Multiple sequence alignment - TraesCS4D01G044000

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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 TraesCS4D01G044000 chr4D 100.000 3101 0 0 1 3101 19926825 19929925 0.000000e+00 5727
1 TraesCS4D01G044000 chr5D 97.575 2804 61 5 300 3101 503216771 503219569 0.000000e+00 4795
2 TraesCS4D01G044000 chr5D 97.183 2804 72 5 300 3101 6187493 6190291 0.000000e+00 4734
3 TraesCS4D01G044000 chr5D 97.146 2803 74 4 300 3101 503279672 503276875 0.000000e+00 4728
4 TraesCS4D01G044000 chr5D 97.279 294 8 0 1 294 503216246 503216539 1.660000e-137 499
5 TraesCS4D01G044000 chr5D 97.279 294 6 1 1 294 329122077 329121786 5.970000e-137 497
6 TraesCS4D01G044000 chrUn 97.504 2804 62 6 300 3101 93411078 93408281 0.000000e+00 4783
7 TraesCS4D01G044000 chrUn 97.254 2804 70 5 300 3101 216520050 216517252 0.000000e+00 4745
8 TraesCS4D01G044000 chrUn 97.966 295 5 1 1 294 93411604 93411310 7.670000e-141 510
9 TraesCS4D01G044000 chr6D 97.468 2804 65 4 300 3101 168253478 168256277 0.000000e+00 4780
10 TraesCS4D01G044000 chr6D 97.627 295 6 1 1 294 168249567 168249861 3.570000e-139 505
11 TraesCS4D01G044000 chr3B 97.432 2804 65 5 300 3101 201525577 201528375 0.000000e+00 4772
12 TraesCS4D01G044000 chr3D 97.325 2804 64 8 300 3101 589280988 589278194 0.000000e+00 4752
13 TraesCS4D01G044000 chr1D 96.898 2805 78 7 300 3101 254399557 254396759 0.000000e+00 4689
14 TraesCS4D01G044000 chr1D 97.279 294 6 2 1 294 254524101 254524392 5.970000e-137 497
15 TraesCS4D01G044000 chr2D 97.959 294 5 1 1 294 272795865 272795573 2.760000e-140 508
16 TraesCS4D01G044000 chr5B 97.279 294 8 0 1 294 545928553 545928260 1.660000e-137 499
17 TraesCS4D01G044000 chr7D 96.949 295 7 2 1 294 231546620 231546913 7.730000e-136 494
18 TraesCS4D01G044000 chr3A 96.610 295 8 2 1 294 672911981 672911688 3.590000e-134 488


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 TraesCS4D01G044000 chr4D 19926825 19929925 3100 False 5727.0 5727 100.0000 1 3101 1 chr4D.!!$F1 3100
1 TraesCS4D01G044000 chr5D 6187493 6190291 2798 False 4734.0 4734 97.1830 300 3101 1 chr5D.!!$F1 2801
2 TraesCS4D01G044000 chr5D 503276875 503279672 2797 True 4728.0 4728 97.1460 300 3101 1 chr5D.!!$R2 2801
3 TraesCS4D01G044000 chr5D 503216246 503219569 3323 False 2647.0 4795 97.4270 1 3101 2 chr5D.!!$F2 3100
4 TraesCS4D01G044000 chrUn 216517252 216520050 2798 True 4745.0 4745 97.2540 300 3101 1 chrUn.!!$R1 2801
5 TraesCS4D01G044000 chrUn 93408281 93411604 3323 True 2646.5 4783 97.7350 1 3101 2 chrUn.!!$R2 3100
6 TraesCS4D01G044000 chr6D 168249567 168256277 6710 False 2642.5 4780 97.5475 1 3101 2 chr6D.!!$F1 3100
7 TraesCS4D01G044000 chr3B 201525577 201528375 2798 False 4772.0 4772 97.4320 300 3101 1 chr3B.!!$F1 2801
8 TraesCS4D01G044000 chr3D 589278194 589280988 2794 True 4752.0 4752 97.3250 300 3101 1 chr3D.!!$R1 2801
9 TraesCS4D01G044000 chr1D 254396759 254399557 2798 True 4689.0 4689 96.8980 300 3101 1 chr1D.!!$R1 2801

