Multiple sequence alignment - TraesCS5D01G040100

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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 TraesCS5D01G040100 chr5D 100.000 2888 0 0 1 2888 41120658 41117771 0.000000e+00 5334
1 TraesCS5D01G040100 chr5D 83.025 595 57 19 1284 1858 41294673 41295243 1.550000e-137 499
2 TraesCS5D01G040100 chr5D 75.123 611 77 45 433 1004 41294102 41294676 1.740000e-52 217
3 TraesCS5D01G040100 chr5A 93.308 2107 82 20 34 2089 29516131 29514033 0.000000e+00 3055
4 TraesCS5D01G040100 chr5A 94.322 317 14 2 2057 2373 29514028 29513716 1.560000e-132 483
5 TraesCS5D01G040100 chr5A 85.421 487 32 20 2410 2888 29513720 29513265 1.210000e-128 470
6 TraesCS5D01G040100 chr5A 85.366 205 30 0 1634 1838 29624427 29624631 2.250000e-51 213
7 TraesCS5D01G040100 chr5B 91.968 2154 87 38 1 2089 35190345 35188213 0.000000e+00 2940
8 TraesCS5D01G040100 chr5B 95.824 455 16 3 2057 2508 35188208 35187754 0.000000e+00 732
9 TraesCS5D01G040100 chr5B 79.872 467 54 22 1823 2271 35286731 35287175 3.620000e-79 305
10 TraesCS5D01G040100 chr5B 81.180 356 27 10 1284 1626 35286408 35286736 1.720000e-62 250
11 TraesCS5D01G040100 chr5B 92.715 151 9 1 2740 2888 35187720 35187570 1.740000e-52 217
12 TraesCS5D01G040100 chr5B 85.714 196 13 10 812 1005 35286230 35286412 2.940000e-45 193


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 TraesCS5D01G040100 chr5D 41117771 41120658 2887 True 5334.000000 5334 100.000000 1 2888 1 chr5D.!!$R1 2887
1 TraesCS5D01G040100 chr5D 41294102 41295243 1141 False 358.000000 499 79.074000 433 1858 2 chr5D.!!$F1 1425
2 TraesCS5D01G040100 chr5A 29513265 29516131 2866 True 1336.000000 3055 91.017000 34 2888 3 chr5A.!!$R1 2854
3 TraesCS5D01G040100 chr5B 35187570 35190345 2775 True 1296.333333 2940 93.502333 1 2888 3 chr5B.!!$R1 2887
4 TraesCS5D01G040100 chr5B 35286230 35287175 945 False 249.333333 305 82.255333 812 2271 3 chr5B.!!$F1 1459

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
195 204 0.250513 GTGGAGTCCATGTCCAGGTC 59.749 60.0 16.67 0.0 45.0 3.85 F
203 212 0.253894 CATGTCCAGGTCCATGCTCA 59.746 55.0 8.38 0.0 32.8 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1440 1.376466 GTCTTCTGCTGCTGGGGAA 59.624 57.895 6.69 2.94 0.0 3.97 R
