Multiple sequence alignment - TraesCS3D01G306000

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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 TraesCS3D01G306000 chr3D 100.000 3379 0 0 1 3379 419882717 419879339 0.000000e+00 6240
1 TraesCS3D01G306000 chr3B 93.625 3451 110 39 1 3379 547060304 547056892 0.000000e+00 5053
2 TraesCS3D01G306000 chr3A 92.733 3440 142 39 1 3379 531446129 531449521 0.000000e+00 4868
3 TraesCS3D01G306000 chr1D 75.727 1203 211 57 1106 2242 422289979 422291166 2.310000e-146 529
4 TraesCS3D01G306000 chr1A 81.132 318 41 15 1106 1406 518046278 518046593 1.570000e-58 237
5 TraesCS3D01G306000 chr1B 77.440 461 59 33 1106 1524 571164574 571165031 2.030000e-57 233


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 TraesCS3D01G306000 chr3D 419879339 419882717 3378 True 6240 6240 100.000 1 3379 1 chr3D.!!$R1 3378
1 TraesCS3D01G306000 chr3B 547056892 547060304 3412 True 5053 5053 93.625 1 3379 1 chr3B.!!$R1 3378
2 TraesCS3D01G306000 chr3A 531446129 531449521 3392 False 4868 4868 92.733 1 3379 1 chr3A.!!$F1 3378
3 TraesCS3D01G306000 chr1D 422289979 422291166 1187 False 529 529 75.727 1106 2242 1 chr1D.!!$F1 1136

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
88 97 0.538977 TCCATCGATCTCCCCGTACC 60.539 60.000 0.00 0.00 0.00 3.34 F
446 474 1.283181 GGTCGATCTGATCCGTCCG 59.717 63.158 11.84 0.98 0.00 4.79 F
754 859 2.938798 GGGTGGTGGGGTGATCCA 60.939 66.667 0.00 0.00 37.22 3.41 F
1767 1966 2.145397 TCCCTGAGTCGCTTCATACT 57.855 50.000 0.00 0.00 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1856 0.392998 GCATCAGGGGACGACATTGT 60.393 55.000 0.0 0.0 0.00 2.71 R
1767 1966 0.850784 GGAGCTTAAGGCCCCCATTA 59.149 55.000 0.0 0.0 43.05 1.90 R
2323 2522 2.322355 ATGCTACAGGACATCAGCAC 57.678 50.000 0.0 0.0 46.02 4.40 R
2930 3131 1.432807 ACCCTGATCACCCAAACCATT 59.567 47.619 0.0 0.0 0.00 3.16 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
88 97 0.538977 TCCATCGATCTCCCCGTACC 60.539 60.000 0.00 0.00 0.00 3.34
295 323 2.300152 TCGAGCTGTTTCCTCTGACAAT 59.700 45.455 0.00 0.00 0.00 2.71
296 324 2.414481 CGAGCTGTTTCCTCTGACAATG 59.586 50.000 0.00 0.00 0.00 2.82
333 361 7.398746 TCGCTTTGTTTAATCGTCATTATCAG 58.601 34.615 0.00 0.00 0.00 2.90
342 370 1.802508 CGTCATTATCAGCGCAGGTCA 60.803 52.381 11.47 0.00 33.74 4.02
446 474 1.283181 GGTCGATCTGATCCGTCCG 59.717 63.158 11.84 0.98 0.00 4.79
664 749 3.149981 TGAGCCACCGTCTATCTATCTG 58.850 50.000 0.00 0.00 0.00 2.90
685 770 4.057428 GGTCAGTCAGGCGTCGCT 62.057 66.667 18.11 0.00 0.00 4.93
