Multiple sequence alignment - TraesCS2D01G350400

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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 TraesCS2D01G350400 chr2D 100.000 6009 0 0 1 6009 448207294 448213302 0 11097
1 TraesCS2D01G350400 chr2A 97.401 5195 99 22 1 5172 592851138 592856319 0 8813
2 TraesCS2D01G350400 chr2A 89.085 852 54 21 5175 6009 592856365 592857194 0 1022
3 TraesCS2D01G350400 chr2B 92.346 5239 256 53 1 5172 528201449 528206609 0 7319
4 TraesCS2D01G350400 chr2B 95.928 835 33 1 5175 6009 528206657 528207490 0 1352
5 TraesCS2D01G350400 chrUn 100.000 416 0 0 4391 4806 477174446 477174031 0 769


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 TraesCS2D01G350400 chr2D 448207294 448213302 6008 False 11097.0 11097 100.000 1 6009 1 chr2D.!!$F1 6008
1 TraesCS2D01G350400 chr2A 592851138 592857194 6056 False 4917.5 8813 93.243 1 6009 2 chr2A.!!$F1 6008
2 TraesCS2D01G350400 chr2B 528201449 528207490 6041 False 4335.5 7319 94.137 1 6009 2 chr2B.!!$F1 6008

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
709 732 0.605860 AGGACTTCTGCAGCTGCTTG 60.606 55.000 36.61 27.98 42.66 4.01 F
1393 1426 1.534175 CCGAGCAAGGAAGTACTAGCG 60.534 57.143 0.00 0.00 0.00 4.26 F
1624 1657 1.926665 TCTCTGCTAAGGAGGAGACCT 59.073 52.381 0.00 0.00 44.52 3.85 F
2072 2106 2.158623 TGTGGATGCAAGTCCTCACTTT 60.159 45.455 7.83 0.00 41.24 2.66 F
3361 3402 2.288152 ACGCCTAATTTGTTGGCACTTG 60.288 45.455 0.00 0.00 46.39 3.16 F
4888 4970 3.199290 CTCCGATCTCCAGGAGTGT 57.801 57.895 16.65 6.59 46.68 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 2480 4.990526 ACATCCAAAATCTCAGTGAAGGT 58.009 39.130 0.0 0.0 0.00 3.50 R
3335 3375 2.986479 GCCAACAAATTAGGCGTTTCAG 59.014 45.455 0.0 0.0 38.86 3.02 R
3543 3584 3.756082 ACCATGAGAATGCCCCTTTAA 57.244 42.857 0.0 0.0 0.00 1.52 R
3687 3758 1.416030 TGAACTAGACTGTGCCTGCAA 59.584 47.619 0.0 0.0 0.00 4.08 R
4918 5000 0.250338 GGACCTGGAGCTTCACGTTT 60.250 55.000 0.0 0.0 0.00 3.60 R
5866 6009 1.404181 CGTCGTGTTCATCCATGTCCT 60.404 52.381 0.0 0.0 0.00 3.85 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
155 168 1.977293 AATCCAAGCCTCGCCCTCTC 61.977 60.000 0.00 0.00 0.00 3.20
156 169 4.168291 CCAAGCCTCGCCCTCTCC 62.168 72.222 0.00 0.00 0.00 3.71
157 170 3.080121 CAAGCCTCGCCCTCTCCT 61.080 66.667 0.00 0.00 0.00 3.69
158 171 2.762043 AAGCCTCGCCCTCTCCTC 60.762 66.667 0.00 0.00 0.00 3.71
159 172 3.310035 AAGCCTCGCCCTCTCCTCT 62.310 63.158 0.00 0.00 0.00 3.69
189 202 0.978146 TCTCCCTCCCAGCAAGTAGC 60.978 60.000 0.00 0.00 46.19 3.58
