Multiple sequence alignment - TraesCS2D01G294500

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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 TraesCS2D01G294500 chr2D 100.000 2348 0 0 1 2348 376813662 376816009 0.000000e+00 4337
1 TraesCS2D01G294500 chr2A 96.785 2364 46 12 1 2345 510803653 510806005 0.000000e+00 3917
2 TraesCS2D01G294500 chr2B 95.053 2365 67 19 1 2348 448250697 448253028 0.000000e+00 3674
3 TraesCS2D01G294500 chr4B 95.952 2174 52 15 189 2348 640325454 640327605 0.000000e+00 3494
4 TraesCS2D01G294500 chr4B 91.324 219 10 5 1 213 640324543 640324758 8.210000e-75 291
5 TraesCS2D01G294500 chr4B 90.411 219 12 5 1 213 640329576 640329361 1.780000e-71 279


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 TraesCS2D01G294500 chr2D 376813662 376816009 2347 False 4337.0 4337 100.000 1 2348 1 chr2D.!!$F1 2347
1 TraesCS2D01G294500 chr2A 510803653 510806005 2352 False 3917.0 3917 96.785 1 2345 1 chr2A.!!$F1 2344
2 TraesCS2D01G294500 chr2B 448250697 448253028 2331 False 3674.0 3674 95.053 1 2348 1 chr2B.!!$F1 2347
3 TraesCS2D01G294500 chr4B 640324543 640327605 3062 False 1892.5 3494 93.638 1 2348 2 chr4B.!!$F1 2347