688 773 4.803426 CAGTCAGGCGTCGCTCCC 62.803 72.222 18.11 0.00 0.00 4.30
692 777 4.821589 CAGGCGTCGCTCCCCTTC 62.822 72.222 18.11 0.00 0.00 3.46
754 859 2.938798 GGGTGGTGGGGTGATCCA 60.939 66.667 0.00 0.00 37.22 3.41
1767 1966 2.145397 TCCCTGAGTCGCTTCATACT 57.855 50.000 0.00 0.00 0.00 2.12
2249 2448 3.229276 CTCGTTCTGAGCTTCACAGAT 57.771 47.619 4.58 0.00 42.68 2.90
2309 2508 5.503662 TTATTGCACATCATTACTGCCAG 57.496 39.130 0.00 0.00 0.00 4.85
2323 2522 8.363390 TCATTACTGCCAGACTATTTAGATCAG 58.637 37.037 0.00 0.00 0.00 2.90
2324 2523 7.661536 TTACTGCCAGACTATTTAGATCAGT 57.338 36.000 0.00 0.00 36.41 3.41
2533 2734 8.704849 TCAATAATAAAGGATTGGGGTGTATG 57.295 34.615 0.00 0.00 34.45 2.39
2535 2736 8.923270 CAATAATAAAGGATTGGGGTGTATGTT 58.077 33.333 0.00 0.00 30.80 2.71
2541 2742 4.079212 AGGATTGGGGTGTATGTTAGCAAT 60.079 41.667 0.00 0.00 0.00 3.56
2868 3069 5.709631 TGCTTTATGGTGAGCATAACTTGAA 59.290 36.000 15.83 1.65 43.46 2.69
2929 3130 2.357517 GGGCACAGGTCACAGACG 60.358 66.667 0.00 0.00 32.65 4.18
2930 3131 2.734591 GGCACAGGTCACAGACGA 59.265 61.111 0.00 0.00 32.65 4.20
2963 3164 1.606313 CAGGGTTTCCGGGTGCATT 60.606 57.895 0.00 0.00 38.33 3.56
2995 3196 7.063662 TGCATACGTATTTTGGTTAGTGTACTG 59.936 37.037 5.03 0.00 0.00 2.74
3125 3326 7.251704 AGGCACAATATATGAGTTCTTTTCG 57.748 36.000 0.00 0.00 0.00 3.46
3154 3355 4.022329 CAGGGTTGTTGAATTGGTCTTACC 60.022 45.833 0.00 0.00 39.22 2.85
3166 3367 2.829720 TGGTCTTACCACAGCTATTCGT 59.170 45.455 0.00 0.00 44.79 3.85
3304 3507 8.516234 GTCGTGTTATGATTAGATAGGACAGAT 58.484 37.037 0.00 0.00 0.00 2.90
3319 3522 1.721389 ACAGATAATAATGCTCGCGCG 59.279 47.619 26.76 26.76 39.65 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.181510 GCTAATCAAGTGCGGTAGTTTGG 60.182 47.826 0.00 0.00 0.00 3.28
88 97 3.989698 CTAGCGTGGCTGGTCGGTG 62.990 68.421 0.00 0.00 40.10 4.94
247 275 2.427453 GGATCGAGGAGCTTACTGACAA 59.573 50.000 0.00 0.00 0.00 3.18
286 314 0.392193 AAGCGGAGGCATTGTCAGAG 60.392 55.000 0.00 0.00 43.41 3.35
295 323 2.731691 AAAGCGAAGAAGCGGAGGCA 62.732 55.000 0.00 0.00 43.41 4.75
296 324 2.035442 AAAGCGAAGAAGCGGAGGC 61.035 57.895 0.00 0.00 43.00 4.70
342 370 2.722201 GGAACGGGATCTCAGCGGT 61.722 63.158 0.00 0.00 0.00 5.68
348 376 0.969894 ATCGATGGGAACGGGATCTC 59.030 55.000 0.00 0.00 0.00 2.75
446 474 0.179108 CCGTCCGATCCTGGAGAAAC 60.179 60.000 1.52 0.00 39.14 2.78
652 728 5.300539 TGACTGACCTTGCAGATAGATAGAC 59.699 44.000 0.00 0.00 39.20 2.59
664 749 2.029844 GACGCCTGACTGACCTTGC 61.030 63.158 0.00 0.00 0.00 4.01
688 773 3.839432 GACTCGCTCGGGGGAAGG 61.839 72.222 2.75 0.00 34.03 3.46