497 511 5.968848 TGAGTTACACTGAATTTTGTTTCGC 59.031 36.000 0.00 0.00 0.00 4.70
589 611 1.884926 GATTTCCTCCGCGCTCAGG 60.885 63.158 13.97 13.97 0.00 3.86
637 659 6.057321 TGAAACGGATAGATTTTACTGGGT 57.943 37.500 0.00 0.00 0.00 4.51
709 732 0.605860 AGGACTTCTGCAGCTGCTTG 60.606 55.000 36.61 27.98 42.66 4.01
719 742 3.547567 AGCTGCTTGAGGCTGTTAG 57.452 52.632 0.00 0.00 42.39 2.34
722 745 1.818642 CTGCTTGAGGCTGTTAGCTT 58.181 50.000 11.79 0.00 41.99 3.74
1173 1206 2.881441 GTTGCTGAACGACTCGTCA 58.119 52.632 4.17 4.32 39.99 4.35
1209 1242 1.972872 CTATGTGGTCATCCTTGGGC 58.027 55.000 0.00 0.00 35.70 5.36
1319 1352 2.559698 TCGGTGAATCCAGCTGAAAA 57.440 45.000 17.39 0.00 38.57 2.29
1393 1426 1.534175 CCGAGCAAGGAAGTACTAGCG 60.534 57.143 0.00 0.00 0.00 4.26
1479 1512 4.250305 AAGTCACTTGGCGGCGGT 62.250 61.111 9.78 2.67 0.00 5.68
1494 1527 2.542907 CGGTGTTCTTGCGCAGGTT 61.543 57.895 19.74 0.00 0.00 3.50
1624 1657 1.926665 TCTCTGCTAAGGAGGAGACCT 59.073 52.381 0.00 0.00 44.52 3.85
1931 1964 8.528044 TTTATTTAGTTATGTTTAGCTGGGGG 57.472 34.615 0.00 0.00 0.00 5.40
2072 2106 2.158623 TGTGGATGCAAGTCCTCACTTT 60.159 45.455 7.83 0.00 41.24 2.66
2074 2108 4.072131 GTGGATGCAAGTCCTCACTTTTA 58.928 43.478 7.83 0.00 41.24 1.52
2406 2441 8.562052 TCTATTGATGTTTGATGTATGTGATGC 58.438 33.333 0.00 0.00 0.00 3.91
2440 2480 5.981088 TTATTCAGCAAATCAGAAAGCCA 57.019 34.783 0.00 0.00 0.00 4.75
2558 2598 5.821097 TGGTGGTTATGTTGGACATGATAA 58.179 37.500 0.00 0.00 39.53 1.75
3201 3241 6.585695 ATGCAATCATATTGGTCCTGATTC 57.414 37.500 0.00 0.21 37.48 2.52
3323 3363 7.596749 TGAATCGAACTGAATCTTTTCCTAC 57.403 36.000 0.00 0.00 0.00 3.18
3326 3366 6.097915 TCGAACTGAATCTTTTCCTACAGT 57.902 37.500 0.00 0.00 39.70 3.55
3327 3367 6.522054 TCGAACTGAATCTTTTCCTACAGTT 58.478 36.000 0.00 0.00 46.39 3.16
3361 3402 2.288152 ACGCCTAATTTGTTGGCACTTG 60.288 45.455 0.00 0.00 46.39 3.16
3543 3584 6.204301 CCATTAGCACAATCGATCATCTTTCT 59.796 38.462 0.00 0.00 0.00 2.52
3638 3708 5.576384 TGAATGCATTTAACTTTGAATCGGC 59.424 36.000 14.33 0.00 0.00 5.54
3687 3758 4.815533 TGACTAGAAGCTTCTTCTGCAT 57.184 40.909 32.70 12.87 38.70 3.96
3898 3969 7.905604 TCTGTGTTGTGATATCTAGGTTTTG 57.094 36.000 3.98 0.00 0.00 2.44
4389 4471 6.650807 GGTCCGAATGTCACACATCATATTAT 59.349 38.462 0.00 0.00 37.97 1.28
4888 4970 3.199290 CTCCGATCTCCAGGAGTGT 57.801 57.895 16.65 6.59 46.68 3.55
4918 5000 4.492160 GACTCGATGGGCACGCGA 62.492 66.667 15.93 3.66 0.00 5.87
5023 5105 1.272490 TCATGACACGGTGAGGAAGTC 59.728 52.381 16.29 1.01 0.00 3.01
5064 5146 6.895756 TCTTACCCTCAACTGTATCATACTGT 59.104 38.462 1.57 1.57 41.72 3.55
