Multiple sequence alignment - TraesCS1A01G130000

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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 TraesCS1A01G130000 chr1A 100.000 2335 0 0 1 2335 168442692 168445026 0.000000e+00 4313.0
1 TraesCS1A01G130000 chr5D 96.602 2354 60 11 1 2335 560880407 560878055 0.000000e+00 3886.0
2 TraesCS1A01G130000 chrUn 96.518 2355 62 10 1 2335 93416408 93418762 0.000000e+00 3877.0
3 TraesCS1A01G130000 chr6A 96.031 2343 82 11 1 2335 271185377 271183038 0.000000e+00 3801.0
4 TraesCS1A01G130000 chr3B 95.924 2355 72 14 1 2335 201522612 201520262 0.000000e+00 3795.0
5 TraesCS1A01G130000 chr3A 95.869 2348 76 13 1 2335 672914403 672916742 0.000000e+00 3779.0
6 TraesCS1A01G130000 chr3A 95.681 1783 63 13 562 2335 692573172 692571395 0.000000e+00 2854.0
7 TraesCS1A01G130000 chr3A 93.370 362 19 2 147 504 471793343 471792983 4.420000e-147 531.0
8 TraesCS1A01G130000 chr1D 96.677 2227 56 10 126 2335 144238516 144236291 0.000000e+00 3687.0
9 TraesCS1A01G130000 chr2D 96.500 2200 60 9 1 2183 272798296 272800495 0.000000e+00 3620.0
10 TraesCS1A01G130000 chr4A 96.009 1829 59 11 136 1953 722779094 722780919 0.000000e+00 2961.0
11 TraesCS1A01G130000 chr2A 87.634 186 20 3 23 208 651278124 651277942 1.820000e-51 213.0
12 TraesCS1A01G130000 chr2A 98.333 120 2 0 346 465 187060400 187060281 6.540000e-51 211.0
13 TraesCS1A01G130000 chr2A 97.500 120 3 0 346 465 187105848 187105967 3.040000e-49 206.0
14 TraesCS1A01G130000 chr2A 100.000 38 0 0 393 430 557180324 557180361 1.160000e-08 71.3


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 TraesCS1A01G130000 chr1A 168442692 168445026 2334 False 4313 4313 100.000 1 2335 1 chr1A.!!$F1 2334
1 TraesCS1A01G130000 chr5D 560878055 560880407 2352 True 3886 3886 96.602 1 2335 1 chr5D.!!$R1 2334
2 TraesCS1A01G130000 chrUn 93416408 93418762 2354 False 3877 3877 96.518 1 2335 1 chrUn.!!$F1 2334
3 TraesCS1A01G130000 chr6A 271183038 271185377 2339 True 3801 3801 96.031 1 2335 1 chr6A.!!$R1 2334
4 TraesCS1A01G130000 chr3B 201520262 201522612 2350 True 3795 3795 95.924 1 2335 1 chr3B.!!$R1 2334
5 TraesCS1A01G130000 chr3A 672914403 672916742 2339 False 3779 3779 95.869 1 2335 1 chr3A.!!$F1 2334
6 TraesCS1A01G130000 chr3A 692571395 692573172 1777 True 2854 2854 95.681 562 2335 1 chr3A.!!$R2 1773
7 TraesCS1A01G130000 chr1D 144236291 144238516 2225 True 3687 3687 96.677 126 2335 1 chr1D.!!$R1 2209
