Multiple sequence alignment - TraesCS5A01G130500

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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 TraesCS5A01G130500 chr5A 100.000 3462 0 0 701 4162 292861897 292858436 0.000000e+00 6394
1 TraesCS5A01G130500 chr5A 100.000 312 0 0 1 312 292862597 292862286 1.000000e-160 577
2 TraesCS5A01G130500 chr5D 95.452 3342 111 13 823 4157 219526662 219523355 0.000000e+00 5291
3 TraesCS5A01G130500 chr5D 91.900 321 15 6 1 312 219527247 219526929 4.940000e-119 438
4 TraesCS5A01G130500 chr5D 99.187 123 0 1 701 822 219526902 219526780 1.950000e-53 220
5 TraesCS5A01G130500 chr5B 92.494 3424 160 33 794 4162 238314870 238318251 0.000000e+00 4809
6 TraesCS5A01G130500 chr5B 91.765 3473 168 48 727 4162 242138544 242135153 0.000000e+00 4721
7 TraesCS5A01G130500 chr5B 95.268 317 10 1 1 312 242139080 242138764 8.040000e-137 497
8 TraesCS5A01G130500 chr5B 94.551 312 15 1 1 312 238312506 238312815 8.090000e-132 481
9 TraesCS5A01G130500 chr3D 94.737 76 4 0 3574 3649 19210039 19209964 7.310000e-23 119


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 TraesCS5A01G130500 chr5A 292858436 292862597 4161 True 3485.5 6394 100.0000 1 4162 2 chr5A.!!$R1 4161
1 TraesCS5A01G130500 chr5D 219523355 219527247 3892 True 1983.0 5291 95.5130 1 4157 3 chr5D.!!$R1 4156
2 TraesCS5A01G130500 chr5B 238312506 238318251 5745 False 2645.0 4809 93.5225 1 4162 2 chr5B.!!$F1 4161
3 TraesCS5A01G130500 chr5B 242135153 242139080 3927 True 2609.0 4721 93.5165 1 4162 2 chr5B.!!$R1 4161

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
929 3032 1.203523 CTGGTCTGTCTTCTTCCTCGG 59.796 57.143 0.0 0.0 0.0 4.63 F
1576 3685 1.202348 ACTCTCATCTTGTCGCATCCG 60.202 52.381 0.0 0.0 0.0 4.18 F
2673 4830 1.227263 CCCCGATGGTCGTGTCATC 60.227 63.158 0.0 0.0 38.4 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 4281 1.065199 CCAGATGAGCCAGGCTTGTTA 60.065 52.381 17.46 3.10 39.88 2.41 R
2935 5092 0.394192 CGCCTGAGAGATGGGCATTA 59.606 55.000 0.00 0.00 45.50 1.90 R
3708 5890 0.899720 CAAATCAGGGTGCAGCCATT 59.100 50.000 34.87 23.52 39.65 3.16 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
47 48 4.518970 AGTGTAAGCACCACACCATTAAAG 59.481 41.667 10.71 0.00 46.01 1.85
116 120 8.592105 TCATTTGTCTCATTCATTTTTCAACC 57.408 30.769 0.00 0.00 0.00 3.77
270 285 2.106684 GGTTGGTCAAAGGAGAGAGGTT 59.893 50.000 0.00 0.00 0.00 3.50
275 290 3.071747 GGTCAAAGGAGAGAGGTTGTTCT 59.928 47.826 0.00 0.00 0.00 3.01
818 2782 7.118390 CCATAGAACTTTGGCATATGCTACTAC 59.882 40.741 26.12 10.51 41.70 2.73
819 2783 6.240549 AGAACTTTGGCATATGCTACTACT 57.759 37.500 26.12 13.98 41.70 2.57
820 2784 6.284459 AGAACTTTGGCATATGCTACTACTC 58.716 40.000 26.12 15.87 41.70 2.59
821 2785 4.962155 ACTTTGGCATATGCTACTACTCC 58.038 43.478 26.12 8.37 41.70 3.85
