Multiple sequence alignment - TraesCS2B01G470600

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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 TraesCS2B01G470600 chr2B 100.000 2942 0 0 1 2942 666934330 666937271 0 5433
1 TraesCS2B01G470600 chr2A 96.263 2970 66 23 1 2942 699129049 699132001 0 4828
2 TraesCS2B01G470600 chr2D 97.286 2211 46 8 1 2198 558481272 558483481 0 3738
3 TraesCS2B01G470600 chr2D 92.954 809 30 9 2151 2942 558483464 558484262 0 1153


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 TraesCS2B01G470600 chr2B 666934330 666937271 2941 False 5433.0 5433 100.000 1 2942 1 chr2B.!!$F1 2941
1 TraesCS2B01G470600 chr2A 699129049 699132001 2952 False 4828.0 4828 96.263 1 2942 1 chr2A.!!$F1 2941
2 TraesCS2B01G470600 chr2D 558481272 558484262 2990 False 2445.5 3738 95.120 1 2942 2 chr2D.!!$F1 2941

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
658 675 0.257616 CCGTCCTCTCTTCTCCTCCT 59.742 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2082 2.721425 TTGTTTCCTTGGGTCGTTCT 57.279 45.0 0.0 0.0 0.0 3.01 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
22 23 5.574815 GTTCCAACCACATTCGAAAAATG 57.425 39.130 0.00 0.00 0.00 2.32
46 52 8.942338 TGTAGCATATACAAAGACTACAAAGG 57.058 34.615 0.00 0.00 37.60 3.11
74 80 2.168936 TGAACCACCAAACTCGTGTAGT 59.831 45.455 0.00 0.00 41.49 2.73
213 219 5.075493 TCTACCCTAAGTCGTATCAATCCC 58.925 45.833 0.00 0.00 0.00 3.85
316 322 0.393402 ACTGTCGCCATGCATCACAT 60.393 50.000 0.00 0.00 40.66 3.21
382 388 2.124942 TGTCACCAGCGCACACAA 60.125 55.556 11.47 0.00 0.00 3.33
401 407 0.673437 AAACACCCATGAAACTGCCG 59.327 50.000 0.00 0.00 0.00 5.69
517 523 2.305927 TGTTCTCCCATCCAAACTCTCC 59.694 50.000 0.00 0.00 0.00 3.71
658 675 0.257616 CCGTCCTCTCTTCTCCTCCT 59.742 60.000 0.00 0.00 0.00 3.69
918 935 8.566260 CACTCTGTTTCAATCTGATTTTTCTCT 58.434 33.333 0.00 0.00 0.00 3.10
2058 2082 0.105964 AGGTTAGAGCACGCACACAA 59.894 50.000 0.00 0.00 0.00 3.33
2065 2089 1.367665 GCACGCACACAAGAACGAC 60.368 57.895 0.00 0.00 0.00 4.34
2162 2186 4.389374 TCATGTTGTCCTCCTTGTTCTTC 58.611 43.478 0.00 0.00 0.00 2.87
2179 2242 9.108284 CTTGTTCTTCTTCTTCTTCTTCTTCTT 57.892 33.333 0.00 0.00 0.00 2.52
2180 2243 8.655651 TGTTCTTCTTCTTCTTCTTCTTCTTC 57.344 34.615 0.00 0.00 0.00 2.87
2184 2247 9.898152 TCTTCTTCTTCTTCTTCTTCTTCTTTT 57.102 29.630 0.00 0.00 0.00 2.27
2289 2352 4.138487 AGTATCCCTCAATTTGTCCGAC 57.862 45.455 0.00 0.00 0.00 4.79
2317 2380 3.388024 GCATGGGTCTAGTCATCTTGGTA 59.612 47.826 0.00 0.00 0.00 3.25
2326 2389 3.614092 AGTCATCTTGGTATTGCTGGTG 58.386 45.455 0.00 0.00 0.00 4.17
2331 2394 3.146066 TCTTGGTATTGCTGGTGTGTTC 58.854 45.455 0.00 0.00 0.00 3.18
2351 2414 5.995282 TGTTCTTTATGTGGACGACAGATTT 59.005 36.000 0.00 0.00 38.23 2.17
2370 2433 3.924114 TTGATTCCAGCCGATAAGGAA 57.076 42.857 0.00 0.00 44.77 3.36
2453 2516 7.936950 ATTAGATAGATCGATGTGTTGTGTG 57.063 36.000 0.54 0.00 0.00 3.82
