Multiple sequence alignment - TraesCS5B01G342900

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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 TraesCS5B01G342900 chr5B 100.000 2426 0 0 1 2426 527041049 527038624 0.000000e+00 4481.0
1 TraesCS5B01G342900 chr5B 79.405 874 148 19 707 1568 527607516 527608369 2.690000e-164 588.0
2 TraesCS5B01G342900 chr5B 77.818 825 146 24 765 1566 528524503 528525313 2.180000e-130 475.0
3 TraesCS5B01G342900 chr5B 77.460 874 143 27 713 1568 527059201 527058364 7.850000e-130 473.0
4 TraesCS5B01G342900 chr5A 95.377 2466 69 9 1 2426 548227692 548225232 0.000000e+00 3880.0
5 TraesCS5B01G342900 chr5A 79.437 817 133 18 765 1568 549153598 549154392 1.640000e-151 545.0
6 TraesCS5B01G342900 chr5A 83.137 255 31 8 713 961 548229084 548228836 3.140000e-54 222.0
7 TraesCS5B01G342900 chr5D 94.880 2422 67 12 1 2384 434330350 434332752 0.000000e+00 3733.0
8 TraesCS5B01G342900 chr5D 95.565 2052 47 9 1 2038 434383032 434381011 0.000000e+00 3245.0
9 TraesCS5B01G342900 chr5D 80.000 875 143 23 707 1568 434568967 434569822 3.430000e-173 617.0
10 TraesCS5B01G342900 chr5D 79.932 877 137 22 717 1568 435237356 435238218 2.060000e-170 608.0
11 TraesCS5B01G342900 chr5D 84.298 242 30 5 723 961 434392087 434391851 1.880000e-56 230.0
12 TraesCS5B01G342900 chr5D 89.796 147 15 0 2278 2424 433992617 433992763 3.180000e-44 189.0
13 TraesCS5B01G342900 chr5D 87.037 54 7 0 359 412 434712985 434712932 7.240000e-06 62.1


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 TraesCS5B01G342900 chr5B 527038624 527041049 2425 True 4481 4481 100.000 1 2426 1 chr5B.!!$R1 2425
1 TraesCS5B01G342900 chr5B 527607516 527608369 853 False 588 588 79.405 707 1568 1 chr5B.!!$F1 861
2 TraesCS5B01G342900 chr5B 528524503 528525313 810 False 475 475 77.818 765 1566 1 chr5B.!!$F2 801
3 TraesCS5B01G342900 chr5B 527058364 527059201 837 True 473 473 77.460 713 1568 1 chr5B.!!$R2 855
4 TraesCS5B01G342900 chr5A 548225232 548229084 3852 True 2051 3880 89.257 1 2426 2 chr5A.!!$R1 2425
5 TraesCS5B01G342900 chr5A 549153598 549154392 794 False 545 545 79.437 765 1568 1 chr5A.!!$F1 803
6 TraesCS5B01G342900 chr5D 434330350 434332752 2402 False 3733 3733 94.880 1 2384 1 chr5D.!!$F2 2383
7 TraesCS5B01G342900 chr5D 434381011 434383032 2021 True 3245 3245 95.565 1 2038 1 chr5D.!!$R1 2037
8 TraesCS5B01G342900 chr5D 434568967 434569822 855 False 617 617 80.000 707 1568 1 chr5D.!!$F3 861
9 TraesCS5B01G342900 chr5D 435237356 435238218 862 False 608 608 79.932 717 1568 1 chr5D.!!$F4 851

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
789 2184 1.810755 AGTGATCATGCTGCAACACTG 59.189 47.619 23.22 12.53 37.24 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 3763 0.957395 CACGCCTTCTGATTGCCACT 60.957 55.0 0.0 0.0 0.0 4.0 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
53 1446 4.096382 GGTATGAATTTTCACAGATGCGGT 59.904 41.667 0.00 0.00 40.49 5.68