904 3007 2.335316 ACTAGAGTAGGCGTCTCCTG 57.665 55.000 0.00 4.97 46.98 3.86
929 3032 1.203523 CTGGTCTGTCTTCTTCCTCGG 59.796 57.143 0.00 0.00 0.00 4.63
932 3035 2.352912 GGTCTGTCTTCTTCCTCGGTTC 60.353 54.545 0.00 0.00 0.00 3.62
992 3095 1.307647 CCAAGCAAGCTACCCCCAT 59.692 57.895 0.00 0.00 0.00 4.00
1134 3237 4.816984 TCTCCCTCCTCGCCGTCC 62.817 72.222 0.00 0.00 0.00 4.79
1238 3341 4.152625 CGGCGAGCAGGAAAAGCG 62.153 66.667 0.00 0.00 37.01 4.68
1576 3685 1.202348 ACTCTCATCTTGTCGCATCCG 60.202 52.381 0.00 0.00 0.00 4.18
1648 3757 5.131475 TCACCAACCTTTACCTGTACTCTTT 59.869 40.000 0.00 0.00 0.00 2.52
1734 3844 4.081862 TGAACTAATCGACCTGATCCGTTT 60.082 41.667 0.00 0.00 35.84 3.60
1743 3853 4.143179 CGACCTGATCCGTTTGAAAGTTAC 60.143 45.833 0.00 0.00 0.00 2.50
1809 3919 3.510388 TTCATGCTCTCCAGTAGTTCG 57.490 47.619 0.00 0.00 0.00 3.95
1843 3953 4.766404 ACTAGTGTAATTGTTTGCCTGC 57.234 40.909 0.00 0.00 0.00 4.85
1844 3954 3.506067 ACTAGTGTAATTGTTTGCCTGCC 59.494 43.478 0.00 0.00 0.00 4.85
1973 4087 5.741388 ATTAGCGTCTTTGGCATCTTAAG 57.259 39.130 0.00 0.00 0.00 1.85
1988 4102 5.883115 GCATCTTAAGCCTCTAATATTCCCC 59.117 44.000 0.00 0.00 0.00 4.81
2035 4159 4.451557 GGTGTCGTAATTTGAGAAACACG 58.548 43.478 0.00 0.00 37.10 4.49
2157 4281 2.762327 GACCATCTCCAATGTGGCATTT 59.238 45.455 0.00 0.00 37.47 2.32
2252 4382 3.829886 TTTGCTGTTTGCCTCTTATCG 57.170 42.857 0.00 0.00 42.00 2.92
2304 4437 4.617959 TGCGTGCCTATGTATTAAGAGAC 58.382 43.478 0.00 0.00 0.00 3.36
2312 4445 7.451566 TGCCTATGTATTAAGAGACAGATAGCA 59.548 37.037 0.00 0.00 30.16 3.49
2322 4455 4.591072 AGAGACAGATAGCAATCCCCTAAC 59.409 45.833 0.00 0.00 31.98 2.34
2326 4459 5.826643 ACAGATAGCAATCCCCTAACAAAA 58.173 37.500 0.00 0.00 31.98 2.44
2327 4460 6.252995 ACAGATAGCAATCCCCTAACAAAAA 58.747 36.000 0.00 0.00 31.98 1.94
2328 4461 6.378280 ACAGATAGCAATCCCCTAACAAAAAG 59.622 38.462 0.00 0.00 31.98 2.27
2342 4475 7.337942 CCCTAACAAAAAGAGACAGATAGCAAT 59.662 37.037 0.00 0.00 0.00 3.56
2453 4610 9.638239 CTTTATTTATACACAATGCAACTTGGT 57.362 29.630 5.11 3.10 0.00 3.67
2468 4625 5.357032 GCAACTTGGTTAATGGCTATGTACT 59.643 40.000 0.00 0.00 0.00 2.73
2519 4676 9.825972 CTATTTTAACTGGTGTATTGTGTCTTG 57.174 33.333 0.00 0.00 0.00 3.02
2673 4830 1.227263 CCCCGATGGTCGTGTCATC 60.227 63.158 0.00 0.00 38.40 2.92
2774 4931 8.676401 CACCTTTTGAATTTTGAAACCATCTTT 58.324 29.630 0.00 0.00 0.00 2.52
2831 4988 1.550130 TTGTGGGGAGCTTCCTACCG 61.550 60.000 23.93 0.00 43.72 4.02
2886 5043 4.349503 AGCCGCAACCATCTGCCA 62.350 61.111 0.00 0.00 39.26 4.92
2891 5048 1.314534 CGCAACCATCTGCCATTCCA 61.315 55.000 0.00 0.00 39.26 3.53
2935 5092 3.231889 CTCCGGTGCTCACAGCTGT 62.232 63.158 15.25 15.25 42.97 4.40
3027 5184 1.138036 CATGCCAATGTGGAGCACG 59.862 57.895 0.00 0.00 40.96 5.34
3068 5225 1.743252 CCTGAACTCAAGCTCCGCC 60.743 63.158 0.00 0.00 0.00 6.13