2454 2517 4.115516 AGATAGATCGATGTGTTGTGTGC 58.884 43.478 0.54 0.00 0.00 4.57
2511 2574 4.345257 AGGTGTTAGATGCCCTATGTGTAG 59.655 45.833 0.00 0.00 0.00 2.74
2586 2649 9.985318 GCTTTGAGCTAACATAATCATATCATC 57.015 33.333 0.00 0.00 38.45 2.92
2628 2698 4.509970 TGTGAGTTTATGTTGGAGTTGTCG 59.490 41.667 0.00 0.00 0.00 4.35
2645 2715 3.355378 TGTCGAATTGGGAATTGCATCT 58.645 40.909 0.00 0.00 0.00 2.90
2664 2734 6.262944 TGCATCTCAATTCACTTGTTACAGTT 59.737 34.615 0.00 0.00 36.20 3.16
2670 2740 8.050778 TCAATTCACTTGTTACAGTTCTTTGT 57.949 30.769 0.00 0.00 36.20 2.83
2751 2828 3.373439 GCATCCTCACAGAAACAAGCTAG 59.627 47.826 0.00 0.00 0.00 3.42
2752 2829 3.045601 TCCTCACAGAAACAAGCTAGC 57.954 47.619 6.62 6.62 0.00 3.42
2783 2864 1.376553 GGAACCCTCAGCTGTCTGC 60.377 63.158 14.67 0.00 40.13 4.26
2789 2870 0.829333 CCTCAGCTGTCTGCCTATGT 59.171 55.000 14.67 0.00 44.23 2.29
2790 2871 1.209019 CCTCAGCTGTCTGCCTATGTT 59.791 52.381 14.67 0.00 44.23 2.71
2791 2872 2.355513 CCTCAGCTGTCTGCCTATGTTT 60.356 50.000 14.67 0.00 44.23 2.83
2792 2873 3.341823 CTCAGCTGTCTGCCTATGTTTT 58.658 45.455 14.67 0.00 44.23 2.43
2793 2874 3.338249 TCAGCTGTCTGCCTATGTTTTC 58.662 45.455 14.67 0.00 44.23 2.29
2794 2875 3.008375 TCAGCTGTCTGCCTATGTTTTCT 59.992 43.478 14.67 0.00 44.23 2.52
2795 2876 3.755378 CAGCTGTCTGCCTATGTTTTCTT 59.245 43.478 5.25 0.00 44.23 2.52
2834 2915 1.544246 CGTTTCCCCCAATGTTCTTCC 59.456 52.381 0.00 0.00 0.00 3.46
2835 2916 2.817839 CGTTTCCCCCAATGTTCTTCCT 60.818 50.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.943909 ACCTTTGTAGTCTTTGTATATGCTAC 57.056 34.615 0.00 0.00 0.00 3.58
44 50 2.621526 GTTTGGTGGTTCAAATCGACCT 59.378 45.455 0.00 0.00 38.64 3.85
45 51 2.621526 AGTTTGGTGGTTCAAATCGACC 59.378 45.455 0.00 0.00 38.64 4.79
46 52 3.606153 CGAGTTTGGTGGTTCAAATCGAC 60.606 47.826 0.00 0.00 38.42 4.20
88 94 1.375908 GCCCTCATCGAGTGCACAA 60.376 57.895 21.04 4.16 33.44 3.33
382 388 0.673437 CGGCAGTTTCATGGGTGTTT 59.327 50.000 0.00 0.00 0.00 2.83
401 407 2.048603 GTGAAGGTGAGGCCCATGC 61.049 63.158 0.00 0.00 38.26 4.06
517 523 5.903198 AAAATAATGGGAGGAGAGAGAGG 57.097 43.478 0.00 0.00 0.00 3.69
1126 1143 2.103340 GTTGCCGTTGCCGTTGTT 59.897 55.556 0.00 0.00 36.33 2.83
1242 1259 3.338250 GCCACCATGTCCCCAGGA 61.338 66.667 0.00 0.00 0.00 3.86
2058 2082 2.721425 TTGTTTCCTTGGGTCGTTCT 57.279 45.000 0.00 0.00 0.00 3.01
2065 2089 4.770795 AGACGATAGATTGTTTCCTTGGG 58.229 43.478 0.00 0.00 41.38 4.12
2179 2242 9.067986 GGAGAGACAAGAAAAGGAAATAAAAGA 57.932 33.333 0.00 0.00 0.00 2.52
2180 2243 9.072375 AGGAGAGACAAGAAAAGGAAATAAAAG 57.928 33.333 0.00 0.00 0.00 2.27
2184 2247 7.316393 TCAGGAGAGACAAGAAAAGGAAATA 57.684 36.000 0.00 0.00 0.00 1.40
2185 2248 6.192970 TCAGGAGAGACAAGAAAAGGAAAT 57.807 37.500 0.00 0.00 0.00 2.17
2186 2249 5.630415 TCAGGAGAGACAAGAAAAGGAAA 57.370 39.130 0.00 0.00 0.00 3.13
