Multiple sequence alignment - TraesCS2D01G205500

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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 TraesCS2D01G205500 chr2D 100.000 4763 0 0 1 4763 157135551 157140313 0.000000e+00 8796
1 TraesCS2D01G205500 chr2B 95.738 3848 130 20 1 3838 214591003 214594826 0.000000e+00 6167
2 TraesCS2D01G205500 chr2B 85.328 518 44 7 3911 4410 214594822 214595325 1.530000e-139 507
3 TraesCS2D01G205500 chr2B 89.076 119 12 1 4401 4518 214596344 214596462 3.840000e-31 147
4 TraesCS2D01G205500 chr2A 97.653 3025 58 4 800 3814 166854950 166857971 0.000000e+00 5180
5 TraesCS2D01G205500 chr2A 91.988 986 36 17 3810 4763 166858092 166859066 0.000000e+00 1343
6 TraesCS2D01G205500 chr2A 90.497 463 30 7 343 798 166854412 166854867 2.450000e-167 599
7 TraesCS2D01G205500 chr2A 88.520 331 20 4 7 332 166851114 166851431 7.480000e-103 385
8 TraesCS2D01G205500 chr2A 95.062 81 2 1 343 421 166854051 166854131 5.000000e-25 126
9 TraesCS2D01G205500 chr4B 89.529 764 53 18 3783 4521 623483670 623482909 0.000000e+00 942
10 TraesCS2D01G205500 chr3D 88.667 150 13 3 4610 4759 182651246 182651391 3.790000e-41 180
11 TraesCS2D01G205500 chr3B 87.662 154 15 3 4610 4763 345400765 345400914 4.900000e-40 176
12 TraesCS2D01G205500 chr5D 87.662 154 14 4 4610 4763 282529462 282529610 1.760000e-39 174
13 TraesCS2D01G205500 chr5D 87.013 154 16 3 4610 4763 138393828 138393977 2.280000e-38 171
14 TraesCS2D01G205500 chr7D 87.013 154 16 2 4610 4763 380074909 380074760 2.280000e-38 171
15 TraesCS2D01G205500 chr7A 87.838 148 14 3 4612 4759 309472295 309472438 2.280000e-38 171
16 TraesCS2D01G205500 chr6B 87.013 154 16 3 4610 4763 665034518 665034667 2.280000e-38 171
17 TraesCS2D01G205500 chr3A 86.364 154 17 3 4610 4763 8228655 8228804 1.060000e-36 165


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 TraesCS2D01G205500 chr2D 157135551 157140313 4762 False 8796.000000 8796 100.000000 1 4763 1 chr2D.!!$F1 4762
1 TraesCS2D01G205500 chr2B 214591003 214596462 5459 False 2273.666667 6167 90.047333 1 4518 3 chr2B.!!$F1 4517
2 TraesCS2D01G205500 chr2A 166851114 166859066 7952 False 1526.600000 5180 92.744000 7 4763 5 chr2A.!!$F1 4756
3 TraesCS2D01G205500 chr4B 623482909 623483670 761 True 942.000000 942 89.529000 3783 4521 1 chr4B.!!$R1 738

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
782 3766 0.109781 GTGGGCTGTATGTGCAAACG 60.110 55.0 0.00 0.0 0.00 3.60 F
1339 4414 0.248094 GATCAAGCGGCGGTTTAAGC 60.248 55.0 22.98 12.3 0.00 3.09 F
1347 4422 0.377203 GGCGGTTTAAGCGAATCAGG 59.623 55.0 20.82 0.0 42.41 3.86 F
1476 4551 0.952497 ACAGTGACGCTCATTGCAGG 60.952 55.0 0.00 0.0 37.59 4.85 F
