Multiple sequence alignment - TraesCS6D01G180900

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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 TraesCS6D01G180900 chr6D 100.000 2204 0 0 1 2204 202266812 202264609 0.000000e+00 4071
1 TraesCS6D01G180900 chr6D 93.388 847 44 6 1 835 58443353 58444199 0.000000e+00 1243
2 TraesCS6D01G180900 chr6D 93.460 841 48 5 1 834 412473303 412472463 0.000000e+00 1242
3 TraesCS6D01G180900 chr6D 93.365 844 45 9 1 835 4362107 4361266 0.000000e+00 1238
4 TraesCS6D01G180900 chr6D 93.112 842 48 8 1 835 414105621 414106459 0.000000e+00 1225
5 TraesCS6D01G180900 chr6A 95.544 1369 24 5 844 2204 309863425 309864764 0.000000e+00 2156
6 TraesCS6D01G180900 chr6B 95.250 821 13 12 845 1648 319525170 319525981 0.000000e+00 1277
7 TraesCS6D01G180900 chr6B 84.955 771 71 24 846 1583 100895189 100895947 0.000000e+00 739
8 TraesCS6D01G180900 chr6B 96.774 372 11 1 1644 2014 319526284 319526655 8.640000e-174 619
9 TraesCS6D01G180900 chr6B 96.296 189 7 0 2014 2202 319528153 319528341 5.910000e-81 311
10 TraesCS6D01G180900 chr1D 93.499 846 43 9 1 835 393530213 393529369 0.000000e+00 1247
11 TraesCS6D01G180900 chr7D 93.365 844 46 6 1 835 536432479 536431637 0.000000e+00 1240
12 TraesCS6D01G180900 chr7D 93.262 846 46 8 1 835 97944276 97945121 0.000000e+00 1236
13 TraesCS6D01G180900 chr3D 93.349 842 46 5 1 835 8822993 8822155 0.000000e+00 1236
14 TraesCS6D01G180900 chr2D 93.254 845 45 7 1 835 111145481 111146323 0.000000e+00 1234


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 TraesCS6D01G180900 chr6D 202264609 202266812 2203 True 4071.000000 4071 100.000000 1 2204 1 chr6D.!!$R2 2203
1 TraesCS6D01G180900 chr6D 58443353 58444199 846 False 1243.000000 1243 93.388000 1 835 1 chr6D.!!$F1 834
2 TraesCS6D01G180900 chr6D 412472463 412473303 840 True 1242.000000 1242 93.460000 1 834 1 chr6D.!!$R3 833
3 TraesCS6D01G180900 chr6D 4361266 4362107 841 True 1238.000000 1238 93.365000 1 835 1 chr6D.!!$R1 834
4 TraesCS6D01G180900 chr6D 414105621 414106459 838 False 1225.000000 1225 93.112000 1 835 1 chr6D.!!$F2 834
5 TraesCS6D01G180900 chr6A 309863425 309864764 1339 False 2156.000000 2156 95.544000 844 2204 1 chr6A.!!$F1 1360
6 TraesCS6D01G180900 chr6B 100895189 100895947 758 False 739.000000 739 84.955000 846 1583 1 chr6B.!!$F1 737
7 TraesCS6D01G180900 chr6B 319525170 319528341 3171 False 735.666667 1277 96.106667 845 2202 3 chr6B.!!$F2 1357
8 TraesCS6D01G180900 chr1D 393529369 393530213 844 True 1247.000000 1247 93.499000 1 835 1 chr1D.!!$R1 834
9 TraesCS6D01G180900 chr7D 536431637 536432479 842 True 1240.000000 1240 93.365000 1 835 1 chr7D.!!$R1 834
10 TraesCS6D01G180900 chr7D 97944276 97945121 845 False 1236.000000 1236 93.262000 1 835 1 chr7D.!!$F1 834
11 TraesCS6D01G180900 chr3D 8822155 8822993 838 True 1236.000000 1236 93.349000 1 835 1 chr3D.!!$R1 834
12 TraesCS6D01G180900 chr2D 111145481 111146323 842 False 1234.000000 1234 93.254000 1 835 1 chr2D.!!$F1 834

