Multiple sequence alignment - TraesCS1A01G240700

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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 TraesCS1A01G240700 chr1A 100.000 2438 0 0 1 2438 427902740 427905177 0 4503
1 TraesCS1A01G240700 chr1A 96.270 2440 85 6 1 2438 66297725 66300160 0 3997
2 TraesCS1A01G240700 chr7A 96.355 2442 83 6 1 2438 579878970 579876531 0 4012
3 TraesCS1A01G240700 chr7A 96.314 2442 84 6 1 2438 618748472 618746033 0 4006
4 TraesCS1A01G240700 chr4A 96.351 2439 86 3 1 2438 81354125 81351689 0 4008
5 TraesCS1A01G240700 chr4A 96.352 2440 82 6 1 2438 501519570 501517136 0 4006
6 TraesCS1A01G240700 chr4A 96.196 2445 85 5 1 2438 482066705 482069148 0 3993
7 TraesCS1A01G240700 chr6B 96.189 2440 90 3 1 2438 526508954 526511392 0 3988
8 TraesCS1A01G240700 chr6A 96.225 2437 87 5 1 2435 73419158 73421591 0 3986


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 TraesCS1A01G240700 chr1A 427902740 427905177 2437 False 4503 4503 100.000 1 2438 1 chr1A.!!$F2 2437
1 TraesCS1A01G240700 chr1A 66297725 66300160 2435 False 3997 3997 96.270 1 2438 1 chr1A.!!$F1 2437
2 TraesCS1A01G240700 chr7A 579876531 579878970 2439 True 4012 4012 96.355 1 2438 1 chr7A.!!$R1 2437
3 TraesCS1A01G240700 chr7A 618746033 618748472 2439 True 4006 4006 96.314 1 2438 1 chr7A.!!$R2 2437
4 TraesCS1A01G240700 chr4A 81351689 81354125 2436 True 4008 4008 96.351 1 2438 1 chr4A.!!$R1 2437
5 TraesCS1A01G240700 chr4A 501517136 501519570 2434 True 4006 4006 96.352 1 2438 1 chr4A.!!$R2 2437
6 TraesCS1A01G240700 chr4A 482066705 482069148 2443 False 3993 3993 96.196 1 2438 1 chr4A.!!$F1 2437
7 TraesCS1A01G240700 chr6B 526508954 526511392 2438 False 3988 3988 96.189 1 2438 1 chr6B.!!$F1 2437
8 TraesCS1A01G240700 chr6A 73419158 73421591 2433 False 3986 3986 96.225 1 2435 1 chr6A.!!$F1 2434