1898 2044 2.038557 GCAGGGAAACAACTCACCTCTA 59.961 50.000 0.00 0.00 0.0 2.43 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
177 186 2.154462 CTGCGAGATTGGGTTCTTTGT 58.846 47.619 0.00 0.00 0.00 2.83
190 199 2.814336 GTTCTTTGTGGAGTCCATGTCC 59.186 50.000 16.67 2.49 35.28 4.02
191 200 2.054021 TCTTTGTGGAGTCCATGTCCA 58.946 47.619 16.67 5.54 42.06 4.02
192 201 2.038952 TCTTTGTGGAGTCCATGTCCAG 59.961 50.000 16.67 7.70 45.00 3.86
193 202 0.692476 TTGTGGAGTCCATGTCCAGG 59.308 55.000 16.67 0.00 45.00 4.45
194 203 0.473694 TGTGGAGTCCATGTCCAGGT 60.474 55.000 16.67 0.00 45.00 4.00
195 204 0.250513 GTGGAGTCCATGTCCAGGTC 59.749 60.000 16.67 0.00 45.00 3.85
196 205 0.909610 TGGAGTCCATGTCCAGGTCC 60.910 60.000 8.12 0.00 39.28 4.46
197 206 0.909610 GGAGTCCATGTCCAGGTCCA 60.910 60.000 3.60 0.00 33.84 4.02
198 207 1.207791 GAGTCCATGTCCAGGTCCAT 58.792 55.000 0.00 0.00 0.00 3.41
199 208 0.914644 AGTCCATGTCCAGGTCCATG 59.085 55.000 12.45 12.45 38.51 3.66
200 209 0.749454 GTCCATGTCCAGGTCCATGC 60.749 60.000 13.47 1.94 37.67 4.06
201 210 0.915872 TCCATGTCCAGGTCCATGCT 60.916 55.000 13.47 0.00 37.67 3.79
202 211 0.465097 CCATGTCCAGGTCCATGCTC 60.465 60.000 13.47 0.00 37.67 4.26
203 212 0.253894 CATGTCCAGGTCCATGCTCA 59.746 55.000 8.38 0.00 32.80 4.26
204 213 1.133884 CATGTCCAGGTCCATGCTCAT 60.134 52.381 8.38 0.00 32.80 2.90
205 214 0.253894 TGTCCAGGTCCATGCTCATG 59.746 55.000 2.97 2.97 38.51 3.07
206 215 0.254178 GTCCAGGTCCATGCTCATGT 59.746 55.000 8.81 0.00 37.11 3.21
207 216 0.994247 TCCAGGTCCATGCTCATGTT 59.006 50.000 8.81 0.00 37.11 2.71
292 323 2.061028 CCGTTGCTTCCAAAGATTTGC 58.939 47.619 0.00 0.00 36.86 3.68
316 353 5.946377 CCCCCTTTGGTTGATAATAGATAGC 59.054 44.000 0.00 0.00 0.00 2.97
424 466 7.039574 GCTAGGTTTTCCCTTTTATTTACCACA 60.040 37.037 0.00 0.00 42.73 4.17
435 477 9.031537 CCTTTTATTTACCACAGATTTTAGGGT 57.968 33.333 0.00 0.00 35.66 4.34
453 500 5.874895 AGGGTTTTTCTGCTTACGATTAC 57.125 39.130 0.00 0.00 0.00 1.89
915 1028 7.030075 AGAAAATCCAAATGTTTTTGCAAGG 57.970 32.000 0.00 0.00 40.77 3.61
933 1046 4.270084 GCAAGGTTTGGTGCTAACTTTTTC 59.730 41.667 0.00 0.00 37.78 2.29
934 1047 4.665833 AGGTTTGGTGCTAACTTTTTCC 57.334 40.909 0.00 0.00 0.00 3.13
1251 1365 2.045045 CCCAGCAAGGCCATCGAA 60.045 61.111 5.01 0.00 35.39 3.71
1500 1619 2.667536 CTGCACTGCTCCAACGCT 60.668 61.111 1.98 0.00 0.00 5.07
1557 1682 2.494918 CTTGCCTACTACGCCGCT 59.505 61.111 0.00 0.00 0.00 5.52