5163 5245 0.320421 TGGCGAACAGGAAGTGTAGC 60.320 55.000 0.00 0.00 39.03 3.58
5172 5254 0.376152 GGAAGTGTAGCGATCGTCGA 59.624 55.000 17.81 0.00 43.74 4.20
5173 5255 1.202110 GGAAGTGTAGCGATCGTCGAA 60.202 52.381 17.81 0.00 43.74 3.71
5320 5447 3.874383 TGAATGTTTCTGGACTTCCCA 57.126 42.857 0.00 0.00 44.25 4.37
5368 5495 2.884639 ACAGGTGAATTTTCCAGTTCCG 59.115 45.455 3.36 0.00 0.00 4.30
5386 5513 2.401766 GCATTGGCTGTCAGGGACG 61.402 63.158 1.14 0.00 34.95 4.79
5390 5524 2.821366 GGCTGTCAGGGACGCATG 60.821 66.667 1.14 0.00 35.22 4.06
5454 5590 5.104277 TGGTGAAACTCCTGGACTTTTAAGA 60.104 40.000 0.00 0.00 36.74 2.10
5552 5694 2.503765 TCTCCGCTCAACCATGGAATTA 59.496 45.455 21.47 0.00 0.00 1.40
5707 5850 1.667154 TTGGACTCGCCCGATCAGAG 61.667 60.000 0.00 0.00 37.96 3.35
5764 5907 4.230002 GCAGCCGGGTATGCCGTA 62.230 66.667 5.47 0.00 36.41 4.02
5808 5951 4.081322 ACCGTTTGTACTGGACTGAATT 57.919 40.909 0.00 0.00 0.00 2.17
5858 6001 0.904865 ATTGAGCGTCTGGGGAGTCA 60.905 55.000 0.00 0.00 0.00 3.41
5866 6009 0.487325 TCTGGGGAGTCAGAGTTGGA 59.513 55.000 0.00 0.00 38.70 3.53
5995 6138 4.722535 AGCTCCGAGGGCCAGGAA 62.723 66.667 19.19 6.23 35.90 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 168 1.720694 GGAGACGAGGCGAGAAGAGG 61.721 65.000 0.00 0.00 0.00 3.69
156 169 1.720694 GGGAGACGAGGCGAGAAGAG 61.721 65.000 0.00 0.00 0.00 2.85
157 170 1.749638 GGGAGACGAGGCGAGAAGA 60.750 63.158 0.00 0.00 0.00 2.87
158 171 1.720694 GAGGGAGACGAGGCGAGAAG 61.721 65.000 0.00 0.00 0.00 2.85
159 172 1.749638 GAGGGAGACGAGGCGAGAA 60.750 63.158 0.00 0.00 0.00 2.87
189 202 2.203126 GGGAATCGGAGGCTGCTG 60.203 66.667 4.02 0.00 0.00 4.41
192 205 1.753368 GAGGAGGGAATCGGAGGCTG 61.753 65.000 0.00 0.00 0.00 4.85
251 264 2.202892 GAGGACGACGGATTGGCC 60.203 66.667 0.00 0.00 37.76 5.36
458 472 2.100605 ACTCAGAACCTCCAATTCGC 57.899 50.000 0.00 0.00 0.00 4.70
497 511 0.745845 CACCAAATCAGCTCCTCCGG 60.746 60.000 0.00 0.00 0.00 5.14
589 611 6.273825 TCCAGAAACGCTCTATAATCTGAAC 58.726 40.000 0.00 0.00 37.14 3.18
637 659 3.357203 AGACAGAAGCTCGGTATCTGAA 58.643 45.455 17.24 0.00 42.48 3.02
709 732 1.079503 CAACCGAAGCTAACAGCCTC 58.920 55.000 0.00 0.00 43.77 4.70
719 742 0.241213 GAGGAAAAGGCAACCGAAGC 59.759 55.000 0.00 0.00 37.17 3.86
722 745 0.183971 TTGGAGGAAAAGGCAACCGA 59.816 50.000 0.00 0.00 37.17 4.69
753 776 2.032549 CGGCACAAGAACTCAACTCAAG 60.033 50.000 0.00 0.00 0.00 3.02
1173 1206 4.022935 CACATAGCAAACATCTGGTGTGTT 60.023 41.667 0.00 0.00 43.78 3.32
1319 1352 2.757124 GCCATTCTCCCGGTCCCAT 61.757 63.158 0.00 0.00 0.00 4.00
