Multiple sequence alignment - TraesCS5D01G171400

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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 TraesCS5D01G171400 chr5D 100.000 1541 0 0 1 1541 268516508 268518048 0.000000e+00 2846.0
1 TraesCS5D01G171400 chr5D 100.000 570 0 0 1920 2489 268518427 268518996 0.000000e+00 1053.0
2 TraesCS5D01G171400 chr5A 91.798 1463 63 17 105 1541 356103730 356105161 0.000000e+00 1984.0
3 TraesCS5D01G171400 chr5A 91.473 258 16 3 1930 2181 356105190 356105447 1.420000e-92 350.0
4 TraesCS5D01G171400 chr5A 86.026 229 16 7 2182 2409 356105848 356106061 5.350000e-57 231.0
5 TraesCS5D01G171400 chr5B 89.484 1550 61 42 44 1513 304124327 304125854 0.000000e+00 1866.0
6 TraesCS5D01G171400 chr5B 87.831 567 60 6 1930 2489 304125905 304126469 0.000000e+00 656.0
7 TraesCS5D01G171400 chr3B 78.656 253 37 9 2251 2489 256779440 256779191 4.290000e-33 152.0
8 TraesCS5D01G171400 chr3D 81.034 174 29 4 2251 2421 178528341 178528169 4.320000e-28 135.0
9 TraesCS5D01G171400 chr3D 81.935 155 24 4 2270 2421 178528676 178528523 7.230000e-26 128.0
10 TraesCS5D01G171400 chr1B 83.065 124 18 3 2287 2408 49751332 49751454 2.620000e-20 110.0
11 TraesCS5D01G171400 chr4D 80.374 107 18 3 2285 2389 475015177 475015282 7.380000e-11 78.7


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 TraesCS5D01G171400 chr5D 268516508 268518996 2488 False 1949.5 2846 100.000000 1 2489 2 chr5D.!!$F1 2488
1 TraesCS5D01G171400 chr5A 356103730 356106061 2331 False 855.0 1984 89.765667 105 2409 3 chr5A.!!$F1 2304
2 TraesCS5D01G171400 chr5B 304124327 304126469 2142 False 1261.0 1866 88.657500 44 2489 2 chr5B.!!$F1 2445

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
518 533 0.669625 AAGGCCGCAACGTTAGAGTC 60.67 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2890 1.798813 CGGCGGCCAGTTTTATATCTC 59.201 52.381 20.71 0.0 0.0 2.75 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
18 19 1.218316 CGTCTCCCTAAGTGTGGGC 59.782 63.158 0.00 0.00 44.23 5.36
19 20 1.602771 GTCTCCCTAAGTGTGGGCC 59.397 63.158 0.00 0.00 44.23 5.80
20 21 1.615424 TCTCCCTAAGTGTGGGCCC 60.615 63.158 17.59 17.59 44.23 5.80
21 22 1.923395 CTCCCTAAGTGTGGGCCCA 60.923 63.158 24.45 24.45 44.23 5.36
22 23 2.198304 CTCCCTAAGTGTGGGCCCAC 62.198 65.000 42.81 42.81 44.23 4.61
35 36 4.778415 CCCACAGGACGCGTCTCG 62.778 72.222 35.50 27.81 45.38 4.04
36 37 4.778415 CCACAGGACGCGTCTCGG 62.778 72.222 35.50 26.71 43.86 4.63
37 38 4.778415 CACAGGACGCGTCTCGGG 62.778 72.222 35.50 24.63 45.13 5.14
58 59 2.592861 GGGCCCTGATGCGTGATC 60.593 66.667 17.04 0.00 0.00 2.92