106 1500 4.267452 GCAAACTGCGAAAATCAGAAACAA 59.733 37.500 0.00 0.00 35.61 2.83
232 1626 8.246180 CAGATTCAGTAATTTATGGCAAGTTGT 58.754 33.333 4.48 0.00 0.00 3.32
255 1649 2.921834 ACACTTGACCCTCCTAGCTA 57.078 50.000 0.00 0.00 0.00 3.32
385 1780 5.055812 GGTGGAAGCAACAATGAAATGAAA 58.944 37.500 0.00 0.00 0.00 2.69
570 1965 7.009179 TGAACAAGTTCCTGATCATTAGTCT 57.991 36.000 10.19 0.00 38.77 3.24
586 1981 8.506168 TCATTAGTCTGACACACTTTCTTTTT 57.494 30.769 10.88 0.00 0.00 1.94
670 2065 7.095270 TGATGATATCTCAACTGAATCCATCG 58.905 38.462 3.98 0.00 34.37 3.84
778 2173 6.820152 TCACAATCTACTCCAAAGTGATCATG 59.180 38.462 0.00 0.00 36.92 3.07
779 2174 5.587844 ACAATCTACTCCAAAGTGATCATGC 59.412 40.000 0.00 0.00 36.92 4.06
780 2175 5.627182 ATCTACTCCAAAGTGATCATGCT 57.373 39.130 0.00 0.00 36.92 3.79
781 2176 4.763073 TCTACTCCAAAGTGATCATGCTG 58.237 43.478 0.00 0.00 36.92 4.41
782 2177 2.089980 ACTCCAAAGTGATCATGCTGC 58.910 47.619 0.00 0.00 33.32 5.25
783 2178 2.089201 CTCCAAAGTGATCATGCTGCA 58.911 47.619 4.13 4.13 0.00 4.41
784 2179 2.490509 CTCCAAAGTGATCATGCTGCAA 59.509 45.455 6.36 0.00 0.00 4.08
785 2180 2.229543 TCCAAAGTGATCATGCTGCAAC 59.770 45.455 6.36 0.00 0.00 4.17
786 2181 2.029739 CCAAAGTGATCATGCTGCAACA 60.030 45.455 6.36 2.26 0.00 3.33
787 2182 2.984471 CAAAGTGATCATGCTGCAACAC 59.016 45.455 6.36 14.19 0.00 3.32
788 2183 2.195741 AGTGATCATGCTGCAACACT 57.804 45.000 20.47 20.47 34.46 3.55
789 2184 1.810755 AGTGATCATGCTGCAACACTG 59.189 47.619 23.22 12.53 37.24 3.66
1150 2598 1.439353 CTGCATCATGTACACGGCCC 61.439 60.000 0.00 0.00 0.00 5.80
1412 2860 3.011566 TGTTGGAGACAGCCAGAAAAA 57.988 42.857 0.00 0.00 44.54 1.94
1675 3135 7.548967 ACAATCTAGCACTAAGTAAGTCCTTC 58.451 38.462 0.00 0.00 35.76 3.46
1726 3186 3.796764 TGACTGTGTGGCACAATCA 57.203 47.368 23.90 21.77 45.99 2.57
1727 3187 1.596603 TGACTGTGTGGCACAATCAG 58.403 50.000 27.24 27.24 43.91 2.90
1747 3207 2.298446 AGTATGCAGTGATGATCCCTCG 59.702 50.000 0.00 0.00 0.00 4.63
1865 3327 6.042208 AGCAGGTCTCTTTAGTAGAAACAAGT 59.958 38.462 0.00 0.00 30.91 3.16
2045 3508 0.675633 ATGGTTTGCAGCTGGTCAAC 59.324 50.000 17.12 6.91 0.00 3.18
2101 3589 9.376075 CTCATCAACAGAACTAAGATACAACAT 57.624 33.333 0.00 0.00 0.00 2.71
2124 3612 7.068103 ACATTGTTCATCAAGTTGTGTTCCTTA 59.932 33.333 2.11 0.00 39.55 2.69
2137 3625 7.441458 AGTTGTGTTCCTTACATCAACTAACTC 59.559 37.037 16.66 0.00 45.93 3.01
2143 3631 7.159322 TCCTTACATCAACTAACTCAGTCTC 57.841 40.000 0.00 0.00 36.04 3.36
2213 3701 4.278170 CACAAACCCAATCAAGTCAGCTTA 59.722 41.667 0.00 0.00 32.87 3.09
2275 3763 1.064463 CCATTCTGGCTAGCTTTCCCA 60.064 52.381 15.72 2.34 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 1403 9.599866 TCATACCAACATATAACTTCTTGTGAG 57.400 33.333 0.00 0.00 0.00 3.51
27 1420 5.512788 CGCATCTGTGAAAATTCATACCAAC 59.487 40.000 0.00 0.00 39.73 3.77
106 1500 5.126869 CGTGCATCATATATTCTCTCTCCCT 59.873 44.000 0.00 0.00 0.00 4.20
232 1626 3.097614 GCTAGGAGGGTCAAGTGTTCTA 58.902 50.000 0.00 0.00 0.00 2.10