1393 1426 1.095807 GCAATAGGCCTCGGAACCAC 61.096 60.000 9.68 0.00 36.11 4.16
1479 1512 0.749818 TCCAAACCTGCGCAAGAACA 60.750 50.000 14.09 0.00 43.02 3.18
1494 1527 2.951269 CTGCTCAACAGGCATCCAA 58.049 52.632 0.00 0.00 43.19 3.53
1931 1964 7.492344 CCTTCATGGGTAAATTCACTATTTTGC 59.508 37.037 0.00 0.00 37.60 3.68
2072 2106 5.772825 GCATCTAGAAATGGCACCAATAA 57.227 39.130 0.00 0.00 0.00 1.40
2440 2480 4.990526 ACATCCAAAATCTCAGTGAAGGT 58.009 39.130 0.00 0.00 0.00 3.50
3335 3375 2.986479 GCCAACAAATTAGGCGTTTCAG 59.014 45.455 0.00 0.00 38.86 3.02
3543 3584 3.756082 ACCATGAGAATGCCCCTTTAA 57.244 42.857 0.00 0.00 0.00 1.52
3638 3708 6.986817 AGGATATCAAGAATCCAGTTAACACG 59.013 38.462 8.61 0.00 44.62 4.49
3687 3758 1.416030 TGAACTAGACTGTGCCTGCAA 59.584 47.619 0.00 0.00 0.00 4.08
4150 4232 3.066342 CAGCATCACATGAAGGGAATGAC 59.934 47.826 0.00 0.00 29.94 3.06
4389 4471 3.053991 TGGTCCTTGTGTTCCTTCAGAAA 60.054 43.478 0.00 0.00 35.85 2.52
4888 4970 0.952010 TCGAGTCCATGACGTCGACA 60.952 55.000 17.16 0.00 37.33 4.35
4918 5000 0.250338 GGACCTGGAGCTTCACGTTT 60.250 55.000 0.00 0.00 0.00 3.60
5040 5122 6.980978 CACAGTATGATACAGTTGAGGGTAAG 59.019 42.308 5.28 0.00 39.69 2.34
5064 5146 2.290514 ACAGCGTAGACTACACCTACCA 60.291 50.000 12.99 0.00 34.51 3.25
5163 5245 2.047040 CTCCATGACATTCGACGATCG 58.953 52.381 14.88 14.88 42.10 3.69
5320 5447 6.484364 AACAAACAGAGAATTTGGAACCAT 57.516 33.333 0.00 0.00 40.64 3.55
5368 5495 2.401766 CGTCCCTGACAGCCAATGC 61.402 63.158 0.00 0.00 37.95 3.56
5390 5524 2.356135 TCCGATTTAAGCTGGCAGTTC 58.644 47.619 17.16 0.00 0.00 3.01
5454 5590 1.366319 AAGATTGTCAGCCAGTCCCT 58.634 50.000 0.00 0.00 30.39 4.20
5552 5694 7.601886 CGATCTCAGCATAGGAAAAACAGATAT 59.398 37.037 0.00 0.00 0.00 1.63
5680 5823 1.212751 GGCGAGTCCAAAATGGCAC 59.787 57.895 0.00 0.00 37.47 5.01
5726 5869 1.874345 GCTGTGCATGCAGGAAGCTT 61.874 55.000 29.37 0.00 45.94 3.74
5729 5872 3.676216 TGCTGTGCATGCAGGAAG 58.324 55.556 23.41 19.35 37.00 3.46
5761 5904 5.517054 GCTTTCCTATCAACAGAACTCTACG 59.483 44.000 0.00 0.00 0.00 3.51
5764 5907 5.753721 AGCTTTCCTATCAACAGAACTCT 57.246 39.130 0.00 0.00 0.00 3.24
5808 5951 5.867330 TGTTCCTATCGGTTGGACTTTAAA 58.133 37.500 0.00 0.00 31.24 1.52
5858 6001 2.837947 TCATCCATGTCCTCCAACTCT 58.162 47.619 0.00 0.00 0.00 3.24
5866 6009 1.404181 CGTCGTGTTCATCCATGTCCT 60.404 52.381 0.00 0.00 0.00 3.85
5970 6113 1.975327 CCCTCGGAGCTGTTTCTCA 59.025 57.895 0.00 0.00 34.84 3.27


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

AutoCloner maintained by Alex Coulton.