8 TraesCS1A01G130000 chr2D 272798296 272800495 2199 False 3620 3620 96.500 1 2183 1 chr2D.!!$F1 2182
9 TraesCS1A01G130000 chr4A 722779094 722780919 1825 False 2961 2961 96.009 136 1953 1 chr4A.!!$F1 1817

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
676 693 3.00611 TCGGAAACATCAGGAACGTAACT 59.994 43.478 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1518 1.937846 CGTCCGCACCTACGAATCG 60.938 63.158 0.0 0.0 41.55 3.34 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
39 40 6.449830 ACCTCAGACCCTTTTAAATGTAGT 57.550 37.500 0.00 0.00 0.00 2.73
74 75 6.150976 TGGAGCTCGAAAATTGATGTGTATTT 59.849 34.615 7.83 0.00 0.00 1.40
134 135 5.334491 CGTGTTGGTGATGTTATTGTTGCTA 60.334 40.000 0.00 0.00 0.00 3.49
148 149 4.514545 TGTTGCTATAATCAAAGACGCG 57.485 40.909 3.53 3.53 0.00 6.01
189 190 6.210287 AGAAAGATCCGAAGTAATTCGAGT 57.790 37.500 25.41 13.56 46.52 4.18
229 230 8.246180 ACATGTAAAGAATTCAAATGCGAAGAT 58.754 29.630 8.44 0.00 0.00 2.40
294 295 5.927819 TGATCAAAAAGGCAATCCAAAAGT 58.072 33.333 0.00 0.00 33.74 2.66
513 529 8.925338 GGAGGAACCTTGAATTAGAGTCTTATA 58.075 37.037 0.00 0.00 35.41 0.98
569 585 8.763049 TCTATAAGAAATGCGGACATGAATAG 57.237 34.615 0.00 0.00 36.36 1.73
647 664 9.462606 AATACTTCTACAAGAGGGTTTTATTGG 57.537 33.333 0.00 0.00 33.34 3.16
676 693 3.006110 TCGGAAACATCAGGAACGTAACT 59.994 43.478 0.00 0.00 0.00 2.24
851 868 7.770897 GGGAATTGCTATTCTTTCTACTTCTCA 59.229 37.037 18.26 0.00 40.07 3.27
1057 1080 7.497925 AGAGAAGCAAAAGTAACTTTCGAAT 57.502 32.000 0.00 0.00 31.99 3.34
1188 1211 1.701847 CTGATGGGGGATAGGGTCAAG 59.298 57.143 0.00 0.00 0.00 3.02
1201 1224 7.339482 GGATAGGGTCAAGATTGAAGTAAGTT 58.661 38.462 0.00 0.00 39.21 2.66
1257 1281 2.649816 ACTTCCCCATAAGGCTTCAAGT 59.350 45.455 1.30 1.23 0.00 3.16
1393 1421 6.712241 TCTAAAATTCAAGCGAAGAGACTG 57.288 37.500 0.00 0.00 33.74 3.51
1488 1518 7.587028 TCGTAAAATTTGTACAAAATGTCGACC 59.413 33.333 23.97 7.56 33.56 4.79
1501 1531 3.993103 CGACCGATTCGTAGGTGC 58.007 61.111 5.20 0.00 43.24 5.01
1561 1591 8.585018 CATAAACAAAGACAGGGGTAATCTTTT 58.415 33.333 0.00 0.00 39.98 2.27
1793 1829 6.369615 ACGTAAGAAAGTGCGTATTGGTTTAT 59.630 34.615 0.00 0.00 43.62 1.40
1845 1881 5.989777 AGAGTGCACGTAGAATAACAAAAGT 59.010 36.000 12.01 0.00 0.00 2.66
1847 1883 5.526111 AGTGCACGTAGAATAACAAAAGTGT 59.474 36.000 12.01 0.00 40.75 3.55
1968 2004 5.068198 TCAAAAGCTCAAGAAAAGCATCACT 59.932 36.000 0.00 0.00 42.35 3.41
1974 2010 5.353678 GCTCAAGAAAAGCATCACTCTATGT 59.646 40.000 0.00 0.00 39.61 2.29
