Multiple sequence alignment - TraesCS1A01G213700

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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 TraesCS1A01G213700 chr1A 100.000 5063 0 0 1 5063 377001820 377006882 0.000000e+00 9350.0
1 TraesCS1A01G213700 chr1D 91.791 3277 161 30 1 3203 302348094 302351336 0.000000e+00 4462.0
2 TraesCS1A01G213700 chr1D 95.386 997 29 10 3236 4223 302351335 302352323 0.000000e+00 1570.0
3 TraesCS1A01G213700 chr1D 89.474 76 7 1 4537 4611 377196492 377196567 1.500000e-15 95.3
4 TraesCS1A01G213700 chr1D 80.645 124 13 9 4620 4735 7431564 7431444 9.030000e-13 86.1
5 TraesCS1A01G213700 chr1D 94.340 53 3 0 4617 4669 42128190 42128138 1.170000e-11 82.4
6 TraesCS1A01G213700 chr1B 93.554 1629 74 18 2602 4223 408617213 408615609 0.000000e+00 2398.0
7 TraesCS1A01G213700 chr1B 90.799 1815 84 27 1 1739 408621085 408619278 0.000000e+00 2350.0
8 TraesCS1A01G213700 chr1B 88.139 548 40 8 1858 2397 408619200 408618670 3.330000e-176 628.0
9 TraesCS1A01G213700 chr1B 89.604 202 7 6 2377 2578 408618564 408618377 1.410000e-60 244.0
10 TraesCS1A01G213700 chr1B 96.000 50 2 0 4620 4669 433138337 433138288 1.170000e-11 82.4
11 TraesCS1A01G213700 chr1B 73.462 260 50 10 4537 4779 57006106 57005849 4.200000e-11 80.5
12 TraesCS1A01G213700 chr6A 83.735 166 21 6 4223 4385 258377834 258377996 8.780000e-33 152.0
13 TraesCS1A01G213700 chr6A 94.340 53 3 0 4617 4669 223405917 223405969 1.170000e-11 82.4
14 TraesCS1A01G213700 chr3A 73.985 542 62 37 4283 4776 158163316 158163826 4.080000e-31 147.0
15 TraesCS1A01G213700 chr6D 74.811 397 51 24 4430 4781 391921171 391921563 3.180000e-27 134.0
16 TraesCS1A01G213700 chr6B 81.250 128 22 2 4654 4780 672200328 672200454 8.970000e-18 102.0
17 TraesCS1A01G213700 chr6B 78.231 147 24 5 4617 4757 8600816 8600672 2.510000e-13 87.9
18 TraesCS1A01G213700 chr7A 81.967 122 18 3 4667 4788 5095778 5095661 3.230000e-17 100.0
19 TraesCS1A01G213700 chr7A 81.416 113 19 2 4672 4784 36335535 36335645 1.940000e-14 91.6
20 TraesCS1A01G213700 chr7A 84.211 95 11 3 4671 4765 696676792 696676702 6.980000e-14 89.8
21 TraesCS1A01G213700 chr4B 79.562 137 23 5 4287 4420 570127823 570127689 5.400000e-15 93.5
22 TraesCS1A01G213700 chr4B 74.539 271 36 19 4430 4669 17070639 17070371 2.510000e-13 87.9
23 TraesCS1A01G213700 chr7B 87.500 72 9 0 4537 4608 166783439 166783368 3.250000e-12 84.2
24 TraesCS1A01G213700 chrUn 94.340 53 3 0 4617 4669 393604415 393604467 1.170000e-11 82.4
25 TraesCS1A01G213700 chr5B 94.340 53 3 0 4617 4669 412680930 412680982 1.170000e-11 82.4
26 TraesCS1A01G213700 chr4D 87.879 66 8 0 4543 4608 477160086 477160021 1.510000e-10 78.7
27 TraesCS1A01G213700 chr2B 83.133 83 14 0 4617 4699 555852460 555852542 5.440000e-10 76.8
28 TraesCS1A01G213700 chr2B 95.455 44 2 0 5020 5063 222140460 222140417 2.530000e-08 71.3
29 TraesCS1A01G213700 chr2A 79.439 107 20 2 4674 4780 612841510 612841614 1.950000e-09 75.0
30 TraesCS1A01G213700 chr3D 81.053 95 15 3 4970 5063 405380816 405380908 7.030000e-09 73.1
31 TraesCS1A01G213700 chr2D 89.286 56 6 0 4725 4780 23120849 23120904 2.530000e-08 71.3
32 TraesCS1A01G213700 chr2D 80.645 93 13 2 4971 5063 174320736 174320649 3.270000e-07 67.6
33 TraesCS1A01G213700 chr3B 90.000 50 2 2 5009 5057 15981588 15981635 1.520000e-05 62.1
34 TraesCS1A01G213700 chr5D 97.059 34 1 0 4575 4608 547517693 547517660 1.970000e-04 58.4


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 TraesCS1A01G213700 chr1A 377001820 377006882 5062 False 9350 9350 100.0000 1 5063 1 chr1A.!!$F1 5062
1 TraesCS1A01G213700 chr1D 302348094 302352323 4229 False 3016 4462 93.5885 1 4223 2 chr1D.!!$F2 4222
2 TraesCS1A01G213700 chr1B 408615609 408621085 5476 True 1405 2398 90.5240 1 4223 4 chr1B.!!$R3 4222


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
993 1036 0.033920 GGAGTCCGTTTTACGTGGGT 59.966 55.0 0.0 0.0 40.58 4.51 F
1795 1881 0.108804 AGCATGTACAACCTCCGTCG 60.109 55.0 0.0 0.0 0.00 5.12 F
1931 2031 0.109342 CACCTTCTGACTGCTGGGTT 59.891 55.0 0.0 0.0 0.00 4.11 F
2303 2422 0.109781 CAACACTAACATGGCCGCAC 60.110 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2076 0.250234 TTGTCTCGCCTTCTCCATGG 59.750 55.0 4.97 4.97 0.00 3.66 R
3771 5198 0.109086 CGACTTGCCGATGTCTCAGT 60.109 55.0 0.00 0.00 0.00 3.41 R
3772 5199 0.171231 TCGACTTGCCGATGTCTCAG 59.829 55.0 0.00 0.00 33.14 3.35 R
4240 5669 0.107993 ACTGTGCGTCCATGATCCTG 60.108 55.0 0.00 0.00 0.00 3.86 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.