68 69 3.372060 TGATGCGTGATCGTAATCAGTC 58.628 45.455 0.00 0.00 42.53 3.51
75 76 3.791887 GTGATCGTAATCAGTCGGTTGAG 59.208 47.826 0.00 0.00 42.53 3.02
76 77 3.442625 TGATCGTAATCAGTCGGTTGAGT 59.557 43.478 0.00 0.00 36.98 3.41
77 78 4.637091 TGATCGTAATCAGTCGGTTGAGTA 59.363 41.667 0.00 0.00 36.98 2.59
78 79 5.124297 TGATCGTAATCAGTCGGTTGAGTAA 59.876 40.000 0.17 0.00 36.98 2.24
79 80 5.375417 TCGTAATCAGTCGGTTGAGTAAA 57.625 39.130 0.17 0.00 30.46 2.01
383 392 2.109387 CCGTCGACAAACCCACCA 59.891 61.111 17.16 0.00 0.00 4.17
390 400 2.882137 TCGACAAACCCACCAAAATCTC 59.118 45.455 0.00 0.00 0.00 2.75
457 467 2.835764 ACCCACCAAAATAGAGCTCGTA 59.164 45.455 8.37 1.66 0.00 3.43
461 471 4.876107 CCACCAAAATAGAGCTCGTAATGT 59.124 41.667 8.37 0.00 0.00 2.71
467 477 6.466885 AAATAGAGCTCGTAATGTACCACT 57.533 37.500 8.37 0.00 0.00 4.00
518 533 0.669625 AAGGCCGCAACGTTAGAGTC 60.670 55.000 0.00 0.00 0.00 3.36
552 571 4.056740 CCTAGAATCGAGCACGTAGAGTA 58.943 47.826 2.86 0.00 40.69 2.59
571 590 4.024670 AGTACGAAAACCTGGAGCTAGAT 58.975 43.478 0.00 0.00 0.00 1.98
610 629 1.552348 GCGTCAGCAGTGAGTGTGTC 61.552 60.000 0.00 0.00 44.35 3.67
818 879 3.058363 CAGGAGCAACAGCTTTCTTCTTC 60.058 47.826 0.00 0.00 39.10 2.87
819 880 3.145286 GGAGCAACAGCTTTCTTCTTCT 58.855 45.455 0.00 0.00 39.10 2.85
820 881 3.188254 GGAGCAACAGCTTTCTTCTTCTC 59.812 47.826 0.00 0.00 39.10 2.87
821 882 4.064388 GAGCAACAGCTTTCTTCTTCTCT 58.936 43.478 0.00 0.00 39.10 3.10
831 892 7.329226 CAGCTTTCTTCTTCTCTCTCAGTTAAG 59.671 40.741 0.00 0.00 0.00 1.85
918 987 2.066999 GTCCGCTCTCCCCCATCTT 61.067 63.158 0.00 0.00 0.00 2.40
956 1036 5.782331 TCTTCTTCTTTCTCTTCAGATCCCA 59.218 40.000 0.00 0.00 0.00 4.37
957 1037 5.413309 TCTTCTTTCTCTTCAGATCCCAC 57.587 43.478 0.00 0.00 0.00 4.61
958 1038 4.840680 TCTTCTTTCTCTTCAGATCCCACA 59.159 41.667 0.00 0.00 0.00 4.17
993 1073 2.494059 GAGCAACTGACCAGCAAGTTA 58.506 47.619 0.00 0.00 0.00 2.24
1059 1139 4.137615 TCCTCCATCCTCGGCCGA 62.138 66.667 29.03 29.03 0.00 5.54
2001 2087 8.671921 ACATAATGTTGATTCTTGAGTGCTTAG 58.328 33.333 0.00 0.00 0.00 2.18
2074 2160 5.449177 CGATGATTGTAAAGAGGAAAAGGGC 60.449 44.000 0.00 0.00 0.00 5.19
2079 2168 3.316868 TGTAAAGAGGAAAAGGGCAAACG 59.683 43.478 0.00 0.00 0.00 3.60
2147 2236 4.759183 GGAATACAATGCCTTTGCCAAAAA 59.241 37.500 0.00 0.00 39.03 1.94
2154 2243 2.135139 GCCTTTGCCAAAAACAGCTAC 58.865 47.619 0.00 0.00 0.00 3.58
2248 2738 5.333513 CAAGAGAGTACAAGATCACGTACC 58.666 45.833 16.73 10.80 39.03 3.34
2257 2747 4.036971 ACAAGATCACGTACCTAGAGCATC 59.963 45.833 0.00 0.00 0.00 3.91
2283 2773 7.997107 TCAATAGATCATGCAAATTTGAAGC 57.003 32.000 22.31 7.20 0.00 3.86
