Multiple sequence alignment - TraesCS5D01G345800

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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 TraesCS5D01G345800 chr5D 100.000 2388 0 0 1 2388 432433806 432436193 0 4410
1 TraesCS5D01G345800 chr5D 98.079 2395 37 6 1 2388 503243819 503246211 0 4159
2 TraesCS5D01G345800 chr6D 98.246 2395 33 6 1 2388 389247275 389244883 0 4181
3 TraesCS5D01G345800 chr7B 98.121 2395 36 6 1 2388 663100878 663098486 0 4165
4 TraesCS5D01G345800 chr7B 97.912 2395 41 6 1 2388 662724951 662727343 0 4137
5 TraesCS5D01G345800 chr3A 98.079 2394 38 6 1 2388 66006585 66004194 0 4159
6 TraesCS5D01G345800 chr3A 97.368 2394 53 7 1 2388 650015965 650013576 0 4063
7 TraesCS5D01G345800 chr3D 98.078 2393 38 6 1 2388 589264976 589262587 0 4157
8 TraesCS5D01G345800 chr2A 97.912 2395 41 6 1 2388 726907908 726905516 0 4137
9 TraesCS5D01G345800 chr3B 97.663 2396 46 6 1 2388 201538068 201540461 0 4106


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 TraesCS5D01G345800 chr5D 432433806 432436193 2387 False 4410 4410 100.000 1 2388 1 chr5D.!!$F1 2387
1 TraesCS5D01G345800 chr5D 503243819 503246211 2392 False 4159 4159 98.079 1 2388 1 chr5D.!!$F2 2387
2 TraesCS5D01G345800 chr6D 389244883 389247275 2392 True 4181 4181 98.246 1 2388 1 chr6D.!!$R1 2387
3 TraesCS5D01G345800 chr7B 663098486 663100878 2392 True 4165 4165 98.121 1 2388 1 chr7B.!!$R1 2387
4 TraesCS5D01G345800 chr7B 662724951 662727343 2392 False 4137 4137 97.912 1 2388 1 chr7B.!!$F1 2387
5 TraesCS5D01G345800 chr3A 66004194 66006585 2391 True 4159 4159 98.079 1 2388 1 chr3A.!!$R1 2387
6 TraesCS5D01G345800 chr3A 650013576 650015965 2389 True 4063 4063 97.368 1 2388 1 chr3A.!!$R2 2387
7 TraesCS5D01G345800 chr3D 589262587 589264976 2389 True 4157 4157 98.078 1 2388 1 chr3D.!!$R1 2387
8 TraesCS5D01G345800 chr2A 726905516 726907908 2392 True 4137 4137 97.912 1 2388 1 chr2A.!!$R1 2387
9 TraesCS5D01G345800 chr3B 201538068 201540461 2393 False 4106 4106 97.663 1 2388 1 chr3B.!!$F1 2387


