Multiple sequence alignment - TraesCS6D01G390500

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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 TraesCS6D01G390500 chr6D 100.000 2183 0 0 1 2183 465542463 465544645 0 4032
1 TraesCS6D01G390500 chr6D 95.463 2182 91 7 1 2179 84778085 84780261 0 3474
2 TraesCS6D01G390500 chr3D 95.646 2182 91 4 1 2179 134566693 134568873 0 3500
3 TraesCS6D01G390500 chr5D 95.509 2182 92 6 1 2179 468048705 468050883 0 3482
4 TraesCS6D01G390500 chr4D 95.700 2163 89 4 1 2160 460577988 460575827 0 3476
5 TraesCS6D01G390500 chr2B 95.419 2183 97 3 1 2180 119789536 119787354 0 3474
6 TraesCS6D01G390500 chr7D 95.280 2182 99 4 1 2179 302035279 302033099 0 3456
7 TraesCS6D01G390500 chr4B 95.277 2181 96 7 1 2178 346139761 346141937 0 3450
8 TraesCS6D01G390500 chr5B 94.918 2184 95 7 1 2179 538310887 538308715 0 3404
9 TraesCS6D01G390500 chr3A 94.775 2182 106 6 1 2179 245614562 245616738 0 3391


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 TraesCS6D01G390500 chr6D 465542463 465544645 2182 False 4032 4032 100.000 1 2183 1 chr6D.!!$F2 2182
1 TraesCS6D01G390500 chr6D 84778085 84780261 2176 False 3474 3474 95.463 1 2179 1 chr6D.!!$F1 2178
2 TraesCS6D01G390500 chr3D 134566693 134568873 2180 False 3500 3500 95.646 1 2179 1 chr3D.!!$F1 2178
3 TraesCS6D01G390500 chr5D 468048705 468050883 2178 False 3482 3482 95.509 1 2179 1 chr5D.!!$F1 2178
4 TraesCS6D01G390500 chr4D 460575827 460577988 2161 True 3476 3476 95.700 1 2160 1 chr4D.!!$R1 2159
5 TraesCS6D01G390500 chr2B 119787354 119789536 2182 True 3474 3474 95.419 1 2180 1 chr2B.!!$R1 2179
6 TraesCS6D01G390500 chr7D 302033099 302035279 2180 True 3456 3456 95.280 1 2179 1 chr7D.!!$R1 2178
7 TraesCS6D01G390500 chr4B 346139761 346141937 2176 False 3450 3450 95.277 1 2178 1 chr4B.!!$F1 2177
8 TraesCS6D01G390500 chr5B 538308715 538310887 2172 True 3404 3404 94.918 1 2179 1 chr5B.!!$R1 2178
9 TraesCS6D01G390500 chr3A 245614562 245616738 2176 False 3391 3391 94.775 1 2179 1 chr3A.!!$F1 2178