1731 1871 4.636435 CCGTCCCAGCACCCGTTT 62.636 66.667 0.00 0.00 0.00 3.60
1807 1950 2.203337 TTGGAGGCAACAGCGCTT 60.203 55.556 7.50 0.00 41.41 4.68
1824 1970 3.914579 TTCTGCTGCTGCTCCTGCC 62.915 63.158 17.00 0.00 40.48 4.85
1898 2044 8.797438 GGAAAGGAAGACATAATTTCTTCTTGT 58.203 33.333 14.87 5.83 45.68 3.16
2143 2339 0.673985 GCCAACCAAAGGGAGTGTTC 59.326 55.000 0.00 0.00 38.05 3.18
2155 2351 4.709250 AGGGAGTGTTCTCTCAAGAAAAC 58.291 43.478 1.04 1.04 46.27 2.43
2229 2432 5.721960 TCCAAGTTCCTAGAGAATAGCACTT 59.278 40.000 0.00 0.00 36.69 3.16
2299 2502 4.350368 TGTTTCTTACAGAGGTCATGCA 57.650 40.909 0.00 0.00 31.68 3.96
2300 2503 4.713553 TGTTTCTTACAGAGGTCATGCAA 58.286 39.130 0.00 0.00 31.68 4.08
2335 2538 3.999001 TGAATTCAGACTACTTGCTGCAG 59.001 43.478 10.11 10.11 32.27 4.41
2405 2608 7.831193 ACATGCTGAAATACCTATTCTTGAACT 59.169 33.333 0.00 0.00 0.00 3.01
2482 2687 5.290386 ACTGTGACTTCTAAGAAGTTTCCG 58.710 41.667 5.04 1.84 0.00 4.30
2504 2709 8.565896 TCCGACTATAGTTGTAGTTAAGAACA 57.434 34.615 17.25 0.00 35.14 3.18
2534 2752 1.298157 TGGCGAACAAGAATGGCTCG 61.298 55.000 0.00 0.00 0.00 5.03
2565 2783 4.164221 GGGAGATCATTTCACTTCAGGGTA 59.836 45.833 0.00 0.00 0.00 3.69
2623 2841 4.659480 CCACTGCATGTTTGTGGC 57.341 55.556 16.61 0.00 43.61 5.01
2624 2842 1.740905 CCACTGCATGTTTGTGGCA 59.259 52.632 16.61 0.00 43.61 4.92
2626 2844 0.598158 CACTGCATGTTTGTGGCACC 60.598 55.000 16.26 0.00 33.34 5.01
2630 2848 1.285641 CATGTTTGTGGCACCGTCC 59.714 57.895 16.26 0.91 0.00 4.79
2631 2849 1.152860 ATGTTTGTGGCACCGTCCA 60.153 52.632 16.26 6.99 0.00 4.02
2632 2850 0.539438 ATGTTTGTGGCACCGTCCAT 60.539 50.000 16.26 9.04 38.57 3.41
2633 2851 0.753479 TGTTTGTGGCACCGTCCATT 60.753 50.000 16.26 0.00 38.57 3.16
2634 2852 0.039527 GTTTGTGGCACCGTCCATTC 60.040 55.000 16.26 0.00 38.57 2.67
2635 2853 0.179004 TTTGTGGCACCGTCCATTCT 60.179 50.000 16.26 0.00 38.57 2.40
2636 2854 0.605319 TTGTGGCACCGTCCATTCTC 60.605 55.000 16.26 0.00 38.57 2.87
2637 2855 1.296715 GTGGCACCGTCCATTCTCT 59.703 57.895 6.29 0.00 38.57 3.10
2638 2856 0.321653 GTGGCACCGTCCATTCTCTT 60.322 55.000 6.29 0.00 38.57 2.85
2639 2857 1.066430 GTGGCACCGTCCATTCTCTTA 60.066 52.381 6.29 0.00 38.57 2.10
2640 2858 1.066430 TGGCACCGTCCATTCTCTTAC 60.066 52.381 0.00 0.00 0.00 2.34