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
826 4445 1.176527 CATGCACGGGTTCAATTCCT 58.823 50.000 0.0 0.0 0.00 3.36 F
1077 4698 1.470458 CCTCTTACTACGGGGCGTTTC 60.470 57.143 0.0 0.0 41.54 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 5462 1.317613 AACGGCAGCAAGTGATTGAA 58.682 45.000 0.00 0.0 0.00 2.69 R
2897 6521 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.0 28.48 6.46 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
294 296 5.132648 AGGGCATGAGGTTCAGTATCATAAA 59.867 40.000 0.00 0.00 32.51 1.40
295 297 6.006449 GGGCATGAGGTTCAGTATCATAAAT 58.994 40.000 0.00 0.00 32.51 1.40
296 298 7.017551 AGGGCATGAGGTTCAGTATCATAAATA 59.982 37.037 0.00 0.00 32.51 1.40
297 299 7.665559 GGGCATGAGGTTCAGTATCATAAATAA 59.334 37.037 0.00 0.00 32.51 1.40
298 300 8.725148 GGCATGAGGTTCAGTATCATAAATAAG 58.275 37.037 0.00 0.00 32.51 1.73
642 4260 2.425312 CGTGTCAGAGCTGATTACTCCT 59.575 50.000 3.19 0.00 42.18 3.69
643 4261 3.119316 CGTGTCAGAGCTGATTACTCCTT 60.119 47.826 3.19 0.00 42.18 3.36
826 4445 1.176527 CATGCACGGGTTCAATTCCT 58.823 50.000 0.00 0.00 0.00 3.36
910 4529 9.616634 TTATGTATTTACTTATAGCGACGAAGG 57.383 33.333 0.00 0.00 0.00 3.46
924 4544 4.288531 CGACGAAGGATAAAACTATCGCT 58.711 43.478 0.00 0.00 33.88 4.93
925 4545 5.446709 CGACGAAGGATAAAACTATCGCTA 58.553 41.667 0.00 0.00 33.88 4.26
929 4549 9.570488 GACGAAGGATAAAACTATCGCTATATT 57.430 33.333 0.00 0.00 33.88 1.28
963 4583 1.656095 CTAGTTCTTCTTCCAAGCGCG 59.344 52.381 0.00 0.00 0.00 6.86
1020 4641 1.767692 GGGAGCTTTCCCTTCACCA 59.232 57.895 3.72 0.00 46.39 4.17
1077 4698 1.470458 CCTCTTACTACGGGGCGTTTC 60.470 57.143 0.00 0.00 41.54 2.78
1431 5053 8.097662 TGTATATGACGATCTCTAGACAGATGT 58.902 37.037 0.00 0.00 32.94 3.06
1510 5132 1.959042 AATCTGCCGAATCGCTCATT 58.041 45.000 0.00 0.00 0.00 2.57
1655 5277 2.783510 GAGACATCCCTATTTTCCCCCA 59.216 50.000 0.00 0.00 0.00 4.96
1672 5294 2.174854 CCCCAGGGGTCTTAATTACCAG 59.825 54.545 18.09 0.00 38.25 4.00
1936 5558 5.100259 GTGATCGATTTCTAGGTTTCGTCA 58.900 41.667 0.00 8.49 33.52 4.35
2299 5922 5.221224 GCCGTCCATGGATCAAATTATTTCA 60.221 40.000 19.62 0.00 0.00 2.69
2395 6018 9.616156 TTTTGCCGTATTATTAAGTATTCTCCA 57.384 29.630 0.00 0.00 0.00 3.86
2437 6061 3.326880 AGAAGTGGAACAGAATAACCCGT 59.673 43.478 0.00 0.00 41.80 5.28
2460 6084 6.036735 CGTTTGAAGGGTAATGATCATACGTT 59.963 38.462 9.04 10.09 40.17 3.99
2561 6185 5.008712 CACCTTAACACCAAAGAAGAGTTCC 59.991 44.000 0.00 0.00 0.00 3.62
2734 6358 8.973378 CCAGTATCGATAAGAATTTGAGTTCTC 58.027 37.037 6.72 0.00 37.46 2.87
2760 6384 9.650371 CATTGTTCTTATGTTATGGTACGAATG 57.350 33.333 0.00 0.00 0.00 2.67
2897 6521 6.475402 CCCGCAAATTTACCAATTATGAGTTC 59.525 38.462 0.00 0.00 31.89 3.01
