Multiple sequence alignment - TraesCS4B01G147300

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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 TraesCS4B01G147300 chr4B 100.000 2594 0 0 1 2594 209299631 209302224 0 4791
1 TraesCS4B01G147300 chr5A 98.002 2602 44 3 1 2594 19248878 19246277 0 4510
2 TraesCS4B01G147300 chr7D 97.924 2601 47 3 1 2594 203499965 203502565 0 4497
3 TraesCS4B01G147300 chr7D 97.924 2601 47 3 1 2594 381923967 381926567 0 4497
4 TraesCS4B01G147300 chr7D 97.848 2602 48 3 1 2594 382050044 382052645 0 4488
5 TraesCS4B01G147300 chr7B 97.958 2596 50 3 1 2594 716878814 716876220 0 4497
6 TraesCS4B01G147300 chr7B 97.728 2597 55 3 1 2594 742989412 742992007 0 4466
7 TraesCS4B01G147300 chr1A 97.843 2596 54 2 1 2594 498691261 498688666 0 4482
8 TraesCS4B01G147300 chr7A 97.804 2596 55 2 1 2594 60279279 60281874 0 4477
9 TraesCS4B01G147300 chr6B 96.333 2291 81 2 1 2289 297473037 297475326 0 3762


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 TraesCS4B01G147300 chr4B 209299631 209302224 2593 False 4791 4791 100.000 1 2594 1 chr4B.!!$F1 2593
1 TraesCS4B01G147300 chr5A 19246277 19248878 2601 True 4510 4510 98.002 1 2594 1 chr5A.!!$R1 2593
2 TraesCS4B01G147300 chr7D 203499965 203502565 2600 False 4497 4497 97.924 1 2594 1 chr7D.!!$F1 2593
3 TraesCS4B01G147300 chr7D 381923967 381926567 2600 False 4497 4497 97.924 1 2594 1 chr7D.!!$F2 2593
4 TraesCS4B01G147300 chr7D 382050044 382052645 2601 False 4488 4488 97.848 1 2594 1 chr7D.!!$F3 2593
5 TraesCS4B01G147300 chr7B 716876220 716878814 2594 True 4497 4497 97.958 1 2594 1 chr7B.!!$R1 2593
6 TraesCS4B01G147300 chr7B 742989412 742992007 2595 False 4466 4466 97.728 1 2594 1 chr7B.!!$F1 2593
7 TraesCS4B01G147300 chr1A 498688666 498691261 2595 True 4482 4482 97.843 1 2594 1 chr1A.!!$R1 2593
8 TraesCS4B01G147300 chr7A 60279279 60281874 2595 False 4477 4477 97.804 1 2594 1 chr7A.!!$F1 2593
9 TraesCS4B01G147300 chr6B 297473037 297475326 2289 False 3762 3762 96.333 1 2289 1 chr6B.!!$F1 2288

