Multiple sequence alignment - TraesCS5A01G528900

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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 TraesCS5A01G528900 chr5A 100.000 2393 0 0 1 2393 688722327 688719935 0.000000e+00 4420.0
1 TraesCS5A01G528900 chr5A 95.560 473 16 1 1921 2393 26593695 26594162 0.000000e+00 752.0
2 TraesCS5A01G528900 chr5A 91.241 137 10 2 325 461 477546071 477545937 4.060000e-43 185.0
3 TraesCS5A01G528900 chr5A 90.909 121 7 1 10 126 477546315 477546195 2.460000e-35 159.0
4 TraesCS5A01G528900 chr6A 97.154 1230 34 1 1164 2393 494044142 494045370 0.000000e+00 2076.0
5 TraesCS5A01G528900 chr6A 98.090 1152 17 3 1 1151 494042895 494044042 0.000000e+00 2001.0
6 TraesCS5A01G528900 chr2A 97.157 1231 32 3 1164 2393 677911349 677912577 0.000000e+00 2076.0
7 TraesCS5A01G528900 chr2A 97.409 849 17 2 307 1151 677910402 677911249 0.000000e+00 1441.0
8 TraesCS5A01G528900 chr2A 86.260 262 32 4 1192 1451 32135550 32135291 5.040000e-72 281.0
9 TraesCS5A01G528900 chr2A 82.653 98 13 3 9 102 738003378 738003475 1.520000e-12 84.2
10 TraesCS5A01G528900 chr3A 97.133 1151 29 3 1 1151 301201597 301202743 0.000000e+00 1940.0
11 TraesCS5A01G528900 chr3A 96.575 730 23 2 1256 1984 301202884 301203612 0.000000e+00 1208.0
12 TraesCS5A01G528900 chr3A 97.330 412 11 0 1982 2393 301203999 301204410 0.000000e+00 701.0
13 TraesCS5A01G528900 chr3A 93.478 46 2 1 1164 1209 301202843 301202887 1.540000e-07 67.6
14 TraesCS5A01G528900 chr1D 97.561 287 7 0 175 461 242019723 242020009 2.140000e-135 492.0
15 TraesCS5A01G528900 chr1D 87.405 262 30 3 1192 1451 71308183 71307923 5.000000e-77 298.0
16 TraesCS5A01G528900 chr1D 97.647 170 4 0 563 732 242021212 242021381 2.330000e-75 292.0
17 TraesCS5A01G528900 chr1D 85.496 262 26 10 175 426 242019134 242019393 1.820000e-66 263.0
18 TraesCS5A01G528900 chr1D 85.496 262 25 7 177 426 19056529 19056789 6.560000e-66 261.0
19 TraesCS5A01G528900 chr1D 95.172 145 3 1 1 141 242018581 242018725 2.390000e-55 226.0
20 TraesCS5A01G528900 chr1D 76.042 192 35 9 731 917 124069850 124070035 3.280000e-14 89.8
21 TraesCS5A01G528900 chr3D 96.540 289 8 1 175 461 16456478 16456190 5.980000e-131 477.0
22 TraesCS5A01G528900 chr3D 95.582 249 10 1 484 731 16455038 16454790 4.790000e-107 398.0
23 TraesCS5A01G528900 chr3D 84.791 263 26 12 175 426 16457077 16456818 3.950000e-63 252.0
24 TraesCS5A01G528900 chr3D 88.660 194 4 2 1 176 16457630 16457437 1.110000e-53 220.0