255 1649 5.923733 TGTCCAAAGTTGTACCATGTTTT 57.076 34.783 0.00 0.00 0.00 2.43
385 1780 1.632409 AGTCCAGCATCTCATGTGGTT 59.368 47.619 0.00 0.00 34.87 3.67
532 1927 9.493173 AGGAACTTGTTCATGGTCTTACCAGTT 62.493 40.741 14.38 1.70 46.39 3.16
570 1965 6.071952 AGCTGAAAGAAAAAGAAAGTGTGTCA 60.072 34.615 0.00 0.00 34.07 3.58
586 1981 2.170397 TGACACTTGACCAGCTGAAAGA 59.830 45.455 17.39 0.00 34.07 2.52
694 2089 3.087031 GGTAGCAATAGCATCATGGCAT 58.913 45.455 0.00 0.00 45.49 4.40
782 2177 1.538075 TGATCAGTGCATGCAGTGTTG 59.462 47.619 40.43 26.78 45.02 3.33
783 2178 1.538512 GTGATCAGTGCATGCAGTGTT 59.461 47.619 40.43 35.47 45.02 3.32
784 2179 1.162698 GTGATCAGTGCATGCAGTGT 58.837 50.000 40.43 31.25 45.02 3.55
785 2180 1.161843 TGTGATCAGTGCATGCAGTG 58.838 50.000 38.57 38.57 45.85 3.66
786 2181 1.743394 CATGTGATCAGTGCATGCAGT 59.257 47.619 23.41 22.90 34.47 4.40
787 2182 1.065551 CCATGTGATCAGTGCATGCAG 59.934 52.381 23.41 10.99 38.79 4.41
788 2183 1.099689 CCATGTGATCAGTGCATGCA 58.900 50.000 18.46 18.46 38.79 3.96
789 2184 0.248907 GCCATGTGATCAGTGCATGC 60.249 55.000 11.82 11.82 38.79 4.06
790 2185 0.384309 GGCCATGTGATCAGTGCATG 59.616 55.000 14.77 14.77 39.54 4.06
791 2186 0.257905 AGGCCATGTGATCAGTGCAT 59.742 50.000 5.01 0.00 0.00 3.96
792 2187 0.038599 AAGGCCATGTGATCAGTGCA 59.961 50.000 5.01 0.00 0.00 4.57
793 2188 0.454600 CAAGGCCATGTGATCAGTGC 59.545 55.000 5.01 0.00 0.00 4.40
794 2189 1.741706 GACAAGGCCATGTGATCAGTG 59.258 52.381 20.20 0.00 32.57 3.66
795 2190 1.340405 GGACAAGGCCATGTGATCAGT 60.340 52.381 20.20 0.00 32.57 3.41
796 2191 1.386533 GGACAAGGCCATGTGATCAG 58.613 55.000 20.20 0.00 32.57 2.90
797 2192 0.034186 GGGACAAGGCCATGTGATCA 60.034 55.000 20.20 0.00 32.57 2.92
798 2193 0.257039 AGGGACAAGGCCATGTGATC 59.743 55.000 20.20 3.86 32.57 2.92
799 2194 0.033796 CAGGGACAAGGCCATGTGAT 60.034 55.000 20.20 0.55 35.12 3.06
800 2195 1.379916 CAGGGACAAGGCCATGTGA 59.620 57.895 20.20 0.00 35.12 3.58
1323 2771 0.391661 GCAATGCCTTCTCGACCTCA 60.392 55.000 0.00 0.00 0.00 3.86
1546 3000 2.164827 CTGCTTGGTTGCTTGCATGATA 59.835 45.455 3.33 0.00 34.79 2.15
1688 3148 8.398665 ACAGTCATTTCACTTTCTTACAGTTTC 58.601 33.333 0.00 0.00 0.00 2.78
1726 3186 2.298446 CGAGGGATCATCACTGCATACT 59.702 50.000 0.00 0.00 24.24 2.12
1727 3187 2.611473 CCGAGGGATCATCACTGCATAC 60.611 54.545 0.00 0.00 24.24 2.39
1747 3207 6.159988 CGATGACCTTCTCAAGTTATATCCC 58.840 44.000 0.00 0.00 30.60 3.85
1808 3270 8.927675 TGCTAAATAAAACCTGGTTTCTCTTA 57.072 30.769 24.02 18.00 34.43 2.10
1932 3395 2.494471 TCATTGAGCATTTTCTGGCCTG 59.506 45.455 3.32 2.92 0.00 4.85
2045 3508 2.016318 TGGCATCCATTTCTTAGTGCG 58.984 47.619 0.00 0.00 33.62 5.34
2101 3589 5.913137 AAGGAACACAACTTGATGAACAA 57.087 34.783 0.00 0.00 36.97 2.83
2124 3612 7.500992 TGAAAAGAGACTGAGTTAGTTGATGT 58.499 34.615 0.00 0.00 40.53 3.06
2213 3701 7.118723 TCAATGGTCTTATTTTAGCAGGTGAT 58.881 34.615 0.00 0.00 0.00 3.06
2275 3763 0.957395 CACGCCTTCTGATTGCCACT 60.957 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.