Multiple sequence alignment - TraesCS5D01G345000

Loading Multiple Alignment...

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 TraesCS5D01G345000 chr5D 100.000 2177 0 0 1 2177 432333371 432331195 0 4021
1 TraesCS5D01G345000 chr5D 97.207 2184 53 6 1 2177 503238784 503236602 0 3688
2 TraesCS5D01G345000 chr5D 97.161 2184 51 7 1 2177 503243030 503240851 0 3679
3 TraesCS5D01G345000 chr6D 97.344 2184 51 5 1 2177 389254927 389252744 0 3705
4 TraesCS5D01G345000 chr3A 97.253 2184 52 6 1 2177 66007374 66009556 0 3694
5 TraesCS5D01G345000 chr3A 96.612 2184 67 5 1 2177 672899763 672901946 0 3616
6 TraesCS5D01G345000 chrUn 96.979 2185 55 6 1 2177 216508360 216510541 0 3659
7 TraesCS5D01G345000 chr3B 96.795 2184 62 6 1 2177 201537278 201535096 0 3639
8 TraesCS5D01G345000 chr2A 96.566 2184 68 5 1 2177 335845070 335842887 0 3611
9 TraesCS5D01G345000 chr2B 96.200 2184 76 5 1 2177 474918688 474916505 0 3567


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 TraesCS5D01G345000 chr5D 432331195 432333371 2176 True 4021.0 4021 100.000 1 2177 1 chr5D.!!$R1 2176
1 TraesCS5D01G345000 chr5D 503236602 503243030 6428 True 3683.5 3688 97.184 1 2177 2 chr5D.!!$R2 2176
2 TraesCS5D01G345000 chr6D 389252744 389254927 2183 True 3705.0 3705 97.344 1 2177 1 chr6D.!!$R1 2176
3 TraesCS5D01G345000 chr3A 66007374 66009556 2182 False 3694.0 3694 97.253 1 2177 1 chr3A.!!$F1 2176
4 TraesCS5D01G345000 chr3A 672899763 672901946 2183 False 3616.0 3616 96.612 1 2177 1 chr3A.!!$F2 2176
5 TraesCS5D01G345000 chrUn 216508360 216510541 2181 False 3659.0 3659 96.979 1 2177 1 chrUn.!!$F1 2176
6 TraesCS5D01G345000 chr3B 201535096 201537278 2182 True 3639.0 3639 96.795 1 2177 1 chr3B.!!$R1 2176
7 TraesCS5D01G345000 chr2A 335842887 335845070 2183 True 3611.0 3611 96.566 1 2177 1 chr2A.!!$R1 2176
8 TraesCS5D01G345000 chr2B 474916505 474918688 2183 True 3567.0 3567 96.200 1 2177 1 chr2B.!!$R1 2176