25 TraesCS5A01G528900 chr3D 79.681 251 51 0 890 1140 1701421 1701171 5.250000e-42 182.0
26 TraesCS5A01G528900 chr2D 87.786 262 29 3 1192 1451 345275149 345274889 1.070000e-78 303.0
27 TraesCS5A01G528900 chr7D 86.121 281 34 5 1175 1451 58108443 58108722 5.000000e-77 298.0
28 TraesCS5A01G528900 chr7D 85.878 262 34 3 1192 1451 127417131 127416871 2.340000e-70 276.0
29 TraesCS5A01G528900 chr5D 87.405 262 30 3 1192 1451 42225125 42224865 5.000000e-77 298.0
30 TraesCS5A01G528900 chr1A 84.351 262 35 6 1192 1451 546526454 546526197 3.950000e-63 252.0
31 TraesCS5A01G528900 chr6B 79.259 270 54 1 871 1140 669532469 669532736 1.130000e-43 187.0
32 TraesCS5A01G528900 chr6B 85.437 103 12 3 165 265 689930757 689930656 1.170000e-18 104.0
33 TraesCS5A01G528900 chr5B 87.671 146 6 8 293 426 71799054 71799199 2.460000e-35 159.0
34 TraesCS5A01G528900 chr1B 87.591 137 12 3 9 141 512804246 512804381 1.150000e-33 154.0


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 TraesCS5A01G528900 chr5A 688719935 688722327 2392 True 4420.00 4420 100.00000 1 2393 1 chr5A.!!$R1 2392
1 TraesCS5A01G528900 chr6A 494042895 494045370 2475 False 2038.50 2076 97.62200 1 2393 2 chr6A.!!$F1 2392
2 TraesCS5A01G528900 chr2A 677910402 677912577 2175 False 1758.50 2076 97.28300 307 2393 2 chr2A.!!$F2 2086
3 TraesCS5A01G528900 chr3A 301201597 301204410 2813 False 979.15 1940 96.12900 1 2393 4 chr3A.!!$F1 2392
4 TraesCS5A01G528900 chr1D 242018581 242021381 2800 False 318.25 492 93.96900 1 732 4 chr1D.!!$F3 731
5 TraesCS5A01G528900 chr3D 16454790 16457630 2840 True 336.75 477 91.39325 1 731 4 chr3D.!!$R2 730

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
946 3070 0.103937 GATAGAGCACGGCAGAAGCT 59.896 55.0 8.05 8.05 42.17 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 4106 0.671781 AGACTGGTGAGTGCATTCGC 60.672 55.0 13.89 13.89 39.24 4.7 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
530 2649 0.106419 TGACGTTTTTGGGCTTCCCT 60.106 50.000 3.27 0.00 45.70 4.20
694 2813 4.760047 CTCGTTCGGGCTGGGGTG 62.760 72.222 0.00 0.00 0.00 4.61
728 2847 1.924524 CGTTCGGCAGTTATCGATGTT 59.075 47.619 8.54 0.00 35.25 2.71
848 2972 2.619697 TTTCCTGCCATCCCAAATGA 57.380 45.000 0.00 0.00 0.00 2.57
946 3070 0.103937 GATAGAGCACGGCAGAAGCT 59.896 55.000 8.05 8.05 42.17 3.74
952 3076 1.816537 CACGGCAGAAGCTAGGCTA 59.183 57.895 0.00 0.00 38.25 3.93
