Multiple sequence alignment - TraesCS6B01G219600

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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 TraesCS6B01G219600 chr6B 100.000 2414 0 0 1 2414 308516968 308514555 0.000000e+00 4458.0
1 TraesCS6B01G219600 chr6D 96.705 1487 41 6 765 2249 260039025 260037545 0.000000e+00 2468.0
2 TraesCS6B01G219600 chr2D 93.543 1657 98 7 765 2414 586840203 586838549 0.000000e+00 2459.0
3 TraesCS6B01G219600 chr2D 93.935 775 33 4 1 767 637373273 637372505 0.000000e+00 1158.0
4 TraesCS6B01G219600 chr1D 94.928 769 34 2 1 767 52355099 52354334 0.000000e+00 1199.0
5 TraesCS6B01G219600 chr3D 93.185 763 44 3 1 761 519602308 519603064 0.000000e+00 1114.0
6 TraesCS6B01G219600 chr3A 92.578 768 52 3 1 766 507620472 507621236 0.000000e+00 1098.0
7 TraesCS6B01G219600 chr6A 92.208 770 54 3 1 768 54008033 54008798 0.000000e+00 1085.0
8 TraesCS6B01G219600 chr5A 91.429 770 61 2 1 768 709415567 709414801 0.000000e+00 1051.0
9 TraesCS6B01G219600 chr5A 91.299 770 62 2 1 768 709420168 709420934 0.000000e+00 1046.0
10 TraesCS6B01G219600 chr4B 91.062 772 60 7 1 768 206810265 206809499 0.000000e+00 1035.0
11 TraesCS6B01G219600 chr4B 88.847 529 54 3 765 1291 450460107 450460632 0.000000e+00 645.0
12 TraesCS6B01G219600 chr2B 90.779 770 67 3 1 768 743338771 743339538 0.000000e+00 1026.0
13 TraesCS6B01G219600 chr2B 96.774 31 1 0 2341 2371 737104717 737104687 4.000000e-03 52.8
14 TraesCS6B01G219600 chr4D 88.280 529 56 5 765 1291 365847704 365848228 1.580000e-176 628.0
15 TraesCS6B01G219600 chr5D 96.774 31 1 0 2341 2371 529746542 529746512 4.000000e-03 52.8
16 TraesCS6B01G219600 chr2A 100.000 28 0 0 2341 2368 568293746 568293773 4.000000e-03 52.8


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 TraesCS6B01G219600 chr6B 308514555 308516968 2413 True 4458 4458 100.000 1 2414 1 chr6B.!!$R1 2413
1 TraesCS6B01G219600 chr6D 260037545 260039025 1480 True 2468 2468 96.705 765 2249 1 chr6D.!!$R1 1484
2 TraesCS6B01G219600 chr2D 586838549 586840203 1654 True 2459 2459 93.543 765 2414 1 chr2D.!!$R1 1649
3 TraesCS6B01G219600 chr2D 637372505 637373273 768 True 1158 1158 93.935 1 767 1 chr2D.!!$R2 766
4 TraesCS6B01G219600 chr1D 52354334 52355099 765 True 1199 1199 94.928 1 767 1 chr1D.!!$R1 766
5 TraesCS6B01G219600 chr3D 519602308 519603064 756 False 1114 1114 93.185 1 761 1 chr3D.!!$F1 760
6 TraesCS6B01G219600 chr3A 507620472 507621236 764 False 1098 1098 92.578 1 766 1 chr3A.!!$F1 765
7 TraesCS6B01G219600 chr6A 54008033 54008798 765 False 1085 1085 92.208 1 768 1 chr6A.!!$F1 767
8 TraesCS6B01G219600 chr5A 709414801 709415567 766 True 1051 1051 91.429 1 768 1 chr5A.!!$R1 767
9 TraesCS6B01G219600 chr5A 709420168 709420934 766 False 1046 1046 91.299 1 768 1 chr5A.!!$F1 767
10 TraesCS6B01G219600 chr4B 206809499 206810265 766 True 1035 1035 91.062 1 768 1 chr4B.!!$R1 767
11 TraesCS6B01G219600 chr4B 450460107 450460632 525 False 645 645 88.847 765 1291 1 chr4B.!!$F1 526