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
388 389 1.299541 CCATACGGTGGTGAATCAGC 58.7 55.0 5.36 5.36 43.44 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2219 0.032813 TAGTTCCTACGGGGTGGAGG 60.033 60.0 0.0 0.0 36.25 4.3 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
254 255 2.125310 CGTGCTACAATGGGCGGA 60.125 61.111 0.00 0.00 0.00 5.54
388 389 1.299541 CCATACGGTGGTGAATCAGC 58.700 55.000 5.36 5.36 43.44 4.26
403 404 3.083997 AGCTCCCGGGCCTTGTAG 61.084 66.667 18.49 8.13 0.00 2.74
430 431 2.860009 CCCGTCACACTATAGGAGCTA 58.140 52.381 4.43 0.00 0.00 3.32
519 520 3.257375 AGTGAAGTCGTAACATGGTAGCA 59.743 43.478 0.00 0.00 0.00 3.49
960 961 5.121811 GGATAGTTCAATGTGCTCATCAGT 58.878 41.667 1.01 0.00 32.56 3.41
1015 1016 1.452953 TAGCATGGCGTACTCCTCCG 61.453 60.000 3.08 0.00 0.00 4.63
1124 1125 1.681793 CTATTCACTCGTGGGATCCGT 59.318 52.381 5.45 0.00 0.00 4.69
1193 1198 7.855375 CATACATCCCTTATCAGTGTATGGAT 58.145 38.462 13.29 0.00 44.23 3.41
1225 1230 0.180406 AGCACAGGTTGAGGTTCGTT 59.820 50.000 0.00 0.00 0.00 3.85
1264 1269 2.420022 GCACCTAACAACGCATCTTCAT 59.580 45.455 0.00 0.00 0.00 2.57
1427 1434 4.909880 GGAAGAACGTGAAATTCTTTTCCG 59.090 41.667 1.24 0.48 44.53 4.30
2090 2100 2.158385 TCTCCTAGGCTTCCCTCATCTC 60.158 54.545 2.96 0.00 41.75 2.75
2192 2202 3.942130 AGCAAAAGGAAGGAAAATCCG 57.058 42.857 0.00 0.00 42.75 4.18
2209 2219 2.750237 GTGGACCGACCCCATTGC 60.750 66.667 0.00 0.00 35.91 3.56
2248 2258 1.522569 GAGATCACCCCAAGGACGG 59.477 63.158 0.00 0.00 36.73 4.79
2370 2380 4.215613 GGGCAATCACTCGTTCTTAAAACT 59.784 41.667 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 255 0.736325 CGAGATCGCGACCCTTTGTT 60.736 55.000 12.93 0.00 0.00 2.83
377 378 2.669133 CCCGGGAGCTGATTCACCA 61.669 63.158 18.48 0.00 0.00 4.17
388 389 1.987855 TGTCTACAAGGCCCGGGAG 60.988 63.158 29.31 12.15 0.00 4.30
403 404 2.221906 ATAGTGTGACGGGCGGTGTC 62.222 60.000 1.11 0.00 36.88 3.67
430 431 3.763897 GGGTAATGACTTCAAACATGGCT 59.236 43.478 0.00 0.00 0.00 4.75
519 520 1.913762 AGCCGCACCTTCCAGTACT 60.914 57.895 0.00 0.00 0.00 2.73
641 642 6.240549 ACGAAAGAAGACTTCCATATCCAT 57.759 37.500 11.67 0.00 35.05 3.41
960 961 1.296392 CACATCTTCGGGTCAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
1015 1016 4.202070 TGGTTTCAAACTCCGATTCAAACC 60.202 41.667 0.00 0.00 41.07 3.27
1193 1198 2.158740 ACCTGTGCTCGAGAGATAGCTA 60.159 50.000 18.75 0.00 40.84 3.32
1225 1230 3.091545 GTGCTCCATTTTCCCATTGAGA 58.908 45.455 0.00 0.00 0.00 3.27
1264 1269 4.639310 GGTGATCTCGTAGTTCTTGGTCTA 59.361 45.833 0.00 0.00 0.00 2.59
1427 1434 1.065126 ACCTGCTCTGCTCCCATTTAC 60.065 52.381 0.00 0.00 0.00 2.01
2042 2050 3.578716 CCCTCCAACTATCGTCCATGTAT 59.421 47.826 0.00 0.00 0.00 2.29
2065 2075 1.383248 GGGAAGCCTAGGAGAGCCA 60.383 63.158 14.75 0.00 36.29 4.75
2090 2100 2.143419 CCTCTTCCCCAGGGATCCG 61.143 68.421 7.25 0.00 44.74 4.18
2192 2202 2.750237 GCAATGGGGTCGGTCCAC 60.750 66.667 0.00 0.00 40.76 4.02
2209 2219 0.032813 TAGTTCCTACGGGGTGGAGG 60.033 60.000 0.00 0.00 36.25 4.30
2329 2339 1.558233 CCTTCTCCGACCCTTACTGT 58.442 55.000 0.00 0.00 0.00 3.55



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

AutoCloner maintained by Alex Coulton.