATGAAACTA 58.519 37.037 0.00 0.00 44.26 2.24
1413 1442 8.310122 AGGGTAGTGAATCGTTATAGGTAAAA 57.690 34.615 0.00 0.00 0.00 1.52
1499 1528 6.710295 TGAACACATACTTCACAAGCAATACT 59.290 34.615 0.00 0.00 0.00 2.12
1618 1647 7.383572 TCAACACAATTGCCACAAAATATACAC 59.616 33.333 5.05 0.00 0.00 2.90
1763 1792 7.517614 TCCTAATTGTTTGAATTGTGTGCTA 57.482 32.000 0.00 0.00 0.00 3.49
1765 1794 7.656707 ATTCCTAATTGTTTGAATTGTGTGC 57.343 32.000 0.00 0.00 0.00 4.57
1766 1795 8.427012 CGAATTCCTAATTGTTTGAATTGTGTG 58.573 33.333 0.00 0.00 37.51 3.82
2181 2215 7.014711 GGGGTTGGTAAGTAATACTACTCCTAC 59.985 44.444 2.69 7.72 37.39 3.18


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

AutoCloner maintained by Alex Coulton.