Multiple sequence alignment - TraesCS5A01G081700

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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 TraesCS5A01G081700 chr5A 100.000 3089 0 0 1 3089 105690273 105687185 0.000000e+00 5705
1 TraesCS5A01G081700 chr5D 95.270 2685 59 22 299 2949 97831839 97834489 0.000000e+00 4193
2 TraesCS5A01G081700 chr5D 95.846 337 9 3 1 335 97831395 97831728 9.750000e-150 540
3 TraesCS5A01G081700 chr5D 98.701 77 1 0 3011 3087 97834491 97834567 1.490000e-28 137
4 TraesCS5A01G081700 chr5B 96.704 2427 55 10 1 2404 107195900 107198324 0.000000e+00 4015
5 TraesCS5A01G081700 chr5B 96.209 554 15 3 2396 2949 107198508 107199055 0.000000e+00 902
6 TraesCS5A01G081700 chr5B 98.701 77 1 0 3011 3087 107199057 107199133 1.490000e-28 137


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 TraesCS5A01G081700 chr5A 105687185 105690273 3088 True 5705.000000 5705 100.000000 1 3089 1 chr5A.!!$R1 3088
1 TraesCS5A01G081700 chr5D 97831395 97834567 3172 False 1623.333333 4193 96.605667 1 3087 3 chr5D.!!$F1 3086
2 TraesCS5A01G081700 chr5B 107195900 107199133 3233 False 1684.666667 4015 97.204667 1 3087 3 chr5B.!!$F1 3086

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
716 870 0.110486 GTCTCCTGCTTCCAAACCCA 59.89 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2560 2944 1.374572 ACCATCGGAAACCCCCTAAA 58.625 50.0 0.0 0.0 0.0 1.85 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
63 64 3.071479 GGCAAACAGACCTAAATCGACA 58.929 45.455 0.00 0.00 0.00 4.35
101 102 2.672651 CATGTTCCCAGCGGCACA 60.673 61.111 1.45 0.00 0.00 4.57
125 126 2.707849 CGGTGATCGGTCCGGTTCT 61.708 63.158 12.29 0.00 42.61 3.01
265 269 4.009675 GCAACCATGGATAACAGAACAGA 58.990 43.478 21.47 0.00 0.00 3.41
266 270 4.095483 GCAACCATGGATAACAGAACAGAG 59.905 45.833 21.47 0.00 0.00 3.35
267 271 4.494091 ACCATGGATAACAGAACAGAGG 57.506 45.455 21.47 0.00 0.00 3.69
612 766 3.673597 TCTCCACCTCCCCTCGCT 61.674 66.667 0.00 0.00 0.00 4.93
613 767 2.685380 CTCCACCTCCCCTCGCTT 60.685 66.667 0.00 0.00 0.00 4.68
614 768 2.683933 TCCACCTCCCCTCGCTTC 60.684 66.667 0.00 0.00 0.00 3.86
655 809 2.035783 GAGAGCCCCACCCAAACC 59.964 66.667 0.00 0.00 0.00 3.27
716 870 0.110486 GTCTCCTGCTTCCAAACCCA 59.890 55.000 0.00 0.00 0.00 4.51
1062 1254 4.493747 GACGAGTTCGGGAGGGCG 62.494 72.222 6.48 0.00 44.95 6.13
