Multiple sequence alignment - TraesCS3D01G185200

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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 TraesCS3D01G185200 chr3D 100.000 3637 0 0 1 3637 170667052 170670688 0.000000e+00 6717
1 TraesCS3D01G185200 chr3D 84.721 877 115 7 1763 2639 170558160 170557303 0.000000e+00 859
2 TraesCS3D01G185200 chr3D 88.026 618 73 1 2029 2646 170564249 170563633 0.000000e+00 730
3 TraesCS3D01G185200 chr3D 87.263 581 74 0 2048 2628 170659786 170660366 0.000000e+00 664
4 TraesCS3D01G185200 chr3D 88.000 175 12 5 579 746 380272030 380271858 7.970000e-47 198
5 TraesCS3D01G185200 chr3D 81.667 240 32 8 1001 1231 170558776 170558540 4.790000e-44 189
6 TraesCS3D01G185200 chr3A 96.369 3663 83 15 1 3637 208233218 208236856 0.000000e+00 5982
7 TraesCS3D01G185200 chr3A 85.114 880 114 8 1763 2639 208086396 208085531 0.000000e+00 883
8 TraesCS3D01G185200 chr3A 88.283 623 73 0 2024 2646 208089594 208088972 0.000000e+00 747
9 TraesCS3D01G185200 chr3A 87.263 581 74 0 2048 2628 208222240 208222820 0.000000e+00 664
10 TraesCS3D01G185200 chr3A 81.197 234 38 3 1000 1227 208090513 208090280 2.230000e-42 183
11 TraesCS3D01G185200 chr3B 96.002 2626 75 11 730 3337 246145239 246147852 0.000000e+00 4241
12 TraesCS3D01G185200 chr3B 85.210 879 107 14 1763 2639 245964146 245963289 0.000000e+00 881
13 TraesCS3D01G185200 chr3B 89.661 590 31 6 1 583 246144681 246145247 0.000000e+00 725
14 TraesCS3D01G185200 chr3B 87.980 599 71 1 2029 2627 245969599 245969002 0.000000e+00 706
15 TraesCS3D01G185200 chr3B 88.124 581 69 0 2048 2628 246129338 246129918 0.000000e+00 691
16 TraesCS3D01G185200 chr3B 96.657 329 9 2 3310 3637 246148017 246148344 2.470000e-151 545
17 TraesCS3D01G185200 chr3B 80.932 236 35 6 1000 1227 245970513 245970280 1.040000e-40 178
18 TraesCS3D01G185200 chr3B 87.755 147 18 0 1085 1231 245964637 245964491 4.830000e-39 172
19 TraesCS3D01G185200 chr7A 91.765 170 14 0 28 197 83784825 83784994 1.690000e-58 237
20 TraesCS3D01G185200 chr4D 92.073 164 13 0 34 197 482703628 482703465 7.850000e-57 231
21 TraesCS3D01G185200 chr2A 92.169 166 10 3 34 197 231352954 231352790 7.850000e-57 231
22 TraesCS3D01G185200 chr2A 88.750 160 14 3 580 735 746803159 746803318 3.710000e-45 193
23 TraesCS3D01G185200 chrUn 92.073 164 12 1 35 197 41419069 41419232 2.820000e-56 230
24 TraesCS3D01G185200 chrUn 90.588 170 16 0 28 197 40706725 40706894 3.650000e-55 226
25 TraesCS3D01G185200 chr4B 90.588 170 15 1 28 197 85758665 85758497 1.310000e-54 224
26 TraesCS3D01G185200 chr4B 89.326 178 17 2 21 197 13282350 13282174 4.730000e-54 222
27 TraesCS3D01G185200 chr4B 89.571 163 10 3 580 735 613157423 613157261 2.210000e-47 200
28 TraesCS3D01G185200 chr7D 89.024 164 10 4 580 735 389188187 389188024 2.870000e-46 196
29 TraesCS3D01G185200 chr6B 88.889 162 12 2 580 735 127605812 127605973 1.030000e-45 195
30 TraesCS3D01G185200 chr6D 88.889 162 11 3 580 735 431160668 431160828 3.710000e-45 193
31 TraesCS3D01G185200 chr5A 87.079 178 14 4 580 750 558675658 558675483 3.710000e-45 193
32 TraesCS3D01G185200 chr1A 88.344 163 13 3 580 736 181769427 181769589 1.330000e-44 191