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
643 648 1.816863 AAGGAAAGAGTCGCAGCCGA 61.817 55.0 0.0 0.0 42.01 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2150 0.039617 GGCGCTGCAACATGTACAAA 60.04 50.0 7.64 0.0 0.0 2.83 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
167 168 2.038033 GGTGGAGCAGCGGGTAATAATA 59.962 50.000 0.00 0.00 0.00 0.98
194 195 6.411376 AGTGGTCGGTGTTATGAATTTCATA 58.589 36.000 13.83 13.83 38.26 2.15
425 429 2.802247 CGCGCTTATTGATCATTGGAGA 59.198 45.455 5.56 0.00 0.00 3.71
507 512 2.288518 GCTATGATCACCGGTCTTCCTC 60.289 54.545 2.59 0.00 0.00 3.71
552 557 2.696864 ACCGATTCTGATGGGTGGT 58.303 52.632 0.00 0.00 42.11 4.16
643 648 1.816863 AAGGAAAGAGTCGCAGCCGA 61.817 55.000 0.00 0.00 42.01 5.54
723 728 3.262420 GACACGGTCAAGACATATGCTT 58.738 45.455 1.58 4.68 32.09 3.91
903 909 7.771183 TGTTTCTTTTTCACTTCATTGCTACT 58.229 30.769 0.00 0.00 0.00 2.57
974 980 4.250464 CAGTTGGACGAAGCCTATTGTAA 58.750 43.478 0.00 0.00 0.00 2.41
1246 1252 9.159364 GCATAAGTGATTATCATGCTTCTATCA 57.841 33.333 10.25 0.00 39.09 2.15
1407 1413 2.421388 GGTGCCCACTCATATGCAACTA 60.421 50.000 0.00 0.00 38.38 2.24
1410 1416 2.158755 GCCCACTCATATGCAACTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
1419 1425 0.250727 TGCAACTAGGTGGTTGAGCC 60.251 55.000 10.43 0.00 46.55 4.70
1570 1577 4.684703 CCGTTCGATGGTGGTAATATTCTC 59.315 45.833 0.00 0.00 0.00 2.87
1587 1595 8.870075 AATATTCTCTTTCTAACTTGCAGGTT 57.130 30.769 18.86 18.86 0.00 3.50
1700 1708 0.467290 TGGAAAACGAGCCCAGCTTT 60.467 50.000 0.00 0.00 39.88 3.51
1828 1836 1.732259 ACCGTTTTTGATGAGCTAGCG 59.268 47.619 9.55 0.00 0.00 4.26
1945 1953 6.417258 TCCATTTGCACTATTCTCATCTTCA 58.583 36.000 0.00 0.00 0.00 3.02
2024 2033 4.787551 ACTGATGAGACCGAGACTATCTT 58.212 43.478 0.00 0.00 0.00 2.40
2053 2062 2.507769 GGCTGGCAAAAGCGATGC 60.508 61.111 0.00 3.23 44.52 3.91
2100 2109 7.723616 TCATTAAGGTTCACATCTCCTTCAAAA 59.276 33.333 0.00 0.00 41.17 2.44
2103 2112 9.581289 TTAAGGTTCACATCTCCTTCAAAATAA 57.419 29.630 0.00 0.00 41.17 1.40
2141 2150 4.045104 GCTACGTTCGATGTCTCATTCAT 58.955 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 6.039941 TGAAATTCATAACACCGACCACTTTT 59.960 34.615 0.00 0.00 0.00 2.27
194 195 6.302269 TGGGGCATTTGTGTTTGAAATAAAT 58.698 32.000 0.00 0.00 0.00 1.40
425 429 0.106149 GGAAACTGTGTGTCTCCGGT 59.894 55.000 0.00 0.00 0.00 5.28
507 512 5.654209 TCATACATAGAGGATTCCCATCGAG 59.346 44.000 0.00 0.00 33.88 4.04
604 609 4.690280 CCTTCTTCTTGTCTTCTGCTTCTC 59.310 45.833 0.00 0.00 0.00 2.87
643 648 2.496899 AATCCACGTGAAAGGAGCAT 57.503 45.000 19.30 0.00 37.34 3.79
723 728 2.885894 TCACGTACCACATGTAGACACA 59.114 45.455 0.00 0.00 39.52 3.72
903 909 5.565592 AACAGCAAGATCGCATTGATAAA 57.434 34.783 0.00 0.00 37.47 1.40
974 980 1.492176 CACCAATACCTCCAGATGGCT 59.508 52.381 0.00 0.00 34.45 4.75
1180 1186 1.138883 GTGTGATCGCGTCCAGCTA 59.861 57.895 5.77 0.00 45.59 3.32
1407 1413 3.161557 GGTGAGGCTCAACCACCT 58.838 61.111 22.05 0.00 45.08 4.00
1410 1416 2.431683 GCAGGTGAGGCTCAACCA 59.568 61.111 28.18 0.00 43.14 3.67
1419 1425 2.124983 CCCGATGTGGCAGGTGAG 60.125 66.667 0.00 0.00 35.87 3.51
1444 1450 1.754226 GGCTGGAACAAACCAAACTGA 59.246 47.619 0.00 0.00 38.70 3.41
1570 1577 5.355350 CCTATCCAACCTGCAAGTTAGAAAG 59.645 44.000 0.00 0.00 0.00 2.62
1587 1595 1.280710 TCCGCTGCTTTTTCCTATCCA 59.719 47.619 0.00 0.00 0.00 3.41
1700 1708 2.265739 GATCGGGCAGTGCTCACA 59.734 61.111 16.85 0.03 0.00 3.58
1789 1797 2.945668 GGTGGGATCTTCCAAAATCTCG 59.054 50.000 0.00 0.00 38.64 4.04
1828 1836 4.988486 GCGTTGTGCTGGTGCTGC 62.988 66.667 0.00 0.00 41.73 5.25
1838 1846 3.120199 CCTTTCCTGACTAATGCGTTGTG 60.120 47.826 0.08 0.00 0.00 3.33
1945 1953 3.928375 CGGTATTAACGTGTTAGGCAAGT 59.072 43.478 0.00 0.00 41.43 3.16
2024 2033 1.976474 GCCAGCCGGGATTGTTTCA 60.976 57.895 2.18 0.00 40.01 2.69
2053 2062 2.383527 GCTCGAAGTGCACCTTCCG 61.384 63.158 14.63 11.96 45.75 4.30
2100 2109 7.867752 ACGTAGCAAAACATGTTAAGTGTTAT 58.132 30.769 12.39 4.58 38.76 1.89
2103 2112 5.744666 ACGTAGCAAAACATGTTAAGTGT 57.255 34.783 12.39 2.01 36.42 3.55
2141 2150 0.039617 GGCGCTGCAACATGTACAAA 60.040 50.000 7.64 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.