2641 2859 1.207329 GGCACCGTCCATTCTCTTACT 59.793 52.381 0.00 0.00 0.00 2.24
2642 2860 2.429610 GGCACCGTCCATTCTCTTACTA 59.570 50.000 0.00 0.00 0.00 1.82
2643 2861 3.118884 GGCACCGTCCATTCTCTTACTAA 60.119 47.826 0.00 0.00 0.00 2.24
2644 2862 3.864003 GCACCGTCCATTCTCTTACTAAC 59.136 47.826 0.00 0.00 0.00 2.34
2645 2863 4.619863 GCACCGTCCATTCTCTTACTAACA 60.620 45.833 0.00 0.00 0.00 2.41
2646 2864 5.475719 CACCGTCCATTCTCTTACTAACAA 58.524 41.667 0.00 0.00 0.00 2.83
2647 2865 5.577164 CACCGTCCATTCTCTTACTAACAAG 59.423 44.000 0.00 0.00 0.00 3.16
2648 2866 5.109903 CCGTCCATTCTCTTACTAACAAGG 58.890 45.833 0.00 0.00 0.00 3.61
2649 2867 5.337330 CCGTCCATTCTCTTACTAACAAGGT 60.337 44.000 0.00 0.00 0.00 3.50
2650 2868 5.577164 CGTCCATTCTCTTACTAACAAGGTG 59.423 44.000 0.00 0.00 0.00 4.00
2651 2869 5.875359 GTCCATTCTCTTACTAACAAGGTGG 59.125 44.000 0.00 0.00 0.00 4.61
2652 2870 5.045869 TCCATTCTCTTACTAACAAGGTGGG 60.046 44.000 0.00 0.00 0.00 4.61
2653 2871 4.903045 TTCTCTTACTAACAAGGTGGGG 57.097 45.455 0.00 0.00 0.00 4.96
2654 2872 2.570302 TCTCTTACTAACAAGGTGGGGC 59.430 50.000 0.00 0.00 0.00 5.80
2655 2873 2.304761 CTCTTACTAACAAGGTGGGGCA 59.695 50.000 0.00 0.00 0.00 5.36
2656 2874 2.304761 TCTTACTAACAAGGTGGGGCAG 59.695 50.000 0.00 0.00 0.00 4.85
2657 2875 0.326927 TACTAACAAGGTGGGGCAGC 59.673 55.000 0.00 0.00 0.00 5.25
2658 2876 1.678970 CTAACAAGGTGGGGCAGCC 60.679 63.158 1.26 1.26 31.60 4.85
2659 2877 3.561120 TAACAAGGTGGGGCAGCCG 62.561 63.158 5.00 0.00 31.60 5.52
2729 2947 8.563123 TCTTCTTTAGAACTCAGAATCGAGTA 57.437 34.615 7.84 0.00 45.56 2.59
2740 2958 4.038042 TCAGAATCGAGTAATAGCTGGGTG 59.962 45.833 0.00 0.00 0.00 4.61
2833 3060 6.983307 CACAGAAAGGTCTCATATTCTACCTG 59.017 42.308 0.00 0.00 41.51 4.00
2851 3078 2.357154 CCTGACAACATAAAGGGAGGGG 60.357 54.545 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 186 0.909610 GGACCTGGACATGGACTCCA 60.910 60.000 0.00 0.00 38.19 3.86
190 199 2.118313 TGAACATGAGCATGGACCTG 57.882 50.000 14.35 0.00 42.91 4.00
191 200 2.422519 GGATGAACATGAGCATGGACCT 60.423 50.000 14.35 2.11 42.91 3.85
192 201 1.952296 GGATGAACATGAGCATGGACC 59.048 52.381 14.35 6.65 42.91 4.46
193 202 2.877168 GAGGATGAACATGAGCATGGAC 59.123 50.000 14.35 8.34 42.91 4.02
194 203 2.775960 AGAGGATGAACATGAGCATGGA 59.224 45.455 14.35 0.00 42.91 3.41
195 204 3.139850 GAGAGGATGAACATGAGCATGG 58.860 50.000 14.35 0.00 42.91 3.66
