Multiple sequence alignment - TraesCS1D01G184800

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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 TraesCS1D01G184800 chr1D 100.000 3660 0 0 1 3660 255494693 255491034 0 6759
1 TraesCS1D01G184800 chr1A 91.935 3732 127 53 1 3660 327532136 327528507 0 5064
2 TraesCS1D01G184800 chr1B 93.386 3190 120 37 1 3143 357424856 357428001 0 4638
3 TraesCS1D01G184800 chr1B 97.699 478 7 1 3187 3660 357429355 357429832 0 819


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 TraesCS1D01G184800 chr1D 255491034 255494693 3659 True 6759.0 6759 100.0000 1 3660 1 chr1D.!!$R1 3659
1 TraesCS1D01G184800 chr1A 327528507 327532136 3629 True 5064.0 5064 91.9350 1 3660 1 chr1A.!!$R1 3659
2 TraesCS1D01G184800 chr1B 357424856 357429832 4976 False 2728.5 4638 95.5425 1 3660 2 chr1B.!!$F1 3659

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
858 906 0.601311 GATCCATTTCCGCCTCCTCG 60.601 60.0 0.0 0.0 0.00 4.63 F
1266 1337 0.878086 GGCATCTACTTCTCCTGCGC 60.878 60.0 0.0 0.0 33.69 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1988 0.462581 ATCGGCCACACATACTGCAG 60.463 55.0 13.48 13.48 0.00 4.41 R
3160 3265 1.043022 AGGAAAAAGCCTTGTGCCTG 58.957 50.0 0.00 0.00 42.71 4.85 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
27 28 9.864034 GAAGTGATGAACCAATACATTATTACG 57.136 33.333 0.00 0.00 0.00 3.18
28 29 9.607988 AAGTGATGAACCAATACATTATTACGA 57.392 29.630 0.00 0.00 0.00 3.43
29 30 9.778741 AGTGATGAACCAATACATTATTACGAT 57.221 29.630 0.00 0.00 0.00 3.73
86 90 1.953686 GCAAACAGCCTAACCAAGTCA 59.046 47.619 0.00 0.00 37.23 3.41
114 118 2.099141 TGCAGTACTGAATGGAGTGC 57.901 50.000 27.08 8.97 0.00 4.40
308 317 3.011517 TGCCTTGGCCTCCTCCTC 61.012 66.667 3.32 0.00 0.00 3.71
850 898 1.705337 AAGCGCGTGATCCATTTCCG 61.705 55.000 8.43 0.00 0.00 4.30
858 906 0.601311 GATCCATTTCCGCCTCCTCG 60.601 60.000 0.00 0.00 0.00 4.63
863 912 2.595009 ATTTCCGCCTCCTCGCTTCC 62.595 60.000 0.00 0.00 0.00 3.46
864 913 4.761058 TCCGCCTCCTCGCTTCCT 62.761 66.667 0.00 0.00 0.00 3.36
1000 1059 1.603739 GCCCCAACCGCTTTTCTCT 60.604 57.895 0.00 0.00 0.00 3.10
1171 1242 2.202946 TCGCCAAGCACAACGTCA 60.203 55.556 0.00 0.00 0.00 4.35
1247 1318 2.302157 ACTCCTTCGTTTTCCTACCCTG 59.698 50.000 0.00 0.00 0.00 4.45
1266 1337 0.878086 GGCATCTACTTCTCCTGCGC 60.878 60.000 0.00 0.00 33.69 6.09
1318 1389 1.968017 CTTCGCCTGCAAAGCCTGA 60.968 57.895 2.96 0.00 0.00 3.86
1349 1420 7.654022 AGATAATACTTCTAGATGCTAGGCC 57.346 40.000 0.00 0.00 0.00 5.19