968 3092 5.187967 GCTAGGCTATAATATGTGGACCTGT 59.812 44.000 0.00 0.00 0.00 4.00
1120 3244 1.375013 GGCTGGACGCGAAGGTAAA 60.375 57.895 15.93 0.00 40.44 2.01
1123 3247 1.347320 CTGGACGCGAAGGTAAAGAC 58.653 55.000 15.93 0.00 0.00 3.01
1151 3275 3.304391 GCATTGTGTTCCTCGCAGTTAAA 60.304 43.478 0.00 0.00 37.85 1.52
1152 3276 4.615912 GCATTGTGTTCCTCGCAGTTAAAT 60.616 41.667 0.00 0.00 37.85 1.40
1153 3277 5.391523 GCATTGTGTTCCTCGCAGTTAAATA 60.392 40.000 0.00 0.00 37.85 1.40
1154 3278 6.607689 CATTGTGTTCCTCGCAGTTAAATAA 58.392 36.000 0.00 0.00 37.85 1.40
1156 3280 6.236017 TGTGTTCCTCGCAGTTAAATAAAG 57.764 37.500 0.00 0.00 32.41 1.85
1157 3281 5.180492 TGTGTTCCTCGCAGTTAAATAAAGG 59.820 40.000 0.00 0.00 32.41 3.11
1159 3283 5.410439 TGTTCCTCGCAGTTAAATAAAGGTC 59.590 40.000 0.00 0.00 0.00 3.85
1160 3284 5.416271 TCCTCGCAGTTAAATAAAGGTCT 57.584 39.130 0.00 0.00 0.00 3.85
1161 3285 5.175859 TCCTCGCAGTTAAATAAAGGTCTG 58.824 41.667 0.00 0.00 0.00 3.51
1163 3287 5.411669 CCTCGCAGTTAAATAAAGGTCTGTT 59.588 40.000 0.00 0.00 0.00 3.16
1164 3288 6.236017 TCGCAGTTAAATAAAGGTCTGTTG 57.764 37.500 0.00 0.00 0.00 3.33
1166 3290 5.048991 CGCAGTTAAATAAAGGTCTGTTGGT 60.049 40.000 0.00 0.00 0.00 3.67
1167 3291 6.149633 GCAGTTAAATAAAGGTCTGTTGGTG 58.850 40.000 0.00 0.00 0.00 4.17
1168 3292 6.149633 CAGTTAAATAAAGGTCTGTTGGTGC 58.850 40.000 0.00 0.00 0.00 5.01
1169 3293 6.016276 CAGTTAAATAAAGGTCTGTTGGTGCT 60.016 38.462 0.00 0.00 0.00 4.40
1170 3294 6.206829 AGTTAAATAAAGGTCTGTTGGTGCTC 59.793 38.462 0.00 0.00 0.00 4.26
1386 3598 1.153539 TTCATGGGAGGTTGGGTTCA 58.846 50.000 0.00 0.00 0.00 3.18
1505 3717 2.460757 ATTGTTCCAGCAATTGCACC 57.539 45.000 30.89 14.06 45.16 5.01
1507 3719 1.080569 GTTCCAGCAATTGCACCCG 60.081 57.895 30.89 16.03 45.16 5.28
1576 3788 1.807814 AGGACTGAAACCACCTGAGT 58.192 50.000 0.00 0.00 0.00 3.41
1622 3834 5.885449 ACAAATAGCAGAGATAAGCCTCT 57.115 39.130 0.00 0.00 43.84 3.69
1635 3847 2.073252 AGCCTCTGTATGATGACCGA 57.927 50.000 0.00 0.00 0.00 4.69
1712 3924 2.881266 GCACGAGCAAACGCACTCA 61.881 57.895 0.00 0.00 41.58 3.41
1728 3940 3.268330 CACTCACTTCTGCAGCATATGT 58.732 45.455 9.47 0.00 0.00 2.29
1777 3989 2.202492 CGCGACGAGGAGGTCTTG 60.202 66.667 0.00 0.00 34.75 3.02
1894 4106 2.346803 CTGGGACAACTAATGTGGACG 58.653 52.381 0.00 0.00 44.12 4.79
2008 4609 4.991687 TCTGTGTAATAACATGTTGCGTCA 59.008 37.500 21.42 11.78 38.08 4.35
2013 4614 7.021196 GTGTAATAACATGTTGCGTCAATCTT 58.979 34.615 21.42 3.63 38.08 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