196 205 4.074627 AGAGAGGATGAACATGAGCATG 57.925 45.455 8.82 8.82 44.15 4.06
197 206 4.452825 CAAGAGAGGATGAACATGAGCAT 58.547 43.478 0.00 1.82 0.00 3.79
198 207 3.370209 CCAAGAGAGGATGAACATGAGCA 60.370 47.826 0.00 0.00 0.00 4.26
199 208 3.118482 TCCAAGAGAGGATGAACATGAGC 60.118 47.826 0.00 0.00 31.23 4.26
200 209 4.750021 TCCAAGAGAGGATGAACATGAG 57.250 45.455 0.00 0.00 31.23 2.90
292 323 5.946377 GCTATCTATTATCAACCAAAGGGGG 59.054 44.000 0.00 0.00 42.91 5.40
316 353 2.292267 GCCACCACCATTACTCATCTG 58.708 52.381 0.00 0.00 0.00 2.90
419 461 5.221441 GCAGAAAAACCCTAAAATCTGTGGT 60.221 40.000 0.00 0.00 37.27 4.16
424 466 6.713450 TCGTAAGCAGAAAAACCCTAAAATCT 59.287 34.615 0.00 0.00 37.18 2.40
435 477 4.011698 GGGGGTAATCGTAAGCAGAAAAA 58.988 43.478 0.00 0.00 37.18 1.94
453 500 4.722700 CTGGCAAGGACGTGGGGG 62.723 72.222 0.00 0.00 0.00 5.40
546 609 0.391966 GCCCTGTTCCCCGTCTATAC 59.608 60.000 0.00 0.00 0.00 1.47
915 1028 5.902681 AGAAGGAAAAAGTTAGCACCAAAC 58.097 37.500 0.00 0.00 0.00 2.93
933 1046 3.389656 GGGGTAGGATTCAGAGAAGAAGG 59.610 52.174 0.00 0.00 0.00 3.46
934 1047 4.033709 TGGGGTAGGATTCAGAGAAGAAG 58.966 47.826 0.00 0.00 0.00 2.85
1326 1440 1.376466 GTCTTCTGCTGCTGGGGAA 59.624 57.895 6.69 2.94 0.00 3.97
1557 1682 2.047655 GCGATGTGTGAACCCGGA 60.048 61.111 0.73 0.00 0.00 5.14
1807 1950 4.405671 GGCAGGAGCAGCAGCAGA 62.406 66.667 3.17 0.00 45.49 4.26
1898 2044 2.038557 GCAGGGAAACAACTCACCTCTA 59.961 50.000 0.00 0.00 0.00 2.43
2096 2291 6.902341 TGCTGCTAAGTTCTGAAATTAACTG 58.098 36.000 10.95 11.07 36.12 3.16
2143 2339 7.589221 GCTACAATCAGTTTGTTTTCTTGAGAG 59.411 37.037 2.15 0.00 46.51 3.20
2155 2351 3.921119 TTGGCAGCTACAATCAGTTTG 57.079 42.857 0.00 0.00 41.36 2.93
2300 2503 9.757227 GTAGTCTGAATTCAGTAAATCTGCTAT 57.243 33.333 29.80 9.69 44.12 2.97
2335 2538 1.521450 ATTGGACTGCTGCACACTGC 61.521 55.000 0.00 0.00 45.29 4.40
2405 2608 7.466746 CCTCAAAAGGAATCCAAAATCAGTA 57.533 36.000 0.61 0.00 46.67 2.74
2482 2687 9.857957 AAGCTGTTCTTAACTACAACTATAGTC 57.142 33.333 5.70 0.00 34.18 2.59
2516 2734 1.298859 ACGAGCCATTCTTGTTCGCC 61.299 55.000 0.00 0.00 35.93 5.54
2534 2752 6.581171 AGTGAAATGATCTCCCTTCAAAAC 57.419 37.500 0.00 0.00 30.03 2.43
2623 2841 5.068234 TGTTAGTAAGAGAATGGACGGTG 57.932 43.478 0.00 0.00 0.00 4.94
