Multiple sequence alignment - TraesCS1B01G192600

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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 TraesCS1B01G192600 chr1B 100.000 4898 0 0 1 4898 344842927 344838030 0.000000e+00 9046.0
1 TraesCS1B01G192600 chr1A 94.518 2955 124 18 1847 4775 334451724 334448782 0.000000e+00 4525.0
2 TraesCS1B01G192600 chr1A 94.050 1042 38 12 710 1733 334452842 334451807 0.000000e+00 1559.0
3 TraesCS1B01G192600 chr1A 94.173 635 31 4 4268 4896 334416718 334416084 0.000000e+00 963.0
4 TraesCS1B01G192600 chr1A 93.651 252 12 3 410 661 334453094 334452847 1.660000e-99 374.0
5 TraesCS1B01G192600 chr1A 90.435 115 6 3 1747 1856 584082913 584082799 3.950000e-31 147.0
6 TraesCS1B01G192600 chr1A 89.024 82 8 1 2519 2600 334451125 334451045 3.120000e-17 100.0
7 TraesCS1B01G192600 chr1D 93.984 2959 135 20 1845 4775 267986754 267989697 0.000000e+00 4438.0
8 TraesCS1B01G192600 chr1D 95.131 1068 31 11 681 1733 267985612 267986673 0.000000e+00 1664.0
9 TraesCS1B01G192600 chr1D 89.000 400 35 5 4219 4616 268461813 268462205 2.050000e-133 486.0
10 TraesCS1B01G192600 chr1D 94.805 231 11 1 410 640 267985368 267985597 4.660000e-95 359.0
11 TraesCS1B01G192600 chr1D 85.714 231 16 5 5 220 267984812 267985040 1.370000e-55 228.0
12 TraesCS1B01G192600 chr1D 81.145 297 29 16 4612 4883 268467360 268467654 3.840000e-51 213.0
13 TraesCS1B01G192600 chr1D 91.463 82 6 1 2519 2600 267987355 267987435 1.440000e-20 111.0
14 TraesCS1B01G192600 chr6A 98.913 92 0 1 1758 1848 503767444 503767535 3.920000e-36 163.0
15 TraesCS1B01G192600 chr4A 97.826 92 2 0 1753 1844 59254318 59254227 5.070000e-35 159.0
16 TraesCS1B01G192600 chr3B 96.842 95 2 1 1755 1849 447014633 447014540 1.830000e-34 158.0
17 TraesCS1B01G192600 chr5D 94.949 99 5 0 1744 1842 364250210 364250308 6.560000e-34 156.0
18 TraesCS1B01G192600 chr6D 95.876 97 1 3 1752 1846 79346548 79346453 2.360000e-33 154.0
19 TraesCS1B01G192600 chr6B 95.789 95 4 0 1750 1844 546656566 546656660 2.360000e-33 154.0
20 TraesCS1B01G192600 chr7B 88.793 116 11 2 1749 1864 20241016 20240903 1.840000e-29 141.0
21 TraesCS1B01G192600 chr3D 91.346 104 6 3 1744 1846 414368803 414368702 6.610000e-29 139.0
22 TraesCS1B01G192600 chr2A 85.714 84 11 1 307 389 706531654 706531571 2.430000e-13 87.9


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 TraesCS1B01G192600 chr1B 344838030 344842927 4897 True 9046.0 9046 100.00000 1 4898 1 chr1B.!!$R1 4897
1 TraesCS1B01G192600 chr1A 334448782 334453094 4312 True 1639.5 4525 92.81075 410 4775 4 chr1A.!!$R3 4365
2 TraesCS1B01G192600 chr1A 334416084 334416718 634 True 963.0 963 94.17300 4268 4896 1 chr1A.!!$R1 628
3 TraesCS1B01G192600 chr1D 267984812 267989697 4885 False 1360.0 4438 92.21940 5 4775 5 chr1D.!!$F3 4770


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
267 413 0.893270 CACCGGGCATGGAAAAGACA 60.893 55.0 6.32 0.0 0.00 3.41 F
268 414 0.893727 ACCGGGCATGGAAAAGACAC 60.894 55.0 6.32 0.0 0.00 3.67 F
269 415 0.893270 CCGGGCATGGAAAAGACACA 60.893 55.0 0.00 0.0 0.00 3.72 F
2003 2203 0.530744 GTCATAGGGTCGAGTGTGCA 59.469 55.0 0.00 0.0 0.00 4.57 F
2139 2339 0.257328 TGGGCTTTGTTGTCCACTCA 59.743 50.0 0.00 0.0 36.71 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2058 0.184451 CTGGGTAGGGCCGTACTCTA 59.816 60.000 30.30 18.84 38.44 2.43 R
1944 2144 5.011533 TCCCTATGCTTCTAGATGCTTCTTC 59.988 44.000 25.75 2.78 33.17 2.87 R
2139 2339 5.247110 AGGAATGACTGACAGTGTGAGTATT 59.753 40.000 15.74 14.20 28.74 1.89 R
3774 3996 1.228124 CGGGCAAGTGGGTTCTTCA 60.228 57.895 0.00 0.00 0.00 3.02 R
4093 4318 4.165372 GGTCCAGGTAGATATTTGGTTCCA 59.835 45.833 0.00 0.00 32.51 3.53 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)



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AutoCloner maintained by Alex Coulton.