Multiple sequence alignment - TraesCS3A01G086200

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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 TraesCS3A01G086200 chr3A 100.000 5253 0 0 1 5253 55715008 55720260 0.000000e+00 9701.0
1 TraesCS3A01G086200 chr3A 96.183 131 5 0 4474 4604 532609643 532609513 1.150000e-51 215.0
2 TraesCS3A01G086200 chr3A 95.420 131 6 0 4478 4608 595058522 595058392 5.330000e-50 209.0
3 TraesCS3A01G086200 chr3D 91.850 2233 102 36 547 2741 43793566 43795756 0.000000e+00 3042.0
4 TraesCS3A01G086200 chr3D 88.235 1479 123 28 2803 4259 43795783 43797232 0.000000e+00 1720.0
5 TraesCS3A01G086200 chr3B 90.684 2265 111 50 528 2741 68449965 68452180 0.000000e+00 2922.0
6 TraesCS3A01G086200 chr3B 89.095 1238 91 25 3262 4480 68452600 68453812 0.000000e+00 1498.0
7 TraesCS3A01G086200 chr3B 86.849 403 37 8 2800 3191 68452204 68452601 2.250000e-118 436.0
8 TraesCS3A01G086200 chr3B 93.671 158 8 2 4603 4759 68453802 68453958 8.790000e-58 235.0
9 TraesCS3A01G086200 chr3B 88.889 189 14 6 5066 5252 68463522 68463705 5.290000e-55 226.0
10 TraesCS3A01G086200 chr3B 96.154 130 4 1 4478 4606 23595106 23594977 1.480000e-50 211.0
11 TraesCS3A01G086200 chr3B 95.122 123 5 1 4950 5071 68454300 68454422 5.370000e-45 193.0
12 TraesCS3A01G086200 chr3B 94.872 78 3 1 4758 4834 68454109 68454186 2.570000e-23 121.0
13 TraesCS3A01G086200 chr3B 100.000 61 0 0 4833 4893 68454238 68454298 4.300000e-21 113.0
14 TraesCS3A01G086200 chrUn 97.638 127 3 0 4477 4603 243391443 243391317 8.860000e-53 219.0
15 TraesCS3A01G086200 chr5D 98.387 124 2 0 4478 4601 303929261 303929138 8.860000e-53 219.0
16 TraesCS3A01G086200 chr5A 98.387 124 2 0 4478 4601 608862350 608862227 8.860000e-53 219.0
17 TraesCS3A01G086200 chr7A 96.212 132 5 0 4476 4607 546640237 546640106 3.190000e-52 217.0
18 TraesCS3A01G086200 chr5B 97.600 125 3 0 4478 4602 399041875 399041999 1.150000e-51 215.0
19 TraesCS3A01G086200 chr5B 95.420 131 6 0 4476 4606 636898708 636898578 5.330000e-50 209.0
20 TraesCS3A01G086200 chr7B 100.000 30 0 0 5152 5181 490356423 490356394 7.350000e-04 56.5


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 TraesCS3A01G086200 chr3A 55715008 55720260 5252 False 9701.000000 9701 100.0000 1 5253 1 chr3A.!!$F1 5252
1 TraesCS3A01G086200 chr3D 43793566 43797232 3666 False 2381.000000 3042 90.0425 547 4259 2 chr3D.!!$F1 3712
2 TraesCS3A01G086200 chr3B 68449965 68454422 4457 False 788.285714 2922 92.8990 528 5071 7 chr3B.!!$F2 4543


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
132 133 0.029567 CTCGCCGTCATCCACTAGAC 59.970 60.0 0.00 0.00 0.00 2.59 F
392 393 0.031721 GACGACCGAAGACCACAAGT 59.968 55.0 0.00 0.00 0.00 3.16 F
489 490 0.035317 CTTGCACTCCCAGTACTGCA 59.965 55.0 17.86 9.22 0.00 4.41 F
2311 2387 0.393808 ACGTGTCCTGGCAGTTTGTT 60.394 50.0 14.43 0.00 0.00 2.83 F
3322 3418 0.456653 CAATAGCCTTGTGCCGTTGC 60.457 55.0 0.00 0.00 42.71 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1911 0.248843 CACCCAGCTCTGTCTTCCTC 59.751 60.000 0.00 0.00 0.00 3.71 R
2381 2457 1.127582 GACAAAGCTCACGTGCTCATC 59.872 52.381 11.67 0.82 43.24 2.92 R
2460 2536 1.000163 TCTTGAGCACGTTGGAGTCTC 60.000 52.381 0.00 0.00 0.00 3.36 R
3393 3489 0.258774 AACTGCCAGGGTGTTCTGTT 59.741 50.000 0.00 0.00 33.14 3.16 R
5228 5550 0.031857 TTTGTTGCGCACCATCCAAG 59.968 50.000 11.12 0.00 0.00 3.61 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.