1467 1659 0.549950 CTGGGATGAGGCATGTTCCT 59.450 55.000 0.00 0.00 39.67 3.36
1667 1859 1.134670 AGCGGTTTCTGAGGATAGTGC 60.135 52.381 0.00 0.00 0.00 4.40
1692 1884 3.270877 CAAAGGGAAGGAGATACAACCG 58.729 50.000 0.00 0.00 0.00 4.44
2271 2463 4.333926 GGCTATCAGTTCCTTACTTGCTTG 59.666 45.833 0.00 0.00 33.85 4.01
2353 2545 2.448153 AATGCAGCGCACGTCTGTTG 62.448 55.000 11.47 0.00 43.04 3.33
2370 2562 4.080807 TCTGTTGTGGTTACCTGAAAGTCA 60.081 41.667 2.07 0.00 0.00 3.41
2429 2813 5.073311 AGACTTTGCACTACATGTCGTAT 57.927 39.130 0.00 0.00 37.27 3.06
2560 2944 2.603075 TTTTGAGCAATAGCCAGGGT 57.397 45.000 0.00 0.00 43.56 4.34
2561 2945 2.603075 TTTGAGCAATAGCCAGGGTT 57.397 45.000 0.00 0.00 43.56 4.11
2564 2948 3.281727 TGAGCAATAGCCAGGGTTTAG 57.718 47.619 0.00 0.00 43.56 1.85
2565 2949 2.092429 TGAGCAATAGCCAGGGTTTAGG 60.092 50.000 0.00 0.00 43.56 2.69
2625 3009 3.882888 TCTGTTGTTGGGTTTCTGATGAC 59.117 43.478 0.00 0.00 0.00 3.06
2636 3020 5.880332 GGGTTTCTGATGACAGTAAGCATAA 59.120 40.000 15.95 0.00 46.18 1.90
2698 3082 7.660208 CAGGTACAGTAGTATTTTGACCAACTT 59.340 37.037 0.00 0.00 31.84 2.66
2828 3212 0.898320 ACTAGGCATGCGTCTTGAGT 59.102 50.000 17.50 11.77 0.00 3.41
2949 3333 9.310449 TGAAGATTAGTGACTAAGTTCCTACTT 57.690 33.333 19.48 12.09 46.18 2.24
2976 3360 9.661954 TTCTTATCTCTGTATGATTCCTTACCT 57.338 33.333 0.00 0.00 0.00 3.08
2994 3378 7.559590 CTTACCTAAAGGATCAAACTCATGG 57.440 40.000 2.23 0.00 38.94 3.66
2995 3379 5.520748 ACCTAAAGGATCAAACTCATGGT 57.479 39.130 2.23 0.00 38.94 3.55
2996 3380 5.892348 ACCTAAAGGATCAAACTCATGGTT 58.108 37.500 2.23 0.00 38.02 3.67
2997 3381 7.027874 ACCTAAAGGATCAAACTCATGGTTA 57.972 36.000 2.23 0.00 36.45 2.85
2998 3382 7.643123 ACCTAAAGGATCAAACTCATGGTTAT 58.357 34.615 2.23 0.00 36.45 1.89
2999 3383 7.557719 ACCTAAAGGATCAAACTCATGGTTATG 59.442 37.037 2.23 0.00 36.45 1.90
3000 3384 5.841957 AAGGATCAAACTCATGGTTATGC 57.158 39.130 0.00 0.00 37.12 3.14
3001 3385 4.858850 AGGATCAAACTCATGGTTATGCA 58.141 39.130 0.00 0.00 37.12 3.96
3002 3386 5.263599 AGGATCAAACTCATGGTTATGCAA 58.736 37.500 0.00 0.00 37.12 4.08
3003 3387 5.126061 AGGATCAAACTCATGGTTATGCAAC 59.874 40.000 0.00 0.00 37.12 4.17
3004 3388 5.126061 GGATCAAACTCATGGTTATGCAACT 59.874 40.000 0.00 0.00 37.12 3.16
3005 3389 5.627499 TCAAACTCATGGTTATGCAACTC 57.373 39.130 0.00 0.00 37.12 3.01