2619 5694 1.680338 GCCGCCTATCAATCCAAAGT 58.320 50.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 4827 2.833794 CGAAGTTCACCCTTCAAGTCA 58.166 47.619 3.32 0.00 40.72 3.41 R
2619 5694 3.689347 AGTCAACTGCTCAATATTGGCA 58.311 40.909 22.26 22.26 34.67 4.92 R
3186 6261 4.676196 GCCATAATTGCAAGACTGACAAGG 60.676 45.833 4.94 0.00 0.00 3.61 R
3456 6531 1.179152 CCATGGCATTGAAGTGCAGA 58.821 50.000 0.00 0.00 46.81 4.26 R
4552 8814 1.134729 TCACCGTCCTATAAAACCCGC 60.135 52.381 0.00 0.00 0.00 6.13 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
41 43 5.823045 AGAACGAAGGAAATTTTCTGACACT 59.177 36.000 0.00 0.00 0.00 3.55
233 240 2.180204 CCAAATGAGCCCGCGTAGG 61.180 63.158 4.92 0.00 40.63 3.18
274 281 1.226746 GGATAGAATTGGGTTCGGCG 58.773 55.000 0.00 0.00 41.84 6.46
275 282 1.202604 GGATAGAATTGGGTTCGGCGA 60.203 52.381 4.99 4.99 41.84 5.54
276 283 2.550208 GGATAGAATTGGGTTCGGCGAT 60.550 50.000 11.76 0.00 41.84 4.58
335 342 3.387699 TGCACAGCATAGGAGCTTATGTA 59.612 43.478 7.16 0.00 43.70 2.29
341 3318 7.875041 CACAGCATAGGAGCTTATGTACTTATT 59.125 37.037 7.16 0.00 43.70 1.40
413 3392 4.843220 ATGTCTTTTCTTTCTGCACCAG 57.157 40.909 0.00 0.00 0.00 4.00
481 3460 4.217767 TGTGCTTTACAGATGTACTCGAGT 59.782 41.667 23.66 23.66 33.42 4.18
497 3476 1.657816 CGAGTACTCGCAGTAGCATCG 60.658 57.143 30.44 5.37 46.50 3.84
560 3544 9.461312 AAAGCTACATGAACATAATTTACCTGA 57.539 29.630 0.00 0.00 0.00 3.86
566 3550 6.509418 TGAACATAATTTACCTGAAGCACC 57.491 37.500 0.00 0.00 0.00 5.01
607 3591 2.457366 AAGCACCGAGTAAGTTCAGG 57.543 50.000 0.00 0.00 0.00 3.86
633 3617 3.903360 CGGGTTCCGCAATCTTTTAAAA 58.097 40.909 0.00 0.00 41.17 1.52
718 3702 2.973694 TTAGCTTCCGTGGTACCATC 57.026 50.000 19.72 10.92 0.00 3.51
719 3703 1.117150 TAGCTTCCGTGGTACCATCC 58.883 55.000 19.72 5.02 0.00 3.51
782 3766 0.109781 GTGGGCTGTATGTGCAAACG 60.110 55.000 0.00 0.00 0.00 3.60
792 3776 6.292865 GCTGTATGTGCAAACGTACATATGAT 60.293 38.462 10.38 0.00 41.85 2.45
801 3866 6.658831 CAAACGTACATATGATTCATGGACC 58.341 40.000 10.38 0.00 34.27 4.46
859 3924 7.120051 GGGCCTATCTACATATCTTCAGTCTA 58.880 42.308 0.84 0.00 0.00 2.59
889 3954 8.934023 ATTGTTTACTTCAATCCTTCTGGTAA 57.066 30.769 0.00 0.00 30.95 2.85
904 3969 7.993183 TCCTTCTGGTAAATTCATCCAAGATAC 59.007 37.037 0.00 0.00 34.23 2.24
906 3971 9.401058 CTTCTGGTAAATTCATCCAAGATACTT 57.599 33.333 0.00 0.00 0.00 2.24
958 4033 5.012893 CCTTTCTGGCTTAGGACATTTTCT 58.987 41.667 0.00 0.00 0.00 2.52
959 4034 5.478332 CCTTTCTGGCTTAGGACATTTTCTT 59.522 40.000 0.00 0.00 0.00 2.52
960 4035 6.349694 CCTTTCTGGCTTAGGACATTTTCTTC 60.350 42.308 0.00 0.00 0.00 2.87
1252 4327 1.077429 ATCCGAGGCCTTGCTTTCC 60.077 57.895 15.36 0.00 0.00 3.13
