Multiple sequence alignment - TraesCS5D01G009000

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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 TraesCS5D01G009000 chr5D 100.000 4244 0 0 1 4244 6196391 6192148 0.000000e+00 7838
1 TraesCS5D01G009000 chr5D 98.446 4247 60 5 2 4244 503225672 503221428 0.000000e+00 7472
2 TraesCS5D01G009000 chr3A 98.281 4247 66 6 2 4244 66010169 66014412 0.000000e+00 7432
3 TraesCS5D01G009000 chr3A 97.552 4248 96 7 2 4244 672902559 672906803 0.000000e+00 7262
4 TraesCS5D01G009000 chrUn 98.069 4246 75 5 2 4244 216511154 216515395 0.000000e+00 7380
5 TraesCS5D01G009000 chrUn 98.069 4246 75 5 2 4244 286272229 286267988 0.000000e+00 7380
6 TraesCS5D01G009000 chr3B 97.905 4249 81 5 2 4244 201534483 201530237 0.000000e+00 7347
7 TraesCS5D01G009000 chr2B 97.857 4246 83 7 2 4244 474915894 474911654 0.000000e+00 7330
8 TraesCS5D01G009000 chr1B 97.786 3975 82 5 2 3973 633746444 633750415 0.000000e+00 6848
9 TraesCS5D01G009000 chr4D 95.033 4248 200 10 2 4244 207362816 207367057 0.000000e+00 6665
10 TraesCS5D01G009000 chr7A 94.840 407 18 3 3838 4244 352601151 352600748 2.150000e-177 632


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 TraesCS5D01G009000 chr5D 6192148 6196391 4243 True 7838 7838 100.000 1 4244 1 chr5D.!!$R1 4243
1 TraesCS5D01G009000 chr5D 503221428 503225672 4244 True 7472 7472 98.446 2 4244 1 chr5D.!!$R2 4242
2 TraesCS5D01G009000 chr3A 66010169 66014412 4243 False 7432 7432 98.281 2 4244 1 chr3A.!!$F1 4242
3 TraesCS5D01G009000 chr3A 672902559 672906803 4244 False 7262 7262 97.552 2 4244 1 chr3A.!!$F2 4242
4 TraesCS5D01G009000 chrUn 216511154 216515395 4241 False 7380 7380 98.069 2 4244 1 chrUn.!!$F1 4242
5 TraesCS5D01G009000 chrUn 286267988 286272229 4241 True 7380 7380 98.069 2 4244 1 chrUn.!!$R1 4242
6 TraesCS5D01G009000 chr3B 201530237 201534483 4246 True 7347 7347 97.905 2 4244 1 chr3B.!!$R1 4242
7 TraesCS5D01G009000 chr2B 474911654 474915894 4240 True 7330 7330 97.857 2 4244 1 chr2B.!!$R1 4242
8 TraesCS5D01G009000 chr1B 633746444 633750415 3971 False 6848 6848 97.786 2 3973 1 chr1B.!!$F1 3971
9 TraesCS5D01G009000 chr4D 207362816 207367057 4241 False 6665 6665 95.033 2 4244 1 chr4D.!!$F1 4242