3187 5347 1.566404 CTGCCGTTTTGTTTTGGTCC 58.434 50.000 0.00 0.00 0.00 4.46
3319 5479 6.379703 CCCTAATCTGATAGAGTGATAGGTGG 59.620 46.154 7.97 0.00 0.00 4.61
3322 5482 3.891977 TCTGATAGAGTGATAGGTGGTGC 59.108 47.826 0.00 0.00 0.00 5.01
3329 5489 3.441101 AGTGATAGGTGGTGCTCTTACA 58.559 45.455 0.00 0.00 0.00 2.41
3432 5596 9.701098 CTTGTAGTACTTTAATCAGTGGTTACA 57.299 33.333 0.00 0.00 0.00 2.41
3460 5625 4.586884 AGTCCATGTCTGAACGTAGTCTA 58.413 43.478 0.00 0.00 45.00 2.59
3484 5649 1.071385 CCTGTTTCCAGAGTCACTGCT 59.929 52.381 0.00 0.00 44.52 4.24
3516 5681 5.734311 ACGTGTGTTACTTTTGATTTCGAG 58.266 37.500 0.00 0.00 0.00 4.04
3596 5778 4.201950 ACGTGTGTTACTTTCGAGTAGTGT 60.202 41.667 11.31 0.00 0.00 3.55
3607 5789 7.960793 ACTTTCGAGTAGTGTAATTTGCATAC 58.039 34.615 1.90 0.00 0.00 2.39
3649 5831 2.587322 TAGGGCCTGTTTGGATCGCG 62.587 60.000 18.53 0.00 38.35 5.87
3686 5868 7.037153 ACCCTACCAAAATCCTATTGTTGACTA 60.037 37.037 0.00 0.00 0.00 2.59
3721 5903 1.526575 CGTTTCAATGGCTGCACCCT 61.527 55.000 0.50 0.00 37.83 4.34
3981 6163 7.372714 CAGCATATTGGTATACACAATTGCAT 58.627 34.615 27.27 19.73 40.55 3.96
4043 6227 8.743099 GTGCTCGGCTTTAAATTAATAAATCAC 58.257 33.333 0.00 0.00 0.00 3.06
4126 6310 0.036732 ATTGCGGAGTCAAAGAGGCA 59.963 50.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.629079 ACAGCTTAAACTATGAAACTGGC 57.371 39.130 0.00 0.00 0.00 4.85
215 230 3.211045 GGACTGCAAAAGTGTACTGGAA 58.789 45.455 0.00 0.00 40.07 3.53
270 285 7.875041 CACTCTCTCTCCATTCTTTAAAGAACA 59.125 37.037 28.38 16.24 46.80 3.18
275 290 6.931281 CACACACTCTCTCTCCATTCTTTAAA 59.069 38.462 0.00 0.00 0.00 1.52
818 2782 4.142359 CCAGTAGCACTGTTGTAGTAGGAG 60.142 50.000 13.06 0.00 44.50 3.69
819 2783 3.762288 CCAGTAGCACTGTTGTAGTAGGA 59.238 47.826 13.06 0.00 44.50 2.94
820 2784 3.510360 ACCAGTAGCACTGTTGTAGTAGG 59.490 47.826 13.06 0.00 44.50 3.18
821 2785 4.486090 CACCAGTAGCACTGTTGTAGTAG 58.514 47.826 13.06 1.52 44.50 2.57
904 3007 2.232696 GGAAGAAGACAGACCAGAGGAC 59.767 54.545 0.00 0.00 0.00 3.85
992 3095 1.485019 CCCTCCCCTCCATGTAGCATA 60.485 57.143 0.00 0.00 0.00 3.14
1047 3150 2.125350 GCTCTGAACAGGCCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
1260 3363 3.347405 CCGTTGCCGTTGCCGTTA 61.347 61.111 0.00 0.00 36.33 3.18
1520 3623 1.342674 TGTCCTAACAGATACCGCCCT 60.343 52.381 0.00 0.00 0.00 5.19
1576 3685 7.711339 AGGAATCACTTTAATAACATCGGAGAC 59.289 37.037 0.00 0.00 42.51 3.36
1648 3757 5.269554 AGGTTGGTGAGAATAAATGGGAA 57.730 39.130 0.00 0.00 0.00 3.97
1843 3953 6.757897 TCACAAGTATTTAAGGATTGCAGG 57.242 37.500 0.00 0.00 0.00 4.85
1844 3954 9.079833 CAAATCACAAGTATTTAAGGATTGCAG 57.920 33.333 0.00 0.00 0.00 4.41
1973 4087 5.940470 CACAATGTAGGGGAATATTAGAGGC 59.060 44.000 0.00 0.00 0.00 4.70
1980 4094 7.911651 CACTAGATCACAATGTAGGGGAATAT 58.088 38.462 0.00 0.00 33.96 1.28