1257 4332 1.844687 GAGGCCTTGCTTTCCAGATT 58.155 50.000 6.77 0.00 0.00 2.40
1263 4338 2.751806 CCTTGCTTTCCAGATTGAGGAC 59.248 50.000 0.00 0.00 34.19 3.85
1299 4374 5.723672 TCACCTACAAGTTAGAGGACAAG 57.276 43.478 8.83 0.00 34.24 3.16
1339 4414 0.248094 GATCAAGCGGCGGTTTAAGC 60.248 55.000 22.98 12.30 0.00 3.09
1347 4422 0.377203 GGCGGTTTAAGCGAATCAGG 59.623 55.000 20.82 0.00 42.41 3.86
1372 4447 1.853319 CGCCGTCTGTCACTGAAAC 59.147 57.895 0.00 0.00 0.00 2.78
1464 4539 5.639506 TGCAATAGAAGCTAGAAACAGTGAC 59.360 40.000 0.00 0.00 0.00 3.67
1476 4551 0.952497 ACAGTGACGCTCATTGCAGG 60.952 55.000 0.00 0.00 37.59 4.85
1543 4618 5.525378 GTCGGCATTGATGAGAGTAAGAATT 59.475 40.000 0.00 0.00 0.00 2.17
1566 4641 4.808558 TGCTGATTAATTGGTTGACAAGC 58.191 39.130 10.46 10.46 43.48 4.01
1752 4827 7.069331 CAGATTATCAGGGAGTTACAGAAGAGT 59.931 40.741 0.00 0.00 0.00 3.24
2619 5694 1.680338 GCCGCCTATCAATCCAAAGT 58.320 50.000 0.00 0.00 0.00 2.66
3186 6261 6.624423 GCAATGCTATCATGAATATGACCCAC 60.624 42.308 0.00 0.00 45.54 4.61
3192 6267 4.780815 TCATGAATATGACCCACCTTGTC 58.219 43.478 0.00 0.00 38.37 3.18
3255 6330 1.830477 CTGGAAGAGCTCTGCTTACCT 59.170 52.381 21.44 1.06 39.88 3.08
3332 6407 2.757868 AGATTGTCTCGTCCTTCTCAGG 59.242 50.000 0.00 0.00 42.50 3.86
3456 6531 2.577772 AGGCCTATGAAGGGAAGAGT 57.422 50.000 1.29 0.00 43.87 3.24
3886 7086 4.219507 AGATCAACGACACTTGAGAGATGT 59.780 41.667 0.00 0.00 33.65 3.06
3967 7174 4.729868 AGAGTAAGTGGCAAGGAAATGTT 58.270 39.130 0.00 0.00 0.00 2.71
3991 7198 6.230472 TGAAAAGCATCTGTGTACACTGTAT 58.770 36.000 25.60 16.52 0.00 2.29
4046 7254 2.029380 AGCCTTATTCGGTTTTGTTGGC 60.029 45.455 0.00 0.00 38.24 4.52
4090 7305 3.496130 CACATCGAAATGGATACCTCAGC 59.504 47.826 0.00 0.00 37.19 4.26
4111 7326 4.464597 AGCAGGTTGGTTGTTGTTTTTCTA 59.535 37.500 0.00 0.00 0.00 2.10
4115 7330 7.148323 GCAGGTTGGTTGTTGTTTTTCTATTTT 60.148 33.333 0.00 0.00 0.00 1.82
4116 7331 9.372369 CAGGTTGGTTGTTGTTTTTCTATTTTA 57.628 29.630 0.00 0.00 0.00 1.52
4177 7410 6.096423 GGACTTCTTGACCCTAAACAAAGTTT 59.904 38.462 0.51 0.51 0.00 2.66
4386 7619 9.769093 TTCTTCTGCGCTTTATCTAAAATTTAC 57.231 29.630 9.73 0.00 0.00 2.01
4417 7650 5.796424 AAAAATGTGGCTTTCTGTGAGAT 57.204 34.783 0.00 0.00 0.00 2.75
4429 8691 5.592104 TTCTGTGAGATAAGTGCGGATAA 57.408 39.130 0.00 0.00 0.00 1.75
4531 8793 3.750652 TGCATACAATTCGACTTGCAAGA 59.249 39.130 32.50 10.88 37.17 3.02
4534 8796 5.726138 GCATACAATTCGACTTGCAAGAGAG 60.726 44.000 32.50 20.78 0.00 3.20
4589 8851 4.387862 ACGGTGATTCGACTTGTAATGTTC 59.612 41.667 0.00 0.00 0.00 3.18
4598 8860 4.034048 CGACTTGTAATGTTCTATGGCACC 59.966 45.833 0.00 0.00 0.00 5.01
