Multiple sequence alignment - TraesCS2D01G598800

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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 TraesCS2D01G598800 chr2D 100.000 3966 0 0 1 3966 650604622 650600657 0.000000e+00 7324.0
1 TraesCS2D01G598800 chr2A 93.724 2438 111 22 1538 3966 771975276 771972872 0.000000e+00 3616.0
2 TraesCS2D01G598800 chr2A 90.454 1477 101 19 1 1459 771979500 771978046 0.000000e+00 1910.0
3 TraesCS2D01G598800 chr2A 91.420 641 44 5 1 639 771991011 771990380 0.000000e+00 869.0
4 TraesCS2D01G598800 chr2A 79.690 773 119 29 2177 2926 771805383 771804626 1.260000e-144 523.0
5 TraesCS2D01G598800 chr2A 93.333 120 8 0 1420 1539 771978049 771977930 1.130000e-40 178.0
6 TraesCS2D01G598800 chr2B 91.886 1972 119 13 44 1995 787803353 787801403 0.000000e+00 2717.0
7 TraesCS2D01G598800 chr2B 97.328 1048 25 3 1994 3038 787801142 787800095 0.000000e+00 1777.0
8 TraesCS2D01G598800 chr2B 89.867 1283 105 12 2125 3399 787027380 787028645 0.000000e+00 1626.0
9 TraesCS2D01G598800 chr2B 94.918 551 19 5 3417 3966 787792314 787791772 0.000000e+00 854.0
10 TraesCS2D01G598800 chr2B 87.571 700 69 6 1422 2109 787026639 787027332 0.000000e+00 795.0
11 TraesCS2D01G598800 chr2B 97.087 412 11 1 3023 3434 787794292 787793882 0.000000e+00 693.0
12 TraesCS2D01G598800 chr2B 87.835 559 47 7 586 1144 787023208 787023745 1.550000e-178 636.0
13 TraesCS2D01G598800 chr2B 87.269 542 49 13 1 540 787022506 787023029 5.670000e-168 601.0
14 TraesCS2D01G598800 chr2B 79.541 567 85 19 2159 2717 787171689 787171146 3.740000e-100 375.0
15 TraesCS2D01G598800 chr2B 75.030 821 156 30 2154 2947 786463009 786463807 6.350000e-88 335.0
16 TraesCS2D01G598800 chr2B 92.424 198 15 0 3769 3966 787031177 787031374 2.330000e-72 283.0
17 TraesCS2D01G598800 chr2B 83.658 257 40 2 2168 2424 787222119 787221865 1.420000e-59 241.0
18 TraesCS2D01G598800 chr2B 90.110 182 13 2 3592 3773 787028647 787028823 8.570000e-57 231.0
19 TraesCS2D01G598800 chr7D 80.387 775 121 17 2177 2926 632654020 632653252 9.620000e-156 560.0
20 TraesCS2D01G598800 chr1D 81.431 517 83 10 2181 2687 12301166 12301679 1.030000e-110 411.0
21 TraesCS2D01G598800 chr5D 81.213 511 86 8 2179 2685 3544208 3544712 1.720000e-108 403.0
22 TraesCS2D01G598800 chr5B 75.000 504 91 29 2192 2682 697125077 697125558 2.420000e-47 200.0
23 TraesCS2D01G598800 chr7B 78.289 152 31 2 2784 2934 744699025 744698875 3.260000e-16 97.1
24 TraesCS2D01G598800 chr7B 80.672 119 21 2 2784 2901 745357214 745357331 1.520000e-14 91.6


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 TraesCS2D01G598800 chr2D 650600657 650604622 3965 True 7324.000000 7324 100.000000 1 3966 1 chr2D.!!$R1 3965
1 TraesCS2D01G598800 chr2A 771972872 771979500 6628 True 1901.333333 3616 92.503667 1 3966 3 chr2A.!!$R3 3965