689 774 3.839432 GGACTCGCTCGGGGGAAG 61.839 72.222 2.75 0.34 34.03 3.46
690 775 4.689549 TGGACTCGCTCGGGGGAA 62.690 66.667 2.75 0.00 34.03 3.97
691 776 4.689549 TTGGACTCGCTCGGGGGA 62.690 66.667 0.66 0.66 0.00 4.81
692 777 3.702048 TTTGGACTCGCTCGGGGG 61.702 66.667 0.00 0.00 0.00 5.40
693 778 2.434359 GTTTGGACTCGCTCGGGG 60.434 66.667 0.00 0.00 0.00 5.73
694 779 2.809601 CGTTTGGACTCGCTCGGG 60.810 66.667 0.00 0.00 0.00 5.14
754 859 2.561569 GCGGAGGTAATGCTAATGTGT 58.438 47.619 0.00 0.00 0.00 3.72
755 860 1.526887 CGCGGAGGTAATGCTAATGTG 59.473 52.381 0.00 0.00 0.00 3.21
756 861 1.411246 TCGCGGAGGTAATGCTAATGT 59.589 47.619 6.13 0.00 0.00 2.71
757 862 2.148916 TCGCGGAGGTAATGCTAATG 57.851 50.000 6.13 0.00 0.00 1.90
758 863 2.299013 TGATCGCGGAGGTAATGCTAAT 59.701 45.455 6.13 0.00 0.00 1.73
759 864 1.684450 TGATCGCGGAGGTAATGCTAA 59.316 47.619 6.13 0.00 0.00 3.09
760 865 1.269723 CTGATCGCGGAGGTAATGCTA 59.730 52.381 6.13 0.00 0.00 3.49
761 866 0.032678 CTGATCGCGGAGGTAATGCT 59.967 55.000 6.13 0.00 0.00 3.79
762 867 1.560860 GCTGATCGCGGAGGTAATGC 61.561 60.000 6.13 0.00 0.00 3.56
1029 1138 4.918201 CGCCCTTCCTCCATCCGC 62.918 72.222 0.00 0.00 0.00 5.54
1030 1139 4.918201 GCGCCCTTCCTCCATCCG 62.918 72.222 0.00 0.00 0.00 4.18
1031 1140 4.918201 CGCGCCCTTCCTCCATCC 62.918 72.222 0.00 0.00 0.00 3.51
1664 1851 1.602323 GGGGACGACATTGTTGGCA 60.602 57.895 12.03 0.00 0.00 4.92
1669 1856 0.392998 GCATCAGGGGACGACATTGT 60.393 55.000 0.00 0.00 0.00 2.71
1767 1966 0.850784 GGAGCTTAAGGCCCCCATTA 59.149 55.000 0.00 0.00 43.05 1.90
2309 2508 6.644592 GGACATCAGCACTGATCTAAATAGTC 59.355 42.308 10.19 11.84 46.57 2.59
2323 2522 2.322355 ATGCTACAGGACATCAGCAC 57.678 50.000 0.00 0.00 46.02 4.40
2556 2757 4.623167 CGAACGAGAAGAATGTCAATGAGT 59.377 41.667 0.00 0.00 0.00 3.41
2566 2767 4.506886 AACTCTCACGAACGAGAAGAAT 57.493 40.909 0.14 0.00 41.43 2.40
2868 3069 8.635765 TGATTAAGGAGAACAAACTAAGCATT 57.364 30.769 0.00 0.00 0.00 3.56
2929 3130 2.102578 CCCTGATCACCCAAACCATTC 58.897 52.381 0.00 0.00 0.00 2.67
2930 3131 1.432807 ACCCTGATCACCCAAACCATT 59.567 47.619 0.00 0.00 0.00 3.16
2963 3164 8.136165 ACTAACCAAAATACGTATGCAAAACAA 58.864 29.630 9.24 0.00 0.00 2.83
3125 3326 3.005791 CCAATTCAACAACCCTGGACTTC 59.994 47.826 0.00 0.00 0.00 3.01
3154 3355 6.408858 AAAACAGACATACGAATAGCTGTG 57.591 37.500 0.00 0.00 36.77 3.66
3166 3367 8.974060 AACAGAAAGGAACTAAAACAGACATA 57.026 30.769 0.00 0.00 38.49 2.29
3319 3522 3.056035 AGTCCCGTAAAGATGACAAGACC 60.056 47.826 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.