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
861 1610 1.232621 ACCCGACGCAAAAGTAAGCC 61.233 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2636 0.759959 TTGAGGCGTGGGAGTTGTAA 59.24 50.0 0.0 0.0 0.0 2.41 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
27 31 3.479489 TGATGTGCATTTGAGACACTGT 58.521 40.909 0.00 0.00 35.33 3.55
28 32 3.884693 TGATGTGCATTTGAGACACTGTT 59.115 39.130 0.00 0.00 35.33 3.16
147 152 5.833406 TTGATGAGCTTCAACTTTCAACA 57.167 34.783 0.00 0.00 30.82 3.33
223 952 4.327357 CACTGTCTAGATGCAGTAAAACCG 59.673 45.833 13.91 0.43 43.27 4.44
295 1025 7.697291 TGTGTTTTAACTTTCGACCAAACATAC 59.303 33.333 0.00 0.00 36.72 2.39
296 1026 7.911727 GTGTTTTAACTTTCGACCAAACATACT 59.088 33.333 0.00 0.00 36.72 2.12
297 1027 9.107177 TGTTTTAACTTTCGACCAAACATACTA 57.893 29.630 0.00 0.00 31.00 1.82
298 1028 9.373750 GTTTTAACTTTCGACCAAACATACTAC 57.626 33.333 0.00 0.00 0.00 2.73
299 1029 8.891671 TTTAACTTTCGACCAAACATACTACT 57.108 30.769 0.00 0.00 0.00 2.57
861 1610 1.232621 ACCCGACGCAAAAGTAAGCC 61.233 55.000 0.00 0.00 0.00 4.35
895 1644 4.477249 TGCATCCATCTCTAGTGATCTCA 58.523 43.478 4.30 0.00 0.00 3.27
896 1645 5.085219 TGCATCCATCTCTAGTGATCTCAT 58.915 41.667 4.30 0.00 0.00 2.90
926 1675 3.559238 AGGTTGCAACAATCGATCAAC 57.441 42.857 29.55 15.10 37.04 3.18
1091 1840 2.671682 GGACTCCTCCAACAGGGC 59.328 66.667 0.00 0.00 43.67 5.19
1170 1919 2.839098 CAGTGGTCCAACAGCCCT 59.161 61.111 0.00 0.00 0.00 5.19
1236 1985 2.446848 CGTCATGCTCCCCCAGGAT 61.447 63.158 0.00 0.00 42.93 3.24
1313 2062 7.436673 GGACAATAGCAACAATAACAACAACAA 59.563 33.333 0.00 0.00 0.00 2.83
1468 2217 7.423844 TCTTCAGTGTAACCATGATATGTCT 57.576 36.000 0.00 0.00 37.80 3.41
1509 2259 2.751259 GGCATATATCCATGTGCTGGTG 59.249 50.000 6.36 0.00 45.70 4.17
1510 2260 3.415212 GCATATATCCATGTGCTGGTGT 58.585 45.455 0.00 0.00 43.74 4.16
1647 2397 8.197988 TCTTCTGTTTCTTACTTTCAAGACAC 57.802 34.615 0.00 0.00 36.30 3.67
1738 2488 0.861837 CTTCTGCGACTTCACACCAC 59.138 55.000 0.00 0.00 0.00 4.16
1883 2636 6.909550 TTAGTTGAACTAACCAATTGGCAT 57.090 33.333 24.79 15.81 40.24 4.40
1944 2697 8.043710 ACCTACTATCCTTGAAAAAGACATCAG 58.956 37.037 0.00 0.00 0.00 2.90
2266 3020 4.460382 GGCTTGAATCACATCAGAAAAGGA 59.540 41.667 0.00 0.00 0.00 3.36
2267 3021 5.047802 GGCTTGAATCACATCAGAAAAGGAA 60.048 40.000 0.00 0.00 0.00 3.36
2270 3024 7.115947 GCTTGAATCACATCAGAAAAGGAAAAG 59.884 37.037 0.00 0.00 0.00 2.27
2341 3097 8.917088 CCTTAATTGTCTTGATTGGAATGGTAT 58.083 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 31 9.874205 GTGATCTTGAATGGAATTTATTTGGAA 57.126 29.630 0.00 0.00 36.07 3.53
28 32 9.033711 TGTGATCTTGAATGGAATTTATTTGGA 57.966 29.630 0.00 0.00 36.07 3.53
147 152 9.920946 ATTATGAGAGTTATTATTGGGTGTGTT 57.079 29.630 0.00 0.00 0.00 3.32
297 1027 9.116067 GACTTCACATATTAGAGTGAGTAGAGT 57.884 37.037 0.00 0.00 44.65 3.24
298 1028 9.337396 AGACTTCACATATTAGAGTGAGTAGAG 57.663 37.037 0.00 0.00 44.65 2.43
653 1402 8.279800 GGTCAATTAGTTTTGTTTAATGCAACC 58.720 33.333 0.00 0.00 0.00 3.77
861 1610 1.971149 TGGATGCATATAGGGAGGGG 58.029 55.000 0.00 0.00 0.00 4.79
895 1644 6.703607 CGATTGTTGCAACCTAGAAGAGATAT 59.296 38.462 26.14 0.00 0.00 1.63
896 1645 6.042777 CGATTGTTGCAACCTAGAAGAGATA 58.957 40.000 26.14 0.21 0.00 1.98
1091 1840 1.064946 GACTCCTCGTCAGCCATCG 59.935 63.158 0.00 0.00 42.37 3.84
1170 1919 2.994995 ACCATGGACGTCGCCTCA 60.995 61.111 21.47 1.71 0.00 3.86
1313 2062 1.027357 CTTCCTGCTGTTGCTGTTGT 58.973 50.000 0.00 0.00 40.48 3.32
1373 2122 1.291184 TTCTTGATGTCGGTGCTGCG 61.291 55.000 0.00 0.00 0.00 5.18
1468 2217 4.769488 TGCCAGCCTCACAATTTTAATACA 59.231 37.500 0.00 0.00 0.00 2.29
1485 2234 2.422479 CAGCACATGGATATATGCCAGC 59.578 50.000 1.35 4.40 39.11 4.85
1647 2397 6.374333 TGAGATTTTCAGGGGTAATCTTTTCG 59.626 38.462 0.00 0.00 38.40 3.46
1883 2636 0.759959 TTGAGGCGTGGGAGTTGTAA 59.240 50.000 0.00 0.00 0.00 2.41
1913 2666 7.707464 GTCTTTTTCAAGGATAGTAGGTAGAGC 59.293 40.741 0.00 0.00 0.00 4.09
2266 3020 9.990360 TTTTAGTTTCCTGTCTGTTTTTCTTTT 57.010 25.926 0.00 0.00 0.00 2.27
2267 3021 9.639601 CTTTTAGTTTCCTGTCTGTTTTTCTTT 57.360 29.630 0.00 0.00 0.00 2.52
2270 3024 6.475727 GCCTTTTAGTTTCCTGTCTGTTTTTC 59.524 38.462 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.