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 TraesCS3D01G185200 chr3D 170667052 170670688 3636 False 6717.000000 6717 100.000000 1 3637 1 chr3D.!!$F2 3636
1 TraesCS3D01G185200 chr3D 170563633 170564249 616 True 730.000000 730 88.026000 2029 2646 1 chr3D.!!$R1 617
2 TraesCS3D01G185200 chr3D 170659786 170660366 580 False 664.000000 664 87.263000 2048 2628 1 chr3D.!!$F1 580
3 TraesCS3D01G185200 chr3D 170557303 170558776 1473 True 524.000000 859 83.194000 1001 2639 2 chr3D.!!$R3 1638
4 TraesCS3D01G185200 chr3A 208233218 208236856 3638 False 5982.000000 5982 96.369000 1 3637 1 chr3A.!!$F2 3636
5 TraesCS3D01G185200 chr3A 208222240 208222820 580 False 664.000000 664 87.263000 2048 2628 1 chr3A.!!$F1 580
6 TraesCS3D01G185200 chr3A 208085531 208090513 4982 True 604.333333 883 84.864667 1000 2646 3 chr3A.!!$R1 1646
7 TraesCS3D01G185200 chr3B 246144681 246148344 3663 False 1837.000000 4241 94.106667 1 3637 3 chr3B.!!$F2 3636
8 TraesCS3D01G185200 chr3B 246129338 246129918 580 False 691.000000 691 88.124000 2048 2628 1 chr3B.!!$F1 580
9 TraesCS3D01G185200 chr3B 245963289 245964637 1348 True 526.500000 881 86.482500 1085 2639 2 chr3B.!!$R1 1554
10 TraesCS3D01G185200 chr3B 245969002 245970513 1511 True 442.000000 706 84.456000 1000 2627 2 chr3B.!!$R2 1627