2 TraesCS2D01G598800 chr2A 771990380 771991011 631 True 869.000000 869 91.420000 1 639 1 chr2A.!!$R2 638
3 TraesCS2D01G598800 chr2A 771804626 771805383 757 True 523.000000 523 79.690000 2177 2926 1 chr2A.!!$R1 749
4 TraesCS2D01G598800 chr2B 787800095 787803353 3258 True 2247.000000 2717 94.607000 44 3038 2 chr2B.!!$R4 2994
5 TraesCS2D01G598800 chr2B 787791772 787794292 2520 True 773.500000 854 96.002500 3023 3966 2 chr2B.!!$R3 943
6 TraesCS2D01G598800 chr2B 787022506 787031374 8868 False 695.333333 1626 89.179333 1 3966 6 chr2B.!!$F2 3965
7 TraesCS2D01G598800 chr2B 787171146 787171689 543 True 375.000000 375 79.541000 2159 2717 1 chr2B.!!$R1 558
8 TraesCS2D01G598800 chr2B 786463009 786463807 798 False 335.000000 335 75.030000 2154 2947 1 chr2B.!!$F1 793
9 TraesCS2D01G598800 chr7D 632653252 632654020 768 True 560.000000 560 80.387000 2177 2926 1 chr7D.!!$R1 749
10 TraesCS2D01G598800 chr1D 12301166 12301679 513 False 411.000000 411 81.431000 2181 2687 1 chr1D.!!$F1 506
11 TraesCS2D01G598800 chr5D 3544208 3544712 504 False 403.000000 403 81.213000 2179 2685 1 chr5D.!!$F1 506

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
286 288 0.325671 TCTCCTCCACACATCCCCTC 60.326 60.0 0.0 0.0 0.0 4.30 F
1214 4024 0.895530 AGGGTACTGGTCGTGATGTG 59.104 55.0 0.0 0.0 0.0 3.21 F
1444 4404 0.417437 TGATGGTTCCTCTCCCTCCA 59.583 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 4404 1.885850 GCGTCGAGGTTGTGTTGGT 60.886 57.895 7.01 0.0 0.0 3.67 R
2717 8699 5.605069 AGGTTAGGGTGCAAAAGGTAAAATT 59.395 36.000 0.00 0.0 0.0 1.82 R
3297 9285 0.806492 GGAATGACGAGGAAGGCGAC 60.806 60.000 0.00 0.0 0.0 5.19 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
38 39 7.601856 TGTGGGCTTTATTAATTTGAAGACAG 58.398 34.615 11.54 0.00 0.00 3.51
114 115 2.420022 GGTGGATGTGGAGAAATGTTCG 59.580 50.000 0.00 0.00 34.02 3.95
116 117 3.372206 GTGGATGTGGAGAAATGTTCGAG 59.628 47.826 0.00 0.00 34.02 4.04
162 164 4.280677 TGCTTGTGGGAATACAGGAAAAAG 59.719 41.667 0.00 0.00 29.97 2.27
163 165 4.522789 GCTTGTGGGAATACAGGAAAAAGA 59.477 41.667 0.00 0.00 29.97 2.52
190 192 2.513753 CACATTGTAGCAGTCCCCAAA 58.486 47.619 0.00 0.00 0.00 3.28
209 211 5.300034 CCCAAAATGTATCTAGCAGCAATGA 59.700 40.000 0.00 0.00 0.00 2.57
249 251 7.572814 TGGTCAATGGACTTATCATCATGTAA 58.427 34.615 0.00 0.00 43.77 2.41
261 263 5.794687 TCATCATGTAAACAAAGTAGGCG 57.205 39.130 0.00 0.00 0.00 5.52
272 274 2.814336 CAAAGTAGGCGCTTTTTCTCCT 59.186 45.455 7.64 0.00 36.64 3.69
286 288 0.325671 TCTCCTCCACACATCCCCTC 60.326 60.000 0.00 0.00 0.00 4.30
352 354 8.894768 CTAGCTAGCAGAAGGTTTTAATACAT 57.105 34.615 18.83 0.00 0.00 2.29
376 378 6.662755 TGGTAATTTGAGCTTCCATAGATGT 58.337 36.000 0.00 0.00 0.00 3.06
451 453 1.617322 AAAAAGTCCCTTTCCTCCGC 58.383 50.000 0.00 0.00 31.99 5.54
460 462 2.582436 TTCCTCCGCGGAATCCAC 59.418 61.111 30.53 0.00 46.80 4.02