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
404 405 1.248785 CGACAACGGAGAGGGAAGGA 61.249 60.0 0.0 0.0 35.72 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1323 2.304221 AAGCCCTTACCCCTTGAAAC 57.696 50.0 0.0 0.0 0.0 2.78 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
61 62 7.893302 ACCACAACTGAGGGAATTAATTTCATA 59.107 33.333 8.74 0.00 35.94 2.15
197 198 2.430367 GCCGGGTCCTTCAAGTGT 59.570 61.111 2.18 0.00 0.00 3.55
219 220 2.397413 CTTCCACCGCACCAACTCCT 62.397 60.000 0.00 0.00 0.00 3.69
404 405 1.248785 CGACAACGGAGAGGGAAGGA 61.249 60.000 0.00 0.00 35.72 3.36
438 439 6.824305 ACATGTCATAAGAAAGGGAGTTTG 57.176 37.500 0.00 0.00 0.00 2.93
627 632 7.439157 TTCAGAGATTGTTCGTGATTGATTT 57.561 32.000 0.00 0.00 0.00 2.17
689 694 7.121974 TGATCTGTTCAGATTTCTTTCGTTC 57.878 36.000 15.16 2.32 0.00 3.95
728 733 4.393680 CGAAAATAAACCGATGAAGTGGGA 59.606 41.667 0.00 0.00 0.00 4.37
736 741 1.813102 GATGAAGTGGGAGAGGGGAT 58.187 55.000 0.00 0.00 0.00 3.85
773 784 2.978156 AAATCAGCAAAGGTGGGAGA 57.022 45.000 0.00 0.00 0.00 3.71
827 845 4.684484 AAAACTGGAAACGAGACTACCT 57.316 40.909 0.00 0.00 0.00 3.08
835 853 2.783609 ACGAGACTACCTACTGCTCA 57.216 50.000 0.00 0.00 0.00 4.26
836 854 3.069079 ACGAGACTACCTACTGCTCAA 57.931 47.619 0.00 0.00 0.00 3.02
837 855 3.011119 ACGAGACTACCTACTGCTCAAG 58.989 50.000 0.00 0.00 0.00 3.02
838 856 2.223386 CGAGACTACCTACTGCTCAAGC 60.223 54.545 0.00 0.00 42.50 4.01
913 931 2.426842 ACTATTTGGGCTTCTGCTCC 57.573 50.000 0.00 0.00 39.40 4.70
1280 1323 3.642848 CCTAATGGGTGAATTTGGGATGG 59.357 47.826 0.00 0.00 31.25 3.51
1786 2156 7.370383 GGCAACAAAGTAATCATCTCTTTTCA 58.630 34.615 0.00 0.00 30.41 2.69
1953 2327 8.472413 TCTACTACCCATGTTATGTTCTGTAAC 58.528 37.037 0.00 0.00 36.07 2.50
2181 4053 5.466127 TCCTTAAGGGCCAATTTCAGTAT 57.534 39.130 21.53 0.00 35.41 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.036996 TGTGGTGGCAAATATAATACACATG 57.963 36.000 0.00 0.0 32.12 3.21
61 62 1.103398 GCTGTGGCTGGCCGATTTAT 61.103 55.000 7.14 0.0 39.42 1.40
245 246 2.671682 GAAGAAGGGCGGCTTCCT 59.328 61.111 9.56 0.0 35.60 3.36
438 439 5.109903 ACAATACATCGAGGAGCAGTAAAC 58.890 41.667 3.06 0.0 0.00 2.01
627 632 9.590451 ACTAGCGCAAGTTATTTAGTAATGTAA 57.410 29.630 11.47 0.0 41.68 2.41
689 694 2.126307 CGCGTCACCCTCTCACAG 60.126 66.667 0.00 0.0 0.00 3.66
757 766 0.401738 CCTTCTCCCACCTTTGCTGA 59.598 55.000 0.00 0.0 0.00 4.26
835 853 3.006247 GAGCCGAAGAAAATCTCTGCTT 58.994 45.455 0.00 0.0 33.37 3.91
836 854 2.626840 GAGCCGAAGAAAATCTCTGCT 58.373 47.619 0.00 0.0 33.37 4.24
837 855 1.325943 CGAGCCGAAGAAAATCTCTGC 59.674 52.381 0.00 0.0 33.37 4.26
838 856 1.325943 GCGAGCCGAAGAAAATCTCTG 59.674 52.381 0.00 0.0 33.37 3.35
839 857 1.066858 TGCGAGCCGAAGAAAATCTCT 60.067 47.619 0.00 0.0 35.13 3.10
840 858 1.359848 TGCGAGCCGAAGAAAATCTC 58.640 50.000 0.00 0.0 0.00 2.75
841 859 1.734465 CTTGCGAGCCGAAGAAAATCT 59.266 47.619 0.00 0.0 0.00 2.40
842 860 1.791914 GCTTGCGAGCCGAAGAAAATC 60.792 52.381 15.66 0.0 43.29 2.17
885 903 8.386264 AGCAGAAGCCCAAATAGTAATATACAT 58.614 33.333 0.00 0.0 43.56 2.29
913 931 0.969149 TAGGACAGCCACACTCACAG 59.031 55.000 0.00 0.0 36.29 3.66
1280 1323 2.304221 AAGCCCTTACCCCTTGAAAC 57.696 50.000 0.00 0.0 0.00 2.78
1715 2085 6.207417 GTCATCAGGAAGAACCAAAAGAATCA 59.793 38.462 0.00 0.0 42.04 2.57
2120 3992 9.033481 CACTTAGAAGATGAACTGAGATCAATC 57.967 37.037 0.00 0.0 0.00 2.67
2166 4038 5.007332 CGTAGTAACATACTGAAATTGGCCC 59.993 44.000 0.00 0.0 39.81 5.80


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

AutoCloner maintained by Alex Coulton.