Multiple sequence alignment - TraesCS6D01G168700

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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 TraesCS6D01G168700 chr6D 100.000 2192 0 0 1 2192 153943321 153941130 0.000000e+00 4048
1 TraesCS6D01G168700 chr6D 95.833 2208 74 9 1 2192 108485201 108487406 0.000000e+00 3552
2 TraesCS6D01G168700 chr3A 96.060 2208 69 9 1 2192 495104767 495102562 0.000000e+00 3579
3 TraesCS6D01G168700 chr2B 96.060 2208 69 9 1 2192 234541167 234538962 0.000000e+00 3579
4 TraesCS6D01G168700 chr4D 95.980 2214 65 9 1 2192 123448993 123446782 0.000000e+00 3574
5 TraesCS6D01G168700 chr1B 95.971 2209 68 12 1 2192 619195338 619193134 0.000000e+00 3567
6 TraesCS6D01G168700 chr1B 96.121 696 15 3 1 685 461440114 461440808 0.000000e+00 1125
7 TraesCS6D01G168700 chr1A 95.969 2208 70 10 1 2192 278521187 278523391 0.000000e+00 3567
8 TraesCS6D01G168700 chrUn 95.879 2208 72 10 1 2192 217907661 217909865 0.000000e+00 3555
9 TraesCS6D01G168700 chrUn 95.798 476 10 2 1 467 366196552 366197026 0.000000e+00 760
10 TraesCS6D01G168700 chrUn 95.152 330 6 2 1 321 472380880 472381208 1.500000e-141 512
11 TraesCS6D01G168700 chr3B 95.879 2208 72 10 1 2192 6010773 6008569 0.000000e+00 3555
12 TraesCS6D01G168700 chr3B 95.837 2210 69 11 1 2192 92296739 92294535 0.000000e+00 3550
13 TraesCS6D01G168700 chr7D 95.696 2207 77 8 1 2192 307146630 307144427 0.000000e+00 3533
14 TraesCS6D01G168700 chr6A 96.689 1933 44 9 1 1918 597253000 597251073 0.000000e+00 3197
15 TraesCS6D01G168700 chr1D 95.789 475 10 2 1 466 351028919 351029392 0.000000e+00 758


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 TraesCS6D01G168700 chr6D 153941130 153943321 2191 True 4048 4048 100.000 1 2192 1 chr6D.!!$R1 2191
1 TraesCS6D01G168700 chr6D 108485201 108487406 2205 False 3552 3552 95.833 1 2192 1 chr6D.!!$F1 2191
2 TraesCS6D01G168700 chr3A 495102562 495104767 2205 True 3579 3579 96.060 1 2192 1 chr3A.!!$R1 2191
3 TraesCS6D01G168700 chr2B 234538962 234541167 2205 True 3579 3579 96.060 1 2192 1 chr2B.!!$R1 2191
4 TraesCS6D01G168700 chr4D 123446782 123448993 2211 True 3574 3574 95.980 1 2192 1 chr4D.!!$R1 2191
5 TraesCS6D01G168700 chr1B 619193134 619195338 2204 True 3567 3567 95.971 1 2192 1 chr1B.!!$R1 2191
6 TraesCS6D01G168700 chr1B 461440114 461440808 694 False 1125 1125 96.121 1 685 1 chr1B.!!$F1 684
7 TraesCS6D01G168700 chr1A 278521187 278523391 2204 False 3567 3567 95.969 1 2192 1 chr1A.!!$F1 2191
8 TraesCS6D01G168700 chrUn 217907661 217909865 2204 False 3555 3555 95.879 1 2192 1 chrUn.!!$F1 2191
9 TraesCS6D01G168700 chr3B 6008569 6010773 2204 True 3555 3555 95.879 1 2192 1 chr3B.!!$R1 2191
10 TraesCS6D01G168700 chr3B 92294535 92296739 2204 True 3550 3550 95.837 1 2192 1 chr3B.!!$R2 2191
11 TraesCS6D01G168700 chr7D 307144427 307146630 2203 True 3533 3533 95.696 1 2192 1 chr7D.!!$R1 2191
12 TraesCS6D01G168700 chr6A 597251073 597253000 1927 True 3197 3197 96.689 1 1918 1 chr6A.!!$R1 1917