461 463 2.287274 TTCCTCCGCGGAATCCACA 61.287 57.895 30.53 4.52 46.80 4.17
612 751 3.754965 CACAGATTGTTCCTTCCTTCCA 58.245 45.455 0.00 0.00 0.00 3.53
618 757 3.492102 TGTTCCTTCCTTCCAGTTCAG 57.508 47.619 0.00 0.00 0.00 3.02
664 804 2.574074 TTTAGTATCCGGGTTCCCCT 57.426 50.000 0.00 0.00 42.67 4.79
778 918 2.219325 CTGACTCCTCGTGGGTGAGC 62.219 65.000 3.23 0.00 34.56 4.26
779 919 1.979693 GACTCCTCGTGGGTGAGCT 60.980 63.158 3.23 0.00 34.56 4.09
1214 4024 0.895530 AGGGTACTGGTCGTGATGTG 59.104 55.000 0.00 0.00 0.00 3.21
1444 4404 0.417437 TGATGGTTCCTCTCCCTCCA 59.583 55.000 0.00 0.00 0.00 3.86
1729 7352 2.491298 TCTCTGCATGTCTCTGTCTGTC 59.509 50.000 0.00 0.00 0.00 3.51
1855 7478 1.878953 AACAATTCGAGCGTGAGGTT 58.121 45.000 0.00 0.00 45.11 3.50
1970 7593 0.581529 CGTTTTCGCAGAGACAGCAA 59.418 50.000 0.00 0.00 38.43 3.91
1975 7598 0.961753 TCGCAGAGACAGCAAAGAGA 59.038 50.000 0.00 0.00 0.00 3.10
1981 7604 4.566360 GCAGAGACAGCAAAGAGATTACTC 59.434 45.833 0.00 0.00 42.90 2.59
2002 7887 4.802307 TCTGCTTGGAATATATGCCCAAA 58.198 39.130 7.33 0.00 39.22 3.28
2054 7939 5.131308 TGGTTCCCGATATCCTGTTCATTTA 59.869 40.000 0.00 0.00 0.00 1.40
2433 8358 8.807118 TGGAACATTGTAAGTTAATGCCATTTA 58.193 29.630 0.00 0.00 38.72 1.40
2652 8611 1.815003 ACCCGGACGTTACTAGAACTG 59.185 52.381 0.73 0.00 0.00 3.16
2688 8650 7.915293 TTTATCGAGCTTGTAAGGAAATTCA 57.085 32.000 0.00 0.00 0.00 2.57
2717 8699 4.803452 AGTTTCCAAATGGACCTCTTTGA 58.197 39.130 16.92 0.43 45.39 2.69
2754 8737 4.218417 CACCCTAACCTTTCAGATGTTTGG 59.782 45.833 0.00 0.00 0.00 3.28
2756 8739 5.073965 ACCCTAACCTTTCAGATGTTTGGTA 59.926 40.000 0.00 0.00 0.00 3.25
2848 8831 8.689972 AGAATAGATTGCCAACAAATAAAGAGG 58.310 33.333 0.00 0.00 39.77 3.69
3355 9343 1.069668 ACCGCTAACACCGAACTCTTT 59.930 47.619 0.00 0.00 0.00 2.52
3425 10998 5.152623 TGAGGACTGGTCTGTAAATTCAG 57.847 43.478 0.67 0.00 36.85 3.02
3468 11041 1.522130 TGATGCGATGCGATGCTGT 60.522 52.632 0.00 0.00 0.00 4.40
3470 11043 0.028505 GATGCGATGCGATGCTGTTT 59.971 50.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.265095 CATTGTGGCCATATGAGCGTC 59.735 52.381 20.50 1.50 0.00 5.19
94 95 3.334691 TCGAACATTTCTCCACATCCAC 58.665 45.455 0.00 0.00 0.00 4.02
179 181 3.565902 GCTAGATACATTTTGGGGACTGC 59.434 47.826 0.00 0.00 0.00 4.40
190 192 7.094248 TGTTGTTTCATTGCTGCTAGATACATT 60.094 33.333 0.00 0.00 0.00 2.71
236 238 7.466725 GCGCCTACTTTGTTTACATGATGATAA 60.467 37.037 0.00 0.00 0.00 1.75
237 239 6.018262 GCGCCTACTTTGTTTACATGATGATA 60.018 38.462 0.00 0.00 0.00 2.15
238 240 5.220854 GCGCCTACTTTGTTTACATGATGAT 60.221 40.000 0.00 0.00 0.00 2.45
249 251 3.004419 GGAGAAAAAGCGCCTACTTTGTT 59.996 43.478 2.29 0.00 39.76 2.83
261 263 2.489722 GGATGTGTGGAGGAGAAAAAGC 59.510 50.000 0.00 0.00 0.00 3.51
272 274 1.279496 CTTCAGAGGGGATGTGTGGA 58.721 55.000 0.00 0.00 0.00 4.02
286 288 1.554160 ACCTGAGATGTGCTCCTTCAG 59.446 52.381 0.00 0.00 43.26 3.02