12 TraesCS6B01G219600 chr2B 743338771 743339538 767 False 1026 1026 90.779 1 768 1 chr2B.!!$F1 767
13 TraesCS6B01G219600 chr4D 365847704 365848228 524 False 628 628 88.280 765 1291 1 chr4D.!!$F1 526

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
885 895 0.17907 GGAGGGCGAAGTTGATCTCC 60.179 60.0 0.0 0.0 34.78 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1811 1.04816 CCCAACCTTTGCCCACTTGT 61.048 55.0 0.0 0.0 0.0 3.16 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
189 192 0.916358 CTGGGGGATGTCCAGGAGTT 60.916 60.000 0.86 0.00 45.95 3.01
259 262 2.040009 CTCGGGTGTGGTGGTGTCTT 62.040 60.000 0.00 0.00 0.00 3.01
337 340 4.033776 GCCTGTGGCTGGGTGCTA 62.034 66.667 0.73 0.00 46.69 3.49
613 622 2.699212 GTCGTATGCGGTTTCGGC 59.301 61.111 2.62 0.00 38.89 5.54
648 657 2.706952 TTAGGGGTGGTGTTGCTGCC 62.707 60.000 0.00 0.00 0.00 4.85
683 692 3.297620 CTGCCTTGGGTGTGTGCC 61.298 66.667 0.00 0.00 0.00 5.01
823 833 1.099879 GCTGGAGCTGATGCCGAATT 61.100 55.000 0.00 0.00 40.80 2.17
884 894 0.827368 AGGAGGGCGAAGTTGATCTC 59.173 55.000 0.00 0.00 0.00 2.75
885 895 0.179070 GGAGGGCGAAGTTGATCTCC 60.179 60.000 0.00 0.00 34.78 3.71
893 903 2.996621 CGAAGTTGATCTCCAGGACAAC 59.003 50.000 11.82 11.82 41.61 3.32
1027 1038 1.601663 CCGTCTCTCCATCGATTGCTC 60.602 57.143 0.00 0.00 0.00 4.26
1194 1205 1.574925 CAGTGAGCTGCAGCAACTG 59.425 57.895 38.19 38.19 45.08 3.16
1384 1396 2.297033 TGGAAGAGGCAATTTCAGCAAC 59.703 45.455 0.00 0.00 0.00 4.17
1401 1413 1.279271 CAACGGTCCAGGAGGAGATTT 59.721 52.381 0.00 0.00 46.92 2.17
1410 1422 0.392998 GGAGGAGATTTGCTTGCGGA 60.393 55.000 0.00 0.00 0.00 5.54
1628 1641 2.357517 GTGGACGTGGCAGAGGTG 60.358 66.667 0.00 0.00 0.00 4.00
1629 1642 2.523168 TGGACGTGGCAGAGGTGA 60.523 61.111 0.00 0.00 0.00 4.02
1649 1662 4.520874 GTGATGTCAGCACTAGAGCCTATA 59.479 45.833 13.95 0.00 33.57 1.31
1687 1700 0.443869 CACACATCGTGCTTACAGGC 59.556 55.000 0.00 0.00 39.19 4.85
2045 2072 4.952071 TCAATTTTGCATGTCCCTTCAA 57.048 36.364 0.00 0.00 0.00 2.69
2064 2091 6.886459 CCTTCAATTCCAGTCAATCTCCTTTA 59.114 38.462 0.00 0.00 0.00 1.85
2066 2093 7.687941 TCAATTCCAGTCAATCTCCTTTAAC 57.312 36.000 0.00 0.00 0.00 2.01
2174 2201 0.888736 TGGAACTGGAACATGGCGTG 60.889 55.000 4.87 4.87 38.20 5.34
2239 2266 0.976641 CTGTAGGAGGTGTTGAGGCA 59.023 55.000 0.00 0.00 0.00 4.75
2252 2279 3.953612 TGTTGAGGCAGAGATTTTGTTGT 59.046 39.130 0.00 0.00 0.00 3.32
2296 2323 6.187682 TCTTTCTTTTGGGAGTTTGAGTCTT 58.812 36.000 0.00 0.00 0.00 3.01
2301 2328 4.981806 TTGGGAGTTTGAGTCTTTTGTG 57.018 40.909 0.00 0.00 0.00 3.33
2327 2354 9.561270 GTCCTGAGTTATTTAAGAAAGCAAATC 57.439 33.333 0.00 0.00 0.00 2.17
2328 2355 9.295825 TCCTGAGTTATTTAAGAAAGCAAATCA 57.704 29.630 0.00 0.00 0.00 2.57
2360 2387 3.065786 AGTGTGTGATGCTTGTGAGTTTG 59.934 43.478 0.00 0.00 0.00 2.93
2376 2403 1.883926 GTTTGGCAAACATACCCGAGT 59.116 47.619 32.22 0.00 41.04 4.18