3006 3390 5.069318 TCAAACTCATGGTTATGCAACTCA 58.931 37.500 0.00 0.00 37.12 3.41
3007 3391 5.534278 TCAAACTCATGGTTATGCAACTCAA 59.466 36.000 0.00 0.00 37.12 3.02
3008 3392 6.040278 TCAAACTCATGGTTATGCAACTCAAA 59.960 34.615 0.00 0.00 37.12 2.69
3009 3393 6.594788 AACTCATGGTTATGCAACTCAAAT 57.405 33.333 0.00 0.00 36.23 2.32
3049 3433 3.330126 TGAGGGAGGGAGGTACTATTG 57.670 52.381 0.00 0.00 41.55 1.90
3087 3471 6.676950 TCCTTTATGTTGCTTGTTACATGTG 58.323 36.000 9.11 0.00 36.46 3.21
3088 3472 6.264292 TCCTTTATGTTGCTTGTTACATGTGT 59.736 34.615 9.11 0.00 36.46 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 5.939883 CCATAACAGGATGAACTGAACAGAA 59.060 40.000 8.87 0.00 40.97 3.02
455 609 0.953960 GTTGGTTTCGCCTCGTGGAT 60.954 55.000 7.92 0.00 38.35 3.41
716 870 3.793888 GGAAATCGGGAGCGGGGT 61.794 66.667 0.00 0.00 0.00 4.95
725 890 2.193536 GGATTGGGCGGGAAATCGG 61.194 63.158 0.00 0.00 34.28 4.18
1311 1503 3.573772 CTTGACGACGCCTGAGCCA 62.574 63.158 0.00 0.00 34.57 4.75
1667 1859 2.239654 TGTATCTCCTTCCCTTTGGCTG 59.760 50.000 0.00 0.00 0.00 4.85
1692 1884 1.387539 GATTTCTCTTGCTCCCAGCC 58.612 55.000 0.00 0.00 41.51 4.85
2204 2396 7.874940 TGAAACATTTCAACATACCTCAAGAG 58.125 34.615 4.56 0.00 43.62 2.85
2353 2545 4.067972 TGTCTGACTTTCAGGTAACCAC 57.932 45.455 9.51 0.00 44.39 4.16
2370 2562 4.426704 ACTACAGTTGGGTATCCTTGTCT 58.573 43.478 0.00 0.00 0.00 3.41
2429 2813 6.697641 ACTCCCAATCTAAAGTTTCTACCA 57.302 37.500 0.00 0.00 0.00 3.25
2560 2944 1.374572 ACCATCGGAAACCCCCTAAA 58.625 50.000 0.00 0.00 0.00 1.85
2561 2945 2.121129 CTACCATCGGAAACCCCCTAA 58.879 52.381 0.00 0.00 0.00 2.69
2564 2948 1.499368 TACTACCATCGGAAACCCCC 58.501 55.000 0.00 0.00 0.00 5.40
2565 2949 2.744166 GCTTACTACCATCGGAAACCCC 60.744 54.545 0.00 0.00 0.00 4.95
2625 3009 8.584157 AGAGAGTAATCAGGATTATGCTTACTG 58.416 37.037 7.48 0.00 40.42 2.74
2636 3020 4.163078 CCCACAACAGAGAGTAATCAGGAT 59.837 45.833 0.00 0.00 0.00 3.24
2771 3155 3.282021 ACTCACACAACTTTCATGCAGT 58.718 40.909 0.00 0.00 0.00 4.40
2862 3246 6.369615 GTGCCATTGATAAAAGAACAAAGCAT 59.630 34.615 0.00 0.00 38.28 3.79
2869 3253 7.865385 TGTTTACTGTGCCATTGATAAAAGAAC 59.135 33.333 0.00 0.00 0.00 3.01
2950 3334 9.661954 AGGTAAGGAATCATACAGAGATAAGAA 57.338 33.333 0.00 0.00 0.00 2.52
2970 3354 7.112779 ACCATGAGTTTGATCCTTTAGGTAAG 58.887 38.462 0.00 0.00 36.34 2.34