1450 1530 2.669300 TCAGATCTGTTCAGCTGCTC 57.331 50.000 21.92 4.90 0.00 4.26
1544 1624 3.733443 AAGCTTGTGTTCCAATTCCAC 57.267 42.857 0.00 0.00 31.20 4.02
1560 1640 1.202758 TCCACACCAGTTACAGCCTTG 60.203 52.381 0.00 0.00 0.00 3.61
1601 1681 2.154462 GCTGTTACATGCACCTTCTGT 58.846 47.619 0.00 0.00 0.00 3.41
1611 1691 7.792374 ACATGCACCTTCTGTAATATTGTAG 57.208 36.000 0.00 0.00 0.00 2.74
1641 1721 2.708051 TGGTCGACTCGTACAAGATCT 58.292 47.619 16.46 0.00 0.00 2.75
1643 1723 2.419324 GGTCGACTCGTACAAGATCTGT 59.581 50.000 16.46 0.00 42.47 3.41
1848 1929 5.456763 GGGTCAATTAAGATGTATCAGGGCT 60.457 44.000 0.00 0.00 0.00 5.19
1849 1930 5.471456 GGTCAATTAAGATGTATCAGGGCTG 59.529 44.000 0.00 0.00 0.00 4.85
1852 1933 7.715249 GTCAATTAAGATGTATCAGGGCTGTTA 59.285 37.037 0.00 0.00 0.00 2.41
1863 1944 2.428171 CAGGGCTGTTAATTCACATGGG 59.572 50.000 0.00 0.00 0.00 4.00
1875 1956 1.074775 ACATGGGCGTGGTTGATGT 59.925 52.632 0.00 0.00 0.00 3.06
1907 1988 2.712057 CCAAAATGGTGTCTCTGCAC 57.288 50.000 0.00 0.00 38.56 4.57
1908 1989 2.233271 CCAAAATGGTGTCTCTGCACT 58.767 47.619 0.00 0.00 39.21 4.40
1983 2064 1.250328 ATGTTCCAGTGTGGCATGTG 58.750 50.000 0.00 0.00 37.47 3.21
2163 2250 3.379650 GGTGTATGATGTCACCCCG 57.620 57.895 9.43 0.00 45.70 5.73
2226 2313 4.757149 GCAGTAACAGGTGAGTCATTTTCT 59.243 41.667 0.00 0.00 0.00 2.52
2231 2318 5.757850 ACAGGTGAGTCATTTTCTTTGTC 57.242 39.130 0.00 0.00 0.00 3.18
2235 2322 6.914757 CAGGTGAGTCATTTTCTTTGTCTTTC 59.085 38.462 0.00 0.00 0.00 2.62
2275 2362 2.797491 AGTTCAAAAGTCTTGCGCAAC 58.203 42.857 21.02 11.97 0.00 4.17
2282 2369 1.071605 AGTCTTGCGCAACTTCGATC 58.928 50.000 21.02 9.62 0.00 3.69
2596 2683 0.380378 GTTGTTGGCGAGTTGCTTCA 59.620 50.000 1.51 0.00 45.43 3.02
2745 2843 7.275183 CACTCTCAGTTCCAAACATCCATATA 58.725 38.462 0.00 0.00 0.00 0.86
2761 2859 9.007494 ACATCCATATATATGCCCAGATTACTT 57.993 33.333 16.08 0.00 32.40 2.24
2798 2899 8.489676 ACATTCTCAACATATGGAGTCTCTAT 57.510 34.615 7.80 3.96 32.93 1.98
2799 2900 8.366401 ACATTCTCAACATATGGAGTCTCTATG 58.634 37.037 8.88 7.99 32.93 2.23
2897 2999 7.848223 TCAGAATAAATATGGGCATCATACG 57.152 36.000 1.80 0.00 40.75 3.06
2984 3089 6.367969 CAGTTATACACGCCTAAAAGAGTTGT 59.632 38.462 0.00 0.00 0.00 3.32
2997 3102 5.869753 AAAGAGTTGTGCAGCACTTATAG 57.130 39.130 25.83 0.00 35.11 1.31
3006 3111 2.223611 GCAGCACTTATAGAGCATGCAG 59.776 50.000 21.98 9.77 36.66 4.41
3103 3208 4.141620 CCTGAATACACCCTCTGCAGTAAT 60.142 45.833 14.67 0.00 0.00 1.89