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
75 76 0.038526 CGTCCGCCACTAGAAACACT 60.039 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 6106 1.478631 CCCTTGCCCCTCATTCTTTC 58.521 55.0 0.0 0.0 0.0 2.62 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
59 60 0.109781 TTACGCGTTACTCACCCGTC 60.110 55.000 20.78 0.00 33.79 4.79
67 68 2.482796 TACTCACCCGTCCGCCACTA 62.483 60.000 0.00 0.00 0.00 2.74
75 76 0.038526 CGTCCGCCACTAGAAACACT 60.039 55.000 0.00 0.00 0.00 3.55
214 216 3.766051 AGCAGATTGGAATTGTCTTTCCC 59.234 43.478 1.03 0.00 43.86 3.97
389 392 7.460214 ACTCACATTGGGTTTAGGGATAATA 57.540 36.000 0.00 0.00 0.00 0.98
405 408 5.511545 GGGATAATAAGGCTCGAACTGATGT 60.512 44.000 0.00 0.00 0.00 3.06
436 439 1.612463 GTCAAGGTGACACTCTACCGT 59.388 52.381 5.39 0.00 46.22 4.83
484 487 8.844244 CCCATCGAGAAAGAGAATTAATGAATT 58.156 33.333 0.00 0.00 38.00 2.17
595 599 3.193479 GGATTCAATTGTCAACTGGTCCC 59.807 47.826 5.13 0.00 0.00 4.46
598 602 3.843422 TCAATTGTCAACTGGTCCCATT 58.157 40.909 5.13 0.00 0.00 3.16
609 613 3.655777 ACTGGTCCCATTGAAAGTAGGAA 59.344 43.478 0.00 0.00 0.00 3.36
714 718 4.699257 AGAAGATCTTGTTCAGCATGTTCC 59.301 41.667 14.00 0.00 37.40 3.62
941 5195 7.550906 ACATGAGGACAAATTACTTCTCTTAGC 59.449 37.037 0.00 0.00 0.00 3.09
942 5196 6.407202 TGAGGACAAATTACTTCTCTTAGCC 58.593 40.000 0.00 0.00 0.00 3.93
1265 5519 2.215942 AAAATGTAGGACTGGTGCCC 57.784 50.000 0.00 0.00 0.00 5.36
1307 5561 2.362503 TCACAGAGCCGGGATCGT 60.363 61.111 6.65 5.35 33.95 3.73
1486 5740 8.140628 CGGATCATATAGATATCCCTTCAACAG 58.859 40.741 0.00 0.00 37.00 3.16
1618 5872 4.285775 ACCCGTCAATTTTGGATCCAATTT 59.714 37.500 27.53 20.03 35.70 1.82
1740 5994 3.310288 GGATAGGGATAGAGGAAGAGGGG 60.310 56.522 0.00 0.00 0.00 4.79
1752 6007 4.935578 AGGAAGAGGGGAAAATCGAAATT 58.064 39.130 0.00 0.00 0.00 1.82
1848 6106 5.423015 TCGAAAAGGATCCTTCTGATTCTG 58.577 41.667 27.20 19.49 38.45 3.02
1929 6187 5.461078 GTGATTTGATCTGCATATGTTTGGC 59.539 40.000 4.29 0.00 0.00 4.52
2022 6280 7.963532 ACTCAATTGGTCTTAGTTAGTCTTCA 58.036 34.615 5.42 0.00 0.00 3.02
2023 6281 8.598041 ACTCAATTGGTCTTAGTTAGTCTTCAT 58.402 33.333 5.42 0.00 0.00 2.57
2025 6283 7.824289 TCAATTGGTCTTAGTTAGTCTTCATGG 59.176 37.037 5.42 0.00 0.00 3.66
2105 6363 1.655329 CGAGGAGCCGTATGAGGTC 59.345 63.158 0.00 0.00 0.00 3.85
2133 6391 4.525487 TCTCATGTACGGTTCTGTAAAGGT 59.475 41.667 0.00 0.00 0.00 3.50
2137 6395 5.528043 TGTACGGTTCTGTAAAGGTACAA 57.472 39.130 0.00 0.00 39.75 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.230976 GAGGGGAACAACAACTGGAAAT 58.769 45.455 0.00 0.00 0.00 2.17
59 60 3.251571 GAAGTAGTGTTTCTAGTGGCGG 58.748 50.000 0.00 0.00 33.11 6.13
67 68 2.624838 TCGAACGGGAAGTAGTGTTTCT 59.375 45.455 0.00 0.00 0.00 2.52
75 76 0.675083 TGCAAGTCGAACGGGAAGTA 59.325 50.000 0.00 0.00 0.00 2.24
186 187 4.828939 AGACAATTCCAATCTGCTTTGTCA 59.171 37.500 13.98 0.00 43.23 3.58
280 282 3.090210 TGACGTGATAGGTAGGGTTCA 57.910 47.619 0.00 0.00 0.00 3.18
281 283 4.501058 GGATTGACGTGATAGGTAGGGTTC 60.501 50.000 0.00 0.00 0.00 3.62
389 392 2.354203 GGAAGACATCAGTTCGAGCCTT 60.354 50.000 0.00 0.00 0.00 4.35
405 408 2.523440 ACCTTGACGTGGTGGAAGA 58.477 52.632 0.00 0.00 36.30 2.87
436 439 3.644738 GACGGGGAAGGGATATAACTCAA 59.355 47.826 0.00 0.00 0.00 3.02
484 487 0.907704 TCTCGCCCCTTTGCCTTAGA 60.908 55.000 0.00 0.00 0.00 2.10
595 599 8.915057 ATCCATAGTCATTCCTACTTTCAATG 57.085 34.615 0.00 0.00 0.00 2.82
598 602 7.069455 TCGAATCCATAGTCATTCCTACTTTCA 59.931 37.037 0.00 0.00 0.00 2.69
609 613 4.199432 GATGGCTCGAATCCATAGTCAT 57.801 45.455 16.24 2.45 43.90 3.06
714 718 7.308710 GGGTTCTTCTCCTACTAGTATCGAATG 60.309 44.444 2.33 0.00 0.00 2.67
771 777 5.044919 ACCCATATCATCTTGACTTGGTTCA 60.045 40.000 6.74 0.00 32.67 3.18
842 848 6.269769 TGGAAATTGAAAAGAAATGTAGCCCT 59.730 34.615 0.00 0.00 0.00 5.19
941 5195 7.021196 CGTTATCCTTTTTCTTGTATGTGTGG 58.979 38.462 0.00 0.00 0.00 4.17
942 5196 7.021196 CCGTTATCCTTTTTCTTGTATGTGTG 58.979 38.462 0.00 0.00 0.00 3.82
1223 5477 3.216187 TCTCTATGGACCGAGGAGAAG 57.784 52.381 7.39 0.00 31.28 2.85
1265 5519 4.058124 TCTTTCTTCCGTGATGAACTGTG 58.942 43.478 2.98 0.00 0.00 3.66
1486 5740 6.143118 CGAGATCTTTTCGATGACCTATGTTC 59.857 42.308 0.00 0.00 40.36 3.18
1618 5872 5.452636 CCGAAACTTCCAAAGAAAAATCCCA 60.453 40.000 0.00 0.00 0.00 4.37
1631 5885 3.572255 CCAATTTCTTCCCGAAACTTCCA 59.428 43.478 0.00 0.00 43.90 3.53
1676 5930 7.092891 TGCATCAATAGAGAACCTTTTCCTCTA 60.093 37.037 0.00 0.00 31.61 2.43
1848 6106 1.478631 CCCTTGCCCCTCATTCTTTC 58.521 55.000 0.00 0.00 0.00 2.62
1994 6252 8.140112 AGACTAACTAAGACCAATTGAGTCAT 57.860 34.615 21.54 15.42 36.68 3.06
2022 6280 1.604378 CCTTCTTCCACTCCGCCAT 59.396 57.895 0.00 0.00 0.00 4.40
2023 6281 2.592993 CCCTTCTTCCACTCCGCCA 61.593 63.158 0.00 0.00 0.00 5.69
2025 6283 2.436824 GCCCTTCTTCCACTCCGC 60.437 66.667 0.00 0.00 0.00 5.54
2105 6363 5.862924 ACAGAACCGTACATGAGATTTTG 57.137 39.130 0.00 0.00 0.00 2.44
2133 6391 8.929260 TCGATAGATAAGTCACCCTTATTGTA 57.071 34.615 0.00 0.00 44.62 2.41
2154 6412 4.514401 GGGTTGATAGTGGAAAAGTCGAT 58.486 43.478 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.