2971 3355 7.027874 ACCATGAGTTTGATCCTTTAGGTAA 57.972 36.000 0.00 0.00 36.34 2.85
2972 3356 6.636454 ACCATGAGTTTGATCCTTTAGGTA 57.364 37.500 0.00 0.00 36.34 3.08
2973 3357 5.520748 ACCATGAGTTTGATCCTTTAGGT 57.479 39.130 0.00 0.00 36.34 3.08
2974 3358 7.469181 GCATAACCATGAGTTTGATCCTTTAGG 60.469 40.741 0.00 0.00 40.05 2.69
2975 3359 7.067372 TGCATAACCATGAGTTTGATCCTTTAG 59.933 37.037 0.00 0.00 40.05 1.85
2976 3360 6.889177 TGCATAACCATGAGTTTGATCCTTTA 59.111 34.615 0.00 0.00 40.05 1.85
2977 3361 5.716228 TGCATAACCATGAGTTTGATCCTTT 59.284 36.000 0.00 0.00 40.05 3.11
2978 3362 5.263599 TGCATAACCATGAGTTTGATCCTT 58.736 37.500 0.00 0.00 40.05 3.36
2979 3363 4.858850 TGCATAACCATGAGTTTGATCCT 58.141 39.130 0.00 0.00 40.05 3.24
2980 3364 5.126061 AGTTGCATAACCATGAGTTTGATCC 59.874 40.000 0.00 0.00 40.05 3.36
2981 3365 6.127925 TGAGTTGCATAACCATGAGTTTGATC 60.128 38.462 0.00 0.00 40.05 2.92
2982 3366 5.711506 TGAGTTGCATAACCATGAGTTTGAT 59.288 36.000 0.00 0.00 40.05 2.57
2983 3367 5.069318 TGAGTTGCATAACCATGAGTTTGA 58.931 37.500 0.00 0.00 40.05 2.69
2984 3368 5.375417 TGAGTTGCATAACCATGAGTTTG 57.625 39.130 0.00 0.65 40.05 2.93
2985 3369 6.403866 TTTGAGTTGCATAACCATGAGTTT 57.596 33.333 0.00 0.00 40.05 2.66
2986 3370 6.209192 TCATTTGAGTTGCATAACCATGAGTT 59.791 34.615 0.00 0.00 42.83 3.01
2987 3371 5.711506 TCATTTGAGTTGCATAACCATGAGT 59.288 36.000 0.00 0.00 37.52 3.41
2988 3372 6.032094 GTCATTTGAGTTGCATAACCATGAG 58.968 40.000 0.00 0.00 37.52 2.90
2989 3373 5.476254 TGTCATTTGAGTTGCATAACCATGA 59.524 36.000 0.00 0.00 37.52 3.07
2990 3374 5.712004 TGTCATTTGAGTTGCATAACCATG 58.288 37.500 0.00 0.00 37.52 3.66
2991 3375 5.477984 ACTGTCATTTGAGTTGCATAACCAT 59.522 36.000 0.00 0.00 37.52 3.55
2992 3376 4.826733 ACTGTCATTTGAGTTGCATAACCA 59.173 37.500 0.00 0.00 37.52 3.67
2993 3377 5.376854 ACTGTCATTTGAGTTGCATAACC 57.623 39.130 0.00 0.00 37.52 2.85
2994 3378 7.189512 GGATACTGTCATTTGAGTTGCATAAC 58.810 38.462 0.00 0.00 37.06 1.89
2995 3379 7.320443 GGATACTGTCATTTGAGTTGCATAA 57.680 36.000 0.00 0.00 0.00 1.90
2996 3380 6.925610 GGATACTGTCATTTGAGTTGCATA 57.074 37.500 0.00 0.00 0.00 3.14
2997 3381 5.824904 GGATACTGTCATTTGAGTTGCAT 57.175 39.130 0.00 0.00 0.00 3.96
3049 3433 6.749923 ACATAAAGGAGAAATTCTGCTGTC 57.250 37.500 17.57 0.00 44.73 3.51


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

AutoCloner maintained by Alex Coulton.