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
563 575 0.878416 GCGAATGTGTGTAAGCCCAA 59.122 50.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1733 0.036765 AACGAGATGCGCCAACCTTA 60.037 50.0 4.18 0.0 46.04 2.69 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
201 202 1.451504 CTGGTGGAGTGGCACAAGA 59.548 57.895 21.41 0.00 44.16 3.02
205 206 1.168714 GTGGAGTGGCACAAGAATCC 58.831 55.000 21.41 17.29 44.16 3.01
248 249 5.882557 AGATATTGATTCCTCCACACAACAC 59.117 40.000 0.00 0.00 0.00 3.32
279 289 3.692593 TCGTATCGAAGAGATGTCAACCA 59.307 43.478 0.00 0.00 43.63 3.67
341 351 1.034356 TCACTGCACAGCAAGCAAAT 58.966 45.000 0.00 0.00 42.17 2.32
368 378 3.443681 GGGGATTCAGTGGTGTAATGTTG 59.556 47.826 0.00 0.00 0.00 3.33
369 379 3.119495 GGGATTCAGTGGTGTAATGTTGC 60.119 47.826 0.00 0.00 0.00 4.17
376 386 1.070914 TGGTGTAATGTTGCGAGGTCA 59.929 47.619 0.00 0.00 0.00 4.02
534 546 2.224159 GGTGAGCTGAGGGGGACAA 61.224 63.158 0.00 0.00 0.00 3.18
563 575 0.878416 GCGAATGTGTGTAAGCCCAA 59.122 50.000 0.00 0.00 0.00 4.12
584 596 7.521669 CCCAATCAAAGATTCCTATTCTAGGT 58.478 38.462 0.35 0.00 46.32 3.08
685 697 3.134127 GCATGAGTTCACCGGGGC 61.134 66.667 6.32 0.00 0.00 5.80
722 734 4.196193 CAAAATCGGCATAGGTTAGGTGA 58.804 43.478 0.00 0.00 0.00 4.02
767 779 6.359804 CCCATCTTTCTCCATATGAAAGTGA 58.640 40.000 3.65 3.34 46.08 3.41
859 871 3.927555 CCGAAAAGGTGGCTGACTA 57.072 52.632 0.00 0.00 34.51 2.59
1183 1195 3.276846 GCCGGTGCTCGTTTGTGT 61.277 61.111 1.90 0.00 37.11 3.72
1240 1252 2.608623 TCGGGGCATCTGAGAATGATA 58.391 47.619 0.00 0.00 0.00 2.15
1349 1371 6.507023 CCTAAGTGAAAGTGCAAAAGTGAAT 58.493 36.000 0.00 0.00 0.00 2.57
1541 1565 6.422333 TGTGATGTCCTAATCAAATGCCTAA 58.578 36.000 0.00 0.00 38.28 2.69
1665 1689 4.236147 GTTCTTAACCGAGACTCAGGTTC 58.764 47.826 25.11 13.30 46.87 3.62
1676 1700 2.298729 GACTCAGGTTCAGCTCTGTCTT 59.701 50.000 0.56 0.00 33.13 3.01
1683 1707 1.423584 TCAGCTCTGTCTTGGAACCA 58.576 50.000 0.00 0.00 0.00 3.67
1927 1954 4.016444 GGTTGTGGCTTGATGAGGATAAA 58.984 43.478 0.00 0.00 0.00 1.40
1932 1959 6.662755 TGTGGCTTGATGAGGATAAATAAGT 58.337 36.000 0.00 0.00 0.00 2.24
1941 1968 5.730550 TGAGGATAAATAAGTTGACACGCT 58.269 37.500 0.00 0.00 0.00 5.07
2013 2041 2.256158 CGGTAGCGTTCGTGGTGA 59.744 61.111 6.07 0.00 0.00 4.02
2037 2065 4.263462 TGCTTCAGGATTCCAATGTACTGT 60.263 41.667 5.29 0.00 0.00 3.55
2064 2092 2.172483 ATCAGAACGAGCTTGCCGGT 62.172 55.000 1.90 0.00 0.00 5.28
2074 2102 3.476031 CTTGCCGGTGGACCACTGT 62.476 63.158 27.97 0.00 38.92 3.55
2117 2145 0.399454 AGCGCTGCCATCTTATCCAT 59.601 50.000 10.39 0.00 0.00 3.41
2138 2166 1.730064 GGAAAACGCGTCAAGCTATCA 59.270 47.619 14.44 0.00 45.59 2.15