350 352 7.230108 ACATCTATGGAAGCTCAAATTACCATG 59.770 37.037 0.00 0.00 38.37 3.66
352 354 6.662755 ACATCTATGGAAGCTCAAATTACCA 58.337 36.000 0.00 0.00 0.00 3.25
376 378 2.105821 ACATCCCGTGTCTCCAAAAAGA 59.894 45.455 0.00 0.00 35.77 2.52
451 453 0.586319 GTGTGTGTGTGTGGATTCCG 59.414 55.000 0.00 0.00 0.00 4.30
458 460 1.102154 ATTGGTGGTGTGTGTGTGTG 58.898 50.000 0.00 0.00 0.00 3.82
459 461 1.748493 GAATTGGTGGTGTGTGTGTGT 59.252 47.619 0.00 0.00 0.00 3.72
460 462 2.023673 AGAATTGGTGGTGTGTGTGTG 58.976 47.619 0.00 0.00 0.00 3.82
461 463 2.435372 AGAATTGGTGGTGTGTGTGT 57.565 45.000 0.00 0.00 0.00 3.72
612 751 3.380320 CGGGGAAACACTTTTTCTGAACT 59.620 43.478 0.00 0.00 0.00 3.01
618 757 2.882927 AAGCGGGGAAACACTTTTTC 57.117 45.000 0.00 0.00 0.00 2.29
664 804 1.536418 CAGTGGTGGAGGTGGAGGA 60.536 63.158 0.00 0.00 0.00 3.71
750 890 1.509004 GAGGAGTCAGTCGGTCTGC 59.491 63.158 0.00 0.00 43.32 4.26
778 918 1.845627 ATCCAGAGTGGGTGTGGCAG 61.846 60.000 0.00 0.00 39.61 4.85
779 919 1.841302 GATCCAGAGTGGGTGTGGCA 61.841 60.000 0.00 0.00 39.61 4.92
951 1091 1.755380 GCCACTAGAACATCCTACGGT 59.245 52.381 0.00 0.00 0.00 4.83
956 1096 1.264749 TGGCGCCACTAGAACATCCT 61.265 55.000 29.03 0.00 0.00 3.24
983 1123 1.303309 CATCTCCTCCGGATTGCAAC 58.697 55.000 3.57 0.00 0.00 4.17
1044 1190 2.000323 CGTCGTCGTCGTTGTCGTT 61.000 57.895 3.67 0.00 38.33 3.85
1050 1196 3.306134 GAGGCTCGTCGTCGTCGTT 62.306 63.158 11.41 0.00 38.33 3.85
1214 4024 2.749621 GGAAGTTGATCACCATCACCAC 59.250 50.000 0.00 0.00 38.86 4.16
1375 4224 2.722201 GGCGTGGAGGTCCCTGTAG 61.722 68.421 0.00 0.00 35.38 2.74
1444 4404 1.885850 GCGTCGAGGTTGTGTTGGT 60.886 57.895 7.01 0.00 0.00 3.67
1493 4459 4.803426 CCGGAGAGCGTGCTGGTC 62.803 72.222 0.00 0.00 45.59 4.02
1729 7352 4.494362 CGGATCGAGTGTAGTTACAGACAG 60.494 50.000 0.00 0.00 36.78 3.51
1975 7598 6.183347 GGGCATATATTCCAAGCAGAGTAAT 58.817 40.000 3.71 0.00 0.00 1.89
1981 7604 4.021719 CCTTTGGGCATATATTCCAAGCAG 60.022 45.833 13.80 10.82 41.00 4.24
2002 7887 7.069331 CCTGACAGATACTTATTGAGACTTCCT 59.931 40.741 3.32 0.00 0.00 3.36
2652 8611 5.921004 AGCTCGATAAATTCATCTGAAGC 57.079 39.130 0.00 1.25 37.48 3.86
2717 8699 5.605069 AGGTTAGGGTGCAAAAGGTAAAATT 59.395 36.000 0.00 0.00 0.00 1.82
2818 8801 9.801873 TTTATTTGTTGGCAATCTATTCTTAGC 57.198 29.630 1.92 0.00 34.18 3.09
3297 9285 0.806492 GGAATGACGAGGAAGGCGAC 60.806 60.000 0.00 0.00 0.00 5.19
3425 10998 8.263940 ACACACTGTGATTAAATATACCACAC 57.736 34.615 16.30 0.00 36.96 3.82
3468 11041 6.493458 TCGGTATCATCATATCAGACCAGAAA 59.507 38.462 0.00 0.00 0.00 2.52
3470 11043 5.416013 GTCGGTATCATCATATCAGACCAGA 59.584 44.000 0.00 0.00 0.00 3.86
3820 13752 1.360820 GTGAAGGCGAGCTAAACCTC 58.639 55.000 2.33 0.00 31.86 3.85


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

AutoCloner maintained by Alex Coulton.