2187 2250 5.368989 GTTCAGGAGAGACAAGAAAAGGAA 58.631 41.667 0.00 0.00 0.00 3.36
2188 2251 4.202367 GGTTCAGGAGAGACAAGAAAAGGA 60.202 45.833 0.00 0.00 0.00 3.36
2189 2252 4.068599 GGTTCAGGAGAGACAAGAAAAGG 58.931 47.826 0.00 0.00 0.00 3.11
2269 2332 3.203716 GGTCGGACAAATTGAGGGATAC 58.796 50.000 10.76 0.00 0.00 2.24
2317 2380 4.022068 CCACATAAAGAACACACCAGCAAT 60.022 41.667 0.00 0.00 0.00 3.56
2326 2389 4.304110 TCTGTCGTCCACATAAAGAACAC 58.696 43.478 0.00 0.00 33.23 3.32
2331 2394 6.668541 ATCAAATCTGTCGTCCACATAAAG 57.331 37.500 0.00 0.00 33.23 1.85
2351 2414 3.038280 TCTTCCTTATCGGCTGGAATCA 58.962 45.455 0.00 0.00 38.91 2.57
2370 2433 7.012044 ACGAACACTAACAGCACTAAATTTTCT 59.988 33.333 0.00 0.00 0.00 2.52
2451 2514 6.983474 AAATAATTACCCAAAAGCATGCAC 57.017 33.333 21.98 0.00 0.00 4.57
2452 2515 7.446625 ACAAAAATAATTACCCAAAAGCATGCA 59.553 29.630 21.98 0.00 0.00 3.96
2453 2516 7.750014 CACAAAAATAATTACCCAAAAGCATGC 59.250 33.333 10.51 10.51 0.00 4.06
2454 2517 8.782144 ACACAAAAATAATTACCCAAAAGCATG 58.218 29.630 0.00 0.00 0.00 4.06
2511 2574 8.630278 AATATACACACATCACTTCGTTAGAC 57.370 34.615 0.00 0.00 0.00 2.59
2543 2606 4.333649 TCAAAGCTGAACTGTTGTGAAGAG 59.666 41.667 0.00 0.00 0.00 2.85
2581 2644 7.721399 ACAACCAGAAAAGAACTAACTGATGAT 59.279 33.333 0.00 0.00 0.00 2.45
2582 2645 7.012327 CACAACCAGAAAAGAACTAACTGATGA 59.988 37.037 0.00 0.00 0.00 2.92
2583 2646 7.012327 TCACAACCAGAAAAGAACTAACTGATG 59.988 37.037 0.00 0.00 0.00 3.07
2584 2647 7.054124 TCACAACCAGAAAAGAACTAACTGAT 58.946 34.615 0.00 0.00 0.00 2.90
2585 2648 6.411376 TCACAACCAGAAAAGAACTAACTGA 58.589 36.000 0.00 0.00 0.00 3.41
2586 2649 6.316390 ACTCACAACCAGAAAAGAACTAACTG 59.684 38.462 0.00 0.00 0.00 3.16
2587 2650 6.415573 ACTCACAACCAGAAAAGAACTAACT 58.584 36.000 0.00 0.00 0.00 2.24
2588 2651 6.679327 ACTCACAACCAGAAAAGAACTAAC 57.321 37.500 0.00 0.00 0.00 2.34
2645 2715 8.050778 ACAAAGAACTGTAACAAGTGAATTGA 57.949 30.769 0.00 0.00 41.83 2.57
2653 2723 6.961554 GTGTGAGAACAAAGAACTGTAACAAG 59.038 38.462 0.00 0.00 0.00 3.16
2751 2828 1.003696 GGGTTCCCCATGAGCTATAGC 59.996 57.143 17.33 17.33 44.65 2.97
2790 2871 9.382275 ACGTTAAGTGGTAGTAAGAAAAAGAAA 57.618 29.630 0.00 0.00 0.00 2.52
2791 2872 8.947055 ACGTTAAGTGGTAGTAAGAAAAAGAA 57.053 30.769 0.00 0.00 0.00 2.52
2792 2873 8.947055 AACGTTAAGTGGTAGTAAGAAAAAGA 57.053 30.769 0.00 0.00 0.00 2.52
2793 2874 9.642312 GAAACGTTAAGTGGTAGTAAGAAAAAG 57.358 33.333 0.00 0.00 0.00 2.27
2794 2875 8.611757 GGAAACGTTAAGTGGTAGTAAGAAAAA 58.388 33.333 0.00 0.00 0.00 1.94
2795 2876 7.226523 GGGAAACGTTAAGTGGTAGTAAGAAAA 59.773 37.037 0.00 0.00 0.00 2.29
2812 2893 2.375014 AGAACATTGGGGGAAACGTT 57.625 45.000 0.00 0.00 0.00 3.99
2834 2915 9.667107 TTTACATTACTCAATAGGACAAGGAAG 57.333 33.333 0.00 0.00 0.00 3.46
2835 2916 9.667107 CTTTACATTACTCAATAGGACAAGGAA 57.333 33.333 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.