1982 4096 6.179906 CACTAGATCACAATGTAGGGGAAT 57.820 41.667 0.00 0.00 33.96 3.01
1988 4102 3.068165 TCCGCCACTAGATCACAATGTAG 59.932 47.826 0.00 0.00 35.41 2.74
2035 4159 1.429463 AATCGGACAAGAACAGCGAC 58.571 50.000 0.00 0.00 0.00 5.19
2157 4281 1.065199 CCAGATGAGCCAGGCTTGTTA 60.065 52.381 17.46 3.10 39.88 2.41
2262 4392 3.204827 CCTCTTGCGCATTCCCGG 61.205 66.667 12.75 3.97 0.00 5.73
2264 4394 1.678970 AACCCTCTTGCGCATTCCC 60.679 57.895 12.75 0.00 0.00 3.97
2304 4437 6.603201 TCTTTTTGTTAGGGGATTGCTATCTG 59.397 38.462 8.06 0.00 0.00 2.90
2312 4445 6.200878 TCTGTCTCTTTTTGTTAGGGGATT 57.799 37.500 0.00 0.00 0.00 3.01
2322 4455 8.077991 TGTTTGATTGCTATCTGTCTCTTTTTG 58.922 33.333 9.55 0.00 0.00 2.44
2326 4459 7.934855 AATGTTTGATTGCTATCTGTCTCTT 57.065 32.000 9.55 0.00 0.00 2.85
2327 4460 7.934855 AAATGTTTGATTGCTATCTGTCTCT 57.065 32.000 9.55 0.00 0.00 3.10
2328 4461 9.495754 GTAAAATGTTTGATTGCTATCTGTCTC 57.504 33.333 9.55 0.00 0.00 3.36
2453 4610 8.321353 CCATCCTCATAAGTACATAGCCATTAA 58.679 37.037 0.00 0.00 0.00 1.40
2519 4676 8.368126 CACGAAATATTTTCAGTTTGAATCAGC 58.632 33.333 1.43 0.00 36.11 4.26
2774 4931 5.287226 GGTCTGTGTTAGAGAACGAAGAAA 58.713 41.667 0.00 0.00 38.51 2.52
2831 4988 2.415857 CTGATGCTGCTTCAGACTGTTC 59.584 50.000 30.83 0.00 42.63 3.18
2870 5027 2.618312 GAATGGCAGATGGTTGCGGC 62.618 60.000 0.00 0.00 45.00 6.53
2935 5092 0.394192 CGCCTGAGAGATGGGCATTA 59.606 55.000 0.00 0.00 45.50 1.90
3068 5225 2.819595 CCGACCATGGTGAAGCCG 60.820 66.667 25.52 18.82 41.21 5.52
3187 5347 3.366679 GCAAAATGTGTCAGTGATGAGGG 60.367 47.826 0.00 0.00 0.00 4.30
3356 5516 4.832266 ACAATGAACAGCCCAGAACAAATA 59.168 37.500 0.00 0.00 0.00 1.40
3432 5596 5.407407 ACGTTCAGACATGGACTTAGAAT 57.593 39.130 0.00 0.00 32.11 2.40
3484 5649 5.866335 AAAGTAACACACGTCAACAGAAA 57.134 34.783 0.00 0.00 0.00 2.52
3649 5831 1.202769 TGGTAGGGTGGTTACTGGCC 61.203 60.000 0.00 0.00 0.00 5.36
3708 5890 0.899720 CAAATCAGGGTGCAGCCATT 59.100 50.000 34.87 23.52 39.65 3.16
3721 5903 2.274104 GCCCGCCCTACCAAATCA 59.726 61.111 0.00 0.00 0.00 2.57
3780 5962 6.378710 TGACTCATGTCTATTTCTAGGTCG 57.621 41.667 0.00 0.00 43.29 4.79
3843 6025 2.373335 ACCACAAGCCCATAACAACA 57.627 45.000 0.00 0.00 0.00 3.33
3850 6032 1.922447 TGGATAGAACCACAAGCCCAT 59.078 47.619 0.00 0.00 34.77 4.00
4000 6182 4.697514 GAGCACATCTTATGCCTCTGTTA 58.302 43.478 0.00 0.00 44.53 2.41
4043 6227 7.337150 ACATTTGACTATTTTGCATGTTTCG 57.663 32.000 0.00 0.00 0.00 3.46
4126 6310 3.174265 GCATGAGGGGGCCTAGCT 61.174 66.667 0.84 0.00 31.76 3.32
4134 6318 3.569491 ACATCTTTTATGGCATGAGGGG 58.431 45.455 10.98 4.43 0.00 4.79
4137 6321 5.471456 GGGAGTACATCTTTTATGGCATGAG 59.529 44.000 10.98 5.67 0.00 2.90


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

AutoCloner maintained by Alex Coulton.