3104 3209 5.070446 CCTGAATACACCCTCTGCAGTAATA 59.930 44.000 14.67 0.00 0.00 0.98
3105 3210 6.161855 TGAATACACCCTCTGCAGTAATAG 57.838 41.667 14.67 3.14 0.00 1.73
3116 3221 6.989169 CCTCTGCAGTAATAGCTGAACTAAAT 59.011 38.462 14.67 0.00 39.05 1.40
3160 3265 1.423794 TTCCCTCCACACCACCCTTC 61.424 60.000 0.00 0.00 0.00 3.46
3241 4656 3.495100 CCACAGTCCAAGAAGTAGCAACT 60.495 47.826 0.00 0.00 37.65 3.16
3315 4734 2.223572 GCACACCAGAAAACAAGACCAG 60.224 50.000 0.00 0.00 0.00 4.00
3650 5069 4.096081 GCTGAAGTTTTCTCCAGGATGATG 59.904 45.833 0.00 0.00 39.69 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.641541 AGCCATTTGGATAATTGAAATCGTAAT 58.358 29.630 0.00 0.00 37.39 1.89
23 24 8.006298 AGCCATTTGGATAATTGAAATCGTAA 57.994 30.769 0.00 0.00 37.39 3.18
24 25 7.581213 AGCCATTTGGATAATTGAAATCGTA 57.419 32.000 0.00 0.00 37.39 3.43
26 27 7.169035 CAAGCCATTTGGATAATTGAAATCG 57.831 36.000 0.00 0.00 37.39 3.34
86 90 1.029681 TCAGTACTGCATATCGCCGT 58.970 50.000 18.45 0.00 41.43 5.68
114 118 2.009108 CGTCCTTGTGCATGATCGG 58.991 57.895 0.00 0.00 0.00 4.18
291 300 3.011517 GAGGAGGAGGCCAAGGCA 61.012 66.667 13.87 0.00 44.11 4.75
850 898 1.142965 GAGAAGGAAGCGAGGAGGC 59.857 63.158 0.00 0.00 0.00 4.70
858 906 1.139947 CCGAGACCGAGAAGGAAGC 59.860 63.158 0.00 0.00 45.00 3.86
863 912 2.202492 CGCACCGAGACCGAGAAG 60.202 66.667 0.00 0.00 38.22 2.85
864 913 2.981909 ACGCACCGAGACCGAGAA 60.982 61.111 0.00 0.00 38.22 2.87
941 1000 2.985456 CTCTCACTCACCTGGGGC 59.015 66.667 0.00 0.00 0.00 5.80
942 1001 2.985456 GCTCTCACTCACCTGGGG 59.015 66.667 0.00 0.00 0.00 4.96
943 1002 1.979155 TCGCTCTCACTCACCTGGG 60.979 63.158 0.00 0.00 0.00 4.45
944 1003 1.214062 GTCGCTCTCACTCACCTGG 59.786 63.158 0.00 0.00 0.00 4.45
945 1004 1.214062 GGTCGCTCTCACTCACCTG 59.786 63.158 0.00 0.00 0.00 4.00
946 1005 1.979693 GGGTCGCTCTCACTCACCT 60.980 63.158 0.00 0.00 0.00 4.00
972 1031 2.281900 GTTGGGGCGCTGTTGGTA 60.282 61.111 7.64 0.00 0.00 3.25
1171 1242 2.753029 GAGCCAGCAGTCCTTGGT 59.247 61.111 0.00 0.00 38.24 3.67
1247 1318 0.878086 GCGCAGGAGAAGTAGATGCC 60.878 60.000 0.30 0.00 33.32 4.40
1266 1337 2.989840 CAAGAAGACTAGCCACAGAACG 59.010 50.000 0.00 0.00 0.00 3.95
1318 1389 9.699410 AGCATCTAGAAGTATTATCTAGCTCAT 57.301 33.333 0.00 0.00 43.92 2.90
1450 1530 6.096036 AGAACATCTCTGTTGACGAAGTATG 58.904 40.000 0.00 0.00 44.04 2.39
1544 1624 2.076863 GCTACAAGGCTGTAACTGGTG 58.923 52.381 0.00 0.00 37.58 4.17
1560 1640 0.250727 TGGAGTGCACCAAAGGCTAC 60.251 55.000 14.63 0.00 36.96 3.58