2624 2842 5.337330 CCTTGTTAGTAAGAGAATGGACGGT 60.337 44.000 0.00 0.00 0.00 4.83
2626 2844 5.577164 CACCTTGTTAGTAAGAGAATGGACG 59.423 44.000 0.00 0.00 0.00 4.79
2630 2848 5.186198 CCCCACCTTGTTAGTAAGAGAATG 58.814 45.833 0.00 0.00 0.00 2.67
2631 2849 4.324331 GCCCCACCTTGTTAGTAAGAGAAT 60.324 45.833 0.00 0.00 0.00 2.40
2632 2850 3.008704 GCCCCACCTTGTTAGTAAGAGAA 59.991 47.826 0.00 0.00 0.00 2.87
2633 2851 2.570302 GCCCCACCTTGTTAGTAAGAGA 59.430 50.000 0.00 0.00 0.00 3.10
2634 2852 2.304761 TGCCCCACCTTGTTAGTAAGAG 59.695 50.000 0.00 0.00 0.00 2.85
2635 2853 2.304761 CTGCCCCACCTTGTTAGTAAGA 59.695 50.000 0.00 0.00 0.00 2.10
2636 2854 2.711542 CTGCCCCACCTTGTTAGTAAG 58.288 52.381 0.00 0.00 0.00 2.34
2637 2855 1.271707 GCTGCCCCACCTTGTTAGTAA 60.272 52.381 0.00 0.00 0.00 2.24
2638 2856 0.326927 GCTGCCCCACCTTGTTAGTA 59.673 55.000 0.00 0.00 0.00 1.82
2639 2857 1.074951 GCTGCCCCACCTTGTTAGT 59.925 57.895 0.00 0.00 0.00 2.24
2640 2858 1.678970 GGCTGCCCCACCTTGTTAG 60.679 63.158 7.66 0.00 0.00 2.34
2641 2859 2.438795 GGCTGCCCCACCTTGTTA 59.561 61.111 7.66 0.00 0.00 2.41
2642 2860 4.974721 CGGCTGCCCCACCTTGTT 62.975 66.667 14.12 0.00 0.00 2.83
2648 2866 4.722700 ACATGTCGGCTGCCCCAC 62.723 66.667 14.12 10.72 0.00 4.61
2649 2867 4.408821 GACATGTCGGCTGCCCCA 62.409 66.667 14.12 10.67 0.00 4.96
2650 2868 4.408821 TGACATGTCGGCTGCCCC 62.409 66.667 20.54 4.46 0.00 5.80
2651 2869 2.821366 CTGACATGTCGGCTGCCC 60.821 66.667 21.34 0.00 0.00 5.36
2652 2870 2.046892 ACTGACATGTCGGCTGCC 60.047 61.111 30.48 9.11 39.55 4.85
2653 2871 2.393768 CCACTGACATGTCGGCTGC 61.394 63.158 30.48 3.79 39.55 5.25
2654 2872 1.742880 CCCACTGACATGTCGGCTG 60.743 63.158 30.48 25.00 39.55 4.85
2655 2873 1.913262 TCCCACTGACATGTCGGCT 60.913 57.895 30.48 16.96 39.55 5.52
2656 2874 1.741770 GTCCCACTGACATGTCGGC 60.742 63.158 30.48 13.08 43.85 5.54
2657 2875 4.598257 GTCCCACTGACATGTCGG 57.402 61.111 29.25 29.25 43.85 4.79
2705 2923 9.796120 ATTACTCGATTCTGAGTTCTAAAGAAG 57.204 33.333 13.63 0.00 46.85 2.85
2723 2941 0.750850 GCCACCCAGCTATTACTCGA 59.249 55.000 0.00 0.00 0.00 4.04
2729 2947 2.182516 ACTCTAGCCACCCAGCTATT 57.817 50.000 0.00 0.00 44.14 1.73
2740 2958 3.874392 TTACCACCGTAAACTCTAGCC 57.126 47.619 0.00 0.00 31.40 3.93
2833 3060 2.356844 GGACCCCTCCCTTTATGTTGTC 60.357 54.545 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.