2021 2057 6.317642 TGCTATTCGTACAATAGGTTTGCAAT 59.682 34.615 18.52 0.00 32.32 3.56
2065 2101 1.484240 GCTGGTAGTGGAAGAGATGCT 59.516 52.381 0.00 0.00 0.00 3.79
2149 2185 1.540146 CCGCATAATGGATGTCGACCA 60.540 52.381 14.12 4.10 41.83 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.638873 TCAATTTTCGAGCTCCACTATTATCTA 58.361 33.333 8.47 0.00 0.00 1.98
74 75 1.117994 CCAGCAGCTCCTATGACTCA 58.882 55.000 0.00 0.00 0.00 3.41
113 114 9.450807 GATTATAGCAACAATAACATCACCAAC 57.549 33.333 0.00 0.00 0.00 3.77
134 135 1.400494 GGGCAACGCGTCTTTGATTAT 59.600 47.619 14.44 0.00 37.60 1.28
148 149 1.106285 CTAGAGGCATTTGGGGCAAC 58.894 55.000 0.00 0.00 35.46 4.17
229 230 8.073467 TGTCATCATAGCGGATTATTATACCA 57.927 34.615 0.00 0.00 0.00 3.25
294 295 1.941294 TCGCGCCAAAAACTTGAGTTA 59.059 42.857 0.00 0.00 37.25 2.24
497 513 7.344612 TGTCCTTGCCTATAAGACTCTAATTCA 59.655 37.037 0.00 0.00 0.00 2.57
513 529 1.630369 TCAGCAATAGTGTCCTTGCCT 59.370 47.619 3.82 0.00 46.99 4.75
569 585 7.314393 AGATACTACTCGAACTGTTCCTTTTC 58.686 38.462 14.48 2.47 0.00 2.29
676 693 6.640499 CGCAAAGTTGAAACCAAGAAATATCA 59.360 34.615 0.00 0.00 0.00 2.15
851 868 5.988561 GCTTCTCGATCTGTCATTATTCCTT 59.011 40.000 0.00 0.00 0.00 3.36
926 943 1.329256 ATTCGAGCACTATAGGCGGT 58.671 50.000 4.43 0.06 36.08 5.68
1057 1080 3.055891 GGTAGGGCTTCCGTAACTAAACA 60.056 47.826 0.00 0.00 29.90 2.83
1201 1224 3.689161 CGTCCCTTGCTTGAATCATAACA 59.311 43.478 0.00 0.00 0.00 2.41
1488 1518 1.937846 CGTCCGCACCTACGAATCG 60.938 63.158 0.00 0.00 41.55 3.34
1499 1529 3.520290 AATGACTCTAATTCGTCCGCA 57.480 42.857 0.00 0.00 0.00 5.69
1501 1531 3.865745 AGCAAATGACTCTAATTCGTCCG 59.134 43.478 0.00 0.00 0.00 4.79
1529 1559 3.502211 CCCTGTCTTTGTTTATGCTTCGT 59.498 43.478 0.00 0.00 0.00 3.85
1793 1829 7.308109 CCTTAAACTAAAACGTGCATTCCTACA 60.308 37.037 0.00 0.00 0.00 2.74
1845 1881 8.845227 TGAAACTAGCTTGAACATGAATAAACA 58.155 29.630 0.00 0.00 0.00 2.83
1847 1883 9.677567 GTTGAAACTAGCTTGAACATGAATAAA 57.322 29.630 0.00 0.00 0.00 1.40
1929 1965 3.500680 GCTTTTGAATCCACAAGTACCGA 59.499 43.478 0.00 0.00 33.72 4.69
1968 2004 4.713553 TGCTGTTCTTTGACCAACATAGA 58.286 39.130 0.00 0.00 35.44 1.98
1974 2010 4.415881 TCTACTGCTGTTCTTTGACCAA 57.584 40.909 0.09 0.00 0.00 3.67
2021 2057 4.843728 CCCTTTACCATAACTTCTGCTCA 58.156 43.478 0.00 0.00 0.00 4.26
2164 2200 7.087639 TGAAAGCGGGTTAATTCTTTTACATG 58.912 34.615 0.00 0.00 0.00 3.21
2165 2201 7.222000 TGAAAGCGGGTTAATTCTTTTACAT 57.778 32.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.