4648 8910 2.760374 CCATACAAGGAAGGATCGAGC 58.240 52.381 0.00 0.00 0.00 5.03
4665 8927 6.920758 GGATCGAGCCAGTAATGATGATATAC 59.079 42.308 16.44 0.00 0.00 1.47
4668 8930 6.434340 TCGAGCCAGTAATGATGATATACAGT 59.566 38.462 0.00 0.00 0.00 3.55
4718 8980 5.111989 TGAAGAGAAGCTTGTCCAATATCG 58.888 41.667 19.26 0.00 36.83 2.92
4732 8994 6.097696 TGTCCAATATCGTCTGAGATGGTTTA 59.902 38.462 1.24 0.00 32.39 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 233 1.935300 GCATACCATCTTCCCTACGCG 60.935 57.143 3.53 3.53 0.00 6.01
265 272 0.672342 TCTAAGCTATCGCCGAACCC 59.328 55.000 0.00 0.00 36.60 4.11
274 281 8.732531 ACCGATCTATACTGTTTCTAAGCTATC 58.267 37.037 0.00 0.00 0.00 2.08
275 282 8.516234 CACCGATCTATACTGTTTCTAAGCTAT 58.484 37.037 0.00 0.00 0.00 2.97
276 283 7.040617 CCACCGATCTATACTGTTTCTAAGCTA 60.041 40.741 0.00 0.00 0.00 3.32
341 3318 8.863872 TCTCATTGATAACATATCTAGGACGA 57.136 34.615 0.00 0.00 0.00 4.20
413 3392 1.023513 AGGCAGCGATTGAGTCTTGC 61.024 55.000 0.00 0.00 35.55 4.01
421 3400 2.589014 GACAAGAAAAGGCAGCGATTG 58.411 47.619 0.00 0.00 0.00 2.67
422 3401 1.541588 GGACAAGAAAAGGCAGCGATT 59.458 47.619 0.00 0.00 0.00 3.34
481 3460 0.248498 GCACGATGCTACTGCGAGTA 60.248 55.000 0.00 0.00 40.96 2.59
566 3550 4.545823 TGTTTACTCTCGGCACAAAAAG 57.454 40.909 0.00 0.00 0.00 2.27
633 3617 5.480422 CCCAAAAGGTTCACTAGCCTAAAAT 59.520 40.000 0.00 0.00 34.15 1.82
731 3715 7.961351 ACAAAGTCATCTTAGCTAGCTCATAT 58.039 34.615 23.26 10.09 33.09 1.78
736 3720 6.042638 TCAACAAAGTCATCTTAGCTAGCT 57.957 37.500 23.12 23.12 33.09 3.32
737 3721 6.292061 CGATCAACAAAGTCATCTTAGCTAGC 60.292 42.308 6.62 6.62 33.09 3.42
738 3722 6.199908 CCGATCAACAAAGTCATCTTAGCTAG 59.800 42.308 0.00 0.00 33.09 3.42
739 3723 6.042777 CCGATCAACAAAGTCATCTTAGCTA 58.957 40.000 0.00 0.00 33.09 3.32
747 3731 2.436417 CCCACCGATCAACAAAGTCAT 58.564 47.619 0.00 0.00 0.00 3.06
782 3766 5.555017 AGCAGGTCCATGAATCATATGTAC 58.445 41.667 1.90 0.00 0.00 2.90
792 3776 4.922206 AGAAACATTAGCAGGTCCATGAA 58.078 39.130 0.00 0.00 0.00 2.57
801 3866 4.561606 GCATTGCAAGAGAAACATTAGCAG 59.438 41.667 4.94 0.00 0.00 4.24
872 3937 7.340232 TGGATGAATTTACCAGAAGGATTGAAG 59.660 37.037 0.00 0.00 38.69 3.02
889 3954 8.773033 AGCCAATAAAGTATCTTGGATGAATT 57.227 30.769 4.79 0.00 41.61 2.17
904 3969 4.275443 GCAAGGAGATGAGAGCCAATAAAG 59.725 45.833 0.00 0.00 0.00 1.85
906 3971 3.457380 AGCAAGGAGATGAGAGCCAATAA 59.543 43.478 0.00 0.00 0.00 1.40
958 4033 2.693074 GTTGGCTTCTTTCAAGGGTGAA 59.307 45.455 0.00 0.00 42.12 3.18
959 4034 2.306847 GTTGGCTTCTTTCAAGGGTGA 58.693 47.619 0.00 0.00 0.00 4.02
960 4035 1.341209 GGTTGGCTTCTTTCAAGGGTG 59.659 52.381 0.00 0.00 0.00 4.61