2343 2834 6.767524 TTAGAAAAGAGCCAACTTCAACAA 57.232 33.333 0.00 0.00 0.00 2.83
2394 2887 8.918202 AAGTAACTCCAACAGATGATACAAAA 57.082 30.769 0.00 0.00 0.00 2.44
2397 2890 6.764308 ACTCCAACAGATGATACAAAATGG 57.236 37.500 0.00 0.00 0.00 3.16
2402 2895 8.493607 TCCAACAGATGATACAAAATGGAGATA 58.506 33.333 0.00 0.00 31.26 1.98
2417 2910 1.798813 GAGATATAAAACTGGCCGCCG 59.201 52.381 4.58 2.21 0.00 6.46
2454 2947 3.620286 CCGCGCGGATCGAAATAA 58.380 55.556 44.86 0.00 41.67 1.40
2458 2951 1.372656 GCGCGGATCGAAATAAAACG 58.627 50.000 8.83 0.00 41.67 3.60
2474 2967 4.961435 AAAACGTCCCGAAAACAACTTA 57.039 36.364 0.00 0.00 0.00 2.24
2482 2975 7.009448 ACGTCCCGAAAACAACTTAAAAATTTC 59.991 33.333 0.00 0.00 0.00 2.17
2483 2976 7.009357 CGTCCCGAAAACAACTTAAAAATTTCA 59.991 33.333 0.00 0.00 0.00 2.69
2484 2977 8.111836 GTCCCGAAAACAACTTAAAAATTTCAC 58.888 33.333 0.00 0.00 0.00 3.18
2485 2978 7.817962 TCCCGAAAACAACTTAAAAATTTCACA 59.182 29.630 0.00 0.00 0.00 3.58
2486 2979 8.608317 CCCGAAAACAACTTAAAAATTTCACAT 58.392 29.630 0.00 0.00 0.00 3.21
2487 2980 9.419737 CCGAAAACAACTTAAAAATTTCACATG 57.580 29.630 0.00 0.00 0.00 3.21
2488 2981 9.965748 CGAAAACAACTTAAAAATTTCACATGT 57.034 25.926 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.778415 CGAGACGCGTCCTGTGGG 62.778 72.222 34.08 14.03 34.64 4.61
19 20 4.778415 CCGAGACGCGTCCTGTGG 62.778 72.222 34.08 25.16 38.67 4.17
20 21 4.778415 CCCGAGACGCGTCCTGTG 62.778 72.222 34.08 20.73 38.67 3.66
38 39 4.864334 CACGCATCAGGGCCCTCC 62.864 72.222 25.77 9.89 0.00 4.30
39 40 3.112205 ATCACGCATCAGGGCCCTC 62.112 63.158 25.77 10.24 0.00 4.30
40 41 3.092511 ATCACGCATCAGGGCCCT 61.093 61.111 22.28 22.28 0.00 5.19
41 42 2.592861 GATCACGCATCAGGGCCC 60.593 66.667 16.46 16.46 0.00 5.80
42 43 2.363711 TACGATCACGCATCAGGGCC 62.364 60.000 0.00 0.00 43.96 5.80
45 46 2.728318 CTGATTACGATCACGCATCAGG 59.272 50.000 17.18 6.24 45.99 3.86
58 59 5.444218 GCTTTTACTCAACCGACTGATTACG 60.444 44.000 0.00 0.00 0.00 3.18
68 69 5.740406 TCTTAAAACGCTTTTACTCAACCG 58.260 37.500 0.00 0.00 35.03 4.44
117 125 2.357517 CAGTCTGTGGGCGTGGAC 60.358 66.667 0.00 0.00 0.00 4.02
128 136 0.605589 GAGAGTCCACACCCAGTCTG 59.394 60.000 0.00 0.00 0.00 3.51
132 140 1.908793 ACGGAGAGTCCACACCCAG 60.909 63.158 0.00 0.00 35.91 4.45
214 223 2.094752 GGTTTGGTGTATGTGACCATGC 60.095 50.000 0.00 0.00 43.13 4.06
383 392 2.877168 GGAGATGCGCAGATGAGATTTT 59.123 45.455 18.32 0.00 0.00 1.82
390 400 1.329906 GAAAGTGGAGATGCGCAGATG 59.670 52.381 18.32 0.00 0.00 2.90
457 467 6.349280 CGAACCAAATCAATCAGTGGTACATT 60.349 38.462 0.00 0.00 43.62 2.71