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
251 253 1.199327 CATGTCACGTCGAGGTACTGT 59.801 52.381 10.91 0.0 41.55 3.55 F
1784 1791 2.288030 CGTCTACGAAGGAGTGTGGTTT 60.288 50.000 0.00 0.0 43.02 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1872 0.042131 TTGGTCGGAGTGGGGATAGT 59.958 55.0 0.00 0.0 0.0 2.12 R
3319 3327 0.250124 CGTAGCGCCCATTCCCATTA 60.250 55.0 2.29 0.0 0.0 1.90 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
251 253 1.199327 CATGTCACGTCGAGGTACTGT 59.801 52.381 10.91 0.00 41.55 3.55
293 295 7.568199 AATCCGATCCAATTTTTCGTAATCT 57.432 32.000 0.00 0.00 0.00 2.40
698 700 6.384224 CAAATAGAGCTCTTGCACATTTTCA 58.616 36.000 23.84 0.00 42.74 2.69
778 782 9.401058 GGAAAAGAATCAATAGAAGGAGAATCA 57.599 33.333 0.00 0.00 36.25 2.57
796 800 6.664515 AGAATCAGACGATATCTTTCTCGAC 58.335 40.000 0.34 0.00 31.46 4.20
898 902 9.050601 AGAAAGAAGAATCTTATGGAAATAGCG 57.949 33.333 0.00 0.00 45.19 4.26
912 916 5.712917 TGGAAATAGCGTGGAATAAGGTTTT 59.287 36.000 0.00 0.00 0.00 2.43
1121 1125 8.893563 TTCCCAGAATGTATCCTAATTTTTGT 57.106 30.769 0.00 0.00 0.00 2.83
1146 1150 6.040504 TCCTAATTCTTCTTCCGATGATCGAA 59.959 38.462 17.52 7.85 43.74 3.71
1158 1162 3.733224 CGATGATCGAATCAACCTCTGAC 59.267 47.826 9.62 0.00 43.74 3.51
1641 1648 4.272261 GGGAGATCGAGCTTCAAGAAATTC 59.728 45.833 11.82 0.00 0.00 2.17
1784 1791 2.288030 CGTCTACGAAGGAGTGTGGTTT 60.288 50.000 0.00 0.00 43.02 3.27
1865 1872 7.070447 ACTCCATAGACATGCAGAAGAGAAATA 59.930 37.037 0.00 0.00 0.00 1.40
2033 2040 3.846360 AGTTCCTACAAAGAATCGGACG 58.154 45.455 0.00 0.00 0.00 4.79
2104 2111 4.707448 GGTTCTCATCCTTCAGAGACTACA 59.293 45.833 0.00 0.00 40.37 2.74
2115 2122 8.107729 TCCTTCAGAGACTACAAGTGTAATAGA 58.892 37.037 0.00 0.00 0.00 1.98
2183 2190 5.010012 GGCTATTGGGAACGAATCAAATCAT 59.990 40.000 0.00 0.00 0.00 2.45
2214 2221 7.735917 TCTATTTCTCAACCTTTCTGACTTGA 58.264 34.615 0.00 0.00 0.00 3.02
2503 2510 1.229209 GACTCCCCCACTCCAGTCA 60.229 63.158 0.00 0.00 36.15 3.41
2648 2655 3.033184 GCATGATTTTGGGGAATCTCCA 58.967 45.455 0.00 0.00 38.64 3.86
2706 2713 4.218417 GCATATTCGTCCATAGGGCAAATT 59.782 41.667 0.00 0.00 0.00 1.82
2834 2841 7.339212 TGCTTGCATTGTATTATTTGGTCTACT 59.661 33.333 0.00 0.00 0.00 2.57
2885 2893 5.070446 TGCAGGATTATACACGAAAGATCCT 59.930 40.000 0.00 0.00 43.00 3.24
3151 3159 7.093377 CCCCTTTAAGATCAAACAATTCCATCA 60.093 37.037 0.00 0.00 0.00 3.07
3265 3273 6.399639 AGCTGCTAGGTCTATTTCTTAGTC 57.600 41.667 0.00 0.00 0.00 2.59
3319 3327 1.794714 AGTAGATCTGTTCCGCCCAT 58.205 50.000 5.18 0.00 0.00 4.00
3337 3345 1.812571 CATAATGGGAATGGGCGCTAC 59.187 52.381 7.64 0.66 0.00 3.58
3441 3449 7.690454 TCTTATTATGAGAAGGGGTCATTCA 57.310 36.000 0.00 0.00 36.11 2.57
3750 3758 5.584551 AATACTCCAAGACTCCACCTTTT 57.415 39.130 0.00 0.00 0.00 2.27
3942 3950 3.069586 TGAGCATTCCCCGTAGAAGTATG 59.930 47.826 0.00 0.00 0.00 2.39
4070 4078 4.081309 TGAACGATCCTAAAAATCCCTCGT 60.081 41.667 0.00 0.00 39.31 4.18
4094 4103 7.985752 CGTAGGAGATAATAAAGAACCCAAAGT 59.014 37.037 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.959311 CACTTTAAATTGAGTATCCGTTTCCG 59.041 38.462 0.00 0.00 0.00 4.30
653 655 2.103771 GCCTCTGCCATTCTATGAGTCA 59.896 50.000 0.00 0.00 0.00 3.41
778 782 5.562506 TTGTGTCGAGAAAGATATCGTCT 57.437 39.130 10.68 10.68 40.97 4.18
796 800 8.532977 TCTCTTTCTTTTCCTTTTTGTTTGTG 57.467 30.769 0.00 0.00 0.00 3.33
912 916 4.435137 ACGGAATCCCCATGAATAGGATA 58.565 43.478 0.00 0.00 39.53 2.59
1641 1648 6.961359 TTGTGTATTGATAAGACCGTTCAG 57.039 37.500 0.00 0.00 0.00 3.02
1784 1791 4.884668 AGAGGTAGGAATTTGTCGAACA 57.115 40.909 0.00 0.00 0.00 3.18
1865 1872 0.042131 TTGGTCGGAGTGGGGATAGT 59.958 55.000 0.00 0.00 0.00 2.12
1982 1989 8.460831 GTAATAACGAACTTGCAAAATGGATT 57.539 30.769 0.00 0.00 0.00 3.01
2104 2111 5.581085 GTCAACGGATGCTTCTATTACACTT 59.419 40.000 0.00 0.00 0.00 3.16
2115 2122 2.582052 TCCTTTTGTCAACGGATGCTT 58.418 42.857 0.00 0.00 0.00 3.91
2183 2190 8.602424 TCAGAAAGGTTGAGAAATAGAACCATA 58.398 33.333 0.00 0.00 41.48 2.74
2452 2459 4.657436 GAGGATTCCTCGCTTCTTTCTA 57.343 45.455 16.79 0.00 41.08 2.10
2503 2510 7.259290 TCGAAGTAACAGAAAGAAAAGCAAT 57.741 32.000 0.00 0.00 0.00 3.56
2648 2655 7.395190 TTCATGCTTGTTTGAGTAATAGCAT 57.605 32.000 0.00 0.00 42.65 3.79
2834 2841 6.198650 TCTCGAATGTTATCAGTTCCGTAA 57.801 37.500 0.00 0.00 0.00 3.18
3265 3273 4.962995 TCCAGTTAGTAAGAGGGATCTTGG 59.037 45.833 0.81 0.00 0.00 3.61
3319 3327 0.250124 CGTAGCGCCCATTCCCATTA 60.250 55.000 2.29 0.00 0.00 1.90
3525 3533 6.904626 AGGATAGATATGTCAAAAGCAGGTT 58.095 36.000 0.00 0.00 0.00 3.50
4094 4103 4.160329 CCCTTGCAGTAGGATACCATCTA 58.840 47.826 5.98 0.00 44.47 1.98
4201 4210 2.325583 AGTCACTTTTTCCTGTCGCA 57.674 45.000 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.