2913 6537 2.674357 GAGTTCGGCGCTTTAACCATTA 59.326 45.455 7.64 0.00 0.00 1.90
2947 6571 5.303333 TGCTTAACAGGGATCATCGTACATA 59.697 40.000 0.00 0.00 0.00 2.29
3062 6686 1.407258 CACCTCTCTGGATCCTCGAAC 59.593 57.143 14.23 0.00 39.71 3.95
3072 6696 4.026744 TGGATCCTCGAACTGAAAGAGAT 58.973 43.478 14.23 0.00 37.43 2.75
3082 6706 6.378564 TCGAACTGAAAGAGATATTGAGAGGT 59.621 38.462 0.00 0.00 37.43 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 124 2.828520 AGAAATTCAGACCTCGAGCTCA 59.171 45.455 15.40 0.00 0.00 4.26
332 562 7.310664 TCGTCGTTAACTGAATTCTGAATAGT 58.689 34.615 18.13 4.57 0.00 2.12
812 4431 0.395312 ACGACAGGAATTGAACCCGT 59.605 50.000 0.00 0.00 0.00 5.28
887 4506 7.263100 TCCTTCGTCGCTATAAGTAAATACA 57.737 36.000 0.00 0.00 0.00 2.29
900 4519 4.288531 CGATAGTTTTATCCTTCGTCGCT 58.711 43.478 0.00 0.00 33.52 4.93
963 4583 0.032515 CAACCCCTTGGGGTTATCCC 60.033 60.000 34.97 0.00 42.24 3.85
1077 4698 2.224066 CGGATCTAAGTGTTGGCTAGGG 60.224 54.545 0.00 0.00 0.00 3.53
1510 5132 9.303116 GAGACCTAGGATGTAGAAGATCATAAA 57.697 37.037 17.98 0.00 0.00 1.40
1601 5223 6.269077 ACCCATAATATGTGGAAGTATCGACA 59.731 38.462 12.60 0.00 46.37 4.35
1655 5277 3.190439 AGCACTGGTAATTAAGACCCCT 58.810 45.455 6.83 0.00 35.99 4.79
1672 5294 3.917988 AGGCAAATTGAAAGCTAAGCAC 58.082 40.909 0.00 0.00 0.00 4.40
1722 5344 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
1840 5462 1.317613 AACGGCAGCAAGTGATTGAA 58.682 45.000 0.00 0.00 0.00 2.69
1964 5586 9.126151 TGAGTGTGGTTTGAACTATTGATTTAA 57.874 29.630 0.00 0.00 0.00 1.52
1984 5606 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
2299 5922 5.336102 ACAGGAAAGTGAAATCCAATCCAT 58.664 37.500 0.00 0.00 38.23 3.41
2411 6035 6.342111 GGGTTATTCTGTTCCACTTCTAGAG 58.658 44.000 0.00 0.00 0.00 2.43
2437 6061 7.392113 ACAAACGTATGATCATTACCCTTCAAA 59.608 33.333 14.65 0.00 0.00 2.69
2460 6084 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.60 0.00 2.41
2503 6127 2.304761 AGCCATCGACTACCTGGAAAAA 59.695 45.455 6.18 0.00 31.38 1.94
2561 6185 5.649782 AGACAGAAATAAAGCATTGGGTG 57.350 39.130 0.00 0.00 0.00 4.61
2666 6290 6.265422 GGGAAAGTCGATTTATGGATGGATTT 59.735 38.462 0.00 0.00 0.00 2.17
2668 6292 5.073691 AGGGAAAGTCGATTTATGGATGGAT 59.926 40.000 0.00 0.00 0.00 3.41
2734 6358 9.650371 CATTCGTACCATAACATAAGAACAATG 57.350 33.333 0.00 0.00 0.00 2.82
2760 6384 7.874016 TCCATACATAACGAATTGGTATGGTAC 59.126 37.037 21.76 0.00 45.91 3.34
2897 6521 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.00 28.48 6.46
3062 6686 9.695526 CTTGATACCTCTCAATATCTCTTTCAG 57.304 37.037 0.00 0.00 34.76 3.02


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

AutoCloner maintained by Alex Coulton.