1611 1691 4.548991 ACGAGTCGACCAATCTATGTAC 57.451 45.455 21.50 0.00 0.00 2.90
1848 1929 1.815613 CCACGCCCATGTGAATTAACA 59.184 47.619 0.00 0.00 42.55 2.41
1849 1930 1.816224 ACCACGCCCATGTGAATTAAC 59.184 47.619 0.00 0.00 42.55 2.01
1852 1933 0.602562 CAACCACGCCCATGTGAATT 59.397 50.000 0.00 0.00 42.55 2.17
1863 1944 0.802494 CTACCCAACATCAACCACGC 59.198 55.000 0.00 0.00 0.00 5.34
1904 1985 1.503542 GCCACACATACTGCAGTGC 59.496 57.895 29.57 17.78 39.30 4.40
1905 1986 1.638388 CGGCCACACATACTGCAGTG 61.638 60.000 29.57 16.03 41.40 3.66
1906 1987 1.375908 CGGCCACACATACTGCAGT 60.376 57.895 25.12 25.12 0.00 4.40
1907 1988 0.462581 ATCGGCCACACATACTGCAG 60.463 55.000 13.48 13.48 0.00 4.41
1908 1989 0.827368 TATCGGCCACACATACTGCA 59.173 50.000 2.24 0.00 0.00 4.41
1983 2064 1.400737 ACTCTAGACCGTATGGCCAC 58.599 55.000 8.16 0.00 39.70 5.01
2111 2198 6.045318 ACACAACATGAGCTGATATAGTCAC 58.955 40.000 0.00 0.00 32.22 3.67
2211 2298 6.603201 TGAAAGACAAAGAAAATGACTCACCT 59.397 34.615 0.00 0.00 0.00 4.00
2226 2313 9.897744 GTCTCATCAACAATTATGAAAGACAAA 57.102 29.630 20.47 3.42 40.17 2.83
2244 2331 7.041780 GCAAGACTTTTGAACTTAGTCTCATCA 60.042 37.037 0.00 0.00 45.81 3.07
2745 2843 9.592196 AACATAATTCAAGTAATCTGGGCATAT 57.408 29.630 0.00 0.00 0.00 1.78
2798 2899 7.450074 AGACACTCCATCAGTACAAAAATACA 58.550 34.615 0.00 0.00 32.21 2.29
2799 2900 7.907214 AGACACTCCATCAGTACAAAAATAC 57.093 36.000 0.00 0.00 32.21 1.89
2807 2908 6.631016 TCAATTGTAGACACTCCATCAGTAC 58.369 40.000 5.13 0.00 32.21 2.73
2888 2990 2.978013 CATCACTGCAACGTATGATGC 58.022 47.619 10.08 10.08 41.31 3.91
2897 2999 1.317613 TGTGGGAACATCACTGCAAC 58.682 50.000 0.00 0.00 46.14 4.17
2984 3089 2.216046 GCATGCTCTATAAGTGCTGCA 58.784 47.619 11.37 0.00 38.03 4.41
2997 3102 2.747822 CGCTGTCACCTGCATGCTC 61.748 63.158 20.33 3.28 35.43 4.26
3103 3208 6.874134 GTCCTGAAAGACATTTAGTTCAGCTA 59.126 38.462 6.72 0.00 43.62 3.32
3104 3209 5.703130 GTCCTGAAAGACATTTAGTTCAGCT 59.297 40.000 6.72 0.00 43.62 4.24
3105 3210 5.470098 TGTCCTGAAAGACATTTAGTTCAGC 59.530 40.000 6.72 0.00 43.62 4.26
3160 3265 1.043022 AGGAAAAAGCCTTGTGCCTG 58.957 50.000 0.00 0.00 42.71 4.85
3177 3282 6.092259 GGTCTTGCAGTGTATTTGTAACTAGG 59.908 42.308 0.00 0.00 0.00 3.02
3241 4656 4.397103 GCAGATTTGTGGATCTTGTCATCA 59.603 41.667 0.00 0.00 34.20 3.07
3315 4734 6.817765 TGAGGTTATGGACAGAAACATTTC 57.182 37.500 0.00 0.00 37.45 2.17
3422 4841 1.751924 ACAAGACAGGATCGAGTAGCC 59.248 52.381 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.