530 2649 1.531739 GCGGACCAGCCCAAAAATGA 61.532 55.000 0.00 0.00 0.00 2.57
694 2813 3.735037 GAACGATCGGCCTGGGGAC 62.735 68.421 20.98 0.00 0.00 4.46
728 2847 5.837770 AATCTCCATAGCCATGATCTTGA 57.162 39.130 10.07 0.00 33.67 3.02
848 2972 3.793559 AGCGAAAACACACTGAAGTACT 58.206 40.909 0.00 0.00 0.00 2.73
917 3041 2.732843 GCTCTATCGGCAGCTCGC 60.733 66.667 0.00 0.00 41.28 5.03
928 3052 1.339610 CTAGCTTCTGCCGTGCTCTAT 59.660 52.381 0.00 0.00 40.80 1.98
946 3070 5.483937 CCACAGGTCCACATATTATAGCCTA 59.516 44.000 0.00 0.00 0.00 3.93
952 3076 4.968719 TGAGTCCACAGGTCCACATATTAT 59.031 41.667 0.00 0.00 0.00 1.28
968 3092 0.250684 TTCGCCAATGCTTGAGTCCA 60.251 50.000 0.00 0.00 34.43 4.02
1120 3244 1.609208 GAACACAATGCAGTGGGTCT 58.391 50.000 23.92 12.92 43.72 3.85
1123 3247 0.883833 GAGGAACACAATGCAGTGGG 59.116 55.000 16.12 16.12 43.72 4.61
1151 3275 2.301870 TCGAGCACCAACAGACCTTTAT 59.698 45.455 0.00 0.00 0.00 1.40
1152 3276 1.689813 TCGAGCACCAACAGACCTTTA 59.310 47.619 0.00 0.00 0.00 1.85
1153 3277 0.468226 TCGAGCACCAACAGACCTTT 59.532 50.000 0.00 0.00 0.00 3.11
1154 3278 0.468226 TTCGAGCACCAACAGACCTT 59.532 50.000 0.00 0.00 0.00 3.50
1156 3280 1.305201 TTTTCGAGCACCAACAGACC 58.695 50.000 0.00 0.00 0.00 3.85
1349 3561 9.822727 TCCCATGAATATAGATTGTAGTAGTCA 57.177 33.333 0.00 0.00 0.00 3.41
1386 3598 1.407258 GCTCTTGCCGTATCTCACTCT 59.593 52.381 0.00 0.00 0.00 3.24
1505 3717 2.736682 CTAACGTTCCCGCTTGCGG 61.737 63.158 25.17 25.17 37.70 5.69
1507 3719 0.947180 TCACTAACGTTCCCGCTTGC 60.947 55.000 2.82 0.00 37.70 4.01
1576 3788 2.914908 GCGCGGCTTTCCTTTTCCA 61.915 57.895 8.83 0.00 0.00 3.53
1622 3834 1.190643 TGCACCTCGGTCATCATACA 58.809 50.000 0.00 0.00 0.00 2.29
1712 3924 2.428530 TCTCGACATATGCTGCAGAAGT 59.571 45.455 20.43 6.67 0.00 3.01
1728 3940 1.613925 CTCTTGTGACCAGGTTCTCGA 59.386 52.381 0.00 0.00 0.00 4.04
1777 3989 1.266989 CTCGTTCCTTTCCTTTGGTGC 59.733 52.381 0.00 0.00 0.00 5.01
1887 4099 2.027073 GAGTGCATTCGCGTCCACA 61.027 57.895 5.77 0.00 42.97 4.17
1894 4106 0.671781 AGACTGGTGAGTGCATTCGC 60.672 55.000 13.89 13.89 39.24 4.70
2001 4602 1.268999 GGCACACAAAGATTGACGCAA 60.269 47.619 0.00 0.00 0.00 4.85
2193 4794 1.202734 ACACAGCAGCTCTTGTGATGT 60.203 47.619 25.91 10.45 45.17 3.06
2318 4919 2.036571 TACCTCTCGTTCGCGCTCA 61.037 57.895 5.56 0.00 41.05 4.26


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

AutoCloner maintained by Alex Coulton.