461 471 4.900684 TCGAACCAAATCAATCAGTGGTA 58.099 39.130 0.00 0.00 43.62 3.25
467 477 8.138074 TGTAAATTGTTCGAACCAAATCAATCA 58.862 29.630 24.78 12.57 0.00 2.57
518 533 5.050972 GCTCGATTCTAGGGTAAACGATTTG 60.051 44.000 0.00 0.00 0.00 2.32
552 571 3.983044 AATCTAGCTCCAGGTTTTCGT 57.017 42.857 0.00 0.00 0.00 3.85
632 660 1.288127 GTTAGCCGTCCTCACGTGT 59.712 57.895 16.51 0.00 45.17 4.49
818 879 5.135508 TCCGTTTTCCTTAACTGAGAGAG 57.864 43.478 0.00 0.00 0.00 3.20
819 880 5.740290 ATCCGTTTTCCTTAACTGAGAGA 57.260 39.130 0.00 0.00 0.00 3.10
820 881 6.043411 CCTATCCGTTTTCCTTAACTGAGAG 58.957 44.000 0.00 0.00 33.27 3.20
821 882 5.105064 CCCTATCCGTTTTCCTTAACTGAGA 60.105 44.000 0.00 0.00 0.00 3.27
831 892 2.737679 CGTCTGTCCCTATCCGTTTTCC 60.738 54.545 0.00 0.00 0.00 3.13
918 987 7.944554 AGAAAGAAGAAGAAGAGAGAGAGAGAA 59.055 37.037 0.00 0.00 0.00 2.87
956 1036 3.966543 CCGGGTCTGGGGCTTTGT 61.967 66.667 0.00 0.00 0.00 2.83
957 1037 3.628646 CTCCGGGTCTGGGGCTTTG 62.629 68.421 0.00 0.00 0.00 2.77
958 1038 3.330720 CTCCGGGTCTGGGGCTTT 61.331 66.667 0.00 0.00 0.00 3.51
993 1073 3.144871 TCGTCGTCCATGCCCGAT 61.145 61.111 7.98 0.00 35.30 4.18
1059 1139 3.663176 TCGACGACGAGCGGGTTT 61.663 61.111 5.75 0.00 46.49 3.27
1936 2019 6.961359 TCATTTGTACAACAAGTATCGAGG 57.039 37.500 8.07 0.00 39.53 4.63
1979 2065 5.709164 AGCTAAGCACTCAAGAATCAACATT 59.291 36.000 0.00 0.00 0.00 2.71
2033 2119 3.882888 TCATCGAGTGCTTTTCCTTGTTT 59.117 39.130 0.00 0.00 0.00 2.83
2074 2160 3.381045 TCTCACTTCACAGCTACGTTTG 58.619 45.455 0.00 0.00 0.00 2.93
2079 2168 5.065704 TCAGATTCTCACTTCACAGCTAC 57.934 43.478 0.00 0.00 0.00 3.58
2147 2236 1.972588 AGGAAGAATGGGGTAGCTGT 58.027 50.000 0.00 0.00 0.00 4.40
2154 2243 2.827921 CAAAGACCAAGGAAGAATGGGG 59.172 50.000 0.00 0.00 41.17 4.96
2219 2709 6.100668 GTGATCTTGTACTCTCTTGGTTACC 58.899 44.000 0.00 0.00 0.00 2.85
2248 2738 7.097834 TGCATGATCTATTGAAGATGCTCTAG 58.902 38.462 18.02 0.00 45.35 2.43
2265 2755 7.585286 TTTACAGCTTCAAATTTGCATGATC 57.415 32.000 13.54 0.00 0.00 2.92
2323 2814 6.042143 TCATTTGTTGAAGTTGGCTCTTTTC 58.958 36.000 0.00 0.00 0.00 2.29
2389 2882 6.183360 CGGCCAGTTTTATATCTCCATTTTGT 60.183 38.462 2.24 0.00 0.00 2.83
2394 2887 3.412386 GCGGCCAGTTTTATATCTCCAT 58.588 45.455 2.24 0.00 0.00 3.41
2397 2890 1.798813 CGGCGGCCAGTTTTATATCTC 59.201 52.381 20.71 0.00 0.00 2.75
2402 2895 3.138128 GCCGGCGGCCAGTTTTAT 61.138 61.111 39.67 0.00 44.06 1.40
2441 2934 2.286008 GGGACGTTTTATTTCGATCCGC 60.286 50.000 0.00 0.00 32.49 5.54
2458 2951 8.111836 GTGAAATTTTTAAGTTGTTTTCGGGAC 58.888 33.333 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.