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
223 224 1.135286 GTTTGGCTAGCATTCCAGTGC 60.135 52.381 18.24 0.0 45.38 4.40 F
1127 1130 0.251341 AAACATCTCTGGGCCCACAC 60.251 55.000 24.45 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1232 0.178992 CCAGAGGCACCAAAGGACAA 60.179 55.000 0.00 0.0 0.00 3.18 R
2378 2391 2.168106 ACAACAACTTGCATTGGCTTCA 59.832 40.909 5.11 0.0 41.91 3.02 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
103 104 7.301420 TCTCCACTATGATAAACTGAGGAGAT 58.699 38.462 0.00 0.00 42.88 2.75
113 114 7.558081 TGATAAACTGAGGAGATAGGATATCCG 59.442 40.741 16.21 0.49 45.21 4.18
223 224 1.135286 GTTTGGCTAGCATTCCAGTGC 60.135 52.381 18.24 0.00 45.38 4.40
290 291 8.148999 CCTCATCAATTCTCAGATGTCTCATTA 58.851 37.037 0.00 0.00 41.74 1.90
328 329 4.101114 TGAGGGAAATAGGAAGCTACACA 58.899 43.478 0.00 0.00 0.00 3.72
350 351 2.205342 TGCTAATTGGGCCCTAGTCTT 58.795 47.619 25.70 9.66 0.00 3.01
352 353 2.952310 GCTAATTGGGCCCTAGTCTTTG 59.048 50.000 25.70 9.11 0.00 2.77
743 745 5.437060 GGATGGTCAATGCCTAAAACTCTA 58.563 41.667 0.00 0.00 0.00 2.43
810 812 2.299867 GCTGGAGGAAATTGCCAAAAGA 59.700 45.455 4.92 0.00 0.00 2.52
815 817 7.256494 TGGAGGAAATTGCCAAAAGAATTAT 57.744 32.000 4.92 0.00 0.00 1.28
930 932 2.506444 GTTCAACCCGTGTTTATCCCA 58.494 47.619 0.00 0.00 30.42 4.37
1127 1130 0.251341 AAACATCTCTGGGCCCACAC 60.251 55.000 24.45 0.00 0.00 3.82
1171 1174 3.634397 TTGGCTCATCCTTCGAATCTT 57.366 42.857 0.00 0.00 35.26 2.40
1292 1295 4.993705 TCAGTAACACCTCCTGGATTTT 57.006 40.909 0.00 0.00 37.04 1.82
1352 1355 1.208293 GAACTGGGCGATTCTCTCCTT 59.792 52.381 0.00 0.00 0.00 3.36
1355 1358 0.683179 TGGGCGATTCTCTCCTTCGA 60.683 55.000 0.00 0.00 34.92 3.71
1427 1430 0.443869 CAGAAACCGTTGGCGATCAG 59.556 55.000 0.00 0.00 41.33 2.90
1439 1442 0.445436 GCGATCAGTTGTGGCTGAAG 59.555 55.000 0.00 0.00 46.93 3.02
1461 1464 1.985116 GCTCGACCTTCTCTGGGGT 60.985 63.158 0.00 0.00 38.70 4.95
1628 1631 1.195115 AGACCATGAAGGCTTCGCTA 58.805 50.000 21.42 5.50 43.14 4.26
1751 1759 6.709018 TGTAGCTTTTCTACCTTTGCTTTT 57.291 33.333 0.00 0.00 45.56 2.27
1795 1803 7.148255 GCTGTATCAGAATATGTTGTGGTTTCA 60.148 37.037 0.00 0.00 32.44 2.69
1834 1842 2.797177 GGAGATGCTCCCTGTTTTCT 57.203 50.000 1.97 0.00 44.36 2.52
1835 1843 3.914426 GGAGATGCTCCCTGTTTTCTA 57.086 47.619 1.97 0.00 44.36 2.10
1930 1940 8.506168 TGTAAGAAAACAATATCCCACATCTC 57.494 34.615 0.00 0.00 0.00 2.75
2037 2047 7.361799 GCTTGGTAAGATTTAAGGACGAATGTT 60.362 37.037 0.00 0.00 0.00 2.71
2347 2360 0.802494 GGGTTGAATACGTGCCACAG 59.198 55.000 0.00 0.00 0.00 3.66
2378 2391 3.099141 CTGAAATGTGGGCCAATAGGTT 58.901 45.455 8.40 0.00 37.19 3.50
2394 2407 2.041701 AGGTTGAAGCCAATGCAAGTT 58.958 42.857 0.00 0.00 41.13 2.66
2423 2436 9.897744 TGTCAATTTAGTCAACAAATGATTCTC 57.102 29.630 0.00 0.00 40.97 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.225293 CCAGAAGGGGTCGGATATCCTA 60.225 54.545 19.61 5.99 0.00 2.94
113 114 8.533569 TTTAATGATTTTATCCAGAAGGGGTC 57.466 34.615 0.00 0.00 37.22 4.46
145 146 3.179339 TTTGCCCCTCCACCCGAA 61.179 61.111 0.00 0.00 0.00 4.30
146 147 3.961414 GTTTGCCCCTCCACCCGA 61.961 66.667 0.00 0.00 0.00 5.14
147 148 3.507377 AAGTTTGCCCCTCCACCCG 62.507 63.158 0.00 0.00 0.00 5.28
223 224 5.418676 GAACTTGAAGAAGGAGAGGAGATG 58.581 45.833 0.00 0.00 32.95 2.90
290 291 4.739793 TCCCTCAAAATCATTCCACAAGT 58.260 39.130 0.00 0.00 0.00 3.16
328 329 2.785857 AGACTAGGGCCCAATTAGCAAT 59.214 45.455 27.56 1.16 0.00 3.56
661 663 7.067008 GCAGACAGAGTAAATAGGCCAAAATTA 59.933 37.037 5.01 0.00 0.00 1.40
810 812 5.509498 TCCAGCTTGGCAGTAAAGATAATT 58.491 37.500 0.00 0.00 37.47 1.40
815 817 2.715046 CATCCAGCTTGGCAGTAAAGA 58.285 47.619 0.00 0.00 37.47 2.52
826 828 1.481871 CAAATCAGGGCATCCAGCTT 58.518 50.000 0.00 0.00 44.79 3.74
930 932 4.322567 GAACTCTCAATTTCCAGACAGCT 58.677 43.478 0.00 0.00 0.00 4.24
1127 1130 9.695526 CAATCTGACTAGAGAAATATTCCTCAG 57.304 37.037 4.38 2.68 36.14 3.35
1229 1232 0.178992 CCAGAGGCACCAAAGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1292 1295 1.218047 CTCAAGACCCGCGGAATGA 59.782 57.895 30.73 22.05 0.00 2.57
1352 1355 1.616865 ACTTGTCCTTGTCCGATTCGA 59.383 47.619 7.83 0.00 0.00 3.71
1355 1358 3.485463 TCAACTTGTCCTTGTCCGATT 57.515 42.857 0.00 0.00 0.00 3.34
1427 1430 0.877743 GAGCCTTCTTCAGCCACAAC 59.122 55.000 0.00 0.00 0.00 3.32
1690 1693 6.525121 TGAACAAGTTCTCTGAATAACACG 57.475 37.500 13.49 0.00 40.14 4.49
1795 1803 1.683011 CCCGGTTCCATTGCTGAGAAT 60.683 52.381 0.00 0.00 0.00 2.40
2347 2360 2.289010 CCCACATTTCAGCCTCCAAAAC 60.289 50.000 0.00 0.00 0.00 2.43
2378 2391 2.168106 ACAACAACTTGCATTGGCTTCA 59.832 40.909 5.11 0.00 41.91 3.02
2394 2407 9.814899 AATCATTTGTTGACTAAATTGACAACA 57.185 25.926 0.00 0.00 45.31 3.33


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

AutoCloner maintained by Alex Coulton.