2410 2437 4.641094 AGTACTGGTCTCCGAAGTAATGAG 59.359 45.833 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.966026 GACGAGCTCGGTCCAACGG 62.966 68.421 36.93 9.41 44.95 4.44
189 192 3.569873 GAAAGATCCCGCCTTTCCA 57.430 52.632 0.00 0.00 42.04 3.53
198 201 0.249114 GAGACGAGCGGAAAGATCCC 60.249 60.000 0.00 0.00 43.37 3.85
259 262 3.727258 CCCCGGCATCCAAGACCA 61.727 66.667 0.00 0.00 0.00 4.02
295 298 4.626081 AAGAGCACCGCGCAACCT 62.626 61.111 8.75 0.00 46.13 3.50
462 465 2.513159 CGACGACGCCTTCAAGAAA 58.487 52.632 0.00 0.00 0.00 2.52
613 622 3.368116 CCCCTAACACTAACGTGAAGAGG 60.368 52.174 5.26 1.94 43.97 3.69
648 657 0.179000 AGGATACAAAGGCGCTGAGG 59.821 55.000 7.64 0.00 41.41 3.86
659 668 1.072266 ACACCCAAGGCAGGATACAA 58.928 50.000 0.00 0.00 41.41 2.41
683 692 2.715005 CACGCCACCACAACACAG 59.285 61.111 0.00 0.00 0.00 3.66
823 833 7.016153 TCTTGCTCCCTTCTAACTTCAATTA 57.984 36.000 0.00 0.00 0.00 1.40
884 894 0.246635 CTCTACACCCGTTGTCCTGG 59.753 60.000 0.00 0.00 39.91 4.45
885 895 0.389948 GCTCTACACCCGTTGTCCTG 60.390 60.000 0.00 0.00 39.91 3.86
1027 1038 3.153676 TGCAATTGCTTCAATCATCCG 57.846 42.857 29.37 0.00 42.66 4.18
1215 1226 4.036567 ACATGTCAATTGCAATGGATCG 57.963 40.909 19.39 12.81 0.00 3.69
1384 1396 0.462759 GCAAATCTCCTCCTGGACCG 60.463 60.000 0.00 0.00 37.46 4.79
1401 1413 1.750018 CCACCATCATCCGCAAGCA 60.750 57.895 0.00 0.00 0.00 3.91
1410 1422 0.625316 TTGCTGCTACCCACCATCAT 59.375 50.000 0.00 0.00 0.00 2.45
1569 1582 3.083997 GTCCTCCACGGCCCTCAT 61.084 66.667 0.00 0.00 0.00 2.90
1628 1641 4.764823 AGTATAGGCTCTAGTGCTGACATC 59.235 45.833 15.85 0.00 0.00 3.06
1629 1642 4.522405 CAGTATAGGCTCTAGTGCTGACAT 59.478 45.833 15.85 7.27 0.00 3.06
1649 1662 1.072806 TGATGTTTCCTCTGCAGCAGT 59.927 47.619 22.10 0.00 32.61 4.40
1687 1700 1.154093 CCATTGTGCTGCTTGCTCG 60.154 57.895 0.00 0.00 43.37 5.03
1798 1811 1.048160 CCCAACCTTTGCCCACTTGT 61.048 55.000 0.00 0.00 0.00 3.16
2045 2072 7.020827 TCAGTTAAAGGAGATTGACTGGAAT 57.979 36.000 10.72 0.00 36.90 3.01
2064 2091 5.615289 ACTGTTTGATAGCAGAACTCAGTT 58.385 37.500 0.00 0.00 36.62 3.16
2066 2093 5.698089 TGAACTGTTTGATAGCAGAACTCAG 59.302 40.000 0.00 0.00 36.62 3.35
2129 2156 2.907042 TCTTCCCAGTCCTCTTTTCCTC 59.093 50.000 0.00 0.00 0.00 3.71
2174 2201 8.807118 TCCTTGATCAATATACCACAGTCTATC 58.193 37.037 8.96 0.00 0.00 2.08
2239 2266 6.403636 GGCGACAATGATACAACAAAATCTCT 60.404 38.462 0.00 0.00 0.00 3.10
2252 2279 4.152647 AGATGTCCTAGGCGACAATGATA 58.847 43.478 2.96 0.00 45.49 2.15
2296 2323 8.349983 GCTTTCTTAAATAACTCAGGACACAAA 58.650 33.333 0.00 0.00 0.00 2.83
2301 2328 9.561270 GATTTGCTTTCTTAAATAACTCAGGAC 57.439 33.333 0.00 0.00 0.00 3.85
2327 2354 5.224888 AGCATCACACACTAATTTGCTTTG 58.775 37.500 0.00 0.00 35.57 2.77
2328 2355 5.458041 AGCATCACACACTAATTTGCTTT 57.542 34.783 0.00 0.00 35.57 3.51
2360 2387 2.981898 AGTTACTCGGGTATGTTTGCC 58.018 47.619 0.00 0.00 0.00 4.52
2376 2403 6.100279 TCGGAGACCAGTACTAGGATAAGTTA 59.900 42.308 15.59 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.