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
570 575 0.466124 GGATAGCAGCCTTCCTTCGT 59.534 55.0 4.28 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2476 0.608035 GACGATTGAAGCCCCCAACA 60.608 55.0 0.0 0.0 0.0 3.33 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
59 60 2.632377 TGGATTGGATCGTTTCTGCTC 58.368 47.619 0.00 0.00 0.00 4.26
161 162 1.988846 CCCCTCCCTCTGTCTTTTTCT 59.011 52.381 0.00 0.00 0.00 2.52
235 236 4.058817 GGAAGAAAGAAAGTCGAAGAGCA 58.941 43.478 0.00 0.00 36.95 4.26
236 237 4.084276 GGAAGAAAGAAAGTCGAAGAGCAC 60.084 45.833 0.00 0.00 36.95 4.40
281 282 1.817740 GCAACACAGGAAAGCACCCTA 60.818 52.381 0.00 0.00 31.64 3.53
307 308 0.998928 TAATCCCTGCAGCTTCCCAA 59.001 50.000 8.66 0.00 0.00 4.12
380 384 2.107378 TGTTTGAGCCTATGTTCACCCA 59.893 45.455 0.00 0.00 30.81 4.51
460 464 2.881111 ACCACTAAAGGAAAGGCTCC 57.119 50.000 0.00 0.00 45.81 4.70
570 575 0.466124 GGATAGCAGCCTTCCTTCGT 59.534 55.000 4.28 0.00 0.00 3.85
572 577 1.137086 GATAGCAGCCTTCCTTCGTGA 59.863 52.381 0.00 0.00 0.00 4.35
762 767 1.596934 GTGTGGAATGGCCGAGAGA 59.403 57.895 0.00 0.00 40.66 3.10
841 846 4.768130 TGGAAAACAACTTTCACGTTCA 57.232 36.364 0.00 0.00 44.61 3.18
935 940 3.949430 ACTTGTGGGGCCCTATCTATTA 58.051 45.455 25.93 0.00 0.00 0.98
994 999 5.710567 TCGGACTCAATCTCTCTTTTGACTA 59.289 40.000 0.00 0.00 0.00 2.59
1126 1131 1.974028 TGCTTCCTATGGGGGTACAA 58.026 50.000 0.00 0.00 35.33 2.41
1128 1133 2.856231 TGCTTCCTATGGGGGTACAATT 59.144 45.455 0.00 0.00 35.33 2.32
1429 1434 4.974645 AATCCTATTTCGGCTATGACCA 57.025 40.909 0.00 0.00 0.00 4.02
1432 1437 3.260884 TCCTATTTCGGCTATGACCATCC 59.739 47.826 0.00 0.00 0.00 3.51
1474 1479 0.326808 AGGAATACCCCCGTTAGCCA 60.327 55.000 0.00 0.00 36.73 4.75
1558 1563 2.447443 CAGTGGGAGTAGTGACTAGCA 58.553 52.381 0.00 0.00 35.45 3.49
1682 1687 2.092267 ACAGATGGGAATGCATGCTACA 60.092 45.455 20.33 10.63 0.00 2.74
1846 1851 0.617820 ATACTGAGGTGCTCCCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
1926 1931 3.256704 ACAGAGGTGACTAATTCCCCAA 58.743 45.455 0.00 0.00 44.43 4.12
2011 2016 0.736325 AAGAACGGCGAAGTCCATCG 60.736 55.000 16.62 0.00 45.41 3.84
2273 2278 5.871465 TCGATTTCGATTTCATGAAACCA 57.129 34.783 22.71 7.19 44.22 3.67
2289 2294 9.076781 TCATGAAACCATTGATTCAAAGAACTA 57.923 29.630 2.68 0.00 38.88 2.24
2362 2369 0.801067 CGTAGTACCCGAAGCACTGC 60.801 60.000 0.00 0.00 0.00 4.40
2533 2545 3.914426 AACGGAGCCTGACTTATTCAT 57.086 42.857 0.00 0.00 32.17 2.57
2562 2574 0.461548 TGGAGCCTATCGAAGCACTG 59.538 55.000 8.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.334676 TCCAATCCATTCGGGGCTTT 59.665 50.000 0.00 0.00 37.22 3.51
59 60 0.109132 GCCTTCATTTCGTTGGCAGG 60.109 55.000 0.00 0.00 42.79 4.85
161 162 2.578021 AGAGGGGAAGATTAGCAAAGCA 59.422 45.455 0.00 0.00 0.00 3.91
206 207 1.420138 ACTTTCTTTCTTCCTCCCGCA 59.580 47.619 0.00 0.00 0.00 5.69
281 282 4.081476 GGAAGCTGCAGGGATTACAAAAAT 60.081 41.667 17.12 0.00 0.00 1.82
570 575 1.573829 GAACGTCGGCAGGCAAATCA 61.574 55.000 0.00 0.00 0.00 2.57
572 577 0.036765 TAGAACGTCGGCAGGCAAAT 60.037 50.000 0.00 0.00 0.00 2.32
668 673 1.072159 GAACCTGCTGCTCAGTGGT 59.928 57.895 0.00 9.63 41.25 4.16
762 767 7.836183 GCTTGGATTATATATCCATTTGGTCCT 59.164 37.037 13.86 0.00 46.51 3.85
935 940 1.573108 TCTTGGGGCTCGAGAGATTT 58.427 50.000 18.75 0.00 40.84 2.17
969 974 5.186797 AGTCAAAAGAGAGATTGAGTCCGAT 59.813 40.000 0.00 0.00 34.90 4.18
994 999 9.849752 ATAGATATCAGGTGCCCACATATATAT 57.150 33.333 5.32 0.00 0.00 0.86
1126 1131 7.042254 GCTGCAGAAAAAGAAGATTTGTTGAAT 60.042 33.333 20.43 0.00 0.00 2.57
1128 1133 5.750067 GCTGCAGAAAAAGAAGATTTGTTGA 59.250 36.000 20.43 0.00 0.00 3.18
1405 1410 4.083271 GGTCATAGCCGAAATAGGATTTGC 60.083 45.833 0.00 0.00 30.49 3.68
1407 1412 5.304686 TGGTCATAGCCGAAATAGGATTT 57.695 39.130 0.00 0.00 0.00 2.17
1429 1434 5.997746 CGTATGAGAACATTGTAATGGGGAT 59.002 40.000 9.22 0.00 40.70 3.85
1432 1437 4.574421 TGCGTATGAGAACATTGTAATGGG 59.426 41.667 9.22 0.00 40.70 4.00
1682 1687 2.317040 TCAGACTCGACCCTGTCTTTT 58.683 47.619 2.51 0.00 41.06 2.27
1846 1851 2.526993 CGCGTCGTTCCAACAACCA 61.527 57.895 0.00 0.00 0.00 3.67
1880 1885 6.782000 TCCCTTCATCTTTTTGAAAGGAATCA 59.218 34.615 2.76 0.00 41.22 2.57
1926 1931 0.966179 GTTTTCCGCCCCAAATGAGT 59.034 50.000 0.00 0.00 0.00 3.41
2011 2016 6.187682 TCTTATTTCTTCATTGGAGGGTTCC 58.812 40.000 0.00 0.00 44.31 3.62
2083 2088 4.601857 TCCCCCACACTTCTTTATTTCTCT 59.398 41.667 0.00 0.00 0.00 3.10
2273 2278 6.183360 GGCTAAGCGTAGTTCTTTGAATCAAT 60.183 38.462 8.50 0.00 0.00 2.57
2362 2369 1.043116 TCCCGGCTACTGGATCACTG 61.043 60.000 0.00 0.00 0.00 3.66
2464 2476 0.608035 GACGATTGAAGCCCCCAACA 60.608 55.000 0.00 0.00 0.00 3.33
2533 2545 0.937441 ATAGGCTCCACTCTCTCCCA 59.063 55.000 0.00 0.00 0.00 4.37
2562 2574 4.438148 GAGCCAAGGATCTTACTCTCAAC 58.562 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.