2139 2167 2.351726 GGAAAACGCGTCAAGCTATCAT 59.648 45.455 14.44 0.00 45.59 2.45
2142 2170 4.419522 AAACGCGTCAAGCTATCATTTT 57.580 36.364 14.44 0.00 45.59 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 249 4.663166 TCTCTTCGATACGAGAAGCAAAG 58.337 43.478 7.01 0.00 43.40 2.77
279 289 2.812011 GTTGTTTCCAGATACGGTTGCT 59.188 45.455 0.00 0.00 0.00 3.91
341 351 1.710244 ACACCACTGAATCCCCAATCA 59.290 47.619 0.00 0.00 0.00 2.57
368 378 1.083806 TTCATGTCGCATGACCTCGC 61.084 55.000 18.10 0.00 44.86 5.03
369 379 0.926155 CTTCATGTCGCATGACCTCG 59.074 55.000 18.10 7.29 44.86 4.63
376 386 4.212847 GCTATCAATGTCTTCATGTCGCAT 59.787 41.667 0.00 0.00 34.19 4.73
534 546 2.058798 CACACATTCGCTCACTTACGT 58.941 47.619 0.00 0.00 0.00 3.57
722 734 5.079643 GGGCTTACCATGTTCCATCAATAT 58.920 41.667 0.00 0.00 39.85 1.28
767 779 0.761187 ACATCTCTATGTGCCCGCAT 59.239 50.000 0.00 0.00 44.79 4.73
859 871 3.694926 CTTTGATCCAGGAGAAAAGCCT 58.305 45.455 11.84 0.00 35.75 4.58
863 875 2.039746 TCCGCTTTGATCCAGGAGAAAA 59.960 45.455 0.00 0.00 0.00 2.29
975 987 1.007037 GGGATAGGGGGAAAGGGGT 59.993 63.158 0.00 0.00 0.00 4.95
1240 1252 0.899720 TTTCCCTTCATACGGCTCGT 59.100 50.000 5.58 5.58 44.35 4.18
1402 1424 4.280436 TGGTCATGAACATCGTAAGGTT 57.720 40.909 10.05 0.00 38.47 3.50
1541 1565 3.812262 TCATCGACTTTGATCATGCCAT 58.188 40.909 0.00 0.00 0.00 4.40
1556 1580 4.072839 AGGACATAGCTTACGATCATCGA 58.927 43.478 15.60 0.00 43.74 3.59
1665 1689 1.517242 GTGGTTCCAAGACAGAGCTG 58.483 55.000 0.00 0.00 0.00 4.24
1676 1700 1.756024 CTAACCCACGGTGGTTCCA 59.244 57.895 24.70 7.06 45.51 3.53
1683 1707 1.277273 GCTTTACTCCTAACCCACGGT 59.723 52.381 0.00 0.00 37.65 4.83
1708 1733 0.036765 AACGAGATGCGCCAACCTTA 60.037 50.000 4.18 0.00 46.04 2.69
1927 1954 3.067106 CAACTCCAGCGTGTCAACTTAT 58.933 45.455 0.00 0.00 0.00 1.73
1932 1959 1.891919 GCCAACTCCAGCGTGTCAA 60.892 57.895 0.00 0.00 0.00 3.18
1941 1968 3.888460 TGCCAGCAGCCAACTCCA 61.888 61.111 0.00 0.00 42.71 3.86
1994 2022 3.980989 ACCACGAACGCTACCGCA 61.981 61.111 0.00 0.00 38.22 5.69
2013 2041 4.885907 CAGTACATTGGAATCCTGAAGCAT 59.114 41.667 0.00 0.00 0.00 3.79
2037 2065 0.532573 GCTCGTTCTGATCCTGGACA 59.467 55.000 0.00 0.00 0.00 4.02
2074 2102 2.832129 AGCTCACTAAAGAATGGGACGA 59.168 45.455 0.00 0.00 0.00 4.20
2117 2145 1.730064 GATAGCTTGACGCGTTTTCCA 59.270 47.619 15.53 3.08 45.59 3.53
2138 2166 6.371809 TCTTTTAGTGCTTCGACACAAAAT 57.628 33.333 8.66 0.00 43.23 1.82
2139 2167 5.804692 TCTTTTAGTGCTTCGACACAAAA 57.195 34.783 8.66 10.65 43.23 2.44
2142 2170 5.220777 CCTTTTCTTTTAGTGCTTCGACACA 60.221 40.000 8.66 0.00 43.23 3.72


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

AutoCloner maintained by Alex Coulton.