1204 4279 2.162681 GAAGCTGGCAGTGGTATTGTT 58.837 47.619 17.16 0.00 0.00 2.83
1252 4327 2.155732 CGTCAACAACGTCCTCAATCTG 59.844 50.000 0.00 0.00 46.42 2.90
1299 4374 0.961019 TCACAGAAAAGCCACCATGC 59.039 50.000 0.00 0.00 0.00 4.06
1339 4414 2.892425 GCGCCAGGTCCTGATTCG 60.892 66.667 21.23 19.22 32.44 3.34
1372 4447 8.768957 TCTAATTTCAGTTTGATGTCTCTCAG 57.231 34.615 0.00 0.00 0.00 3.35
1476 4551 7.422399 GGAAGTATGAAGTCTGATCTGTAGAC 58.578 42.308 3.97 3.97 43.77 2.59
1543 4618 5.229423 GCTTGTCAACCAATTAATCAGCAA 58.771 37.500 0.00 0.00 31.20 3.91
1566 4641 6.683974 ATTACATTCTCCTGTTGGAAATCG 57.316 37.500 0.00 0.00 42.66 3.34
1752 4827 2.833794 CGAAGTTCACCCTTCAAGTCA 58.166 47.619 3.32 0.00 40.72 3.41
1845 4920 5.453057 CCAGACATCATCTAGAACCAGAAGG 60.453 48.000 0.00 0.00 35.15 3.46
2619 5694 3.689347 AGTCAACTGCTCAATATTGGCA 58.311 40.909 22.26 22.26 34.67 4.92
3186 6261 4.676196 GCCATAATTGCAAGACTGACAAGG 60.676 45.833 4.94 0.00 0.00 3.61
3192 6267 8.570488 TCATTTATAGCCATAATTGCAAGACTG 58.430 33.333 4.94 1.62 32.04 3.51
3332 6407 4.690280 CCAACAAGGTAATGTTTTCATGGC 59.310 41.667 0.00 0.00 41.44 4.40
3456 6531 1.179152 CCATGGCATTGAAGTGCAGA 58.821 50.000 0.00 0.00 46.81 4.26
3949 7156 5.860941 TTTCAACATTTCCTTGCCACTTA 57.139 34.783 0.00 0.00 0.00 2.24
3967 7174 4.450976 ACAGTGTACACAGATGCTTTTCA 58.549 39.130 27.06 0.00 0.00 2.69
3991 7198 5.842328 TCCCTTGTTTCTAACTCAGGTTCTA 59.158 40.000 0.00 0.00 36.92 2.10
4046 7254 5.283294 TGTTGTGCATTTTCAACATCTCAG 58.717 37.500 14.57 0.00 45.50 3.35
4090 7305 7.841915 AAATAGAAAAACAACAACCAACCTG 57.158 32.000 0.00 0.00 0.00 4.00
4177 7410 6.888105 TGATTCCTGATGCAGAGTTATACAA 58.112 36.000 0.00 0.00 32.44 2.41
4185 7418 3.878103 CCTCTTTGATTCCTGATGCAGAG 59.122 47.826 0.00 0.00 32.44 3.35
4417 7650 7.468084 GCCTGACAAATTTATTATCCGCACTTA 60.468 37.037 0.00 0.00 0.00 2.24
4429 8691 7.099120 GGAAATGTTCAGCCTGACAAATTTAT 58.901 34.615 0.00 0.00 0.00 1.40
4552 8814 1.134729 TCACCGTCCTATAAAACCCGC 60.135 52.381 0.00 0.00 0.00 6.13
4561 8823 2.758979 ACAAGTCGAATCACCGTCCTAT 59.241 45.455 0.00 0.00 0.00 2.57
4589 8851 1.369091 GCCAACACTCGGTGCCATAG 61.369 60.000 4.23 0.00 36.98 2.23
4598 8860 1.462283 CATCTCAACAGCCAACACTCG 59.538 52.381 0.00 0.00 0.00 4.18
4648 8910 8.127150 TCCTGACTGTATATCATCATTACTGG 57.873 38.462 0.00 0.00 0.00 4.00
4665 8927 2.472029 ACCCCAACTCTATCCTGACTG 58.528 52.381 0.00 0.00 0.00 3.51
4668 8930 2.863238 TCCTACCCCAACTCTATCCTGA 59.137 50.000 0.00 0.00 0.00 3.86
4718 8980 9.817809 TTTGTATATGACTAAACCATCTCAGAC 57.182 33.333 0.00 0.00 0.00 3.51
4732 8994 3.181450 GGAGGCCTGCTTTGTATATGACT 60.181 47.826 18.47 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.