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
109 110 2.742589 GTCCGATCACTTTGGGTCTTTC 59.257 50.000 0.0 0.0 0.0 2.62 F
164 165 3.202906 CTGTTTTCAAGACTCGAACCCA 58.797 45.455 0.0 0.0 0.0 4.51 F
1997 5692 2.691409 TTCTTTCCCAGATAGCACGG 57.309 50.000 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 5385 1.548986 GGCACATGCAACGAAATAGC 58.451 50.000 6.15 0.0 44.36 2.97 R
2090 5793 3.137459 CTCGCGCCCAGAGAGTCT 61.137 66.667 0.00 0.0 41.13 3.24 R
3082 6785 2.097036 TGTGGTGTATCCTAGTGGTCG 58.903 52.381 0.00 0.0 37.07 4.79 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
109 110 2.742589 GTCCGATCACTTTGGGTCTTTC 59.257 50.000 0.00 0.00 0.00 2.62
164 165 3.202906 CTGTTTTCAAGACTCGAACCCA 58.797 45.455 0.00 0.00 0.00 4.51
329 335 9.897744 CAACTTTGCAGAACTTTCATAAGAATA 57.102 29.630 0.00 0.00 35.30 1.75
352 358 3.576078 TGTTCTTCAAGTGGTGATGGT 57.424 42.857 0.00 0.00 35.70 3.55
362 368 7.669089 TCAAGTGGTGATGGTACTATTGATA 57.331 36.000 0.00 0.00 0.00 2.15
402 409 5.699001 AGTGTGCATTTGTATTAACTCGTCA 59.301 36.000 0.00 0.00 0.00 4.35
488 495 6.280643 ACCAAATCACCAAAGCTTAAAGTTC 58.719 36.000 0.00 0.00 0.00 3.01
602 610 9.860393 AGTTACTCCCTCCATTCCTAAATATAT 57.140 33.333 0.00 0.00 0.00 0.86
605 613 8.525729 ACTCCCTCCATTCCTAAATATATGTT 57.474 34.615 0.00 0.00 0.00 2.71
1511 5178 8.663167 TCCTAGGCTAAACTTTTAGTTTTACCT 58.337 33.333 20.25 20.25 45.38 3.08
1690 5385 4.379813 GCATGTACCTGTCCAATGAAACTG 60.380 45.833 0.00 0.00 0.00 3.16
1742 5437 7.707893 GTGTAGTACCAGTAACTTTTTCTGACA 59.292 37.037 0.00 0.00 0.00 3.58
1860 5555 3.001406 CTCCGGGGGTTCGAGGTT 61.001 66.667 0.00 0.00 0.00 3.50
1932 5627 2.932234 CGCCGATATCCTCGCCCTT 61.932 63.158 0.00 0.00 46.25 3.95
1997 5692 2.691409 TTCTTTCCCAGATAGCACGG 57.309 50.000 0.00 0.00 0.00 4.94
2022 5717 4.870123 AAACAATGCAGCCAGTATTTGA 57.130 36.364 0.00 0.00 29.42 2.69
2159 5862 0.476771 CCAACAACACCCTACCCACT 59.523 55.000 0.00 0.00 0.00 4.00
2192 5895 0.824109 TCAATCGCCTCGGTCTCAAT 59.176 50.000 0.00 0.00 0.00 2.57
2486 6189 0.034337 TTACCAAGAGCGCGGAAACT 59.966 50.000 8.83 0.00 0.00 2.66
2628 6331 1.572085 CTGCAGGAGGCTCAACAACG 61.572 60.000 17.69 0.00 45.15 4.10
2859 6562 5.774498 ACCAAGTTCTCACTTCCAAATTC 57.226 39.130 0.00 0.00 41.69 2.17
2869 6572 2.827921 ACTTCCAAATTCCACTCATGGC 59.172 45.455 0.00 0.00 46.80 4.40
3028 6731 8.055181 TCTTGTTATGCCTCCAAGAAATATCTT 58.945 33.333 0.00 0.00 46.91 2.40
3082 6785 0.380378 TTGACCAAGTTTGCGCTGAC 59.620 50.000 9.73 7.33 0.00 3.51
3105 6808 3.704566 GACCACTAGGATACACCACATCA 59.295 47.826 0.00 0.00 42.04 3.07
3132 6835 4.058817 GCTGTGCCATACTAGGTTCATAC 58.941 47.826 0.00 0.00 0.00 2.39
3210 6913 2.855963 CAGCACAAGTTGTTCAAAGCTG 59.144 45.455 23.02 23.02 36.52 4.24
3216 6919 0.102844 GTTGTTCAAAGCTGGCAGCA 59.897 50.000 38.09 17.61 45.56 4.41
3368 7263 8.812972 AGGAATTATCACACAGTAAACTAGTCA 58.187 33.333 0.00 0.00 0.00 3.41
3408 7303 9.000486 CATAGTAATCAGAGATGCAAATCATGT 58.000 33.333 0.00 0.00 35.05 3.21
3556 7451 3.949754 ACGAGAGGTGTAATCATTACCGA 59.050 43.478 5.05 0.00 39.46 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 0.928229 GTAGGGAAATGCTGCGTACG 59.072 55.000 11.84 11.84 28.88 3.67
324 330 6.591935 TCACCACTTGAAGAACAACTATTCT 58.408 36.000 0.00 0.00 40.78 2.40
329 335 3.885297 CCATCACCACTTGAAGAACAACT 59.115 43.478 0.00 0.00 37.92 3.16
362 368 4.821260 TGCACACTGTAACACTGATGAAAT 59.179 37.500 0.00 0.00 0.00 2.17
438 445 8.546083 AGACAAGTGTAGATGGAGATTCTTAT 57.454 34.615 0.00 0.00 0.00 1.73
488 495 5.924254 TCATTTCTGGTGTTGTAGTTACTCG 59.076 40.000 0.00 0.00 0.00 4.18
504 511 5.049474 TGTCATGTTTCGGTCTTCATTTCTG 60.049 40.000 0.00 0.00 0.00 3.02
629 637 7.907389 AGTGTAGATTCACTCATTTTACTCCA 58.093 34.615 0.00 0.00 44.07 3.86
1511 5178 7.559486 CATTGTAGGCAGGCTATCTTATCATA 58.441 38.462 7.03 0.00 0.00 2.15
1690 5385 1.548986 GGCACATGCAACGAAATAGC 58.451 50.000 6.15 0.00 44.36 2.97
1932 5627 3.755628 GTAGAGTCACGGGCGGCA 61.756 66.667 12.47 0.00 0.00 5.69
1997 5692 4.718940 ATACTGGCTGCATTGTTTAACC 57.281 40.909 0.50 0.00 0.00 2.85
2090 5793 3.137459 CTCGCGCCCAGAGAGTCT 61.137 66.667 0.00 0.00 41.13 3.24
2159 5862 3.876914 GGCGATTGAACTTGGTGATGATA 59.123 43.478 0.00 0.00 0.00 2.15
2486 6189 2.666190 GCCTTCACGAGTGCTGCA 60.666 61.111 0.00 0.00 0.00 4.41
2628 6331 4.159506 AGGAGCTTCAGTAACTCAGTGATC 59.840 45.833 0.00 0.00 36.47 2.92
2869 6572 4.518590 TGTTGAACAATAGGTGGATGTGTG 59.481 41.667 0.00 0.00 0.00 3.82
3082 6785 2.097036 TGTGGTGTATCCTAGTGGTCG 58.903 52.381 0.00 0.00 37.07 4.79
3210 6913 4.156556 TCATCAAAAGATAACACTGCTGCC 59.843 41.667 0.00 0.00 0.00 4.85
3216 6919 5.413833 CCAGCTGTCATCAAAAGATAACACT 59.586 40.000 13.81 0.00 0.00 3.55
3278 6981 2.978156 TTTTGGGCACTTCTCCTCAT 57.022 45.000 0.00 0.00 0.00 2.90
3368 7263 8.768397 TCTGATTACTATGGTGAAACTTGGTAT 58.232 33.333 0.00 0.00 36.74 2.73
3370 7265 7.016153 TCTGATTACTATGGTGAAACTTGGT 57.984 36.000 0.00 0.00 36.74 3.67
3408 7303 9.558396 ACAGATCCTTGAATTTATTTTTGCAAA 57.442 25.926 8.05 8.05 0.00 3.68
3518 7413 4.082190 CCTCTCGTCCATGAGTTCTAACAA 60.082 45.833 0.00 0.00 37.28 2.83
3556 7451 2.375174 TGCTGGAACCAAGTATCCTGTT 59.625 45.455 0.00 0.00 37.10 3.16


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

AutoCloner maintained by Alex Coulton.